Minia, Egypt: Principal Component Analysis

PubMed

Abdelrehim, Marwa G; Mahfouz, Eman M; Ewis, Ashraf A; Seedhom, Amany E; Afifi, Hassan M; Shebl, Fatma M

2018-02-26

Background: Pancreatic cancer (PC) is a serious and rapidly progressing malignancy. Identifying risk factors including dietary elements is important to develop preventive strategies. This study focused on possible links between diet and PC. Methods: We conducted a case-control study including all PC patients diagnosed at Minia Cancer Center and controls from general population from June 2014 to December 2015. Dietary data were collected directly through personal interviews. Principal component analysis (PCA) was performed to identify dietary groups. The data were analyzed using crude odds ratios (ORs) and multivariable logistic regression with adjusted ORs and 95% confidence intervals (CIs). Results: A total of 75 cases and 149 controls were included in the study. PCA identified six dietary groups, labeled as cereals and grains, vegetables, proteins, dairy products, fruits, and sugars. Bivariate analysis showed that consumption of vegetables, fruits, sugars, and total energy intake were associated with change in PC risk. In multivariable-adjusted models comparing highest versus lowest levels of intake, we observed significant lower odds of PC in association with vegetable intake (OR 0.24; 95% CI, 0.07-0.85, P=0.012) and a higher likelihood with the total energy intake (OR 9.88; 95% CI, 2.56-38.09, P<0.0001). There was also a suggested link between high fruit consumption and reduced odds of PC. Conclusions: The study supports the association between dietary factors and the odds of PC development in Egypt. It was found that higher energy intake is associated with an increase in likelihood of PC, while increased vegetable consumption is associated with a lower odds ratio. Creative Commons Attribution License

Understanding deformation mechanisms during powder compaction using principal component analysis of compression data.

PubMed

Roopwani, Rahul; Buckner, Ira S

2011-10-14

Principal component analysis (PCA) was applied to pharmaceutical powder compaction. A solid fraction parameter (SF(c/d)) and a mechanical work parameter (W(c/d)) representing irreversible compression behavior were determined as functions of applied load. Multivariate analysis of the compression data was carried out using PCA. The first principal component (PC1) showed loadings for the solid fraction and work values that agreed with changes in the relative significance of plastic deformation to consolidation at different pressures. The PC1 scores showed the same rank order as the relative plasticity ranking derived from the literature for common pharmaceutical materials. The utility of PC1 in understanding deformation was extended to binary mixtures using a subset of the original materials. Combinations of brittle and plastic materials were characterized using the PCA method. The relationships between PC1 scores and the weight fractions of the mixtures were typically linear showing ideal mixing in their deformation behaviors. The mixture consisting of two plastic materials was the only combination to show a consistent positive deviation from ideality. The application of PCA to solid fraction and mechanical work data appears to be an effective means of predicting deformation behavior during compaction of simple powder mixtures. Copyright © 2011 Elsevier B.V. All rights reserved.

Kicking against the PRCs – A Domesticated Transposase Antagonises Silencing Mediated by Polycomb Group Proteins and Is an Accessory Component of Polycomb Repressive Complex 2

PubMed Central

Perera, Pumi; Mora-García, Santiago; de Leau, Erica; Thornton, Harry; de Alves, Flavia Lima; Rapsilber, Juri; Yang, Suxin; James, Geo Velikkakam; Schneeberger, Korbinian; Finnegan, E. Jean; Turck, Franziska; Goodrich, Justin

2015-01-01

The Polycomb group (PcG) and trithorax group (trxG) genes play crucial roles in development by regulating expression of homeotic and other genes controlling cell fate. Both groups catalyse modifications of chromatin, particularly histone methylation, leading to epigenetic changes that affect gene activity. The trxG antagonizes the function of PcG genes by activating PcG target genes, and consequently trxG mutants suppress PcG mutant phenotypes. We previously identified the ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN1 (ALP1) gene as a genetic suppressor of mutants in the Arabidopsis PcG gene LIKE HETEROCHROMATIN PROTEIN1 (LHP1). Here, we show that ALP1 interacts genetically with several other PcG and trxG components and that it antagonizes PcG silencing. Transcriptional profiling reveals that when PcG activity is compromised numerous target genes are hyper-activated in seedlings and that in most cases this requires ALP1. Furthermore, when PcG activity is present ALP1 is needed for full activation of several floral homeotic genes that are repressed by the PcG. Strikingly, ALP1 does not encode a known chromatin protein but rather a protein related to PIF/Harbinger class transposases. Phylogenetic analysis indicates that ALP1 is broadly conserved in land plants and likely lost transposase activity and acquired a novel function during angiosperm evolution. Consistent with this, immunoprecipitation and mass spectrometry (IP-MS) show that ALP1 associates, in vivo, with core components of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a widely conserved PcG protein complex which functions as a H3K27me3 histone methyltransferase. Furthermore, in reciprocal pulldowns using the histone methyltransferase CURLY LEAF (CLF), we identify not only ALP1 and the core PRC2 components but also plant-specific accessory components including EMBRYONIC FLOWER 1 (EMF1), a transcriptional repressor previously associated with PRC1-like complexes. Taken together our data suggest that ALP1 inhibits PcG silencing by blocking the interaction of the core PRC2 with accessory components that promote its HMTase activity or its role in inhibiting transcription. ALP1 is the first example of a domesticated transposase acquiring a novel function as a PcG component. The antagonistic interaction of a modified transposase with the PcG machinery is novel and may have arisen as a means for the cognate transposon to evade host surveillance or for the host to exploit features of the transposition machinery beneficial for epigenetic regulation of gene activity. PMID:26642436

[Study on discrimination of varieties of fire resistive coating for steel structure based on near-infrared spectroscopy].

PubMed

Xue, Gang; Song, Wen-qi; Li, Shu-chao

2015-01-01

In order to achieve the rapid identification of fire resistive coating for steel structure of different brands in circulating, a new method for the fast discrimination of varieties of fire resistive coating for steel structure by means of near infrared spectroscopy was proposed. The raster scanning near infrared spectroscopy instrument and near infrared diffuse reflectance spectroscopy were applied to collect the spectral curve of different brands of fire resistive coating for steel structure and the spectral data were preprocessed with standard normal variate transformation(standard normal variate transformation, SNV) and Norris second derivative. The principal component analysis (principal component analysis, PCA)was used to near infrared spectra for cluster analysis. The analysis results showed that the cumulate reliabilities of PC1 to PC5 were 99. 791%. The 3-dimentional plot was drawn with the scores of PC1, PC2 and PC3 X 10, which appeared to provide the best clustering of the varieties of fire resistive coating for steel structure. A total of 150 fire resistive coating samples were divided into calibration set and validation set randomly, the calibration set had 125 samples with 25 samples of each variety, and the validation set had 25 samples with 5 samples of each variety. According to the principal component scores of unknown samples, Mahalanobis distance values between each variety and unknown samples were calculated to realize the discrimination of different varieties. The qualitative analysis model for external verification of unknown samples is a 10% recognition ration. The results demonstrated that this identification method can be used as a rapid, accurate method to identify the classification of fire resistive coating for steel structure and provide technical reference for market regulation.

Multivariate analysis of sexual size dimorphism in local turkeys (Meleagris gallopavo) in Nigeria.

PubMed

Ajayi, Oyeyemi O; Yakubu, Abdulmojeed; Jayeola, Oluwaseun O; Imumorin, Ikhide G; Takeet, Michael I; Ozoje, Michael O; Ikeobi, Christian O N; Peters, Sunday O

2012-06-01

Sexual size dimorphism is a key evolutionary feature that can lead to important biological insights. To improve methods of sexing live birds in the field, we assessed sexual size dimorphism in Nigerian local turkeys (Meleagris gallopavo) using multivariate techniques. Measurements were taken on 125 twenty-week-old birds reared under the intensive management system. The body parameters measured were body weight, body length, breast girth, thigh length, shank length, keel length, wing length and wing span. Univariate analysis revealed that toms (males) had significantly (P < 0.05) higher mean values than hens (females) in all the measured traits. Positive phenotypic correlations between body weight and body measurements ranged from 0.445 to 0.821 in toms and 0.053-0.660 in hens, respectively. Three principal components (PC1, PC2 and PC3) were extracted in toms, each accounting for 63.70%, 19.42% and 5.72% of the total variance, respectively. However, four principal components (PC1, PC2, PC3 and PC4) were extracted in hens, which explained 54.03%, 15.29%, 11.68% and 6.95%, respectively of the generalised variance. A stepwise discriminant function analysis of the eight morphological traits indicated that body weight, body length, tail length and wing span were the most discriminating variables in separating the sexes. The single discriminant function obtained was able to correctly classify 100% of the birds into their source population. The results obtained from the present study could aid future management decisions, ecological studies and conservation of local turkeys in a developing economy.

Influence of Different Factors on Relative Air Humidity in Zaragoza, Spain

NASA Astrophysics Data System (ADS)

Cuadrat, José M.

2015-03-01

In this study, the spatial patterns of relative air humidity and its relation to urban, geographical and meteorological factors in the city of Zaragoza (Spain) is discussed. We created a relative humidity database by means of 32 urban transects. Data were taken on different days and with different weather types. This data set was used to map the mean spatial distribution of urban dry island (UDI). Using stepwise multiple regression analysis and Landsat ETM+ images the relationships between mean UDI and the main geographic-urban factors: topography, land cover and surface reflectivity, have been analyzed. Different spatial patterns of UDI were determined using Principal Component Analysis (Varimax rotation). The three components extracted accounted for 91% of the total variance. PC1 accounted for the most general patterns (similar to mean UDI); PC2 showed a shift of dry areas to the SE and PC3 a shift to NW. Using data on wind direction in Zaragoza, we have found that the displacement of dry areas to the SE (PC 2) was greater during NW winds while the shift to the NW (PC 3) was produced mainly by SE winds.

Relationships between NIR spectra and sensory attributes of Thai commercial fish sauces.

PubMed

Ritthiruangdej, Pitiporn; Suwonsichon, Thongchai

2007-07-01

Twenty Thai commercial fish sauces were characterized by sensory descriptive analysis and near-infrared (NIR) spectroscopy. The main objectives were i) to investigate the relationships between sensory attributes and NIR spectra of samples and ii) to characterize the sensory characteristics of fish sauces based on NIR data. A generic descriptive analysis with 12 trained panels was used to characterize the sensory attributes. These attributes consisted of 15 descriptors: brown color, 5 aromatics (sweet, caramelized, fermented, fishy, and musty), 4 tastes (sweet, salty, bitter, and umami), 3 aftertastes (sweet, salty and bitter) and 2 flavors (caramelized and fishy). The results showed that Thai fish sauce samples exhibited significant differences in all of sensory attribute values (p < 0.05). NIR transflectance spectra were obtained from 1100 to 2500 nm. Prior to investigation of the relationships between sensory attributes and NIR spectra, principal component analysis (PCA) was applied to reduce the dimensionality of the spectral data from 622 wavelengths to two uncorrelated components (NIR1 and NIR2) which explained 92 and 7% of the total variation, respectively. NIR1 was highly correlated with the wavelength regions of 1100 - 1544, 1774 - 2062, 2092 - 2308, and 2358 - 2440 nm, while NIR2 was highly correlated with the wavelength regions of 1742 - 1764, 2066 - 2088, and 2312 - 2354 nm. Subsequently, the relationships among these two components and all sensory attributes were also investigated by PCA. The results showed that the first three principal components (PCs) named as fishy flavor component (PC1), sweet component (PC2) and bitterness component (PC3), respectively, explained a total of 66.86% of the variation. NIR1 was mainly correlated to the sensory attributes of fishy aromatic, fishy flavor and sweet aftertaste on PC1. In addition, the PCA using only the factor loadings of NIR1 and NIR2 could be used to classify samples into three groups which showed high, medium and low degrees of fishy aromatic, fishy flavor and sweet aftertaste.

The Same Story or a Unique Novel? Within-Participant Principle Component Analysis of Training Load Measures in Professional Rugby Union Skills Training.

PubMed

Weaving, Dan; Dalton, Nicholas E; Black, Christopher; Darrall-Jones, Joshua; Phibbs, Padraic J; Gray, Michael; Jones, Ben; Roe, Gregory A B

2018-03-27

The study aimed to identify which combination of external and internal training load (TL) metrics capture similar or unique information for individual professional players during skills training in rugby union using principal component analysis (PCA). TL data were collected from twenty-one male professional rugby union players across a competitive season. This included PlayerLoad™, total distance (TD), and individualised high-speed distance (HSD; >61% maximal velocity; all external TL) obtained from a micro-technology device worn by each player (Optimeye X4, Catapult Innovations, Melbourne, Australia) and the session-rating of perceived exertion (sRPE; internal TL). PCA was conducted on each individual to extract the underlying combinations of the four TL measures that best describe the total information (variance) provided by the measures. TL measures with PC "loadings" (PC L ) above 0.7 were deemed to possess well-defined relationships with the extracted PC. The findings show that from the four TL measures, the majority of an individual's TL information (1 st PC: 55 to 70%) during skills training can be explained by either sRPE (PC L : 0.72 to 0.95), TD (PC L : 0.86 to 0.98) or PlayerLoad™ (PC L : 0.71 to 0.98). HSD was the only variable to relate to the 2nd PC (PC L : 0.72 to 1.00), which captured additional TL information (+19 to 28%). Findings suggest practitioners could quantify the TL of rugby union skills training with one of PlayerLoad™, TD, or sRPE plus HSD whilst limiting omitted information of the TL imposed during professional rugby union skills training.

A Principal Component Analysis of the Diffuse Interstellar Bands

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

Ensor, T.; Cami, J.; Bhatt, N. H.

2017-02-20

We present a principal component (PC) analysis of 23 line-of-sight parameters (including the strengths of 16 diffuse interstellar bands, DIBs) for a well-chosen sample of single-cloud sightlines representing a broad range of environmental conditions. Our analysis indicates that the majority (∼93%) of the variations in the measurements can be captured by only four parameters The main driver (i.e., the first PC) is the amount of DIB-producing material in the line of sight, a quantity that is extremely well traced by the equivalent width of the λ 5797 DIB. The second PC is the amount of UV radiation, which correlates wellmore » with the λ 5797/ λ 5780 DIB strength ratio. The remaining two PCs are more difficult to interpret, but are likely related to the properties of dust in the line of sight (e.g., the gas-to-dust ratio). With our PCA results, the DIBs can then be used to estimate these line-of-sight parameters.« less

Direct identification of various copper phthalocyanine pigments in automotive paints and paint smears by laser desorption ionization mass spectrometry.

PubMed

Mukai, Tadashi; Nakazumi, Hiroyuki; Kawabata, Shin-ichirou; Kusatani, Masaru; Nakai, Seita; Honda, Sadao

2008-01-01

Direct identification of copper phthalocyanine (CuPc) and chlorinated CuPcs in paints for discrimination between blue automobile paints by means of laser desorption mass spectrometry (LDMS) in the absence of a matrix is reported. The models consisted of eight commercially available CuPc pigments applied to a piece of plain white coating paper. The relationship between the peak intensity at m/z 575 of the CuPc, the number of pulsed laser shots, and laser power was compared to optimize laser abrasion. LDMS analysis of the model paints demonstrated that all characteristic components of the CuPc pigments in the paint films were in good agreement with those in the powder pigments. Further, the chlorinated CuPcs in the paint films could be distinguished. A quantity of 42 blue paint films, representing the paints used for painting Japanese domestic trucks, was examined by LDMS analysis. Results indicate that the paints can be classified into four categories based on the chlorinated CuPc components of the paints. Therefore, LDMS spectra of CuPc pigments would be useful for the identification of paints in forensic investigations. Herein, we report the successful identification of the CuPcs in a paint smear on the frame of a bicycle damaged in a hit-and-run accident, using the LDMS spectra.

Principal component and clustering analysis on molecular dynamics data of the ribosomal L11·23S subdomain.

PubMed

Wolf, Antje; Kirschner, Karl N

2013-02-01

With improvements in computer speed and algorithm efficiency, MD simulations are sampling larger amounts of molecular and biomolecular conformations. Being able to qualitatively and quantitatively sift these conformations into meaningful groups is a difficult and important task, especially when considering the structure-activity paradigm. Here we present a study that combines two popular techniques, principal component (PC) analysis and clustering, for revealing major conformational changes that occur in molecular dynamics (MD) simulations. Specifically, we explored how clustering different PC subspaces effects the resulting clusters versus clustering the complete trajectory data. As a case example, we used the trajectory data from an explicitly solvated simulation of a bacteria's L11·23S ribosomal subdomain, which is a target of thiopeptide antibiotics. Clustering was performed, using K-means and average-linkage algorithms, on data involving the first two to the first five PC subspace dimensions. For the average-linkage algorithm we found that data-point membership, cluster shape, and cluster size depended on the selected PC subspace data. In contrast, K-means provided very consistent results regardless of the selected subspace. Since we present results on a single model system, generalization concerning the clustering of different PC subspaces of other molecular systems is currently premature. However, our hope is that this study illustrates a) the complexities in selecting the appropriate clustering algorithm, b) the complexities in interpreting and validating their results, and c) by combining PC analysis with subsequent clustering valuable dynamic and conformational information can be obtained.

Guided filter and principal component analysis hybrid method for hyperspectral pansharpening

NASA Astrophysics Data System (ADS)

Qu, Jiahui; Li, Yunsong; Dong, Wenqian

2018-01-01

Hyperspectral (HS) pansharpening aims to generate a fused HS image with high spectral and spatial resolution through integrating an HS image with a panchromatic (PAN) image. A guided filter (GF) and principal component analysis (PCA) hybrid HS pansharpening method is proposed. First, the HS image is interpolated and the PCA transformation is performed on the interpolated HS image. The first principal component (PC1) channel concentrates on the spatial information of the HS image. Different from the traditional PCA method, the proposed method sharpens the PAN image and utilizes the GF to obtain the spatial information difference between the HS image and the enhanced PAN image. Then, in order to reduce spectral and spatial distortion, an appropriate tradeoff parameter is defined and the spatial information difference is injected into the PC1 channel through multiplying by this tradeoff parameter. Once the new PC1 channel is obtained, the fused image is finally generated by the inverse PCA transformation. Experiments performed on both synthetic and real datasets show that the proposed method outperforms other several state-of-the-art HS pansharpening methods in both subjective and objective evaluations.

Raman spectra of pigmented skin conditions

NASA Astrophysics Data System (ADS)

Bitar, Renata; Moreno, Marcelo; Oliveira, Andréa; Cartaxo, Sidney; Martinho, Herculano; Espírito Santo, Ana Maria do; Santos, Ivan Dunshee; Ferreira, Lydia Massako; Martin, Airton

2007-02-01

Melanoma is the most aggressive skin cancer and is invariably fatal if left untreated. Melanoma removal at early stages is almost always curative and therefore early detection is essential. Removal of every pigmented lesion is unacceptable for the patient, especially in the case of multiple skin lesions or lesions localized in cosmetically important parts of the body such as the face because of risk of scarring. The development of a technique to detect these changes in a noninvasive way is therefore crucial for melanoma detection. In this study, we have used FT-Raman Spectroscopy to investigate through PCA analysis the alterations in the molecular structure of 90 skin spectra, being 30 Pigmented Nevi, 30 Primary Melanoma, and 30 Metastasis, for 6 patients. For projection of data, the scores (Principal Components) PC1 to PC3 were calculated. PC1 versus PC3 for the 800 to 1800 cm -1 spectral region. PC1 versus PC2 for the 1200 to 1400 cm -1 spectral region. In both analysis, we could differentiate the three different types of tissues.

Spatial assessment of water quality using chemometrics in the Pearl River Estuary, China

NASA Astrophysics Data System (ADS)

Wu, Meilin; Wang, Youshao; Dong, Junde; Sun, Fulin; Wang, Yutu; Hong, Yiguo

2017-03-01

A cruise was commissioned in the summer of 2009 to evaluate water quality in the Pearl River Estuary (PRE). Chemometrics such as Principal Component Analysis (PCA), Cluster analysis (CA) and Self-Organizing Map (SOM) were employed to identify anthropogenic and natural influences on estuary water quality. The scores of stations in the surface layer in the first principal component (PC1) were related to NH4-N, PO4-P, NO2-N, NO3-N, TP, and Chlorophyll a while salinity, turbidity, and SiO3-Si in the second principal component (PC2). Similarly, the scores of stations in the bottom layers in PC1 were related to PO4-P, NO2-N, NO3-N, and TP, while salinity, Chlorophyll a, NH4-N, and SiO3-Si in PC2. Results of the PCA identified the spatial distribution of the surface and bottom water quality, namely the Guangzhou urban reach, Middle reach, and Lower reach of the estuary. Both cluster analysis and PCA produced the similar results. Self-organizing map delineated the Guangzhou urban reach of the Pearl River that was mainly influenced by human activities. The middle and lower reaches of the PRE were mainly influenced by the waters in the South China Sea. The information extracted by PCA, CA, and SOM would be very useful to regional agencies in developing a strategy to carry out scientific plans for resource use based on marine system functions.

The Bolivian "Altiplano" and "Valle" sheep are two different peripatric breeds.

PubMed

Parés-Casanova, Pere M; Pérezgrovas Garza, Raúl

2014-06-01

Forty-nine sheep belonged to the Andean Altiplano region ("Altiplano") and 30 in the lowland regions of Bolivia ("Valle"), aged 1 to 4 years, were wool sampled to determine the extent of difference between these local breeds. Fibre length and the percentage of each type of fibre (long-thick, short-thin and kemp), yield and fibre diameter were measured. There was a highly significant difference between the two sheep populations that were not clearly separated in the first two principal component of a principal components analysis (PC); the first PC explained 67.1 % and the second PC explained 26.6 % of the total variation. The variables that contributed most to the separation of the sheep populations were the percentage of long-thick and short-thin fibres in the first PC and yield in the second PC. A discriminant analysis, which was used to classify individuals with respect to their breeding, achieved an accurate classification rate of 84.2 %. Thus, the Altiplano and Valle sheep must be viewed as two closely peripatric breeds rather than different "ecotypes", as more than 80 % could be correctly assigned to one of the breeds; however, the differences are based on composition of long-thick and short-thin fibres and yield after alcohol scouring.

Cardiorespiratory Coordination after Training and Detraining. A Principal Component Analysis Approach

PubMed Central

Balagué, Natàlia; González, Jacob; Javierre, Casimiro; Hristovski, Robert; Aragonés, Daniel; Álamo, Juan; Niño, Oscar; Ventura, Josep L.

2016-01-01

Our purpose was to study the effects of different training modalities and detraining on cardiorespiratory coordination (CRC). Thirty-two young males were randomly assigned to four training groups: aerobic (AT), resistance (RT), aerobic plus resistance (AT + RT), and control (C). They were assessed before training, after training (6 weeks) and after detraining (3 weeks) by means of a graded maximal test. A principal component (PC) analysis of selected cardiovascular and cardiorespiratory variables was performed to evaluate CRC. The first PC (PC1) coefficient of congruence in the three conditions (before training, after training and after detraining) was compared between groups. Two PCs were identified in 81% of participants before the training period. After this period the number of PCs and the projection of the selected variables onto them changed only in the groups subject to a training programme. The PC1 coefficient of congruence was significantly lower in the training groups compared with the C group [H(3, N=32) = 11.28; p = 0.01]. In conclusion, training produced changes in CRC, reflected by the change in the number of PCs and the congruence values of PC1. These changes may be more sensitive than the usually explored cardiorespiratory reserve, and they probably precede it. PMID:26903884

Principal component analysis-based pattern analysis of dose-volume histograms and influence on rectal toxicity.

PubMed

Söhn, Matthias; Alber, Markus; Yan, Di

2007-09-01

The variability of dose-volume histogram (DVH) shapes in a patient population can be quantified using principal component analysis (PCA). We applied this to rectal DVHs of prostate cancer patients and investigated the correlation of the PCA parameters with late bleeding. PCA was applied to the rectal wall DVHs of 262 patients, who had been treated with a four-field box, conformal adaptive radiotherapy technique. The correlated changes in the DVH pattern were revealed as "eigenmodes," which were ordered by their importance to represent data set variability. Each DVH is uniquely characterized by its principal components (PCs). The correlation of the first three PCs and chronic rectal bleeding of Grade 2 or greater was investigated with uni- and multivariate logistic regression analyses. Rectal wall DVHs in four-field conformal RT can primarily be represented by the first two or three PCs, which describe approximately 94% or 96% of the DVH shape variability, respectively. The first eigenmode models the total irradiated rectal volume; thus, PC1 correlates to the mean dose. Mode 2 describes the interpatient differences of the relative rectal volume in the two- or four-field overlap region. Mode 3 reveals correlations of volumes with intermediate doses ( approximately 40-45 Gy) and volumes with doses >70 Gy; thus, PC3 is associated with the maximal dose. According to univariate logistic regression analysis, only PC2 correlated significantly with toxicity. However, multivariate logistic regression analysis with the first two or three PCs revealed an increased probability of bleeding for DVHs with more than one large PC. PCA can reveal the correlation structure of DVHs for a patient population as imposed by the treatment technique and provide information about its relationship to toxicity. It proves useful for augmenting normal tissue complication probability modeling approaches.

Comparative analysis of different weight matrices in subspace system identification for structural health monitoring

NASA Astrophysics Data System (ADS)

Shokravi, H.; Bakhary, NH

2017-11-01

Subspace System Identification (SSI) is considered as one of the most reliable tools for identification of system parameters. Performance of a SSI scheme is considerably affected by the structure of the associated identification algorithm. Weight matrix is a variable in SSI that is used to reduce the dimensionality of the state-space equation. Generally one of the weight matrices of Principle Component (PC), Unweighted Principle Component (UPC) and Canonical Variate Analysis (CVA) are used in the structure of a SSI algorithm. An increasing number of studies in the field of structural health monitoring are using SSI for damage identification. However, studies that evaluate the performance of the weight matrices particularly in association with accuracy, noise resistance, and time complexity properties are very limited. In this study, the accuracy, noise-robustness, and time-efficiency of the weight matrices are compared using different qualitative and quantitative metrics. Three evaluation metrics of pole analysis, fit values and elapsed time are used in the assessment process. A numerical model of a mass-spring-dashpot and operational data is used in this research paper. It is observed that the principal components obtained using PC algorithms are more robust against noise uncertainty and give more stable results for the pole distribution. Furthermore, higher estimation accuracy is achieved using UPC algorithm. CVA had the worst performance for pole analysis and time efficiency analysis. The superior performance of the UPC algorithm in the elapsed time is attributed to using unit weight matrices. The obtained results demonstrated that the process of reducing dimensionality in CVA and PC has not enhanced the time efficiency but yield an improved modal identification in PC.

The Use of Multi-Component Statistical Techniques in Understanding Subduction Zone Arc Granitic Geochemical Data Sets

NASA Astrophysics Data System (ADS)

Pompe, L.; Clausen, B. L.; Morton, D. M.

2015-12-01

Multi-component statistical techniques and GIS visualization are emerging trends in understanding large data sets. Our research applies these techniques to a large igneous geochemical data set from southern California to better understand magmatic and plate tectonic processes. A set of 480 granitic samples collected by Baird from this area were analyzed for 39 geochemical elements. Of these samples, 287 are from the Peninsular Ranges Batholith (PRB) and 164 from part of the Transverse Ranges (TR). Principal component analysis (PCA) summarized the 39 variables into 3 principal components (PC) by matrix multiplication and for the PRB are interpreted as follows: PC1 with about 30% of the variation included mainly compatible elements and SiO2 and indicates extent of differentation; PC2 with about 20% of the variation included HFS elements and may indicate crustal contamination as usually identified by Sri; PC3 with about 20% of the variation included mainly HRE elements and may indicate magma source depth as often diplayed using REE spider diagrams and possibly Sr/Y. Several elements did not fit well in any of the three components: Cr, Ni, U, and Na2O.For the PRB, the PC1 correlation with SiO2 was r=-0.85, the PC2 correlation with Sri was r=0.80, and the PC3 correlation with Gd/Yb was r=-0.76 and with Sr/Y was r=-0.66 . Extending this method to the TR, correlations were r=-0.85, -0.21, -0.06, and -0.64, respectively. A similar extent of correlation for both areas was visually evident using GIS interpolation.PC1 seems to do well at indicating differentiation index for both the PRB and TR and correlates very well with SiO2, Al2O3, MgO, FeO*, CaO, K2O, Sc, V, and Co, but poorly with Na2O and Cr. If the crustal component is represented by Sri, PC2 correlates well and less expesively with this indicator in the PRB, but not in the TR. Source depth has been related to the slope on REE spidergrams, and PC3 based on only the HREE and using the Sr/Y ratios gives a reasonable correlation for both PRB and TR, but the Gd/Yb ratio gives a reasonable correlation for only the PRB. The PRB data provide reasonable correlation between principal components and standard geochemical indicators, perhaps because of the well-recognized monotonic variation from SW to NE. Data sets from the TR give similar results in some cases, but poor correlation in others.

Classification of the degenerative grade of lesions of supraspinatus rotator cuff tendons by FT-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Palma Fogazza, Bianca; da Silva Carvalho, Carolina; Godoy Penteado, Sergio; Meneses, Cláudio S.; Abrahão Martin, Airton; da Silva Martinho, Herculano

2007-02-01

FT-Raman spectroscopy was employed to access the biochemical alterations occurring on the degenerative process of the rotator cuff supraspinatus tendons. The spectral characteristic variations in the 351 spectra of samples of 39 patients were identified with the help of Principal Components Analysis. The main variations occurred in the 840-911; 1022- 1218; 1257; 1270; 1300; 1452; 1663; and 1751 cm -1 regions corresponding to the vibrational bands of proline, hydroxiproline, lipids, nucleic acids, carbohydrates, collagen, and elastin. These alterations are compatible with the pathology alterations reported on the literature. Scattering plots of PC 4 vs PC 2 and PC 3 vs PC 2 contrasted with histopathological analysis has enabled the spectral classification of the data into normal and degenerated groups of tendons. By depicting empiric lines the estimated sensibility and specificity were 39,6 % and 97,8 %, respectively for PC 4 vs PC 2 and 36,0 % and 100 %, respectively for PC 3 vs PC 2. These results indicate that Raman spectroscopy can be used to probe the general tendon quality and could be applied as co adjuvant element in the usual arthroscopy surgery apparatus to guide the procedure and possibly infer about the probability of rerupture.

RP-HPLC method using 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate incorporated with normalization technique in principal component analysis to differentiate the bovine, porcine and fish gelatins.

PubMed

Azilawati, M I; Hashim, D M; Jamilah, B; Amin, I

2015-04-01

The amino acid compositions of bovine, porcine and fish gelatin were determined by amino acid analysis using 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate as derivatization reagent. Sixteen amino acids were identified with similar spectral chromatograms. Data pre-treatment via centering and transformation of data by normalization were performed to provide data that are more suitable for analysis and easier to be interpreted. Principal component analysis (PCA) transformed the original data matrix into a number of principal components (PCs). Three principal components (PCs) described 96.5% of the total variance, and 2 PCs (91%) explained the highest variances. The PCA model demonstrated the relationships among amino acids in the correlation loadings plot to the group of gelatins in the scores plot. Fish gelatin was correlated to threonine, serine and methionine on the positive side of PC1; bovine gelatin was correlated to the non-polar side chains amino acids that were proline, hydroxyproline, leucine, isoleucine and valine on the negative side of PC1 and porcine gelatin was correlated to the polar side chains amino acids that were aspartate, glutamic acid, lysine and tyrosine on the negative side of PC2. Verification on the database using 12 samples from commercial products gelatin-based had confirmed the grouping patterns and the variables correlations. Therefore, this quantitative method is very useful as a screening method to determine gelatin from various sources. Copyright © 2014 Elsevier Ltd. All rights reserved.

Application of principal component analysis to ecodiversity assessment of postglacial landscape (on the example of Debnica Kaszubska commune, Middle Pomerania)

NASA Astrophysics Data System (ADS)

Wojciechowski, Adam

2017-04-01

In order to assess ecodiversity understood as a comprehensive natural landscape factor (Jedicke 2001), it is necessary to apply research methods which recognize the environment in a holistic way. Principal component analysis may be considered as one of such methods as it allows to distinguish the main factors determining landscape diversity on the one hand, and enables to discover regularities shaping the relationships between various elements of the environment under study on the other hand. The procedure adopted to assess ecodiversity with the use of principal component analysis involves: a) determining and selecting appropriate factors of the assessed environment qualities (hypsometric, geological, hydrographic, plant, and others); b) calculating the absolute value of individual qualities for the basic areas under analysis (e.g. river length, forest area, altitude differences, etc.); c) principal components analysis and obtaining factor maps (maps of selected components); d) generating a resultant, detailed map and isolating several classes of ecodiversity. An assessment of ecodiversity with the use of principal component analysis was conducted in the test area of 299,67 km2 in Debnica Kaszubska commune. The whole commune is situated in the Weichselian glaciation area of high hypsometric and morphological diversity as well as high geo- and biodiversity. The analysis was based on topographical maps of the commune area in scale 1:25000 and maps of forest habitats. Consequently, nine factors reflecting basic environment elements were calculated: maximum height (m), minimum height (m), average height (m), the length of watercourses (km), the area of water reservoirs (m2), total forest area (ha), coniferous forests habitats area (ha), deciduous forest habitats area (ha), alder habitats area (ha). The values for individual factors were analysed for 358 grid cells of 1 km2. Based on the principal components analysis, four major factors affecting commune ecodiversity were distinguished: hypsometric component (PC1), deciduous forest habitats component (PC2), river valleys and alder habitats component (PC3), and lakes component (PC4). The distinguished factors characterise natural qualities of postglacial area and reflect well the role of the four most important groups of environment components in shaping ecodiversity of the area under study. The map of ecodiversity of Debnica Kaszubska commune was created on the basis of the first four principal component scores and then five classes of diversity were isolated: very low, low, average, high and very high. As a result of the assessment, five commune regions of very high ecodiversity were separated. These regions are also very attractive for tourists and valuable in terms of their rich nature which include protected areas such as Slupia Valley Landscape Park. The suggested method of ecodiversity assessment with the use of principal component analysis may constitute an alternative methodological proposition to other research methods used so far. Literature Jedicke E., 2001. Biodiversität, Geodiversität, Ökodiversität. Kriterien zur Analyse der Landschaftsstruktur - ein konzeptioneller Diskussionsbeitrag. Naturschutz und Landschaftsplanung, 33(2/3), 59-68.

Consistent Principal Component Modes from Molecular Dynamics Simulations of Proteins.

PubMed

Cossio-Pérez, Rodrigo; Palma, Juliana; Pierdominici-Sottile, Gustavo

2017-04-24

Principal component analysis is a technique widely used for studying the movements of proteins using data collected from molecular dynamics simulations. In spite of its extensive use, the technique has a serious drawback: equivalent simulations do not afford the same PC-modes. In this article, we show that concatenating equivalent trajectories and calculating the PC-modes from the concatenated one significantly enhances the reproducibility of the results. Moreover, the consistency of the modes can be systematically improved by adding more individual trajectories to the concatenated one.

Does long time spending on the electronic devices affect the reading abilities? A cross-sectional study among Chinese school-aged children.

PubMed

He, Zhen; Shao, Shanshan; Zhou, Jie; Ke, Juntao; Kong, Rui; Guo, Shengnan; Zhang, Jiajia; Song, Ranran

2014-12-01

Home literacy environment (HLE) is one of most important modifiable risk factors to dyslexia. With the development in technology, we include the electronic devices usage at home, such as computers and televisions, to the definition of HLE and investigate its impact on dyslexia based on the on-going project of Tongji's Reading Environment and Dyslexia Study. The data include 5063 children, primary school students (grade 3-grade 6), from a middle-sized city in China. We apply the principal component analysis (PCA) to reduce the large dimension of variables in HLE, and find the first three components, denoted as PC1, PC2 and PC3, can explain 95.45% of HLE information. PC1 and PC2 demonstrate strong positive association with 'total time spending on electronic devices' and 'literacy-related activity', respectively. PC3 demonstrates strong negative association with 'restrictions on using electronic devices'. From the generalized linear model, we find that PC1 significantly increases the risk of dyslexia (OR = 1.043, 95% CI: 1.018-1.070), while PC2 significantly decreases the risk of dyslexia (OR = 0.839, 95% CI: 0.795-0.886). Therefore, reducing the total time spending on electronic devices and increasing the literacy-related activity would be the potential protective factors for dyslexic children in China. Copyright © 2014 Elsevier Ltd. All rights reserved.

Principle Component Analysis of the Evolution of the Saharan Air Layer and Dust Transport: Comparisons between a Model Simulation and MODIS Retrievals

NASA Technical Reports Server (NTRS)

Wong, S.; Colarco, P. R.; Dessler, A.

2006-01-01

The onset and evolution of Saharan Air Layer (SAL) episodes during June-September 2002 are diagnosed by applying principal component analysis to the NCEP reanalysis temperature anomalies at 850 hPa, where the largest SAL-induced temperature anomalies are located. The first principal component (PC) represents the onset of SAL episodes, which are associated with large warm anomalies located at the west coast of Africa. The second PC represents two opposite phases of the evolution of the SAL. The positive phase of the second PC corresponds to the southwestward extension of the warm anomalies into the tropical-subtropical North Atlantic Ocean, and the negative phase corresponds to the northwestward extension into the subtropical to mid-latitude North Atlantic Ocean and the southwest Europe. A dust transport model (CARMA) and the MODIS retrievals are used to study the associated effects on dust distribution and deposition. The positive (negative) phase of the second PC corresponds to a strengthening (weakening) of the offshore flows in the lower troposphere around 10deg - 20degN, causing more (less) dust being transported along the tropical to subtropical North Atlantic Ocean. The variation of the offshore flow indicates that the subseasonal variation of African Easterly Jet is associated with the evolution of the SAL. Significant correlation is found between the second PC time series and the daily West African monsoon index, implying a dynamical linkage between West African monsoon and the evolution of the SAL and Saharan dust transport.

Multivariate analysis of mixed contaminants (PAHs and heavy metals) at manufactured gas plant site soils.

PubMed

Thavamani, Palanisami; Megharaj, Mallavarapu; Naidu, Ravi

2012-06-01

Principal component analysis (PCA) was used to provide an overview of the distribution pattern of polycyclic aromatic hydrocarbons (PAHs) and heavy metals in former manufactured gas plant (MGP) site soils. PCA is the powerful multivariate method to identify the patterns in data and expressing their similarities and differences. Ten PAHs (naphthalene, acenapthylene, acenaphthene, fluorene, phenanthrene, anthracene, fluoranthene, pyrene, chrysene, benzo[a]pyrene) and four toxic heavy metals - lead (Pb), cadmium (Cd), chromium (Cr) and zinc (Zn) - were detected in the site soils. PAH contamination was contributed equally by both low and high molecular weight PAHs. PCA was performed using the varimax rotation method in SPSS, 17.0. Two principal components accounting for 91.7% of the total variance was retained using scree test. Principle component 1 (PC1) substantially explained the dominance of PAH contamination in the MGP site soils. All PAHs, except anthracene, were positively correlated in PC1. There was a common thread in high molecular weight PAHs loadings, where the loadings were inversely proportional to the hydrophobicity and molecular weight of individual PAHs. Anthracene, which was less correlated with other individual PAHs, deviated well from the origin which can be ascribed to its lower toxicity and different origin than its isomer phenanthrene. Among the four major heavy metals studied in MGP sites, Pb, Cd and Cr were negatively correlated in PC1 but showed strong positive correlation in principle component 2 (PC2). Although metals may not have originated directly from gaswork processes, the correlation between PAHs and metals suggests that the materials used in these sites may have contributed to high concentrations of Pb, Cd, Cr and Zn. Thus, multivariate analysis helped to identify the sources of PAHs, heavy metals and their association in MGP site, and thereby better characterise the site risk, which would not be possible if one uses chemical analysis alone.

State and group dynamics of world stock market by principal component analysis

NASA Astrophysics Data System (ADS)

Nobi, Ashadun; Lee, Jae Woo

2016-05-01

We study the dynamic interactions and structural changes by a principal component analysis (PCA) to cross-correlation coefficients of global financial indices in the years 1998-2012. The variances explained by the first PC increase with time and show a drastic change during the crisis. A sharp change in PC coefficient implies a transition of market state, a situation which occurs frequently in the American and Asian indices. However, the European indices remain stable over time. Using the first two PC coefficients, we identify indices that are similar and more strongly correlated than the others. We observe that the European indices form a robust group over the observation period. The dynamics of the individual indices within the group increase in similarity with time, and the dynamics of indices are more similar during the crises. Furthermore, the group formation of indices changes position in two-dimensional spaces due to crises. Finally, after a financial crisis, the difference of PCs between the European and American indices narrows.

Characterization and source apportionment of particle number concentration at a semi-urban tropical environment.

PubMed

Khan, Md Firoz; Latif, Mohd Talib; Amil, Norhaniza; Juneng, Liew; Mohamad, Noorlin; Nadzir, Mohd Shahrul Mohd; Hoque, Hossain Mohammed Syedul

2015-09-01

Principal component analysis (PCA) and correlation have been used to study the variability of particle mass and particle number concentrations (PNC) in a tropical semi-urban environment. PNC and mass concentration (diameter in the range of 0.25->32.0 μm) have been measured from 1 February to 26 February 2013 using an in situ Grimm aerosol sampler. We found that the 24-h average total suspended particulates (TSP), particulate matter ≤10 μm (PM10), particulate matter ≤2.5 μm (PM2.5) and particulate matter ≤1 μm (PM1) were 14.37 ± 4.43, 14.11 ± 4.39, 12.53 ± 4.13 and 10.53 ± 3.98 μg m(-3), respectively. PNC in the accumulation mode (<500 nm) was the most abundant (at about 99 %). Five principal components (PCs) resulted from the PCA analysis where PC1 (43.8 % variance) predominates with PNC in the fine and sub-microme tre range. PC2, PC3, PC4 and PC5 explain 16.5, 12.4, 6.0 and 5.6 % of the variance to address the coarse, coarser, accumulation and giant fraction of PNC, respectively. Our particle distribution results show good agreement with the moderate resolution imaging spectroradiometer (MODIS) distribution.

CARES/PC - CERAMICS ANALYSIS AND RELIABILITY EVALUATION OF STRUCTURES

NASA Technical Reports Server (NTRS)

Szatmary, S. A.

1994-01-01

The beneficial properties of structural ceramics include their high-temperature strength, light weight, hardness, and corrosion and oxidation resistance. For advanced heat engines, ceramics have demonstrated functional abilities at temperatures well beyond the operational limits of metals. This is offset by the fact that ceramic materials tend to be brittle. When a load is applied, their lack of significant plastic deformation causes the material to crack at microscopic flaws, destroying the component. CARES/PC performs statistical analysis of data obtained from the fracture of simple, uniaxial tensile or flexural specimens and estimates the Weibull and Batdorf material parameters from this data. CARES/PC is a subset of the program CARES (COSMIC program number LEW-15168) which calculates the fast-fracture reliability or failure probability of ceramic components utilizing the Batdorf and Weibull models to describe the effects of multi-axial stress states on material strength. CARES additionally requires that the ceramic structure be modeled by a finite element program such as MSC/NASTRAN or ANSYS. The more limited CARES/PC does not perform fast-fracture reliability estimation of components. CARES/PC estimates ceramic material properties from uniaxial tensile or from three- and four-point bend bar data. In general, the parameters are obtained from the fracture stresses of many specimens (30 or more are recommended) whose geometry and loading configurations are held constant. Parameter estimation can be performed for single or multiple failure modes by using the least-squares analysis or the maximum likelihood method. Kolmogorov-Smirnov and Anderson-Darling goodness-of-fit tests measure the accuracy of the hypothesis that the fracture data comes from a population with a distribution specified by the estimated Weibull parameters. Ninety-percent confidence intervals on the Weibull parameters and the unbiased value of the shape parameter for complete samples are provided when the maximum likelihood technique is used. CARES/PC is written and compiled with the Microsoft FORTRAN v5.0 compiler using the VAX FORTRAN extensions and dynamic array allocation supported by this compiler for the IBM/MS-DOS or OS/2 operating systems. The dynamic array allocation routines allow the user to match the number of fracture sets and test specimens to the memory available. Machine requirements include IBM PC compatibles with optional math coprocessor. Program output is designed to fit 80-column format printers. Executables for both DOS and OS/2 are provided. CARES/PC is distributed on one 5.25 inch 360K MS-DOS format diskette in compressed format. The expansion tool PKUNZIP.EXE is supplied on the diskette. CARES/PC was developed in 1990. IBM PC and OS/2 are trademarks of International Business Machines. MS-DOS and MS OS/2 are trademarks of Microsoft Corporation. VAX is a trademark of Digital Equipment Corporation.

The risk of misclassifying subjects within principal component based asset index

PubMed Central

2014-01-01

The asset index is often used as a measure of socioeconomic status in empirical research as an explanatory variable or to control confounding. Principal component analysis (PCA) is frequently used to create the asset index. We conducted a simulation study to explore how accurately the principal component based asset index reflects the study subjects’ actual poverty level, when the actual poverty level is generated by a simple factor analytic model. In the simulation study using the PC-based asset index, only 1% to 4% of subjects preserved their real position in a quintile scale of assets; between 44% to 82% of subjects were misclassified into the wrong asset quintile. If the PC-based asset index explained less than 30% of the total variance in the component variables, then we consistently observed more than 50% misclassification across quintiles of the index. The frequency of misclassification suggests that the PC-based asset index may not provide a valid measure of poverty level and should be used cautiously as a measure of socioeconomic status. PMID:24987446

Combination of 1H nuclear magnetic resonance spectroscopy and principal component analysis to evaluate the lipid fluidity of flutamide-encapsulated lipid nanoemulsions.

PubMed

Takegami, Shigehiko; Ueyama, Keita; Konishi, Atsuko; Kitade, Tatsuya

2018-06-06

The lipid fluidity of various lipid nanoemulsions (LNEs) without and with flutamide (FT) and containing one of two neutral lipids, one of four phosphatidylcholines as a surfactant, and sodium palmitate as a cosurfactant was investigated by the combination of 1 H nuclear magnetic resonance (NMR) spectroscopy and principal component analysis (PCA). In the 1 H NMR spectra, the peaks from the methylene groups of the neutral lipids and surfactants for all LNE preparations showed downfield shifts with increasing temperature from 20 to 60 °C. PCA was applied to the 1 H NMR spectral data obtained for the LNEs. The PCA resulted in a model in which the first two principal components (PCs) extracted 88% of the total spectral variation; the first PC (PC-1) axis and second PC (PC-2) axis accounted for 73 and 15%, respectively, of the total spectral variation. The Score-1 values for PC-1 plotted against temperature revealed the existence of two clusters, which were defined by the neutral lipid of the LNE preparations. Meanwhile, the Score-2 values decreased with rising temperature and reflected the increase in lipid fluidity of each LNE preparation, consistent with fluorescence anisotropy measurements. In addition, the changes of Score-2 values with temperature for LNE preparations with FT were smaller than those for LNE preparations without FT. This indicates that FT encapsulated in LNE particles markedly suppressed the increase in lipid fluidity of LNE particles with rising temperature. Thus, PCA of 1 H NMR spectra will become a powerful tool to analyze the lipid fluidity of lipid nanoparticles. Graphical abstract ᅟ.

A PCA-Based method for determining craniofacial relationship and sexual dimorphism of facial shapes.

PubMed

Shui, Wuyang; Zhou, Mingquan; Maddock, Steve; He, Taiping; Wang, Xingce; Deng, Qingqiong

2017-11-01

Previous studies have used principal component analysis (PCA) to investigate the craniofacial relationship, as well as sex determination using facial factors. However, few studies have investigated the extent to which the choice of principal components (PCs) affects the analysis of craniofacial relationship and sexual dimorphism. In this paper, we propose a PCA-based method for visual and quantitative analysis, using 140 samples of 3D heads (70 male and 70 female), produced from computed tomography (CT) images. There are two parts to the method. First, skull and facial landmarks are manually marked to guide the model's registration so that dense corresponding vertices occupy the same relative position in every sample. Statistical shape spaces of the skull and face in dense corresponding vertices are constructed using PCA. Variations in these vertices, captured in every principal component (PC), are visualized to observe shape variability. The correlations of skull- and face-based PC scores are analysed, and linear regression is used to fit the craniofacial relationship. We compute the PC coefficients of a face based on this craniofacial relationship and the PC scores of a skull, and apply the coefficients to estimate a 3D face for the skull. To evaluate the accuracy of the computed craniofacial relationship, the mean and standard deviation of every vertex between the two models are computed, where these models are reconstructed using real PC scores and coefficients. Second, each PC in facial space is analysed for sex determination, for which support vector machines (SVMs) are used. We examined the correlation between PCs and sex, and explored the extent to which the choice of PCs affects the expression of sexual dimorphism. Our results suggest that skull- and face-based PCs can be used to describe the craniofacial relationship and that the accuracy of the method can be improved by using an increased number of face-based PCs. The results show that the accuracy of the sex classification is related to the choice of PCs. The highest sex classification rate is 91.43% using our method. Copyright © 2017 Elsevier Ltd. All rights reserved.

Gas, dust, stars, star formation, and their evolution in M 33 at giant molecular cloud scales

NASA Astrophysics Data System (ADS)

Komugi, Shinya; Miura, Rie E.; Kuno, Nario; Tosaki, Tomoka

2018-06-01

We report on a multi-parameter analysis of giant molecular clouds (GMCs) in the nearby spiral galaxy M 33. A catalog of GMCs identifed in 12CO(J = 3-2) was used to compile associated 12CO(J = 1-0), dust, stellar mass, and star formation rate. Each of the 58 GMCs are categorized by their evolutionary stage. Applying the principal component analysis on these parameters, we construct two principal components, PC1 and PC2, which retain 75% of the information from the original data set. PC1 is interpreted as expressing the total interstellar matter content, and PC2 as the total activity of star formation. Young (< 10 Myr) GMCs occupy a distinct region in the PC1-PC2 plane, with lower interstellar medium (ISM) content and star formation activity compared to intermediate-age and older clouds. Comparison of average cloud properties in different evolutionary stages imply that GMCs may be heated or grow denser and more massive via aggregation of diffuse material in their first ˜ 10 Myr. The PCA also objectively identified a set of tight relations between ISM and star formation. The ratio of the two CO lines is nearly constant, but weakly modulated by massive star formation. Dust is more strongly correlated with the star formation rate than the CO lines, supporting recent findings that dust may trace molecular gas better than CO. Stellar mass contributes weakly to the star formation rate, reminiscent of an extended form of the Schmidt-Kennicutt relation with the molecular gas term substituted by dust.

Gas, dust, stars, star formation, and their evolution in M 33 at giant molecular cloud scales

NASA Astrophysics Data System (ADS)

Komugi, Shinya; Miura, Rie E.; Kuno, Nario; Tosaki, Tomoka

2018-04-01

We report on a multi-parameter analysis of giant molecular clouds (GMCs) in the nearby spiral galaxy M 33. A catalog of GMCs identifed in 12CO(J = 3-2) was used to compile associated 12CO(J = 1-0), dust, stellar mass, and star formation rate. Each of the 58 GMCs are categorized by their evolutionary stage. Applying the principal component analysis on these parameters, we construct two principal components, PC1 and PC2, which retain 75% of the information from the original data set. PC1 is interpreted as expressing the total interstellar matter content, and PC2 as the total activity of star formation. Young (< 10 Myr) GMCs occupy a distinct region in the PC1-PC2 plane, with lower interstellar medium (ISM) content and star formation activity compared to intermediate-age and older clouds. Comparison of average cloud properties in different evolutionary stages imply that GMCs may be heated or grow denser and more massive via aggregation of diffuse material in their first ˜ 10 Myr. The PCA also objectively identified a set of tight relations between ISM and star formation. The ratio of the two CO lines is nearly constant, but weakly modulated by massive star formation. Dust is more strongly correlated with the star formation rate than the CO lines, supporting recent findings that dust may trace molecular gas better than CO. Stellar mass contributes weakly to the star formation rate, reminiscent of an extended form of the Schmidt-Kennicutt relation with the molecular gas term substituted by dust.

Serum metabolomics differentiating pancreatic cancer from new-onset diabetes

PubMed Central

He, Xiangyi; Zhong, Jie; Wang, Shuwei; Zhou, Yufen; Wang, Lei; Zhang, Yongping; Yuan, Yaozong

2017-01-01

To establish a screening strategy for pancreatic cancer (PC) based on new-onset diabetic mellitus (NO-DM), serum metabolomics analysis and a search for the metabolic pathways associated with PC related DM were performed. Serum samples from patients with NO-DM (n = 30) and patients with pancreatic cancer and NO-DM were examined by liquid chromatography-mass spectrometry. Data were analyzed using principal components analysis (PCA) and orthogonal projection to latent structures (OPLS) of the most significant metabolites. The diagnostic model was constructed using logistic regression analysis. Metabolic pathways were analyzed using the web-based tool MetPA. PC patients with NO-DM were older and had a lower BMI and shorter duration of DM than those with NO-DM. The metabolomic profiles of patients with PC and NO-DM were significantly different from those of patients with NO-DM in the PCA and OPLS models. Sixty two differential metabolites were identified by the OPLS model. The logistic regression model using a panel of two metabolites including N_Succinyl_L_diaminopimelic_acid and PE (18:2) had high sensitivity (93.3%) and specificity (93.1%) for PC. The top three metabolic pathways associated with PC related DM were valine, leucine and isoleucine biosynthesis and degradation, primary bile acid biosynthesis, and sphingolipid metabolism. In conclusion, screening for PC based on NO-DM using serum metabolomics in combination with clinic characteristics and CA19-9 is a potential useful strategy. Several metabolic pathways differed between PC related DM and type 2 DM. PMID:28418859

Transcriptional regulation of crystallin, redox, and apoptotic genes by C-Phycocyanin in the selenite-induced cataractogenic rat model

PubMed Central

Kumari, Rasiah Pratheepa; Ramkumar, Srinivasagan; Thankappan, Bency; Natarajaseenivasan, Kalimuthusamy; Balaji, Sadhasivam

2015-01-01

Purpose This study was designed to examine the constrictive potential of C-Phycocyanin (C-PC) in regulating changes imposed on gene expression in the selenite-induced cataract model. Methods Wistar rat pups were divided into three groups of eight each. On P10, Group I received an intraperitoneal injection of normal saline. Groups II and III received a subcutaneous injection of sodium selenite (19 μmol/kg bodyweight); Group III also received an intraperitoneal injection of C-PC (200 mg/kg bodyweight) on P9–14. Total RNA was isolated on P16, and the relative abundance of mRNA of the crystallin structural genes, redox components, and apoptotic cascade were ascertained with real-time PCR with reference to the internal control β-actin. Results Real-time PCR analysis showed the crystallin genes (αA-, βB1-, γD-) and redox cycle components (Cat, SOD-1, Gpx) were downregulated, the apoptotic components were upregulated, and antiapoptotic Bcl-2 was downregulated in Group II. Treatment with 200 mg/kg bodyweight C-PC (Group III) transcriptionally regulated the instability of the expression of these genes, thus ensuring C-PC is a prospective anticataractogenic agent that probably delays the onset and progression of cataractogenesis induced by sodium selenite. Conclusions C-PC treatment possibly prevented cataractogenesis triggered by sodium selenite, by regulating the lens crystallin, redox genes, and apoptotic cascade mRNA expression and thus maintains lens transparency. C-PC may be developed as a potential antioxidant compound applied in the future to prevent and treat age-related cataract. PMID:25593511

Genus- and species-level identification of dermatophyte fungi by surface-enhanced Raman spectroscopy.

PubMed

Witkowska, Evelin; Jagielski, Tomasz; Kamińska, Agnieszka

2018-03-05

This paper demonstrates that surface-enhanced Raman spectroscopy (SERS) coupled with principal component analysis (PCA) can serve as a fast and reliable technique for detection and identification of dermatophyte fungi at both genus and species level. Dermatophyte infections are the most common mycotic diseases worldwide, affecting a quarter of the human population. Currently, there is no optimal method for detection and identification of fungal diseases, as each has certain limitations. Here, for the first time, we have achieved with a high accuracy, differentiation of dermatophytes representing three major genera, i.e. Trichophyton, Microsporum, and Epidermophyton. Two first principal components (PC), namely PC-1 and PC-2, gave together 97% of total variance. Additionally, species-level identification within the Trichophyton genus has been performed. PC-1 and PC-2, which are the most diagnostically significant, explain 98% of the variance in the data obtained from spectra of: Trichophyton rubrum, Trichophyton menatgrophytes, Trichophyton interdigitale and Trichophyton tonsurans. This study offers a new diagnostic approach for the identification of dermatophytes. Being fast, reliable and cost-effective, it has the potential to be incorporated in the clinical practice to improve diagnostics of medically important fungi. Copyright © 2017 Elsevier B.V. All rights reserved.

Genus- and species-level identification of dermatophyte fungi by surface-enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

Witkowska, Evelin; Jagielski, Tomasz; Kamińska, Agnieszka

2018-03-01

This paper demonstrates that surface-enhanced Raman spectroscopy (SERS) coupled with principal component analysis (PCA) can serve as a fast and reliable technique for detection and identification of dermatophyte fungi at both genus and species level. Dermatophyte infections are the most common mycotic diseases worldwide, affecting a quarter of the human population. Currently, there is no optimal method for detection and identification of fungal diseases, as each has certain limitations. Here, for the first time, we have achieved with a high accuracy, differentiation of dermatophytes representing three major genera, i.e. Trichophyton, Microsporum, and Epidermophyton. Two first principal components (PC), namely PC-1 and PC-2, gave together 97% of total variance. Additionally, species-level identification within the Trichophyton genus has been performed. PC-1 and PC-2, which are the most diagnostically significant, explain 98% of the variance in the data obtained from spectra of: Trichophyton rubrum, Trichophyton menatgrophytes, Trichophyton interdigitale and Trichophyton tonsurans. This study offers a new diagnostic approach for the identification of dermatophytes. Being fast, reliable and cost-effective, it has the potential to be incorporated in the clinical practice to improve diagnostics of medically important fungi.

Genetic algorithm applied to the selection of factors in principal component-artificial neural networks: application to QSAR study of calcium channel antagonist activity of 1,4-dihydropyridines (nifedipine analogous).

PubMed

Hemmateenejad, Bahram; Akhond, Morteza; Miri, Ramin; Shamsipur, Mojtaba

2003-01-01

A QSAR algorithm, principal component-genetic algorithm-artificial neural network (PC-GA-ANN), has been applied to a set of newly synthesized calcium channel blockers, which are of special interest because of their role in cardiac diseases. A data set of 124 1,4-dihydropyridines bearing different ester substituents at the C-3 and C-5 positions of the dihydropyridine ring and nitroimidazolyl, phenylimidazolyl, and methylsulfonylimidazolyl groups at the C-4 position with known Ca(2+) channel binding affinities was employed in this study. Ten different sets of descriptors (837 descriptors) were calculated for each molecule. The principal component analysis was used to compress the descriptor groups into principal components. The most significant descriptors of each set were selected and used as input for the ANN. The genetic algorithm (GA) was used for the selection of the best set of extracted principal components. A feed forward artificial neural network with a back-propagation of error algorithm was used to process the nonlinear relationship between the selected principal components and biological activity of the dihydropyridines. A comparison between PC-GA-ANN and routine PC-ANN shows that the first model yields better prediction ability.

Short communication: Principal components and factor analytic models for test-day milk yield in Brazilian Holstein cattle.

PubMed

Bignardi, A B; El Faro, L; Rosa, G J M; Cardoso, V L; Machado, P F; Albuquerque, L G

2012-04-01

A total of 46,089 individual monthly test-day (TD) milk yields (10 test-days), from 7,331 complete first lactations of Holstein cattle were analyzed. A standard multivariate analysis (MV), reduced rank analyses fitting the first 2, 3, and 4 genetic principal components (PC2, PC3, PC4), and analyses that fitted a factor analytic structure considering 2, 3, and 4 factors (FAS2, FAS3, FAS4), were carried out. The models included the random animal genetic effect and fixed effects of the contemporary groups (herd-year-month of test-day), age of cow (linear and quadratic effects), and days in milk (linear effect). The residual covariance matrix was assumed to have full rank. Moreover, 2 random regression models were applied. Variance components were estimated by restricted maximum likelihood method. The heritability estimates ranged from 0.11 to 0.24. The genetic correlation estimates between TD obtained with the PC2 model were higher than those obtained with the MV model, especially on adjacent test-days at the end of lactation close to unity. The results indicate that for the data considered in this study, only 2 principal components are required to summarize the bulk of genetic variation among the 10 traits. Copyright © 2012 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Genetic Evaluation of Dual-Purpose Buffaloes (Bubalus bubalis) in Colombia Using Principal Component Analysis

PubMed Central

Agudelo-Gómez, Divier; Pineda-Sierra, Sebastian; Cerón-Muñoz, Mario Fernando

2015-01-01

Genealogy and productive information of 48621 dual-purpose buffaloes born in Colombia between years 1996 and 2014 was used. The following traits were assessed using one-trait models: milk yield at 270 days (MY270), age at first calving (AFC), weaning weight (WW), and weights at the following ages: first year (W12), 18 months (W18), and 2 years (W24). Direct additive genetic and residual random effects were included in all the traits. Maternal permanent environmental and maternal additive genetic effects were included for WW and W12. The fixed effects were: contemporary group (for all traits), sex (for WW, W12, W18, and W24), parity (for WW, W12, and MY270). Age was included as covariate for WW, W12, W18 and W24. Principal component analysis (PCA) was conducted using the genetic values of 133 breeding males whose breeding-value reliability was higher than 50% for all the traits in order to define the number of principal components (PC) which would explain most of the variation. The highest heritabilities were for W18 and MY270, and the lowest for AFC; with 0.53, 0.23, and 0.17, respectively. The first three PCs represented 66% of the total variance. Correlation of the first PC with meat production traits was higher than 0.73, and it was -0.38 with AFC. Correlations of the second PC with maternal genetic component traits for WW and W12 were above 0.75. The third PC had 0.84 correlation with MY270. PCA is an alternative approach for analyzing traits in dual-purpose buffaloes and reduces the dimension of the traits. PMID:26230093

Seasonal and Spatial Variability of Anthropogenic and Natural Factors Influencing Groundwater Quality Based on Source Apportionment

PubMed Central

Guo, Xueru; Zuo, Rui; Meng, Li; Wang, Jinsheng; Teng, Yanguo; Liu, Xin; Chen, Minhua

2018-01-01

Globally, groundwater resources are being deteriorated by rapid social development. Thus, there is an urgent need to assess the combined impacts of natural and enhanced anthropogenic sources on groundwater chemistry. The aim of this study was to identify seasonal characteristics and spatial variations in anthropogenic and natural effects, to improve the understanding of major hydrogeochemical processes based on source apportionment. 34 groundwater points located in a riverside groundwater resource area in northeast China were sampled during the wet and dry seasons in 2015. Using principal component analysis and factor analysis, 4 principal components (PCs) were extracted from 16 groundwater parameters. Three of the PCs were water-rock interaction (PC1), geogenic Fe and Mn (PC2), and agricultural pollution (PC3). A remarkable difference (PC4) was organic pollution originating from negative anthropogenic effects during the wet season, and geogenic F enrichment during the dry season. Groundwater exploitation resulted in dramatic depression cone with higher hydraulic gradient around the water source area. It not only intensified dissolution of calcite, dolomite, gypsum, Fe, Mn and fluorine minerals, but also induced more surface water recharge for the water source area. The spatial distribution of the PCs also suggested the center of the study area was extremely vulnerable to contamination by Fe, Mn, COD, and F−. PMID:29415516

Quality of life in adults with congenital adrenal hyperplasia relates to glucocorticoid treatment, adiposity and insulin resistance: United Kingdom Congenital adrenal Hyperplasia Adult Study Executive (CaHASE)

PubMed Central

Han, Thang S; Krone, Nils; Willis, Debbie S; Conway, Gerard S; Hahner, Stefanie; Rees, D Aled; Stimson, Roland H; Walker, Brian R; Arlt, Wiebke; Ross, Richard J

2013-01-01

Context Quality of life (QoL) has been variously reported as normal or impaired in adults with congenital adrenal hyperplasia (CAH). To explore the reasons for this discrepancy we investigated the relationship between QoL, glucocorticoid treatment and other health outcomes in CAH adults. Methods Cross-sectional analysis of 151 adults with 21-hydroxylase deficiency aged 18–69 years in whom QoL (assessed using the Short Form Health Survey), glucocorticoid regimen, anthropometric and metabolic measures were recorded. Relationships were examined between QoL, type of glucocorticoid (hydrocortisone, prednisolone and dexamethasone) and dose of glucocorticoid expressed as prednisolone dose equivalent (PreDEq). QoL was expressed as z-scores calculated from matched controls (14 430 subjects from UK population). Principal components analysis (PCA) was undertaken to identify clusters of associated clinical and biochemical features and the principal component (PC) scores used in regression analysis as predictor of QoL. Results QoL scores were associated with type of glucocorticoid treatment for vitality (P=0.002) and mental health (P=0.011), with higher z-scores indicating better QoL in patients on hydrocortisone monotherapy (P<0.05). QoL did not relate to PreDEq or mutation severity. PCA identified three PCs (PC1, disease control; PC2, adiposity and insulin resistance and PC3, blood pressure and mutations) that explained 61% of the variance in observed variables. Stepwise multiple regression analysis demonstrated that PC2, reflecting adiposity and insulin resistance (waist circumference, serum triglycerides, homeostasis model assessment of insulin resistance and HDL-cholesterol), related to QoL scores, specifically impaired physical functioning, bodily pain, general health, Physical Component Summary Score (P<0.001) and vitality (P=0.002). Conclusions Increased adiposity, insulin resistance and use of prednisolone or dexamethasone are associated with impaired QoL in adults with CAH. Intervention trials are required to establish whether choice of glucocorticoid treatment and/or weight loss can improve QoL in CAH adults. PMID:23520247

Impact of 4-epi-oxytetracycline on the gut microbiota and blood metabolomics of Wistar rats

PubMed Central

Han, Hongxing; Xiao, Hailong; Zhang, Kai; Lu, Zhenmei

2016-01-01

The impact of 4-epi-oxytetracycline (4-EOTC), one of the main oxytetracycline (OTC) metabolites, on the gut microbiota and physiological metabolism of Wistar rats was analyzed to explore the dynamic alterations apparent after repeated oral exposure (0.5, 5.0 or 50.0 mg/kg bw) for 15 days as shown by 16S rRNA pyrosequencing and UPLC-Q-TOF/MS analysis. Both principal component analysis and cluster analysis showed consistently altered patterns with distinct differences in the treated groups versus the control groups. 4-EOTC treatment at 5.0 or 50.0 mg/kg increased the relative abundance of the Actinobacteria, specifically Bifidobacteriaceae, and improved the synthesis of lysophosphatidylcholine (LysoPC), as shown by the lipid biomarkers LysoPC(16:0), LysoPC(18:3), LysoPC(20:3), and LysoPC(20:4). The metabolomic analysis of urine samples also identified four other decreased metabolites: diacylglycerol, sphingomyelin, triacylglycerol, and phosphatidylglycerol. Notably, the significant changes observed in these biomarkers demonstrated the ongoing disorder induced by 4-EOTC. Blood and urine analysis revealed that residual 4-EOTC accumulated in the rats, even two weeks after oral 4-EOTC administration, ceased. Thus, through thorough analysis, it can be concluded that the alteration of the gut microbiota and disorders in blood metabolomics are correlated with 4-EOTC treatment. PMID:26976662

Impact of 4-epi-oxytetracycline on the gut microbiota and blood metabolomics of Wistar rats.

PubMed

Han, Hongxing; Xiao, Hailong; Zhang, Kai; Lu, Zhenmei

2016-03-15

The impact of 4-epi-oxytetracycline (4-EOTC), one of the main oxytetracycline (OTC) metabolites, on the gut microbiota and physiological metabolism of Wistar rats was analyzed to explore the dynamic alterations apparent after repeated oral exposure (0.5, 5.0 or 50.0 mg/kg bw) for 15 days as shown by 16S rRNA pyrosequencing and UPLC-Q-TOF/MS analysis. Both principal component analysis and cluster analysis showed consistently altered patterns with distinct differences in the treated groups versus the control groups. 4-EOTC treatment at 5.0 or 50.0 mg/kg increased the relative abundance of the Actinobacteria, specifically Bifidobacteriaceae, and improved the synthesis of lysophosphatidylcholine (LysoPC), as shown by the lipid biomarkers LysoPC(16:0), LysoPC(18:3), LysoPC(20:3), and LysoPC(20:4). The metabolomic analysis of urine samples also identified four other decreased metabolites: diacylglycerol, sphingomyelin, triacylglycerol, and phosphatidylglycerol. Notably, the significant changes observed in these biomarkers demonstrated the ongoing disorder induced by 4-EOTC. Blood and urine analysis revealed that residual 4-EOTC accumulated in the rats, even two weeks after oral 4-EOTC administration, ceased. Thus, through thorough analysis, it can be concluded that the alteration of the gut microbiota and disorders in blood metabolomics are correlated with 4-EOTC treatment.

77 FR 42225 - Airworthiness Directives; PILATUS AIRCRAFT LTD. Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-18

... (AD) for all PILATUS AIRCRAFT LTD. Models PC 12, PC 12/45, PC 12/47, and PC 12/47E airplanes that... instructions and airworthiness limitations applicable to the Structure and Components of the PC-12 are... Pilatus Aircraft LTD. Models PC 12, PC 12/45, PC 12/47, and PC-12/47E airplanes, all manufacturer serial...

Method of mounting a PC board to a hybrid

NASA Technical Reports Server (NTRS)

O'Coin, James R. (Inventor)

1999-01-01

A system for mounting a hybrid electronic component to a PC board is disclosed. The system includes a set of brackets for mutually engaging a first surface of the PC board and a cover surface of the hybrid electronic component, wherein the cover surface has an arcuate shape when in a vacuum environment. The brackets are designed with legs having lengths and thicknesses for providing clearance between the cover surface of the hybrid and the first surface of the PC board for use when the hybrid electronic component is in a vacuum environment.

Spectral decomposition of asteroid Itokawa based on principal component analysis

NASA Astrophysics Data System (ADS)

Koga, Sumire C.; Sugita, Seiji; Kamata, Shunichi; Ishiguro, Masateru; Hiroi, Takahiro; Tatsumi, Eri; Sasaki, Sho

2018-01-01

The heliocentric stratification of asteroid spectral types may hold important information on the early evolution of the Solar System. Asteroid spectral taxonomy is based largely on principal component analysis. However, how the surface properties of asteroids, such as the composition and age, are projected in the principal-component (PC) space is not understood well. We decompose multi-band disk-resolved visible spectra of the Itokawa surface with principal component analysis (PCA) in comparison with main-belt asteroids. The obtained distribution of Itokawa spectra projected in the PC space of main-belt asteroids follows a linear trend linking the Q-type and S-type regions and is consistent with the results of space-weathering experiments on ordinary chondrites and olivine, suggesting that this trend may be a space-weathering-induced spectral evolution track for S-type asteroids. Comparison with space-weathering experiments also yield a short average surface age (< a few million years) for Itokawa, consistent with the cosmic-ray-exposure time of returned samples from Itokawa. The Itokawa PC score distribution exhibits asymmetry along the evolution track, strongly suggesting that space weathering has begun saturated on this young asteroid. The freshest spectrum found on Itokawa exhibits a clear sign for space weathering, indicating again that space weathering occurs very rapidly on this body. We also conducted PCA on Itokawa spectra alone and compared the results with space-weathering experiments. The obtained results indicate that the first principal component of Itokawa surface spectra is consistent with spectral change due to space weathering and that the spatial variation in the degree of space weathering is very large (a factor of three in surface age), which would strongly suggest the presence of strong regional/local resurfacing process(es) on this small asteroid.

Real time gamma-ray signature identifier

DOEpatents

Rowland, Mark [Alamo, CA; Gosnell, Tom B [Moraga, CA; Ham, Cheryl [Livermore, CA; Perkins, Dwight [Livermore, CA; Wong, James [Dublin, CA

2012-05-15

A real time gamma-ray signature/source identification method and system using principal components analysis (PCA) for transforming and substantially reducing one or more comprehensive spectral libraries of nuclear materials types and configurations into a corresponding concise representation/signature(s) representing and indexing each individual predetermined spectrum in principal component (PC) space, wherein an unknown gamma-ray signature may be compared against the representative signature to find a match or at least characterize the unknown signature from among all the entries in the library with a single regression or simple projection into the PC space, so as to substantially reduce processing time and computing resources and enable real-time characterization and/or identification.

Comprehensive two-dimensional PC-3 prostate cancer cell membrane chromatography for screening anti-tumor components from Radix Sophorae flavescentis.

PubMed

Wang, Qiang; Xu, Junnan; Li, Xiang; Zhang, Dawei; Han, Yong; Zhang, Xu

2017-07-01

Radix Sophorae flavescentis is generally used for the treatment of different stages of prostate cancer in China. It has ideal effects when combined with surgical treatment and chemotherapy. However, its active components are still ambiguous. We devised a comprehensive two-dimensional PC-3 prostate cancer cell membrane chromatography system for screening anti-prostate cancer components in Radix Sophorae flavescentis. Gefitinib and dexamethasone were chosen as positive and negative drugs respectively for validation and optimization the selectivity and suitability of the comprehensive two-dimensional chromatographic system. Five compounds, sophocarpine, matrine, oxymatrine, oxysophocarpine, and xanthohumol were found to have significant retention behaviors on the PC-3 cell membrane chromatography and were unambiguously identified by time-of-flight mass spectrometry. Cell proliferation and apoptosis assays confirmed that all five compounds had anti-prostate cancer effects. Matrine and xanthohumol had good inhibitory effects, with half maximal inhibitory concentration values of 0.893 and 0.137 mg/mL, respectively. Our comprehensive two-dimensional PC-3 prostate cancer cell membrane chromatographic system promotes the efficient recognition and rapid analysis of drug candidates, and it will be practical for the discovery of prostate cancer drugs from complex traditional Chinese medicines. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Use of Principal Components Analysis and Kriging to Predict Groundwater-Sourced Rural Drinking Water Quality in Saskatchewan

PubMed Central

McLeod, Lianne; Bharadwaj, Lalita; Epp, Tasha; Waldner, Cheryl L.

2017-01-01

Groundwater drinking water supply surveillance data were accessed to summarize water quality delivered as public and private water supplies in southern Saskatchewan as part of an exposure assessment for epidemiologic analyses of associations between water quality and type 2 diabetes or cardiovascular disease. Arsenic in drinking water has been linked to a variety of chronic diseases and previous studies have identified multiple wells with arsenic above the drinking water standard of 0.01 mg/L; therefore, arsenic concentrations were of specific interest. Principal components analysis was applied to obtain principal component (PC) scores to summarize mixtures of correlated parameters identified as health standards and those identified as aesthetic objectives in the Saskatchewan Drinking Water Quality Standards and Objective. Ordinary, universal, and empirical Bayesian kriging were used to interpolate arsenic concentrations and PC scores in southern Saskatchewan, and the results were compared. Empirical Bayesian kriging performed best across all analyses, based on having the greatest number of variables for which the root mean square error was lowest. While all of the kriging methods appeared to underestimate high values of arsenic and PC scores, empirical Bayesian kriging was chosen to summarize large scale geographic trends in groundwater-sourced drinking water quality and assess exposure to mixtures of trace metals and ions. PMID:28914824

Use of Principal Components Analysis and Kriging to Predict Groundwater-Sourced Rural Drinking Water Quality in Saskatchewan.

PubMed

McLeod, Lianne; Bharadwaj, Lalita; Epp, Tasha; Waldner, Cheryl L

2017-09-15

Groundwater drinking water supply surveillance data were accessed to summarize water quality delivered as public and private water supplies in southern Saskatchewan as part of an exposure assessment for epidemiologic analyses of associations between water quality and type 2 diabetes or cardiovascular disease. Arsenic in drinking water has been linked to a variety of chronic diseases and previous studies have identified multiple wells with arsenic above the drinking water standard of 0.01 mg/L; therefore, arsenic concentrations were of specific interest. Principal components analysis was applied to obtain principal component (PC) scores to summarize mixtures of correlated parameters identified as health standards and those identified as aesthetic objectives in the Saskatchewan Drinking Water Quality Standards and Objective. Ordinary, universal, and empirical Bayesian kriging were used to interpolate arsenic concentrations and PC scores in southern Saskatchewan, and the results were compared. Empirical Bayesian kriging performed best across all analyses, based on having the greatest number of variables for which the root mean square error was lowest. While all of the kriging methods appeared to underestimate high values of arsenic and PC scores, empirical Bayesian kriging was chosen to summarize large scale geographic trends in groundwater-sourced drinking water quality and assess exposure to mixtures of trace metals and ions.

Polarization-resolved second-harmonic generation microscopy as a method to visualize protein-crystal domains

PubMed Central

DeWalt, Emma L.; Begue, Victoria J.; Ronau, Judith A.; Sullivan, Shane Z.; Das, Chittaranjan; Simpson, Garth J.

2013-01-01

Polarization-resolved second-harmonic generation (PR-SHG) microscopy is described and applied to identify the presence of multiple crystallographic domains within protein-crystal conglomerates, which was confirmed by synchrotron X-ray diffraction. Principal component analysis (PCA) of PR-SHG images resulted in principal component 2 (PC2) images with areas of contrasting negative and positive values for conglomerated crystals and PC2 images exhibiting uniformly positive or uniformly negative values for single crystals. Qualitative assessment of PC2 images allowed the identification of domains of different internal ordering within protein-crystal samples as well as differentiation between multi-domain conglomerated crystals and single crystals. PR-SHG assessments of crystalline domains were in good agreement with spatially resolved synchrotron X-ray diffraction measurements. These results have implications for improving the productive throughput of protein structure determination through early identification of multi-domain crystals. PMID:23275165

Strategies for reducing large fMRI data sets for independent component analysis.

PubMed

Wang, Ze; Wang, Jiongjiong; Calhoun, Vince; Rao, Hengyi; Detre, John A; Childress, Anna R

2006-06-01

In independent component analysis (ICA), principal component analysis (PCA) is generally used to reduce the raw data to a few principal components (PCs) through eigenvector decomposition (EVD) on the data covariance matrix. Although this works for spatial ICA (sICA) on moderately sized fMRI data, it is intractable for temporal ICA (tICA), since typical fMRI data have a high spatial dimension, resulting in an unmanageable data covariance matrix. To solve this problem, two practical data reduction methods are presented in this paper. The first solution is to calculate the PCs of tICA from the PCs of sICA. This approach works well for moderately sized fMRI data; however, it is highly computationally intensive, even intractable, when the number of scans increases. The second solution proposed is to perform PCA decomposition via a cascade recursive least squared (CRLS) network, which provides a uniform data reduction solution for both sICA and tICA. Without the need to calculate the covariance matrix, CRLS extracts PCs directly from the raw data, and the PC extraction can be terminated after computing an arbitrary number of PCs without the need to estimate the whole set of PCs. Moreover, when the whole data set becomes too large to be loaded into the machine memory, CRLS-PCA can save data retrieval time by reading the data once, while the conventional PCA requires numerous data retrieval steps for both covariance matrix calculation and PC extractions. Real fMRI data were used to evaluate the PC extraction precision, computational expense, and memory usage of the presented methods.

Principal component analysis of early alcohol, drug and tobacco use with major depressive disorder in US adults.

PubMed

Wang, Kesheng; Liu, Ying; Ouedraogo, Youssoufou; Wang, Nianyang; Xie, Xin; Xu, Chun; Luo, Xingguang

2018-05-01

Early alcohol, tobacco and drug use prior to 18 years old are comorbid and correlated. This study included 6239 adults with major depressive disorder (MDD) in the past year and 72,010 controls from the combined data of 2013 and 2014 National Survey on Drug Use and Health (NSDUH). To deal with multicollinearity existing among 17 variables related to early alcohol, tobacco and drug use prior to 18 years old, we used principal component analysis (PCA) to infer PC scores and then use weighted multiple logistic regression analyses to estimate the associations of potential factors and PC scores with MDD. The odds ratios (ORs) with 95% confidence intervals (CIs) were estimated. The overall prevalence of MDD was 6.7%. The first four PCs could explain 57% of the total variance. Weighted multiple logistic regression showed that PC 1 (a measure of psychotherapeutic drugs and illicit drugs other than marijuana use), PC 2 (a measure of cocaine and hallucinogens), PC 3 (a measure of early alcohol, cigarettes, and marijuana use), and PC 4 (a measure of cigar, smokeless tobacco use and illicit drugs use) revealed significant associations with MDD (OR = 1.12, 95% CI = 1.08-1.16, OR = 1.08, 95% CI = 1.04-1.12, OR = 1.13, 95% CI = 1.07-1.18, and OR = 1.15, 95% CI = 1.09-1.21, respectively). In conclusion, PCA can be used to reduce the indicators in complex survey data. Early alcohol, tobacco and drug use prior to 18 years old were found to be associated with increased odds of adult MDD. Copyright © 2018 Elsevier Ltd. All rights reserved.

Principal component analysis and hydrochemical facies characterization to evaluate groundwater quality in Varahi river basin, Karnataka state, India

NASA Astrophysics Data System (ADS)

Ravikumar, P.; Somashekar, R. K.

2017-05-01

The present study envisages the importance of graphical representations like Piper trilinear diagram and Chadha's plot, respectively to determine variation in hydrochemical facies and understand the evolution of hydrochemical processes in the Varahi river basin. The analytical values obtained from the groundwater samples when plotted on Piper's and Chadha's plots revealed that the alkaline earth metals (Ca2+, Mg2+) are significantly dominant over the alkalis (Na+, K+), and the strong acidic anions (Cl-, SO4 2-) dominant over the weak acidic anions (CO3 2-, HCO3 -). Further, Piper trilinear diagram classified 93.48 % of the samples from the study area under Ca2+-Mg2+-Cl--SO4 2- type and only 6.52 % samples under Ca2+-Mg2+-HCO3 - type. Interestingly, Chadha's plot also demonstrated the dominance of reverse ion exchange water having permanent hardness (viz., Ca-Mg-Cl type) in majority of the samples over recharging water with temporary hardness (i.e., Ca-Mg-HCO3 type). Thus, evaluation of hydrochemical facies from both the plots highlighted the contribution from the reverse ion exchange processes in controlling geochemistry of groundwater in the study area. Further, PCA analysis yielded four principal components (PC1, PC2, PC3 and PC4) with higher eigen values of 1.0 or more, accounting for 65.55, 10.17, 6.88 and 6.52 % of the total variance, respectively. Consequently, majority of the physico-chemical parameters (87.5 %) loaded under PC1 and PC2 were having strong positive loading (>0.75) and these are mainly responsible for regulating the hydrochemistry of groundwater in the study area.

Robust inference of population structure for ancestry prediction and correction of stratification in the presence of relatedness.

PubMed

Conomos, Matthew P; Miller, Michael B; Thornton, Timothy A

2015-05-01

Population structure inference with genetic data has been motivated by a variety of applications in population genetics and genetic association studies. Several approaches have been proposed for the identification of genetic ancestry differences in samples where study participants are assumed to be unrelated, including principal components analysis (PCA), multidimensional scaling (MDS), and model-based methods for proportional ancestry estimation. Many genetic studies, however, include individuals with some degree of relatedness, and existing methods for inferring genetic ancestry fail in related samples. We present a method, PC-AiR, for robust population structure inference in the presence of known or cryptic relatedness. PC-AiR utilizes genome-screen data and an efficient algorithm to identify a diverse subset of unrelated individuals that is representative of all ancestries in the sample. The PC-AiR method directly performs PCA on the identified ancestry representative subset and then predicts components of variation for all remaining individuals based on genetic similarities. In simulation studies and in applications to real data from Phase III of the HapMap Project, we demonstrate that PC-AiR provides a substantial improvement over existing approaches for population structure inference in related samples. We also demonstrate significant efficiency gains, where a single axis of variation from PC-AiR provides better prediction of ancestry in a variety of structure settings than using 10 (or more) components of variation from widely used PCA and MDS approaches. Finally, we illustrate that PC-AiR can provide improved population stratification correction over existing methods in genetic association studies with population structure and relatedness. © 2015 WILEY PERIODICALS, INC.

Evaluation of the temporal variations of air quality in Taipei City, Taiwan, from 1994 to 2003.

PubMed

Chang, Shuenn-Chin; Lee, Chung-Te

2008-03-01

Data collected from the five air-quality monitoring stations established by the Taiwan Environmental Protection Administration in Taipei City from 1994 to 2003 are analyzed to assess the temporal variations of air quality. Principal component analysis (PCA) is adopted to convert the original measuring pollutants into fewer independent components through linear combinations while still retaining the majority of the variance of the original data set. Two principal components (PCs) are retained together explaining 82.73% of the total variance. PC1, which represents primary pollutants such as CO, NO(x), and SO(2), shows an obvious decrease over the last 10 years. PC2, which represents secondary pollutants such as ozone, displays a yearly increase over the time period when a reduction of primary pollutants is obvious. In order to track down the control measures put forth by the authorities, 47 days of high PM(10) concentrations caused by transboundary transport have been eliminated in analyzing the long-term trend of PM(10) in Taipei City. The temporal variations over the past 10 years show that the moderate peak in O(3) demonstrates a significant upward trend even when the local primary pollutants have been well under control. Monthly variations of PC scores demonstrate that primary pollution is significant from January to April, while ozone increases from April to August. The results of the yearly variations of PC scores show that PM(10) has gradually shifted from a strong correlation with PC1 during the early years to become more related to PC2 in recent years. This implies that after a reduction of primary pollutants, the proportion of secondary aerosols in PM(10) may increase. Thus, reducing the precursor concentrations of secondary aerosols will be an effective way to lower PM(10) concentrations.

Research of seafloor topographic analyses for a staged mineral exploration

NASA Astrophysics Data System (ADS)

Ikeda, M.; Kadoshima, K.; Koizumi, Y.; Yamakawa, T.; Asakawa, E.; Sumi, T.; Kose, M.

2016-12-01

J-MARES (Research and Development Partnership for Next Generation Technology of Marine Resources Survey, JAPAN) has been designing a low-cost and high-efficiency exploration system for seafloor hydrothermal massive sulfide (SMS) deposits in "Cross-ministerial Strategic Innovation Promotion Program (SIP)" granted by the Cabinet Office, Government of Japan since 2014. We proposed the multi-stage approach, which is designed from the regional scaled to the detail scaled survey stages through semi-detail scaled, focusing a prospective area by seafloor topographic analyses. We applied this method to the area of more than 100km x 100km around Okinawa Trough, including some well-known mineralized deposits. In the regional scale survey, we assume survey areas are more than 100 km x 100km. Then the spatial resolution of topography data should be bigger than 100m. The 500 m resolution data which is interpolated into 250 m resolution was used for extracting depression and performing principal component analysis (PCA) by the wavelength obtained from frequency analysis. As the result, we have successfully extracted the areas having the topographic features quite similar to well-known mineralized deposits. In the semi-local survey stage, we use the topography data obtained by bathymetric survey using multi-narrow beam echo-sounder. The 30m-resolution data was used for extracting depression, relative-large mounds, hills, lineaments as fault, and also for performing frequency analysis. As the result, wavelength as principal component constituting in the target area was extracted by PCA of wavelength obtained from frequency analysis. Therefore, color image was composited by using the second principal component (PC2) to the forth principal component (PC4) in which the continuity of specific wavelength was observed, and consistent with extracted lineaments. In addition, well-known mineralized deposits were discriminated in the same clusters by using clustering from PC2 to PC4.We applied the results described above to a new area, and successfully extract the quite similar area in vicinity to one of the well-known mineralized deposits. So we are going to verify the extracted areas by using geophysical methods, such as vertical cable seismic and time-domain EM survey, developed in this SIP project.

Study of Geochemical System in Constructed Wetland Using Multivariate Statistical Analysis

NASA Astrophysics Data System (ADS)

Chen, V.

2015-12-01

People have recognized that the human activities lead to the degradation of the environment, and constructed wetland is one of the well-known technologies for water treatment. In constructed wetland, complicated processes should be considered such as redox reactions, acid-base reactions, adsorption-desorption between water and sediment and biochemical reactions associated with plant and microorganism. In this study, most of inorganic components were analyzed and principal component analysis (PCA) was followed for depicting the controlling biochemical reaction in the constructed wetland. The results could be a guide to operate the constructed wetland. The constructed wetland in this study is located in Taoyuan County, north Taiwan. It's a horizontal subsurface flow constructed wetland composed of ten cells. The water in wetland was pumped from Nankan River, which collects wastewater from Hwaya technology park, Linkou, Guishan and Nankan industrial zone. The water of inflow and outflow from each cell were collected for analyzing inorganic components with ICP-MS and IC. In general, the results show that water quality had dramatically changed in the first three cells and became stable in the following seven cells. In this study, PCA extracted two major factors (PCs), which can respectively explain 52.76%（PC1）and 28.32%（PC2）of variance of water quality data. PC1 separates samples of the first three cells from those of the other following cells. It is believed that there was another pollution source involved in the 4th cell because PC1 is characterized by high loadings of most of trace heavy metals. On the other hand, the hydrochemistry of water mainly evolve along PC2 axis. PC2 is composed of Fe, Mn, NH4, dissolved oxygen, pH, etc with high loadings. These chemical components are predominately controlled by redox reactions. Moreover, the deep water from the 4th cell contains high concentrations of many heavy metals, especially Cu and Ga. This confirms the previous derivation based on PCA. The rare earth elements (REEs) were also measured in this study. After normalized to North American shale, the REEs shows an uncommon pattern with Eu and Gd positive anomalies and Tm negative anomaly, which probably result from industrial contamination. However, more studies would be needed to prove it.

Crosstalk between stromal cells and cancer cells in pancreatic cancer: New insights into stromal biology.

PubMed

Zhan, Han-Xiang; Zhou, Bin; Cheng, Yu-Gang; Xu, Jian-Wei; Wang, Lei; Zhang, Guang-Yong; Hu, San-Yuan

2017-04-28

Pancreatic cancer (PC) remains one of the most lethal malignancies worldwide. Increasing evidence has confirmed the pivotal role of stromal components in the regulation of carcinogenesis, invasion, metastasis, and therapeutic resistance in PC. Interaction between neoplastic cells and stromal cells builds a specific microenvironment, which further modulates the malignant properties of cancer cells. Instead of being a "passive bystander", stroma may play a role as a "partner in crime" in PC. However, the role of stromal components in PC is complex and requires further investigation. In this article, we review recent advances regarding the regulatory roles and mechanisms of stroma biology, especially the cellular components such as pancreatic stellate cells, macrophages, neutrophils, adipocytes, epithelial cells, pericytes, mast cells, and lymphocytes, in PC. Crosstalk between stromal cells and cancer cells is thoroughly investigated. We also review the prognostic value and molecular therapeutic targets of stroma in PC. This review may help us further understand the molecular mechanisms of stromal biology and its role in PC development and therapeutic resistance. Moreover, targeting stroma components may provide new therapeutic strategies for this stubborn disease. Copyright © 2017 Elsevier B.V. All rights reserved.

The USL NASA PC R and D project: Detailed specifications of objects

NASA Technical Reports Server (NTRS)

Dominick, Wayne D. (Editor); Chum, Frank Y.; Hall, Philip P.; Moreau, Dennis R.; Triantafyllopoulos, Spiros

1984-01-01

The specifications for a number of projects which are to be implemented within the University of Southwestern Louisiana NASA PC R and D Project are discussed. The goals and objectives of the PC development project and the interrelationships of the various components are discussed. Six projects are described. They are a NASA/RECON simulator, a user interface to multiple remote information systems, evaluation of various personal computer systems, statistical analysis software development, interactive presentation system development, and the development of a distributed processing environment. The relationships of these projects to one another and to the goals and objectives of the overall project are discussed.

Local Prediction Models on Mid-Atlantic Ridge MORB by Principal Component Regression

NASA Astrophysics Data System (ADS)

Ling, X.; Snow, J. E.; Chin, W.

2017-12-01

The isotopic compositions of the daughter isotopes of long-lived radioactive systems (Sr, Nd, Hf and Pb ) can be used to map the scale and history of mantle heterogeneities beneath mid-ocean ridges. Our goal is to relate the multidimensional structure in the existing isotopic dataset with an underlying physical reality of mantle sources. The numerical technique of Principal Component Analysis is useful to reduce the linear dependence of the data to a minimum set of orthogonal eigenvectors encapsulating the information contained (cf Agranier et al 2005). The dataset used for this study covers almost all the MORBs along mid-Atlantic Ridge (MAR), from 54oS to 77oN and 8.8oW to -46.7oW, including replicating the dataset of Agranier et al., 2005 published plus 53 basalt samples dredged and analyzed since then (data from PetDB). The principal components PC1 and PC2 account for 61.56% and 29.21%, respectively, of the total isotope ratios variability. The samples with similar compositions to HIMU and EM and DM are identified to better understand the PCs. PC1 and PC2 are accountable for HIMU and EM whereas PC2 has limited control over the DM source. PC3 is more strongly controlled by the depleted mantle source than PC2. What this means is that all three principal components have a high degree of significance relevant to the established mantle sources. We also tested the relationship between mantle heterogeneity and sample locality. K-means clustering algorithm is a type of unsupervised learning to find groups in the data based on feature similarity. The PC factor scores of each sample are clustered into three groups. Cluster one and three are alternating on the north and south MAR. Cluster two exhibits on 45.18oN to 0.79oN and -27.9oW to -30.40oW alternating with cluster one. The ridge has been preliminarily divided into 16 sections considering both the clusters and ridge segments. The principal component regression models the section based on 6 isotope ratios and PCs. The prediction residual is about 1-2km. It means that the combined 5 isotopes are a strong predictor of geographic location along the ridge, a slightly surprising result. PCR is a robust and powerful method for both visualizing and manipulating the multidimensional representation of isotope data.

Lifetime shift work exposure: association with anthropometry, body composition, blood pressure, glucose and heart rate variability.

PubMed

Souza, Breno Bernardes; Monteze, Nayara Mussi; de Oliveira, Fernando Luiz Pereira; de Oliveira, José Magalhães; de Freitas Nascimento, Silvia; Marques do Nascimento Neto, Raimundo; Sales, Maria Lilian; Souza, Gabriela Guerra Leal

2015-03-01

To evaluate the association between lifetime exposure to shift work and blood pressure, fasting glucose (FG), anthropometric variables, body composition and heart rate variability (HRV). Male shift workers (N=438) were evaluated using principal component (PC) analysis. The variables used were: weight, body mass index (BMI), waist circumference (WC), neck circumference (NC), hip circumference (HC), waist-to-hip ratio (WHR), waist-to-height ratio (WHtR), body fat mass (BFKg), body fat percentage (BF%), visceral fat area (VFA), FG, systolic (SBP) and diastolic blood pressure (DBP), and HRV variables. ECG was performed, extracting heart rate (HR), root mean square of the successive differences (RMSSD), high frequency (HF), low frequency (LF) and the LF/HF ratio. Using linear regression models, the lifetime shift work exposure was associated with each PC. Five PCs were obtained, which accounted for 79.6% of the total variation of the data. PC1 (weight, BMI, WC, NC, HC, WHR, WHtR, BFKg, BF% and VFA) was designated as body obesity; PC2 (HF, RMSSD and LF) as good cardiac regulation; PC3 (SBP and DBP) as blood pressure; PC4 (LF/HF ratio and HR) as bad cardiac regulation and PC5 (WHR and FG) as insulin resistance. After age adjustment, the regression analysis showed that lifetime shift work was negatively associated with PC2 and positively associated with PC3. The association of lifetime shift work exposure with PC2 and PC3 suggests that shift work promotes unfavourable changes in autonomic cardiac control related to a decrease in parasympathetic modulation and an increase in blood pressure. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Dynamic of consumer groups and response of commodity markets by principal component analysis

NASA Astrophysics Data System (ADS)

Nobi, Ashadun; Alam, Shafiqul; Lee, Jae Woo

2017-09-01

This study investigates financial states and group dynamics by applying principal component analysis to the cross-correlation coefficients of the daily returns of commodity futures. The eigenvalues of the cross-correlation matrix in the 6-month timeframe displays similar values during 2010-2011, but decline following 2012. A sharp drop in eigenvalue implies the significant change of the market state. Three commodity sectors, energy, metals and agriculture, are projected into two dimensional spaces consisting of two principal components (PC). We observe that they form three distinct clusters in relation to various sectors. However, commodities with distinct features have intermingled with one another and scattered during severe crises, such as the European sovereign debt crises. We observe the notable change of the position of two dimensional spaces of groups during financial crises. By considering the first principal component (PC1) within the 6-month moving timeframe, we observe that commodities of the same group change states in a similar pattern, and the change of states of one group can be used as a warning for other group.

Analysis of Floral Volatile Components and Antioxidant Activity of Different Varieties of Chrysanthemum morifolium.

PubMed

Yang, Lu; Cheng, Ping; Wang, Jin-Hui; Li, Hong

2017-10-23

This study investigated the volatile flavor compounds and antioxidant properties of the essential oil of chrysanthemums that was extracted from the fresh flowers of 10 taxa of Chrysanthemum morifolium from three species; namely Dendranthema morifolium (Ramat.) Yellow, Dendranthema morifolium (Ramat.) Red, Dendranthema morifolium (Ramat.) Pink, Dendranthema morifolium (Ramat.) White, Pericallis hybrid Blue, Pericallis hybrid Pink, Pericallis hybrid Purple, Bellis perennis Pink, Bellis perennis Yellow, and Bellis perennis White. The antioxidant capacity of the essential oil was assayed by spectrophotometric analysis. The volatile flavor compounds from the fresh flowers were collected using dynamic headspace collection, analyzed using auto thermal desorber-gas chromatography/mass spectrometry, and identified with quantification using the external standard method. The antioxidant activities of Chrysanthemum morifolium were evaluated by DPPH and FRAP assays, and the results showed that the antioxidant activity of each sample was not the same. The different varieties of fresh Chrysanthemum morifolium flowers were distinguished and classified by fingerprint similarity evaluation, principle component analysis (PCA), and cluster analysis. The results showed that the floral volatile component profiles were significantly different among the different Chrysanthemum morifolium varieties. A total of 36 volatile flavor compounds were identified with eight functional groups: hydrocarbons, terpenoids, aromatic compounds, alcohols, ketones, ethers, aldehydes, and esters. Moreover, the variability among Chrysanthemum morifolium in basis to the data, and the first three principal components (PC1, PC2, and PC3) accounted for 96.509% of the total variance (55.802%, 30.599%, and 10.108%, respectively). PCA indicated that there were marked differences among Chrysanthemum morifolium varieties. The cluster analysis confirmed the results of the PCA analysis. In conclusion, the results of this study provide a basis for breeding Chrysanthemum cultivars with desirable floral scents, and they further support the view that some plants are promising sources of natural antioxidants.

Adaptive non-local means on local principle neighborhood for noise/artifacts reduction in low-dose CT images.

PubMed

Zhang, Yuanke; Lu, Hongbing; Rong, Junyan; Meng, Jing; Shang, Junliang; Ren, Pinghong; Zhang, Junying

2017-09-01

Low-dose CT (LDCT) technique can reduce the x-ray radiation exposure to patients at the cost of degraded images with severe noise and artifacts. Non-local means (NLM) filtering has shown its potential in improving LDCT image quality. However, currently most NLM-based approaches employ a weighted average operation directly on all neighbor pixels with a fixed filtering parameter throughout the NLM filtering process, ignoring the non-stationary noise nature of LDCT images. In this paper, an adaptive NLM filtering scheme on local principle neighborhoods (PC-NLM) is proposed for structure-preserving noise/artifacts reduction in LDCT images. Instead of using neighboring patches directly, in the PC-NLM scheme, the principle component analysis (PCA) is first applied on local neighboring patches of the target patch to decompose the local patches into uncorrelated principle components (PCs), then a NLM filtering is used to regularize each PC of the target patch and finally the regularized components is transformed to get the target patch in image domain. Especially, in the NLM scheme, the filtering parameter is estimated adaptively from local noise level of the neighborhood as well as the signal-to-noise ratio (SNR) of the corresponding PC, which guarantees a "weaker" NLM filtering on PCs with higher SNR and a "stronger" filtering on PCs with lower SNR. The PC-NLM procedure is iteratively performed several times for better removal of the noise and artifacts, and an adaptive iteration strategy is developed to reduce the computational load by determining whether a patch should be processed or not in next round of the PC-NLM filtering. The effectiveness of the presented PC-NLM algorithm is validated by experimental phantom studies and clinical studies. The results show that it can achieve promising gain over some state-of-the-art methods in terms of artifact suppression and structure preservation. With the use of PCA on local neighborhoods to extract principal structural components, as well as adaptive NLM filtering on PCs of the target patch using filtering parameter estimated based on the local noise level and corresponding SNR, the proposed PC-NLM method shows its efficacy in preserving fine anatomical structures and suppressing noise/artifacts in LDCT images. © 2017 American Association of Physicists in Medicine.

ARDS User Manual

NASA Technical Reports Server (NTRS)

Fleming, David P.

2001-01-01

Personal computers (PCs) are now used extensively for engineering analysis. their capability exceeds that of mainframe computers of only a few years ago. Programs originally written for mainframes have been ported to PCs to make their use easier. One of these programs is ARDS (Analysis of Rotor Dynamic Systems) which was developed at Arizona State University (ASU) by Nelson et al. to quickly and accurately analyze rotor steady state and transient response using the method of component mode synthesis. The original ARDS program was ported to the PC in 1995. Several extensions were made at ASU to increase the capability of mainframe ARDS. These extensions have also been incorporated into the PC version of ARDS. Each mainframe extension had its own user manual generally covering only that extension. Thus to exploit the full capability of ARDS required a large set of user manuals. Moreover, necessary changes and enhancements for PC ARDS were undocumented. The present document is intended to remedy those problems by combining all pertinent information needed for the use of PC ARDS into one volume.

Characterization of Hatay honeys according to their multi-element analysis using ICP-OES combined with chemometrics.

PubMed

Yücel, Yasin; Sultanoğlu, Pınar

2013-09-01

Chemical characterisation has been carried out on 45 honey samples collected from Hatay region of Turkey. The concentrations of 17 elements were determined by inductively coupled plasma optical emission spectrometry (ICP-OES). Ca, K, Mg and Na were the most abundant elements, with mean contents of 219.38, 446.93, 49.06 and 95.91 mg kg(-1) respectively. The trace element mean contents ranged between 0.03 and 15.07 mg kg(-1). Chemometric methods such as principal component analysis (PCA) and cluster analysis (CA) techniques were applied to classify honey according to mineral content. The first most important principal component (PC) was strongly associated with the value of Al, B, Cd and Co. CA showed eight clusters corresponding to the eight botanical origins of honey. PCA explained 75.69% of the variance with the first six PC variables. Chemometric analysis of the analytical data allowed the accurate classification of the honey samples according to origin. Copyright © 2013 Elsevier Ltd. All rights reserved.

Global and system-specific resting-state fMRI fluctuations are uncorrelated: principal component analysis reveals anti-correlated networks.

PubMed

Carbonell, Felix; Bellec, Pierre; Shmuel, Amir

2011-01-01

The influence of the global average signal (GAS) on functional-magnetic resonance imaging (fMRI)-based resting-state functional connectivity is a matter of ongoing debate. The global average fluctuations increase the correlation between functional systems beyond the correlation that reflects their specific functional connectivity. Hence, removal of the GAS is a common practice for facilitating the observation of network-specific functional connectivity. This strategy relies on the implicit assumption of a linear-additive model according to which global fluctuations, irrespective of their origin, and network-specific fluctuations are super-positioned. However, removal of the GAS introduces spurious negative correlations between functional systems, bringing into question the validity of previous findings of negative correlations between fluctuations in the default-mode and the task-positive networks. Here we present an alternative method for estimating global fluctuations, immune to the complications associated with the GAS. Principal components analysis was applied to resting-state fMRI time-series. A global-signal effect estimator was defined as the principal component (PC) that correlated best with the GAS. The mean correlation coefficient between our proposed PC-based global effect estimator and the GAS was 0.97±0.05, demonstrating that our estimator successfully approximated the GAS. In 66 out of 68 runs, the PC that showed the highest correlation with the GAS was the first PC. Since PCs are orthogonal, our method provides an estimator of the global fluctuations, which is uncorrelated to the remaining, network-specific fluctuations. Moreover, unlike the regression of the GAS, the regression of the PC-based global effect estimator does not introduce spurious anti-correlations beyond the decrease in seed-based correlation values allowed by the assumed additive model. After regressing this PC-based estimator out of the original time-series, we observed robust anti-correlations between resting-state fluctuations in the default-mode and the task-positive networks. We conclude that resting-state global fluctuations and network-specific fluctuations are uncorrelated, supporting a Resting-State Linear-Additive Model. In addition, we conclude that the network-specific resting-state fluctuations of the default-mode and task-positive networks show artifact-free anti-correlations.

Relations of Principal Components Analysis Site Scores to Algal-Biomass, Habitat, Basin-Characteristics, Nutrient, and Biological-Community Data in the West Fork White River Basin, Indiana, 2001

USGS Publications Warehouse

Frey, Jeffrey W.; Caskey, Brian J.; Lowe, B. Scott

2007-01-01

Data were gathered from July through September 2001 at 34 randomly selected sites in the West Fork White River Basin, Indiana for algal biomass, habitat, nutrients, and biological communities (fish and invertebrates). Basin characteristics (drainage area and land use) and biological-community attributes and metric scores were determined for the basin of each sampling site. Yearly Principal Components Analysis site scores were calculated for algal biomass (periphyton and seston). The yearly Principal Components Analysis site scores for the first axis (PC1) were related, using Spearman's rho, to the seasonal algal-biomass, basin-characteristics, habitat, seasonal nutrient, biological-community attribute and metric score data. The periphyton PC1 site score, which was most influenced by ash-free dry mass, was negatively related to one (percent closed canopy) of nine habitat variables examined. Of the 43 fish-community attributes and metric scores examined, the periphyton PC1 was positively related to one fish-community attribute (percent tolerant). Of the 21 invertebrate-community attributes and metric scores examined, the periphyton PC1 was positively related to one attribute (Ephemeroptera, Plecoptera, and Trichoptera (EPT) index) and one metric score (EPT index metric score). The periphyton PC1 was not related to the five basin-characteristic or 12 nutrient variables examined. The seston PC1 site score, which was most influenced by particulate organic carbon, was negatively related to two of the 12 nutrient variables examined: total Kjeldahl nitrogen (July) and total phosphorus (July). Of the 43 fish-community attributes and metric scores examined, the seston PC1 was negatively related to one attribute (large-river percent). Of the 21 invertebrate-community attributes and metric scores examined, the seston PC1 was negatively related to one attribute (EPT-to-total ratio). The seston PC1 was not related to the five basin-characteristics or nine habitat variables examined. To understand how the choice of sampling sites might have affected the results, an analysis of the drainage area and land use was done. The 34 randomly selected sites in the West Fork White River Basin in 2001 were skewed to small streams. The dominant mean land use of the sites sampled was agriculture, followed by forest, and urban. The values for nutrients (nitrate, total Kjeldahl nitrogen, total nitrogen, and total phosphorus) and chlorophyll a (periphyton and seston) were compared to published U.S. Environmental Protection Agency (USEPA) values for Aggregate Nutrient Ecoregions VI and IX and Level III Ecoregions 55 and 72. Several nutrient values were greater than the 25th percentile of the published USEPA values. Chlorophyll a (periphyton and seston) values were either greater than the 25th percentile of published USEPA values or extended data ranges in the Aggregate Nutrient Ecoregions and Level III Ecoregions. If the proposed values for the 25th percentile were adopted as nutrient water-quality criteria, many samples in the West Fork White River Basin would have exceeded the criteria.

[Discrimination of varieties of borneol using terahertz spectra based on principal component analysis and support vector machine].

PubMed

Li, Wu; Hu, Bing; Wang, Ming-wei

2014-12-01

In the present paper, the terahertz time-domain spectroscopy (THz-TDS) identification model of borneol based on principal component analysis (PCA) and support vector machine (SVM) was established. As one Chinese common agent, borneol needs a rapid, simple and accurate detection and identification method for its different source and being easily confused in the pharmaceutical and trade links. In order to assure the quality of borneol product and guard the consumer's right, quickly, efficiently and correctly identifying borneol has significant meaning to the production and transaction of borneol. Terahertz time-domain spectroscopy is a new spectroscopy approach to characterize material using terahertz pulse. The absorption terahertz spectra of blumea camphor, borneol camphor and synthetic borneol were measured in the range of 0.2 to 2 THz with the transmission THz-TDS. The PCA scores of 2D plots (PC1 X PC2) and 3D plots (PC1 X PC2 X PC3) of three kinds of borneol samples were obtained through PCA analysis, and both of them have good clustering effect on the 3 different kinds of borneol. The value matrix of the first 10 principal components (PCs) was used to replace the original spectrum data, and the 60 samples of the three kinds of borneol were trained and then the unknown 60 samples were identified. Four kinds of support vector machine model of different kernel functions were set up in this way. Results show that the accuracy of identification and classification of SVM RBF kernel function for three kinds of borneol is 100%, and we selected the SVM with the radial basis kernel function to establish the borneol identification model, in addition, in the noisy case, the classification accuracy rates of four SVM kernel function are above 85%, and this indicates that SVM has strong generalization ability. This study shows that PCA with SVM method of borneol terahertz spectroscopy has good classification and identification effects, and provides a new method for species identification of borneol in Chinese medicine.

Investigation of using wavelet analysis for classifying pattern of cyclic voltammetry signals

NASA Astrophysics Data System (ADS)

Jityen, Arthit; Juagwon, Teerasak; Jaisuthi, Rawat; Osotchan, Tanakorn

2017-09-01

Wavelet analysis is an excellent technique for data processing analysis based on linear vector algebra since it has an ability to perform local analysis and is able to analyze an unspecific localized area of a large signal. In this work, the wavelet analysis of cyclic waveform was investigated in order to find the distinguishable feature from the cyclic data. The analyzed wavelet coefficients were proposed to be used as selected cyclic feature parameters. The cyclic voltammogram (CV) of different electrodes consisting of carbon nanotube (CNT) and several types of metal phthalocyanine (MPc) including CoPc, FePc, ZnPc and MnPc powders was used as several sets of cyclic data for various types of coffee. The mixture powder was embedded in a hollow Teflon rod and used as working electrodes. Electrochemical response of the fabricated electrodes in Robusta, blend coffee I, blend coffee II, chocolate malt and cocoa at the same concentrations was measured with scanning rate of 0.05V/s from -1.5 to 1.5V respectively to Ag/AgCl electrode for five scanning loops. The CV of blended CNT electrode with some MPc electrodes indicated the ionic interaction which can be the effect of catalytic oxidation of saccharides and/or polyphenol on the sensor surface. The major information of CV response can be extracted by using several mother wavelet families viz. daubechies (dB1 to dB3), coiflets (coiflet1), biorthogonal (Bior1.1) and symlets (sym2) and then the discrimination of these wavelet coefficients of each data group can be separated by principal component analysis (PCA). The PCA results indicated the clearly separate groups with total contribution more than 62.37% representing from PC1 and PC2.

Expression of Extracellular Signal-regulated Kinase 5 and Ankyrin Repeat Domain 1 in Composite Pheochromocytoma and Ganglioneuroblastoma Detected Incidentally in the Adult Adrenal Gland

PubMed Central

Suenaga, Shinta; Ichiyanagi, Osamu; Ito, Hiromi; Naito, Sei; Kato, Tomoyuki; Nagaoka, Akira; Kato, Tomoya; Yamakawa, Mitsunori; Obara, Yutaro; Tsuchiya, Norihiko

2016-01-01

Composite pheochromocytoma (cPC) is extremely rare, arising in the adrenal medulla as a mixture of PC and other tumors of neural origin. We herein report on a case of adrenal incidentaloma post-operatively diagnosed as cPC with ganglioneuroblastoma (GNBL). The PC component had 7 points on the PASS, a Ki-67 index of 5.1%, a focal absence of sustentacular cells, and no genetic aberrations in succinate dehydrogenase subunit B. The GNBL component exhibited no N-myc amplification. Tumor cells of both components were stained positively for extracellular signal-regulated kinase 5 and ankyrin repeat domain 1. The aberrant activation of growth signaling may play a role in the marginal malignancy of cPC. PMID:27980262

The Siberian High and precipitation over Cyprus

NASA Astrophysics Data System (ADS)

Lingis, P.; Michaelides, S. C.

2009-04-01

The aim of this study is to find possible teleconnection patterns associated with the Siberian High (SH) and precipitation in Cyprus. In this respect, the study examines the impacts that the SH exerts on local climate in areas far beyond the area of its domination; in particular, the relation of the teleconnection patterns derived from the SH Sea Level Pressure (SLP) characteristics and precipitation over Cyprus are examined. Four indices are used describing the characteristics of the SH (strength and geographical displacement). In an attempt to identify possible relations between precipitation, on the one hand, and the SH indices, on the other hand, a network of 32 rain gauge stations in Cyprus, both coastal and inland, was carefully selected to cover the whole island. Precipitation in Cyprus is mainly the result of baroclinic depressions traveling in the eastern Mediterranean Basin. SH as one of the dominant centers of action in the northern hemisphere, acts as one of the regulators of the preferred paths of these frontal depressions. The overall effect of the SH on these depressions is connected to characteristics and behavior of the SH, such as its intensity and location, as it may act as a blocking system preventing the propagation of migratory depressions eastwards or diverting them towards the North or South. The depressions arriving or forming over the island have a short lifespan and they are not frequent. The mean monthly sea-level pressure (SLP) was obtained from the dataset of the Climatic Research Unit of the University of East Anglia, with horizontal analysis of 5 degree latitude and 10 degree longitude grid. The 5 degree resolution global mean monthly temperature anomaly values taken were also taken from the same source. Monthly total precipitation amounts from 32 rain gauges in Cyprus were obtained from the Cyprus Meteorological Service for the period 1961 - 2000. Finally, use has been made of the reanalysis data at 2.5x2.5 degree resolution of global monthly mean SLP and precipitation rate from the National Centers for Environmental Prediction (NCEP). Principal Component Analysis (PCA) for the gridded SLP dataset for each month was performed. From this analysis, the first four Principal Components (PC) were obtained, explaining for the winter months 89-90% of the total variance and for all months 81- 90%. From the PCA and for each of the four Principal Components (hereafter denoted as PC1, PC2, PC3 and PC4), graphs of the loading distributions and the respective time series resulting from the scores of each PC were constructed. The scores were used as indices for further calculations. Susequently, the correlation coefficients between the PC scores and mean SLP for each month were calculated. The data from the 32 rain gauges were used to calculate the monthly mean precipitation over Cyprus. Extrapolation using distance weighted average algorithm was used to plot the spatial distribution of precipitation of each month over the island. Correlation coefficients were calculated between the four PC indices and the precipitation at each one of the rain gauge stations; these correlation coefficients were subsequently plotted on geographical maps in an attempt to visualize any recognizable patterns. Also, to investigate the overall effect of the four indices (i.e. PC1 to PC4) on precipitation over Cyprus, multiple correlation analysis was employed between these four indices and the total amount of precipitation of each month (the sum of all rain gauges used for each month).

Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies

PubMed Central

Ciucci, Sara; Ge, Yan; Durán, Claudio; Palladini, Alessandra; Jiménez-Jiménez, Víctor; Martínez-Sánchez, Luisa María; Wang, Yuting; Sales, Susanne; Shevchenko, Andrej; Poser, Steven W.; Herbig, Maik; Otto, Oliver; Androutsellis-Theotokis, Andreas; Guck, Jochen; Gerl, Mathias J.; Cannistraci, Carlo Vittorio

2017-01-01

Omic science is rapidly growing and one of the most employed techniques to explore differential patterns in omic datasets is principal component analysis (PCA). However, a method to enlighten the network of omic features that mostly contribute to the sample separation obtained by PCA is missing. An alternative is to build correlation networks between univariately-selected significant omic features, but this neglects the multivariate unsupervised feature compression responsible for the PCA sample segregation. Biologists and medical researchers often prefer effective methods that offer an immediate interpretation to complicated algorithms that in principle promise an improvement but in practice are difficult to be applied and interpreted. Here we present PC-corr: a simple algorithm that associates to any PCA segregation a discriminative network of features. Such network can be inspected in search of functional modules useful in the definition of combinatorial and multiscale biomarkers from multifaceted omic data in systems and precision biomedicine. We offer proofs of PC-corr efficacy on lipidomic, metagenomic, developmental genomic, population genetic, cancer promoteromic and cancer stem-cell mechanomic data. Finally, PC-corr is a general functional network inference approach that can be easily adopted for big data exploration in computer science and analysis of complex systems in physics. PMID:28287094

Nutrient Patterns and Their Association with Socio-Demographic, Lifestyle Factors and Obesity Risk in Rural South African Adolescents

PubMed Central

Pisa, Pedro T.; Pedro, Titilola M.; Kahn, Kathleen; Tollman, Stephen M.; Pettifor, John M.; Norris, Shane A.

2015-01-01

The aim of this study was to identify and describe the diversity of nutrient patterns and how they associate with socio-demographic and lifestyle factors including body mass index in rural black South African adolescents. Nutrient patterns were identified from quantified food frequency questionnaires (QFFQ) in 388 rural South African adolescents between the ages of 11–15 years from the Agincourt Health and Socio-demographic Surveillance System (AHDSS). Principle Component Analysis (PCA) was applied to 25 nutrients derived from QFFQs. Multiple linear regression and partial R2 models were fitted and computed respectively for each of the retained principal component (PC) scores on socio-demographic and lifestyle characteristics including body mass index (BMI) for age Z scores. Four nutrient patterns explaining 79% of the total variance were identified: PCI (26%) was characterized by animal derived nutrients; PC2 (21%) by vitamins, fibre and vegetable oil nutrients; PC3 (19%) by both animal and plant derived nutrients (mixed diet driven nutrients); and PC4 (13%) by starch and folate. A positive and significant association was observed with BMI for age Z scores per 1 standard deviation (SD) increase in PC1 (0.13 (0.02; 0.24); p = 0.02) and PC4 (0.10 (−0.01; 0.21); p = 0.05) scores only. We confirmed variability in nutrient patterns that were significantly associated with various lifestyle factors including obesity. PMID:25984738

Mineral constituents profile of biochar derived from diversified waste biomasses: implications for agricultural applications.

PubMed

Zhao, Ling; Cao, Xinde; Wang, Qun; Yang, Fan; Xu, Shi

2013-01-01

The wide distribution and high heterogeneity of different elements in biochars derived from diverse feedstocks make it difficult to regulate their application in soil and to evaluate the maximum potential contribution of the nutrients and trace metals as well as the potential risk of toxic metals. This study classified 20 biochars, covering six typical categories, into three clusters according to their similarity and distance on nutrients and minerals using cluster analysis. Four principle components (PC) were extracted using factor analysis to reduce dimension and clearly characterize the mineral profile of these biochars. The contribution of each group of elements in the PCs to every cluster was clarified. PC1 had a high loading for Mg, Cu, Zn, Al, and Fe; PC2 was related to N, K, and Mn; and PC3 and PC4 mainly represented P and Ca. Cluster 1 included bone dregs and eggshell biochars with PC3 and PC4 as the main contributors. Cluster 2 included waterweeds and waste paper biochars, which were close to shrimp hull and chlorella biochars, with the main contributions being from PC2 and PC4. Cluster 3 included biochars with PC1 as the main contributor. At a soil biochar amendment rate of 50 t ha, the soil nutrients were significantly elevated, whereas the rise in toxic metals was negligible compared with Class I of the China Environmental Quality Standards for Soil. Biochar can potentially supply soil nutrients and trace metals, and different cluster biochars can be applied appropriately to different soils so that excessive or deficient nutrient and metal applications can be avoided. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Coagulation mechanism of salt solution-extracted active component in Moringa oleifera seeds.

PubMed

Okuda, T; Baes, A U; Nishijima, W; Okada, M

2001-03-01

This study focuses on the coagulation mechanism by the purified coagulant solution (MOC-SC-PC) with the coagulation active component extracted from M. oleifera seeds using salt solution. The addition of MOC-SC-PC tap water formed insoluble matters. This formation was responsible for kaolin coagulation. On the other hand, insoluble matters were not formed when the MOC-SC-PC was added into distilled water. The formation was affected by Ca2+ or other bivalent cations which may connect each molecule of the active coagulation component in MOC-SC-PC and form a net-like structure. The coagulation mechanism of MOC-SC-PC seemed to be an enmeshment of Kaolin by the insoluble matters with the net-like structure. In case of Ca2+ ion (bivalent cations), at least 0.2 mM was necessary for coagulation at 0.3 mgC l-1 dose of MOC-SC-PC. Other coagulation mechanisms like compression of double layer, interparticle bridging or charge neutralization were not responsible for the coagulation by MOC-SC-PC.

Factors associated with successful transition among children with disabilities in eight European countries

PubMed Central

2017-01-01

Introduction This research paper aims to assess factors reported by parents associated with the successful transition of children with complex additional support requirements that have undergone a transition between school environments from 8 European Union member states. Methods Quantitative data were collected from 306 parents within education systems from 8 EU member states (Bulgaria, Cyprus, Greece, Ireland, the Netherlands, Romania, Spain and the UK). The data were derived from an online questionnaire and consisted of 41 questions. Information was collected on: parental involvement in their child’s transition, child involvement in transition, child autonomy, school ethos, professionals’ involvement in transition and integrated working, such as, joint assessment, cooperation and coordination between agencies. Survey questions that were designed on a Likert-scale were included in the Principal Components Analysis (PCA), additional survey questions, along with the results from the PCA, were used to build a logistic regression model. Results Four principal components were identified accounting for 48.86% of the variability in the data. Principal component 1 (PC1), ‘child inclusive ethos,’ contains 16.17% of the variation. Principal component 2 (PC2), which represents child autonomy and involvement, is responsible for 8.52% of the total variation. Principal component 3 (PC3) contains questions relating to parental involvement and contributed to 12.26% of the overall variation. Principal component 4 (PC4), which involves transition planning and coordination, contributed to 11.91% of the overall variation. Finally, the principal components were included in a logistic regression to evaluate the relationship between inclusion and a successful transition, as well as whether other factors that may have influenced transition. All four principal components were significantly associated with a successful transition, with PC1 being having the most effect (OR: 4.04, CI: 2.43–7.18, p<0.0001). Discussion To support a child with complex additional support requirements through transition from special school to mainstream, governments and professionals need to ensure children with additional support requirements and their parents are at the centre of all decisions that affect them. It is important that professionals recognise the educational, psychological, social and cultural contexts of a child with additional support requirements and their families which will provide a holistic approach and remove barriers for learning. PMID:28636649

Factors associated with successful transition among children with disabilities in eight European countries.

PubMed

Ravenscroft, John; Wazny, Kerri; Davis, John M

2017-01-01

This research paper aims to assess factors reported by parents associated with the successful transition of children with complex additional support requirements that have undergone a transition between school environments from 8 European Union member states. Quantitative data were collected from 306 parents within education systems from 8 EU member states (Bulgaria, Cyprus, Greece, Ireland, the Netherlands, Romania, Spain and the UK). The data were derived from an online questionnaire and consisted of 41 questions. Information was collected on: parental involvement in their child's transition, child involvement in transition, child autonomy, school ethos, professionals' involvement in transition and integrated working, such as, joint assessment, cooperation and coordination between agencies. Survey questions that were designed on a Likert-scale were included in the Principal Components Analysis (PCA), additional survey questions, along with the results from the PCA, were used to build a logistic regression model. Four principal components were identified accounting for 48.86% of the variability in the data. Principal component 1 (PC1), 'child inclusive ethos,' contains 16.17% of the variation. Principal component 2 (PC2), which represents child autonomy and involvement, is responsible for 8.52% of the total variation. Principal component 3 (PC3) contains questions relating to parental involvement and contributed to 12.26% of the overall variation. Principal component 4 (PC4), which involves transition planning and coordination, contributed to 11.91% of the overall variation. Finally, the principal components were included in a logistic regression to evaluate the relationship between inclusion and a successful transition, as well as whether other factors that may have influenced transition. All four principal components were significantly associated with a successful transition, with PC1 being having the most effect (OR: 4.04, CI: 2.43-7.18, p<0.0001). To support a child with complex additional support requirements through transition from special school to mainstream, governments and professionals need to ensure children with additional support requirements and their parents are at the centre of all decisions that affect them. It is important that professionals recognise the educational, psychological, social and cultural contexts of a child with additional support requirements and their families which will provide a holistic approach and remove barriers for learning.

Current Source Mapping by Spontaneous MEG and ECoG in Piglets Model

PubMed Central

Gao, Lin; Wang, Jue; Stephen, Julia; Zhang, Tongsheng

2016-01-01

The previous research reveals the presence of relatively strong spatial correlations from spontaneous activity over cortex in Electroencephalography (EEG) and Magnetoencephalography (MEG) measurement. A critical obstacle in MEG current source mapping is that strong background activity masks the relatively weak local information. In this paper, the hypothesis is that the dominant components of this background activity can be captured by the first Principal Component (PC) after employing Principal Component Analysis (PCA), thus discarding the first PC before the back projection would enhance the exposure of the information carried by a subset of sensors that reflects the local neuronal activity. By detecting MEG signals densely (one measurement per 2×2 mm2) in three piglets neocortical models over an area of 18×26 mm2 with a special shape of lesion by means of a μSQUID, this basic idea was demonstrated by the fact that a strong activity could be imaged in the lesion region after removing the first PC in Delta, Theta and Alpha band, while the original recordings did not show such activity clearly. Thus, the PCA decomposition can be employed to expose the local activity, which is around the lesion in the piglets’ neocortical models, by removing the dominant components of the background activity. PMID:27570537

Piscivory limits diversification of feeding morphology in centrarchid fishes.

PubMed

Collar, David C; O'Meara, Brian C; Wainwright, Peter C; Near, Thomas J

2009-06-01

Proximity to an adaptive peak influences a lineage's potential to diversify. We tested whether piscivory, a high quality but functionally demanding trophic strategy, represents an adaptive peak that limits morphological diversification in the teleost fish clade, Centrarchidae. We synthesized published diet data and applied a well-resolved, multilocus and time-calibrated phylogeny to reconstruct ancestral piscivory. We measured functional features of the skull and performed principal components analysis on species' values for these variables. To assess the role of piscivory on morphological diversification, we compared the fit of several models of evolution for each principal component (PC), where model parameters were allowed to vary between lineages that differed in degree of piscivory. According to the best-fitting model, two adaptive peaks influenced PC 1 evolution, one peak shared between highly and moderately piscivorous lineages and another for nonpiscivores. Brownian motion better fit PCs 2, 3, and 4, but the best Brownian models infer a slow rate of PC 2 evolution shared among all piscivores and a uniquely slow rate of PC 4 evolution in highly piscivorous lineages. These results suggest that piscivory limits feeding morphology diversification, but this effect is most severe in lineages that exhibit an extreme form of this diet.

Dog sperm head morphometry: its diversity and evolution.

PubMed

Soler, Carles; Alambiaga, Ana; Martí, Maria A; García-Molina, Almudena; Valverde, Anthony; Contell, Jesús; Campos, Marcos

2017-01-01

Dogs have been under strong artificial selection as a consequence of their relationship with man. Differences between breeds are evident that could be reflected in seminal characteristics. The present study was to evaluate differences in sperm head morphometry between seven well-defined breeds of dog: the British Bulldog, Chihuahua, German Shepherd, Labrador Retriever, Spanish Mastiff, Staffordshire Terrier, and Valencian Rat Hunting dog. Semen samples were obtained by masturbation and smears stained with Diff-Quik. Morphometric analysis (CASA-Morph) produced four size and four shape parameters. Length, Ellipticity, and Elongation showed higher differences between breeds. MANOVA revealed differences among all breeds. Considering the whole dataset, principal component analysis (PCA) showed that PC1 was related to head shape and PC2 to size. Procluster analysis showed the British Bulldog to be the most isolated breed, followed by the German Shepherd. The PCA breed by breed showed the Chihuahua, Labrador Retriever, Spanish Mastiff, and Staffordshire Terrier to have PC1 related to shape and PC2 to size, whereas the British Bulldog, Valencia Rat Hunting dog, and German Shepherd had PC1 related to size and PC2 to shape. The dendrogram for cluster groupings and the distance between them showed the British Bulldog to be separated from the rest of the breeds. Future work on dog semen must take into account the large differences in the breeds' sperm characteristics. The results provide a base for future work on phylogenetic and evolutionary studies of dogs, based on their seminal characteristics.

Dog sperm head morphometry: its diversity and evolution

PubMed Central

Soler, Carles; Alambiaga, Ana; Martí, Maria A; García-Molina, Almudena; Valverde, Anthony; Contell, Jesús; Campos, Marcos

2017-01-01

Dogs have been under strong artificial selection as a consequence of their relationship with man. Differences between breeds are evident that could be reflected in seminal characteristics. The present study was to evaluate differences in sperm head morphometry between seven well-defined breeds of dog: the British Bulldog, Chihuahua, German Shepherd, Labrador Retriever, Spanish Mastiff, Staffordshire Terrier, and Valencian Rat Hunting dog. Semen samples were obtained by masturbation and smears stained with Diff-Quik. Morphometric analysis (CASA-Morph) produced four size and four shape parameters. Length, Ellipticity, and Elongation showed higher differences between breeds. MANOVA revealed differences among all breeds. Considering the whole dataset, principal component analysis (PCA) showed that PC1 was related to head shape and PC2 to size. Procluster analysis showed the British Bulldog to be the most isolated breed, followed by the German Shepherd. The PCA breed by breed showed the Chihuahua, Labrador Retriever, Spanish Mastiff, and Staffordshire Terrier to have PC1 related to shape and PC2 to size, whereas the British Bulldog, Valencia Rat Hunting dog, and German Shepherd had PC1 related to size and PC2 to shape. The dendrogram for cluster groupings and the distance between them showed the British Bulldog to be separated from the rest of the breeds. Future work on dog semen must take into account the large differences in the breeds’ sperm characteristics. The results provide a base for future work on phylogenetic and evolutionary studies of dogs, based on their seminal characteristics. PMID:27751991

A reexamination of ATS 6 magnetometer data for radially polarized Pc 3 magnetic pulsations

NASA Technical Reports Server (NTRS)

Takahashi, K.; Mcpherron, R. L.

1983-01-01

The polarization of Pc 3 (22-100 MHz) magnetic pulsations measured by the ATS 6 fluxgate magnetometer at synchronous orbit has been examined by using dynamic autospectral analysis. In contrast to the result obtained by Arthur et al. (1977) using the same data set, very few cases of radially polarized Pc 3 pulsations are found. It is suggested that satellite noise in the radial component, which depends on frequency f as 0.015/f (nT-squared/Hz), is responsible for this disagreement. In the presence of this type of noise, diagonalization of the spectral matrix can produce an erroneous major axis of polarization. Most Pc 3 pulsations classified as radially polarized by Arthur et al. appear to be a consequence of small amplitude azimuthal pulsations contaminated by satellite noise.

Early palliative care in advanced lung cancer: a qualitative study.

PubMed

Yoong, Jaclyn; Park, Elyse R; Greer, Joseph A; Jackson, Vicki A; Gallagher, Emily R; Pirl, William F; Back, Anthony L; Temel, Jennifer S

2013-02-25

BACKGROUND Early ambulatory palliative care (PC) is an emerging practice, and its key elements have not been defined. We conducted a qualitative analysis of data from a randomized controlled trial that demonstrated improved quality of life, mood, and survival in patients with newly diagnosed metastatic non-small cell lung cancer who received early PC integrated with standard oncologic care vs standard oncologic care alone. Our objectives were to (1) identify key elements of early PC clinic visits, (2) explore the timing of key elements, and (3) compare the content of PC and oncologic visit notes at the critical time points of clinical deterioration and radiographic disease progression. METHODS We randomly selected 20 patients who received early PC and survived within 4 periods: less than 3 months (n = 5), 3 to 6 months (n = 5), 6 to 12 months (n = 5), and 12 to 24 months (n = 5). We performed content analysis on PC and oncologic visit notes from the electronic health records of these patients. RESULTS Addressing symptoms and coping were the most prevalent components of the PC clinic visits. Initial visits focused on building relationships and rapport with patients and their families and on illness understanding, including prognostic awareness. Discussions about resuscitation preferences and hospice predominantly occurred during later visits. Comparing PC and oncologic care visits around critical time points, both included discussions about symptoms and illness status; however, PC visits emphasized psychosocial elements, such as coping, whereas oncologic care visits focused on cancer treatment and management of medical complications. CONCLUSIONS Early PC clinic visits emphasize managing symptoms, strengthening coping, and cultivating illness understanding and prognostic awareness in a responsive and time-sensitive model. During critical clinical time points, PC and oncologic care visits have distinct features that suggest a key role for PC involvement and enable oncologists to focus on cancer treatment and managing medical complications.

Puma (Puma concolor) epididymal sperm morphometry

PubMed Central

Cucho, Hernán; Alarcón, Virgilio; Ordóñez, César; Ampuero, Enrique; Meza, Aydee; Soler, Carles

2016-01-01

The Andean puma (Puma concolor) has not been widely studied, particularly in reference to its semen characteristics. The aim of the present study was to define the morphometry of puma sperm heads and classify their subpopulations by cluster analysis. Samples were recovered postmortem from two epididymides from one animal and prepared for morphological observation after staining with the Hemacolor kit. Morphometric data were obtained from 581 spermatozoa using a CASA-Morph system, rendering 13 morphometric parameters. The principal component (PC) analysis was performed followed by cluster analysis for the establishment of subpopulations. Two PC components were obtained, the first related to size and the second to shape. Three subpopulations were observed, corresponding to elongated and intermediate-size sperm heads and acrosomes, to large heads with large acrosomes, and to small heads with short acrosomes. In conclusion, puma spermatozoa showed no uniform sperm morphology but three clear subpopulations. These results should be used for future work in the establishment of an adequate germplasm bank of this species. PMID:27678466

Puma (Puma concolor) epididymal sperm morphometry.

PubMed

Cucho, Hernán; Alarcón, Virgilio; Ordóñez, César; Ampuero, Enrique; Meza, Aydee; Soler, Carles

2016-01-01

The Andean puma (Puma concolor) has not been widely studied, particularly in reference to its semen characteristics. The aim of the present study was to define the morphometry of puma sperm heads and classify their subpopulations by cluster analysis. Samples were recovered postmortem from two epididymides from one animal and prepared for morphological observation after staining with the Hemacolor kit. Morphometric data were obtained from 581 spermatozoa using a CASA-Morph system, rendering 13 morphometric parameters. The principal component (PC) analysis was performed followed by cluster analysis for the establishment of subpopulations. Two PC components were obtained, the first related to size and the second to shape. Three subpopulations were observed, corresponding to elongated and intermediate-size sperm heads and acrosomes, to large heads with large acrosomes, and to small heads with short acrosomes. In conclusion, puma spermatozoa showed no uniform sperm morphology but three clear subpopulations. These results should be used for future work in the establishment of an adequate germplasm bank of this species.

Molecular Characteristics of Mantle Cell Lymphoma Presenting with Clonal Plasma Cell Component

PubMed Central

Visco, Carlo; Hoeller, Sylvia; Malik, Jeffrey T.; Xu-Monette, Zijun Y.; Wiggins, Michele L.; Liu, Jessica; Sanger, Warren G.; Liu, Zhongfeng; Chang, Julie; Ranheim, Erik A.; Gradowski, Joel F.; Serrrano, Sergio; Wang, Huan-You; Liu, Qingquan; Dave, Sandeep; Olsen, Brian; Gascoyne, Randy D.; Campo, Elias; Swerdlow, Steven H.; Chan, Wing C.; Tzankov, Alexander; Young, Ken H.

2011-01-01

The normal counterparts of mantle cell lymphoma (MCL) are naïve quiescent B-cells that have not been processed through the germinal center (GC). For this reason, while lymphomas arising from GC or post-GC B-cells often exhibit plasmacytic differentiation, MCL rarely presents with plasmacytic features. Seven cases of MCL with a monotypic plasma cell (PC) population were collected from six centers and studied by immunohistochemistry, FICTION (Fluorescence immunophenotyping and Interphase Cytogenetics as a Tool for the Investigation of Neoplasms), capillary gel electrophoresis, and restriction fragment length polymorphism of immunoglobulin heavy chain analysis (RFLP/IgH) of microdissections of each of the MCL and PC populations to assess their clonal relationship. Clinical presentation was rather unusual compared to typical MCL, with two cases arising from extranodal soft-tissues of the head. All MCL cases were morphologically and immunohistochemically typical, bearing the t(11;14)(q13;q32). In all cases PC populations were clonal. In 5 of the 7 cases, the MCL and PC clones showed identical restriction fragments, indicating a common clonal origin of the neoplastic populations. The two cases with clonal diversity denoted the coexistence of two different tumors in a composite lymphoma/plasma cell neoplasm. Our findings suggest that MCL can present with a PC component that is often clonally related to the lymphoma, representing a rare but unique biological variant of this tumor. PMID:21263238

Coherent response of the Indo-African boreal summer monsoon to Pacific SST captured in Ethiopian rain δ18O

NASA Astrophysics Data System (ADS)

Madhavan, M.; Palliyil, L. R.; Ramesh, R.

2017-12-01

Pacific Sea Surface Temperature (SST) plays an important role in the inter-annual to inter-decadal variability of boreal monsoons. We identified a common mode of inter annual variability in the Indian and African boreal summer monsoon (June to September) rainfalls, which is linked to Pacific SSTs, using Empirical Orthogonal Function (EOF) analysis. Temporal coefficients (Principle component: PC1) of the leading mode of variability (EOF-1) is well correlated with the Indian summer monsoon rainfall and Sahel rainfall. About forty year long monthly observations of δ18O (and δD) at Addis Ababa, Ethiopia show a strong association with PC1 (r=0.69 for δ18O and r=0.75 for δD). Analysis of SST, sea level pressure and lower tropospheric winds suggest that 18O depletion in Ethiopian rainfall (and wet phases of PC1) is associated with cooler eastern tropical Pacific and warmer western Pacific and strengthening of Pacific subtropical high in both the hemispheres. Associated changes in the trade winds cause enhanced westerly moisture transport into the Indian subcontinent and northern Africa and cause enhanced rainfall. The intrusion of Atlantic westerly component of moisture transport at Addis Ababa during wet phases of PC1 is clearly recorded in δ18O of rain. We also observe the same common mode of variability (EOF1) of Indo-African boreal summer monsoon rain on decadal time scales. A 100 year long δ18O record of actively growing speleothem from the Mechara cave, Ethiopia, matches very well with the PC1 on the decadal time scale. This highlights the potential of speleothem δ18O and leaf wax δD from Ethiopia to investigate the natural variability and teleconnections of Indo-African boreal monsoon.

Coordinative structuring of gait kinematics during adaptation to variable and asymmetric split-belt treadmill walking - A principal component analysis approach.

PubMed

Hinkel-Lipsker, Jacob W; Hahn, Michael E

2018-06-01

Gait adaptation is a task that requires fine-tuned coordination of all degrees of freedom in the lower limbs by the central nervous system. However, when individuals change their gait it is unknown how this coordination is organized, and how it can be influenced by contextual interference during practice. Such knowledge could provide information about measurement of gait adaptation during rehabilitation. Able-bodied individuals completed an acute bout of asymmetric split-belt treadmill walking, where one limb was driven at a constant velocity and the other according to one of three designed practice paradigms: serial practice, where the variable limb belt velocity increased over time; random blocked practice, where every 20 strides the variable limb belt velocity changed randomly; random practice, where every stride the variable limb belt velocity changed randomly. On the second day, subjects completed one of two different transfer tests; one with a belt asymmetry close to that experienced on the acquisition day (transfer 1; 1.5:1), and one with a greater asymmetry (transfer 2; 2:1) . To reduce this inherently high-dimensional dataset, principal component analyses were used for kinematic data collected throughout the acquisition and transfer phases; resulting in extraction of the first two principal components (PCs). For acquisition, PC1 and PC2 were related to sagittal and frontal plane control. For transfer 1, PC1 and PC2 were related to frontal plane control of the base of support and whole-body center of mass. For transfer 2, PC1 did not have any variables with high enough coefficients deemed to be relevant, and PC2 was related to sagittal plane control. Observations of principal component scores indicate that variance structuring differs among practice groups during acquisition and transfer 1, but not transfer 2. These results demonstrate the main kinematic coordinative structures that exist during gait adaptation, and that control of sagittal plane and frontal plane motion are perhaps a trade-off during acquisition of a novel asymmetric gait pattern. Copyright © 2018 Elsevier B.V. All rights reserved.

Weather conditions influence the number of psychiatric emergency room patients

NASA Astrophysics Data System (ADS)

Brandl, Eva Janina; Lett, Tristram A.; Bakanidze, George; Heinz, Andreas; Bermpohl, Felix; Schouler-Ocak, Meryam

2017-12-01

The specific impact of weather factors on psychiatric disorders has been investigated only in few studies with inconsistent results. We hypothesized that meteorological conditions influence the number of cases presenting in a psychiatric emergency room as a measure of mental health conditions. We analyzed the number of patients consulting the emergency room (ER) of a psychiatric hospital in Berlin, Germany, between January 1, 2008, and December 31, 2014. A total of N = 22,672 cases were treated in the ER over the study period. Meteorological data were obtained from a publicly available data base. Due to collinearity among the meteorological variables, we performed a principal component (PC) analysis. Association of PCs with the daily number of patients was analyzed with autoregressive integrated moving average model. Delayed effects were investigated using Granger causal modeling. Daily number of patients in the ER was significantly higher in spring and summer compared to fall and winter (p < 0.001). Three PCs explained 76.8% percent of the variance with PC1 loading mostly on temperature, PC2 on cloudiness and low pressure, and PC3 on windiness. PC1 and PC2 showed strong association with number of patients in the emergency room (p < 0.010) indicating higher patient numbers on warmer and on cloudy days. Further, PC1, PC2, and PC3 predicted the number of patients presenting in the emergency room for up to 7 days (p < 0.050). A secondary analysis revealed that the effect of temperature on number of patients was mostly due to lower patient numbers on cold days. Although replication of our findings is required, our results suggest that weather influences the number of psychiatric patients consulting the emergency room. In particular, our data indicate lower patient numbers during very cold temperatures.

Weather conditions influence the number of psychiatric emergency room patients

NASA Astrophysics Data System (ADS)

Brandl, Eva Janina; Lett, Tristram A.; Bakanidze, George; Heinz, Andreas; Bermpohl, Felix; Schouler-Ocak, Meryam

2018-05-01

The specific impact of weather factors on psychiatric disorders has been investigated only in few studies with inconsistent results. We hypothesized that meteorological conditions influence the number of cases presenting in a psychiatric emergency room as a measure of mental health conditions. We analyzed the number of patients consulting the emergency room (ER) of a psychiatric hospital in Berlin, Germany, between January 1, 2008, and December 31, 2014. A total of N = 22,672 cases were treated in the ER over the study period. Meteorological data were obtained from a publicly available data base. Due to collinearity among the meteorological variables, we performed a principal component (PC) analysis. Association of PCs with the daily number of patients was analyzed with autoregressive integrated moving average model. Delayed effects were investigated using Granger causal modeling. Daily number of patients in the ER was significantly higher in spring and summer compared to fall and winter ( p < 0.001). Three PCs explained 76.8% percent of the variance with PC1 loading mostly on temperature, PC2 on cloudiness and low pressure, and PC3 on windiness. PC1 and PC2 showed strong association with number of patients in the emergency room ( p < 0.010) indicating higher patient numbers on warmer and on cloudy days. Further, PC1, PC2, and PC3 predicted the number of patients presenting in the emergency room for up to 7 days ( p < 0.050). A secondary analysis revealed that the effect of temperature on number of patients was mostly due to lower patient numbers on cold days. Although replication of our findings is required, our results suggest that weather influences the number of psychiatric patients consulting the emergency room. In particular, our data indicate lower patient numbers during very cold temperatures.

Decomposing the Apoptosis Pathway Into Biologically Interpretable Principal Components

PubMed Central

Wang, Min; Kornblau, Steven M; Coombes, Kevin R

2018-01-01

Principal component analysis (PCA) is one of the most common techniques in the analysis of biological data sets, but applying PCA raises 2 challenges. First, one must determine the number of significant principal components (PCs). Second, because each PC is a linear combination of genes, it rarely has a biological interpretation. Existing methods to determine the number of PCs are either subjective or computationally extensive. We review several methods and describe a new R package, PCDimension, that implements additional methods, the most important being an algorithm that extends and automates a graphical Bayesian method. Using simulations, we compared the methods. Our newly automated procedure is competitive with the best methods when considering both accuracy and speed and is the most accurate when the number of objects is small compared with the number of attributes. We applied the method to a proteomics data set from patients with acute myeloid leukemia. Proteins in the apoptosis pathway could be explained using 6 PCs. By clustering the proteins in PC space, we were able to replace the PCs by 6 “biological components,” 3 of which could be immediately interpreted from the current literature. We expect this approach combining PCA with clustering to be widely applicable. PMID:29881252

A proteomic approach to the analysis of the components of the phycobilisomes from two cyanobacteria with complementary chromatic adaptation: Fremyella diplosiphon UTEX B590 and Tolypothrix PCC 7601.

PubMed

Pérez-Gómez, Bertha; Mendoza-Hernández, Guillermo; Cabellos-Avelar, Tecilli; Leyva-Castillo, Lourdes Elizabeth; Gutiérrez-Cirlos, Emma Berta; Gómez-Lojero, Carlos

2012-10-01

Tolypothrix PCC 7601 and Fremyella diplosiphon UTEX B590 can produce two alternative phycobilisome (PBS) rods. PE-PBSs with one phycocyanin (PC) disk and multiple phycoerythrin (PE) disks are found in cells grown under green light (GL). PC-PBSs with only PC disks are obtained from cells grown under red light (RL). In this manuscript, we show the localization of the linker proteins and ferredoxin-NADP(+) oxidoreductase (FNR) in the PC-PBS and of PE-PBS rods using visible spectroscopy and mass spectrometry. PE-PBSs with different [PE]/[PC] ratios and PC-PBSs with different [PC]/[AP] (AP, allophycocyanin) ratios were isolated. CpeC was the primary rod linker protein found in the PBSs with a [PE]/[PC] ratio of 1.1, which indicates that this is the rod linker at the interphase PC-PE. CpeC and CpeD were identified in the PBSs with a [PE]/[PC] ratio of 1.6, which indicates that CpcD is the linker between the first and the second PE hexamers. Finally, CpeC, CpeD, and CpeE were found in the PBSs with a [PE]/[PC] ratio of 2.9, indicating the position of CpeE between the second and third PE moieties. CpcI2 was identified in the two PC-PBSs obtained from cells grown under RL, which indicates that CpcI2 is the linker between the first and second PC hexamers. CpcH2 was identified only in the PC-PBSs from Tolypothrix with a high [PC]/[AP] ratio of 1.92, which indicates that CpcH2 is the linker between the second and third PC hexamers. The PC-PBSs contained the rod cap protein L(R)(10) (CpcD), but this protein was absent in the PE-PBSs. PE-PBSs (lacking L(R)(10)) incorporated exogenous rFNR in a stoichiometry of up to five FNRs per PBS. A maximum of two FNRs per PBS were found in PC-PBSs (with L(R)(10)). These observations support the hypothesis that FNR binds at the distal ends of the PBS rods in the vacant site of CpcD L(R)(10). Finally, the molecular mass of the core membrane linker (L(CM)) was determined to be 102 kDa from a mass spectrometry analysis.

Quantitative evaluation of changes in eyeball shape in emmetropization and myopic changes based on elliptic fourier descriptors.

PubMed

Ishii, Kotaro; Iwata, Hiroyoshi; Oshika, Tetsuro

2011-11-04

To evaluate changes in eyeball shape in emmetropization and myopic changes using magnetic resonance imaging (MRI) and elliptic Fourier descriptors (EFDs). The subjects were 105 patients (age range, 1 month-19 years) who underwent head MRI. The refractive error was determined in 30 patients, and eyeball shape was expressed numerically by principal components analysis of standardized EFDs. In the first principal component (PC1; the oblate-to-prolate change), the proportion of variance/total variance in the development of the eyeball shape was 76%. In all subjects, PC1 showed a significant correlation with age (Pearson r = -0.314; P = 0.001), axial length (AL, r = -0.378; P < 0.001), width (r = -0.200, P = 0.0401), oblateness (r = 0.657, P < 0.001), and spherical equivalent refraction (SER, r = 0.438; P = 0.0146; n = 30). In the group containing patients aged 1 month to 6 years (n = 49), PC1 showed a significant correlation with age (r = -0.366; P = 0.0093). In the group containing patients aged 7 to 19 years (n = 56), PC1 showed a significant correlation with SER (r = 0.640; P = 0.0063). The main deformation pattern in the development of the eyeball shape from oblate to prolate was clarified by quantitative analysis based on EFDs. The results showed clear differences between age groups with regard to changes in the shape of the eyeball, the correlation between these changes, and refractive status changes.

Relations of Principal Components Analysis Site Scores to Algal-Biomass, Habitat, Basin-Characteristics, Nutrient, and Biological-Community Data in the Whitewater River and East Fork White River Basins, Indiana, 2002

USGS Publications Warehouse

Caskey, Brian J.; Frey, Jeffrey W.; Lowe, B. Scott

2007-01-01

Data were gathered from May through September 2002 at 76 randomly selected sites in the Whitewater River and East Fork White River Basins, Indiana, for algal biomass, habitat, nutrients, and biological communities (fish and invertebrates). Basin characteristics (land use and drainage area) and biolog-ical-community attributes and metric scores were determined for the basin of each sampling site. Yearly Principal Compo-nents Analysis site scores were calculated for algal biomass (periphyton and seston). The yearly Principal Components Analysis site scores for the first axis (PC1) were related using Spearman's rho to the seasonal algal-biomass, basin-charac-teristics, habitat, seasonal nutrient, and biological-community attribute and metric score data. The periphyton PC1 site score was not significantly related to the nine habitat or 12 nutrient variables examined. One land-use variable, drainage area, was negatively related to the periphyton PC1. Of the 43 fish-community attributes and metrics examined, the periphyton PC1 was negatively related to one attribute (large-river percent) and one metric score (car-nivore percent metric score). It was positively related to three fish-community attributes (headwater percent, pioneer percent, and simple lithophil percent). The periphyton PC1 was not statistically related to any of the 21 invertebrate-community attributes or metric scores examined. Of the 12 nutrient variables examined two were nega-tively related to the seston PC1 site score in two seasons: total Kjeldahl nitrogen (July and September), and TP (May and September). There were no statistically significant relations between the seston PC1 and the five basin-characteristics or nine habitat variables examined. Of the 43 fish-community attributes and metrics examined, the seston PC1 was positively related to one attribute (headwater percent) and negatively related to one metric score (large-river percent metric score) . Of the 21 invertebrate-community attributes and metrics exam-ined, the seston PC1 was negatively related to one metric score (number of individuals metric score). To understand how the choice of sampling sites might have affected the results, an analysis of the drainage area and land use was done. The sites selected in the Whitewater River Basin were generally small drainage basins; compared to Whitewater River Basin sites, the sites selected in the East Fork White River Basin were generally larger drainage basins. Although both basins were dominated by agricultural land use the Whitewater River Basin sites had more land in agriculture than the East Fork White River Basin sites. The values for nutrients (nitrate, total Kjeldahl nitrogen, total nitrogen, and total phosphorus) and chlorophyll a (per-iphyton and seston) were compared to published U.S. Environmental Protection Agency (USEPA) values for Aggregate Nutrient Ecoregions VI and IX and USEPA Level III Ecore-gions 55 and 71. Several nutrient values were greater than the 25th percentile of published USEPA values. Chlorophyll a (periphyton and seston) values were either greater than the 25thpercentile of published USEPA values or they extended data ranges in the Aggregate Nutrient and Level III Ecore-gions. If the values for the 25th percentile as proposes by the USEPA were adopted as nutrient water-quality criteria, many samples in the Whitewater River and East Fork White River Basins would have exceeded the criteria.

The Speed of Serial Attention Shifts in Visual Search: Evidence from the N2pc Component.

PubMed

Grubert, Anna; Eimer, Martin

2016-02-01

Finding target objects among distractors in visual search display is often assumed to be based on sequential movements of attention between different objects. However, the speed of such serial attention shifts is still under dispute. We employed a search task that encouraged the successive allocation of attention to two target objects in the same search display and measured N2pc components to determine how fast attention moved between these objects. Each display contained one digit in a known color (fixed-color target) and another digit whose color changed unpredictably across trials (variable-color target) together with two gray distractor digits. Participants' task was to find the fixed-color digit and compare its numerical value with that of the variable-color digit. N2pc components to fixed-color targets preceded N2pc components to variable-color digits, demonstrating that these two targets were indeed selected in a fixed serial order. The N2pc to variable-color digits emerged approximately 60 msec after the N2pc to fixed-color digits, which shows that attention can be reallocated very rapidly between different target objects in the visual field. When search display durations were increased, thereby relaxing the temporal demands on serial selection, the two N2pc components to fixed-color and variable-color targets were elicited within 90 msec of each other. Results demonstrate that sequential shifts of attention between different target locations can operate very rapidly at speeds that are in line with the assumptions of serial selection models of visual search.

Motion and properties of nuclear radio components in Seyfert galaxies seen with VLBI

NASA Astrophysics Data System (ADS)

Middelberg, E.; Roy, A. L.; Nagar, N. M.; Krichbaum, T. P.; Norris, R. P.; Wilson, A. S.; Falcke, H.; Colbert, E. J. M.; Witzel, A.; Fricke, K. J.

2004-04-01

We report EVN, MERLIN and VLBA observations at 18 cm, 6 cm and 3.6 cm of the Seyfert galaxies NGC 7674, NGC 5506, NGC 2110 and Mrk 1210 to study their structure and proper motions on pc scales and to add some constraints on the many possible causes of the radio-quietness of Seyferts. The component configurations in NGC 7674 and NGC 2110 are simple, linear structures, whereas the configurations in NGC 5506 and Mrk 1210 have multiple components with no clear axis of symmetry. We suggest that NGC 7674 is a low-luminosity compact symmetric object. Comparing the images at different epochs, we find a proper motion in NGC 7674 of (0.92±0.07) c between the two central components separated by 282 pc and, in NGC 5506, we find a 3 σ upper limit of 0.50 c for the components separated by 3.8 pc. Our results confirm and extend earlier work showing that the outward motion of radio components in Seyfert galaxies is non-relativistic on pc scales. We briefly discuss whether this non-relativistic motion is intrinsic to the jet-formation process or results from deceleration of an initially relativistic jet by interaction with the pc or sub-pc scale interstellar medium. We combined our sample with a list compiled from the literature of VLBI observations made of Seyfert galaxies, and found that most Seyfert nuclei have at least one flat-spectrum component on the VLBI scale, which was not seen in the spectral indices measured at arcsec resolution. We found also that the bimodal alignment of pc and kpc radio structures displayed by radio galaxies and quasars is not displayed by this sample of Seyferts, which shows a uniform distribution of misalignment between 0° and 90°. The frequent misalignment could result from jet precession or from deflection of the jet by interaction with gas in the interstellar medium.

[Effect of climate change on the fisheries conununity pattern in the overwintering ground of open waters of northern East China Sea].

PubMed

Liu, Zun-lei; Yuan, Xing-wei; Yang, Lin-lin; Yan, Li-ping; Tian, Yong-jun; Chen, Jia-hua

2015-03-01

Data sets of 26 fisheries target species from the fishery-depen-dent and fishery-independent surveys in the overwintering ground of open waters of northern East China Sea (OW-NECS), combined sea surface temperature (SST), were used to examine the links between diversity index, pattern of common variability and climate changes based on the principal component analysis (PCA) and generalized additive model (GAM). The results showed that the shift from a cold regime to a warm regime was detected in SST during the 1970s-2011 with step changes around 1982/ 1983. SST increased during the cold regime and the warm regime before 1998 (warming trend period, 1972-1998), and decreased during the warm regime after 1998 (cooling trend period, 1999-2011). Shannon diversity index was largely dependent on the filefish, which contributed up to 50% of the total production as a single species, with low diversity in the waters of the OW-NECS, during the late 1980s and early 1990s. Excluding the filefish, the diversity index linearly increased and decreased during 1972-1998 and 1999-2011, respectively. The variation pattern generally corresponds with the trend in water temperature, strongly suggesting the effect of the SST on the diversity. The first two components (PC1 and PC2) of PCA for target species, which accounted for 32.43% of the total variance, showed evident decadal variation patterns with a step change during 1992-1999 and inter-annual variability with short-period fluctuation, respectively. It seems that PC1 was associated with large scale climatic change, while PC2 was related to inter-annual oceanographic variability such as ENSO events. Linear fitting results showed winEOF1 had significant effect on PC1, and GAM analysis for PC1 showed that winter EOF1 (winEOF1) and summer EOF2 (sumEOF2) can explain 88.9% of the total variance. Nonlinear effect was also found between PC2 and win EOF1, indicating that the fish community structure, which had predominantly decadal/inter-annual variation patterns, was influenced by inter-annual variations in oceanographic conditions.

Anti-tumor immunity of BAM-SiPc-mediated vascular photodynamic therapy in a BALB/c mouse model.

PubMed

Yeung, Hing-Yuen; Lo, Pui-Chi; Ng, Dennis K P; Fong, Wing-Ping

2017-02-01

In recent decades, accumulating evidence from both animal and clinical studies has suggested that a sufficiently activated immune system may strongly augment various types of cancer treatment, including photodynamic therapy (PDT). Through the generation of reactive oxygen species, PDT eradicates tumors by triggering localized tumor damage and inducing anti-tumor immunity. As the major component of anti-tumor immunity, the involvement of a cell-mediated immune response in PDT has been well investigated in the past decade, whereas the role of humoral immunity has remained relatively unexplored. In the present investigation, using the photosensitizer BAM-SiPc and the CT26 tumor-bearing BALB/c mouse model, it was demonstrated that both cell-mediated and humoral adaptive immune components could be involved in PDT. With a vascular PDT (VPDT) regimen, BAM-SiPc could eradicate the tumors of ∼70% of tumor-bearing mice and trigger an anti-tumor immune response that could last for more than 1 year. An elevation of Th2 cytokines was detected ex vivo after VPDT, indicating the potential involvement of a humoral response. An analysis of serum from the VPDT-cured mice also revealed elevated levels of tumor-specific antibodies. Moreover, this serum could effectively hinder tumor growth and protect the mice against further re-challenge in a T-cell-dependent manner. Taken together, these results show that the humoral components induced after BAM-SiPc-VPDT could assist the development of anti-tumor immunity.

Lateral Distribution of NBD-PC Fluorescent Lipid Analogs in Membranes Probed by Molecular Dynamics-Assisted Analysis of Förster Resonance Energy Transfer (FRET) and Fluorescence Quenching

PubMed Central

Loura, Luís M. S.

2012-01-01

Förster resonance energy transfer (FRET) is a powerful tool used for many problems in membrane biophysics, including characterization of the lateral distribution of lipid components and other species of interest. However, quantitative analysis of FRET data with a topological model requires adequate choices for the values of several input parameters, some of which are difficult to obtain experimentally in an independent manner. For this purpose, atomistic molecular dynamics (MD) simulations can be potentially useful as they provide direct detailed information on transverse probe localization, relative probe orientation, and membrane surface area, all of which are required for analysis of FRET data. This is illustrated here for the FRET pairs involving 1,6-diphenylhexatriene (DPH) as donor and either 1-palmitoyl,2-(6-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino] hexanoyl)- sn-glycero-3-phosphocholine (C6-NBD-PC) or 1-palmitoyl,2-(12-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]dodecanoyl)-sn-glycero-3-phosphocholine (C12-NBD-PC) as acceptors, in fluid vesicles of 1,2-dipalmitoyl-sn-3-glycerophosphocholine (DPPC, 50 °C). Incorporation of results from MD simulations improves the statistical quality of model fitting to the experimental FRET data. Furthermore, the decay of DPH in the presence of moderate amounts of C12-NBD-PC (>0.4 mol%) is consistent with non-random lateral distribution of the latter, at variance with C6-NBD-PC, for which aggregation is ruled out up to 2.5 mol% concentration. These conclusions are supported by analysis of NBD-PC fluorescence self-quenching. Implications regarding the relative utility of these probes in membrane studies are discussed. PMID:23203080

Lateral distribution of NBD-PC fluorescent lipid analogs in membranes probed by molecular dynamics-assisted analysis of Förster Resonance Energy Transfer (FRET) and fluorescence quenching.

PubMed

Loura, Luís M S

2012-11-08

Förster resonance energy transfer (FRET) is a powerful tool used for many problems in membrane biophysics, including characterization of the lateral distribution of lipid components and other species of interest. However, quantitative analysis of FRET data with a topological model requires adequate choices for the values of several input parameters, some of which are difficult to obtain experimentally in an independent manner. For this purpose, atomistic molecular dynamics (MD) simulations can be potentially useful as they provide direct detailed information on transverse probe localization, relative probe orientation, and membrane surface area, all of which are required for analysis of FRET data. This is illustrated here for the FRET pairs involving 1,6-diphenylhexatriene (DPH) as donor and either 1-palmitoyl,2-(6-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino] hexanoyl)- sn-glycero-3-phosphocholine (C6-NBD-PC) or 1-palmitoyl,2-(12-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]dodecanoyl)-sn-glycero-3-phosphocholine (C12-NBD-PC) as acceptors, in fluid vesicles of 1,2-dipalmitoyl-sn-3-glycerophosphocholine (DPPC, 50 °C). Incorporation of results from MD simulations improves the statistical quality of model fitting to the experimental FRET data. Furthermore, the decay of DPH in the presence of moderate amounts of C12-NBD-PC (>0.4 mol%) is consistent with non-random lateral distribution of the latter, at variance with C6-NBD-PC, for which aggregation is ruled out up to 2.5 mol% concentration. These conclusions are supported by analysis of NBD-PC fluorescence self-quenching. Implications regarding the relative utility of these probes in membrane studies are discussed.

Potential for the use of reconstructed IASI radiances in the detection of atmospheric trace gases

NASA Astrophysics Data System (ADS)

Atkinson, N. C.; Hilton, F. I.; Illingworth, S. M.; Eyre, J. R.; Hultberg, T.

2010-07-01

Principal component (PC) analysis has received considerable attention as a technique for the extraction of meteorological signals from hyperspectral infra-red sounders such as the Infrared Atmospheric Sounding Interferometer (IASI) and the Atmospheric Infrared Sounder (AIRS). In addition to achieving substantial bit-volume reductions for dissemination purposes, the technique can also be used to generate reconstructed radiances in which random instrument noise has been reduced. Studies on PC analysis of hyperspectral infrared sounder data have been undertaken in the context of numerical weather prediction, instrument monitoring and geophysical variable retrieval, as well as data compression. This study examines the potential of PC analysis for chemistry applications. A major concern in the use of PC analysis for chemistry is that the spectral features associated with trace gases may not be well represented in the reconstructed spectra, either due to deficiencies in the training set or due to the limited number of PC scores used in the radiance reconstruction. In this paper we show examples of reconstructed IASI radiances for several trace gases: ammonia, sulphur dioxide, methane and carbon monoxide. It is shown that care must be taken in the selection of spectra for the initial training set: an iterative technique, in which outlier spectra are added to a base training set, gives the best results. For the four trace gases examined, key features of the chemical signatures are retained in the reconstructed radiances, whilst achieving a substantial reduction in instrument noise. A new regional re-transmission service for IASI is scheduled to start in 2010, as part of the EUMETSAT Advanced Retransmission Service (EARS). For this EARS-IASI service it is intended to include PC scores as part of the data stream. The paper describes the generation of the reference eigenvectors for this new service.

Turkish Population Structure and Genetic Ancestry Reveal Relatedness among Eurasian Populations

PubMed Central

Hodoğlugil, Uğur; Mahley, Robert W.

2013-01-01

Summary Turkey connects the Middle East, Europe, and Asia and has experienced major population movements. We examined the population structure and genetic relatedness of samples from three regions of Turkey using over 500,000 SNP genotypes. The data were analyzed together with Human Genome Diversity Panel data. To obtain a more representative sampling from Central Asia, Kyrgyz samples (Bishkek, Kyrgyzstan) were genotyped and analyzed. Principal component (PC) analysis reveals a significant overlap between Turks and Middle Easterners and a relationship with Europeans and South and Central Asians; however, the Turkish genetic structure is unique. FRAPPE, STRUCTURE, and phylogenetic analyses support the PC analysis depending upon the number of parental ancestry components chosen. For example, supervised STRUCTURE (K = 3) illustrates a genetic ancestry for the Turks of 45% Middle Eastern (95% CI, 42–49), 40% European (95% CI, 36–44), and 15% Central Asian (95% CI, 13–16), whereas at K = 4 the genetic ancestry of the Turks was 38% European (95% CI, 35–42), 35% Middle Eastern (95% CI, 33–38), 18% South Asian (95% CI, 16–19), and 9% Central Asian (95% CI, 7–11). PC analysis and FRAPPE/STRUCTURE results from three regions in Turkey (Aydin, Istanbul, and Kayseri) were superimposed, without clear subpopulation structure, suggesting the selected samples were rather homogeneous. Thus, this study demonstrates admixture of Turkish people reflecting the population migration patterns. PMID:22332727

Dietary Components Affect the Plasma and Tissue Levels of Lutein in Aged Rats with Lutein Deficiency--A Repeated Gavage and Dietary Study.

PubMed

Sheshappa, Mamatha Bangera; Ranganathan, Arunkumar; Bhatiwada, Nidhi; Talahalli, Ramprasad Ravichandra; Vallikannan, Baskaran

2015-10-01

The aim of this study was to find out the influence of selected dietary components on plasma and tissue response of repeated micellar and dietary lutein in aged rats with lutein deficiency. In repeated (16 d) gavage study, micellar lutein was co-ingested with either phosphatidylcholine (PC), lyso-phosphatidylcholine (lysoPC), β-carotene, dietary fiber or vegetable fat (3% soybean oil). In dietary study, rats were fed (4 wk) semi-synthetic diet either with lutein + PC, lutein + dietary fiber or B. alba (lutein source) + PC. The post-prandial plasma and tissue response of lutein was measured by HPLC. Results showed that micellar fat, PC and lysoPC significantly (P ≤ 0.05) increased the lutein levels in plasma (31.1%, 26.8%, and 34.9%), liver (27.4%, 29.5%, and 8.6%), and eyes (63.5%, 90.2%, and 86%) compared to the control group (group gavaged micelles with no dietary components studied). Similarly, dietary study showed an enhanced plasma, liver, and eye lutein levels by 44.8%, 24.1%, and 42.0% (lutein + PC group) and 51.7%, 39.8%, and 31.7% (B.alba + PC group), respectively compared to control. The activity of antioxidant enzymes in plasma and liver of both the studies were also affected compared to control. Result reveals, that PC enhance the intestinal absorption of both micellar and dietary lutein which is either in free or bound form with food matrices in aged rats with lutein deficiency. Hence, PC at a concentration used in this study can be considered to improve the lutein bioavailability in lutein deficiency. Lutein and zeaxanthin are macular pigments acquired mostly from greens, that play an significant role in protecting vision from Age related macular degeneration (AMD). However, their biological availability is poor and affected by dietary components. This study demonstrates the positive influence of dietary PC and lyso PC in improving intestinal uptake of lutein. Our previous and present finding shows there is a possibility of developing functional/supplemental foods with PC and lyso PC targeted to elderly populace thus minimizing or delaying the vision complication associated like AMD. © 2015 Institute of Food Technologists®

RING1 is associated with the polycomb group protein complex and acts as a transcriptional repressor.

PubMed

Satijn, D P; Gunster, M J; van der Vlag, J; Hamer, K M; Schul, W; Alkema, M J; Saurin, A J; Freemont, P S; van Driel, R; Otte, A P

1997-07-01

The Polycomb (Pc) protein is a component of a multimeric, chromatin-associated Polycomb group (PcG) protein complex, which is involved in stable repression of gene activity. The identities of components of the PcG protein complex are largely unknown. In a two-hybrid screen with a vertebrate Pc homolog as a target, we identify the human RING1 protein as interacting with Pc. RING1 is a protein that contains the RING finger motif, a specific zinc-binding domain, which is found in many regulatory proteins. So far, the function of the RING1 protein has remained enigmatic. Here, we show that RING1 coimmunoprecipitates with a human Pc homolog, the vertebrate PcG protein BMI1, and HPH1, a human homolog of the PcG protein Polyhomeotic (Ph). Also, RING1 colocalizes with these vertebrate PcG proteins in nuclear domains of SW480 human colorectal adenocarcinoma and Saos-2 human osteosarcoma cells. Finally, we show that RING1, like Pc, is able to repress gene activity when targeted to a reporter gene. Our findings indicate that RING1 is associated with the human PcG protein complex and that RING1, like PcG proteins, can act as a transcriptional repressor.

Discrimination of various paper types using diffuse reflectance ultraviolet-visible near-infrared (UV-Vis-NIR) spectroscopy: forensic application to questioned documents.

PubMed

Kumar, Raj; Kumar, Vinay; Sharma, Vishal

2015-06-01

Diffuse reflectance ultraviolet-visible-near-infrared (UV-Vis-NIR) spectroscopy is applied as a means of differentiating various types of writing, office, and photocopy papers (collected from stationery shops in India) on the basis of reflectance and absorbance spectra that otherwise seem to be almost alike in different illumination conditions. In order to minimize bias, spectra from both sides of paper were obtained. In addition, three spectra from three different locations (from one side) were recorded covering the upper, middle, and bottom portions of the paper sample, and the mean average reflectivity of both the sides was calculated. A significant difference was observed in mean average reflectivity of Side A and Side B of the paper using Student's pair >t-test. Three different approaches were used for discrimination: (1) qualitative features of the whole set of samples, (2) principal component analysis, and (3) a combination of both approaches. On the basis of the first approach, i.e., qualitative features, 96.49% discriminating power (DP) was observed, which shows highly significant results with the UV-Vis-NIR technique. In the second approach the discriminating power is further enhanced by incorporating the principal component analysis (PCA) statistical method, where this method describes each UV-Vis spectrum in a group through numerical loading values connected to the first few principal components. All components described 100% variance of the samples, but only the first three PCs are good enough to explain the variance (PC1 = 51.64%, PC2 = 47.52%, and PC3 = 0.54%) of the samples; i.e., the first three PCs described 99.70% of the data, whereas in the third approach, the four samples, C, G, K, and N, out of a total 19 samples, which were not differentiated using qualitative features (approach no. 1), were therefore subjected to PCA. The first two PCs described 99.37% of the spectral features. The discrimination was achieved by using a loading plot between PC1 and PC2. It is therefore concluded that maximum discrimination of writing, office, and photocopy paper could be achieved on the basis of the second approach. Hence, the present inexpensive analytical method can be appropriate for application to routine questioned document examination work in forensic laboratories because it provides nondestructive, quantitative, reliable, and repeatable results.

Browning Index of Anthocyanin-Rich Fruit Juice Depends on pH and Anthocyanin Loss More Than the Gain of Soluble Polymeric Pigments.

PubMed

Dorris, Matthew R; Voss, Danielle M; Bollom, Mark A; Krawiec-Thayer, Mitchell P; Bolling, Bradley W

2018-04-01

Browning index (BI, ABS 520 nm /ABS 420 nm ) is a measure of anthocyanin-rich fruit juice pigmentation quality. This study sought to determine the extent to which BI describes anthocyanin quality and degradation in fruit juices. Commercial fruit juices were assayed for monomeric anthocyanin (MA) content, percent polymeric color (%PC), pH, and BI. BI varied, 0.29 to 1.72, among cranberry, cherry, grape, aronia, and pomegranate juices. Principal component analysis (PCA) revealed that BI was strongly inversely associated with %PC, and positively correlated with MAs to a lesser extent. The BI of grape and cherry juices varied linearly with pH from 2.0 to 4.0 in pH-adjusted juices. Cherry and grape juices at pH approximately 2.0 to 4.0 were incubated at 50 °C to induce juice browning. BI and MA decreased, and %PC increased, but the amount of MA degradation was not explained by %PC. In the aged juices, BI and MA were strongly correlated using PCA. In aged grape juice, chromatographic analysis was used characterize anthocyanins, proanthocyanidins, and anthocyanin scission products. Anthocyanin loss and a gain of unresolved components absorbing at 420 nm decreased BI. Proanthocyanidins and co-eluting pigments with varying BI decreased during aging. Scission products did not account for anthocyanin loss. Thus, MA loss more so than the gain in pigments associated with juice proanthocyanidins contribute to the increase in %PC and decline of the BI during accelerated aging of grape juice. Thus, BI is a useful marker of fruit juice quality within juices of the same pH and anthocyanin composition. Fruit juice pigmentation depends on anthocyanins, pH, and other matrix components. Spectrophotometric methods to determine pigmentation include the browning index (ABS 520 nm /ABS 420 nm ), pH differential method for monomeric anthocyanin (MA) content, and bisulfite bleaching to determine percent polymeric color (%PC). In this study, anthocyanin-rich fruit juice browning index was strongly dependent on pH and MA content. MA loss, and to a lesser extent, a gain in newly-formed pigments at 420 nm contributed to the browning index change during aging. Therefore, browning index is strongly associated with MA content and is useful for assessing fruit juice quality. © 2018 Institute of Food Technologists®.

Global and System-Specific Resting-State fMRI Fluctuations Are Uncorrelated: Principal Component Analysis Reveals Anti-Correlated Networks

PubMed Central

Carbonell, Felix; Bellec, Pierre

2011-01-01

Abstract The influence of the global average signal (GAS) on functional-magnetic resonance imaging (fMRI)–based resting-state functional connectivity is a matter of ongoing debate. The global average fluctuations increase the correlation between functional systems beyond the correlation that reflects their specific functional connectivity. Hence, removal of the GAS is a common practice for facilitating the observation of network-specific functional connectivity. This strategy relies on the implicit assumption of a linear-additive model according to which global fluctuations, irrespective of their origin, and network-specific fluctuations are super-positioned. However, removal of the GAS introduces spurious negative correlations between functional systems, bringing into question the validity of previous findings of negative correlations between fluctuations in the default-mode and the task-positive networks. Here we present an alternative method for estimating global fluctuations, immune to the complications associated with the GAS. Principal components analysis was applied to resting-state fMRI time-series. A global-signal effect estimator was defined as the principal component (PC) that correlated best with the GAS. The mean correlation coefficient between our proposed PC-based global effect estimator and the GAS was 0.97±0.05, demonstrating that our estimator successfully approximated the GAS. In 66 out of 68 runs, the PC that showed the highest correlation with the GAS was the first PC. Since PCs are orthogonal, our method provides an estimator of the global fluctuations, which is uncorrelated to the remaining, network-specific fluctuations. Moreover, unlike the regression of the GAS, the regression of the PC-based global effect estimator does not introduce spurious anti-correlations beyond the decrease in seed-based correlation values allowed by the assumed additive model. After regressing this PC-based estimator out of the original time-series, we observed robust anti-correlations between resting-state fluctuations in the default-mode and the task-positive networks. We conclude that resting-state global fluctuations and network-specific fluctuations are uncorrelated, supporting a Resting-State Linear-Additive Model. In addition, we conclude that the network-specific resting-state fluctuations of the default-mode and task-positive networks show artifact-free anti-correlations. PMID:22444074

Geological and Structural Patterns on Titan Enhanced Through Cassini's SAR PCA and High-Resolution Radiometry

NASA Astrophysics Data System (ADS)

Paganelli, F.; Schubert, G.; Lopes, R. M. C.; Malaska, M.; Le Gall, A. A.; Kirk, R. L.

2016-12-01

The current SAR data coverage on Titan encompasses several areas in which multiple radar passes are present and overlapping, providing additional information to aid the interpretation of geological and structural features. We exploit the different combinations of look direction and variable incidence angle to examine Cassini Synthetic Aperture RADAR (SAR) data using the Principal Component Analysis (PCA) technique and high-resolution radiometry, as a tool to aid in the interpretation of geological and structural features. Look direction and variable incidence angle is of particular importance in the analysis of variance in the images, which aid in the perception and identification of geological and structural features, as extensively demonstrated in Earth and planetary examples. The PCA enhancement technique uses projected non-ortho-rectified SAR imagery in order to maintain the inherent differences in scattering and geometric properties due to the different look directions, while enhancing the geometry of surface features. The PC2 component provides a stereo view of the areas in which complex surface features and structural patterns can be enhanced and outlined. We focus on several areas of interest, in older and recently acquired flybys, in which evidence of geological and structural features can be enhanced and outlined in the PC1 and PC2 components. Results of this technique provide enhanced geometry and insights into the interpretation of the observed geological and structural features, thus allowing a better understanding towards the geology and tectonics on Titan.

Analysis of Hand and Wrist Postural Synergies in Tolerance Grasping of Various Objects

PubMed Central

Liu, Yuan; Jiang, Li; Yang, Dapeng; Liu, Hong

2016-01-01

Human can successfully grasp various objects in different acceptable relative positions between human hand and objects. This grasp functionality can be described as the grasp tolerance of human hand, which is a significant functionality of human grasp. To understand the motor control of human hand completely, an analysis of hand and wrist postural synergies in tolerance grasping of various objects is needed. Ten healthy right-handed subjects were asked to perform the tolerance grasping with right hand using 6 objects of different shapes, sizes and relative positions between human hand and objects. Subjects were wearing CyberGlove attaching motion tracker on right hand, allowing a measurement of the hand and wrist postures. Correlation analysis of joints and inter-joint/inter-finger modules were carried on to explore the coordination between joints or modules. As the correlation between hand and wrist module is not obvious in tolerance grasping, individual analysis of wrist synergies would be more practical. In this case, postural synergies of hand and wrist were then presented separately through principal component analysis (PCA), expressed through the principal component (PC) information transmitted ratio, PC elements distribution and reconstructed angle error of joints. Results on correlation comparison of different module movements can be well explained by the influence factors of the joint movement correlation. Moreover, correlation analysis of joints and modules showed the wrist module had the lowest correlation among all inter-finger and inter-joint modules. Hand and wrist postures were both sufficient to be described by a few principal components. In terms of the PC elements distribution of hand postures, compared with previous investigations, there was a greater proportion of movement in the thumb joints especially the interphalangeal (IP) and opposition rotation (ROT) joint. The research could serve to a complete understanding of hand grasp, and the design, control of the anthropomorphic hand and wrist. PMID:27580298

Principal components derived from CSF inflammatory profiles predict outcome in survivors after severe traumatic brain injury.

PubMed

Kumar, Raj G; Rubin, Jonathan E; Berger, Rachel P; Kochanek, Patrick M; Wagner, Amy K

2016-03-01

Studies have characterized absolute levels of multiple inflammatory markers as significant risk factors for poor outcomes after traumatic brain injury (TBI). However, inflammatory marker concentrations are highly inter-related, and production of one may result in the production or regulation of another. Therefore, a more comprehensive characterization of the inflammatory response post-TBI should consider relative levels of markers in the inflammatory pathway. We used principal component analysis (PCA) as a dimension-reduction technique to characterize the sets of markers that contribute independently to variability in cerebrospinal (CSF) inflammatory profiles after TBI. Using PCA results, we defined groups (or clusters) of individuals (n=111) with similar patterns of acute CSF inflammation that were then evaluated in the context of outcome and other relevant CSF and serum biomarkers collected days 0-3 and 4-5 post-injury. We identified four significant principal components (PC1-PC4) for CSF inflammation from days 0-3, and PC1 accounted for the greatest (31%) percentage of variance. PC1 was characterized by relatively higher CSF sICAM-1, sFAS, IL-10, IL-6, sVCAM-1, IL-5, and IL-8 levels. Cluster analysis then defined two distinct clusters, such that individuals in cluster 1 had highly positive PC1 scores and relatively higher levels of CSF cortisol, progesterone, estradiol, testosterone, brain derived neurotrophic factor (BDNF), and S100b; this group also had higher serum cortisol and lower serum BDNF. Multinomial logistic regression analyses showed that individuals in cluster 1 had a 10.9 times increased likelihood of GOS scores of 2/3 vs. 4/5 at 6 months compared to cluster 2, after controlling for covariates. Cluster group did not discriminate between mortality compared to GOS scores of 4/5 after controlling for age and other covariates. Cluster groupings also did not discriminate mortality or 12 month outcomes in multivariate models. PCA and cluster analysis establish that a subset of CSF inflammatory markers measured in days 0-3 post-TBI may distinguish individuals with poor 6-month outcome, and future studies should prospectively validate these findings. PCA of inflammatory mediators after TBI could aid in prognostication and in identifying patient subgroups for therapeutic interventions. Copyright © 2015 Elsevier Inc. All rights reserved.

High-resolution Anorectal Manometry for Identifying Defecatory Disorders and Rectal Structural Abnormalities in Women.

PubMed

Prichard, David O; Lee, Taehee; Parthasarathy, Gopanandan; Fletcher, Joel G; Zinsmeister, Alan R; Bharucha, Adil E

2017-03-01

Contrary to conventional wisdom, the rectoanal gradient during evacuation is negative in many healthy people, undermining the utility of anorectal high-resolution manometry (HRM) for diagnosing defecatory disorders. We aimed to compare HRM and magnetic resonance imaging (MRI) for assessing rectal evacuation and structural abnormalities. We performed a retrospective analysis of 118 patients (all female; 51 with constipation, 48 with fecal incontinence, and 19 with rectal prolapse; age, 53 ± 1 years) assessed by HRM, the rectal balloon expulsion test (BET), and MRI at Mayo Clinic, Rochester, Minnesota, from February 2011 through March 2013. Thirty healthy asymptomatic women (age, 37 ± 2 years) served as controls. We used principal components analysis of HRM variables to identify rectoanal pressure patterns associated with rectal prolapse and phenotypes of patients with prolapse. Compared with patients with normal findings from the rectal BET, patients with an abnormal BET had lower median rectal pressure (36 vs 22 mm Hg, P = .002), a more negative median rectoanal gradient (-6 vs -29 mm Hg, P = .006) during evacuation, and a lower proportion of evacuation on the basis of MRI analysis (median of 40% vs 80%, P < .0001). A score derived from rectal pressure and anorectal descent during evacuation and a patulous anal canal was associated (P = .005) with large rectoceles (3 cm or larger). A principal component (PC) logistic model discriminated between patients with and without prolapse with 96% accuracy. Among patients with prolapse, there were 2 phenotypes, which were characterized by high (PC1) or low (PC2) anal pressures at rest and squeeze along with higher rectal and anal pressures (PC1) or a higher rectoanal gradient during evacuation (PC2). In a retrospective analysis of patients assessed by HRM, measurements of rectal evacuation by anorectal HRM, BET, and MRI were correlated. HRM alone and together with anorectal descent during evacuation may identify rectal prolapse and large rectoceles, respectively, and also identify unique phenotypes of rectal prolapse. Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

Meteorology-induced variations in the spatial behavior of summer ozone pollution in Central California

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

Jin, Ling; Harley, Robert A.; Brown, Nancy J.

Cluster analysis was applied to daily 8 h ozone maxima modeled for a summer season to characterize meteorology-induced variations in the spatial distribution of ozone. Principal component analysis is employed to form a reduced dimension set to describe and interpret ozone spatial patterns. The first three principal components (PCs) capture {approx}85% of total variance, with PC1 describing a general spatial trend, and PC2 and PC3 each describing a spatial contrast. Six clusters were identified for California's San Joaquin Valley (SJV) with two low, three moderate, and one high-ozone cluster. The moderate ozone clusters are distinguished by elevated ozone levels inmore » different parts of the valley: northern, western, and eastern, respectively. The SJV ozone clusters have stronger coupling with the San Francisco Bay area (SFB) than with the Sacramento Valley (SV). Variations in ozone spatial distributions induced by anthropogenic emission changes are small relative to the overall variations in ozone amomalies observed for the whole summer. Ozone regimes identified here are mostly determined by the direct and indirect meteorological effects. Existing measurement sites are sufficiently representative to capture ozone spatial patterns in the SFB and SV, but the western side of the SJV is under-sampled.« less

Increased phosphatidylcholine (16:0/16:0) in the folliculus lymphaticus of Warthin tumor.

PubMed

He, Qian; Takizawa, Yoshinori; Hayasaka, Takahiro; Masaki, Noritaka; Kusama, Yukiko; Su, Jiping; Mineta, Hiroyuki; Setou, Mitsutoshi

2014-09-01

Warthin tumor (War-T), the second most common benign salivary gland tumor, consists mainly of neoplastic epithelium and lymphoid stroma. Some proteins and genes thought to be involved in War-T were evaluated by molecular biology and immunology. However, lipids as an important component of many tumor cells have not been well studied in War-T. To elucidate the molecular biology and pathogenesis of War-T, we investigated the visualized distribution of phosphatidylcholines (PCs) by imaging mass spectrometry (IMS). In our IMS analysis of a typical case, 10 signals were significantly different in intensity (p < 0.01) between the War-T and non-tumor (Non-T) regions. Five specific PCs were frequently found in the War-T regions of all of the samples: [PC (16:0/16:0) + K](+) (m/z 772.5), [PC (16:0/20:4) + K](+) (m/z 820.5), [PC (16:0/20:3) + K](+) (m/z 822.5), [PC (18:2/20:4) + K](+) (m/z 844.5), and [PC (18:0/20:5) + K](+) (m/z 846.5). PC (16:0/16:0) was increased specifically in the folliculus lymphaticus of War-T lymphoid stroma, suggesting a different metabolism. Localization of PC (16:0/16:0) might reflect inflammation activity participating in the pathogenesis of War-T. Thus, our IMS analysis revealed the profile of PCs specific to the War-T region. The molecules identified in our study provide important information for further studies of War-T pathogenesis.

Genome-wide association analysis of host genotype and plastic wing morphological variation of an endoparasitoid wasp Asobara japonica (Hymenoptera: Braconidae).

PubMed

Yamashita, Shinpei; Takigahira, Tomohiro; Takahashi, Kazuo H

2018-06-01

Accumulating evidence suggests that genotype of host insects influences the development of koinobiont endoparasitoids. Although there are many potential genetic variations that lead to the internal body environmental variations of host insects, association between the host genotype and the parasitoid development has not been examined in a genome-wide manner. In the present study, we used highly inbred whole genome sequenced strains of Drosophila melanogaster to associate single nucleotide polymorphisms (SNPs) of host flies with morphological traits of Asobara japonica, a larval-pupal parasitoid wasp that infected those hosts. We quantified the outline shape of the forewings of A. japonica with two major principal components (PC1 and PC2) calculated from Fourier coefficients obtained from elliptic Fourier analysis. We also quantified wing size and estimated wasp survival. We then examined the association between the PC scores, wing size and 1,798,561 SNPs and  the association between the estimated wasp survival and 1,790,544 SNPs. As a result, we obtained 22, 24 and 14 SNPs for PC1, PC2 and wing size and four SNPs for the estimated survival with P values smaller than 10 -5 . Based on the location of the SNPs, 12, 17, 11 and five protein coding genes were identified as potential candidates for PC1, PC2, wing size and the estimated survival, respectively. Based on the function of the candidate genes, it is suggested that the host genetic variation associated with the cell growth and morphogenesis may influence the wasp's morphogenetic variation.

Effect of polymer blend types and gamma radiation on the physico-chemical properties of polycarbonate

NASA Astrophysics Data System (ADS)

Nouh, S. A.; Magida, M. M.; Al-Shekify, L. S.; Bashter, I. I.

2016-12-01

Samples from polycarbonate (PC) were classified into two main groups. The first group was blended with Abietic acid (Rosin) with different compositions, while the second group was blended with ethylene-vinyl acetate (EVA) copolymer with almost the same composition. A comparative study of the effect of both Rosin and EVA concentration on the thermal stability of PC has been investigated using thermogravimetric analysis. The results show that blending with Rosin causes the dominance of degradation. Samples from PC with 20% Rosin blend were irradiated with gamma at the dose of range 20-300 kGy. The resultant effect of gamma radiation on the structural properties of the 20% Rosin/ 80%PC blend has been investigated using Fourier Transform Infrared FTIR spectroscopy. The results indicate that degradation of the polymer blend dominates, thus increases the creation of hot free radicals that leads to the formation of color centers in PC. In addition, the transmission of the 20% Rosin/80%PC samples as well as color changes was studied. The color intensity ΔE was greatly increased with increasing the gamma dose up to 300 kGy, accompanied by a significant increase in the blue color component.

[Identification of varieties of textile fibers by using Vis/NIR infrared spectroscopy technique].

PubMed

Wu, Gui-Fang; He, Yong

2010-02-01

The aim of the present paper was to provide new insight into Vis/NIR spectroscopic analysis of textile fibers. In order to achieve rapid identification of the varieties of fibers, the authors selected 5 kinds of fibers of cotton, flax, wool, silk and tencel to do a study with Vis/NIR spectroscopy. Firstly, the spectra of each kind of fiber were scanned by spectrometer, and principal component analysis (PCA) method was used to analyze the characteristics of the pattern of Vis/NIR spectra. Principal component scores scatter plot (PC1 x PC2 x PC3) of fiber indicated the classification effect of five varieties of fibers. The former 6 principal components (PCs) were selected according to the quantity and size of PCs. The PCA classification model was optimized by using the least-squares support vector machines (LS-SVM) method. The authors used the 6 PCs extracted by PCA as the inputs of LS-SVM, and PCA-LS-SVM model was built to achieve varieties validation as well as mathematical model building and optimization analysis. Two hundred samples (40 samples for each variety of fibers) of five varieties of fibers were used for calibration of PCA-LS-SVM model, and the other 50 samples (10 samples for each variety of fibers) were used for validation. The result of validation showed that Vis/NIR spectroscopy technique based on PCA-LS-SVM had a powerful classification capability. It provides a new method for identifying varieties of fibers rapidly and real time, so it has important significance for protecting the rights of consumers, ensuring the quality of textiles, and implementing rationalization production and transaction of textile materials and its production.

Blocking phosphatidylcholine utilization in Pseudomonas aeruginosa, via mutagenesis of fatty acid, glycerol and choline degradation pathways, confirms the importance of this nutrient source in vivo.

PubMed

Sun, Zhenxin; Kang, Yun; Norris, Michael H; Troyer, Ryan M; Son, Mike S; Schweizer, Herbert P; Dow, Steven W; Hoang, Tung T

2014-01-01

Pseudomonas aeruginosa can grow to very high-cell-density (HCD) during infection of the cystic fibrosis (CF) lung. Phosphatidylcholine (PC), the major component of lung surfactant, has been hypothesized to support HCD growth of P. aeruginosa in vivo. The phosphorylcholine headgroup, a glycerol molecule, and two long-chain fatty acids (FAs) are released by enzymatic cleavage of PC by bacterial phospholipase C and lipases. Three different bacterial pathways, the choline, glycerol, and fatty acid degradation pathways, are then involved in the degradation of these PC components. Here, we identified five potential FA degradation (Fad) related fadBA-operons (fadBA1-5, each encoding 3-hydroxyacyl-CoA dehydrogenase and acyl-CoA thiolase). Through mutagenesis and growth analyses, we showed that three (fadBA145) of the five fadBA-operons are dominant in medium-chain and long-chain Fad. The triple fadBA145 mutant also showed reduced ability to degrade PC in vitro. We have previously shown that by partially blocking Fad, via mutagenesis of fadBA5 and fadDs, we could significantly reduce the ability of P. aeruginosa to replicate on FA and PC in vitro, as well as in the mouse lung. However, no studies have assessed the ability of mutants, defective in choline and/or glycerol degradation in conjunction with Fad, to grow on PC or in vivo. Hence, we constructed additional mutants (ΔfadBA145ΔglpD, ΔfadBA145ΔbetAB, and ΔfadBA145ΔbetABΔglpD) significantly defective in the ability to degrade FA, choline, and glycerol and, therefore, PC. The analysis of these mutants in the BALB/c mouse lung infection model showed significant inability to utilize PC in vitro, resulted in decreased replication fitness and competitiveness in vivo compared to the complement strain, although there was little to no variation in typical virulence factor production (e.g., hemolysin, lipase, and protease levels). This further supports the hypothesis that lung surfactant PC serves as an important nutrient for P. aeruginosa during CF lung infection.

Waveform and polarization of compressional Pc 5 waves at geosynchronous orbit

NASA Astrophysics Data System (ADS)

Higuchi, Tomoyuki; Kokubun, Susumu

1988-12-01

The factors controlling the occurrence and the properties of compressional Pc 5 waves were examined by studying the statistical characteristics of compressional Pc 5 waves, using magnetic-field data obtained by GOES 2 and GOES 3 satellites during the August 1978 - August 1980 period. The compressional Pc 5 waves could be classified into the harmonic, transitional, and normal types, on the basis of the second-harmonic component in the compressional component of the magnetic field oscillation. It was found that the harmonic and the transitional waves have significant azimuthal perturbations and show right-handed polarization with respect to the local magnetic field, while most of the normal-type waves have small amplitude in the azimuthal component. The polarization properties of transverse perturbation, which may reflect the spatial inhomogeneity of the medium, are investigated.

Characterisation of volatile profiles in 50 native Peruvian chili pepper using solid phase microextraction-gas chromatography mass spectrometry (SPME-GCMS).

PubMed

Patel, Kirti; Ruiz, Candy; Calderon, Rosa; Marcelo, Mavel; Rojas, Rosario

2016-11-01

The volatiles were characterised by headspace solid phase micro extraction (HS-SPME), gas chromatography mass spectrometry (GC-FID/MS). A total of 127 compounds were identified with terpenes (including mono terpenes and sesquiterpenes - a total of 45 compounds), esters (31 compounds) and hydrocarbons (20 compounds) were the predominant volatile compounds. Principal component analysis (PCA) of the volatile compounds yielded 2 significant PC's, which together accounted for 90.3% of the total variance in the data set and the scatter plot generated between PC1 and PC2 successfully segregated the 50 chili pepper samples into 7 groups. Clusters of hydrocarbons, esters, terpenes, aldehyde and ketones formed the major determinants of the difference. Copyright © 2016 Elsevier Ltd. All rights reserved.

Phenotype diversity analysis of red-grained rice landraces from Yuanyang Hani's terraced fields, China

NASA Astrophysics Data System (ADS)

Li, Lianjie; Cheng, Long

2017-10-01

There are many areas in the world have terraced fields, Yuanyang Rani's terraced fields are examples in the world, and their unique ecological diversity is beyond other terraced fields, rice landraces are very rich. In order to provide useful information for protection and utilization of red-grained rice landraces from Rani's terraced fields, 61 red-grained rice landraces were assessed based 20 quantitative traits. Principal component analysis (PCA) suggested that 20 quantitative characters could be simplified to seven principal components, and their accumulative contribution ration amounted to 78.699%. The first principal component (PC1) explained 18.375% of the total variance, which was contributed by filled grain number, 1000-grain weight, spikelets per panicle, secondary branch number, grain length, and grain thickness. PC2 accounted for 16.548% of the variance and featured flag leaf width, flag leaf area, panicle neck length and primary branch number. These traits were the most effective parameters to discriminate individuals. At the request of the proceedings editor and with the approval of all authors, article 040111 titled, "Phenotype diversity analysis of red-grained rice landraces from Yuanyang Hani's terraced fields, China," is being retracted from the public record due to the fact that it is a duplication of article 040110 published in the same volume.

Rotordynamics on the PC: Further Capabilities of ARDS

NASA Technical Reports Server (NTRS)

Fleming, David P.

1997-01-01

Rotordynamics codes for personal computers are now becoming available. One of the most capable codes is Analysis of RotorDynamic Systems (ARDS) which uses the component mode synthesis method to analyze a system of up to 5 rotating shafts. ARDS was originally written for a mainframe computer but has been successfully ported to a PC; its basic capabilities for steady-state and transient analysis were reported in an earlier paper. Additional functions have now been added to the PC version of ARDS. These functions include: 1) Estimation of the peak response following blade loss without resorting to a full transient analysis; 2) Calculation of response sensitivity to input parameters; 3) Formulation of optimum rotor and damper designs to place critical speeds in desirable ranges or minimize bearing loads; 4) Production of Poincard plots so the presence of chaotic motion can be ascertained. ARDS produces printed and plotted output. The executable code uses the full array sizes of the mainframe version and fits on a high density floppy disc. Examples of all program capabilities are presented and discussed.

Application of Elliptic Fourier Analysis to Describe the Lamina Cribrosa Shape with Age and Intraocular Pressure

PubMed Central

Sanfilippo, P.G.; Grimm, J.L.; Flanagan, J.G.; Lathrop, K.L.; Sigal, I.A.

2014-01-01

The lamina cribrosa (LC) plays an important biomechanical role in the optic nerve head (ONH). We developed a statistical shape model of the LC and tested if the shape varies with age or IOP. The ONHs of 18 donor eyes (47 to 91 years, mean 76 years) fixed at either 5 or 50 mm Hg of IOP were sectioned, stained, and imaged under a microscope. A 3D model of each ONH was reconstructed and the outline of the vertical sagittal section closest to the geometric centre of the LC extracted. The outline shape was described using elliptic Fourier analysis, and principal components analysis (PCA) employed to identify the primary modes of LC shape variation. Linear mixed effect models were used to determine if the shape measurements were associated with age or IOP. The analysis revealed several modes of shape variation: thickness and depth directly (PC1), or inversely (PC2) related, and superior-inferior asymmetry (PC3). Only PC3 was associated with IOP, with higher IOP correlating with greater curvature of the LC superiorly compared to inferiorly. Our analysis enabled a concise and complete characterization of LC shape, revealing variations without defining them a priori. No association between LC shape and age was found for the relatively old population studied. Superior-inferior asymmetry of LC shape was associated with IOP, with more asymmetry at higher IOP. Increased IOP was not associated with LC thickness or depth. PMID:25193035

Application of Elliptic Fourier analysis to describe the lamina cribrosa shape with age and intraocular pressure.

PubMed

Sanfilippo, P G; Grimm, J L; Flanagan, J G; Lathrop, K L; Sigal, I A

2014-11-01

The lamina cribrosa (LC) plays an important biomechanical role in the optic nerve head (ONH). We developed a statistical shape model of the LC and tested if the shape varies with age or IOP. The ONHs of 18 donor eyes (47-91 years, mean 76 years) fixed at either 5 or 50 mmHg of IOP were sectioned, stained, and imaged under a microscope. A 3D model of each ONH was reconstructed and the outline of the vertical sagittal section closest to the geometric center of the LC extracted. The outline shape was described using Elliptic Fourier analysis, and principal components analysis (PCA) employed to identify the primary modes of LC shape variation. Linear mixed effect models were used to determine if the shape measurements were associated with age or IOP. The analysis revealed several modes of shape variation: thickness and depth directly (PC 1), or inversely (PC 2) related, and superior-inferior asymmetry (PC 3). Only PC 3 was associated with IOP, with higher IOP correlating with greater curvature of the LC superiorly compared to inferiorly. Our analysis enabled a concise and complete characterization of LC shape, revealing variations without defining them a priori. No association between LC shape and age was found for the relatively old population studied. Superior-inferior asymmetry of LC shape was associated with IOP, with more asymmetry at higher IOP. Increased IOP was not associated with LC thickness or depth. Copyright © 2014 Elsevier Ltd. All rights reserved.

A principal component analysis of the dynamics of subdomains and binding sites in human serum albumin.

PubMed

Paris, Guillaume; Ramseyer, Christophe; Enescu, Mironel

2014-05-01

The conformational dynamics of human serum albumin (HSA) was investigated by principal component analysis (PCA) applied to three molecular dynamics trajectories of 200 ns each. The overlap of the essential subspaces spanned by the first 10 principal components (PC) of different trajectories was about 0.3 showing that the PCA based on a trajectory length of 200 ns is not completely convergent for this protein. The contributions of the relative motion of subdomains and of the subdomains (internal) distortion to the first 10 PCs were found to be comparable. Based on the distribution of the first 3 PC, 10 protein conformers are identified showing relative root mean square deviations (RMSD) between 2.3 and 4.6 Å. The main PCs are found to be delocalized over the whole protein structure indicating that the motions of different protein subdomains are coupled. This coupling is considered as being related to the allosteric effects observed upon ligand binding to HSA. On the other hand, the first PC of one of the three trajectories describes a conformational transition of the protein domain I that is close to that experimentally observed upon myristate binding. This is a theoretical support for the older hypothesis stating that changes of the protein onformation favorable to binding can precede the ligand complexation. A detailed all atoms PCA performed on the primary Sites 1 and 2 confirms the multiconformational character of the HSA binding sites as well as the significant coupling of their motions. Copyright © 2013 Wiley Periodicals, Inc.

[Identification of varieties of cashmere by Vis/NIR spectroscopy technology based on PCA-SVM].

PubMed

Wu, Gui-Fang; He, Yong

2009-06-01

One mixed algorithm was presented to discriminate cashmere varieties with principal component analysis (PCA) and support vector machine (SVM). Cashmere fiber has such characteristics as threadlike, softness, glossiness and high tensile strength. The quality characters and economic value of each breed of cashmere are very different. In order to safeguard the consumer's rights and guarantee the quality of cashmere product, quickly, efficiently and correctly identifying cashmere has significant meaning to the production and transaction of cashmere material. The present research adopts Vis/NIRS spectroscopy diffuse techniques to collect the spectral data of cashmere. The near infrared fingerprint of cashmere was acquired by principal component analysis (PCA), and support vector machine (SVM) methods were used to further identify the cashmere material. The result of PCA indicated that the score map made by the scores of PC1, PC2 and PC3 was used, and 10 principal components (PCs) were selected as the input of support vector machine (SVM) based on the reliabilities of PCs of 99.99%. One hundred cashmere samples were used for calibration and the remaining 75 cashmere samples were used for validation. A one-against-all multi-class SVM model was built, the capabilities of SVM with different kernel function were comparatively analyzed, and the result showed that SVM possessing with the Gaussian kernel function has the best identification capabilities with the accuracy of 100%. This research indicated that the data mining method of PCA-SVM has a good identification effect, and can work as a new method for rapid identification of cashmere material varieties.

PC index as a proxy of the solar wind energy that entered into the magnetosphere and energy accumulated in the magnetosphere

NASA Astrophysics Data System (ADS)

Troshichev, Oleg; Sormakov, Dmitry

The PC index has been approved by the International Association of Geomagnetism and Aeronomy (Merida, Mexico, 2013) as a new international index of magnetic activity. Application of the PC index as a proxy of a solar wind energy that entered into the magnetosphere determines a principal distinction of the PC index from AL and Dst indices, which are regarded as characteristics of the energy that realized in magnetosphere in form of substorms and magnetic storms. This conclusion is based on results of analysis of relationships between the polar cap magnetic activity (PC-index) and parameters of the solar wind, on the one hand, relationships between changes of PC and development of magnetospheric substorms (AL-index) and magnetic storms (Dst-index), on the other hand. In this study the relationships between the PC and Dst indices in course of more than 200 magnetic storms observed in epoch of solar maximum (1998-2004) have been examined for different classes of storms separated by their kind and intensity. Results of statistical analysis demonstrate that depression of geomagnetic field starts to develop as soon as PC index steadily excess the threshold level ~1.5 mV/m; the storm intensity (DstMIN) follows, with delay ~ 1 hour, the maximum of PC in course of the storm. Main features of magnetic storms are determined, irrespective of their class and intensity, by the accumulated-mean PC value (PCAM): storm is developed as long as PCAM increases, comes to maximal intensity when PCAM attains the maximum, and starts to decay as soon as PCAM value displays decline. The run of “anomalous” magnetic storm on January 21-22, 2005, lasting many hours (with intensity of ≈ -100 nT) under conditions of northward or close to zero BZ component, is perfectly governed by behavior of the accumulated-mean PCAM index and, therefore, this storm should be regarded as an ordinary phenomenon. The conclusion is made that the PC index provides the unique on-line information on solar wind energy that entered into magnetosphere and PCAM index provides information on energy that accumulated in the magnetosphere.

The bio-optical properties of CDOM as descriptor of lake stratification.

PubMed

Bracchini, Luca; Dattilo, Arduino Massimo; Hull, Vincent; Loiselle, Steven Arthur; Martini, Silvia; Rossi, Claudio; Santinelli, Chiara; Seritti, Alfredo

2006-11-01

Multivariate statistical techniques are used to demonstrate the fundamental role of CDOM optical properties in the description of water masses during the summer stratification of a deep lake. PC1 was linked with dissolved species and PC2 with suspended particles. In the first principal component that the role of CDOM bio-optical properties give a better description of the stratification of the Salto Lake with respect to temperature. The proposed multivariate approach can be used for the analysis of different stratified aquatic ecosystems in relation to interaction between bio-optical properties and stratification of the water body.

Determinants and Consequences of Arsenic Metabolism Efficiency among 4,794 Individuals: Demographics, Lifestyle, Genetics, and Toxicity.

PubMed

Jansen, Rick J; Argos, Maria; Tong, Lin; Li, Jiabei; Rakibuz-Zaman, Muhammad; Islam, Md Tariqul; Slavkovich, Vesna; Ahmed, Alauddin; Navas-Acien, Ana; Parvez, Faruque; Chen, Yu; Gamble, Mary V; Graziano, Joseph H; Pierce, Brandon L; Ahsan, Habibul

2016-02-01

Exposure to inorganic arsenic (iAs), a class I carcinogen, affects several hundred million people worldwide. Once absorbed, iAs is converted to monomethylated (MMA) and then dimethylated forms (DMA), with methylation facilitating urinary excretion. The abundance of each species in urine relative to their sum (iAs%, MMA%, and DMA%) varies across individuals, reflecting differences in arsenic metabolism capacity. The association of arsenic metabolism phenotypes with participant characteristics and arsenical skin lesions was characterized among 4,794 participants in the Health Effects of Arsenic Longitudinal Study (Araihazar, Bangladesh). Metabolism phenotypes include those obtained from principal component (PC) analysis of arsenic species. Two independent PCs were identified: PC1 appears to represent capacity to produce DMA (second methylation step), and PC2 appears to represent capacity to convert iAs to MMA (first methylation step). PC1 was positively associated (P <0.05) with age, female sex, and BMI, while negatively associated with smoking, arsenic exposure, education, and land ownership. PC2 was positively associated with age and education but negatively associated with female sex and BMI. PC2 was positively associated with skin lesion status, while PC1 was not. 10q24.32/AS3MT region polymorphisms were strongly associated with PC1, but not PC2. Patterns of association for most variables were similar for PC1 and DMA%, and for PC2 and MMA% with the exception of arsenic exposure and SNP associations. Two distinct arsenic metabolism phenotypes show unique associations with age, sex, BMI, 10q24.32 polymorphisms, and skin lesions. This work enhances our understanding of arsenic metabolism kinetics and toxicity risk profiles. ©2015 American Association for Cancer Research.

Phthalocyanine tetrasulfonates affect the amyloid formation and cytotoxicity of alpha-synuclein.

PubMed

Lee, Eui-Nam; Cho, Hyun-Ju; Lee, Choong-Hwan; Lee, Daekyun; Chung, Kwang Chul; Paik, Seung R

2004-03-30

Alpha-synuclein is a pathological component of Parkinson's disease by constituting the filamentous component of Lewy bodies. Phthalocyanine (Pc) effects on the amyloidosis of alpha-synuclein have been examined. The copper complex of phthalocyanine tetrasulfonate (PcTS-Cu(2+)) caused the self-oligomerization of alpha-synuclein while Pc-Cu(2+) did not affect the protein, indicating that introduction of the sulfonate groups was critical for the selective protein interaction. The PcTS-Cu(2+) interaction with alpha-synuclein has occurred predominantly at the N-terminal region of the protein with a K(d) of 0.83 microM apart from the hydrophobic NAC (non-Abeta component of Alzheimer's disease amyloid) segment. Phthalocyanine tetrasulfonate (PcTS) lacking the intercalated copper ion also showed a considerable affinity toward alpha-synuclein with a K(d) of 3.12 microM, and its binding site, on the other hand, was located at the acidic C-terminus. These mutually exclusive interactions between PcTS and PcTS-Cu(2+) toward alpha-synuclein resulted in distinctive features on the kinetics of protein aggregation, morphologies of the final aggregates, and their in vitro cytotoxicities. The PcTS actually suppressed the fibrous amyloid formation of alpha-synuclein, but it produced the chopped-wood-looking protein aggregates. The aggregates showed rather low toxicity (9.5%) on human neuroblastoma cells (SH-SY5Y). In fact, the PcTS was shown to effectively rescue the cell death of alpha-synuclein overexpressing cells caused by the lactacystin treatment as a proteasome inhibitor. The anti-aggregative and anti-amyloidogenic properties of PcTS were also demonstrated with alcohol dehydrogenase, glutathione S-transferase, and amyloid beta/A4 protein under their aggregative conditions. The PcTS-Cu(2+), on the other hand, promoted the protein aggregation of alpha-synuclein, which gave rise to the fibrillar protein aggregates whose cytotoxicity became significant to 35.8%. Taken together, the data provided in this study indicate that PcTS/PcTS-Cu(2+) could be considered as possible candidates for the development of therapeutic or prophylactic strategies against the alpha-synuclein-related neurodegenerative disorders.

Sperm kinematic, head morphometric and kinetic-morphometric subpopulations in the blue fox (Alopex lagopus).

PubMed

Soler, Carles; Contell, Jesús; Bori, Lorena; Sancho, María; García-Molina, Almudena; Valverde, Anthony; Segarvall, Jan

2017-01-01

This work provides information on the blue fox ejaculated sperm quality needed for seminal dose calculations. Twenty semen samples, obtained by masturbation, were analyzed for kinematic and morphometric parameters by using CASA-Mot and CASA-Morph system and principal component (PC) analysis. For motility, eight kinematic parameters were evaluated, which were reduced to PC1, related to linear variables, and PC2, related to oscillatory movement. The whole population was divided into three independent subpopulations: SP1, fast cells with linear movement; SP2, slow cells and nonoscillatory motility; and SP3, medium speed cells and oscillatory movement. In almost all cases, the subpopulation distribution by animal was significantly different. Head morphology analysis generated four size and four shape parameters, which were reduced to PC1, related to size, and PC2, related to shape of the cells. Three morphometric subpopulations existed: SP1: large oval cells; SP2: medium size elongated cells; and SP3: small and short cells. The subpopulation distribution differed between animals. Combining the kinematic and morphometric datasets produced PC1, related to morphometric parameters, and PC2, related to kinematics, which generated four sperm subpopulations - SP1: high oscillatory motility, large and short heads; SP2: medium velocity with small and short heads; SP3: slow motion small and elongated cells; and SP4: high linear speed and large elongated cells. Subpopulation distribution was different in all animals. The establishment of sperm subpopulations from kinematic, morphometric, and combined variables not only improves the well-defined fox semen characteristics and offers a good conceptual basis for fertility and sperm preservation techniques in this species, but also opens the door to use this approach in other species, included humans.

Sperm kinematic, head morphometric and kinetic-morphometric subpopulations in the blue fox (Alopex lagopus)

PubMed Central

Soler, Carles; Contell, Jesús; Bori, Lorena; Sancho, María; García-Molina, Almudena; Valverde, Anthony; Segarvall, Jan

2017-01-01

This work provides information on the blue fox ejaculated sperm quality needed for seminal dose calculations. Twenty semen samples, obtained by masturbation, were analyzed for kinematic and morphometric parameters by using CASA-Mot and CASA-Morph system and principal component (PC) analysis. For motility, eight kinematic parameters were evaluated, which were reduced to PC1, related to linear variables, and PC2, related to oscillatory movement. The whole population was divided into three independent subpopulations: SP1, fast cells with linear movement; SP2, slow cells and nonoscillatory motility; and SP3, medium speed cells and oscillatory movement. In almost all cases, the subpopulation distribution by animal was significantly different. Head morphology analysis generated four size and four shape parameters, which were reduced to PC1, related to size, and PC2, related to shape of the cells. Three morphometric subpopulations existed: SP1: large oval cells; SP2: medium size elongated cells; and SP3: small and short cells. The subpopulation distribution differed between animals. Combining the kinematic and morphometric datasets produced PC1, related to morphometric parameters, and PC2, related to kinematics, which generated four sperm subpopulations – SP1: high oscillatory motility, large and short heads; SP2: medium velocity with small and short heads; SP3: slow motion small and elongated cells; and SP4: high linear speed and large elongated cells. Subpopulation distribution was different in all animals. The establishment of sperm subpopulations from kinematic, morphometric, and combined variables not only improves the well-defined fox semen characteristics and offers a good conceptual basis for fertility and sperm preservation techniques in this species, but also opens the door to use this approach in other species, included humans. PMID:27751987

DCE-MRI defined subvolumes of a brain metastatic lesion by principle component analysis and fuzzy-c-means clustering for response assessment of radiation therapy

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

Farjam, Reza; Tsien, Christina I.; Lawrence, Theodore S.

Purpose: To develop a pharmacokinetic modelfree framework to analyze the dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data for assessment of response of brain metastases to radiation therapy. Methods: Twenty patients with 45 analyzable brain metastases had MRI scans prior to whole brain radiation therapy (WBRT) and at the end of the 2-week therapy. The volumetric DCE images covering the whole brain were acquired on a 3T scanner with approximately 5 s temporal resolution and a total scan time of about 3 min. DCE curves from all voxels of the 45 brain metastases were normalized and then temporally aligned. Amore » DCE matrix that is constructed from the aligned DCE curves of all voxels of the 45 lesions obtained prior to WBRT is processed by principal component analysis to generate the principal components (PCs). Then, the projection coefficient maps prior to and at the end of WBRT are created for each lesion. Next, a pattern recognition technique, based upon fuzzy-c-means clustering, is used to delineate the tumor subvolumes relating to the value of the significant projection coefficients. The relationship between changes in different tumor subvolumes and treatment response was evaluated to differentiate responsive from stable and progressive tumors. Performance of the PC-defined tumor subvolume was also evaluated by receiver operating characteristic (ROC) analysis in prediction of nonresponsive lesions and compared with physiological-defined tumor subvolumes. Results: The projection coefficient maps of the first three PCs contain almost all response-related information in DCE curves of brain metastases. The first projection coefficient, related to the area under DCE curves, is the major component to determine response while the third one has a complimentary role. In ROC analysis, the area under curve of 0.88 ± 0.05 and 0.86 ± 0.06 were achieved for the PC-defined and physiological-defined tumor subvolume in response assessment. Conclusions: The PC-defined subvolume of a brain metastasis could predict tumor response to therapy similar to the physiological-defined one, while the former is determined more rapidly for clinical decision-making support.« less

DCE-MRI defined subvolumes of a brain metastatic lesion by principle component analysis and fuzzy-c-means clustering for response assessment of radiation therapy

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

Farjam, Reza; Tsien, Christina I.; Lawrence, Theodore S.

2014-01-15

Purpose: To develop a pharmacokinetic modelfree framework to analyze the dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data for assessment of response of brain metastases to radiation therapy. Methods: Twenty patients with 45 analyzable brain metastases had MRI scans prior to whole brain radiation therapy (WBRT) and at the end of the 2-week therapy. The volumetric DCE images covering the whole brain were acquired on a 3T scanner with approximately 5 s temporal resolution and a total scan time of about 3 min. DCE curves from all voxels of the 45 brain metastases were normalized and then temporally aligned. Amore » DCE matrix that is constructed from the aligned DCE curves of all voxels of the 45 lesions obtained prior to WBRT is processed by principal component analysis to generate the principal components (PCs). Then, the projection coefficient maps prior to and at the end of WBRT are created for each lesion. Next, a pattern recognition technique, based upon fuzzy-c-means clustering, is used to delineate the tumor subvolumes relating to the value of the significant projection coefficients. The relationship between changes in different tumor subvolumes and treatment response was evaluated to differentiate responsive from stable and progressive tumors. Performance of the PC-defined tumor subvolume was also evaluated by receiver operating characteristic (ROC) analysis in prediction of nonresponsive lesions and compared with physiological-defined tumor subvolumes. Results: The projection coefficient maps of the first three PCs contain almost all response-related information in DCE curves of brain metastases. The first projection coefficient, related to the area under DCE curves, is the major component to determine response while the third one has a complimentary role. In ROC analysis, the area under curve of 0.88 ± 0.05 and 0.86 ± 0.06 were achieved for the PC-defined and physiological-defined tumor subvolume in response assessment. Conclusions: The PC-defined subvolume of a brain metastasis could predict tumor response to therapy similar to the physiological-defined one, while the former is determined more rapidly for clinical decision-making support.« less

Multi-mode humidity sensing with water-soluble copper phthalocyanine for increased sensitivity and dynamic range

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

Muckley, Eric S.; Jacobs, Christopher B.; Vidal, Keith

Aqueous solubility of copper phthalocyanine-3,4',4',4"'-tetrasulfonic acid tetrasodium salt (CuPcTs) enables fabrication of flexible electronic devices by low cost inkjet printing. We (1) investigate water adsorption kinetics on CuPcTs for better understanding the effects of relative humidity (RH) on hydrophilic phthalocyanines, and (2) assess CuPcTs as a humidity-sensing material. Reaction models show that H 2O undergoes 2-site adsorption which can be represented by a pair of sequentially-occurring pseudo-first order reactions. Using high frequency (300–700 THz) and low frequency (1–8 MHz) dielectric spectroscopy combined with gravimetric measurements and principal component analysis, we observe that significant opto-electrical changes in CuPcTs occur at RHmore » ≈ 60%. The results suggest that rapid H 2O adsorption takes place at hydrophilic sulfonyl/salt groups on domain surfaces at low RH, while slow adsorption and diffusion of H 2O into CuPcTs crystallites leads to a mixed CuPcTs-H 2O phase at RH > 60%, resulting in high frequency dielectric screening of the film by water and dissociation of Na+ from CuPc(SO 3-) 4 ions. Lastly, the CuPcTs-H 2O interaction can be tracked using a combination of gravimetric, optical, and electrical sensing modes, enabling accurate ( ± 2.5%) sensing in the ~0–95% RH range with a detection limit of less than 0.1% RH.« less

Multi-mode humidity sensing with water-soluble copper phthalocyanine for increased sensitivity and dynamic range

DOE PAGES

Muckley, Eric S.; Jacobs, Christopher B.; Vidal, Keith; ...

2017-08-30

Aqueous solubility of copper phthalocyanine-3,4',4',4"'-tetrasulfonic acid tetrasodium salt (CuPcTs) enables fabrication of flexible electronic devices by low cost inkjet printing. We (1) investigate water adsorption kinetics on CuPcTs for better understanding the effects of relative humidity (RH) on hydrophilic phthalocyanines, and (2) assess CuPcTs as a humidity-sensing material. Reaction models show that H 2O undergoes 2-site adsorption which can be represented by a pair of sequentially-occurring pseudo-first order reactions. Using high frequency (300–700 THz) and low frequency (1–8 MHz) dielectric spectroscopy combined with gravimetric measurements and principal component analysis, we observe that significant opto-electrical changes in CuPcTs occur at RHmore » ≈ 60%. The results suggest that rapid H 2O adsorption takes place at hydrophilic sulfonyl/salt groups on domain surfaces at low RH, while slow adsorption and diffusion of H 2O into CuPcTs crystallites leads to a mixed CuPcTs-H 2O phase at RH > 60%, resulting in high frequency dielectric screening of the film by water and dissociation of Na+ from CuPc(SO 3-) 4 ions. Lastly, the CuPcTs-H 2O interaction can be tracked using a combination of gravimetric, optical, and electrical sensing modes, enabling accurate ( ± 2.5%) sensing in the ~0–95% RH range with a detection limit of less than 0.1% RH.« less

Multi-mode humidity sensing with water-soluble copper phthalocyanine for increased sensitivity and dynamic range.

PubMed

Muckley, Eric S; Jacobs, Christopher B; Vidal, Keith; Lavrik, Nickolay V; Sumpter, Bobby G; Ivanov, Ilia N

2017-08-30

Aqueous solubility of copper phthalocyanine-3,4',4″,4″'-tetrasulfonic acid tetrasodium salt (CuPcTs) enables fabrication of flexible electronic devices by low cost inkjet printing. We (1) investigate water adsorption kinetics on CuPcTs for better understanding the effects of relative humidity (RH) on hydrophilic phthalocyanines, and (2) assess CuPcTs as a humidity-sensing material. Reaction models show that H 2 O undergoes 2-site adsorption which can be represented by a pair of sequentially-occurring pseudo-first order reactions. Using high frequency (300-700 THz) and low frequency (1-8 MHz) dielectric spectroscopy combined with gravimetric measurements and principal component analysis, we observe that significant opto-electrical changes in CuPcTs occur at RH ≈ 60%. The results suggest that rapid H 2 O adsorption takes place at hydrophilic sulfonyl/salt groups on domain surfaces at low RH, while slow adsorption and diffusion of H 2 O into CuPcTs crystallites leads to a mixed CuPcTs-H 2 O phase at RH > 60%, resulting in high frequency dielectric screening of the film by water and dissociation of Na + from CuPc(SO 3 - ) 4 ions. The CuPcTs-H 2 O interaction can be tracked using a combination of gravimetric, optical, and electrical sensing modes, enabling accurate ( ± 2.5%) sensing in the ~0-95% RH range with a detection limit of less than 0.1% RH.

Thermodynamic efficiency analysis and cycle optimization of deeply precooled combined cycle engine in the air-breathing mode

NASA Astrophysics Data System (ADS)

Zhang, Jianqiang; Wang, Zhenguo; Li, Qinglian

2017-09-01

The efficiency calculation and cycle optimization were carried out for the Synergistic Air-Breathing Rocket Engine (SABRE) with deeply precooled combined cycle. A component-level model was developed for the engine, and exergy efficiency analysis based on the model was carried out. The methods to improve cycle efficiency have been proposed. The results indicate cycle efficiency of SABRE is between 29.7% and 41.7% along the flight trajectory, and most of the wasted exergy is occupied by the unburned hydrogen in exit gas. Exergy loss exists in each engine component, and the sum losses of main combustion chamber(CC), pre-burner(PB), precooler(PC) and 3# heat exchanger(HX3) are greater than 71.3% of the total loss. Equivalence ratio is the main influencing factor of cycle, and it can be regulated by adjusting parameters of helium loop. Increase the maximum helium outlet temperature of PC by 50 K, the total assumption of hydrogen will be saved by 4.8%, and the cycle efficiency is advanced by 3% averagely in the trajectory. Helium recirculation scheme introduces a helium recirculation loop to increase local helium flow rate of PC. It turns out the total assumption of hydrogen will be saved by 9%, that's about 1740 kg, and the cycle efficiency is advanced by 5.6% averagely.

Differential Metabolic Impact of Gastric Bypass Surgery Versus Dietary Intervention in Obese Diabetic Subjects Despite Identical Weight Loss

PubMed Central

Laferrère, Blandine; Reilly, David; Arias, Sara; Swerdlow, Nicholas; Gorroochurn, Prakash; Bawa, Baani; Bose, Mousumi; Teixeira, Julio; Stevens, Robert D.; Wenner, Brett R.; Bain, James R.; Muehlbauer, Michael J.; Haqq, Andrea; Lien, Lillian; Shah, Svati H.; Svetkey, Laura P.; Newgard, Christopher B.

2013-01-01

Glycemic control is improved more after gastric bypass surgery (GBP) than after equivalent diet-induced weight loss in patients with morbid obesity and type 2 diabetes mellitus. We applied metabolomic profiling to understand the mechanisms of this better metabolic response after GBP. Circulating amino acids (AAs) and acylcarnitines (ACs) were measured in plasma from fasted subjects by targeted tandem mass spectrometry before and after a matched 10-kilogram weight loss induced by GBP or diet. Total AAs and branched-chain AAs (BCAAs) decreased after GBP, but not after dietary intervention. Metabolites derived from BCAA oxidation also decreased only after GBP. Principal components (PC) analysis identified two major PCs, one composed almost exclusively of ACs (PC1) and another with BCAAs and their metabolites as major contributors (PC2). PC1 and PC2 were inversely correlated with pro-insulin concentrations, the C-peptide response to oral glucose, and the insulin sensitivity index after weight loss, whereas PC2 was uniquely correlated with levels of insulin resistance (HOMA-IR). These data suggest that the enhanced decrease in circulating AAs after GBP occurs by mechanisms other than weight loss and may contribute to the better improvement in glucose homeostasis observed with the surgical intervention. PMID:21525399

Exploring spatial-temporal dynamics of fire regime features in mainland Spain

NASA Astrophysics Data System (ADS)

Jiménez-Ruano, Adrián; Rodrigues Mimbrero, Marcos; de la Riva Fernández, Juan

2017-10-01

This paper explores spatial-temporal dynamics in fire regime features, such as fire frequency, burnt area, large fires and natural- and human-caused fires, as an essential part of fire regime characterization. Changes in fire features are analysed at different spatial - regional and provincial/NUTS3 - levels, together with summer and winter temporal scales, using historical fire data from Spain for the period 1974-2013. Temporal shifts in fire features are investigated by means of change point detection procedures - Pettitt test, AMOC (at most one change), PELT (pruned exact linear time) and BinSeg (binary segmentation) - at a regional level to identify changes in the time series of the features. A trend analysis was conducted using the Mann-Kendall and Sen's slope tests at both the regional and NUTS3 level. Finally, we applied a principal component analysis (PCA) and varimax rotation to trend outputs - mainly Sen's slope values - to summarize overall temporal behaviour and to explore potential links in the evolution of fire features. Our results suggest that most fire features show remarkable shifts between the late 1980s and the first half of the 1990s. Mann-Kendall outputs revealed negative trends in the Mediterranean region. Results from Sen's slope suggest high spatial and intra-annual variability across the study area. Fire activity related to human sources seems to be experiencing an overall decrease in the northwestern provinces, particularly pronounced during summer. Similarly, the Hinterland and the Mediterranean coast are gradually becoming less fire affected. Finally, PCA enabled trends to be synthesized into four main components: winter fire frequency (PC1), summer burnt area (PC2), large fires (PC3) and natural fires (PC4).

Gene Expression Profiling in Pachyonychia Congenita Skin

PubMed Central

Cao, Yu-An; Hickerson, Robyn P.; Seegmiller, Brandon L.; Grapov, Dmitry; Gross, Maren M.; Bessette, Marc R.; Phinney, Brett S.; Flores, Manuel A.; Speaker, Tycho J.; Vermeulen, Annaleen; Bravo, Albert A.; Bruckner, Anna L.; Milstone, Leonard M.; Schwartz, Mary E.; Rice, Robert H.; Kaspar, Roger L.

2015-01-01

Background Pachyonychia congenita (PC) is a skin disorder resulting from mutations in keratin (K) proteins including K6a, K6b, K16, and K17. One of the major symptoms is painful plantar keratoderma. The pathogenic sequelae resulting from the keratin mutations remain unclear. Objective To better understand PC pathogenesis. Methods RNA profiling was performed on biopsies taken from PC-involved and uninvolved plantar skin of seven genotyped PC patients (two K6a, one K6b, three K16, and one K17) as well as from control volunteers. Protein profiling was generated from tape-stripping samples. Results A comparison of PC-involved skin biopsies to adjacent uninvolved plantar skin identified 112 differentially-expressed mRNAs common to patient groups harboring K6 (i.e., both K6a and K6b) and K16 mutations. Among these mRNAs, 25 encode structural proteins including keratins, small proline-rich and late cornified envelope proteins, 20 are related to metabolism and 16 encode proteases, peptidases, and their inhibitors including kallikrein-related peptidases (KLKs), and serine protease inhibitors (SERPINs). mRNAs were also identified to be differentially expressed only in K6 (81) or K16 (141) patient samples. Furthermore, 13 mRNAs were identified that may be involved in pain including nociception and neuropathy. Protein profiling, comparing three K6a plantar tape-stripping samples to non-PC controls, showed changes in the PC corneocytes similar, but not identical, to the mRNA analysis. Conclusion Many differentially-expressed genes identified in PC-involved skin encode components critical for skin barrier homeostasis including keratinocyte proliferation, differentiation, cornification, and desquamation. The profiling data provide a foundation for unraveling the pathogenesis of PC and identifying targets for developing effective PC therapeutics. PMID:25656049

Apple Procyanidins Suppress Amyloid β-Protein Aggregation

PubMed Central

Toda, Toshihiko; Sunagawa, Tadahiro; Kanda, Tomomasa; Tagashira, Motoyuki; Shirasawa, Takuji; Shimizu, Takahiko

2011-01-01

Procyanidins (PCs) are major components of the apple polyphenols (APs). We previously reported that treatment with PC extended the mean lifespan of Caenorhabditis elegans (Sunagawa et al., 2011). In order to estimate the neuroprotective effects of PC, we investigated the antiaggregative activity of PC on amyloid β-protein (Aβ) aggregation, which is a pathological hallmark of Alzheimer's disease. We herein report that PC significantly suppressed Aβ42 aggregation and dissociated Aβ42 aggregates in a dose-dependent manner, indicating that PC is a potent suppressor of Aβ aggregation. Furthermore, PC significantly inhibited Aβ42 neurotoxicity and stimulated proliferation in PC-12 cells. These results suggested that the PC and AP acted as neuroprotective factors against toxic Aβ aggregates. PMID:21826271

Behavior of ambient concentrations of natural radionuclides (7)Be, (210)Pb, (40)K in the Mediterranean coastal city of Málaga (Spain).

PubMed

Gordo, E; Dueñas, C; Fernández, M C; Liger, E; Cañete, S

2015-05-01

During a 4-year period (January 2009-December 2012), the (7)Be, (210)Pb, and (40)K activity concentrations in airborne particulate matter were weekly determined at the Málaga (Spain) located in the southern Iberian Peninsula. Totally 209 polypropylene filters were analyzed in the mentioned period. In 100% of the filters, (7)Be and (40)K activity concentrations were detected while (210)Pb activity concentration was detected in 96% of the filters. The results from individual measurements of (7)Be, (210)Pb, and (40)K concentrations were analyzed to derive the statistical estimates characterizing the distributions. Principal components analysis (PCA) was applied to the datasets and the results of the study reveal that aerosol behavior is represented by two principal components which explain 73.2% of total variance. Components PC1 and PC2 respectively explain 46.0 and 27.2% of total variance. PC1 was related positively to dust content, (7)Be and (40)K concentrations and negatively to sunspot numbers. In contrast, PC2 was related positively to temperature and (210)Pb activity and negatively to precipitation and relative humidity. The (7)Be levels showed a significant correlation with sunspot numbers due to the cosmogenic origin. (40)K activities showed a good correlation with dust deposition in filters mainly because it was transported to the air as resuspended particle from the soil. An inverse relationship was observed between the (210)Pb concentrations and monthly rainfall, indicating washout of atmospheric aerosols carrying these radionuclides and a pronounced positive correlation with the average monthly temperature of air.

Heritability of the somatotype components in Biscay families.

PubMed

Rebato, E; Jelenkovic, A; Salces, I

2007-01-01

The anthropometric somatotype is a quantitative description of body shape and composition. Familial studies indicate the existence of a familial resemblance for this phenotype and they suggest a substantial action by genetic factors on this aggregation. The aim of this study is to examine the degree of familial resemblance of the somatotype components and of a factor of shape, in a sample of Biscay nuclear families (Basque Country, Spain). One thousand three hundred and thirty nuclear families were analysed. The anthropometric somatotype components [Carter, J.E.L., Heath, B.H., 1990. Somatotyping. Development and applications. Cambridge University Press, Cambridge, p. 503] were computed. Each component was fitted for the other two through a stepwise multiple regression, and also fitted through the LMS method [Cole, T., 1988. Fitting smoothed centile curves to reference data. J. Roy. Stat. Soc. 151, 385-418] in order to eliminate the age, sex and generation effects. The three raw components were introduced in a PCA from which a shape factor (PC1) was extracted for each generation. The correlations analysis was performed with the SEGPATH package [Province, M.A., Rao, D.C., 1995. General purpose model and computer programme for combined segregation and path analysis (SEGPATH): automatically creating computer from symbolic language model specifications. Genet. Epidemiol. 12, 203-219]. A general model of transmission and nine reduced models were tested. Maximal heritability was estimated with the formula of [Rice, T., Warwick, D.E., Gagnon, J., Bouchard, C., Leon, A.S., Skinner, J.S., Wilmore, J.H., Rao, D.C., 1997. Familial resemblance for body composition measures: the HERITAGE family study. Obes. Res. 5, 557-562]. The correlations were higher between offspring than in parents and offspring and a significant resemblance between mating partners existed. Maximum heritabilities were 55%, 52% and 46% for endomorphy, mesomorphy and ectomorphy, respectively, and 52% for PC1. In conclusion, the somatotype presents a moderate degree of familial aggregation. For the somatotype components, as well as for PC1, the degree of familial resemblance depends on age. The sex only has a significant effect on ectomorphy.

Effects of plant polyphenols and α-tocopherol on lipid oxidation, microbiological characteristics, and biogenic amines formation in dry-cured bacons.

PubMed

Wang, Yongli; Li, Feng; Zhuang, Hong; Li, Lianghao; Chen, Xiao; Zhang, Jianhao

2015-03-01

Effects of plant polyphenols (tea polyphenol [TP], grape seed extract [GSE], and gingerol) and α-tocopherol on physicochemical parameters, microbiological counts, and biogenic amines were determined in dry-cured bacons at the end of ripening. Results showed that plant polyphenols and α-tocopherol significantly decreased pH, thiobarbituric acid reactive substances content, and total volatile basic nitrogen (TVBN) compared with the control (P < 0.05). Microbial counts and biogenic amine contents in dry-cured bacons were affected by plant polyphenols or α-tocopherol, with TP being the most effective (P < 0.05) in reducing aerobic plate counts, Enterobacteriaceae, Micrococcaceae, yeast, and molds, as well as in inhibiting formation of putrescine, cadaverine, tyramine, and spermine. Principal component analysis indicated that the first 2 principal components (PC) explained about 85.5% of the total variation. PC1 was related with physicochemical factors, parts of biogenic amines, and spoilage microorganisms, whereas PC2 grouped the TVBN, tyramine, 2-phenylethylamine, yeast, and molds. These findings suggest that plant polyphenols, especially TP, could be used to process dry-cured bacons to improve the quality and safety of finished products. © 2015 Institute of Food Technologists®

78 FR 17865 - Airworthiness Directives; PILATUS AIRCRAFT LTD. Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-25

... TBO were moved from Chapter 5: Time Limits/Maintenance Checks, to Chapter 4: Structural, Component and... Directives; PILATUS AIRCRAFT LTD. Airplanes AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: Final... all PILATUS AIRCRAFT LTD. Models PC-12, PC-12/45, and PC-12/47 airplanes. This AD results from...

Discrete Event Simulation Modeling and Analysis of Key Leader Engagements

DTIC Science & Technology

2012-06-01

to offer. GreenPlayer agents require four parameters, pC, pKLK, pTK, and pRK , which give probabilities for being corrupt, having key leader...HandleMessageRequest component. The same parameter constraints apply to these four parameters. The parameter pRK is the same parameter from the CreatePlayers component...whether the local Green player has resource critical knowledge by using the parameter pRK . It schedules an EndResourceKnowledgeRequest event, passing

Quantitative Analysis and Biological Efficacies regarding the Neuroprotective and Antineuroinflammatory Actions of the Herbal Formula Jodeungsan in HT22 Hippocampal Cells and BV-2 Microglia

PubMed Central

Lim, Hye-Sun

2017-01-01

Jodeungsan (JDS) is a traditional herbal formula that comprises seven medicinal herbs and is broadly utilized to treat hypertension, dementia, and headache. However, the effects of JDS and its herbal components on neurodegenerative diseases have not been reported. We examined the inhibitory effects of JDS and its seven components on neuronal cell death and inflammation using HT22 hippocampal cells and BV-2 microglia, respectively. Among its seven herbal components, Uncaria sinensis (US), Chrysanthemum morifolium (CM), Zingiber officinale (ZO), Pinellia ternata (PT), Citrus unshiu (CU), and Poria cocos (PC) exhibited significant neuroprotective effects in HT22 cells. In BV-2 cells, JDS significantly suppressed the production of tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6), indicating the antineuroinflammatory activity of JDS. In addition, the herbal extracts from ZO, Panax ginseng (PG), PT, CU, and PC exhibited inhibitory effects on the inflammatory response in microglia. These data imply that the JDS effect on neurodegeneration occurs via coordination among its seven components. To establish a quality control for JDS, a simultaneous analysis using five standard compounds identified hesperidin (37.892 ± 1.228 mg/g) as the most abundant phytochemical of JDS. Further investigation of the combinatorial activities of two or more standard compounds will be necessary to verify their antineurodegenerative regulatory mechanisms. PMID:29391873

Relationship between polycystic ovary syndrome and ancestry in European Americans.

PubMed

Bjonnes, Andrew C; Saxena, Richa; Welt, Corrine K

2016-12-01

To determine whether European Americans with polycystic ovary syndrome (PCOS) exhibit genetic differences associated with PCOS status and phenotypic features. Case-control association study in European Americans. Academic center. Women with PCOS diagnosed with the use of the National Institutes of Health criteria (n = 532) and control women with regular menstrual cycles and no evidence of hyperandrogenism (n = 432). Blood was drawn for measurement of sex steroids, metabolic parameters, and genotyping. Associations among PCOS status, phenotype, and genetic background identified with the use of principal component analysis. Principal component analysis identified five principal components (PCs). PC1 captured northwest-to-southeast European genetic variation and was associated with PCOS status. Acanthosis was associated with southern European ancestry, and larger waist:hip ratio was associated with northern European ancestry. PC2 was associated with east-to-west European genetic variation and cholesterol levels. These data provide evidence for genetic influence based on European ethnicity in women with PCOS. There is also evidence for a genetic component in the phenotypic features of PCOS within a mixed European population. The data point to the need to control for population stratification in genetic studies in women of mixed European ethnicity. They also emphasize the need for better studies of PCOS prevalence and phenotype as a function of genetic background. Copyright © 2016 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Acute inflammatory proteins constitute the organic matrix of prostatic corpora amylacea and calculi in men with prostate cancer

PubMed Central

Sfanos, Karen S.; Wilson, Brice A.; De Marzo, Angelo M.; Isaacs, William B.

2009-01-01

Corpora amylacea (CA) are a frequent microscopic finding in radical prostatectomy specimens from men undergoing treatment for prostate cancer. Although often observed histologically to be associated with inflammation, the contribution of CA to prostatitis-related symptoms of unknown etiology or to prostate carcinogenesis remains unclear. Prostatic calculi (PC), which potentially represent calcified forms of CA, are less common but can cause urological disease including urinary retention and prostatitis. We conducted a comprehensive compositional analysis of CA/PC to gain insight into their biogenesis. Infrared spectroscopy analysis of calculi collected from 23 patients confirmed a prevalence of calcium phosphate in the form of hydroxyapatite. This result sets PC apart from most urinary stones, which largely are composed of calcium oxalate. Tandem mass spectrometry-based proteomic analysis of CA/PC revealed that lactoferrin is the predominant protein component, a result that was confirmed by Western blot analysis. Other proteins identified, including calprotectin, myeloperoxidase, and α-defensins, are proteins contained in neutrophil granules. Immunohistochemistry (IHC) suggested the source of lactoferrin to be prostate-infiltrating neutrophils as well as inflamed prostate epithelium; however, IHC for calprotectin suggested prostate-infiltrating neutrophils as a major source of the protein, because it was absent from other prostate compartments. This study represents a definitive analysis of the protein composition of prostatic CA and calculi and suggests that acute inflammation has a role in their biogenesis—an intriguing finding, given the prevalence of CA in prostatectomy specimens and the hypothesized role for inflammation in prostate carcinogenesis. PMID:19202053

Interface doping of conjugated organic films by means of diffusion of atomic components from the surfaces of semiconductors and of metal oxides.

PubMed

Komolov, A S; Akhremtchik, S N; Lazneva, E F

2011-08-15

The paper reports the results on the interface formation of 5-10 nm thick conjugated layers of Cu-phthalocyanine (CuPc) with a number of solid surfaces: polycrystalline Au, (SiO(2))n-Si, ZnO(0 0 0 1), Si(1 0 0), Ge(1 1 1), CdS(0 0 0 1) and GaAs(1 0 0). The results were obtained using Auger electron spectroscopy (AES) and low-energy target current electron spectroscopy (TCS). The organic overlayers were thermally deposited in situ in UHV onto substrate surfaces. The island-like organic deposits were excluded from the analysis so that only uniform organic deposits were considered. In the cases of polycrystalline Au, Si(1 0 0) and Ge(1 1 1) substrates the AES peaks of the substrate material attenuated down to the zero noise level upon the increase of the CuPc film thickness of 8-10 nm. The peaks corresponding to oxygen atoms in the case of SiO(2) substrate, and to atoms from the ZnO, GaAs and CdS substrates were clearly registered in the AES spectra of the 8-10 nm thick CuPc deposits. The relative concentration of the substrate atomic components diffused into the film was different from their relative concentration at the pure substrate surface. The concentration of the substrate dopant atoms in the CuPc film was estimated as one atom per one CuPc molecule. Using the target current electron spectroscopy, it was shown that the substrate atoms admixed in the CuPc film account for the appearance of a new peak in the density of unoccupied electronic states. Formation of intermediate TCS spectra until the CuPc deposit reaches 2-3 nm was observed in the cases of GaAs(1 0 0), ZnO(0 0 0 1), Ge(1 1 1) surfaces. The intermediate spectra show a less pronounced peak structure different from the one typical for the CuPc films. It was suggested that the intermediate layer was formed by the CuPc molecules fully or partially decomposed due to the interaction with the relatively reactive semiconductor surfaces. Copyright © 2010 Elsevier B.V. All rights reserved.

Morphological analysis of Trichomycterus areolatus Valenciennes, 1846 from southern Chilean rivers using a truss-based system (Siluriformes, Trichomycteridae).

PubMed

Colihueque, Nelson; Corrales, Olga; Yáñez, Miguel

2017-01-01

Trichomycterus areolatus Valenciennes, 1846 is a small endemic catfish inhabiting the Andean river basins of Chile. In this study, the morphological variability of three T. areolatus populations, collected in two river basins from southern Chile, was assessed with multivariate analyses, including principal component analysis (PCA) and discriminant function analysis (DFA). It is hypothesized that populations must segregate morphologically from each other based on the river basin that they were sampled from, since each basin presents relatively particular hydrological characteristics. Significant morphological differences among the three populations were found with PCA (ANOSIM test, r = 0.552, p < 0.0001) and DFA (Wilks's λ = 0.036, p < 0.01). PCA accounted for a total variation of 56.16% by the first two principal components. The first Principal Component (PC1) and PC2 explained 34.72 and 21.44% of the total variation, respectively. The scatter-plot of the first two discriminant functions (DF1 on DF2) also validated the existence of three different populations. In group classification using DFA, 93.3% of the specimens were correctly-classified into their original populations. Of the total of 22 transformed truss measurements, 17 exhibited highly significant ( p < 0.01) differences among populations. The data support the existence of T. areolatus morphological variation across different rivers in southern Chile, likely reflecting the geographic isolation underlying population structure of the species.

Biomimicry 1: PC.

PubMed

Cumberland, D C; Gunn, J; Malik, N; Holt, C M

1998-01-01

The surface properties of stents can be modified by coating them, for example with a polymer. Phosphorylcoline (PC) is the major component of the outer layer of the cell membrane. The haemo- and biocompatibility of a PC-containing polymer is thus based on biomimicry, and has been confirmed by several experiments showing much reduced thrombogenicity of PC-coated surfaces, and porcine coronary artery implants showing no sign of adverse effect. Clinical experience with the PC-coated BiodivYsio appears favourable. The PC coating can be tailored for take up and controlled elution of various drugs for stent-based local delivery, a property which is being actively explored.

Environmental risk of heavy metal pollution and contamination sources using multivariate analysis in the soils of Varanasi environs, India.

PubMed

Singh, Shubhra; Raju, N Janardhana; Nazneen, Sadaf

2015-06-01

This study assessed soil pollution in the Varanasi environs of Uttar Pradesh in India. Assessing the concentration of potentially harmful heavy metals in the soils is imperative in order to evaluate the potential risks to human. To identify the concentration and sources of heavy metals and assess the soil environmental quality, 23 samples were collected from different locations covering dumping, road and agricultural area. The average concentrations of the heavy metals were all below the permissible limits according to soil quality guidelines except Cu (copper) and Pb (lead) in dumping and road soils. Soil heavy metal contamination was assessed on the basis of geoaccumulation index (Igeo), pollution index (PI) and integrated pollution index (IPI). The IPI of the metals ranged from 0.59 to 9.94, with the highest IPI observed in the dumping and road soils. A very significant correlation was found between Pb and Cu. The result of principal component analysis suggested that PC1 was mainly affected by the use of agrochemicals, PC2 was affected by vehicular emission and PC3 was affected by dumping waste. Meanwhile, PC4 was mainly controlled by parent material along with anthropogenic activities. Appropriate measures should be taken to minimize the heavy metal levels in soils and thus protect human health.

Statistical analysis of aerosol species, trace gasses, and meteorology in Chicago.

PubMed

Binaku, Katrina; O'Brien, Timothy; Schmeling, Martina; Fosco, Tinamarie

2013-09-01

Both canonical correlation analysis (CCA) and principal component analysis (PCA) were applied to atmospheric aerosol and trace gas concentrations and meteorological data collected in Chicago during the summer months of 2002, 2003, and 2004. Concentrations of ammonium, calcium, nitrate, sulfate, and oxalate particulate matter, as well as, meteorological parameters temperature, wind speed, wind direction, and humidity were subjected to CCA and PCA. Ozone and nitrogen oxide mixing ratios were also included in the data set. The purpose of statistical analysis was to determine the extent of existing linear relationship(s), or lack thereof, between meteorological parameters and pollutant concentrations in addition to reducing dimensionality of the original data to determine sources of pollutants. In CCA, the first three canonical variate pairs derived were statistically significant at the 0.05 level. Canonical correlation between the first canonical variate pair was 0.821, while correlations of the second and third canonical variate pairs were 0.562 and 0.461, respectively. The first canonical variate pair indicated that increasing temperatures resulted in high ozone mixing ratios, while the second canonical variate pair showed wind speed and humidity's influence on local ammonium concentrations. No new information was uncovered in the third variate pair. Canonical loadings were also interpreted for information regarding relationships between data sets. Four principal components (PCs), expressing 77.0 % of original data variance, were derived in PCA. Interpretation of PCs suggested significant production and/or transport of secondary aerosols in the region (PC1). Furthermore, photochemical production of ozone and wind speed's influence on pollutants were expressed (PC2) along with overall measure of local meteorology (PC3). In summary, CCA and PCA results combined were successful in uncovering linear relationships between meteorology and air pollutants in Chicago and aided in determining possible pollutant sources.

Comparison of factor-analytic and reduced rank models for test-day milk yield in Gyr dairy cattle (Bos indicus).

PubMed

Pereira, R J; Ayres, D R; El Faro, L; Verneque, R S; Vercesi Filho, A E; Albuquerque, L G

2013-09-27

We analyzed 46,161 monthly test-day records of milk production from 7453 first lactations of crossbred dairy Gyr (Bos indicus) x Holstein cows. The following seven models were compared: standard multivariate model (M10), three reduced rank models fitting the first 2, 3, or 4 genetic principal components, and three models considering a 2-, 3-, or 4-factor structure for the genetic covariance matrix. Full rank residual covariance matrices were considered for all models. The model fitting the first two principal components (PC2) was the best according to the model selection criteria. Similar phenotypic, genetic, and residual variances were obtained with models M10 and PC2. The heritability estimates ranged from 0.14 to 0.21 and from 0.13 to 0.21 for models M10 and PC2, respectively. The genetic correlations obtained with model PC2 were slightly higher than those estimated with model M10. PC2 markedly reduced the number of parameters estimated and the time spent to reach convergence. We concluded that two principal components are sufficient to model the structure of genetic covariances between test-day milk yields.

TWO-DIMENSIONAL MAPPING OF YOUNG STARS IN THE INNER 180 pc OF NGC 1068: CORRELATION WITH MOLECULAR GAS RING AND STELLAR KINEMATICS

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

Storchi-Bergmann, Thaisa; Riffel, Rogerio; Vale, Tiberio Borges

We report the first two-dimensional mapping of the stellar population and non-stellar continua within the inner 180 pc (radius) of NGC 1068 at a spatial resolution of 8 pc, using integral field spectroscopy in the near-infrared. We have applied the technique of spectral synthesis to data obtained with the instrument NIFS and the adaptive optics module ALTAIR at the Gemini North Telescope. Two episodes of recent star formation are found to dominate the stellar population contribution: the first occurred 300 Myr ago, extending over most of the nuclear region; the second occurred just 30 Myr ago, in a ring-like structuremore » at Almost-Equal-To 100 pc from the nucleus, where it is coincident with an expanding ring of H{sub 2} emission. Inside the ring, where a decrease in the stellar velocity dispersion is observed, the stellar population is dominated by the 300 Myr age component. In the inner 35 pc, the oldest age component (age {>=} 2 Gyr) dominates the mass, while the flux is dominated by blackbody components with temperatures in the range 700 K {<=} T {<=} 800 K which we attribute to the dusty torus. We also find some contribution from blackbody and power-law components beyond the nucleus which we attribute to dust emission and scattered light.« less

Intelligent tutoring systems for systems engineering methodologies

NASA Technical Reports Server (NTRS)

Meyer, Richard J.; Toland, Joel; Decker, Louis

1991-01-01

The general goal is to provide the technology required to build systems that can provide intelligent tutoring in IDEF (Integrated Computer Aided Manufacturing Definition Method) modeling. The following subject areas are covered: intelligent tutoring systems for systems analysis methodologies; IDEF tutor architecture and components; developing cognitive skills for IDEF modeling; experimental software; and PC based prototype.

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

Yang, Chao

Sparx, a new environment for Cryo-EM image processing; Cryo-EM, Single particle reconstruction, principal component analysis; Hardware Req.: PC, MAC, Supercomputer, Mainframe, Multiplatform, Workstation. Software Req.: operating system is Unix; Compiler C++; type of files: source code, object library, executable modules, compilation instructions; sample problem input data. Location/transmission: http://sparx-em.org; User manual & paper: http://sparx-em.org;

ULF geomagnetic activity effects on tropospheric temperature, specific humidity, and cloud cover in Antarctica, during 2003-2010

NASA Astrophysics Data System (ADS)

Regi, Mauro; Redaelli, Gianluca; Francia, Patrizia; De Lauretis, Marcello

2017-06-01

In the present study we investigated the possible relationship between the ULF geomagnetic activity and the variations of several atmospheric parameters. In particular, we compared the ULF activity in the Pc1-2 frequency band (100 mHz-5 Hz), computed from geomagnetic field measurements at Terra Nova Bay in Antarctica, with the tropospheric temperature T, specific humidity Q, and cloud cover (high cloud cover, medium cloud cover, and low cloud cover) obtained from reanalysis data set. The statistical analysis was conducted during the years 2003-2010, using correlation and Superposed Epoch Analysis approaches. The results show that the atmospheric parameters significantly change following the increase of geomagnetic activity within 2 days. These changes are evident in particular when the interplanetary magnetic field Bz component is oriented southward (Bz<0) and the By component duskward (By>0). We suggest that both the precipitation of electrons induced by Pc1-2 activity and the intensification of the polar cap potential difference, modulating the microphysical processes in the clouds, can affect the atmosphere conditions.

Wave number determination of Pc 1-2 mantle waves considering He++ ions: A Cluster study

NASA Astrophysics Data System (ADS)

Grison, B.; Escoubet, C. P.; Santolík, O.; Cornilleau-Wehrlin, N.; Khotyaintsev, Y.

2014-09-01

The present case study concerns narrowband electromagnetic emission detected in the distant cusp region simultaneously with upgoing plasma flows. The wave properties match the usual properties of the Pc 1-2 mantle waves: small angle between the wave vector and the magnetic field line, left-hand polarization, and propagation toward the ionosphere. We report here the first direct wave vector measurement of these waves (about 1.2 × 10- 2 rad/km) through multi spacecraft analysis using the three magnetic components and, at the same time, through single spacecraft analysis based on the refractive index analysis using the three magnetic components and two electric components. The refractive index analysis offers a simple way to estimate wave numbers in this frequency range. Numerical calculations are performed under the observed plasma conditions. The obtained results show that the ion distribution functions are unstable to ion cyclotron instability at the observed wave vector value, due to the large ion temperature anisotropy. We thus show that these electromagnetic ion cyclotron (EMIC) waves are amplified in the distant cusp region. The Poynting flux of the waves is counterstreaming with respect to the plasma flow. This sense of propagation is consistent with the time necessary to amplify the emissions to the observed level. We point out the role of the wave damping at the He++ gyrofrequency to explain that such waves cannot be observed from the ground at the cusp foot print location.

Direct characterization of the energy level alignments and molecular components in an organic hetero-junction by integrated photoemission spectroscopy and reflection electron energy loss spectroscopy analysis.

PubMed

Yun, Dong-Jin; Shin, Weon-Ho; Bulliard, Xavier; Park, Jong Hwan; Kim, Seyun; Chung, Jae Gwan; Kim, Yongsu; Heo, Sung; Kim, Seong Heon

2016-08-26

A novel, direct method for the characterization of the energy level alignments at bulk-heterojunction (BHJ)/electrode interfaces on the basis of electronic spectroscopy measurements is proposed. The home-made in situ photoemission system is used to perform x-ray/ultraviolet photoemission spectroscopy (XPS/UPS), reflection electron energy loss spectroscopy (REELS) and inverse photoemission spectroscopy of organic-semiconductors (OSCs) deposited onto a Au substrate. Through this analysis system, we are able to obtain the electronic structures of a boron subphthalocyanine chloride:fullerene (SubPC:C60) BHJ and those of the separate OSC/electrode structures (SubPC/Au and C60/Au). Morphology and chemical composition analyses confirm that the original SubPC and C60 electronic structures remain unchanged in the electrodes prepared. Using this technique, we ascertain that the position and area of the nearest peak to the Fermi energy (EF = 0 eV) in the UPS (REELS) spectra of SubPC:C60 BHJ provide information on the highest occupied molecular orbital level (optical band gap) and combination ratio of the materials, respectively. Thus, extracting the adjusted spectrum from the corresponding SubPC:C60 BHJ UPS (REELS) spectrum reveals its electronic structure, equivalent to that of the C60 materials. This novel analytical approach allows complete energy-level determination for each combination ratio by separating its electronic structure information from the BHJ spectrum.

Describing temperament in an ungulate: a multidimensional approach.

PubMed

Graunke, Katharina L; Nürnberg, Gerd; Repsilber, Dirk; Puppe, Birger; Langbein, Jan

2013-01-01

Studies on animal temperament have often described temperament using a one-dimensional scale, whereas theoretical framework has recently suggested two or more dimensions using terms like "valence" or "arousal" to describe these dimensions. Yet, the valence or assessment of a situation is highly individual. The aim of this study was to provide support for the multidimensional framework with experimental data originating from an economically important species (Bos taurus). We tested 361 calves at 90 days post natum (dpn) in a novel-object test. Using a principal component analysis (PCA), we condensed numerous behaviours into fewer variables to describe temperament and correlated these variables with simultaneously measured heart rate variability (HRV) data. The PCA resulted in two behavioural dimensions (principal components, PC): novel-object-related (PC 1) and exploration-activity-related (PC 2). These PCs explained 58% of the variability in our data. The animals were distributed evenly within the two behavioural dimensions independent of their sex. Calves with different scores in these PCs differed significantly in HRV, and thus in the autonomous nervous system's activity. Based on these combined behavioural and physiological data we described four distinct temperament types resulting from two behavioural dimensions: "neophobic/fearful--alert", "interested--stressed", "subdued/uninterested--calm", and "neoophilic/outgoing--alert". Additionally, 38 calves were tested at 90 and 197 dpn. Using the same PCA-model, they correlated significantly in PC 1 and tended to correlate in PC 2 between the two test ages. Of these calves, 42% expressed a similar behaviour pattern in both dimensions and 47% in one. No differences in temperament scores were found between sexes or breeds. In conclusion, we described distinct temperament types in calves based on behavioural and physiological measures emphasising the benefits of a multidimensional approach.

Principal components analysis of Jupiter VIMS spectra

USGS Publications Warehouse

Bellucci, G.; Formisano, V.; D'Aversa, E.; Brown, R.H.; Baines, K.H.; Bibring, J.-P.; Buratti, B.J.; Capaccioni, F.; Cerroni, P.; Clark, R.N.; Coradini, A.; Cruikshank, D.P.; Drossart, P.; Jaumann, R.; Langevin, Y.; Matson, D.L.; McCord, T.B.; Mennella, V.; Nelson, R.M.; Nicholson, P.D.; Sicardy, B.; Sotin, Christophe; Chamberlain, M.C.; Hansen, G.; Hibbits, K.; Showalter, M.; Filacchione, G.

2004-01-01

During Cassini - Jupiter flyby occurred in December 2000, Visual-Infrared mapping spectrometer (VIMS) instrument took several image cubes of Jupiter at different phase angles and distances. We have analysed the spectral images acquired by the VIMS visual channel by means of a principal component analysis technique (PCA). The original data set consists of 96 spectral images in the 0.35-1.05 ??m wavelength range. The product of the analysis are new PC bands, which contain all the spectral variance of the original data. These new components have been used to produce a map of Jupiter made of seven coherent spectral classes. The map confirms previously published work done on the Great Red Spot by using NIMS data. Some other new findings, presently under investigation, are presented. ?? 2004 Published by Elsevier Ltd on behalf of COSPAR.

A low-cost PC-based telemetry data-reduction system

NASA Astrophysics Data System (ADS)

Simms, D. A.; Butterfield, C. P.

1990-04-01

The Solar Energy Research Institute's (SERI) Wind Research Branch is using Pulse Code Modulation (PCM) telemetry data-acquisition systems to study horizontal-axis wind turbines. PCM telemetry systems are used in test installations that require accurate multiple-channel measurements taken from a variety of different locations. SERI has found them ideal for use in tests requiring concurrent acquisition of data-reduction system to facilitate quick, in-the-field multiple-channel data analysis. Called the PC-PCM System, it consists of two basic components. First, AT-compatible hardware boards are used for decoding and combining PCM data streams. Up to four hardware boards can be installed in a single PC, which provides the capability to combine data from four PCM streams directly to PC disk or memory. Each stream can have up to 62 data channels. Second, a software package written for the DOS operating system was developed to simplify data-acquisition control and management. The software provides a quick, easy-to-use interface between the PC and PCM data streams. Called the Quick-Look Data Management Program, it is a comprehensive menu-driven package used to organize, acquire, process, and display information from incoming PCM data streams. This paper describes both hardware and software aspects of the SERI PC-PCM system, concentrating on features that make it useful in an experiment test environment to quickly examine and verify incoming data. Also discussed are problems and techniques associated with PC-based telemetry data acquisition, processing, and real-time display.

An endophytic Coniochaeta velutina producing broad spectrum antimycotics.

PubMed

Xie, Jie; Strobel, Gary A; Feng, Tao; Ren, Huishuang; Mends, Morgan T; Zhou, Zeyang; Geary, Brad

2015-06-01

An endophyte (PC27-5) was isolated from stem tissue of Western hemlock (Tsuga heterophylla) in a Pacific Northwest temperate rainforest. Phylogenetic analyses, based on ITS-5.8S rDNA and 18S rDNA sequence data, combined with cultural and morphological analysis showed that endophyte PC27-5 exhibited all characteristics of a fungus identical to Coniochaeta velutina. Furthermore, wide spectrum antimycotics were produced by this endophyte that were active against such plant pathogens as Sclerotinia sclerotiorum, Pythium ultimum, and Verticillium dahliae and lethal to Phythophthora cinnamomi, Pythium ultimum, and Phytophthora palmivora in plate tests. The bioactive components were purified through organic solvent extraction, followed by silica column chromatography, and finally preparative HPLC. The minimum inhibitory concentration of the active fraction to Pythium ultimum, which was gained from preparative HPLC, was 11 μg/ml. UPLC-HRMS analysis showed there were two similar components in the antimycotic fraction. Their molecular formulae were established as C30H22O11 (compound I) and C30H22O10 (compound II) respectively, and preliminary spectral results indicate that they are anthroquinone glycosides. Other non-biologically active compounds were identified in culture fluids of this fungus by spectral means as emodin and chrysophanol--anthroquinone derivatives. This is the first report that Coniochaeta velutina as an endophyte produces bioactive antifungal components.

Pectus Carinatum Evaluation Questionnaire (PCEQ): a novel tool to improve the follow-up in patients treated with brace compression.

PubMed

Pessanha, Inês; Severo, Milton; Correia-Pinto, Jorge; Estevão-Costa, José; Henriques-Coelho, Tiago

2016-03-01

A questionnaire (Pectus Carinatum Evaluation Questionnaire, PCEQ) was developed to be applied in follow-up of patients with Pectus Carinatum (PC). After validation of the PCEQ, we aimed to quantify the compliance to brace compression and to assess factors that could influence this treatment in patients with PC. From July 2008 to July 2014, 56 patients with PC were treated with the Calgary Protocol of compressive bracing at Paediatric Surgery Department of Hospital São João. Forty patients (71%) completed the questionnaire. The PCEQ was divided into four sections: (i) compliance; (ii) symptoms; (iii) social influence; (iv) activities. For the validation process of the PCEQ, principal components analysis (PCA), orthogonal varimax or oblimin rotation and Cronbach's α coefficient were used. To evaluate the association between compliance and other sections of the questionnaire, we estimated the Pearson's correlation between compliance factor scores ('Compliance Days' and 'Compliance Hours') and the final score of each new questionnaire component identified by PCA ('Chest Pain', 'Dyspnoea', 'Back Pain', 'Parents' Influence', 'Friends' Influence', 'Activities', 'Time To Compliance'). For the sections 'Symptoms', 'Social Influence' and 'Activities', we estimated final scores as the sum of the questions that constitute each component. For the section 'Compliance', the factor scores were estimated by the regression method. After PCA analysis, the PCEQ found nine different components with high reliability. When analysing the compliance of our study group, the final score for 'Activities' revealed a significant correlation with the factor score for 'Compliance Hours' (r = 0.382, P = 0.015). The final score for 'Time To Compliance' showed a significant correlation with both factor scores for 'Compliance Hours' (r = -0.765, P < 0.001) and 'Compliance Days' (r = -0.345, P < 0.029). The PCEQ seems to be an important tool to follow up patients with PC treated by brace compression. Practical steps, such as developing a tight schedule in the early follow-up period or applying the PCEQ in first visits after initiating brace therapy, can be taken in order to increase compliance with brace therapy and improve the quality of life. © The Author 2015. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Discriminating the Mineralogical Composition in Drill Cuttings Based on Absorption Spectra in the Terahertz Range.

PubMed

Miao, Xinyang; Li, Hao; Bao, Rima; Feng, Chengjing; Wu, Hang; Zhan, Honglei; Li, Yizhang; Zhao, Kun

2017-02-01

Understanding the geological units of a reservoir is essential to the development and management of the resource. In this paper, drill cuttings from several depths from an oilfield were studied using terahertz time domain spectroscopy (THz-TDS). Cluster analysis (CA) and principal component analysis (PCA) were employed to classify and analyze the cuttings. The cuttings were clearly classified based on CA and PCA methods, and the results were in agreement with the lithology. Moreover, calcite and dolomite have stronger absorption of a THz pulse than any other minerals, based on an analysis of the PC1 scores. Quantitative analyses of minor minerals were also realized by building a series of linear and non-linear models between contents and PC2 scores. The results prove THz technology to be a promising means for determining reservoir lithology as well as other properties, which will be a significant supplementary method in oil fields.

[Design of hand-held heart rate variability acquisition and analysis system].

PubMed

Li, Kaiyuan; Wang, Buqing; Wang, Weidong

2012-07-01

A design of handheld heart rate variability acquisition and analysis system is proposed. The system collects and stores the patient's ECG every five minutes through both hands touching on the electrodes, and then -uploads data to a PC through USB port. The system uses software written in LabVIEW to analyze heart rate variability parameters, The parameters calculated function is programmed and generated to components in Matlab.

Determination of water-soluble elements in PM2.5, PM10, and PM2.5-10 collected in the surroundings of power plants

NASA Astrophysics Data System (ADS)

Zajusz-Zubek, Elwira; Mainka, Anna; Kaczmarek, Konrad

2018-01-01

The analysis reported in this study was performed to characterize the concentrations and water-soluble content of trace elements (As, Cd, Co, Cr, Hg, Mn, Ni, Pb, Sb and Se) in PM2.5, PM10 and PM2.5-10 samples collected in the surroundings of power plants in southern Poland. The solubility of trace elements bound to PM2.5 and PM10 was higher than for PM2.5-10, and in most cases, significant differences were revealed in the relative percentage concentrations of the water-soluble fractions. The occurrence of Cd, Cr, Mn, Ni, Pb and Se in first PCA (Principal Component Analysis) factor (PC1) - indicate coal combustion processes as the potential source of these elements. Other factors indicate two further anthropogenic sources: the resuspension of road dust due to vehicular activities and waste burning in domestic sources - factor (PC2), and, soil dust sources affected by fugitive dust from the mining processes and unpaved roads, as well as transportation and deposition of coal -factor (PC3).

Sex-based differences in lifting technique under increasing load conditions: A principal component analysis.

PubMed

Sheppard, P S; Stevenson, J M; Graham, R B

2016-05-01

The objective of the present study was to determine if there is a sex-based difference in lifting technique across increasing-load conditions. Eleven male and 14 female participants (n = 25) with no previous history of low back disorder participated in the study. Participants completed freestyle, symmetric lifts of a box with handles from the floor to a table positioned at 50% of their height for five trials under three load conditions (10%, 20%, and 30% of their individual maximum isometric back strength). Joint kinematic data for the ankle, knee, hip, and lumbar and thoracic spine were collected using a two-camera Optotrak motion capture system. Joint angles were calculated using a three-dimensional Euler rotation sequence. Principal component analysis (PCA) and single component reconstruction were applied to assess differences in lifting technique across the entire waveforms. Thirty-two PCs were retained from the five joints and three axes in accordance with the 90% trace criterion. Repeated-measures ANOVA with a mixed design revealed no significant effect of sex for any of the PCs. This is contrary to previous research that used discrete points on the lifting curve to analyze sex-based differences, but agrees with more recent research using more complex analysis techniques. There was a significant effect of load on lifting technique for five PCs of the lower limb (PC1 of ankle flexion, knee flexion, and knee adduction, as well as PC2 and PC3 of hip flexion) (p < 0.005). However, there was no significant effect of load on the thoracic and lumbar spine. It was concluded that when load is standardized to individual back strength characteristics, males and females adopted a similar lifting technique. In addition, as load increased male and female participants changed their lifting technique in a similar manner. Copyright © 2016. Published by Elsevier Ltd.

Immunological dysregulation in multiple myeloma microenvironment.

PubMed

Romano, Alessandra; Conticello, Concetta; Cavalli, Maide; Vetro, Calogero; La Fauci, Alessia; Parrinello, Nunziatina Laura; Di Raimondo, Francesco

2014-01-01

Multiple Myeloma (MM) is a systemic hematologic disease due to uncontrolled proliferation of monoclonal plasma cells (PC) in bone marrow (BM). Emerging in other solid and liquid cancers, the host immune system and the microenvironment have a pivotal role for PC growth, proliferation, survival, migration, and resistance to drugs and are responsible for some clinical manifestations of MM. In MM, microenvironment is represented by the cellular component of a normal bone marrow together with extracellular matrix proteins, adhesion molecules, cytokines, and growth factors produced by both stromal cells and PC themselves. All these components are able to protect PC from cytotoxic effect of chemo- and radiotherapy. This review is focused on the role of immunome to sustain MM progression, the emerging role of myeloid derived suppressor cells, and their potential clinical implications as novel therapeutic target.

Digital video timing analyzer for the evaluation of PC-based real-time simulation systems

NASA Astrophysics Data System (ADS)

Jones, Shawn R.; Crosby, Jay L.; Terry, John E., Jr.

2009-05-01

Due to the rapid acceleration in technology and the drop in costs, the use of commercial off-the-shelf (COTS) PC-based hardware and software components for digital and hardware-in-the-loop (HWIL) simulations has increased. However, the increase in PC-based components creates new challenges for HWIL test facilities such as cost-effective hardware and software selection, system configuration and integration, performance testing, and simulation verification/validation. This paper will discuss how the Digital Video Timing Analyzer (DiViTA) installed in the Aviation and Missile Research, Development and Engineering Center (AMRDEC) provides quantitative characterization data for PC-based real-time scene generation systems. An overview of the DiViTA is provided followed by details on measurement techniques, applications, and real-world examples of system benefits.

NASA's Agency-Wide Strategy for Environmental Regulatory Risk Analysis and Communication

NASA Technical Reports Server (NTRS)

Duda, Kristen; Scroggins, Sharon

2008-01-01

NASA's mission is to pioneer the future in space exploration, scientific discovery, and aeronautics research. To help enable existing and future programs to pursue this mission, NASA has established the Principal Center for Regulatory Risk Analysis and Communication (RRAC PC) to proactively identify, analyze, and communicate environmental regulatory risks to the NASA community. The RRAC PC is chartered to evaluate the risks posed to NASA Programs and facilities by environmentally related drivers. The RRAC PC focuses on emerging environmental regulations, as well as risks related to operational changes that can trigger existing environmental requirements. Changing regulations have the potential to directly affect program activities. For example, regulatory changes can restrict certain activities or operations by mandating changes in how operations may be done or limiting where or how certain operations can take place. Regulatory changes also can directly affect the ability to use certain materials by mandating a production phase-out or restricting usage applications of certain materials. Such changes can result in NASA undertaking material replacement efforts. Even if a regulation does not directly affect NASA operations, U.S. and international regulations can pose program risks indirectly through requirements levied on manufacturers and vendors of components and materials. For example, manufacturers can change their formulations to comply with new regulatory requirements. Such changes can require time-consuming and costly requalification certification for use in human spaceflight programs. The RRAC PC has implemented several strategies for proactively managing regulatory change to minimize potential adverse impacts to NASA Programs and facilities. This presentation highlights the lessons learned through establishing the RRAC PC, the process by which the RRAC PC monitors and distributes information about emerging regulatory requirements, and the cross-Agency cooperation that is vital to supporting NASA's mission.

LANL seismic screening method for existing buildings

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

Dickson, S.L.; Feller, K.C.; Fritz de la Orta, G.O.

1997-01-01

The purpose of the Los Alamos National Laboratory (LANL) Seismic Screening Method is to provide a comprehensive, rational, and inexpensive method for evaluating the relative seismic integrity of a large building inventory using substantial life-safety as the minimum goal. The substantial life-safety goal is deemed to be satisfied if the extent of structural damage or nonstructural component damage does not pose a significant risk to human life. The screening is limited to Performance Category (PC) -0, -1, and -2 buildings and structures. Because of their higher performance objectives, PC-3 and PC-4 buildings automatically fail the LANL Seismic Screening Method andmore » will be subject to a more detailed seismic analysis. The Laboratory has also designated that PC-0, PC-1, and PC-2 unreinforced masonry bearing wall and masonry infill shear wall buildings fail the LANL Seismic Screening Method because of their historically poor seismic performance or complex behavior. These building types are also recommended for a more detailed seismic analysis. The results of the LANL Seismic Screening Method are expressed in terms of separate scores for potential configuration or physical hazards (Phase One) and calculated capacity/demand ratios (Phase Two). This two-phase method allows the user to quickly identify buildings that have adequate seismic characteristics and structural capacity and screen them out from further evaluation. The resulting scores also provide a ranking of those buildings found to be inadequate. Thus, buildings not passing the screening can be rationally prioritized for further evaluation. For the purpose of complying with Executive Order 12941, the buildings failing the LANL Seismic Screening Method are deemed to have seismic deficiencies, and cost estimates for mitigation must be prepared. Mitigation techniques and cost-estimate guidelines are not included in the LANL Seismic Screening Method.« less

NASA's Agency-wide Strategy for Environmental Regulatory Risk Analysis and Communication

NASA Technical Reports Server (NTRS)

Duda, Kristen; Scroggins. Sharon

2008-01-01

NASA's mission is to pioneer the future in space exploration, scientific discovery, and aeronautics research. To help enable existing and future programs to pursue this mission, NASA has established the Principal Center for Regulatory Risk Analysis and Communication (RRAC PC) to proactively identify, analyze, and communicate environmental regulatory risks to the NASA community. The RRAC PC is chartered to evaluate the risks posed to NASA Programs and facilities by environmentally related drivers. The RRAC PC focuses on emerging environmental regulations, as well as risks related to operational changes that can trigger existing environmental requirements. Changing regulations have the potential to directly affect program activities. For example, regulatory changes can restrict certain activities or operations by mandating changes in how operations may be done or limiting where or how certain operations can take place. Regulatory changes also can directly affect the ability to use certain materials by mandating a production phase-out or restricting usage aPi'iications of certain materials. Such changes can result in NASA undertaking material replacement efforts. Even if a regulation does not directly affect NASA operations, U.S. and international regulations can pose program risks indirectly through requirements levied on manufacturers and vendors of components and materials. For example, manufacturers can change their formulations to comply with new regulatory requirements. Such changes can require time-consuming and costly requalification certification for use in human spaceflight programs. The RRAC PC has implemented several strategies for proactively managing regulatory change to minimize potential adverse impacts to NASA Programs and facilities. This presentation highlights the lessons learned through establishing the RRAC PC, the process by which the RRAC PC monitors and distributes information about emerging regulatory requirements, and the cross-Agency cooperation that is vital to supporting NASA's mission.

Potential for the use of reconstructed IASI radiances in the detection of atmospheric trace gases

NASA Astrophysics Data System (ADS)

Atkinson, N. C.; Hilton, F. I.; Illingworth, S. M.; Eyre, J. R.; Hultberg, T.

2010-02-01

Principal component (PC) analysis has received considerable attention as a technique for the extraction of meteorological signals from hyperspectral infra-red sounders such as the Infrared Atmospheric Sounding Interferometer (IASI) and the Atmospheric Infrared Sounder (AIRS). In addition to achieving substantial bit-volume reductions for dissemination purposes, the technique can also be used to generate reconstructed radiances in which random instrument noise has been suppressed. To date, most studies have been in the context of Numerical Weather Prediction (NWP). This study examines the potential of PC analysis for chemistry applications. A major concern in the use of PC analysis for chemistry has been that the spectral features associated with trace gases may not be well represented in the reconstructed spectra, either due to deficiencies in the training set or due to the limited number of PC scores used in the radiance reconstruction. In this paper we show examples of reconstructed IASI radiances for several trace gases: ammonia, sulphur dioxide, methane and carbon monoxide. It is shown that care must be taken in the selection of spectra for the initial training set: an iterative technique, in which outlier spectra are added to a base training set, gives the best results. For the four trace gases examined, the chemical signatures are retained in the reconstructed radiances, whilst achieving a substantial reduction in instrument noise. A new regional re-transmission service for IASI is scheduled to start in 2010, as part of the EUMETSAT Advanced Retransmission Service (EARS). For this EARS-IASI service it is intended to include PC scores as part of the data stream. The paper describes the generation of the reference eigenvectors for this new service.

Underlying mechanisms of cyclic peptide inhibitors interrupting the interaction of CK2α/CK2β: comparative molecular dynamics simulation studies.

PubMed

Zhou, Yue; Zhang, Na; Chen, Wenjuan; Zhao, Lijiao; Zhong, Rugang

2016-04-07

Protein-protein interactions (PPIs) are fundamental to all biological processes. Recently, the CK2β-derived cyclic peptide Pc has been demonstrated to efficiently antagonize the CK2α/CK2β interaction and strongly affect the phosphorylation of CK2β-dependent CK2 substrate specificity. The binding affinity of Pc to CK2α is destroyed to different extents by two single-point mutations of Tyr188 to Ala (Y188A) and Phe190 to Ala (F190A), which exert negative effects on the inhibitory activity (IC50) of Pc against the CK2α/CK2β interaction from 3.0 μM to 54.0 μM and ≫100 μM, respectively. However, the structural influences of Y188A and F190A mutations on the CK2α-Pc complex remain unclear. In this study, comparative molecular dynamics (MD) simulations, principal component analysis (PCA), domain cross-correlation map (DCCM) analysis and energy calculations were performed on wild type (WT), Y188A mutant, and F190A mutant systems. The results revealed that ordered communications between hydrophobic and polar interactions were essential for CK2α-Pc binding in the WT system. In addition to the loss of the hydrogen bond between Gln36 of CK2α and Gly189 of Pc in the two mutants, the improper recognition mechanisms occurred through different pathways. These pathways included the weakened hydrophobic interactions in the Y188A mutant as well as decreased polar and hydrophobic interactions in the F190A mutant. The energy analysis results qualitatively elucidated the instability of the two mutants and energetic contributions of the key residues. This study not only revealed the structural mechanisms for the decreased binding affinity of Y188A and F190A mutant CK2α-Pc complexes, but also provided valuable clues for the rational design of CK2α/CK2β subunit interaction inhibitors with high affinity and specificity.

Using the AUDIT-PC to predict alcohol withdrawal in hospitalized patients.

PubMed

Pecoraro, Anna; Ewen, Edward; Horton, Terry; Mooney, Ruth; Kolm, Paul; McGraw, Patty; Woody, George

2014-01-01

Alcohol withdrawal syndrome (AWS) occurs when alcohol-dependent individuals abruptly reduce or stop drinking. Hospitalized alcohol-dependent patients are at risk. Hospitals need a validated screening tool to assess withdrawal risk, but no validated tools are currently available. To examine the admission Alcohol Use Disorders Identification Test-(Piccinelli) Consumption (AUDIT-PC) ability to predict the subsequent development of AWS among hospitalized medical-surgical patients admitted to a non-intensive care setting. Retrospective case–control study of patients discharged from the hospital with a diagnosis of AWS. All patients with AWS were classified as presenting with AWS or developing AWS later during admission. Patients admitted to an intensive care setting and those missing AUDIT-PC scores were excluded from analysis. A hierarchical (by hospital unit) logistic regression was performed and receiver-operating characteristics were examined on those developing AWS after admission and randomly selected controls. Because those diagnosing AWS were not blinded to the AUDIT-PC scores, a sensitivity analysis was performed. The study cohort included all patients age ≥18 years admitted to any medical or surgical units in a single health care system from 6 October 2009 to 7 October 2010. After exclusions, 414 patients were identified with AWS. The 223 (53.9 %) who developed AWS after admission were compared to 466 randomly selected controls without AWS. An AUDIT-PC score ≥4 at admission provides 91.0 % sensitivity and 89.7 % specificity (AUC=0.95; 95 % CI, 0.94–0.97) for AWS, and maximizes the correct classification while resulting in 17 false positives for every true positive identified. Performance remained excellent on sensitivity analysis (AUC=0.92; 95 % CI, 0.90–0.93). Increasing AUDIT-PC scores were associated with an increased risk of AWS (OR=1.68, 95 % CI 1.55–1.82, p<0.001). The admission AUDIT-PC score is an excellent discriminator of AWS and could be an important component of future clinical prediction rules. Calibration and further validation on a large prospectivecohort is indicated.

Principal Component Noise Filtering for NAST-I Radiometric Calibration

NASA Technical Reports Server (NTRS)

Tian, Jialin; Smith, William L., Sr.

2011-01-01

The National Polar-orbiting Operational Environmental Satellite System (NPOESS) Airborne Sounder Testbed- Interferometer (NAST-I) instrument is a high-resolution scanning interferometer that measures emitted thermal radiation between 3.3 and 18 microns. The NAST-I radiometric calibration is achieved using internal blackbody calibration references at ambient and hot temperatures. In this paper, we introduce a refined calibration technique that utilizes a principal component (PC) noise filter to compensate for instrument distortions and artifacts, therefore, further improve the absolute radiometric calibration accuracy. To test the procedure and estimate the PC filter noise performance, we form dependent and independent test samples using odd and even sets of blackbody spectra. To determine the optimal number of eigenvectors, the PC filter algorithm is applied to both dependent and independent blackbody spectra with a varying number of eigenvectors. The optimal number of PCs is selected so that the total root-mean-square (RMS) error is minimized. To estimate the filter noise performance, we examine four different scenarios: apply PC filtering to both dependent and independent datasets, apply PC filtering to dependent calibration data only, apply PC filtering to independent data only, and no PC filters. The independent blackbody radiances are predicted for each case and comparisons are made. The results show significant reduction in noise in the final calibrated radiances with the implementation of the PC filtering algorithm.

Early forest fire detection using principal component analysis of infrared video

NASA Astrophysics Data System (ADS)

Saghri, John A.; Radjabi, Ryan; Jacobs, John T.

2011-09-01

A land-based early forest fire detection scheme which exploits the infrared (IR) temporal signature of fire plume is described. Unlike common land-based and/or satellite-based techniques which rely on measurement and discrimination of fire plume directly from its infrared and/or visible reflectance imagery, this scheme is based on exploitation of fire plume temporal signature, i.e., temperature fluctuations over the observation period. The method is simple and relatively inexpensive to implement. The false alarm rate is expected to be lower that of the existing methods. Land-based infrared (IR) cameras are installed in a step-stare-mode configuration in potential fire-prone areas. The sequence of IR video frames from each camera is digitally processed to determine if there is a fire within camera's field of view (FOV). The process involves applying a principal component transformation (PCT) to each nonoverlapping sequence of video frames from the camera to produce a corresponding sequence of temporally-uncorrelated principal component (PC) images. Since pixels that form a fire plume exhibit statistically similar temporal variation (i.e., have a unique temporal signature), PCT conveniently renders the footprint/trace of the fire plume in low-order PC images. The PC image which best reveals the trace of the fire plume is then selected and spatially filtered via simple threshold and median filter operations to remove the background clutter, such as traces of moving tree branches due to wind.

Using Fourier transform infrared spectroscopy to evaluate biological effects induced by photodynamic therapy.

PubMed

Lima, Cassio A; Goulart, Viviane P; Correa, Luciana; Zezell, Denise M

2016-07-01

Vibrational spectroscopic methods associated with multivariate statistical techniques have been succeeded in discriminating skin lesions from normal tissues. However, there is no study exploring the potential of these techniques to assess the alterations promoted by photodynamic effect in tissue. The present study aims to demonstrate the ability of Fourier Transform Infrared (FTIR) spectroscopy on Attenuated total reflection (ATR) sampling mode associated with principal component-linear discriminant analysis (PC-LDA) to evaluate the biochemical changes caused by photodynamic therapy (PDT) in skin neoplastic tissue. Cutaneous neoplastic lesions, precursors of squamous cell carcinoma (SCC), were chemically induced in Swiss mice and submitted to a single session of 5-aminolevulinic acid (ALA)-mediated PDT. Tissue sections with 5 μm thickness were obtained from formalin-fixed paraffin-embedded (FFPE) and processed prior to the histopathological analysis and spectroscopic measurements. Spectra were collected in mid-infrared region using a FTIR spectrometer on ATR sampling mode. Principal Component-Linear Discriminant Analysis (PC-LDA) was applied on preprocessed second derivatives spectra. Biochemical changes were assessed using PCA-loadings and accuracy of classification was obtained from PC-LDA . Sub-bands of Amide I (1,624 and 1,650 cm(-1) ) and Amide II (1,517 cm(-1) ) indicated a protein overexpression in non-treated and post-PDT neoplastic tissue compared with healthy skin, as well as a decrease in collagen fibers (1,204, 1,236, 1,282, and 1,338 cm(-1) ) and glycogen (1,028, 1,082, and 1,151 cm(-1) ) content. Photosensitized neoplastic tissue revealed shifted peak position and decreased β-sheet secondary structure of proteins (1,624 cm(-1) ) amount in comparison to non-treated neoplastic lesions. PC-LDA score plots discriminated non-treated neoplastic skin spectra from post-PDT cutaneous lesions with accuracy of 92.8%, whereas non-treated neoplastic skin was discriminated from healthy tissue with 93.5% accuracy and post-PDT cutaneous lesions was discriminated from healthy tissue with 89.7% accuracy. PC-LDA was able to discriminate ATR-FTIR spectra of non-treated and post-PDT neoplastic lesions, as well as from healthy skin. Thus, the method can be used for early diagnosis of premalignant skin lesions, as well as to evaluate the response to photodynamic treatment. Lasers Surg. Med. 48:538-545, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Comparison between Two Linear Supervised Learning Machines' Methods with Principle Component Based Methods for the Spectrofluorimetric Determination of Agomelatine and Its Degradants.

PubMed

Elkhoudary, Mahmoud M; Naguib, Ibrahim A; Abdel Salam, Randa A; Hadad, Ghada M

2017-05-01

Four accurate, sensitive and reliable stability indicating chemometric methods were developed for the quantitative determination of Agomelatine (AGM) whether in pure form or in pharmaceutical formulations. Two supervised learning machines' methods; linear artificial neural networks (PC-linANN) preceded by principle component analysis and linear support vector regression (linSVR), were compared with two principle component based methods; principle component regression (PCR) as well as partial least squares (PLS) for the spectrofluorimetric determination of AGM and its degradants. The results showed the benefits behind using linear learning machines' methods and the inherent merits of their algorithms in handling overlapped noisy spectral data especially during the challenging determination of AGM alkaline and acidic degradants (DG1 and DG2). Relative mean squared error of prediction (RMSEP) for the proposed models in the determination of AGM were 1.68, 1.72, 0.68 and 0.22 for PCR, PLS, SVR and PC-linANN; respectively. The results showed the superiority of supervised learning machines' methods over principle component based methods. Besides, the results suggested that linANN is the method of choice for determination of components in low amounts with similar overlapped spectra and narrow linearity range. Comparison between the proposed chemometric models and a reported HPLC method revealed the comparable performance and quantification power of the proposed models.

Chemometric and multivariate statistical analysis of time-of-flight secondary ion mass spectrometry spectra from complex Cu-Fe sulfides.

PubMed

Kalegowda, Yogesh; Harmer, Sarah L

2012-03-20

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) spectra of mineral samples are complex, comprised of large mass ranges and many peaks. Consequently, characterization and classification analysis of these systems is challenging. In this study, different chemometric and statistical data evaluation methods, based on monolayer sensitive TOF-SIMS data, have been tested for the characterization and classification of copper-iron sulfide minerals (chalcopyrite, chalcocite, bornite, and pyrite) at different flotation pulp conditions (feed, conditioned feed, and Eh modified). The complex mass spectral data sets were analyzed using the following chemometric and statistical techniques: principal component analysis (PCA); principal component-discriminant functional analysis (PC-DFA); soft independent modeling of class analogy (SIMCA); and k-Nearest Neighbor (k-NN) classification. PCA was found to be an important first step in multivariate analysis, providing insight into both the relative grouping of samples and the elemental/molecular basis for those groupings. For samples exposed to oxidative conditions (at Eh ~430 mV), each technique (PCA, PC-DFA, SIMCA, and k-NN) was found to produce excellent classification. For samples at reductive conditions (at Eh ~ -200 mV SHE), k-NN and SIMCA produced the most accurate classification. Phase identification of particles that contain the same elements but a different crystal structure in a mixed multimetal mineral system has been achieved.

Characterization of Leaf Extracts of Schinus terebinthifolius Raddi by GC-MS and Chemometric Analysis

PubMed Central

Carneiro, Fabíola B.; Lopes, Pablo Q.; Ramalho, Ricardo C.; Scotti, Marcus T.; Santos, Sócrates G.; Soares, Luiz A. L.

2017-01-01

Background: Schinus terebinthifolius Raddi belongs to Anacardiacea family and is widely known as “aroeira.” This species originates from South America, and its extracts are used in folk medicine due to its therapeutic properties, which include antimicrobial, anti-inflammatory, and antipyretic effects. The complexity and variability of the chemical constitution of the herbal raw material establishes the quality of the respective herbal medicine products. Objective: Thus, the purpose of this study was to investigate the variability of the volatile compounds from leaves of S. terebinthifolius. Materials and Methods: The samples were collected from different states of the Northeast region of Brazil and analyzed with a gas chromatograph coupled to a mass spectrometer (GC-MS). The collected data were analyzed using multivariate data analysis. Results: The samples’ chromatograms, obtained by GC-MS, showed similar chemical profiles in a number of peaks, but some differences were observed in the intensity of these analytical markers. The chromatographic fingerprints obtained by GC-MS were suitable for discrimination of the samples; these results along with a statistical treatment (principal component analysis [PCA]) were used as a tool for comparative analysis between the different samples of S. terebinthifolius. Conclusion: The experimental data show that the PCA used in this study clustered the samples into groups with similar chemical profiles, which builds an appropriate approach to evaluate the similarity in the phytochemical pattern found in the different leaf samples. SUMMARY The leave extracts of Schinus terebinthifolius were obtained by turbo-extractionThe extracts were partitioned with hexane and analyzed by GC-MSThe chromatographic data were analyzed using the principal component analysis (PCA)The PCA plots showed the main compounds (phellandrene, limonene, and carene), which were used to group the samples from a different geographical location in accordance to their chemical similarity. Abbreviations used: AL: Alagoas, BA: Bahia, CE: Ceará, CPETEC: Center for Weather Forecasting and Climate Studies, GC-MS: Gas chromatograph coupled to a mass spectrometer, MA: Maranhão, MVA: Multivariate data analysis, PB: Paraíba, PC1: Direction that describes the maximum variance of the original data, PC2: Maximum direction variance of the data in the subspace orthogonal to PC1, PCA: Principal component analysis, PE: Pernambuco, PI: Piauí, RN: Rio Grande do Norte, SE: Sergipe. PMID:29142431

The X-ray Spectrum of the North Polar Spur

NASA Technical Reports Server (NTRS)

Willingale, Richard; Hands, A. D. P.; Warwick, R. S.; Snowden, S. L.; Burrows, David N.

2003-01-01

An analysis is presented of the soft X-ray background spectrum measured by the EPIC MOS cameras on XMM-Newton in three observations targeted on the North Polar Spur (NPS). Three distinct Galactic plasma components are identified, a cool Local Hot Bubble (LHB) component, T(sub lo) approx. 0.1 keV, a cool Galactic Halo component at a similar temperature and a hotter component, T(sub hi) approx. 0.26 keV, associated with the NPS itself. Using the new data in combination with the Rosat All-Sky Survey count rates measured in the 0.1-0.4 keV band, we estimate the emission measure of the LHB material to be 0.0040-0.0052 cm(exp -6) pc, which implies an electron density of 0.008-0.011 cm(exp -3) and pressure of approx. 22000 cm(exp -3) K. The halo and NPS components lie behind at least 50% of the line-of-sight cold gas for which the total Galactic column density is in the range (2 - 8) x 10(exp 20) cm(exp -2). Modelling the X-ray emitting superbubble as a sphere at distance 210 pc, radius 140 pc and center l(sub II) = 352 deg, b(sub II) = 15 deg, the implied electron density in the NPS is approx. 0.03 cm(exp -3) with pressure approx. 150000 cm(exp -3) K. The observed spectral line complexes from OVII, OVIII, FeXVII, NeIX, NeX and MgXI provide constraints on the composition of the plasma. The hot component in the NPS is depleted in oxygen, neon and, to some extent, magnesium and iron. Assuming the effective line of sight across the halo emission is 1 kpc, the electron density in the halo is 0.007-0.011 cm(exp -3) and the pressure is approx. 16500 cm(exp -3) K, conditions very similar to those in the LHB.

Assessment of Parylene C Thin Films for Heart Valve Tissue Engineering

PubMed Central

Marei, Isra; Chester, Adrian; Carubelli, Ivan; Prodromakis, Themistoklis; Trantidou, Tatiana

2015-01-01

Background: Scaffolds are a key component of tissue-engineered heart valves (TEHVs). Several approaches had been adopted in the design of scaffolds using both natural and synthetic resources. We have investigated the suitability of parylene C (PC), a vapor deposited polymeric material, for the use as a scaffold in TEHV. Aims: To evaluate the adsorption of extracellular matrix components onto plasma-activated PC and study the biocompatibility of PC by measuring cellular adhesion, viability, apoptosis, and phenotypic expression of valve endothelial and interstitial cells. Finally, the mechanical properties of PC were compared with those of native aortic valve cusp tissue. Methods: PC slides were plasma activated and then coated with gelatin, type I collagen, or fibronectin. Porcine pulmonary valve endothelial and interstitial cells were then grown on plasma oxidized PC with different types of coatings and their adhesion was observed after 20 h of incubation. Cell viability was tested using the MTS assay, and apoptosis was estimated using TUNEL staining. The mechanical properties of PC and valve tissue were measured using a Bose Mechanical Tester. Finally, cell-seeded PC films were exposed to pulsatile pressure and aortic shear stress, respectively, to test their durability in a dynamic environment. Results: Our findings show that collagen and fibronectin could bind to plasma oxidized PC. Both valve endothelial and interstitial cells adhered to protein-coated ECM. PC had a profile of mechanical stiffness and ultimate tensile strength that were comparable with or in excess of those seen in porcine aortic valve cusps. Cells were still attached to PC films after 3 days of exposure to up to 50 mmHg pulsatile pressure or aortic levels of shear stress. Conclusion: PC is a promising candidate for use as a scaffold in tissue engineering heart valves. Additional studies are required to determine both the durability and long-term performance of cell-seeded PC when in a similar hemodynamic environment to that of the aortic valve. PMID:26101808

VLBI observations of the nucleus of Centaurus A

NASA Technical Reports Server (NTRS)

Preston, R. A.; Wehrle, A. E.; Morabito, D. D.; Jauncey, D. L.; Batty, M. J.; Haynes, R. F.; Wright, A. E.; Nicolson, G. D.

1983-01-01

VLBI observations of the nucleus of Centaurus A made at 2.3 GHz on baselines with minimum fringe spacings of 0.15 and 0.0027 arcsec are presented. Results show that the nuclear component is elongated with a maximum extent of approximately 0.05 arcsec which is equivalent to a size of approximately 1 pc at the 5 Mpc distance of Centaurus A. The position angle of the nucleus is found to be 30 + or - 20 degrees, while the ratio of nuclear jet length to width is less than or approximately equal to 20. The nuclear flux density is determined to be 6.8 Jy, while no core component is found with an extent less than or approximately equal to 0.001 (less than or approximately equal to 0.02 pc) with a flux density of greater than or approximately equal to 20 mJy. A model of the Centaurus A nucleus composed of at least two components is developed on the basis of these results in conjunction with earlier VLBI and spectral data. The first component is an elongated source of approximately 0.05 arcsec (approximately 1 pc) size which contains most of the 2.3 GHz nuclear flux, while the second component is a source of approximately 0.0005 arcsec (approximately 0.01 pc) size which is nearly completely self-absorbed at 2.3 GHz but strengthens at higher frequencies.

Influence of Multidimensionality on Convergence of Sampling in Protein Simulation

NASA Astrophysics Data System (ADS)

Metsugi, Shoichi

2005-06-01

We study the problem of convergence of sampling in protein simulation originating in the multidimensionality of protein’s conformational space. Since several important physical quantities are given by second moments of dynamical variables, we attempt to obtain the time of simulation necessary for their sufficient convergence. We perform a molecular dynamics simulation of a protein and the subsequent principal component (PC) analysis as a function of simulation time T. As T increases, PC vectors with smaller amplitude of variations are identified and their amplitudes are equilibrated before identifying and equilibrating vectors with larger amplitude of variations. This sequential identification and equilibration mechanism makes protein simulation a useful method although it has an intrinsic multidimensional nature.

Metabolic fingerprint of Brazilian maize landraces silk (stigma/styles) using NMR spectroscopy and chemometric methods.

PubMed

Kuhnen, Shirley; Bernardi Ogliari, Juliana; Dias, Paulo Fernando; da Silva Santos, Maiara; Ferreira, Antônio Gilberto; Bonham, Connie C; Wood, Karl Vernon; Maraschin, Marcelo

2010-02-24

Aqueous extract from maize silks is used by traditional medicine for the treatment of several ailments, mainly related to the urinary system. This work focuses on the application of NMR spectroscopy and chemometric analysis for the determination of metabolic fingerprint and pattern recognition of silk extracts from seven maize landraces cultivated in southern Brazil. Principal component analysis (PCA) of the (1)H NMR data set showed clear discrimination among the maize varieties by PC1 and PC2, pointing out three distinct metabolic profiles. Target compounds analysis showed significant differences (p < 0.05) in the contents of protocatechuic acid, gallic acid, t-cinnamic acid, and anthocyanins, corroborating the discrimination of the genotypes in this study as revealed by PCA analysis. Thus the combination of (1)H NMR and PCA is a useful tool for the discrimination of maize silks in respect to their chemical composition, including rapid authentication of the raw material of current pharmacological interest.

Bile acids-mediated overexpression of MUC4 via FAK-dependent c-Jun activation in pancreatic cancer.

PubMed

Joshi, Suhasini; Cruz, Eric; Rachagani, Satyanarayana; Guha, Sushovan; Brand, Randall E; Ponnusamy, Moorthy P; Kumar, Sushil; Batra, Surinder K

2016-08-01

The majority of pancreatic cancer (PC) patients are clinically presented with obstructive jaundice with elevated levels of circulatory bilirubin and alkaline phosphatases. In the current study, we examined the implications of bile acids (BA), an important component of bile, on the pathophysiology of PC and investigated their mechanistic association in tumor-promoting functions. Integration of results from PC patient samples and autochthonous mouse models showed an elevated levels of BA (p < 0.05) in serum samples compared to healthy controls. Similarly, an elevated BA levels was observed in pancreatic juice derived from PC patients (p < 0.05) than non-pancreatic non-healthy (NPNH) controls, further establishing the clinical association of BA with the pathogenesis of PC. The tumor-promoting functions of BA were established by observed transcriptional upregulation of oncogenic MUC4 expression. Luciferase reporter assay revealed distal MUC4 promoter as the primary responsive site to BA. In silico analysis recognized two c-Jun binding sites at MUC4 distal promoter, which was biochemically established using ChIP assay. Interestingly, BA treatment led to an increased transcription and activation of c-Jun in a FAK-dependent manner. Additionally, BA receptor, namely FXR, which is also upregulated at transcriptional level in PC patient samples, was demonstrated as an upstream molecule in BA-mediated FAK activation, plausibly by regulating Src activation. Altogether, these results demonstrate that elevated levels of BA increase the tumorigenic potential of PC cells by inducing FXR/FAK/c-Jun axis to upregulate MUC4 expression, which is overexpressed in pancreatic tumors and is known to be associated with progression and metastasis of PC. Published by Elsevier B.V.

A PC-based telemetry system for acquiring and reducing data from multiple PCM streams

NASA Astrophysics Data System (ADS)

Simms, D. A.; Butterfield, C. P.

1991-07-01

The Solar Energy Research Institute's (SERI) Wind Research Program is using Pulse Code Modulation (PCM) Telemetry Data-Acquisition Systems to study horizontal-axis wind turbines. Many PCM systems are combined for use in test installations that require accurate measurements from a variety of different locations. SERI has found them ideal for data-acquisition from multiple wind turbines and meteorological towers in wind parks. A major problem has been in providing the capability to quickly combine and examine incoming data from multiple PCM sources in the field. To solve this problem, SERI has developed a low-cost PC-based PCM Telemetry Data-Reduction System (PC-PCM System) to facilitate quick, in-the-field multiple-channel data analysis. The PC-PCM System consists of two basic components. First, PC-compatible hardware boards are used to decode and combine multiple PCM data streams. Up to four hardware boards can be installed in a single PC, which provides the capability to combine data from four PCM streams directly to PC disk or memory. Each stream can have up to 62 data channels. Second, a software package written for use under DOS was developed to simplify data-acquisition control and management. The software, called the Quick-Look Data Management Program, provides a quick, easy-to-use interface between the PC and multiple PCM data streams. The Quick-Look Data Management Program is a comprehensive menu-driven package used to organize, acquire, process, and display information from incoming PCM data streams. The paper describes both hardware and software aspects of the SERI PC-PCM system, concentrating on features that make it useful in an experiment test environment to quickly examine and verify incoming data from multiple PCM streams. Also discussed are problems and techniques associated with PC-based telemetry data-acquisition, processing, and real-time display.

Parvovirus B19 Passive Transmission by Transfusion of Intercept® Blood System-Treated Platelet Concentrate

PubMed Central

Gowland, Peter; Fontana, Stefano; Stolz, Martin; Andina, Nicola; Niederhauser, Christoph

2016-01-01

Summary Background Pathogen reduction methods for blood components are effective for a large number of viruses though less against small, non-enveloped viruses such as Parvovirus B19 (B19V). This article describes the passive transmission by transfusion of two B19V-contaminated pooled platelet concentrates (PCs) which were treated with the Intercept® blood pathogen reduction system. Case Reports Two transfusion cases of B19V-contaminated Intercept-treated pooled PCs were described. Due to the analysis delay, the PCs were already transfused. The viral content of each donation was 4.87 × 1010 IU/ml in case 1and 1.46 × 108 IU/ml in case 2. B19V (52 IU/ml) was detected in the recipient of the case 1 PC, whereas no virus could be detected in the case 2 PC recipient. A B19V IgM response and a transient boost of the underlying B19V IgG immune status and was observed in recipient 1. Recipient of the case 2 PC remained B19V IgG- and IgM-negative. B19V DNA sequence and phylogenetic analysis revealed a 100% homology between donor and recipient. Conclusion This report describes passive B19V transmission by a PC with very high B19 viral load which elicited a transient boost of the B19V immunity, but not by a PC with a lower B19V content, suggesting that there is a B19 viral load threshold value at which B19V inactivation is exceeded. PMID:27403092

Withaferin A Induces Cell Death Selectively in Androgen-Independent Prostate Cancer Cells but Not in Normal Fibroblast Cells

PubMed Central

Nishikawa, Yukihiro; Okuzaki, Daisuke; Fukushima, Kohshiro; Mukai, Satomi; Ohno, Shouichi; Ozaki, Yuki; Yabuta, Norikazu; Nojima, Hiroshi

2015-01-01

Withaferin A (WA), a major bioactive component of the Indian herb Withania somnifera, induces cell death (apoptosis/necrosis) in multiple types of tumor cells, but the molecular mechanism underlying this cytotoxicity remains elusive. We report here that 2 μM WA induced cell death selectively in androgen-insensitive PC-3 and DU-145 prostate adenocarcinoma cells, whereas its toxicity was less severe in androgen-sensitive LNCaP prostate adenocarcinoma cells and normal human fibroblasts (TIG-1 and KD). WA also killed PC-3 cells in spheroid-forming medium. DNA microarray analysis revealed that WA significantly increased mRNA levels of c-Fos and 11 heat-shock proteins (HSPs) in PC-3 and DU-145, but not in LNCaP and TIG-1. Western analysis revealed increased expression of c-Fos and reduced expression of the anti-apoptotic protein c-FLIP(L). Expression of HSPs such as HSPA6 and Hsp70 was conspicuously elevated; however, because siRNA-mediated depletion of HSF-1, an HSP-inducing transcription factor, reduced PC-3 cell viability, it is likely that these heat-shock genes were involved in protecting against cell death. Moreover, WA induced generation of reactive oxygen species (ROS) in PC-3 and DU-145, but not in normal fibroblasts. Immunocytochemistry and immuno-electron microscopy revealed that WA disrupted the vimentin cytoskeleton, possibly inducing the ROS generation, c-Fos expression and c-FLIP(L) suppression. These observations suggest that multiple events followed by disruption of the vimentin cytoskeleton play pivotal roles in WA-mediated cell death. PMID:26230090

Morphological analysis of Trichomycterus areolatus Valenciennes, 1846 from southern Chilean rivers using a truss-based system (Siluriformes, Trichomycteridae)

PubMed Central

Colihueque, Nelson; Corrales, Olga; Yáñez, Miguel

2017-01-01

Abstract Trichomycterus areolatus Valenciennes, 1846 is a small endemic catfish inhabiting the Andean river basins of Chile. In this study, the morphological variability of three T. areolatus populations, collected in two river basins from southern Chile, was assessed with multivariate analyses, including principal component analysis (PCA) and discriminant function analysis (DFA). It is hypothesized that populations must segregate morphologically from each other based on the river basin that they were sampled from, since each basin presents relatively particular hydrological characteristics. Significant morphological differences among the three populations were found with PCA (ANOSIM test, r = 0.552, p < 0.0001) and DFA (Wilks’s λ = 0.036, p < 0.01). PCA accounted for a total variation of 56.16% by the first two principal components. The first Principal Component (PC1) and PC2 explained 34.72 and 21.44% of the total variation, respectively. The scatter-plot of the first two discriminant functions (DF1 on DF2) also validated the existence of three different populations. In group classification using DFA, 93.3% of the specimens were correctly-classified into their original populations. Of the total of 22 transformed truss measurements, 17 exhibited highly significant (p < 0.01) differences among populations. The data support the existence of T. areolatus morphological variation across different rivers in southern Chile, likely reflecting the geographic isolation underlying population structure of the species. PMID:29134012

Source Determination of Red Gel Pen Inks using Raman Spectroscopy and Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy combined with Pearson's Product Moment Correlation Coefficients and Principal Component Analysis.

PubMed

Mohamad Asri, Muhammad Naeim; Mat Desa, Wan Nur Syuhaila; Ismail, Dzulkiflee

2018-01-01

The potential combination of two nondestructive techniques, that is, Raman spectroscopy (RS) and attenuated total reflectance-fourier transform infrared (ATR-FTIR) spectroscopy with Pearson's product moment correlation (PPMC) coefficient (r) and principal component analysis (PCA) to determine the actual source of red gel pen ink used to write a simulated threatening note, was examined. Eighteen (18) red gel pens purchased from Japan and Malaysia from November to December 2014 where one of the pens was used to write a simulated threatening note were analyzed using RS and ATR-FTIR spectroscopy, respectively. The spectra of all the red gel pen inks including the ink deposited on the simulated threatening note gathered from the RS and ATR-FTIR analyses were subjected to PPMC coefficient (r) calculation and principal component analysis (PCA). The coefficients r = 0.9985 and r = 0.9912 for pairwise combination of RS and ATR-FTIR spectra respectively and similarities in terms of PC1 and PC2 scores of one of the inks to the ink deposited on the simulated threatening note substantiated the feasibility of combining RS and ATR-FTIR spectroscopy with PPMC coefficient (r) and PCA for successful source determination of red gel pen inks. The development of pigment spectral library had allowed the ink deposited on the threatening note to be identified as XSL Poppy Red (CI Pigment Red 112). © 2017 American Academy of Forensic Sciences.

42 CFR 414.50 - Physician or other supplier billing for diagnostic tests performed or interpreted by a physician...

Code of Federal Regulations, 2011 CFR

2011-10-01

...) or professional component (PC) of a diagnostic test that was ordered by the physician or other... behalf of the beneficiary) for the TC or PC of the diagnostic test may not exceed the lowest of the... who supervised the TC, and with respect to the PC, the performing supplier is the physician who...

Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster.

PubMed

Tolhuis, Bas; de Wit, Elzo; Muijrers, Inhua; Teunissen, Hans; Talhout, Wendy; van Steensel, Bas; van Lohuizen, Maarten

2006-06-01

Polycomb group (PcG) proteins maintain transcriptional repression of developmentally important genes and have been implicated in cell proliferation and stem cell self-renewal. We used a genome-wide approach to map binding patterns of PcG proteins (Pc, esc and Sce) in Drosophila melanogaster Kc cells. We found that Pc associates with large genomic regions of up to approximately 150 kb in size, hereafter referred to as 'Pc domains'. Sce and esc accompany Pc in most of these domains. PcG-bound chromatin is trimethylated at histone H3 Lys27 and is generally transcriptionally silent. Furthermore, PcG proteins preferentially bind to developmental genes. Many of these encode transcriptional regulators and key components of signal transduction pathways, including Wingless, Hedgehog, Notch and Delta. We also identify several new putative functions of PcG proteins, such as in steroid hormone biosynthesis. These results highlight the extensive involvement of PcG proteins in the coordination of development through the formation of large repressive chromatin domains.

A Homolog Pentameric Complex Dictates Viral Epithelial Tropism, Pathogenicity and Congenital Infection Rate in Guinea Pig Cytomegalovirus.

PubMed

Coleman, Stewart; Choi, K Yeon; Root, Matthew; McGregor, Alistair

2016-07-01

In human cytomegalovirus (HCMV), tropism to epithelial and endothelial cells is dependent upon a pentameric complex (PC). Given the structure of the placenta, the PC is potentially an important neutralizing antibody target antigen against congenital infection. The guinea pig is the only small animal model for congenital CMV. Guinea pig cytomegalovirus (GPCMV) potentially encodes a UL128-131 HCMV PC homolog locus (GP128-GP133). In transient expression studies, GPCMV gH and gL glycoproteins interacted with UL128, UL130 and UL131 homolog proteins (designated GP129 and GP131 and GP133 respectively) to form PC or subcomplexes which were determined by immunoprecipitation reactions directed to gH or gL. A natural GP129 C-terminal deletion mutant (aa 107-179) and a chimeric HCMV UL128 C-terminal domain swap GP129 mutant failed to form PC with other components. GPCMV infection of a newly established guinea pig epithelial cell line required a complete PC and a GP129 mutant virus lacked epithelial tropism and was attenuated in the guinea pig for pathogenicity and had a low congenital transmission rate. Individual knockout of GP131 or 133 genes resulted in loss of viral epithelial tropism. A GP128 mutant virus retained epithelial tropism and GP128 was determined not to be a PC component. A series of GPCMV mutants demonstrated that gO was not strictly essential for epithelial infection whereas gB and the PC were essential. Ectopic expression of a GP129 cDNA in a GP129 mutant virus restored epithelial tropism, pathogenicity and congenital infection. Overall, GPCMV forms a PC similar to HCMV which enables evaluation of PC based vaccine strategies in the guinea pig model.

A Homolog Pentameric Complex Dictates Viral Epithelial Tropism, Pathogenicity and Congenital Infection Rate in Guinea Pig Cytomegalovirus

PubMed Central

McGregor, Alistair

2016-01-01

In human cytomegalovirus (HCMV), tropism to epithelial and endothelial cells is dependent upon a pentameric complex (PC). Given the structure of the placenta, the PC is potentially an important neutralizing antibody target antigen against congenital infection. The guinea pig is the only small animal model for congenital CMV. Guinea pig cytomegalovirus (GPCMV) potentially encodes a UL128-131 HCMV PC homolog locus (GP128-GP133). In transient expression studies, GPCMV gH and gL glycoproteins interacted with UL128, UL130 and UL131 homolog proteins (designated GP129 and GP131 and GP133 respectively) to form PC or subcomplexes which were determined by immunoprecipitation reactions directed to gH or gL. A natural GP129 C-terminal deletion mutant (aa 107–179) and a chimeric HCMV UL128 C-terminal domain swap GP129 mutant failed to form PC with other components. GPCMV infection of a newly established guinea pig epithelial cell line required a complete PC and a GP129 mutant virus lacked epithelial tropism and was attenuated in the guinea pig for pathogenicity and had a low congenital transmission rate. Individual knockout of GP131 or 133 genes resulted in loss of viral epithelial tropism. A GP128 mutant virus retained epithelial tropism and GP128 was determined not to be a PC component. A series of GPCMV mutants demonstrated that gO was not strictly essential for epithelial infection whereas gB and the PC were essential. Ectopic expression of a GP129 cDNA in a GP129 mutant virus restored epithelial tropism, pathogenicity and congenital infection. Overall, GPCMV forms a PC similar to HCMV which enables evaluation of PC based vaccine strategies in the guinea pig model. PMID:27387220

Penetration studies of an extremely lipophilic active model substance from an oil-in-water emulsion: influence of the lipophilicity of the formulation in human skin - part 2.

PubMed

Naumann, S; Lange, S; Polak, G; Kalhoelfer, V; Motlagh, L; Goebel, A; Wohlrab, J; Neubert, R H H

2014-01-01

The effect of the lipophilicity of a carrier on human skin penetration of an extremely lipophilic active model substance was evaluated by using Franz type diffusion cells. Oil-in-water model emulsions containing different amounts of the oily phase were prepared, and Myritol® PC (M-PC) was selected as lipophilic marker component of the oily phase. The penetrated amounts of the lipophilic model substance salicyloyl phytosphingosine (SP) were determined by high-performance liquid chromatography with ultraviolet detection, while M-PC was detected using gas chromatography coupled with mass spectrometry. It has been ascertained that the amount of the lipid phase within the emulsion influenced the penetration profile of the active ingredient SP. The emulsion containing the lowest proportion of the lipid phase provides the best conditions for SP penetration. Surprisingly, the penetration behavior of M-PC was influenced by the oily phase in the same way. Regarding the M-PC and the SP penetration profiles from each emulsion, a solvent drag mechanism can be assumed whereby M-PC acts as penetration enhancer. In conclusion, the penetration rate of the active ingredient SP and the marker component M-PC are in reverse proportion to the oil content of the formulations. The lipophilicity of SP and M-PC, their solubility and their thermodynamic activity within the vehicle could have an effect on their penetration behavior. Additionally, M-PC has the property to enhance the penetration rates of extremely lipophilic substances even at low concentrations.

The X-ray Emitting Components towards l = 111 deg: The Local Hot Bubble and Beyond

NASA Technical Reports Server (NTRS)

Kuntz, K. D.; Snowden, S. L.

2006-01-01

We have obtained an XMM-Newton spectrum of the diffuse X-ray emission towards (l, b) = (111.14,1.11), a line of sight with a relatively simple distribution of absorbing clouds; > 9 x 10(exp 19)/sq cm at R>170 pc, a 6 x 10(exp 21)/sq cm molecular cloud at 2.5-3.3 kpc, and a total column of 1.2 x 10(exp 22)/sq cm. We find that the analysis of the XMM-Newton spectrum in conjunction with the RASS spectral energy distribution for the same direction requires three thermal components to be well fit: a "standard" Local Hot Bubble component with kT = 0.089, a component beyond the molecular cloud with kT = 0.59, and a component before the molecular cloud with kT = 0.21. The strength of the O VII 0.56 keV line from the Local Hot Bubble, 2.1+/-0.7 photons/sq cm/s/sr, is consistent with other recent measures. The 0.21 keV component has an emission measure of 0.0022+/-0.0006 pc and is not localized save as diffuse emission within the Galactic plane; it is the best candidate for a pervasive hot medium. The spatial separation of the approx. 0.2 keV component from the approx. 0.6 keV component suggests that the spectral decompositions of the emission from late-type spiral disks found in the literature do represent real temperature components rather than reflecting more complex temperature distributions.

Cardiorespiratory Coordination in Repeated Maximal Exercise

PubMed Central

Garcia-Retortillo, Sergi; Javierre, Casimiro; Hristovski, Robert; Ventura, Josep L.; Balagué, Natàlia

2017-01-01

Increases in cardiorespiratory coordination (CRC) after training with no differences in performance and physiological variables have recently been reported using a principal component analysis approach. However, no research has yet evaluated the short-term effects of exercise on CRC. The aim of this study was to delineate the behavior of CRC under different physiological initial conditions produced by repeated maximal exercises. Fifteen participants performed 2 consecutive graded and maximal cycling tests. Test 1 was performed without any previous exercise, and Test 2 6 min after Test 1. Both tests started at 0 W and the workload was increased by 25 W/min in males and 20 W/min in females, until they were not able to maintain the prescribed cycling frequency of 70 rpm for more than 5 consecutive seconds. A principal component (PC) analysis of selected cardiovascular and cardiorespiratory variables (expired fraction of O2, expired fraction of CO2, ventilation, systolic blood pressure, diastolic blood pressure, and heart rate) was performed to evaluate the CRC defined by the number of PCs in both tests. In order to quantify the degree of coordination, the information entropy was calculated and the eigenvalues of the first PC (PC1) were compared between tests. Although no significant differences were found between the tests with respect to the performed maximal workload (Wmax), maximal oxygen consumption (VO2 max), or ventilatory threshold (VT), an increase in the number of PCs and/or a decrease of eigenvalues of PC1 (t = 2.95; p = 0.01; d = 1.08) was found in Test 2 compared to Test 1. Moreover, entropy was significantly higher (Z = 2.33; p = 0.02; d = 1.43) in the last test. In conclusion, despite the fact that no significant differences were observed in the conventionally explored maximal performance and physiological variables (Wmax, VO2 max, and VT) between tests, a reduction of CRC was observed in Test 2. These results emphasize the interest of CRC evaluation in the assessment and interpretation of cardiorespiratory exercise testing. PMID:28638349

A Multi-Variable Approach to Diagnosing the Monthly Covariability of the Amazonian Radiative and Convective Diurnal Cycles

NASA Astrophysics Data System (ADS)

Dodson, J. B.; Taylor, P. C.

2016-12-01

The diurnal cycle of convection (CDC) greatly influences the water, radiative, and energy budgets in convectively active regions. For example, previous research of the Amazonian CDC has identified significant monthly covariability between the satellite-observed radiative and precipitation diurnal and multiple reanalysis-derived atmospheric state variables (ASVs) representing convective instability. However, disagreements between retrospective analysis products (reanalyses) over monthly ASV anomalies create significant uncertainty in the resulting covariability. Satellite observations of convective clouds can be used to characterize monthly anomalies in convective activity. CloudSat observes multiple properties of both deep convective cores and the associated anvils, and so is useful as an alternative to the use of reanalyses. CloudSat cannot observe the full diurnal cycle, but it can detect differences between daytime and nighttime convection. Initial efforts to use CloudSat data to characterize convective activity showed that the results are highly dependent on the choice of variable used to characterize the cloud. This is caused by a series of inverse relationships between convective frequency, cloud top height, radar reflectivity vertical profile, and other variables. A single, multi-variable index for convective activity based on CloudSat data may be useful to clarify the results. Principal component analysis (PCA) provides a method to create a multivariable index, where the first principal component (PC1) corresponds with convective instability. The time series of PC1 can then be used as a proxy for monthly variability in convective activity. The primary challenge presented involves determining the utility of PCA for creating a robust index for convective activity that accounts for the complex relationships of multiple convective cloud variables, and yields information about the interactions between convection, the convective environment, and radiation beyond the previous single-variable approaches. The choice of variables used to calculate PC1 may influence any results based on PC1, so it is necessary to test the sensitivity of the results to different variable combinations.

Surface-enhanced Raman spectroscopy introduced into the International Standard Organization (ISO) regulations as an alternative method for detection and identification of pathogens in the food industry.

PubMed

Witkowska, Evelin; Korsak, Dorota; Kowalska, Aneta; Księżopolska-Gocalska, Monika; Niedziółka-Jönsson, Joanna; Roźniecka, Ewa; Michałowicz, Weronika; Albrycht, Paweł; Podrażka, Marta; Hołyst, Robert; Waluk, Jacek; Kamińska, Agnieszka

2017-02-01

We show that surface-enhanced Raman spectroscopy (SERS) coupled with principal component analysis (PCA) can serve as a fast, reliable, and easy method for detection and identification of food-borne bacteria, namely Salmonella spp., Listeria monocytogenes, and Cronobacter spp., in different types of food matrices (salmon, eggs, powdered infant formula milk, mixed herbs, respectively). The main aim of this work was to introduce the SERS technique into three ISO (6579:2002; 11290-1:1996/A1:2004; 22964:2006) standard procedures required for detection of these bacteria in food. Our study demonstrates that the SERS technique is effective in distinguishing very closely related bacteria within a genus grown on solid and liquid media. The advantages of the proposed ISO-SERS method for bacteria identification include simplicity and reduced time of analysis, from almost 144 h required by standard methods to 48 h for the SERS-based approach. Additionally, PCA allows one to perform statistical classification of studied bacteria and to identify the spectrum of an unknown sample. Calculated first and second principal components (PC-1, PC-2) account for 96, 98, and 90% of total variance in the spectra and enable one to identify the Salmonella spp., L. monocytogenes, and Cronobacter spp., respectively. Moreover, the presented study demonstrates the excellent possibility for simultaneous detection of analyzed food-borne bacteria in one sample test (98% of PC-1 and PC-2) with a goal of splitting the data set into three separated clusters corresponding to the three studied bacteria species. The studies described in this paper suggest that SERS represents an alternative to standard microorganism diagnostic procedures. Graphical Abstract New approach of the SERS strategy for detection and identification of food-borne bacteria, namely S. enterica, L. monocytogenes, and C. sakazakii in selected food matrices.

The metabolic signature associated with the Western dietary pattern: a cross-sectional study.

PubMed

Bouchard-Mercier, Annie; Rudkowska, Iwona; Lemieux, Simone; Couture, Patrick; Vohl, Marie-Claude

2013-12-11

Metabolic profiles have been shown to be associated to obesity status and insulin sensitivity. Dietary intakes influence metabolic pathways and therefore, different dietary patterns may relate to modifications in metabolic signatures. The objective was to verify associations between dietary patterns and metabolic profiles composed of amino acids (AAs) and acylcarnitines (ACs). 210 participants were recruited in the greater Quebec City area between September 2009 and December 2011. Dietary patterns had been previously derived using principal component analysis (PCA). The Prudent dietary pattern was characterised by higher intakes of vegetables, fruits, whole grain products, non-hydrogenated fat and lower intakes of refined grain products, whereas the Western dietary pattern was associated with higher intakes of refined grain products, desserts, sweets and processed meats. Targeted metabolites were quantified in 37 participants with the Biocrates Absolute IDQ p150 (Biocrates Life Sciences AG, Austria) mass spectrometry method (including 14 amino acids and 41 acylcarnitines). PCA analysis with metabolites including AAs and ACs revealed two main components explaining the most variance in overall data (13.8%). PC1 was composed mostly of medium- to long-chain ACs (C16:2, C14:2, C14:2-OH, C16, C14:1-OH, C14:1, C10:2, C5-DC/C6-OH, C12, C18:2, C10, C4:1-DC/C6, C8:1 and C2) whereas PC2 included certain AAs and short-chain ACs (xLeu, Met, Arg, Phe, Pro, Orn, His, C0, C3, C4 and C5). The Western dietary pattern correlated negatively with PC1 and positively with PC2 (r = -0.34, p = 0.05 and r = 0.38, p = 0.03, respectively), independently of age, sex and BMI. These findings suggest that the Western dietary pattern is associated with a specific metabolite signature characterized by increased levels of AAs including branched-chain AAs (BCAAs) and short-chain ACs.

Drought tolerance of selected bottle gourd [Lagenaria siceraria (Molina) Standl.] landraces assessed by leaf gas exchange and photosynthetic efficiency.

PubMed

Mashilo, Jacob; Odindo, Alfred O; Shimelis, Hussein A; Musenge, Pearl; Tesfay, Samson Z; Magwaza, Lembe S

2017-11-01

Successful cultivation of bottle gourd in arid and semi-arid areas of sub-Saharan Africa and globally requires the identification of drought tolerant parents for developing superior genotypes with increased drought resistance. The objective of this study was to determine the level of drought tolerance among genetically diverse South African bottle gourd landraces based on leaf gas exchange and photosynthetic efficiency and identify promising genotypes for breeding. The responses of 12 bottle gourd landraces grown in glasshouse under non-stressed (NS) and drought-stressed (DS) conditions were studied. A significant genotype x water regime interaction was observed for gs, T, A, A/C i , IWUE, WUE ins , F m ', F v '/F m ', Ф PSII , qP, qN, ETR, ETR/A and AES indicating variability in response among the studied bottle gourd landraces under NS and DS conditions. Principal component analysis identified three principal components (PC's) under drought stress condition contributing to 82.9% of total variation among leaf gas exchange and chlorophyll fluorescence parameters measured. PC1 explained 36% of total variation contributed by gs, T, F 0 ', F m ', F v '/F m ' and qN, while PC2 explained 28% of the variation and highly correlated with A, A/C i , IWUE, WUE ins ETR/A and AES. PC3 explained 14% of total variation contributed by Ф PSII , qP and ETR. Principal biplot analysis allowed the identification of drought tolerant genotypes such as BG-27, BG-48, BG-58, BG-79, BG-70 and BG-78 which were grouped based on high gs, A, F m 'F v '/F m ', qN, ETR/A and AES under DS condition. The study suggests that the identified physiological traits could be useful indicators in the selection of bottle gourd genotypes for increased drought tolerance. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Analysis and Application of European Genetic Substructure Using 300 K SNP Information

PubMed Central

Tian, Chao; Plenge, Robert M; Ransom, Michael; Lee, Annette; Villoslada, Pablo; Selmi, Carlo; Klareskog, Lars; Pulver, Ann E; Qi, Lihong; Gregersen, Peter K; Seldin, Michael F

2008-01-01

European population genetic substructure was examined in a diverse set of >1,000 individuals of European descent, each genotyped with >300 K SNPs. Both STRUCTURE and principal component analyses (PCA) showed the largest division/principal component (PC) differentiated northern from southern European ancestry. A second PC further separated Italian, Spanish, and Greek individuals from those of Ashkenazi Jewish ancestry as well as distinguishing among northern European populations. In separate analyses of northern European participants other substructure relationships were discerned showing a west to east gradient. Application of this substructure information was critical in examining a real dataset in whole genome association (WGA) analyses for rheumatoid arthritis in European Americans to reduce false positive signals. In addition, two sets of European substructure ancestry informative markers (ESAIMs) were identified that provide substantial substructure information. The results provide further insight into European population genetic substructure and show that this information can be used for improving error rates in association testing of candidate genes and in replication studies of WGA scans. PMID:18208329

Arabidopsis florigen FT binds to diurnally oscillating phospholipids that accelerate flowering.

PubMed

Nakamura, Yuki; Andrés, Fernando; Kanehara, Kazue; Liu, Yu-chi; Dörmann, Peter; Coupland, George

2014-04-04

Arabidopsis FT protein is a component of florigen, which transmits photoperiodic flowering signals from leaf companion cells to the shoot apex. Here, we show that FT specifically binds phosphatidylcholine (PC) in vitro. A transgenic approach to increase PC levels in vivo in the shoot meristem accelerates flowering whereas reduced PC levels delay flowering, demonstrating that PC levels are correlated with flowering time. The early flowering is related to FT activity, because expression of FT-effector genes is increased in these plants. Simultaneous increase of FT and PC in the shoot apical meristem further stimulates flowering, whereas a loss of FT function leads to an attenuation of the effect of increased PC. Specific molecular species of PC oscillate diurnally, and night-dominant species are not the preferred ligands of FT. Elevating night-dominant species during the day delays flowering. We suggest that FT binds to diurnally changing molecular species of PC to promote flowering.

Quality Evaluation of Potentilla fruticosa L. by High Performance Liquid Chromatography Fingerprinting Associated with Chemometric Methods.

PubMed

Liu, Wei; Wang, Dongmei; Liu, Jianjun; Li, Dengwu; Yin, Dongxue

2016-01-01

The present study was performed to assess the quality of Potentilla fruticosa L. sampled from distinct regions of China using high performance liquid chromatography (HPLC) fingerprinting coupled with a suite of chemometric methods. For this quantitative analysis, the main active phytochemical compositions and the antioxidant activity in P. fruticosa were also investigated. Considering the high percentages and antioxidant activities of phytochemicals, P. fruticosa samples from Kangding, Sichuan were selected as the most valuable raw materials. Similarity analysis (SA) of HPLC fingerprints, hierarchical cluster analysis (HCA), principle component analysis (PCA), and discriminant analysis (DA) were further employed to provide accurate classification and quality estimates of P. fruticosa. Two principal components (PCs) were collected by PCA. PC1 separated samples from Kangding, Sichuan, capturing 57.64% of the variance, whereas PC2 contributed to further separation, capturing 18.97% of the variance. Two kinds of discriminant functions with a 100% discrimination ratio were constructed. The results strongly supported the conclusion that the eight samples from different regions were clustered into three major groups, corresponding with their morphological classification, for which HPLC analysis confirmed the considerable variation in phytochemical compositions and that P. fruticosa samples from Kangding, Sichuan were of high quality. The results of SA, HCA, PCA, and DA were in agreement and performed well for the quality assessment of P. fruticosa. Consequently, HPLC fingerprinting coupled with chemometric techniques provides a highly flexible and reliable method for the quality evaluation of traditional Chinese medicines.

Quality Evaluation of Potentilla fruticosa L. by High Performance Liquid Chromatography Fingerprinting Associated with Chemometric Methods

PubMed Central

Liu, Wei; Wang, Dongmei; Liu, Jianjun; Li, Dengwu; Yin, Dongxue

2016-01-01

The present study was performed to assess the quality of Potentilla fruticosa L. sampled from distinct regions of China using high performance liquid chromatography (HPLC) fingerprinting coupled with a suite of chemometric methods. For this quantitative analysis, the main active phytochemical compositions and the antioxidant activity in P. fruticosa were also investigated. Considering the high percentages and antioxidant activities of phytochemicals, P. fruticosa samples from Kangding, Sichuan were selected as the most valuable raw materials. Similarity analysis (SA) of HPLC fingerprints, hierarchical cluster analysis (HCA), principle component analysis (PCA), and discriminant analysis (DA) were further employed to provide accurate classification and quality estimates of P. fruticosa. Two principal components (PCs) were collected by PCA. PC1 separated samples from Kangding, Sichuan, capturing 57.64% of the variance, whereas PC2 contributed to further separation, capturing 18.97% of the variance. Two kinds of discriminant functions with a 100% discrimination ratio were constructed. The results strongly supported the conclusion that the eight samples from different regions were clustered into three major groups, corresponding with their morphological classification, for which HPLC analysis confirmed the considerable variation in phytochemical compositions and that P. fruticosa samples from Kangding, Sichuan were of high quality. The results of SA, HCA, PCA, and DA were in agreement and performed well for the quality assessment of P. fruticosa. Consequently, HPLC fingerprinting coupled with chemometric techniques provides a highly flexible and reliable method for the quality evaluation of traditional Chinese medicines. PMID:26890416

[Soil microbial community structure in Picea asperata plantations with different ages in subalpine of western Sichuan, Southwest China.

PubMed

Luo, Da; Liu, Shun; Shi, Zuo Min; Feng, Qiu Hong; Liu, Qian Li; Zhang, Li; Huang, Quan; He, Jian She

2017-02-01

The effects of four Picea asperata plantations with different ages (50-, 38-, 27- and 20-year-old), in subalpine of western Sichuan, on the characteristics of soil microbial diversity and microbial community structure were studied by the method of phospholipid fatty acid (PLFA) profiles. The results showed that, with the increase of age, the contents of soil organic carbon and total nitrogen gradually improved, while Shannon's diversity index and Pielou's evenness index of soil microorganisms increased at first and then decreased. The amounts of microbial total PLFAs, bacterial PLFAs, fungal PLFAs, actinobacterial PLFAs, and arbuscular mycorrhizal fungal (AMF) PLFAs in soils consistently increased with increasing age. The principal component analysis (PCA) indicated that the soil microbial communities in different plantations were structurally distinct from each other. The first principal component (PC1) and the second principal component (PC2) together accounted for 66.8% of total variation of the soil microbial community structure. The redundancy analysis (RDA) of soil microbial community structure and environmental factors showed that soil organic carbon, total nitrogen, total potassium, and fine root mass were the key determinants influencing the microbial community structure. Our study suggested that, with the extension of artificialafforestation time, the soil fertility and microbial biomass were enhanced, and the restoration processes of forest ecosystem were stable.

PC-based Multiple Information System Interface (PC/MISI) detailed design and implementation plan

NASA Technical Reports Server (NTRS)

Dominick, Wayne D. (Editor); Hall, Philip P.

1985-01-01

The design plan for the personal computer multiple information system interface (PC/MISI) project is discussed. The document is intended to be used as a blueprint for the implementation of the system. Each component is described in the detail necessary to allow programmers to implement the system. A description of the system data flow and system file structures is given.

Correlating the amount of urea, creatinine, and glucose in urine from patients with diabetes mellitus and hypertension with the risk of developing renal lesions by means of Raman spectroscopy and principal component analysis

NASA Astrophysics Data System (ADS)

Bispo, Jeyse Aliana Martins; de Sousa Vieira, Elzo Everton; Silveira, Landulfo; Fernandes, Adriana Barrinha

2013-08-01

Patients with diabetes mellitus and hypertension (HT) diseases are predisposed to kidney diseases. The objective of this study was to identify potential biomarkers in the urine of diabetic and hypertensive patients through Raman spectroscopy in order to predict the evolution to complications and kidney failure. Urine samples were collected from control subjects (CTR) and patients with diabetes and HT with no complications (lower risk, LR), high degree of complications (higher risk, HR), and doing blood dialysis (DI). Urine samples were stored frozen (-20°C) before spectral analysis. Raman spectra were obtained using a dispersive spectrometer (830-nm, 300-mW power, and 20-s accumulation). Spectra were then submitted to principal component analysis (PCA) followed by discriminant analysis. The first PCA loading vectors revealed spectral features of urea, creatinine, and glucose. It has been found that the amounts of urea and creatinine decreased as disease evoluted from CTR to LR/HR and DI (PC1, p<0.05), and the amount of glucose increased in the urine of LR/HR compared to CTR (PC3, p<0.05). The discriminating model showed better overall classification rate of 70%. These results could lead to diagnostic information of possible complications and a better disease prognosis.

Correlating the amount of urea, creatinine, and glucose in urine from patients with diabetes mellitus and hypertension with the risk of developing renal lesions by means of Raman spectroscopy and principal component analysis.

PubMed

Bispo, Jeyse Aliana Martins; de Sousa Vieira, Elzo Everton; Silveira, Landulfo; Fernandes, Adriana Barrinha

2013-08-01

Patients with diabetes mellitus and hypertension (HT) diseases are predisposed to kidney diseases. The objective of this study was to identify potential biomarkers in the urine of diabetic and hypertensive patients through Raman spectroscopy in order to predict the evolution to complications and kidney failure. Urine samples were collected from control subjects (CTR) and patients with diabetes and HT with no complications (lower risk, LR), high degree of complications (higher risk, HR), and doing blood dialysis (DI). Urine samples were stored frozen (-20°C) before spectral analysis. Raman spectra were obtained using a dispersive spectrometer (830-nm, 300-mW power, and 20-s accumulation). Spectra were then submitted to principal component analysis (PCA) followed by discriminant analysis. The first PCA loading vectors revealed spectral features of urea, creatinine, and glucose. It has been found that the amounts of urea and creatinine decreased as disease evoluted from CTR to LR/HR and DI (PC1, p<0.05), and the amount of glucose increased in the urine of LR/HR compared to CTR (PC3, p<0.05). The discriminating model showed better overall classification rate of 70%. These results could lead to diagnostic information of possible complications and a better disease prognosis.

Principal Component-Based Radiative Transfer Model (PCRTM) for Hyperspectral Sensors. Part I; Theoretical Concept

NASA Technical Reports Server (NTRS)

Liu, Xu; Smith, William L.; Zhou, Daniel K.; Larar, Allen

2005-01-01

Modern infrared satellite sensors such as Atmospheric Infrared Sounder (AIRS), Cosmic Ray Isotope Spectrometer (CrIS), Thermal Emission Spectrometer (TES), Geosynchronous Imaging Fourier Transform Spectrometer (GIFTS) and Infrared Atmospheric Sounding Interferometer (IASI) are capable of providing high spatial and spectral resolution infrared spectra. To fully exploit the vast amount of spectral information from these instruments, super fast radiative transfer models are needed. This paper presents a novel radiative transfer model based on principal component analysis. Instead of predicting channel radiance or transmittance spectra directly, the Principal Component-based Radiative Transfer Model (PCRTM) predicts the Principal Component (PC) scores of these quantities. This prediction ability leads to significant savings in computational time. The parameterization of the PCRTM model is derived from properties of PC scores and instrument line shape functions. The PCRTM is very accurate and flexible. Due to its high speed and compressed spectral information format, it has great potential for super fast one-dimensional physical retrievals and for Numerical Weather Prediction (NWP) large volume radiance data assimilation applications. The model has been successfully developed for the National Polar-orbiting Operational Environmental Satellite System Airborne Sounder Testbed - Interferometer (NAST-I) and AIRS instruments. The PCRTM model performs monochromatic radiative transfer calculations and is able to include multiple scattering calculations to account for clouds and aerosols.

Colour-specific differences in attentional deployment for equiluminant pop-out colours: evidence from lateralised potentials.

PubMed

Pomerleau, Vincent Jetté; Fortier-Gauthier, Ulysse; Corriveau, Isabelle; Dell'Acqua, Roberto; Jolicœur, Pierre

2014-03-01

We investigated how target colour affected behavioural and electrophysiological results in a visual search task. Perceptual and attentional mechanisms were tracked using the N2pc component of the event-related potential and other lateralised components. Four colours (red, green, blue, or yellow) were calibrated for each participant for luminance through heterochromatic flicker photometry and equated to the luminance of grey distracters. Each visual display contained 10 circles, 1 colored and 9 grey, each of which contained an oriented line segment. The task required deploying attention to the colored circle, which was either in the left or right visual hemifield. Three lateralised ERP components relative to the side of the lateral coloured circle were examined: a posterior contralateral positivity (Ppc) prior to N2pc, the N2pc, reflecting the deployment of visual spatial attention, and a temporal and contralateral positivity (Ptc) following N2pc. Red or blue stimuli, as compared to green or yellow, had an earlier N2pc. Both the Ppc and Ptc had higher amplitudes to red stimuli, suggesting particular selectivity for red. The results suggest that attention may be deployed to red and blue more quickly than to other colours and suggests special caution when designing ERP experiments involving stimuli in different colours, even when all colours are equiluminant. Copyright © 2013 Elsevier B.V. All rights reserved.

PUZZLE - A program for computer-aided design of printed circuit artwork

NASA Technical Reports Server (NTRS)

Harrell, D. A. W.; Zane, R.

1971-01-01

Program assists in solving spacing problems encountered in printed circuit /PC/ design. It is intended to have maximum use for two-sided PC boards carrying integrated circuits, and also aids design of discrete component circuits.

Climatic niche evolution in New World monkeys (Platyrrhini).

PubMed

Duran, Andressa; Meyer, Andreas L S; Pie, Marcio R

2013-01-01

Despite considerable interest in recent years on species distribution modeling and phylogenetic niche conservatism, little is known about the way in which climatic niches change over evolutionary time. This knowledge is of major importance to understand the mechanisms underlying limits of species distributions, as well as to infer how different lineages might be affected by anthropogenic climate change. In this study we investigate the tempo and mode climatic niche evolution in New World monkeys (Platyrrhini). Climatic conditions found throughout the distribution of 140 primate species were investigated using a principal component analysis, which indicated that mean temperature (particularly during the winter) is the most important climatic correlate of platyrrhine geographical distributions, accounting for nearly half of the interspecific variation in climatic niches. The effects of precipitation were associated with the second principal component, particularly with respect to the dry season. When models of trait evolution were fit to scores on each of the principal component axes, significant phylogenetic signal was detected for PC1 scores, but not for PC2 scores. Interestingly, although all platyrrhine families occupied comparable regions of climatic space, some aotid species such as Aotus lemurinus, A. jorgehernandezi, and A. miconax show highly distinctive climatic niches associated with drier conditions (high PC2 scores). This shift might have been made possible by their nocturnal habits, which could serve as an exaptation that allow them to be less constrained by humidity during the night. These results underscore the usefulness of investigating explicitly the tempo and mode of climatic niche evolution and its role in determining species distributions.

Dynamics of trace elements in shallow groundwater of an agricultural land in the northeast of Mexico

NASA Astrophysics Data System (ADS)

Mora, Abrahan; Mahlknecht, Jürgen; Hernández-Antonio, Arturo

2017-04-01

The citrus zone located in northeastern Mexico covers an area of 8000 km2 and produces 10% of the Mexican citrus production. The aquifer system of this zone constitutes the major source of water for drinking and irrigation purposes for local population and provides base flows to surface water supplied to the city of Monterrey ( 4.5 million inhabitants). Although the study area is near the recharge zones, several works have reported nitrate pollution in shallow groundwater of this agricultural area, mainly due to animal manure and human waste produced by infiltration of urban sewers and septic tanks. Thus, the goals of this work were to assess the dynamics of selected trace elements in this aquifer system and determine if the trace element content in groundwater poses a threat to the population living in the area. Thirty-nine shallow water wells were sampled in 2010. These water samples were filtered through 0,45 µm pore size membranes and preserved with nitric acid for storage. The concentrations of Cd, Cs, Cu, Mo, Pb, Rb, Si, Ti, U, Y, and Zn were measured by ICP-MS. Also, sulfate concentrations were measured by ion chromatography in unacidified samples. Principal Component Analysis (PCA) performed in the data set show five principal components (PC). PC1 includes elements derived from silicate weathering, such as Si and Ti. The relationship found between Mo and U with sulfates in PC2 indicates that both elements show a high mobility in groundwater. Indeed, the concentrations of sulfate, Mo and U are increased as groundwater moves eastward. PC3 includes the alkali trace elements (Rb and Cs), indicating that both elements could be derived from the same source of origin. PC4 represents the heavy trace elements (Cd and Pb) whereas PC5 includes divalent trace elements such as Zn and Cu. None of the water samples showed trace element concentrations higher than the guideline values for drinking water proposed by the World Health Organization, which indicates that the analyzed trace elements in groundwater do not pose any significant threat to the population living in this area.

Principal component analysis of PiB distribution in Parkinson and Alzheimer diseases

PubMed Central

Markham, Joanne; Flores, Hubert; Hartlein, Johanna M.; Goate, Alison M.; Cairns, Nigel J.; Videen, Tom O.; Perlmutter, Joel S.

2013-01-01

Objective: To use principal component analyses (PCA) of Pittsburgh compound B (PiB) PET imaging to determine whether the pattern of in vivo β-amyloid (Aβ) in Parkinson disease (PD) with cognitive impairment is similar to the pattern found in symptomatic Alzheimer disease (AD). Methods: PiB PET scans were obtained from participants with PD with cognitive impairment (n = 53), participants with symptomatic AD (n = 35), and age-matched controls (n = 67). All were assessed using the Clinical Dementia Rating and APOE genotype was determined in 137 participants. PCA was used to 1) determine the PiB binding pattern in AD, 2) determine a possible unique PD pattern, and 3) directly compare the PiB binding patterns in PD and AD groups. Results: The first 2 principal components (PC1 and PC2) significantly separated the AD and control participants (p < 0.001). Participants with PD with cognitive impairment also were significantly different from participants with symptomatic AD on both components (p < 0.001). However, there was no difference between PD and controls on either component. Even those participants with PD with elevated mean cortical binding potentials were significantly different from participants with AD on both components. Conclusion: Using PCA, we demonstrated that participants with PD with cognitive impairment do not exhibit the same PiB binding pattern as participants with AD. These data suggest that Aβ deposition may play a different pathophysiologic role in the cognitive impairment of PD compared to that in AD. PMID:23825179

Nanoscale Packing Differences in Sphingomyelin and Phosphatidylcholine Revealed by BODIPY Fluorescence in Monolayers: Physiological Implications

PubMed Central

2015-01-01

Phosphatidycholines (PC) with two saturated acyl chains (e.g., dipalmitoyl) mimic natural sphingomyelin (SM) by promoting raft formation in model membranes. However, sphingoid-based lipids, such as SM, rather than saturated-chain PCs have been implicated as key components of lipid rafts in biomembranes. These observations raise questions about the physical packing properties of the phase states that can be formed by these two major plasma membrane lipids with identical phosphocholine headgroups. To investigate, we developed a monolayer platform capable of monitoring changes in surface fluorescence by acquiring multiple spectra during measurement of a lipid force–area isotherm. We relied on the concentration-dependent emission changes of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY)-labeled PC to detect nanoscale alterations in lipid packing and phase state induced by monolayer lateral compression. The BODIPY-PC probe contained an indacene ring with four symmetrically located methyl (Me) substituents to enhance localization to the lipid hydrocarbon region. Surface fluorescence spectra indicated changes in miscibility even when force–area isotherms showed no deviation from ideal mixing behavior in the surface pressure versus cross-sectional molecular area response. We detected slightly better mixing of Me4-BODIPY-8-PC with the fluid-like, liquid expanded phase of 1-palmitoyl-2-oleoyl-PC compared to N-oleoyl-SM. Remarkably, in the gel-like, liquid condensed phase, Me4-BODIPY-8-PC mixed better with N-palmitoyl-SM than dipalmitoyl-PC, suggesting naturally abundant SMs with saturated acyl chains form gel-like lipid phase(s) with enhanced ability to accommodate deeply embedded components compared to dipalmitoyl-PC gel phase. The findings reveal a fundamental difference in the lateral packing properties of SM and PC that occurs even when their acyl chains match. PMID:24564829

Shear in high strength concrete bridge girders : technical report.

DOT National Transportation Integrated Search

2013-04-01

Prestressed Concrete (PC) I-girders are used extensively as the primary superstructure components in Texas highway bridges. : A simple semi-empirical equation was developed at the University of Houston (UH) to predict the shear strength of PC I-girde...

Identification of protein expression alterations in gefitinib-resistant human lung adenocarcinoma: PCNT and mPR play key roles in the development of gefitinib-associated resistance

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

Lin, Chi-Chen; Institute of Biomedical Science, and Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taiwan; Department of Medical Research and Education, Taichung Veterans General Hospital, Taichung, Taiwan

2015-11-01

Gefitinib is the first-line chemotherapeutic drug for treating non-small cell lung cancer (NSCLC), which comprises nearly 85% of all lung cancer cases worldwide. However, most patients eventually develop drug resistance after 12–18 months of treatment. Hence, investigating the drug resistance mechanism and resistance-associated biomarkers is necessary. Two lung adenocarcinoma cell lines, PC9 and gefitinib-resistant PC9/Gef, were established for examining resistance mechanisms and identifying potential therapeutic targets. Two-dimensional differential gel electrophoresis and matrix-assisted laser desorption ionization time-of-flight mass spectrometry were used for examining global protein expression changes between PC9 and PC9/Gef. The results revealed that 164 identified proteins were associated withmore » the formation of gefitinib resistance in PC9 cells. Additional studies using RNA interference showed that progesterone receptor membrane component 1 and pericentrin proteins have major roles in gefitinib resistance. In conclusion, the proteomic approach enabled identifying of numerous proteins involved in gefitinib resistance. The results provide useful diagnostic markers and therapeutic candidates for treating gefitinib-resistant NSCLC. - Highlights: • 164 proteins associated with gefitinib resistance were identified through proteomic analysis. • In this study, a lung adenocarcinoma and its gefitinib resistant partner were established. • mPR and PCNT proteins have evidenced to play important roles in gefitinib resistance.« less

Morphological correlates of swimming activity in wild largemouth bass (Micropterus salmoides) in their natural environment.

PubMed

Hanson, K C; Hasler, C T; Suski, C D; Cooke, S J

2007-12-01

Individual variation in morphology has been linked to organismal performance in numerous taxa. Recently, the relationship between functional morphology and swimming performance in teleost fishes has been studied in laboratory experiments. In this study, we evaluate the relationship between morphology and swimming activity of wild largemouth bass (Micropterus salmoides) during the reproductive period, providing the first data derived on free-swimming fish not exposed to forced swim trials in the laboratory. Sixteen male largemouth bass were angled from their nests, telemetered, and subsequently monitored by a whole-lake acoustic hydrophone array with sub-meter accuracy. Additionally, eleven morphological measurements were taken from digital images of each fish. A principal components analysis of the morphological measurements described 79.8% of the variance. PC1 was characterized by measures of overall body stoutness, PC2 was characterized by measures of the length and depth of the caudal region, and PC3 characterized individuals with relatively large anterior portions of the body and relatively small caudal areas. Of these variables, only PC3 showed significant relationships to swimming activity throughout the parental care period. PC3 was negatively correlated with multiple measures of swimming activity across the parental care period. Furthermore, swimming performance of individual male bass was noted to be repeatable across the parental care period indicating that this phenomenon extends beyond the laboratory.

Principal component analysis of physicochemical and sensory characteristics of beef rounds extended with gum arabic from Acacia senegal var. kerensis.

PubMed

Mwove, Johnson K; Gogo, Lilian A; Chikamai, Ben N; Omwamba, Mary; Mahungu, Symon M

2018-03-01

Principal component analysis (PCA) was carried out to study the relationship between 24 meat quality measurements taken from beef round samples that were injected with curing brines containing gum arabic (1%, 1.5%, 2%, 2.5%, and 3%) and soy protein concentrate (SPC) (3.5%) at two injection levels (30% and 35%). The measurements used to describe beef round quality were expressible moisture, moisture content, cook yield, possible injection, achieved gum arabic level in beef round, and protein content, as well as descriptive sensory attributes for flavor, texture, basic tastes, feeling factors, color, and overall acceptability. Several significant correlations were found between beef round quality parameters. The highest significant negative and positive correlations were recorded between color intensity and gray color and between color intensity and brown color, respectively. The first seven principal components (PCs) were extracted explaining over 95% of the total variance. The first PC was characterized by texture attributes (hardness and denseness), feeling factors (chemical taste and chemical burn), and two physicochemical properties (expressible moisture and achieved gum arabic level). Taste attribute (saltiness), physicochemical attributes (cook yield and possible injection), and overall acceptability were useful in defining the second PC, while the third PC was characterized by metallic taste, gray color, brown color, and physicochemical attributes (moisture and protein content). The correlation loading plot showed that the distribution of the samples on the axes of the first two PCs allowed for differentiation of samples injected to 30% injection level which were placed on the upper side of the biplot from those injected to 35% which were placed on the lower side. Similarly, beef samples extended with gum arabic and those containing SPC were also visible when scores for the first and third PCs were plotted. Thus, PCA was efficient in analyzing the quality characteristics of beef rounds extended with gum arabic.

Profound and pervasive degradation of Madagascar's freshwater wetlands and links with biodiversity.

PubMed

Bamford, Andrew J; Razafindrajao, Felix; Young, Richard P; Hilton, Geoff M

2017-01-01

Reflecting a global trend, freshwater wetlands in Madagascar have received little conservation or research attention. Madagascar is a global conservation priority due to its high level of species endemism but most work has focused on protecting forests. For the first time, we investigated the state of wetlands across the country to determine the effects of human disturbance. We conducted a rapid survey of 37 wetlands, using waterbirds and benthic invertebrates as ecological indicators. We recorded nine variables relating to human disturbance, revealing widespread wetland destruction. Principal Components Analysis reduced the nine variables to a single Principal Component (PC) that explained 50% of the dataset variance, demonstrating that different forms of human disturbance are ubiquitous and inseparable. The disturbance PC provides an index of how pristine a lake is and in Generalized Linear Models (GLMs) was significantly inversely related to the number of waterbird species present and the density of Chironomidae. The disturbance PC was estimated for every wetland in a GIS-derived dataset of wetland locations in Madagascar, giving a country-wide frequency distribution of disturbance. To validate the estimated PC values, we used the GLMs to predict the number of endemic bird species at an independent sample of 22 lakes. The predicted values correlated with the observed number of species, demonstrating that our procedure can identify lakes with high biodiversity value. The disturbance PC provides a convenient method for ranking sites, and a country-wide ranking demonstrates that the only near-pristine lakes in Madagascar are small sites that have been preserved by remoteness from human activity and not conservation management. The strategy of conserving high biodiversity remnants is insufficient because existing remnants suffer some degree of degradation and only support small populations of threatened species. Large-scale restoration of degraded wetlands is required for the long-term conservation of Madagascar's freshwater biodiversity.

Profound and pervasive degradation of Madagascar’s freshwater wetlands and links with biodiversity

PubMed Central

Razafindrajao, Felix; Young, Richard P.; Hilton, Geoff M.

2017-01-01

Reflecting a global trend, freshwater wetlands in Madagascar have received little conservation or research attention. Madagascar is a global conservation priority due to its high level of species endemism but most work has focused on protecting forests. For the first time, we investigated the state of wetlands across the country to determine the effects of human disturbance. We conducted a rapid survey of 37 wetlands, using waterbirds and benthic invertebrates as ecological indicators. We recorded nine variables relating to human disturbance, revealing widespread wetland destruction. Principal Components Analysis reduced the nine variables to a single Principal Component (PC) that explained 50% of the dataset variance, demonstrating that different forms of human disturbance are ubiquitous and inseparable. The disturbance PC provides an index of how pristine a lake is and in Generalized Linear Models (GLMs) was significantly inversely related to the number of waterbird species present and the density of Chironomidae. The disturbance PC was estimated for every wetland in a GIS-derived dataset of wetland locations in Madagascar, giving a country-wide frequency distribution of disturbance. To validate the estimated PC values, we used the GLMs to predict the number of endemic bird species at an independent sample of 22 lakes. The predicted values correlated with the observed number of species, demonstrating that our procedure can identify lakes with high biodiversity value. The disturbance PC provides a convenient method for ranking sites, and a country-wide ranking demonstrates that the only near-pristine lakes in Madagascar are small sites that have been preserved by remoteness from human activity and not conservation management. The strategy of conserving high biodiversity remnants is insufficient because existing remnants suffer some degree of degradation and only support small populations of threatened species. Large-scale restoration of degraded wetlands is required for the long-term conservation of Madagascar’s freshwater biodiversity. PMID:28792516

Impact of a New Palliative Care Program on Health System Finances: An Analysis of the Palliative Care Program Inpatient Unit and Consultations at Johns Hopkins Medical Institutions.

PubMed

Isenberg, Sarina R; Lu, Chunhua; McQuade, John; Chan, Kelvin K W; Gill, Natasha; Cardamone, Michael; Torto, Deirdre; Langbaum, Terry; Razzak, Rab; Smith, Thomas J

2017-05-01

Palliative care inpatient units (PCUs) can improve symptoms, family perception of care, and lower per-diem costs compared with usual care. In March 2013, Johns Hopkins Medical Institutions (JHMI) added a PCU to the palliative care (PC) program. We studied the financial impact of the PC program on JHMI from March 2013 to March 2014. This study considered three components of the PC program: PCU, PC consultations, and professional fees. Using 13 months of admissions data, the team calculated the per-day variable cost pre-PCU (ie, in another hospital unit) and after transfer to the PCU. These fees were multiplied by the number of patients transferred to the PCU and by the average length of stay in the PCU. Consultation savings were estimated using established methods. Professional fees assumed a collection rate of 50%. The total positive financial impact of the PC program was $3,488,863.17. There were 153 transfers to the PCU, 60% with cancer, and an average length of stay of 5.11 days. The daily loss pretransfer to the PCU of $1,797.67 was reduced to $1,345.34 in the PCU (-25%). The PCU saved JHMI $353,645.17 in variable costs, or $452.33 per transfer. Cost savings for PC consultations in the hospital, 60% with cancer, were estimated at $2,765,218. $370,000 was collected in professional fees savings. The PCU and PC program had a favorable impact on JHMI while providing expert patient-centered care. As JHMI moves to an accountable care organization model, value-based patient-centered care and increased intensive care unit availability are desirable.

Metabolomics of dates (Phoenix dactylifera) reveals a highly dynamic ripening process accounting for major variation in fruit composition.

PubMed

Diboun, Ilhame; Mathew, Sweety; Al-Rayyashi, Maryam; Elrayess, Mohamed; Torres, Maria; Halama, Anna; Méret, Michaël; Mohney, Robert P; Karoly, Edward D; Malek, Joel; Suhre, Karsten

2015-12-16

Dates are tropical fruits with appreciable nutritional value. Previous attempts at global metabolic characterization of the date metabolome were constrained by small sample size and limited geographical sampling. In this study, two independent large cohorts of mature dates exhibiting substantial diversity in origin, varieties and fruit processing conditions were measured by metabolomics techniques in order to identify major determinants of the fruit metabolome. Multivariate analysis revealed a first principal component (PC1) significantly associated with the dates' countries of production. The availability of a smaller dataset featuring immature dates from different development stages served to build a model of the ripening process in dates, which helped reveal a strong ripening signature in PC1. Analysis revealed enrichment in the dry type of dates amongst fruits with early ripening profiles at one end of PC1 as oppose to an overrepresentation of the soft type of dates with late ripening profiles at the other end of PC1. Dry dates are typical to the North African region whilst soft dates are more popular in the Gulf region, which partly explains the observed association between PC1 and geography. Analysis of the loading values, expressing metabolite correlation levels with PC1, revealed enrichment patterns of a comprehensive range of metabolite classes along PC1. Three distinct metabolic phases corresponding to known stages of date ripening were observed: An early phase enriched in regulatory hormones, amines and polyamines, energy production, tannins, sucrose and anti-oxidant activity, a second phase with on-going phenylpropanoid secondary metabolism, gene expression and phospholipid metabolism and a late phase with marked sugar dehydration activity and degradation reactions leading to increased volatile synthesis. These data indicate the importance of date ripening as a main driver of variation in the date metabolome responsible for their diverse nutritional and economical values. The biochemistry of the ripening process in dates is consistent with other fruits but natural dryness may prevent degenerative senescence in dates following ripening. Based on the finding that mature dates present varying extents of ripening, our survey of the date metabolome essentially revealed snapshots of interchanging metabolic states during ripening empowering an in-depth characterization of underlying biology.

Radiometric and spectral calibrations of the Geostationary Imaging Fourier Transform Spectrometer (GIFTS) using principle component analysis

NASA Astrophysics Data System (ADS)

Tian, Jialin; Smith, William L.; Gazarik, Michael J.

2008-10-01

The ultimate remote sensing benefits of the high resolution Infrared radiance spectrometers will be realized with their geostationary satellite implementation in the form of imaging spectrometers. This will enable dynamic features of the atmosphere's thermodynamic fields and pollutant and greenhouse gas constituents to be observed for revolutionary improvements in weather forecasts and more accurate air quality and climate predictions. As an important step toward realizing this application objective, the Geostationary Imaging Fourier Transform Spectrometer (GIFTS) Engineering Demonstration Unit (EDU) was successfully developed under the NASA New Millennium Program, 2000-2006. The GIFTS-EDU instrument employs three focal plane arrays (FPAs), which gather measurements across the long-wave IR (LWIR), short/mid-wave IR (SMWIR), and visible spectral bands. The raw GIFTS interferogram measurements are radiometrically and spectrally calibrated to produce radiance spectra, which are further processed to obtain atmospheric profiles via retrieval algorithms. The radiometric calibration is achieved using internal blackbody calibration references at ambient (260 K) and hot (286 K) temperatures. The absolute radiometric performance of the instrument is affected by several factors including the FPA off-axis effect, detector/readout electronics induced nonlinearity distortions, and fore-optics offsets. The GIFTS-EDU, being the very first imaging spectrometer to use ultra-high speed electronics to readout its large area format focal plane array detectors, operating at wavelengths as large as 15 microns, possessed non-linearity's not easily removable in the initial calibration process. In this paper, we introduce a refined calibration technique that utilizes Principle Component (PC) analysis to compensate for instrument distortions and artifacts remaining after the initial radiometric calibration process, thus, further enhance the absolute calibration accuracy. This method is applied to data collected during an atmospheric measurement experiment with the GIFTS, together with simultaneous observations by the accurately calibrated AERI (Atmospheric Emitted Radiance Interferometer), both simultaneously zenith viewing the sky through the same external scene mirror at ten-minute intervals throughout a cloudless day at Logan Utah on September 13, 2006. The PC vectors of the calibrated radiance spectra are defined from the AERI observations and regression matrices relating the initial GIFTS radiance PC scores to the AERI radiance PC scores are calculated using the least squares inverse method. A new set of accurately calibrated GIFTS radiances are produced using the first four PC scores in the regression model. Temperature and moisture profiles retrieved from the PC-calibrated GIFTS radiances are verified against radiosonde measurements collected throughout the GIFTS sky measurement period.

Reparameterization of PAM50 Expression Identifies Novel Breast Tumor Dimensions and Leads to Discovery of a Genome-Wide Significant Breast Cancer Locus at 12q15.

PubMed

Madsen, Michael J; Knight, Stacey; Sweeney, Carol; Factor, Rachel; Salama, Mohamed; Stijleman, Inge J; Rajamanickam, Venkatesh; Welm, Bryan E; Arunachalam, Sasi; Jones, Brandt; Rachamadugu, Rakesh; Rowe, Kerry; Cessna, Melissa H; Thomas, Alun; Kushi, Lawrence H; Caan, Bette J; Bernard, Philip S; Camp, Nicola J

2018-06-01

Background: Breast tumor subtyping has failed to provide impact in susceptibility genetics. The PAM50 assay categorizes breast tumors into: Luminal A, Luminal B, HER2-enriched and Basal-like. However, tumors are often more complex than simple categorization can describe. The identification of heritable tumor characteristics has potential to decrease heterogeneity and increase power for gene finding. Methods: We used 911 sporadic breast tumors with PAM50 expression data to derive tumor dimensions using principal components (PC). Dimensions in 238 tumors from high-risk pedigrees were compared with the sporadic tumors. Proof-of-concept gene mapping, informed by tumor dimension, was performed using Shared Genomic Segment (SGS) analysis. Results: Five dimensions (PC1-5) explained the majority of the PAM50 expression variance: three captured intrinsic subtype, two were novel (PC3, PC5). All five replicated in 745 TCGA tumors. Both novel dimensions were significantly enriched in the high-risk pedigrees (intrinsic subtypes were not). SGS gene-mapping in a pedigree identified a 0.5 Mb genome-wide significant region at 12q15 This region segregated through 32 meioses to 8 breast cancer cases with extreme PC3 tumors ( P = 2.6 × 10 -8 ). Conclusions: PC analysis of PAM50 gene expression revealed multiple independent, quantitative measures of tumor diversity. These tumor dimensions show evidence for heritability and potential as powerful traits for gene mapping. Impact: Our study suggests a new approach to describe tumor expression diversity, provides new avenues for germline studies, and proposes a new breast cancer locus. Similar reparameterization of expression patterns may inform other studies attempting to model the effects of tumor heterogeneity. Cancer Epidemiol Biomarkers Prev; 27(6); 644-52. ©2018 AACR . ©2018 American Association for Cancer Research.

Topside Ionospheric Response to Solar EUV Variability

NASA Astrophysics Data System (ADS)

Anderson, P. C.; Hawkins, J.

2015-12-01

We present an analysis of 23 years of thermal plasma measurements in the topside ionosphere from several DMSP spacecraft at ~800 km. The solar cycle variations of the daily averaged densities, temperatures, and H+/O+ ratios show a strong relationship to the solar EUV as described by the E10.7 solar EUV proxy with cross-correlation coefficients (CCCs) with the density greater than 0.85. The H+/O+ varies dramatically from solar maximum when it is O+ dominated to solar minimum when it is H+ dominated. These ionospheric parameters also vary strongly with season, particularly at latitudes well away from the equator where the solar zenith angle (SZA) varies greatly with season. There are strong 27-day solar rotation periodicities in the density, associated with the periodicities in the solar EUV as measured by the TIMED SEE and SDO EVE instruments, with CCCs at times greater than 0.9 at selected wavelengths. Empirical Orthogonal Function (EOF) analysis captures over 95% of the variation in the density over the 23 years in the first two principle components. The first principle component (PC1) is clearly associated with the solar EUV showing a 0.91 CCC with the E10.7 proxy while the PC1 EOFs remain relatively constant with latitude indicating that the solar EUV effects are relatively independent of latitude. The second principle component (PC2) is clearly associated with the SZA variation, showing strong correlations with the SZA and the concomitant density variations at latitudes away from the equator and with the PC2 EOFs having magnitudes near zero at the equator and maximum at high latitude. The magnitude of the variation of the response of the topside ionosphere to solar EUV variability is shown to be closely related to the composition. This is interpreted as the result of the effect of composition on the scale height in the topside ionosphere and the "pivot effect" in which the variation in density near the F2 peak is expected to be amplified by a factor of e at an altitude a scale height above the F2 peak. When the topside ionosphere is H+ dominated, DMSP may be much less than a scale height above the F2 peak while when it is O+ dominated, DMSP may be several scale heights above the F2 peak.

An Empirical Cumulus Parameterization Scheme for a Global Spectral Model

NASA Technical Reports Server (NTRS)

Rajendran, K.; Krishnamurti, T. N.; Misra, V.; Tao, W.-K.

2004-01-01

Realistic vertical heating and drying profiles in a cumulus scheme is important for obtaining accurate weather forecasts. A new empirical cumulus parameterization scheme based on a procedure to improve the vertical distribution of heating and moistening over the tropics is developed. The empirical cumulus parameterization scheme (ECPS) utilizes profiles of Tropical Rainfall Measuring Mission (TRMM) based heating and moistening derived from the European Centre for Medium- Range Weather Forecasts (ECMWF) analysis. A dimension reduction technique through rotated principal component analysis (RPCA) is performed on the vertical profiles of heating (Q1) and drying (Q2) over the convective regions of the tropics, to obtain the dominant modes of variability. Analysis suggests that most of the variance associated with the observed profiles can be explained by retaining the first three modes. The ECPS then applies a statistical approach in which Q1 and Q2 are expressed as a linear combination of the first three dominant principal components which distinctly explain variance in the troposphere as a function of the prevalent large-scale dynamics. The principal component (PC) score which quantifies the contribution of each PC to the corresponding loading profile is estimated through a multiple screening regression method which yields the PC score as a function of the large-scale variables. The profiles of Q1 and Q2 thus obtained are found to match well with the observed profiles. The impact of the ECPS is investigated in a series of short range (1-3 day) prediction experiments using the Florida State University global spectral model (FSUGSM, T126L14). Comparisons between short range ECPS forecasts and those with the modified Kuo scheme show a very marked improvement in the skill in ECPS forecasts. This improvement in the forecast skill with ECPS emphasizes the importance of incorporating realistic vertical distributions of heating and drying in the model cumulus scheme. This also suggests that in the absence of explicit models for convection, the proposed statistical scheme improves the modeling of the vertical distribution of heating and moistening in areas of deep convection.

Mg II Spectra of Late Type Stars Used to Probe the LISM

NASA Technical Reports Server (NTRS)

Beckman, J. E.; Crivellari, L.; Franco, M.; Molaro, P.; Vladilo, G.

1984-01-01

IUE spectra of Mg II h and k in late type dwarfs and giants were used to detect and measure absorption components due to the LISM. This technique gives a method of probing the awkward range from d = 3 pc to d = 80 pc from the Sun. In spite of interpretational uncertainties the HI component of the LISM can be plotted well enough to confirm it as a cloud some 20 to 30 pc in extent, peaking sharply in density towards l(II)-25 deg., moving towards the Sun from l(II)-25 deg, b(II) = + 10 deg., at 28 Km/sec. The hole towards l(II) = 150 deg is confirmed, suggesting a solar position close to the cloud's edge in this direction.

Active suppression after involuntary capture of attention.

PubMed

Sawaki, Risa; Luck, Steven J

2013-04-01

After attention has been involuntarily captured by a distractor, how is it reoriented toward a target? One possibility is that attention to the distractor passively fades over time, allowing the target to become attended. Another possibility is that the captured location is actively suppressed so that attention can be directed toward the target location. The present study investigated this issue with event-related potentials (ERPs), focusing on the N2pc component (a neural measure of attentional deployment) and the Pd component (a neural measure of attentional suppression). Observers identified a color-defined target in a search array, which was preceded by a task-irrelevant cue array. When the cue array contained an item that matched the target color, this item captured attention (as measured both behaviorally and with the N2pc component). This capture of attention was followed by active suppression (indexed by the Pd component), and this was then followed by a reorienting of attention toward the target in the search array (indexed by the N2pc component). These findings indicate that the involuntary capture of attention by a distractor is followed by an active suppression process that presumably facilitates the subsequent voluntary orienting of attention to the target.

Multivariate optimization of a synergistic blend of oleoresin sage (Salvia officinalis L.) and ascorbyl palmitate to stabilize sunflower oil.

PubMed

Upadhyay, Rohit; Mishra, Hari Niwas

2016-04-01

The simultaneous optimization of a synergistic blend of oleoresin sage (SAG) and ascorbyl palmitate (AP) in sunflower oil (SO) was performed using central composite and rotatable design coupled with principal component analysis (PCA) and response surface methodology (RSM). The physicochemical parameters viz., peroxide value, anisidine value, free fatty acids, induction period, total polar matter, antioxidant capacity and conjugated diene value were considered as response variables. PCA reduced the original set of correlated responses to few uncorrelated principal components (PC). The PC1 (eigen value, 5.78; data variance explained, 82.53 %) was selected for optimization using RSM. The quadratic model adequately described the data (R (2) = 0. 91, p < 0.05) and lack of fit was insignificant (p > 0.05). The contour plot of PC 1 score indicated the optimal synergistic combination of 1289.19 and 218.06 ppm for SAG and AP, respectively. This combination of SAG and AP resulted in shelf life of 320 days at 25 °C estimated using linear shelf life prediction model. In conclusion, the versatility of PCA-RSM approach has resulted in an easy interpretation in multiple response optimizations. This approach can be considered as a useful guide to develop new oil blends stabilized with food additives from natural sources.

Principal Component 2-D Long Short-Term Memory for Font Recognition on Single Chinese Characters.

PubMed

Tao, Dapeng; Lin, Xu; Jin, Lianwen; Li, Xuelong

2016-03-01

Chinese character font recognition (CCFR) has received increasing attention as the intelligent applications based on optical character recognition becomes popular. However, traditional CCFR systems do not handle noisy data effectively. By analyzing in detail the basic strokes of Chinese characters, we propose that font recognition on a single Chinese character is a sequence classification problem, which can be effectively solved by recurrent neural networks. For robust CCFR, we integrate a principal component convolution layer with the 2-D long short-term memory (2DLSTM) and develop principal component 2DLSTM (PC-2DLSTM) algorithm. PC-2DLSTM considers two aspects: 1) the principal component layer convolution operation helps remove the noise and get a rational and complete font information and 2) simultaneously, 2DLSTM deals with the long-range contextual processing along scan directions that can contribute to capture the contrast between character trajectory and background. Experiments using the frequently used CCFR dataset suggest the effectiveness of PC-2DLSTM compared with other state-of-the-art font recognition methods.

Divergent prion strain evolution driven by PrPC expression level in transgenic mice

PubMed Central

Le Dur, Annick; Laï, Thanh Lan; Stinnakre, Marie-George; Laisné, Aude; Chenais, Nathalie; Rakotobe, Sabine; Passet, Bruno; Reine, Fabienne; Soulier, Solange; Herzog, Laetitia; Tilly, Gaëlle; Rézaei, Human; Béringue, Vincent; Vilotte, Jean-Luc; Laude, Hubert

2017-01-01

Prions induce a fatal neurodegenerative disease in infected host brain based on the refolding and aggregation of the host-encoded prion protein PrPC into PrPSc. Structurally distinct PrPSc conformers can give rise to multiple prion strains. Constrained interactions between PrPC and different PrPSc strains can in turn lead to certain PrPSc (sub)populations being selected for cross-species transmission, or even produce mutation-like events. By contrast, prion strains are generally conserved when transmitted within the same species, or to transgenic mice expressing homologous PrPC. Here, we compare the strain properties of a representative sheep scrapie isolate transmitted to a panel of transgenic mouse lines expressing varying levels of homologous PrPC. While breeding true in mice expressing PrPC at near physiological levels, scrapie prions evolve consistently towards different strain components in mice beyond a certain threshold of PrPC overexpression. Our results support the view that PrPC gene dosage can influence prion evolution on homotypic transmission. PMID:28112164

Opportunities for Palliative Care in Public Health.

PubMed

De Lima, Liliana; Pastrana, Tania

2016-01-01

In May 2014, the World Health Assembly, of the World Health Organization (WHO), unanimously adopted a palliative care (PC) resolution, which outlines clear recommendations to the United Nations member states, such as including PC in national health policies and in the undergraduate curricula for health care professionals, and highlights the critical need for countries to ensure that there is an adequate supply of essential PC medicines, especially those needed to alleviate pain. This resolution also carries great challenges: Every year over 20 million patients (of which 6% are children) need PC at the end of life (EOL). However, in 2011, approximately three million patients received PC, and only one in ten people in need is currently receiving it. We describe this public health situation and systems failure, the history and evolution of PC, and the components of the WHO public health model. We propose a role for public health for PC integration in community settings to advance PC and relieve suffering in the world.

Factors Affecting Outcomes in Cochlear Implant Recipients Implanted With a Perimodiolar Electrode Array Located in Scala Tympani.

PubMed

Holden, Laura K; Firszt, Jill B; Reeder, Ruth M; Uchanski, Rosalie M; Dwyer, Noël Y; Holden, Timothy A

2016-12-01

To identify primary biographic and audiologic factors contributing to cochlear implant (CI) performance variability in quiet and noise by controlling electrode array type and electrode position within the cochlea. Although CI outcomes have improved over time, considerable outcome variability still exists. Biographic, audiologic, and device-related factors have been shown to influence performance. Examining CI recipients with consistent array type and electrode position may allow focused investigation into outcome variability resulting from biographic and audiologic factors. Thirty-nine adults (40 ears) implanted for at least 6 months with a perimodiolar electrode array known (via computed tomography [CT] imaging) to be in scala tympani participated. Test materials, administered CI only, included monosyllabic words, sentences in quiet and noise, and spectral ripple discrimination. In quiet, scores were high with mean word and sentence scores of 76 and 87%, respectively; however, sentence scores decreased by an average of 35 percentage points when noise was added. A principal components (PC) analysis of biographic and audiologic factors found three distinct factors, PC1 Age, PC2 Duration, and PC3 Pre-op Hearing. PC1 Age was the only factor that correlated, albeit modestly, with speech recognition in quiet and noise. Spectral ripple discrimination strongly correlated with speech measures. For these recipients with consistent electrode position, PC1 Age was related to speech recognition performance. Consistent electrode position may have contributed to high speech understanding in quiet. Inter-subject variability in noise may have been influenced by auditory/cognitive processing, known to decline with age, and mechanisms that underlie spectral resolution ability.

Identifying Clinical Factors Which Predict for Early Failure Patterns Following Resection for Pancreatic Adenocarcinoma in Patients Who Received Adjuvant Chemotherapy Without Chemoradiation.

PubMed

Walston, Steve; Salloum, Joseph; Grieco, Carmine; Wuthrick, Evan; Diaz, Dayssy A; Barney, Christian; Manilchuk, Andrei; Schmidt, Carl; Dillhoff, Mary; Pawlik, Timothy M; Williams, Terence M

2018-05-04

The role of radiation therapy (RT) in resected pancreatic cancer (PC) remains incompletely defined. We sought to determine clinical variables which predict for local-regional recurrence (LRR) to help select patients for adjuvant RT. We identified 73 patients with PC who underwent resection and adjuvant gemcitabine-based chemotherapy alone. We performed detailed radiologic analysis of first patterns of failure. LRR was defined as recurrence of PC within standard postoperative radiation volumes. Univariate analyses (UVA) were conducted using the Kaplan-Meier method and multivariate analyses (MVA) utilized the Cox proportional hazard ratio model. Factors significant on UVA were used for MVA. At median follow-up of 20 months, rates of local-regional recurrence only (LRRO) were 24.7%, LRR as a component of any failure 68.5%, metastatic recurrence (MR) as a component of any failure 65.8%, and overall disease recurrence (OR) 90.5%. On UVA, elevated postoperative CA 19-9 (>90 U/mL), pathologic lymph node positive (pLN+) disease, and higher tumor grade were associated with increased LRR, MR, and OR. On MVA, elevated postoperative CA 19-9 and pLN+ were associated with increased MR and OR. In addition, positive resection margin was associated with increased LRRO on both UVA and MVA. About 25% of patients with PC treated without adjuvant RT develop LRRO as initial failure. The only independent predictor of LRRO was positive margin, while elevated postoperative CA 19-9 and pLN+ were associated with predicting MR and overall survival. These data may help determine which patients benefit from intensification of local therapy with radiation.

Differences in levels of platelet-derived microparticles in platelet components prepared using the platelet rich plasma, buffy coat, and apheresis procedures.

PubMed

Noulsri, Egarit; Udomwinijsilp, Prapaporn; Lerdwana, Surada; Chongkolwatana, Viroje; Permpikul, Parichart

2017-04-01

There has been an increased interest in platelet-derived microparticles (PMPs) in transfusion medicine. Little is known about PMP status during the preparation of platelet concentrates for transfusion. The aim of this study is to compare the PMP levels in platelet components prepared using the buffy coat (BC), platelet-rich plasma platelet concentrate (PRP-PC), and apheresis (AP) processes. Platelet components were prepared using the PRP-PC and BC processes. Apheresis platelets were prepared using the Trima Accel and Amicus instruments. The samples were incubated with annexin A5-FITC, CD41-PE, and CD62P-APC. At day 1 after processing, the PMPs and activated platelets were determined using flow cytometry. Both the percentage and number of PMPs were higher in platelet components prepared using the Amicus instrument (2.6±1.8, 32802±19036 particles/μL) than in platelet components prepared using the Trima Accel instrument (0.5±0.4, 7568±5298 particles/μL), BC (1.2±0.6, 12,920±6426 particles/μL), and PRP-PC (0.9±0.6, 10731±5514 particles/μL). Both the percentage and number of activated platelets were higher in platelet components prepared using the Amicus instrument (33.2±13.9, 427553±196965 cells/μL) than in platelet components prepared using the Trima Accel instrument (16.2±6.1, 211209±87706 cells/μL), BC (12.9±3.2, 140624±41003 cells/μL), and PRP-PC (21.1±6.3, 265210±86257 cells/μL). The study suggests high variability of PMPs and activated platelets in platelet components prepared using different processes. This result may be important in validating the instruments involved in platelet blood collection and processing. Copyright © 2016 Elsevier Ltd. All rights reserved.

Thin Rechargeable Batteries for CMOS SRAM Memory Protection

NASA Technical Reports Server (NTRS)

Crouse, Dennis N.

1993-01-01

New rechargeable battery technology is described and compared with classical primary battery back-up of SRAM PC cards. Thin solid polymer electrolyte cells with the thickness of TSOP memory components (1 mm nominal, 1.1 mm max) and capacities of 14 mAh/sq cm can replace coin cells. The SRAM PC cards with permanently installed rechargeable cells and optional electrochromic low battery voltage indicators will free the periodic PC card user from having to 'feed' their PC cards with coin cells and will allow a quick visual check of stored cards for their battery voltage status.

The control of attentional target selection in a colour/colour conjunction task.

PubMed

Berggren, Nick; Eimer, Martin

2016-11-01

To investigate the time course of attentional object selection processes in visual search tasks where targets are defined by a combination of features from the same dimension, we measured the N2pc component as an electrophysiological marker of attentional object selection during colour/colour conjunction search. In Experiment 1, participants searched for targets defined by a combination of two colours, while ignoring distractor objects that matched only one of these colours. Reliable N2pc components were triggered by targets and also by partially matching distractors, even when these distractors were accompanied by a target in the same display. The target N2pc was initially equal in size to the sum of the two N2pc components to the two different types of partially matching distractors and became superadditive from approximately 250 ms after search display onset. Experiment 2 demonstrated that the superadditivity of the target N2pc was not due to a selective disengagement of attention from task-irrelevant partially matching distractors. These results indicate that attention was initially deployed separately and in parallel to all target-matching colours, before attentional allocation processes became sensitive to the presence of both matching colours within the same object. They suggest that attention can be controlled simultaneously and independently by multiple features from the same dimension and that feature-guided attentional selection processes operate in parallel for different target-matching objects in the visual field.

Cost-effectiveness analysis of pharmaceutical care for hypertensive patients from the perspective of the public health system in Brazil.

PubMed

Cazarim, Maurílio de Souza; Pereira, Leonardo Régis Leira

2018-01-01

Only 20% of patients with systemic arterial hypertension (SAH) have blood pressure within recommended parameters. SAH has been the main risk factor for morbidity and mortality of cardiovascular diseases, which affects the burden of the Public Health System (PHS). Some studies have shown the effectiveness of Pharmaceutical Care (PC) in the care of hypertensive patients. To perform a cost-effectiveness analysis to compare SAH treatment with PC management and conventional treatment for hypertensive patients offered by the PHS. A cost-effectiveness study nested to a quasi-experimental study was conducted, in which 104 hypertensive patients were followed up in a PC program. Blood pressure control was considered as the outcome for the economic analysis and the costs were direct and non-direct medical costs. PC was dominant for two years in the post-PC period compared with the pre-PC year. The mean cost effectiveness ratio (CER) for the CERPre-PC, CERPC, and CERPost-PC periods were: US$ 364.65, US$ 415.39, and US$ 231.14 respectively. The incremental cost effectiveness ratio (ICER) analysis presented ICER of US$ 478.41 in the PC period and US$ 42.95 in the post PC period. Monte Carlo sensitivity analysis presented mean ICERPC and ICERPost-PC equal to US$ 605.09 and US$ 128.03, reaching US$ 1,725.00 and US$ 740.00 respectively. Even for the highest ICER, the values were below the cost effectiveness threshold, which means that PC was a cost effective strategy for the care of hypertensive patients in the PHS.

Docosahexaenoic acid-containing choline phospholipid modulates LPS-induced neuroinflammation in vivo and in microglia in vitro.

PubMed

Fourrier, Célia; Remus-Borel, Julie; Greenhalgh, Andrew D; Guichardant, Michel; Bernoud-Hubac, Nathalie; Lagarde, Michel; Joffre, Corinne; Layé, Sophie

2017-08-24

Neuroinflammatory processes are considered a double-edged sword, having both protective and detrimental effects in the brain. Microglia, the brain's resident innate immune cells, are a key component of neuroinflammatory response. There is a growing interest in developing drugs to target microglia and control neuroinflammatory processes. In this regard, docosahexaenoic acid (DHA), the brain's n-3 polyunsaturated fatty acid, is a promising molecule to regulate pro-inflammatory microglia and cytokine production. Several works reported that the bioavailability of DHA to the brain is higher when DHA is acylated to phospholipid. In this work, we analyzed the anti-inflammatory activity of DHA-phospholipid, either acetylated at the sn-1 position (AceDoPC, a stable form thought to have superior access to the brain) or acylated with palmitic acid at the sn-1 position (PC-DHA) using a lipopolysaccharide (LPS)-induced neuroinflammation model both in vitro and in vivo. In vivo, adult C57Bl6/J mice were injected intravenously (i.v.) with either AceDoPC or PC-DHA 24 h prior to LPS (i.p.). For in vitro studies, immortalized murine microglia cells BV-2 were co-incubated with DHA forms and LPS. AceDoPC and PC-DHA effect on brain or BV-2 PUFA content was assessed by gas chromatography. LPS-induced pro-inflammatory cytokines interleukin IL-1β, IL-6, and tumor necrosis factor (TNF) α production were measured by quantitative PCR (qPCR) or multiplex. IL-6 receptors and associated signaling pathway STAT3 were assessed by FACS analysis and western-blot in vitro. In vivo, a single injection of AceDoPC or PC-DHA decreased LPS-induced IL-6 production in the hippocampus of mice. This effect could be linked to their direct effect on microglia, as revealed in vitro. In addition, AceDoPC or PC-DHA reduced IL-6 receptor while only AceDoPC decreased IL-6-induced STAT3 phosphorylation. These results highlight the potency of administered DHA-acetylated to phospholipids-to rapidly regulate LPS-induced neuroinflammatory processes through their effect on microglia. In particular, both IL-6 production and signaling are targeted by AceDoPC in microglia.

Study on nondestructive discrimination of genuine and counterfeit wild ginsengs using NIRS

NASA Astrophysics Data System (ADS)

Lu, Q.; Fan, Y.; Peng, Z.; Ding, H.; Gao, H.

2012-07-01

A new approach for the nondestructive discrimination between genuine wild ginsengs and the counterfeit ones by near infrared spectroscopy (NIRS) was developed. Both discriminant analysis and back propagation artificial neural network (BP-ANN) were applied to the model establishment for discrimination. Optimal modeling wavelengths were determined based on the anomalous spectral information of counterfeit samples. Through principal component analysis (PCA) of various wild ginseng samples, genuine and counterfeit, the cumulative percentages of variance of the principal components were obtained, serving as a reference for principal component (PC) factor determination. Discriminant analysis achieved an identification ratio of 88.46%. With sample' truth values as its outputs, a three-layer BP-ANN model was built, which yielded a higher discrimination accuracy of 100%. The overall results sufficiently demonstrate that NIRS combined with BP-ANN classification algorithm performs better on ginseng discrimination than discriminant analysis, and can be used as a rapid and nondestructive method for the detection of counterfeit wild ginsengs in food and pharmaceutical industry.

Use of genotype-environment interactions to elucidate the pattern of maize root plasticity to nitrogen deficiency.

PubMed

Li, Pengcheng; Zhuang, Zhongjuan; Cai, Hongguang; Cheng, Shuai; Soomro, Ayaz Ali; Liu, Zhigang; Gu, Riliang; Mi, Guohua; Yuan, Lixing; Chen, Fanjun

2016-03-01

Maize (Zea mays L.) root morphology exhibits a high degree of phenotypic plasticity to nitrogen (N) deficiency, but the underlying genetic architecture remains to be investigated. Using an advanced BC4 F3 population, we investigated the root growth plasticity under two contrasted N levels and identified the quantitative trait loci (QTLs) with QTL-environment (Q × E) interaction effects. Principal components analysis (PCA) on changes of root traits to N deficiency (ΔLN-HN) showed that root length and biomass contributed for 45.8% in the same magnitude and direction on the first PC, while root traits scattered highly on PC2 and PC3. Hierarchical cluster analysis on traits for ΔLN-HN further assigned the BC4 F3 lines into six groups, in which the special phenotypic responses to N deficiency was presented. These results revealed the complicated root plasticity of maize in response to N deficiency that can be caused by genotype-environment (G × E) interactions. Furthermore, QTL mapping using a multi-environment analysis identified 35 QTLs for root traits. Nine of these QTLs exhibited significant Q × E interaction effects. Taken together, our findings contribute to understanding the phenotypic and genotypic pattern of root plasticity to N deficiency, which will be useful for developing maize tolerance cultivars to N deficiency. © 2015 Institute of Botany, Chinese Academy of Sciences.

Kinematics and subpopulations' structure definition of blue fox (Alopex lagopus) sperm motility using the ISAS® V1 CASA system.

PubMed

Soler, C; García, A; Contell, J; Segervall, J; Sancho, M

2014-08-01

Over recent years, technological advances have brought innovation in assisted reproduction to the agriculture. Fox species are of great economical interest in some countries, but their semen characteristics have not been studied enough. To advance the knowledge of function of fox spermatozoa, five samples were obtained by masturbation, in the breeding season. Kinetic analysis was performed using ISAS® v1 system. Usual kinematic parameters (VCL, VSL, VAP, LIN, STR, WOB, ALH and BCF) were considered. To establish the standardization for the analysis of samples, the minimum number of cells to analyse and the minimum number of fields to capture were defined. In the second step, the presence of subpopulations in blue fox semen was analysed. The minimum number of cells to test was 30, because kinematic parameters remained constant along the groups of analysis. Also, the effectiveness of ISAS® D4C20 counting chamber was studied, showing that the first five squares presented equivalent results, while in the squares six and seven, the kinematic parameters showed a reduction in all of them, but not in the concentration or motility percentage. Kinematic variables were grouped into two principal components (PC). A linear movement characterized PC1, while PC2 showed an oscillatory movement. Three subpopulations were found, varying in structure among different animals. © 2014 Blackwell Verlag GmbH.

Active site formation mechanism of carbon-based oxygen reduction catalysts derived from a hyperbranched iron phthalocyanine polymer.

PubMed

Hiraike, Yusuke; Saito, Makoto; Niwa, Hideharu; Kobayashi, Masaki; Harada, Yoshihisa; Oshima, Masaharu; Kim, Jaehong; Nabae, Yuta; Kakimoto, Masa-Aki

2015-01-01

Carbon-based cathode catalysts derived from a hyperbranched iron phthalocyanine polymer (HB-FePc) were characterized, and their active-site formation mechanism was studied by synchrotron-based spectroscopy. The properties of the HB-FePc catalyst are compared with those of a catalyst with high oxygen reduction reaction (ORR) activity synthesized from a mixture of iron phthalocyanine and phenolic resin (FePc/PhRs). Electrochemical measurements demonstrate that the HB-FePc catalyst does not lose its ORR activity up to 900°C, whereas that of the FePc/PhRs catalyst decreases above 700°C. Hard X-ray photoemission spectra reveal that the HB-FePc catalysts retain more nitrogen components than the FePc/PhRs catalysts between pyrolysis temperatures of 600°C and 800°C. This is because the linked structure of the HB-FePc precursor has high thermostability against nitrogen desorption. Consequently, effective doping of active nitrogen species into the sp (2) carbon network of the HB-FePc catalysts may occur up to 900°C.

Reconstruction of sediment transport pathways in modern microtidal sand flat by multiple classification analysis

NASA Astrophysics Data System (ADS)

Yamashita, S.; Nakajo, T.; Naruse, H.

2009-12-01

In this study, we statistically classified the grain size distribution of the bottom surface sediment on a microtidal sand flat to analyze the depositional processes of the sediment. Multiple classification analysis revealed that two types of sediment populations exist in the bottom surface sediment. Then, we employed the sediment trend model developed by Gao and Collins (1992) for the estimation of sediment transport pathways. As a result, we found that statistical discrimination of the bottom surface sediment provides useful information for the sediment trend model while dealing with various types of sediment transport processes. The microtidal sand flat along the Kushida River estuary, Ise Bay, central Japan, was investigated, and 102 bottom surface sediment samples were obtained. Then, their grain size distribution patterns were measured by the settling tube method, and each grain size distribution parameter (mud and gravel contents, mean grain size, coefficient of variance (CV), skewness, kurtosis, 5, 25, 50, 75, and 95 percentile) was calculated. Here, CV is the normalized sorting value divided by the mean grain size. Two classical statistical methods—principal component analysis (PCA) and fuzzy cluster analysis—were applied. The results of PCA showed that the bottom surface sediment of the study area is mainly characterized by grain size (mean grain size and 5-95 percentile) and the CV value, indicating predominantly large absolute values of factor loadings in primal component (PC) 1. PC1 is interpreted as being indicative of the grain-size trend, in which a finer grain-size distribution indicates better size sorting. The frequency distribution of PC1 has a bimodal shape and suggests the existence of two types of sediment populations. Therefore, we applied fuzzy cluster analysis, the results of which revealed two groupings of the sediment (Cluster 1 and Cluster 2). Cluster 1 shows a lower value of PC1, indicating coarse and poorly sorted sediments. Cluster 1 sediments are distributed around the branched channel from Kushida River and show an expanding distribution from the river mouth toward the northeast direction. Cluster 2 shows a higher value of PC1, indicating fine and well-sorted sediments; this cluster is distributed in a distant area from the river mouth, including the offshore region. Therefore, Cluster 1 and Cluster 2 are interpreted as being deposited by fluvial and wave processes, respectively. Finally, on the basis of this distribution pattern, the sediment trend model was applied in areas dominated separately by fluvial and wave processes. Resultant sediment transport patterns showed good agreement with those obtained by field observations. The results of this study provide an important insight into the numerical models of sediment transport.

Inhibition of human prostate cancer (PC-3) cells and targeting of PC-3-derived prostate cancer stem cells with koenimbin, a natural dietary compound from Murraya koenigii (L) Spreng.

PubMed

Kamalidehghan, Behnam; Ghafouri-Fard, Soudeh; Motevaseli, Elahe; Ahmadipour, Fatemeh

2018-01-01

Inhibition of prostate cancer stem cells (PCSCs) is an efficient curative maintenance protocol for the prevention of prostate cancer. The objectives of this study were to assess the efficiency of koenimbin, a major biologically active component of Murraya koenigii (L) Spreng, in the suppression of PC-3 cells and to target PC-3-derived cancer stem cells (CSCs) through apoptotic and CSC signaling pathways in vitro. The antiproliferative activity of koenimbin was examined using MTT, and the apoptotic detection was carried out by acridine orange/propidium iodide (AO/PI) double-staining and multiparametric high-content screening (HCS) assays. Caspase bioluminescence assay, reverse transcription polymerase chain reaction (RT-PCR), and immunoblotting were conducted to confirm the expression of apoptotic-associated proteins. Cell cycle analysis was investigated using flow cytometry. Involvement of nuclear factor-kappa B (NF-κB) was analyzed using HCS assay. Aldefluor™ and prostasphere formation examinations were used to evaluate the impact of koenimbin on PC-3 CSCs in vitro. Koenimbin remarkably inhibited cell proliferation in a dose-dependent manner. Koenimbin induced nuclear condensation, formation of apoptotic bodies, and G 0 /G 1 phase arrest of PC-3 cells. Koenimbin triggered the activation of caspase-3/7 and caspase-9 and the release of cytochrome c , decreased anti-apoptotic Bcl-2 and HSP70 proteins, increased pro-apoptotic Bax proteins, and inhibited NF-κB translocation from the cytoplasm to the nucleus, leading to the activation of the intrinsic apoptotic pathway. Koenimbin significantly ( P <0.05) reduced the aldehyde dehydrogenase-positive cell population of PC-3 CSCs and the size and number of PC-3 CSCs in primary, secondary, and tertiary prostaspheres in vitro. Koenimbin has chemotherapeutic potential that may be employed for future treatment through decreasing the recurrence of cancer, resulting in the improvement of cancer management strategies and patient survival.

Prostate Cancer Associated Lipid Signatures in Serum Studied by ESI-Tandem Mass Spectrometryas Potential New Biomarkers.

PubMed

Duscharla, Divya; Bhumireddy, Sudarshana Reddy; Lakshetti, Sridhar; Pospisil, Heike; Murthy, P V L N; Walther, Reinhard; Sripadi, Prabhakar; Ummanni, Ramesh

2016-01-01

Prostate cancer (PCa) is one amongst the most common cancersin western men. Incidence rate ofPCa is on the rise worldwide. The present study deals with theserum lipidome profiling of patients diagnosed with PCa to identify potential new biomarkers. We employed ESI-MS/MS and GC-MS for identification of significantly altered lipids in cancer patient's serum compared to controls. Lipidomic data revealed 24 lipids are significantly altered in cancer patinet's serum (n = 18) compared to normal (n = 18) with no history of PCa. By using hierarchical clustering and principal component analysis (PCA) we could clearly separate cancer patients from control group. Correlation and partition analysis along with Formal Concept Analysis (FCA) have identified that PC (39:6) and FA (22:3) could classify samples with higher certainty. Both the lipids, PC (39:6) and FA (22:3) could influence the cataloging of patients with 100% sensitivity (all 18 control samples are classified correctly) and 77.7% specificity (of 18 tumor samples 4 samples are misclassified) with p-value of 1.612×10-6 in Fischer's exact test. Further, we performed GC-MS to denote fatty acids altered in PCa patients and found that alpha-linolenic acid (ALA) levels are altered in PCa. We also performed an in vitro proliferation assay to determine the effect of ALA in survival of classical human PCa cell lines LNCaP and PC3. We hereby report that the altered lipids PC (39:6) and FA (22:3) offer a new set of biomarkers in addition to the existing diagnostic tests that could significantly improve sensitivity and specificity in PCa diagnosis.

Prostate Cancer Associated Lipid Signatures in Serum Studied by ESI-Tandem Mass Spectrometryas Potential New Biomarkers

PubMed Central

Duscharla, Divya; Bhumireddy, Sudarshana Reddy; Lakshetti, Sridhar; Pospisil, Heike; Murthy, P. V. L. N.; Walther, Reinhard; Sripadi, Prabhakar; Ummanni, Ramesh

2016-01-01

Prostate cancer (PCa) is one amongst the most common cancersin western men. Incidence rate ofPCa is on the rise worldwide. The present study deals with theserum lipidome profiling of patients diagnosed with PCa to identify potential new biomarkers. We employed ESI-MS/MS and GC-MS for identification of significantly altered lipids in cancer patient’s serum compared to controls. Lipidomic data revealed 24 lipids are significantly altered in cancer patinet’s serum (n = 18) compared to normal (n = 18) with no history of PCa. By using hierarchical clustering and principal component analysis (PCA) we could clearly separate cancer patients from control group. Correlation and partition analysis along with Formal Concept Analysis (FCA) have identified that PC (39:6) and FA (22:3) could classify samples with higher certainty. Both the lipids, PC (39:6) and FA (22:3) could influence the cataloging of patients with 100% sensitivity (all 18 control samples are classified correctly) and 77.7% specificity (of 18 tumor samples 4 samples are misclassified) with p-value of 1.612×10−6 in Fischer’s exact test. Further, we performed GC-MS to denote fatty acids altered in PCa patients and found that alpha-linolenic acid (ALA) levels are altered in PCa. We also performed an in vitro proliferation assay to determine the effect of ALA in survival of classical human PCa cell lines LNCaP and PC3. We hereby report that the altered lipids PC (39:6) and FA (22:3) offer a new set of biomarkers in addition to the existing diagnostic tests that could significantly improve sensitivity and specificity in PCa diagnosis. PMID:26958841

Supernova-regulated ISM. V. Space and Time Correlations

NASA Astrophysics Data System (ADS)

Hollins, J. F.; Sarson, G. R.; Shukurov, A.; Fletcher, A.; Gent, F. A.

2017-11-01

We apply correlation analysis to random fields in numerical simulations of the supernova-driven interstellar medium (ISM) with the magnetic field produced by dynamo action. We solve the magnetohydrodynamic (MHD) equations in a shearing Cartesian box representing a local region of the ISM, subject to thermal and kinetic energy injection by supernova explosions, and parameterized, optically thin radiative cooling. We consider the cold, warm, and hot phases of the ISM separately; the analysis mostly considers the warm gas, which occupies the bulk of the domain. Various physical variables have different correlation lengths in the warm phase: 40,50, and 60 {pc} for the random magnetic field, density, and velocity, respectively, in the midplane. The correlation time of the random velocity is comparable to the eddy turnover time, about {10}7 {year}, although it may be shorter in regions with a higher star formation rate. The random magnetic field is anisotropic, with the standard deviations of its components {b}x/{b}y/{b}z having approximate ratios 0.5/0.6/0.6 in the midplane. The anisotropy is attributed to the global velocity shear from galactic differential rotation and locally inhomogeneous outflow to the galactic halo. The correlation length of Faraday depth along the z axis, 120 {pc}, is greater than for electron density, 60{--}90 {pc}, and the vertical magnetic field, 60 {pc}. Such comparisons may be sensitive to the orientation of the line of sight. Uncertainties of the structure functions of synchrotron intensity rapidly increase with the scale. This feature is hidden in a power spectrum analysis, which can undermine the usefulness of power spectra for detailed studies of interstellar turbulence.

MALDI-Mass Spectrometric Imaging Revealing Hypoxia-Driven Lipids and Proteins in a Breast Tumor Model

DOE PAGES

Jiang, Lu; Chughtai, Kamila; Purvine, Samuel O.; ...

2015-05-20

Hypoxic areas are a common feature of rapidly growing malignant tumors and their metastases, and are typically spatially heterogeneous. Hypoxia has a strong impact on tumor cell biology and contributes to tumor progression in multiple ways. To date, only a few molecular key players in tumor hypoxia, such as for example hypoxia-inducible factor-1 (HIF-1), have been discovered. The distribution of biomolecules is frequently heterogeneous in the tumor volume, and may be driven by hypoxia and HIF-1α. Understanding the spatially heterogeneous hypoxic response of tumors is critical. Mass spectrometric imaging (MSI) provides a unique way of imaging biomolecular distributions in tissuemore » sections with high spectral and spatial resolution. In this paper, breast tumor xenografts grown from MDA-MB-231-HRE-tdTomato cells, with a red fluorescent tdTomato protein construct under the control of a hypoxia response element (HRE)-containing promoter driven by HIF-1α, were used to detect the spatial distribution of hypoxic regions. We elucidated the 3D spatial relationship between hypoxic regions and the localization of small molecules, metabolites, lipids, and proteins by using principal component analysis – linear discriminant analysis (PCA-LDA) on 3D rendered MSI volume data from MDA-MB-231-HRE-tdTomato breast tumor xenografts. In this study we identified hypoxia-regulated proteins active in several distinct pathways such as glucose metabolism, regulation of actin cytoskeleton, protein folding, translation/ribosome, splicesome, the PI3K-Akt signaling pathway, hemoglobin chaperone, protein processing in endoplasmic reticulum, detoxification of reactive oxygen species, aurora B signaling/apoptotic execution phase, the RAS signaling pathway, the FAS signaling pathway/caspase cascade in apoptosis and telomere stress induced senescence. In parallel we also identified co-localization of hypoxic regions and various lipid species such as PC(16:0/18:1), PC(16:0/18:2), PC(18:0/18:1), PC(18:1/18:1), PC(18:1/18:2), PC(16:1/18:4), PC(18:0/20:3), PC(16:0/22:1), among others. Lastly, our findings shed light on the biomolecular composition of hypoxic tumor regions, which may be responsible for a given tumor’s resistance to radiation or chemotherapy.« less

MALDI-Mass Spectrometric Imaging Revealing Hypoxia-Driven Lipids and Proteins in a Breast Tumor Model

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

Jiang, Lu; Chughtai, Kamila; Purvine, Samuel O.

Hypoxic areas are a common feature of rapidly growing malignant tumors and their metastases, and are typically spatially heterogeneous. Hypoxia has a strong impact on tumor cell biology and contributes to tumor progression in multiple ways. To date, only a few molecular key players in tumor hypoxia, such as for example hypoxia-inducible factor-1 (HIF-1), have been discovered. The distribution of biomolecules is frequently heterogeneous in the tumor volume, and may be driven by hypoxia and HIF-1α. Understanding the spatially heterogeneous hypoxic response of tumors is critical. Mass spectrometric imaging (MSI) provides a unique way of imaging biomolecular distributions in tissuemore » sections with high spectral and spatial resolution. In this paper, breast tumor xenografts grown from MDA-MB-231-HRE-tdTomato cells, with a red fluorescent tdTomato protein construct under the control of a hypoxia response element (HRE)-containing promoter driven by HIF-1α, were used to detect the spatial distribution of hypoxic regions. We elucidated the 3D spatial relationship between hypoxic regions and the localization of small molecules, metabolites, lipids, and proteins by using principal component analysis – linear discriminant analysis (PCA-LDA) on 3D rendered MSI volume data from MDA-MB-231-HRE-tdTomato breast tumor xenografts. In this study we identified hypoxia-regulated proteins active in several distinct pathways such as glucose metabolism, regulation of actin cytoskeleton, protein folding, translation/ribosome, splicesome, the PI3K-Akt signaling pathway, hemoglobin chaperone, protein processing in endoplasmic reticulum, detoxification of reactive oxygen species, aurora B signaling/apoptotic execution phase, the RAS signaling pathway, the FAS signaling pathway/caspase cascade in apoptosis and telomere stress induced senescence. In parallel we also identified co-localization of hypoxic regions and various lipid species such as PC(16:0/18:1), PC(16:0/18:2), PC(18:0/18:1), PC(18:1/18:1), PC(18:1/18:2), PC(16:1/18:4), PC(18:0/20:3), PC(16:0/22:1), among others. Lastly, our findings shed light on the biomolecular composition of hypoxic tumor regions, which may be responsible for a given tumor’s resistance to radiation or chemotherapy.« less

How Adequate are One- and Two-Dimensional Free Energy Landscapes for Protein Folding Dynamics?

NASA Astrophysics Data System (ADS)

Maisuradze, Gia G.; Liwo, Adam; Scheraga, Harold A.

2009-06-01

The molecular dynamics trajectories of protein folding or unfolding, generated with the coarse-grained united-residue force field for the B domain of staphylococcal protein A, were analyzed by principal component analysis (PCA). The folding or unfolding process was examined by using free-energy landscapes (FELs) in PC space. By introducing a novel multidimensional FEL, it was shown that the low-dimensional FELs are not always sufficient for the description of folding or unfolding processes. Similarities between the topographies of FELs along low- and high-indexed principal components were observed.

Comparison of three-dimensional fluorescence analysis methods for predicting formation of trihalomethanes and haloacetic acids.

PubMed

Peleato, Nicolás M; Andrews, Robert C

2015-01-01

This work investigated the application of several fluorescence excitation-emission matrix analysis methods as natural organic matter (NOM) indicators for use in predicting the formation of trihalomethanes (THMs) and haloacetic acids (HAAs). Waters from four different sources (two rivers and two lakes) were subjected to jar testing followed by 24hr disinfection by-product formation tests using chlorine. NOM was quantified using three common measures: dissolved organic carbon, ultraviolet absorbance at 254 nm, and specific ultraviolet absorbance as well as by principal component analysis, peak picking, and parallel factor analysis of fluorescence spectra. Based on multi-linear modeling of THMs and HAAs, principle component (PC) scores resulted in the lowest mean squared prediction error of cross-folded test sets (THMs: 43.7 (μg/L)(2), HAAs: 233.3 (μg/L)(2)). Inclusion of principle components representative of protein-like material significantly decreased prediction error for both THMs and HAAs. Parallel factor analysis did not identify a protein-like component and resulted in prediction errors similar to traditional NOM surrogates as well as fluorescence peak picking. These results support the value of fluorescence excitation-emission matrix-principal component analysis as a suitable NOM indicator in predicting the formation of THMs and HAAs for the water sources studied. Copyright © 2014. Published by Elsevier B.V.

Assessment of major ions and trace elements in groundwater supplied to the Monterrey metropolitan area, Nuevo León, Mexico.

PubMed

Mora, Abrahan; Mahlknecht, Jürgen; Rosales-Lagarde, Laura; Hernández-Antonio, Arturo

2017-08-01

The Monterrey metropolitan area (MMA) is the third greatest urban area and the second largest economic city of Mexico. More than four million people living in this megacity use groundwater for drinking, industrial and household purposes. Thus, major ion and trace element content were assessed in order to investigate the main hydrochemical properties of groundwater and determine if groundwater of the area poses a threat to the MMA population. Hierarchical cluster analysis using all the groundwater chemical data showed five groups of water. The first two groups were classified as recharge waters (Ca-HCO 3 ) coming from the foothills of mountain belts. The third group was also of Ca-HCO 3 water type flowing through lutites and limestones. Transition zone waters of group four (Ca-HCO 3 -SO 4 ) flow through the valley of Monterrey, whereas discharge waters of group 5 (Ca-SO 4 ) were found toward the north and northeast of the MMA. Principal component analysis performed in groundwater data indicates four principal components (PCs). PC1 included major ions Si, Co, Se, and Zn, suggesting that these are derived by rock weathering. Other trace elements such as As, Mo, Mn, and U are coupled in PC2 because they show redox-sensitive properties. PC3 indicates that Pb and Cu could be the less mobile elements in groundwater. Although groundwater supplied to MMA showed a high-quality, high mineralized waters of group 5 have NO 3 - concentrations higher than the maximum value proposed by international guidelines and SO 4 2- , NO 3 - , and total dissolved solid concentrations higher than the maximum levels allowed by the Mexican normative.

Near-infrared-excited confocal Raman spectroscopy advances in vivo diagnosis of cervical precancer.

PubMed

Duraipandian, Shiyamala; Zheng, Wei; Ng, Joseph; Low, Jeffrey J H; Ilancheran, Arunachalam; Huang, Zhiwei

2013-06-01

Raman spectroscopy is a unique optical technique that can probe the changes of vibrational modes of biomolecules associated with tissue premalignant transformation. This study evaluates the clinical utility of confocal Raman spectroscopy over near-infrared (NIR) autofluorescence (AF) spectroscopy and composite NIR AF/Raman spectroscopy for improving early diagnosis of cervical precancer in vivo at colposcopy. A rapid NIR Raman system coupled with a ball-lens fiber-optic confocal Raman probe was utilized for in vivo NIR AF/Raman spectral measurements of the cervix. A total of 1240 in vivo Raman spectra [normal (n=993), dysplasia (n=247)] were acquired from 84 cervical patients. Principal components analysis (PCA) and linear discriminant analysis (LDA) together with a leave-one-patient-out, cross-validation method were used to extract the diagnostic information associated with distinctive spectroscopic modalities. The diagnostic ability of confocal Raman spectroscopy was evaluated using the PCA-LDA model developed from the significant principal components (PCs) [i.e., PC4, 0.0023%; PC5, 0.00095%; PC8, 0.00022%, (p<0.05)], representing the primary tissue Raman features (e.g., 854, 937, 1095, 1253, 1311, 1445, and 1654 cm(-1)). Confocal Raman spectroscopy coupled with PCA-LDA modeling yielded the diagnostic accuracy of 84.1% (a sensitivity of 81.0% and a specificity of 87.1%) for in vivo discrimination of dysplastic cervix. The receiver operating characteristic curves further confirmed that the best classification was achieved using confocal Raman spectroscopy compared to the composite NIR AF/Raman spectroscopy or NIR AF spectroscopy alone. This study illustrates that confocal Raman spectroscopy has great potential to improve early diagnosis of cervical precancer in vivo during clinical colposcopy.

Analysis of field-aligned structure of compressional Pc 5 waves and associated energetic ion modulations observed by Polar at L~9.5

NASA Astrophysics Data System (ADS)

Capman, E.; Engebretson, M. J.; Pilipenko, V.; Russell, C. T.; Peterson, W. K.

2012-12-01

Nearly all previous studies of storm-time compressional Pc 5 waves have used data from low-inclination satellites, so the field-aligned structure of these waves could be determined only statistically or by inference. However, the high inclination of the Polar satellite's orbit allowed it to approximately follow a flux tube across the equator. In this study we present examples of compressional Pc 5 events identified during Polar's 2001-02 and 2002-03 duskside passages. The focus of this presentation is on exploring the field-aligned structure of the observed waves near the geomagnetic equator. At least two frequencies were identified in each event. In many cases these are a 1st (fundamental) harmonic with a node in the field-aligned (Bz) component near the geomagnetic equator, and a 2nd harmonic with an anti-node near the equator. To verify this assumption we applied the analytical signal method, verified by manual hodogram analysis, to monitor the amplitude and phase variations of the radial (Bx) and compressional (Bz) components at certain frequencies. The following transitions occurred near the time when Polar crossed the geomagnetic equator: The phase difference was 0° in the southern hemisphere and then 180° out of phase in the northern hemisphere. The waves were often linearly polarized, and the inclination angle of the polarization ellipse in the Bx-Bz plane was negative in the southern hemisphere and positive in the northern hemisphere. The ellipticity still had a slight positive bias in the southern hemisphere and a slight negative bias in the northern hemisphere. These observational results are compared with the results of modeling of coupled MHD Alfven and slow magnetosonic modes.

Detection of Cell Wall Chemical Variation in Zea Mays Mutants Using Near-Infrared Spectroscopy

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

Buyck, N.; Thomas, S.

Corn stover is regarded as the prime candidate feedstock material for commercial biomass conversion in the United States. Variations in chemical composition of Zea mays cell walls can affect biomass conversion process yields and economics. Mutant lines were constructed by activating a Mu transposon system. The cell wall chemical composition of 48 mutant families was characterized using near-infrared (NIR) spectroscopy. NIR data were analyzed using a multivariate statistical analysis technique called Principal Component Analysis (PCA). PCA of the NIR data from 349 maize leaf samples reveals 57 individuals as outliers on one or more of six Principal Components (PCs) atmore » the 95% confidence interval. Of these, 19 individuals from 16 families are outliers on either PC3 (9% of the variation) or PC6 (1% of the variation), the two PCs that contain information about cell wall polymers. Those individuals for which altered cell wall chemistry is confirmed with wet chemical analysis will then be subjected to fermentation analysis to determine whether or not biomass conversion process kinetics, yields and/or economics are significantly affected. Those mutants that provide indications for a decrease in process cost will be pursued further to identify the gene(s) responsible for the observed changes in cell wall composition and associated changes in process economics. These genes will eventually be incorporated into maize breeding programs directed at the development of a truly dual use crop.« less

Selective Localization and Migration of Multiwalled Carbon Nanotubes in Blends of Polycarbonate and Poly(styrene-acrylonitrile).

PubMed

Göldel, Andreas; Kasaliwal, Gaurav; Pötschke, Petra

2009-03-19

Multiwalled carbon nanotubes (MWNTs) have been introduced into blends of polycarbonate (PC) and poly(styrene-acrylonitrile) (SAN) by melt mixing in a microcompounder. Co-continuous blends are prepared by either pre-compounding low amounts of nanotubes into PC or SAN or by mixing all three components together. Interestingly, in all blends, regardless of the way of introducing the nanotubes, the MWNTs were exclusively located within the PC phase, which resulted in much lower electrical resistivities as compared to PC or SAN composites with the same MWNT content. The migration of MWNTs from the SAN phase into the PC phase during common mixing is explained by interfacial effects. Copyright © 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Primary analysis for clinical efficacy of immunotherapy in patients with pancreatic cancer.

PubMed

Chen, Linghua; Zhang, Xiaoyan

2016-02-01

Immunotherapy is an important treatment for pancreatic cancer (PC) patients. To evaluate the therapeutic efficacy of immunotherapy in the treatment of PC, we performed a systemic review and meta-analysis of the relevant published clinical trials, collectively referred to as DC, DC-CIK, LAK, NK and GM-CSF secreting PC cell lines.  A total of 413 patients in 11 eligible trials with PC were selected for the present meta-analysis. The estimated pooled overall survival showed a significant improvement for PC patients who received immunotherapy compared with nonimmunotherapy. The lymphocyte subsets, immune cytokine levels and serum cancer markers in the peripheral blood of PC patients were significantly improved after immunotherapy. The results showed that immunotherapy can improve the efficacy of the treatment of PC patients.

Optimization of replacement and inspection decisions for multiple components on a power system

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

Mauney, D.A.

1994-12-31

The use of optimization on the rescheduling of replacement dates provided a very proactive approach to deciding when components on individual units need to be addressed with a run/repair/replace decision. Including the effects of time value of money and taxes and unit need inside the spreadsheet model allowed the decision maker to concentrate on the effects of engineering input and replacement date decisions on the final net present value (NPV). The personal computer (PC)-based model was applied to a group of 140 forced outage critical fossil plant tube components across a power system. The estimated resulting NPV of the optimizationmore » was in the tens of millions of dollars. This PC spreadsheet model allows the interaction of inputs from structural reliability risk assessment models, plant foreman interviews, and actual failure history on a by component by unit basis across a complete power production system. This model includes not only the forced outage performance of these components caused by tube failures but, in addition, the forecasted need of the individual units on the power system and the expected cost of their replacement power if forced off line. The use of cash flow analysis techniques in the spreadsheet model results in the calculation of an NPV for a whole combination of replacement dates. This allows rapid assessments of {open_quotes}what if{close_quotes} scenarios of major maintenance projects on a systemwide basis and not just on a unit-by-unit basis.« less

The Relationship Between Polycystic Ovary Syndrome and Ancestry in European Americans

PubMed Central

Bjonnes, Andrew C.; Saxena, Richa; Welt, Corrine K.

2016-01-01

Objective To determine whether European Americans with PCOS would exhibit genetic differences associated with PCOS status and phenotypic features. Design The study was a case-control association study in European Americans. Setting Subjects were studied in an academic center. Subjects Women with PCOS diagnosed using the NIH criteria (n=532) and controls with regular menstrual cycles and no evidence of hyperandrogenism (n=432) were studied. Interventions Blood was drawn for measurement of sex steroids, metabolic parameters and genotyping. Main outcome measure Associations were identified between PCOS status, phenotype and genetic background determined using principal components. Results Principal component analysis identified 5 principal components (PCs). PC1 captured northwest to southeast European genetic variation and was associated with PCOS status. Acanthosis was associated with southern European ancestry, while larger waist:hip ratio was associated with northern European ancestry. PC2 was associated with east to west European genetic variation and cholesterol levels. Conclusions These data provide evidence for genetic influence based on European ethnicity in women with PCOS. There is also evidence for a genetic component in the phenotypic features of PCOS within a mixed European population. The data point to the need to control for population stratification in genetic studies in women of mixed European ethnicity. They also emphasize the need for better studies of PCOS prevalence and phenotype as a function of genetic background. PMID:27666562

Behavioral effects of bidirectional selection for behavior towards human in virgin and lactate Norway rats.

PubMed

Konoshenko, Maria Yu; Plyusnina, Irina Z

2012-06-01

Although numerous studies have demonstrated strong differences in behavioral, hormonal and neurobiological characteristics between male rats selected for elimination (tame) and enhancement (aggressive) of aggressiveness towards humans, few studies have examined changes in female behavior under this selection. The objective of the current work was to evaluate the effects of bidirectional selection for aggressiveness towards humans on behavioral profiles of virgin and lactating rats compared with the behavior in tame, aggressive and unselected (wild-type) females. The behavior of virgin females was studied using the light-dark box, the startle response test and the modified glove test. Tame females were less anxious and more tolerant towards humans than unselected and aggressive rats. Principal component analysis of all behavioral parameters produced three independent factors, explaining 66.37% of the total variability. The measures of behavior towards humans and the measures of anxiety mainly loaded on PC1 (first principal component) which separated the tame females from the unselected and aggressive ones. These data suggest the genetic correlation between the selected behavior towards humans and anxiety-related behavior in virgin rats. No significant effect of line was found for PC2 scores, associated with risk assessment behavior. Measurements of freezing behavior mainly loaded on PC3, and this component separated rats of different genetic groups from each other. The behavior of lactating rats was studied in maternal defense and pup retrieval tests. Females of selected lines did not significantly differ in behavioral measurements of these tests and were characterized by higher maternal motivation than unselected rats. It is suggested that long-term breeding of tame and aggressive rats in captivity has reduced the threshold for maternal behavior. Copyright © 2012 Elsevier B.V. All rights reserved.

Principal components of hand kinematics and neurophysiological signals in motor cortex during reach to grasp movements

PubMed Central

Aggarwal, Vikram; Thakor, Nitish V.; Schieber, Marc H.

2014-01-01

A few kinematic synergies identified by principal component analysis (PCA) account for most of the variance in the coordinated joint rotations of the fingers and wrist used for a wide variety of hand movements. To examine the possibility that motor cortex might control the hand through such synergies, we collected simultaneous kinematic and neurophysiological data from monkeys performing a reach-to-grasp task. We used PCA, jPCA and isomap to extract kinematic synergies from 18 joint angles in the fingers and wrist and analyzed the relationships of both single-unit and multiunit spike recordings, as well as local field potentials (LFPs), to these synergies. For most spike recordings, the maximal absolute cross-correlations of firing rates were somewhat stronger with an individual joint angle than with any principal component (PC), any jPC or any isomap dimension. In decoding analyses, where spikes and LFP power in the 100- to 170-Hz band each provided better decoding than other LFP-based signals, the first PC was decoded as well as the best decoded joint angle. But the remaining PCs and jPCs were predicted with lower accuracy than individual joint angles. Although PCs, jPCs or isomap dimensions might provide a more parsimonious description of kinematics, our findings indicate that the kinematic synergies identified with these techniques are not represented in motor cortex more strongly than the original joint angles. We suggest that the motor cortex might act to sculpt the synergies generated by subcortical centers, superimposing an ability to individuate finger movements and adapt the hand to grasp a wide variety of objects. PMID:24990564

Comparison of fMRI data analysis by SPM99 on different operating systems.

PubMed

Shinagawa, Hideo; Honda, Ei-ichi; Ono, Takashi; Kurabayashi, Tohru; Ohyama, Kimie

2004-09-01

The hardware chosen for fMRI data analysis may depend on the platform already present in the laboratory or the supporting software. In this study, we ran SPM99 software on multiple platforms to examine whether we could analyze fMRI data by SPM99, and to compare their differences and limitations in processing fMRI data, which can be attributed to hardware capabilities. Six normal right-handed volunteers participated in a study of hand-grasping to obtain fMRI data. Each subject performed a run that consisted of 98 images. The run was measured using a gradient echo-type echo planar imaging sequence on a 1.5T apparatus with a head coil. We used several personal computer (PC), Unix and Linux machines to analyze the fMRI data. There were no differences in the results obtained on several PC, Unix and Linux machines. The only limitations in processing large amounts of the fMRI data were found using PC machines. This suggests that the results obtained with different machines were not affected by differences in hardware components, such as the CPU, memory and hard drive. Rather, it is likely that the limitations in analyzing a huge amount of the fMRI data were due to differences in the operating system (OS).

Interstellar scintillations of PSR B1919+21: space-ground interferometry

NASA Astrophysics Data System (ADS)

Shishov, V. I.; Smirnova, T. V.; Gwinn, C. R.; Andrianov, A. S.; Popov, M. V.; Rudnitskiy, A. G.; Soglasnov, V. A.

2017-07-01

We carried out observations of pulsar PSR B1919+21 at 324 MHz to study the distribution of interstellar plasma in the direction of this pulsar. We used the RadioAstron (RA) space radio telescope, together with two ground telescopes: Westerbork (WB) and Green Bank (GB). The maximum baseline projection for the space-ground interferometer was about 60 000 km. We show that interstellar scintillation of this pulsar consists of two components: diffractive scintillations from inhomogeneities in a layer of turbulent plasma at a distance z1 = 440 pc from the observer or homogeneously distributed scattering material to the pulsar; and weak scintillations from a screen located near the observer at z2 = 0.14 ± 0.05 pc. Furthermore, in the direction to the pulsar we detected a prism that deflects radiation, leading to a shift in observed source position. We show that the influence of the ionosphere can be ignored for the space-ground baseline. Analysis of the spatial coherence function for the space-ground baseline (RA-GB) yielded a scattering angle in the observer plane of θscat = 0.7 mas. An analysis of the time-frequency correlation function for weak scintillations yielded an angle of refraction in the direction to the pulsar θref, 0 = 110 ms and a distance to the prism zprism ≤ 2 pc.

An assessment of groundwater potential and vulnerability in the Upper Manyame Sub-Catchment of Zimbabwe

NASA Astrophysics Data System (ADS)

Misi, Alfred; Gumindoga, Webster; Hoko, Zvikomborero

2018-06-01

Severe depletion and pollution of groundwater resources are of rising concern in the Upper Manyame Sub-Catchment (UMSC); Zimbabwe's most urbanised sub-catchment. Despite groundwater playing a pivotal role in the provision of potable water in the sub-catchment, it is under serious threat from anthropogenic stressors which include sewage effluents and leachates from landfills, among others. Inadequate scientific knowledge pertaining to the spatio-temporal variability of groundwater storage and vulnerability in the UMSC is further compromising its sustainability. Therefore, comprehensive assessments of UMSC's Groundwater Potential (GP) and vulnerability are crucial for its effective management. This study assessed GP and vulnerability in the UMSC using Geographic Information Systems and Remote Sensing techniques. Groundwater conditioning factors: geology, slope, land-use, drainage density, topographic index, altitude, recharge and rainfall were used to develop GP zones. Validation of the GP map was done by correlating estimated GP with historical borehole yields. An assessment of groundwater vulnerability was done at micro-catchment level (Marimba) using the GOD model; a three parameter Index Overlay Model. Marimba is the most urbanised and has the second highest borehole density. It also exhibits similar landuse characteristics as the UMSC. Furthermore, groundwater quality in Marimba was assessed from 15 sampling sites. Fifteen drinking water parameters were analysed based on the standard methods for Water and Wastewater Examination. The potability of groundwater was then assessed by comparing the measured water quality parameters with the Standards Association of Zimbabwe (SAZ) drinking water standards and/or WHO guidelines for drinking water. Repeated Measures ANOVA and Principal Component Analysis (PCA) were used to assess the spatio-temporal variations in groundwater quality and to identify key parameters, respectively. About 72% (2725.9 km2) of the UMSC was found to be of moderate GP, while 19% and 9% accounted for high and low GP, respectively. Marimba vulnerability status was dominantly moderate (77.3%). Parameters: EC, pH, coliforms, TDS, total hardness, Fe, NH4+ and turbidity exceeded SAZ and/or WHO drinking water limits on most sampling sites with DO, total and faecal coliforms showing significant variations (p < 0.05). Four Principal Components representing 84% of the cumulative variance were extracted; with PC1, PC2, PC3 and PC4 contributing 38%, 19.1%, 14.3% and 12.85%, respectively. PC1 was characterized by pH, TDS, EC and total hardness. PC2's variance was associated with elevated levels of Cl-, Zn and Cu. PC3 had high loadings of total and faecal coliforms, Fl- and turbidity while PC4 was characterized by high loadings of Pb, Fe, ammonia and turbidity. The variation in the nature of the parameters across PCs explains the complexity of pollutants within the micro-catchment. PC2 and PC4 were largely characterized by metallic compounds, suggesting pollution from mineral dissolution into the aquifers e.g. from industrial areas and dumpsites. PC3 indicate the contribution of domestic waste e.g. faecal waste from waste pipe leakages and poorly constructed pit latrines. The findings of this study are useful decision-making tools on groundwater utilisation and groundwater protection.

Changes of Attention during Value-Based Reversal Learning Are Tracked by N2pc and Feedback-Related Negativity

PubMed Central

Oemisch, Mariann; Watson, Marcus R.; Womelsdorf, Thilo; Schubö, Anna

2017-01-01

Previously learned reward values can have a pronounced impact, behaviorally and neurophysiologically, on the allocation of selective attention. All else constant, stimuli previously associated with a high value gain stronger attentional prioritization than stimuli previously associated with a low value. The N2pc, an ERP component indicative of attentional target selection, has been shown to reflect aspects of this prioritization, by changes of mean amplitudes closely corresponding to selective enhancement of high value target processing and suppression of high value distractor processing. What has remained unclear so far is whether the N2pc also reflects the flexible and repeated behavioral adjustments needed in a volatile task environment, in which the values of stimuli are reversed often and unannounced. Using a value-based reversal learning task, we found evidence that the N2pc amplitude flexibly and reversibly tracks value-based choices during the learning of reward associated stimulus colors. Specifically, successful learning of current value-contingencies was associated with reduced N2pc amplitudes, and this effect was more apparent for distractor processing, compared with target processing. In addition, following a value reversal the feedback related negativity(FRN), an ERP component that reflects feedback processing, was amplified and co-occurred with increased N2pc amplitudes in trials following low-value feedback. Importantly, participants that showed the greatest adjustment in N2pc amplitudes based on feedback were also the most efficient learners. These results allow further insight into how changes in attentional prioritization in an uncertain and volatile environment support flexible adjustments of behavior. PMID:29163113

Changes of Attention during Value-Based Reversal Learning Are Tracked by N2pc and Feedback-Related Negativity.

PubMed

Oemisch, Mariann; Watson, Marcus R; Womelsdorf, Thilo; Schubö, Anna

2017-01-01

Previously learned reward values can have a pronounced impact, behaviorally and neurophysiologically, on the allocation of selective attention. All else constant, stimuli previously associated with a high value gain stronger attentional prioritization than stimuli previously associated with a low value. The N2pc, an ERP component indicative of attentional target selection, has been shown to reflect aspects of this prioritization, by changes of mean amplitudes closely corresponding to selective enhancement of high value target processing and suppression of high value distractor processing. What has remained unclear so far is whether the N2pc also reflects the flexible and repeated behavioral adjustments needed in a volatile task environment, in which the values of stimuli are reversed often and unannounced. Using a value-based reversal learning task, we found evidence that the N2pc amplitude flexibly and reversibly tracks value-based choices during the learning of reward associated stimulus colors. Specifically, successful learning of current value-contingencies was associated with reduced N2pc amplitudes, and this effect was more apparent for distractor processing, compared with target processing. In addition, following a value reversal the feedback related negativity(FRN), an ERP component that reflects feedback processing, was amplified and co-occurred with increased N2pc amplitudes in trials following low-value feedback. Importantly, participants that showed the greatest adjustment in N2pc amplitudes based on feedback were also the most efficient learners. These results allow further insight into how changes in attentional prioritization in an uncertain and volatile environment support flexible adjustments of behavior.

On the robustness of EC-PC spike detection method for online neural recording.

PubMed

Zhou, Yin; Wu, Tong; Rastegarnia, Amir; Guan, Cuntai; Keefer, Edward; Yang, Zhi

2014-09-30

Online spike detection is an important step to compress neural data and perform real-time neural information decoding. An unsupervised, automatic, yet robust signal processing is strongly desired, thus it can support a wide range of applications. We have developed a novel spike detection algorithm called "exponential component-polynomial component" (EC-PC) spike detection. We firstly evaluate the robustness of the EC-PC spike detector under different firing rates and SNRs. Secondly, we show that the detection Precision can be quantitatively derived without requiring additional user input parameters. We have realized the algorithm (including training) into a 0.13 μm CMOS chip, where an unsupervised, nonparametric operation has been demonstrated. Both simulated data and real data are used to evaluate the method under different firing rates (FRs), SNRs. The results show that the EC-PC spike detector is the most robust in comparison with some popular detectors. Moreover, the EC-PC detector can track changes in the background noise due to the ability to re-estimate the neural data distribution. Both real and synthesized data have been used for testing the proposed algorithm in comparison with other methods, including the absolute thresholding detector (AT), median absolute deviation detector (MAD), nonlinear energy operator detector (NEO), and continuous wavelet detector (CWD). Comparative testing results reveals that the EP-PC detection algorithm performs better than the other algorithms regardless of recording conditions. The EC-PC spike detector can be considered as an unsupervised and robust online spike detection. It is also suitable for hardware implementation. Copyright © 2014 Elsevier B.V. All rights reserved.

Metal mixtures in urban and rural populations in the US: The Multi-Ethnic Study of Atherosclerosis and the Strong Heart Study.

PubMed

Pang, Yuanjie; Peng, Roger D; Jones, Miranda R; Francesconi, Kevin A; Goessler, Walter; Howard, Barbara V; Umans, Jason G; Best, Lyle G; Guallar, Eliseo; Post, Wendy S; Kaufman, Joel D; Vaidya, Dhananjay; Navas-Acien, Ana

2016-05-01

Natural and anthropogenic sources of metal exposure differ for urban and rural residents. We searched to identify patterns of metal mixtures which could suggest common environmental sources and/or metabolic pathways of different urinary metals, and compared metal-mixtures in two population-based studies from urban/sub-urban and rural/town areas in the US: the Multi-Ethnic Study of Atherosclerosis (MESA) and the Strong Heart Study (SHS). We studied a random sample of 308 White, Black, Chinese-American, and Hispanic participants in MESA (2000-2002) and 277 American Indian participants in SHS (1998-2003). We used principal component analysis (PCA), cluster analysis (CA), and linear discriminant analysis (LDA) to evaluate nine urinary metals (antimony [Sb], arsenic [As], cadmium [Cd], lead [Pb], molybdenum [Mo], selenium [Se], tungsten [W], uranium [U] and zinc [Zn]). For arsenic, we used the sum of inorganic and methylated species (∑As). All nine urinary metals were higher in SHS compared to MESA participants. PCA and CA revealed the same patterns in SHS, suggesting 4 distinct principal components (PC) or clusters (∑As-U-W, Pb-Sb, Cd-Zn, Mo-Se). In MESA, CA showed 2 large clusters (∑As-Mo-Sb-U-W, Cd-Pb-Se-Zn), while PCA showed 4 PCs (Sb-U-W, Pb-Se-Zn, Cd-Mo, ∑As). LDA indicated that ∑As, U, W, and Zn were the most discriminant variables distinguishing MESA and SHS participants. In SHS, the ∑As-U-W cluster and PC might reflect groundwater contamination in rural areas, and the Cd-Zn cluster and PC could reflect common sources from meat products or metabolic interactions. Among the metals assayed, ∑As, U, W and Zn differed the most between MESA and SHS, possibly reflecting disproportionate exposure from drinking water and perhaps food in rural Native communities compared to urban communities around the US. Copyright © 2016 Elsevier Inc. All rights reserved.

Raw material variability of an active pharmaceutical ingredient and its relevance for processability in secondary continuous pharmaceutical manufacturing.

PubMed

Stauffer, F; Vanhoorne, V; Pilcer, G; Chavez, P-F; Rome, S; Schubert, M A; Aerts, L; De Beer, T

2018-06-01

Active Pharmaceutical Ingredients (API) raw material variability is not always thoroughly considered during pharmaceutical process development, mainly due to low quantities of drug substance available. However, synthesis, crystallization routes and production sites evolve during product development and product life cycle leading to changes in physical material attributes which can potentially affect their processability. Recent literature highlights the need for a global approach to understand the link between material synthesis, material variability, process and product quality. The study described in this article aims at explaining the raw material variability of an API using extensive material characterization on a restricted number of representative batches using multivariate data analysis. It is part of a larger investigation trying to link the API drug substance manufacturing process, the resulting physical API raw material attributes and the drug product continuous manufacturing process. Eight API batches produced using different synthetic routes, crystallization, drying, delumping processes and processing equipment were characterized, extensively. Seventeen properties from seven characterization techniques were retained for further analysis using Principal Component Analysis (PCA). Three principal components (PCs) were sufficient to explain 92.9% of the API raw material variability. The first PC was related to crystal length, agglomerate size and fraction, flowability and electrostatic charging. The second PC was driven by the span of the particle size distribution and the agglomerates strength. The third PC was related to surface energy. Additionally, the PCA allowed to summarize the API batch-to-batch variability in only three PCs which can be used in future drug product development studies to quantitatively evaluate the impact of the API raw material variability upon the drug product process. The approach described in this article could be applied to any other compound which is prone to batch-to-batch variability. Copyright © 2018 Elsevier B.V. All rights reserved.

Organic micropollutant removal from wastewater effluent-impacted drinking water sources during bank filtration and artificial recharge.

PubMed

Maeng, Sung Kyu; Ameda, Emmanuel; Sharma, Saroj K; Grützmacher, Gesche; Amy, Gary L

2010-07-01

Natural treatment systems such as bank filtration (BF) and artificial recharge (via an infiltration basin) are a robust barrier for many organic micropollutants (OMPs) and may represent a low-cost alternative compared to advanced drinking water treatment systems. This study analyzes a comprehensive database of OMPs at BF and artificial recharge (AR) sites located near Lake Tegel in Berlin (Germany). The focus of the study was on the derivation of correlations between the removal efficiencies of OMPs and key factors influencing the performance of BF and AR. At the BF site, shallow monitoring wells located close to the Lake Tegel source exhibited oxic conditions followed by prolonged anoxic conditions in deep monitoring wells and a production well. At the AR site, oxic conditions prevailed from the recharge pond along monitoring wells to the production well. Long residence times of up to 4.5 months at the BF site reduced the temperature variation during soil passage between summer and winter. The temperature variations were greater at the AR site as a consequence of shorter residence times. Deep monitoring wells and the production well located at the BF site were under the influence of ambient groundwater and old bank filtrate (up to several years of age). Thus, it is important to account for mixing with native groundwater and other sources (e.g., old bank filtrate) when estimating the performance of BF with respect to removal of OMPs. Principal component analysis (PCA) was used to investigate correlations between OMP removals and hydrogeochemical conditions with spatial and temporal parameters (e.g., well distance, residence time and depth) from both sites. Principal component-1 (PC1) embodied redox conditions (oxidation-reduction potential and dissolved oxygen), and principal component-2 (PC2) embodied degradation potential (e.g., total organic carbon and dissolved organic carbon) with the calcium carbonate dissolution potential (Ca(2+) and HCO(3)(-)) for the BF site. These two PCs explained a total variance of 55% at the BF site. At the AR site, PCA revealed redox conditions (PC1) and degradation potential with temperature (PC2) as principal components, which explained a total variance of 56%. Copyright 2010 Elsevier Ltd. All rights reserved.

Sensibilization of polymer/fullerene photovoltaic cells using Zinc Phtalocyanine studied by combinatorial technique

NASA Astrophysics Data System (ADS)

Godovsky, D.; Chen, L.; Petterson, L.; Inganäs, O.

2000-11-01

The influence of Zinc Phtalocyanine admixture to fullerene layers on top of PTOPT to the photovoltaic cells performance was studied. In order to investigate all the possible combinations of ZnPc and C60 the combinatorial technique was developed consisting in thermal co-evaporation of ZnPc and C60 from two different boats. The significant increase in solar cells photocurrent was observed, coming from ZnPc absorbance bands, especially for the layers containing 1:1 molar ratio of the components.

A data analysis expert system for large established distributed databases

NASA Technical Reports Server (NTRS)

Gnacek, Anne-Marie; An, Y. Kim; Ryan, J. Patrick

1987-01-01

A design for a natural language database interface system, called the Deductively Augmented NASA Management Decision support System (DANMDS), is presented. The DANMDS system components have been chosen on the basis of the following considerations: maximal employment of the existing NASA IBM-PC computers and supporting software; local structuring and storing of external data via the entity-relationship model; a natural easy-to-use error-free database query language; user ability to alter query language vocabulary and data analysis heuristic; and significant artificial intelligence data analysis heuristic techniques that allow the system to become progressively and automatically more useful.

Physiological investigation of C4-phosphoenolpyruvate-carboxylase-introduced rice line shows that sucrose metabolism is involved in the improved drought tolerance.

PubMed

Zhang, Chen; Li, Xia; He, Yafei; Zhang, Jinfei; Yan, Ting; Liu, Xiaolong

2017-06-01

We compared the drought tolerance of wild-type (WT) and transgenic rice plants (PC) over-expressing the maize C 4 PEPC gene, which encodes phosphoenolpyruvate carboxylase (PEPC, EC 4.1.1.31) gene, and evaluated the roles of saccharide and sugar-related enzymes in the drought response. Pot-grown seedlings were subjected to real drought conditions outdoors, and the yield components were compared between PC and untransformed wild-type (WT) plants. The stable yield from PC plants was associated with higher net photosynthetic rate under the real drought treatment. The physiological characters of WT and PC seedlings under a simulated drought treatment (25% (w/v) polyethylene glycol-6000 for 3 h; PEG 6000 treatment) were analyzed in detail for the early response of drought. The relative water content was higher in PC than in WT, and PEPC activity and the C 4 -PEPC transcript level in PC were elevated under the simulated drought conditions. The endogenous saccharide responses also differed between PC and WT under simulated drought stress. The higher sugar decomposition rate in PC than in WT under drought analog stress was related to the increased activities of sucrose phosphate synthase, sucrose synthase, acid invertase, and neutral invertase, increased transcript levels of VIN1, CIN1, NIN1, SUT2, SUT4, and SUT5, and increased activities of superoxide dismutase and peroxidase in the leaves. The greater antioxidant defense capacity of PC and its relationship with saccharide metabolism was one of the reasons for the improved drought tolerance. In conclusion, PEPC effectively alleviated oxidative damage and enhanced the drought tolerance in rice plants, which were more related to the increase of the endogenous saccharide decomposition. These findings show that components of C 4 photosynthesis can be used to increase the yield of rice under drought conditions. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

A principal component meta-analysis on multiple anthropometric traits identifies novel loci for body shape

PubMed Central

Ried, Janina S.; Jeff M., Janina; Chu, Audrey Y.; Bragg-Gresham, Jennifer L.; van Dongen, Jenny; Huffman, Jennifer E.; Ahluwalia, Tarunveer S.; Cadby, Gemma; Eklund, Niina; Eriksson, Joel; Esko, Tõnu; Feitosa, Mary F.; Goel, Anuj; Gorski, Mathias; Hayward, Caroline; Heard-Costa, Nancy L.; Jackson, Anne U.; Jokinen, Eero; Kanoni, Stavroula; Kristiansson, Kati; Kutalik, Zoltán; Lahti, Jari; Luan, Jian'an; Mägi, Reedik; Mahajan, Anubha; Mangino, Massimo; Medina-Gomez, Carolina; Monda, Keri L.; Nolte, Ilja M.; Pérusse, Louis; Prokopenko, Inga; Qi, Lu; Rose, Lynda M.; Salvi, Erika; Smith, Megan T.; Snieder, Harold; Stančáková, Alena; Ju Sung, Yun; Tachmazidou, Ioanna; Teumer, Alexander; Thorleifsson, Gudmar; van der Harst, Pim; Walker, Ryan W.; Wang, Sophie R.; Wild, Sarah H.; Willems, Sara M.; Wong, Andrew; Zhang, Weihua; Albrecht, Eva; Couto Alves, Alexessander; Bakker, Stephan J. L.; Barlassina, Cristina; Bartz, Traci M.; Beilby, John; Bellis, Claire; Bergman, Richard N.; Bergmann, Sven; Blangero, John; Blüher, Matthias; Boerwinkle, Eric; Bonnycastle, Lori L.; Bornstein, Stefan R.; Bruinenberg, Marcel; Campbell, Harry; Chen, Yii-Der Ida; Chiang, Charleston W. K.; Chines, Peter S.; Collins, Francis S; Cucca, Fracensco; Cupples, L Adrienne; D'Avila, Francesca; de Geus, Eco J .C.; Dedoussis, George; Dimitriou, Maria; Döring, Angela; Eriksson, Johan G.; Farmaki, Aliki-Eleni; Farrall, Martin; Ferreira, Teresa; Fischer, Krista; Forouhi, Nita G.; Friedrich, Nele; Gjesing, Anette Prior; Glorioso, Nicola; Graff, Mariaelisa; Grallert, Harald; Grarup, Niels; Gräßler, Jürgen; Grewal, Jagvir; Hamsten, Anders; Harder, Marie Neergaard; Hartman, Catharina A.; Hassinen, Maija; Hastie, Nicholas; Hattersley, Andrew Tym; Havulinna, Aki S.; Heliövaara, Markku; Hillege, Hans; Hofman, Albert; Holmen, Oddgeir; Homuth, Georg; Hottenga, Jouke-Jan; Hui, Jennie; Husemoen, Lise Lotte; Hysi, Pirro G.; Isaacs, Aaron; Ittermann, Till; Jalilzadeh, Shapour; James, Alan L.; Jørgensen, Torben; Jousilahti, Pekka; Jula, Antti; Marie Justesen, Johanne; Justice, Anne E.; Kähönen, Mika; Karaleftheri, Maria; Tee Khaw, Kay; Keinanen-Kiukaanniemi, Sirkka M.; Kinnunen, Leena; Knekt, Paul B.; Koistinen, Heikki A.; Kolcic, Ivana; Kooner, Ishminder K.; Koskinen, Seppo; Kovacs, Peter; Kyriakou, Theodosios; Laitinen, Tomi; Langenberg, Claudia; Lewin, Alexandra M.; Lichtner, Peter; Lindgren, Cecilia M.; Lindström, Jaana; Linneberg, Allan; Lorbeer, Roberto; Lorentzon, Mattias; Luben, Robert; Lyssenko, Valeriya; Männistö, Satu; Manunta, Paolo; Leach, Irene Mateo; McArdle, Wendy L.; Mcknight, Barbara; Mohlke, Karen L.; Mihailov, Evelin; Milani, Lili; Mills, Rebecca; Montasser, May E.; Morris, Andrew P.; Müller, Gabriele; Musk, Arthur W.; Narisu, Narisu; Ong, Ken K.; Oostra, Ben A.; Osmond, Clive; Palotie, Aarno; Pankow, James S.; Paternoster, Lavinia; Penninx, Brenda W.; Pichler, Irene; Pilia, Maria G.; Polašek, Ozren; Pramstaller, Peter P.; Raitakari, Olli T; Rankinen, Tuomo; Rao, D. C.; Rayner, Nigel W.; Ribel-Madsen, Rasmus; Rice, Treva K.; Richards, Marcus; Ridker, Paul M.; Rivadeneira, Fernando; Ryan, Kathy A.; Sanna, Serena; Sarzynski, Mark A.; Scholtens, Salome; Scott, Robert A.; Sebert, Sylvain; Southam, Lorraine; Sparsø, Thomas Hempel; Steinthorsdottir, Valgerdur; Stirrups, Kathleen; Stolk, Ronald P.; Strauch, Konstantin; Stringham, Heather M.; Swertz, Morris A.; Swift, Amy J.; Tönjes, Anke; Tsafantakis, Emmanouil; van der Most, Peter J.; Van Vliet-Ostaptchouk, Jana V.; Vandenput, Liesbeth; Vartiainen, Erkki; Venturini, Cristina; Verweij, Niek; Viikari, Jorma S.; Vitart, Veronique; Vohl, Marie-Claude; Vonk, Judith M.; Waeber, Gérard; Widén, Elisabeth; Willemsen, Gonneke; Wilsgaard, Tom; Winkler, Thomas W.; Wright, Alan F.; Yerges-Armstrong, Laura M.; Hua Zhao, Jing; Carola Zillikens, M.; Boomsma, Dorret I.; Bouchard, Claude; Chambers, John C.; Chasman, Daniel I.; Cusi, Daniele; Gansevoort, Ron T.; Gieger, Christian; Hansen, Torben; Hicks, Andrew A.; Hu, Frank; Hveem, Kristian; Jarvelin, Marjo-Riitta; Kajantie, Eero; Kooner, Jaspal S.; Kuh, Diana; Kuusisto, Johanna; Laakso, Markku; Lakka, Timo A.; Lehtimäki, Terho; Metspalu, Andres; Njølstad, Inger; Ohlsson, Claes; Oldehinkel, Albertine J.; Palmer, Lyle J.; Pedersen, Oluf; Perola, Markus; Peters, Annette; Psaty, Bruce M.; Puolijoki, Hannu; Rauramaa, Rainer; Rudan, Igor; Salomaa, Veikko; Schwarz, Peter E. H.; Shudiner, Alan R.; Smit, Jan H.; Sørensen, Thorkild I. A.; Spector, Timothy D.; Stefansson, Kari; Stumvoll, Michael; Tremblay, Angelo; Tuomilehto, Jaakko; Uitterlinden, André G.; Uusitupa, Matti; Völker, Uwe; Vollenweider, Peter; Wareham, Nicholas J.; Watkins, Hugh; Wilson, James F.; Zeggini, Eleftheria; Abecasis, Goncalo R.; Boehnke, Michael; Borecki, Ingrid B.; Deloukas, Panos; van Duijn, Cornelia M.; Fox, Caroline; Groop, Leif C.; Heid, Iris M.; Hunter, David J.; Kaplan, Robert C.; McCarthy, Mark I.; North, Kari E.; O'Connell, Jeffrey R.; Schlessinger, David; Thorsteinsdottir, Unnur; Strachan, David P.; Frayling, Timothy; Hirschhorn, Joel N.; Müller-Nurasyid, Martina; Loos, Ruth J. F.

2016-01-01

Large consortia have revealed hundreds of genetic loci associated with anthropometric traits, one trait at a time. We examined whether genetic variants affect body shape as a composite phenotype that is represented by a combination of anthropometric traits. We developed an approach that calculates averaged PCs (AvPCs) representing body shape derived from six anthropometric traits (body mass index, height, weight, waist and hip circumference, waist-to-hip ratio). The first four AvPCs explain >99% of the variability, are heritable, and associate with cardiometabolic outcomes. We performed genome-wide association analyses for each body shape composite phenotype across 65 studies and meta-analysed summary statistics. We identify six novel loci: LEMD2 and CD47 for AvPC1, RPS6KA5/C14orf159 and GANAB for AvPC3, and ARL15 and ANP32 for AvPC4. Our findings highlight the value of using multiple traits to define complex phenotypes for discovery, which are not captured by single-trait analyses, and may shed light onto new pathways. PMID:27876822

Hereditary pancreatic cancer: molecular bases and their application in diagnosis and clinical management: a guideline of the TTD group.

PubMed

Segura, P Pérez; Ponce, C Guillén; Ramón Y Cajal, T; Blanch, R Serrano; Aranda, E

2012-08-01

Pancreatic carcinoma (PC) represents the fourth leading cause of cancer death in Spain with a death rate of 2,400 males and 2,000 females per year. Poor outcome related to its silent nature and the lack of reliable secondary prevention measures translate into advanced-stage diagnosis, 75 % of deaths within the first year of diagnosis and 5-year survival rate of <5 %. Family history was first recognized as a risk factor for PC. Further population-based and case-control studies subsequently found that 7.8 % of patients with PC have a family history of the same tumor and individuals with a first-degree relative with PC have a 3.2-fold increased risk of developing PC. Overall, it is estimated that up to 10 % of PC have a familial component. However, known genetic syndromes account for <20 % of the observed familial aggregation of PC. We review the most important aspects in epidemiology, molecular biology and clinical management of familial PC.

Target objects defined by a conjunction of colour and shape can be selected independently and in parallel.

PubMed

Jenkins, Michael; Grubert, Anna; Eimer, Martin

2017-11-01

It is generally assumed that during search for targets defined by a feature conjunction, attention is allocated sequentially to individual objects. We tested this hypothesis by tracking the time course of attentional processing biases with the N2pc component in tasks where observers searched for two targets defined by a colour/shape conjunction. In Experiment 1, two displays presented in rapid succession (100 ms or 10 ms SOA) each contained a target and a colour-matching or shape-matching distractor on opposite sides. Target objects in both displays elicited N2pc components of similar size that overlapped in time when the SOA was 10 ms, suggesting that attention was allocated in parallel to both targets. Analogous results were found in Experiment 2, where targets and partially matching distractors were both accompanied by an object without target-matching features. Colour-matching and shape-matching distractors also elicited N2pc components, and the target N2pc was initially identical to the sum of the two distractor N2pcs, suggesting that the initial phase of attentional object selection was guided independently by feature templates for target colour and shape. Beyond 230 ms after display onset, the target N2pc became superadditive, indicating that attentional selection processes now started to be sensitive to the presence of feature conjunctions. Results show that independent attentional selection processes can be activated in parallel by two target objects in situations where these objects are defined by a feature conjunction.

Resolved Structure of the Arp 220 Nuclei at λ ≈ 3 mm

NASA Astrophysics Data System (ADS)

Sakamoto, Kazushi; Aalto, Susanne; Barcos-Muñoz, Loreto; Costagliola, Francesco; Evans, Aaron S.; Harada, Nanase; Martín, Sergio; Wiedner, Martina; Wilner, David

2017-11-01

We analyze the 3 mm emission of the ultraluminous infrared galaxy Arp 220 for the spatially resolved structure and the spectral properties of the merger nuclei. ALMA archival data at ˜0.″05 resolution are used for extensive visibility fitting and deep imaging of the continuum emission. The data are fitted well by two concentric components for each nucleus, such as two Gaussians or one Gaussian plus one exponential disk. The larger components in the individual nuclei are similar in shape and extent, ˜100-150 pc, to the centimeter wave emission due to supernovae. They are therefore identified with the known starburst nuclear disks. The smaller components in both nuclei have about a few 10 pc sizes and peak brightness temperatures ({T}{{b}}) more than twice higher than those in previous single-Gaussian fitting. They correspond to the dust emission that we find centrally concentrated in both nuclei by subtracting the plasma emission measured at 33 GHz. The dust emission in the western nucleus is found to have a peak {T}{{b}}≈ 530 K and an FWHM of about 20 pc. This component is estimated to have a bolometric luminosity on the order of {10}12.5 {L}⊙ and a 20 pc scale luminosity surface density {10}15.5 {{L}}⊙ {{{k}}{{p}}{{c}}}-2. A luminous active galactic nucleus is a plausible energy source for these high values while other explanations remain to be explored. Our continuum image also reveals a third structural component of the western nucleus—a pair of faint spurs perpendicular to the disk major axis. We attribute it to a bipolar outflow from the highly inclined (I≈ 60^\\circ ) western nuclear disk.

Relative effectiveness of kinetic analysis vs single point readings for classifying environmental samples based on community-level physiological profiles (CLPP)

NASA Technical Reports Server (NTRS)

Garland, J. L.; Mills, A. L.; Young, J. S.

2001-01-01

The relative effectiveness of average-well-color-development-normalized single-point absorbance readings (AWCD) vs the kinetic parameters mu(m), lambda, A, and integral (AREA) of the modified Gompertz equation fit to the color development curve resulting from reduction of a redox sensitive dye from microbial respiration of 95 separate sole carbon sources in microplate wells was compared for a dilution series of rhizosphere samples from hydroponically grown wheat and potato ranging in inoculum densities of 1 x 10(4)-4 x 10(6) cells ml-1. Patterns generated with each parameter were analyzed using principal component analysis (PCA) and discriminant function analysis (DFA) to test relative resolving power. Samples of equivalent cell density (undiluted samples) were correctly classified by rhizosphere type for all parameters based on DFA analysis of the first five PC scores. Analysis of undiluted and 1:4 diluted samples resulted in misclassification of at least two of the wheat samples for all parameters except the AWCD normalized (0.50 abs. units) data, and analysis of undiluted, 1:4, and 1:16 diluted samples resulted in misclassification for all parameter types. Ordination of samples along the first principal component (PC) was correlated to inoculum density in analyses performed on all of the kinetic parameters, but no such influence was seen for AWCD-derived results. The carbon sources responsible for classification differed among the variable types with the exception of AREA and A, which were strongly correlated. These results indicate that the use of kinetic parameters for pattern analysis in CLPP may provide some additional information, but only if the influence of inoculum density is carefully considered. c2001 Elsevier Science Ltd. All rights reserved.

From cow to cheese: genetic parameters of the flavour fingerprint of cheese investigated by direct-injection mass spectrometry (PTR-ToF-MS).

PubMed

Bergamaschi, Matteo; Cecchinato, Alessio; Biasioli, Franco; Gasperi, Flavia; Martin, Bruno; Bittante, Giovanni

2016-11-16

Volatile organic compounds determine important quality traits in cheese. The aim of this work was to infer genetic parameters of the profile of volatile compounds in cheese as revealed by direct-injection mass spectrometry of the headspace gas from model cheeses that were produced from milk samples from individual cows. A total of 1075 model cheeses were produced using raw whole-milk samples that were collected from individual Brown Swiss cows. Single spectrometry peaks and a combination of these peaks obtained by principal component analysis (PCA) were analysed. Using a Bayesian approach, we estimated genetic parameters for 240 individual spectrometry peaks and for the first ten principal components (PC) extracted from them. Our results show that there is some genetic variability in the volatile compound fingerprint of these model cheeses. Most peaks were characterized by a substantial heritability and for about one quarter of the peaks, heritability (up to 21.6%) was higher than that of the best PC. Intra-herd heritability of the PC ranged from 3.6 to 10.2% and was similar to heritabilities estimated for milk fat, specific fatty acids, somatic cell count and some coagulation parameters in the same population. We also calculated phenotypic correlations between PC (around zero as expected), the corresponding genetic correlations (from -0.79 to 0.86) and correlations between herds and sampling-processing dates (from -0.88 to 0.66), which confirmed that there is a relationship between cheese flavour and the dairy system in which cows are reared. This work reveals the existence of a link between the cow's genetic background and the profile of volatile compounds in cheese. Analysis of the relationships between the volatile organic compound (VOC) content and the sensory characteristics of cheese as perceived by the consumer, and of the genetic basis of these relationships could generate new knowledge that would open up the possibility of controlling and improving the sensory properties of cheese through genetic selection of cows. More detailed investigations are necessary to connect VOC with the sensory properties of cheese and gain a better understanding of the significance of these new phenotypes.

Characterising the VHE diffuse emission in the central 200 parsecs of our Galaxy with H.E.S.S.

NASA Astrophysics Data System (ADS)

H.E.S.S. Collaboration; Abdalla, H.; Abramowski, A.; Aharonian, F.; Ait Benkhali, F.; Akhperjanian, A. G.; Andersson, T.; Angüner, E. O.; Arakawa, M.; Arrieta, M.; Aubert, P.; Backes, M.; Balzer, A.; Barnard, M.; Becherini, Y.; Becker Tjus, J.; Berge, D.; Bernhard, S.; Bernlöhr, K.; Blackwell, R.; Böttcher, M.; Boisson, C.; Bolmont, J.; Bonnefoy, S.; Bordas, P.; Bregeon, J.; Brun, F.; Brun, P.; Bryan, M.; Büchele, M.; Bulik, T.; Capasso, M.; Carr, J.; Casanova, S.; Cerruti, M.; Chakraborty, N.; Chaves, R. C. G.; Chen, A.; Chevalier, J.; Coffaro, M.; Colafrancesco, S.; Cologna, G.; Condon, B.; Conrad, J.; Cui, Y.; Davids, I. D.; Decock, J.; Degrange, B.; Deil, C.; Devin, J.; deWilt, P.; Dirson, L.; Djannati-Ataï, A.; Domainko, W.; Donath, A.; Drury, L. O.'C.; Dutson, K.; Dyks, J.; Edwards, T.; Egberts, K.; Eger, P.; Ernenwein, J.-P.; Eschbach, S.; Farnier, C.; Fegan, S.; Fernandes, M. V.; Fiasson, A.; Fontaine, G.; Förster, A.; Funk, S.; Füßling, M.; Gabici, S.; Gallant, Y. A.; Garrigoux, T.; Giavitto, G.; Giebels, B.; Glicenstein, J. F.; Gottschall, D.; Goyal, A.; Grondin, M.-H.; Hahn, J.; Haupt, M.; Hawkes, J.; Heinzelmann, G.; Henri, G.; Hermann, G.; Hinton, J. A.; Hofmann, W.; Hoischen, C.; Holch, T. L.; Holler, M.; Horns, D.; Ivascenko, A.; Iwasaki, H.; Jacholkowska, A.; Jamrozy, M.; Janiak, M.; Jankowsky, D.; Jankowsky, F.; Jingo, M.; Jogler, T.; Jouvin, L.; Jung-Richardt, I.; Kastendieck, M. A.; Katarzyński, K.; Katsuragawa, M.; Katz, U.; Kerszberg, D.; Khangulyan, D.; Khélifi, B.; King, J.; Klepser, S.; Klochkov, D.; Kluźniak, W.; Kolitzus, D.; Komin, Nu.; Kosack, K.; Krakau, S.; Kraus, M.; Krüger, P. P.; Laffon, H.; Lamanna, G.; Lau, J.; Lees, J.-P.; Lefaucheur, J.; Lefranc, V.; Lemière, A.; Lemoine-Goumard, M.; Lenain, J.-P.; Leser, E.; Lohse, T.; Lorentz, M.; Liu, R.; López-Coto, R.; Lypova, I.; Marandon, V.; Marcowith, A.; Mariaud, C.; Marx, R.; Maurin, G.; Maxted, N.; Mayer, M.; Meintjes, P. J.; Meyer, M.; Mitchell, A. M. W.; Moderski, R.; Mohamed, M.; Mohrmann, L.; Morå, K.; Moulin, E.; Murach, T.; Nakashima, S.; de Naurois, M.; Niederwanger, F.; Niemiec, J.; Oakes, L.; O'Brien, P.; Odaka, H.; Ohm, S.; Ostrowski, M.; Oya, I.; Padovani, M.; Panter, M.; Parsons, R. D.; Pekeur, N. W.; Pelletier, G.; Perennes, C.; Petrucci, P.-O.; Peyaud, B.; Piel, Q.; Pita, S.; Poon, H.; Prokhorov, D.; Prokoph, H.; Pühlhofer, G.; Punch, M.; Quirrenbach, A.; Raab, S.; Rauth, R.; Reimer, A.; Reimer, O.; Renaud, M.; de los Reyes, R.; Richter, S.; Rieger, F.; Romoli, C.; Rowell, G.; Rudak, B.; Rulten, C. B.; Sahakian, V.; Saito, S.; Salek, D.; Sanchez, D. A.; Santangelo, A.; Sasaki, M.; Schlickeiser, R.; Schüssler, F.; Schulz, A.; Schwanke, U.; Schwemmer, S.; Seglar-Arroyo, M.; Settimo, M.; Seyffert, A. S.; Shafi, N.; Shilon, I.; Simoni, R.; Sol, H.; Spanier, F.; Spengler, G.; Spies, F.; Stawarz, Ł.; Steenkamp, R.; Stegmann, C.; Stycz, K.; Sushch, I.; Takahashi, T.; Tavernet, J.-P.; Tavernier, T.; Taylor, A. M.; Terrier, R.; Tibaldo, L.; Tiziani, D.; Tluczykont, M.; Trichard, C.; Tsuji, N.; Tuffs, R.; Uchiyama, Y.; van der Walt, D. J.; van Eldik, C.; van Rensburg, C.; van Soelen, B.; Vasileiadis, G.; Veh, J.; Venter, C.; Viana, A.; Vincent, P.; Vink, J.; Voisin, F.; Völk, H. J.; Vuillaume, T.; Wadiasingh, Z.; Wagner, S. J.; Wagner, P.; Wagner, R. M.; White, R.; Wierzcholska, A.; Willmann, P.; Wörnlein, A.; Wouters, D.; Yang, R.; Zaborov, D.; Zacharias, M.; Zanin, R.; Zdziarski, A. A.; Zech, A.; Zefi, F.; Ziegler, A.; Żywucka, N.

2018-04-01

The diffuse very high-energy (VHE; >100 GeV) γ-ray emission observed in the central 200 pc of the Milky Way by H.E.S.S. was found to follow dense matter distribution in the central molecular zone (CMZ) up to a longitudinal distance of about 130 pc to the Galactic centre (GC), where the flux rapidly decreases. This was initially interpreted as the result of a burst-like injection of energetic particles 104 yr ago, but a recent more sensitive H.E.S.S. analysis revealed that the cosmic-ray (CR) density profile drops with the distance to the centre, making data compatible with a steady cosmic PeVatron at the GC. In this paper, we extend this analysis to obtain, for the first time, a detailed characterisation of the correlation with matter and to search for additional features and individual γ-ray sources in the inner 200 pc. Taking advantage of 250 h of H.E.S.S. data and improved analysis techniques, we perform a detailed morphology study of the diffuse VHE emission observed from the GC ridge and reconstruct its total spectrum. To test the various contributions to the total γ-ray emission, we used an iterative 2D maximum-likelihood approach that allows us to build a phenomenological model of the emission by summing a number of different spatial components. We show that the emission correlated with dense matter covers the full CMZ and that its flux is about half the total diffuse emission flux. We also detect some emission at higher latitude that is likely produced by hadronic collisions of CRs in less dense regions of the GC interstellar medium. We detect an additional emission component centred on the GC and extending over about 15 pc that is consistent with the existence of a strong CR density gradient and confirms the presence of a CR accelerator at the very centre of our Galaxy. We show that the spectrum of full ridge diffuse emission is compatible with that previously derived from the central regions, suggesting that a single population of particles fills the entire CMZ. Finally, we report the discovery of a VHE γ-ray source near the GC radio arc and argue that it is produced by the pulsar wind nebula candidate G0.13-0.11.

Poynting vector measurements of electromagnetic ion cyclotron waves in the plasmasphere

NASA Technical Reports Server (NTRS)

Labelle, J.; Treumann, R. A.

1992-01-01

Results are presented from an analysis of the June 6, 1985 Pc 2 measurements for which E, B, and delta-N were all analyzed. The event occurred in the duskside overlap region between the plasmaspheric bulge and the ion ring current. Results of the Poynting vector analysis of the R and L mode components show both of them to be characterized by northward Poynting vector, indicating energy flux away from the equator. The value of the Poynting vector was found to be about 3 microW/sq m.

Platelet Distribution Width to Platelet Count Ratio as an Index of Severity of Illness.

PubMed

Purbiya, Pragati; Golwala, Zainab Mohammedi; Manchanda, Ayush; Sreenivas, V; Puliyel, Jacob M

2018-01-01

To prospectively validate association between the ratio of platelet distribution width (PDW)/platelet count (PCT) and pediatric intensive care unit (PICU) mortality. The study was done in the pediatric intensive care unit (PICU). Platelet indices in the first sample taken after admission were used. In this case control analysis, cases were the patients who died in PICU and the survivors served as controls. Consecutive 209 eligible patients over a period of 15 mo from January 2014 through March 2015 were included. Exposure was PDW/PC above 0.07. Of them 174 survived and 35 died. The mean PDW for survivors was 16.77 (±0.92) and for those who died it was 17.33 (±1.03) (p 0.0015). Mean platelet count (PC) for survivors was 3,46,000 (±1,64,700) and for those who died it was 1,75,800 (±1,61,500) (p < 0.001). PDW/PC for survivors was 0.12 (±0.46) and for those who died it was 0.336 (±0.53) (p 0.0014). Using the cut-off of 0.07 for PDW/PC described by Golwala et al., 77.14% above the cut-off died, compared to 22.85% below that cut-off. The odds ratio (OR) for death was 10.6 (95% CI: 4.48 to 25.12). The area under the receiver operating curve (ROC) curve for PDW/PC ratio was 0.81. The ratio of PDW/PC, higher than 0.07 in the first sample after admission can be considered as an independent predictor of mortality with sensitivity and specificity of 77.1% and 77.5%, respectively. It may be a useful component for inclusion in composite scores for predicting mortality.

Cultural Adaptation and Psychometric Evaluation of the Spanish Version of the Nursing Outcome "Pain Control" in Primary Care Patients with Chronic Pain.

PubMed

Bellido-Vallejo, José Carlos; Pancorbo-Hidalgo, Pedro Luis

2017-10-01

The control of chronic pain is a major challenge for patients and health care professionals. To culturally adapt the Nursing Outcomes Classification outcome "Pain control" (PC) to the Spanish health care setting and to analyze its psychometric properties and sensitivity to change. A study of three stages was designed: (1) Translation and cultural adaptation by translation-back-translation method, (2) content validation by a group of experts, and (3) observational-longitudinal study in patients with chronic pain. Patient sampling was nonprobabilistic, and participants completed forms and questionnaires and responded to a question on pain. Statistical analysis included descriptive analysis, content validity index (for global PC and each indicator), principal component analysis, Spearman's test, Cronbach's α, Cohen's κ coefficient, and Wilcoxon range test. The new Spanish version of "Pain control" was semantically equivalent to the original, with a mean content validity index of 0.96. The clinical study included 88 patients with long-term pain, and the mean (standard deviation) interval between assessments (baseline and final) was 29.33 (8.05) days. Thirteen indicators were organized into two components. There was divergent but not convergent validity with the Change Pain Scale and Brief Pain Inventory. Between-observer agreement was κ = 0.48 and internal consistency was α = 0.85. No differences were found between mean baseline and final scores. The Spanish version of "Pain control," culturally adapted and structured in two components (13 indicators), is useful to assess and monitor pain control in patients with chronic pain. Copyright © 2017 American Society for Pain Management Nursing. Published by Elsevier Inc. All rights reserved.

GAC: Gene Associations with Clinical, a web based application.

PubMed

Zhang, Xinyan; Rupji, Manali; Kowalski, Jeanne

2017-01-01

We present GAC, a shiny R based tool for interactive visualization of clinical associations based on high-dimensional data. The tool provides a web-based suite to perform supervised principal component analysis (SuperPC), an approach that uses both high-dimensional data, such as gene expression, combined with clinical data to infer clinical associations. We extended the approach to address binary outcomes, in addition to continuous and time-to-event data in our package, thereby increasing the use and flexibility of SuperPC.  Additionally, the tool provides an interactive visualization for summarizing results based on a forest plot for both binary and time-to-event data.  In summary, the GAC suite of tools provide a one stop shop for conducting statistical analysis to identify and visualize the association between a clinical outcome of interest and high-dimensional data types, such as genomic data. Our GAC package has been implemented in R and is available via http://shinygispa.winship.emory.edu/GAC/. The developmental repository is available at https://github.com/manalirupji/GAC.

Rapid discrimination of the causal agents of urinary tract infection using ToF-SIMS with chemometric cluster analysis

NASA Astrophysics Data System (ADS)

Fletcher, John S.; Henderson, Alexander; Jarvis, Roger M.; Lockyer, Nicholas P.; Vickerman, John C.; Goodacre, Royston

2006-07-01

Advances in time of flight secondary ion mass spectrometry (ToF-SIMS) have enabled this technique to become a powerful tool for the analysis of biological samples. Such samples are often very complex and as a result full interpretation of the acquired data can be extremely difficult. To simplify the interpretation of these information rich data, the use of chemometric techniques is becoming widespread in the ToF-SIMS community. Here we discuss the application of principal components-discriminant function analysis (PC-DFA) to the separation and classification of a number of bacterial samples that are known to be major causal agents of urinary tract infection. A large data set has been generated using three biological replicates of each isolate and three machine replicates were acquired from each biological replicate. Ordination plots generated using the PC-DFA are presented demonstrating strain level discrimination of the bacteria. The results are discussed in terms of biological differences between certain species and with reference to FT-IR, Raman spectroscopy and pyrolysis mass spectrometric studies of similar samples.

Impact of peer counselling breast-feeding support programme protocols on any and exclusive breast-feeding discontinuation in low-income women.

PubMed

Rozga, Mary R; Kerver, Jean M; Olson, Beth H

2015-02-01

Peer counselling (PC) programmes have been shown to improve breast-feeding outcomes in populations at risk for early discontinuation. Our objective was to describe associations between programme components (individual and combinations) and breast-feeding outcomes (duration and exclusivity) in a PC programme for low-income women. Secondary analysis of programme data. Multivariable-adjusted Cox proportional hazards models were used to examine associations between type and quantity of peer contacts with breast-feeding outcomes. Types of contacts included in-person (hospital or home), phone or other (e.g. mail, text). Quantities of contacts were considered 'optimal' if they adhered to standard programme guidelines. Programme data collected from 2005 to 2011 in Michigan's Breastfeeding Initiative Peer Counseling Program. Low-income (n 5886) women enrolled prenatally. For each additional home, phone and other PC contact there was a significant reduction in the hazard of discontinuing any breast-feeding by 6 months (hazard ratio (HR)=0·90 (95% CI 0·88, 0·92); HR=0·89 (95% CI 0·87, 0·90); and HR=0·93 (95% CI 0·90, 0·96), respectively) and exclusive breast-feeding by 3 months (HR=0·92 (95% CI 0·89, 0·95); HR=0·90 (95% CI 0·88, 0·91); and HR=0·93 (95% CI 0·89, 0·97), respectively). Participants receiving greater than optimal in-person and less than optimal phone contacts had a reduced hazard of any and exclusive breast-feeding discontinuation compared with those who were considered to have optimum quantities of contacts (HR=0·17 (95% CI 0·14, 0·20) and HR=0·28 (95% CI 0·23, 0·35), respectively). Specific components of a large PC programme appeared to have an appreciable impact on breast-feeding outcomes. In-person contacts were essential to improving breast-feeding outcomes, but defining optimal programme components is complex.

The potential of statistical shape modelling for geometric morphometric analysis of human teeth in archaeological research

PubMed Central

Fernee, Christianne; Browne, Martin; Zakrzewski, Sonia

2017-01-01

This paper introduces statistical shape modelling (SSM) for use in osteoarchaeology research. SSM is a full field, multi-material analytical technique, and is presented as a supplementary geometric morphometric (GM) tool. Lower mandibular canines from two archaeological populations and one modern population were sampled, digitised using micro-CT, aligned, registered to a baseline and statistically modelled using principal component analysis (PCA). Sample material properties were incorporated as a binary enamel/dentin parameter. Results were assessed qualitatively and quantitatively using anatomical landmarks. Finally, the technique’s application was demonstrated for inter-sample comparison through analysis of the principal component (PC) weights. It was found that SSM could provide high detail qualitative and quantitative insight with respect to archaeological inter- and intra-sample variability. This technique has value for archaeological, biomechanical and forensic applications including identification, finite element analysis (FEA) and reconstruction from partial datasets. PMID:29216199

Jungle Honey Enhances Immune Function and Antitumor Activity

PubMed Central

Fukuda, Miki; Kobayashi, Kengo; Hirono, Yuriko; Miyagawa, Mayuko; Ishida, Takahiro; Ejiogu, Emenike C.; Sawai, Masaharu; Pinkerton, Kent E.; Takeuchi, Minoru

2011-01-01

Jungle honey (JH) is collected from timber and blossom by wild honey bees that live in the tropical forest of Nigeria. JH is used as a traditional medicine for colds, skin inflammation and burn wounds as well as general health care. However, the effects of JH on immune functions are not clearly known. Therefore, we investigated the effects of JH on immune functions and antitumor activity in mice. Female C57BL/6 mice were injected with JH (1 mg/mouse/day, seven times intra-peritoneal). After seven injections, peritoneal cells (PC) were obtained. Antitumor activity was assessed by growth of Lewis Lung Carcinoma/2 (LL/2) cells. PC numbers were increased in JH-injected mice compared to control mice. In Dot Plot analysis by FACS, a new cell population appeared in JH-injected mice. The percent of Gr-1 surface antigen and the intensity of Gr-1 antigen expression of PC were increased in JH-injected mice. The new cell population was neutrophils. JH possessed chemotactic activity for neutrophils. Tumor incidence and weight were decreased in JH-injected mice. The ratio of reactive oxygen species (ROS) producing cells was increased in JH-injected mice. The effective component in JH was fractionized by gel filtration using HPLC and had an approximate molecular weight (MW) of 261. These results suggest that neutrophils induced by JH possess potent antitumor activity mediated by ROS and the effective immune component of JH is substrate of MW 261. PMID:19141489

Revealing anti-inflammation mechanism of water-extract and oil of forsythiae fructus on carrageenan-Induced edema rats by serum metabolomics.

PubMed

Yuan, An; Gong, Lihong; Luo, Lin; Dang, Jue; Gong, Xiaohong; Zhao, Mengjie; Li, Yan; Li, Yunxia; Peng, Cheng

2017-11-01

Forsythiae Fructus is an important Chinese medicine which shows a significant effect against inflammation. This study aimed to investigate the preventive anti-inflammation mechanism of Forsythiae Fructus by serum metabolomics strategy and compare the difference of the metabolism pathways between Forsythia extract and Forsythia oil in rat. Four groups (control group, model group, Forsythia extract group and Forsythia oil group) were orally administered 10mL/kg 0.5% Tween 80 solution, 10mL/kg 0.5% Tween 80 solution, 5g/kg Forsythia extract and 0.48mL/kg Forsythia oil respectively. 30min after drug administration, rat acute inflammation was induced by subcutaneous injection of carrageenan in the right paw in model group, Forsythia extract group and Forsythia oil group. After being administered Forsythia extract and Forsythia oil, the percentage of rat paw edema was significantly decreased (P<0.05) compared with model group. Metabolomics based on UPLC-Q-TOF-MS/MS was used to analyze the collected serum sample. Multivariate analysis was established for metabolomics analysis. According to Principal component analysis (PCA) and partial least squares-discriminate analysis (PLS-DA) results, four groups were clearly separated. And thirteen alterative biomarkers were identified in the serum, namely PC (19:0/0:0), LysoPC (20:0), LysoPC (20:1), LysoPC (17:0), Sphingosine, Linoleic acid, 3R-hydroxy-butanoic acid (3-HB), 2-hydroxyhexadecanoic acid, Lactic acid, L-Threonine, L-Leucine, Maleic acid, Adipic acid. The change of biomarkers suggested that Forsythia extract affected Linoleic acid metabolism, Valine, leucine and isoleucine biosynthesis, Sphingolipid metabolism and Glycerophospholipid metabolism. Forsythia oil affected Sphingolipid metabolism and Glycerophospholipid metabolism. It indicated that Forsythia extract and Forsythia oil both showed significant preventive anti-inflammatory effect through acting on different metabolism pathways. Moreover, efficacy mechanism of Forsythiae Fructus could recover metabolites disturb in the body through affecting particular drug targets associated with the inflammatory pathway. Copyright © 2017. Published by Elsevier Masson SAS.

Principal component directed partial least squares analysis for combining nuclear magnetic resonance and mass spectrometry data in metabolomics: application to the detection of breast cancer.

PubMed

Gu, Haiwei; Pan, Zhengzheng; Xi, Bowei; Asiago, Vincent; Musselman, Brian; Raftery, Daniel

2011-02-07

Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) are the two most commonly used analytical tools in metabolomics, and their complementary nature makes the combination particularly attractive. A combined analytical approach can improve the potential for providing reliable methods to detect metabolic profile alterations in biofluids or tissues caused by disease, toxicity, etc. In this paper, (1)H NMR spectroscopy and direct analysis in real time (DART)-MS were used for the metabolomics analysis of serum samples from breast cancer patients and healthy controls. Principal component analysis (PCA) of the NMR data showed that the first principal component (PC1) scores could be used to separate cancer from normal samples. However, no such obvious clustering could be observed in the PCA score plot of DART-MS data, even though DART-MS can provide a rich and informative metabolic profile. Using a modified multivariate statistical approach, the DART-MS data were then reevaluated by orthogonal signal correction (OSC) pretreated partial least squares (PLS), in which the Y matrix in the regression was set to the PC1 score values from the NMR data analysis. This approach, and a similar one using the first latent variable from PLS-DA of the NMR data resulted in a significant improvement of the separation between the disease samples and normals, and a metabolic profile related to breast cancer could be extracted from DART-MS. The new approach allows the disease classification to be expressed on a continuum as opposed to a binary scale and thus better represents the disease and healthy classifications. An improved metabolic profile obtained by combining MS and NMR by this approach may be useful to achieve more accurate disease detection and gain more insight regarding disease mechanisms and biology. Copyright © 2010 Elsevier B.V. All rights reserved.

Statistical study of ULF wave occurrence in the dayside magnetosphere

NASA Technical Reports Server (NTRS)

Cao, M.; Mcpherron, R. L.; Russell, C. T.

1994-01-01

Ultralow-frequency (ULF) waves are observed almost everywhere in the dayside magnetosphere. The mechanism by which these waves are generated and transformed in the dayside magnetosphere is still not understood. Here we report a statistical study of these waves based on magnetic field data from the International Sun-Earth Explorer 1 (ISEE 1) spacecraft. Data from the first traversal of the spacecraft through the entire dayside magnetosphere have been examined to determine the spatial distribution of wave occurrence. Successive 20-min segments of data were transformed to a field-aligned coordinate system. The parallel component was detrended and all three components of the field spectrally analyzed. Wave occurrence was defined by the presence of significant peaks in the power spectra. Wave events were categorized by three wave frequency bands: Pc 3 with T approximately 10-45 s; Pc 4 with T approximately 45-150 s; the short-period part of the Pc 5 wave band with T approximately 150-324 s. Properties of the spectral peaks were then entered into a data base. The data base was next sorted to determine the spatial occurrence pattern for the waves. Our results show that Pc 3 waves most frequently occur just outside synchronous orbit and are approximately centered on local noon. Pc 4 waves have a similar distribution with its peak further out. Pc 5 waves have high occurrence rate at the two flanks of the magnetosphere. Peaks in spectra obtained near the magnetopause are less clearly defined than those deeper in the magnetosphere.

High-resolution responses of sedimentary δ15N to climate change in the southern California for the past 2000 years

NASA Astrophysics Data System (ADS)

Wang, Y.; Hendy, I. L.; Thunell, R.

2017-12-01

The short duration of instrumental records limits our understanding of nitrogen loss to denitrification on interannual to centennial time scales. Bulk sediment δ15N is widely applied as a proxy for water column denitrification in oxygen minimum zones (OMZ). Lying within the California OMZ, Santa Barbara Basin (SBB) provides an ideal location for producing a high-resolution δ15N record for denitrification reconstruction. Here we present a high-resolution ( 1-2 y) 2000-year record of δ15N from SPR0901-03KC (34°16.99'N, 120°2.408'W; 586 m depth). Grey flood layer sediments are associated with abrupt decreases of 0.9 to 2.5 ‰ in the δ15N record. After removal of flood-affected samples from the record, δ15N varies from 6.8 to 8.7 ‰ with an average of 7.7 ‰. After 1800 AD δ15N experienced a sustained decrease to its minimum at the core top. Comparison with the principal components (PCs) of scanning X-ray fluorescence (XRF) elemental counts allow for further investigation of factors driving δ15N variations. The first PC (PC1) of scanning XRF elemental records contains high loadings for lithogenic sediment components while the second PC (PC2) has high loadings for biogenic components. The δ15N record is positively correlated with PC2 (r=0.2521, p<0.01) throughout the core while negatively correlated with PC1 relationship (r=-0.2596, p<0.01) between AD 1000-1800. Peaks of δ15N and PC2 (high primary productivity) coincide with intensified upwelling intervals supported by high anchovy scale counts, and bloom-forming diatoms (Rhizosolenia spp.) and silicoflagellates (D. speculum) from a nearby core. These upwelling intervals coincide with low PC1 (low river runoff). The coherent variability appears to indicate an atmospheric influence on the marine environment through the relative intensity of North Pacific High (NPH). Enhanced NPH induces stronger coastal upwelling with associated upward advection of δ15N-enriched subsurface water and higher primary productivity in the surface ocean. Subsurface waters are fed by California Undercurrent originated from the north Eastern Tropical Pacific, where active water column denitrification occurs generating high δ15N values.

DigiSeis—A software component for digitizing seismic signals using the PC sound card

NASA Astrophysics Data System (ADS)

Amin Khan, Khalid; Akhter, Gulraiz; Ahmad, Zulfiqar

2012-06-01

An innovative software-based approach to develop an inexpensive experimental seismic recorder is presented. This approach requires no hardware as the built-in PC sound card is used for digitization of seismic signals. DigiSeis, an ActiveX component is developed to capture the digitized seismic signals from the sound card and deliver them to applications for processing and display. A seismic recorder application software SeisWave is developed over this component, which provides real-time monitoring and display of seismic events picked by a pair of external geophones. This recorder can be used as an educational aid for conducting seismic experiments. It can also be connected with suitable seismic sensors to record earthquakes. The software application and the ActiveX component are available for download. This component can be used to develop seismic recording applications according to user specific requirements.

Early and late selection processes have separable influences on the neural substrates of attention.

PubMed

Drisdelle, Brandi Lee; Jolicoeur, Pierre

2018-05-01

To improve our understanding of the mechanisms of target selection, we examined how the spatial separation of salient items and their similarity to a pre-defined target interact using lateralised electrophysiological correlates of visual spatial attention (N2pc component) and visual short-term memory (VSTM; SPCN component). Using these features of target selection, we sought to expand on previous work proposing a model of early and late selection, where the N2pc is suggested to reflect the selection probability of visual stimuli (Aubin and Jolicoeur, 2016). The authors suggested that early-selection processes could be enhanced when items are adjacent. In the present work, the stimuli were short oriented lines, all of which were grey except for two that were blue and hence salient. A decrease in N2pc amplitude with decreasing spatial separation between salient items was observed. The N2pc increased in amplitude with increasing similarity of salient distractors to the target template, but only in target-absent trials. There was no interaction between these two factors, suggesting that separable attentional mechanisms influenced the N2pc. The findings suggest that selection is initially based on easily-distinguished attributes (i.e., both blue items) followed by a later identification-based process (if necessary), which depends on feature similarity to a target template. For the SPCN component, the results were in line with previous work: for target-present trials, an increase in similarity of salient distractors was associated with an increase in SPCN amplitude, suggesting more information was maintained in VSTM. In sum, results suggest there is a need for further inspection of salient distractors when they are similar to the target, increasing the need for focal attention, demonstrated by an increase in N2pc amplitude, followed by a higher probability of transfer to VSTM, demonstrated by an increase in SPCN amplitude. Copyright © 2018 Elsevier B.V. All rights reserved.

Unifying measures of gene function and evolution.

PubMed

Wolf, Yuri I; Carmel, Liran; Koonin, Eugene V

2006-06-22

Recent genome analyses revealed intriguing correlations between variables characterizing the functioning of a gene, such as expression level (EL), connectivity of genetic and protein-protein interaction networks, and knockout effect, and variables describing gene evolution, such as sequence evolution rate (ER) and propensity for gene loss. Typically, variables within each of these classes are positively correlated, e.g. products of highly expressed genes also have a propensity to be involved in many protein-protein interactions, whereas variables between classes are negatively correlated, e.g. highly expressed genes, on average, evolve slower than weakly expressed genes. Here, we describe principal component (PC) analysis of seven genome-related variables and propose biological interpretations for the first three PCs. The first PC reflects a gene's 'importance', or the 'status' of a gene in the genomic community, with positive contributions from knockout lethality, EL, number of protein-protein interaction partners and the number of paralogues, and negative contributions from sequence ER and gene loss propensity. The next two PCs define a plane that seems to reflect the functional and evolutionary plasticity of a gene. Specifically, PC2 can be interpreted as a gene's 'adaptability' whereby genes with high adaptability readily duplicate, have many genetic interaction partners and tend to be non-essential. PC3 also might reflect the role of a gene in organismal adaptation albeit with a negative rather than a positive contribution of genetic interactions; we provisionally designate this PC 'reactivity'. The interpretation of PC2 and PC3 as measures of a gene's plasticity is compatible with the observation that genes with high values of these PCs tend to be expressed in a condition- or tissue-specific manner. Functional classes of genes substantially vary in status, adaptability and reactivity, with the highest status characteristic of the translation system and cytoskeletal proteins, highest adaptability seen in cellular processes and signalling genes, and top reactivity characteristic of metabolic enzymes.

Temporal patterns of the trunk muscles remain altered in a low back-injured population despite subjective reports of recovery.

PubMed

Moreside, Janice M; Quirk, D Adam; Hubley-Kozey, Cheryl L

2014-04-01

To compare temporal activation patterns from 24 abdominal and lumbar muscles between healthy subjects and those who reported recovery from recent low back injury (LBI). Cross-sectional comparative study. University neuromuscular function laboratory. Healthy adult volunteers (N=81; 30 LBI, 51 asymptomatic subjects). Trunk muscle electromyographic activity was collected during 2 difficulty levels of a supine trunk stability test aimed at challenging lumbopelvic control. Principal component (PC) analysis was applied to determine differences in temporal and/or amplitude electromyographic patterns between groups. Mixed-model analyses of variance were performed on PC scores that explained more than 89% of the variance (α=.05). Four PCs explained 89% and 96% of the variance for the abdominal and back muscles, respectively, with both muscle groups having similar shapes in the first 3 PCs. Significant interactions or group main effects were found for all PC scores except PC4 for the back extensors. Overall activation amplitudes for both the abdominal and back muscles (PC1 scores) were significantly (P<.05) higher for the LBI group, with both abdominal and back muscles of the LBI group demonstrating an increased response to the leg-loading phase (PC2 scores) compared with the asymptomatic group. Differences were also found between groups in their preparatory activity (PC3 scores), with the LBI group having a higher early relative amplitude of abdominal and back extensor activity. Despite perceived readiness to return to work and low pain scores, muscle activation patterns remained altered in this LBI group, including reduced synergistic coactivation and increased overall amplitudes as well as greater relative amplitude differences during specific phases of the movement. Electromyographic measures provide objective information to help guide therapy and may assist with determining the level of healing and return-to-work readiness after an LBI. Copyright © 2014 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Land use impact on soil quality in eastern Himalayan region of India.

PubMed

Singh, A K; Bordoloi, L J; Kumar, Manoj; Hazarika, S; Parmar, Brajendra

2014-04-01

Quantitative assessment of soil quality is required to determine the sustainability of land uses in terms of environmental quality and plant productivity. Our objective was to identify the most appropriate soil quality indicators and to evaluate the impact of six most prevalent land use types (natural forestland, cultivated lowland, cultivated upland terrace, shifting cultivation, plantation land, and grassland) on soil quality in eastern Himalayan region of India. We collected 120 soil samples (20 cm depth) and analyzed them for 29 physical, chemical, and biological soil attributes. For selection of soil quality indicators, principal component analysis (PCA) was performed on the measured attributes, which provided four principal components (PC) with eigenvalues >1 and explaining at least 5% of the variance in dataset. The four PCs together explained 92.6% of the total variance. Based on rotated factor loadings of soil attributes, selected indicators were: soil organic carbon (SOC) from PC-1, exchangeable Al from PC-2, silt content from PC-3, and available P and Mn from PC-4. Indicators were transformed into scores (linear scoring method) and soil quality index (SQI) was determined, on a scale of 0-1, using the weighting factors obtained from PCA. SQI rating was the highest for the least-disturbed sites, i.e., natural forestland (0.93) and grassland (0.87), and the lowest for the most intensively cultivated site, i.e., cultivated upland terrace (0.44). Ratings for the other land uses were shifting cultivation (0.60) > cultivated low land (0.57) > plantation land (0.54). Overall contribution (in percent) of the indicators in determination of SQI was in the order: SOC (58%) > exch. Al (17.1%) > available P (8.9%) > available Mn (8.2%) > silt content (7.8%). Results of this study suggest SOC and exch. Al as the two most powerful indicators of soil quality in study area. Thus, organic C and soil acidity management holds the key to improve soil quality under many exploitatively cultivated land use systems in eastern Himalayan region of India.

Anatomy of the AGN in NGC 5548. VI. Long-term variability of the warm absorber

NASA Astrophysics Data System (ADS)

Ebrero, J.; Kaastra, J. S.; Kriss, G. A.; Di Gesu, L.; Costantini, E.; Mehdipour, M.; Bianchi, S.; Cappi, M.; Boissay, R.; Branduardi-Raymont, G.; Petrucci, P.-O.; Ponti, G.; Pozo Núñez, F.; Seta, H.; Steenbrugge, K. C.; Whewell, M.

2016-03-01

Context. We observed the archetypal Seyfert 1 galaxy NGC 5548 in 2013-2014 in the context of an extensive multiwavelength campaign involving several satellites, which revealed the source to be in an extraordinary state of persistent heavy obscuration. Aims: We re-analyzed the archival grating spectra obtained by XMM-Newton and Chandra between 1999 and 2007 in order to characterize the classic warm absorber (WA) using consistent models and up-to-date photoionization codes and atomic physics databases and to construct a baseline model that can be used as a template for the physical state of the WA in the 2013 observations. Methods: We used the latest version of the photoionization code CLOUDY and the SPEX fitting package to model the X-ray grating spectra of the different archival observations of NGC 5548. Results: We find that the WA in NGC 5548 is composed of six distinct ionization phases outflowing in four kinematic regimes. The components seem to be in the form of a stratified wind with several layers intersected by our line of sight. Assuming that the changes in the WA are solely due to ionization or recombination processes in response to variations in the ionizing flux among the different observations, we are able to estimate lower limits on the density of the absorbing gas, finding that the farthest components are less dense and have a lower ionization. These limits are used to put stringent upper limits on the distance of the WA components from the central ionizing source, with the lowest ionization phases at several pc distances (<50, <20, and <5 pc, respectively), while the intermediately ionized components lie at pc-scale distances from the center (<3.6 and <2.2 pc, respectively). The highest ionization component is located at ~0.6 pc or closer to the AGN central engine. The mass outflow rate summed over all WA components is ~0.3 M⊙ yr-1, about six times the nominal accretion rate of the source. The total kinetic luminosity injected into the surrounding medium is a small fraction (~0.03%) of the bolometric luminosity of the source. After adding the contribution of the UV absorbers, this value augments to ~0.2% of the bolometric luminosity, well below the minimum amount of energy required by current feedback models to regulate galaxy evolution.

Whole genome population genetics analysis of Sudanese goats identifies regions harboring genes associated with major traits.

PubMed

Rahmatalla, Siham A; Arends, Danny; Reissmann, Monika; Said Ahmed, Ammar; Wimmers, Klaus; Reyer, Henry; Brockmann, Gudrun A

2017-10-23

Sudan is endowed with a variety of indigenous goat breeds which are used for meat and milk production and which are well adapted to the local environment. The aim of the present study was to determine the genetic diversity and relationship within and between the four main Sudanese breeds of Nubian, Desert, Taggar and Nilotic goats. Using the 50 K SNP chip, 24 animals of each breed were genotyped. More than 96% of high quality SNPs were polymorphic with an average minor allele frequency of 0.3. In all breeds, no significant difference between observed (0.4) and expected (0.4) heterozygosity was found and the inbreeding coefficients (F IS ) did not differ from zero. F st coefficients for the genetic distance between breeds also did not significantly deviate from zero. In addition, the analysis of molecular variance revealed that 93% of the total variance in the examined population can be explained by differences among individuals, while only 7% result from differences between the breeds. These findings provide evidence for high genetic diversity and little inbreeding within breeds on one hand, and low diversity between breeds on the other hand. Further examinations using Nei's genetic distance and STRUCTURE analysis clustered Taggar goats distinct from the other breeds. In a principal component (PC) analysis, PC1 could separate Taggar, Nilotic and a mix of Nubian and Desert goats into three groups. The SNPs that contributed strongly to PC1 showed high F st values in Taggar goat versus the other goat breeds. PCA allowed us to identify target genomic regions which contain genes known to influence growth, development, bone formation and the immune system. The information on the genetic variability and diversity in this study confirmed that Taggar goat is genetically different from the other goat breeds in Sudan. The SNPs identified by the first principal components show high F st values in Taggar goat and allowed to identify candidate genes which can be used in the development of breed selection programs to improve local breeds and find genetic factors contributing to the adaptation to harsh environments.

Spirituality as an ethical challenge in Indian palliative care: A systematic review.

PubMed

Gielen, Joris; Bhatnagar, Sushma; Chaturvedi, Santosh K

2016-10-01

Spiritual care is recognized as an essential component of palliative care (PC). However, patients' experience of spirituality is heavily context dependent. In addition, Western definitions and findings regarding spirituality may not be applicable to patients of non-Western origin, such as Indian PC patients. Given the particular sociocultural, religious, and economic conditions in which PC programs in India operate, we decided to undertake a systematic review of the literature on spirituality among Indian PC patients. We intended to assess how spirituality has been interpreted and operationalized in studies of this population, to determine which dimensions of spirituality are important for patients, and to analyze its ethical implications. In January of 2015, we searched five databases (ATLA, CINAHL, EMBASE, PsycINFO, and PubMed) using a combination of controlled and noncontrolled vocabulary. A content analysis of all selected reports was undertaken to assess the interpretation and dimensions of spirituality. Data extraction from empirical studies was done using a data-extraction sheet. A total of 39 empirical studies (12 qualitative, 21 quantitative, and 6 mixed-methods) and 18 others (10 reviews, 4 opinion articles, and 4 case studies) were retrieved. To date, no systematic review on spirituality in Indian PC has been published. Spirituality was the main focus of only six empirical studies. The content analysis revealed three dimensions of spirituality: (1) the relational dimension, (2) the existential dimension, and (3) the values dimension. Religion is prominent in all these dimensions. Patients' experiences of spirituality are determined by the specifically Indian context, which leads to particular ethical issues. Since spiritual well-being greatly impacts quality of life, and because of the substantial presence of people of Indian origin living outside the subcontinent, the findings of our review have international relevance. Moreover, our review illustrates that spirituality can be an ethical challenge and that more ethical reflection on provision of spiritual care is needed.

The Three-Dimensional Morphological Effects of Captivity

PubMed Central

Hartstone-Rose, Adam; Selvey, Hannah; Villari, Joseph R.; Atwell, Madeline; Schmidt, Tammy

2014-01-01

Many captive animals are fed diets that are drastically different in mechanical properties than their wild diet. Most captive pantherines are fed a nutritionally supplemented diet consisting almost entirely of ground meat. While many zoos supplement this diet with bones, the fact remains that large captive felids are fed diets that require substantially less masticatory effort than those of their wild counterparts. The osteological effects of this dietary difference have not been fully evaluated. To this end, we compared linear measurements and 3D geometric morphometric landmarks of captive and wild lions and tigers. Using Principal Component (PC) analysis of the linear measurements, not only were the sexes and species statistically distinct, but so too was the population clearly divisible in terms of captivity status. The 3D analysis supported these findings: although the most influential variable in the sample (PC1, 21.5% of the variation) separates the two species, the second most influential contributor (PC2) to the overall skull shape is driven not by the sex differences in these highly dimorphic species, but rather by their captivity status. In fact, captivity status drives nearly twice as much of the 3D variation as sexual dimorphism (14.8% vs. 8.0% for PC2 vs. PC3). Thus the shape is influenced nearly twice as much by whether the animal was captive or wild than by whether it was male or female. If a causal relationship can be demonstrated between dietary mechanical properties and morphology, people who oversee the diets of captive carnivores should consider modifying these diets to account for not only nutritional but also the mechanical properties of a carcass-based diet as well. In addition to the husbandry implications, our analyses show the ways in which captive specimens are different than their wild counterparts – findings that have implications for morphologists when considering anatomical samples. PMID:25409498

Relationship between changes in crystalline lens shape and axial elongation in young children.

PubMed

Ishii, Kotaro; Yamanari, Masahiro; Iwata, Hiroyoshi; Yasuno, Yoshiaki; Oshika, Tetsuro

2013-01-28

To evaluate the relationship between changes in crystalline lens shape and axial elongation during growth in young children. Twenty-five patients (age: 1 month to 6 years) who underwent head magnetic resonance imaging (MRI) were included in the analysis. Refractive error was measured with an autorefractor in 22 patients. Crystalline lens dimensions and axial length (AL) were obtained from the MR images. The radius of curvature and asphericity of the crystalline lens were measured using reconstructed MR images. Crystalline lens shape and eyeball shape were numerically expressed by elliptic Fourier descriptors (EFDs) on the basis of MR images. The contours of the crystalline lens and eyeball were evaluated by principal component analysis of the EFDs. The average anterior and posterior radii of curvature were 6.21 mm (range across ages from 3.89-7.26 mm) and -4.81 mm (range across ages from -2.93 to -5.67 mm). These were closely correlated with age by logarithmic analysis. The first principal component (PC1) of the crystalline lens explained 89.15% of the total variance in lens shape, and it was also significantly correlated with age (Pearson's r = 0.648, P < 0.001) and AL (r = 0.847, P < 0.001). In the multiple linear regression analysis in which AL was a dependent variable, only the PC1 of the crystalline lens was associated with AL. Axial elongation is related to the entire contour of the crystalline lens. This result shows that axial elongation progresses in parallel to change in the crystalline lens shape.

The Sub-Parsec Radio Jet in NGC 4151

NASA Astrophysics Data System (ADS)

Roy, A. L.; Ulvestad, J. S.; Colbert, E. J. M.; Wilson, A. S.

1997-05-01

We are surveying eight nearby Seyfert galaxies (four Sy1s and four Sy2s) that have compact radio cores, using the VLBA. We are interested in parsec-scale morphology and low-frequency absorption effects, and so are observing three frequencies per galaxy (1.6, 4.8, and 8.4 or 15 GHz) to get spectral-index diagnostics. VLBA imaging of NGC 4151 at 1.6 and 4.8 GHz reveals the following results: * NGC 4151 contains a remarkable chain of knots strongly resembling a jet, emerging in component C4 and extending for 0.8 pc. * The jet propagates NNE for 0.5 pc then turns sharply eastward and becomes the known MERLIN jet. * Curiously, by propagating northwards at first, the jet initially makes an angle of 60d with the axis of the ionization cones seen by HST. This breaks the cylindrical symmetry required by orientation unification, and may indicate that the BLR and torus have a symmetry axis unrelated to the axis of the NLR. * The nucleus looks to be in the C4 eastern component from our radio continuum morphology and from limited radio spectral information, rather than being in the C4 western component as Mundell et al. (1995, MNRAS, 272, 355) infer from HI absorbing columns. * The components located at 6 and 30 pc from the C4 eastern component have apparent speeds relative to that component of < 0.1 c to 0.2 c.

Primary Care-Mental Health Integration in the Veterans Affairs Health System: Program Characteristics and Performance.

PubMed

Cornwell, Brittany L; Brockmann, Laurie M; Lasky, Elaine C; Mach, Jennifer; McCarthy, John F

2018-06-01

The Veterans Health Administration (VHA) has achieved substantial national implementation of primary care-mental health integration (PC-MHI) services. However, little is known regarding program characteristics, variation in characteristics across settings, or associations between program fidelity and performance. This study identified core elements of PC-MHI services and evaluated their associations with program characteristics and performance. A principal-components analysis (PCA) of reports from 349 sites identified factors associated with PC-MHI fidelity. Analyses assessed the correlation among factors and between each factor and facility type (medical center or community-based outpatient clinic), primary care population size, and performance indicators (receipt of PC-MHI services, same-day access to mental health and primary care services, and extended duration of services). PCA identified seven factors: core implementation, care management (CM) assessments and supervision, CM supervision receipt, colocated collaborative care (CCC) by prescribing providers, CCC by behavioral health providers, participation in patient aligned care teams (PACTs) for special populations, and treatment of complex mental health conditions. Sites serving larger populations had greater core implementation scores. Medical centers and sites serving larger populations had greater scores for CCC by prescribing providers, CM assessments and supervision, and participation in PACTs. Greater core implementation scores were associated with greater same-day access. Sites with greater scores for CM assessments and supervision had lower scores for treatment of complex conditions. Outpatient clinics and sites serving smaller populations experienced challenges in integrated care implementation. To enhance same-day access, VHA should continue to prioritize PC-MHI implementation. Providing brief, problem-focused care may enhance CM implementation.

Association Between Pituitary-Adrenal Axis Dominance Over the Renin-Angiotensin-Aldosterone System and Hypertension.

PubMed

Daimon, Makoto; Kamba, Aya; Murakami, Hiroshi; Takahashi, Kazuhisa; Otaka, Hideyuki; Makita, Koushi; Yanagimachi, Miyuki; Terui, Ken; Kageyama, Kazunori; Nigawara, Takeshi; Sawada, Kaori; Takahashi, Ippei; Nakaji, Shigeyuki

2016-03-01

The hypothalamus-pituitary-adrenal (HPA) axis and the renin-angiotensin aldosterone system (RAAS) are well known to be associated with hypertension. However, the extent of the effects is not yet well elucidated in general conditions. To separately determine the effect of the HPA axis and the RAAS on hypertension in a general population. A population-based study of 859 Japanese individuals enrolled in the 2014 Iwaki study and without hypertension or steroid treatment (age, 50.2 ± 14.7 years). Hypertension prevalence, plasma concentration of aldosterone, ACTH, cortisol, and plasma renin activity. Principal component (PC) analysis using these four hormones identified two PCs (PC1 and PC2), which represent levels of these hormones as a whole, and dominance between the HPA axis (ACTH and cortisol) and the RAAS (plasma renin activity and plasma concentration of aldosterone), respectively. Association between these PCs and hypertension was significant (PC1, high vs low, odds ratio [OR], 1.48; 95% confidence interval [CI], 1.09-2.02; and PC2, HPA axis vs RAAS dominancy, OR, 2.08; and 95% CI, 1.51-2.85). However, association between the hormone levels as a whole and hypertension became insignificant after adjustment for multiple factors including these PCs together. However, association between the HPA axis dominance and hypertension remained significant even after the adjustment (the HPA axis vs the RAAS, OR, 1.73; 95% CI, 1.20-2.48). The HPA axis dominance over the RAAS is significantly associated with hypertension in a Japanese population.

The intrinsic cause of color fading in sliced cooked cured beef during chilled storage.

PubMed

Ma, Jing; Yu, Chensha; Guo, Juanjuan; Wu, Mengting; Xu, Yunqiang; Yi, Hongchao; Sun, Weiqing

2017-10-01

The relationship between color change and other physical and chemical characteristics of sliced cooked cured beef (SCCB) during chilled storage were investigated using principal components analysis (PCA) to determine the color fading causes. Samples were prepared and stored at 8°C for up to 35 days in a vacuum package to simulate a supermarket storage environment; related indicators were measured periodically every week. The results showed that the first PC explained 59.82% of the total variation, and the second explained 22.28%. PC1 was a concentrated reflection of color changes of SCCB during storage and PC2 was an environment factor causing the change of color. The change in apparent redness is mainly caused by redox reaction of the nitroso hemochromogen (NH) (eigenvectors of a*, C and NH in PC1 were all the maximum value of 0.28); a* was correlated with NH (0.96), free sulfhydryls (0.98), carbonyl derivatives (-0.95) formed during protein oxidation, and malondialdehyde (-0.98) and dienes (-0.92) formed by lipid oxidation. Color fading was significantly correlated with oxidizing and reducing power, existing forms of nitrogen and with the pH of the meat matrix. Changes in the internal environment of the sample initially influenced L* and b* values, and subsequently a*. © 2017 Japanese Society of Animal Science.

Analysis of Triplet Exciton Loss Pathways in PTB7:PC71BM Bulk Heterojunction Solar Cells

NASA Astrophysics Data System (ADS)

Kraus, Hannes; Heiber, Michael C.; Väth, Stefan; Kern, Julia; Deibel, Carsten; Sperlich, Andreas; Dyakonov, Vladimir

2016-07-01

A strategy for increasing the conversion efficiency of organic photovoltaics has been to increase the VOC by tuning the energy levels of donor and acceptor components. However, this opens up a new loss pathway from an interfacial charge transfer state to a triplet exciton (TE) state called electron back transfer (EBT), which is detrimental to device performance. To test this hypothesis, we study triplet formation in the high performing PTB7:PC71BM blend system and determine the impact of the morphology-optimizing additive 1,8-diiodoctane (DIO). Using photoluminescence and spin-sensitive optically detected magnetic resonance (ODMR) measurements at low temperature, we find that TEs form on PC71BM via intersystem crossing from singlet excitons and on PTB7 via EBT mechanism. For DIO blends with smaller fullerene domains, an increased density of PTB7 TEs is observed. The EBT process is found to be significant only at very low temperature. At 300 K, no triplets are detected via ODMR, and electrically detected magnetic resonance on optimized solar cells indicates that TEs are only present on the fullerenes. We conclude that in PTB7:PC71BM devices, TE formation via EBT is impacted by fullerene domain size at low temperature, but at room temperature, EBT does not represent a dominant loss pathway.

Key elements of optimal treatment decision-making for surgeons and older patients with colorectal or pancreatic cancer: A qualitative study.

PubMed

Geessink, Noralie H; Schoon, Yvonne; van Herk, Hanneke C P; van Goor, Harry; Olde Rikkert, Marcel G M

2017-03-01

To identify key elements of optimal treatment decision-making for surgeons and older patients with colorectal (CRC) or pancreatic cancer (PC). Six focus groups with different participants were performed: three with older CRC/PC patients and relatives, and three with physicians. Supplementary in-depth interviews were conducted in another seven patients. Framework analysis was used to identify key elements in decision-making. 23 physicians, 22 patients and 14 relatives participated. Three interacting components were revealed: preconditions, content and facilitators of decision-making. To provide optimal information about treatments' impact on an older patient's daily life, physicians should obtain an overall picture and take into account patients' frailty. Depending on patients' preferences and capacities, dividing decision-making into more sessions will be helpful and simultaneously emphasize patients' own responsibility. GPs may have a valuable contribution because of their background knowledge and supportive role. Stakeholders identified several crucial elements in the complex surgical decision-making of older CRC/PC patients. Structured qualitative research may also be of great help in optimizing other treatment directed decision-making processes. Surgeons should be trained in examining preconditions and useful facilitators in decision-making in older CRC/PC patients to optimize its content and to improve the quality of shared care. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Finite Element Analysis of IPS Empress II Ceramic Bridge Reinforced by Zirconia Bar

PubMed Central

Kermanshah, H.; Bitaraf, T.; Geramy, A.

2012-01-01

Objective: The aim of this study was to determine the effect of trenched zirconia bar on the von Mises stress distribution of IPS –Empress II core ceramics. Materials and Methods: The three-dimensional model including a three-unit bridge from the second premolar to the second molar was designed. The model was reinforced with zirconia bar (ZB), zirconia bar with vertical trench (VZB) and zirconia bar with horizontal trench (HZB) (cross sections of these bars were circular). The model without zirconia bar was designed as the control. The bridges were loaded by 200 N and 500 N on the occlusal surface at the middle of the pontic component and von Mises stresses were evaluated along a defined path. Results: In the connector area, von Mises stress in MPa were approximately identical in the specimens with ZB (at molar connector (MC): 4.75 and at premolar connector (PC): 6.40) and without ZB (MC: 5.50, PC: 6.68), and considerable differences were not recognized. Whereas, Von-Mises stress (MPa) in the specimens with horizontal trenched Zirconia bar (HZB) (MC: 3.91, PC: 2.44) and Vertical trenched Zirconia bar (VZB) (MC: 2.53, PC: 2.56) was decreased considerably. Conclusion: Embeded trenched zirconia bar could reinforce IPS-Empress II at the connector area which is a main failure region in all ceramic fixed partial dentures. PMID:23323181

Finite Element Analysis of IPS Empress II Ceramic Bridge Reinforced by Zirconia Bar.

PubMed

Kermanshah, H; Bitaraf, T; Geramy, A

2012-01-01

The aim of this study was to determine the effect of trenched zirconia bar on the von Mises stress distribution of IPS -Empress II core ceramics. The three-dimensional model including a three-unit bridge from the second premolar to the second molar was designed. The model was reinforced with zirconia bar (ZB), zirconia bar with vertical trench (VZB) and zirconia bar with horizontal trench (HZB) (cross sections of these bars were circular). The model without zirconia bar was designed as the control. The bridges were loaded by 200 N and 500 N on the occlusal surface at the middle of the pontic component and von Mises stresses were evaluated along a defined path. IN THE CONNECTOR AREA, VON MISES STRESS IN MPA WERE APPROXIMATELY IDENTICAL IN THE SPECIMENS WITH ZB (AT MOLAR CONNECTOR (MC): 4.75 and at premolar connector (PC): 6.40) and without ZB (MC: 5.50, PC: 6.68), and considerable differences were not recognized. Whereas, Von-Mises stress (MPa) in the specimens with horizontal trenched Zirconia bar (HZB) (MC: 3.91, PC: 2.44) and Vertical trenched Zirconia bar (VZB) (MC: 2.53, PC: 2.56) was decreased considerably. Embeded trenched zirconia bar could reinforce IPS-Empress II at the connector area which is a main failure region in all ceramic fixed partial dentures.

Effect of photodegradation and biodegradation on the concentration and composition of dissolved organic matter in diverse waterbodies

NASA Astrophysics Data System (ADS)

Manalilkada Sasidharan, S.; Dash, P.; Singh, S.; Lu, Y.

2017-12-01

The objective of this research was to quantify the effects of photodegradation and biodegradation on the dissolved organic matter (DOM) concentration and composition in five distinct waterbodies with diverse types of watershed land use and land cover in the southeastern United States. The water bodies included an agricultural pond, a lake in a predominantly forested watershed, a man-made reservoir, an estuary, and a bay. Two sets of samples were prepared from these water bodies by dispensing filtered water samples to unfiltered samples in 10:1 ratio. The first set was kept in the sunlight during the day (12 hours), and colored dissolved organic matter (CDOM) absorption and fluorescence were measured periodically over a 30-day period for examining the effects of combined photo- and biodegradation. The second set of samples was kept in the dark for examining the effects of biodegradation alone, and CDOM absorption and fluorescence were measured at the same time as the sunlight-exposed samples. Subsequently, spectrometric results in tandem with multivariate statistical analysis were used to interpret the lability vs. composition of DOM. Parallel factor analysis (PARAFAC) revealed the presence of four DOM components (C1-C4). C1 and C4 were microbial tryptophan-like, labile lighter components, while C2 and C3 were terrestrial humic like or fulvic acid type, larger aromatic refractory components. The principal component analysis (PCA) also revealed two distinct groups of DOM - C1 and C4 vs. C2 and C3. The negative PC1 loadings of C2, C3, HIX, a254 and SUVA indicated humic-like or fulvic-like structurally complex refractory aromatic DOM originated from higher plants in forested areas. C1, C4, SR, FI and BI had positive PC1 loadings, which indicated structurally simpler labile DOM were derived from agricultural areas or microbial activity. There was a decrease in dissolved organic carbon (DOC) due to combined photo- and biodegradation, and transformation of components C2, C3 into components C1, C4 was at a much faster rate than only biodegradation. This observation suggests that the presence of sunlight facilitated the degradation of larger, recalcitrant, terrestrial humic-like compounds into smaller, labile microbial components.

Scanning tunneling microscopy investigation of copper phthalocyanine and truxenone derivative binary superstructures on graphite.

PubMed

Liu, Jia; Wang, Dong; Wang, Jie-Yu; Pei, Jian; Wan, Li-Jun

2011-02-01

The binary self-assembly of copper phthalocyanine (CuPc) and 2,3,7,8,12,13-hexahexyloxy-truxenone (TrO23) at the solid/liquid interface of highly oriented pyrolytic graphite (HOPG) was investigated by using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS). Pseduohexagonal and linear patterned superstructures of CuPc are obtained by co-adsorbing with TrO23. High-resolution STM images reveal the structural details of the arrangement of TrO23 and CuPc in the binary assembly structures. The molecular ratio between CuPc and TrO23 in the adlayer can be modulated by the CuPc concentration in liquid phase. The electronic properties of CuPc and TrO23 in the co-adsorbed self-assembly are investigated by STS. The results presented here are helpful to the design and fabrication of multi-component functional molecular nanostructures. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Encapsulation of antioxidant phenolic compounds extracted from spent coffee grounds by freeze-drying and spray-drying using different coating materials.

PubMed

Ballesteros, Lina F; Ramirez, Monica J; Orrego, Carlos E; Teixeira, José A; Mussatto, Solange I

2017-12-15

Freeze-drying and spray-drying techniques were evaluated for encapsulation of phenolic compounds (PC) extracted from spent coffee grounds. Additionally, the use of maltodextrin, gum arabic and a mixture of these components (ratio 1:1) as wall material to retain the PC and preserve their antioxidant activity was also assessed. The contents of PC and flavonoids (FLA), as well as the antioxidant activity of the encapsulated samples were determined in order to verify the efficiency of each studied condition. Additional analyses for characterization of the samples were also performed. Both the technique and the coating material greatly influenced the encapsulation of antioxidant PC. The best results were achieved when PC were encapsulated by freeze-drying using maltodextrin as wall material. Under these conditions, the amount of PC and FLA retained in the encapsulated sample corresponded to 62% and 73%, respectively, and 73-86% of the antioxidant activity present in the original extract was preserved. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cocoa bean quality assessment by using hyperspectral images and fuzzy logic techniques

NASA Astrophysics Data System (ADS)

Soto, Juan; Granda, Guillermo; Prieto, Flavio; Ipanaque, William; Machacuay, Jorge

2015-04-01

Nowadays, cocoa bean exportation from Piura-Peru is having a positive international market response due to their inherent high quality. Nevertheless, when using subjective techniques for quality assessment, such as the cut test, a wastefulness of grains is generated, additional to a restriction in the selection as well as improvement approaches in earlier stages for optimizing the quality. Thus, in an attempt to standardize the internal features analyzed by the cut test, for instance, crack formation and internal color changes during the fermentation, this research is submitted as an approach which aims to make use of hyperspectral images, with the purpose of having a quick and accurate analysis. Hyperspectral cube size was reduced by using Principal Component Analysis (PCA). The image generated by principal component PC1 provides enough information to clearly distinguish the internal cracks of the cocoa bean, since the zones where these cracks are, have a negative correlation with PC1. The features taken were processed through a fuzzy block, which is able to describe the cocoa bean quality. Three membership functions were defined in the output: unfermented, partly fermented and well fermented, by using trapezoidal-shaped and triangular-shaped functions. A total of twelve rules were propounded. Furthermore, the bisector method was chosen for the defuzzification. Begin the abstract two lines below author names and addresses.

Near-infrared Raman spectroscopy for estimating biochemical changes associated with different pathological conditions of cervix

NASA Astrophysics Data System (ADS)

Daniel, Amuthachelvi; Prakasarao, Aruna; Ganesan, Singaravelu

2018-02-01

The molecular level changes associated with oncogenesis precede the morphological changes in cells and tissues. Hence molecular level diagnosis would promote early diagnosis of the disease. Raman spectroscopy is capable of providing specific spectral signature of various biomolecules present in the cells and tissues under various pathological conditions. The aim of this work is to develop a non-linear multi-class statistical methodology for discrimination of normal, neoplastic and malignant cells/tissues. The tissues were classified as normal, pre-malignant and malignant by employing Principal Component Analysis followed by Artificial Neural Network (PC-ANN). The overall accuracy achieved was 99%. Further, to get an insight into the quantitative biochemical composition of the normal, neoplastic and malignant tissues, a linear combination of the major biochemicals by non-negative least squares technique was fit to the measured Raman spectra of the tissues. This technique confirms the changes in the major biomolecules such as lipids, nucleic acids, actin, glycogen and collagen associated with the different pathological conditions. To study the efficacy of this technique in comparison with histopathology, we have utilized Principal Component followed by Linear Discriminant Analysis (PC-LDA) to discriminate the well differentiated, moderately differentiated and poorly differentiated squamous cell carcinoma with an accuracy of 94.0%. And the results demonstrated that Raman spectroscopy has the potential to complement the good old technique of histopathology.

A new ULF wave analysis for Seismo-Electromagnetics using CPMN/MAGDAS data

NASA Astrophysics Data System (ADS)

Yumoto, K.; Ikemoto, S.; Cardinal, M. G.; Hayakawa, M.; Hattori, K.; Liu, J. Y.; Saroso, S.; Ruhimat, M.; Husni, M.; Widarto, D.; Ramos, E.; McNamara, D.; Otadoy, R. E.; Yumul, G.; Ebora, R.; Servando, N.

The Space Environment Research Center of Kyushu University has obtained geomagnetic data in the Circum-pan Pacific Magnetometer Network (CPMN) region for over 10 years, and has recently deployed a new real-time Magnetic Data Acquisition System (MAGDAS) in the CPMN region and an FM-CW radar network along the 210° magnetic meridian (MM) for space weather research and applications. This project intends to get the MAGDAS network fully operational and provide data for studies on space and lithosphere weather. In connection with this project, we propose a new ultra-low frequency (ULF) wave analysis method to study ULF anomalies associated with large earthquakes using magnetic data. From a case study of the 1999/05/12 Kushiro earthquake with magnitude M = 6.4, we found a peculiar increase of H-component power ratio AR/ AM of Pc 3 magnetic pulsations a few weeks before the earthquake, where AR is the power obtained at Rikubetsu station ( r = 61 km) near the epicenter and AM is the power obtained at a remote reference station, Moshiri ( r = 205 km). It is also found that the H-component power ratio AD/ AY of Pc 3 increased three times just a few weeks before the earthquake and after one week decreased to the normal level, where AD is one-day power at Rikubetsu station and AY is the one-year-average power.

Carcass characteristics of Criollo Cordobés kid goats under an extensive management system: effects of gender and liveweight at slaughter.

PubMed

Bonvillani, A; Peña, F; de Gea, G; Gómez, G; Petryna, A; Perea, J

2010-11-01

Thirty males and thirty females suckling Criollo Cordobes kid goats of approximately 60 to 90 days old were used in this study. Kids were slaughtered at <9.5 kg, >9.5<11 kg and >11 kg of empty body weight. The carcasses showed a medium conformation index. The meat and fat colour, and internal subcutaneous fatness were mainly scored as either pink, cream, slight and low-medium, respectively. The shoulder comprised 66-67% muscle, 24-27% bone and 4-6% fat. The slaughter weight had significant effects on the following characteristics: dressing yield, carcass measures and indices, subcutaneous fatness, meat colour, and muscle/fat ratio. The effect of gender was smaller: the female kids presented the highest fatness values for all parameters studied. Also, these animals displayed the lowest percentage of joints of extra class. The meat of female kids contained significantly less muscle and bone and a higher proportion of fat than that of male kids. The allometric analysis displays an early growth in the carcass measures and indices, fifth quarter, joints and bone proportion of shoulder. Internal and dissectible fats show a late growth. Principal component (PC) analysis was performed to study the relationship between carcass quality variables. The six first PC's explained about 85% of the total variability. The weight and yield of the carcasses were more effective to define the first PC. The projection of the carcass quality data in the first two PC's allowed distinguishing between carcass weight and carcass conformation groups, but not between gender and fatness. Copyright © 2010 The American Meat Science Association. Published by Elsevier Ltd. All rights reserved.

Spatial variability assessment of soil nutrients in an intense agricultural area, a case study of Rugao County in Yangtze River Delta Region, China

NASA Astrophysics Data System (ADS)

Zhao, Yongcun; Xu, Xianghua; Darilek, Jeremy Landon; Huang, Biao; Sun, Weixia; Shi, Xuezheng

2009-05-01

Topsoil samples (0-20 cm) ( n = 237) were collected from Rugao County, China. Geostatistical variogram analysis, sequential Gaussian simulation (SGS), and principal component (PC) analysis were applied to assess spatial variability of soil nutrients, identify the possible areas of nutrient deficiency, and explore spatial scale of variability of soil nutrients in the county. High variability of soil nutrient such as soil organic matter (SOM), total nitrogen (TN), available P, K, Fe, Mn, Cu, Zn, and B concentrations were observed. Soil nutrient properties displayed significant differences in their spatial structures, with available Cu having strong spatial dependence, SOM and available P having weak spatial dependence, and other nutrient properties having moderate spatial dependence. The soil nutrient deficiency, defined here as measured nutrient concentrations which do not meet the advisory threshold values specific to the county for dominant crops, namely rice, wheat, and rape seeds, was observed in available K and Zn, and the deficient areas covered 38 and 11%, respectively. The first three PCs of the nine soil nutrient properties explained 62.40% of the total variance. TN and SOM with higher loadings on PC1 are closely related to soil texture derived from different parent materials. The PC2 combined intermediate response variables such as available Zn and P that are likely to be controlled by land use and soil pH. Available B has the highest loading on PC3 and its variability of concentrations may be primarily ascribed to localized anthropogenic influence. The amelioration of soil physical properties (i.e. soil texture) and soil pH may improve the availability of soil nutrients and the sustainability of the agricultural system of Rugao County.

Chemical and Biological Properties of S-1-Propenyl-l-Cysteine in Aged Garlic Extract.

PubMed

Kodera, Yukihioro; Ushijima, Mitsuyasu; Amano, Hirotaka; Suzuki, Jun-Ichiro; Matsutomo, Toshiaki

2017-03-31

S-1-Propenyl-l-cysteine (S1PC) is a stereoisomer of S-1-Propenyl-l-cysteine (SAC), an important sulfur-containing amino acid that plays a role for the beneficial pharmacological effects of aged garlic extract (AGE). The existence of S1PC in garlic preparations has been known since the 1960's. However, there was no report regarding the biological and/or pharmacological activity of S1PC until 2016. Recently, we performed a series of studies to examine the chemical, biological, pharmacological and pharmacokinetic properties of S1PC, and obtained some interesting results. S1PC existed only in trace amounts in raw garlic, but its concentration increased almost up to the level similar of SAC through aging process of AGE. S1PC showed immunomodulatory effects in vitro and in vivo, and reduced blood pressure in a hypertensive animal model. A pharmacokinetic study revealed that S1PC was readily absorbed after oral administration in rats and dogs with bioavailability of 88-100%. Additionally, S1PC had little inhibitory influence on human cytochrome P450 activities, even at a concentration of 1 mM. Based on these findings, S1PC was suggested to be another important, pharmacologically active and safe component of AGE similar to SAC. In this review, we highlight some results from recent studies on S1PC and discuss the potential medicinal value of S1PC.

Structural Factors and Mechanisms Underlying the Improved Photodynamic Cell Killing with Silicon Phthalocyanine Photosensitizers Directed to Lysosomes Versus Mitochondria

PubMed Central

Rodriguez, Myriam E.; Zhang, Ping; Azizuddin, Kashif; Delos Santos, Grace B.; Chiu, Song-mao; Xue, Liang-yan; Berlin, Jeffery C.; Peng, Xinzhan; Wu, Hongqiao; Lam, Minh; Nieminen, Anna-Liisa; Kenney, Malcolm E.; Oleinick, Nancy L.

2012-01-01

The phthalocyanine photosensitizer Pc 4 has been shown to bind preferentially to mitochondrial and endoplasmic reticulum membranes. Upon photoirradiation of Pc 4-loaded cells, membrane components, especially Bcl-2, are photodamaged and apoptosis, as indicated by activation of caspase-3 and cleavage of poly(ADP-ribose) polymerase, is triggered. A series of analogs of Pc 4 were synthesized, and the results demonstrate that Pcs with the aminopropylsiloxy ligand of Pc 4 or a similar one on one side of the Pc ring and a second large axial ligand on the other side of the ring have unexpected properties, including enhanced cell uptake, greater monomerization resulting in greater intracellular fluorescence and three-fold higher affinity constants for liposomes. The hydroxyl-bearing axial ligands tend to reduce aggregation of the Pc and direct it to lysosomes, resulting in four to six times more killing of cells, as defined by loss of clonogenicity, than with Pc 4. Whereas Pc 4-PDT photodamages Bcl-2 and Bcl-xL, Pc 181-PDT causes much less photodamage to Bcl-2 over the same dose–response range relative to cell killing, with earlier cleavage of Bid and slower caspase-3-dependent apoptosis. Therefore, within this series of photosensitizers, these hydroxyl-bearing axial ligands are less aggregated than is Pc 4, tend to localize to lysosomes and are more effective in overall cell killing than is Pc 4, but induce apoptosis more slowly and by a modified pathway. PMID:19508642

Cognitive versus Software-Assisted Registration: Development of a New Nomogram Predicting Prostate Cancer at MRI-Targeted Biopsies.

PubMed

Kaufmann, Sascha; Russo, Giorgio I; Thaiss, Wolfgang; Notohamiprodjo, Mike; Bamberg, Fabian; Bedke, Jens; Morgia, Giuseppe; Nikolaou, Konstantin; Stenzl, Arnulf; Kruck, Stephan

2018-04-03

Multiparametric magnetic resonance imaging (mpMRI) is gaining acceptance to guide targeted biopsy (TB) in prostate cancer (PC) diagnosis. We aimed to compare the detection rate of software-assisted fusion TB (SA-TB) versus cognitive fusion TB (COG-TB) for PC and to evaluate potential clinical features in detecting PC and clinically significant PC (csPC) at TB. This was a retrospective cohort study of patients with rising and/or persistently elevated prostate-specific antigen (PSA) undergoing mpMRI followed by either transperineal SA-TB or transrectal COG-TB. The analysis showed a matched-paired analysis between SA-TB versus COG-TB without differences in clinical or radiological characteristics. Differences among detection of PC/csPC among groups were analyzed. A multivariable logistic regression model predicting PC at TB was fitted. The model was evaluated using the receiver operating characteristic-derived area under the curve, goodness of fit test, and decision-curve analyses. One hundred ninety-one and 87 patients underwent SA-TB or COG-TB, respectively. The multivariate logistic analysis showed that SA-TB was associated with overall PC (odds ratio [OR], 5.70; P < .01) and PC at TB (OR, 3.00; P < .01) but not with overall csPC (P = .40) and csPC at TB (P = .40). A nomogram predicting PC at TB was constructed using the Prostate Imaging Reporting and Data System version 2.0, age, PSA density and biopsy technique, showing improved clinical risk prediction against a threshold probability of 10% with a c-index of 0.83. In patients with suspected PC, software-assisted biopsy detects most cancers and outperforms the cognitive approach in targeting magnetic resonance imaging-visible lesions. Furthermore, we introduced a prebiopsy nomogram for the probability of PC in TB. Copyright © 2018 Elsevier Inc. All rights reserved.

TU-AB-BRC-03: Accurate Tissue Characterization for Monte Carlo Dose Calculation Using Dual-and Multi-Energy CT Data

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

Lalonde, A; Bouchard, H

Purpose: To develop a general method for human tissue characterization with dual-and multi-energy CT and evaluate its performance in determining elemental compositions and the associated proton stopping power relative to water (SPR) and photon mass absorption coefficients (EAC). Methods: Principal component analysis is used to extract an optimal basis of virtual materials from a reference dataset of tissues. These principal components (PC) are used to perform two-material decomposition using simulated DECT data. The elemental mass fraction and the electron density in each tissue is retrieved by measuring the fraction of each PC. A stoichiometric calibration method is adapted to themore » technique to make it suitable for clinical use. The present approach is compared with two others: parametrization and three-material decomposition using the water-lipid-protein (WLP) triplet. Results: Monte Carlo simulations using TOPAS for four reference tissues shows that characterizing them with only two PC is enough to get a submillimetric precision on proton range prediction. Based on the simulated DECT data of 43 references tissues, the proposed method is in agreement with theoretical values of protons SPR and low-kV EAC with a RMS error of 0.11% and 0.35%, respectively. In comparison, parametrization and WLP respectively yield RMS errors of 0.13% and 0.29% on SPR, and 2.72% and 2.19% on EAC. Furthermore, the proposed approach shows potential applications for spectral CT. Using five PC and five energy bins reduces the SPR RMS error to 0.03%. Conclusion: The proposed method shows good performance in determining elemental compositions from DECT data and physical quantities relevant to radiotherapy dose calculation and generally shows better accuracy and unbiased results compared to reference methods. The proposed method is particularly suitable for Monte Carlo calculations and shows promise in using more than two energies to characterize human tissue with CT.« less

Assessing the role of feed water constituents in irreversible membrane fouling of pilot-scale ultrafiltration drinking water treatment systems.

PubMed

Peiris, R H; Jaklewicz, M; Budman, H; Legge, R L; Moresoli, C

2013-06-15

Fluorescence excitation-emission matrix (EEM) approach together with principal component analysis (PCA) was used for assessing hydraulically irreversible fouling of three pilot-scale ultrafiltration (UF) systems containing full-scale and bench-scale hollow fiber membrane modules in drinking water treatment. These systems were operated for at least three months with extensive cycles of permeation, combination of back-pulsing and scouring and chemical cleaning. The principal component (PC) scores generated from the PCA of the fluorescence EEMs were found to be related to humic substances (HS), protein-like and colloidal/particulate matter content. PC scores of HS- and protein-like matter of the UF feed water, when considered separately, showed reasonably good correlations with the rate of hydraulically irreversible fouling for long-term UF operations. In contrast, comparatively weaker correlations for PC scores of colloidal/particulate matter and the rate of hydraulically irreversible fouling were obtained for all UF systems. Since, individual correlations could not fully explain the evolution of the rate of irreversible fouling, multi-linear regression models were developed to relate the combined effect of HS-like, protein-like and colloidal/particulate matter PC scores to the rate of hydraulically irreversible fouling for each specific UF system. These multi-linear regression models revealed significant individual and combined contribution of HS- and protein-like matter to the rate of hydraulically irreversible fouling, with protein-like matter generally showing the greatest contribution. The contribution of colloidal/particulate matter to the rate of hydraulically irreversible fouling was not as significant. The addition of polyaluminum chloride, as coagulant, to UF feed appeared to have a positive impact in reducing hydraulically irreversible fouling by these constituents. The proposed approach has applications in quantifying the individual and synergistic contribution of major natural water constituents to the rate of hydraulically irreversible membrane fouling and shows potential for controlling UF irreversible fouling in the production of drinking water. Copyright © 2013 Elsevier Ltd. All rights reserved.

Nutrient patterns and their food sources in an International Study Setting: report from the EPIC study.

PubMed

Moskal, Aurelie; Pisa, Pedro T; Ferrari, Pietro; Byrnes, Graham; Freisling, Heinz; Boutron-Ruault, Marie-Christine; Cadeau, Claire; Nailler, Laura; Wendt, Andrea; Kühn, Tilman; Boeing, Heiner; Buijsse, Brian; Tjønneland, Anne; Halkjær, Jytte; Dahm, Christina C; Chiuve, Stephanie E; Quirós, Jose R; Buckland, Genevieve; Molina-Montes, Esther; Amiano, Pilar; Huerta Castaño, José M; Gurrea, Aurelio Barricarte; Khaw, Kay-Tee; Lentjes, Marleen A; Key, Timothy J; Romaguera, Dora; Vergnaud, Anne-Claire; Trichopoulou, Antonia; Bamia, Christina; Orfanos, Philippos; Palli, Domenico; Pala, Valeria; Tumino, Rosario; Sacerdote, Carlotta; de Magistris, Maria Santucci; Bueno-de-Mesquita, H Bas; Ocké, Marga C; Beulens, Joline W J; Ericson, Ulrika; Drake, Isabel; Nilsson, Lena M; Winkvist, Anna; Weiderpass, Elisabete; Hjartåker, Anette; Riboli, Elio; Slimani, Nadia

2014-01-01

Compared to food patterns, nutrient patterns have been rarely used particularly at international level. We studied, in the context of a multi-center study with heterogeneous data, the methodological challenges regarding pattern analyses. We identified nutrient patterns from food frequency questionnaires (FFQ) in the European Prospective Investigation into Cancer and Nutrition (EPIC) Study and used 24-hour dietary recall (24-HDR) data to validate and describe the nutrient patterns and their related food sources. Associations between lifestyle factors and the nutrient patterns were also examined. Principal component analysis (PCA) was applied on 23 nutrients derived from country-specific FFQ combining data from all EPIC centers (N = 477,312). Harmonized 24-HDRs available for a representative sample of the EPIC populations (N = 34,436) provided accurate mean group estimates of nutrients and foods by quintiles of pattern scores, presented graphically. An overall PCA combining all data captured a good proportion of the variance explained in each EPIC center. Four nutrient patterns were identified explaining 67% of the total variance: Principle component (PC) 1 was characterized by a high contribution of nutrients from plant food sources and a low contribution of nutrients from animal food sources; PC2 by a high contribution of micro-nutrients and proteins; PC3 was characterized by polyunsaturated fatty acids and vitamin D; PC4 was characterized by calcium, proteins, riboflavin, and phosphorus. The nutrients with high loadings on a particular pattern as derived from country-specific FFQ also showed high deviations in their mean EPIC intakes by quintiles of pattern scores when estimated from 24-HDR. Center and energy intake explained most of the variability in pattern scores. The use of 24-HDR enabled internal validation and facilitated the interpretation of the nutrient patterns derived from FFQs in term of food sources. These outcomes open research opportunities and perspectives of using nutrient patterns in future studies particularly at international level.

PcG and trxG in plants - friends or foes.

PubMed

Pu, Li; Sung, Zinmay Renee

2015-05-01

The highly-conserved Polycomb group (PcG) and trithorax group (trxG) proteins play major roles in regulating gene expression and maintaining developmental states in many organisms. However, neither the recruitment of Polycomb repressive complexes (PRC) nor the mechanisms of PcG and trxG-mediated gene silencing and activation are well understood. Recent progress in Arabidopsis research challenges the dominant model of PRC2-dependent recruitment of PRC1 to target genes. Moreover, evidence indicates that diverse forms of PRC1, with shared components, are a common theme in plants and mammals. Although trxG is known to antagonize PcG, emerging data reveal that trxG can also repress gene expression, acting cooperatively with PcG. We discuss these recent findings and highlight the employment of diverse epigenetic mechanisms during development in plants and animals. Copyright © 2015 Elsevier Ltd. All rights reserved.

A DNA sequence analysis package for the IBM personal computer.

PubMed Central

Lagrimini, L M; Brentano, S T; Donelson, J E

1984-01-01

We present here a collection of DNA sequence analysis programs, called "PC Sequence" (PCS), which are designed to run on the IBM Personal Computer (PC). These programs are written in IBM PC compiled BASIC and take full advantage of the IBM PC's speed, error handling, and graphics capabilities. For a modest initial expense in hardware any laboratory can use these programs to quickly perform computer analysis on DNA sequences. They are written with the novice user in mind and require very little training or previous experience with computers. Also provided are a text editing program for creating and modifying DNA sequence files and a communications program which enables the PC to communicate with and collect information from mainframe computers and DNA sequence databases. PMID:6546433

Traceability of Opuntia ficus-indica L. Miller by ICP-MS multi-element profile and chemometric approach.

PubMed

Mottese, Antonio Francesco; Naccari, Clara; Vadalà, Rossella; Bua, Giuseppe Daniel; Bartolomeo, Giovanni; Rando, Rossana; Cicero, Nicola; Dugo, Giacomo

2018-01-01

Opuntia ficus-indica L. Miller fruits, particularly 'Ficodindia dell'Etna' of Biancavilla (POD), 'Fico d'india tradizionale di Roccapalumba' with protected brand and samples from an experimental field in Pezzolo (Sicily) were analyzed by inductively coupled plasma mass spectrometry in order to determine the multi-element profile. A multivariate chemometric approach, specifically principal component analysis (PCA), was applied to individuate how mineral elements may represent a marker of geographic origin, which would be useful for traceability. PCA has allowed us to verify that the geographical origin of prickly pear fruits is significantly influenced by trace element content, and the results found in Biancavilla PDO samples were linked to the geological composition of this volcanic areas. It was observed that two principal components accounted for 72.03% of the total variance in the data and, in more detail, PC1 explains 45.51% and PC2 26.52%, respectively. This study demonstrated that PCA is an integrated tool for the traceability of food products and, at the same time, a useful method of authentication of typical local fruits such as prickly pear. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

A Mini-BAL Outflow at 900 pc from the Central Source: VLT/X-shooter Observations

NASA Astrophysics Data System (ADS)

Xu, Xinfeng; Arav, Nahum; Miller, Timothy; Benn, Chris

2018-05-01

We determine the physical conditions and location of the outflow material seen in the mini-BAL quasar SDSS J1111+1437 (z = 2.138). These results are based on the analysis of a high S/N, medium-resolution VLT/X-shooter spectrum. The main outflow component spans the velocity range ‑1500 to ‑3000 km s‑1 and has detected absorption troughs from both high-ionization species: C IV, N V, O VI, Si IV, P V, and S IV; and low-ionization species: H I, C II, Mg II, Al II, Al III, Si II, and Si III. Measurements of these troughs allow us to derive an accurate photoionization solution for this absorption component: a hydrogen column density, {log}({N}{{H}})={21.47}-0.27+0.21 cm‑2 and ionization parameter, {log}({U}{{H}})=-{1.23}-0.25+0.20. Troughs produced from the ground and excited states of S IV combined with the derived {U}{{H}} value allow us to determine an electron number density of {log}({n}{{e}})={3.62}-0.11+0.09 cm‑3 and to obtain the distance of the ionized gas from the central source: R={880}-260+210 pc.

Optical system for tablet variety discrimination using visible/near-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Shao, Yongni; He, Yong; Hu, Xingyue

2007-12-01

An optical system based on visible/near-infrared spectroscopy (Vis/NIRS) for variety discrimination of ginkgo (Ginkgo biloba L.) tablets was developed. This system consisted of a light source, beam splitter system, sample chamber, optical detector (diffuse reflection detector), and data collection. The tablet varieties used in the research include Da na kang, Xin bang, Tian bao ning, Yi kang, Hua na xing, Dou le, Lv yuan, Hai wang, and Ji yao. All samples (n=270) were scanned in the Vis/NIR region between 325 and 1075 nm using a spectrograph. The chemometrics method of principal component artificial neural network (PC-ANN) was used to establish discrimination models of them. In PC-ANN models, the scores of the principal components were chosen as the input nodes for the input layer of ANN, and the best discrimination rate of 91.1% was reached. Principal component analysis was also executed to select several optimal wavelengths based on loading values. Wavelengths at 481, 458, 466, 570, 1000, 662, and 400 nm were then used as the input data of stepwise multiple linear regression, the regression equation of ginkgo tablets was obtained, and the discrimination rate was researched 84.4%. The results indicated that this optical system could be applied to discriminating ginkgo (Ginkgo biloba L.) tablets, and it supplied a new method for fast ginkgo tablet variety discrimination.

Rapid top-down control over template-guided attention shifts to multiple objects.

PubMed

Grubert, Anna; Fahrenfort, Johannes; Olivers, Christian N L; Eimer, Martin

2017-02-01

Previous research has shown that when observers search for targets defined by a particular colour, attention can be directed rapidly and independently to two target objects that appear in close temporal proximity. We investigated how such rapid attention shifts are modulated by task instructions to selectively attend versus ignore one of these objects. Two search displays that both contained a colour-defined target and a distractor in a different colour were presented in rapid succession, with a stimulus onset asynchrony (SOA) of 100ms. In different blocks, participants were instructed to attend and respond to target-colour objects in the first display and to ignore these objects in the second display, or vice versa. N2pc components were measured to track the allocation of spatial attention to target-colour objects in these two displays. When participants responded to the second display, irrelevant target-colour objects in the first display still triggered N2pc components, demonstrating task-set contingent attentional capture while a feature-specific target template is active. Critically, when participants responded to the first display instead, no N2pc was elicited by target-colour items in the second display, indicating that they no longer rapidly captured attention. However, these items still elicited a longer-latency contralateral negativity (SPCN component), suggesting that attention was oriented towards template-matching objects in working memory. This dissociation between N2pc and SPCN components shows that rapid attentional capture and subsequent attentional selection processes within working memory can be independent. We suggest that early attentional orienting mechanisms can be inhibited when task-set matching objects are no longer task-relevant, and that this type of inhibitory control is a rapid but transient process. Copyright © 2016 Elsevier Inc. All rights reserved.

Age-Related Occipito-Temporal Hypoactivation during Visual Search: Relationships between mN2pc Sources and Performance

ERIC Educational Resources Information Center

Lorenzo-Lopez, L.; Gutierrez, R.; Moratti, S.; Maestu, F.; Cadaveira, F.; Amenedo, E.

2011-01-01

Recently, an event-related potential (ERP) study (Lorenzo-Lopez et al., 2008) provided evidence that normal aging significantly delays and attenuates the electrophysiological correlate of the allocation of visuospatial attention (N2pc component) during a feature-detection visual search task. To further explore the effects of normal aging on the…

Peak Pc Prediction in Conjunction Analysis: Conjunction Assessment Risk Analysis. Pc Behavior Prediction Models

NASA Technical Reports Server (NTRS)

Vallejo, J.J.; Hejduk, M.D.; Stamey, J. D.

2015-01-01

Satellite conjunction risk typically evaluated through the probability of collision (Pc). Considers both conjunction geometry and uncertainties in both state estimates. Conjunction events initially discovered through Joint Space Operations Center (JSpOC) screenings, usually seven days before Time of Closest Approach (TCA). However, JSpOC continues to track objects and issue conjunction updates. Changes in state estimate and reduced propagation time cause Pc to change as event develops. These changes a combination of potentially predictable development and unpredictable changes in state estimate covariance. Operationally useful datum: the peak Pc. If it can reasonably be inferred that the peak Pc value has passed, then risk assessment can be conducted against this peak value. If this value is below remediation level, then event intensity can be relaxed. Can the peak Pc location be reasonably predicted?

Field-aligned structure of the storm time Pc 5 wave of November 14-15, 1979

NASA Astrophysics Data System (ADS)

Takahashi, K.; Higbie, P. R.; Fennell, J. F.; Amata, E.

1987-06-01

Magnetic field data from the four satellites SCATHA (P78-2), GOES 2, GOES 3, and GOES 2 have been analyzed to examine the magnetic field-aligned structure of a storm time Pc 5 wave that occurred on November 14-15, 1979. The wave had both transverse and compressional components. At a given instance, the compressional and the radial components oscillated in phase or 180 deg out of phase, and the compressional and the azimuthal components oscillated +90 deg or -90 deg out of phase. In addition, each component changed its amplitude with magnetic latitude: the compressional component had a minimum at the magnetic equator, whereas the transverse components had a maximum at the equator and minima several degrees off the equator. A 180 deg relative phase switching among the components occurred across the latitudes of amplitude minima. From these observations, the field line displacement of the wave is confirmed to have an antisymmetric standing structure about the magnetic equator with a parallel wave length of a few earth radii.

Geographic variation in floral allometry suggests repeated transitions between selfing and outcrossing in a mixed mating plant.

PubMed

Summers, Holly E; Hartwick, Sally M; Raguso, Robert A

2015-05-01

Isometric and allometric scaling of a conserved floral plan could provide a parsimonious mechanism for rapid and reversible transitions between breeding systems. This scaling may occur during transitions between predominant autogamy and xenogamy, contributing to the maintenance of a stable mixed mating system. We compared nine disjunct populations of the polytypic, mixed mating species Oenothera flava (Onagraceae) to two parapatric relatives, the obligately xenogamous species O. acutissima and the mixed mating species O. triloba. We compared floral morphology of all taxa using principal component analysis (PCA) and developmental trajectories of floral organs using ANCOVA homogeneity of slopes. The PCA revealed both isometric and allometric scaling of a conserved floral plan. Three principal components (PCs) explained 92.5% of the variation in the three species. PC1 predominantly loaded on measures of floral size and accounts for 36% of the variation. PC2 accounted for 35% of the variation, predominantly in traits that influence pollinator handling. PC3 accounted for 22% of the variation, primarily in anther-stigma distance (herkogamy). During O. flava subsp. taraxacoides development, style elongation was accelerated relative to anthers, resulting in positive herkogamy. During O. flava subsp. flava development, style elongation was decelerated, resulting in zero or negative herkogamy. Of the two populations with intermediate morphology, style elongation was accelerated in one population and decelerated in the other. Isometric and allometric scaling of floral organs in North American Oenothera section Lavauxia drive variation in breeding system. Multiple developmental paths to intermediate phenotypes support the likelihood of multiple mating system transitions. © 2015 Botanical Society of America, Inc.

Systolic blood pressure variability in patients with early severe sepsis or septic shock: a prospective cohort study.

PubMed

Tang, Yi; Sorenson, Jeff; Lanspa, Michael; Grissom, Colin K; Mathews, V J; Brown, Samuel M

2017-06-17

Severe sepsis and septic shock are often lethal syndromes, in which the autonomic nervous system may fail to maintain adequate blood pressure. Heart rate variability has been associated with outcomes in sepsis. Whether systolic blood pressure (SBP) variability is associated with clinical outcomes in septic patients is unknown. The propose of this study is to determine whether variability in SBP correlates with vasopressor independence and mortality among septic patients. We prospectively studied patients with severe sepsis or septic shock, admitted to an intensive care unit (ICU) with an arterial catheter. We analyzed SBP variability on the first 5-min window immediately following ICU admission. We performed principal component analysis of multidimensional complexity, and used the first principal component (PC 1 ) as input for Firth logistic regression, controlling for mean systolic pressure (SBP) in the primary analyses, and Acute Physiology and Chronic Health Evaluation (APACHE) II score or NEE dose in the ancillary analyses. Prespecified outcomes were vasopressor independence at 24 h (primary), and 28-day mortality (secondary). We studied 51 patients, 51% of whom achieved vasopressor independence at 24 h. Ten percent died at 28 days. PC 1 represented 26% of the variance in complexity measures. PC 1 was not associated with vasopressor independence on Firth logistic regression (OR 1.04; 95% CI: 0.93-1.16; p = 0.54), but was associated with 28-day mortality (OR 1.16, 95% CI: 1.01-1.35, p = 0.040). Early SBP variability appears to be associated with 28-day mortality in patients with severe sepsis and septic shock.

A spectroscopic study of mechanochemically activated kaolinite with the aid of chemometrics.

PubMed

Carmody, Onuma; Kristóf, János; Frost, Ray L; Makó, Eva; Kloprogge, J Theo; Kokot, Serge

2005-07-01

The study of kaolinite surfaces is of industrial importance. In this work we report the application of chemometrics to the study of modified kaolinite surfaces. DRIFT spectra of mechanochemically activated kaolinites (Kiralyhegy, Zettlitz, Szeg, and Birdwood) were analyzed using principal component analysis (PCA) and multicriteria decision making (MCDM) methods, PROMETHEE and GAIA. The clear discrimination of the Kiralyhegy spectral objects on the two PC scores plots (400-800 and 800-2030 cm(-1)) indicated the dominance of quartz. Importantly, no ordering of any spectral objects appeared to be related to grinding time in the PC plots of these spectral regions. Thus, neither the kaolinite nor the quartz, are systematically responsive to grinding time according to the spectral criteria investigated. The third spectral region (2600-3800 cm(-1)OH vibrations), showed apparent systematic ordering of the Kiralyhegy and, to a lesser extent, Zettlitz spectral objects with grinding time. This was attributed to the effect of the natural quartz on the delamination of kaolinite and the accompanying phenomena (i.e., formation of kaolinite spheres and water). With the MCDM methods, it was shown that useful information on the basis of chemical composition, physical properties and grinding time can be obtained. For example, the effects of the minor chemical components (e.g., MgO, K(2)O, etc.) indicated that the Birdwood kaolinite is arguably the most pure one analyzed. In another MCDM experiment, some support was obtained for the apparent trend with grinding time noted in the PC plot of the OH spectral region.

NIST Libraries of Peptide Fragmentation Mass Spectra Databass

National Institute of Standards and Technology Data Gateway

SRD 4 NIST Libraries of Peptide Fragmentation Mass Spectra Databass (PC database for purchase)   Interactive computer program for predicting thermodynamic and transport properties of pure fluids and fluid mixtures containing up to 20 components. The components are selected from a database of 196 components, mostly hydrocarbons.

An In-depth Chandra ACIS View Of The Circumnuclear Region Of NGC 4151: The Jet, The Biconical Outflow, And A Leaky Torus

NASA Astrophysics Data System (ADS)

Wang, Junfeng; Fabbiano, G.; Elvis, M.; Risaliti, G.; Karovska, M.; Zezas, A.; Mundell, C. G.

2011-05-01

We report on the imaging analysis of 200 ks Chandra ACIS-S observations of the nearby Seyfert 1 galaxy NGC 4151. Structured soft X-ray emission is observed to extend from 30 pc to 1.5 kpc. We find strong evidence for jet-gas cloud interaction in the inner 150 pc region, confirming our previous HRC results. Self-consistent photoionization models provide good descriptions of the spectra of the optical bi-cone, supporting the dominant role of nuclear photoionization. Presence of both low and high ionization spectral components and extended emission in the X-ray image perpendicular to the bi-cone indicates leakage of nuclear ionization. Using spatially resolved features, we estimate the kinematic power of the outflow in NGC 4151 to be 0.3% of its bolometric luminosity. This work is supported by NASA grant GO8-9101X and GO1-12009X.

Evaluation of three pumpkin species: correlation with physicochemical, antioxidant properties and classification using SPME-GC-MS and E-nose methods.

PubMed

Zhou, Chun-Li; Mi, Li; Hu, Xue-Yan; Zhu, Bi-Hua

2017-09-01

To ascertain the most discriminant variables for three pumpkin species principal component analysis (PCA) was performed. Twenty-four parameters (pH, conductivity, sucrose, glucose, total soluble solids, L* , a* , b* , individual weight, edible rate, firmness, citric acid, fumaric acid, l-ascorbic acid, malic acid, PPO activity, POD activity, total flavonoids, vitamin E, total phenolics, DPPH, FRAP, β-carotene, and aroma) were considered. The studied pumpkin species were Cucurbita maxima , Cucurbita moschata , and Cucurbita pepo . Three pumpkin species were classified by PCA based on aroma, physicochemical and antioxidant properties because the sum of PC1 and PC2 were both greater than 85% (85.06 and 93.64% respectively). Results were validated by the PCA and showed that PPO activity, total flavonoid, sucrose, glucose, TSS, a* , pH, malic acid, vitamin E, DPPH, FRAP and β-carotene, and aroma are highly useful parameters to classify pumpkin species.

NCOA3-mediated upregulation of mucin expression via transcriptional and post-translational changes during the development of pancreatic cancer

PubMed Central

Kumar, S; Das, S; Rachagani, S; Kaur, S; Joshi, S; Johansson, SL; Ponnusamy, MP; Jain, M; Batra, SK

2015-01-01

Pancreatic cancer (PC) is characterized by aberrant overexpression of mucins that contribute to its pathogenesis. Although the inflammatory cytokines contribute to mucin overexpression, the mucin profile of PC is markedly distinct from that of normal or inflamed pancreas. We postulated that de novo expression of various mucins in PC involves chromatin modifications. Analysis of chromatin modifying enzymes by PCR array identified differential expression of NCOA3 in MUC4-expressing PC cell lines. Immunohistochemistry analysis in tumor tissues from patients and spontaneous mouse models, and microarray analysis following the knockdown of NCOA3 were performed to elucidate its role in mucin regulation and overall impact on PC. Silencing of NCOA3 in PC cell lines resulted in significant downregulation of two most differentially expressed mucins in PC, MUC4 and MUC1 (P<0.01). Immunohistochemistry analysis in PC tissues and metastatic lesions established an association between NCOA3 and mucin (MUC1 and MUC4) expression. Spontaneous mouse model of PC (K-rasG12D; Pdx-1cre) showed early expression of Ncoa3 during preneoplastic lesions. Mechanistically, NCOA3 knockdown abrogated retinoic acid-mediated MUC4 upregulation by restricting MUC4 promoter accessibility as demonstrated by micrococcus nuclease digestion (P<0.05) and chromatin immuno-precipitation analysis. NCOA3 also created pro-inflammatory conditions by upregulating chemokines like CXCL1, 2, 5 and CCL20 (P<0.001). AKT, ubiquitin C, ERK1/2 and NF-κB occupied dominant nodes in the networks significantly modulated after NCOA3 silencing. In addition, NCOA3 stabilized mucins post translationally through fucosylation by FUT8, as the knockdown of FUT8 resulted in the downregulation of MUC4 and MUC1 at protein levels. PMID:25531332

Serum Immunoglobulin G4 in Discriminating Autoimmune Pancreatitis From Pancreatic Cancer: A Diagnostic Meta-analysis.

PubMed

Dai, Cong; Cao, Qin; Jiang, Min; Sun, Ming-Jun

2018-03-01

Differentiation between autoimmune pancreatitis (AIP) and pancreatic cancer (PC) is a clinical challenge. Emerging published data on the accuracy of serum immunoglobulin G4 (IgG4) for the differential diagnosis between AIP and PC are inconsistent. The objective of our study was to perform a meta-analysis evaluating the clinical utility of serum IgG4 in the differential diagnosis between AIP and PC. We performed a systematic literature search of multiple electronic databases. The methodological quality of each study was assessed according to the Quality Assessment of Diagnostic Accuracy Studies checklist. Random-effects model was used to summarize the diagnostic odds ratio and other measures of accuracy. Eleven studies comprising 523 AIP patients and 771 PC patients were included in the meta-analysis. The summary estimates for serum IgG4 in distinguishing AIP from PC were as follows: diagnostic odds ratio, 57.30 (95% confidence interval [CI], 23.17-141.67); sensitivity, 0.72 (95% CI, 0.68-0.76); specificity, 0.93 (95% CI, 0.91-0.94). The area under the curve of serum IgG4 in distinguishing AIP from PC was 0.9200. Our meta-analysis found that serum IgG4 has high specificity and relatively low sensitivity in the differential diagnosis between AIP and PC. Therefore, serum IgG4 is useful in distinguishing AIP from PC.

CARA Status and Upcoming Enhancements

NASA Technical Reports Server (NTRS)

Johnson, Megan

2017-01-01

CAS 8.4.3 was deployed to operations on 13 June 2017. Discrepancies Between 3D Pc Estimates and advanced Monte Carlo Equinoctial-Sampling Pc Estimates discovered and discussed at 23 May 2017 Useras (Registered Trademark) Forum. The patch created the Reporting Pc, which is the greater value between the calculated 2D and 3D Pc values This changed the Pc reported in the CDMs to the Reporting Pc This changed the Pc reported on the Summary Report to the Reporting Pc This changed the Pc reported on Maneuver Screening Analysis (MSA) Report to the Reporting Pc. Both the 2D and 3D Pc added to the Summary Report details section The patch also updated the 3D Pc algorithm to eliminate velocity covariance from the Pc calculation This will bring 2D and 3D Pc into close alignment for vast majority of events, particularly for the events in which the 2D/3D discrepancy was found.

A multivariate and stochastic approach to identify key variables to rank dairy farms on profitability.

PubMed

Atzori, A S; Tedeschi, L O; Cannas, A

2013-05-01

The economic efficiency of dairy farms is the main goal of farmers. The objective of this work was to use routinely available information at the dairy farm level to develop an index of profitability to rank dairy farms and to assist the decision-making process of farmers to increase the economic efficiency of the entire system. A stochastic modeling approach was used to study the relationships between inputs and profitability (i.e., income over feed cost; IOFC) of dairy cattle farms. The IOFC was calculated as: milk revenue + value of male calves + culling revenue - herd feed costs. Two databases were created. The first one was a development database, which was created from technical and economic variables collected in 135 dairy farms. The second one was a synthetic database (sDB) created from 5,000 synthetic dairy farms using the Monte Carlo technique and based on the characteristics of the development database data. The sDB was used to develop a ranking index as follows: (1) principal component analysis (PCA), excluding IOFC, was used to identify principal components (sPC); and (2) coefficient estimates of a multiple regression of the IOFC on the sPC were obtained. Then, the eigenvectors of the sPC were used to compute the principal component values for the original 135 dairy farms that were used with the multiple regression coefficient estimates to predict IOFC (dRI; ranking index from development database). The dRI was used to rank the original 135 dairy farms. The PCA explained 77.6% of the sDB variability and 4 sPC were selected. The sPC were associated with herd profile, milk quality and payment, poor management, and reproduction based on the significant variables of the sPC. The mean IOFC in the sDB was 0.1377 ± 0.0162 euros per liter of milk (€/L). The dRI explained 81% of the variability of the IOFC calculated for the 135 original farms. When the number of farms below and above 1 standard deviation (SD) of the dRI were calculated, we found that 21 farms had dRI<-1 SD, 32 farms were between -1 SD and 0, 67 farms were between 0 and +1 SD, and 15 farms had dRI>+1 SD. The top 10% of the farms had a dRI greater than 0.170 €/L, whereas the bottom 10% farms had a dRI lower than 0.116 €/L. This stochastic approach allowed us to understand the relationships among the inputs of the studied dairy farms and to develop a ranking index for comparison purposes. The developed methodology may be improved by using more inputs at the dairy farm level and considering the actual cost to measure profitability. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Effectiveness of multicomponent interventions in primary healthcare settings to promote continuous smoking cessation in adults: a systematic review

PubMed Central

Martín Cantera, Carlos; Puigdomènech, Elisa; Ballvé, Jose Luis; Arias, Olga Lucía; Clemente, Lourdes; Casas, Ramon; Roig, Lydia; Pérez-Tortosa, Santiago; Díaz-Gete, Laura; Granollers, Sílvia

2015-01-01

Objective The objective of the present review is to evaluate multicomponent/complex primary care (PC) interventions for their effectiveness in continuous smoking abstinence by adult smokers. Design A systematic review of randomised and non-randomised controlled trials was undertaken. Eligibility criteria for included studies Selected studies met the following criteria: evaluated effects of a multicomponent/complex intervention (with 2 or more intervention components) in achieving at least 6-month abstinence in adult smokers who visited a PC, biochemical confirmation of abstinence, intention-to-treat analysis and results published in English/Spanish. Methods We followed PRISMA statement to report the review. We searched the following data sources: MEDLINE, Web of Science, Scopus (from inception to February 2014), 3 key journals and a tobacco research bulletin. The Scottish Intercollegiate Guidelines Network checklists were used to evaluate methodological quality. Data selection, evaluation and extraction were done independently, using a paired review approach. Owing to the heterogeneity of interventions in the studies included, a meta-analysis was not conducted. Results Of 1147 references identified, 9 studies were selected (10 204 participants, up to 48 months of follow-up, acceptable methodological quality). Methodologies used were mainly individual or group sessions, telephone conversations, brochures or quit-smoking kits, medications and economic incentives for doctors and no-cost medications for smokers. Complex interventions achieved long-term continuous abstinence ranging from 7% to 40%. Behavioural interventions were effective and had a dose–response effect. Both nicotine replacement and bupropion therapy were safe and effective, with no observed differences. Conclusions Multicomponent/complex interventions in PC are effective and safe, appearing to achieve greater long-term continuous smoking cessation than usual care and counselling alone. Selected studies were heterogeneous and some had significant losses to follow-up. Our results show that smoking interventions should include more than one component and a strong follow-up of the patient to maximise results. PMID:26428333

Remote Sensing for Mapping Soybean Crop in the Brazilian Cerrado

NASA Astrophysics Data System (ADS)

Trabaquini, K.; Bernardes, T.; Mello, M. P.; Formaggio, A.; Rosa, V. G.

2011-12-01

The soybean expansion in the Brazilian Cerrado has been strongly affected by internal and external markets. The main factors driving that expansion are the climatic conditions, the development of technologies and genetic improvement. Recent studies have shown that the soybean expansion has become a major cause of reduction of native vegetation in Mato Grosso State - Brazil, responding for 17% of deforestation from 2000 to 2004. This work aims to map soybean areas in the Brazilian Cerrado in Mato Grosso State, using MODIS data. Thirteen MODIS images (MOD13 - 16 days composition), acquired from September, 2005 to March, 2006, were used to run principal component analysis (PCA) in order to reduce the dimensionality of the data. The first three components (PC1, PC2 and PC3), which contained about 90% of data variability were segmented and utilized as input for an unsupervised classification using the ISOSEG classifier, implemented in the SPRING software. Eighty field work points were randomly selected for the accuracy assessment. An intersection between the soybean map and a map generated by the "Project Monitoring Deforestation of Brazilian Biomes Satellite - PMDBBS", which aimed at identifying anthropic areas, was conducted in order to evaluate the distribution of soybeans within those areas. Moreover a soil map was used in order to evaluate the soybean distribution over the classes of soil. The classification result presented overall index of 83% and the kappa coefficient of 0.64 for the soybean map, which presented a total soybean area of about 42,317 square kilometers. Furthermore, it was verified that 27% of anthropic area was covered by soybean. In relation to the soil analysis, 87% of the total soybean area was planted in Oxisoils. Despite the economic gain related to the soybean production, an adequate management is needed to avoid soil acidification, soil erosion and pollution, aiming at providing a sustainable environment.

Principal Component Analysis for Normal-Distribution-Valued Symbolic Data.

PubMed

Wang, Huiwen; Chen, Meiling; Shi, Xiaojun; Li, Nan

2016-02-01

This paper puts forward a new approach to principal component analysis (PCA) for normal-distribution-valued symbolic data, which has a vast potential of applications in the economic and management field. We derive a full set of numerical characteristics and variance-covariance structure for such data, which forms the foundation for our analytical PCA approach. Our approach is able to use all of the variance information in the original data than the prevailing representative-type approach in the literature which only uses centers, vertices, etc. The paper also provides an accurate approach to constructing the observations in a PC space based on the linear additivity property of normal distribution. The effectiveness of the proposed method is illustrated by simulated numerical experiments. At last, our method is applied to explain the puzzle of risk-return tradeoff in China's stock market.

Menstrual cycle perturbation by organohalogens and elements in the Cree of James Bay, Canada.

PubMed

Wainman, Bruce C; Kesner, James S; Martin, Ian D; Meadows, Juliana W; Krieg, Edward F; Nieboer, Evert; Tsuji, Leonard J

2016-04-01

Persistent organohalogens (POHs) and metals have been linked to alterations in menstrual cycle function and fertility in humans. The Cree First Nations people living near James Bay in Ontario and Quebec, Canada, have elevated levels of POHs, mercury and lead compared to other Canadians. The present study examines the interrelationships between selected POHs and elements on menstrual cycle function in these Cree women. Menstrual cycle characteristics were derived from structured daily diaries and endocrine measurements from daily urine samples collected during one cycle for 42 women age 19-42. We measured 31 POHs in blood plasma and 18 elements in whole blood, for 31 of the participants. POHs and elements detected in ≥ 70% of the participants were transformed by principal component (PC) analysis to reduce the contaminant exposure data to fewer, uncorrelated PCA variables. Multiple regression analysis revealed that, after adjusting for confounders, PC-3 values showed significant negative association with cycle length, after adjusting for confounders (p = 0.002). PC-3 accounted for 9.2% of the variance and shows positive loadings for cadmium, selenium, and PBDE congeners 47 and 153, and a negative loading for copper. Sensitivity analysis of the model to quantify likely effect sizes showed a range of menstrual cycle length from 25.3 to 28.3 days using the lower and upper 95% confidence limits of mean measured contaminant concentrations to predict cycle length. Our observations support the hypothesis that the menstrual cycle function of these women may be altered by exposure to POHs and elements from their environment. Copyright © 2015. Published by Elsevier Ltd.

Morphometry and subpopulation structure of Holstein bull spermatozoa: variations in ejaculates and cryopreservation straws

PubMed Central

Valverde, Anthony; Arenán, Héctor; Sancho, María; Contell, Jesús; Yániz, Jesús; Fernández, Alejandro; Soler, Carles

2016-01-01

Sperm quality is evaluated for the calculation of sperm dosage in artificial reproductive programs. The most common parameter used is motility, but morphology has a higher potential as a predictor of genetic quality. Morphometry calculations from CASA-Morph technology improve morphological evaluation and allow mathematical approaches to the problem. Semen from 28 Holstein bulls was collected by artificial vagina, and several ejaculates were studied. After general evaluation, samples were diluted, packaged in 0.25 ml straws, and stored in liquid nitrogen. Two straws per sample were thawed, and slides were processed and stained with Diff-Quik. Samples were analyzed by a CASA-Morph system for eight morphometric parameters. In addition to the “classical” statistical approach, based on variance analysis (revealing differences between animals, ejaculates, and straws), principal component (PC) analysis showed that the variables were grouped into PC1, related to size, and PC2 to shape. Subpopulation structure analysis showed four groups, namely, big, small, short, and narrow from their dominant characteristics, representing 31.0%, 27.3%, 24.1%, and 17.7% of the total population, respectively. The distributions varied between animals and ejaculates, but between straws, there were no differences in only four animals. This modern approach of considering an ejaculate sperm population as divided into subpopulations reflecting quantifiable parameters generated by CASA-Morph systems technology opens a new view on sperm function. This is the first study applying this approach to evaluate different ejaculates and straws from the same individual. More work must be done to improve seminal dose calculations in assisted reproductive programs. PMID:27678464

Morphometry and subpopulation structure of Holstein bull spermatozoa: variations in ejaculates and cryopreservation straws.

PubMed

Valverde, Anthony; Arenán, Héctor; Sancho, María; Contell, Jesús; Yániz, Jesús; Fernández, Alejandro; Soler, Carles

2016-01-01

Sperm quality is evaluated for the calculation of sperm dosage in artificial reproductive programs. The most common parameter used is motility, but morphology has a higher potential as a predictor of genetic quality. Morphometry calculations from CASA-Morph technology improve morphological evaluation and allow mathematical approaches to the problem. Semen from 28 Holstein bulls was collected by artificial vagina, and several ejaculates were studied. After general evaluation, samples were diluted, packaged in 0.25 ml straws, and stored in liquid nitrogen. Two straws per sample were thawed, and slides were processed and stained with Diff-Quik. Samples were analyzed by a CASA-Morph system for eight morphometric parameters. In addition to the "classical" statistical approach, based on variance analysis (revealing differences between animals, ejaculates, and straws), principal component (PC) analysis showed that the variables were grouped into PC1, related to size, and PC2 to shape. Subpopulation structure analysis showed four groups, namely, big, small, short, and narrow from their dominant characteristics, representing 31.0%, 27.3%, 24.1%, and 17.7% of the total population, respectively. The distributions varied between animals and ejaculates, but between straws, there were no differences in only four animals. This modern approach of considering an ejaculate sperm population as divided into subpopulations reflecting quantifiable parameters generated by CASA-Morph systems technology opens a new view on sperm function. This is the first study applying this approach to evaluate different ejaculates and straws from the same individual. More work must be done to improve seminal dose calculations in assisted reproductive programs.

Phosphatidylcholine transfer protein interacts with thioesterase superfamily member 2 to attenuate insulin signaling.

PubMed

Ersoy, Baran A; Tarun, Akansha; D'Aquino, Katharine; Hancer, Nancy J; Ukomadu, Chinweike; White, Morris F; Michel, Thomas; Manning, Brendan D; Cohen, David E

2013-07-30

Phosphatidylcholine transfer protein (PC-TP) is a phospholipid-binding protein that is enriched in liver and that interacts with thioesterase superfamily member 2 (THEM2). Mice lacking either protein exhibit improved hepatic glucose homeostasis and are resistant to diet-induced diabetes. Insulin receptor substrate 2 (IRS2) and mammalian target of rapamycin complex 1 (mTORC1) are key effectors of insulin signaling, which is attenuated in diabetes. We found that PC-TP inhibited IRS2, as evidenced by insulin-independent IRS2 activation after knockdown, genetic ablation, or chemical inhibition of PC-TP. In addition, IRS2 was activated after knockdown of THEM2, providing support for a role for the interaction of PC-TP with THEM2 in suppressing insulin signaling. Additionally, we showed that PC-TP bound to tuberous sclerosis complex 2 (TSC2) and stabilized the components of the TSC1-TSC2 complex, which functions to inhibit mTORC1. Preventing phosphatidylcholine from binding to PC-TP disrupted interactions of PC-TP with THEM2 and TSC2, and disruption of the PC-TP-THEM2 complex was associated with increased activation of both IRS2 and mTORC1. In livers of mice with genetic ablation of PC-TP or that had been treated with a PC-TP inhibitor, steady-state amounts of IRS2 were increased, whereas those of TSC2 were decreased. These findings reveal a phospholipid-dependent mechanism that suppresses insulin signaling downstream of its receptor.

Phosphatidylcholine Transfer Protein Interacts with Thioesterase Superfamily Member 2 to Attenuate Insulin Signaling

PubMed Central

Ersoy, Baran A.; Tarun, Akansha; D’Aquino, Katharine; Hancer, Nancy J.; Ukomadu, Chinweike; White, Morris F.; Michel, Thomas; Manning, Brendan D.; Cohen, David E.

2014-01-01

Phosphatidylcholine transfer protein (PC-TP) is a phospholipid-binding protein that is enriched in liver and that interacts with thioesterase superfamily member 2 (THEM2). Mice lacking either protein exhibit improved hepatic glucose homeostasis and are resistant to diet-induced diabetes. Insulin receptor substrate 2 (IRS2) and mammalian target of rapamycin complex 1 (mTORC1) are key effectors of insulin signaling, which is attenuated in diabetes. We found that PC-TP inhibited IRS2, as evidenced by insulin-independent IRS2 activation following knockdown, genetic ablation, or chemical inhibition of PC-TP. In addition, IRS2 was activated after knockdown of THEM2, providing support for a role for the interaction of PC-TP with THEM2 in suppressing insulin signaling. Additionally, we showed that PC-TP bound to tuberous sclerosis complex 2 (TSC2) and stabilized the components of the TSC1-TSC2 complex, which functions to inhibit mTORC1. Preventing phosphatidylcholine from binding to PC-TP disrupted interactions of PC-TP with THEM2 and TSC2, and disruption of the PC-TP–THEM2 complex was associated with increased activation of both IRS2 and mTORC1. In livers of mice with genetic ablation of PC-TP or that had been treated with a PC-TP inhibitor, steady-state amounts of IRS2 were increased, whereas those of TSC2 were decreased. These findings reveal a phospholipid-dependent mechanism that suppresses insulin signaling downstream of its receptor. PMID:23901139

Imaging the molecular outflows of the prototypical ULIRG NGC 6240 with ALMA

NASA Astrophysics Data System (ADS)

Saito, T.; Iono, D.; Ueda, J.; Espada, D.; Sliwa, K.; Nakanishi, K.; Lu, N.; Xu, C. K.; Michiyama, T.; Kaneko, H.; Yamashita, T.; Ando, M.; Yun, M. S.; Motohara, K.; Kawabe, R.

2018-03-01

We present 0.97 × 0.53 arcsec2 (470 pc × 250 pc) resolution CO (J = 2-1) observations towards the nearby luminous merging galaxy NGC 6240 with the Atacama Large Millimeter/submillimeter Array. We confirmed a strong CO concentration within the central 700 pc, which peaks between the double nuclei, surrounded by extended CO features along the optical dust lanes (˜11 kpc). We found that the CO emission around the central, a few kpc, has extremely broad velocity wings with full width at zero intensity ˜ 2000 km s-1, suggesting a possible signature of molecular outflow(s). In order to extract and visualize the high-velocity components in NGC 6240, we performed a multiple Gaussian fit to the CO data cube. The distribution of the broad CO components shows four extremely large line width regions (˜1000 km s-1) located 1-2 kpc away from both nuclei. Spatial coincidence of the large line width regions with H α, near-IR H2, and X-ray suggests that the broad CO (2-1) components are associated with nuclear outflows launched from the double nuclei.

GAC: Gene Associations with Clinical, a web based application

PubMed Central

Zhang, Xinyan; Rupji, Manali; Kowalski, Jeanne

2018-01-01

We present GAC, a shiny R based tool for interactive visualization of clinical associations based on high-dimensional data. The tool provides a web-based suite to perform supervised principal component analysis (SuperPC), an approach that uses both high-dimensional data, such as gene expression, combined with clinical data to infer clinical associations. We extended the approach to address binary outcomes, in addition to continuous and time-to-event data in our package, thereby increasing the use and flexibility of SuperPC.  Additionally, the tool provides an interactive visualization for summarizing results based on a forest plot for both binary and time-to-event data.  In summary, the GAC suite of tools provide a one stop shop for conducting statistical analysis to identify and visualize the association between a clinical outcome of interest and high-dimensional data types, such as genomic data. Our GAC package has been implemented in R and is available via http://shinygispa.winship.emory.edu/GAC/. The developmental repository is available at https://github.com/manalirupji/GAC. PMID:29263780

Development a computer codes to couple PWR-GALE output and PC-CREAM input

NASA Astrophysics Data System (ADS)

Kuntjoro, S.; Budi Setiawan, M.; Nursinta Adi, W.; Deswandri; Sunaryo, G. R.

2018-02-01

Radionuclide dispersion analysis is part of an important reactor safety analysis. From the analysis it can be obtained the amount of doses received by radiation workers and communities around nuclear reactor. The radionuclide dispersion analysis under normal operating conditions is carried out using the PC-CREAM code, and it requires input data such as source term and population distribution. Input data is derived from the output of another program that is PWR-GALE and written Population Distribution data in certain format. Compiling inputs for PC-CREAM programs manually requires high accuracy, as it involves large amounts of data in certain formats and often errors in compiling inputs manually. To minimize errors in input generation, than it is make coupling program for PWR-GALE and PC-CREAM programs and a program for writing population distribution according to the PC-CREAM input format. This work was conducted to create the coupling programming between PWR-GALE output and PC-CREAM input and programming to written population data in the required formats. Programming is done by using Python programming language which has advantages of multiplatform, object-oriented and interactive. The result of this work is software for coupling data of source term and written population distribution data. So that input to PC-CREAM program can be done easily and avoid formatting errors. Programming sourceterm coupling program PWR-GALE and PC-CREAM is completed, so that the creation of PC-CREAM inputs in souceterm and distribution data can be done easily and according to the desired format.

The economic and clinical impact of an inpatient palliative care consultation service: a multifaceted approach.

PubMed

Ciemins, Elizabeth L; Blum, Linda; Nunley, Marsha; Lasher, Andrew; Newman, Jeffrey M

2007-12-01

While there has been a rapid increase of inpatient palliative care (PC) programs, the financial and clinical benefits have not been well established. Determine the effect of an inpatient PC consultation service on costs and clinical outcomes. Multifaceted study included: (1) interrupted time-series design utilizing mean daily costs preintervention and postintervention; (2) matched cohort analysis comparing PC to usual care patients; and (3) analysis of symptom control after consultation. Large private, not-for-profit, academic medical center in San Francisco, California, 2004-2006. Time series analysis included 282 PC patients; matched cohorts included 27 PC with 128 usual care patients; clinical outcome analysis of 48 PC patients. Mean daily patient costs and length of stay (LOS); pain, dyspnea, and secretions assessment scores. Mean daily costs were reduced 33% (p < 0.01) from preintervention to postintervention period. Mean length of stay (LOS) was reduced 30%. Mean daily costs for PC patients were 14.5% lower compared to usual care patients (p < 0.01). Pain, dyspnea, and secretions scores were reduced by 86%, 64%, and 87%, respectively. Over the study period, time to PC referral as well as overall ALOS were reduced by 50%. The large reduction in mean daily costs and LOS resulted in an estimated annual savings of $2.2 million in the study hospital. Our results extend the evidence base of financial and clinical benefits associated with inpatient PC programs. We recommend additional study of best practices for identifying patients and providing consultation services, in addition to progressive management support and reimbursement policy.

CARA Risk Assessment Thresholds

NASA Technical Reports Server (NTRS)

Hejduk, M. D.

2016-01-01

Warning remediation threshold (Red threshold): Pc level at which warnings are issued, and active remediation considered and usually executed. Analysis threshold (Green to Yellow threshold): Pc level at which analysis of event is indicated, including seeking additional information if warranted. Post-remediation threshold: Pc level to which remediation maneuvers are sized in order to achieve event remediation and obviate any need for immediate follow-up maneuvers. Maneuver screening threshold: Pc compliance level for routine maneuver screenings (more demanding than regular Red threshold due to additional maneuver uncertainty).

Graphene-enhanced intermolecular interaction at interface between copper- and cobalt-phthalocyanines

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

Dou, Wei-Dong; Center of Super-Diamond and Advanced Films; Huang, Shu-Ping

2015-10-07

Interfacial electronic structures of copper-phthalocyanine (CuPc), cobalt-phthalocyanine (CoPc), and graphene were investigated experimentally by using photoelectron spectroscopy. While the CuPc/graphene interface shows flat band structure and negligible interfacial dipole indicating quite weak molecule-substrate interaction, the CuPc/CoPc/graphene interface shows a large interfacial dipole and obvious energy level bending. Controlled experiments ruled out possible influences from the change in film structure of CuPc and pure π–π interaction between CoPc and CuPc. Analysis based on X-ray photoelectron spectroscopy and density functional theory reveals that the decrease in the work function for the CuPc/CoPc/graphene system is induced by the intermolecular interaction between CuPc andmore » CoPc which is enhanced owning to the peculiar electronic properties at the CoPc-graphene interface.« less

Ecological characteristics of Simulium breeding sites in West Africa.

PubMed

Cheke, Robert A; Young, Stephen; Garms, Rolf

2017-03-01

Twenty-nine taxa of Simulium were identified amongst 527 collections of larvae and pupae from untreated rivers and streams in Liberia (362 collections in 1967-71 & 1989), Togo (125 in 1979-81), Benin (35 in 1979-81) and Ghana (5 in 1980-81). Presence or absence of associations between different taxa were used to group them into six clusters using Ward agglomerative hierarchical cluster analysis. Environmental data associated with the pre-imaginal habitats were then analysed in relation to the six clusters by one way ANOVA. The results revealed significant effects in determining the clusters of maximum river width (all P<0.001 unless stated otherwise), water temperature, dry bulb air temperature, relative humidity, altitude, type of water (on a range from trickle to large river), water level, slope, current, vegetation, light conditions, discharge, length of breeding area, environs, terrain, river bed type (P<0.01), and the supports to which the insects were attached (P<0.01). When four non-significant contributors (wet bulb temperature, river features, height of waterfall and depth) were excluded and the reduced data-set analysed by principal components analysis (PCA), the first two principal components (PCs) accounted for 87% of the variance, with geographical features dominant in PC1 and hydrological characteristics in PC2. The analyses also revealed the ecological characteristics of each taxon's pre-imaginal habitats, which are discussed with particular reference to members of the Simulium damnosum species complex, whose breeding site distributions were further analysed by canonical correspondence analysis (CCA), a method also applied to the data on non-vector species. Copyright © 2016 Elsevier B.V. All rights reserved.

The fractal characteristic of facial anthropometric data for developing PCA fit test panels for youth born in central China.

PubMed

Yang, Lei; Wei, Ran; Shen, Henggen

2017-01-01

New principal component analysis (PCA) respirator fit test panels had been developed for current American and Chinese civilian workers based on anthropometric surveys. The PCA panels used the first two principal components (PCs) obtained from a set of 10 facial dimensions. Although the PCA panels for American and Chinese subjects adopted the bivairate framework with two PCs, the number of the PCs retained in the PCA analysis was different between Chinese subjects and Americans. For the Chinese youth group, the third PC should be retained in the PCA analysis for developing new fit test panels. In this article, an additional number label (ANL) is used to explain the third PC in PCA analysis when the first two PCs are used to construct the PCA half-facepiece respirator fit test panel for Chinese group. The three-dimensional box-counting method is proposed to estimate the ANLs by calculating fractal dimensions of the facial anthropometric data of the Chinese youth. The linear regression coefficients of scale-free range R 2 are all over 0.960, which demonstrates that the facial anthropometric data of the Chinese youth has fractal characteristic. The youth subjects born in Henan province has an ANL of 2.002, which is lower than the composite facial anthropometric data of Chinese subjects born in many provinces. Hence, Henan youth subjects have the self-similar facial anthropometric characteristic and should use the particular ANL (2.002) as the important tool along with using the PCA panel. The ANL method proposed in this article not only provides a new methodology in quantifying the characteristics of facial anthropometric dimensions for any ethnic/racial group, but also extends the scope of PCA panel studies to higher dimensions.

Survey and Alighment for the ALS Project at LBL Berkeley

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

Keller, R.; Lauritzen, T.; /LBL, Berkeley

2005-08-12

The Advanced Light Source (ALS), now under construction at Lawrence Berkeley Laboratory, is a synchrotron radiation source of the third generation designed to produce extremely bright photon beams in the UV and soft X-ray regions. Its main accelerator components are a 1-1.9 GeV electron storage ring with 196.8 m circumference and 12 super-periods, a 1.5 GeV booster synchrotron with 75.0 m circumference and 4 super-periods, and a 50 MeV linac, as shown in Fig. 1. The storage ring has particularly tight positioning tolerances for lattice magnets and other components to assure the required operational characteristics. The general survey and alignmentmore » concept for the ALS is based on a network of fixed monuments installed in the building floor, to which all component positions are referred. Measurements include electronic distance measurements and separate sightings for horizontal and vertical directions, partially with automated electronic data capture. Most of the data processing is accomplished by running a customized version of PC-GEONET. It provides raw data storage, data reduction, and the calculation of adjusted coordinates, as well as an option for error analysis. PC-GEONET has also been used to establish an observation plan for the monuments and calculate their expected position accuracies, based on approximate coordinates. Additionally, for local survey tasks, the commercial software package ECDS is used. In this paper, the ALS survey and alignment strategy and techniques are presented and critically discussed. First experiences with the alignment of the linac and booster components are described.« less

Deconvolution of ferredoxin, plastocyanin, and P700 transmittance changes in intact leaves with a new type of kinetic LED array spectrophotometer.

PubMed

Klughammer, Christof; Schreiber, Ulrich

2016-05-01

A newly developed compact measuring system for assessment of transmittance changes in the near-infrared spectral region is described; it allows deconvolution of redox changes due to ferredoxin (Fd), P700, and plastocyanin (PC) in intact leaves. In addition, it can also simultaneously measure chlorophyll fluorescence. The major opto-electronic components as well as the principles of data acquisition and signal deconvolution are outlined. Four original pulse-modulated dual-wavelength difference signals are measured (785-840 nm, 810-870 nm, 870-970 nm, and 795-970 nm). Deconvolution is based on specific spectral information presented graphically in the form of 'Differential Model Plots' (DMP) of Fd, P700, and PC that are derived empirically from selective changes of these three components under appropriately chosen physiological conditions. Whereas information on maximal changes of Fd is obtained upon illumination after dark-acclimation, maximal changes of P700 and PC can be readily induced by saturating light pulses in the presence of far-red light. Using the information of DMP and maximal changes, the new measuring system enables on-line deconvolution of Fd, P700, and PC. The performance of the new device is demonstrated by some examples of practical applications, including fast measurements of flash relaxation kinetics and of the Fd, P700, and PC changes paralleling the polyphasic fluorescence rise upon application of a 300-ms pulse of saturating light.

Raman and coherent anti-Stokes Raman scattering microscopy studies of changes in lipid content and composition in hormone-treated breast and prostate cancer cells

NASA Astrophysics Data System (ADS)

Potcoava, Mariana C.; Futia, Gregory L.; Aughenbaugh, Jessica; Schlaepfer, Isabel R.; Gibson, Emily A.

2014-11-01

Increasing interest in the role of lipids in cancer cell proliferation and resistance to drug therapies has motivated the need to develop better tools for cellular lipid analysis. Quantification of lipids in cells is typically done by destructive chromatography protocols that do not provide spatial information on lipid distribution and prevent dynamic live cell studies. Methods that allow the analysis of lipid content in live cells are therefore of great importance. Using micro-Raman spectroscopy and coherent anti-Stokes Raman scattering (CARS) microscopy, we generated a lipid profile for breast (T47D, MDA-MB-231) and prostate (LNCaP, PC3) cancer cells upon exposure to medroxyprogesterone acetate (MPA) and synthetic androgen R1881. Combining Raman spectra with CARS imaging, we can study the process of hormone-mediated lipogenesis. Our results show that hormone-treated cancer cells T47D and LNCaP have an increased number and size of intracellular lipid droplets and higher degree of saturation than untreated cells. MDA-MB-231 and PC3 cancer cells showed no significant changes upon treatment. Principal component analysis with linear discriminant analysis of the Raman spectra was able to differentiate between cancer cells that were treated with MPA, R1881, and untreated.

Density Functional Theory Research into the Reduction Mechanism for the Solvent/Additive in a Sodium-Ion Battery.

PubMed

Liu, Qi; Mu, Daobin; Wu, Borong; Wang, Lei; Gai, Liang; Wu, Feng

2017-02-22

The solid-electrolyte interface (SEI) film in a sodium-ion battery is closely related to capacity fading and cycling stability of the battery. However, there are few studies on the SEI film of sodium-ion batteries and the mechanism of SEI film formation is unclear. The mechanism for the reduction of ethylene carbonate (EC), propylene carbonate (PC), vinylene carbonate (VC), ethylene sulfite (ES), 1,3-propylene sulfite (PS), and fluorinated ethylene carbonate (FEC) is studied by DFT. The reaction activation energies, Gibbs free energies, enthalpies, and structures of the transition states are calculated. It is indicated that VC, ES, and PS additives in the electrolyte are all easier to form organic components in the anode SEI film by one-electron reduction. The priority of one-electron reduction to produce organic SEI components is in the order of VC>PC>EC; two-electron reduction to produce the inorganic Na 2 CO 3 component is different and follows the order of EC>PC>VC. Two-electron reduction for sulfites ES and PS to form inorganic Na 2 SO 3 is harder than that of carbonate ester reduction. It is also suggested that the one- and two-electron reductive decomposition pathway for FEC is more feasible to produce inorganic NaF components. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ligand-independent activation of EphA2 by arachidonic acid induces metastasis-like behaviour in prostate cancer cells

PubMed Central

Tawadros, T; Brown, M D; Hart, C A; Clarke, N W

2012-01-01

Background: High intake of omega-6 polyunsaturated fatty acids (PUFA) has been associated with clinical progression in prostate cancer (CaP). This study investigates the signalling mechanism by which the omega-6 PUFA arachidonic acid (AA) induces prostatic cellular migration to bone marrow stroma. Methods: Western blot analysis of the PC-3, PC3-GFP, DU 145 and LNCaP cells or their lipid raft (LR) components post AA stimulation was conducted in association with assays for adhesion and invasion through the bone marrow endothelial monolayers. Results: Arachidonic acid increased transendothelial migration of PC3-GFP cells (adhesion 37%±0.08, P=0.0124; transmigration 270%±0.145, P=0.0008). Akt, Src and focal adhesion kinase (FAK) pathways were induced by AA and integrally involved in transendothelial migration. LR were critical in AA uptake and induced Akt activity. Ephrin receptor A2 (EphA2), localised in LR, is expressed in DU 145 and PC-3 cells. Arachidonic acid induced a rapid increase of EphA2 Akt-dependent/ligand-independent activation, while knockdown of the EphrinA1 ligand decreased AA induced transendothelial migration, with an associated decrease in Src and FAK activity. Arachidonic acid activated Akt in EphA2− LNCaP cells but failed to induce BMEC transendothelial invasion. Conclusion: Arachidonic acid induced stimulation of EphA2 in vitro is associated fundamentally with CaP epithelial migration across the endothelial barrier. PMID:23037715

Enhancing Nutritional Contents of Lentinus sajor-caju Using Residual Biogas Slurry Waste of Detoxified Mahua Cake Mixed with Wheat Straw

PubMed Central

Gupta, Aditi; Sharma, Satyawati; Kumar, Ashwani; Alam, Pravej; Ahmad, Parvaiz

2016-01-01

Residual biogas slurries (BGS) of detoxified mahua cake and cow dung were used as supplements to enhance the yield and nutritional quality of Lentinus sajor-caju on wheat straw (WS). Supplementation with 20% BGS gave a maximum yield of 1155 gkg-1 fruit bodies, furnishing an increase of 95.1% over WS control. Significant increase (p ≤ 0.05) in protein content (29.6-38.9%), sugars (29.1-32.3%) and minerals (N, P, K, Fe, Zn) was observed in the fruit bodies. Principle component analysis (PCA) was performed to see the pattern of correlation within a set of observed variables and how these different variables varied in different treatments. PC1 and PC2 represented 90% of total variation in the observed variables. Moisture (%), lignin (%), celluloses (%), and C/N ratio were closely correlated in comparison to Fe, N, and saponins. PCA of amino acids revealed that, PC1 and PC2 represented 74% of total variation in the data set. HPLC confirmed the absence of any saponin residues (characteristic toxins of mahua cake) in fruit bodies and mushroom spent. FTIR studies showed significant degradation of celluloses (22.2-32.4%), hemicelluloses (14.1-23.1%) and lignin (27.4-39.23%) in the spent, along with an increase in nutrition content. The study provided a simple, cost effective approach to improve the yield and nutritional quality of L. sajor-caju by resourceful utilization of BGS. PMID:27790187

New ALMA constraints on the star-forming interstellar medium at low metallicity: a 50 pc view of the blue compact dwarf galaxy SBS 0335-052

NASA Astrophysics Data System (ADS)

Cormier, D.; Bendo, G. J.; Hony, S.; Lebouteiller, V.; Madden, S. C.; Galliano, F.; Glover, S. C. O.; Klessen, R. S.; Abel, N. P.; Bigiel, F.; Clark, P. C.

2017-06-01

Properties of the cold interstellar medium of low-metallicity galaxies are not well known due to the faintness and extremely small scale on which emission is expected. We present deep ALMA band 6 (230 GHz) observations of the nearby, low-metallicity (12 + log (O/H) = 7.25) blue compact dwarf galaxy SBS 0335-052 at an unprecedented resolution of 0.2 arcsec (52 pc). The 12CO J = 2→1 line is not detected and we report a 3σ upper limit of LCO(2-1) = 3.6 × 104 K km s-1 pc2. Assuming that molecular gas is converted into stars with a given depletion time, ranging from 0.02 to 2 Gyr, we find lower limits on the CO-to-H2 conversion factor αCO in the range 102-104 M⊙ pc-2 (K km s-1)-1. The continuum emission is detected and resolved over the two main super star clusters. Re-analysis of the IR-radio spectral energy distribution suggests that the mm-fluxes are not only free-free emission but are most likely also associated with a cold dust component coincident with the position of the brightest cluster. With standard dust properties, we estimate its mass to be as large as 105 M⊙. Both line and continuum results suggest the presence of a large cold gas reservoir unseen in CO even with ALMA.

Optical characteristics of a one-dimensional photonic crystal with an additional regular layer

NASA Astrophysics Data System (ADS)

Tolmachev, V. A.; Baldycheva, A. V.; Krutkova, E. Yu.; Perova, T. S.; Berwick, K.

2009-06-01

In this paper, the forbidden Photonic Band Gaps (PBGs) of a one-dimensional Photonic Crystal (1D PC) with additional regular layer, t for the constant value of the lattice constant A and at normal incident of light beam were investigated. The additional regular layer was formed from both sides of the high-refractive index layer H. The gap map approach and the Transfer Matrix Method were used for numerical analysis of this structure. The limitation of filling fraction values caused by the presence of t-layer was taking into account during calculations of the Stop-Band (SB) regions for threecomponent PC. The red shift of SBs was observed at the introduction of t-layer to conventional two-component 1D PC with optical contrast of N=3.42/1. The blue edge of the first PBG occupied the intermediate position between the blue edges of SBs regions of conventional PCs with different optical contrast N. This gives the opportunity of tuning the optical contrast of PC by introduction of the additional layer, rather than using the filler, as well as fine tuning of the SB edge. The influence of the number of periods m and the optical contrast N on the properties of SBs was also investigated. The effect of the PBG disappearance in the gap map and in the regions of the PBGs of high order was revealed at certain parameters of the additional layer.

ACS sampling system: design, implementation, and performance evaluation

NASA Astrophysics Data System (ADS)

Di Marcantonio, Paolo; Cirami, Roberto; Chiozzi, Gianluca

2004-09-01

By means of ACS (ALMA Common Software) framework we designed and implemented a sampling system which allows sampling of every Characteristic Component Property with a specific, user-defined, sustained frequency limited only by the hardware. Collected data are sent to various clients (one or more Java plotting widgets, a dedicated GUI or a COTS application) using the ACS/CORBA Notification Channel. The data transport is optimized: samples are cached locally and sent in packets with a lower and user-defined frequency to keep network load under control. Simultaneous sampling of the Properties of different Components is also possible. Together with the design and implementation issues we present the performance of the sampling system evaluated on two different platforms: on a VME based system using VxWorks RTOS (currently adopted by ALMA) and on a PC/104+ embedded platform using Red Hat 9 Linux operating system. The PC/104+ solution offers, as an alternative, a low cost PC compatible hardware environment with free and open operating system.

Efficient On-Off Ratiometric Fluorescence Probe for Cyanide Ion Based on Perturbation of the Interaction between Gold Nanoclusters and a Copper(II)-Phthalocyanine Complex.

PubMed

Shojaeifard, Zahra; Hemmateenejad, Bahram; Shamsipur, Mojtaba

2016-06-22

A new ratiometric fluorescent sensor was developed for the sensitive and selective detection of cyanide ion (CN(-)) in aqueous media. The ratiometric sensing system is based on CN(-) modulated recovery of copper(II) phthalocyanine (Cu(PcTs)) fluorescence signal at the expense of diminished fluorescence intensity of gold nanoclusters (AuNCs). Preliminary experiments revealed that the AuNCs and Cu(PcTs) possess a turn-off effect on each other, the interaction of which being verified through studying their interactions by principle component analysis (PCA) and multivariate cure resolution-alternating least-squares (MCR-ALS) methods. In the presence of CN(-) anion, the AuNCs and Cu(PcTs) interaction was perturbed, so that the fluorescence of Cu (PcTs), already quenched by AuNCs, was found to be efficiently recovered, while the fluorescence intensity of AuNCs was quenched via the formation of a stable [Au(CN)2](-) species. The ratiometric variation of AuNCs and Cu(PcTs) fluorescence intensities leads to designing a highly sensitive probe for CN(-) ion detection. Under the optimal conditions, CN(-) anion was detected without needing any etching time, over the concentration range of 100 nM-220 μM, with a detection limit of 75 nM, which is much lower than the allowable level of CN(-) in water permitted by the World Health Organization (WHO). Moreover, the detection of CN(-) was developed based on the CN(-) effects on the blue and red florescent colors of Cu(PcTs) and AuNCs, respectively. The designed probe displays a continuous color change from red to blue by addition of CN(-), which can be clearly observed by the naked eye in the range of 7-350 μM, under UV lamp. The prepared AuNCs/Cu(PcTs) probe was successfully utilized for the selective and sensitive determination of CN(-) anion in two different types of natural water (Rodbal dam and rainwater) and also in blood serum as a biological sample.

Composition, distribution, and potential toxicity of organochlorine mixtures in bed sediments of streams

USGS Publications Warehouse

Phillips, Patrick J.; Nowell, Lisa H.; Gilliom, Robert J.; Nakagaki, Naomi; Murray, Karen; VanAlstyne, Carolyn

2010-01-01

Mixtures of organochlorine compounds have the potential for additive or interactive toxicity to organisms exposed in the stream. This study uses a variety of methods to identify mixtures and a modified concentration-addition approach to estimate their potential toxicity at 845 stream sites across the United States sampled between 1992 and 2001 for organochlorine pesticides and polychlorinated biphenyls (PCBs) in bed sediment. Principal-component (PC) analysis identified five PCs that account for 77% of the total variance in 14 organochlorine compounds in the original dataset. The five PCs represent: (1) chlordane-related compounds and dieldrin; (2) p,p′-DDT and its degradates; (3) o,p′-DDT and its degradates; (4) the pesticide degradates oxychlordane and heptachlor epoxide; and (5) PCBs. The PC analysis grouped compounds that have similar chemical structure (such as parent compound and degradate), common origin (in the same technical pesticide mixture), and(or) similar relation of concentrations to land use. For example, the highest concentrations of chlordane compounds and dieldrin occurred at urban sites, reflecting past use of parent pesticides for termite control. Two approaches to characterizing mixtures—PC-based mixtures and unique mixtures—were applied to all 299 samples with a detection of two or more organochlorine compounds. PC-based mixtures are defined by the presence (in the sample) of one or more compounds associated with that PC. Unique mixtures are defined as a specific combination of two or more compounds detected in a sample, regardless of how many other compounds were also detected in that sample. The simplest PC-based mixtures (containing compounds from 1 or 2 PCs) commonly occurred in a variety of land use settings. Complex mixtures (containing compounds from 3 or more PCs) were most common in samples from urban and mixed/urban sites, especially in the Northeast, reflecting high concentrations of multiple chlordane, dieldrin, DDT-related compounds, and(or) PCBs. The most commonly occurring unique mixture (p,p′-DDE, p,p′-DDD) occurred in both simple and complex PC-based mixtures, and at both urban and agricultural sites. Mean Probable Effect Concentration Quotients (PEC-Q) values, which estimate the potential toxicity of organochlorine contaminant mixtures, were highest for complex mixtures. Mean PEC-Q values were highest for urban sites in the Northeast, followed by mixed/urban sites in the Northeast and agricultural sites in cotton growing areas. These results demonstrate that the PEC-Q approach can be used in combination with PC-based and unique mixture analyses to relate potential aquatic toxicity of contaminant mixtures to mixture complexity, land use, and other surrogates for contaminant sources.

Synthesis, Spectral and Photophysical Properties of Anthracene Substituted Phthalocyanines; A Study as Polyurethane Electrospun Nanofibers.

PubMed

Ku, Kyo-Sun; Kumar, Rangaraju Satish; Son, Young-A

2018-03-01

We have designed and synthesized novel symmetrical anthracene substituted zinc(II), copper(II), cobalt(II) and nickel(II) phthalocyanines (PC1, PC2, PC3 and PC4) in this work. For this synthesis, we started from base-catalysed aromatic displacement reaction of 4-nitrophthalonitrile with 9-hydroxyanthracene. The resulting four phthalocyanines (PCs) have been fully characterized by a series of spectroscopic methods including electronic absorption, elemental analysis, MALDI-TOF mass, and IR spectroscopy. The aggregation behavior of these PCs was investigated in different concentrations of chloroform solution. Further thermal stability also investigated by TG analysis. Finally we successfully made phthalocyanine (PC1) blended polyurethane electrospun (ES) nanofibers.

METCAN-PC - METAL MATRIX COMPOSITE ANALYZER

NASA Technical Reports Server (NTRS)

Murthy, P. L.

1994-01-01

High temperature metal matrix composites offer great potential for use in advanced aerospace structural applications. The realization of this potential however, requires concurrent developments in (1) a technology base for fabricating high temperature metal matrix composite structural components, (2) experimental techniques for measuring their thermal and mechanical characteristics, and (3) computational methods to predict their behavior. METCAN (METal matrix Composite ANalyzer) is a computer program developed to predict this behavior. METCAN can be used to computationally simulate the non-linear behavior of high temperature metal matrix composites (HT-MMC), thus allowing the potential payoff for the specific application to be assessed. It provides a comprehensive analysis of composite thermal and mechanical performance. METCAN treats material nonlinearity at the constituent (fiber, matrix, and interphase) level, where the behavior of each constituent is modeled accounting for time-temperature-stress dependence. The composite properties are synthesized from the constituent instantaneous properties by making use of composite micromechanics and macromechanics. Factors which affect the behavior of the composite properties include the fabrication process variables, the fiber and matrix properties, the bonding between the fiber and matrix and/or the properties of the interphase between the fiber and matrix. The METCAN simulation is performed as point-wise analysis and produces composite properties which are readily incorporated into a finite element code to perform a global structural analysis. After the global structural analysis is performed, METCAN decomposes the composite properties back into the localized response at the various levels of the simulation. At this point the constituent properties are updated and the next iteration in the analysis is initiated. This cyclic procedure is referred to as the integrated approach to metal matrix composite analysis. METCAN-PC is written in FORTRAN 77 for IBM PC series and compatible computers running MS-DOS. An 80286 machine with an 80287 math co-processor is required for execution. The executable requires at least 640K of RAM and DOS 3.1 or higher. The package includes sample executables which were compiled under Microsoft FORTRAN v. 5.1. The standard distribution medium for this program is one 5.25 inch 360K MS-DOS format diskette. The contents of the diskette are compressed using the PKWARE archiving tools. The utility to unarchive the files, PKUNZIP.EXE, is included. METCAN-PC was developed in 1992.

Category-based guidance of spatial attention during visual search for feature conjunctions.

PubMed

Nako, Rebecca; Grubert, Anna; Eimer, Martin

2016-10-01

The question whether alphanumerical category is involved in the control of attentional target selection during visual search remains a contentious issue. We tested whether category-based attentional mechanisms would guide the allocation of attention under conditions where targets were defined by a combination of alphanumerical category and a basic visual feature, and search displays could contain both targets and partially matching distractor objects. The N2pc component was used as an electrophysiological marker of attentional object selection in tasks where target objects were defined by a conjunction of color and category (Experiment 1) or shape and category (Experiment 2). Some search displays contained the target or a nontarget object that matched either the target color/shape or its category among 3 nonmatching distractors. In other displays, the target and a partially matching nontarget object appeared together. N2pc components were elicited not only by targets and by color- or shape-matching nontargets, but also by category-matching nontarget objects, even on trials where a target was present in the same display. On these trials, the summed N2pc components to the 2 types of partially matching nontargets were initially equal in size to the target N2pc, suggesting that attention was allocated simultaneously and independently to all objects with target-matching features during the early phase of attentional processing. Results demonstrate that alphanumerical category is a genuine guiding feature that can operate in parallel with color or shape information to control the deployment of attention during visual search. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Mutations disrupting the Kennedy phosphatidylcholine pathway in humans with congenital lipodystrophy and fatty liver disease.

PubMed

Payne, Felicity; Lim, Koini; Girousse, Amandine; Brown, Rebecca J; Kory, Nora; Robbins, Ann; Xue, Yali; Sleigh, Alison; Cochran, Elaine; Adams, Claire; Dev Borman, Arundhati; Russel-Jones, David; Gorden, Phillip; Semple, Robert K; Saudek, Vladimir; O'Rahilly, Stephen; Walther, Tobias C; Barroso, Inês; Savage, David B

2014-06-17

Phosphatidylcholine (PC) is the major glycerophospholipid in eukaryotic cells and is an essential component in all cellular membranes. The biochemistry of de novo PC synthesis by the Kennedy pathway is well established, but less is known about the physiological functions of PC. We identified two unrelated patients with defects in the Kennedy pathway due to biallellic loss-of-function mutations in phosphate cytidylyltransferase 1 alpha (PCYT1A), the rate-limiting enzyme in this pathway. The mutations lead to a marked reduction in PCYT1A expression and PC synthesis. The phenotypic consequences include some features, such as severe fatty liver and low HDL cholesterol levels, that are predicted by the results of previously reported liver-specific deletion of murine Pcyt1a. Both patients also had lipodystrophy, severe insulin resistance, and diabetes, providing evidence for an additional and essential role for PCYT1A-generated PC in the normal function of white adipose tissue and insulin action.

Mutations disrupting the Kennedy phosphatidylcholine pathway in humans with congenital lipodystrophy and fatty liver disease

PubMed Central

Payne, Felicity; Lim, Koini; Girousse, Amandine; Brown, Rebecca J.; Kory, Nora; Robbins, Ann; Xue, Yali; Sleigh, Alison; Cochran, Elaine; Adams, Claire; Dev Borman, Arundhati; Russel-Jones, David; Gorden, Phillip; Semple, Robert K.; Saudek, Vladimir; O’Rahilly, Stephen; Walther, Tobias C.; Barroso, Inês; Savage, David B.

2014-01-01

Phosphatidylcholine (PC) is the major glycerophospholipid in eukaryotic cells and is an essential component in all cellular membranes. The biochemistry of de novo PC synthesis by the Kennedy pathway is well established, but less is known about the physiological functions of PC. We identified two unrelated patients with defects in the Kennedy pathway due to biallellic loss-of-function mutations in phosphate cytidylyltransferase 1 alpha (PCYT1A), the rate-limiting enzyme in this pathway. The mutations lead to a marked reduction in PCYT1A expression and PC synthesis. The phenotypic consequences include some features, such as severe fatty liver and low HDL cholesterol levels, that are predicted by the results of previously reported liver-specific deletion of murine Pcyt1a. Both patients also had lipodystrophy, severe insulin resistance, and diabetes, providing evidence for an additional and essential role for PCYT1A-generated PC in the normal function of white adipose tissue and insulin action. PMID:24889630

Characterization of the PcCdc42 small G protein from Pneumocystis carinii, which interacts with the PcSte20 life cycle regulatory kinase

PubMed Central

Krajicek, Bryan J.; Kottom, Theodore J.; Villegas, Leah

2010-01-01

Pneumocystis carinii (Pc) causes severe pneumonia in immunocompromised hosts. The binding of Pc trophic forms to alveolar epithelial cells is a central feature of infection, inducing the expression and activation of PcSte20, a gene participating in mating, proliferation, and pseudohyphal growth. In related fungi, Ste20 proteins are generally activated by immediate upstream small G proteins of the Cdc42-like family. PcCdc42 has not been previously described in Pneumocystis. To address the potential role of such a G protein in Pneumocystis, PcCdc42 was cloned from a Pc cDNA library. Using the full-length 576-bp PcCdc42 cDNA sequence, a CHEF blot of genomic DNA yielded a single band, providing evidence that this gene is present as a single copy within the genome. The total length of PcCdc42 cDNA was 576 bp with an estimated molecular mass of ∼38 kDa. BLASTP analysis demonstrated greater than 80% homology with other fungal Cdc42p proteins. Northern analysis indicated equal mRNA expression in both cystic and trophic life forms. Heterologous expression of PcCdc42 in Saccharomyces cerevisiae (Sc) demonstrated that PcCdc42p was able to restore growth in an ScCdc42Δ yeast strain. Additional assays with purified PcCdc42 protein demonstrated GTP binding and intrinsic GTPase activity, which was partially but significantly suppressed by Clostridium difficile toxin B, characteristic of Cdc42 GTPases. Furthermore, PcCdc42 protein was also shown to bind to the downstream PCSte20 kinase partner in the presence (but not the absence) of GTP. These data indicate that Pc possesses a Cdc42 gene expressing an active G protein, which binds the downstream regulatory kinase PcSte20, important in Pc life cycle regulation. PMID:19915161

Multivariate analyses reveal a new assemblage of diverse and small archosauriforms (Reptilia, Diapsida) from the Upper Triassic of India

NASA Astrophysics Data System (ADS)

Shafi Bhat, Mohd; Ray, Sanghamitra; Mohan Datta, Pradipendra

2017-04-01

The study is based on a large collection of vertebrate microfossils collected from the Upper Triassic Tiki Formation of the Rewa Gondwana basin of India, which is a mud-dominated fluvial succession. About 8600 kg of mudrocks from the Tiki Formation were screen washed to yield 1865 vertebrate microfossils, of which 67% are isolated teeth. Of these, there are about 450 well-preserved teeth, which are leaf-shaped, slightly recurved and have subtriangular crowns with expanded and asymmetric bases, and distinct denticles both on the posterior or anterior carinae. The morphology of these teeth suggests that these belong to Archosauriformes (Heckert, 2004; Irmis et al., 2007). Since the teeth were found isolated, without being associated with any other skeletal elements, it is not possible to ascertain their taxonomic position up to the generic and species level. However, based on their distinct dental attributes, twelve morphotypes are identified, of which five show similarity with the teeth of the basal saurischian dinosaurs. Principal Component and Canonical Variate analyses (PCA and CVA) are performed on these isolated teeth to evaluate the differentiation of the specimens based on the variance of their variables and to assess the consistency of identification by qualitative and quantitative methods (Hammer and Harper, 2006). PCA and CVA are applied to the variance-covariance matrix of the logarithmically transformed variables, the latter including six measured dimensions characterizing the different crown proportions. Since the first three principal components (PCs) account for more than 98% of the total variance, PC4 is discarded. Principal component scores are plotted on PC 1 and PC 2, and PC 2 and PC 3 to show the scatter of the archosauriform teeth examined. Although distinct clustering of specimens belonging to the different morphotypes is seen, there is considerable overlapping as represented by the convex hull polygons. The quantitative analyses show that many of the teeth collected from the Tiki Formation are similar to that of other known Late Triassic archosauriforms such as Protecovasaurus, Revueltosaurus, Pekinosaurus and Crosbysaurus Although more analyses are required for precise taxonomic identification, the current study highlights a large array of Late Triassic archosauriforms from India, which so far remained unknown. References: Hammer, O., Harper, D.A.T. 2006. Paleontological data analysis. Blackwell Publishing, Ltd., Malden, USA. Heckert, A.B. 2004. Late Triassic microvertebrates from the Upper Triassic Chinle Group (Otischalkian-Adamanian: Carnian), southwestern U.S.A.: New Mexico Museum of Natural History and Science Bulletin 27:1-170. Irmis, R.B., Parker, W.G., Nesbitt, S.J., Liu, J. 2007. Early ornithischian dinosaurs: the Triassic record. Historical Biology 19: 3-22.

The marijuana component cannabidiol inhibits beta-amyloid-induced tau protein hyperphosphorylation through Wnt/beta-catenin pathway rescue in PC12 cells.

PubMed

Esposito, Giuseppe; De Filippis, Daniele; Carnuccio, Rosa; Izzo, Angelo A; Iuvone, Teresa

2006-03-01

Alzheimer's disease (AD) is the most common age-related neurodegenerative disorder. A massive accumulation of beta-amyloid (Abeta) peptide aggregates has been proposed as pivotal event in AD. Abeta-induced toxicity is accompanied by a variegated combination of events including oxidative stress. The Wnt pathway has multiple actions in the cascade of events triggered by Abeta, and drugs that rescue Wnt activity may be considered as novel therapeutics for AD treatment. Cannabidiol, a non-psychoactive marijuana component, has been recently proposed as an antioxidant neuroprotective agent in neurodegenerative diseases. Moreover, it has been shown to rescue PC12 cells from toxicity induced by Abeta peptide. However, the molecular mechanism of cannabidiol-induced neuroprotective effect is still unknown. Here, we report that cannabidiol inhibits hyperphosphorylation of tau protein in Abeta-stimulated PC12 neuronal cells, which is one of the most representative hallmarks in AD. The effect of cannabidiol is mediated through the Wnt/beta-catenin pathway rescue in Abeta-stimulated PC12 cells. These results provide new molecular insight regarding the neuroprotective effect of cannabidiol and suggest its possible role in the pharmacological management of AD, especially in view of its low toxicity in humans.

Finite element analysis performed on radius and tibia HR-pQCT images and fragility fractures at all sites in men.

PubMed

Vilayphiou, Nicolas; Boutroy, Stephanie; Szulc, Pawel; van Rietbergen, Bert; Munoz, Francoise; Delmas, Pierre D; Chapurlat, Roland

2011-05-01

Few studies have investigated bone microarchitecture and biomechanical properties in men. This study assessed in vivo both aspects in a population of 185 men (aged 71 ± 10 years) with prevalent fragility fractures, compared to 185 controls matched for age, height, and weight, from the Structure of the Aging Men's Bones (STRAMBO) cohort. In this case-control study, areal BMD (aBMD) was measured by DXA, bone microarchitecture was assessed by high resolution (HR)-pQCT, and finite element (µFE) analysis was based on HR-pQCT images of distal radius and tibia. A principal component (PC) analysis (PCA) was used to study the association of synthetic PCs with fracture by computing their odds ratio (OR [95%CI]) per SD change. Specific associations with vertebral fracture (n = 100), and nonvertebral fracture (n = 85) were also computed. At both sites, areal and volumetric BMD, cortical thickness and trabecular number, separation, and distribution were significantly worse in cases than in controls, with differences ranging from -6% to 15%. µFE-derived stiffness and failure load were 8% to 9% lower in fractures (p < .01). No difference in load distribution was found between the two groups. After adjustment for aBMD, only differences of µFE-derived stresses, stiffness, and failure load at the tibia remained significant (p < .05). PCA resulted in defining 4 independent PCs, explaining 83% of the total variability of bone characteristics. Nonvertebral fractures were associated with PC1, reflecting bone quantity and strength at the radius (tibia) with OR = 1.64 [1.27-2.12] (2.21 [1.60-3.04]), and with PC2, defined by trabecular microarchitecture, with OR = 1.27 [1.00-1.61]. Severe vertebral fractures were associated with PC1, with OR = 1.56 [1.16-2.09] (2.21 [1.59-3.07]), and with PC2, with OR = 1.55 [1.17-2.06] (1.45 [1.06-1.98]). In conclusion, microarchitecture and biomechanical properties derived from µFE were associated with all types of fractures in men, showing that radius and tibia mechanical properties were relatively representative of distant bone site properties. Copyright © 2011 American Society for Bone and Mineral Research.

Geochemical Study on an Abandoned Copper Smelting Plant Using Rare Earth Elements

NASA Astrophysics Data System (ADS)

Sun, S. H.

2017-12-01

The Shuei Nan Dong Copper Smelting Plant smelting is located on the northern coast of New Taipei City, Taiwan. The plant built in 1906 for but has been shut down since 1987. However, the watershed is continuing to discharge acid mine water into the sea; and, the acid mine drainage releases high amounts of sulfate, heavy metals without any treatment. In this study, the water samples were sequentially collected along the main channel and its tributaries in the watershed. The results of hydrochemical analysis show that the untreated inflow water can be characterized with low pH value of <3 and enriched sulfate, copper and arsenic. However, the water is much less contaminated in the upstream area until a major tributary converge. The results of principal component analysis (PCA) demonstrate that the first principal component (PC) can explain >80% of the total variance and almost all chemical components have high loadings in the PC. Therefore, the hydrochemical properties in the watershed are mainly dominated by the mixing process between main channel and the major tributary but the geochemical reactions during flow down the channel is insignificant. Rare earth elements (REE) are an excellent tracer, which can indicate sources of chemical components and geochemical reactions in water. The analysis results demonstrate two distinct REE patterns. The water with low REE can be characterized by prominent Eu positive anomaly and Ce negative anomaly, which may result from the alteration of Na-plagioclase in sandstone and oxidation reaction when contact with air, respectively. On the contrary, the water with high REE shows only minor Ce negative anomaly and insignificant Eu positive anomaly. In addition, there is an enrichment of middle REE in high-REE water, which is quite different with the REE pattern of pyrite. According to the Grawunder's study (2014), it corresponds to the complexation to sulphite during pyrite oxidation. It is worth noting that REE show no considerable fractionation along the channel and confirms the results from PCA. It can be derived that the water may not reached equilibrium condition. A simple aerated retention pool could dramatically reduce the pollutants due to coprecipitation of iron oxide and aluminum oxide.

Widespread differential maternal and paternal genome effects on fetal bone phenotype at mid-gestation.

PubMed

Xiang, Ruidong; Lee, Alice M C; Eindorf, Tanja; Javadmanesh, Ali; Ghanipoor-Samami, Mani; Gugger, Madeleine; Fitzsimmons, Carolyn J; Kruk, Zbigniew A; Pitchford, Wayne S; Leviton, Alison J; Thomsen, Dana A; Beckman, Ian; Anderson, Gail I; Burns, Brian M; Rutley, David L; Xian, Cory J; Hiendleder, Stefan

2014-11-01

Parent-of-origin-dependent (epi)genetic factors are important determinants of prenatal development that program adult phenotype. However, data on magnitude and specificity of maternal and paternal genome effects on fetal bone are lacking. We used an outbred bovine model to dissect and quantify effects of parental genomes, fetal sex, and nongenetic maternal effects on the fetal skeleton and analyzed phenotypic and molecular relationships between fetal muscle and bone. Analysis of 51 bone morphometric and weight parameters from 72 fetuses recovered at day 153 gestation (54% term) identified six principal components (PC1-6) that explained 80% of the variation in skeletal parameters. Parental genomes accounted for most of the variation in bone wet weight (PC1, 72.1%), limb ossification (PC2, 99.8%), flat bone size (PC4, 99.7%), and axial skeletal growth (PC5, 96.9%). Limb length showed lesser effects of parental genomes (PC3, 40.8%) and a significant nongenetic maternal effect (gestational weight gain, 29%). Fetal sex affected bone wet weight (PC1, p < 0.0001) and limb length (PC3, p < 0.05). Partitioning of variation explained by parental genomes revealed strong maternal genome effects on bone wet weight (74.1%, p < 0.0001) and axial skeletal growth (93.5%, p < 0.001), whereas paternal genome controlled limb ossification (95.1%, p < 0.0001). Histomorphometric data revealed strong maternal genome effects on growth plate height (98.6%, p < 0.0001) and trabecular thickness (85.5%, p < 0.0001) in distal femur. Parental genome effects on fetal bone were mirrored by maternal genome effects on fetal serum 25-hydroxyvitamin D (96.9%, p < 0.001) and paternal genome effects on alkaline phosphatase (90.0%, p < 0.001) and their correlations with maternally controlled bone wet weight and paternally controlled limb ossification, respectively. Bone wet weight and flat bone size correlated positively with muscle weight (r = 0.84 and 0.77, p < 0.0001) and negatively with muscle H19 expression (r = -0.34 and -0.31, p < 0.01). Because imprinted maternally expressed H19 regulates growth factors by miRNA interference, this suggests muscle-bone interaction via epigenetic factors. © 2014 American Society for Bone and Mineral Research.

Innovative Techniques Simplify Vibration Analysis

NASA Technical Reports Server (NTRS)

2010-01-01

In the early years of development, Marshall Space Flight Center engineers encountered challenges related to components in the space shuttle main engine. To assess the problems, they evaluated the effects of vibration and oscillation. To enhance the method of vibration signal analysis, Marshall awarded Small Business Innovation Research (SBIR) contracts to AI Signal Research, Inc. (ASRI), in Huntsville, Alabama. ASRI developed a software package called PC-SIGNAL that NASA now employs on a daily basis, and in 2009, the PKP-Module won Marshall s Software of the Year award. The technology is also used in many industries: aircraft and helicopter, rocket engine manufacturing, transportation, and nuclear power."

Propagation characteristics of Pc 3 compressional waves generated at the dayside magnetopause

NASA Technical Reports Server (NTRS)

Zhang, X.; Comfort, R. H.; Musielak, Z. E.; Moore, T. E.; Gallagher, D. L.; Green, J. L.

1993-01-01

New, 3D ray tracing of Pc 3 compressional waves from the magnetosheath reveals that the magnetosphere can present a major propagation barrier to the penetration of these waves to the plasmasphere. This barrier is the ion-ion cutoff between the He(+) and O(+) gyroresonances. As a result of the frequency-dependent location of this cutoff, the magnetosphere behaves like a filter for Pc 3 compressional waves, and only low-frequency components of Pc 3 compressional waves can penetrate to inner magnetosphere. Results are in agreement with previous satellite observations. This 'filter action' strongly depends on the relative concentration of He(+) and O(+) and is therefore sensitive to solar and magnetic activity. Ray-tracing results are based on a cold plasma dispersion relation, a semiempirical model of plasma density, and the Mead-Fairfield (1975) magnetic field model.

Correlations among Galaxy Properties from the Sloan Digital Sky Survey

NASA Astrophysics Data System (ADS)

Li, Zhongmu; Mao, Caiyan

2013-07-01

Galaxies are complex systems with many properties. Correlations among galaxy properties can supply important clues for studying the formation and evolution of galaxies. Using principal component analysis and least-squares fitting, this paper investigates the correlations among galactic parameters involving more properties (color, morphology, stellar population, and absolute magnitude) than previous studies. We use a volume-limited sample (whole sample) of 75,423 galaxies that was selected from the Sloan Digital Sky Survey Data Release 2 and divided into two subsamples (blue and red samples) using a critical color of (g - r) = 0.70 mag. In addition to recovering some previous results, we also obtain some new results. First, all separators for dividing galaxies into two groups can be related via good parameter-first principal component (PC1) correlations. A critical PC1 that indicates whether or not stellar age (or the evolution of a stellar population over time) is important can be used to separate galaxies. This suggests that a statistical parameter, PC1, is helpful in understanding the physical separators of galaxies. In addition, stellar age is shown to be unimportant for red galaxies, while both stellar age and mass are dominating parameters of blue galaxies. This suggests that the various numbers of dominating parameters of galaxies may result from the use of different samples. Finally, some parameters are shown to be correlated, and quantitative fits for a few correlations are obtained, e.g., log(t) = 8.57 + 1.65 (g - r) for the age (log t) and color (g - r) of blue galaxies and log (M *) = 4.31 - 0.30 M r for the stellar mass (log M *) and absolute magnitude (M r) of red galaxies. The median relationships between various parameter pairs are also presented for comparison.

Evaluating methods to visualize patterns of genetic differentiation on a landscape.

PubMed

House, Geoffrey L; Hahn, Matthew W

2018-05-01

With advances in sequencing technology, research in the field of landscape genetics can now be conducted at unprecedented spatial and genomic scales. This has been especially evident when using sequence data to visualize patterns of genetic differentiation across a landscape due to demographic history, including changes in migration. Two recent model-based visualization methods that can highlight unusual patterns of genetic differentiation across a landscape, SpaceMix and EEMS, are increasingly used. While SpaceMix's model can infer long-distance migration, EEMS' model is more sensitive to short-distance changes in genetic differentiation, and it is unclear how these differences may affect their results in various situations. Here, we compare SpaceMix and EEMS side by side using landscape genetics simulations representing different migration scenarios. While both methods excel when patterns of simulated migration closely match their underlying models, they can produce either un-intuitive or misleading results when the simulated migration patterns match their models less well, and this may be difficult to assess in empirical data sets. We also introduce unbundled principal components (un-PC), a fast, model-free method to visualize patterns of genetic differentiation by combining principal components analysis (PCA), which is already used in many landscape genetics studies, with the locations of sampled individuals. Un-PC has characteristics of both SpaceMix and EEMS and works well with simulated and empirical data. Finally, we introduce msLandscape, a collection of tools that streamline the creation of customizable landscape-scale simulations using the popular coalescent simulator ms and conversion of the simulated data for use with un-PC, SpaceMix and EEMS. © 2017 John Wiley & Sons Ltd.

Mission Risk Reduction Regulatory Change Management

NASA Technical Reports Server (NTRS)

Scroggins, Sharon

2007-01-01

NASA Headquarters Environmental Management Division supports NASA's mission to pioneer the future in space exploration, scientific discovery, and aeronautics research by integrating environmental considerations into programs and projects early-on, thereby proactively reducing NASA's exposure to institutional, programmatic and operational risk. As part of this effort, NASA established the Principal Center for Regulatory Risk Analysis and Communication (RRAC PC) as a resource for detecting, analyzing, and communicating environmental regulatory risks to the NASA stakeholder community. The RRAC PC focuses on detecting emerging environmental regulations and other operational change drivers that may pose risks to NASA programs and facilities, and effectively communicating the potential risks. For example, regulatory change may restrict how and where certain activities or operations may be conducted. Regulatory change can also directly affect the ability to use certain materials by mandating a production phase-out or restricting usage applications of certain materials. Regulatory change can result in significant adverse impacts to NASA programs and facilities due to NASA's stringent performance requirements for materials and components related to human-rated space vehicles. Even if a regulation does not directly affect NASA operations, U.S. and international regulations can pose program risks indirectly through requirements levied on manufacturers and vendors of components and materials. For example, manufacturers can change their formulations to comply with new regulatory requirements. Such changes can require time-consuming and costly requalification certification for use in human spaceflight programs. The RRAC PC has implemented a system for proactively managing regulatory change to minimize potential adverse impacts to NASA programs and facilities. This presentation highlights the process utilized by the RRACPC to communicate regulatory change and the associated potential risks within NASA, as well as the process for communicating and cooperating with other government agencies and industry partners, both domestic and international, to ensure mission success.

A Weak Bar Potential and Massive Core in the Seyfert 2 Galaxy NGC 3079: CO(1--0) observations using the Nobeyama Millimeter Array

NASA Astrophysics Data System (ADS)

Koda, J.; Sofue, Y.; Kohno, K.; Okumura, S. K.; Irwin, Judith A.

We present our recent 12CO (1-0) observations in the central molecular disk of the Hα/radio lobe galaxy NGC 3079 with the Nobeyama Millimeter Array. We show four kinematically distinct components in the observed molecular disk: a main disk, spiral arms, a nuclear disk and a nuclear core. We discuss their possible origins using a simple orbit-analysis model in a weak bar potential. We show that three of the four components are well-understood by typical gaseous orbits in a weak bar, such as gaseous x1- and x2-orbits. The main disk and spiral arms are well-understood as the gaseous x1-orbits and their associated crowding, respectively. The nuclear disk is naturally explained by the x2-orbits. However, the nuclear core, showing a high velocity of about 200kmps at a radius of about 100pc, cannot be explained by those gaseous orbits in a bar. Furthermore, no other orbits, derived by bars, cannot be responsible for the nuclear core. Thus we discuss that this component should be attributed to a central massive core with a dynamical mass of about 109Msun within the central 100pc radius. This mass is three orders of magnitude more massive than that of a central black hole in this galaxy. More detailed descriptions are presented in Koda et al. (2002).

Modification of isoflavone profiles in a fermented soy food with almond powder.

PubMed

Park, MinHee; Jeong, Min Kyu; Kim, MiJa; Lee, JaeHwan

2012-01-01

Isoflavone profiles of a fermented soy food, cheonggukjang, were modified using almond powder. Isoflavones were analyzed by high performance liquid chromatography (HPLC) with an ultraviolet detector. Malonyl derivatives of isoflavones decreased and aglycones of isoflavones increased in samples with almond powder for 48 h. As added, almond powder increased from 0%, 5%, and 10% (w/w), amounts of aglycones increased to 21.11%, 26.63%, and 32.45% for 48 h, respectively. β-Glucosidase activity in 5% and 10% almond added samples was significantly higher than samples without addition of almond (P < 0.05). The content of succinyl daidzin and succinyl genistin, new metabolites from isoflavones, in almond-added cheonggukjang was significantly lower than control samples, implying that β-glucosidase activity from almond affected negatively the formation of succinyl derivatives (P < 0.05). Principal component analysis (PCA) for isoflavone distribution showed that first principal component (PC1) and second principal component (PC2) expressed 64.78% and 22.26% of the data variability, respectively. Biotransformation of isoflavones in any fermented soy foods can be achieved using natural products containing high β-glucosidase activity such as almond. The results of this study can help to modify the structural transformation of phytochemicals in any fermented soy foods using natural products. Adjusting the content of almond powder can achieve wanted profiles, for example, high aglycones content. Also, content of metabolites such as succinyl derivatives can be controlled using proper amounts of almond and fermentation time. © 2011 Institute of Food Technologists®

Molecular Weight Affected Antioxidant, Hypoglycemic and Hypotensive Activities of Cold Water Extract from Pleurotus citrinopileatus.

PubMed

Chen, Pao-Huei; Weng, Yih-Ming; Lin, Shu-Mei; Yu, Zer-Ran; Wang, Be-Jen

2017-10-01

Cold water extract of P. citrinopileatus (CWEPC) was fractioned into 4 fractions, PC-I (<1 kDa), PC-II (1-3.5 kDa), PC-III (3.5-10 kDa), and PC-IV (>10 kDa), by ultrafiltration. The antioxidant activities, the inhibition of pancreatic α-amylase, intestinal α-glucosidase, and hypertension-linked angiotensin converting enzyme (ACE), as well as the contents of polysaccharides, protein, and phenolic compounds of 4 fractions were determined. The results showed that lower MW fractions exerted a higher antioxidant activity, which was correlated to phenolic contents. The high molecular fraction (PC-IV) exhibited significantly higher inhibitory activity on α-amylase, α-glucosidase, and ACE compared to CWEPC and the other 3 lower MW fractions (<10 kDa), which was more related to protein contents. The inhibition capability of CWEPC and PC-IV on α-amylase activity was 1/13.4 to 1/2.7 relative to that of acarbose, respectively. Kinetic data revealed that PC-IV fraction followed a noncompetitive inhibition pattern on α-glucosidase activity. The study demonstrated that various MW fractions and types of components contribute to different biological functions of P. citrinopileatus and it is protein constituents but not peptides responsible for the hypoglycemic potential of CWEPC. © 2017 Institute of Food Technologists®.

Quantitation of isobaric phosphatidylcholine species in human plasma using a hybrid quadrupole linear ion trap mass spectrometer

USDA-ARS?s Scientific Manuscript database

Phosphatidylcholine (PC) species in human plasma are used as biomarkers of disease. PC biomarkers are often limited by the inability to separate isobaric PC. In this work, we developed a targeted shotgun approach for analysis of isobaric and isomeric PC. This approach is comprised of two mass spectr...

Quantification of phytochelatins in Chlamydomonas reinhardtii using ferrocene-based derivatization.

PubMed

Bräutigam, Anja; Bomke, Susanne; Pfeifer, Thorben; Karst, Uwe; Krauss, Gerd-Joachim; Wesenberg, Dirk

2010-08-01

A method for the identification and quantification of canonic and isoforms of phytochelatins (PCs) from Chlamydomonas reinhardtii was developed. After disulfide reduction with tris(2-carboxyethyl)phosphine (TCEP) PCs were derivatized with ferrocenecarboxylic acid (2-maleimidoyl)ethylamide (FMEA) in order to avoid oxidation of the free thiol functions during analysis. Liquid chromatography (LC) coupled to electrospray mass spectrometry (ESI-MS) and inductively coupled plasma-mass spectrometry (ICP-MS) was used for rapid and quantitative analysis of the precolumn derivatized PCs. PC(2-4), CysGSH, CysPC(2-4), CysPC(2)desGly, CysPC(2)Glu and CysPC(2)Ala were determined in the algal samples depending on the exposure of the cells to cadmium ions.

Lipophilic organic pollutants induce changes in phospholipid and membrane protein composition leading to Vero cell morphological change.

PubMed

Liao, Ting T; Wang, Lei; Jia, Ru W; Fu, Xiao H; Chua, Hong

2014-01-01

Membrane damage related to morphological change in Vero cells is a sensitive index of the composite biotoxicity of trace lipophilic chemicals. However, judging whether the morphological change in Vero cells happens and its ratio are difficult because it is not a quantitative characteristic. To find biomarkers of cell morphological change for quantitatively representing the ratio of morphological changed cell, the mechanism of cell membrane damage driven by typical lipophilic chemicals, such as trichlorophenol (TCP) and perfluorooctanesulphonate (PFOS), was explored. The ratio of morphologically changed cells generally increased with increased TCP or PFOS concentrations, and the level of four major components of phospholipids varied with concentrations of TCP or PFOS, but only the ratio of phosphatidylcholine (PC)/phosphatidylethanolamine (PE) decreased regularly as TCP or PFOS concentrations increased. Analysis of membrane proteins showed that the level of vimentin in normal cell membranes is high, while it decreases or vanishes after TCP exposure. These variations in phospholipid and membrane protein components may result in membrane leakage and variation in rigid structure, which leads to changes in cell morphology. Therefore, the ratio of PC/PE and amount of vimentin may be potential biomarkers for representing the ratio of morphological changed Vero cell introduced by trace lipophilic compounds, thus their composite bio-toxicity.

Geochemical speciation and pollution assessment of heavy metals in surface sediments from Nansi Lake, China.

PubMed

Yang, Liyuan; Wang, Longfeng; Wang, Yunqian; Zhang, Wei

2015-05-01

Sixteen surface sediment samples were collected from Nansi Lake to analyze geochemical speciation of heavy metals including Cd, As, Pb, Cr, and Zn, assess their pollution level, and determine the spatial distribution of the non-residual fraction. Results showed that Cd had higher concentrations in water-soluble and exchangeable fractions. As and Pb were mainly observed as humic acid and reducible fractions among the non-residual fractions, while Cr and Zn were mostly locked up in a residual fraction. The mean pollution index (P i) values revealed that the lower lake generally had a higher enrichment degree than the upper lake. Cd (2.73) and As (2.05) were in moderate level of pollution, while the pollution of Pb (1.80), Cr (1.27), and Zn (1.02) appeared at low-level pollution. The calculated pollution load index (PLI) suggested the upper lake suffered from borderline moderate pollution, while the lower lake showed moderate to heavy pollution. Spatial principle component analysis showed that the first principal component (PC1) including Cd, As, and Pb could explain 56.18 % of the non-residual fraction. High values of PC1 were observed mostly in the southern part of Weishan Lake, which indicated greater bioavailability and toxicity of Cd, As, and Pb in this area.

Antiallergic activity of unripe Citrus hassaku fruits extract and its flavanone glycosides on chemical substance-induced dermatitis in mice.

PubMed

Itoh, Kimihisa; Masuda, Megumi; Naruto, Shunsuke; Murata, Kazuya; Matsuda, Hideaki

2009-10-01

Oral administration of a 50% ethanolic extract (CH-ext) obtained from unripe Citrus hassaku fruits collected in July exhibited a potent dose-dependent inhibition of IgE (immunoglobulin E)-mediated triphasic cutaneous reaction at 1 h [immediate phase response (IPR)], 24 h [late phase response (LPR)] and 8 days [very late phase response (vLPR)] after dinitrofluorobenzene challenge in mice. Naringin, a major flavanone glycoside component of CH-ext, showed a potent dose-dependent inhibition against IPR, LPR and vLPR. Neohesperidin, another major glycoside component of CH-ext, showed an inhibition against vLPR. The effect of CH-ext on type IV allergic reaction was examined by determining inhibitory activity against ear swelling in mice by using the picryl chloride-induced contact dermatitis (PC-CD) model. Oral administration (p.o.) of CH-ext and subcutaneous administration (s.c.) of prednisolone inhibited ear swelling during the induction phase of PC-CD. The inhibitory activities of combinations of CH-ext (p.o.) and prednisolone (s.c.) against PC-CD in mice were more potent than those of CH-ext alone and prednisolone alone, without enhancing the adverse effects. Other combinations of prednisolone (s.c.) and flavanone glycoside (p.o.) components of CH-ext, i.e. naringin and neohesperidin, exerted similar synergistic effects.

GeneOnEarth: fitting genetic PC plots on the globe.

PubMed

Torres-Sánchez, Sergio; Medina-Medina, Nuria; Gignoux, Chris; Abad-Grau, María M; González-Burchard, Esteban

2013-01-01

Principal component (PC) plots have become widely used to summarize genetic variation of individuals in a sample. The similarity between genetic distance in PC plots and geographical distance has shown to be quite impressive. However, in most situations, individual ancestral origins are not precisely known or they are heterogeneously distributed; hence, they are hardly linked to a geographical area. We have developed GeneOnEarth, a user-friendly web-based tool to help geneticists to understand whether a linear isolation-by-distance model may apply to a genetic data set; thus, genetic distances among a set of individuals resemble geographical distances among their origins. Its main goal is to allow users to first apply a by-view Procrustes method to visually learn whether this model holds. To do that, the user can choose the exact geographical area from an on line 2D or 3D world map by using, respectively, Google Maps or Google Earth, and rotate, flip, and resize the images. GeneOnEarth can also compute the optimal rotation angle using Procrustes analysis and assess statistical evidence of similarity when a different rotation angle has been chosen by the user. An online version of GeneOnEarth is available for testing and using purposes at http://bios.ugr.es/GeneOnEarth.

Spatial decorrelation stretch of annual (2003-2014) Daymet precipitation summaries on a 1-km grid for California, Nevada, Arizona, and Utah.

PubMed

Ch Miliaresis, George

2016-06-01

A method is presented for elevation (H) and spatial position (X, Y) decorrelation stretch of annual precipitation summaries on a 1-km grid for SW USA for the period 2003 to 2014. Multiple linear regression analysis of the first and second principal component (PC) quantifies the variance in the multi-temporal precipitation imagery that is explained by X, Y, and elevation (h). The multi-temporal dataset is reconstructed from the PC1 and PC2 residual images and the later PCs by taking into account the variance that is not related to X, Y, and h. Clustering of the reconstructed precipitation dataset allowed the definition of positive (for example, in Sierra Nevada, Salt Lake City) and negative (for example, in San Joaquin Valley, Nevada, Colorado Plateau) precipitation anomalies. The temporal and spatial patterns defined from the spatially standardized multi-temporal precipitation imagery provide a tool of comparison for regions in different geographic environments according to the deviation from the precipitation amount that they are expected to receive as function of X, Y, and h. Such a standardization allows the definition of less or more sensitive to climatic change regions and gives an insight in the spatial impact of atmospheric circulation that causes the annual precipitation.

Detection and Site Localization of Phosphorylcholine-Modified Peptides by NanoLC-ESI-MS/MS Using Precursor Ion Scanning and Multiple Reaction Monitoring Experiments

NASA Astrophysics Data System (ADS)

Timm, Thomas; Lenz, Christof; Merkel, Dietrich; Sadiffo, Christian; Grabitzki, Julia; Klein, Jochen; Lochnit, Guenter

2015-03-01

Phosphorylcholine (PC)-modified biomolecules like lipopolysaccharides, glycosphingolipids, and (glyco)proteins are widespread, highly relevant antigens of parasites, since this small hapten shows potent immunomodulatory capacity, which allows the establishment of long-lasting infections of the host. Especially for PC-modified proteins, structural data is rare because of the zwitterionic nature of the PC substituent, resulting in low sensitivities and unusual but characteristic fragmentation patterns. We have developed a targeted mass spectrometric approach using hybrid triple quadrupole/linear ion trap (QTRAP) mass spectrometry coupled to nanoflow chromatography for the sensitive detection of PC-modified peptides from complex proteolytic digests, and the localization of the PC-modification within the peptide backbone. In a first step, proteolytic digests are screened using precursor ion scanning for the marker ions of choline ( m/z 104.1) and phosphorylcholine ( m/z 184.1) to establish the presence of PC-modified peptides. Potential PC-modified precursors are then subjected to a second analysis using multiple reaction monitoring (MRM)-triggered product ion spectra for the identification and site localization of the modified peptides. The approach was first established using synthetic PC-modified synthetic peptides and PC-modified model digests. Following the optimization of key parameters, we then successfully applied the method to the detection of PC-peptides in the background of a proteolytic digest of a whole proteome. This methodological invention will greatly facilitate the detection of PC-substituted biomolecules and their structural analysis.

Fourier transform infrared spectroscopy and chemometrics for the characterization and discrimination of writing/photocopier paper types: Application in forensic document examinations

NASA Astrophysics Data System (ADS)

Kumar, Raj; Kumar, Vinay; Sharma, Vishal

2017-01-01

The aim of the present work is to explore the non-destructive application of ATR-FTIR technique for characterization and discrimination of paper samples which could be helpful to give forensic aid in resolving legal cases. Twenty-four types of paper brands were purchased from local market in and around Chandigarh, India. All the paper samples were subjected to ATR-FTIR analysis from 400 to 4000 cm- 1 wavenumber range. The qualitative feature and Chemometrics of the obtained spectral data are used for characterization and discrimination. Characterization is achieved by matching the peaks with standards of cellulose and inorganic fillers, a usual constituents of paper. Three different regions of IR, i.e. 400-2000 cm- 1, 2000-4000 cm- 1 and 400-4000 cm- 1 were selected for differentiation by Chemometrics analysis. The discrimination is achieved on the basis of three principal components, i.e. PC 1, PC 2 and PC 3. It is observed that maximum discrimination was procured in the wave number range of i.e. 2000-4000 cm- 1. Discriminating power was calculated on the basis of qualitative features as well, and it is found that the discrimination of paper samples was better achieved by Chemometrics analysis rather than qualitative features. The discriminating power by Chemometrics is 99.64% and which is larger as ever achieved by any group for present number of samples. The present result confirms that this study will be highly useful in forensic document examination work in the legal cases, where the authenticity of the document is challenged. The results are completely analytical and, therefore, overcome the problem encounter in traditional routine light/radiation scanning methods which are still in practice by various questioned document laboratories.

Immunization-induced perturbation of human blood plasma cell pool: progressive maturation, IL-6 responsiveness, and high PRDI-BF1/BLIMP1 expression are critical distinctions between antigen-specific and nonspecific plasma cells.

PubMed

González-García, Inés; Ocaña, Esther; Jiménez-Gómez, Gema; Campos-Caro, Antonio; Brieva, José A

2006-04-01

The present study shows that reimmunization with tetanus toxoid (tet) caused a transient increase of the human blood plasma cell (PC) pool, detectable from 6th to 15th day postboost, as well as the temporal alteration of several PC features. Labeling of specific PC with FITC-tet C fragment (tetC) allowed kinetics analysis of the tetC(+) and tetC(-) PC, and revealed remarkable differences between them: 1) the kinetics of tetC(+) PC occurrence was exponential, and most of them appeared in a narrow time frame (5th to 8th day postboost), whereas the tetC(-) PC increase was lower (three to five times) and more prolonged (4th to 15th day postboost). 2) The tetC(+) PC subset contained a fraction of cycling cells, expressed high levels of DR, CD138, and CD126, and responded to IL-6 by improving their survival and Ig secretion; in contrast, the tetC(-) PC showed higher CXCR4 and lower DR and CD138, did not respond to IL-6, and contained a fraction of apoptotic cells. 3) Sequential phenotypic analysis revealed maturational changes within the tetC(+), but not tetC(-), PC subset; sequencing of tetC(+) PC IgVH genes showed clear features of Ag selection. 4) The tetC(+) PC expressed several times more positive regulatory domain I- binding factor 1/B lymphocyte-induced maturation protein 1 transcription factor than the tetC(-) PC. 5) The tetC(-) PC and bone marrow resident PC similarly expressed low DR and high CXCR4, but differed in that the latter exhibited higher levels of CD31, CD138, and positive regulatory domain I- binding factor 1/B lymphocyte-induced maturation protein 1. These findings support the view that tetC(+) PC contain bone marrow PC precursors, and tetC(-) PC probably belong to a removable compartment of aged PC.

PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics1[OPEN

PubMed Central

Poeschl, Yvonne; Plötner, Romina

2017-01-01

Pavement cells (PCs) are the most frequently occurring cell type in the leaf epidermis and play important roles in leaf growth and function. In many plant species, PCs form highly complex jigsaw-puzzle-shaped cells with interlocking lobes. Understanding of their development is of high interest for plant science research because of their importance for leaf growth and hence for plant fitness and crop yield. Studies of PC development, however, are limited, because robust methods are lacking that enable automatic segmentation and quantification of PC shape parameters suitable to reflect their cellular complexity. Here, we present our new ImageJ-based tool, PaCeQuant, which provides a fully automatic image analysis workflow for PC shape quantification. PaCeQuant automatically detects cell boundaries of PCs from confocal input images and enables manual correction of automatic segmentation results or direct import of manually segmented cells. PaCeQuant simultaneously extracts 27 shape features that include global, contour-based, skeleton-based, and PC-specific object descriptors. In addition, we included a method for classification and analysis of lobes at two-cell junctions and three-cell junctions, respectively. We provide an R script for graphical visualization and statistical analysis. We validated PaCeQuant by extensive comparative analysis to manual segmentation and existing quantification tools and demonstrated its usability to analyze PC shape characteristics during development and between different genotypes. PaCeQuant thus provides a platform for robust, efficient, and reproducible quantitative analysis of PC shape characteristics that can easily be applied to study PC development in large data sets. PMID:28931626

Oxidative stress and neurobehavioral problems in pediatric acute lymphoblastic leukemia patients undergoing chemotherapy.

PubMed

Stenzel, Stephanie L; Krull, Kevin R; Hockenberry, Marilyn; Jain, Neelam; Kaemingk, Kris; Miketova, Petra; Moore, Ida M

2010-03-01

Neurobehavioral problems after chemotherapy treatment for pediatric acute lymphoblastic leukemia (ALL) have been a recent focus of investigation. This study extended previous research that suggested oxidative stress as a potential mechanism for chemotherapy-induced central nervous system injury by examining early markers of oxidative stress in relation to subsequent neurobehavioral problems. Oxidized and unoxidized components of phosphatidylcholine (PC) were measured in the cerebrospinal fluid of 87 children with ALL at diagnosis, induction, and consolidation. Behavioral assessments were conducted postconsolidation and at the end of chemotherapy. Results revealed a significant association between physiologic reactivity (high vs. low PC changes from diagnosis) and behavioral outcomes (high vs. low pathology). Elevated oxidized PC fraction change was predictive of increased problems with aggression at the end of therapy as well as postconsolidation adaptability. Furthermore, symptoms of hyperactivity systematically changed over time in relation to both unoxidized PC and oxidized PC fraction reactivity. These findings suggest that symptoms of behavioral problems occur early in the course of chemotherapy and that increases in the cerebrospinal fluid PC markers of oxidative stress during induction and consolidation may help to predict certain future behavioral problems.

Global Prostate Cancer Incidence and Mortality Rates According to the Human Development Index.

PubMed

Khazaei, Salman; Rezaeian, Shahab; Ayubi, Erfan; Gholamaliee, Behzad; Pishkuhi, Mahin Ahmadi; Khazaei, Somayeh; Mansori, Kamyar; Nematollahi, Shahrzad; Sani, Mohadeseh; Hanis, Shiva Mansouri

2016-01-01

Prostate cancer (PC) is one of the leading causes of death, especially in developed countries. The human development index (HDI) and its dimensions seem correlated with incidence and mortality rates of PC. This study aimed to assess the association of the specific components of HDI (life expectancy at birth, education, gross national income per 1000 capita, health, and living standards) with burden indicators of PC worldwide. Information of the incidence and mortality rates of PC was obtained from the GLOBOCAN cancer project in year 2012 and data about the HDI 2013 were obtained from the World Bank database. The correlation between incidence, mortality rates, and the HDI parameters were assessed using STATA software. A significant inequality of PC incidence rates was observed according to concentration indexes=0.25 with 95% CI (0.22, 0.34) and a negative mortality concentration index of -0.04 with 95% CI (-0.09, 0.01) was observed. A positive significant correlation was detected between the incidence rates of PC and the HDI and its dimensions including life expectancy at birth, education, income, urbanization level and obesity. However, there was a negative significant correlation between the standardized mortality rates and the life expectancy, income and HDI.

Assessment of Pb, Cd, Cr and Ag leaching from electronics waste using four extraction methods.

PubMed

Keith, Ashley; Keesling, Kara; Fitzwater, Kendra K; Pichtel, John; Houy, Denise

2008-12-01

Heavy metals present in electronic components may leach upon disposal and therefore pose significant environmental hazards. The potential leaching of Pb, Cd, Cr and Ag from PC cathode ray tubes, printed circuit boards (PCBs), PC mice, TV remote controls, and mobile phones was assessed. After controlled crushing, each component was extracted using the Toxicity Characteristic Leaching Procedure (TCLP), EPA Method 1312 (SPLP), NEN 7371 (Dutch Environmental Agency), and DIN S4 (Germany). The TCLP consistently leached the greatest amounts of Pb from all components. The SPLP, NEN 7371 and DIN S4 extracted relatively small amounts of metals compared with the TCLP and were not considered effective as leaching tests for e-waste. The smallest size fraction (< 2 mm) of CRT glass and PCBs leached significantly (p < 0.05) highest Pb via the TCLP. A modified TCLP removed 50.9% more extractable Pb compared with the conventional procedure.

Diatom responses to precipitation and anthropogenic disturbances in an azorean lake during the last seven centuries

NASA Astrophysics Data System (ADS)

Vázquez-Loureiro, David; Bao, Roberto; Gonçalves, Vitor; Rubio-Inglés, Maria J.; Sáez, Alberto; Hernández, Armand; Raposeiro, Pedro M.; Pueyo, Juan J.; Masqué, Pere; Trigo, Ricardo; Giralt, Santiago

2015-04-01

Sedimentary lacustrine records provide an important source of knowledge of past environmental changes at regional and local scales. Here we perform a diatom-based paleoenvironmental reconstruction, complemented with geochemical proxies, of the recent history of Lake Azul (37° 52' 21' N - 25° 46' 26' W), located in the crater caldera of Sete Cidades volcano, São Miguel Island. A 132 cm long sediment core from the offshore and deepest part of the lake was selected, from a total of fourteen cores extracted in 2011, and dated with21Pb and137Cs, as well as AMS14C. Two main litological intervals were described: at the lower part there are hard volcanic rocks interbedding silty lacustrine episodes, whereas the upper part is made up by silty mud lacustrine sediments. Eight terrestrial-nearshore levels with high values of TOC/TN ratio, low values of δ13C and high abundances of aerophilic diatoms, plus nine volcanic levels, were removed from any further analysis in order to assess changes in in-lake processes. Main environmental gradients driving the composition of the diatom assemblages were explored by a Principal Component Analysis (PCA) on the diatom relative abundance data, and four statistically significant Diatom Assemblage Zones (DAZs) were defined with a cluster analysis (CONISS). The first axis of PCA (PC1), explaining 47.3% of total variance, confronts benthic vs tychoplanktonic and euplanktonic taxa, suggesting a relationship with water depth. The second axis (PC2) explained 23.1% of total variance, showing high positive values for eutrophic taxa of the genus Aulacoseira, and negative values for oligotrophic taxa and diatoms of a broad trophic spectrum. This axis is very likely related to a trophic gradient. DAZ-1 (c. 1280 - 1400 cal yr AD), dominated by benthic taxa, is characterized by positive values of PC1 and PC2, indicating relative shallow lake conditions and a high trophic level, respectively. A transition from a benthic to a facultatively planktonic community (lower PC1 values) occurs in DAZ-2 (c. 1400 - 1800 cal yr AD), suggesting a rise in water level, probably triggered by an increase in precipitation. Negative values of PC2 in this zone and DAZ-3 (c. 1800 - 1960 cal yr AD) might be explained by the dilution of nutrients in a larger water volume. The sharp transition to high positive values of PC2 in DAZ-4 (c. 1960 cal yr AD) coincides with the start in the use of nitrate- and phosphate-rich fertilizers in the surrounding farming area. Long-term changes in diatoms assemblages since the late XIII century in Lake Azul are driven by two factors of natural and anthropogenic origin, respectively; the strong inter-annual variability of the precipitation (largely controlled by the North Atlantic Oscillation, NAO), and the eutrophication of lakes in recent decades.

Clinical Outcomes of Specific Immunotherapy in Advanced Pancreatic Cancer: A Systematic Review and Meta-Analysis

PubMed Central

Qi, Xing-Shun

2017-01-01

Specific immunotherapies, including vaccines with autologous tumor cells and tumor antigen-specific monoclonal antibodies, are important treatments for PC patients. To evaluate the clinical outcomes of PC-specific immunotherapy, we performed a systematic review and meta-analysis of the relevant published clinical trials. The effects of specific immunotherapy were compared with those of nonspecific immunotherapy and the meta-analysis was executed with results regarding the overall survival (OS), immune responses data, and serum cancer markers data. The pooled analysis was performed by using the random-effects model. We found that significantly improved OS was noted for PC patients utilizing specific immunotherapy and an improved immune response was also observed. In conclusion, specific immunotherapy was superior in prolonging the survival time and enhancing immunological responses in PC patients. PMID:28265583

Cohort profile: the chronic kidney disease prognosis consortium.

PubMed

Matsushita, Kunihiro; Ballew, Shoshana H; Astor, Brad C; Jong, Paul E de; Gansevoort, Ron T; Hemmelgarn, Brenda R; Levey, Andrew S; Levin, Adeera; Wen, Chi-Pang; Woodward, Mark; Coresh, Josef

2013-12-01

The Chronic Kidney Disease Prognosis Consortium (CKD-PC) was established in 2009 to provide comprehensive evidence about the prognostic impact of two key kidney measures that are used to define and stage CKD, estimated glomerular filtration rate (eGFR) and albuminuria, on mortality and kidney outcomes. CKD-PC currently consists of 46 cohorts with data on these kidney measures and outcomes from >2 million participants spanning across 40 countries/regions all over the world. CKD-PC published four meta-analysis articles in 2010-11, providing key evidence for an international consensus on the definition and staging of CKD and an update for CKD clinical practice guidelines. The consortium continues to work on more detailed analysis (subgroups, different eGFR equations, other exposures and outcomes, and risk prediction). CKD-PC preferably collects individual participant data but also applies a novel distributed analysis model, in which each cohort runs statistical analysis locally and shares only analysed outputs for meta-analyses. This distributed model allows inclusion of cohorts which cannot share individual participant level data. According to agreement with cohorts, CKD-PC will not share data with third parties, but is open to including further eligible cohorts. Each cohort can opt in/out for each topic. CKD-PC has established a productive and effective collaboration, allowing flexible participation and complex meta-analyses for studying CKD.

PV-Diesel Hybrid SCADA Experiment Network Design

NASA Technical Reports Server (NTRS)

Kalu, Alex; Durand, S.; Emrich, Carol; Ventre, G.; Wilson, W.; Acosta, R.

1999-01-01

The essential features of an experimental network for renewable power system satellite based supervisory, control and data acquisition (SCADA) are communication links, controllers, diagnostic equipment and a hybrid power system. Required components for implementing the network consist of two satellite ground stations, to satellite modems, two 486 PCs, two telephone receivers, two telephone modems, two analog telephone lines, one digital telephone line, a hybrid-power system equipped with controller and a satellite spacecraft. In the technology verification experiment (TVE) conducted by Savannah State University and Florida Solar Energy Center, the renewable energy hybrid system is the Apex-1000 Mini-Hybrid which is equipped with NGC3188 for user interface and remote control and the NGC2010 for monitoring and basic control tasks. This power system is connected to a satellite modem via a smart interface, RS232. Commands are sent to the power system control unit through a control PC designed as PC1. PC1 is thus connected to a satellite model through RS232. A second PC, designated PC2, the diagnostic PC is connected to both satellite modems via separate analog telephone lines for checking modems'health. PC2 is also connected to PC1 via a telephone line. Due to the unavailability of a second ground station for the ACTS, one ground station is used to serve both the sending and receiving functions in this experiment. Signal is sent from the control PC to the Hybrid system at a frequency f(sub 1), different from f(sub 2), the signal from the hybrid system to the control PC. f(sub l) and f(sub 2) are sufficiently separated to avoid interference.

Illuminating the conceptual structure of the space of moral violations with searchlight representational similarity analysis.

PubMed

Wasserman, E A; Chakroff, A; Saxe, R; Young, L

2017-10-01

Characterizing how representations of moral violations are organized, cognitively and neurally, is central to understanding how people conceive and judge them. Past work has identified brain regions that represent morally relevant features and distinguish moral domains, but has not yet advanced a broader account of where and on what basis neural representations of moral violations are organized. With searchlight representational similarity analysis, we investigate where category membership drives similarity in neural patterns during moral judgment of violations from two key moral domains: Harm and Purity. Representations converge across domains in a network of regions resembling the mentalizing network. However, Harm and Purity violation representations respectively converge in different regions: precuneus (PC) and left inferior frontal gyrus (LIFG). Examining substructure within moral domains, Harm violations converge in PC regardless of subdomain (physical harms, psychological harms), while Purity subdomains (pathogen-related violations, sex-related violations) converge in distinct sets of regions - mirroring a dissociation observed in principal-component analysis of behavioral data. Further, we find initial evidence for representation of morally relevant features within these two domain-encoding regions. The present analyses offer a case study for understanding how organization within the complex conceptual space of moral violations is reflected in the organization of neural patterns across the cortex. Copyright © 2017 Elsevier Inc. All rights reserved.

An Upper Bound on High Speed Satellite Collision Probability When Only One Object has Position Uncertainty Information

NASA Technical Reports Server (NTRS)

Frisbee, Joseph H., Jr.

2015-01-01

Upper bounds on high speed satellite collision probability, PC †, have been investigated. Previous methods assume an individual position error covariance matrix is available for each object. The two matrices being combined into a single, relative position error covariance matrix. Components of the combined error covariance are then varied to obtain a maximum PC. If error covariance information for only one of the two objects was available, either some default shape has been used or nothing could be done. An alternative is presented that uses the known covariance information along with a critical value of the missing covariance to obtain an approximate but potentially useful Pc upper bound.

SU-E-J-44: A Novel Approach to Quantify Patient Setup and Target Motion for Real-Time Image-Guided Radiotherapy (IGRT)

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

Li, S; Charpentier, P; Sayler, E

2015-06-15

Purpose Isocenter shifts and rotations to correct patient setup errors and organ motion cannot remedy some shape changes of large targets. We are investigating new methods in quantification of target deformation for realtime IGRT of breast and chest wall cancer. Methods Ninety-five patients of breast or chest wall cancer were accrued in an IRB-approved clinical trial of IGRT using 3D surface images acquired at daily setup and beam-on time via an in-room camera. Shifts and rotations relating to the planned reference surface were determined using iterative-closest-point alignment. Local surface displacements and target deformation are measured via a ray-surface intersection andmore » principal component analysis (PCA) of external surface, respectively. Isocenter shift, upper-abdominal displacement, and vectors of the surface projected onto the two principal components, PC1 and PC2, were evaluated for sensitivity and accuracy in detection of target deformation. Setup errors for some deformed targets were estimated by superlatively registering target volume, inner surface, or external surface in weekly CBCT or these outlines on weekly EPI. Results Setup difference according to the inner-surface, external surface, or target volume could be 1.5 cm. Video surface-guided setup agreed with EPI results to within < 0.5 cm while CBCT results were sometimes (∼20%) different from that of EPI (>0.5 cm) due to target deformation for some large breasts and some chest walls undergoing deep-breath-hold irradiation. Square root of PC1 and PC2 is very sensitive to external surface deformation and irregular breathing. Conclusion PCA of external surfaces is quick and simple way to detect target deformation in IGRT of breast and chest wall cancer. Setup corrections based on the target volume, inner surface, and external surface could be significant different. Thus, checking of target shape changes is essential for accurate image-guided patient setup and motion tracking of large deformable targets. NIH grant for the first author as cionsultant and the last author as the PI.« less

Influence of storage temperature and time on the physicochemical and bioactive properties of roselle-fruit juice blends in plastic bottle

PubMed Central

Mgaya-Kilima, Beatrice; Remberg, Siv Fagertun; Chove, Bernard Elias; Wicklund, Trude

2014-01-01

Roselle-fruit juice blends were made from roselle extract and mango, papaya, and guava juices at the ratio of 80:20, 60:40, 40:60, and 20:80, % roselle: fruit juice, respectively. The blends were pasteurized at 82.5°C for 20 min and stored in 100 mL plastic bottles at 28 and 4°C for 6 months. The effects of storage time and temperature on physicochemical and bioactive properties were evaluated. Total soluble solids, pH, and reducing sugars increased significantly (P < 0.05) in some blends while titratable acidity decrease with increasing storage time. Vitamin C, total monomeric anthocyanins (TMA), total phenols (TPC), and antioxidant activity (ferric reducing ability of plasma, FRAP) in all roselle-fruit blends (40% roselle) decreased significantly (P < 0.05) at 28 and 4°C as storage progressed. Vitamin C in all roselle-fruit blends (40% roselle) decreased from 58–55% to 43–42% when stored at 28 and 4°C, respectively. TMA losses were 86–65% at 28°C and 75–53% at 4°C while TPC losses were 66–58% at 28°C and 51–22% at 4°C. Loss of antioxidant capacity (FRAP) was 18–46% at 28°C and 17–35% at 4°C. A principal component analysis (PCA) differentiated roselle-juice fruit blends into two clusters with two principle components PC1 and PC2, which explained 97 and 3% (blends stored at ambient temperature) and 96 and 4% (blends stored at refrigerated temperature) of the variation, respectively. PC1 differentiated roselle-guava juice blends which were characterized by vitamin C, TPC, FRAP, and pH, while PC2 from another cluster of roselle-mango and roselle-papaya juice blends and was characterized by TSS, RS, and color parameters (L* a* b*). However, TMA was the main variable with the highest effect on all roselle-fruit juice blends regardless of the storage time and temperature. PMID:24804077

The association of lean and fat mass with all-cause mortality in older adults: The Cardiovascular Health Study.

PubMed

Spahillari, A; Mukamal, K J; DeFilippi, C; Kizer, J R; Gottdiener, J S; Djoussé, L; Lyles, M F; Bartz, T M; Murthy, V L; Shah, R V

2016-11-01

Understanding contributions of lean and fat tissue to cardiovascular and non-cardiovascular mortality may help clarify areas of prevention in older adults. We aimed to define distributions of lean and fat tissue in older adults and their contributions to cause-specific mortality. A total of 1335 participants of the Cardiovascular Health Study (CHS) who underwent dual-energy x-ray absorptiometry (DEXA) scans were included. We used principal components analysis (PCA) to define two independent sources of variation in DEXA-derived body composition, corresponding to principal components composed of lean ("lean PC") and fat ("fat PC") tissue. We used Cox proportional hazards regression using these PCs to investigate the relationship between body composition with cardiovascular and non-cardiovascular mortality. Mean age was 76.2 ± 4.8 years (56% women) with mean body mass index 27.1 ± 4.4 kg/m 2 . A greater lean PC was associated with lower all-cause (HR = 0.91, 95% CI 0.84-0.98, P = 0.01) and cardiovascular mortality (HR = 0.84, 95% CI 0.74-0.95, P = 0.005). The lowest quartile of the fat PC (least adiposity) was associated with a greater hazard of all-cause mortality (HR = 1.24, 95% CI 1.04-1.48, P = 0.02) relative to fat PCs between the 25th-75th percentile, but the highest quartile did not have a significantly greater hazard (P = 0.70). Greater lean tissue mass is associated with improved cardiovascular and overall mortality in the elderly. The lowest levels of fat tissue mass are linked with adverse prognosis, but the highest levels show no significant mortality protection. Prevention efforts in the elderly frail may be best targeted toward improvements in lean muscle mass. Copyright © 2016 The Italian Society of Diabetology, the Italian Society for the Study of Atherosclerosis, the Italian Society of Human Nutrition, and the Department of Clinical Medicine and Surgery, Federico II University. Published by Elsevier B.V. All rights reserved.

Hardware accelerator design for tracking in smart camera

NASA Astrophysics Data System (ADS)

Singh, Sanjay; Dunga, Srinivasa Murali; Saini, Ravi; Mandal, A. S.; Shekhar, Chandra; Vohra, Anil

2011-10-01

Smart Cameras are important components in video analysis. For video analysis, smart cameras needs to detect interesting moving objects, track such objects from frame to frame, and perform analysis of object track in real time. Therefore, the use of real-time tracking is prominent in smart cameras. The software implementation of tracking algorithm on a general purpose processor (like PowerPC) could achieve low frame rate far from real-time requirements. This paper presents the SIMD approach based hardware accelerator designed for real-time tracking of objects in a scene. The system is designed and simulated using VHDL and implemented on Xilinx XUP Virtex-IIPro FPGA. Resulted frame rate is 30 frames per second for 250x200 resolution video in gray scale.

Phospholipase Dζ Enhances Diacylglycerol Flux into Triacylglycerol

DOE PAGES

Yang, Wenyu; Wang, Geliang; Li, Jia; ...

2017-03-21

Plant seeds are the primary source of triacylglycerols (TAG) for food, feed, fuel, and industrial applications. As TAG is produced from diacylglycerol (DAG), successful engineering strategies to enhance TAG levels have focused on the conversion of DAG to TAG. However, the production of TAG can be limited by flux through the enzymatic reactions that supply DAG. In this study, two Arabidopsis phospholipase Dζ genes (AtPLDζ 1 and AtPLDζ 2) were coexpressed in Camelina sativa to test whether the conversion of phosphatidylcholine to DAG impacts TAG levels in seeds. The resulting transgenic plants produced 2% to 3% more TAG as amore » component of total seed biomass and had increased 18:3 and 20:1 fatty acid levels relative to wild type. Increased DAG and decreased PC levels were examined through the kinetics of lipid assembly by [ 14C]acetate and [ 14C]glycerol incorporation into glycerolipids. [ 14C]acetate was rapidly incorporated into TAG in both wild-type and overexpression lines, indicating a significant flux of nascent and elongated acyl-CoAs into the sn-3 position of TAG. Stereochemical analysis revealed that newly synthesized fatty acids were preferentially incorporated into the sn-2 position of PC, but the sn-1 position of de novo DAG and indicated similar rates of nascent acyl groups into the Kennedy pathway and acyl editing. [ 14C]glycerol studies demonstrated PC-derived DAG is the major source of DAG for TAG synthesis in both tissues. The results emphasize that the interconversions of DAG and PC pools can impact oil production and composition.« less

Rapid determination of biogenic amines in cooked beef using hyperspectral imaging with sparse representation algorithm

NASA Astrophysics Data System (ADS)

Yang, Dong; Lu, Anxiang; Ren, Dong; Wang, Jihua

2017-11-01

This study explored the feasibility of rapid detection of biogenic amines (BAs) in cooked beef during the storage process using hyperspectral imaging technique combined with sparse representation (SR) algorithm. The hyperspectral images of samples were collected in the two spectral ranges of 400-1000 nm and 1000-1800 nm, separately. The spectral data were reduced dimensionality by SR and principal component analysis (PCA) algorithms, and then integrated the least square support vector machine (LS-SVM) to build the SR-LS-SVM and PC-LS-SVM models for the prediction of BAs values in cooked beef. The results showed that the SR-LS-SVM model exhibited the best predictive ability with determination coefficients (RP2) of 0.943 and root mean square errors (RMSEP) of 1.206 in the range of 400-1000 nm of prediction set. The SR and PCA algorithms were further combined to establish the best SR-PC-LS-SVM model for BAs prediction, which had high RP2of 0.969 and low RMSEP of 1.039 in the region of 400-1000 nm. The visual map of the BAs was generated using the best SR-PC-LS-SVM model with imaging process algorithms, which could be used to observe the changes of BAs in cooked beef more intuitively. The study demonstrated that hyperspectral imaging technique combined with sparse representation were able to detect effectively the BAs values in cooked beef during storage and the built SR-PC-LS-SVM model had a potential for rapid and accurate determination of freshness indexes in other meat and meat products.

Phospholipase Dζ Enhances Diacylglycerol Flux into Triacylglycerol

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

Yang, Wenyu; Wang, Geliang; Li, Jia

Plant seeds are the primary source of triacylglycerols (TAG) for food, feed, fuel, and industrial applications. As TAG is produced from diacylglycerol (DAG), successful engineering strategies to enhance TAG levels have focused on the conversion of DAG to TAG. However, the production of TAG can be limited by flux through the enzymatic reactions that supply DAG. In this study, two Arabidopsis phospholipase Dζ genes (AtPLDζ 1 and AtPLDζ 2) were coexpressed in Camelina sativa to test whether the conversion of phosphatidylcholine to DAG impacts TAG levels in seeds. The resulting transgenic plants produced 2% to 3% more TAG as amore » component of total seed biomass and had increased 18:3 and 20:1 fatty acid levels relative to wild type. Increased DAG and decreased PC levels were examined through the kinetics of lipid assembly by [ 14C]acetate and [ 14C]glycerol incorporation into glycerolipids. [ 14C]acetate was rapidly incorporated into TAG in both wild-type and overexpression lines, indicating a significant flux of nascent and elongated acyl-CoAs into the sn-3 position of TAG. Stereochemical analysis revealed that newly synthesized fatty acids were preferentially incorporated into the sn-2 position of PC, but the sn-1 position of de novo DAG and indicated similar rates of nascent acyl groups into the Kennedy pathway and acyl editing. [ 14C]glycerol studies demonstrated PC-derived DAG is the major source of DAG for TAG synthesis in both tissues. The results emphasize that the interconversions of DAG and PC pools can impact oil production and composition.« less

Radio Astronomy Software Defined Receiver Project

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

Vacaliuc, Bogdan; Leech, Marcus; Oxley, Paul

The paper describes a Radio Astronomy Software Defined Receiver (RASDR) that is currently under development. RASDR is targeted for use by amateurs and small institutions where cost is a primary consideration. The receiver will operate from HF thru 2.8 GHz. Front-end components such as preamps, block down-converters and pre-select bandpass filters are outside the scope of this development and will be provided by the user. The receiver includes RF amplifiers and attenuators, synthesized LOs, quadrature down converters, dual 8 bit ADCs and a Signal Processor that provides firmware processing of the digital bit stream. RASDR will interface to a usermore » s PC via a USB or higher speed Ethernet LAN connection. The PC will run software that provides processing of the bit stream, a graphical user interface, as well as data analysis and storage. Software should support MAC OS, Windows and Linux platforms and will focus on such radio astronomy applications as total power measurements, pulsar detection, and spectral line studies.« less

Parameters of Six Selected Galactic Potential Models

NASA Astrophysics Data System (ADS)

Bajkova, Anisa; Bobylev, Vadim

2017-11-01

This paper is devoted to the refinement of the parameters of the six three-component (bulge, disk, halo) axisymmetric Galactic gravitational potential models on the basis of modern data on circular velocities of Galactic objects located at distances up to 200 kpc from the Galactic center. In all models the bulge and disk are described by the Miyamoto-Nagai expressions. To describe the halo, the models of Allen-Santillán (I), Wilkinson-Evans (II), Navarro- Frenk-White (III), Binney (IV), Plummer (V), and Hernquist (VI) are used. The sought-for parameters of potential models are determined by fitting the model rotation curves to the measured velocities, taking into account restrictions on the local dynamical matter density p⊙ - 0.1M⊙ pc-3 and the vertical force |Kz=1.1|/2πG = 77M⊙ pc-2. A comparative analysis of the refined potential models is made and for each of the models the estimates of a number of the Galactic characteristics are presented.

Differences in Viscosity of Superior and Inferior Spikelets of Japonica Rice with Various Percentages of Apparent Amylose Content.

PubMed

Ma, Zhao-Hui; Cheng, Hai-Tao; Nitta, Y; Aoki, Naohiro; Chen, Yun; Chen, Heng-Xue; Ohsugi, Ryu; Lyu, Wen-Yan

2017-05-31

Viscosity, a crucial characteristic for rice palatability, is affected by endosperm characters. We compared correlations between differences in viscosity of japonica rice with various palatability and endosperm characters. Changes in apparent amylose and protein contents (AAC% and PC%, respectively) and amylopectin side-chain distribution and the relationship of these traits with palatability were investigated in superior and inferior spikelets of good cultivars with low amylose content from Hokkaido and common cultivars from northeastern Japan, using rapid visco analyzer characteristics and rice-grain microstructures. Significant differences occurred in PC%, AAC%, breakdown, setback, peak time, and pasting temperature of different cultivars and grain positions. Amylopectin components showed remarkable differences in grain surfaces, surface layers, and section structure between the grain varieties. Hokkaido cultivars showed better viscosity than northeastern cultivars, particularly initial stage grains. Correlation analysis indicated viscosity was mainly AAC%-dependent, whereas differences in endosperm characteristics between spikelet positions were mainly due to grain-filling temperature.

Inventory-driven costs.

PubMed

Callioni, Gianpaolo; de Montgros, Xavier; Slagmulder, Regine; Van Wassenhove, Luk N; Wright, Linda

2005-03-01

In the 199os, Hewlett-Packard's PC business was struggling to turn a dollar, despite the company's success in winning market share. By 1997, margins on its PCs were as thin as a silicon wafer, and some product lines hadn't turned a profit since 1993. The problem had everything to do with the PC industry's notoriously short product cycles and brutal product and component price deflation. A common rule of thumb was that the value of a fully assembled PC decreased 1% a week. In such an environment, inventory costs become critical. But not just the inventory costs companies traditionally track, HP found, after a thorough review of the problem. The standard "holding cost of inventory"--the capital and physical costs of inventory--accounted for only about 10% of HP's inventory costs. The greater risks, it turned out, resided in four other, essentially hidden costs, which stemmed from mismatches between demand and supply: Component devaluation costs for components still held in production; Price protection costs incurred when product prices drop on the goods distributors still have on their shelves; Product return costs that have to be absorbed when distributors return and receive refunds on overstock items, and; Obsolescence costs for products still unsold when new models are introduced. By developing metrics to track those costs in a consistent way throughout the PC division, HP has found it can manage its supply chains with much more sophistication. Gone are the days of across-the-board measures such as,"Everyone must cut inventories by 20% by the end of the year," which usually resulted in a flurry of cookie-cutter lean production and just-in-time initiatives. Now, each product group is free to choose the supply chain configuration that best suits its needs. Other companies can follow HP's example.

Molecular clouds in the NGC 6334 and NGC 6357 region: Evidence for a 100 pc-scale cloud-cloud collision triggering the Galactic mini-starbursts

NASA Astrophysics Data System (ADS)

Fukui, Yasuo; Kohno, Mikito; Yokoyama, Keiko; Torii, Kazufumi; Hattori, Yusuke; Sano, Hidetoshi; Nishimura, Atsushi; Ohama, Akio; Yamamoto, Hiroaki; Tachihara, Kengo

2018-03-01

We carried out new CO (J = 1-0, 2-1, and 3-2) observations with NANTEN2 and ASTE in the region of the twin Galactic mini-starbursts NGC 6334 and NGC 6357. We detected two velocity molecular components of 12 km s-1 velocity separation, which is continuous over 3° along the plane. In NGC 6334 the two components show similar two-peaked intensity distributions toward the young H II regions and are linked by a bridge feature. In NGC 6357 we found spatially complementary distribution between the two velocity components as well as a bridge feature in velocity. Based on these results we hypothesize that the two clouds in the two regions collided with each other in the past few Myr and triggered the formation of the starbursts over ˜ 100 pc. We suggest that the formation of the starbursts happened toward the collisional region of extent ˜ 10 pc with initial high molecular column densities. For NGC 6334 we present a scenario which includes spatial variation of the colliding epoch due to non-uniform cloud separation. The scenario possibly explains the apparent age differences among the young O stars in NGC 6334, which range from 104 yr to 106 yr; the latest collision happened within 105 yr toward the youngest stars in NGC 6334 I(N) and I which exhibit molecular outflows without H II regions. For NGC 6357 the O stars were formed a few Myr ago, and the cloud dispersal by the O stars is significant. We conclude that cloud-cloud collision offers a possible explanation of the mini-starburst over a 100 pc scale.

Molecular clouds in the NGC 6334 and NGC 6357 region; Evidence for a 100-pc-scale cloud-cloud collision triggering the Galactic mini-starbursts

NASA Astrophysics Data System (ADS)

Fukui, Yasuo; Kohno, Mikito; Yokoyama, Keiko; Torii, Kazufumi; Hattori, Yusuke; Sano, Hidetoshi; Nishimura, Atsushi; Ohama, Akio; Yamamoto, Hiroaki; Tachihara, Kengo

2018-03-01

We carried out new CO (J = 1-0, 2-1, and 3-2) observations with NANTEN2 and ASTE in the region of the twin Galactic mini-starbursts NGC 6334 and NGC 6357. We detected two velocity molecular components of 12 km s-1 velocity separation, which is continuous over 3° along the plane. In NGC 6334 the two components show similar two-peaked intensity distributions toward the young H II regions and are linked by a bridge feature. In NGC 6357 we found spatially complementary distribution between the two velocity components as well as a bridge feature in velocity. Based on these results we hypothesize that the two clouds in the two regions collided with each other in the past few Myr and triggered the formation of the starbursts over ˜ 100 pc. We suggest that the formation of the starbursts happened toward the collisional region of extent ˜ 10 pc with initial high molecular column densities. For NGC 6334 we present a scenario which includes spatial variation of the colliding epoch due to non-uniform cloud separation. The scenario possibly explains the apparent age differences among the young O stars in NGC 6334, which range from 104 yr to 106 yr; the latest collision happened within 105 yr toward the youngest stars in NGC 6334 I(N) and I which exhibit molecular outflows without H II regions. For NGC 6357 the O stars were formed a few Myr ago, and the cloud dispersal by the O stars is significant. We conclude that cloud-cloud collision offers a possible explanation of the mini-starburst over a 100-pc scale.

Molecular clouds in the NGC 6334 and NGC 6357 region: Evidence for a 100 pc-scale cloud-cloud collision triggering the Galactic mini-starbursts

NASA Astrophysics Data System (ADS)

Fukui, Yasuo; Kohno, Mikito; Yokoyama, Keiko; Torii, Kazufumi; Hattori, Yusuke; Sano, Hidetoshi; Nishimura, Atsushi; Ohama, Akio; Yamamoto, Hiroaki; Tachihara, Kengo

2018-05-01

We carried out new CO (J = 1-0, 2-1, and 3-2) observations with NANTEN2 and ASTE in the region of the twin Galactic mini-starbursts NGC 6334 and NGC 6357. We detected two velocity molecular components of 12 km s-1 velocity separation, which is continuous over 3° along the plane. In NGC 6334 the two components show similar two-peaked intensity distributions toward the young H II regions and are linked by a bridge feature. In NGC 6357 we found spatially complementary distribution between the two velocity components as well as a bridge feature in velocity. Based on these results we hypothesize that the two clouds in the two regions collided with each other in the past few Myr and triggered the formation of the starbursts over ˜ 100 pc. We suggest that the formation of the starbursts happened toward the collisional region of extent ˜ 10 pc with initial high molecular column densities. For NGC 6334 we present a scenario which includes spatial variation of the colliding epoch due to non-uniform cloud separation. The scenario possibly explains the apparent age differences among the young O stars in NGC 6334, which range from 104 yr to 106 yr; the latest collision happened within 105 yr toward the youngest stars in NGC 6334 I(N) and I which exhibit molecular outflows without H II regions. For NGC 6357 the O stars were formed a few Myr ago, and the cloud dispersal by the O stars is significant. We conclude that cloud-cloud collision offers a possible explanation of the mini-starburst over a 100 pc scale.

Object-based target templates guide attention during visual search.

PubMed

Berggren, Nick; Eimer, Martin

2018-05-03

During visual search, attention is believed to be controlled in a strictly feature-based fashion, without any guidance by object-based target representations. To challenge this received view, we measured electrophysiological markers of attentional selection (N2pc component) and working memory (sustained posterior contralateral negativity; SPCN) in search tasks where two possible targets were defined by feature conjunctions (e.g., blue circles and green squares). Critically, some search displays also contained nontargets with two target features (incorrect conjunction objects, e.g., blue squares). Because feature-based guidance cannot distinguish these objects from targets, any selective bias for targets will reflect object-based attentional control. In Experiment 1, where search displays always contained only one object with target-matching features, targets and incorrect conjunction objects elicited identical N2pc and SPCN components, demonstrating that attentional guidance was entirely feature-based. In Experiment 2, where targets and incorrect conjunction objects could appear in the same display, clear evidence for object-based attentional control was found. The target N2pc became larger than the N2pc to incorrect conjunction objects from 250 ms poststimulus, and only targets elicited SPCN components. This demonstrates that after an initial feature-based guidance phase, object-based templates are activated when they are required to distinguish target and nontarget objects. These templates modulate visual processing and control access to working memory, and their activation may coincide with the start of feature integration processes. Results also suggest that while multiple feature templates can be activated concurrently, only a single object-based target template can guide attention at any given time. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Singular value decomposition for photon-processing nuclear imaging systems and applications for reconstruction and computing null functions.

PubMed

Jha, Abhinav K; Barrett, Harrison H; Frey, Eric C; Clarkson, Eric; Caucci, Luca; Kupinski, Matthew A

2015-09-21

Recent advances in technology are enabling a new class of nuclear imaging systems consisting of detectors that use real-time maximum-likelihood (ML) methods to estimate the interaction position, deposited energy, and other attributes of each photon-interaction event and store these attributes in a list format. This class of systems, which we refer to as photon-processing (PP) nuclear imaging systems, can be described by a fundamentally different mathematical imaging operator that allows processing of the continuous-valued photon attributes on a per-photon basis. Unlike conventional photon-counting (PC) systems that bin the data into images, PP systems do not have any binning-related information loss. Mathematically, while PC systems have an infinite-dimensional null space due to dimensionality considerations, PP systems do not necessarily suffer from this issue. Therefore, PP systems have the potential to provide improved performance in comparison to PC systems. To study these advantages, we propose a framework to perform the singular-value decomposition (SVD) of the PP imaging operator. We use this framework to perform the SVD of operators that describe a general two-dimensional (2D) planar linear shift-invariant (LSIV) PP system and a hypothetical continuously rotating 2D single-photon emission computed tomography (SPECT) PP system. We then discuss two applications of the SVD framework. The first application is to decompose the object being imaged by the PP imaging system into measurement and null components. We compare these components to the measurement and null components obtained with PC systems. In the process, we also present a procedure to compute the null functions for a PC system. The second application is designing analytical reconstruction algorithms for PP systems. The proposed analytical approach exploits the fact that PP systems acquire data in a continuous domain to estimate a continuous object function. The approach is parallelizable and implemented for graphics processing units (GPUs). Further, this approach leverages another important advantage of PP systems, namely the possibility to perform photon-by-photon real-time reconstruction. We demonstrate the application of the approach to perform reconstruction in a simulated 2D SPECT system. The results help to validate and demonstrate the utility of the proposed method and show that PP systems can help overcome the aliasing artifacts that are otherwise intrinsically present in PC systems.

Singular value decomposition for photon-processing nuclear imaging systems and applications for reconstruction and computing null functions

NASA Astrophysics Data System (ADS)

Jha, Abhinav K.; Barrett, Harrison H.; Frey, Eric C.; Clarkson, Eric; Caucci, Luca; Kupinski, Matthew A.

2015-09-01

Recent advances in technology are enabling a new class of nuclear imaging systems consisting of detectors that use real-time maximum-likelihood (ML) methods to estimate the interaction position, deposited energy, and other attributes of each photon-interaction event and store these attributes in a list format. This class of systems, which we refer to as photon-processing (PP) nuclear imaging systems, can be described by a fundamentally different mathematical imaging operator that allows processing of the continuous-valued photon attributes on a per-photon basis. Unlike conventional photon-counting (PC) systems that bin the data into images, PP systems do not have any binning-related information loss. Mathematically, while PC systems have an infinite-dimensional null space due to dimensionality considerations, PP systems do not necessarily suffer from this issue. Therefore, PP systems have the potential to provide improved performance in comparison to PC systems. To study these advantages, we propose a framework to perform the singular-value decomposition (SVD) of the PP imaging operator. We use this framework to perform the SVD of operators that describe a general two-dimensional (2D) planar linear shift-invariant (LSIV) PP system and a hypothetical continuously rotating 2D single-photon emission computed tomography (SPECT) PP system. We then discuss two applications of the SVD framework. The first application is to decompose the object being imaged by the PP imaging system into measurement and null components. We compare these components to the measurement and null components obtained with PC systems. In the process, we also present a procedure to compute the null functions for a PC system. The second application is designing analytical reconstruction algorithms for PP systems. The proposed analytical approach exploits the fact that PP systems acquire data in a continuous domain to estimate a continuous object function. The approach is parallelizable and implemented for graphics processing units (GPUs). Further, this approach leverages another important advantage of PP systems, namely the possibility to perform photon-by-photon real-time reconstruction. We demonstrate the application of the approach to perform reconstruction in a simulated 2D SPECT system. The results help to validate and demonstrate the utility of the proposed method and show that PP systems can help overcome the aliasing artifacts that are otherwise intrinsically present in PC systems.

Multivariate Statistical Analysis of Water Quality data in Indian River Lagoon, Florida

NASA Astrophysics Data System (ADS)

Sayemuzzaman, M.; Ye, M.

2015-12-01

The Indian River Lagoon, is part of the longest barrier island complex in the United States, is a region of particular concern to the environmental scientist because of the rapid rate of human development throughout the region and the geographical position in between the colder temperate zone and warmer sub-tropical zone. Thus, the surface water quality analysis in this region always brings the newer information. In this present study, multivariate statistical procedures were applied to analyze the spatial and temporal water quality in the Indian River Lagoon over the period 1998-2013. Twelve parameters have been analyzed on twelve key water monitoring stations in and beside the lagoon on monthly datasets (total of 27,648 observations). The dataset was treated using cluster analysis (CA), principle component analysis (PCA) and non-parametric trend analysis. The CA was used to cluster twelve monitoring stations into four groups, with stations on the similar surrounding characteristics being in the same group. The PCA was then applied to the similar groups to find the important water quality parameters. The principal components (PCs), PC1 to PC5 was considered based on the explained cumulative variances 75% to 85% in each cluster groups. Nutrient species (phosphorus and nitrogen), salinity, specific conductivity and erosion factors (TSS, Turbidity) were major variables involved in the construction of the PCs. Statistical significant positive or negative trends and the abrupt trend shift were detected applying Mann-Kendall trend test and Sequential Mann-Kendall (SQMK), for each individual stations for the important water quality parameters. Land use land cover change pattern, local anthropogenic activities and extreme climate such as drought might be associated with these trends. This study presents the multivariate statistical assessment in order to get better information about the quality of surface water. Thus, effective pollution control/management of the surface waters can be undertaken.

Genetic determinism of anatomical and hydraulic traits within an apple progeny.

PubMed

Lauri, Pierre-Éric; Gorza, Olivier; Cochard, Hervé; Martinez, Sébastien; Celton, Jean-Marc; Ripetti, Véronique; Lartaud, Marc; Bry, Xavier; Trottier, Catherine; Costes, Evelyne

2011-08-01

The apple tree is known to have an isohydric behaviour, maintaining rather constant leaf water potential in soil with low water status and/or under high evaporative demand. However, little is known on the xylem water transport from roots to leaves from the two perspectives of efficiency and safety, and on its genetic variability. We analysed 16 traits related to hydraulic efficiency and safety, and anatomical traits in apple stems, and the relationships between them. Most variables were found heritable, and we investigated the determinism underlying their genetic control through a quantitative trait loci (QTL) analysis on 90 genotypes from the same progeny. Principal component analysis (PCA) revealed that all traits related to efficiency, whether hydraulic conductivity, vessel number and area or wood area, were included in the first PC, whereas the second PC included the safety variables, thus confirming the absence of trade-off between these two sets of traits. Our results demonstrated that clustered variables were characterized by common genomic regions. Together with previous results on the same progeny, our study substantiated that hydraulic efficiency traits co-localized with traits identified for tree growth and fruit production. © 2011 Blackwell Publishing Ltd.

Genetic differentiation and origin of the Jordanian population: an analysis of Alu insertion polymorphisms.

PubMed

Bahri, Raoudha; El Moncer, Wifak; Al-Batayneh, Khalid; Sadiq, May; Esteban, Esther; Moral, Pedro; Chaabani, Hassen

2012-05-01

Although much of Jordan is covered by desert, its north-western region forms part of the Fertile Crescent region that had given a rich past to Jordanians. This past, scarcely described by historians, is not yet clarified by sufficient genetic data. Thus in this paper we aim to determine the genetic differentiation of the Jordanian population and to discuss its origin. A total of 150 unrelated healthy Jordanians were investigated for ten Alu insertion polymorphisms. Genetic relationships among populations were estimated by a principal component (PC) plot based on the analyses of the R-matrix software. Statistical analysis showed that the Jordanian population is not significantly different from the United Arab Emirates population or the North Africans. This observation, well represented in PC plot, suggests a common origin of these populations belonging respectively to ancient Mesopotamia, Arabia, and North Africa. Our results are compatible with ancient peoples' movements from Arabia to ancient Mesopotamia and North Africa as proposed by historians and supported by previous genetic results. The original genetic profile of the Jordanian population, very likely Arabian Semitic, has not been subject to significant change despite the succession of several civilizations.

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

Shaw, Guinevere C.; Bannister, Mark E.; Biewer, Theodore M.

Laser-induced breakdown spectroscopy (LIBS) results are presented that provide depth-resolved identification of He implanted in polycrystalline tungsten (PC-W) targets by a 200 keV He+ ion beam, with a surface temperature of approximately 900 °C and a peak fluence of 10 23 m –2. He retention, and the influence of He on deuterium and tritium recycling, permeation, and retention in PC-W plasma facing components are important questions for the divertor and plasma facing components in a fusion reactor, yet are difficult to quantify. The purpose of this work is to demonstrate the ability of LIBS to identify helium in tungsten; tomore » investigate the sensitivity of laser parameters including, laser energy and gate delay, that directly influence the sensitivity and depth resolution of LIBS; and to perform a proof-of-principle experiment using LIBS to measure relative He intensities as a function of depth. In conclusion, the results presented demonstrate the potential not only to identify helium but also to develop a methodology to quantify gaseous impurity concentration in PC-W as a function of depth.« less

The detection of He in tungsten following ion implantation by laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Shaw, G.; Bannister, M.; Biewer, T. M.; Martin, M. Z.; Meyer, F.; Wirth, B. D.

2018-01-01

Laser-induced breakdown spectroscopy (LIBS) results are presented that provide depth-resolved identification of He implanted in polycrystalline tungsten (PC-W) targets by a 200 keV He+ ion beam, with a surface temperature of approximately 900 °C and a peak fluence of 1023 m-2. He retention, and the influence of He on deuterium and tritium recycling, permeation, and retention in PC-W plasma facing components are important questions for the divertor and plasma facing components in a fusion reactor, yet are difficult to quantify. The purpose of this work is to demonstrate the ability of LIBS to identify helium in tungsten; to investigate the sensitivity of laser parameters including, laser energy and gate delay, that directly influence the sensitivity and depth resolution of LIBS; and to perform a proof-of-principle experiment using LIBS to measure relative He intensities as a function of depth. The results presented demonstrate the potential not only to identify helium but also to develop a methodology to quantify gaseous impurity concentration in PC-W as a function of depth.

Lysophosphatidylcholine Regulates Sexual Stage Differentiation in the Human Malaria Parasite Plasmodium falciparum.

PubMed

Brancucci, Nicolas M B; Gerdt, Joseph P; Wang, ChengQi; De Niz, Mariana; Philip, Nisha; Adapa, Swamy R; Zhang, Min; Hitz, Eva; Niederwieser, Igor; Boltryk, Sylwia D; Laffitte, Marie-Claude; Clark, Martha A; Grüring, Christof; Ravel, Deepali; Blancke Soares, Alexandra; Demas, Allison; Bopp, Selina; Rubio-Ruiz, Belén; Conejo-Garcia, Ana; Wirth, Dyann F; Gendaszewska-Darmach, Edyta; Duraisingh, Manoj T; Adams, John H; Voss, Till S; Waters, Andrew P; Jiang, Rays H Y; Clardy, Jon; Marti, Matthias

2017-12-14

Transmission represents a population bottleneck in the Plasmodium life cycle and a key intervention target of ongoing efforts to eradicate malaria. Sexual differentiation is essential for this process, as only sexual parasites, called gametocytes, are infective to the mosquito vector. Gametocyte production rates vary depending on environmental conditions, but external stimuli remain obscure. Here, we show that the host-derived lipid lysophosphatidylcholine (LysoPC) controls P. falciparum cell fate by repressing parasite sexual differentiation. We demonstrate that exogenous LysoPC drives biosynthesis of the essential membrane component phosphatidylcholine. LysoPC restriction induces a compensatory response, linking parasite metabolism to the activation of sexual-stage-specific transcription and gametocyte formation. Our results reveal that malaria parasites can sense and process host-derived physiological signals to regulate differentiation. These data close a critical knowledge gap in parasite biology and introduce a major component of the sexual differentiation pathway in Plasmodium that may provide new approaches for blocking malaria transmission. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

MOLECULAR GAS VELOCITY DISPERSIONS IN THE ANDROMEDA GALAXY

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

Caldú-Primo, Anahi; Schruba, Andreas, E-mail: caldu@mpia.de, E-mail: schruba@mpe.mpg.de

In order to characterize the distribution of molecular gas in spiral galaxies, we study the line profiles of CO (1 – 0) emission in Andromeda, our nearest massive spiral galaxy. We compare observations performed with the IRAM 30 m single-dish telescope and with the CARMA interferometer at a common resolution of 23 arcsec ≈ 85 pc × 350 pc and 2.5 km s{sup −1}. When fitting a single Gaussian component to individual spectra, the line profile of the single dish data is a factor of 1.5 ± 0.4 larger than the interferometric data one. This ratio in line widths ismore » surprisingly similar to the ratios previously observed in two other nearby spirals, NGC 4736 and NGC 5055, but measured at ∼0.5–1 kpc spatial scale. In order to study the origin of the different line widths, we stack the individual spectra in five bins of increasing peak intensity and fit two Gaussian components to the stacked spectra. We find a unique narrow component of FWHM = 7.5 ± 0.4 km s{sup −1} visible in both the single dish and the interferometric data. In addition, a broad component with FWHM = 14.4 ± 1.5 km s{sup −1} is present in the single-dish data, but cannot be identified in the interferometric data. We interpret this additional broad line width component detected by the single dish as a low brightness molecular gas component that is extended on spatial scales >0.5 kpc, and thus filtered out by the interferometer. We search for evidence of line broadening by stellar feedback across a range of star formation rates but find no such evidence on ∼100 pc spatial scale when characterizing the line profile by a single Gaussian component.« less

Evolution of the Phosphatidylcholine Biosynthesis Pathways in Green Algae: Combinatorial Diversity of Methyltransferases.

PubMed

Hirashima, Takashi; Toyoshima, Masakazu; Moriyama, Takashi; Sato, Naoki

2018-01-01

Phosphatidylcholine (PC) is one of the most common phospholipids in eukaryotes, although some green algae such as Chlamydomonas reinhardtii are known to lack PC. Recently, we detected PC in four species in the genus Chlamydomonas: C. applanata NIES-2202, C. asymmetrica NIES-2207, C. debaryana NIES-2212, and C. sphaeroides NIES-2242. To reveal the PC biosynthesis pathways in green algae and the evolutionary scenario involved in their diversity, we analyzed the PC biosynthesis genes in these four algae using draft genome sequences. Homology searches suggested that PC in these species is synthesized by phosphoethanolamine-N-methyltransferase (PEAMT) and/or phosphatidylethanolamine-N-methyltransferase (PEMT), both of which are absent in C. reinhardtii. Recombinant PEAMTs from these algae showed methyltransferase activity for phosphoethanolamine but not for monomethyl phosphoethanolamine in vitro, in contrast to land plant PEAMT, which catalyzes the three methylations from phosphoethanolamine to phosphocholine. This suggested an involvement of other methyltransferases in PC biosynthesis. Here, we characterized the putative phospholipid-N-methyltransferase (PLMT) genes of these species by genetic and phylogenetic analysis. Complementation assays using a PC biosynthesis-deficient yeast suggested that the PLMTs of these algae can synthesize PC from phosphatidylethanolamine. These results indicated that the PC biosynthesis pathways in green algae differ from those of land plants, although the enzymes involved are homologous. Phylogenetic analysis suggested that the PEAMTs and PLMTs in these algae were inherited from the common ancestor of green algae. The absence of PC biosynthesis in many Chlamydomonas species is likely a result of parallel losses of PEAMT and PLMT in this genus.

Determination of critical epitope of PcMab-47 against human podocalyxin.

PubMed

Itai, Shunsuke; Yamada, Shinji; Kaneko, Mika K; Kato, Yukinari

2018-07-01

Podocalyxin (PODXL) is a type I transmembrane protein, which is highly glycosylated. PODXL is expressed in some types of human cancer tissues including oral, breast, and lung cancer tissues and may promote tumor growth, invasion, and metastasis. We previously produced PcMab-47, a novel anti-PODXL monoclonal antibody (mAb) which reacts with endogenous PODXL-expressing cancer cell lines and normal cells independently of glycosylation in Western blot, flow cytometry, and immunohistochemical analysis. In this study, we used enzyme-linked immunosorbent assay (ELISA), flow cytometry, and immunohistochemical analysis to determine the epitope of PcMab-47. The minimum epitope of PcMab-47 was found to be Asp207, His208, Leu209, and Met210. A blocking peptide containing this minimum epitope completely neutralized PcMab-47 reaction against oral cancer cells by flow cytometry and immunohistochemical analysis. These findings could lead to the production of more functional anti-PODXL mAbs, which are advantageous for antitumor activities.

NIR camera and spectrograph SWIMS for TAO 6.5m telescope: array control system and its performance

NASA Astrophysics Data System (ADS)

Terao, Yasunori; Motohara, Kentaro; Konishi, Masahiro; Takahashi, Hidenori; Kato, Natsuko M.; Kitagawa, Yutaro; Kobayakawa, Yutaka; Ohashi, Hirofumi; Tateuchi, Ken; Todo, Soya

2016-08-01

SWIMS (Simultaneous-color Wide-field Infrared Multi-object Spectrograph) is a near-infrared imager and multi-object spectrograph as one of the first generation instruments for the University of Tokyo Atacama Observatory (TAO) 6.5m telescope. In this paper, we describe an array control system of SWIMS and results of detector noise performance evaluation. SWIMS incorporates four (and eight in future) HAWAII-2RG focal plane arrays for detectors, each driven by readout electronics components: a SIDECAR ASIC and a JADE2 Card. The readout components are controlled by a HAWAII-2RG Testing Software running on a virtual Windows machine on a Linux PC called array control PC. All of those array control PCs are then supervised by a SWIMS control PC. We have developed an "array control software system", which runs on the array control PC to control the HAWAII-2RG Testing Software, and consists of a socket client and a dedicated server called device manager. The client runs on the SWIMS control PC, and the device manager runs on the array control PC. An exposure command, issued by the client on the SWIMS control PC, is sent to the multiple device managers on the array control PCs, and then multiple HAWAII-2RGs are driven simultaneously. Using this system, we evaluate readout noise performances of the detectors, both in a test dewar and in a SWIMS main dewar. In the test dewar, we confirm the readout noise to be 4.3 e- r.m.s. by 32 times multiple sampling when we operate only a single HAWAII-2RG, whereas in the case of simultaneous driving of two HAWAII-2RGs, we still obtain sufficiently low readout noise of 10 e- r.m.s. In the SWIMS main dewar, although there are some differences between the detectors, the readout noise is measured to be 4:1-4:6 e- r.m.s. with simultaneous driving by 64 times multiple sampling, which meets the requirement for background-limited observations in J band of 14 e- r.m.s..

Examining the Relationship Between Pain Catastrophizing and Suicide Risk in Patients with Rheumatic Disease: the Mediating Role of Depression, Perceived Social Support, and Perceived Burdensomeness.

PubMed

Shim, Eun -Jung; Song, Yeong Wook; Park, Seung-Hee; Lee, Kwang-Min; Go, Dong Jin; Hahm, Bong-Jin

2017-08-01

Little research has examined the role of pain catastrophizing (PC) in predicting suicide among patients with rheumatic disease or the mechanisms through which it works. This study examines whether depression, perceived social support (PSS), and perceived burdensomeness (PB) mediate the relationship between PC and suicide risk. It also examines the relative importance of sociodemographic, clinical, and psychological factors in predicting suicide risk. Three hundred sixty patients from a rheumatology clinic in Korea completed measures of pain catastrophizing, social support, depression, and perceived burdensomeness. In hierarchical multiple regression analysis, the PC magnification, PB, physical disability, and PSS were significantly related to suicide risk. Results of the serial multiple mediation analysis indicated that the total indirect effect of PC magnification on suicide risk was significant while the direct effect was not. Four specific indirect effects of PC magnification were found to be statistically significant. First of all, PC magnification was associated with suicide risk through PB and through depression and PB. PC magnification was also associated with suicide risk through depression and PSS. Lastly, PC magnification was associated with suicide risk through depression, PSS, and PB. The identified pathways through which PC affects suicide risk suggest the importance of depression, PSS, and PB. Evaluation and intervention targeted at physical disability and the psychological factors of PC magnification, depression, PSS, and PB may be integrated into the management of suicide risk in patients with rheumatic disease.

Palliative Care Consultations in the Neuro-ICU: A Qualitative Study.

PubMed

Tran, Len N; Back, Anthony L; Creutzfeldt, Claire J

2016-10-01

Integration of palliative care (PC) into the neurological intensive care unit (neuro-ICU) is increasingly recommended, but evidence regarding the best practice is lacking. We conducted a qualitative analysis exploring current practices and key themes of specialist PC consultations in patients admitted to a single neuro-ICU. We retrospectively identified all patients who were admitted to the neuro-ICU for ≥24 h and received a PC consultation between January and August 2014. We reviewed PC consultation notes and neuro-ICU progress notes from the electronic health records of these patients. We performed content analysis on the PC notes. Twenty-five neuro-ICU patients (4 %) received a PC consultation over 8 months with the most prevalent reason of clarifying goals of care. The main distinctions between patients with and those without (n = 580) a PC consultation were ICU length of stay (median 8.2 vs. 2.8 days) and death in the neuro-ICU (56 % vs. 11 %). The most prevalent themes addressed in the PC consultation notes were (1) discussing prognosis, (2) eliciting patient and family values, (3) understanding medical options, and (4) identifying conflict. PC consultations in the neuro-ICU emphasize family coping and decision-making by helping discuss prognosis and exploring patient and family values as well as their ability to understand the medical information. Several features suggest that earlier integration of PC into neuro-ICU care may enhance both coping and the decision-making process.

Genome-wide analysis of Polycomb targets in Drosophila

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

Schwartz, Yuri B.; Kahn, Tatyana G.; Nix, David A.

2006-04-01

Polycomb Group (PcG) complexes are multiprotein assemblages that bind to chromatin and establish chromatin states leading to epigenetic silencing. PcG proteins regulate homeotic genes in flies and vertebrates but little is known about other PcG targets and the role of the PcG in development, differentiation and disease. We have determined the distribution of the PcG proteins PC, E(Z) and PSC and of histone H3K27 trimethylation in the Drosophila genome. At more than 200 PcG target genes, binding sites for the three PcG proteins colocalize to presumptive Polycomb Response Elements (PREs). In contrast, H3 me3K27 forms broad domains including the entiremore » transcription unit and regulatory regions. PcG targets are highly enriched in genes encoding transcription factors but receptors, signaling proteins, morphogens and regulators representing all major developmental pathways are also included.« less

Anticancer effects on human pancreatic cancer cells of triterpenoids, polysaccharides and 1,3-β-D-glucan derived from the fruiting body of Antrodia camphorata.

PubMed

Lee, Chu-I; Wu, Chih-Chung; Hsieh, Shu-Ling; Lee, Chun-Lin; Chang, Yueh-Ping; Chang, Chih-Chuan; Wang, Yi-Zhen; Wang, Jyh-Jye

2014-12-01

Antrodia camphorata is a fungus native to Taiwan, and it is considered a precious medicinal agent. We analyzed triterpenoids, polysaccharides and 1,3-β-D-glucan, three major effective components in A. camphorata extracts (ACE). ACE exhibited a selective cytotoxic effect on BxPC-3 human pancreatic cancer cells. ACE markedly inhibited the migration ability of BxPC-3 cells. Treatment of BxPC-3 cells with ACE resulted in the increase of cells in the sub-G1 phase and G2/M phase arrest. Apoptosis was confirmed by validating phosphatidylserine externalization, the observation of characteristic chromatin condensation, and nuclear DNA fragmentation. ACE induced apoptosis in BxPC-3 cells through a mitochondria-dependent pathway by triggering an appropriate balance of bax/bcl-2, cytochrome c release, activation of caspase-9 and -3, and poly(ADP-ribose) polymerase cleavage. ACE shows great therapeutic potential due to its cytotoxic effects against BxPC-3 cells which include inhibiting cell migration and inducing mitochondria-mediated apoptosis.

PaCeQuant: A Tool for High-Throughput Quantification of Pavement Cell Shape Characteristics.

PubMed

Möller, Birgit; Poeschl, Yvonne; Plötner, Romina; Bürstenbinder, Katharina

2017-11-01

Pavement cells (PCs) are the most frequently occurring cell type in the leaf epidermis and play important roles in leaf growth and function. In many plant species, PCs form highly complex jigsaw-puzzle-shaped cells with interlocking lobes. Understanding of their development is of high interest for plant science research because of their importance for leaf growth and hence for plant fitness and crop yield. Studies of PC development, however, are limited, because robust methods are lacking that enable automatic segmentation and quantification of PC shape parameters suitable to reflect their cellular complexity. Here, we present our new ImageJ-based tool, PaCeQuant, which provides a fully automatic image analysis workflow for PC shape quantification. PaCeQuant automatically detects cell boundaries of PCs from confocal input images and enables manual correction of automatic segmentation results or direct import of manually segmented cells. PaCeQuant simultaneously extracts 27 shape features that include global, contour-based, skeleton-based, and PC-specific object descriptors. In addition, we included a method for classification and analysis of lobes at two-cell junctions and three-cell junctions, respectively. We provide an R script for graphical visualization and statistical analysis. We validated PaCeQuant by extensive comparative analysis to manual segmentation and existing quantification tools and demonstrated its usability to analyze PC shape characteristics during development and between different genotypes. PaCeQuant thus provides a platform for robust, efficient, and reproducible quantitative analysis of PC shape characteristics that can easily be applied to study PC development in large data sets. © 2017 American Society of Plant Biologists. All Rights Reserved.

Procyanidins-crosslinked aortic elastin scaffolds with distinctive anti-calcification and biological properties.

PubMed

Wang, Xiaoya; Zhai, Wanyin; Wu, Chengtie; Ma, Bing; Zhang, Jiamin; Zhang, Hongfeng; Zhu, Ziyan; Chang, Jiang

2015-04-01

Elastin, a main component of decellularized extracellular matrices and elastin-containing materials, has been used for tissue engineering applications due to their excellent biocompatibility. However, elastin is easily calcified, leading to the decrease of life span for elastin-based substitutes. How to inhibit the calcification of elastin-based scaffolds, but maintain their good biocompatibility, still remains significantly challenging. Procyanidins (PC) are a type of natural polyphenols with crosslinking ability. To investigate whether pure elastin could be crosslinked by PC with anti-calcification effect, PC was first used to crosslink aortic elastin. Results show that PC can crosslink elastin and effectively inhibit elastin-initiated calcification. Further experiments reveal the possible mechanisms for the anti-calcification of PC crosslinking including (1) inhibiting inflammation cell attachment, and secretion of inflammatory factors such as MMPs and TNF-α, (2) preventing elastin degradation by elastase, and (3) direct inhibition of mineral nucleation in elastin. Moreover, the PC-crosslinked aortic elastin maintains natural structure with high pore volume (1111 μL/g), large pore size (10-300 μm) and high porosity (75.1%) which facilitates recellularization of scaffolds in vivo, and displays excellent hemocompatibility, anti-thrombus and anti-inflammatory potential. The advantages of PC-crosslinked porous aortic elastin suggested that it can serve as a promising scaffold for tissue engineering. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Optical diagnosis of the progression and reversal of CCl4-induced liver injury in rodent model using minimally invasive autofluorescence spectroscopy.

PubMed

Nazeer, Shaiju S; Sandhyamani, S; Jayasree, Ramapurath S

2015-06-07

Worldwide, liver cancer is the fifth most common cancer in men and seventh most common cancer in women. Intoxicant-induced liver injury is one of the major causes for severe structural damage with fibrosis and functional derangement of the liver leading to cancer in its later stages. This report focuses on the minimally invasive autofluorescence spectroscopic (AFS) studies on intoxicant, carbon tetrachloride (CCl4)-induced liver damage in a rodent model. Different stages of liver damage, including the reversed stage, on stoppage of the intoxicant are examined. Emission from prominent fluorophores, such as collagen, nicotinamide adenine dinucleotide (NADH), and flavin adenine dinucleotide (FAD), and variations in redox ratio have been studied. A direct correlation between the severity of the disease and the levels of collagen and redox ratio was observed. On withdrawal of the intoxicant, a gradual reversal of the disease to normal conditions was observed as indicated by the decrease in collagen levels and redox ratio. Multivariate statistical techniques and principal component analysis followed by linear discriminant analysis (PC-LDA) were used to develop diagnostic algorithms for distinguishing different stages of the liver disease based on spectral features. The PC-LDA modeling on a minimally invasive AFS dataset yielded diagnostic sensitivities of 93%, 87% and 87% and specificities of 90%, 98% and 98% for pairwise classification among normal, fibrosis, cirrhosis and reversal conditions. We conclude that AFS along with PC-LDA algorithm has the potential for rapid and accurate minimally invasive diagnosis and detection of structural changes due to liver injury resulting from various intoxicants.

Specificity and rate of human and mouse liver and plasma phosphatidylcholine synthesis analyzed in vivo[S

PubMed Central

Pynn, Christopher J.; Henderson, Neil G.; Clark, Howard; Koster, Grielof; Bernhard, Wolfgang; Postle, Anthony D.

2011-01-01

Phosphatidylcholine (PC) synthesis by the direct cytidine diphosphate choline (CDP-choline) pathway in rat liver generates predominantly mono- and di-unsaturated molecular species, while polyunsaturated PC species are synthesized largely by the phosphatidylethanolamine-N-methyltransferase (PEMT) pathway. Although altered PC synthesis has been suggested to contribute to development of hepatocarcinoma and nonalcoholic steatohepatitis, analysis of the specificity of hepatic PC metabolism in human patients has been limited by the lack of sensitive and safe methodologies. Here we incorporated a deuterated methyl-d9-labled choline chloride, to quantify biosynthesis fluxes through both of the PC synthetic pathways in vivo in human volunteers and compared these fluxes with those in mice. Rates and molecular specificities of label incorporated into mouse liver and plasma PC were very similar and strongly suggest that label incorporation into human plasma PC can provide a direct measure of hepatic PC synthesis in human subjects. Importantly, we demonstrate for the first time that the PEMT pathway in human liver is selective for polyunsaturated PC species, especially those containing docosahexaenoic acid. Finally, we present a multiple isotopomer distribution analysis approach, based on transfer of deuterated methyl groups to S-adenosylmethionine and subsequent sequential methylations of PE, to quantify absolute flux rates through the PEMT pathway that are applicable to studies of liver dysfunction in clinical studies. PMID:21068006

Structural and magnetic characterization of copper sulfonated phthalocyanine grafted onto treated polyethylene

NASA Astrophysics Data System (ADS)

Reznickova, A.; Kolska, Z.; Orendac, M.; Cizmar, E.; Sajdl, P.; Svorcik, V.

2016-08-01

This study focuses on high density polyethylene (HDPE) activated by Ar plasma treatment, subsequently grafted with copper sulfonated phthalocyanine (CuPc) especially pointing out to the surface and magnetic properties of those composites. Properties of pristine PE and their plasma treated counterparts were studied by different experimental techniques: X-ray photoelectron spectroscopy (XPS), UV-vis spectroscopy, zeta potential and by electron spin resonance (ESR). XPS analysis confirmed the successful grafting of phthalocyanine. The highest absorption was found for the sample grafted with bCuPc for 1 h. Electrokinetic analysis also confirmed the plasma treatment and also subsequent CuPc grafting influence significantly the surface chemistry and charge. These results correspond well with XPS determination. ESR studies confirmed the presence of CuPc grafted on HDPE. It was found, that grafting is mediated by magnetically inactive functional groups, rather than radicals. Magnetic properties of CuPc do not seem to change significantly after grafting CuPc on polyethylene surface.

A STUDY OF THE η^'π^- SYSTEM PRODUCED IN THE REACTION π^-parrowη^'π^- p AT 18 GeV/c

NASA Astrophysics Data System (ADS)

Ivanov-Tatar, Emil

2000-04-01

The η^'π^- system has been studied in the reaction π^-parrowη^'π^- p at 18 GeV/c. The partial wave analysis of 6040 kinematically-identified events shows that the reaction is dominated by natural parity exchange. The production of an exotic isovector state π_1(1600) is observed in the I^G(J^PC) = 1^-(1^-+) wave. The mass and the width of that state are estimated via simultaneous mass-dependent fits of the I^G(J^PC) = 1^-(1^-+) and I^G(J^PC) = 1^-(2^++) waves. The a_2^-(1320) and a wide structure at 1.8 GeV/c^2 are observed in the I^G(J^PC) = 1^-(2^++) wave. The amplitude analysis of the mass interval above 1.8 GeV/c^2 indicates an interference between I^G(J^PC) = 1^-(2^++) and I^G(J^PC) = 1^-(4^++) waves.

Could texture features from preoperative CT image be used for predicting occult peritoneal carcinomatosis in patients with advanced gastric cancer?

PubMed

Kim, Hae Young; Kim, Young Hoon; Yun, Gabin; Chang, Won; Lee, Yoon Jin; Kim, Bohyoung

2018-01-01

To retrospectively investigate whether texture features obtained from preoperative CT images of advanced gastric cancer (AGC) patients could be used for the prediction of occult peritoneal carcinomatosis (PC) detected during operation. 51 AGC patients with occult PC detected during operation from January 2009 to December 2012 were included as occult PC group. For the control group, other 51 AGC patients without evidence of distant metastasis including PC, and whose clinical T and N stage could be matched to those of the patients of the occult PC group, were selected from the period of January 2011 to July 2012. Each group was divided into test (n = 41) and validation cohort (n = 10). Demographic and clinical data of these patients were acquired from the hospital database. Texture features including average, standard deviation, kurtosis, skewness, entropy, correlation, and contrast were obtained from manually drawn region of interest (ROI) over the omentum on the axial CT image showing the omentum at its largest cross sectional area. After using Fisher's exact and Wilcoxon signed-rank test for comparison of the clinical and texture features between the two groups of the test cohort, conditional logistic regression analysis was performed to determine significant independent predictor for occult PC. Using the optimal cut-off value from receiver operating characteristic (ROC) analysis for the significant variables, diagnostic sensitivity and specificity were determined in the test cohort. The cut-off value of the significant variables obtained from the test cohort was then applied to the validation cohort. Bonferroni correction was used to adjust P value for multiple comparisons. Between the two groups, there was no significant difference in the clinical features. Regarding the texture features, the occult PC group showed significantly higher average, entropy, standard deviation, and significantly lower correlation (P value < 0.004 for all). Conditional logistic regression analysis demonstrated that entropy was significant independent predictor for occult PC. When the cut-off value of entropy (> 7.141) was applied to the validation cohort, sensitivity and specificity for the prediction of occult PC were 80% and 90%, respectively. For AGC patients whose PC cannot be detected with routine imaging such as CT, texture analysis may be a useful adjunct for the prediction of occult PC.

Multivariate analysis of FTIR and ion chromatographic data for the quality control of tequila.

PubMed

Lachenmeier, Dirk W; Richling, Elke; López, Mercedes G; Frank, Willi; Schreier, Peter

2005-03-23

Principal component analysis (PCA) was applied to the chromatographic and spectroscopic data of authentic Mexican tequilas (n = 14) and commercially available samples purchased in Mexico and Germany (n = 24). The scores scatter plot of the first two principal components (PC) of the anions chloride, nitrate, sulfate, acetate, and oxalate accounting for 78% of the variability allowed a classification between tequilas bottled in Mexico and overseas; however, no discrimination between tequila categories was possible. Mexican products had a significantly (p = 0.0014) lower inorganic anion concentration (range = 1.5-5.1 mg/L; mean = 2.5 mg/L) than the products bottled in the importing countries (range = 3.3-62.6 mg/L; mean = 26.3 mg/L). FTIR allowed a rapid screening of density and ethanol as well as the volatile compounds methanol, ethyl acetate, propanol-1, isobutanol, and 2-/3-methyl-1-butanol using partial least-squares regression (precisions = 5.3-29.3%). Using PCA of the volatile compounds, a differentiation between tequila derived from "100% agave" (Agave tequilana Weber var. azul, Agavaceae) and tequila produced with other fermentable sugars ("mixed"tequila) was possible. The first two PCs describe 89% of the total variability of the data. Methanol and isobutanol influenced the variability in PC1, which led to discrimination. The concentrations of methanol and isobutanol were significantly higher (methanol, p = 0.004; isobutanol, p = 0.005) in the 100% agave (methanol, 297.9 +/- 49.5; isobutanol, 251.3 +/- 34.9) than in the mixed tequilas (methanol, 197.8 +/- 118.5; isobutanol, 151.4 +/- 52.8).

Multicomponent kinetic spectrophotometric determination of pefloxacin and norfloxacin in pharmaceutical preparations and human plasma samples with the aid of chemometrics

NASA Astrophysics Data System (ADS)

Ni, Yongnian; Wang, Yong; Kokot, Serge

2008-10-01

A spectrophotometric method for the simultaneous determination of the important pharmaceuticals, pefloxacin and its structurally similar metabolite, norfloxacin, is described for the first time. The analysis is based on the monitoring of a kinetic spectrophotometric reaction of the two analytes with potassium permanganate as the oxidant. The measurement of the reaction process followed the absorbance decrease of potassium permanganate at 526 nm, and the accompanying increase of the product, potassium manganate, at 608 nm. It was essential to use multivariate calibrations to overcome severe spectral overlaps and similarities in reaction kinetics. Calibration curves for the individual analytes showed linear relationships over the concentration ranges of 1.0-11.5 mg L -1 at 526 and 608 nm for pefloxacin, and 0.15-1.8 mg L -1 at 526 and 608 nm for norfloxacin. Various multivariate calibration models were applied, at the two analytical wavelengths, for the simultaneous prediction of the two analytes including classical least squares (CLS), principal component regression (PCR), partial least squares (PLS), radial basis function-artificial neural network (RBF-ANN) and principal component-radial basis function-artificial neural network (PC-RBF-ANN). PLS and PC-RBF-ANN calibrations with the data collected at 526 nm, were the preferred methods—%RPE T ˜ 5, and LODs for pefloxacin and norfloxacin of 0.36 and 0.06 mg L -1, respectively. Then, the proposed method was applied successfully for the simultaneous determination of pefloxacin and norfloxacin present in pharmaceutical and human plasma samples. The results compared well with those from the alternative analysis by HPLC.

Ring-patterned plasmonic photonic crystal thermal light source for miniaturized near-infrared spectrometers

NASA Astrophysics Data System (ADS)

Labib, Shady R.; Elsayed, Ahmed A.; Sabry, Yasser M.; Khalil, Diaa

2018-02-01

There is a growing number of spectroscopy applications in the near-infrared (NIR) range including gas sensing, food analysis, pharmaceutical and industrial applications that requires highly efficient, more compact and low-cost miniaturized spectrometers. One of the key components for such systems is the wideband light source that can be fabricated using Silicon technology and hence integrated with other components on the same chip. In this work, we report a ring-patterned plasmonic photonic crystal (PC) thermal light source for miniaturized near-infrared spectrometers. The design is based on silicon and tuned to achieve wavelength selectivity in the emitted spectrum. The design is optimized by using Rigorous Coupled-Wave Analysis (RCWA) simulation, which is used to compute the power reflectance and transmittance that are used to predict the emissivity of the structure. The design consists of a PC of silicon rings coated with platinum. The period of the structure is about 2 μm and the silicon is highly-doped with n-type doping level in the order of 1019-1020 cm-3 to enhance the free-carrier absorption. The ring etching depth, diameter and shell thickness are optimized to increase its emissivity within a specific wavelength range of interest. The simulation results show an emissivity exceeding 0.9 in the NIR range up to 2.5 μm, while the emissivity is decreased significantly for longer wavelengths suppressing the emission out of the range of interest, and hence increasing the efficiency for the source. The reported results open the door for black body radiation engineering in integrated silicon sources for spectrometer miniaturization.

Bayesian bivariate meta-analysis of diagnostic test studies with interpretable priors.

PubMed

Guo, Jingyi; Riebler, Andrea; Rue, Håvard

2017-08-30

In a bivariate meta-analysis, the number of diagnostic studies involved is often very low so that frequentist methods may result in problems. Using Bayesian inference is particularly attractive as informative priors that add a small amount of information can stabilise the analysis without overwhelming the data. However, Bayesian analysis is often computationally demanding and the selection of the prior for the covariance matrix of the bivariate structure is crucial with little data. The integrated nested Laplace approximations method provides an efficient solution to the computational issues by avoiding any sampling, but the important question of priors remain. We explore the penalised complexity (PC) prior framework for specifying informative priors for the variance parameters and the correlation parameter. PC priors facilitate model interpretation and hyperparameter specification as expert knowledge can be incorporated intuitively. We conduct a simulation study to compare the properties and behaviour of differently defined PC priors to currently used priors in the field. The simulation study shows that the PC prior seems beneficial for the variance parameters. The use of PC priors for the correlation parameter results in more precise estimates when specified in a sensible neighbourhood around the truth. To investigate the usage of PC priors in practice, we reanalyse a meta-analysis using the telomerase marker for the diagnosis of bladder cancer and compare the results with those obtained by other commonly used modelling approaches. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

A Western Dietary Pattern Increases Prostate Cancer Risk: A Systematic Review and Meta-Analysis.

PubMed

Fabiani, Roberto; Minelli, Liliana; Bertarelli, Gaia; Bacci, Silvia

2016-10-12

Dietary patterns were recently applied to examine the relationship between eating habits and prostate cancer (PC) risk. While the associations between PC risk with the glycemic index and Mediterranean score have been reviewed, no meta-analysis is currently available on dietary patterns defined by "a posteriori" methods. A literature search was carried out (PubMed, Web of Science) to identify studies reporting the relationship between dietary patterns and PC risk. Relevant dietary patterns were selected and the risks estimated were calculated by a random-effect model. Multivariable-adjusted odds ratios (ORs), for a first-percentile increase in dietary pattern score, were combined by a dose-response meta-analysis. Twelve observational studies were included in the meta-analysis which identified a "Healthy pattern" and a "Western pattern". The Healthy pattern was not related to PC risk (OR = 0.96; 95% confidence interval (CI): 0.88-1.04) while the Western pattern significantly increased it (OR = 1.34; 95% CI: 1.08-1.65). In addition, the "Carbohydrate pattern", which was analyzed in four articles, was positively associated with a higher PC risk (OR = 1.64; 95% CI: 1.35-2.00). A significant linear trend between the Western ( p = 0.011) pattern, the Carbohydrate ( p = 0.005) pattern, and the increment of PC risk was observed. The small number of studies included in the meta-analysis suggests that further investigation is necessary to support these findings.

A Western Dietary Pattern Increases Prostate Cancer Risk: A Systematic Review and Meta-Analysis

PubMed Central

Fabiani, Roberto; Minelli, Liliana; Bertarelli, Gaia; Bacci, Silvia

2016-01-01

Dietary patterns were recently applied to examine the relationship between eating habits and prostate cancer (PC) risk. While the associations between PC risk with the glycemic index and Mediterranean score have been reviewed, no meta-analysis is currently available on dietary patterns defined by “a posteriori” methods. A literature search was carried out (PubMed, Web of Science) to identify studies reporting the relationship between dietary patterns and PC risk. Relevant dietary patterns were selected and the risks estimated were calculated by a random-effect model. Multivariable-adjusted odds ratios (ORs), for a first-percentile increase in dietary pattern score, were combined by a dose-response meta-analysis. Twelve observational studies were included in the meta-analysis which identified a “Healthy pattern” and a “Western pattern”. The Healthy pattern was not related to PC risk (OR = 0.96; 95% confidence interval (CI): 0.88–1.04) while the Western pattern significantly increased it (OR = 1.34; 95% CI: 1.08–1.65). In addition, the “Carbohydrate pattern”, which was analyzed in four articles, was positively associated with a higher PC risk (OR = 1.64; 95% CI: 1.35–2.00). A significant linear trend between the Western (p = 0.011) pattern, the Carbohydrate (p = 0.005) pattern, and the increment of PC risk was observed. The small number of studies included in the meta-analysis suggests that further investigation is necessary to support these findings. PMID:27754328

Cyst fluid analysis in the differential diagnosis of pancreatic cystic lesions: a pooled analysis.

PubMed

van der Waaij, Laurens A; van Dullemen, Hendrik M; Porte, Robert J

2005-09-01

Pancreatic cystic tumors commonly include serous cystadenoma (SCA), mucinous cystadenoma (MCA), and mucinous cystadenocarcinoma (MCAC). A differential diagnosis with pseudocysts (PC) can be difficult. Radiologic criteria are not reliable. The objective of the study is to investigate the value of cyst fluid analysis in the differential diagnosis of benign (SCA, PC) vs. premalignant or malignant (MCA, MCAC) lesions. A search in PubMed was performed with the search terms cyst, pancrea, and fluid. Articles about cyst fluid analysis of pancreatic lesions that contained the individual data of at least 7 patients were included in the study. Data of all individual patients were combined and were plotted in scatter grams. Cutoff levels were determined. Twelve studies were included, which comprised data of 450 patients. Cysts with an amylase concentration <250 U/L were SCA, MCA, or MCAC (sensitivity 44%, specificity 98%) and, thus, virtually excluded PC. A carcinoembryonic antigen (CEA) <5 ng/mL suggested a SCA or PC (sensitivity 50%, specificity 95%). A CEA >800 ng/mL strongly suggested MCA or MCAC (sensitivity 48%, specificity 98%). A carbohydrate-associated antigen (CA) 19-9 <37 U/mL strongly suggested PC or SCA (sensitivity 19%, specificity 98%). Cytologic examination revealed malignant cells in 48% of MCAC (n = 111). Most pancreatic cystic tumors should be resected without the need for cyst fluid analysis. However, in asymptomatic patients, in patients with an increased surgical risk, and, in patients in whom there is a diagnostic uncertainty about the presence of a PC, cyst fluid analysis helps to determine the optimal therapeutic strategy.

SRGULL - AN ADVANCED ENGINEERING MODEL FOR THE PREDICTION OF AIRFRAME INTEGRATED SCRAMJET CYCLE PERFORMANCE

NASA Technical Reports Server (NTRS)

Walton, J. T.

1994-01-01

The development of a single-stage-to-orbit aerospace vehicle intended to be launched horizontally into low Earth orbit, such as the National Aero-Space Plane (NASP), has concentrated on the use of the supersonic combustion ramjet (scramjet) propulsion cycle. SRGULL, a scramjet cycle analysis code, is an engineer's tool capable of nose-to-tail, hydrogen-fueled, airframe-integrated scramjet simulation in a real gas flow with equilibrium thermodynamic properties. This program facilitates initial estimates of scramjet cycle performance by linking a two-dimensional forebody, inlet and nozzle code with a one-dimensional combustor code. Five computer codes (SCRAM, SEAGUL, INLET, Progam HUD, and GASH) originally developed at NASA Langley Research Center in support of hypersonic technology are integrated in this program to analyze changing flow conditions. The one-dimensional combustor code is based on the combustor subroutine from SCRAM and the two-dimensional coding is based on an inviscid Euler program (SEAGUL). Kinetic energy efficiency input for sidewall area variation modeling can be calculated by the INLET program code. At the completion of inviscid component analysis, Program HUD, an integral boundary layer code based on the Spaulding-Chi method, is applied to determine the friction coefficient which is then used in a modified Reynolds Analogy to calculate heat transfer. Real gas flow properties such as flow composition, enthalpy, entropy, and density are calculated by the subroutine GASH. Combustor input conditions are taken from one-dimensionalizing the two-dimensional inlet exit flow. The SEAGUL portions of this program are limited to supersonic flows, but the combustor (SCRAM) section can handle supersonic and dual-mode operation. SRGULL has been compared to scramjet engine tests with excellent results. SRGULL was written in FORTRAN 77 on an IBM PC compatible using IBM's FORTRAN/2 or Microway's NDP386 F77 compiler. The program is fully user interactive, but can also run in batch mode. It operates under the UNIX, VMS, NOS, and DOS operating systems. The source code is not directly compatible with all PC compilers (e.g., Lahey or Microsoft FORTRAN) due to block and segment size requirements. SRGULL executable code requires about 490K RAM and a math coprocessor on PC's. The SRGULL program was developed in 1989, although the component programs originated in the 1960's and 1970's. IBM, IBM PC, and DOS are registered trademarks of International Business Machines. VMS is a registered trademark of Digital Equipment Corporation. UNIX is a registered trademark of Bell Laboratories. NOS is a registered trademark of Control Data Corporation.

Alterations of idiotypic profiles: The cellular basis of T15 dominance in BALB/c mice

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

Wemhoff, G.A.; Quintans, J.

1987-01-01

Phosphorylcholine (PC) is a component of cell walls and membranes from a variety of widely distributed microorganisms. It is highly immunogenic in mice and most murine strains have circulating anti-PC antibodies which are known to confer protection against certain bacterial infections. BALB/c mice offer a striking example of a high responsiveness to PC, a propensity to generate PC-binding myelomas, and a great restriction of idiotype expression in anti-PC antibodies; in fact, most BALB/c anti-PC IgM antibodies express the T15 idiotype marker. Although it has been suspected that T15 dominance is somewhat related to the continuous antigenic load presented by microorganismalmore » flora found in conventional mice, a complete experimental account of how antigenic selection brings about such extreme idiotypic dominance is not yet available. In the studies presented below, we investigated the role played by the host environment, T cells, and antigen in affecting the generation of the anti-PC T15 idiotype profile in lethally irradiated adoptive hosts reconstituted with syngeneic neonatal liver cells. The results presented herein indicate that the transfer of mature carrier-primed T cells with neonatal liver cells does not influence the generation of the T15 idiotype profile. We also demonstrated that anti-T15 idiotype suppressed mice, used as lethally irradiated hosts of immature immunocompetent cells, allow an increased rate of reconstitution of the anti-PC response when compared to nonsuppressed hosts. Since the administration of a T15+ anti-PC antibody inhibits both reconstitution and idiotype expansion, we conclude that T15+ B cells do not self-promote themselves. In contrast, we observed that exposure of adoptive hosts to PC antigens can enhance the anti-PC response and alter the idiotypic profile in favor of T15-bearing clones.« less

[Construction and functional identification of eukaryotic expression vector carrying Sprague-Dawley rat MSX-2 gene].

PubMed

Yang, Xian-Xian; Zhang, Mei; Yan, Zhao-Wen; Zhang, Ru-Hong; Mu, Xiong-Zheng

2008-01-01

To construct a high effective eukaryotic expressing plasmid PcDNA 3.1-MSX-2 encoding Sprague-Dawley rat MSX-2 gene for the further study of MSX-2 gene function. The full length SD rat MSX-2 gene was amplified by PCR, and the full length DNA was inserted in the PMD1 8-T vector. It was isolated by restriction enzyme digest with BamHI and Xhol, then ligated into the cloning site of the PcDNA3.1 expression plasmid. The positive recombinant was identified by PCR analysis, restriction endonudease analysis and sequence analysis. Expression of RNA and protein was detected by RT-PCR and Western blot analysis in PcDNA3.1-MSX-2 transfected HEK293 cells. Sequence analysis and restriction endonudease analysis of PcDNA3.1-MSX-2 demonstrated that the position and size of MSX-2 cDNA insertion were consistent with the design. RT-PCR and Western blot analysis showed specific expression of mRNA and protein of MSX-2 in the transfected HEK293 cells. The high effective eukaryotic expression plasmid PcDNA3.1-MSX-2 encoding Sprague-Dawley Rat MSX-2 gene which is related to craniofacial development can be successfully reconstructed. It may serve as the basis for the further study of MSX-2 gene function.

Substrate analysis of the Pneumocystis carinii protein kinases PcCbk1 and PcSte20 using yeast proteome microarrays provides a novel method for Pneumocystis signalling biology.

PubMed

Kottom, Theodore J; Limper, Andrew H

2011-10-01

Pneumocystis carinii (Pc) undergoes morphological transitions between cysts and trophic forms. We have previously described two Pc serine/threonine kinases, termed PcCbk1 and PcSte20, with PcSte20 belonging to a family of kinases involved in yeast mating, while PcCbk1 is a member of a group of protein kinases involved in regulation of cell cycle, shape, and proliferation. As Pc remains genetically intractable, knowledge on specific substrates phosphorylated by these kinases remains limited. Utilizing the phylogenetic relatedness of Pc to Saccharomyces cerevisiae, we interrogated a yeast proteome microarray containing >4000 purified protein based peptides, leading to the identification of 18 potential PcCbk1 and 15 PcSte20 substrates (Z-score > 3.0). A number of these potential protein substrates are involved in bud site selection, polarized growth, and response to mating α factor and pseudohyphal and invasive growth. Full-length open reading frames suggested by the PcCbk1 and PcSte20 protoarrays were amplified and expressed. These five proteins were used as substrates for PcCbk1 or PcSte20, with each being highly phosphorylated by the respective kinase. Finally, to demonstrate the utility of this method to identify novel PcCbk1 and PcSte20 substrates, we analysed DNA sequence data from the partially complete Pc genome database and detected partial sequence information of potential PcCbk1 kinase substrates PcPxl1 and PcInt1. We additionally identified the potential PcSte20 kinase substrate PcBdf2. Full-length Pc substrates were cloned and expressed in yeast, and shown to be phosphorylated by the respective Pc kinases. In conclusion, the yeast protein microarray represents a novel crossover technique for identifying unique potential Pc kinase substrates. Copyright © 2011 John Wiley & Sons, Ltd.

Dectin-2 Is a C-Type Lectin Receptor that Recognizes Pneumocystis and Participates in Innate Immune Responses.

PubMed

Kottom, Theodore J; Hebrink, Deanne M; Jenson, Paige E; Marsolek, Paige L; Wüthrich, Marcel; Wang, Huafeng; Klein, Bruce; Yamasaki, Sho; Limper, Andrew H

2018-02-01

Pneumocystis is an important fungal pathogen that causes life-threatening pneumonia in patients with AIDS and malignancy. Lung fungal pathogens are recognized by C-type lectin receptors (CLRs), which bind specific ligands and stimulate innate immune responses. The CLR Dectin-1 was previously shown to mediate immune responses to Pneumocystis spp. For this reason, we investigated a potential role for Dectin-2. Rats with Pneumocystis pneumonia (PCP) exhibited elevated Dectin-2 mRNA levels. Soluble Dectin-2 carbohydrate-recognition domain fusion protein showed binding to intact Pneumocystis carinii (Pc) and to native Pneumocystis major surface glycoprotein/glycoprotein A (Msg/gpA). RAW macrophage cells expressing V5-tagged Dectin-2 displayed enhanced binding to Pc and increased protein tyrosine phosphorylation. Furthermore, the binding of Pc to Dectin-2 resulted in Fc receptor-γ-mediated intracellular signaling. Alveolar macrophages from Dectin-2-deficient mice (Dectin-2 -/- ) showed significant decreases in phospho-Syk activation after challenge with Pc cell wall components. Stimulation of Dectin-2 -/- alveolar macrophages with Pc components showed significant decreases in the proinflammatory cytokines IL-6 and TNF-α. Finally, during infection with Pneumocystis murina, Dectin-2 -/- mice displayed downregulated mRNA expression profiles of other CLRs implicated in fungal immunity. Although Dectin-2 -/- alveolar macrophages had reduced proinflammatory cytokine release in vitro, Dectin-2 -/- deficiency did not reduce the overall resistance of these mice in the PCP model, and organism burdens were statistically similar in the long-term immunocompromised and short-term immunocompetent PCP models. These results suggest that Dectin-2 participates in the initial innate immune signaling response to Pneumocystis, but its deficiency does not impair resistance to the organism.

In-Silico Integration Approach to Identify a Key miRNA Regulating a Gene Network in Aggressive Prostate Cancer

PubMed Central

Colaprico, Antonio; Bontempi, Gianluca; Castiglioni, Isabella

2018-01-01

Like other cancer diseases, prostate cancer (PC) is caused by the accumulation of genetic alterations in the cells that drives malignant growth. These alterations are revealed by gene profiling and copy number alteration (CNA) analysis. Moreover, recent evidence suggests that also microRNAs have an important role in PC development. Despite efforts to profile PC, the alterations (gene, CNA, and miRNA) and biological processes that correlate with disease development and progression remain partially elusive. Many gene signatures proposed as diagnostic or prognostic tools in cancer poorly overlap. The identification of co-expressed genes, that are functionally related, can identify a core network of genes associated with PC with a better reproducibility. By combining different approaches, including the integration of mRNA expression profiles, CNAs, and miRNA expression levels, we identified a gene signature of four genes overlapping with other published gene signatures and able to distinguish, in silico, high Gleason-scored PC from normal human tissue, which was further enriched to 19 genes by gene co-expression analysis. From the analysis of miRNAs possibly regulating this network, we found that hsa-miR-153 was highly connected to the genes in the network. Our results identify a four-gene signature with diagnostic and prognostic value in PC and suggest an interesting gene network that could play a key regulatory role in PC development and progression. Furthermore, hsa-miR-153, controlling this network, could be a potential biomarker for theranostics in high Gleason-scored PC. PMID:29562723

Automated visual inspection system based on HAVNET architecture

NASA Astrophysics Data System (ADS)

Burkett, K.; Ozbayoglu, Murat A.; Dagli, Cihan H.

1994-10-01

In this study, the HAusdorff-Voronoi NETwork (HAVNET) developed at the UMR Smart Engineering Systems Lab is tested in the recognition of mounted circuit components commonly used in printed circuit board assembly systems. The automated visual inspection system used consists of a CCD camera, a neural network based image processing software and a data acquisition card connected to a PC. The experiments are run in the Smart Engineering Systems Lab in the Engineering Management Dept. of the University of Missouri-Rolla. The performance analysis shows that the vision system is capable of recognizing different components under uncontrolled lighting conditions without being effected by rotation or scale differences. The results obtained are promising and the system can be used in real manufacturing environments. Currently the system is being customized for a specific manufacturing application.

Practical and generalizable architecture for an intelligent tutoring system

NASA Astrophysics Data System (ADS)

Kaplan, Randy M.; Trenholm, Harriet

1993-03-01

In this paper we describe an intelligent tutoring system (ITS) called HYDRIVE (hydraulics interactive video experience). This system is built using several novel approaches to intelligent tutoring. The underlying rationale for HYDRIVE is based on the results of a cognitive task analysis. The reasoning component of the system makes extensive use of a hierarchical knowledge representation. Reasoning within the system is accomplished using a logic-based approach and is linked to a highly interactive interface using multimedia. The knowledge representation contains information that drives the multimedia elements of the system, and the reasoning components select the appropriate information to assess student knowledge or guide the student at any particular moment. As this system will be deployed throughout the Air Force maintenance function, the implementation platform is the IBM PC.

A Mobile Computing Solution for Collecting Functional Analysis Data on a Pocket PC

ERIC Educational Resources Information Center

Jackson, James; Dixon, Mark R.

2007-01-01

The present paper provides a task analysis for creating a computerized data system using a Pocket PC and Microsoft Visual Basic. With Visual Basic software and any handheld device running the Windows MOBLE operating system, this task analysis will allow behavior analysts to program and customize their own functional analysis data-collection…

Insights into the Morphological Instability of Bulk Heterojunction PTB7-Th/PCBM Solar Cells upon High-Temperature Aging

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

Hsieh, Yen-Ju; Huang, Yu-Ching; Liu, Wei-Shin

The impact of the morphological stability of the donor/acceptor mixture under thermal stress on the photovoltaic properties of bulk heterojunction (BHJ) solar cells based on the poly[4,8-bis(5-(2-ethylhexyl)thiophen-2-yl)benzo[1,2-b;4,5-b']-di-thiophene-2,6-diyl-alt-(4-(2 ethylhexyl)-3-fluorothieno[3,4-b]-thiophene)-2-carboxylate-2,6-diyl]/phenyl-C61-butyric acid methylester (PTB7-Th/PC61BM) blend is extensively investigated. Both optical microscopy and transmission electron microscopy micrographs show that long-term high-temperature aging stimulates the formation of microscale clusters, the size of which, however, is about 1 order of magnitude smaller than those observed in thermally annealed poly(3hexylthiophene)/PC61BM composite film. The multilength-scale evolution of the morphology of PTB7-Th/PC61BM film from the scattering profiles of grazing incidence small-angle and wide-angle X-ray scattering indicates the PC61BM moleculesmore » spatially confine the self-organization of polymer chains into large domains during cast drying and upon thermal activation. Moreover, some PC61BM molecules accumulate into ~30-40 nm clusters, the number of which increases with heating time. Therefore, the hole mobility in the active layer decays much more rapidly than the electron mobility, leading to unbalanced charge transport and degraded cell performance. Importantly, the three-component blend that is formed by replacing a small amount of PC61BM in the active layer with the bis-adduct of PC61BM (bis-P61M) exhibits robust morphology against thermal stress. Accordingly, the PTB7-Th/PC61BM:bis-PC61BM (8 wt %) device has an extremely stable power conversion efficiency.« less

Lysophosphatidylcholine-induced cytotoxicity in osteoblast-like MG-63 cells: involvement of transient receptor potential vanilloid 2 (TRPV2) channels.

PubMed

Fallah, Abdallah; Pierre, Rachel; Abed, Elie; Moreau, Robert

2013-01-01

Epidemiological studies indicate that patients suffering from atherosclerosis are predisposed to develop osteoporosis. Accordingly, atherogenic determinants such as oxidized low density lipoprotein (OxLDL) particles have been shown to alter bone cell functions. In this work, we investigated the cytotoxicity of lysophosphatidylcholine (lysoPC), a major phospholipid component generated upon LDL oxidation, on bone-forming MG-63 osteoblast-like cells. Cell viability was reduced by lysoPC in a concentration-dependent manner with a LC50 of 18.7±0.7 μM. LysoPC-induced cell death was attributed to induction of both apoptosis and necrosis. Since impairment of intracellular calcium homeostasis is often involved in mechanism of cell death, we determined the involvement of calcium in lysoPC-induced cytotoxicity. LysoPC promoted a rapid and transient increase in intracellular calcium attributed to mobilization from calcium stores, followed by a sustained influx. Intracellular calcium mobilization was associated to phospholipase C (PLC)-dependent mobilization of calcium from the endoplasmic reticulum since inhibition of PLC or calcium depletion of reticulum endoplasmic with thapsigargin prevented the calcium mobilization. The calcium influx induced by lysoPC was abolished by inhibition of transient receptor potential vanilloid (TRPV) channels with ruthenium red whereas gadolinium, which inhibits canonical TRP (TRPC) channels, was without effect. Accordingly, expression of TRPV2 and TRPV4 were shown in MG-63 cells. The addition of TRPV2 inhibitor Tranilast in the incubation medium prevent the calcium influx triggered by lysoPC and reduced lysoPC-induced cytotoxicity whereas TRPV4 inhibitor RN 1734 was without effect, which confirms the involvement of TRPV2 activation in lysoPC-induced cell death.

Abbreviation of the Follow-Up NIH Stroke Scale Using Factor Analysis

PubMed Central

Raza, Syed Ali; Frankel, Michael R.; Rangaraju, Srikant

2017-01-01

Background The NIH Stroke Scale (NIHSS) is a 15-item measure of stroke-related neurologic deficits that, when measured at 24 h, is highly predictive of long-term functional outcome. We hypothesized that a simplified 24-h scale that incorporates the most predictive components of the NIHSS can retain prognostic accuracy and have improved interrater reliability. Methods In a post hoc analysis of the Interventional Management of Stroke-3 (IMS-3) trial, we performed principal component (PC) analysis to resolve the 24-h NIHSS into PCs. In the PCs that explained the largest proportions of variance, key variables were identified. Using these key variables, the prognostic accuracies (area under the curve [AUC]) for good outcome (3-month modified Rankin Scale [mRS] 0–2) and poor outcome (mRS 5–6) of various abbreviated NIHSS iterations were compared with the total 24-h NIHSS. The results were validated in the NINDS intravenous tissue plasminogen activator (NINDS-TPA) study cohort. Based on previously published data, interrater reliability of the abbreviated 24-h NIHSS (aNIHSS) was compared to the total 24-h NIHSS. Results In 545 IMS-3 participants, 2 PCs explained 60.8% of variance in the 24-h NIHSS. The key variables in PC1 included neglect, arm and leg weakness; while PC2 included level-of-consciousness (LOC) questions, LOC commands, and aphasia. A 3-variable aNIHSS (aphasia, neglect, arm weakness) retained excellent prognostic accuracy for good outcome (AUC = 0.90) as compared to the total 24-h NIHSS (AUC = 0.91), and it was more predictive (p < 0.001) than the baseline NIHSS (AUC = 0.73). The prognostic accuracy of the aNIHSS for good outcome was validated in the NINDS-TPA trial cohort (aNIHSS: AUC = 0.89 vs. total 24-h NIHSS: 0.92). An aNIHSS >9 predicted very poor outcomes (mRS 0–2: 0%, mRS 4–6: 98.5%). The estimated interrater reliability of the aNIHSS was higher than that of the total 24-h NIHSS across 6 published datasets (mean weighted kappa 0.80 vs. 0.73, p < 0.001). Conclusions At 24 h following ischemic stroke, aphasia, neglect, and arm weakness are the most prognostically relevant neurologic findings. The aNIHSS appears to have excellent prognostic accuracy with higher reliability and may be clinically useful. PMID:28968607

Association Between Lung Microbiome and Disease Progression in IPF: A Prospective Cohort Study

PubMed Central

Han, MeiLan K.; Zhou, Yueren; Murray, Susan; Tayob, Nabihah; Noth, Imre; Lama, Vibha N.; Moore, Bethany B.; White, Eric S.; Flaherty, Kevin R.; Huffnagle, Gary B.; Martinez, Fernando J.

2014-01-01

Background The lung microbiome’s contribution to IPF pathogenesisis unknown. Using COMET-IPF (Correlating Outcomes with biochemical Markers to Estimate Time-progression in Idiopathic Pulmonary Fibrosis), the goal of this study was to determine whether unique microbial signatures would associate with disease progression. Methods IPF subjects within four years of diagnosis aged 35–80 were eligible for inclusion. Subjects were followed for up to a maximum of 80 weeks. This completed observational study is registered with ClinicalTrials.gov, number NCT01071707. Progression-free survival was defined as death, acute exacerbation, lung transplant, or decline in FVC of 10% or DLCO of 15%.DNA was isolated from 55 bronchoscopic alveolar lavage (BAL) samples. 454 pyrosequencing was used to assign operational taxonomic units (OTUs) based on a 3% sequence divergence. Adjusted Cox models identified OTUs significantly associated with progression-free survival at a p<0·10 level. These OTUs were then used in principal components (PC) analysis. The association between PCs and microbes with high factor loadings from the PC analysis and progression-free survival were examined via Cox regression analyses. Findings Mean FVC was 70·1% and mean DLCO 42·3 %predicted. Significant associations with disease progression were noted with increased % relative abundance of two OTUs identified by PC analysis, a Streptococcus OTU. (p<0·0009) and a Staphylococcus OTU(p=0·01). Strength of associations using PCs versus two OTUs alone was similar. Threshold analysis helped define a cut point for % relative abundance for each OTU associated with progression-free survival, >3·9% for the Streptococcus OTU, HR 10·19 (95% CI 2·94, 35·35; p=0·0002) and >1·8% for the Staphylococcus OTU, HR 5·06 (1·71, 14·93; p=0·003). Interpretation These preliminary data suggest IPF disease progression is associated with presence of specific members within the Staphylococcus and Streptococcus genera. PMID:24767767

Transcriptional Networks in Single Perivascular Cells Sorted from Human Adipose Tissue Reveal a Hierarchy of Mesenchymal Stem Cells.

PubMed

Hardy, W Reef; Moldovan, Nicanor I; Moldovan, Leni; Livak, Kenneth J; Datta, Krishna; Goswami, Chirayu; Corselli, Mirko; Traktuev, Dmitry O; Murray, Iain R; Péault, Bruno; March, Keith

2017-05-01

Adipose tissue is a rich source of multipotent mesenchymal stem-like cells, located in the perivascular niche. Based on their surface markers, these have been assigned to two main categories: CD31 - /CD45 - /CD34 + /CD146 - cells (adventitial stromal/stem cells [ASCs]) and CD31 - /CD45 - /CD34 - /CD146 + cells (pericytes [PCs]). These populations display heterogeneity of unknown significance. We hypothesized that aldehyde dehydrogenase (ALDH) activity, a functional marker of primitivity, could help to better define ASC and PC subclasses. To this end, the stromal vascular fraction from a human lipoaspirate was simultaneously stained with fluorescent antibodies to CD31, CD45, CD34, and CD146 antigens and the ALDH substrate Aldefluor, then sorted by fluorescence-activated cell sorting. Individual ASCs (n = 67) and PCs (n = 73) selected from the extremities of the ALDH-staining spectrum were transcriptionally profiled by Fluidigm single-cell quantitative polymerase chain reaction for a predefined set (n = 429) of marker genes. To these single-cell data, we applied differential expression and principal component and clustering analysis, as well as an original gene coexpression network reconstruction algorithm. Despite the stochasticity at the single-cell level, covariation of gene expression analysis yielded multiple network connectivity parameters suggesting that these perivascular progenitor cell subclasses possess the following order of maturity: (a) ALDH br ASC (most primitive); (b) ALDH dim ASC; (c) ALDH br PC; (d) ALDH dim PC (least primitive). This order was independently supported by specific combinations of class-specific expressed genes and further confirmed by the analysis of associated signaling pathways. In conclusion, single-cell transcriptional analysis of four populations isolated from fat by surface markers and enzyme activity suggests a developmental hierarchy among perivascular mesenchymal stem cells supported by markers and coexpression networks. Stem Cells 2017;35:1273-1289. © 2017 AlphaMed Press.