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.

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.

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.

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.

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.

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.

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.

Shape Analysis of 3D Head Scan Data for U.S. Respirator Users

NASA Astrophysics Data System (ADS)

Zhuang, Ziqing; Slice, DennisE; Benson, Stacey; Lynch, Stephanie; Viscusi, DennisJ

2010-12-01

In 2003, the National Institute for Occupational Safety and Health (NIOSH) conducted a head-and-face anthropometric survey of diverse, civilian respirator users. Of the 3,997 subjects measured using traditional anthropometric techniques, surface scans and 26 three-dimensional (3D) landmark locations were collected for 947 subjects. The objective of this study was to report the size and shape variation of the survey participants using the 3D data. Generalized Procrustes Analysis (GPA) was conducted to standardize configurations of landmarks associated with individuals into a common coordinate system. The superimposed coordinates for each individual were used as commensurate variables that describe individual shape and were analyzed using Principal Component Analysis (PCA) to identify population variation. The first four principal components (PC) account for 49% of the total sample variation. The first PC indicates that overall size is an important component of facial variability. The second PC accounts for long and narrow or short and wide faces. Longer narrow orbits versus shorter wider orbits can be described by PC3, and PC4 represents variation in the degree of ortho/prognathism. Geometric Morphometrics provides a detailed and interpretable assessment of morphological variation that may be useful in assessing respirators and devising new test and certification standards.

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.

Use of Principal Components Analysis to Explain Controls on Nutrient Fluxes to the Chesapeake Bay

NASA Astrophysics Data System (ADS)

Rice, K. C.; Mills, A. L.

2017-12-01

The Chesapeake Bay watershed, on the east coast of the United States, encompasses about 166,000-square kilometers (km2) of diverse land use, which includes a mixture of forested, agricultural, and developed land. The watershed is now managed under a Total Daily Maximum Load (TMDL), which requires implementation of management actions by 2025 that are sufficient to reduce nitrogen, phosphorus, and suspended-sediment fluxes to the Chesapeake Bay and restore the bay's water quality. We analyzed nutrient and sediment data along with land-use and climatic variables in nine sub watersheds to better understand the drivers of flux within the watershed and to provide relevant management implications. The nine sub watersheds range in area from 300 to 30,000 km2, and the analysis period was 1985-2014. The 31 variables specific to each sub watershed were highly statistically significantly correlated, so Principal Components Analysis was used to reduce the dimensionality of the dataset. The analysis revealed that about 80% of the variability in the whole dataset can be explained by discharge, flux, and concentration of nutrients and sediment. The first two principal components (PCs) explained about 68% of the total variance. PC1 loaded strongly on discharge and flux, and PC2 loaded on concentration. The PC scores of both PC1 and PC2 varied by season. Subsequent analysis of PC1 scores versus PC2 scores, broken out by sub watershed, revealed management implications. Some of the largest sub watersheds are largely driven by discharge, and consequently large fluxes. In contrast, some of the smaller sub watersheds are more variable in nutrient concentrations than discharge and flux. Our results suggest that, given no change in discharge, a reduction in nutrient flux to the streams in the smaller watersheds could result in a proportionately larger decrease in fluxes of nutrients down the river to the bay, than in the larger watersheds.

Clustering of immunological, metabolic and genetic features in latent autoimmune diabetes in adults: evidence from principal component analysis.

PubMed

Pes, Giovanni Mario; Delitala, Alessandro Palmerio; Errigo, Alessandra; Delitala, Giuseppe; Dore, Maria Pina

2016-06-01

Latent autoimmune diabetes in adults (LADA) which accounts for more than 10 % of all cases of diabetes is characterized by onset after age 30, absence of ketoacidosis, insulin independence for at least 6 months, and presence of circulating islet-cell antibodies. Its marked heterogeneity in clinical features and immunological markers suggests the existence of multiple mechanisms underlying its pathogenesis. The principal component (PC) analysis is a statistical approach used for finding patterns in data of high dimension. In this study the PC analysis was applied to a set of variables from a cohort of Sardinian LADA patients to identify a smaller number of latent patterns. A list of 11 variables including clinical (gender, BMI, lipid profile, systolic and diastolic blood pressure and insulin-free time period), immunological (anti-GAD65, anti-IA-2 and anti-TPO antibody titers) and genetic features (predisposing gene variants previously identified as risk factors for autoimmune diabetes) retrieved from clinical records of 238 LADA patients referred to the Internal Medicine Unit of University of Sassari, Italy, were analyzed by PC analysis. The predictive value of each PC on the further development of insulin dependence was evaluated using Kaplan-Meier curves. Overall 4 clusters were identified by PC analysis. In component PC-1, the dominant variables were: BMI, triglycerides, systolic and diastolic blood pressure and duration of insulin-free time period; in PC-2: genetic variables such as Class II HLA, CTLA-4 as well as anti-GAD65, anti-IA-2 and anti-TPO antibody titers, and the insulin-free time period predominated; in PC-3: gender and triglycerides; and in PC-4: total cholesterol. These components explained 18, 15, 12, and 12 %, respectively, of the total variance in the LADA cohort. The predictive power of insulin dependence of the four components was different. PC-2 (characterized mostly by high antibody titers and presence of predisposing genetic markers) showed a faster beta-cells failure and PC-3 (characterized mostly by gender and high triglycerides) and PC-4 (high cholesterol) showed a slower beta-cells failure. PC-1 (including dislipidemia and other metabolic dysfunctions), showed a mild beta-cells failure. In conclusion variable clustering might be consistent with different pathogenic pathways and/or distinct immune mechanisms in LADA and could potentially help physicians improve the clinical management of these patients.

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

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.

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.

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.

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.

[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.

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

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.

Comparison of centre of gravity and centre of pressure patterns in the golf swing.

PubMed

Smith, Aimée C; Roberts, Jonathan R; Kong, Pui Wah; Forrester, Stephanie E

2017-03-01

Analysing the centre of pressure (COP) and centre of gravity (COG) could reveal stabilising strategies used by golfers throughout the golf swing. This study identified and compared golfers' COP and COG patterns throughout the golf swing in medial-lateral (ML) and anterior-posterior (AP) directions using principal component analysis (PCA) and examined their relationship to clubhead velocity. Three-dimensional marker trajectories were collected using Vicon motion analysis and force plate data from two Kistler force plates for 22 low-handicap golfers during drives. Golfers' COG and COP were expressed as a percentage distance between their feet. PCA was performed on COG and COP in ML and AP directions. Relationships between principal component (PC) scores were examined using Pearson correlation and regression analysis used to examine the relationship with clubhead velocity. ML COP movements varied in magnitude (PC1), rate of change and timing (PC2 and PC3). The COP and COG PC1 scores were strongly correlated in both directions (ML: r = 0.90, P < .05; AP: r = 0.81, P < .05). Clubhead velocity, explained by three PCs (74%), related to timing and rate of change in COP ML near downswing (PC2 and PC3) and timing of COG ML late backswing (PC2). The relationship between COP ML and COG ML PC1 scores identified extremes of COP and COG patterns in golfers and could indicate a golfer's dynamic balance. Golfers with earlier movement of COP to the front foot (PC2) and rate of change (PC3) patterns in ML COP, prior to the downswing, may be more likely to generate higher clubhead velocity.

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

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.

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

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

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

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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

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.

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.

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.

[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.

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.

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

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.

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

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.

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®

Study on fast discrimination of varieties of yogurt using Vis/NIR-spectroscopy

NASA Astrophysics Data System (ADS)

He, Yong; Feng, Shuijuan; Deng, Xunfei; Li, Xiaoli

2006-09-01

A new approach for discrimination of varieties of yogurt by means of VisINTR-spectroscopy was present in this paper. Firstly, through the principal component analysis (PCA) of spectroscopy curves of 5 typical kinds of yogurt, the clustering of yogurt varieties was processed. The analysis results showed that the cumulate reliabilities of PC1 and PC2 (the first two principle components) were more than 98.956%, and the cumulate reliabilities from PC1 to PC7 (the first seven principle components) was 99.97%. Secondly, a discrimination model of Artificial Neural Network (ANN-BP) was set up. The first seven principles components of the samples were applied as ANN-BP inputs, and the value of type of yogurt were applied as outputs, then the three-layer ANN-BP model was build. In this model, every variety yogurt includes 27 samples, the total number of sample is 135, and the rest 25 samples were used as prediction set. The results showed the distinguishing rate of the five yogurt varieties was 100%. It presented that this model was reliable and practicable. So a new approach for the rapid and lossless discrimination of varieties of yogurt was put forward.

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.

[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.

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

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.

Data for Known Geothermal Resource Areas (KGRA) and Identified Hydrothermal Resource Areas (IHRA) in Southern Idaho and Southeastern Oregon

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

Neupane, Ghanashyam; McLing, Travis; Mattson, Earl

The presented database includes water chemistry data and structural rating values for various geothermal features used for performing principal component (PC) and cluster analyses work to identify promising KGRAs and IHRAs in southern Idaho and southeastern Oregon. A brief note on various KGRAs/IHRAs is also included herewith. Results of PC and cluster analyses are presented as a separate paper (Lindsey et al., 2017) that is, as of the time of this submission, in 'revision' status.

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.

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

[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.

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.

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.

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.

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.

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.

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

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

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.

Investigating the composition characteristics of dissolved and particulate/colloidal organic matter in effluent-dominated stream using fluorescence spectroscopy combined with multivariable analysis.

PubMed

Yu, Min-Da; He, Xiao-Song; Xi, Bei-Dou; Gao, Ru-Tai; Zhao, Xian-Wei; Zhang, Hui; Huang, Cai-Hong; Tan, Wenbing

2018-03-01

Fluorescence excitation-emission matrix (EEM) spectroscopy combined with principal component analysis (PCA) and parallel factor analysis (PARAFAC) were used to investigate the compositional characteristics of dissolved and particulate/colloidal organic matter and its correlations with nitrogen, phosphorus, and heavy metals in an effluent-dominated stream, Northern China. The results showed that dissolved organic matter (DOM) was comprised of fulvic-like, humic-like, and protein-like components in the water samples, and fulvic-like substances were the main fraction of DOM among them. Particulate/colloidal organic matter (PcOM) consisted of fulvic-like and protein-like matter. Fulvic-like substances existed in the larger molecular form in PcOM, and they comprised a large amount of nitrogen and polar functional groups. On the other hand, protein-like components in PcOM were low in benzene ring and bound to heavy metals. It could be concluded that nitrogen, phosphorus, and heavy metals in effluent had an effect on the compositional characteristics of natural DOM and PcOM, which may deepen our understanding about the environmental behaviors of organic matter in effluent.

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.

Population genetics related to adaptation in elite oat germplasm

USDA-ARS?s Scientific Manuscript database

Six hundred thirty five oat lines and 2,635 SNP loci were used to evaluate population structure, linkage disequilibrium (LD) and genotype-phenotype association with heading date. The first five principal components (PC) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 2...

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.

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.

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.

Comparing Independent Component Analysis with Principle Component Analysis in Detecting Alterations of Porphyry Copper Deposit (case Study: Ardestan Area, Central Iran)

NASA Astrophysics Data System (ADS)

Mahmoudishadi, S.; Malian, A.; Hosseinali, F.

2017-09-01

The image processing techniques in transform domain are employed as analysis tools for enhancing the detection of mineral deposits. The process of decomposing the image into important components increases the probability of mineral extraction. In this study, the performance of Principal Component Analysis (PCA) and Independent Component Analysis (ICA) has been evaluated for the visible and near-infrared (VNIR) and Shortwave infrared (SWIR) subsystems of ASTER data. Ardestan is located in part of Central Iranian Volcanic Belt that hosts many well-known porphyry copper deposits. This research investigated the propylitic and argillic alteration zones and outer mineralogy zone in part of Ardestan region. The two mentioned approaches were applied to discriminate alteration zones from igneous bedrock using the major absorption of indicator minerals from alteration and mineralogy zones in spectral rang of ASTER bands. Specialized PC components (PC2, PC3 and PC6) were used to identify pyrite and argillic and propylitic zones that distinguish from igneous bedrock in RGB color composite image. Due to the eigenvalues, the components 2, 3 and 6 account for 4.26% ,0.9% and 0.09% of the total variance of the data for Ardestan scene, respectively. For the purpose of discriminating the alteration and mineralogy zones of porphyry copper deposit from bedrocks, those mentioned percentages of data in ICA independent components of IC2, IC3 and IC6 are more accurately separated than noisy bands of PCA. The results of ICA method conform to location of lithological units of Ardestan region, as well.

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.

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.

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.

Using PC Software To Enhance the Student's Ability To Learn the Exporting Process.

ERIC Educational Resources Information Center

Buckles, Tom A.; Lange, Irene

This paper describes the advantages of using computer simulations in the classroom or managerial environment and the major premise and principal components of Export to Win!, a computer simulation used in international marketing seminars. A rationale for using computer simulations argues that they improve the quality of teaching by building…

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;

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®

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.

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 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.

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 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.

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).

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.

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.

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.

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

Long-term growth-increment chronologies reveal diverse influences of climate forcing on freshwater and forest biota in the Pacific Northwest

USGS Publications Warehouse

Black, Bryan A.; Dunham, Jason B.; Blundon, Brett W.; Brim-Box, Jayne; Tepley, Alan J.

2015-01-01

Analyses of how organisms are likely to respond to a changing climate have focused largely on the direct effects of warming temperatures, though changes in other variables may also be important, particularly the amount and timing of precipitation. Here, we develop a network of eight growth-increment width chronologies for freshwater mussel species in the Pacific Northwest, United States and integrate them with tree-ring data to evaluate how terrestrial and aquatic indicators respond to hydroclimatic variability, including river discharge and precipitation. Annual discharge averaged across water years (October 1–September 30) was highly synchronous among river systems and imparted a coherent pattern among mussel chronologies. The leading principal component of the five longest mussel chronologies (1982–2003; PC1mussel) accounted for 47% of the dataset variability and negatively correlated with the leading principal component of river discharge (PC1discharge; r = −0.88; P < 0.0001). PC1mussel and PC1discharge were closely linked to regional wintertime precipitation patterns across the Pacific Northwest, the season in which the vast majority of annual precipitation arrives. Mussel growth was also indirectly related to tree radial growth, though the nature of the relationships varied across the landscape. Negative correlations occurred in forests where tree growth tends to be limited by drought while positive correlations occurred in forests where tree growth tends to be limited by deep or lingering snowpack. Overall, this diverse assemblage of chronologies illustrates the importance of winter precipitation to terrestrial and freshwater ecosystems and suggests that a complexity of climate responses must be considered when estimating the biological impacts of climate variability and change.

Long-term growth-increment chronologies reveal diverse influences of climate forcing on freshwater and forest biota in the Pacific Northwest.

PubMed

Black, Bryan A; Dunham, Jason B; Blundon, Brett W; Brim-Box, Jayne; Tepley, Alan J

2015-02-01

Analyses of how organisms are likely to respond to a changing climate have focused largely on the direct effects of warming temperatures, though changes in other variables may also be important, particularly the amount and timing of precipitation. Here, we develop a network of eight growth-increment width chronologies for freshwater mussel species in the Pacific Northwest, United States and integrate them with tree-ring data to evaluate how terrestrial and aquatic indicators respond to hydroclimatic variability, including river discharge and precipitation. Annual discharge averaged across water years (October 1-September 30) was highly synchronous among river systems and imparted a coherent pattern among mussel chronologies. The leading principal component of the five longest mussel chronologies (1982-2003; PC1(mussel)) accounted for 47% of the dataset variability and negatively correlated with the leading principal component of river discharge (PC1(discharge); r = -0.88; P < 0.0001). PC1(mussel) and PC1(discharge) were closely linked to regional wintertime precipitation patterns across the Pacific Northwest, the season in which the vast majority of annual precipitation arrives. Mussel growth was also indirectly related to tree radial growth, though the nature of the relationships varied across the landscape. Negative correlations occurred in forests where tree growth tends to be limited by drought while positive correlations occurred in forests where tree growth tends to be limited by deep or lingering snowpack. Overall, this diverse assemblage of chronologies illustrates the importance of winter precipitation to terrestrial and freshwater ecosystems and suggests that a complexity of climate responses must be considered when estimating the biological impacts of climate variability and change. © 2014 John Wiley & Sons Ltd.

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.

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 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.

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

Identification and apportionment of hazardous elements in the sediments in the Yangtze River estuary.

PubMed

Wang, Jiawei; Liu, Ruimin; Wang, Haotian; Yu, Wenwen; Xu, Fei; Shen, Zhenyao

2015-12-01

In this study, positive matrix factorization (PMF) and principal components analysis (PCA) were combined to identify and apportion pollution-based sources of hazardous elements in the surface sediments in the Yangtze River estuary (YRE). Source identification analysis indicated that PC1, including Al, Fe, Mn, Cr, Ni, As, Cu, and Zn, can be defined as a sewage component; PC2, including Pb and Sb, can be considered as an atmospheric deposition component; and PC3, containing Cd and Hg, can be considered as an agricultural nonpoint component. To better identify the sources and quantitatively apportion the concentrations to their sources, eight sources were identified with PMF: agricultural/industrial sewage mixed (18.6 %), mining wastewater (15.9 %), agricultural fertilizer (14.5 %), atmospheric deposition (12.8 %), agricultural nonpoint (10.6 %), industrial wastewater (9.8 %), marine activity (9.0 %), and nickel plating industry (8.8 %). Overall, the hazardous element content seems to be more connected to anthropogenic activity instead of natural sources. The PCA results laid the foundation for the PMF analysis by providing a general classification of sources. PMF resolves more factors with a higher explained variance than PCA; PMF provided both the internal analysis and the quantitative analysis. The combination of the two methods can provide more reasonable and reliable results.

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.

QSAR modeling of flotation collectors using principal components extracted from topological indices.

PubMed

Natarajan, R; Nirdosh, Inderjit; Basak, Subhash C; Mills, Denise R

2002-01-01

Several topological indices were calculated for substituted-cupferrons that were tested as collectors for the froth flotation of uranium. The principal component analysis (PCA) was used for data reduction. Seven principal components (PC) were found to account for 98.6% of the variance among the computed indices. The principal components thus extracted were used in stepwise regression analyses to construct regression models for the prediction of separation efficiencies (Es) of the collectors. A two-parameter model with a correlation coefficient of 0.889 and a three-parameter model with a correlation coefficient of 0.913 were formed. PCs were found to be better than partition coefficient to form regression equations, and inclusion of an electronic parameter such as Hammett sigma or quantum mechanically derived electronic charges on the chelating atoms did not improve the correlation coefficient significantly. The method was extended to model the separation efficiencies of mercaptobenzothiazoles (MBT) and aminothiophenols (ATP) used in the flotation of lead and zinc ores, respectively. Five principal components were found to explain 99% of the data variability in each series. A three-parameter equation with correlation coefficient of 0.985 and a two-parameter equation with correlation coefficient of 0.926 were obtained for MBT and ATP, respectively. The amenability of separation efficiencies of chelating collectors to QSAR modeling using PCs based on topological indices might lead to the selection of collectors for synthesis and testing from a virtual database.

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.

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.

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.

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

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.

Identifying overarching excipient properties towards an in-depth understanding of process and product performance for continuous twin-screw wet granulation.

PubMed

Willecke, N; Szepes, A; Wunderlich, M; Remon, J P; Vervaet, C; De Beer, T

2017-04-30

The overall objective of this work is to understand how excipient characteristics influence the process and product performance for a continuous twin-screw wet granulation process. The knowledge gained through this study is intended to be used for a Quality by Design (QbD)-based formulation design approach and formulation optimization. A total of 9 preferred fillers and 9 preferred binders were selected for this study. The selected fillers and binders were extensively characterized regarding their physico-chemical and solid state properties using 21 material characterization techniques. Subsequently, principal component analysis (PCA) was performed on the data sets of filler and binder characteristics in order to reduce the variety of single characteristics to a limited number of overarching properties. Four principal components (PC) explained 98.4% of the overall variability in the fillers data set, while three principal components explained 93.4% of the overall variability in the data set of binders. Both PCA models allowed in-depth evaluation of similarities and differences in the excipient properties. Copyright © 2017. Published by Elsevier B.V.

Improving the Power of GWAS and Avoiding Confounding from Population Stratification with PC-Select

PubMed Central

Tucker, George; Price, Alkes L.; Berger, Bonnie

2014-01-01

Using a reduced subset of SNPs in a linear mixed model can improve power for genome-wide association studies, yet this can result in insufficient correction for population stratification. We propose a hybrid approach using principal components that does not inflate statistics in the presence of population stratification and improves power over standard linear mixed models. PMID:24788602

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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.

Evaluating cumulative effects of anthropogenic inputs in Prince Edward Island estuaries using the mummichog (Fundulus heteroclitus).

PubMed

Finley, Megan A; Courtenay, Simon C; Teather, Kevin L; Hewitt, L Mark; Holdway, D A; Hogan, Natacha S; van den Heuvel, Michael R

2013-07-01

Estuarine eutrophication as a result of agricultural land use, including the use of chemical fertilizers, is increasing worldwide. Prince Edward Island (PEI), Canada has very high agricultural intensity by international standards with approximately 44% of the land area under production, and some watersheds in excess of 75% agricultural land-use. The type of agriculture is also intensive with primarily row crops that have high chemical fertilizer and pesticide usage. In light of these stressors, the hypothesis of this study was that mummichog (Fundulus heteroclitus) population parameters would change with point and nonpoint source pollution, and that multivariate statistics could be used to draw associations with specific stressors. Fish were sampled on a monthly basis from May through August at 7 estuaries spanning a range of land use, nutrient, and contaminant loadings. A suite of environmental variables were simplified into 3 principal components: PC1 representing agricultural land use, N loading, and plant habitat, PC2 being dominated by sediment sand and silt distribution, and PC3 largely reflecting P loading and sediment organic matter. There were significant differences in abundance of both adult and young-of-the-year mummichog, and these changes associated most strongly with PC1, the largely N-driven agricultural influences. In contrast, somatic variables such as liver and gonad size did not show strong association with the environmental quality principal component scores. The sand and silt PC2 appeared to have the opposite association with the biological data, with siltier environments correlating to older, larger, less dense populations of mummichog. Although pesticide residues were detected in estuarine sediment, there was no clear relationship between these and watershed agricultural intensity or biochemical indicators. There was, however, a strong relationship between agricultural environmental variables (PC1) and in vitro steroid production that is suggestive of a potential chemical effect. Eutrophication appeared to be a primary stressor affecting mummichog populations, as nutrient enrichment was associated with changes in habitat variables and these in turn were associated with high mummichog density. Thus, mummichog population demographics appear to have use as an indicator of adverse or worsening conditions in estuaries. We concluded that, based on the subset of environmental factors evaluated, the nonpoint-source inputs of sediments and nutrients exerted the greatest influence on mummichog populations in PEI estuaries. Copyright © 2013 SETAC.

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

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.

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.

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.

Spectral gene set enrichment (SGSE).

PubMed

Frost, H Robert; Li, Zhigang; Moore, Jason H

2015-03-03

Gene set testing is typically performed in a supervised context to quantify the association between groups of genes and a clinical phenotype. In many cases, however, a gene set-based interpretation of genomic data is desired in the absence of a phenotype variable. Although methods exist for unsupervised gene set testing, they predominantly compute enrichment relative to clusters of the genomic variables with performance strongly dependent on the clustering algorithm and number of clusters. We propose a novel method, spectral gene set enrichment (SGSE), for unsupervised competitive testing of the association between gene sets and empirical data sources. SGSE first computes the statistical association between gene sets and principal components (PCs) using our principal component gene set enrichment (PCGSE) method. The overall statistical association between each gene set and the spectral structure of the data is then computed by combining the PC-level p-values using the weighted Z-method with weights set to the PC variance scaled by Tracy-Widom test p-values. Using simulated data, we show that the SGSE algorithm can accurately recover spectral features from noisy data. To illustrate the utility of our method on real data, we demonstrate the superior performance of the SGSE method relative to standard cluster-based techniques for testing the association between MSigDB gene sets and the variance structure of microarray gene expression data. Unsupervised gene set testing can provide important information about the biological signal held in high-dimensional genomic data sets. Because it uses the association between gene sets and samples PCs to generate a measure of unsupervised enrichment, the SGSE method is independent of cluster or network creation algorithms and, most importantly, is able to utilize the statistical significance of PC eigenvalues to ignore elements of the data most likely to represent noise.

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.

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

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

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.

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

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

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

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.

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.

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.

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.

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.

Occurrence of Emerging Micropollutants in Water Systems in Gauteng, Mpumalanga, and North West Provinces, South Africa.

PubMed

Wanda, Elijah M M; Nyoni, Hlengilizwe; Mamba, Bhekie B; Msagati, Titus A M

2017-01-13

The ubiquitous occurrence of emerging micropollutants (EMPs) in water is an issue of growing environmental-health concern worldwide. However, there remains a paucity of data regarding their levels and occurrence in water. This study determined the occurrence of EMPs namely: carbamazepine (CBZ), galaxolide (HHCB), caffeine (CAF), tonalide (AHTN), 4-nonylphenol (NP), and bisphenol A (BPA) in water from Gauteng, Mpumalanga, and North West provinces, South Africa using comprehensive two-dimensional gas chromatography coupled to high resolution time-of-flight mass spectrometry (GCxGC-HRTOFMS). Kruskal-Wallis test and ANOVA were performed to determine temporal variations in occurrence of the EMPs. Principal component analysis (PCA) and Surfer Golden Graphics software for surface mapping were used to determine spatial variations in levels and occurrence of the EMPs. The mean levels ranged from 11.22 ± 18.8 ng/L for CAF to 158.49 ± 662 ng/L for HHCB. There was no evidence of statistically significant temporal variations in occurrence of EMPs in water. Nevertheless, their levels and occurrence vary spatially and are a function of two principal components (PCs, PC1 and PC2) which controlled 89.99% of the variance. BPA was the most widely distributed EMP, which was present in 62% of the water samples. The detected EMPs pose ecotoxicological risks in water samples, especially those from Mpumalanga province.

Occurrence of Emerging Micropollutants in Water Systems in Gauteng, Mpumalanga, and North West Provinces, South Africa

PubMed Central

Wanda, Elijah M. M.; Nyoni, Hlengilizwe; Mamba, Bhekie B.; Msagati, Titus A. M.

2017-01-01

The ubiquitous occurrence of emerging micropollutants (EMPs) in water is an issue of growing environmental-health concern worldwide. However, there remains a paucity of data regarding their levels and occurrence in water. This study determined the occurrence of EMPs namely: carbamazepine (CBZ), galaxolide (HHCB), caffeine (CAF), tonalide (AHTN), 4-nonylphenol (NP), and bisphenol A (BPA) in water from Gauteng, Mpumalanga, and North West provinces, South Africa using comprehensive two-dimensional gas chromatography coupled to high resolution time-of-flight mass spectrometry (GCxGC-HRTOFMS). Kruskal-Wallis test and ANOVA were performed to determine temporal variations in occurrence of the EMPs. Principal component analysis (PCA) and Surfer Golden Graphics software for surface mapping were used to determine spatial variations in levels and occurrence of the EMPs. The mean levels ranged from 11.22 ± 18.8 ng/L for CAF to 158.49 ± 662 ng/L for HHCB. There was no evidence of statistically significant temporal variations in occurrence of EMPs in water. Nevertheless, their levels and occurrence vary spatially and are a function of two principal components (PCs, PC1 and PC2) which controlled 89.99% of the variance. BPA was the most widely distributed EMP, which was present in 62% of the water samples. The detected EMPs pose ecotoxicological risks in water samples, especially those from Mpumalanga province. PMID:28098799

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.

Is Allelopathic Activity of Ipomoea murucoides Induced by Xylophage Damage?

PubMed

Flores-Palacios, Alejandro; Corona-López, Angélica María; Rios, María Yolanda; Aguilar-Guadarrama, Berenice; Toledo-Hernández, Víctor Hugo; Rodríguez-López, Verónica; Valencia-Díaz, Susana

2015-01-01

Herbivory activates the synthesis of allelochemicals that can mediate plant-plant interactions. There is an inverse relationship between the activity of xylophages and the abundance of epiphytes on Ipomoea murucoides. Xylophagy may modify the branch chemical constitution, which also affects the liberation of allelochemicals with defense and allelopathic properties. We evaluated the bark chemical content and the effect of extracts from branches subjected to treatments of exclusion, mechanical damage and the presence/absence of epiphytes, on the seed germination of the epiphyte Tillandsia recurvata. Principal component analysis showed that branches without any treatment separate from branches subjected to treatments; damaged and excluded branches had similar chemical content but we found no evidence to relate intentional damage with allelopathy; however 1-hexadecanol, a defense volatile compound correlated positively with principal component (PC) 1. The chemical constitution of branches subject to exclusion plus damage or plus epiphytes was similar among them. PC2 indicated that palmitic acid (allelopathic compound) and squalene, a triterpene that attracts herbivore enemies, correlated positively with the inhibition of seed germination of T. recurvata. Inhibition of seed germination of T. recurvata was mainly correlated with the increment of palmitic acid and this compound reached higher concentrations in excluded branches treatments. Then, it is likely that the allelopathic response of I. murucoides would increase to the damage (shade, load) that may be caused by a high load of epiphytes than to damage caused by the xylophages.

Digital staining for histopathology multispectral images by the combined application of spectral enhancement and spectral transformation.

PubMed

Bautista, Pinky A; Yagi, Yukako

2011-01-01

In this paper we introduced a digital staining method for histopathology images captured with an n-band multispectral camera. The method consisted of two major processes: enhancement of the original spectral transmittance and the transformation of the enhanced transmittance to its target spectral configuration. Enhancement is accomplished by shifting the original transmittance with the scaled difference between the original transmittance and the transmittance estimated with m dominant principal component (PC) vectors;the m-PC vectors were determined from the transmittance samples of the background image. Transformation of the enhanced transmittance to the target spectral configuration was done using an nxn transformation matrix, which was derived by applying a least square method to the enhanced and target spectral training data samples of the different tissue components. Experimental results on the digital conversion of a hematoxylin and eosin (H&E) stained multispectral image to its Masson's trichrome stained (MT) equivalent shows the viability of the method.

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.

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.

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.

Chemical and microstructural characterizations of plasma polymer films by time-of-flight secondary ion mass spectrometry and principal component analysis

NASA Astrophysics Data System (ADS)

Cossement, Damien; Renaux, Fabian; Thiry, Damien; Ligot, Sylvie; Francq, Rémy; Snyders, Rony

2015-11-01

It is accepted that the macroscopic properties of functional plasma polymer films (PPF) are defined by their functional density and their crosslinking degree (χ) which are quantities that most of the time behave in opposite trends. If the PPF chemistry is relatively easy to evaluate, it is much more challenging for χ. This paper reviews the recent work developed in our group on the application of principal component analysis (PCA) to time-of-flight secondary ion mass spectrometric (ToF-SIMS) positive spectra data in order to extract the relative cross-linking degree (χ) of PPF. NH2-, COOR- and SH-containing PPF synthesized in our group by plasma enhanced chemical vapor deposition (PECVD) varying the applied radiofrequency power (PRF), have been used as model surfaces. For the three plasma polymer families, the scores of the first computed principal component (PC1) highlighted significant differences in the chemical composition supported by X-Ray photoelectron spectroscopy (XPS) data. The most important fragments contributing to PC1 (loadings > 90%) were used to compute an average C/H ratio index for samples synthesized at low and high PRF. This ratio being an evaluation of χ, these data, accordingly to the literature, indicates an increase of χ with PRF excepted for the SH-PPF. These results have been cross-checked by the evaluation of functional properties of the plasma polymers namely a linear correlation with the stability of NH2-PPF in ethanol and a correlation with the mechanical properties of the COOR-PPF. For the SH-PPF family, the peculiar evolution of χ is supported by the understanding of the growth mechanism of the PPF from plasma diagnostic. The whole set of data clearly demonstrates the potential of the PCA method for extracting information on the microstructure of plasma polymers from ToF-SIMS measurements.

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.

Use of insoluble polyacrylate polymers to aid phytostabilization of mine soils: effects on plant growth and soil characteristics.

PubMed

Qu, G; de Varennes, A; Cunha-Queda, C

2010-01-01

We evaluated the use of polyacrylate polymers to aid phytostabilization of mine soils. In a pot experiment, perennial ryegrass was grown in a mine soil and in uncontaminated soil. Growth was stimulated in the polymer-amended mine soil compared with an unamended control, and water-extractable levels of soil Cu and Zn decreased after polymer application. In an experiment performed in six 60-cm-diameter cylinders filled with fertilized mine soil, polymers were applied to three cylinders, with the remainder used as unamended control. Total biomass produced by indigenous plant species sown in polymer-amended soil was 1.8 (Spring-Summer) or 2.4 times (Fall-Winter) greater than that of plants from unamended soil. The application of polymers to the mine soil led to the greatest activity of soil enzymes. Soil pH, biomass of Spergularia purpurea and Chaetopogon fasciculatus, and activities of protease and cellulase had large loadings on principal component (PC)1, whereas growth of Briza maxima and the activities of urease, acid phosphatase, and beta-glucosidase had large loadings on PC2. The treatments corresponding to controls were located on the negative side of PC1 and PC2. Amended treatments were on the positive side of PC2 (Spring-Summer) or on the positive side of PC1 (Fall-Winter), demonstrating differential responses of plants and soil parameters in the two growth cycles.

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.

Modelling Ecuador's rainfall distribution according to geographical characteristics.

NASA Astrophysics Data System (ADS)

Tobar, Vladimiro; Wyseure, Guido

2017-04-01

It is known that rainfall is affected by terrain characteristics and some studies had focussed on its distribution over complex terrain. Ecuador's temporal and spatial rainfall distribution is affected by its location on the ITCZ, the marine currents in the Pacific, the Amazon rainforest, and the Andes mountain range. Although all these factors are important, we think that the latter one may hold a key for modelling spatial and temporal distribution of rainfall. The study considered 30 years of monthly data from 319 rainfall stations having at least 10 years of data available. The relatively low density of stations and their location in accessible sites near to main roads or rivers, leave large and important areas ungauged, making it not appropriate to rely on traditional interpolation techniques to estimate regional rainfall for water balance. The aim of this research was to come up with a useful model for seasonal rainfall distribution in Ecuador based on geographical characteristics to allow its spatial generalization. The target for modelling was the seasonal rainfall, characterized by nine percentiles for each one of the 12 months of the year that results in 108 response variables, later on reduced to four principal components comprising 94% of the total variability. Predictor variables for the model were: geographic coordinates, elevation, main wind effects from the Amazon and Coast, Valley and Hill indexes, and average and maximum elevation above the selected rainfall station to the east and to the west, for each one of 18 directions (50-135°, by 5°) adding up to 79 predictors. A multiple linear regression model by the Elastic-net algorithm with cross-validation was applied for each one of the PC as response to select the most important ones from the 79 predictor variables. The Elastic-net algorithm deals well with collinearity problems, while allowing variable selection in a blended approach between the Ridge and Lasso regression. The model fitting produced explained variances of 59%, 81%, 49% and 17% for PC1, PC2, PC3 and PC4, respectively, backing up the hypothesis of good correlation between geographical characteristics and seasonal rainfall patterns (comprised in the four principal components). With the obtained coefficients from the regression, the 108 rainfall percentiles for each station were back estimated giving very good results when compared with the original ones, with an overall 60% explained variance.

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.

Classification of time-of-flight secondary ion mass spectrometry spectra from complex Cu-Fe sulphides by principal component analysis and artificial neural networks.

PubMed

Kalegowda, Yogesh; Harmer, Sarah L

2013-01-08

Artificial neural network (ANN) and a hybrid principal component analysis-artificial neural network (PCA-ANN) classifiers have been successfully implemented for classification of static time-of-flight secondary ion mass spectrometry (ToF-SIMS) mass spectra collected from complex Cu-Fe sulphides (chalcopyrite, bornite, chalcocite and pyrite) at different flotation conditions. ANNs are very good pattern classifiers because of: their ability to learn and generalise patterns that are not linearly separable; their fault and noise tolerance capability; and high parallelism. In the first approach, fragments from the whole ToF-SIMS spectrum were used as input to the ANN, the model yielded high overall correct classification rates of 100% for feed samples, 88% for conditioned feed samples and 91% for Eh modified samples. In the second approach, the hybrid pattern classifier PCA-ANN was integrated. PCA is a very effective multivariate data analysis tool applied to enhance species features and reduce data dimensionality. Principal component (PC) scores which accounted for 95% of the raw spectral data variance, were used as input to the ANN, the model yielded high overall correct classification rates of 88% for conditioned feed samples and 95% for Eh modified samples. Copyright © 2012 Elsevier B.V. All rights reserved.

Signal-to-noise contribution of principal component loads in reconstructed near-infrared Raman tissue spectra.

PubMed

Grimbergen, M C M; van Swol, C F P; Kendall, C; Verdaasdonk, R M; Stone, N; Bosch, J L H R

2010-01-01

The overall quality of Raman spectra in the near-infrared region, where biological samples are often studied, has benefited from various improvements to optical instrumentation over the past decade. However, obtaining ample spectral quality for analysis is still challenging due to device requirements and short integration times required for (in vivo) clinical applications of Raman spectroscopy. Multivariate analytical methods, such as principal component analysis (PCA) and linear discriminant analysis (LDA), are routinely applied to Raman spectral datasets to develop classification models. Data compression is necessary prior to discriminant analysis to prevent or decrease the degree of over-fitting. The logical threshold for the selection of principal components (PCs) to be used in discriminant analysis is likely to be at a point before the PCs begin to introduce equivalent signal and noise and, hence, include no additional value. Assessment of the signal-to-noise ratio (SNR) at a certain peak or over a specific spectral region will depend on the sample measured. Therefore, the mean SNR over the whole spectral region (SNR(msr)) is determined in the original spectrum as well as for spectra reconstructed from an increasing number of principal components. This paper introduces a method of assessing the influence of signal and noise from individual PC loads and indicates a method of selection of PCs for LDA. To evaluate this method, two data sets with different SNRs were used. The sets were obtained with the same Raman system and the same measurement parameters on bladder tissue collected during white light cystoscopy (set A) and fluorescence-guided cystoscopy (set B). This method shows that the mean SNR over the spectral range in the original Raman spectra of these two data sets is related to the signal and noise contribution of principal component loads. The difference in mean SNR over the spectral range can also be appreciated since fewer principal components can reliably be used in the low SNR data set (set B) compared to the high SNR data set (set A). Despite the fact that no definitive threshold could be found, this method may help to determine the cutoff for the number of principal components used in discriminant analysis. Future analysis of a selection of spectral databases using this technique will allow optimum thresholds to be selected for different applications and spectral data quality levels.

Relationship between rice yield and climate variables in southwest Nigeria using multiple linear regression and support vector machine analysis

NASA Astrophysics Data System (ADS)

Oguntunde, Philip G.; Lischeid, Gunnar; Dietrich, Ottfried

2018-03-01

This study examines the variations of climate variables and rice yield and quantifies the relationships among them using multiple linear regression, principal component analysis, and support vector machine (SVM) analysis in southwest Nigeria. The climate and yield data used was for a period of 36 years between 1980 and 2015. Similar to the observed decrease ( P < 0.001) in rice yield, pan evaporation, solar radiation, and wind speed declined significantly. Eight principal components exhibited an eigenvalue > 1 and explained 83.1% of the total variance of predictor variables. The SVM regression function using the scores of the first principal component explained about 75% of the variance in rice yield data and linear regression about 64%. SVM regression between annual solar radiation values and yield explained 67% of the variance. Only the first component of the principal component analysis (PCA) exhibited a clear long-term trend and sometimes short-term variance similar to that of rice yield. Short-term fluctuations of the scores of the PC1 are closely coupled to those of rice yield during the 1986-1993 and the 2006-2013 periods thereby revealing the inter-annual sensitivity of rice production to climate variability. Solar radiation stands out as the climate variable of highest influence on rice yield, and the influence was especially strong during monsoon and post-monsoon periods, which correspond to the vegetative, booting, flowering, and grain filling stages in the study area. The outcome is expected to provide more in-depth regional-specific climate-rice linkage for screening of better cultivars that can positively respond to future climate fluctuations as well as providing information that may help optimized planting dates for improved radiation use efficiency in the study area.

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

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.

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.

Minerals and Trace Elements in Human Breast Milk Are Associated with Guatemalan Infant Anthropometric Outcomes within the First 6 Months.

PubMed

Li, Chen; Solomons, Noel W; Scott, Marilyn E; Koski, Kristine G

2016-10-01

Breast milk is the recommended source of nutrients for infant growth, but its adequacy to meet infants' mineral and trace element needs is unknown. We used breast-milk mineral and trace element concentrations of Guatemalan mothers at 3 lactation stages to estimate total daily intakes and to determine whether intakes were associated with early infant growth. In this cross-sectional study, breast-milk samples were collected from Mam-Mayan mothers during transitional (5-17 d, n = 56), early (18-46 d, n = 75), and established (4-6 mo, n = 103) lactation; z scores for weight (WAZ), length (LAZ), and head circumference (HCAZ) were measured. Concentrations of 11 minerals (calcium, potassium, magnesium, sodium, copper, iron, manganese, rubidium, selenium, strontium, and zinc) were analyzed by inductively coupled plasma-mass spectrometry (ICP-MS). WHO equations were used to calculate the estimated energy requirement, which was divided by the energy density of breast milk to estimate daily milk volume, and this number was multiplied by breast-milk mineral concentrations to estimate intakes. Principal component analyses identified clusters of minerals; principal components (PCs) were used in regression analyses for anthropometric outcomes. Estimated breast-milk intakes during established lactation were insufficient to compensate for the lower milk sodium, copper, manganese, and zinc concentrations in male infants and the lower sodium, iron and manganese concentrations in female infants. Estimated intakes of calcium, magnesium, potassium, sodium, and selenium were below the Institute of Medicine Adequate Intake for both sexes at all 3 stages of lactation. In early lactation, multiple linear regressions showed that PC1 (calcium, magnesium, potassium, rubidium, and strontium intakes) was positively associated with WAZ, LAZ, and HCAZ. In established lactation, the same PC with sodium added was positively associated with all 3 anthropometric outcomes; a second PC (PC2: zinc, copper, and selenium intakes) was associated with WAZ and LAZ but not HCAZ. Breast milk may be inadequate in selected minerals and trace elements where higher estimated intakes were associated with greater infant growth. © 2016 American Society for Nutrition.

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.

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.

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.

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

Characterization of yakju brewed from glutinous rice and wild-type yeast strains isolated from nuruks.

PubMed

Kim, Hye Ryun; Kim, Jae-Ho; Bae, Dong-Hoon; Ahn, Byung-Hak

2010-12-01

Korean traditional rice wines yakju and takju are generally brewed with nuruk as the source of the saccharogenic enzymes by natural fermentation. To improve the quality of Korean rice wine, the microorganisms in the nuruk need to be studied. The objective of this research was to improve the quality of Korean wine with the wild-type yeast strains isolated from the fermentation starter, nuruk. Only strain YA-6 showed high activity in 20% ethanol. Precipitation of Y89-5-3 was similar to that of very flocculent yeast (〉80%) at 75.95%. Using 18S rRNA sequencing, all 10 strains were identified as Saccharomyces cerevisiae. Volatile compounds present in yakju were analyzed by gas chromatography-mass selective detector. The principal component analysis (PCA) of the volatile compounds grouped long-chain esters on the right side of the first principal component, PC1; these compounds were found in yakju that was made with strains YA-6, Y89-5-3, Y89-5- 2, Y90-9, and Y89-1-1. On the other side of PC1 were short-chain esters; these compounds were found in wines that were brewed with strains Y183-2, Y268-3, Y54-3, Y98-4, and Y88-4. Overall, the results indicated that using different wild-type yeast strains in the fermentation process significantly affects the chemical characteristics of the glutinous rice wine.

Is Allelopathic Activity of Ipomoea murucoides Induced by Xylophage Damage?

PubMed Central

Flores-Palacios, Alejandro; Corona-López, Angélica María; Rios, María Yolanda; Aguilar-Guadarrama, Berenice; Toledo-Hernández, Víctor Hugo; Rodríguez-López, Verónica; Valencia-Díaz, Susana

2015-01-01

Herbivory activates the synthesis of allelochemicals that can mediate plant-plant interactions. There is an inverse relationship between the activity of xylophages and the abundance of epiphytes on Ipomoea murucoides. Xylophagy may modify the branch chemical constitution, which also affects the liberation of allelochemicals with defense and allelopathic properties. We evaluated the bark chemical content and the effect of extracts from branches subjected to treatments of exclusion, mechanical damage and the presence/absence of epiphytes, on the seed germination of the epiphyte Tillandsia recurvata. Principal component analysis showed that branches without any treatment separate from branches subjected to treatments; damaged and excluded branches had similar chemical content but we found no evidence to relate intentional damage with allelopathy; however 1-hexadecanol, a defense volatile compound correlated positively with principal component (PC) 1. The chemical constitution of branches subject to exclusion plus damage or plus epiphytes was similar among them. PC2 indicated that palmitic acid (allelopathic compound) and squalene, a triterpene that attracts herbivore enemies, correlated positively with the inhibition of seed germination of T. recurvata. Inhibition of seed germination of T. recurvata was mainly correlated with the increment of palmitic acid and this compound reached higher concentrations in excluded branches treatments. Then, it is likely that the allelopathic response of I. murucoides would increase to the damage (shade, load) that may be caused by a high load of epiphytes than to damage caused by the xylophages. PMID:26625350

Spatial Patterns and Risk Assessment of Heavy Metals in Soils in a Resource-Exhausted City, Northeast China

PubMed Central

Chen, Hongwei; An, Jing; Wei, Shuhe; Gu, Jian

2015-01-01

Northeast China is an intensive area of resource-exhausted city, which is facing the challenges of industry conversion and sustainable development. In order to evaluate the soil environmental quality influenced by mining activities over decades, the concentration and spatial distribution of arsenic (As), cadmium (Cd), chromium (Cr), copper (Cu), nickel (Ni), lead (Pb), and Zinc (Zn) in surface soils (0-20cm) of a typical resource-exhausted city were investigated by analyzing 306 soil samples. The results showed that the average concentrations in the samples were 6.17 mg/kg for As, 0.19 mg/kg for Cd, 51.08 mg/kg for Cr, 23.27 mg/kg for Cu, 31.15 mg/kg for Ni, 22.17 mg/kg for Pb, and 54.21 mg/kg for Zn. Metals distribution maps produced by using the inverse distance weighted interpolation method and results revealed that all investigated metals showed distinct geographical patterns, and the concentrations were higher in urban and industrial areas than in farmland. Pearson correlation and principal component analysis showed that there were significant positive correlations (p<0.05) between all of the metals, and As, Cd, Cr, Mn, Ni, Pb, and Zn were closely associated with the first principal component (PC1), which explained 39.81% of the total variance. Cu and As were mainly associated with the second component (PC2). Based on the calculated Nemerow pollution index, percentage for slightly polluted (1

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

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.

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.

Mitochondrial lipids in Bufo arenarum full-grown oocytes.

PubMed

Gili, Valeria; Alonso, Telma S

2004-05-01

Both the content and composition of polar and neutral lipids from the mitochondrial fraction of ovarian full-grown Bufo arenarum oocytes were analysed in the present study. Triacylglycerols (TAG) represent 33% of the total lipids, followed by phosphatidylcholine (PC), free fatty acids (FFA) and phosphatidylethanolamine (PE). Diphosphatidylglycerol (DPG) or cardiolipin, a specific component of the inner mitochondrial membrane, represents about 4% of the total lipid content. Palmitic (16:0) and arachidonic (20:4n6) acids are the most abundant fatty acids in PC and PE, respectively. DPG is enriched in fatty acids with carbon chain lengths of 18, the principal component being linoleic acid. In phosphatidylinositol (PI), 20:4n6 and stearic acid (18:0) represent about 72 mol% of the total acyl group level. The main fatty acids in TAG are linoleic (18:2), oleic (18:1), and palmitic acids. The fatty acid composition of FFA and diacylglycerols (DAG) is similar, 16:0 being the most abundant acyl group. PE is the most unsaturated lipid and sphingomyelin (SM) has the lowest unsaturation index.

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.

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.

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.

Quantitative structure-activity relationship of the curcumin-related compounds using various regression methods

NASA Astrophysics Data System (ADS)

Khazaei, Ardeshir; Sarmasti, Negin; Seyf, Jaber Yousefi

2016-03-01

Quantitative structure activity relationship were used to study a series of curcumin-related compounds with inhibitory effect on prostate cancer PC-3 cells, pancreas cancer Panc-1 cells, and colon cancer HT-29 cells. Sphere exclusion method was used to split data set in two categories of train and test set. Multiple linear regression, principal component regression and partial least squares were used as the regression methods. In other hand, to investigate the effect of feature selection methods, stepwise, Genetic algorithm, and simulated annealing were used. In two cases (PC-3 cells and Panc-1 cells), the best models were generated by a combination of multiple linear regression and stepwise (PC-3 cells: r2 = 0.86, q2 = 0.82, pred_r2 = 0.93, and r2m (test) = 0.43, Panc-1 cells: r2 = 0.85, q2 = 0.80, pred_r2 = 0.71, and r2m (test) = 0.68). For the HT-29 cells, principal component regression with stepwise (r2 = 0.69, q2 = 0.62, pred_r2 = 0.54, and r2m (test) = 0.41) is the best method. The QSAR study reveals descriptors which have crucial role in the inhibitory property of curcumin-like compounds. 6ChainCount, T_C_C_1, and T_O_O_7 are the most important descriptors that have the greatest effect. With a specific end goal to design and optimization of novel efficient curcumin-related compounds it is useful to introduce heteroatoms such as nitrogen, oxygen, and sulfur atoms in the chemical structure (reduce the contribution of T_C_C_1 descriptor) and increase the contribution of 6ChainCount and T_O_O_7 descriptors. Models can be useful in the better design of some novel curcumin-related compounds that can be used in the treatment of prostate, pancreas, and colon cancers.

Regionalization of precipitation characteristics in Iran's Lake Urmia basin

NASA Astrophysics Data System (ADS)

Fazel, Nasim; Berndtsson, Ronny; Uvo, Cintia Bertacchi; Madani, Kaveh; Kløve, Bjørn

2018-04-01

Lake Urmia in northwest Iran, once one of the largest hypersaline lakes in the world, has shrunk by almost 90% in area and 80% in volume during the last four decades. To improve the understanding of regional differences in water availability throughout the region and to refine the existing information on precipitation variability, this study investigated the spatial pattern of precipitation for the Lake Urmia basin. Daily rainfall time series from 122 precipitation stations with different record lengths were used to extract 15 statistical descriptors comprising 25th percentile, 75th percentile, and coefficient of variation for annual and seasonal total precipitation. Principal component analysis in association with cluster analysis identified three main homogeneous precipitation groups in the lake basin. The first sub-region (group 1) includes stations located in the center and southeast; the second sub-region (group 2) covers mostly northern and northeastern part of the basin, and the third sub-region (group 3) covers the western and southern edges of the basin. Results of principal component (PC) and clustering analyses showed that seasonal precipitation variation is the most important feature controlling the spatial pattern of precipitation in the lake basin. The 25th and 75th percentiles of winter and autumn are the most important variables controlling the spatial pattern of the first rotated principal component explaining about 32% of the total variance. Summer and spring precipitation variations are the most important variables in the second and third rotated principal components, respectively. Seasonal variation in precipitation amount and seasonality are explained by topography and influenced by the lake and westerly winds that are related to the strength of the North Atlantic Oscillation. Despite using incomplete time series with different lengths, the identified sub-regions are physically meaningful.

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).

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

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

Quantitative structure-activity relationship study of P2X7 receptor inhibitors using combination of principal component analysis and artificial intelligence methods.

PubMed

Ahmadi, Mehdi; Shahlaei, Mohsen

2015-01-01

P2X7 antagonist activity for a set of 49 molecules of the P2X7 receptor antagonists, derivatives of purine, was modeled with the aid of chemometric and artificial intelligence techniques. The activity of these compounds was estimated by means of combination of principal component analysis (PCA), as a well-known data reduction method, genetic algorithm (GA), as a variable selection technique, and artificial neural network (ANN), as a non-linear modeling method. First, a linear regression, combined with PCA, (principal component regression) was operated to model the structure-activity relationships, and afterwards a combination of PCA and ANN algorithm was employed to accurately predict the biological activity of the P2X7 antagonist. PCA preserves as much of the information as possible contained in the original data set. Seven most important PC's to the studied activity were selected as the inputs of ANN box by an efficient variable selection method, GA. The best computational neural network model was a fully-connected, feed-forward model with 7-7-1 architecture. The developed ANN model was fully evaluated by different validation techniques, including internal and external validation, and chemical applicability domain. All validations showed that the constructed quantitative structure-activity relationship model suggested is robust and satisfactory.

Quantitative structure–activity relationship study of P2X7 receptor inhibitors using combination of principal component analysis and artificial intelligence methods

PubMed Central

Ahmadi, Mehdi; Shahlaei, Mohsen

2015-01-01

P2X7 antagonist activity for a set of 49 molecules of the P2X7 receptor antagonists, derivatives of purine, was modeled with the aid of chemometric and artificial intelligence techniques. The activity of these compounds was estimated by means of combination of principal component analysis (PCA), as a well-known data reduction method, genetic algorithm (GA), as a variable selection technique, and artificial neural network (ANN), as a non-linear modeling method. First, a linear regression, combined with PCA, (principal component regression) was operated to model the structure–activity relationships, and afterwards a combination of PCA and ANN algorithm was employed to accurately predict the biological activity of the P2X7 antagonist. PCA preserves as much of the information as possible contained in the original data set. Seven most important PC's to the studied activity were selected as the inputs of ANN box by an efficient variable selection method, GA. The best computational neural network model was a fully-connected, feed-forward model with 7−7−1 architecture. The developed ANN model was fully evaluated by different validation techniques, including internal and external validation, and chemical applicability domain. All validations showed that the constructed quantitative structure–activity relationship model suggested is robust and satisfactory. PMID:26600858

Determination of the Characteristics and Classification of Near-Infrared Spectra of Patchouli Oil (Pogostemon Cablin Benth.) from Different Origin

NASA Astrophysics Data System (ADS)

Diego, M. C. R.; Purwanto, Y. A.; Sutrisno; Budiastra, I. W.

2018-05-01

Research related to the non-destructive method of near-infrared (NIR) spectroscopy in aromatic oil is still in development in Indonesia. The objectives of the study were to determine the characteristics of the near-infrared spectra of patchouli oil and classify it based on its origin. The samples were selected from seven different places in Indonesia (Bogor and Garut from West Java, Aceh, and Jambi from Sumatra and Konawe, Masamba and Kolaka from Sulawesi Island). The spectral data of patchouli oil was obtained by FT-NIR spectrometer at the wavelength of 1000-2500 nm, and after that, the samples were subjected to composition analysis using Gas Chromatography-Mass Spectrometry. The transmittance and absorbance spectra were analyzed and then principal component analysis (PCA) was carried out. Discriminant analysis (DA) of the principal component was developed to classify patchouli oil based on its origin. The result shows that the data of both spectra (transmittance and absorbance spectra) by the PC analysis give a similar result for discriminating the seven types of patchouli oil due to their distribution and behavior. The DA of the three principal component in both data processed spectra could classify patchouli oil accurately. This result exposed that NIR spectroscopy can be successfully used as a correct method to classify patchouli oil based on its origin.

[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.

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.

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.

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.

Local or global? How to choose the training set for principal component compression of hyperspectral satellite measurements: a hybrid approach

NASA Astrophysics Data System (ADS)

Hultberg, Tim; August, Thomas; Lenti, Flavia

2017-09-01

Principal Component (PC) compression is the method of choice to achieve band-width reduction for dissemination of hyper spectral (HS) satellite measurements and will become increasingly important with the advent of future HS missions (such as IASI-NG and MTG-IRS) with ever higher data-rates. It is a linear transformation defined by a truncated set of the leading eigenvectors of the covariance of the measurements as well as the mean of the measurements. We discuss the strategy for generation of the eigenvectors, based on the operational experience made with IASI. To compute the covariance and mean, a so-called training set of measurements is needed, which ideally should include all relevant spectral features. For the dissemination of IASI PC scores a global static training set consisting of a large sample of measured spectra covering all seasons and all regions is used. This training set was updated once after the start of the dissemination of IASI PC scores in April 2010 by adding spectra from the 2010 Russian wildfires, in which spectral features not captured by the previous training set were identified. An alternative approach, which has sometimes been proposed, is to compute the eigenvectors on the fly from a local training set, for example consisting of all measurements in the current processing granule. It might naively be thought that this local approach would improve the compression rate by reducing the number of PC scores needed to represent the measurements within each granule. This false belief is apparently confirmed, if the reconstruction scores (root mean square of the reconstruction residuals) is used as the sole criteria for choosing the number of PC scores to retain, which would overlook the fact that the decrease in reconstruction score (for the same number of PCs) is achieved only by the retention of an increased amount of random noise. We demonstrate that the local eigenvectors retain a higher amount of noise and a lower amount of atmospheric signal than global eigenvectors. Local eigenvectors do not increase the compression rate, but increase the amount of atmospheric loss and should be avoided. Only extremely rare situations, resulting in spectra with features which have not been observed previously, can lead to problems for the global approach. To cope with such situations we investigate a hybrid approach, which first apply the global eigenvectors and then apply local compression to the residuals in order to identify and disseminate in addition any directions in the local signal, which are orthogonal to the subspace spanned by the global eigenvectors.

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®.

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

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).

Modelling above Ground Biomass of Mangrove Forest Using SENTINEL-1 Imagery

NASA Astrophysics Data System (ADS)

Labadisos Argamosa, Reginald Jay; Conferido Blanco, Ariel; Balidoy Baloloy, Alvin; Gumbao Candido, Christian; Lovern Caboboy Dumalag, John Bart; Carandang Dimapilis, Lee, , Lady; Camero Paringit, Enrico

2018-04-01

Many studies have been conducted in the estimation of forest above ground biomass (AGB) using features from synthetic aperture radar (SAR). Specifically, L-band ALOS/PALSAR (wavelength 23 cm) data is often used. However, few studies have been made on the use of shorter wavelengths (e.g., C-band, 3.75 cm to 7.5 cm) for forest mapping especially in tropical forests since higher attenuation is observed for volumetric objects where energy propagated is absorbed. This study aims to model AGB estimates of mangrove forest using information derived from Sentinel-1 C-band SAR data. Combinations of polarisations (VV, VH), its derivatives, grey level co-occurrence matrix (GLCM), and its principal components were used as features for modelling AGB. Five models were tested with varying combinations of features; a) sigma nought polarisations and its derivatives; b) GLCM textures; c) the first five principal components; d) combination of models a-c; and e) the identified important features by Random Forest variable importance algorithm. Random Forest was used as regressor to compute for the AGB estimates to avoid over fitting caused by the introduction of too many features in the model. Model e obtained the highest r2 of 0.79 and an RMSE of 0.44 Mg using only four features, namely, σ°VH GLCM variance, σ°VH GLCM contrast, PC1, and PC2. This study shows that Sentinel-1 C-band SAR data could be used to produce acceptable AGB estimates in mangrove forest to compensate for the unavailability of longer wavelength SAR.

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.

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.

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.

Activities of some stress enzymes as indicators of slaughter cattle welfare and their relationship with physico-chemical characteristics of beef.

PubMed

Chulayo, A-Y; Muchenje, V

2017-09-01

The study determined the activities of creatine kinase (CK) and lactate dehydrogenase (LDH) in transported cattle as indicators of welfare and how they relate to beef quality. A total of 219 (n=219) (85 Beefmaster, 48 Charolaise, 32 Holstein-Friesian and 54 nondescript) cattle brought to the abattoir for slaughter were used in the study. Disposable vacutainer tubes with anticoagulant (ethylenediaminetetraacetic acid) were used to collect 4 ml of blood samples to determine the activities of CK and LDH. The measurements of pHu and colour coordinates (L*, a* and b*) were carried out at 48 h after slaughter on the representative samples of muscularis longissimuss thoracis et. lumborum (LTL). Longer distance travelled by cattle had a significant effect (P3000 to 5000) and those that travelled for 1263 km had lower CK activities (1000). The activities of LDH were observed in cattle that travelled for 366 and 1012 km (7000) and for those that travelled for 877 and 922 km (6000). Results of the principal component analysis showed that the first three principal components (PCs) explained about 53% of the total variability. The first PC was correlated with meat quality attributes (pHu, Tm, a* and b* values). The activities of CK and LDH were related and useful to define the second PC. However, CK and LDH were not related to beef quality. Therefore, CK and LDH can be used as indicators of welfare in slaughter cattle but cannot be used to predict the quality of meat.

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.

Global metabolomic profiling targeting childhood obesity in the Hispanic population.

PubMed

Butte, Nancy F; Liu, Yan; Zakeri, Issa F; Mohney, Robert P; Mehta, Nitesh; Voruganti, V Saroja; Göring, Harald; Cole, Shelley A; Comuzzie, Anthony G

2015-08-01

Metabolomics may unravel important biological pathways involved in the pathophysiology of childhood obesity. We aimed to 1) identify metabolites that differ significantly between nonobese and obese Hispanic children; 2) collapse metabolites into principal components (PCs) associated with obesity and metabolic risk, specifically hyperinsulinemia, hypertriglyceridemia, hyperleptinemia, and hyperuricemia; and 3) identify metabolites associated with energy expenditure and fat oxidation. This trial was a cross-sectional observational study of metabolomics by using gas chromatography-mass spectrometry and ultrahigh-performance liquid chromatography-tandem mass spectrometry analyses performed on fasting plasma samples from 353 nonobese and 450 obese Hispanic children. Branched-chained amino acids (BCAAs) (Leu, Ile, and Val) and their catabolites, propionylcarnitine and butyrylcarnitine, were significantly elevated in obese children. Strikingly lower lysolipids and dicarboxylated fatty acids were seen in obese children. Steroid derivatives were markedly higher in obese children as were markers of inflammation and oxidative stress. PC6 (BCAAs and aromatic AAs) and PC10 (asparagine, glycine, and serine) made the largest contributions to body mass index, and PC10 and PC12 (acylcarnitines) made the largest contributions to adiposity. Metabolic risk factors and total energy expenditure were associated with PC6, PC9 (AA and tricarboxylic acid cycle metabolites), and PC10. Fat oxidation was inversely related to PC8 (lysolipids) and positively related to PC16 (acylcarnitines). Global metabolomic profiling in nonobese and obese children replicates the increased BCAA and acylcarnitine catabolism and changes in nucleotides, lysolipids, and inflammation markers seen in obese adults; however, a strong signature of reduced fatty acid catabolism and increased steroid derivatives may be unique to obese children. Metabolic flexibility in fuel use observed in obese children may occur through the activation of alternative intermediary pathways. Insulin resistance, hyperleptinemia, hypertriglyceridemia, hyperuricemia, and oxidative stress and inflammation evident in obese children are associated with distinct metabolomic profiles. © 2015 American Society for Nutrition.

[Source identification and potential ecological hazards assessment of trace metalloid/heavy metals in the soil of Tianshan Mountains, Xinjiang, China].

PubMed

Zhang, Zhao-Yong; Jilili, Abuduwailil; Jiang, Feng-Qing

2014-11-01

In this study, the contents of ten metalloid/heavy metals (As, Pb, Ni, Cd, Co, Hg, Cu, Mn, Zn and Cr) in soil samples collected from three sections including the central Urumqi-Akesu, eastern Blikun-Yiwu and western Zhaosu-Tekesi in Tianshan Mountains were determined, and their sources were identified by using typical statistical and multivariate statistical methods. The potential ecological risks of these heavy metals were assessed by employing pollution index method, potential ecological risk index and the background values of Tianshan Mountains, and Xinjiang, and also the Second National Standard of the Soil Qualities of China. The results showed that the contents of the heavy metals (Pb, Ni, Cd, Co, Hg, Cu, Mn Zn and Cr) and metalloid As were all higher than the soil background values of the Tianshan Mountain or Xinjiang, and their variation co- efficients belonged to the medium variation. In general, the contents of the ten metalloid/heavy metals in the soil of Tianshan Mountains were low. Principal component analysis showed that the ten metalloid/heavy metals could be identified as two principal components, among which PC1 (Cd, Pb, Hg, Mn and Zn) could be seen as 'human influence sources factor', PC2 (Cu, Ni, Cr, Co and As) as 'natural sources factor'. Mn and As had larger loads both in PC1 and PC2, and they could be co-influenced by human and natural sources. The pollution assessment showed that Hg and Cd in central Urumuqi-Akesu section and As in western Zhaosu-Tekesi section were all at alert level, while the other heavy metals in other sections were all at security level. From the comprehensive pollution indices (P(z)) of heavy metals, it was found that the ten metalloid/heavy metals in the soils of central Urumqi-Akesu section were at low pollution level, but those in the other two sections were at clean level. The potential ecological risk assessment showed that the potential ecological risk coefficient (E(i)r) and the ecological damage index (RI) of Hg and Cd in central Urumqi-Akesu section and that of As in western Zhaosu-Tekesi section were relatively high.

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).

Variety identification of brown sugar using short-wave near infrared spectroscopy and multivariate calibration

NASA Astrophysics Data System (ADS)

Yang, Haiqing; Wu, Di; He, Yong

2007-11-01

Near-infrared spectroscopy (NIRS) with the characteristics of high speed, non-destructiveness, high precision and reliable detection data, etc. is a pollution-free, rapid, quantitative and qualitative analysis method. A new approach for variety discrimination of brown sugars using short-wave NIR spectroscopy (800-1050nm) was developed in this work. The relationship between the absorbance spectra and brown sugar varieties was established. The spectral data were compressed by the principal component analysis (PCA). The resulting features can be visualized in principal component (PC) space, which can lead to discovery of structures correlative with the different class of spectral samples. It appears to provide a reasonable variety clustering of brown sugars. The 2-D PCs plot obtained using the first two PCs can be used for the pattern recognition. Least-squares support vector machines (LS-SVM) was applied to solve the multivariate calibration problems in a relatively fast way. The work has shown that short-wave NIR spectroscopy technique is available for the brand identification of brown sugar, and LS-SVM has the better identification ability than PLS when the calibration set is small.

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.

Spatial Organization In Europe of Decadal and Interdecadal Fluctuations In Annual Rainfall

NASA Astrophysics Data System (ADS)

Lucero, O. A.; Rodriguez, N. C.

In this research the spatial patterns of decadal and bidecadal fluctuations in annual rainfall in Europe are identified. Filtering of time series of anomaly of annual rainfall is carried out using the Morlet wavelet technique. Reconstruction is achieved by sum- ming the contributions from bands of wavelet timescales; the decadal band and the bidecadal band are composed of contributions from the band of (10- to 17-year] and (17- to 27- year] timescales respectively. Results indicate that 1) the spatial organi- zation of decadal and bidecadal components of annual rainfall are standing wave-like organized patterns. Three standing decadal fluctuations zonally aligned formed the spatial pattern from 1900 until 1931; thereafter the pattern changed into a NW-SE orientation. The decadal band shows an average 12-year period. 2) The spatial orga- nization of bidecadal component was composed of three standing fluctuations since 1903 to 1986. After 1987 two standing bidecadal fluctuations were located on Europe. The orientation of bidecadal fluctuations changed during the period under study. Until 1913 the spatial pattern of the bidecadal component was zonally aligned. Since 1913 until 1986 the three bidecadal fluctuations composing the spatial pattern were aligned SW U NE; starting 1987 the spatial pattern is composed of two standing fluctuations zonally aligned. The bidecadal spatial pattern shows an average period of 20- to 22- year length. 3) At decadal and bidecadal timescales, the first principal component of the spatial field of anomaly of annual rainfall and the NAO index are connected. The upper positive third (lower negative third) of values of first principal component are indicative of extensive area with positive (negative) anomaly of annual rainfall. 4) At decadal timescale the relative phase between the first PC and the NAO index changes through the period under study; these changes define three regimes: 1) Dur- ing the regime covering the period 1900 (start of period under study) to about 1945, at the time of peak values of decadal NAO-index it takes place a transition between extremes (a neutral state) of the decadal rainfall spatial pattern (first PC takes small absolute values). Besides, for positive (negative) peak value of NAO index the spatial pattern of annual rainfall is evolving toward an area of predominantly positive (nega- tive) anomaly. 2) The second regime starts about 1946 and reaches up to early 1980s. At the time of negative (positive) peak of decadal NAO there is a prevailing spatial pattern of positive (negative) anomaly of decadal rainfall. 3) The third regime starts 1 about late 1970s and reaches to the end of the period under study (in 1996). There is a change of relative phase within this period in late 1980s. In this regime a spatial pattern of prevailing positive or negative anomaly of decadal rainfall takes place dur- ing values of decadal NAO close to zero. 5) At bidecadal timescale the relative phase between the first PC and the NAO index remains almost constant through the period under study. The first PC of the transformed bidecadal component of annual rainfall anomaly attains its positive (negative) peak about three years before the bidecadal component of NAO reaches its negative (positive) peak. 2

Structured mating: Patterns and implications

PubMed Central

Sebro, Ronnie; Peloso, Gina M.; Risch, Neil J.

2017-01-01

Genetic similarity of spouses can reflect factors influencing mate choice, such as physical/behavioral characteristics, and patterns of social endogamy. Spouse correlations for both genetic ancestry and measured traits may impact genotype distributions (Hardy Weinberg and linkage equilibrium), and therefore genetic association studies. Here we evaluate white spouse-pairs from the Framingham Heart Study (FHS) original and offspring cohorts (N = 124 and 755, respectively) to explore spousal genetic similarity and its consequences. Two principal components (PCs) of the genome-wide association (GWA) data were identified, with the first (PC1) delineating clines of Northern/Western to Southern European ancestry and the second (PC2) delineating clines of Ashkenazi Jewish ancestry. In the original (older) cohort, there was a striking positive correlation between the spouses in PC1 (r = 0.73, P = 3x10-22) and also for PC2 (r = 0.80, P = 7x10-29). In the offspring cohort, the spouse correlations were lower but still highly significant for PC1 (r = 0.38, P = 7x10-28) and for PC2 (r = 0.45, P = 2x10-39). We observed significant Hardy-Weinberg disequilibrium for single nucleotide polymorphisms (SNPs) loading heavily on PC1 and PC2 across 3 generations, and also significant linkage disequilibrium between unlinked SNPs; both decreased with time, consistent with reduced ancestral endogamy over generations and congruent with theoretical calculations. Ignoring ancestry, estimates of spouse kinship have a mean significantly greater than 0, and more so in the earlier generations. Adjusting kinship estimates for genetic ancestry through the use of PCs led to a mean spouse kinship not different from 0, demonstrating that spouse genetic similarity could be fully attributed to ancestral assortative mating. These findings also have significance for studies of heritability that are based on distantly related individuals (kinship less than 0.05), as we also demonstrate the poor correlation of kinship estimates in that range when ancestry is or is not taken into account. PMID:28384154

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.

An Intervention to Control Vasomotor Symptoms for Advanced PC Patients on Hormone Therapy

DTIC Science & Technology

2014-08-01

Symptoms for Advanced PC Patients on Hormone Therapy PRINCIPAL INVESTIGATOR: Michael A. Diefenbach, Ph.D. CONTRACTING ORGANIZATION...Control Vasomotor Symptoms for Advanced PC Patients on Hormone Therapy 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-11-1-0604 5c...NOTES 14. ABSTRACT Vasomotor Symptom (Hot Flashes) is a common side-effect of hormone therapy for prostate cancer survivors who experience a rising

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.

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.

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.

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.

Use of Topical PC-NSAIDs to Treat Burn Injury and Pain

DTIC Science & Technology

2015-08-01

1R41CA171408 (PI: Lichtenberger) 05/03/2013-04/30/2014 NIH/NCI 1.2 calendar mo. $85,000/yr Aspirin -PC for Chemoprevention of Colorectal Cancer The...major goal of this Phase I STTR grant is to test aspirin -PC for chemopreventive activity in an animal model of colon cancer. Role: Principal...calendar months $155,000/yr Effects of anti-platelet drugs on colon cancer in the elderly The major goal of this R21 grant is to test Aspirin -PC and

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.

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.

Effect of Low-Level Laser Therapy in an Experimental Model of Osteoarthritis in Rats Evaluated Through Raman Spectroscopy

PubMed Central

Mangueira, Nilton Maciel; Xavier, Murilo; de Souza, Renato Aparecido; Salgado, Miguel Angel Castillo; Silveira, Landulfo

2015-01-01

Abstract Objective: This work aimed to investigate the biochemical changes associated with low-level laser therapy (LLLT) using 660 and 780 nm, on a well-established experimental model of osteoarthritis (OA) in the knees of rats with induced collagenase, using histomorphometry and Raman spectroscopy. Materials and methods: Thirty-six Wistar rats were divided into four groups: control (GCON, n=9), collagenase without treatment (GCOL, n=9), collagenase with LLLT 660 nm treatment (G660, n=8), and collagenase with LLLT 780 nm treatment (G780, n=10). LLLT protocol was: 30 mW power output, 10 sec irradiation time, 0.04 cm2 spot size, 0.3 J energy, 0.75 W/cm2 irradiance, and 7.5 J/cm2 fluence per session per day, during 14 days. Then, knees were withdrawn and submitted to histomorphometry and Raman spectroscopy analysis. Principal components analysis (PCA) and Mahalanobis distance were employed to characterize the spectral findings. Results: Histomorphometry revealed a significant increase in the amount of collagen III for the group irradiated with 660 nm. The Raman bands at 1247, 1273, and 1453 cm−1 (from principal component score PC2), attributed to collagen type II, and 1460 cm−1 (from PC3), attributed to collagen type III, suggested that the LLLT causes acceleration in cellular activity, especially on the cells that repair cartilage, accelerating the breakdown of cartilage destroyed by collagenase and stimulating the fibroblast to synthesize repairing collagen III. Conclusions: LLLT accelerated the initial breakdown of cartilage destroyed by collagenase and stimulated the fibroblast to synthesize the repairing collagen III, suggesting a beneficial effect of LLLT on OA. PMID:25714387

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.

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.

Performance of Optimized Actuator and Sensor Arrays in an Active Noise Control System

NASA Technical Reports Server (NTRS)

Palumbo, D. L.; Padula, S. L.; Lyle, K. H.; Cline, J. H.; Cabell, R. H.

1996-01-01

Experiments have been conducted in NASA Langley's Acoustics and Dynamics Laboratory to determine the effectiveness of optimized actuator/sensor architectures and controller algorithms for active control of harmonic interior noise. Tests were conducted in a large scale fuselage model - a composite cylinder which simulates a commuter class aircraft fuselage with three sections of trim panel and a floor. Using an optimization technique based on the component transfer functions, combinations of 4 out of 8 piezoceramic actuators and 8 out of 462 microphone locations were evaluated against predicted performance. A combinatorial optimization technique called tabu search was employed to select the optimum transducer arrays. Three test frequencies represent the cases of a strong acoustic and strong structural response, a weak acoustic and strong structural response and a strong acoustic and weak structural response. Noise reduction was obtained using a Time Averaged/Gradient Descent (TAGD) controller. Results indicate that the optimization technique successfully predicted best and worst case performance. An enhancement of the TAGD control algorithm was also evaluated. The principal components of the actuator/sensor transfer functions were used in the PC-TAGD controller. The principal components are shown to be independent of each other while providing control as effective as the standard TAGD.

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.

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.

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.

Multimodal imaging of language reorganization in patients with left temporal lobe epilepsy.

PubMed

Chang, Yu-Hsuan A; Kemmotsu, Nobuko; Leyden, Kelly M; Kucukboyaci, N Erkut; Iragui, Vicente J; Tecoma, Evelyn S; Kansal, Leena; Norman, Marc A; Compton, Rachelle; Ehrlich, Tobin J; Uttarwar, Vedang S; Reyes, Anny; Paul, Brianna M; McDonald, Carrie R

2017-07-01

This study explored the relationships among multimodal imaging, clinical features, and language impairment in patients with left temporal lobe epilepsy (LTLE). Fourteen patients with LTLE and 26 controls underwent structural MRI, functional MRI, diffusion tensor imaging, and neuropsychological language tasks. Laterality indices were calculated for each imaging modality and a principal component (PC) was derived from language measures. Correlations were performed among imaging measures, as well as to the language PC. In controls, better language performance was associated with stronger left-lateralized temporo-parietal and temporo-occipital activations. In LTLE, better language performance was associated with stronger right-lateralized inferior frontal, temporo-parietal, and temporo-occipital activations. These right-lateralized activations in LTLE were associated with right-lateralized arcuate fasciculus fractional anisotropy. These data suggest that interhemispheric language reorganization in LTLE is associated with alterations to perisylvian white matter. These concurrent structural and functional shifts from left to right may help to mitigate language impairment in LTLE. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

A Filtering of Incomplete GNSS Position Time Series with Probabilistic Principal Component Analysis

NASA Astrophysics Data System (ADS)

Gruszczynski, Maciej; Klos, Anna; Bogusz, Janusz

2018-04-01

For the first time, we introduced the probabilistic principal component analysis (pPCA) regarding the spatio-temporal filtering of Global Navigation Satellite System (GNSS) position time series to estimate and remove Common Mode Error (CME) without the interpolation of missing values. We used data from the International GNSS Service (IGS) stations which contributed to the latest International Terrestrial Reference Frame (ITRF2014). The efficiency of the proposed algorithm was tested on the simulated incomplete time series, then CME was estimated for a set of 25 stations located in Central Europe. The newly applied pPCA was compared with previously used algorithms, which showed that this method is capable of resolving the problem of proper spatio-temporal filtering of GNSS time series characterized by different observation time span. We showed, that filtering can be carried out with pPCA method when there exist two time series in the dataset having less than 100 common epoch of observations. The 1st Principal Component (PC) explained more than 36% of the total variance represented by time series residuals' (series with deterministic model removed), what compared to the other PCs variances (less than 8%) means that common signals are significant in GNSS residuals. A clear improvement in the spectral indices of the power-law noise was noticed for the Up component, which is reflected by an average shift towards white noise from - 0.98 to - 0.67 (30%). We observed a significant average reduction in the accuracy of stations' velocity estimated for filtered residuals by 35, 28 and 69% for the North, East, and Up components, respectively. CME series were also subjected to analysis in the context of environmental mass loading influences of the filtering results. Subtraction of the environmental loading models from GNSS residuals provides to reduction of the estimated CME variance by 20 and 65% for horizontal and vertical components, respectively.

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.

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.

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.

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.

Dietary patterns of the Andean population of Puna and Quebrada of Humahuaca, Jujuy, Argentina.

PubMed

Romaguera, D; Samman, N; Rossi, A; Miranda, C; Pons, A; Tur, J A

2008-02-01

The aim of the present study was to describe dietary patterns in a representative sample from Puna and Quebrada of Humahuaca, Jujuy, Argentina. A cross-sectional nutritional survey was carried out in a representative sample (n 1236) of individuals from these regions. For the present study, only children aged 2-9 years (n 360), adolescents aged 10-18 years (n 223) and adults aged 18 years or over (n 465) were considered. Breast-fed children, pregnant women and lactating women were excluded. Dietary data collection methods comprised one 24 h recall and a semi-quantitative FFQ. We used principal component (PC) analyses to identify prevailing dietary patterns. Multiple linear regression analyses were performed to assess the determinants of the identified dietary patterns. Two dominant PC were identified: PC1 reflected a 'Western-like' diet with an emphasis on not-autochthon foods. This pattern tended to be present in urban areas of the Quebrada region and was associated with a younger age, a higher level of development, and a worse diet quality. PC2 reflected an 'Andean-like' diet including a variety of autochthon crops. This was preferred by individuals living in rural areas from Puna with a high level of development during the post-harvest season, and was associated with a greater diet quality. These results suggest that the nutrition transition phenomenon is a reality in certain sectors of this population and might be one of the leading causes of the observed double burden of malnutrition.

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.

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.

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.

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.

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.

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.

Trends and interannual variability of mass and steric sea level in the Tropical Asian Seas

NASA Astrophysics Data System (ADS)

Kleinherenbrink, Marcel; Riva, Riccardo; Frederikse, Thomas; Merrifield, Mark; Wada, Yoshihide

2017-08-01

The mass and steric components of sea level changes have been separated in the Tropical Asian Seas (TAS) using a statistically optimal combination of Jason satellite altimetry, GRACE satellite gravimetry, and ocean reanalyses. Using observational uncertainties, statistically optimally weighted time series for both components have been obtained in four regions within the TAS over the period January 2005 to December 2012. The mass and steric sea level variability is regressed with the first two principal components (PC1&2) of Pacific equatorial wind stress and the Dipole Mode Index (DMI). Sea level in the South China Sea is not affected by any of the indices. Steric variability in the TAS is largest in the deep Banda and Celebes seas and is affected by both PCs and the DMI. Mass variability is largest on the continental shelves, which is primarily controlled by PC1. We argue that a water flux from the Western Tropical Pacific Ocean is the cause for mass variability in the TAS. The steric trends are about 2 mm yr-1 larger than the mass trends in the TAS. A significant part of the mass trend can be explained by the aforementioned indices and the nodal cycle. Trends obtained from fingerprints of mass redistribution are statistically equal to mass trends after subtracting the nodal cycle and the indices. Ultimately, the effect of omitting the TAS in global sea level budgets is estimated to be 0.3 mm yr-1.

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.

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

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.

Biomolecular Characterization of Diazotrophs Isolated from the Tropical Soil in Malaysia

PubMed Central

Naher, Umme Aminun; Othman, Radziah; Latif, Mohammad Abdul; Panhwar, Qurban Ali; Amaddin, Puteri Aminatulhawa Megat; Shamsuddin, Zulkifli H

2013-01-01

This study was conducted to evaluate selected biomolecular characteristics of rice root-associated diazotrophs isolated from the Tanjong Karang rice irrigation project area of Malaysia. Soil and rice plant samples were collected from seven soil series belonging to order Inceptisol (USDA soil taxonomy). A total of 38 diazotrophs were isolated using a nitrogen-free medium. The biochemical properties of the isolated bacteria, such as nitrogenase activity, indoleacetic acid (IAA) production and sugar utilization, were measured. According to a cluster analysis of Jaccard’s similarity coefficients, the genetic similarities among the isolated diazotrophs ranged from 10% to 100%. A dendogram constructed using the unweighted pair-group method with arithmetic mean (UPGMA) showed that the isolated diazotrophs clustered into 12 groups. The genomic DNA rep-PCR data were subjected to a principal component analysis, and the first four principal components (PC) accounted for 52.46% of the total variation among the 38 diazotrophs. The 10 diazotrophs that tested highly positive in the acetylene reduction assay (ARA) were identified as Bacillus spp. (9 diazotrophs) and Burkholderia sp. (Sb16) using the partial 16S rRNA gene sequence analysis. In the analysis of the biochemical characteristics, three principal components were accounted for approximately 85% of the total variation among the identified diazotrophs. The examination of root colonization using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) proved that two of the isolated diazotrophs (Sb16 and Sb26) were able to colonize the surface and interior of rice roots and fixed 22%–24% of the total tissue nitrogen from the atmosphere. In general, the tropical soils (Inceptisols) of the Tanjong Karang rice irrigation project area in Malaysia harbor a diverse group of diazotrophs that exhibit a large variation of biomolecular characteristics. PMID:23999588

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.

RSM 1.0 user's guide: A resupply scheduler using integer optimization

NASA Technical Reports Server (NTRS)

Viterna, Larry A.; Green, Robert D.; Reed, David M.

1991-01-01

The Resupply Scheduling Model (RSM) is a PC based, fully menu-driven computer program. It uses integer programming techniques to determine an optimum schedule to replace components on or before a fixed replacement period, subject to user defined constraints such as transportation mass and volume limits or available repair crew time. Principal input for RSJ includes properties such as mass and volume and an assembly sequence. Resource constraints are entered for each period corresponding to the component properties. Though written to analyze the electrical power system on the Space Station Freedom, RSM is quite general and can be used to model the resupply of almost any system subject to user defined resource constraints. Presented here is a step by step procedure for preparing the input, performing the analysis, and interpreting the results. Instructions for installing the program and information on the algorithms are given.

Activation of Nrf2 target enzymes conferring protection against oxidative stress in PC12 cells by ginger principal constituent 6-shogaol.

PubMed

Peng, Shoujiao; Yao, Juan; Liu, Yaping; Duan, Dongzhu; Zhang, Xiaolong; Fang, Jianguo

2015-08-01

Natural compounds containing phenoxyl groups and/or Michael acceptor units appear to possess antioxidant and cytoprotective properties. The ginger principal constituent 6-shogaol (6-S) represents one of such compounds. In this study, we reported that 6-S efficiently scavenges various free radicals in vitro, and displays remarkable cytoprotection against oxidative stress-induced cell damage in the neuron-like rat pheochromocytoma cell line, PC12 cells. Pretreatment of PC12 cells with 6-S significantly upregulates a series of phase II antioxidant molecules, such as glutathione, heme oxygenase 1, NAD(P)H: quinone oxidoreductase 1, thioredoxin reductase 1, and thioredoxin 1. A mechanistic study revealed that 6-S enhanced the translocation of Nrf2 from the cytosol to the nucleus and knockdown of Nrf2 abolished such protection, indicating that this cytoprotection is mediated by the activation of the transcription factor Nrf2. Another ginger constituent 6-gingerol (6-G), having a similar structure of 6-S but lacking the alpha,beta-unsaturated ketone structure (Michael acceptor moiety), failed to shelter PC12 cells from oxidative stress. Our results demonstrate that 6-S is a novel small molecule activator of Nrf2 in PC12 cells, and suggest that 6-S might be a potential candidate for the prevention of oxidative stress-mediated neurodegenerative disorders.

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

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

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

Pang, Yuanjie, E-mail: yuanjie.p@gmail.com

Background: 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). Methods: 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 analysismore » (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). Results: 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. Conclusions: 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. - Highlights: • We identified and compared environmental sources of urinary metals in MESA and SHS. • ∑As-U-W in SHS may reflect groundwater contamination in rural areas. • Cd-Zn in SHS may reflect common sources from meat products or metabolic interaction. • ∑As, U, W, and Zn differed the most between MESA and SHS participants.« less

Formation of biogenic amines and growth of spoilage-related microorganisms in pork stored under different packaging conditions applying PCA.

PubMed

Li, Miaoyun; Tian, Lu; Zhao, Gaiming; Zhang, Qiuhui; Gao, Xiaoping; Huang, Xianqing; Sun, Lingxia

2014-02-01

The objective of this study was to investigate the evolution of biogenic amines and spoilage-related microorganisms of chilled pork stored at 5 °C under various atmospheric conditions. The experimental packaging systems were pallet packaging, vacuum packaging (VP) and modified atmosphere packaging methods (MAP, 40%O2+40%CO2+20%N2), respectively. The results showed that about 74.26% of the variability could be explained by two first principal components analyzed by PCA in the pallet packaging, while in the vacuum and modified atmosphere packagings were about 85.21% and 79.14%, respectively. PC1 differentiated the indicators from packaging conditions. All the five microbial indicators and partial biogenic amines, gathering together, had high values at the positive side of PC1. Putrescine and cadaverine could reflect the spoilage evolution of fresh pork except for those in the pallet. Therefore, putrescine and cadaverine could be used as the spoilage indicators of chilled pork, of which the contents might reflect the spoilage degree. © 2013.

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.

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

METLIN-PC: An applications-program package for problems of mathematical programming

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

Pshenichnyi, B.N.; Sobolenko, L.A.; Sosnovskii, A.A.

1994-05-01

The METLIN-PC applications-program package (APP) was developed at the V.M. Glushkov Institute of Cybernetics of the Academy of Sciences of Ukraine on IBM PC XT and AT computers. The present version of the package was written in Turbo Pascal and Fortran-77. The METLIN-PC is chiefly designed for the solution of smooth problems of mathematical programming and is a further development of the METLIN prototype, which was created earlier on a BESM-6 computer. The principal property of the previous package is retained - the applications modules employ a single approach based on the linearization method of B.N. Pschenichnyi. Hence the namemore » {open_quotes}METLIN.{close_quotes}« less

Storm surge along the Pacific coast of North America

NASA Astrophysics Data System (ADS)

Bromirski, Peter D.; Flick, Reinhard E.; Miller, Arthur J.

2017-01-01

Storm surge is an important factor that contributes to coastal flooding and erosion. Storm surge magnitude along eastern North Pacific coasts results primarily from low sea level pressure (SLP). Thus, coastal regions where high surge occurs identify the dominant locations where intense storms make landfall, controlled by storm track across the North Pacific. Here storm surge variability along the Pacific coast of North America is characterized by positive nontide residuals at a network of tide gauge stations from southern California to Alaska. The magnitudes of mean and extreme storm surge generally increase from south to north, with typically high amplitude surge north of Cape Mendocino and lower surge to the south. Correlation of mode 1 nontide principal component (PC1) during winter months (December-February) with anomalous SLP over the northeast Pacific indicates that the dominant storm landfall region is along the Cascadia/British Columbia coast. Although empirical orthogonal function spatial patterns show substantial interannual variability, similar correlation patterns of nontide PC1 over the 1948-1975 and 1983-2014 epochs with anomalous SLP suggest that, when considering decadal-scale time periods, storm surge and associated tracks have generally not changed appreciably since 1948. Nontide PC1 is well correlated with PC1 of both anomalous SLP and modeled wave height near the tide gauge stations, reflecting the interrelationship between storms, surge, and waves. Weaker surge south of Cape Mendocino during the 2015-2016 El Niño compared with 1982-1983 may result from changes in Hadley circulation. Importantly from a coastal impacts perspective, extreme storm surge events are often accompanied by high waves.

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.

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.

Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface

PubMed Central

Cheng, Sara Y.; Chou, George; Buie, Creighton; Vaughn, Mark W.; Compton, Campbell; Cheng, Kwan H.

2016-01-01

We used molecular dynamics simulations to explore the effects of asymmetric transbilayer distribution of anionic phosphatidylserine (PS) lipids on the structure of a protein on the membrane surface and subsequent protein–lipid interactions. Our simulation systems consisted of an amyloidogenic, beta-sheet rich dimeric protein (D42) absorbed to the phosphatidylcholine (PC) leaflet, or protein-contact PC leaflet, of two membrane systems: a single-component PC bilayer and double PC/PS bilayers. The latter comprised of a stable but asymmetric transbilayer distribution of PS in the presence of counterions, with a 1-component PC leaflet coupled to a 1-component PS leaflet in each bilayer. The maximally asymmetric PC/PS bilayer had a non-zero transmembrane potential (TMP) difference and higher lipid order packing, whereas the symmetric PC bilayer had a zero TMP difference and lower lipid order packing under physiologically relevant conditions. Analysis of the adsorbed protein structures revealed weaker protein binding, more folding in the N-terminal domain, more aggregation of the N- and C-terminal domains and larger tilt angle of D42 on the PC leaflet surface of the PC/PS bilayer versus the PC bilayer. Also, analysis of protein-induced membrane structural disruption revealed more localized bilayer thinning in the PC/PS versus PC bilayer. Although the electric field profile in the non-protein-contact PS leaflet of the PC/PS bilayer differed significantly from that in the non-protein-contact PC leaflet of the PC bilayer, no significant difference in the electric field profile in the protein-contact PC leaflet of either bilayer was evident. We speculate that lipid packing has a larger effect on the surface adsorbed protein structure than the electric field for a maximally asymmetric PC/PS bilayer. Our results support the mechanism that the higher lipid packing in a lipid leaflet promotes stronger protein–protein but weaker protein–lipid interactions for a dimeric protein on membrane surfaces. PMID:26827904

Source field effects in the auroral zone: Evidence from the Slave craton (NW Canada)

NASA Astrophysics Data System (ADS)

Lezaeta, Pamela; Chave, Alan; Jones, Alan G.; Evans, Rob

2007-09-01

We present an investigation of source field effects on the magnetic fields from multiple long period magnetotelluric (MT) data collected on the floors of lakes throughout the Slave craton (NW Canada) from 1998 to 2000. Monthly and daily power spectra of the magnetic fields suggest a dynamic and seasonally varying source, with atypical geomagnetic activity in year 2000. Bounded influence MT and GDS responses were obtained for periods ranging between 80 and 25,000 s over selected monthly time segments. The responses at periods over 4000 s vary, suggesting source field effects. A frequency domain principal component (PC) method was applied to the array to investigate the spatial form of the source field variations. The PC analysis was tested with synthetic data from a regional 3D model with a uniform external source to study the sensitivity of the eigenvectors to conductivity structure, demonstrating a negligible influence with increasing penetration depth. We conclude that magnetic fields at periods near one half day are subject to a 1D polarized source of relatively homogeneous morphology over the survey area during any month recorded, except for the summer month of July 2000 that had particularly high geomagnetic activity. In general, the source space approaches two polarizations at periods below one half day, with the dominant NS component seen quasi-homogeneous over the survey area at periods over 1000 s.

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.

Enlarging the gene-geography of Europe and the Mediterranean area to STR loci of common forensic use: longitudinal and latitudinal frequency gradients.

PubMed

Messina, Francesco; Finocchio, Andrea; Akar, Nejat; Loutradis, Aphrodite; Michalodimitrakis, Emmanuel I; Brdicka, Radim; Jodice, Carla; Novelletto, Andrea

2018-02-01

Tetranucleotide Short Tandem Repeats (STRs) for human identification and common use in forensic cases have recently been used to address the population genetics of the North-Eastern Mediterranean area. However, to gain confidence in the inferences made using STRs, this kind of analysis should be challenged with changes in three main aspects of the data, i.e. the sizes of the samples, their distance across space and the genetic background from which they are drawn. To test the resilience of the gradients previously detected in the North-Eastern Mediterranean to the enlargement of the surveyed area and population set, using revised data. STR genotype profiles were obtained from a publicly available database (PopAffilietor databank) and a dataset was assembled including >7000 subjects from the Arabian Peninsula to Scandinavia, genotyped at eight loci. Spatial principal component analysis (sPCA) was applied and the frequency maps of the nine alleles which contributed most strongly to sPC1 were examined in detail. By far the greatest part of diversity was summarised by a single spatial principal component (sPC1), oriented along a SouthEast-to-NorthWest axis. The alleles with the top 5% squared loadings were TH01(9.3), D19S433(14), TH01(6), D19S433(15.2), FGA(20), FGA(24), D3S1358(14), FGA(21) and D2S1338(19). These results confirm a clinal pattern over the whole range for at least four loci (TH01, D19S433, FGA, D3S1358). Four of the eight STR loci (or even alleles) considered here can reproducibly capture continental arrangements of diversity. This would, in principle, allow for the exploitation of forensic data to clarify important aspects in the formation of local gene pools.

Sea ice concentration temporal variability over the Weddell Sea and its relationship with tropical sea surface temperature

USGS Publications Warehouse

Barreira, S.; Compagnucci, R.

2007-01-01

Principal Components Analysis (PCA) in S-Mode (correlation between temporal series) was performed on sea ice monthly anomalies, in order to investigate which are the main temporal patterns, where are the homogenous areas located and how are they related to the sea surface temperature (SST). This analysis provides 9 patterns (4 in the Amundsen and Bellingshausen Seas and 5 in the Weddell Sea) that represent the most important temporal features that dominated sea ice concentration anomalies (SICA) variability in the Weddell, Amundsen and Bellingshausen Seas over the 1979-2000 period. Monthly Polar Gridded Sea Ice Concentrations data set derived from satellite information generated by NASA Team algorithm and acquired from the National Snow and Ice Data Center (NSIDC) were used. Monthly means SST are provided by the National Center for Environmental Prediction reanalysis. The first temporal pattern series obtained by PCA has its homogeneous area located at the external region of the Weddell and Bellingshausen Seas and Drake Passage, mostly north of 60°S. The second region is centered in 30°W and located at the southeast of the Weddell. The third area is localized east of 30°W and north of 60°S. South of the first area, the fourth PC series has its homogenous region, between 30° and 60°W. The last area is centered at 0° W and south of 60°S. Correlation charts between the five Principal Components series and SST were performed. Positive correlations over the Tropical Pacific Ocean were found for the five PCs when SST series preceded SICA PC series. The sign of the correlation could relate the occurrence of an El Niño/Southern Oscillation (ENSO) warm (cold) event with posterior positive (negative) anomalies of sea ice concentration over the Weddell Sea.

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.

Biochemical Constituents and in Vitro Antioxidant and Anticholinesterase Potential of Seeds from Native Korean Persimmon Genotypes.

PubMed

Bilal, Saqib; Khan, Abdul Latif; Waqas, Muhammad; Shahzad, Raheem; Kim, Il-Doo; Lee, In-Jung; Shin, Dong-Hyun

2016-07-08

In the current study, the functional and biochemical potential of the seeds of four persimmon cultivars (PC1, PC2, PC3 and PC4) and their role against oxidative stress and acetylcholinesterase (AChE) inhibition were evaluated. In terms of biochemical compositions, free amino acids, fatty acids and organic acids analysis was performed. The free amino acids ranged from 2617.31 (PC2) to 3773.01 μg∙g(-1) dry weight (PC4). Oleic acid and linoleic acid were the principal fatty acids, which were significantly higher in PC4 and PC1, respectively. PC4 presented the highest amount of organic acid content (4212 mg∙kg(-1)), whereas PC2 presented the lowest (2498 mg∙kg(-1)). PC2 contained higher total phenolic content and flavonoid content, whereas PC3 had the lowest amount as compared to other cultivars. The in vitro DPPH, ABTS and superoxide anion radicals scavenging activity increased in a dose-dependent manner, whereas PC2 showed significantly higher scavenging activities as compared to PC1, PC2 and PC4 types. In the case of AChE inhibition, PC4 showed a moderate activity (67.34% ± 1.8%). In conclusion, the current findings reveal that the studied persimmon seeds cultivars are a source of bioactive natural antioxidants and AChE inhibitors. Such natural products could be employed in pharmaceutical and food industries, whilst can also be considered for the treatment of neurodegenerative diseases such as Alzheimer's.

FTIR analysis on aging characteristics of ABS/PC blend under UV-irradiation in air

NASA Astrophysics Data System (ADS)

Li, Jiarong; Chen, Fu; Yang, Long; Jiang, Long; Dan, Yi

2017-09-01

Fourier Transform Infrared Spectroscopy (FTIR) is adopted to study the aging characteristics of poly(acrylonitrile-butadiene-styrene)/polycarbonate (ABS/PC) blend under UV-irradiation in air by analyzing the variation of the three main absorbance at about 967 cm- 1, 1720 cm- 1 and 3420 cm- 1 associated with carbon-hydrogen bonds belonging to 1,4 butadiene, carbonyl and hydroxyl groups, respectively. Results indicate that, under UV-irradiation in air, the photo-oxidation of the blend is not a simple combination of the photo-oxidation of corresponding ABS and PC themselves and takes place predominantly at the ABS component. Due to the interaction between the two components and the Fries rearrangement taken place in the PC component during the UV-irradiation in air, the ABS/PC blends behave higher photo-stability than ABS has.

Whole-body patterns of the range of joint motion in young adults: masculine type and feminine type.

PubMed

Moromizato, Keiichi; Kimura, Ryosuke; Fukase, Hitoshi; Yamaguchi, Kyoko; Ishida, Hajime

2016-10-01

Understanding the whole-body patterns of joint flexibility and their related biological and physical factors contributes not only to clinical assessments but also to the fields of human factors and ergonomics. In this study, ranges of motion (ROMs) at limb and trunk joints of young adults were analysed to understand covariation patterns of different joint motions and to identify factors associated with the variation in ROM. Seventy-eight healthy volunteers (42 males and 36 females) living on Okinawa Island, Japan, were recruited. Passive ROM was measured at multiple joints through the whole body (31 measurements) including the left and right side limbs and trunk. Comparisons between males and females, dominant and non-dominant sides, and antagonistic motions indicated that body structures influence ROMs. In principal component analysis (PCA) on the ROM data, the first principal component (PC1) represented the sex difference and a similar covariation pattern appeared in the analysis within each sex. Multiple regression analysis showed that this component was associated with sex, age, body fat %, iliospinale height, and leg extension strength. The present study identified that there is a spectrum of "masculine" and "feminine" types in the whole-body patterns of joint flexibility. This study also suggested that body proportion and composition, muscle mass and strength, and possibly skeletal structures partly explain such patterns. These results would be important to understand individual variation in susceptibility to joint injuries and diseases and in one's suitable and effective postures and motions.

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.

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.

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

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.

Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface.

PubMed

Cheng, Sara Y; Chou, George; Buie, Creighton; Vaughn, Mark W; Compton, Campbell; Cheng, Kwan H

2016-03-01

We used molecular dynamics simulations to explore the effects of asymmetric transbilayer distribution of anionic phosphatidylserine (PS) lipids on the structure of a protein on the membrane surface and subsequent protein-lipid interactions. Our simulation systems consisted of an amyloidogenic, beta-sheet rich dimeric protein (D42) absorbed to the phosphatidylcholine (PC) leaflet, or protein-contact PC leaflet, of two membrane systems: a single-component PC bilayer and double PC/PS bilayers. The latter comprised of a stable but asymmetric transbilayer distribution of PS in the presence of counterions, with a 1-component PC leaflet coupled to a 1-component PS leaflet in each bilayer. The maximally asymmetric PC/PS bilayer had a non-zero transmembrane potential (TMP) difference and higher lipid order packing, whereas the symmetric PC bilayer had a zero TMP difference and lower lipid order packing under physiologically relevant conditions. Analysis of the adsorbed protein structures revealed weaker protein binding, more folding in the N-terminal domain, more aggregation of the N- and C-terminal domains and larger tilt angle of D42 on the PC leaflet surface of the PC/PS bilayer versus the PC bilayer. Also, analysis of protein-induced membrane structural disruption revealed more localized bilayer thinning in the PC/PS versus PC bilayer. Although the electric field profile in the non-protein-contact PS leaflet of the PC/PS bilayer differed significantly from that in the non-protein-contact PC leaflet of the PC bilayer, no significant difference in the electric field profile in the protein-contact PC leaflet of either bilayer was evident. We speculate that lipid packing has a larger effect on the surface adsorbed protein structure than the electric field for a maximally asymmetric PC/PS bilayer. Our results support the mechanism that the higher lipid packing in a lipid leaflet promotes stronger protein-protein but weaker protein-lipid interactions for a dimeric protein on membrane surfaces. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

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

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.

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.

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

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.

QTL mapping of genes controlling plasma insulin and leptin concentrations: metabolic effect of obesity QTLs identified in an F2 intercross between C57BL/6J and DDD.Cg-A(y) inbred mice.

PubMed

Suto, Jun-ichi

2013-07-31

DDD.Cg-A(y) female mice developed massive obesity as compared with B6.Cg-A(y) female mice. We previously identified quantitative trait loci (QTLs) for obesity on chromosomes 1, 6, 9 and 17 in F2 female mice, including F2A(y) (F2 mice with the A(y) allele) and F2 non- A(y) mice (F2 mice without the A(y) allele), produced by crossing C57BL/6J and DDD.Cg-A(y) strains. We here addressed the question whether the obesity QTLs share genetic bases with putative QTLs for plasma glucose, insulin and leptin concentrations. We performed QTL analyses for the first principal component (PC1) extracted from these metabolic measurements to identify the genes that contributed to the comprehensive evaluation of metabolic traits. By single QTL scans, we identified two significant QTLs for insulin concentration on chromosomes 6 and 12, three for leptin concentration on chromosomes 1, 6 and 17, and five for PC1 on chromosomes 1, 6, 12 (two loci) and 17. Although insulin and leptin concentrations and PC1 were not normally distributed in combined F2 mice, results of single QTL scans by parametric and non-parametric methods were very similar. Therefore, QTL scan by the parametric method was performed with the agouti locus genotype as a covariate. A significant QTL × covariate interaction was found for PC1 on chromosome 9. All obesity QTLs had significant metabolic effects. Thus, obesity- and diabetes-related traits in DDD.Cg-A(y) mice were largely controlled by QTLs on chromosomes 1, 6, 9, 12 and 17.

Online Early Resilience Intervention for Combat-Related PTSD in Military Primary Healthcare Settings: A Randomized Trial of DESTRESS-PC

DTIC Science & Technology

2009-08-01

Bryant, R, Engel, CC (2004). A therapist-assisted internet self-help program for traumatic stress . Professional Psychology: Research and Practice, 35...Combat-Related PTSD in Military Primary Healthcare Settings: A Randomized Trial of “DESTRESS-PC” PRINCIPAL INVESTIGATOR: Charles Engel...Early Resilience Intervention for Combat-Related PTSD in Military Primary Healthcare Settings: A Randomized Trial of DESTRESS-PC 5b. GRANT NUMBER

Creating Indices Representing the Atmospheric Conditions throughout Japan by Using Frontal Zone Data

NASA Astrophysics Data System (ADS)

Takahashi, N.

2015-12-01

The climate of Japan exhibits mid-latitude and east coast condition characteristics within the continent, which leads to the large meridional range of the frontal migration and the resultant large annual seasonal change. Therefore, describing the long-term behavior of frontal zones is important for understanding the seasonal, interannual, and long-term variations of the Japanese climate. The purpose of this work is to create indices representing the atmospheric conditions throughout Japan by using frontal zone data created by an objective method at pentad intervals for the period 1948-2013. The indexation was conducted by principal component analyses on the distribution maps of the frontal frequencies near frontal zones, which are defined as the latitude indicating the maximum of the frontal frequencies along each longitude in the climatological mean field. This work focuses on the first four factors, PC1-4, which indicate high contribution rates. The distribution maps of factor loadings were interpreted in the following manner as variations of the frontal zone: PC1, north-south variations in the locations of the frontal zone; PC2, frontal frequencies around the frontal zone; PC3, the running direction of the frontal zone, whether northwest-southeast or southwest-northeast; and PC4, west-east variations of the frontal frequencies. These factors could be regarded as the indices representing the atmospheric conditions throughout Japan. The result of correlation analysis among the indices in this work and those representing global climatic phenomena such as Niño3 sea surface temperature (SST), in addition to Pacific decadal and Arctic oscillations, indicated the comprehensive relationships revealed in previous research. Furthermore, several long-term trend characteristics were exhibited, such as the southward shift of frontal zones in mid- and late spring and the increase of frontal frequencies around frontal zones in mid- and late summer. Thus, the simple indices created in this work verify the effectiveness in the investigation of climate change with regard to the seasonal march.

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

Study of relation between Pc 3 micropulsations and magnetosheath fluctuations, and multisatellite investigation of earth's bow shock

NASA Technical Reports Server (NTRS)

Greenstadt, E. W.

1975-01-01

The validity is investigated of a suggested model according to which Pc 3 and/or Pc 4 micropulsations are excited by magnetosheath field (and plasma) fluctuations arising in the quasi-parallel structure of the subsolar bow shock. The influence of solar wind plasma parameters on local shock structure and on the configuration of the entire bow shock system is included. Simultaneous data from two or more spacecraft and from multiple diagnostics is used to evaluate the geometrical factor, field-to-shock normal angle, or its B-X equivalent, and the principal plasma parameters. Results are presented and discussed.

Warm season tree growth and precipitation over Mexico

NASA Astrophysics Data System (ADS)

Therrell, Matthew D.; Stahle, David W.; Cleaveland, Malcolm K.; Villanueva-Diaz, Jose

2002-07-01

We have developed a network of 18 new tree ring chronologies to examine the history of warm season tree growth over Mexico from 1780 to 1992. The chronologies include Douglas fir (Pseudotsuga menziesii (Mirb.) Franco) and Montezuma pine (Pinus montezumae Lamb.) latewood width, and Montezuma bald cypress (Taxodium mucronatum Ten.) total ring width. They are located in southwestern Texas, the Sierra Madre Oriental, Sierra Madre Occidental, and southern Mexico as far south as Oaxaca. Seven of these chronologies are among the first precipitation sensitive tree ring records from the American tropics. Principal component analysis of the chronologies indicates that the primary modes of tree growth variability are divided north and south by the Tropic of Cancer. The tree ring data in northern Mexico (PC1) are most sensitive to June-August rainfall, while the data from southern Mexico (PC2) are sensitive to rainfall in April-June. We find that the mode of tree growth variability over southern Mexico is significantly correlated with the onset of the North American Monsoon. Anomalies in monsoon onset, spring precipitation, and tree growth in southern Mexico all tend to be followed by precipitation anomalies of opposite sign later in the summer over most of central Mexico.

North Polar Radiative Flux Variability from 2002 Through 2014

NASA Technical Reports Server (NTRS)

Rutan, David; Rose, Fred; Doelling, David; Kato, Seiji; Smith, Bill, Jr.

2017-01-01

NASA's Clouds and the Earth's Radiant Energy System (CERES) project produces the SYN1Deg data product. SYN1deg provides global, 1deg gridded, hourly estimates of Top of Atmosphere (TOA) (CERES observations and calculations) and atmospheric and surface radiative flux (calculations). Examples of 12 year North Polar averages of some variables are shown to the right. Given recent interest in polar science we focus here on TOA and Surface validation of calculated irradiant fluxes. TOA upward longwave irradiance calculations match the CERES observations well both spatially and temporally with correlations remaining strong through PC 6. Compare SYN1Deg Calculations & Meteorological Teleconnections. TOA reflected shortwave irradiance calculations match the CERES observations well both spatially and temporally with correlations remaining string through PC 7. Comparing SYN1Deg calculations to teleconnection patterns requires expanding the area to 30N for EOF analyses. Correlating the Principal Components of various variables to teleconnection time series indicates which variable is most highly correlated with which teleconnection signal. The tables indicate the Pacific North American Oscillation is most correlated to the OLR EOF 1, and the North American Oscillation is correlated most closely to surface LW flux down EOF 1.

Small area estimation (SAE) model: Case study of poverty in West Java Province

NASA Astrophysics Data System (ADS)

Suhartini, Titin; Sadik, Kusman; Indahwati

2016-02-01

This paper showed the comparative of direct estimation and indirect/Small Area Estimation (SAE) model. Model selection included resolve multicollinearity problem in auxiliary variable, such as choosing only variable non-multicollinearity and implemented principal component (PC). Concern parameters in this paper were the proportion of agricultural venture poor households and agricultural poor households area level in West Java Province. The approach for estimating these parameters could be performed based on direct estimation and SAE. The problem of direct estimation, three area even zero and could not be conducted by directly estimation, because small sample size. The proportion of agricultural venture poor households showed 19.22% and agricultural poor households showed 46.79%. The best model from agricultural venture poor households by choosing only variable non-multicollinearity and the best model from agricultural poor households by implemented PC. The best estimator showed SAE better then direct estimation both of the proportion of agricultural venture poor households and agricultural poor households area level in West Java Province. The solution overcame small sample size and obtained estimation for small area was implemented small area estimation method for evidence higher accuracy and better precision improved direct estimator.

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.

Soil-vegetation relationships and community structure in a "terra-firme"-white-sand vegetation gradient in Viruá National Park, northern Amazon, Brazil.

PubMed

Mendonça, Bruno A F DE; Fernandes, Elpídio I; Schaefer, Carlos E G R; Mendonça, Júlia G F DE; Vasconcelos, Bruno N F

2017-01-01

Viruá National Park encompasses a vast and complex system of hydromorphic sandy soils covered largely by the white sand vegetation ("Campinarana") ecosystem. The purpose of this study was to investigate a vegetation gradient of "terra-firme"-white sand vegetation at the Viruá National Park. Nine plots representing three physiognomic units were installed for floristic and phytosociological surveys as well as to collect composite soil samples. The data were subjected to assessments of floristic diversity and similarity, phytosociological parameters and to statistical analyses, focused on principal components (PC) and canonical correspondence analysis (CCA). The vegetation of the Campinaranas types and Forest differed in biomass and species density. Ten species, endemic to Brazil, were particularly well-represented. PC and CCA indicated a clear distinction between the studied plots, based on measured soil variables, especially base sum and clay, which were the most differentiating properties between Campinarana and Forest; For the separation of the Campinarana types, the main distinguishing variable was organic matter content and cation exchange capacity. Higher similarity of Campinaranas was associated to a monodominant species and the lower similarity of Forest was related to the high occurrence of locally rare species.

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

Transformations of the chemical compositions of high molecular weight DOM along a salinity transect: Using two dimensional correlation spectroscopy and principal component analysis approaches

NASA Astrophysics Data System (ADS)

Abdulla, Hussain A. N.; Minor, Elizabeth C.; Dias, Robert F.; Hatcher, Patrick G.

2013-10-01

In a study of chemical transformations of estuarine high-molecular-weight (HMW, >1000 Da) dissolved organic matter (DOM) collected over a period of two years along a transect through the Elizabeth River/Chesapeake Bay system to the coastal Atlantic Ocean off Virginia, USA, δ13C values, N/C ratios, and principal component analysis (PCA) of the solid-state 13C NMR (nuclear magnetic resonance) spectra of HMW-DOM show an abrupt change in both its sources and chemical structural composition occurring around salinity 20. HMW-DOM in the lower salinity region had lighter isotopic values, higher aromatic and lower carbohydrate contents relative to that in the higher salinity region. These changes around a salinity of 20 are possibly due to introduction of a significant amount of new carbon (autotrophic DOM) to the transect. PC-1 loadings plot shows that spatially differing DOM components are similar to previously reported 13C NMR spectra of heteropolysaccharides (HPS) and carboxyl-rich alicyclic molecules (CRAM). Applying two dimensional correlation spectroscopy techniques to 1H NMR spectra from the same samples reveals increases in the contribution of N-acetyl amino sugars, 6-deoxy sugars, and sulfated polysaccharides to HPS components along the salinity transect, which suggests a transition from plant derived carbohydrates to marine produced carbohydrates within the HMW-DOM pool. In contrast to what has been suggested previously, our combined results from 13C NMR, 1H NMR, and FTIR indicate that CRAM consists of at least two different classes of compounds (aliphatic polycarboxyl compounds and lignin-like compounds).

Using Structural Equation Modeling To Fit Models Incorporating Principal Components.

ERIC Educational Resources Information Center

Dolan, Conor; Bechger, Timo; Molenaar, Peter

1999-01-01

Considers models incorporating principal components from the perspectives of structural-equation modeling. These models include the following: (1) the principal-component analysis of patterned matrices; (2) multiple analysis of variance based on principal components; and (3) multigroup principal-components analysis. Discusses fitting these models…

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.

Hydraulic connectivity and evaporation control the water quality and sources of chromophoric dissolved organic matter in Lake Bosten in arid northwest China.

PubMed

Zhou, Lei; Zhou, Yongqiang; Hu, Yang; Cai, Jian; Bai, Chengrong; Shao, Keqiang; Gao, Guang; Zhang, Yunlin; Jeppesen, Erik; Tang, Xiangming

2017-12-01

Lake Bosten is the largest oligosaline lake in arid northwestern China, and water from its tributaries and evaporation control the water balance of the lake. In this study, water quality and chromophoric dissolved organic matter (CDOM) absorption and fluorescence were investigated in different seasons to elucidate how hydraulic connectivity and evaporation may affect the water quality and variability of CDOM in the lake. Mean suspended solids and turbidity were significantly higher in the upstream tributaries than in the lake, the difference being notably more pronounced in the wet than in the dry season. A markedly higher mean first principal component (PC1) score, which was significantly positively related to protein-like components, and a considerably lower fluorescence peak integration ratio - I C :I T , indicative of the terrestrial humic-like CDOM contribution percentage, were observed in the lake than in the upstream tributaries. Correspondingly, notably higher contribution percentages of terrestrial humic-like components were observed in the river mouth areas than in the remaining lake regions. Furthermore, significantly higher mean turbidity, and notably lower mean conductivity and salinity, were recorded in the southwestern Kaidu river mouth than in the remaining lake regions in the wet season. Notably higher mean salinity is recorded in Lake Bosten than in upstream tributaries. Autochthonous protein-like associated amino-acids and also PC1 scores increased significantly with increasing salinity. We conclude that the dynamics of water quality and CDOM composition in remote arid Lake Bosten are strongly driven by evaporation and also the hydraulic connectivity between the upstream tributaries and the downstream lake. Copyright © 2017 Elsevier Ltd. All rights reserved.

Three-dimensional geometry of coronal loops inferred by the Principal Component Analysis

NASA Astrophysics Data System (ADS)

Nisticò, Giuseppe; Nakariakov, Valery

We propose a new method for the determination of the three dimensional (3D) shape of coronal loops from stereoscopy. The common approach requires to find a 1D geometric curve, as circumference or ellipse, that best-fits the 3D tie-points which sample the loop shape in a given coordinate system. This can be easily achieved by the Principal Component (PC) analysis. It mainly consists in calculating the eigenvalues and eigenvectors of the covariance matrix of the 3D tie-points: the eigenvalues give a measure of the variability of the distribution of the tie-points, and the corresponding eigenvectors define a new cartesian reference frame directly related to the loop. The eigenvector associated with the smallest eigenvalues defines the normal to the loop plane, while the other two determine the directions of the loop axes: the major axis is related to the largest eigenvalue, and the minor axis with the second one. The magnitude of the axes is directly proportional to the square roots of these eigenvalues. The technique is fast and easily implemented in some examples, returning best-fitting estimations of the loop parameters and 3D reconstruction with a reasonable small number of tie-points. The method is suitable for serial reconstruction of coronal loops in active regions, providing a useful tool for comparison between observations and theoretical magnetic field extrapolations from potential or force-free fields.

Integrating Multiple Correlated Phenotypes for Genetic Association Analysis by Maximizing Heritability

PubMed Central

Zhou, Jin J.; Cho, Michael H.; Lange, Christoph; Lutz, Sharon; Silverman, Edwin K.; Laird, Nan M.

2015-01-01

Many correlated disease variables are analyzed jointly in genetic studies in the hope of increasing power to detect causal genetic variants. One approach involves assessing the relationship between each phenotype and each single nucleotide polymorphism (SNP) individually and using a Bonferroni correction for the effective number of tests conducted. Alternatively, one can apply a multivariate regression or a dimension reduction technique, such as principal component analysis (PCA), and test for the association with the principal components (PC) of the phenotypes rather than the individual phenotypes. Inspired by the previous approaches of combining phenotypes to maximize heritability at individual SNPs, in this paper, we propose to construct a maximally heritable phenotype (MaxH) by taking advantage of the estimated total heritability and co-heritability. The heritability and co-heritability only need to be estimated once, therefore our method is applicable to genome-wide scans. MaxH phenotype is a linear combination of the individual phenotypes with increased heritability and power over the phenotypes being combined. Simulations show that the heritability and power achieved agree well with the theory for large samples and two phenotypes. We compare our approach with commonly used methods and assess both the heritability and the power of the MaxH phenotype. Moreover we provide suggestions for how to choose the phenotypes for combination. An application of our approach to a COPD genome-wide association study shows the practical relevance. PMID:26111731

Fast Principal-Component Analysis Reveals Convergent Evolution of ADH1B in Europe and East Asia

PubMed Central

Galinsky, Kevin J.; Bhatia, Gaurav; Loh, Po-Ru; Georgiev, Stoyan; Mukherjee, Sayan; Patterson, Nick J.; Price, Alkes L.

2016-01-01

Searching for genetic variants with unusual differentiation between subpopulations is an established approach for identifying signals of natural selection. However, existing methods generally require discrete subpopulations. We introduce a method that infers selection using principal components (PCs) by identifying variants whose differentiation along top PCs is significantly greater than the null distribution of genetic drift. To enable the application of this method to large datasets, we developed the FastPCA software, which employs recent advances in random matrix theory to accurately approximate top PCs while reducing time and memory cost from quadratic to linear in the number of individuals, a computational improvement of many orders of magnitude. We apply FastPCA to a cohort of 54,734 European Americans, identifying 5 distinct subpopulations spanning the top 4 PCs. Using the PC-based test for natural selection, we replicate previously known selected loci and identify three new genome-wide significant signals of selection, including selection in Europeans at ADH1B. The coding variant rs1229984∗T has previously been associated to a decreased risk of alcoholism and shown to be under selection in East Asians; we show that it is a rare example of independent evolution on two continents. We also detect selection signals at IGFBP3 and IGH, which have also previously been associated to human disease. PMID:26924531

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.

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.

The numbers of 2- 5 and 6-9 mm ovarian follicles are inversely correlated in both normal women and in polycystic ovary syndrome patients: what is the missing link?

PubMed

Peigné, M; Catteau-Jonard, S; Robin, G; Dumont, A; Pigny, P; Dewailly, D

2018-04-01

Is the negative correlation between the numbers of 2-5 and 6-9 mm follicles influenced by ovarian and/or metabolic parameter(s) in young control women and in patients with polycystic ovarian syndrome (PCOS)? Our study confirmed that the negative correlation between numbers of follicles sized 2-5 and 6-9 mm was stronger in PCOS than in young control women and was not linked to any ovarian or metabolic parameter. Previous reports described a direct negative correlation between the number of small antral follicles (2-5 mm) and large antral follicle (6-9 mm) during the early follicular phase (cycle Days 2-5) in normal and PCOS women. Numerous factors, that could be either intrinsic to the ovary or secondary to metabolic influence and/or gonadotropin regulation, might account for this. Six hundred and thirty-nine patients with PCOS according to Rotterdam Criteria and 157 control women were recruited in this retrospective cross-sectional study from January 2009 to January 2016. Data were obtained from a database of clinical, hormonal and ultrasound (U/S) features recorded consecutively in a single reproductive medicine centre. Univariate correlations between the various parameters were analysed by the Spearman's correlation test. All variables significantly related to the 2-5 and/or 6-9 mm follicle numbers were included in a principal component analysis (PCA) in order to structure the data and to obtain collections of uncorrelated variables, called principal components (PC), which are linear combinations of the original variables. By univariate analysis, the 2-5 and 6-9 mm follicle numbers were strongly but negatively correlated in both populations. Many other variables were correlated to the 2-5 and/or 6-9 mm follicle numbers and to each other. By PCA, these relationships were gathered into four independent PCs in each population. In both groups, the 2-5 and 6-9 mm follicle numbers correlated strongly and inversely to a specific PC. Among the other variables tested, only serum oestradiol level correlated weakly to this PC in the control group. Two other uncorrelated PCs gathered relationships between variables linked to the metabolic status and the gonadotropin regulation both in control and PCOS women. Lastly, a fourth PC included relationships which linked to ovarian ageing in controls and to follicle dysregulation in patients with PCOS. Our controls did not represent the general population since they were recruited in an ART centre; we used a modified Rotterdam classification for PCOS using follicle count and/or serum AMH level with in-house thresholds to define the follicle excess; the AMH assay used is no longer commercially available. Factor(s) regulating specifically the equilibrium between the 2-5 and 6-9 mm follicle numbers still need(s) to be identified. More attention should be paid to the oocyte. None.

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.

Flavor of fresh blueberry juice and the comparison to amount of sugars, acids, anthocyanidins, and physicochemical measurements.

PubMed

Bett-Garber, Karen L; Lea, Jeanne M; Watson, Michael A; Grimm, Casey C; Lloyd, Steven W; Beaulieu, John C; Stein-Chisholm, Rebecca E; Andrzejewski, Brett P; Marshall, Donna A

2015-04-01

Six cultivars of southern highbush (SHB) and rabbiteye (RE) blueberry samples were harvested on 2 different dates. Each treatment combination was pressed 2 times for repeated measures. Fresh juice was characterized for 18 flavor/taste/feeling factor attributes by a descriptive flavor panel. Each sample was measured for sugars, acids, anthocyanidins, Folin-Ciocalteu, soluble solids (BRIX), titratable acidity (TA), and antioxidant capacity (ORACFL ). Flavors were correlated with the composition and physicochemical data. Blueberry flavor correlated with 3 parameters, and negatively correlated with 2. Strawberry correlated with oxalic acid and negatively correlated with sucrose and quinic acid. Sweet aroma correlated with oxalic and citric acid, but negatively correlated with sucrose, quinic, and total acids. Sweet taste correlated with 11 parameters, including the anthocyanidins; and negatively correlated with 3 parameters. Neither bitter nor astringent correlated with any of the antioxidant parameters, but both correlated with total acids. Sour correlated with total acids and TA, while negatively correlating with pH and BRIX:TA. Throat burn correlated with total acids and TA. Principal component analysis negatively related blueberry, sweet aroma, and sweet to sour, bitter, astringent, tongue tingle, and tongue numbness. The information in this component was related to pH, TA, and BRIX:TA ratio. Another principal component related the nonblueberry fruit flavors to BRIX. This PC, also divided the SHB berries from the RE. This work shows that the impact of juice composition on flavor is very complicated and that estimating flavor with physicochemical parameters is complicated by the composition of the juice. © 2015 Institute of Food Technologists®

Discrimination between diffuse and point sources of arsenic at Zimapán, Hidalgo state, Mexico.

PubMed

Sracek, Ondra; Armienta, María Aurora; Rodríguez, Ramiro; Villaseñor, Guadalupe

2010-01-01

There are two principal sources of arsenic in Zimapán. Point sources are linked to mining and smelting activities and especially to mine tailings. Diffuse sources are not well defined and are linked to regional flow systems in carbonate rocks. Both sources are caused by the oxidation of arsenic-rich sulfidic mineralization. Point sources are characterized by Ca-SO(4)-HCO(3) ground water type and relatively enriched values of deltaD, delta(18)O, and delta(34)S(SO(4)). Diffuse sources are characterized by Ca-Na-HCO(3) type of ground water and more depleted values of deltaD, delta(18)O, and delta(34)S(SO(4)). Values of deltaD and delta(18)O indicate similar altitude of recharge for both arsenic sources and stronger impact of evaporation for point sources in mine tailings. There are also different values of delta(34)S(SO(4)) for both sources, presumably due to different types of mineralization or isotopic zonality in deposits. In Principal Component Analysis (PCA), the principal component 1 (PC1), which describes the impact of sulfide oxidation and neutralization by the dissolution of carbonates, has higher values in samples from point sources. In spite of similar concentrations of As in ground water affected by diffuse sources and point sources (mean values 0.21 mg L(-1) and 0.31 mg L(-1), respectively, in the years from 2003 to 2008), the diffuse sources have more impact on the health of population in Zimapán. This is caused by the extraction of ground water from wells tapping regional flow system. In contrast, wells located in the proximity of mine tailings are not generally used for water supply.

Mapping watershed integrity for the conterminous United States.

PubMed

Thornbrugh, Darren J; Leibowitz, Scott G; Hill, Ryan A; Weber, Marc H; Johnson, Zachary C; Olsen, Anthony R; Flotemersch, Joseph E; Stoddard, John L; Peck, David V

2018-02-01

Watershed integrity is the capacity of a watershed to support and maintain the full range of ecological processes and functions essential to sustainability. Using information from EPA's StreamCat dataset, we calculated and mapped an Index of Watershed Integrity (IWI) for 2.6 million watersheds in the conterminous US with first-order approximations of relationships between stressors and six watershed functions: hydrologic regulation, regulation of water chemistry, sediment regulation, hydrologic connectivity, temperature regulation, and habitat provision. Results show high integrity in the western US, intermediate integrity in the southern and eastern US, and the lowest integrity in the temperate plains and lower Mississippi Valley. Correlation between the six functional components was high ( r = 0.85-0.98). A related Index of Catchment Integrity (ICI) was developed using local drainages of individual stream segments (i.e., excluding upstream information). We evaluated the ability of the IWI and ICI to predict six continuous site-level indicators with regression analyses - three biological indicators and principal components derived from water quality, habitat, and combined water quality and habitat variables - using data from EPA's National Rivers and Streams Assessment. Relationships were highly significant, but the IWI only accounted for 1-12% of the variation in the four biological and habitat variables. The IWI accounted for over 25% of the variation in the water quality and combined principal components nationally, and 32-39% in the Northern and Southern Appalachians. We also used multinomial logistic regression to compare the IWI with the categorical forms of the three biological indicators. Results were consistent: we found positive associations but modest results. We compared how the IWI and ICI predicted the water quality PC relative to agricultural and urban land use. The IWI or ICI are the best predictors of the water quality PC for the CONUS and six of the nine ecoregions, but they only perform marginally better than agriculture in most instances. However, results suggest that agriculture would not be appropriate in all parts of the country, and the index is meant to be responsive to all stressors. The IWI in its present form (available through the StreamCat website; https://www.epa.gov/national-aquatic-resource-surveys/streamcat) could be useful for management efforts at multiple scales, especially when combined with information on site condition. The IWI could be improved by incorporating empirical or literature-derived relationships between functional components and stressors. However, limitations concerning the absence of data for certain stressors should be considered.

Cost Savings from Palliative Care Teams and Guidance for a Financially Viable Palliative Care Program

PubMed Central

McCarthy, Ian M; Robinson, Chessie; Huq, Sakib; Philastre, Martha; Fine, Robert L

2015-01-01

Objectives To quantify the cost savings of palliative care (PC) and identify differences in savings according to team structure, patient diagnosis, and timing of consult. Data Sources Hospital administrative records on all inpatient stays at five hospital campuses from January 2009 through June 2012. Study Design The analysis matched PC patients to non-PC patients (separately by discharge status) using propensity score methods. Weighted generalized linear model regressions of hospital costs were estimated for the matched groups. Data Collection Data were restricted to patients at least 18 years old with inpatient stays of between 7 and 30 days. Variables available included patient demographics, primary and secondary diagnoses, hospital costs incurred for the inpatient stay, and when/if the patient had a PC consult. Principal Findings We found overall cost savings from PC of $3,426 per patient for those dying in the hospital. No significant cost savings were found for patients discharged alive; however, significant cost savings for patients discharged alive could be achieved for certain diagnoses, PC team structures, or if consults occurred within 10 days of admission. Conclusions Appropriately selected and timed PC consults with physician and RN involvement can help ensure a financially viable PC program via cost savings to the hospital. PMID:25040226

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.

Asteroid age distributions determined by space weathering and collisional evolution models

NASA Astrophysics Data System (ADS)

Willman, Mark; Jedicke, Robert

2011-01-01

We provide evidence of consistency between the dynamical evolution of main belt asteroids and their color evolution due to space weathering. The dynamical age of an asteroid's surface (Bottke, W.F., Durda, D.D., Nesvorný, D., Jedicke, R., Morbidelli, A., Vokrouhlický, D., Levison, H. [2005]. Icarus 175 (1), 111-140; Nesvorný, D., Jedicke, R., Whiteley, R.J., Ivezić, Ž. [2005]. Icarus 173, 132-152) is the time since its last catastrophic disruption event which is a function of the object's diameter. The age of an S-complex asteroid's surface may also be determined from its color using a space weathering model (e.g. Willman, M., Jedicke, R., Moskovitz, N., Nesvorný, D., Vokrouhlický, D., Mothé-Diniz, T. [2010]. Icarus 208, 758-772; Jedicke, R., Nesvorný, D., Whiteley, R.J., Ivezić, Ž., Jurić, M. [2004]. Nature 429, 275-277; Willman, M., Jedicke, R., Nesvorny, D., Moskovitz, N., Ivezić, Ž., Fevig, R. [2008]. Icarus 195, 663-673. We used a sample of 95 S-complex asteroids from SMASS and obtained their absolute magnitudes and u, g, r, i, z filter magnitudes from SDSS. The absolute magnitudes yield a size-derived age distribution. The u, g, r, i, z filter magnitudes lead to the principal component color which yields a color-derived age distribution by inverting our color-age relationship, an enhanced version of the 'dual τ' space weathering model of Willman et al. (2010). We fit the size-age distribution to the enhanced dual τ model and found characteristic weathering and gardening times of τw = 2050 ± 80 Myr and τg=4400-500+700Myr respectively. The fit also suggests an initial principal component color of -0.05 ± 0.01 for fresh asteroid surface with a maximum possible change of the probable color due to weathering of Δ PC = 1.34 ± 0.04. Our predicted color of fresh asteroid surface matches the color of fresh ordinary chondritic surface of PC1 = 0.17 ± 0.39.

Can profiles of poly- and Perfluoroalkyl substances (PFASs) in human serum provide information on major exposure sources?

PubMed

Hu, Xindi C; Dassuncao, Clifton; Zhang, Xianming; Grandjean, Philippe; Weihe, Pál; Webster, Glenys M; Nielsen, Flemming; Sunderland, Elsie M

2018-02-01

Humans are exposed to poly- and perfluoroalkyl substances (PFASs) from diverse sources and this has been associated with negative health impacts. Advances in analytical methods have enabled routine detection of more than 15 PFASs in human sera, allowing better profiling of PFAS exposures. The composition of PFASs in human sera reflects the complexity of exposure sources but source identification can be confounded by differences in toxicokinetics affecting uptake, distribution, and elimination. Common PFASs, such as perfluorooctanoic acid (PFOA), perfluorooctane sulfonic acid (PFOS) and their precursors are ubiquitous in multiple exposure sources. However, their composition varies among sources, which may impact associated adverse health effects. We use available PFAS concentrations from several demographic groups in a North Atlantic seafood consuming population (Faroe Islands) to explore whether chemical fingerprints in human sera provide insights into predominant exposure sources. We compare serum PFAS profiles from Faroese individuals to other North American populations to investigate commonalities in potential exposure sources. We compare individuals with similar demographic and physiological characteristics and samples from the same years to reduce confounding by toxicokinetic differences and changing environmental releases. Using principal components analysis (PCA) confirmed by hierarchical clustering, we assess variability in serum PFAS concentrations across three Faroese groups. The first principal component (PC)/cluster consists of C9-C12 perfluoroalkyl carboxylates (PFCAs) and is consistent with measured PFAS profiles in consumed seafood. The second PC/cluster includes perfluorohexanesulfonic acid (PFHxS) and the PFOS precursor N-ethyl perfluorooctane sulfonamidoacetate (N-EtFOSAA), which are directly used or metabolized from fluorochemicals in consumer products such as carpet and food packaging. We find that the same compounds are associated with the same exposure sources in two North American populations, suggesting generalizability of results from the Faroese population. We conclude that PFAS homologue profiles in serum provide valuable information on major exposure sources. It is essential to compare samples collected at similar time periods and to correct for demographic groups that are highly affected by differences in physiological processes (e.g., pregnancy). Information on PFAS homologue profiles is crucial for attributing adverse health effects to the proper mixtures or individual PFASs.

Determining quality of caviar from Caspian Sea based on Raman spectroscopy and using artificial neural networks.

PubMed

Mohamadi Monavar, H; Afseth, N K; Lozano, J; Alimardani, R; Omid, M; Wold, J P

2013-07-15

The purpose of this study was to evaluate the feasibility of Raman spectroscopy for predicting purity of caviars. The 93 wild caviar samples of three different types, namely; Beluga, Asetra and Sevruga were analysed by Raman spectroscopy in the range 1995 cm(-1) to 545 cm(-1). Also, 60 samples from combinations of every two types were examined. The chemical origin of the samples was identified by reference measurements on pure samples. Linear chemometric methods like Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) were used for data visualisation and classification which permitted clear distinction between different caviars. Non-linear methods like Artificial Neural Networks (ANN) were used to classify caviar samples. Two different networks were tested in the classification: Probabilistic Neural Network with Radial-Basis Function (PNN) and Multilayer Feed Forward Networks with Back Propagation (BP-NN). In both cases, scores of principal components (PCs) were chosen as input nodes for the input layer in PC-ANN models in order to reduce the redundancy of data and time of training. Leave One Out (LOO) cross validation was applied in order to check the performance of the networks. Results of PCA indicated that, features like type and purity can be used to discriminate different caviar samples. These findings were also supported by LDA with efficiency between 83.77% and 100%. These results were confirmed with the results obtained by developed PC-ANN models, able to classify pure caviar samples with 93.55% and 71.00% accuracy in BP network and PNN, respectively. In comparison, LDA, PNN and BP-NN models for predicting caviar types have 90.3%, 73.1% and 91.4% accuracy. Partial least squares regression (PLSR) models were built under cross validation and tested with different independent data sets, yielding determination coefficients (R(2)) of 0.86, 0.83, 0.92 and 0.91 with root mean square error (RMSE) of validation of 0.32, 0.11, 0.03 and 0.09 for fatty acids of 16.0, 20.5, 22.6 and fat, respectively. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

Lipid Rafts and Clathrin Cooperate in the Internalization of PrPC in Epithelial FRT Cells

PubMed Central

Casanova, Philippe; Puri, Claudia; Paladino, Simona; Tivodar, Simona S.; Campana, Vincenza; Tacchetti, Carlo; Zurzolo, Chiara

2009-01-01

Background The cellular prion protein (PrPC) plays a key role in the pathogenesis of Transmissible Spongiform Encephalopathies in which the protein undergoes post-translational conversion to the infectious form (PrPSc). Although endocytosis appears to be required for this conversion, the mechanism of PrPC internalization is still debated, as caveolae/raft- and clathrin-dependent processes have all been reported to be involved. Methodology/Principal Findings We have investigated the mechanism of PrPC endocytosis in Fischer Rat Thyroid (FRT) cells, which lack caveolin-1 (cav-1) and caveolae, and in FRT/cav-1 cells which form functional caveolae. We show that PrPC internalization requires activated Cdc-42 and is sensitive to cholesterol depletion but not to cav-1 expression suggesting a role for rafts but not for caveolae in PrPC endocytosis. PrPC internalization is also affected by knock down of clathrin and by the expression of dominant negative Eps15 and Dynamin 2 mutants, indicating the involvement of a clathrin-dependent pathway. Notably, PrPC co-immunoprecipitates with clathrin and remains associated with detergent-insoluble microdomains during internalization thus indicating that PrPC can enter the cell via multiple pathways and that rafts and clathrin cooperate in its internalization. Conclusions/Significance These findings are of particular interest if we consider that the internalization route/s undertaken by PrPC can be crucial for the ability of different prion strains to infect and to replicate in different cell lines. PMID:19503793

Discrimination of a chestnut-oak forest unit for geologic mapping by means of a principal component enhancement of Landsat multispectral scanner data.

USGS Publications Warehouse

Krohn, M.D.; Milton, N.M.; Segal, D.; Enland, A.

1981-01-01

A principal component image enhancement has been effective in applying Landsat data to geologic mapping in a heavily forested area of E Virginia. The image enhancement procedure consists of a principal component transformation, a histogram normalization, and the inverse principal componnet transformation. The enhancement preserves the independence of the principal components, yet produces a more readily interpretable image than does a single principal component transformation. -from Authors

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

Principal component regression analysis with SPSS.

PubMed

Liu, R X; Kuang, J; Gong, Q; Hou, X L

2003-06-01

The paper introduces all indices of multicollinearity diagnoses, the basic principle of principal component regression and determination of 'best' equation method. The paper uses an example to describe how to do principal component regression analysis with SPSS 10.0: including all calculating processes of the principal component regression and all operations of linear regression, factor analysis, descriptives, compute variable and bivariate correlations procedures in SPSS 10.0. The principal component regression analysis can be used to overcome disturbance of the multicollinearity. The simplified, speeded up and accurate statistical effect is reached through the principal component regression analysis with SPSS.

[Cancer and its association with dietary patterns in Córdoba (Argentina)].

PubMed

Pou, Sonia Alejandra; Niclis, Camila; Aballay, Laura Rosana; Tumas, Natalia; Román, María Dolores; Muñoz, Sonia Edith; Coquet, Julia Becaria; Díaz, María del Pilar

2014-03-01

Feeding habits play a prominent role in carcinogenesis. The dietary patterns approach applied to the study of chronic diseases is of increasing interest in nutritional epidemiology. Nevertheless, it has been seldom used in Latin America. To identify dietary patterns in adult population in Córdoba (Argentina) and to estimate their effects on the risk of colon-rectal (CRC), urothelial (UC), breast (BC) and prostate (PC) cancers. Four case control studies were conducted, 2006-2012 for CRC, PC, BC and UC. To identify the dietary patterns, a Principal Components Factor Analysis was conducted. A multilevel logistic regression was adjusted for the risk analyses. Characteristic dietary patterns in the whole population, and in women and men independently, were identified. In the whole population South Cone and Sweet Beverages patterns behaved as promoters for CRC and UC while the Prudent Pattern had a protective effect. Female South Cone, Rural and Starchy patterns were associated to a higher BC risk. Prudent Pattern lowered BC risk. In men, South Cone, Sweet Beverages and Typical Measured patterns promoted PC. It is necessary to promote a regular intake of vegetables, fruits and diary products (although a moderate intake for men), and to reduce red meat (especially fat meat), processed meat, starchy vegetables, wine and sweet beverages intakes, to prevent the occurrence of cancer. In men, it is recommended a moderate intake of egg. In women, it is advised a moderate intake of refined grains, bakery products, oils and mayonnaise intake. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. 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.

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.

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...

Method of determining the optimal dilution ratio for fluorescence fingerprint of food constituents.

PubMed

Trivittayasil, Vipavee; Tsuta, Mizuki; Kokawa, Mito; Yoshimura, Masatoshi; Sugiyama, Junichi; Fujita, Kaori; Shibata, Mario

2015-01-01

Quantitative determination by fluorescence spectroscopy is possible because of the linear relationship between the intensity of emitted fluorescence and the fluorophore concentration. However, concentration quenching may cause the relationship to become nonlinear, and thus, the optimal dilution ratio has to be determined. In the case of fluorescence fingerprint (FF) measurement, fluorescence is measured under multiple wavelength conditions and a method of determining the optimal dilution ratio for multivariate data such as FFs has not been reported. In this study, the FFs of mixed solutions of tryptophan and epicatechin of different concentrations and composition ratios were measured. Principal component analysis was applied, and the resulting loading plots were found to contain useful information about each constituent. The optimal concentration ranges could be determined by identifying the linear region of the PC score plotted against total concentration.

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.

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.

Age-related changes in trunk neuromuscular activation patterns during a controlled functional transfer task include amplitude and temporal synergies.

PubMed

Quirk, D Adam; Hubley-Kozey, Cheryl L

2014-12-01

While healthy aging is associated with physiological changes that can impair control of trunk motion, few studies examine how spinal muscle responses change with increasing age. This study examined whether older (over 65 years) compared to younger (20-45 years) adults had higher overall amplitude and altered temporal recruitment patterns of trunk musculature when performing a functional transfer task. Surface electromyograms from twelve bilateral trunk muscle (24) sites were analyzed using principal component analysis, extracting amplitude and temporal features (PCs) from electromyographic waveforms. Two PCs explained 96% of the waveform variance. Three factor ANOVA models tested main effects (group, muscle and reach) and interactions for PC scores. Significant (p<.0125) group interactions were found for all PC scores. Post hoc analysis revealed that relative to younger adults, older adults recruited higher agonist and antagonistic activity, demonstrated continuous activation levels in specific muscle sites despite changing external moments, and had altered temporal synergies within abdominal and back musculature. In summary both older and younger adults recruit highly organized activation patterns in response to changing external moments. Differences in temporal trunk musculature recruitment patterns suggest that older adults experience different dynamic spinal stiffness and loading compared to younger adults during a functional lifting task. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Morphometric comparison by the ISAS® CASA-DNAf system of two techniques for the evaluation of DNA fragmentation in human spermatozoa

PubMed Central

Sadeghi, Sara; García-Molina, Almudena; Celma, Ferran; Valverde, Anthony; Fereidounfar, Sogol; Soler, Carles

2016-01-01

DNA fragmentation has been shown to be one of the causes of male infertility, particularly related to repeated abortions, and different methods have been developed to analyze it. In the present study, two commercial kits based on the SCD technique (Halosperm® and SDFA) were evaluated by the use of the DNA fragmentation module of the ISAS® v1 CASA system. Seven semen samples from volunteers were analyzed. To compare the results between techniques, the Kruskal–Wallis test was used. Data were used for calculation of Principal Components (two PCs were obtained), and subsequent subpopulations were identified using the Halo, Halo/Core Ratio, and PC data. Results from both kits were significantly different (P < 0.001). In each case, four subpopulations were obtained, independently of the classification method used. The distribution of subpopulations differed depending on the kit used. From the PC data, a discriminant analysis matrix was obtained and a good a posteriori classification was obtained (97.1% for Halosperm and 96.6% for SDFA). The present results are the first approach on morphometric evaluation of DNA fragmentation from the SCD technique. This approach could be used for the future definition of a classification matrix surpassing the current subjective evaluation of this important sperm factor. PMID:27678463

Morphometric comparison by the ISAS® CASA-DNAf system of two techniques for the evaluation of DNA fragmentation in human spermatozoa.

PubMed

Sadeghi, Sara; García-Molina, Almudena; Celma, Ferran; Valverde, Anthony; Fereidounfar, Sogol; Soler, Carles

2016-01-01

DNA fragmentation has been shown to be one of the causes of male infertility, particularly related to repeated abortions, and different methods have been developed to analyze it. In the present study, two commercial kits based on the SCD technique (Halosperm ® and SDFA) were evaluated by the use of the DNA fragmentation module of the ISAS ® v1 CASA system. Seven semen samples from volunteers were analyzed. To compare the results between techniques, the Kruskal-Wallis test was used. Data were used for calculation of Principal Components (two PCs were obtained), and subsequent subpopulations were identified using the Halo, Halo/Core Ratio, and PC data. Results from both kits were significantly different (P < 0.001). In each case, four subpopulations were obtained, independently of the classification method used. The distribution of subpopulations differed depending on the kit used. From the PC data, a discriminant analysis matrix was obtained and a good a posteriori classification was obtained (97.1% for Halosperm and 96.6% for SDFA). The present results are the first approach on morphometric evaluation of DNA fragmentation from the SCD technique. This approach could be used for the future definition of a classification matrix surpassing the current subjective evaluation of this important sperm factor.

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

Control of interjoint coordination during the swing phase of normal gait at different speeds

PubMed Central

Shemmell, Jonathan; Johansson, Jennifer; Portra, Vanessa; Gottlieb, Gerald L; Thomas, James S; Corcos, Daniel M

2007-01-01

Background It has been suggested that the control of unconstrained movements is simplified via the imposition of a kinetic constraint that produces dynamic torques at each moving joint such that they are a linear function of a single motor command. The linear relationship between dynamic torques at each joint has been demonstrated for multijoint upper limb movements. The purpose of the current study was to test the applicability of such a control scheme to the unconstrained portion of the gait cycle – the swing phase. Methods Twenty-eight neurologically normal individuals walked along a track at three different speeds. Angular displacements and dynamic torques produced at each of the three lower limb joints (hip, knee and ankle) were calculated from segmental position data recorded during each trial. We employed principal component (PC) analysis to determine (1) the similarity of kinematic and kinetic time series at the ankle, knee and hip during the swing phase of gait, and (2) the effect of walking speed on the range of joint displacement and torque. Results The angular displacements of the three joints were accounted for by two PCs during the swing phase (Variance accounted for – PC1: 75.1 ± 1.4%, PC2: 23.2 ± 1.3%), whereas the dynamic joint torques were described by a single PC (Variance accounted for – PC1: 93.8 ± 0.9%). Increases in walking speed were associated with increases in the range of motion and magnitude of torque at each joint although the ratio describing the relative magnitude of torque at each joint remained constant. Conclusion Our results support the idea that the control of leg swing during gait is simplified in two ways: (1) the pattern of dynamic torque at each lower limb joint is produced by appropriately scaling a single motor command and (2) the magnitude of dynamic torque at all three joints can be specified with knowledge of the magnitude of torque at a single joint. Walking speed could therefore be altered by modifying a single value related to the magnitude of torque at one joint. PMID:17466065

Characterization and selection of suitable grades of lactose as functional fillers for capsule filling: part 1.

PubMed

Moolchandani, Vikas; Augsburger, Larry L; Gupta, Abhay; Khan, Mansoor; Langridge, John; Hoag, Stephen W

2015-01-01

The purpose of this work is to characterize thermal, physical and mechanical properties of different grades of lactose and better understand the relationships between these properties and capsule filling performance. Eight grades of commercially available lactose were evaluated: Pharmatose 110 M, 125 M, 150 M, 200 M, 350 M (α-lactose monohydrate), AL (anhydrous lactose containing ∼80% β-AL), DCL11 (spray dried α-lactose monohydrate containing ∼15% amorphous lactose) and DCL15 (granulated α-lactose monohydrate containing ∼12% β-AL). In this study, different lactose grades were characterized by thermal, solid state, physical and mechanical properties and later evaluated using principal component analysis (PCA) to assess the inter-relationships among some of these properties. The lactose grades were characterized by differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), X-ray diffraction (XRD), moisture sorption/desorption isotherms, particle size distribution; the flow was characterized by Carr Index (CI), critical orifice diameter (COD) and angle of friction. Plug mechanical strength was estimated from its diametric crushing strength. The first and second principal components (PC) captured 47.6% and 27.4% of variation in the physical and mechanical property data, respectively. The PCA plot grouped together 110 M, AL, DCL11 and DCL15 on the one side of plot which possessed superior properties for capsule formulation and these grades were selected for future formulation development studies (part II of this work).

Quarry identification of historical building materials by means of laser induced breakdown spectroscopy, X-ray fluorescence and chemometric analysis

NASA Astrophysics Data System (ADS)

Colao, F.; Fantoni, R.; Ortiz, P.; Vazquez, M. A.; Martin, J. M.; Ortiz, R.; Idris, N.

2010-08-01

To characterize historical building materials according to the geographic origin of the quarries from which they have been mined, the relative content of major and trace elements were determined by means of Laser Induced Breakdown Spectroscopy (LIBS) and X-ray Fluorescence (XRF) techniques. 48 different specimens were studied and the entire samples' set was divided in two different groups: the first, used as reference set, was composed by samples mined from eight different quarries located in Seville province; the second group was composed by specimens of unknown provenance collected in several historical buildings and churches in the city of Seville. Data reduction and analysis on laser induced breakdown spectroscopy and X-ray fluorescence measurements was performed using multivariate statistical approach, namely the Linear Discriminant Analysis (LDA), Principal Component Analysis (PCA) and Soft Independent Modeling of Class Analogy (SIMCA). A clear separation among reference sample materials mined from different quarries was observed in Principal Components (PC) score plots, then a supervised soft independent modeling of class analogy classification was trained and run, aiming to assess the provenance of unknown samples according to their elemental content. The obtained results were compared with the provenance assignments made on the basis of petrographical description. This work gives experimental evidence that laser induced breakdown spectroscopy measurements on a relatively small set of elements is a fast and effective method for the purpose of origin identification.

Relationships between nuclear magnetic resonance parameters used to characterize weathering spilled oil and soil toxicity in central Patagonia.

PubMed

Ríos, Stella Maris; Barquin, Mercedes; Katusich, Ofelia; Nudelman, Norma

2014-01-01

Oil spill in the Central Patagonian zone was studied to evaluate if any relationship exists between the parameters used to characterize weathering spilled oil and soil toxicity for two plant species and to evaluate if the phytotoxicity to local species would be a good index for the soil contamination. Nuclear magnetic resonance (NMR) structural indexes and column chromatography compositional indexes were determined to characterize the oil spill in the soil samples. Bioassays were also carried out using Lactuca sativa L (reference) and Atriplex lampa (native species) as test organisms. Measurements of the total petroleum hydrocarbon (TPH) and the electrical conductivity (EC) of the soil were carried out to evaluate the effect on the bioassays. The principal components analysis of the parameters determined by NMR, compositional indexes, EC, TPH, and toxicology data shows that the first three principal components accounted for the 78% of the total variance (40%, 25%, and 13% for the first, second, and third PC, respectively). A good agreement was found between information obtained by compositional indexes and NMR structural indexes. Soil toxicity increases with the increase of EC and TPH. Other factors, such as, the presence of branched and aromatic hydrocarbons is also significant. The statistical evaluation showed that the Euclidean distances (3D) between the background and each one of the samples might be a better indicator of the soil contamination, compared with chemical criterion of TPH.

A Data-driven Study of RR Lyrae Near-IR Light Curves: Principal Component Analysis, Robust Fits, and Metallicity Estimates

NASA Astrophysics Data System (ADS)

Hajdu, Gergely; Dékány, István; Catelan, Márcio; Grebel, Eva K.; Jurcsik, Johanna

2018-04-01

RR Lyrae variables are widely used tracers of Galactic halo structure and kinematics, but they can also serve to constrain the distribution of the old stellar population in the Galactic bulge. With the aim of improving their near-infrared photometric characterization, we investigate their near-infrared light curves, as well as the empirical relationships between their light curve and metallicities using machine learning methods. We introduce a new, robust method for the estimation of the light-curve shapes, hence the average magnitudes of RR Lyrae variables in the K S band, by utilizing the first few principal components (PCs) as basis vectors, obtained from the PC analysis of a training set of light curves. Furthermore, we use the amplitudes of these PCs to predict the light-curve shape of each star in the J-band, allowing us to precisely determine their average magnitudes (hence colors), even in cases where only one J measurement is available. Finally, we demonstrate that the K S-band light-curve parameters of RR Lyrae variables, together with the period, allow the estimation of the metallicity of individual stars with an accuracy of ∼0.2–0.25 dex, providing valuable chemical information about old stellar populations bearing RR Lyrae variables. The methods presented here can be straightforwardly adopted for other classes of variable stars, bands, or for the estimation of other physical quantities.

Operational Implementation of a Pc Uncertainty Construct for Conjunction Assessment Risk Analysis

NASA Technical Reports Server (NTRS)

Newman, Lauri K.; Hejduk, Matthew D.; Johnson, Lauren C.

2016-01-01

Earlier this year the NASA Conjunction Assessment and Risk Analysis (CARA) project presented the theoretical and algorithmic aspects of a method to include the uncertainties in the calculation inputs when computing the probability of collision (Pc) between two space objects, principally uncertainties in the covariances and the hard-body radius. The output of this calculation approach is to produce rather than a single Pc value an entire probability density function that will represent the range of possible Pc values given the uncertainties in the inputs and bring CA risk analysis methodologies more in line with modern risk management theory. The present study provides results from the exercise of this method against an extended dataset of satellite conjunctions in order to determine the effect of its use on the evaluation of conjunction assessment (CA) event risk posture. The effects are found to be considerable: a good number of events are downgraded from or upgraded to a serious risk designation on the basis of consideration of the Pc uncertainty. The findings counsel the integration of the developed methods into NASA CA operations.

Identifying potential selective fluorescent probes for cancer-associated protein carbonic anhydrase IX using a computational approach.

PubMed

Kamstra, Rhiannon L; Floriano, Wely B

2014-11-01

Carbonic anhydrase IX (CAIX) is a biomarker for tumor hypoxia. Fluorescent inhibitors of CAIX have been used to study hypoxic tumor cell lines. However, these inhibitor-based fluorescent probes may have a therapeutic effect that is not appropriate for monitoring treatment efficacy. In the search for novel fluorescent probes that are not based on known inhibitors, a database of 20,860 fluorescent compounds was virtually screened against CAIX using hierarchical virtual ligand screening (HierVLS). The screening database contained 14,862 compounds tagged with the ATTO680 fluorophore plus an additional 5998 intrinsically fluorescent compounds. Overall ranking of compounds to identify hit molecular probe candidates utilized a principal component analysis (PCA) approach. Four potential binding sites, including the catalytic site, were identified within the structure of the protein and targeted for virtual screening. Available sequence information for 23 carbonic anhydrase isoforms was used to prioritize the four sites based on the estimated "uniqueness" of each site in CAIX relative to the other isoforms. A database of 32 known inhibitors and 478 decoy compounds was used to validate the methodology. A receiver-operating characteristic (ROC) analysis using the first principal component (PC1) as predictive score for the validation database yielded an area under the curve (AUC) of 0.92. AUC is interpreted as the probability that a binder will have a better score than a non-binder. The use of first component analysis of binding energies for multiple sites is a novel approach for hit selection. The very high prediction power for this approach increases confidence in the outcome from the fluorescent library screening. Ten of the top scoring candidates for isoform-selective putative binding sites are suggested for future testing as fluorescent molecular probe candidates. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

Hooking injury, physiological status and short-term mortality of juvenile lemon sharks (Negaprion bevirostris) following catch-and-release recreational angling

PubMed Central

Danylchuk, Andy J.; Suski, Cory D.; Mandelman, John W.; Murchie, Karen J.; Haak, Christopher R.; Brooks, Annabelle M. L.; Cooke, Steven J.

2014-01-01

Sport fishing for sharks, including fishing with the intent to release, is becoming more prevalent within the recreational angling community. Common targets of recreational anglers are juvenile lemon sharks (Negaprion brevirostris) that frequent shallow tropical nearshore habitats. In this study, we captured 32 juvenile lemon sharks (530–875 mm total length) with conventional angling gear (i.e. spinning rods, dead fish bait and 5/0 barbed circle hooks) from the coastal waters of Eleuthera, The Bahamas, to determine the consequences of capture for individual sharks. Each shark was examined for hooking injuries, blood sampled to quantify physiological disturbance, assessed for reflex impairment and then monitored to assess post-release behaviour and mortality. Four sharks (12.5%) died following release during the 15 min tracking period. Principal components (PC) analysis revealed four axes describing 66.5% of the variance for blood physiology parameters, total length and water temperature. The PC1 and PC3 scores, characterized by positive factor loadings for indicators of exercise-induced stress and blood ion concentrations, respectively, were significantly related to fight time but were not associated with short-term mortality. Short-term mortality was significantly related to factor scores for PC4 that loaded heavily for water temperature and total length. Ten sharks (31%) exhibited impaired reflexes, with loss of bite reflex being most prevalent. Sharks that died had the following characteristics: (i) they had two or more impaired reflexes; (ii) they were hooked in the basihyal; (iii) they exhibited no movement after the initial bout of directional swimming; and (iv) they experienced high water temperatures (i.e. >31°C). Collectively, these results indicate that for juvenile lemon sharks inhabiting tropical flats, fight time can influence the degree of physiological disturbance, while water temperature contributes to the likelihood of survival following release. PMID:27293620

Hooking injury, physiological status and short-term mortality of juvenile lemon sharks (Negaprion bevirostris) following catch-and-release recreational angling.

PubMed

Danylchuk, Andy J; Suski, Cory D; Mandelman, John W; Murchie, Karen J; Haak, Christopher R; Brooks, Annabelle M L; Cooke, Steven J

2014-01-01

Sport fishing for sharks, including fishing with the intent to release, is becoming more prevalent within the recreational angling community. Common targets of recreational anglers are juvenile lemon sharks (Negaprion brevirostris) that frequent shallow tropical nearshore habitats. In this study, we captured 32 juvenile lemon sharks (530-875 mm total length) with conventional angling gear (i.e. spinning rods, dead fish bait and 5/0 barbed circle hooks) from the coastal waters of Eleuthera, The Bahamas, to determine the consequences of capture for individual sharks. Each shark was examined for hooking injuries, blood sampled to quantify physiological disturbance, assessed for reflex impairment and then monitored to assess post-release behaviour and mortality. Four sharks (12.5%) died following release during the 15 min tracking period. Principal components (PC) analysis revealed four axes describing 66.5% of the variance for blood physiology parameters, total length and water temperature. The PC1 and PC3 scores, characterized by positive factor loadings for indicators of exercise-induced stress and blood ion concentrations, respectively, were significantly related to fight time but were not associated with short-term mortality. Short-term mortality was significantly related to factor scores for PC4 that loaded heavily for water temperature and total length. Ten sharks (31%) exhibited impaired reflexes, with loss of bite reflex being most prevalent. Sharks that died had the following characteristics: (i) they had two or more impaired reflexes; (ii) they were hooked in the basihyal; (iii) they exhibited no movement after the initial bout of directional swimming; and (iv) they experienced high water temperatures (i.e. >31°C). Collectively, these results indicate that for juvenile lemon sharks inhabiting tropical flats, fight time can influence the degree of physiological disturbance, while water temperature contributes to the likelihood of survival following release.

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.

Mechanism of Fructus Aurantii Flavonoids Promoting Gastrointestinal Motility: From Organic and Inorganic Endogenous Substances Combination Point of View.

PubMed

Wang, Shuai; Bao, Yong-Rui; Li, Tian-Jiao; Yu, Ting; Chang, Xin; Yang, Guan-Lin; Meng, Xian-Sheng

2017-01-01

Fructus Aurantii (FA) derived from the dried, and unripe fruit of Citrus aurantium L. is one of the commonly used traditional Chinese medicines to treat gastrointestinal motility dysfunction diseases. According to the literature research, FA flavonoids (FAF) are important active ingredients of FA promoting gastrointestinal motility, but the exact material basis and mechanism of action are still not very clear. This experiment was designed to illustrate the material basis of FAF promoting gastrointestinal motility and explore the mechanism of action from an organic and inorganic combination point of view. In this experiment, high-performance liquid chromatography (HPLC) method was used to analyze the composition and content of FAF. Based on the prominent prokinetic effect of FAF on mice, the mechanism of action was speculated through a combination of HPLC coupled with quadrupole time-of-flight mass spectrometry (HPLC-QTOF-MS) and inductively coupled plasma mass spectrometry (ICP-MS). With the method of HPLC, ten dominating components of FAF including neoeriocitrin, narirutin, rhoifolin, naringin, hesperidin, neohesperidin, neoponcirin, naringenin, hesperetin, and nobiletin accounting for more than 86% of FAF were identified. Combined HPLC-QTOF-MS with ICP-MS, the endogenous substances with difference in the blood of mice were analyzed, in which 4-dimethylallyltryptophan, corticosterone, phytosphingosine, sphinganine, LysoPC (20:4(5Z, 8Z, 11Z, 14Z)), LysoPC(18:2 (9Z, 12Z)), and Ca 2+ , Mg 2+ , Zn 2+ metal ions had significant changes, involving tryptophan metabolism, corticosterone metabolism, sphingolipid metabolism, and other pathways. The results preliminarily elaborated the mechanism of FAF promoting gastrointestinal motility from an organic and inorganic point of view, which provide valuable information for researching and developing new multi-component Chinese medicine curing gastrointestinal underpower associated diseases. Fructus Aurantii flavonoids are one of the main components of Fructus Aurantii that possess prominent gastrointestinal motility promoting efficacyThe mainly material basis of Fructus Aurantii flavonoids promoting gastrointestinal motility were neoeriocitrin, narirutin, rhoifolin, naringin, hesperidin, neohesperidin, neoponcirin, naringenin, hesperetin, and nobiletinFructus Aurantii flavonoids can regulate the content of 4-dimethylallyltryptophan, corticosterone, phytosphingosine, sphinganine, LysoPC (20:4(5Z, 8Z, 11Z, 14Z)), LysoPC.(18:2(9Z, 12Z)) and Ca 2+ , Mg 2+ , Zn 2+ -metal ions, through tryptophan metabolism, corticosterone metabolism, sphingolipid metabolism, and other pathways to present its gastrointestinal motility promoting efficacy. Abbreviations used: FA: Fructus Aurantii; FAF: Fructus Aurantii flavonoids; HPLC: High performance liquid chromatography; HPLC-QTOF-MS: High performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry; ICP-MS: Inductively coupled plasma mass spectrometry; PCA: Principal components analysis; CG: Control group; FAFLG: Low-dosage group of Fructus Aurantii flavonoids; FAFMG: Middle-dosage group of Fructus Aurantii flavonoids; FAFHG: High-dosage group of Fructus Aurantii flavonoids; DPG: Domperidone group.

Statistical evaluation of fatty acid profile and cholesterol content in fish (common carp) lipids obtained by different sample preparation procedures.

PubMed

Spiric, Aurelija; Trbovic, Dejana; Vranic, Danijela; Djinovic, Jasna; Petronijevic, Radivoj; Matekalo-Sverak, Vesna

2010-07-05

Studies performed on lipid extraction from animal and fish tissues do not provide information on its influence on fatty acid composition of the extracted lipids as well as on cholesterol content. Data presented in this paper indicate the impact of extraction procedures on fatty acid profile of fish lipids extracted by the modified Soxhlet and ASE (accelerated solvent extraction) procedure. Cholesterol was also determined by direct saponification method, too. Student's paired t-test used for comparison of the total fat content in carp fish population obtained by two extraction methods shows that differences between values of the total fat content determined by ASE and modified Soxhlet method are not statistically significant. Values obtained by three different methods (direct saponification, ASE and modified Soxhlet method), used for determination of cholesterol content in carp, were compared by one-way analysis of variance (ANOVA). The obtained results show that modified Soxhlet method gives results which differ significantly from the results obtained by direct saponification and ASE method. However the results obtained by direct saponification and ASE method do not differ significantly from each other. The highest quantities for cholesterol (37.65 to 65.44 mg/100 g) in the analyzed fish muscle were obtained by applying direct saponification method, as less destructive one, followed by ASE (34.16 to 52.60 mg/100 g) and modified Soxhlet extraction method (10.73 to 30.83 mg/100 g). Modified Soxhlet method for extraction of fish lipids gives higher values for n-6 fatty acids than ASE method (t(paired)=3.22 t(c)=2.36), while there is no statistically significant difference in the n-3 content levels between the methods (t(paired)=1.31). The UNSFA/SFA ratio obtained by using modified Soxhlet method is also higher than the ratio obtained using ASE method (t(paired)=4.88 t(c)=2.36). Results of Principal Component Analysis (PCA) showed that the highest positive impact to the second principal component (PC2) is recorded by C18:3 n-3, and C20:3 n-6, being present in a higher amount in the samples treated by the modified Soxhlet extraction, while C22:5 n-3, C20:3 n-3, C22:1 and C20:4, C16 and C18 negatively influence the score values of the PC2, showing significantly increased level in the samples treated by ASE method. Hotelling's paired T-square test used on the first three principal components for confirmation of differences in individual fatty acid content obtained by ASE and Soxhlet method in carp muscle showed statistically significant difference between these two data sets (T(2)=161.308, p<0.001). Copyright 2010 Elsevier B.V. All rights reserved.

A functional approach to the body condition assessment of lactating donkeys as a tool for welfare evaluation

PubMed Central

Raspa, Federica; Giribaldi, Marzia; Barbero, Raffaella; Bergagna, Stefania; Antoniazzi, Sara; Mc Lean, Amy K.; Minero, Michela; Cavallarin, Laura

2017-01-01

Background The breeding of lactating donkeys is increasing in Western Europe; with it the evaluation of body condition is growing in importance since it is considered a key principle for their welfare. However, assessment of body condition is a complex task, since several factors are involved. The aim of the present study is to investigate which animal-based indicators are the most reliable to describe the body condition of lactating donkeys. For this purpose, new animal-based indicators, which are easy to measure in field conditions (including body measurements, fatty neck score (FNS), dental score), are recorded and their relationship with BCS (a proxy measure for overall adiposity) was assessed. The ones that reveal an association with the BCS are included in an integrated principal component analysis to understand which are the most related to BCS. Methods Fifty-three healthy lactating donkeys of various breeds, including 7 Martina Franca, 10 Ragusano, 2 Romagnolo and 34 crossbreeds, were evaluated. The animal-based indicators that were recorded were: length (OP, olecranon tuber-pinbone and SH, shoulder-hip), heart girth (HG), abdominal circumference (AC), neck length (NL), neck height (NH) and neck thickness (NT) at 0.50 and neck circumference (NC) at 0.25, 0.50 and 0.75, body condition score (BCS) and fatty neck score (FNS). The owners’ evaluation of the BCS was also considered. A dental assessment was performed and the month of lactation and age of each animal was recorded. Results No correlation was found between BCS and the other morphometric body measurements. On the contrary the FNS was correlated with the morphometric measurements of the neck (positive correlation to 0.50 NH and 0.50 NT, 0.50 NC, 0.75 mean NC, and negative correlation to the mean NC:NH and mean NC:NT, 0.50 NC:NT and 0.50 NC:NH ratios). A significant inverse relationship was identified between BCS and dental score. A Principal Component analysis (PCA) separated the BCS classes on the first principal component (PC1). PC1 revealed a meaningful positive correlation between the BCS and the neck measurements (NT, NH and FNS), with high positive loadings, while a negative correlation was found for dental abnormalities. The owners’ evaluation of BCS was different from the expert evaluator’ assessment, since they tended to give higher score that was slightly but significantly correlated to AC. Discussion A new scoring system, called Fatty Neck Score (FNS), has been proposed for the judgement of the adiposity status of donkey neck. The results suggest that caregivers might use the proposed animal based indicators (BCS, FNS and dental scores) together as a tool for the evaluation of the body condition of lactating donkeys. Our findings highlight that caregivers need to be trained in order to be able to properly record these indicators. Ultimately use of these indicators may help to improve the welfare of lactating donkeys. PMID:28367363

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.

On the Fallibility of Principal Components in Research

ERIC Educational Resources Information Center

Raykov, Tenko; Marcoulides, George A.; Li, Tenglong

2017-01-01

The measurement error in principal components extracted from a set of fallible measures is discussed and evaluated. It is shown that as long as one or more measures in a given set of observed variables contains error of measurement, so also does any principal component obtained from the set. The error variance in any principal component is shown…

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.

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

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

NASA Technical Reports Server (NTRS)

Scroggins, Sharon; Duda, Kristen

2008-01-01

This viewgraph presentation gives an overview of NASA's risk analysis communication programs associated with changing environmental policies. The topics include: 1) NASA Program Transition; 2) Principal Center for Regulatory Risk Analysis and Communication (RRAC PC); and 3) Regulatory Tracking and Communication Process.

Recovery of a spectrum based on a compressive-sensing algorithm with weighted principal component analysis

NASA Astrophysics Data System (ADS)

Dafu, Shen; Leihong, Zhang; Dong, Liang; Bei, Li; Yi, Kang

2017-07-01

The purpose of this study is to improve the reconstruction precision and better copy the color of spectral image surfaces. A new spectral reflectance reconstruction algorithm based on an iterative threshold combined with weighted principal component space is presented in this paper, and the principal component with weighted visual features is the sparse basis. Different numbers of color cards are selected as the training samples, a multispectral image is the testing sample, and the color differences in the reconstructions are compared. The channel response value is obtained by a Mega Vision high-accuracy, multi-channel imaging system. The results show that spectral reconstruction based on weighted principal component space is superior in performance to that based on traditional principal component space. Therefore, the color difference obtained using the compressive-sensing algorithm with weighted principal component analysis is less than that obtained using the algorithm with traditional principal component analysis, and better reconstructed color consistency with human eye vision is achieved.

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.

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.

Advanced methods in NDE using machine learning approaches

NASA Astrophysics Data System (ADS)

Wunderlich, Christian; Tschöpe, Constanze; Duckhorn, Frank

2018-04-01

Machine learning (ML) methods and algorithms have been applied recently with great success in quality control and predictive maintenance. Its goal to build new and/or leverage existing algorithms to learn from training data and give accurate predictions, or to find patterns, particularly with new and unseen similar data, fits perfectly to Non-Destructive Evaluation. The advantages of ML in NDE are obvious in such tasks as pattern recognition in acoustic signals or automated processing of images from X-ray, Ultrasonics or optical methods. Fraunhofer IKTS is using machine learning algorithms in acoustic signal analysis. The approach had been applied to such a variety of tasks in quality assessment. The principal approach is based on acoustic signal processing with a primary and secondary analysis step followed by a cognitive system to create model data. Already in the second analysis steps unsupervised learning algorithms as principal component analysis are used to simplify data structures. In the cognitive part of the software further unsupervised and supervised learning algorithms will be trained. Later the sensor signals from unknown samples can be recognized and classified automatically by the algorithms trained before. Recently the IKTS team was able to transfer the software for signal processing and pattern recognition to a small printed circuit board (PCB). Still, algorithms will be trained on an ordinary PC; however, trained algorithms run on the Digital Signal Processor and the FPGA chip. The identical approach will be used for pattern recognition in image analysis of OCT pictures. Some key requirements have to be fulfilled, however. A sufficiently large set of training data, a high signal-to-noise ratio, and an optimized and exact fixation of components are required. The automated testing can be done subsequently by the machine. By integrating the test data of many components along the value chain further optimization including lifetime and durability prediction based on big data becomes possible, even if components are used in different versions or configurations. This is the promise behind German Industry 4.0.

Food patterns and dietary quality associated with organic food consumption during pregnancy; data from a large cohort of pregnant women in Norway.

PubMed

Torjusen, Hanne; Lieblein, Geir; Næs, Tormod; Haugen, Margaretha; Meltzer, Helle Margrete; Brantsæter, Anne Lise

2012-08-06

Little is known about the consumption of organic food during pregnancy. The aim of this study was to describe dietary characteristics associated with frequent consumption of organic food among pregnant women participating in the Norwegian Mother and Child Cohort Study (MoBa). The present study includes 63 808 women who during the years 2002-2007 answered two questionnaires, a general health questionnaire at gestational weeks 15 and a food frequency questionnaire at weeks 17-22. The exploration of food patterns by Principal component analyses (PCA) was followed by ANOVA analyses investigating how these food patterns as well as intake of selected food groups were associated with consumption of organic food. The first principal component (PC1) identified by PCA, accounting for 12% of the variation, was interpreted as a 'health and sustainability component', with high positive loadings for vegetables, fruit and berries, cooking oil, whole grain bread and cereal products and negative loadings for meat, including processed meat, white bread, and cakes and sweets. Frequent consumption of organic food, which was reported among 9.1% of participants (n = 5786), was associated with increased scores on the 'health and sustainability component' (p < 0.001). The increase in score represented approximately 1/10 of the total variation and was independent of sociodemographic and lifestyle characteristics. Participants with frequent consumption of organic food had a diet with higher density of fiber and most nutrients such as folate, beta-carotene and vitamin C, and lower density of sodium compared to participants with no or low organic consumption. The present study showed that pregnant Norwegian women reporting frequent consumption of organically produced food had dietary pattern and quality more in line with public advice for healthy and sustainable diets. A methodological implication is that the overall diet needs to be included in future studies of potential health outcomes related to consumption of organic food during pregnancy.

Ultrasonic sensing of GMAW: Laser/EMAT defect detection system

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

Carlson, N.M.; Johnson, J.A.; Larsen, E.D.

1992-08-01

In-process ultrasonic sensing of welding allows detection of weld defects in real time. A noncontacting ultrasonic system is being developed to operate in a production environment. The principal components are a pulsed laser for ultrasound generation and an electromagnetic acoustic transducer (EMAT) for ultrasound reception. A PC-based data acquisition system determines the quality of the weld on a pass-by-pass basis. The laser/EMAT system interrogates the area in the weld volume where defects are most likely to occur. This area of interest is identified by computer calculations on a pass-by-pass basis using weld planning information provided by the off-line programmer. Themore » absence of a signal above the threshold level in the computer-calculated time interval indicates a disruption of the sound path by a defect. The ultrasonic sensor system then provides an input signal to the weld controller about the defect condition. 8 refs.« less

Surface-enhanced Raman spectra of hemoglobin for esophageal cancer diagnosis

NASA Astrophysics Data System (ADS)

Zhou, Xue; Diao, Zhenqi; Fan, Chunzhen; Guo, Huiqiang; Xiong, Yang; Tang, Weiyue

2014-03-01

Surface-enhanced Raman scattering (SERS) spectra of hemoglobin from 30 esophageal cancer patients and 30 healthy persons have been detected and analyzed. The results indicate that, there are more iron ions in low spin state and less in high for the hemoglobin of esophageal cancer patients than normal persons, which is consistent with the fact that it is easier to hemolyze for the blood of cancer patients. By using principal component analysis (PCA) and discriminate analysis, we can get a three-dimensional scatter plot of PC scores from the SERS spectra of healthy persons and cancer patients, from which the two groups can be discriminated. The total accuracy of this method is 90%, while the diagnostic specificity is 93.3% and sensitivity is 86.7%. Thus SERS spectra of hemoglobin analysis combined with PCA may be a new technique for the early diagnose of esophageal cancer.

Genetic diversity studies in pea (Pisum sativum L.) using simple sequence repeat markers.

PubMed

Kumari, P; Basal, N; Singh, A K; Rai, V P; Srivastava, C P; Singh, P K

2013-03-13

The genetic diversity among 28 pea (Pisum sativum L.) genotypes was analyzed using 32 simple sequence repeat markers. A total of 44 polymorphic bands, with an average of 2.1 bands per primer, were obtained. The polymorphism information content ranged from 0.657 to 0.309 with an average of 0.493. The variation in genetic diversity among these cultivars ranged from 0.11 to 0.73. Cluster analysis based on Jaccard's similarity coefficient using the unweighted pair-group method with arithmetic mean (UPGMA) revealed 2 distinct clusters, I and II, comprising 6 and 22 genotypes, respectively. Cluster II was further differentiated into 2 subclusters, IIA and IIB, with 12 and 10 genotypes, respectively. Principal component (PC) analysis revealed results similar to those of UPGMA. The first, second, and third PCs contributed 21.6, 16.1, and 14.0% of the variation, respectively; cumulative variation of the first 3 PCs was 51.7%.

A Multivariate Methodological Workflow for the Analysis of FTIR Chemical Mapping Applied on Historic Paint Stratigraphies

PubMed Central

Sciutto, Giorgia; Oliveri, Paolo; Catelli, Emilio; Bonacini, Irene

2017-01-01

In the field of applied researches in heritage science, the use of multivariate approach is still quite limited and often chemometric results obtained are often underinterpreted. Within this scenario, the present paper is aimed at disseminating the use of suitable multivariate methodologies and proposes a procedural workflow applied on a representative group of case studies, of considerable importance for conservation purposes, as a sort of guideline on the processing and on the interpretation of this FTIR data. Initially, principal component analysis (PCA) is performed and the score values are converted into chemical maps. Successively, the brushing approach is applied, demonstrating its usefulness for a deep understanding of the relationships between the multivariate map and PC score space, as well as for the identification of the spectral bands mainly involved in the definition of each area localised within the score maps. PMID:29333162

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.

Comparison of HR MAS MR spectroscopic profiles of breast cancer tissue with clinical parameters.

PubMed

Sitter, Beathe; Lundgren, Steinar; Bathen, Tone F; Halgunset, Jostein; Fjosne, Hans E; Gribbestad, Ingrid S

2006-02-01

Breast cancer is the most frequent form of cancer in women and improved diagnostic methods are desirable. Malignant cells have altered metabolism and metabolic mapping might become a tool in cancer diagnostics. High-resolution magic angle spinning (HR MAS) MR spectroscopy of tissue biopsies provides detailed information on metabolic composition. The 600 MHz 1H HR MAS spectra were acquired of breast cancer tissue from 85 patients and adjacent non-involved tissue from 18 of these patients. Tissue specimens were investigated by microscopy after MR analysis. The resulting spectra were examined by three different approaches. Relative intensities of glycerophosphocholine (GPC), phosphocholine (PC) and choline were compared for cancerous and non-involved specimens. Eight metabolites, choline, creatine, beta-glucose, GPC, glycine, myo-inositol, PC and taurine, were quantified from the recorded spectra and compared with tumor histological type and size, patient's lymph node status and tissue composition of sample. The spectra were also compared with tumor histological type and size, lymph node status and tissue composition of samples using principal component analysis (PCA). Tumor samples could be distinguished from non-involved samples (82% sensitivity, 100% specificity) based on relative intensities of signals from GPC, PC and choline in 1H HR MAS spectra. Tissue concentrations of metabolites showed few differences between groups of samples, which can be caused by limitations in the quantification procedure. Choline and glycine concentrations were found to be significantly higher in tumors larger than 2 cm compared with smaller tumors. PCA of MAS spectra from patients with invasive ductal carcinomas indicated a possible prediction of spread to axillary lymph nodes. Metabolite estimates and PCA of MAS spectra were influenced by the percentage of tumor cells in the investigated specimens. 2006 John Wiley & Sons, Ltd.

Comparison of geometric morphometric outline methods in the discrimination of age-related differences in feather shape

PubMed Central

Sheets, H David; Covino, Kristen M; Panasiewicz, Joanna M; Morris, Sara R

2006-01-01

Background Geometric morphometric methods of capturing information about curves or outlines of organismal structures may be used in conjunction with canonical variates analysis (CVA) to assign specimens to groups or populations based on their shapes. This methodological paper examines approaches to optimizing the classification of specimens based on their outlines. This study examines the performance of four approaches to the mathematical representation of outlines and two different approaches to curve measurement as applied to a collection of feather outlines. A new approach to the dimension reduction necessary to carry out a CVA on this type of outline data with modest sample sizes is also presented, and its performance is compared to two other approaches to dimension reduction. Results Two semi-landmark-based methods, bending energy alignment and perpendicular projection, are shown to produce roughly equal rates of classification, as do elliptical Fourier methods and the extended eigenshape method of outline measurement. Rates of classification were not highly dependent on the number of points used to represent a curve or the manner in which those points were acquired. The new approach to dimensionality reduction, which utilizes a variable number of principal component (PC) axes, produced higher cross-validation assignment rates than either the standard approach of using a fixed number of PC axes or a partial least squares method. Conclusion Classification of specimens based on feather shape was not highly dependent of the details of the method used to capture shape information. The choice of dimensionality reduction approach was more of a factor, and the cross validation rate of assignment may be optimized using the variable number of PC axes method presented herein. PMID:16978414

A Common Variation in EDAR Is a Genetic Determinant of Shovel-Shaped Incisors

PubMed Central

Kimura, Ryosuke; Yamaguchi, Tetsutaro; Takeda, Mayako; Kondo, Osamu; Toma, Takashi; Haneji, Kuniaki; Hanihara, Tsunehiko; Matsukusa, Hirotaka; Kawamura, Shoji; Maki, Koutaro; Osawa, Motoki; Ishida, Hajime; Oota, Hiroki

2009-01-01

Shovel shape of upper incisors is a common characteristic in Asian and Native American populations but is rare or absent in African and European populations. Like other common dental traits, genetic polymorphisms involved in the tooth shoveling have not yet been clarified. In ectodysplasin A receptor (EDAR), where dysfunctional mutations cause hypohidrotic ectodermal dysplasia, there is a nonsynonymous-derived variant, 1540C (rs3827760), that has a geographic distribution similar to that of the tooth shoveling. This allele has been recently reported to be associated with Asian-specific hair thickness. We aimed to clarify whether EDAR 1540C is also associated with dental morphology. For this purpose, we measured crown diameters and tooth-shoveling grades and analyzed the correlations between the dental traits and EDAR genotypes in two Japanese populations, inhabitants around Tokyo and in Sakishima Islands. The number of EDAR 1540C alleles in an individual was strongly correlated with the tooth-shoveling grade (p = 7.7 × 10−10). The effect of the allele was additive and explained 18.9% of the total variance in the shoveling grade, which corresponds to about one-fourth of the heritability of the trait reported previously. For data reduction of individual-level metric data, we applied a principal-component analysis, which yielded PC1-4, corresponding to four patterns of tooth size; this result implies that multiple factors are involved in dental morphology. The 1540C allele also significantly affected PC1 (p = 4.9 × 10−3), which denotes overall tooth size, and PC2 (p = 2.6 × 10−3), which denotes the ratio of mesiodistal diameter to buccolingual diameter. PMID:19804850

A common variation in EDAR is a genetic determinant of shovel-shaped incisors.

PubMed

Kimura, Ryosuke; Yamaguchi, Tetsutaro; Takeda, Mayako; Kondo, Osamu; Toma, Takashi; Haneji, Kuniaki; Hanihara, Tsunehiko; Matsukusa, Hirotaka; Kawamura, Shoji; Maki, Koutaro; Osawa, Motoki; Ishida, Hajime; Oota, Hiroki

2009-10-01

Shovel shape of upper incisors is a common characteristic in Asian and Native American populations but is rare or absent in African and European populations. Like other common dental traits, genetic polymorphisms involved in the tooth shoveling have not yet been clarified. In ectodysplasin A receptor (EDAR), where dysfunctional mutations cause hypohidrotic ectodermal dysplasia, there is a nonsynonymous-derived variant, 1540C (rs3827760), that has a geographic distribution similar to that of the tooth shoveling. This allele has been recently reported to be associated with Asian-specific hair thickness. We aimed to clarify whether EDAR 1540C is also associated with dental morphology. For this purpose, we measured crown diameters and tooth-shoveling grades and analyzed the correlations between the dental traits and EDAR genotypes in two Japanese populations, inhabitants around Tokyo and in Sakishima Islands. The number of EDAR 1540C alleles in an individual was strongly correlated with the tooth-shoveling grade (p = 7.7 x 10(-10)). The effect of the allele was additive and explained 18.9% of the total variance in the shoveling grade, which corresponds to about one-fourth of the heritability of the trait reported previously. For data reduction of individual-level metric data, we applied a principal-component analysis, which yielded PC1-4, corresponding to four patterns of tooth size; this result implies that multiple factors are involved in dental morphology. The 1540C allele also significantly affected PC1 (p = 4.9 x 10(-3)), which denotes overall tooth size, and PC2 (p = 2.6 x 10(-3)), which denotes the ratio of mesiodistal diameter to buccolingual diameter.

Principal Component and Linkage Analysis of Cardiovascular Risk Traits in the Norfolk Isolate

PubMed Central

Cox, Hannah C.; Bellis, Claire; Lea, Rod A.; Quinlan, Sharon; Hughes, Roger; Dyer, Thomas; Charlesworth, Jac; Blangero, John; Griffiths, Lyn R.

2009-01-01

Objective(s) An individual's risk of developing cardiovascular disease (CVD) is influenced by genetic factors. This study focussed on mapping genetic loci for CVD-risk traits in a unique population isolate derived from Norfolk Island. Methods This investigation focussed on 377 individuals descended from the population founders. Principal component analysis was used to extract orthogonal components from 11 cardiovascular risk traits. Multipoint variance component methods were used to assess genome-wide linkage using SOLAR to the derived factors. A total of 285 of the 377 related individuals were informative for linkage analysis. Results A total of 4 principal components accounting for 83% of the total variance were derived. Principal component 1 was loaded with body size indicators; principal component 2 with body size, cholesterol and triglyceride levels; principal component 3 with the blood pressures; and principal component 4 with LDL-cholesterol and total cholesterol levels. Suggestive evidence of linkage for principal component 2 (h2 = 0.35) was observed on chromosome 5q35 (LOD = 1.85; p = 0.0008). While peak regions on chromosome 10p11.2 (LOD = 1.27; p = 0.005) and 12q13 (LOD = 1.63; p = 0.003) were observed to segregate with principal components 1 (h2 = 0.33) and 4 (h2 = 0.42), respectively. Conclusion(s): This study investigated a number of CVD risk traits in a unique isolated population. Findings support the clustering of CVD risk traits and provide interesting evidence of a region on chromosome 5q35 segregating with weight, waist circumference, HDL-c and total triglyceride levels. PMID:19339786

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...

A 3 million year index for North African humidity/aridity and the implication of potential pan-African Humid periods

NASA Astrophysics Data System (ADS)

Grant, Katharine M.; Rohling, Eelco J.; Westerhold, Thomas; Zabel, Matthias; Heslop, David; Konijnendijk, Tiuri; Lourens, Lucas

2017-09-01

Mediterranean sediments are valuable archives of both African monsoon variability and higher-latitude climate processes, and can also be used to provide an environmental context for early human migrations and settlements. However, the long history of Mediterranean palaeoclimate studies largely pre-dates the advent of widespread x-ray fluorescence (XRF) core-scanning, so there are few continuous and high-resolution geochemical records from this key region that extend beyond the last glacial cycle. Here we present XRF core-scanning results for ODP Site 967 (Eastern Mediterranean) that have been fully-calibrated into element concentrations spanning the last 3 million years (My). Comparison with independent geochemical data from conventional XRF highlights disparities for certain element/element ratios, thus suggesting the need for caution when taking ratios of scanning XRF data. Principal component analysis of the calibrated XRF dataset reveals two dominant components: detrital inputs (PC1) and a 'sapropel' (≈monsoon run-off) signal (PC2), which we use to establish a new orbitally-tuned chronology. We observe inverse covariation between PC2 and a previously published aeolian dust record from ODP Site 967 (Larrasoaña et al., 2003), and combine these records to produce a composite index of humidity and aridity for the wider North African region over the past 3 My. We propose that by combining run-off and dust signals in a single metric, our index captures the effects of both strengthening/northward migration (increased run-off) and weakening/southward retreat (increased dust) of the North African monsoon. Comparison of the index with published records of Northwest and East African palaeohumidity suggests that it tracks the timing of ;Green Sahara Periods; throughout the Plio-Pleistocene, and that at least 30 of these intervals coincided with increased humidity across East Africa. We tentatively suggest that these specific episodes may be termed ;pan-African Humid Periods;, as a means to highlight large-scale climate trends and to provide an environmental framework for palaeo-anthropological research.

Cloning, Expression, and Characterization of Sorbitol Transporters from Developing Sour Cherry Fruit and Leaf Sink Tissues1

PubMed Central

Gao, Zhifang; Maurousset, Laurence; Lemoine, Remi; Yoo, Sang-Dong; van Nocker, Steven; Loescher, Wayne

2003-01-01

The acyclic polyol sorbitol is a primary photosynthetic product and the principal photosynthetic transport substance in many economically important members of the family Rosaceace (e.g. almond [Prunus dulcis (P. Mill.) D.A. Webber], apple [Malus pumila P. Mill.], cherry [Prunus spp.], peach [Prunus persica L. Batsch], and pear [Pyrus communis]). To understand key steps in long-distance transport and particularly partitioning and accumulation of sorbitol in sink tissues, we have cloned two sorbitol transporter genes (PcSOT1 and PcSOT2) from sour cherry (Prunus cerasus) fruit tissues that accumulate large quantities of sorbitol. Sorbitol uptake activities and other characteristics were measured by heterologous expression of PcSOT1 and PcSOT2 in yeast (Saccharomyces cerevisiae). Both genes encode proton-dependent, sorbitol-specific transporters with similar affinities (Km sorbitol of 0.81 mm for PcSOT1 and 0.64 mm for PcSOT2). Analyses of gene expression of these transporters, however, suggest different roles during leaf and fruit development. PcSOT1 is expressed throughout fruit development, but especially when growth and sorbitol accumulation rates are highest. In leaves, PcSOT1 expression is highest in young, expanding tissues, but substantially less in mature leaves. In contrast, PcSOT2 is mainly expressed only early in fruit development and not in leaves. Compositional analyses suggest that transport mediated by PcSOT1 and PcSOT2 plays a major role in sorbitol and dry matter accumulation in sour cherry fruits. Presence of these transporters and the high fruit sorbitol concentrations suggest that there is an apoplastic step during phloem unloading and accumulation in these sink tissues. Expression of PcSOT1 in young leaves before completion of the transition from sink to source is further evidence for a role in determining sink activity. PMID:12692316

Discrimination of gender-, speed-, and shoe-dependent movement patterns in runners using full-body kinematics.

PubMed

Maurer, Christian; Federolf, Peter; von Tscharner, Vinzenz; Stirling, Lisa; Nigg, Benno M

2012-05-01

Changes in gait kinematics have often been analyzed using pattern recognition methods such as principal component analysis (PCA). It is usually just the first few principal components that are analyzed, because they describe the main variability within a dataset and thus represent the main movement patterns. However, while subtle changes in gait pattern (for instance, due to different footwear) may not change main movement patterns, they may affect movements represented by higher principal components. This study was designed to test two hypotheses: (1) speed and gender differences can be observed in the first principal components, and (2) small interventions such as changing footwear change the gait characteristics of higher principal components. Kinematic changes due to different running conditions (speed - 3.1m/s and 4.9 m/s, gender, and footwear - control shoe and adidas MicroBounce shoe) were investigated by applying PCA and support vector machine (SVM) to a full-body reflective marker setup. Differences in speed changed the basic movement pattern, as was reflected by a change in the time-dependent coefficient derived from the first principal. Gender was differentiated by using the time-dependent coefficient derived from intermediate principal components. (Intermediate principal components are characterized by limb rotations of the thigh and shank.) Different shoe conditions were identified in higher principal components. This study showed that different interventions can be analyzed using a full-body kinematic approach. Within the well-defined vector space spanned by the data of all subjects, higher principal components should also be considered because these components show the differences that result from small interventions such as footwear changes. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

Spatial analysis of sunshine duration by combination of satellite and station data

NASA Astrophysics Data System (ADS)

Frei, C.; Stöckli, R.; Dürr, B.

2009-09-01

Sunshine duration can exhibit rich fine scale patterns associated with special meteorological phenomena, such as fog layers and topographically triggered clouds. Networks of climate stations are mostly too coarse and poorly representative to resolve these patterns explicitly. We present a method which combines station observations with satellite-derived cloud-cover data to produce km-scale fields of sunshine duration. The method is not relying on contemporous satellite information, hence it can be applied over climatological time scales. We apply and evaluate the combination method over the territory of Switzerland. The combination method is based on Universal Kriging. First, the satellite data (a Heliosat clear sky index from MSG, extending over a 5 year preiod) is subjected to a S-mode Principal Component (PC) Analysis. Second, a set of leading PC loadings (seasonally stratified) is introduced as external drift covariates and their optimal linear combination is estimated from the station data (70 stations). Finally, the stochastic component is an autocorrelated field with an exponential variogram, estimated climatologically for each calendar month. For Switzerland the leading PCs of the clear sky index depict familiar patterns of cloud variability which are inhereted in the combination process. The resulting sunshine duration fields exhibit fine-scale structures that are physically plausible, linked to the topography and characteristic of the regional climate. These patterns could not be inferred from station data and/or topographic predictors alone. A cross-validation reveals that the combination method explains between 80-90% of the spatial variance in winter and autumn months. In spring and summer the relative performance is lower (60-75% explained spatial variance) but absolute errors are smaller. Our presentation will also discuss some results from a climatology of the derived sunshine duration fields.

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.

MANGANESE INDUCES NEURITE OUTGROWTH IN PC12 CELLS VIA UPREGULATION OF ALPHA(V) INTEGRINS. (R826248)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

MANGANESE-INDUCED RAT PHEOCHROMOCYTOMA (PC12) CELL DEATH IS INDEPENDENT OF CASPASE ACTIVATION. (R826248)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

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.

Principal Component Relaxation Mode Analysis of an All-Atom Molecular Dynamics Simulation of Human Lysozyme

NASA Astrophysics Data System (ADS)

Nagai, Toshiki; Mitsutake, Ayori; Takano, Hiroshi

2013-02-01

A new relaxation mode analysis method, which is referred to as the principal component relaxation mode analysis method, has been proposed to handle a large number of degrees of freedom of protein systems. In this method, principal component analysis is carried out first and then relaxation mode analysis is applied to a small number of principal components with large fluctuations. To reduce the contribution of fast relaxation modes in these principal components efficiently, we have also proposed a relaxation mode analysis method using multiple evolution times. The principal component relaxation mode analysis method using two evolution times has been applied to an all-atom molecular dynamics simulation of human lysozyme in aqueous solution. Slow relaxation modes and corresponding relaxation times have been appropriately estimated, demonstrating that the method is applicable to protein systems.

Functional principal component analysis of glomerular filtration rate curves after kidney transplant.

PubMed

Dong, Jianghu J; Wang, Liangliang; Gill, Jagbir; Cao, Jiguo

2017-01-01

This article is motivated by some longitudinal clinical data of kidney transplant recipients, where kidney function progression is recorded as the estimated glomerular filtration rates at multiple time points post kidney transplantation. We propose to use the functional principal component analysis method to explore the major source of variations of glomerular filtration rate curves. We find that the estimated functional principal component scores can be used to cluster glomerular filtration rate curves. Ordering functional principal component scores can detect abnormal glomerular filtration rate curves. Finally, functional principal component analysis can effectively estimate missing glomerular filtration rate values and predict future glomerular filtration rate values.

A 400 MHz Wireless Neural Signal Processing IC With 625 $\\times$ On-Chip Data Reduction and Reconfigurable BFSK/QPSK Transmitter Based on Sequential Injection Locking.

PubMed

Teng, Kok-Hin; Wu, Tong; Liu, Xiayun; Yang, Zhi; Heng, Chun-Huat

2017-06-01

An 8-channel wireless neural signal processing IC, which can perform real-time spike detection, alignment, and feature extraction, and wireless data transmission is proposed. A reconfigurable BFSK/QPSK transmitter (TX) at MICS/MedRadio band is incorporated to support different data rate requirement. By using an Exponential Component-Polynomial Component (EC-PC) spike processing unit with an incremental principal component analysis (IPCA) engine, the detection of neural spikes with poor SNR is possible while achieving 625× data reduction. For the TX, a dual-channel at 401 MHz and 403.8 MHz are supported by applying sequential injection locked techniques while attaining phase noise of -102 dBc/Hz at 100 kHz offset. From the measurement, error vector magnitude (EVM) of 4.60%/9.55% with power amplifier (PA) output power of -15 dBm is achieved for the QPSK at 8 Mbps and the BFSK at 12.5 kbps. Fabricated in 65 nm CMOS with an active area of 1 mm 2 , the design consumes a total current of 5  ∼ 5.6 mA with a maximum energy efficiency of 0.7 nJ/b.

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.

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.

Leaving out control groups: an internal contrast analysis of gene expression profiles in atrial fibrillation patients--a systems biology approach to clinical categorization.

PubMed

Vanhoutte, Kurt; de Asmundis, Carlo; Francesconi, Anna; Figysl, Jurgen; Steurs, Griet; Boussy, Tim; Roos, Markus; Mueller, Andreas; Massimo, Lucio; Paparella, Gaetano; Van Caelenberg, Kristien; Chierchia, Gian Battista; Sarkozy, Andrea; Terradellas, Pedro Brugada Y; Zizi, Martin

2009-01-01

Atrial fibrillation (AF) is a frequent chronic dysrythmia with an incidence that increases with age (>40). Because of its medical and socio-economic impacts it is expected to become an increasing burden on most health care systems. AF is a multi-factorial disease for which the identification of subtypes is warranted. Novel approaches based on the broad concepts of systems biology may overcome the blurred notion of normal and pathological phenotype, which is inherent to high throughput molecular arrays analysis. Here we apply an internal contrast algorithm on AF patient data with an analytical focus on potential entry pathways into the disease. We used a RMA (Robust Multichip Average) normalized Affymetrix micro-array data set from 10 AF patients (geo_accession #GSE2240). Four series of probes were selected based on physiopathogenic links with AF entryways: apoptosis (remodeling), MAP kinase (cell remodeling), OXPHOS (ability to sustain hemodynamic workload) and glycolysis (ischemia). Annotated probe lists were polled with Bioconductor packages in R (version 2.7.1). Genetic profile contrasts were analysed with hierarchical clustering and principal component analysis. The analysis revealed distinct patient groups for all probe sets. A substantial part (54% till 67%) of the variance is explained in the first 2 principal components. Genes in PC1/2 with high discriminatory value were selected and analyzed in detail. We aim for reliable molecular stratification of AF. We show that stratification is possible based on physiologically relevant gene sets. Genes with high contrast value are likely to give pathophysiological insight into permanent AF subtypes.

Locomotor Recovery in Spinal Cord Injury: Insights Beyond Walking Speed and Distance.

PubMed

Awai, Lea; Curt, Armin

2016-08-01

Recovery of locomotor function after incomplete spinal cord injury (iSCI) is clinically assessed through walking speed and distance, while improvements in these measures might not be in line with a normalization of gait quality and are, on their own, insensitive at revealing potential mechanisms underlying recovery. The objective of this study was to relate changes of gait parameters to the recovery of walking speed while distinguishing between parameters that rather reflect speed improvements from factors contributing to overall recovery. Kinematic data of 16 iSCI subjects were repeatedly recorded during in-patient rehabilitation. The responsiveness of gait parameters to walking speed was assessed by linear regression. Principal component analysis (PCA) was applied on the multivariate data across time to identify factors that contribute to recovery after iSCI. Parameters of gait cycle and movement dynamics were both responsive and closely related to the recovery of walking speed, which increased by 96%. Multivariate analysis revealed specific gait parameters (intralimb shape normality and consistency) that, although less related to speed increments, loaded highly on principal component one (PC1) (58.6%) explaining the highest proportion of variance (i.e., recovery of outcome over time). Interestingly, measures of hip, knee, and ankle range of motion showed varying degrees of responsiveness (from very high to very low) while not contributing to gait recovery as revealed by PCA. The conjunct application of two analysis methods distinguishes gait parameters that simply reflect increased walking speed from parameters that actually contribute to gait recovery in iSCI. This distinction may be of value for the evaluation of interventions for locomotor recovery.

Classification and quantification analysis of peach kernel from different origins with near-infrared diffuse reflection spectroscopy

PubMed Central

Liu, Wei; Wang, Zhen-Zhong; Qing, Jian-Ping; Li, Hong-Juan; Xiao, Wei

2014-01-01

Background: Peach kernels which contain kinds of fatty acids play an important role in the regulation of a variety of physiological and biological functions. Objective: To establish an innovative and rapid diffuse reflectance near-infrared spectroscopy (DR-NIR) analysis method along with chemometric techniques for the qualitative and quantitative determination of a peach kernel. Materials and Methods: Peach kernel samples from nine different origins were analyzed with high-performance liquid chromatography (HPLC) as a reference method. DR-NIR is in the spectral range 1100-2300 nm. Principal component analysis (PCA) and partial least squares regression (PLSR) algorithm were applied to obtain prediction models, The Savitzky-Golay derivative and first derivative were adopted for the spectral pre-processing, PCA was applied to classify the varieties of those samples. For the quantitative calibration, the models of linoleic and oleinic acids were established with the PLSR algorithm and the optimal principal component (PC) numbers were selected with leave-one-out (LOO) cross-validation. The established models were evaluated with the root mean square error of deviation (RMSED) and corresponding correlation coefficients (R2). Results: The PCA results of DR-NIR spectra yield clear classification of the two varieties of peach kernel. PLSR had a better predictive ability. The correlation coefficients of the two calibration models were above 0.99, and the RMSED of linoleic and oleinic acids were 1.266% and 1.412%, respectively. Conclusion: The DR-NIR combined with PCA and PLSR algorithm could be used efficiently to identify and quantify peach kernels and also help to solve variety problem. PMID:25422544

Multivariate analysis to evaluate genetic groups and production traits of crossbred Holstein × Zebu cows.

PubMed

Fraga, Angelina Bossi; de Lima Silva, Fabiane; Hongyu, Kuang; Da Silva Santos, Darlim; Murphy, Thomas Wayne; Lopes, Fernando Brito

2016-03-01

The objective of this research was to try to unveil the relationship between production traits and genotypic proportions of crossbred dairy cattle using principal component analysis (PCA) and cluster analysis. The herd consists of crossbred animals of Holstein (H) and Zebu (Z) (Gir and Guzerat) in different genotypic proportions; the composition of which varies from 12.5 to 100.0 % of the genetic group H. For this study, 834 milk production records from 257 cows from the years 1997 to 2014 were analyzed. The animals were all managed at a farm located in northeastern Brazil. The variables in the PCA were total milk yield per lactation (MY), milk yield adjusted to 305 days (MY305), lactation length (LL), and proportion of H and Z breeding. This analysis reduced the size of the sample space from the original five variables to two principal components (PCs) that together explained 89.4 % of the total variation. MY, MY305, LL, and genotypic proportion of H all contributed positively to PC1. The genotypic proportion of Z contributed negatively, which established a contrast between H and Z. Further cluster analysis identified two distinct groups when considering production performance and genotype of the animals. The high-performance group was predominantly Holstein breeding, while the lower performing group consisted mostly of Zebu. Under the environmental and management conditions in which this research was conducted, the best performances for the traits considered were achieved from cows whose genotypic proportion was between 38.0 and 94.0 % Holstein breeding.

Morphology, sociality, and ecology: can morphology predict pairing behavior in coral reef fishes?

NASA Astrophysics Data System (ADS)

Brandl, S. J.; Bellwood, D. R.

2013-09-01

Morphology can contain valuable information about the ecological performance of reef fishes, but it has rarely been used in combination with social traits. Social behavior is known to influence the ecological role of fishes; however, the ecological basis for pairing in reef fishes is not well understood. Field observations of 2,753 individuals, in 47 species in six families of biting reef fishes (Acanthuridae, Chaetodontidae, Kyphosidae, Labridae, Pomacanthidae, Siganidae), were used in combination with six morphological measurements, to examine the morphology of fishes in different social systems. A principal components analysis of morphological traits segregated species with high proportions of pairing individuals from non-pairing species along principal component 1, explaining 40.8 % of the variation. Pairing species were characterized by large eyes, concave foreheads, pointed snouts, deep bodies, and small maximum sizes. There was a significant positive relationship between these morphological traits (i.e., scores on PC1) and the prevalence of pairing within the Chaetodontidae ( r 2 = 0.59; P = 0.026), Siganidae ( r 2 = 0.72; P = 0.004), and Acanthuridae ( r 2 = 0.82; P < 0.001). This was consistent when traits were corrected for phylogenetic effects. No pattern was evident in the scarine Labridae ( r 2 = 0.15; P = 0.17). The morphological characteristics found among pairing species suggest that pairing species share common ecological traits, including foraging for small prey items in micro-topographically complex environments such as reef crevices. These ecological traits may have played a role in the evolution of pairing behavior and subsequently led to the development of reproductive patterns based on monogamy.

Origin and z-distribution of Galactic diffuse [C II] emission

NASA Astrophysics Data System (ADS)

Velusamy, T.; Langer, W. D.

2014-12-01

Context. The [C ii] emission is an important probe of star formation in the Galaxy and in external galaxies. The GOT C+ survey and its follow up observations of spectrally resolved 1.9 THz [C ii] emission using Herschel HIFI provides the data needed to quantify the Galactic interstellar [C ii] gas components as tracers of star formation. Aims: We determine the source of the diffuse [C ii] emission by studying its spatial (radial and vertical) distributions by separating and evaluating the fractions of [C ii] and CO emissions in the Galactic ISM gas components. Methods: We used the HIFI [C ii] Galactic survey (GOT C+), along with ancillary H i, 12CO, 13CO, and C18O data toward 354 lines of sight, and several HIFI [C ii] and [C i] position-velocity maps. We quantified the emission in each spectral line profile by evaluating the intensities in 3 km s-1 wide velocity bins, "spaxels". Using the detection of [C ii] with CO or [C i], we separated the dense and diffuse gas components. We derived 2D Galactic disk maps using the spaxel velocities for kinematic distances. We separated the warm and cold H2 gases by comparing CO emissions with and without associated [C ii]. Results: We find evidence of widespread diffuse [C ii] emission with a z-scale distribution larger than that for the total [C ii] or CO. The diffuse [C ii] emission consists of (i) diffuse molecular (CO-faint) H2 clouds and (ii) diffuse H i clouds and/or WIM. In the inner Galaxy we find a lack of [C ii] detections in a majority (~62%) of H i spaxels and show that the diffuse component primarily comes from the WIM (~21%) and that the H i gas is not a major contributor to the diffuse component (~6%). The warm-H2 radial profile shows an excess in the range 4 to 7 kpc, consistent with enhanced star formation there. Conclusions: We derive, for the first time, the 2D [C ii] spatial distribution in the plane and the z-distributions of the individual [C ii] gas component. From the GOT C+ detections we estimate the fractional [C ii] emission tracing (i) H2 gas in dense and diffuse molecular clouds as ~48% and ~14%, respectively, (ii) in the H i gas ~18%, and (iii) in the WIM ~21%. Including non-detections from H i increases the [C ii] in H i to ~27%. The z-scale distributions FWHM from smallest to largest are [C ii] sources with CO, ~130 pc, (CO-faint) diffuse H2 gas, ~200 pc, and the diffuse H i and WIM, ~330 pc. When combined with [C ii], CO observations probe the warm-H2 gas, tracing star formation. Herschel is an ESA space observatory with science instruments provided by European-led Principal Investigator consortia and with important participation from NASA.

Wavelet decomposition based principal component analysis for face recognition using MATLAB

NASA Astrophysics Data System (ADS)

Sharma, Mahesh Kumar; Sharma, Shashikant; Leeprechanon, Nopbhorn; Ranjan, Aashish

2016-03-01

For the realization of face recognition systems in the static as well as in the real time frame, algorithms such as principal component analysis, independent component analysis, linear discriminate analysis, neural networks and genetic algorithms are used for decades. This paper discusses an approach which is a wavelet decomposition based principal component analysis for face recognition. Principal component analysis is chosen over other algorithms due to its relative simplicity, efficiency, and robustness features. The term face recognition stands for identifying a person from his facial gestures and having resemblance with factor analysis in some sense, i.e. extraction of the principal component of an image. Principal component analysis is subjected to some drawbacks, mainly the poor discriminatory power and the large computational load in finding eigenvectors, in particular. These drawbacks can be greatly reduced by combining both wavelet transform decomposition for feature extraction and principal component analysis for pattern representation and classification together, by analyzing the facial gestures into space and time domain, where, frequency and time are used interchangeably. From the experimental results, it is envisaged that this face recognition method has made a significant percentage improvement in recognition rate as well as having a better computational efficiency.

Assessing Wetland Hydroperiod and Soil Moisture With Remote Sensing: A Demonstration for the NASA Plum Brook Station Year 2

NASA Technical Reports Server (NTRS)

Brooks, Colin; Bourgeau-Chavez, Laura; Endres, Sarah; Battaglia, Michael; Shuchman, Robert

2015-01-01

Primary Goal: Assist with the evaluation and measuring of wetlands hydroperiod at the PlumBrook Station using multi-source remote sensing data as part of a larger effort on projecting climate change-related impacts on the station's wetland ecosystems. MTRI expanded on the multi-source remote sensing capabilities to help estimate and measure hydroperiod and the relative soil moisture of wetlands at NASA's Plum Brook Station. Multi-source remote sensing capabilities are useful in estimating and measuring hydroperiod and relative soil moisture of wetlands. This is important as a changing regional climate has several potential risks for wetland ecosystem function. The year two analysis built on the first year of the project by acquiring and analyzing remote sensing data for additional dates and types of imagery, combined with focused field work. Five deliverables were planned and completed: 1) Show the relative length of hydroperiod using available remote sensing datasets 2) Date linked table of wetlands extent over time for all feasible non-forested wetlands 3) Utilize LIDAR data to measure topographic height above sea level of all wetlands, wetland to catchment area radio, slope of wetlands, and other useful variables 4) A demonstration of how analyzed results from multiple remote sensing data sources can help with wetlands vulnerability assessment 5) A MTRI style report summarizing year 2 results. This report serves as a descriptive summary of our completion of these our deliverables. Additionally, two formal meetings were held with Larry Liou and Amanda Sprinzl to provide project updates and receive direction on outputs. These were held on 2/26/15 and 9/17/15 at the Plum Brook Station. Principal Component Analysis (PCA) is a multivariate statistical technique used to identify dominant spatial and temporal backscatter signatures. PCA reduces the information contained in the temporal dataset to the first few new Principal Component (PC) images. Some advantages of PCA include the ability to filter out temporal autocorrelation and reduce speckle to the higher order PC images. A PCA was performed using ERDAS Imagine on a time series of PALSAR dates. Hydroperiod maps were created by separating the PALSAR dates into two date ranges, 2006-2008 and 2010, and performing an unsupervised classification on the PCAs.

Performance evaluation of a hybrid-passive landfill leachate treatment system using multivariate statistical techniques

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

Wallace, Jack, E-mail: jack.wallace@ce.queensu.ca; Champagne, Pascale, E-mail: champagne@civil.queensu.ca; Monnier, Anne-Charlotte, E-mail: anne-charlotte.monnier@insa-lyon.fr

Highlights: • Performance of a hybrid passive landfill leachate treatment system was evaluated. • 33 Water chemistry parameters were sampled for 21 months and statistically analyzed. • Parameters were strongly linked and explained most (>40%) of the variation in data. • Alkalinity, ammonia, COD, heavy metals, and iron were criteria for performance. • Eight other parameters were key in modeling system dynamics and criteria. - Abstract: A pilot-scale hybrid-passive treatment system operated at the Merrick Landfill in North Bay, Ontario, Canada, treats municipal landfill leachate and provides for subsequent natural attenuation. Collected leachate is directed to a hybrid-passive treatment system,more » followed by controlled release to a natural attenuation zone before entering the nearby Little Sturgeon River. The study presents a comprehensive evaluation of the performance of the system using multivariate statistical techniques to determine the interactions between parameters, major pollutants in the leachate, and the biological and chemical processes occurring in the system. Five parameters (ammonia, alkalinity, chemical oxygen demand (COD), “heavy” metals of interest, with atomic weights above calcium, and iron) were set as criteria for the evaluation of system performance based on their toxicity to aquatic ecosystems and importance in treatment with respect to discharge regulations. System data for a full range of water quality parameters over a 21-month period were analyzed using principal components analysis (PCA), as well as principal components (PC) and partial least squares (PLS) regressions. PCA indicated a high degree of association for most parameters with the first PC, which explained a high percentage (>40%) of the variation in the data, suggesting strong statistical relationships among most of the parameters in the system. Regression analyses identified 8 parameters (set as independent variables) that were most frequently retained for modeling the five criteria parameters (set as dependent variables), on a statistically significant level: conductivity, dissolved oxygen (DO), nitrite (NO{sub 2}{sup −}), organic nitrogen (N), oxidation reduction potential (ORP), pH, sulfate and total volatile solids (TVS). The criteria parameters and the significant explanatory parameters were most important in modeling the dynamics of the passive treatment system during the study period. Such techniques and procedures were found to be highly valuable and could be applied to other sites to determine parameters of interest in similar naturalized engineered systems.« less

Effects of castration and time-on-feed on Mertolenga breed beef quality.

PubMed

Monteiro, A C G; Navas, D R; Lemos, J P C

2014-04-01

Physicochemical characteristics were determined in the longissimus lumborum muscle, after 8 days of ageing of steers (n=12) and bulls (n=12) from Mertolenga breed slaughtered directly from pasture (day 0) or after a finishing period of 50, 100 and 150 days in a feed-lot facility. Bulls and steers presented similar live weight (averaging 388 kg), carcass weight (CW; averaging 213 kg), dressing percentage (averaging 60%), carcass fatness (11.9% CW) and carcass fat thickness (averaging 3.03 mm). Live weight, CW, carcass fatness and fat thickness increased along time-on-feed. Gender only had a negligible effect on meat characteristics, with b and h being the only parameters of colour affected by gender, also presenting a significant interaction gender × time-on-feed. Nevertheless, both the genders presented a high-quality grade concerning tenderness (Warner-Bratzler shear force (WBSF)). L increased until 50 days on feed and decreased afterwards, whereas a and C values increased along time-on-feed. Pigment content was also affected by time-on-feed and showed a gender × time-on-feed interaction. Beef colour became darker and redder along time-on-feed, but still in a colour range highly acceptable by Portuguese consumers. Despite the increase in intramuscular fat and myofibrillar fragmentation index, as well as the decrease in collagen content of steers and bulls along time-on-feed, it did not affect the tenderness/hardness, indicating a small effect of time-on-feed in meat characteristics. Despite only small differences in carcass characteristics and meat-quality parameters that have been noticed along time-on-feed, those differences were only significant after 100 days on feed. Principal component analysis (PCA) was performed. The first PC axis (39.6% of the total variance) included colour variables a, b and C, and carcass fatness, fat thickness, CW and live weight, whereas the second one (12.7% of the total variance) included h, cooking losses and dressing-out. The principal component (PC) analysis confirmed the lack of differences between bulls and steers and indicates a differentiation of the first two periods of feeding (0 and 50 days on feed) from the two latter (100 and 150 days on feed) periods of feeding.

Sounds Scary? Lack of Habituation following the Presentation of Novel Sounds

PubMed Central

Biedenweg, Tine A.; Parsons, Michael H.; Fleming, Patricia A.; Blumstein, Daniel T.

2011-01-01

Background Animals typically show less habituation to biologically meaningful sounds than to novel signals. We might therefore expect that acoustic deterrents should be based on natural sounds. Methodology We investigated responses by western grey kangaroos (Macropus fulignosus) towards playback of natural sounds (alarm foot stomps and Australian raven (Corvus coronoides) calls) and artificial sounds (faux snake hiss and bull whip crack). We then increased rate of presentation to examine whether animals would habituate. Finally, we varied frequency of playback to investigate optimal rates of delivery. Principal Findings Nine behaviors clustered into five Principal Components. PC factors 1 and 2 (animals alert or looking, or hopping and moving out of area) accounted for 36% of variance. PC factor 3 (eating cessation, taking flight, movement out of area) accounted for 13% of variance. Factors 4 and 5 (relaxing, grooming and walking; 12 and 11% of variation, respectively) discontinued upon playback. The whip crack was most evocative; eating was reduced from 75% of time spent prior to playback to 6% following playback (post alarm stomp: 32%, raven call: 49%, hiss: 75%). Additionally, 24% of individuals took flight and moved out of area (50 m radius) in response to the whip crack (foot stomp: 0%, raven call: 8% and 4%, hiss: 6%). Increasing rate of presentation (12x/min ×2 min) caused 71% of animals to move out of the area. Conclusions/Significance The bull whip crack, an artificial sound, was as effective as the alarm stomp at eliciting aversive behaviors. Kangaroos did not fully habituate despite hearing the signal up to 20x/min. Highest rates of playback did not elicit the greatest responses, suggesting that ‘more is not always better’. Ultimately, by utilizing both artificial and biological sounds, predictability may be masked or offset, so that habituation is delayed and more effective deterrents may be produced. PMID:21267451

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

The Relation between Factor Score Estimates, Image Scores, and Principal Component Scores

ERIC Educational Resources Information Center

Velicer, Wayne F.

1976-01-01

Investigates the relation between factor score estimates, principal component scores, and image scores. The three methods compared are maximum likelihood factor analysis, principal component analysis, and a variant of rescaled image analysis. (RC)

The Butterflies of Principal Components: A Case of Ultrafine-Grained Polyphase Units

NASA Astrophysics Data System (ADS)

Rietmeijer, F. J. M.

1996-03-01

Dusts in the accretion regions of chondritic interplanetary dust particles [IDPs] consisted of three principal components: carbonaceous units [CUs], carbon-bearing chondritic units [GUs] and carbon-free silicate units [PUs]. Among others, differences among chondritic IDP morphologies and variable bulk C/Si ratios reflect variable mixtures of principal components. The spherical shapes of the initially amorphous principal components remain visible in many chondritic porous IDPs but fusion was documented for CUs, GUs and PUs. The PUs occur as coarse- and ultrafine-grained units that include so called GEMS. Spherical principal components preserved in an IDP as recognisable textural units have unique proporties with important implications for their petrological evolution from pre-accretion processing to protoplanet alteration and dynamic pyrometamorphism. Throughout their lifetime the units behaved as closed-systems without chemical exchange with other units. This behaviour is reflected in their mineralogies while the bulk compositions of principal components define the environments wherein they were formed.

INTRA-AGGREGATE MASS TRANSPORT-LIMITED BIOAVAILABILITY OF POLYCYCLIC AROMATIC HYDROCARBONS TO MYCOBACTERIUM STRAIN PC01. (R825303)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

EFFECT OF THE IRON CHELATOR DESFERRIOXAMINE ON MANGANESE-INDUCED TOXICITY OF RAT PHEOCHROMOCYTOMA (PC12) CELLS. (R826248)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Assessment of Cr, Ni and Pb Pollution in Rural Agricultural Soils of Tonalite-Trondjhemite Series in Central India.

PubMed

Shukla, Kriti; Kumar, Bijendra; Agrawal, Rahul; Priyanka, Kumari; Venkatesh, Madavi; Anshumali

2017-06-01

Chromium (Cr), nickel (Ni) and lead (Pb) contamination was investigated in wheat cultivated rain-fed and irrigated rural agricultural soils (n = 31) of Tonalite-Trondjhemite Series in Central India. The soil sampling was carried out by using stratified random sampling method. The mean concentrations of Cr, Ni and Pb were 54.8, 38.1 and 68.9 mg/kg, respectively. The average values of enrichment factor (EF), geoaccumulation index (I geo ) and contamination factor (CF) followed the order as: Pb > Ni > Cr. Distribution patterns of soil parent material and weathering processes govern mineral enrichments, irrespective of rainfed or irrigated agricultural practices. Principal component analysis (PCA) showed strong loading of Cr and Ni (PC1) and Pb and clay (PC3). The strong loading on Cr and Ni indicates soils are originating from basic and volcanic rocks in the study area. The strong loading of Pb and clay indicates Pb is strongly adsorbed on clay minerals and Fe-oxides. The cancer risk (CR) index showed negligible carcinogenic risk to the residing population. However, hazard index (HI) values for children exceed the safe limit (HI > 1) for Cr and Pb. Spatial distribution of pollution load index suggest highest pollution in the northeastern part of the district. The study revealed that geogenically enriched soils of the area are suitable for agricultural activities under present conditions.

Difference in tree growth responses to climate at the upper treeline: Qilian Juniper in the Anyemaqen Mountains.

PubMed

Peng, Jianfeng; Gou, Xiaohua; Chen, Fahu; Li, Jinbao; Liu, Puxing; Zhang, Yong; Fang, Keyan

2008-08-01

Three ring-width chronologies were developed from Qilian Juniper (Sabina przewalskii Kom.) at the upper treeline along a west-east gradient in the Anyemaqen Mountains. Most chronological statistics, except for mean sensitivity (MS), decreased from west to east. The first principal component (PC1) loadings indicated that stands in a similar climate condition were most important to the variability of radial growth. PC2 loadings decreased from west to east, suggesting the difference of tree-growth between eastern and western Anyemaqen Mountains. Correlations between standard chronologies and climatic factors revealed different climatic influences on radial growth along a west-east gradient in the study area. Temperature of warm season (July-August) was important to the radial growth at the upper treeline in the whole study area. Precipitation of current May was an important limiting factor of tree growth only in the western (drier) upper treeline, whereas precipitation of current September limited tree growth in the eastern (wetter) upper treeline. Response function analysis results showed that there were regional differences between tree growth and climatic factors in various sampling sites of the whole study area. Temperature and precipitation were the important factors influencing tree growth in western (drier) upper treeline. However, tree growth was greatly limited by temperature at the upper treeline in the middle area, and was more limited by precipitation than temperature in the eastern (wetter) upper treeline.

In vivo Raman spectroscopy of human uterine cervix: exploring the utility of vagina as an internal control

NASA Astrophysics Data System (ADS)

Shaikh, Rubina; Dora, Tapas Kumar; Chopra, Supriya; Maheshwari, Amita; Kedar K., Deodhar; Bharat, Rekhi; Krishna, C. Murali

2014-08-01

In vivo Raman spectroscopy is being projected as a new, noninvasive method for cervical cancer diagnosis. In most of the reported studies, normal areas in the cancerous cervix were used as control. However, in the Indian subcontinent, the majority of cervical cancers are detected at advanced stages, leaving no normal sites for acquiring control spectra. Moreover, vagina and ectocervix are reported to have similar biochemical composition. Thus, in the present study, we have evaluated the feasibility of classifying normal and cancerous conditions in the Indian population and we have also explored the utility of the vagina as an internal control. A total of 228 normal and 181 tumor in vivo Raman spectra were acquired from 93 subjects under clinical supervision. The spectral features in normal conditions suggest the presence of collagen, while DNA and noncollagenous proteins were abundant in tumors. Principal-component linear discriminant analysis (PC-LDA) yielded 97% classification efficiency between normal and tumor groups. An analysis of a normal cervix and vaginal controls of cancerous and noncancerous subjects suggests similar spectral features between these groups. PC-LDA of tumor, normal cervix, and vaginal controls further support the utility of the vagina as an internal control. Overall, findings of the study corroborate with earlier studies and facilitate objective, noninvasive, and rapid Raman spectroscopic-based screening/diagnosis of cervical cancers.

Biological and mechanical interplay at the Macro- and Microscales Modulates the Cell-Niche Fate.

PubMed

Sarig, Udi; Sarig, Hadar; Gora, Aleksander; Krishnamoorthi, Muthu Kumar; Au-Yeung, Gigi Chi Ting; de-Berardinis, Elio; Chaw, Su Yin; Mhaisalkar, Priyadarshini; Bogireddi, Hanumakumar; Ramakrishna, Seeram; Boey, Freddy Yin Chiang; Venkatraman, Subbu S; Machluf, Marcelle

2018-03-02

Tissue development, regeneration, or de-novo tissue engineering in-vitro, are based on reciprocal cell-niche interactions. Early tissue formation mechanisms, however, remain largely unknown given complex in-vivo multifactoriality, and limited tools to effectively characterize and correlate specific micro-scaled bio-mechanical interplay. We developed a unique model system, based on decellularized porcine cardiac extracellular matrices (pcECMs)-as representative natural soft-tissue biomaterial-to study a spectrum of common cell-niche interactions. Model monocultures and 1:1 co-cultures on the pcECM of human umbilical vein endothelial cells (HUVECs) and human mesenchymal stem cells (hMSCs) were mechano-biologically characterized using macro- (Instron), and micro- (AFM) mechanical testing, histology, SEM and molecular biology aspects using RT-PCR arrays. The obtained data was analyzed using developed statistics, principal component and gene-set analyses tools. Our results indicated biomechanical cell-type dependency, bi-modal elasticity distributions at the micron cell-ECM interaction level, and corresponding differing gene expression profiles. We further show that hMSCs remodel the ECM, HUVECs enable ECM tissue-specific recognition, and their co-cultures synergistically contribute to tissue integration-mimicking conserved developmental pathways. We also suggest novel quantifiable measures as indicators of tissue assembly and integration. This work may benefit basic and translational research in materials science, developmental biology, tissue engineering, regenerative medicine and cancer biomechanics.

In vivo Raman spectroscopy of human uterine cervix: exploring the utility of vagina as an internal control.

PubMed

Shaikh, Rubina; Dora, Tapas Kumar; Chopra, Supriya; Maheshwari, Amita; Kedar K, Deodhar; Bharat, Rekhi; Krishna, C Murali

2014-08-01

In vivo Raman spectroscopy is being projected as a new, noninvasive method for cervical cancer diagnosis. In most of the reported studies, normal areas in the cancerous cervix were used as control. However, in the Indian subcontinent, the majority of cervical cancers are detected at advanced stages, leaving no normal sites for acquiring control spectra. Moreover, vagina and ectocervix are reported to have similar biochemical composition. Thus, in the present study, we have evaluated the feasibility of classifying normal and cancerous conditions in the Indian population and we have also explored the utility of the vagina as an internal control. A total of 228 normal and 181 tumor in vivo Raman spectra were acquired from 93 subjects under clinical supervision. The spectral features in normal conditions suggest the presence of collagen, while DNA and noncollagenous proteins were abundant in tumors. Principal-component linear discriminant analysis (PC-LDA) yielded 97% classification efficiency between normal and tumor groups. An analysis of a normal cervix and vaginal controls of cancerous and noncancerous subjects suggests similar spectral features between these groups. PC-LDA of tumor, normal cervix, and vaginal controls further support the utility of the vagina as an internal control. Overall, findings of the study corroborate with earlier studies and facilitate objective, noninvasive, and rapid Raman spectroscopic-based screening/diagnosis of cervical cancers.

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.

The influence of iliotibial band syndrome history on running biomechanics examined via principal components analysis.

PubMed

Foch, Eric; Milner, Clare E

2014-01-03

Iliotibial band syndrome (ITBS) is a common knee overuse injury among female runners. Atypical discrete trunk and lower extremity biomechanics during running may be associated with the etiology of ITBS. Examining discrete data points limits the interpretation of a waveform to a single value. Characterizing entire kinematic and kinetic waveforms may provide additional insight into biomechanical factors associated with ITBS. Therefore, the purpose of this cross-sectional investigation was to determine whether female runners with previous ITBS exhibited differences in kinematics and kinetics compared to controls using a principal components analysis (PCA) approach. Forty participants comprised two groups: previous ITBS and controls. Principal component scores were retained for the first three principal components and were analyzed using independent t-tests. The retained principal components accounted for 93-99% of the total variance within each waveform. Runners with previous ITBS exhibited low principal component one scores for frontal plane hip angle. Principal component one accounted for the overall magnitude in hip adduction which indicated that runners with previous ITBS assumed less hip adduction throughout stance. No differences in the remaining retained principal component scores for the waveforms were detected among groups. A smaller hip adduction angle throughout the stance phase of running may be a compensatory strategy to limit iliotibial band strain. This running strategy may have persisted after ITBS symptoms subsided. © 2013 Published by Elsevier Ltd.

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...

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.

Selenium and 17 other largely essential and toxic metals in muscle and organ meats of Red Deer (Cervus elaphus)--consequences to human health.

PubMed

Jarzyńska, Grażyna; Falandysz, Jerzy

2011-07-01

Concentrations, composition and interrelationships of selenium and metallic elements (Ag, Ba, Cd, Co, Cr, Cs, Cu, Ga, Mn, Mo, Pb, Rb, Sb, Sr, Tl, V and Zn) have been examined in muscle and organ meats of Red Deer hunted in Poland. The analytical data obtained were also discussed in terms of Se supplementation and deficit to Deer as well as the benefits and risk to humans associated with the essential and toxic metals intake resulting from consumption of Deer meat and products. These elements were determined in 20 adult animals of both sexes that were obtained in the 2000/2001 hunting season from Warmia and Mazury in the north-eastern part of Poland. The whole kidneys contained Ba, Cd, Cr, Ga, Pb, Se, Sr and Tl at statistically greater concentrations than liver or muscle tissue from the same animal. Liver showed statistically greater concentrations of Ag, Co, Cu, Mn and Mo than kidneys or muscle tissue, and muscle tissue was richer in Zn, when compared to the kidneys or liver. Cs and Rb were similarly distributed between all three tissue types, while V was less abundant in liver than kidneys or muscle tissue. There were significant associations between some metallic elements retained in Red Deer demonstrated by Principal Component Analysis (PCA) of the data set. In organ and muscle meats (kidneys, liver and muscle tissue considered together) the first principal component (PC1) was strongly influenced by positively correlated variables describing Se, Ba and Cd and negatively correlated variables describing Ag, Co, Cs, Mn, Pb, Tl and V; PC2, respectively, by Cu, Mn and Mo (+) and Zn (-); PC3 by Ga (+) and PC4 by Sb (+). Selenium occurred in muscle tissue, liver and kidneys at median concentrations of 0.13, 0.19 and 4.0mg/g dry weight, respectively. These values can be defined as marginally deficient (< 0.6mg Se/kg liver dw) or satisfactory (≤ 3.0mg Se/kg kidneys dw) for the amount required to maintain the Deer's body condition and health, depending on the criterion for supplementation used. In terms of human nutritional needs, a relatively high selenium content of kidneys can be beneficial. The muscle meat, liver and kidneys of Red Deer can be considered as a very good source of essential Co, Cr, Cu, Mo, Mn, Se and Zn in the human diet. Lead is generally considered as toxic, and the concentrations found in Red Deer (via the food chain intake) were well below the European Union tolerance limit. Pb from the lead bullets can always create food hygienic problem, if not well recognized during sanitary inspection, and this was noted for one muscle meat sample in this study (5% surveyed). There is no tolerance limit of Cd in game animal meats. The median values of Cd noted in fresh muscle tissue, liver and whole kidneys were 0.07, 0.18, and 3.3mg/kg wet weight, respectively. Cd exists as a chemical element present at trace levels in plants and mushrooms in Deer's food chain in background (uncontaminated) areas. When these are consumed by the Deer, the amount of Cd sequestered with metallothioneins and retained in the organ and muscle meat in this study is low enough to be considered safe for human consumption. Copyright © 2011 Elsevier Ltd. All rights reserved.

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.

In-line solid state prediction during pharmaceutical hot-melt extrusion in a 12 mm twin screw extruder using Raman spectroscopy.

PubMed

Saerens, Lien; Ghanam, Dima; Raemdonck, Cedric; Francois, Kjell; Manz, Jürgen; Krüger, Rainer; Krüger, Susan; Vervaet, Chris; Remon, Jean Paul; De Beer, Thomas

2014-08-01

The aim of this research was to use Raman spectroscopy for the in-line monitoring of the solid state of materials during pharmaceutical hot-melt extrusion in the die head of a 12 mm (development scale) twin-screw extruder during formulation development. A full factorial (mixed) design was generated to determine the influence of variations in concentration of Celecoxib (CEL) in Eudragit® E PO, three different screw configurations and varying barrel temperature profiles on the solid state, 'melt temperature' and die pressure of continuously produced extrudates in real-time. Off-line XRD and DSC analysis were used to evaluate the suitability of Raman spectroscopy for solid state predictions. First, principal component analysis (PCA) was performed on all in-line collected Raman spectra from the experimental design. The resulting PC 1 versus PC 2 scores plot showed clustering according to solid state of the extrudates, and two classes, one class where crystalline CEL is still present and a second class where no crystalline CEL was detected, were found. Then, a soft independent modelling of class analogy (SIMCA) model was developed, by modelling these two classes separately by disjoint PCA models. These two separate PCA models were then used for the classification of new produced extrudates and allowed distinction between glassy solid solutions of CEL and crystalline dispersions of CEL. All extrudates were classified similarly by Raman spectroscopy, XRD and DSC measurements, with exception of the extrudates with a 30% CEL concentration extruded at 130 °C. The Raman spectra of these experiments showed bands which were sharper than the amorphous spectra, but broader than the crystalline spectra, indicating the presence of CEL that has dissolved into the matrix and CEL in its crystalline state. XRD and DSC measurements did not detect this. Modifications in the screw configuration did not affect the solid state and did not have an effect on the solid state prediction of new produced extrudates. Secondly, the influence of variations in die pressure on the Raman spectra was examined. The applied drug concentration, processing temperature and feeder performance influence the die pressure, which is reflected in the Raman spectra as a change in spectral intensity. When applying PCA on the raw spectra from the experimental design, the first principal component describes the influence of die pressure on the spectra, which was seen as a decrease in Raman intensity of the whole spectrum when the pressure in the sample increased. Clustering according to processing temperature was found, although the temperature in the die remained constant, indicating that a difference in viscosity, resulting in a changed die pressure, was detected. When the feeder was stopped, the score values of the first principal component almost simultaneously decreased, and only stabilized once the die pressure became stable. Since Raman spectra collected in the extrusion die are influenced by changes in die pressure, disturbances upstream of the extrusion process can be observed and identified in the Raman measurements. Copyright © 2014 Elsevier B.V. All rights reserved.

[Development of a measurement of intellectual capital for hospital nursing organizations].

PubMed

Kim, Eun A; Jang, Keum Seong

2011-02-01

This study was done to develop an instrument for measuring intellectual capital and assess its validity and reliability in identifying the components, human capital, structure capital and customer capital of intellectual capital in hospital nursing organizations. The participants were 950 regular clinical nurses who had worked for over 13 months in 7 medical hospitals including 4 national university hospitals and 3 private university hospitals. The data were collected through a questionnaire survey done from July 2 to August 25, 2009. Data from 906 nurses were used for the final analysis. Data were analyzed using descriptive statistics, Cronbach's alpha coefficients, item analysis, factor analysis (principal component analysis, Varimax rotation) with the SPSS PC+ 17.0 for Windows program. Developing the instrument for measuring intellectual capital in hospital nursing organizations involved a literature review, development of preliminary items, and verification of validity and reliability. The final instrument was in a self-report form on a 5-point Likert scale. There were 29 items on human capital (5 domains), 21 items on customer capital (4 domains), 26 items on structure capital (4 domains). The results of this study may be useful to assess the levels of intellectual capital of hospital nursing organizations.

Use of visible and near-infrared spectroscopy to predict pork longissimus lean color stability.

PubMed

King, D A; Shackelford, S D; Wheeler, T L

2011-12-01

This study evaluated the use of visible and near-infrared (VISNIR) spectroscopy to predict lean color stability in pork loin chops. Spectra were collected immediately after and approximately 1 h after rib removal on 1,208 loins. Loins were aged for 14 d before a 2.54-cm chop was placed in simulated retail display. Spectra were collected on aged loins immediately after removal from the vacuum package and on chops 10 min after cutting. Instrumental color measurements [L*, a*, b*, hue angle, chroma, and E (overall color change)] were determined on d 0, 1, 7, 11, and 14 of display. Principal components analysis of display d 0 and 14 values of these traits identified a factor (first principal component; PC1) explaining 67% of the variance that was related to color change. Partial least squares regression was used to develop 3 models to predict PC1 values by using VISNIR spectra collected in the plant, on aged loins, and on chops. Loins with predicted PC1 values less than 0 were classified as having a stable color, whereas values greater than 0 were classified as having a labile lean color. Loins classified as stable by the in-plant model had smaller (P < 0.05) L* values than those classified as labile. Hue angle and ΔE values were less (P < 0.05) and a* and chroma values were greater (P < 0.05) after d 7 of display in loins predicted to have a stable color than in loins predicted to have a labile lean color. Similarly, chops from loins classified as stable using the aged loin model had smaller (P < 0.05) L* values than those from loins classified as labile. Furthermore, loins predicted to be stable had smaller (P < 0.05) hue angle and ΔE values and greater (P < 0.05) a* and chroma values after d 7 of display than did loins predicted to be labile. Results for the chop model were similar to those from the 2 loin models. Chops predicted to have a stable lean color had smaller (P < 0.05) L* values than did those predicted to have a labile lean color. Chops classified as stable had smaller (P < 0.05) hue angle and ΔE values and greater (P < 0.05) a* and chroma values after d 7 of display compared with chops classified as labile. All 3 models effectively segregated chops based on color stability, particularly with regard to redness. Regardless of the model being used, d 14 display values for a*, hue angle, and ΔE in loins classified as stable were similar to the d 7 values of loins classified as labile. Thus, these results suggest that VISNIR spectroscopy would be an effective technology for sorting pork loins with regard to lean color stability.

ACTIVATION OF ERK1 AND ERK2 IS REQUIRED FOR MANGANESE-INDUCED NEURITE OUTGROWTH IN RAT PHEOCHROMOCYTOMA (PC12) CELLS. (R826248)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

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.

Uncertainty quantification for personalized analyses of human proximal femurs.

PubMed

Wille, Hagen; Ruess, Martin; Rank, Ernst; Yosibash, Zohar

2016-02-29

Computational models for the personalized analysis of human femurs contain uncertainties in bone material properties and loads, which affect the simulation results. To quantify the influence we developed a probabilistic framework based on polynomial chaos (PC) that propagates stochastic input variables through any computational model. We considered a stochastic E-ρ relationship and a stochastic hip contact force, representing realistic variability of experimental data. Their influence on the prediction of principal strains (ϵ1 and ϵ3) was quantified for one human proximal femur, including sensitivity and reliability analysis. Large variabilities in the principal strain predictions were found in the cortical shell of the femoral neck, with coefficients of variation of ≈40%. Between 60 and 80% of the variance in ϵ1 and ϵ3 are attributable to the uncertainty in the E-ρ relationship, while ≈10% are caused by the load magnitude and 5-30% by the load direction. Principal strain directions were unaffected by material and loading uncertainties. The antero-superior and medial inferior sides of the neck exhibited the largest probabilities for tensile and compression failure, however all were very small (pf<0.001). In summary, uncertainty quantification with PC has been demonstrated to efficiently and accurately describe the influence of very different stochastic inputs, which increases the credibility and explanatory power of personalized analyses of human proximal femurs. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

Changes in the Indian summer monsoon intensity in Sri Lanka during the last 30 ky - A multiproxy record from a marine sediment core.

NASA Astrophysics Data System (ADS)

Ranasinghage, P. N.; Nanayakkara, N. U.; Kodithuwakku, S.; Siriwardana, S.; Luo, C.; Fenghua, Z.

2016-12-01

Indian monsoon plays a vital role in determining climate events happening in the Asian region. There is no sufficient work in Sri Lanka to fully understand how the summer monsoonal variability affected Sri Lanka during the quaternary. Sri Lanka is situated at an ideal location with a unique geography to isolate Indian summer monsoon record from iris counterpart, Indian winter monsoon. Therefore, this study was carried out to investigate its variability and understand the forcing factors. For this purpose a 1.82 m long gravity core, extracted from western continental shelf off Colombo, Sri Lanka by Shiyan 1 research vessel, was used. Particle size, chemical composition and colour reflectance were measured using laser particle size analyzer at 2 cm resolution, X-Ray Fluorescence spectrometer (XRF) at 2 cm resolution, and color spectrophotometer at 1 cm resolution respectively. Radio carbon dating of foraminifera tests by gas bench technique yielded the sediment age. Finally, principal component analysis (PCA) of XRF and color reflectance (DSR) data was performed to identify groups of correlating elements and mineralogical composition of sediments. Particle size results indicate that Increasing temperature and strengthening monsoonal rainfall after around 18000 yrs BP, at the end of last glacial period, enhanced chemical weathering over physical weathering. Proxies for terrestrial influx (XRF PC1, DSR PC1) and upwelling and nutrient supply driven marine productivity (XRF PC3 and DSR PC2) indicate that strengthening of summer monsoon started around 15000 yrs BP and maximized around 8000-10000 yrs BP after a short period of weakening during Younger Dryas (around 11000 yrs BP). The 8.2 cold event was recorded as a period of low terrestrial influx indicating weakening of rainfall. After that terrestrial input was low till around 2000 yrs BP indicating decrease in rainfall. However, marine productivity remained increasing throughout the Holocene indicating an increase in monsoonal driven upwelling. Authors recorded similar increase in monsoonal wind strength during the late Holocene, with no increase in rainfall in another sediment core extracted from the western continental shelf of Sri Lanka.

Microbial metabolites profile during in vitro human colonic fermentation of breakfast menus consumed by Mexican school children.

PubMed

Zamora-Gasga, Victor Manuel; Montalvo-González, Efigenia; Loarca-Piña, Guadalupe; Vázquez-Landaverde, Pedro Alberto; Tovar, Juscelino; Sáyago-Ayerdi, Sonia G

2017-07-01

The nutrition transition promotes the development of childhood obesity. Currently, Mexico is affected by this serious public health problem. The nutritional and functional characterization of a whole menu has a number of advantages over the study of single nutrients. Since breakfast is considered the most important meal of the day, this study aimed to evaluate the metabolite profile produced by in vitro human colonic fermentation of the isolated indigestible fraction (IF) from three different Mexican breakfast (M-B) menus (Modified "MM-B", traditional "TM-B", and alternative "AM-B"), previously identified as commonly consumed by Mexican schoolchildren in Nayarit State, Mexico. The M-B's consist of egg, corn tortilla, beans (higher in TM-B), sugar and chocolate powder (higher in AM-B) and milk, combined in different proportions. The IF in all breakfasts was about 4.7-5.6g/100g FW, with a relatively high content of protein (≈21%), which might have negative physiological implications. Fermentation of IF from TM-B resulted in the largest pH decrease after 72h (pH=6.07), with a low short chain fatty acid (SCFA) production (0.75 to 47.23mmol/L), but greater relative concentration of other fatty acids (FA) (C7, C8, C9). Besides, 55 volatile compounds were detected in the fermentation media by SPME-GC-MS and three principal components (PC) were identified. PC1 was influenced by SCFA production, low FA esters production (<8C), and low volatile organic acids production. PC2 was influenced by the decrease in pH and an increase in antioxidant capacity (p<0.0001). These results suggest that the production of different metabolites in the luminal medium may affect the pH and antioxidant status in the colon. Fermentation of IF from TM-M, assessed after 48 and 72h, showed the highest correlation for PC2; the metabolic pattern registered for this IF maybe considered beneficial. Copyright © 2017 Elsevier Ltd. All rights reserved.

Nonlinear Principal Components Analysis: Introduction and Application

ERIC Educational Resources Information Center

Linting, Marielle; Meulman, Jacqueline J.; Groenen, Patrick J. F.; van der Koojj, Anita J.

2007-01-01

The authors provide a didactic treatment of nonlinear (categorical) principal components analysis (PCA). This method is the nonlinear equivalent of standard PCA and reduces the observed variables to a number of uncorrelated principal components. The most important advantages of nonlinear over linear PCA are that it incorporates nominal and ordinal…

Selective principal component regression analysis of fluorescence hyperspectral image to assess aflatoxin contamination in corn

USDA-ARS?s Scientific Manuscript database

Selective principal component regression analysis (SPCR) uses a subset of the original image bands for principal component transformation and regression. For optimal band selection before the transformation, this paper used genetic algorithms (GA). In this case, the GA process used the regression co...

Similarities between principal components of protein dynamics and random diffusion

NASA Astrophysics Data System (ADS)

Hess, Berk

2000-12-01

Principal component analysis, also called essential dynamics, is a powerful tool for finding global, correlated motions in atomic simulations of macromolecules. It has become an established technique for analyzing molecular dynamics simulations of proteins. The first few principal components of simulations of large proteins often resemble cosines. We derive the principal components for high-dimensional random diffusion, which are almost perfect cosines. This resemblance between protein simulations and noise implies that for many proteins the time scales of current simulations are too short to obtain convergence of collective motions.

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.

Directly Reconstructing Principal Components of Heterogeneous Particles from Cryo-EM Images

PubMed Central

Tagare, Hemant D.; Kucukelbir, Alp; Sigworth, Fred J.; Wang, Hongwei; Rao, Murali

2015-01-01

Structural heterogeneity of particles can be investigated by their three-dimensional principal components. This paper addresses the question of whether, and with what algorithm, the three-dimensional principal components can be directly recovered from cryo-EM images. The first part of the paper extends the Fourier slice theorem to covariance functions showing that the three-dimensional covariance, and hence the principal components, of a heterogeneous particle can indeed be recovered from two-dimensional cryo-EM images. The second part of the paper proposes a practical algorithm for reconstructing the principal components directly from cryo-EM images without the intermediate step of calculating covariances. This algorithm is based on maximizing the (posterior) likelihood using the Expectation-Maximization algorithm. The last part of the paper applies this algorithm to simulated data and to two real cryo-EM data sets: a data set of the 70S ribosome with and without Elongation Factor-G (EF-G), and a data set of the inluenza virus RNA dependent RNA Polymerase (RdRP). The first principal component of the 70S ribosome data set reveals the expected conformational changes of the ribosome as the EF-G binds and unbinds. The first principal component of the RdRP data set reveals a conformational change in the two dimers of the RdRP. PMID:26049077

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.

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.

Turbulent flux variability and energy balance closure in the TERENO prealpine observatory: a hydrometeorological data analysis

NASA Astrophysics Data System (ADS)

Soltani, Mohsen; Mauder, Matthias; Laux, Patrick; Kunstmann, Harald

2017-07-01

The temporal multiscale variability of the surface heat fluxes is assessed by the analysis of the turbulent heat and moisture fluxes using the eddy covariance (EC) technique at the TERrestrial ENvironmental Observatories (TERENO) prealpine region. The fast and slow response variables from three EC sites located at Fendt, Rottenbuch, and Graswang are gathered for the period of 2013 to 2014. Here, the main goals are to characterize the multiscale variations and drivers of the turbulent fluxes, as well as to quantify the energy balance closure (EBC) and analyze the possible reasons for the lack of EBC at the EC sites. To achieve these goals, we conducted a principal component analysis (PCA) and a climatological turbulent flux footprint analysis. The results show significant differences in the mean diurnal variations of the sensible heat (H) and latent heat (LE) fluxes, because of variations in the solar radiation, precipitation patterns, soil moisture, and the vegetation fraction throughout the year. LE was the main consumer of net radiation. Based on the first principal component (PC1), the radiation and temperature components with a total mean contribution of 29.5 and 41.3%, respectively, were found to be the main drivers of the turbulent fluxes at the study EC sites. A general lack of EBC is observed, where the energy imbalance values amount 35, 44, and 35% at the Fendt, Rottenbuch, and Graswang sites, respectively. An average energy balance ratio (EBR) of 0.65 is obtained in the region. The best closure occurred in the afternoon peaking shortly before sunset with a different pattern and intensity between the study sites. The size and shape of the annual mean half-hourly turbulent flux footprint climatology was analyzed. On average, 80% of the flux footprint was emitted from a radius of approximately 250 m around the EC stations. Moreover, the overall shape of the flux footprints was in good agreement with the prevailing wind direction for all three TERENO EC sites.

Principal component analysis for the early detection of mastitis and lameness in dairy cows.

PubMed

Miekley, Bettina; Traulsen, Imke; Krieter, Joachim

2013-08-01

This investigation analysed the applicability of principal component analysis (PCA), a latent variable method, for the early detection of mastitis and lameness. Data used were recorded on the Karkendamm dairy research farm between August 2008 and December 2010. For mastitis and lameness detection, data of 338 and 315 cows in their first 200 d in milk were analysed, respectively. Mastitis as well as lameness were specified according to veterinary treatments. Diseases were defined as disease blocks. The different definitions used (two for mastitis, three for lameness) varied solely in the sequence length of the blocks. Only the days before the treatment were included in the blocks. Milk electrical conductivity, milk yield and feeding patterns (feed intake, number of feeding visits and time at the trough) were used for recognition of mastitis. Pedometer activity and feeding patterns were utilised for lameness detection. To develop and verify the PCA model, the mastitis and the lameness datasets were divided into training and test datasets. PCA extracted uncorrelated principle components (PC) by linear transformations of the raw data so that the first few PCs captured most of the variations in the original dataset. For process monitoring and disease detection, these resulting PCs were applied to the Hotelling's T 2 chart and to the residual control chart. The results show that block sensitivity of mastitis detection ranged from 77·4 to 83·3%, whilst specificity was around 76·7%. The error rates were around 98·9%. For lameness detection, the block sensitivity ranged from 73·8 to 87·8% while the obtained specificities were between 54·8 and 61·9%. The error rates varied from 87·8 to 89·2%. In conclusion, PCA seems to be not yet transferable into practical usage. Results could probably be improved if different traits and more informative sensor data are included in the analysis.

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.

An Introductory Application of Principal Components to Cricket Data

ERIC Educational Resources Information Center

Manage, Ananda B. W.; Scariano, Stephen M.

2013-01-01

Principal Component Analysis is widely used in applied multivariate data analysis, and this article shows how to motivate student interest in this topic using cricket sports data. Here, principal component analysis is successfully used to rank the cricket batsmen and bowlers who played in the 2012 Indian Premier League (IPL) competition. In…

Least Principal Components Analysis (LPCA): An Alternative to Regression Analysis.

ERIC Educational Resources Information Center

Olson, Jeffery E.

Often, all of the variables in a model are latent, random, or subject to measurement error, or there is not an obvious dependent variable. When any of these conditions exist, an appropriate method for estimating the linear relationships among the variables is Least Principal Components Analysis. Least Principal Components are robust, consistent,…

Identifying apple surface defects using principal components analysis and artifical neural networks

USDA-ARS?s Scientific Manuscript database

Artificial neural networks and principal components were used to detect surface defects on apples in near-infrared images. Neural networks were trained and tested on sets of principal components derived from columns of pixels from images of apples acquired at two wavelengths (740 nm and 950 nm). I...

Cost and utilization outcomes of patients receiving hospital-based palliative care consultation.

PubMed

Penrod, Joan D; Deb, Partha; Luhrs, Carol; Dellenbaugh, Cornelia; Zhu, Carolyn W; Hochman, Tsivia; Maciejewski, Matthew L; Granieri, Evelyn; Morrison, R Sean

2006-08-01

To compare per diem total direct, ancillary (laboratory and radiology) and pharmacy costs of palliative care (PC) compared to usual care (UC) patients during a terminal hospitalization; to examine the association between PC and ICU admission. Retrospective, observational cost analysis using a VA (payer) perspective. Two urban VA medical centers. Demographic and health characteristics of 314 veterans admitted during two years were obtained from VA administrative data. Hospital costs came from the VA cost accounting system. Generalized linear models (GLM) were estimated for total direct, ancillary and pharmacy costs. Predictors included patient age, principal diagnosis, comorbidity, whether patient stay was medical or surgical, site and whether the patient was seen by the palliative care consultation team. A probit regression was used to analyze probability of ICU admission. Propensity score matching was used to improve balance in observed covariates. PC patients were 42 percentage points (95% CI, -56% [corrected] to -31%) less likely to be admitted to ICU. Total direct costs per day were $239 (95% CI, -387 to -122) lower and ancillary costs were $98 (95% CI, -133 to -57) lower than costs for UC patients. There was no difference in pharmacy costs. The results were similar using propensity score matching. PC was associated with significantly lower likelihood of ICU use and lower inpatient costs compared to UC. Our findings coupled with those indicating better patient and family outcomes with PC suggest both a cost and quality incentive for hospitals to develop PC programs.

Leaving out control groups: an internal contrast analysis of gene expression profiles in atrial fibrillation patients ‐ A systems biology approach to clinical categorization

PubMed Central

Vanhoutte, Kurt; de Asmundis, Carlo; Francesconi, Anna; Figys1, Jurgen; Steurs, Griet; Boussy, Tim; Roos, Markus; Mueller, Andreas; Massimo, Lucio; Paparella, Gaetano; Van Caelenberg, Kristien; Chierchia, Gian Battista; Sarkozy, Andrea; Y Terradellas, Pedro Brugada; Zizi, Martin

2009-01-01

Atrial fibrillation (AF) is a frequent chronic dysrythmia with an incidence that increases with age (>40). Because of its medical and socio-economic impacts it is expected to become an increasing burden on most health care systems. AF is a multi-factorial disease for which the identification of subtypes is warranted. Novel approaches based on the broad concepts of systems biology may overcome the blurred notion of normal and pathological phenotype, which is inherent to high throughput molecular arrays analysis. Here we apply an internal contrast algorithm on AF patient data with an analytical focus on potential entry pathways into the disease. We used a RMA (Robust Multichip Average) normalized Affymetrix micro-array data set from 10 AF patients (geo_accession #GSE2240). Four series of probes were selected based on physiopathogenic links with AF entryways: apoptosis (remodeling), MAP kinase (cell remodeling), OXPHOS (ability to sustain hemodynamic workload) and glycolysis (ischemia). Annotated probe lists were polled with Bioconductor packages in R (version 2.7.1). Genetic profile contrasts were analysed with hierarchical clustering and principal component analysis. The analysis revealed distinct patient groups for all probe sets. A substantial part (54% till 67%) of the variance is explained in the first 2 principal components. Genes in PC1/2 with high discriminatory value were selected and analyzed in detail. We aim for reliable molecular stratification of AF. We show that stratification is possible based on physiologically relevant gene sets. Genes with high contrast value are likely to give pathophysiological insight into permanent AF subtypes. PMID:19255648

A principal component analysis of the relationship between the external body shape and internal skeleton for the upper body.

PubMed

Nerot, A; Skalli, W; Wang, X

2016-10-03

Recent progress in 3D scanning technologies allows easy access to 3D human body envelope. To create personalized human models with an articulated linkage for realistic re-posturing and motion analyses, an accurate estimation of internal skeleton points, including joint centers, from the external envelope is required. For this research project, 3D reconstructions of both internal skeleton and external envelope from low dose biplanar X-rays of 40 male adults were obtained. Using principal component analysis technique (PCA), a low-dimensional dataset was used to predict internal points of the upper body from the trunk envelope. A least squares method was used to find PC scores that fit the PCA-based model to the envelope of a new subject. To validate the proposed approach, estimated internal points were evaluated using a leave-one-out (LOO) procedure, i.e. successively considering each individual from our dataset as an extra-subject. In addition, different methods were proposed to reduce the variability in data and improve the performance of the PCA-based prediction. The best method was considered as the one providing the smallest errors between estimated and reference internal points with an average error of 8.3mm anterior-posteriorly, 6.7mm laterally and 6.5mm vertically. As the proposed approach relies on few or no bony landmarks, it could be easily applicable and generalizable to surface scans from any devices. Combined with automatic body scanning techniques, this study could potentially constitute a new step towards automatic generation of external/internal subject-specific manikins. Copyright © 2016 Elsevier Ltd. All rights reserved.

Simulations of cloudy hyperspectral infrared radiances using the HT-FRTC, a fast PC-based multipurpose radiative transfer code

NASA Astrophysics Data System (ADS)

Havemann, S.; Aumann, H. H.; Desouza-Machado, S. G.

2017-12-01

The HT-FRTC uses principal components which cover the spectrum at a very high spectral resolution allowing very fast line-by-line-like, hyperspectral and broadband simulations for satellite-based, airborne and ground-based sensors. Using data from IASI and from the Airborne Research Interferometer Evaluation System (ARIES) on board the FAAM BAE 146 aircraft, variational retrievals in principal component space with HT-FRTC as forward model have demonstrated that valuable information on temperature and humidity profiles and on the cirrus cloud properties can be obtained simultaneously. The NASA/JPL/UMBC cloudy RTM inter-comparison project has been working on a global dataset consisting of 7377 AIRS spectra. Initial simulations with HT-FRTC for this dataset have been promising. A next step taken here is to investigate how sensitive the results are with respect to different assumptions in the cloud modelling. One aspect of this is to study how assumptions about the microphysical and related optical properties of liquid/ice clouds impact the statistics of the agreement between model and observations. The other aspect is about the cloud overlap scheme. Different schemes have been tested (maximum, random, maximum random). As the computational cost increases linearly with the number of cloud columns, it will be investigated if there is an optimal number of columns beyond which there is little additional benefit to be gained. During daytime the high wave number channels of AIRS are affected by solar radiation. With full scattering calculations using a monochromatic version of the Edwards-Slingo radiation code the HT-FRTC can model solar radiation reasonably well, but full scattering calculations are relatively expensive. Pure Chou scaling on the other hand can not properly describe scattering of solar radiation by clouds and requires additional refinements.

Multivariate image analysis of laser-induced photothermal imaging used for detection of caries tooth

NASA Astrophysics Data System (ADS)

El-Sherif, Ashraf F.; Abdel Aziz, Wessam M.; El-Sharkawy, Yasser H.

2010-08-01

Time-resolved photothermal imaging has been investigated to characterize tooth for the purpose of discriminating between normal and caries areas of the hard tissue using thermal camera. Ultrasonic thermoelastic waves were generated in hard tissue by the absorption of fiber-coupled Q-switched Nd:YAG laser pulses operating at 1064 nm in conjunction with a laser-induced photothermal technique used to detect the thermal radiation waves for diagnosis of human tooth. The concepts behind the use of photo-thermal techniques for off-line detection of caries tooth features were presented by our group in earlier work. This paper illustrates the application of multivariate image analysis (MIA) techniques to detect the presence of caries tooth. MIA is used to rapidly detect the presence and quantity of common caries tooth features as they scanned by the high resolution color (RGB) thermal cameras. Multivariate principal component analysis is used to decompose the acquired three-channel tooth images into a two dimensional principal components (PC) space. Masking score point clusters in the score space and highlighting corresponding pixels in the image space of the two dominant PCs enables isolation of caries defect pixels based on contrast and color information. The technique provides a qualitative result that can be used for early stage caries tooth detection. The proposed technique can potentially be used on-line or real-time resolved to prescreen the existence of caries through vision based systems like real-time thermal camera. Experimental results on the large number of extracted teeth as well as one of the thermal image panoramas of the human teeth voltanteer are investigated and presented.

Application of multi-scale wavelet entropy and multi-resolution Volterra models for climatic downscaling

NASA Astrophysics Data System (ADS)

Sehgal, V.; Lakhanpal, A.; Maheswaran, R.; Khosa, R.; Sridhar, Venkataramana

2018-01-01

This study proposes a wavelet-based multi-resolution modeling approach for statistical downscaling of GCM variables to mean monthly precipitation for five locations at Krishna Basin, India. Climatic dataset from NCEP is used for training the proposed models (Jan.'69 to Dec.'94) and are applied to corresponding CanCM4 GCM variables to simulate precipitation for the validation (Jan.'95-Dec.'05) and forecast (Jan.'06-Dec.'35) periods. The observed precipitation data is obtained from the India Meteorological Department (IMD) gridded precipitation product at 0.25 degree spatial resolution. This paper proposes a novel Multi-Scale Wavelet Entropy (MWE) based approach for clustering climatic variables into suitable clusters using k-means methodology. Principal Component Analysis (PCA) is used to obtain the representative Principal Components (PC) explaining 90-95% variance for each cluster. A multi-resolution non-linear approach combining Discrete Wavelet Transform (DWT) and Second Order Volterra (SoV) is used to model the representative PCs to obtain the downscaled precipitation for each downscaling location (W-P-SoV model). The results establish that wavelet-based multi-resolution SoV models perform significantly better compared to the traditional Multiple Linear Regression (MLR) and Artificial Neural Networks (ANN) based frameworks. It is observed that the proposed MWE-based clustering and subsequent PCA, helps reduce the dimensionality of the input climatic variables, while capturing more variability compared to stand-alone k-means (no MWE). The proposed models perform better in estimating the number of precipitation events during the non-monsoon periods whereas the models with clustering without MWE over-estimate the rainfall during the dry season.

Detecting most influencing courses on students grades using block PCA

NASA Astrophysics Data System (ADS)

Othman, Osama H.; Gebril, Rami Salah

2014-12-01

One of the modern solutions adopted in dealing with the problem of large number of variables in statistical analyses is the Block Principal Component Analysis (Block PCA). This modified technique can be used to reduce the vertical dimension (variables) of the data matrix Xn×p by selecting a smaller number of variables, (say m) containing most of the statistical information. These selected variables can then be employed in further investigations and analyses. Block PCA is an adapted multistage technique of the original PCA. It involves the application of Cluster Analysis (CA) and variable selection throughout sub principal components scores (PC's). The application of Block PCA in this paper is a modified version of the original work of Liu et al (2002). The main objective was to apply PCA on each group of variables, (established using cluster analysis), instead of involving the whole large pack of variables which was proved to be unreliable. In this work, the Block PCA is used to reduce the size of a huge data matrix ((n = 41) × (p = 251)) consisting of Grade Point Average (GPA) of the students in 251 courses (variables) in the faculty of science in Benghazi University. In other words, we are constructing a smaller analytical data matrix of the GPA's of the students with less variables containing most variation (statistical information) in the original database. By applying the Block PCA, (12) courses were found to `absorb' most of the variation or influence from the original data matrix, and hence worth to be keep for future statistical exploring and analytical studies. In addition, the course Independent Study (Math.) was found to be the most influencing course on students GPA among the 12 selected courses.

Quantitative tolerance values for common stream benthic macroinvertebrates in the Yangtze River Delta, Eastern China.

PubMed

Qin, Chun-Yan; Zhou, Jin; Cao, Yong; Zhang, Yong; Hughes, Robert M; Wang, Bei-Xin

2014-09-01

Aquatic organisms' tolerance to water pollution is widely used to monitor and assess freshwater ecosystem health. Tolerance values (TVs) estimated based on statistical analyses of species-environment relationships are more objective than those assigned by expert opinion. Region-specific TVs are the basis for developing accurate bioassessment metrics particularly in developing countries, where both aquatic biota and their responses to human disturbances have been poorly documented. We used principal component analysis to derive a synthetic gradient for four stressor variables (total nitrogen, total phosphorus, dissolved oxygen, and % silt) based on 286 sampling sites in the Taihu Lake and Qiantang River basins (Yangtze River Delta), China. We used the scores of taxa on the first principal component (PC1), which explained 49.8% of the variance, to estimate the tolerance values (TV(r)) of 163 macroinvertebrates taxa that were collected from at least 20 sites, 81 of which were not included in the Hilsenhoff TV lists (TV(h)) of 1987. All estimates were scaled into the range of 1-10 as in TV(h). Of all the taxa with different TVs, 46.3% of TV(r) were lower and 52.4% were higher than TV(h). TV(r) were significantly (p < 0.01, Fig. 2), but weakly (r(2) = 0.34), correlated with TVh. Seven biotic metrics based on TVr were more strongly correlated with the main stressors and were more effective at discriminating references sites from impacted sites than those based on TV(h). Our results highlight the importance of developing region-specific TVs for macroinvertebrate-based bioassessment and to facilitate assessment of streams in China, particularly in the Yangtze River Delta.

A quick responding quartz crystal microbalance sensor array based on molecular imprinted polyacrylic acids coating for selective identification of aldehydes in body odor.

PubMed

Jha, Sunil K; Hayashi, Kenshi

2015-03-01

In present work, a novel quartz crystal microbalance (QCM) sensor array has been developed for prompt identification of primary aldehydes in human body odor. Molecularly imprinted polymers (MIP) are prepared using the polyacrylic acid (PAA) polymer matrix and three organic acids (propenoic acid, hexanoic acid and octanoic acid) as template molecules, and utilized as QCM surface coating layer. The performance of MIP films is characterized by 4-element QCM sensor array (three coated with MIP layers and one with pure PAA for reference) dynamic and static responses to target aldehydes: hexanal, heptanal, and nonanal in single, binary, and tertiary mixtures at distinct concentrations. The target aldehydes were selected subsequent to characterization of body odor samples with solid phase-micro extraction gas chromatography mass spectrometer (SPME-GC-MS). The hexanoic acid and octanoic acid imprinted PAA exhibit fast response, and better sensitivity, selectivity and reproducibility than the propenoic acid, and non-imprinted PAA in array. The response time and recovery time for hexanoic acid imprinted PAA are obtained as 5 s and 12 s respectively to typical concentrations of binary and tertiary mixtures of aldehydes using the static response. Dynamic sensor array response matrix has been processed with principal component analysis (PCA) for visual, and support vector machine (SVM) classifier for quantitative identification of target odors. Aldehyde odors were identified successfully in principal component (PC) space. SVM classifier results maximum recognition rate 79% for three classes of binary odors and 83% including single, binary, and tertiary odor classes in 3-fold cross validation. Copyright © 2014 Elsevier B.V. All rights reserved.

Finding Planets in K2: A New Method of Cleaning the Data

NASA Astrophysics Data System (ADS)

Currie, Miles; Mullally, Fergal; Thompson, Susan E.

2017-01-01

We present a new method of removing systematic flux variations from K2 light curves by employing a pixel-level principal component analysis (PCA). This method decomposes the light curves into its principal components (eigenvectors), each with an associated eigenvalue, the value of which is correlated to how much influence the basis vector has on the shape of the light curve. This method assumes that the most influential basis vectors will correspond to the unwanted systematic variations in the light curve produced by K2’s constant motion. We correct the raw light curve by automatically fitting and removing the strongest principal components. The strongest principal components generally correspond to the flux variations that result from the motion of the star in the field of view. Our primary method of calculating the strongest principal components to correct for in the raw light curve estimates the noise by measuring the scatter in the light curve after using an algorithm for Savitsy-Golay detrending, which computes the combined photometric precision value (SG-CDPP value) used in classic Kepler. We calculate this value after correcting the raw light curve for each element in a list of cumulative sums of principal components so that we have as many noise estimate values as there are principal components. We then take the derivative of the list of SG-CDPP values and take the number of principal components that correlates to the point at which the derivative effectively goes to zero. This is the optimal number of principal components to exclude from the refitting of the light curve. We find that a pixel-level PCA is sufficient for cleaning unwanted systematic and natural noise from K2’s light curves. We present preliminary results and a basic comparison to other methods of reducing the noise from the flux variations.

DIFFERENTIAL LOCALIZATION OF DIVALENT METAL TRANSPORTER (DMT1) WITH AND WITHOUT IRON RESPONSE ELEMENT (IRE) IN RAT PC12 AND SYMPATHETIC NEURONAL CELLS. (R826248)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

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.

Directly reconstructing principal components of heterogeneous particles from cryo-EM images.

PubMed

Tagare, Hemant D; Kucukelbir, Alp; Sigworth, Fred J; Wang, Hongwei; Rao, Murali

2015-08-01

Structural heterogeneity of particles can be investigated by their three-dimensional principal components. This paper addresses the question of whether, and with what algorithm, the three-dimensional principal components can be directly recovered from cryo-EM images. The first part of the paper extends the Fourier slice theorem to covariance functions showing that the three-dimensional covariance, and hence the principal components, of a heterogeneous particle can indeed be recovered from two-dimensional cryo-EM images. The second part of the paper proposes a practical algorithm for reconstructing the principal components directly from cryo-EM images without the intermediate step of calculating covariances. This algorithm is based on maximizing the posterior likelihood using the Expectation-Maximization algorithm. The last part of the paper applies this algorithm to simulated data and to two real cryo-EM data sets: a data set of the 70S ribosome with and without Elongation Factor-G (EF-G), and a data set of the influenza virus RNA dependent RNA Polymerase (RdRP). The first principal component of the 70S ribosome data set reveals the expected conformational changes of the ribosome as the EF-G binds and unbinds. The first principal component of the RdRP data set reveals a conformational change in the two dimers of the RdRP. Copyright © 2015 Elsevier Inc. 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.

40 CFR 60.2998 - What are the principal components of the model rule?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 6 2010-07-01 2010-07-01 false What are the principal components of... December 9, 2004 Model Rule-Use of Model Rule § 60.2998 What are the principal components of the model rule... management plan. (c) Operator training and qualification. (d) Emission limitations and operating limits. (e...

40 CFR 60.2570 - What are the principal components of the model rule?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 6 2010-07-01 2010-07-01 false What are the principal components of... Construction On or Before November 30, 1999 Use of Model Rule § 60.2570 What are the principal components of... (k) of this section. (a) Increments of progress toward compliance. (b) Waste management plan. (c...

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.

Effects of adding red wine on the physicochemical properties and sensory characteristics of uncured frankfurter-type sausage.

PubMed

Feng, Xi; Sebranek, Joseph G; Lee, Hyun Yong; Ahn, Dong Uk

2016-11-01

The aim of this work was to evaluate the quality and sensory characteristics of RTE frankfurter-type sausage cured with celery juice powder and including red wine. Four frankfurter treatments including a conventionally cured treatment without red wine (control) and three treatments cured with pre-converted vegetable juice powder and 0%, 5% or 10% (v/w) red wine were prepared. Results showed that adding 5% red wine increased the a*-value, and the textural resilience, cohesiveness and springiness of the frankfurters, as well as decreased lipid/protein oxidation of the final products. Added wine also introduced new volatiles (alcohol and ester compounds) to the frankfurters. The principal component (PC) analysis showed that the pre-converted vegetable juice powder achieved the same effects as the conventional curing agents for typical frankfurter properties. However, the addition of excess amounts of red wine (10%) to the meat batter decreased the pH of meat batter and accelerated lipid oxidation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ultrasonic sensing of GMAW: Laser/EMAT defect detection system. [Gas Metal Arc Welding (GMAW), Electromagnetic acoustic transducer (EMAT)

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

Carlson, N.M.; Johnson, J.A.; Larsen, E.D.

1992-01-01

In-process ultrasonic sensing of welding allows detection of weld defects in real time. A noncontacting ultrasonic system is being developed to operate in a production environment. The principal components are a pulsed laser for ultrasound generation and an electromagnetic acoustic transducer (EMAT) for ultrasound reception. A PC-based data acquisition system determines the quality of the weld on a pass-by-pass basis. The laser/EMAT system interrogates the area in the weld volume where defects are most likely to occur. This area of interest is identified by computer calculations on a pass-by-pass basis using weld planning information provided by the off-line programmer. Themore » absence of a signal above the threshold level in the computer-calculated time interval indicates a disruption of the sound path by a defect. The ultrasonic sensor system then provides an input signal to the weld controller about the defect condition. 8 refs.« less

Compressive light field imaging

NASA Astrophysics Data System (ADS)

Ashok, Amit; Neifeld, Mark A.

2010-04-01

Light field imagers such as the plenoptic and the integral imagers inherently measure projections of the four dimensional (4D) light field scalar function onto a two dimensional sensor and therefore, suffer from a spatial vs. angular resolution trade-off. Programmable light field imagers, proposed recently, overcome this spatioangular resolution trade-off and allow high-resolution capture of the (4D) light field function with multiple measurements at the cost of a longer exposure time. However, these light field imagers do not exploit the spatio-angular correlations inherent in the light fields of natural scenes and thus result in photon-inefficient measurements. Here, we describe two architectures for compressive light field imaging that require relatively few photon-efficient measurements to obtain a high-resolution estimate of the light field while reducing the overall exposure time. Our simulation study shows that, compressive light field imagers using the principal component (PC) measurement basis require four times fewer measurements and three times shorter exposure time compared to a conventional light field imager in order to achieve an equivalent light field reconstruction quality.

Paper spray mass spectrometry and chemometric tools for a fast and reliable identification of counterfeit blended Scottish whiskies.

PubMed

Teodoro, Janaína Aparecida Reis; Pereira, Hebert Vinicius; Sena, Marcelo Martins; Piccin, Evandro; Zacca, Jorge Jardim; Augusti, Rodinei

2017-12-15

A direct method based on the application of paper spray mass spectrometry (PS-MS) combined with a chemometric supervised method (partial least square discriminant analysis, PLS-DA) was developed and applied to the discrimination of authentic and counterfeit samples of blended Scottish whiskies. The developed methodology employed the negative ion mode MS, included 44 authentic whiskies from diverse brands and batches and 44 counterfeit samples of the same brands seized during operations of the Brazilian Federal Police, totalizing 88 samples. An exploratory principal component analysis (PCA) model showed a reasonable discrimination of the counterfeit whiskies in PC2. In spite of the samples heterogeneity, a robust, reliable and accurate PLS-DA model was generated and validated, which was able to correctly classify the samples with nearly 100% success rate. The use of PS-MS also allowed the identification of the main marker compounds associated with each type of sample analyzed: authentic or counterfeit. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rapid identification of pork for halal authentication using the electronic nose and gas chromatography mass spectrometer with headspace analyzer.

PubMed

Nurjuliana, M; Che Man, Y B; Mat Hashim, D; Mohamed, A K S

2011-08-01

The volatile compounds of pork, other meats and meat products were studied using an electronic nose and gas chromatography mass spectrometer with headspace analyzer (GCMS-HS) for halal verification. The zNose™ was successfully employed for identification and differentiation of pork and pork sausages from beef, mutton and chicken meats and sausages which were achieved using a visual odor pattern called VaporPrint™, derived from the frequency of the surface acoustic wave (SAW) detector of the electronic nose. GCMS-HS was employed to separate and analyze the headspace gasses from samples into peaks corresponding to individual compounds for the purpose of identification. Principal component analysis (PCA) was applied for data interpretation. Analysis by PCA was able to cluster and discriminate pork from other types of meats and sausages. It was shown that PCA could provide a good separation of the samples with 67% of the total variance accounted by PC1. Copyright © 2011 Elsevier Ltd. All rights reserved.

Genetic architecture of natural variation in cuticular hydrocarbon composition in Drosophila melanogaster.

PubMed

Dembeck, Lauren M; Böröczky, Katalin; Huang, Wen; Schal, Coby; Anholt, Robert R H; Mackay, Trudy F C

2015-11-14

Insect cuticular hydrocarbons (CHCs) prevent desiccation and serve as chemical signals that mediate social interactions. Drosophila melanogaster CHCs have been studied extensively, but the genetic basis for individual variation in CHC composition is largely unknown. We quantified variation in CHC profiles in the D. melanogaster Genetic Reference Panel (DGRP) and identified novel CHCs. We used principal component (PC) analysis to extract PCs that explain the majority of CHC variation and identified polymorphisms in or near 305 and 173 genes in females and males, respectively, associated with variation in these PCs. In addition, 17 DGRP lines contain the functional Desat2 allele characteristic of African and Caribbean D. melanogaster females (more 5,9-C27:2 and less 7,11-C27:2, female sex pheromone isomers). Disruption of expression of 24 candidate genes affected CHC composition in at least one sex. These genes are associated with fatty acid metabolism and represent mechanistic targets for individual variation in CHC composition.

Development of a platform-independent receiver control system for SISIFOS

NASA Astrophysics Data System (ADS)

Lemke, Roland; Olberg, Michael

1998-05-01

Up to now receiver control software was a time consuming development usually written by receiver engineers who had mainly the hardware in mind. We are presenting a low-cost and very flexible system which uses a minimal interface to the real hardware, and which makes it easy to adapt to new receivers. Our system uses Tcl/Tk as a graphical user interface (GUI), SpecTcl as a GUI builder, Pgplot as plotting software, a simple query language (SQL) database for information storage and retrieval, Ethernet socket to socket communication and SCPI as a command control language. The complete system is in principal platform independent but for cost saving reasons we are using it actually on a PC486 running Linux 2.0.30, which is a copylefted Unix. The only hardware dependent part are the digital input/output boards, analog to digital and digital to analog convertors. In the case of the Linux PC we are using a device driver development kit to integrate the boards fully into the kernel of the operating system, which indeed makes them look like an ordinary device. The advantage of this system is firstly the low price and secondly the clear separation between the different software components which are available for many operating systems. If it is not possible, due to CPU performance limitations, to run all the software in a single machine,the SQL-database or the graphical user interface could be installed on separate computers.

Microbial Community Structure and Enzyme Activities in Semiarid Agricultural Soils

NASA Astrophysics Data System (ADS)

Acosta-Martinez, V. A.; Zobeck, T. M.; Gill, T. E.; Kennedy, A. C.

2002-12-01

The effect of agricultural management practices on the microbial community structure and enzyme activities of semiarid soils of different textures in the Southern High Plains of Texas were investigated. The soils (sandy clay loam, fine sandy loam and loam) were under continuous cotton (Gossypium hirsutum L.) or in rotations with peanut (Arachis hypogaea L.), sorghum (Sorghum bicolor L.) or wheat (Triticum aestivum L.), and had different water management (irrigated or dryland) and tillage (conservation or conventional). Microbial community structure was investigated using fatty acid methyl ester (FAME) analysis by gas chromatography and enzyme activities, involved in C, N, P and S cycling of soils, were measured (mg product released per kg soil per h). The activities of b-glucosidase, b-glucosaminidase, alkaline phosphatase, and arylsulfatase were significantly (P<0.05) increased in soils under cotton rotated with sorghum or wheat, and due to conservation tillage in comparison to continuous cotton under conventional tillage. Principal component analysis showed FAME profiles of these soils separated distinctly along PC1 (20 %) and PC2 (13 %) due to their differences in soil texture and management. No significant differences were detected in FAME profiles due to management practices for the same soils in this sampling period. Enzyme activities provide early indications of the benefits in microbial populations and activities and soil organic matter under crop rotations and conservation tillage in comparison to the typical practices in semiarid regions of continuous cotton and conventional tillage.