Characterization of Multidrug Resistant E. faecalis Strains from Pigs of Local Origin by ADSRRS-Fingerprinting and MALDI -TOF MS; Evaluation of the Compatibility of Methods Employed for Multidrug Resistance Analysis

PubMed Central

Nowakiewicz, Aneta; Ziółkowska, Grażyna; Zięba, Przemysław; Gnat, Sebastian; Trościańczyk, Aleksandra; Adaszek, Łukasz

2017-01-01

The aim of this study was to characterize multidrug resistant E. faecalis strains from pigs of local origin and to analyse the relationship between resistance and genotypic and proteomic profiles by amplification of DNA fragments surrounding rare restriction sites (ADSRRS-fingerprinting) and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI -TOF MS). From the total pool of Enterococcus spp. isolated from 90 pigs, we selected 36 multidrug resistant E. faecalis strains, which represented three different phenotypic resistance profiles. Phenotypic resistance to tetracycline, macrolides, phenicols, and lincomycin and high-level resistance to aminoglycosides were confirmed by the occurrence of at least one corresponding resistance gene in each strain. Based on the analysis of the genotypic and phenotypic resistance of the strains tested, five distinct resistance profiles were generated. As a complement of this analysis, profiles of virulence genes were determined and these profiles corresponded to the phenotypic resistance profiles. The demonstration of resistance to a wide panel of antimicrobials by the strains tested in this study indicates the need of typing to determine the spread of resistance also at the local level. It seems that in the case of E. faecalis, type and scope of resistance strongly determines the genotypic pattern obtained with the ADSRRS-fingerprinting method. The ADSRRS-fingerprinting analysis showed consistency of the genetic profiles with the resistance profiles, while analysis of data with the use of the MALDI- TOF MS method did not demonstrate direct reproduction of the clustering pattern obtained with this method. Our observations were confirmed by statistical analysis (Simpson’s index of diversity, Rand and Wallace coefficients). Even though the MALDI -TOF MS method showed slightly higher discrimination power than ADSRRS-fingerprinting, only the latter method allowed reproduction of the clustering pattern of isolates based on phenotypic resistance and analysis of resistance and virulence genes (Wallace coefficient 1.0). This feature seems to be the most useful for epidemiological purposes and short-term analysis. PMID:28135327

Profile Analysis of Psychological Symptoms Associated With Misophonia: A Community Sample.

PubMed

McKay, Dean; Kim, Se-Kang; Mancusi, Lauren; Storch, Eric A; Spankovich, Christopher

2018-03-01

Misophonia is characterized by extreme aversive reactions to certain classes of sounds. It has recently been recognized as a condition associated with significant disability. Research has begun to evaluate psychopathological correlates of misophonia. This study sought to identify profiles of psychopathology that characterize misophonia in a large community sample. A total of N = 628 adult participants completed a battery of measures assessing anxiety and anxiety sensitivity, depression, stress responses, anger, dissociative experiences, obsessive-compulsive symptoms and beliefs, distress tolerance, bodily perceptions, as well as misophonia severity. Profile Analysis via Multidimensional Scaling (PAMS) was employed to evaluate profiles associated with elevated misophonia and those without symptoms. Three profiles were extracted. The first two accounted for 70% total variance and did not show distinctions between groups. The third profile accounted for 11% total variance, and showed that misophonia is associated with lower obsessive-compulsive symptoms for neutralizing, obsessions generally, and washing compared to those not endorsing misophonia, and higher levels of obsessive-compulsive symptoms associated with ordering and harm avoidance. This third profile extracted also showed significant differences between those with and without misophonia on the scale assessing physical concerns (that is, sensitivity to interoceptive sensations) as assessed with the ASI-3. Further research is called for involving diagnostic interviewing and experimental methods to clarify these putative mechanisms associated with misophonia. Copyright © 2017. Published by Elsevier Ltd.

A ranking index for quality assessment of forensic DNA profiles forensic DNA profiles

PubMed Central

2010-01-01

Background Assessment of DNA profile quality is vital in forensic DNA analysis, both in order to determine the evidentiary value of DNA results and to compare the performance of different DNA analysis protocols. Generally the quality assessment is performed through manual examination of the DNA profiles based on empirical knowledge, or by comparing the intensities (allelic peak heights) of the capillary electrophoresis electropherograms. Results We recently developed a ranking index for unbiased and quantitative quality assessment of forensic DNA profiles, the forensic DNA profile index (FI) (Hedman et al. Improved forensic DNA analysis through the use of alternative DNA polymerases and statistical modeling of DNA profiles, Biotechniques 47 (2009) 951-958). FI uses electropherogram data to combine the intensities of the allelic peaks with the balances within and between loci, using Principal Components Analysis. Here we present the construction of FI. We explain the mathematical and statistical methodologies used and present details about the applied data reduction method. Thereby we show how to adapt the ranking index for any Short Tandem Repeat-based forensic DNA typing system through validation against a manual grading scale and calibration against a specific set of DNA profiles. Conclusions The developed tool provides unbiased quality assessment of forensic DNA profiles. It can be applied for any DNA profiling system based on Short Tandem Repeat markers. Apart from crime related DNA analysis, FI can therefore be used as a quality tool in paternal or familial testing as well as in disaster victim identification. PMID:21062433

Statistical analysis of stratospheric temperature and ozone profile data for trends and model comparison

NASA Technical Reports Server (NTRS)

Tiao, G. C.

1992-01-01

Work performed during the project period July 1, 1990 to June 30, 1992 on the statistical analysis of stratospheric temperature data, rawinsonde temperature data, and ozone profile data for the detection of trends is described. Our principal topics of research are trend analysis of NOAA stratospheric temperature data over the period 1978-1989; trend analysis of rawinsonde temperature data for the period 1964-1988; trend analysis of Umkehr ozone profile data for the period 1977-1991; and comparison of observed ozone and temperature trends in the lower stratosphere. Analysis of NOAA stratospheric temperature data indicates the existence of large negative trends at 0.4 mb level, with magnitudes increasing with latitudes away from the equator. Trend analysis of rawinsonde temperature data over 184 stations shows significant positive trends about 0.2 C per decade at surface to 500 mb range, decreasing to negative trends about -0.3 C at 100 to 50 mb range, and increasing slightly at 30 mb level. There is little evidence of seasonal variation in trends. Analysis of Umkehr ozone data for 12 northern hemispheric stations shows significant negative trends about -.5 percent per year in Umkehr layers 7-9 and layer 3, but somewhat less negative trends in layers 4-6. There is no pronounced seasonal variation in trends, especially in layers 4-9. A comparison was made of empirical temperature trends from rawinsonde data in the lower stratosphere with temperature changes determined from a one-dimensional radiative transfer calculation that prescribed a given ozone change over the altitude region, surface to 50 km, obtained from trend analysis of ozonsonde and Umkehr profile data. The empirical and calculated temperature trends are found in substantive agreement in profile shape and magnitude.

Differential identification of Candida species and other yeasts by analysis of (/sup 35/S)methionine-labeled polypeptide profiles

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

Shen, H.D.; Choo, K.B.; Tsai, W.C.

1988-12-01

This paper describes a scheme for differential identification of Candida species and other yeasts based on autoradiographic analysis of protein profiles of (/sup 35/S)methionine-labeled cellular proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Using ATCC strains as references, protein profile analysis showed that different Candida and other yeast species produced distinctively different patterns. Good agreement in results obtained with this approach and with other conventional systems was observed. Being accurate and reproducible, this approach provides a basis for the development of an alternative method for the identification of yeasts isolated from clinical specimens.

Investigation of the aroma of commercial peach (Prunus persica L. Batsch) types by Proton Transfer Reaction-Mass Spectrometry (PTR-MS) and sensory analysis.

PubMed

Bianchi, Tiago; Weesepoel, Yannick; Koot, Alex; Iglesias, Ignasi; Eduardo, Iban; Gratacós-Cubarsí, Marta; Guerrero, Luis; Hortós, Maria; van Ruth, Saskia

2017-09-01

The aim of this study was to investigate the aroma and sensory profiles of various types of peaches (Prunus persica L. Batsch.). Forty-three commercial cultivars comprising peaches, flat peaches, nectarines, and canning peaches (pavías) were grown over two consecutive harvest years. Fruits were assessed for chemical aroma and sensory profiles. Chemical aroma profile was obtained by proton transfer reaction-mass spectrometry (PTR-MS) and spectral masses were tentatively identified with PTR-Time of Flight-MS (PTR-Tof-MS). Sensory analysis was performed at commercial maturity considering seven aroma/flavor attributes. The four types of peaches showed both distinct chemical aroma and sensory profiles. Flat peaches and canning peaches showed most distinct patterns according to discriminant analysis. The sensory data were related to the volatile compounds by partial least square regression. γ-Hexalactone, γ-octalactone, hotrienol, acetic acid and ethyl acetate correlated positively, and benzeneacetaldehyde, trimethylbenzene and acetaldehyde negatively to the intensities of aroma and ripe fruit sensory scores. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation of the LIA-ANA-Profile-17S for the detection of autoantibodies to nuclear antigens.

PubMed

Yi, Ahram; Lee, Chang-Hoon; Moon, Hee-Won; Kim, Hanah; Hur, Mina; Yun, Yeo-Min

2018-05-01

The diagnostic tests for autoimmune disease include screening for autoantibodies for nuclear antigens (ANA) and antibodies against extractable nuclear antigens (ENA). Using the line immunoassay (LIA) method, various kinds of ENA antibodies can be detected simultaneously. We evaluated the performance of the newly launched LIA-ANA-Profile-17S (Shenzhen YHLO Biotech, Shenzhen, China) as compared to a conventional LIA kit. Residual samples were collected from 200 patients who had been tested for ANA using indirect immunofluorescence. The LIA-ANA-Profile-17S was compared to the EuroLine ANA (Euroimmun, Oberlausitz, Germany) for the analysis of 17 different autoantibodies. The concordance rate and agreement between assays were determined. Samples showing discrepancies between the LIA-ANA-Profile-17S and EuroLine tests were further examined through additional analysis. The overall agreement was moderate (kappa = 0.759, 95% CI = 0.712-0.805). Agreement between assays ranged from weak to almost perfect, except for those tests targeting nucleosomes, histones, and PM-Scl. Of the 57 disparate results between LIA-ANA-Profile-17S and EuroLine, 38 (66.7%) samples tested positive under an additional assay, showing variable patterns between types of autoantibodies. The positive rate of each autoantibody between LIA-ANA-Profile-17S and EuroLine did not differ significantly, except for anti-nucleosome and anti-histone assays in samples from patients diagnosed with systemic lupus erythematosus (P = 0.004 and 0.001, respectively). Compared to those from the conventional EuroLine assay, the LIA-ANA-Profile-17S results showed variable agreement in samples showing different prevalence of each autoantibody. The most frequently detected antibodies showed almost perfect agreement. The LIA-ANA-Profile-17S could play a role in the diagnosis of systemic autoimmune disease in ANA-positive samples. Copyright © 2018 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Integrated lipidomics and transcriptomic analysis of peripheral blood reveals significantly enriched pathways in type 2 diabetes mellitus.

PubMed

Zhao, Chen; Mao, Jinghe; Ai, Junmei; Shenwu, Ming; Shi, Tieliu; Zhang, Daqing; Wang, Xiaonan; Wang, Yunliang; Deng, Youping

2013-01-01

Insulin resistance is a key element in the pathogenesis of type 2 diabetes mellitus. Plasma free fatty acids were assumed to mediate the insulin resistance, while the relationship between lipid and glucose disposal remains to be demonstrated across liver, skeletal muscle and blood. We profiled both lipidomics and gene expression of 144 total peripheral blood samples, 84 from patients with T2D and 60 from healthy controls. Then, factor and partial least squares models were used to perform a combined analysis of lipidomics and gene expression profiles to uncover the bioprocesses that are associated with lipidomic profiles in type 2 diabetes. According to factor analysis of the lipidomic profile, several species of lipids were found to be correlated with different phenotypes, including diabetes-related C23:2CE, C23:3CE, C23:4CE, ePE36:4, ePE36:5, ePE36:6; race-related (African-American) PI36:1; and sex-related PE34:1 and LPC18:2. The major variance of gene expression profile was not caused by known factors and no significant difference can be directly derived from differential gene expression profile. However, the combination of lipidomic and gene expression analyses allows us to reveal the correlation between the altered lipid profile with significantly enriched pathways, such as one carbon pool by folate, arachidonic acid metabolism, insulin signaling pathway, amino sugar and nucleotide sugar metabolism, propanoate metabolism, and starch and sucrose metabolism. The genes in these pathways showed a good capability to classify diabetes samples. Combined analysis of gene expression and lipidomic profiling reveals type 2 diabetes-associated lipid species and enriched biological pathways in peripheral blood, while gene expression profile does not show direct correlation. Our findings provide a new clue to better understand the mechanism of disordered lipid metabolism in association with type 2 diabetes.

Association between Pesticide Profiles Used on Agricultural Fields near Maternal Residences during Pregnancy and IQ at Age 7 Years.

PubMed

Coker, Eric; Gunier, Robert; Bradman, Asa; Harley, Kim; Kogut, Katherine; Molitor, John; Eskenazi, Brenda

2017-05-09

We previously showed that potential prenatal exposure to agricultural pesticides was associated with adverse neurodevelopmental outcomes in children, yet the effects of joint exposure to multiple pesticides is poorly understood. In this paper, we investigate associations between the joint distribution of agricultural use patterns of multiple pesticides (denoted as "pesticide profiles") applied near maternal residences during pregnancy and Full-Scale Intelligence Quotient (FSIQ) at 7 years of age. Among a cohort of children residing in California's Salinas Valley, we used Pesticide Use Report (PUR) data to characterize potential exposure from use within 1 km of maternal residences during pregnancy for 15 potentially neurotoxic pesticides from five different chemical classes. We used Bayesian profile regression (BPR) to examine associations between clustered pesticide profiles and deficits in childhood FSIQ. BPR identified eight distinct clusters of prenatal pesticide profiles. Two of the pesticide profile clusters exhibited some of the highest cumulative pesticide use levels and were associated with deficits in adjusted FSIQ of -6.9 (95% credible interval: -11.3, -2.2) and -6.4 (95% credible interval: -13.1, 0.49), respectively, when compared with the pesticide profile cluster that showed the lowest level of pesticides use. Although maternal residence during pregnancy near high agricultural use of multiple neurotoxic pesticides was associated with FSIQ deficit, the magnitude of the associations showed potential for sub-additive effects. Epidemiologic analysis of pesticides and their potential health effects can benefit from a multi-pollutant approach to analysis.

Global gyrokinetic simulations of intrinsic rotation in ASDEX Upgrade Ohmic L-mode plasmas

NASA Astrophysics Data System (ADS)

Hornsby, W. A.; Angioni, C.; Lu, Z. X.; Fable, E.; Erofeev, I.; McDermott, R.; Medvedeva, A.; Lebschy, A.; Peeters, A. G.; The ASDEX Upgrade Team

2018-05-01

Non-linear, radially global, turbulence simulations of ASDEX Upgrade (AUG) plasmas are performed and the nonlinear generated intrinsic flow shows agreement with the intrinsic flow gradients measured in the core of Ohmic L-mode plasmas at nominal parameters. Simulations utilising the kinetic electron model show hollow intrinsic flow profiles as seen in a predominant number of experiments performed at similar plasma parameters. In addition, significantly larger flow gradients are seen than in a previous flux-tube analysis (Hornsby et al 2017 Nucl. Fusion 57 046008). Adiabatic electron model simulations can show a flow profile with opposing sign in the gradient with respect to a kinetic electron simulation, implying a reversal in the sign of the residual stress due to kinetic electrons. The shaping of the intrinsic flow is strongly determined by the density gradient profile. The sensitivity of the residual stress to variations in density profile curvature is calculated and seen to be significantly stronger than to neoclassical flows (Hornsby et al 2017 Nucl. Fusion 57 046008). This variation is strong enough on its own to explain the large variations in the intrinsic flow gradients seen in some AUG experiments. Analysis of the symmetry breaking properties of the turbulence shows that profile shearing is the dominant mechanism in producing a finite parallel wave-number, with turbulence gradient effects contributing a smaller portion of the parallel wave-vector.

Transform analysis of the resonance Raman excitation profile of lycopene

NASA Astrophysics Data System (ADS)

Hoskins, L. C.

1992-10-01

The resonance Raman excitation profiles (RREPs) of the ν 1, ν 2 and ν 3 vibrations of lycopene in acetone, ethyl alcohol, toluene and carbon disulphide solvents have been analyzed using the transform method for calculating resonance Raman excitation profiles. The tests show excellent agreement between the calculated and observed profiles for the ν 2 and ν 3 RREPs, but greater difference between experiment and theory occurs for the ν 1 RREP, especially in carbon disulphide solvent.

Profiles of childhood adversities in pathological gamblers - A latent class analysis.

PubMed

Lotzin, Annett; Ulas, Mehmet; Buth, Sven; Milin, Sascha; Kalke, Jens; Schäfer, Ingo

2018-06-01

Despite of high rates of adverse childhood experiences (ACEs) in pathological gamblers, researchers have rarely studied which types of ACEs often co-occur and how these profiles of ACEs are related to current psychopathology. We aimed to identify profiles of ACEs in pathological gamblers and examined how these profiles were related to gambling-related characteristics and current general psychopathology. In 329 current or lifetime pathological gamblers, diagnosed with the Composite Diagnostic Interview for DSM-IV, 10 types of ACEs were measured using the Adverse Childhood Experiences Questionnaire. Global psychopathology was assessed using the Symptom Checklist SCL-27. ACE profiles were identified using latent class analysis. Differences between ACE profiles in gambling-related characteristics and global psychopathology were analyzed using MANOVA. We found that four out of five gamblers (n=257, 78.1%) reported at least one ACE. Four distinct ACE profiles were identified: 'Low ACE', 'High ACE', 'Physical and emotional abuse', and 'Neglect'. The number of the fulfilled pathological gambling criteria and the severity of current global psychopathology differed between the ACE profiles: Gamblers with a 'High ACE' profile fulfilled more pathological gambling criteria and showed a more severe current psychopathology than gamblers of the 'Low ACE' profile. Gamblers with a 'Physical and emotional abuse' or an 'Emotion neglect' profile showed an intermediate severity of psychopathology. Our findings indicate that four different ACE profiles can be distinguished in pathological gamblers that differed in their gambling-related characteristics and current psychopathology. Systematic assessment of profiles of ACEs in pathological gamblers may inform about the severity of current global psychopathology that might be important to be addressed in addition to gambling-specific treatment. Copyright © 2018 Elsevier Ltd. All rights reserved.

DNA Barcoding of the Mexican Sedative and Anxiolytic Plant Galphimia glauca

PubMed Central

Sharma, Ashutosh; Folch, Jorge Luis; Cardoso-Taketa, Alexandre; Lorence, Argelia; Villarreal, María Luisa

2015-01-01

Ethnopharmacology relevance Galphimiaglauca (Malpighiaceae) is a Mexican plant popularly used as a tranquilizer in the treatment of nervous system disorders, although it is also used to treat other common illnesses. Aim of the study The aim of this investigation is to find out if populations of Galphimiaglauca collected in different regions and ecosystems in Mexico actually belong to the same species by using the contemporary technique of DNA barcodes. Our previous metabolic profiling study demonstrates that different collections of this plant obtained from various geographical areas exhibited diverse chemical profiles in terms of the active compounds named Galphimines. We expected the DNA barcodes apart from indicating the different species of Galphimia would indicate the active populations. Materials and methods We employed matK, rpoC1 and rbcL DNA barcodes to indicate the different species. Furthermore to investigate the possible impact of the several different ecosystems where the seven populations were collected, thin layer chromatography was employed to create a partial chemical profile, which was then compared with the metabolic profiles obtained by 1H-NMR and multivariate data analysis. Results and conclusions This study showed that the seven populations here analyzed contain at least three different species of the genus Galphimia, although each individual population is homogeneous. Interestingly our TLC analysis clearly showed that the active populations displayed a distinctively unique chemical profile. This work also showed that the use of DNA barcodes combined with chemical profile analysis is an excellent approach to solve the problems of quality control in the development of Galphimia-based medicines, as well as for any breeding programs for this species. PMID:23010364

Psychosocial Outcomes 3 to 10 Years After Donation in the Adult to Adult Living Donor Liver Transplantation Cohort Study (A2ALL)

PubMed Central

Dew, Mary Amanda; DiMartini, Andrea F.; Ladner, Daniela P.; Simpson, Mary Ann; Pomfret, Elizabeth A.; Gillespie, Brenda W.; Merion, Robert M.; Zee, Jarcy; Smith, Abigail R.; Holtzman, Susan; Sherker, Averell H.; Weinrieb, Robert; Fisher, Robert A.; Emond, Jean C.; Freise, Chris E.; Burton, James R.; Butt, Zeeshan

2016-01-01

Background Studies of liver donors’ psychosocial outcomes focus on the short-term and rely largely on quality-of-life measures not specific to donation. We sought to examine long-term donation effects on three psychosocial domains: perceived physical, emotional, and socioeconomic outcomes. Methods Individuals donating 3–10 years previously at nine centers were eligible for telephone surveys. Survey responses were examined descriptively. Cluster analysis was used to identify distinct donor groups based on response profiles across psychosocial domains. Potential predictors of response profiles were evaluated with regression analysis. Results 517 donors (66%) participated (M=5.8 years postdonation, SD=1.9). 15%–48% of donors endorsed current donation-related physical health problems and concerns, and 7%–60% reported socioeconomic concerns (e.g., insurance difficulties, financial expenditures). However, on average, donors experienced high psychological growth, and 90% felt positively about donation. Cluster analysis revealed five donor groups. One group showed high psychological benefit, with little endorsement of physical or socioeconomic concerns (15% of donors). Four groups showed less favorable profiles, with varying combinations of difficulties. The largest such group showed high endorsement of physical concerns and financial expenditures, and only modest psychological benefit (31% of donors). Men and non-Hispanic whites were most likely to have unfavorable response profiles (p<.01). Compared with donors aged 19–30, older donors were less likely to have unfavorable profiles; these differences were significant for donors aged >40–50 (p’s<.008). Conclusions Even many years postdonation, donors report adverse physical and socioeconomic effects, but positive emotional effects as well. Identification of response profiles and predictors may improve targeting of postdonation surveillance and care. PMID:27152918

Chemotaxonomy of heterocystous cyanobacteria using FAME profiling as species markers.

PubMed

Shukla, Ekta; Singh, Satya Shila; Singh, Prashant; Mishra, Arun Kumar

2012-07-01

The fatty acid methyl ester (FAME) analysis of the 12 heterocystous cyanobacterial strains showed different fatty acid profiling based on the presence/absence and the percentage of 13 different types of fatty acids. The major fatty acids viz. palmitic acid (16:0), hexadecadienoic acid (16:2), stearic acid (18:0), oleic acid (18:1), linoleic (18:2), and linolenic acid (18:3) were present among all the strains except Cylindrospermum musicola where oleic acid (18:1) was absent. All the strains showed high levels of polyunsaturated fatty acid (PUFAs; 41-68.35%) followed by saturated fatty acid (SAFAs; 1.82-40.66%) and monounsaturated fatty acid (0.85-24.98%). Highest percentage of PUFAs and essential fatty acid (linolenic acid; 18:3) was reported in Scytonema bohnerii which can be used as fatty acid supplement in medical and biotechnological purpose. The cluster analysis based on FAME profiling suggests the presence of two distinct clusters with Euclidean distance ranging from 0 to 25. S. bohnerii of cluster I was distantly related to the other strains of cluster II. The genotypes of cluster II were further divided into two subclusters, i.e., IIa with C. musicola showing great divergence with the other genotypes of IIb which was further subdivided into two groups. Subsubcluster IIb(1) was represented by a genotype, Anabaena sp. whereas subsubcluster IIb(2) was distinguished by two groups, i.e., one group having significant similarity among their three genotypes showed distant relation with the other group having closely related six genotypes. To test the validity of the fatty acid profiles as a marker, cluster analysis has also been generated on the basis of morphological attributes. Our results suggest that FAME profiling might be used as species markers in the study of polyphasic approach based taxonomy and phylogenetic relationship.

Automated tumor analysis for molecular profiling in lung cancer

PubMed Central

Boyd, Clinton; James, Jacqueline A.; Loughrey, Maurice B.; Hougton, Joseph P.; Boyle, David P.; Kelly, Paul; Maxwell, Perry; McCleary, David; Diamond, James; McArt, Darragh G.; Tunstall, Jonathon; Bankhead, Peter; Salto-Tellez, Manuel

2015-01-01

The discovery and clinical application of molecular biomarkers in solid tumors, increasingly relies on nucleic acid extraction from FFPE tissue sections and subsequent molecular profiling. This in turn requires the pathological review of haematoxylin & eosin (H&E) stained slides, to ensure sample quality, tumor DNA sufficiency by visually estimating the percentage tumor nuclei and tumor annotation for manual macrodissection. In this study on NSCLC, we demonstrate considerable variation in tumor nuclei percentage between pathologists, potentially undermining the precision of NSCLC molecular evaluation and emphasising the need for quantitative tumor evaluation. We subsequently describe the development and validation of a system called TissueMark for automated tumor annotation and percentage tumor nuclei measurement in NSCLC using computerized image analysis. Evaluation of 245 NSCLC slides showed precise automated tumor annotation of cases using Tissuemark, strong concordance with manually drawn boundaries and identical EGFR mutational status, following manual macrodissection from the image analysis generated tumor boundaries. Automated analysis of cell counts for % tumor measurements by Tissuemark showed reduced variability and significant correlation (p < 0.001) with benchmark tumor cell counts. This study demonstrates a robust image analysis technology that can facilitate the automated quantitative analysis of tissue samples for molecular profiling in discovery and diagnostics. PMID:26317646

A Meta-Analysis of Differences in IQ Profiles between Individuals with Asperger's Disorder and High-Functioning Autism

ERIC Educational Resources Information Center

Chiang, Hsu-Min; Tsai, Luke Y.; Cheung, Ying Kuen; Brown, Alice; Li, Huacheng

2014-01-01

A meta-analysis was performed to examine differences in IQ profiles between individuals with Asperger's disorder (AspD) and high-functioning autism (HFA). Fifty-two studies were included for this study. The results showed that (a) individuals with AspD had significantly higher full-scale IQ, verbal IQ (VIQ), and performance IQ (PIQ) than did…

Profiling of Piper betle Linn. cultivars by direct analysis in real time mass spectrometric technique.

PubMed

Bajpai, Vikas; Sharma, Deepty; Kumar, Brijesh; Madhusudanan, K P

2010-12-01

Piper betle Linn. is a traditional plant associated with the Asian and southeast Asian cultures. Its use is also recorded in folk medicines in these regions. Several of its medicinal properties have recently been proven. Phytochemical analysis showed the presence of mainly terpenes and phenols in betel leaves. These constituents vary in the different cultivars of Piper betle. In this paper we have attempted to profile eight locally available betel cultivars using the recently developed mass spectral ionization technique of direct analysis in real time (DART). Principal component analysis has also been employed to analyze the DART MS data of these betel cultivars. The results show that the cultivars of Piper betle could be differentiated using DART MS data. Copyright © 2010 John Wiley & Sons, Ltd.

Impurity profiling of trinitrotoluene using vacuum-outlet gas chromatography-mass spectrometry.

PubMed

Brust, Hanneke; Willemse, Sander; Zeng, Tuoyu; van Asten, Arian; Koeberg, Mattijs; van der Heijden, Antoine; Bolck, Annabel; Schoenmakers, Peter

2014-12-29

In this work, a reliable and robust vacuum-outlet gas chromatography-mass spectrometry (GC-MS) method is introduced for the identification and quantification of impurities in trinitrotoluene (TNT). Vacuum-outlet GC-MS allows for short analysis times; the analysis of impurities in TNT was performed in 4min. This study shows that impurity profiling of TNT can be used to investigate relations between TNT samples encountered in forensic casework. A wide variety of TNT samples were analyzed with the developed method. Dinitrobenzene, dinitrotoluene, trinitrotoluene and amino-dinitrotoluene isomers were detected at very low levels (<1wt.%) by applying the MS in selected-ion monitoring (SIM) mode. Limits of detection ranged from 6ng/mL for 2,6-dinitrotoluene to 43ng/mL for 4-amino-2,6-dinitrotoluene. Major impurities in TNT were 2,4-dinitrotoluene and 2,3,4-trinitrotoluene. Impurity profiles based on seven compounds showed to be useful to TNT samples from different sources. Statistical analysis of these impurity profiles using likelihood ratios demonstrated the potential to investigate whether two questioned TNT samples encountered in forensic casework are from the same source. Copyright © 2014 Elsevier B.V. All rights reserved.

Inversion of TEM data and analysis of the 2D induced magnetic field applied to the aquifers characterization in the Paraná basin, Brazil

NASA Astrophysics Data System (ADS)

Realpe Campaña, Julian David; Porsani, Jorge Luís; Bortolozo, Cassiano Antonio; Serejo de Oliveira, Gabriela; Monteiro dos Santos, Fernando Acácio

2017-03-01

Results of a TEM profile by using the fixed-loop array and an analysis of the induced magnetic field are presented in this work performed in the northwest region of São Paulo State, Brazil, Paraná Basin. The objectives of this research were to map the sedimentary and crystalline aquifers in the area and analyzing the behavior of the magnetic field by observation of magnetic profiles. TEM measurements in the three spatial components were taken to create magnetic profiles of the induced (secondary) magnetic field. The TEM data were acquired using a fixed transmitter loop of 200 m × 200 m and a 3D coil receiver moving along a profile line of 1000 m. Magnetic profiles of dBz, dBx and dBy components showed symmetrical spatial behavior related with loop geometry. z-component showed a behavior probably related to superparamagnetic effect (SPM). dBz data was used to perform individual 1D inversion for each position and to generate an interpolated pseudo-2D geoelectric profile. The results showed two low resistivity zones: the first shallow, between 10 m and 70 m deep, probably related to the Adamantina Formation (sedimentary aquifer). The second between 200 m and 300 m depth, probably related to a fractured zone filled with water or clay inside the basalt layer of the Serra Geral Formation (crystalline aquifer). These results agree with the well logs information available in the studied region.

Cluster analysis of particulate matter (PM10) and black carbon (BC) concentrations

NASA Astrophysics Data System (ADS)

Žibert, Janez; Pražnikar, Jure

2012-09-01

The monitoring of air-pollution constituents like particulate matter (PM10) and black carbon (BC) can provide information about air quality and the dynamics of emissions. Air quality depends on natural and anthropogenic sources of emissions as well as the weather conditions. For a one-year period the diurnal concentrations of PM10 and BC in the Port of Koper were analysed by clustering days into similar groups according to the similarity of the BC and PM10 hourly derived day-profiles without any prior assumptions about working and non-working days, weather conditions or hot and cold seasons. The analysis was performed by using k-means clustering with the squared Euclidean distance as the similarity measure. The analysis showed that 10 clusters in the BC case produced 3 clusters with just one member day and 7 clusters that encompasses more than one day with similar BC profiles. Similar results were found in the PM10 case, where one cluster has a single-member day, while 7 clusters contain several member days. The clustering analysis revealed that the clusters with less pronounced bimodal patterns and low hourly and average daily concentrations for both types of measurements include the most days in the one-year analysis. A typical day profile of the BC measurements includes a bimodal pattern with morning and evening peaks, while the PM10 measurements reveal a less pronounced bimodality. There are also clusters with single-peak day-profiles. The BC data in such cases exhibit morning peaks, while the PM10 data consist of noon or afternoon single peaks. Single pronounced peaks can be explained by appropriate cluster wind speed profiles. The analysis also revealed some special day-profiles. The BC cluster with a high midnight peak at 30/04/2010 and the PM10 cluster with the highest observed concentration of PM10 at 01/05/2010 (208.0 μg m-3) coincide with 1 May, which is a national holiday in Slovenia and has very strong tradition of bonfire parties. The clustering of the diurnal concentration showed that various different day-profiles are presented in a cold period, while this is not the case for the hot season. Additional analysis of ship traffic and rain fall data showed that there is no statistically significant difference between the ship gross (bruto) registered tonnage (BRT) values in the case of BC and PM10 clusters, but that there is statistically significant differences between the rain fall in the BC and PM10 clusters. The wind-rose for clusters which included most days in the sampling period indicating that emitted PM10 and BC from Port of Koper were manly transported in the west direction over the sea and in the east direction, where there is in no populated area. Presented analysis showed that both BC and PM10 concentrations were driven by rain intensity and wind speed.

Influence of anteroposterior mandibular positions on facial attractiveness in Japanese adults.

PubMed

Kuroda, Shingo; Sugahara, Takako; Takabatake, Souichirou; Taketa, Hiroaki; Ando, Ryoko; Takano-Yamamoto, Teruko

2009-01-01

Our aims in this study were to determine the anteroposterior facial relationship that is regarded as most attractive by Japanese laypersons in a questionnaire survey and to evaluate which analysis of the soft-tissue profile is most suitable for Japanese people. We showed 262 Japanese laypersons (121 male, 141 female) 9 morphed profile images with Point B and menton anteriorly or distally moved by software and asked them to number them sequentially according to their attractiveness. To examine which analysis best reflects facial attractiveness as judged by laypersons, we made 5 types of analyses of the facial profile with 11 variables in the 9 images. The normal face was judged favorably; however, an attractive profile might be different for each subject. The 3 highest ranking profiles (normal face and moderate mandibular retrusions) were often favorites, and 2 profiles (severe mandibular protrusions) were liked the least for most subjects. However, the other images showed a wide range of distribution. Mandibular retrusion was generally more favored than mandibular protrusion and bimaxillary protrusion (severe chin retrusion) had a high attractiveness ranking and was well accepted in the Japanese population. To evaluate the profiles of Japanese subjects, it is important to evaluate not only the esthetic line defined by the nose and chin, but also the balance of the upper and lower lips defined by the posterior reference line--ie, Burstone's Sn-Pog' line.

Secondary metabolite profiling of Curcuma species grown at different locations using GC/TOF and UPLC/Q-TOF MS.

PubMed

Lee, Jueun; Jung, Youngae; Shin, Jeoung-Hwa; Kim, Ho Kyoung; Moon, Byeong Cheol; Ryu, Do Hyun; Hwang, Geum-Sook

2014-07-04

Curcuma, a genus of rhizomatous herbaceous species, has been used as a spice, traditional medicine, and natural dye. In this study, the metabolite profile of Curcuma extracts was determined using gas chromatography-time of flight mass spectrometry (GC/TOF MS) and ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS) to characterize differences between Curcuma aromatica and Curcuma longa grown on the Jeju-do or Jin-do islands, South Korea. Previous studies have performed primary metabolite profiling of Curcuma species grown in different regions using NMR-based metabolomics. This study focused on profiling of secondary metabolites from the hexane extract of Curcuma species. Principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) plots showed significant differences between the C. aromatica and C. longa metabolite profiles, whereas geographical location had little effect. A t-test was performed to identify statistically significant metabolites, such as terpenoids. Additionally, targeted profiling using UPLC/Q-TOF MS showed that the concentration of curcuminoids differed depending on the plant origin. Based on these results, a combination of GC- and LC-MS allowed us to analyze curcuminoids and terpenoids, the typical bioactive compounds of Curcuma, which can be used to discriminate Curcuma samples according to species or geographical origin.

Kinetic simulations of the stability of a plasma confined by the magnetic field of a current rod

NASA Astrophysics Data System (ADS)

Tonge, J.; Leboeuf, J. N.; Huang, C.; Dawson, J. M.

2003-09-01

The kinetic stability of a plasma in the magnetic field of a current rod is investigated for various temperature and density profiles using three-dimensional particle-in-cell simulations. Such a plasma obeys similar physics to a plasma in a dipole magnetic field, while it is easier to perform computer simulations, and do theoretical analysis, of a plasma in the field of a current rod. Simple energy principle calculations and simulations with a variety of temperature and density profiles show that the plasma is stable to interchange for pressure profiles proportional to r-10/3. As predicted by theory the simulations also show that the density profile will be stationary as long as density is proportional to r-2 even though the temperature profile may not be stable.

Tensile properties of cooked meat sausages and their correlation with texture profile analysis (TPA) parameters and physico-chemical characteristics.

PubMed

Herrero, A M; de la Hoz, L; Ordóñez, J A; Herranz, B; Romero de Ávila, M D; Cambero, M I

2008-11-01

The possibilities of using breaking strength (BS) and energy to fracture (EF) for monitoring textural properties of some cooked meat sausages (chopped, mortadella and galantines) were studied. Texture profile analysis (TPA), folding test and physico-chemical measurements were also performed. Principal component analysis enabled these meat products to be grouped into three textural profiles which showed significant (p<0.05) differences mainly for BS, hardness, adhesiveness and cohesiveness. Multivariate analysis indicated that BS, EF and TPA parameters were correlated (p<0.05) for every individual meat product (chopped, mortadella and galantines) and all products together. On the basis of these results, TPA parameters could be used for constructing regression models to predict BS. The resulting regression model for all cooked meat products was BS=-0.160+6.600∗cohesiveness-1.255∗adhesiveness+0.048∗hardness-506.31∗springiness (R(2)=0.745, p<0.00005). Simple linear regression analysis showed significant coefficients of determination between BS (R(2)=0.586, p<0.0001) versus folding test grade (FG) and EF versus FG (R(2)=0.564, p<0.0001).

TEXTINFO: a tool for automatic determination of patient clinical profiles using text analysis.

PubMed Central

Borst, F.; Lyman, M.; Nhàn, N. T.; Tick, L. J.; Sager, N.; Scherrer, J. R.

1991-01-01

The clinical data contained in narrative patient documents is made available via grammatical and semantic processing. Retrievals from the resulting relational database tables are matched against a set of clinical descriptors to obtain clinical profiles of the patients in terms of the descriptors present in the documents. Discharge summaries of 57 Dept. of Digestive Surgery patients were processed in this manner. Factor analysis and discriminant analysis procedures were then applied, showing the profiles to be useful for diagnosis definitions (by establishing relations between diagnoses and clinical findings), for diagnosis assessment (by viewing the match between a definition and observed events recorded in a patient text), and potentially for outcome evaluation based on the classification abilities of clinical signs. PMID:1807679

Searching for a neurologic injury's Wechsler Adult Intelligence Scale-Third Edition profile.

PubMed

Gonçalves, Marta A; Moura, Octávio; Castro-Caldas, Alexandre; Simões, Mário R

2017-01-01

This study aimed to investigate the presence of a Wechsler Adult Intelligence Scale-Third Edition (WAIS-III) cognitive profile in a Portuguese neurologic injured sample. The Portuguese WAIS-III was administered to 81 mixed neurologic patients and 81 healthy matched controls selected from the Portuguese standardization sample. Although the mixed neurologic injury group performed significantly lower than the healthy controls for the majority of the WAIS-III scores (i.e., composite measures, discrepancies, and subtests), the mean scores were within the normal range and, therefore, at risk of being unobserved in a clinical evaluation. ROC curves analysis showed poor to acceptable diagnostic accuracy for the WAIS-III composite measures and subtests (Working Memory Index and Digit Span revealed the highest accuracy for discriminating between participants, respectively). Multiple regression analysis showed that both literacy and the presence of brain injury were significant predictors for all of the composite measures. In addition, multiple regression analysis also showed that literacy, age of injury onset, and years of survival predicted all seven composite measures for the mixed neurologic injured group. Despite the failure to find a WAIS-III cognitive profile for mixed neurologic patients, the results showed a significant influence of brain lesion and literacy in the performance of the WAIS-III.

Novel and successful free comments method for sensory characterization of chocolate ice cream: A comparative study between pivot profile and comment analysis.

PubMed

Fonseca, Fernando G A; Esmerino, Erick A; Filho, Elson R Tavares; Ferraz, Juliana P; da Cruz, Adriano G; Bolini, Helena M A

2016-05-01

Rapid sensory profiling methods have gained space in the sensory evaluation field. Techniques using direct analysis of the terms generated by consumers are considered easy to perform, without specific training requirements, thus improving knowledge about consumer perceptions on various products. This study aimed to determine the sensory profile of different commercial samples of chocolate ice cream, labeled as conventional and light or diet, using the "comment analysis" and "pivot profile" methods, based on consumers' perceptions. In the comment analysis task, consumers responded to 2 separate open questions describing the sensory attributes they liked or disliked in each sample. In the pivot profile method, samples were served in pairs (consisting of a coded sample and pivot), and consumers indicated the higher and lower intensity attributes in the target sample compared with the pivot. We observed that both methods were able to characterize the different chocolate ice cream samples using consumer perception, with high correlation results and configurational similarity (regression vector coefficient=0.917) between them. However, it is worth emphasizing that comment analysis is performed intuitively by consumers, whereas the pivot profile method showed high analytical and discriminative power even using consumers, proving to be a promising technique for routine application when classical descriptive methods cannot be used. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Identifying patterns of motor performance, executive functioning, and verbal ability in preschool children: A latent profile analysis.

PubMed

Houwen, Suzanne; Kamphorst, Erica; van der Veer, Gerda; Cantell, Marja

2018-04-30

A relationship between motor performance and cognitive functioning is increasingly being recognized. Yet, little is known about the precise nature of the relationship between both domains, especially in early childhood. To identify distinct constellations of motor performance, executive functioning (EF), and verbal ability in preschool aged children; and to explore how individual and contextual variables are related to profile membership. The sample consisted of 119 3- to 4-year old children (62 boys; 52%). The home based assessments consisted of a standardized motor test (Movement Assessment Battery for Children - 2), five performance-based EF tasks measuring inhibition and working memory, and the Receptive Vocabulary subtest from the Wechsler Preschool and Primary Scale of Intelligence Third Edition. Parents filled out the Behavior Rating Inventory of Executive Function - Preschool version. Latent profile analysis (LPA) was used to delineate profiles of motor performance, EF, and verbal ability. Chi-square statistics and multinomial logistic regression analysis were used to examine whether profile membership was predicted by age, gender, risk of motor coordination difficulties, ADHD symptomatology, language problems, and socioeconomic status (SES). LPA yielded three profiles with qualitatively distinct response patterns of motor performance, EF, and verbal ability. Quantitatively, the profiles showed most pronounced differences with regard to parent ratings and performance-based tests of EF, as well as verbal ability. Risk of motor coordination difficulties and ADHD symptomatology were associated with profile membership, whereas age, gender, language problems, and SES were not. Our results indicate that there are distinct subpopulations of children who show differential relations with regard to motor performance, EF, and verbal ability. The fact that we found both quantitative as well as qualitative differences between the three patterns of profiles underscores the need for a person-centered approach with a focus on patterns of individual characteristics. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Influence of the Aspheric Profiles for Transition Zone on Optical Performance of Human Eye After Conventional Ablation

NASA Astrophysics Data System (ADS)

Fang, L.

2014-12-01

The analysis in the impact of transition zone on the optical performance of human eye after laser refractive surgery is important for improving visual correction technology. By designing the ablation profiles of aspheric transition zone and creating the ablation profile for conventional refractive surgery in optical zone, the influence of aspheric transition zone on residual aberrations was studied. The results indicated that the ablation profiles of transition zone had a significant influence on the residual wavefront aberrations. For a hyperopia correction, the profile #9 shows a larger induced coma and spherical aberration when the translation of the centre of pupil remains constant. However, for a myopia astigmatism correction, the induced coma and spherical aberration in profile #1 shows relatively larger RMS values than those in other profiles. Therefore, the residual higher order aberrations may be decreased by optimizing ablation profiles of transition zone, but they cannot be eliminated. In order to achieve the best visual performance, the design of ablation pattern of transition zone played a crucial role.

Neuro- and social-cognitive clustering highlights distinct profiles in adults with anorexia nervosa.

PubMed

Renwick, Beth; Musiat, Peter; Lose, Anna; DeJong, Hannah; Broadbent, Hannah; Kenyon, Martha; Loomes, Rachel; Watson, Charlotte; Ghelani, Shreena; Serpell, Lucy; Richards, Lorna; Johnson-Sabine, Eric; Boughton, Nicky; Treasure, Janet; Schmidt, Ulrike

2015-01-01

This study aimed to explore the neuro- and social-cognitive profile of a consecutive series of adult outpatients with anorexia nervosa (AN) when compared with widely available age and gender matched historical control data. The relationship between performance profiles, clinical characteristics, service utilization, and treatment adherence was also investigated. Consecutively recruited outpatients with a broad diagnosis of AN (restricting subtype AN-R: n = 44, binge-purge subtype AN-BP: n = 33 or Eating Disorder Not Otherwise Specified-AN subtype EDNOS-AN: n = 23) completed a comprehensive set of neurocognitive (set-shifting, central coherence) and social-cognitive measures (Emotional Theory of Mind). Data were subjected to hierarchical cluster analysis and a discriminant function analysis. Three separate, meaningful clusters emerged. Cluster 1 (n = 45) showed overall average to high average neuro- and social- cognitive performance, Cluster 2 (n = 38) showed mixed performance characterized by distinct strengths and weaknesses, and Cluster 3 (n = 17) showed poor overall performance (Autism Spectrum disorder (ASD) like cluster). The three clusters did not differ in terms of eating disorder symptoms, comorbid features or service utilization and treatment adherence. A discriminant function analysis confirmed that the clusters were best characterized by performance in perseveration and set-shifting measures. The findings suggest that considerable neuro- and social-cognitive heterogeneity exists in patients with AN, with a subset showing ASD-like features. The value of this method of profiling in predicting longer term patient outcomes and in guiding development of etiologically targeted treatments remains to be seen. © 2014 Wiley Periodicals, Inc.

The Development and Use of Internal Amplification Controls (IACs) with DNA Profiling Kits for Forensic DNA Analysis.

PubMed

Zahra, Nathalie; Goodwin, William

2016-01-01

Biological samples recovered for forensic investigations are often degraded and/or have low amounts of DNA; in addition, in some instances the samples may be contaminated with chemicals that can act as PCR inhibitors. As a consequence this can make interpretation of the results challenging with the possibility of having partial profiles and false negative results. Because of the impact of DNA analysis on forensic investigations, it is important to monitor the process of DNA profiling, in particular the amplification reaction. In this chapter we describe a method for the in-house generation and use of internal amplification controls (IACs) with DNA profiling kits to monitor the success of the PCR proces. In the example we show the use of the SGM Plus® kit. These controls can also be used to aid the interpretation of the DNA profile.

Measurements of Reynolds stress profiles in unstratified tidal flow

USGS Publications Warehouse

Stacey, M.T.; Monismith, Stephen G.; Burau, J.R.

1999-01-01

In this paper we present a method for measuring profiles of turbulence quantities using a broadband acoustic doppler current profiler (ADCP). The method follows previous work on the continental shelf and extends the analysis to develop estimates of the errors associated with the estimation methods. ADCP data was collected in an unstratified channel and the results of the analysis are compared to theory. This comparison shows that the method provides an estimate of the Reynolds stresses, which is unbiased by Doppler noise, and an estimate of the turbulent kinetic energy (TKE) which is biased by an amount proportional to the Doppler noise. The noise in each of these quantities as well as the bias in the TKE match well with the theoretical values produced by the error analysis. The quantification of profiles of Reynolds stresses simultaneous with the measurement of mean velocity profiles allows for extensive analysis of the turbulence of the flow. In this paper, we examine the relation between the turbulence and the mean flow through the calculation of u*, the friction velocity, and Cd, the coefficient of drag. Finally, we calculate quantities of particular interest in turbulence modeling and analysis, the characteristic lengthscales, including a lengthscale which represents the stream-wise scale of the eddies which dominate the Reynolds stresses. Copyright 1999 by the American Geophysical Union.

Experimental verification, and domain definition, of structural alerts for protein binding: epoxides, lactones, nitroso, nitros, aldehydes and ketones.

PubMed

Nelms, M D; Cronin, M T D; Schultz, T W; Enoch, S J

2013-01-01

This study outlines how a combination of in chemico and Tetrahymena pyriformis data can be used to define the applicability domain of selected structural alerts within the profilers of the OECD QSAR Toolbox. Thirty-three chemicals were profiled using the OECD and OASIS profilers, enabling the applicability domain of six structural alerts to be defined, the alerts being: epoxides, lactones, nitrosos, nitros, aldehydes and ketones. Analysis of the experimental data showed the applicability domains for the epoxide, nitroso, aldehyde and ketone structural alerts to be well defined. In contrast, the data showed the applicability domains for the lactone and nitro structural alerts needed modifying. The accurate definition of the applicability domain for structural alerts within in silico profilers is important due to their use in the chemical category in predictive and regulatory toxicology. This study highlights the importance of utilizing multiple profilers in category formation.

Association between Pesticide Profiles Used on Agricultural Fields near Maternal Residences during Pregnancy and IQ at Age 7 Years

PubMed Central

Coker, Eric; Gunier, Robert; Bradman, Asa; Harley, Kim; Kogut, Katherine; Molitor, John; Eskenazi, Brenda

2017-01-01

We previously showed that potential prenatal exposure to agricultural pesticides was associated with adverse neurodevelopmental outcomes in children, yet the effects of joint exposure to multiple pesticides is poorly understood. In this paper, we investigate associations between the joint distribution of agricultural use patterns of multiple pesticides (denoted as “pesticide profiles”) applied near maternal residences during pregnancy and Full-Scale Intelligence Quotient (FSIQ) at 7 years of age. Among a cohort of children residing in California’s Salinas Valley, we used Pesticide Use Report (PUR) data to characterize potential exposure from use within 1 km of maternal residences during pregnancy for 15 potentially neurotoxic pesticides from five different chemical classes. We used Bayesian profile regression (BPR) to examine associations between clustered pesticide profiles and deficits in childhood FSIQ. BPR identified eight distinct clusters of prenatal pesticide profiles. Two of the pesticide profile clusters exhibited some of the highest cumulative pesticide use levels and were associated with deficits in adjusted FSIQ of −6.9 (95% credible interval: −11.3, −2.2) and −6.4 (95% credible interval: −13.1, 0.49), respectively, when compared with the pesticide profile cluster that showed the lowest level of pesticides use. Although maternal residence during pregnancy near high agricultural use of multiple neurotoxic pesticides was associated with FSIQ deficit, the magnitude of the associations showed potential for sub-additive effects. Epidemiologic analysis of pesticides and their potential health effects can benefit from a multi-pollutant approach to analysis. PMID:28486423

Missing Pages? A Study of Textbooks for Dutch Early Childhood Teacher Education

ERIC Educational Resources Information Center

Fukkink, Ruben G.

2010-01-01

A content analysis of the textbooks used in the Dutch early childhood teacher education shows clear inconsistencies with the intended curriculum. Neither the content standards found in the professional profile for teachers nor the content standards from the educational profile of their training courses are adequately covered in the books. Whilst…

Integrative Analysis of Longitudinal Metabolomics Data from a Personal Multi-Omics Profile

PubMed Central

Stanberry, Larissa; Mias, George I.; Haynes, Winston; Higdon, Roger; Snyder, Michael; Kolker, Eugene

2013-01-01

The integrative personal omics profile (iPOP) is a pioneering study that combines genomics, transcriptomics, proteomics, metabolomics and autoantibody profiles from a single individual over a 14-month period. The observation period includes two episodes of viral infection: a human rhinovirus and a respiratory syncytial virus. The profile studies give an informative snapshot into the biological functioning of an organism. We hypothesize that pathway expression levels are associated with disease status. To test this hypothesis, we use biological pathways to integrate metabolomics and proteomics iPOP data. The approach computes the pathways’ differential expression levels at each time point, while taking into account the pathway structure and the longitudinal design. The resulting pathway levels show strong association with the disease status. Further, we identify temporal patterns in metabolite expression levels. The changes in metabolite expression levels also appear to be consistent with the disease status. The results of the integrative analysis suggest that changes in biological pathways may be used to predict and monitor the disease. The iPOP experimental design, data acquisition and analysis issues are discussed within the broader context of personal profiling. PMID:24958148

Gene Expression Profile Change and Associated Physiological and Pathological Effects in Mouse Liver Induced by Fasting and Refeeding

PubMed Central

Zhang, Fang; Xu, Xiang; Zhou, Ben; He, Zhishui; Zhai, Qiwei

2011-01-01

Food availability regulates basal metabolism and progression of many diseases, and liver plays an important role in these processes. The effects of food availability on digital gene expression profile, physiological and pathological functions in liver are yet to be further elucidated. In this study, we applied high-throughput sequencing technology to detect digital gene expression profile of mouse liver in fed, fasted and refed states. Totally 12162 genes were detected, and 2305 genes were significantly regulated by food availability. Biological process and pathway analysis showed that fasting mainly affected lipid and carboxylic acid metabolic processes in liver. Moreover, the genes regulated by fasting and refeeding in liver were mainly enriched in lipid metabolic process or fatty acid metabolism. Network analysis demonstrated that fasting mainly regulated Drug Metabolism, Small Molecule Biochemistry and Endocrine System Development and Function, and the networks including Lipid Metabolism, Small Molecule Biochemistry and Gene Expression were affected by refeeding. In addition, FunDo analysis showed that liver cancer and diabetes mellitus were most likely to be affected by food availability. This study provides the digital gene expression profile of mouse liver regulated by food availability, and demonstrates the main biological processes, pathways, gene networks and potential hepatic diseases regulated by fasting and refeeding. These results show that food availability mainly regulates hepatic lipid metabolism and is highly correlated with liver-related diseases including liver cancer and diabetes. PMID:22096593

Identifying arsenic trioxide (ATO) functions in leukemia cells by using time series gene expression profiles.

PubMed

Yang, Hong; Lin, Shan; Cui, Jingru

2014-02-10

Arsenic trioxide (ATO) is presently the most active single agent in the treatment of acute promyelocytic leukemia (APL). In order to explore the molecular mechanism of ATO in leukemia cells with time series, we adopted bioinformatics strategy to analyze expression changing patterns and changes in transcription regulation modules of time series genes filtered from Gene Expression Omnibus database (GSE24946). We totally screened out 1847 time series genes for subsequent analysis. The KEGG (Kyoto encyclopedia of genes and genomes) pathways enrichment analysis of these genes showed that oxidative phosphorylation and ribosome were the top 2 significantly enriched pathways. STEM software was employed to compare changing patterns of gene expression with assigned 50 expression patterns. We screened out 7 significantly enriched patterns and 4 tendency charts of time series genes. The result of Gene Ontology showed that functions of times series genes mainly distributed in profiles 41, 40, 39 and 38. Seven genes with positive regulation of cell adhesion function were enriched in profile 40, and presented the same first increased model then decreased model as profile 40. The transcription module analysis showed that they mainly involved in oxidative phosphorylation pathway and ribosome pathway. Overall, our data summarized the gene expression changes in ATO treated K562-r cell lines with time and suggested that time series genes mainly regulated cell adhesive. Furthermore, our result may provide theoretical basis of molecular biology in treating acute promyelocytic leukemia. Copyright © 2013 Elsevier B.V. All rights reserved.

Gene expression profile change and associated physiological and pathological effects in mouse liver induced by fasting and refeeding.

PubMed

Zhang, Fang; Xu, Xiang; Zhou, Ben; He, Zhishui; Zhai, Qiwei

2011-01-01

Food availability regulates basal metabolism and progression of many diseases, and liver plays an important role in these processes. The effects of food availability on digital gene expression profile, physiological and pathological functions in liver are yet to be further elucidated. In this study, we applied high-throughput sequencing technology to detect digital gene expression profile of mouse liver in fed, fasted and refed states. Totally 12162 genes were detected, and 2305 genes were significantly regulated by food availability. Biological process and pathway analysis showed that fasting mainly affected lipid and carboxylic acid metabolic processes in liver. Moreover, the genes regulated by fasting and refeeding in liver were mainly enriched in lipid metabolic process or fatty acid metabolism. Network analysis demonstrated that fasting mainly regulated Drug Metabolism, Small Molecule Biochemistry and Endocrine System Development and Function, and the networks including Lipid Metabolism, Small Molecule Biochemistry and Gene Expression were affected by refeeding. In addition, FunDo analysis showed that liver cancer and diabetes mellitus were most likely to be affected by food availability. This study provides the digital gene expression profile of mouse liver regulated by food availability, and demonstrates the main biological processes, pathways, gene networks and potential hepatic diseases regulated by fasting and refeeding. These results show that food availability mainly regulates hepatic lipid metabolism and is highly correlated with liver-related diseases including liver cancer and diabetes.

The temporal change in the cortical activations due to salty and sweet tastes in humans: fMRI and time-intensity sensory evaluation.

PubMed

Nakamura, Yuko; Goto, Tazuko K; Tokumori, Kenji; Yoshiura, Takashi; Kobayashi, Koji; Nakamura, Yasuhiko; Honda, Hiroshi; Ninomiya, Yuzo; Yoshiura, Kazunori

2012-04-18

It remains unclear how the cerebral cortex of humans perceives taste temporally, and whether or not such objective data about the brain show a correlation with the current widely used conventional methods of taste-intensity sensory evaluation. The aim of this study was to investigate the difference in the time-intensity profile between salty and sweet tastes in the human brain. The time-intensity profiles of functional MRI (fMRI) data of the human taste cortex were analyzed using finite impulse response analysis for a direct interpretation in terms of the peristimulus time signal. Also, time-intensity sensory evaluations for tastes were performed under the same condition as fMRI to confirm the reliability of the temporal profile in the fMRI data. The time-intensity profile for the brain activations due to a salty taste changed more rapidly than those due to a sweet taste in the human brain cortex and was also similar to the time-intensity sensory evaluation, confirming the reliability of the temporal profile of the fMRI data. In conclusion, the time-intensity profile using finite impulse response analysis for fMRI data showed that there was a temporal difference in the neural responses between salty and sweet tastes over a given period of time. This indicates that there might be taste-specific temporal profiles of activations in the human brain.

Terminal restriction fragment length polymorphism profiling of bacterial flora derived from single human hair shafts can discriminate individuals.

PubMed

Nishi, Eiji; Watanabe, Kota; Tashiro, Yukihiro; Sakai, Kenji

2017-03-01

Human hairs are the trace evidence most commonly encountered at many crime scenes. However, they have not been effectively utilized for actual criminal investigations because of the low accuracy of their morphological inspection, low detection rate of short tandem repeat (STR) typing, and the problem of heteroplasmy in mitochondrial DNA analysis. Here, we examined the possibility of individual discrimination by comparing profiles of bacterial flora on hair. We carried out the profiling of terminal restriction fragment length polymorphisms (T-RFLP) of the amplified bacterial 16S ribosomal RNA (rRNA) gene from hair samples. Compared with existing STR typing methods that use hair roots, this method using hair shafts allowed the detection of stable bacterial DNA. We successfully obtained the T-RFLP profile from single hair shafts of all volunteers tested. The profiles were specific to each individual, and multiple profiles obtained from the individual him/herself showed higher similarity than those from different individuals. These individual-specific profiles were stably obtained from samples from most volunteers, when collected again after 6months. Storage of the collected hair samples at -30°C was effective for obtaining reproducible T-RF profiles. When unidentified hair samples collected in the laboratory were compared with a pre-constructed database, 17 of 22 hairs were assigned to a small group of people, including the corresponding individuals. These results show that T-RFLP analysis of bacterial flora on a hair shaft found at a crime scene could provide useful information for narrowing down a suspect. Copyright © 2017 Elsevier B.V. All rights reserved.

Verification of key odorants in rose oil by gas chromatography-olfactometry/aroma extract dilution analysis, odour activity value and aroma recombination.

PubMed

Xiao, Zuobing; Li, Jing; Niu, Yunwei; Liu, Qiang; Liu, Junhua

2017-10-01

Rose oil is much too expensive but very popular. It's well known that the flower oil's aroma profile hasn't been intensively investigated. In order to verify the aroma profile of rose oil, the synthetic blend of odorants was prepared and then compared with the original rose oil using electronic nose analysis (ENA) combined with quantitative descriptive analysis (QDA). The odorants from rose oils were screened out by Gas Chromatography-Olfactometry/aroma extract dilution analysis (GC-O/AEDA) combined with odour activity value (OAV). Both ENA and QDA indicated the recombination model derived from OAV and GC-O/AEDA closely resembled the original rose oil. The experiment results show that rose oxide, linalool, α-pinene, β-pinene, nonanal, heptanal citronellal, phenyl ethyl alcohol, benzyl alcohol, eugenol, methyl eugenol, β-citronellol, hexyl acetate, β-ionone, nerol, etc. are very important constituent to rose oil aroma profile.

Brightness analysis of an electron beam with a complex profile

NASA Astrophysics Data System (ADS)

Maesaka, Hirokazu; Hara, Toru; Togawa, Kazuaki; Inagaki, Takahiro; Tanaka, Hitoshi

2018-05-01

We propose a novel analysis method to obtain the core bright part of an electron beam with a complex phase-space profile. This method is beneficial to evaluate the performance of simulation data of a linear accelerator (linac), such as an x-ray free electron laser (XFEL) machine, since the phase-space distribution of a linac electron beam is not simple, compared to a Gaussian beam in a synchrotron. In this analysis, the brightness of undulator radiation is calculated and the core of an electron beam is determined by maximizing the brightness. We successfully extracted core electrons from a complex beam profile of XFEL simulation data, which was not expressed by a set of slice parameters. FEL simulations showed that the FEL intensity was well remained even after extracting the core part. Consequently, the FEL performance can be estimated by this analysis without time-consuming FEL simulations.

Latent profile analysis of students' motivation and outcomes in mathematics: an organismic integration theory perspective.

PubMed

Wang, Chee Keng John; Liu, Woon Chia; Nie, Youyan; Chye, Yen Leng Stefanie; Lim, Boon San Coral; Liem, Gregory Arief; Tay, Eng Guan; Hong, Ying-Yi; Chiu, Chi-Yue

2017-05-01

The purpose of the current study was to identify the motivation profiles at the intraindividual level using a latent profile analyses (LPA) approach. A total of 1151 secondary school students aged 13 to 17 years old from Singapore took part in the study. Using LPA, four distinct motivational profiles were identified based on four motivation regulations. Profile 1 has very low introjected and low autonomous motivation (6% of sample). Profile 2 had high external and identified regulations and very low intrinsic regulation (10%). Profile 3 consisted of students with high identified and intrinsic regulations (51%). Profile 4 had moderately low identified and intrinsic regulations (33%). The results showed that the four profiles differed significantly in terms of effort, competence, value, and time spent on math beyond homework. The best profile (Profile 3) reported highest scores in effort, value, competence and time spent on Math beyond homework. The worst profile (Profile 1) reported lowest scores in all the four outcome variables.

Genome-wide analysis and expression profiling of the Solanum tuberosum aquaporins.

PubMed

Venkatesh, Jelli; Yu, Jae-Woong; Park, Se Won

2013-12-01

Aquaporins belongs to the major intrinsic proteins involved in the transcellular membrane transport of water and other small solutes. A comprehensive genome-wide search for the homologues of Solanum tuberosum major intrinsic protein (MIP) revealed 41 full-length potato aquaporin genes. All potato aquaporins are grouped into five subfamilies; plasma membrane intrinsic proteins (PIPs), tonoplast intrinsic proteins (TIPs), NOD26-like intrinsic proteins (NIPs), small basic intrinsic proteins (SIPs) and x-intrinsic proteins (XIPs). Functional predictions based on the aromatic/arginine (ar/R) selectivity filters and Froger's positions showed a remarkable difference in substrate transport specificity among subfamilies. The expression pattern of potato aquaporins, examined by qPCR analysis, showed distinct expression profiles in various organs and tuber developmental stages. Furthermore, qPCR analysis of potato plantlets, subjected to various abiotic stresses revealed the marked effect of stresses on expression levels of aquaporins. Taken together, the expression profiles of aquaporins imply that aquaporins play important roles in plant growth and development, in addition to maintaining water homeostasis in response to environmental stresses. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Meta-analysis of pemetrexed plus carboplatin doublet safety profile in first-line non-squamous non-small cell lung cancer studies.

PubMed

Okamoto, Isamu; Schuette, Wolfgang H W; Stinchcombe, Thomas E; Rodrigues-Pereira, José; San Antonio, Belén; Chen, Jian; Liu, Jingyi; John, William J; Zinner, Ralph G

2017-05-01

This meta-analysis compared safety profiles (selected drug-related treatment-emergent adverse events [TEAEs]) of first-line pemetrexed plus carboplatin (PCb) area under the concentration-time curve 5 mg/min•mL (PCb5) or 6 mg/min•mL (PCb6), two widely used regimens in clinical practice for advanced non-squamous non-small cell lung cancer. All patients received pemetrexed 500 mg/m 2 every 21 days with either of two carboplatin doses for up to 4-6 cycles. Safety profiles of PCb doses were compared using three statistical analysis methods: frequency table analysis (FTA), generalized linear mixed effect model (GLMM), and the propensity score method. Efficacy outcomes of PCb5 and PCb6 regimens were summarized. A total of 486 patients mainly from the US, Europe, and East Asia were included in the analysis; 22% (n = 105) received PCb5 in one trial and 78% (n = 381) received PCb6 in four trials. The FTA comparison demonstrated that PCb5 vs PCb6 was associated with a statistically significantly lower incidence of TEAEs, including all-grade thrombocytopenia, anemia, fatigue, and vomiting, and grade 3/4 thrombocytopenia. In the GLMM analysis, PCb5 patients were numerically less likely to experience all-grade and grade 3/4 neutropenia, anemia, and thrombocytopenia. The propensity score regression analysis showed PCb5 group patients were significantly less likely than PCb6 group patients to experience all-grade hematologic TEAEs and grade 3/4 thrombocytopenia and anemia. After applying propensity score 1:1 matching, FTA analysis showed that the PCb5 group had significantly less all-grade and grade 3/4 hematologic toxicities. Overall efficacy outcomes, including overall survival, progression-free survival, and response rate, were similar between the two carboplatin doses. Acknowledging the limitations of this meta-analysis of five trials, heterogeneous in patient's characteristics and trial designs, the results show that the PCb5 regimen was generally associated with a better safety profile than PCb6 across three statistical approaches, with no apparent impact on survival outcomes.

The role of turbulent suppression in the triggering ITBs on C-Mod

NASA Astrophysics Data System (ADS)

Zhurovich, K.; Fiore, C. L.; Ernst, D. R.; Bonoli, P. T.; Greenwald, M. J.; Hubbard, A. E.; Hughes, J. W.; Marmar, E. S.; Mikkelsen, D. R.; Phillips, P.; Rice, J. E.

2007-11-01

Internal transport barriers can be routinely produced in C-Mod steady EDA H-mode plasmas by applying ICRF at |r/a|>= 0.5. Access to the off-axis ICRF heated ITBs may be understood within the paradigm of marginal stability. Analysis of the Te profiles shows a decrease of R/LTe in the ITB region as the RF resonance is moved off axis. Ti profiles broaden as the ICRF power deposition changes from on-axis to off-axis. TRANSP calculations of the Ti profiles support this trend. Linear GS2 calculations do not reveal any difference in ETG growth rate profiles for ITB vs. non-ITB discharges. However, they do show that the region of stability to ITG modes widens as the ICRF resonance is moved outward. Non-linear simulations show that the outward turbulent particle flux exceeds the Ware pinch by factor of 2 in the outer plasma region. Reducing the temperature gradient significantly decreases the diffusive flux and allows the Ware pinch to peak the density profile. Details of these experiments and simulations will be presented.

Clinical symptoms in fibromyalgia are associated to overweight and lipid profile.

PubMed

Cordero, Mario D; Alcocer-Gómez, Elísabet; Cano-García, Francisco J; Sánchez-Domínguez, Benito; Fernández-Riejo, Patricia; Moreno Fernández, Ana M; Fernández-Rodríguez, Ana; De Miguel, Manuel

2014-03-01

In order to analyze the association between body mass index (BMI), lipid profile and clinical symptoms in patients with fibromyalgia, we assessed BMI levels, lipid profile and its association with clinical symptoms in 183 patients with fibromyalgia. The patients were evaluated using tender points, FIQ and Visual Analogue Scales of pain (VAS). Serum lipid profile analysis (total cholesterol, triglyceride, HDL, LDL and VLDL), and biochemical parameters were measured in the biochemistry laboratory. The BMI distribution of the nonobese, overweight and obese patients' groups were relatively even with 37.7, 35.5 and 26.8%, respectively, with a mean BMI of 27.3 ± 4.9. The number of tender points showed significantly positive correlation with higher BMI (P < 0.05). A total of 57.9% of patients showed increased levels of total cholesterol, 63.4 % increased levels of LDL cholesterol and 19.9% high levels of triglycerides. BMI, total cholesterol and triglycerides showed high association with some clinical parameters. Overweight and lipid profile could be associated with fibromyalgia symptoms. A treatment program with weight loss strategies, and control in diet and increased physical activity is advised to patients.

Analysis of DGGE profiles to explore the relationship between prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin.

PubMed

Fry, John C; Webster, Gordon; Cragg, Barry A; Weightman, Andrew J; Parkes, R John

2006-10-01

The aim of this work was to relate depth profiles of prokaryotic community composition with geochemical processes in the deep subseafloor biosphere at two shallow-water sites on the Peru Margin in the Pacific Ocean (ODP Leg 201, sites 1228 and 1229). Principal component analysis of denaturing gradient gel electrophoresis banding patterns of deep-sediment Bacteria, Archaea, Euryarchaeota and the novel candidate division JS1, followed by multiple regression, showed strong relationships with prokaryotic activity and geochemistry (R(2)=55-100%). Further correlation analysis, at one site, between the principal components from the community composition profiles for Bacteria and 12 other variables quantitatively confirmed their relationship with activity and geochemistry, which had previously only been implied. Comparison with previously published cell counts enumerated by fluorescent in situ hybridization with rRNA-targeted probes confirmed that these denaturing gradient gel electrophoresis profiles described an active prokaryotic community.

Trace element profiles in modern horse molar enamel as tracers of seasonality: Evidence from micro-XRF, LA-ICP-MS and stable isotope analysis

NASA Astrophysics Data System (ADS)

de Winter, Niels; Goderis, Steven; van Malderen, Stijn; Vanhaecke, Frank; Claeys, Philippe

2016-04-01

A combination of laboratory micro-X-ray Fluorescence (μXRF) and stable carbon and oxygen isotope analysis shows that trace element profiles from modern horse molars reveal a seasonal pattern that co-varies with seasonality in the oxygen isotope records of enamel carbonate from the same teeth. A combination of six cheek teeth (premolars and molars) from the same individual yields a seasonal isotope and trace element record of approximately three years recorded during the growth of the molars. This record shows that reproducible measurements of various trace element ratios (e.g., Sr/Ca, Zn/Ca, Fe/Ca, K/Ca and S/Ca) lag the seasonal pattern in oxygen isotope records by 2-3 months. Laser Ablation-ICP-Mass Spectrometry (LA-ICP-MS) analysis on a cross-section of the first molar of the same individual is compared to the bench-top tube-excitation μXRF results to test the robustness of the measurements and to compare both methods. Furthermore, trace element (e.g. Sr, Zn, Mg & Ba) profiles perpendicular to the growth direction of the same tooth, as well as profiles parallel to the growth direction are measured with LA-ICP-MS and μXRF to study the internal distribution of trace element ratios in two dimensions. Results of this extensive complementary line-scanning procedure shows the robustness of state of the art laboratory micro-XRF scanning for the measurement of trace elements in bioapatite. The comparison highlights the advantages and disadvantages of both methods for trace element analysis and illustrates their complementarity. Results of internal variation within the teeth shed light on the origins of trace elements in mammal teeth and their potential use for paleo-environmental reconstruction.

Proton irradiation studies on Al and Al5083 alloy

NASA Astrophysics Data System (ADS)

Bhattacharyya, P.; Gayathri, N.; Bhattacharya, M.; Gupta, A. Dutta; Sarkar, Apu; Dhar, S.; Mitra, M. K.; Mukherjee, P.

2017-10-01

The change in the microstructural parameters and microhardness values in 6.5 MeV proton irradiated pure Al and Al5083 alloy samples have been evaluated using different model based techniques of X-ray diffraction Line Profile Analysis (XRD) and microindendation techniques. The detailed line profile analysis of the XRD data showed that the domain size increases and saturates with irradiation dose both in the case of Al and Al5083 alloy. The corresponding microstrain values did not show any change with irradiation dose in the case of the pure Al but showed an increase at higher irradiation doses in the case of Al5083 alloy. The microindendation results showed that unirradiated Al5083 alloy has higher hardness value compared to that of unirradiated pure Al. The hardness increased marginally with irradiation dose in the case of Al5083, whereas for pure Al, there was no significant change with dose.

Instrumental texture profile analysis of gelatin gel extracted from grouper skin and commercial (bovine and porcine) gelatin gels.

PubMed

Rahman, Mohammad Shafiur; Al-Mahrouqi, Abdullah Issa

2009-01-01

Mechanical compression was used to study the gelling characteristics of gelatin gels. Texture profile analysis (TPA) showed that the hardness of fish and mammalian gelatin increased significantly as the concentrations of gels increased. TPA attributes of 10% fish skin gel showed significant differences from those obtained from 20% and 30% gels. In bovine and porcine cases, such generic trends were not observed. Mechanical characteristics of 10% gels of gelatin from fish skin, determined from one cycle compression, were significantly lower than other sources of gelatin gels, while bovine and porcine gels did not show any significant differences. In the case of TPA, hardness of bovine gelatin gel was highest at 41 N for 10% gel, followed by porcine (30 N) then fish skin (5 N) gelatin gels. The gels prepared from different sources did not show any generic trends when all other mechanical attributes were considered.

Inclusive Education and ELT Policies in Colombia: Views from Some "PROFILE" Journal Authors

ERIC Educational Resources Information Center

Robayo Acuña, Lina María; Cárdenas, Melba Libia

2017-01-01

This article reports on a study aimed at exploring inclusive policies in the teaching of English as a foreign language in Colombia, as evidenced in the articles published in the "PROFILE" Journal by Colombian authors. The use of the documentary research method and critical discourse analysis showed that some policies--mainly The National…

Magnetotelluric 2D Modelling Provides Insight on the Structural Characteristics of the Guadalajara (Mexico) Triple Junction Domains

NASA Astrophysics Data System (ADS)

Arboleda Zapata, M. D. J., Sr.; Arzate-Flores, J.; Guevara Betancourt, R. E., Sr.

2017-12-01

The Jalisco Block is a continental microplate produced by the extension along three large structures: the Tepic-Zacoalco rift (TZR), the Colima rift (CR) and the Chapala rift that converge in a triple junction 50 km southwest of Guadalajara, Mexico, with orientation NW-SE, N-S, and E-W respectively. The present study focuses on investigating the deep structure of the north Colima and eastern Zacoalco grabens close to the Guadalajara triple junction (GTJ). This is a first study of its type that provide insight on the grabens structures and crustal characteristics underneath. We measured along two magnetotellurics (MT) profiles that cut perpendicularly the TZR (profile ZAC), and the northern CR (profile SAY) comprising a total of 24 broad band MT soundings. The ZAC profile has 11 stations and has a NE orientation, and the SAY profile has 14 station aligned E-W. Standard processing and editing procedures were completed, and distortion analysis was applied to the data set in order to define the dimensionality and electric strike of the separated profiles. Static shift was corrected using geology information to distinguish the different types of soundings and later averaging for those soundings located over the same lithology. The Bahr dimensionality parameters showed that the medium is mainly 3D for the SAY profile and 2D for the ZAC profile; furthermore, the regional geoelectric strike azimuth calculated with Bahr methodology were -4° and -48° respectively, with good concordance with the main surface structures. The tipper analysis permitted validated these results, as the real induction vectors were nearly perpendicular to main fault structures. All soundings were rotated to the respective regional strike and a 2D simultaneous inversion of the transverse electric (TE) mode, the transvers magnetic (TM) mode and the Tipper was completed. The RMS fitting error yield 3.2% for ZAC profile and 3.7% for SAY profile. Both profiles show a shallow conductive zone at north of the Colima Rift and the south of the Zacoalco rift, which are interpreted as lacustrine and fluvial sediments having maximum thickness of 1.5 and 1.0 km respectively. The profiles show a faulted resistive upper crust, 35 to 40 km thick, that is reliably correlated with mapped surface structures and consistent with two types of extensional processes.

MicroRNA profiling reveals new aspects of HIV neurodegeneration: caspase-6 regulates astrocyte survival.

PubMed

Noorbakhsh, Farshid; Ramachandran, Rithwik; Barsby, Nicola; Ellestad, Kristofor K; LeBlanc, Andrea; Dickie, Peter; Baker, Glen; Hollenberg, Morley D; Cohen, Eric A; Power, Christopher

2010-06-01

MicroRNAs (miRNAs) are small noncoding RNA molecules, which are known to regulate gene expression in physiological and pathological conditions. miRNA profiling was performed using brain tissue from patients with HIV encephalitis (HIVE), a neuroinflammatory/degenerative disorder caused by HIV infection of the brain. Microarray analysis showed differential expression of multiple miRNAs in HIVE compared to control brains. Target prediction and gene ontology enrichment analysis disclosed targeting of several gene families/biological processes by differentially expressed miRNAs (DEMs), with cell death-related genes, including caspase-6, showing a bias toward down-regulated DEMs. Consistent with the miRNA data, HIVE brains exhibited higher levels of caspase-6 transcripts compared with control patients. Immunohistochemical analysis showed localization of the cleaved form of caspase-6 in astrocytes in HIVE brain sections. Exposure of cultured human primary astrocytes to HIV viral protein R (Vpr) induced p53 up-regulation, loss of mitochondrial membrane potential, and caspase-6 activation followed by cell injury. Transgenic mice, expressing Vpr in microglial cells, demonstrated astrocyte apoptosis in brain, which was associated with caspase-6 activation and neurobehavioral abnormalities. Overall, these data point to previously unrecognized alterations in miRNA profile in the brain during HIV infection, which contribute to cell death through dysregulation of cell death machinery.

Profiles of Motor Laterality in Young Athletes' Performance of Complex Movements: Merging the MOTORLAT and PATHoops Tools

PubMed Central

Castañer, Marta; Andueza, Juan; Hileno, Raúl; Puigarnau, Silvia; Prat, Queralt; Camerino, Oleguer

2018-01-01

Laterality is a key aspect of the analysis of basic and specific motor skills. It is relevant to sports because it involves motor laterality profiles beyond left-right preference and spatial orientation of the body. The aim of this study was to obtain the laterality profiles of young athletes, taking into account the synergies between the support and precision functions of limbs and body parts in the performance of complex motor skills. We applied two instruments: (a) MOTORLAT, a motor laterality inventory comprising 30 items of basic, specific, and combined motor skills, and (b) the Precision and Agility Tapping over Hoops (PATHoops) task, in which participants had to perform a path by stepping in each of 14 hoops arranged on the floor, allowing the observation of their feet, left-right preference and spatial orientation. A total of 96 young athletes performed the PATHoops task and the 30 MOTORLAT items, allowing us to obtain data about limb dominance and spatial orientation of the body in the performance of complex motor skills. Laterality profiles were obtained by means of a cluster analysis and a correlational analysis and a contingency analysis were applied between the motor skills and spatial orientation actions performed. The results obtained using MOTORLAT show that the combined motor skills criterion (for example, turning while jumping) differentiates athletes' uses of laterality, showing a clear tendency toward mixed laterality profiles in the performance of complex movements. In the PATHoops task, the best spatial orientation strategy was “same way” (same foot and spatial wing) followed by “opposite way” (opposite foot and spatial wing), in keeping with the research assumption that actions unfolding in a horizontal direction in front of an observer's eyes are common in a variety of sports. PMID:29930527

Two different protein expression profiles of oral squamous cell carcinoma analyzed by immunoprecipitation high-performance liquid chromatography.

PubMed

Kim, Soung Min; Jeong, Dasul; Kim, Min Keun; Lee, Sang Shin; Lee, Suk Keun

2017-08-08

Oral squamous cell carcinoma (OSCC) is one of the most dangerous cancers in the body, producing serious complications with individual behaviors. Many different pathogenetic factors are involved in the carcinogenesis of OSCC. Cancer cells derived from oral keratinocytes can produce different carcinogenic signaling pathways through differences in protein expression, but their protein expression profiles cannot be easily explored with ordinary detection methods. The present study compared the protein expression profiles between two different types of OSCCs, which were analyzed through immunoprecipitation high-performance liquid chromatography (IP-HPLC). Two types of squamous cell carcinoma (SCC) occurred in a mandibular (SCC-1) and maxillary gingiva (SCC-2), but their clinical features and progression were quite different from each other. SCC-1 showed a large gingival ulceration with severe halitosis and extensive bony destruction, while SCC-2 showed a relatively small papillary gingival swelling but rapidly grew to form a large submucosal mass, followed by early cervical lymph node metastasis. In the histological observation, SCC-1 was relatively well differentiated with a severe inflammatory reaction, while SCC-2 showed severely infiltrative growth of each cancer islets accompanied with a mild inflammatory reaction. IP-HPLC analysis revealed contrary protein expression profiles analyzed by 72 different oncogenic proteins. SCC-1 showed more cellular apoptosis and invasive growth than SCC-2 through increased expression of caspases, MMPs, p53 signaling, FAS signaling, TGF-β1 signaling, and angiogenesis factors, while SCC-2 showed more cellular growth and survival than SCC-1 through the increased expression of proliferating factors, RAS signaling, eIF5A signaling, WNT signaling, and survivin. The increased trends of cellular apoptosis and invasiveness in the protein expression profiles of SCC-1 were implicative of its extensive gingival ulceration and bony destruction, while the increased trends of cellular proliferation and survival in the protein profile of SCC-2 were implicative of its rapid growing tumor mass and early lymph node metastasis. These analyses of the essential oncogenic protein expression profiles in OSCC provide important information for genetic counseling or customized gene therapy in cancer treatment. Therefore, protein expression profile analysis through IP-HPLC is helpful not only for the molecular genetic diagnosis of cancer but also in identifying target molecules for customized gene therapy in near future.

Comparison of three officinal species of Callicarpa based on a biochemome profiling strategy with UHPLC-IT-MS and chemometrics analysis.

PubMed

Chen, Meng-Lu; Chang, Wen-Qi; Zhou, Jian-Liang; Yin, Ying-Hao; Xia, Wen-Rui; Liu, Jian-Qun; Liu, Li-Fang; Xin, Gui-Zhong

2017-10-25

Traditional Chinese medicine (TCM) materials with closely related species are frequently fungible in clinical use. Therefore, holistic comparison of the composition in bioactive compounds is essential to evaluate whether they are equivalent in efficacy. Taking three officinal species of Callicarpa as a case, we proposed and validated a standardized strategy for the discrimination of closely related TCM materials, which focused on the extraction, profiling and multivariate statistical analysis of their biochemome. Firstly, serial liquid-liquid extractions were utilized to prepare different batches of Callicarpa biochemome, and the preparation yields were utilized for the normalization of sampling quantity prior to UHPLC-IT-MS analysis. Secondly, 34 compounds, including 19 phenylethanoid glycosides, 10 flavonoids and 5 terpenoids, were identified based on an untargeted UHPLC-IT-MS method. Thirdly, method validation of linearity, precision and stability showed that the UHPLC-IT-MS system was qualified (R 2 >0.995, RSD<15%) for subsequent biochemome profiling. After PCA and PLS-DA analysis, 30 marker compounds were screened and demonstrated to be of good predictability using genetic algorithm optimized support vector machines. Finally, a heatmap visualization was employed for clarifying the distribution of marker compounds, which could be helpful to determine whether the three Callicarpa species are, in fact, equivalent substitutes. This study provides a standardized biochemome profiling strategy for systemic comparison analysis of closely related TCM materials, which shows promising perspectives in tracking the supply chain of pharmaceutical suppliers. Copyright © 2017 Elsevier B.V. All rights reserved.

KSC 50-MHz Doppler Radar Wind Profiler (DRWP) Operational Acceptance Test (OAT) Report

NASA Technical Reports Server (NTRS)

Barbre, Robert E.

2015-01-01

This report documents analysis results of the Kennedy Space Center updated 50-MHz Doppler Radar Wind Profiler (DRWP) Operational Acceptance Test (OAT). This test was designed to demonstrate that the new DRWP operates in a similar manner to the previous DRWP for use as a situational awareness asset for mission operations at the Eastern Range to identify rapid changes in the wind environment that weather balloons cannot depict. Data examination and two analyses showed that the updated DRWP meets the specifications in the OAT test plan and performs at least as well as the previous DRWP. Data examination verified that the DRWP provides complete profiles every five minutes from 1.8-19.5 km in vertical increments of 150 m. Analysis of 5,426 wind component reports from 49 concurrent DRWP and balloon profiles presented root mean square (RMS) wind component differences around 2.0 m/s. The DRWP's effective vertical resolution (EVR) was found to be 300 m for both the westerly and southerly wind component, which the best EVR possible given the DRWP's vertical sampling interval. A third analysis quantified the sensitivity to rejecting data that do not have adequate signal by assessing the number of first-guess propagations at each altitude. This report documents the data, quality control procedures, methodology, and results of each analysis. It also shows that analysis of the updated DRWP produced results that were at least as good as the previous DRWP with proper rationale. The report recommends acceptance of the updated DRWP for situational awareness usage as per the OAT's intent.

Fast nuclear staining of head hair roots as a screening method for successful STR analysis in forensics.

PubMed

Lepez, Trees; Vandewoestyne, Mado; Van Hoofstat, David; Deforce, Dieter

2014-11-01

The success rate of STR profiling of hairs found at a crime scene is quite low and negative results of hair analysis are frequently reported. To increase the success rate of DNA analysis of hairs in forensics, nuclei in hair roots can be counted after staining the hair root with DAPI. Two staining methods were tested: a longer method with two 1h incubations in respectively a DAPI- and a wash-solution, and a fast, direct staining of the hair root on microscope slides. The two staining methods were not significantly different. The results of the STR analysis for both procedures showed that 20 nuclei are necessary to obtain at least partial STR profiles. When more than 50 nuclei were counted, full STR profiles were always obtained. In 96% of the cases where no nuclei were detected, no STR profile could be obtained. However, 4% of the DAPI-negative hair roots resulted in at least partial STR profiles. Therefore, each forensic case has to be evaluated separately in function of the importance of the evidential value of the found hair. The fast staining method was applied in 36 forensic cases on 279 hairs in total. A fast screening method using DAPI can be used to increase the success rate of hair analysis in forensics. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

MPEG-7-based description infrastructure for an audiovisual content analysis and retrieval system

NASA Astrophysics Data System (ADS)

Bailer, Werner; Schallauer, Peter; Hausenblas, Michael; Thallinger, Georg

2005-01-01

We present a case study of establishing a description infrastructure for an audiovisual content-analysis and retrieval system. The description infrastructure consists of an internal metadata model and access tool for using it. Based on an analysis of requirements, we have selected, out of a set of candidates, MPEG-7 as the basis of our metadata model. The openness and generality of MPEG-7 allow using it in broad range of applications, but increase complexity and hinder interoperability. Profiling has been proposed as a solution, with the focus on selecting and constraining description tools. Semantic constraints are currently only described in textual form. Conformance in terms of semantics can thus not be evaluated automatically and mappings between different profiles can only be defined manually. As a solution, we propose an approach to formalize the semantic constraints of an MPEG-7 profile using a formal vocabulary expressed in OWL, which allows automated processing of semantic constraints. We have defined the Detailed Audiovisual Profile as the profile to be used in our metadata model and we show how some of the semantic constraints of this profile can be formulated using ontologies. To work practically with the metadata model, we have implemented a MPEG-7 library and a client/server document access infrastructure.

Comprehensive profiling and characterization of cellular miRNAs in response to hepatitis A virus infection in human fibroblasts.

PubMed

Shi, Jiandong; Sun, Jing; Wu, Meini; Wang, Haixuan; Hu, Ningzhu; Hu, Yunzhang

2016-11-01

Hepatitis A virus (HAV), the causative agent of acute hepatitis, grows slowly without causing any cytopathic effect (CPE) and lead to a persistent infection in the fibroblasts in vitro. miRNAs play a key role in the viral pathogenesis and virus-host interactions. In this study, the comprehensive miRNA expression profiles of HAV-infected and uninfected fibroblasts were investigated by sRNA-seq and validated by RT-qPCR. The results showed that a total of 94 miRNAs were differentially expressed during HAV infection, including 11 up-regulated miRNAs and 83 down-regulated miRNAs. RT-qPCR analysis showed the expression levels of specific miRNAs were consistent with sRNA-seq data. Further, target prediction analysis showed 729 putative target genes that included many immune-related transcripts were revealed. The GO enrichment analysis and the KEGG pathway analysis of the target genes showed that various biological pathways, including JAK-STAT cascade, type I interferon signaling pathway could be affected by HAV infection by the alteration of host miRNAs. The core regulatory relationship between miRNAs and their targets were revealed by miRNA-gene-network. Collectively, this study provides an overall analysis of miRNA profile in cell culture infected with HAV. The present results imply the alteration of miRNAs expression induced by HAV infection which may be related to the establishment of persistent HAV infection and might provide new clues for understanding the persistent HAV infections in vitro and the unique biological characteristics associated with HAV during infection. Copyright © 2016 Elsevier B.V. All rights reserved.

Reliable screening of various foodstuffs with respect to their irradiation status: A comparative study of different analytical techniques

NASA Astrophysics Data System (ADS)

Ahn, Jae-Jun; Akram, Kashif; Kwak, Ji-Young; Jeong, Mi-Seon; Kwon, Joong-Ho

2013-10-01

Cost-effective and time-efficient analytical techniques are required to screen large food lots in accordance to their irradiation status. Gamma-irradiated (0-10 kGy) cinnamon, red pepper, black pepper, and fresh paprika were investigated using photostimulated luminescence (PSL), direct epifluorescent filter technique/the aerobic plate count (DEFT/APC), and electronic-nose (e-nose) analyses. The screening results were also confirmed with thermoluminescence analysis. PSL analysis discriminated between irradiated (positive, >5000 PCs) and non-irradiated (negative, <700 PCs) cinnamon and red peppers. Black pepper had intermediate results (700-5000 PCs), while paprika had low sensitivity (negative results) upon irradiation. The DEFT/APC technique also showed clear screening results through the changes in microbial profiles, where the best results were found in paprika, followed by red pepper and cinnamon. E-nose analysis showed a dose-dependent discrimination in volatile profiles upon irradiation through principal component analysis. These methods can be used considering their potential applications for the screening analysis of irradiated foods.

Shilling Attacks Detection in Recommender Systems Based on Target Item Analysis

PubMed Central

Zhou, Wei; Wen, Junhao; Koh, Yun Sing; Xiong, Qingyu; Gao, Min; Dobbie, Gillian; Alam, Shafiq

2015-01-01

Recommender systems are highly vulnerable to shilling attacks, both by individuals and groups. Attackers who introduce biased ratings in order to affect recommendations, have been shown to negatively affect collaborative filtering (CF) algorithms. Previous research focuses only on the differences between genuine profiles and attack profiles, ignoring the group characteristics in attack profiles. In this paper, we study the use of statistical metrics to detect rating patterns of attackers and group characteristics in attack profiles. Another question is that most existing detecting methods are model specific. Two metrics, Rating Deviation from Mean Agreement (RDMA) and Degree of Similarity with Top Neighbors (DegSim), are used for analyzing rating patterns between malicious profiles and genuine profiles in attack models. Building upon this, we also propose and evaluate a detection structure called RD-TIA for detecting shilling attacks in recommender systems using a statistical approach. In order to detect more complicated attack models, we propose a novel metric called DegSim’ based on DegSim. The experimental results show that our detection model based on target item analysis is an effective approach for detecting shilling attacks. PMID:26222882

Electrical Load Profile Analysis Using Clustering Techniques

NASA Astrophysics Data System (ADS)

Damayanti, R.; Abdullah, A. G.; Purnama, W.; Nandiyanto, A. B. D.

2017-03-01

Data mining is one of the data processing techniques to collect information from a set of stored data. Every day the consumption of electricity load is recorded by Electrical Company, usually at intervals of 15 or 30 minutes. This paper uses a clustering technique, which is one of data mining techniques to analyse the electrical load profiles during 2014. The three methods of clustering techniques were compared, namely K-Means (KM), Fuzzy C-Means (FCM), and K-Means Harmonics (KHM). The result shows that KHM is the most appropriate method to classify the electrical load profile. The optimum number of clusters is determined using the Davies-Bouldin Index. By grouping the load profile, the demand of variation analysis and estimation of energy loss from the group of load profile with similar pattern can be done. From the group of electric load profile, it can be known cluster load factor and a range of cluster loss factor that can help to find the range of values of coefficients for the estimated loss of energy without performing load flow studies.

Improved intra-array and interarray normalization of peptide microarray phosphorylation for phosphorylome and kinome profiling by rational selection of relevant spots

PubMed Central

Scholma, Jetse; Fuhler, Gwenny M.; Joore, Jos; Hulsman, Marc; Schivo, Stefano; List, Alan F.; Reinders, Marcel J. T.; Peppelenbosch, Maikel P.; Post, Janine N.

2016-01-01

Massive parallel analysis using array technology has become the mainstay for analysis of genomes and transcriptomes. Analogously, the predominance of phosphorylation as a regulator of cellular metabolism has fostered the development of peptide arrays of kinase consensus substrates that allow the charting of cellular phosphorylation events (often called kinome profiling). However, whereas the bioinformatical framework for expression array analysis is well-developed, no advanced analysis tools are yet available for kinome profiling. Especially intra-array and interarray normalization of peptide array phosphorylation remain problematic, due to the absence of “housekeeping” kinases and the obvious fallacy of the assumption that different experimental conditions should exhibit equal amounts of kinase activity. Here we describe the development of analysis tools that reliably quantify phosphorylation of peptide arrays and that allow normalization of the signals obtained. We provide a method for intraslide gradient correction and spot quality control. We describe a novel interarray normalization procedure, named repetitive signal enhancement, RSE, which provides a mathematical approach to limit the false negative results occuring with the use of other normalization procedures. Using in silico and biological experiments we show that employing such protocols yields superior insight into cellular physiology as compared to classical analysis tools for kinome profiling. PMID:27225531

Motivational profiles and their relationships with basic psychological needs, academic performance, study strategies, self-esteem, and vitality in dental students in Chile.

PubMed

Orsini, Cesar A; Binnie, Vivian I; Tricio, Jorge A

2018-01-01

To determine dental students' motivational profiles through a person-centred approach and to analyse the associations with the satisfaction of their basic psychological needs, study strategies, academic performance, self-esteem, and vitality. A total of 924 students from the University of San Sebastian (Chile) participated in this cross-sectional cor¬relational study in spring 2016. Data were collected through 5 self-reported instruments, in addition to students' academic performance. The Cronbach alpha, descriptive statistics, and correla¬tion scores were computed. A k-means cluster analysis with intrinsic and controlled motivation was conducted to identify different mo-tivational profiles. Subsequently, multivariate analysis of covariance controlling for the effects of gender and year of study was carried out to assess differences among the retained motivational profiles and learning variables. All instruments showed acceptable Cronbach alpha scores. A 4-cluster solution was retained for the motivational profile over a 3- or 5-cluster solution. Students' motiva-tional profiles were characterized by different degrees of intrinsic and controlled motivation. The high intrinsic motivation groups showed higher perceptions of their basic psychological, a greater propensity for a deep rather than surface study strategy, better academic performance, and higher scores for self-esteem and vitality than the low intrinsic motivation groups, regardless of the degree of controlled motivation. Students with a high intrinsic motivation profile, regardless of their controlled motivation scores, reported better learning characteristics. Therefore, special attention should be paid to students' motivational profiles, as the quality of motivation might serve as a basis for interventions to support their academic success and well-being.

Elemental profiling and geographical differentiation of Ethiopian coffee samples through inductively coupled plasma-optical emission spectroscopy (ICP-OES), ICP-mass spectrometry (ICP-MS) and direct mercury analyzer (DMA).

PubMed

Habte, Girum; Hwang, In Min; Kim, Jae Sung; Hong, Joon Ho; Hong, Young Sin; Choi, Ji Yeon; Nho, Eun Yeong; Jamila, Nargis; Khan, Naeem; Kim, Kyong Su

2016-12-01

This study was aimed to establish the elemental profiling and provenance of coffee samples collected from eleven major coffee producing regions of Ethiopia. A total of 129 samples were analyzed for forty-five elements using inductively coupled plasma (ICP)-optical emission spectroscopy (OES), ICP-mass spectrometry (MS) and direct mercury analyzer (DMA). Among the macro elements, K showed the highest levels whereas Fe was found to have the lowest concentration values. In all the samples, Ca, K, Mg, P and S contents were statistically significant (p<0.05). Micro elements showed the concentrations order of: Mn>Cu>Sr>Zn>Rb>Ni>B. Contents of the trace elements were lower than the permissible standard values. Inter-regions differentiation by cluster analysis (CA), linear discriminant analysis (LDA) and principal component analysis (PCA) showed that micro and trace elements are the best chemical descriptors of the analyzed coffee samples. Copyright © 2016 Elsevier Ltd. All rights reserved.

The female soft tissue profile as presented in fashion magazines during the 1900s: a photographic analysis.

PubMed

Auger, T A; Turley, P K

1999-01-01

Numerous studies have emphasized the importance of the facial profile in orthodontic treatment planning, with some arguing that the esthetic ideal has remained unchanged for thousands of years. To evaluate changes in the white female facial profile, we measured 14 soft tissue variables on profile photographs presented in fashion magazines during the 1900s. Five time frames were studied, with a sample of 25 photographs from each period corrected for size and orientation. Between-group differences were examined by use of analysis of variance, using a P value corrected for a multivariable analysis. Significant between-group differences (P < 0.0001) were found for anteroposterior lip position, amount of visible lip tissue, and interlabial angle, with the more recent groups displaying fuller and more anteriorly positioned lips. No significant differences were found for measurements calculated superior to subnasale (frontonasal angle, nasal tip angle, and nasolabial angle) or in the relationship of the chin to the upper face (total facial angle). The results of this study suggest that standards for the esthetic white female facial profile are not static and show a trend in this century toward fuller and more anteriorly positioned lips.

Correlation-based network analysis of metabolite and enzyme profiles reveals a role of citrate biosynthesis in modulating N and C metabolism in zea mays

USDA-ARS?s Scientific Manuscript database

To investigate the natural variability of leaf metabolism and enzymatic activity in a maize inbred population, statistical and network analyses were employed on metabolite and enzyme profiles. The test of coefficient of variation showed that sugars and amino acids displayed opposite trends in their ...

Metabolic profiles are principally different between cancers of the liver, pancreas and breast.

PubMed

Budhu, Anuradha; Terunuma, Atsushi; Zhang, Geng; Hussain, S Perwez; Ambs, Stefan; Wang, Xin Wei

2014-01-01

Molecular profiling of primary tumors may facilitate the classification of patients with cancer into more homogenous biological groups to aid clinical management. Metabolomic profiling has been shown to be a powerful tool in characterizing the biological mechanisms underlying a disease but has not been evaluated for its ability to classify cancers by their tissue of origin. Thus, we assessed metabolomic profiling as a novel tool for multiclass cancer characterization. Global metabolic profiling was employed to identify metabolites in paired tumor and non-tumor liver (n=60), breast (n=130) and pancreatic (n=76) tissue specimens. Unsupervised principal component analysis showed that metabolites are principally unique to each tissue and cancer type. Such a difference can also be observed even among early stage cancers, suggesting a significant and unique alteration of global metabolic pathways associated with each cancer type. Our global high-throughput metabolomic profiling study shows that specific biochemical alterations distinguish liver, pancreatic and breast cancer and could be applied as cancer classification tools to differentiate tumors based on tissue of origin.

SU-F-T-179: Fast and Accurate Profile Acquisition for Proton Beam Using Multi-Ion Chamber Arrays

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

Wang, X; Zou, J; Chen, T

2016-06-15

Purpose: Proton beam profile measurement is more time-consuming than photon beam. Due to the energy modulation during proton delivery, chambers have to move step-by-step instead of continuously. Multi-ion chamber arrays are appealing to this task since multiple measurements can be performed at once. However, their utilization suffers from sparse spatial resolution and potential intrinsic volume-averaging effect of the disk-shaped ion chambers. We proposed an approach to measure proton beam profiles accurately and efficiently. Methods: Mevion S250 proton system and IBA Matrixx ion chamber arrays were used in this study. Matrixx has interchamber distance of 7.62 mm, and chamber diameter ofmore » 4.5 mm. We measured the same beam profile by moving the Matrixx seven times with 1 mm each time along y axis. All 7 measurements were superimposed to get a “finer” profile with 1 mm spatial resolution. Coarser resolution profiles of 2 mm and 3 mm were also generated by using subsets of measurements. Those profiles were compared to the TPS calculated beam profile. Gamma analysis was performed for 2D dose maps to evaluate the difference to TPS dose plane. Results: Preliminary results showed a large discrepancy between the TPS calculated profile and the single measurement profile with 7.6 mm resolution. A good match could be achieved when the resolution reduced to 3 mm by adding one extra measurement. Gamma analysis for 2D dose map of a 10×10 field showed a passing rate (γ ≤ 1) of 90.6% using a 3% and 3mm criterion for single measurement, which increased to 92.3% for 2-measurement superimposition, and slightly further increased to 92.9% for 7-measurement superimposition. Conclusion: The results indicated that 2 measurements shifted by 3mm using Matrixx generated a smooth proton beam profile with good matching to Eclipse beam profile. We suggest using this 2-measurement approach in clinic for double scattering proton beam profile measurement.« less

Trends in stratospheric ozone profiles using functional mixed models

NASA Astrophysics Data System (ADS)

Park, A. Y.; Guillas, S.; Petropavlovskikh, I.

2013-05-01

This paper is devoted to the modeling of altitude-dependent patterns of ozone variations over time. Umkher ozone profiles (quarter of Umkehr layer) from 1978 to 2011 are investigated at two locations: Boulder (USA) and Arosa (Switzerland). The study consists of two statistical stages. First we approximate ozone profiles employing an appropriate basis. To capture primary modes of ozone variations without losing essential information, a functional principal component analysis is performed as it penalizes roughness of the function and smooths excessive variations in the shape of the ozone profiles. As a result, data driven basis functions are obtained. Secondly we estimate the effects of covariates - month, year (trend), quasi biennial oscillation, the Solar cycle, arctic oscillation and the El Niño/Southern Oscillation cycle - on the principal component scores of ozone profiles over time using generalized additive models. The effects are smooth functions of the covariates, and are represented by knot-based regression cubic splines. Finally we employ generalized additive mixed effects models incorporating a more complex error structure that reflects the observed seasonality in the data. The analysis provides more accurate estimates of influences and trends, together with enhanced uncertainty quantification. We are able to capture fine variations in the time evolution of the profiles such as the semi-annual oscillation. We conclude by showing the trends by altitude over Boulder. The strongly declining trends over 2003-2011 for altitudes of 32-64 hPa show that stratospheric ozone is not yet fully recovering.

Evaluation of inter-day and inter-individual variability of tear peptide/protein profiles by MALDI-TOF MS analyses

PubMed Central

González, Nerea; Iloro, Ibon; Durán, Juan A.; Elortza, Félix

2012-01-01

Purpose To characterize the tear film peptidome and low molecular weight protein profiles of healthy control individuals, and to evaluate changes due to day-to-day and individual variation and tear collection methods, by using solid phase extraction coupled to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling. Methods The tear protein profiles of six healthy volunteers were analyzed over seven days and inter-day and inter-individual variability was evaluated. The bilaterality of tear film and the effect of tear collection methods on protein profiles were also analyzed in some of these patients. MALDI-TOF MS analyses were performed on tear samples purified by using a solid phase extraction (SPE) method based on C18 functionalized magnetic beads for peptide and low molecular weight protein enrichment, focusing spectra acquisition on the 1 to 20 kDa range. Spectra were analyzed using principal component analysis (PCA) with MultiExperiment Viewer (TMeV) software. Volunteers were examined in terms of tear production status (Schirmer I test), clinical assessment of palpebral lids and meibomian glands, and a subjective OSD questionnaire before tear collection by a glass micro-capillary. Results Analysis of peptides and proteins in the 1–20 kDa range showed no significant inter-day differences in tear samples collected from six healthy individuals during seven days of monitoring, but revealed subtle intrinsic inter-individual differences. Profile analyses of tears collected from the right and left eyes confirmed tear bilaterality in four healthy patients. The addition of physiologic serum for tear sample collection did not affect the peptide and small protein profiles with respect to the number of resolved peaks, but it did reduce the signal intensity of the peaks, and increased variability. Magnetic beads were found to be a suitable method for tear film purification for the profiling study. Conclusions No significant variability in tear peptide and protein profiles below 20 kDa was found in healthy controls over a seven day period, nor in right versus left eye profiles from the same individual. Subtle inter-individual differences can be observed upon tear profiling analysis and confirm intrinsic variability between control subjects. Addition of physiologic serum for tear collection affects the proteome and peptidome in terms of peak intensities, but not in the composition of the profiles themselves. This work shows that MALDI-TOF MS coupled with C18 magnetic beads is an effective and reproducible methodology for tear profiling studies in the clinical monitoring of patients. PMID:22736947

Lagrangian analysis of the laminar flat plate boundary layer

NASA Astrophysics Data System (ADS)

Gabr, Mohammad

2016-10-01

The flow properties at the leading edge of a flat plate represent a singularity to the Blasius laminar boundary layer equations; by applying the Lagrangian approach, the leading edge velocity profiles of the laminar boundary layer over a flat plate are studied. Experimental observations as well as the theoretical analysis show an exact Gaussian distribution curve as the original starting profile of the laminar flow. Comparisons between the Blasius solution and the Gaussian curve solution are carried out providing a new insight into the physics of the laminar flow.

Analysis and test of low profile aluminum aerospace tank dome

NASA Astrophysics Data System (ADS)

Ahmed, R.; Wilhelm, J. M.

1993-12-01

In order to increase the structural performance of cryogenic tanks, the aerospace industry is beginning to employ low-profile bulkheads in new generation launch vehicle designs. This report details the analysis and test of one such dome made from 2219 aluminum. Such domes have two potential failure modes under internal pressure, general tensile failure and hoop compression buckling (in regions near the equator). The test determined the buckling load and ultimate tensile load of the hardware and showed that both compared well with the analysis predictions. This effort was conducted under the auspices of NASA and the General Dynamics Cryogenic Tank Technology Program (CTTP).

Analysis and test of low profile aluminum aerospace tank dome

NASA Technical Reports Server (NTRS)

Ahmed, R.; Wilhelm, J. M.

1993-01-01

In order to increase the structural performance of cryogenic tanks, the aerospace industry is beginning to employ low-profile bulkheads in new generation launch vehicle designs. This report details the analysis and test of one such dome made from 2219 aluminum. Such domes have two potential failure modes under internal pressure, general tensile failure and hoop compression buckling (in regions near the equator). The test determined the buckling load and ultimate tensile load of the hardware and showed that both compared well with the analysis predictions. This effort was conducted under the auspices of NASA and the General Dynamics Cryogenic Tank Technology Program (CTTP).

Multivariate data analysis and metabolic profiling of artemisinin and related compounds in high yielding varieties of Artemisia annua field-grown in Madagascar.

PubMed

Suberu, John; Gromski, Piotr S; Nordon, Alison; Lapkin, Alexei

2016-01-05

An improved liquid chromatography-tandem mass spectrometry (LC-MS/MS) protocol for rapid analysis of co-metabolites of A. annua in raw extracts was developed and extensively characterized. The new method was used to analyse metabolic profiles of 13 varieties of A. annua from an in-field growth programme in Madagascar. Several multivariate data analysis techniques consistently show the association of artemisinin with dihydroartemisinic acid. These data support the hypothesis of dihydroartemisinic acid being the late stage precursor to artemisinin in its biosynthetic pathway. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Analysis of tidal currents in the North Sea from shipboard acoustic Doppler current profiler data

NASA Astrophysics Data System (ADS)

Vindenes, Håvard; Orvik, Kjell Arild; Søiland, Henrik; Wehde, Henning

2018-06-01

North Sea tidal currents are determined by applying harmonic analysis to ship-borne acoustic Doppler current profiler data recorded from 1999 to 2016, covering large areas of the northern North Sea. Direct current measurement data sets of this magnitude are rare in the otherwise well investigated North Sea, and thus it is a valuable asset in studying and expanding our understanding of its tidal currents and circulation in general. The harmonic analysis is applied to a least squares fit of the current observations at a set of knot points. Results from the harmonic analysis compare favorably to tidal parameters estimated from observations from moored instruments. The analysis shows that the tides are characterized by strong semi-diurnal component, with amplitudes of the principal Lunar constituent ranging from 1.6 cm/s in the Skagerrak to 67 cm/s in the Fair Isle Channel. Diurnal tides are found to be approximately one fifth the strength of the predominant semi-diurnal constituent. Output from a regional barotropic tide model compares well to tidal current determined from the harmonic analysis of the Acoustic Doppler Current Profiler data.

Oral administration of kefiran exerts a bifidogenic effect on BALB/c mice intestinal microbiota.

PubMed

Hamet, M F; Medrano, M; Pérez, P F; Abraham, A G

2016-01-01

The activity of kefiran, the exopolysaccharide present in kefir grains, was evaluated on intestinal bacterial populations in BALB/c mice. Animals were orally administered with kefiran and Eubacteria, lactobacilli and bifidobacteria populations were monitored in faeces of mice at days 0, 2, 7, 14 and 21. Profiles obtained by Denaturing Gradient Gel Electrophoresis (DGGE) with primers for Eubacteria were compared by principal component analysis and clearly defined clusters, correlating with the time of kefiran consumption, were obtained. Furthermore, profile analysis of PCR products amplified with specific oligonucleotides for bifidobacteria showed an increment in the number of DGGE bands in the groups administered with kefiran. Fluorescent In Situ Hybridisation (FISH) with specific probes for bifidobacteria showed an increment of this population in faeces, in accordance to DGGE results. The bifidobacteria population was also studied on distal colon content after 0, 2 and 7 days of kefiran administration. Analysis of PCR products by DGGE with Eubacteria primers showed an increment in the number and intensity of bands with high GC content of mice administered with kefiran. Sequencing of DGGE bands confirmed that bifidobacteria were one of the bacterial populations modified by kefiran administration. DGGE profiles of PCR amplicons obtained by using Bifidobacterium or Lactobacillus specific primers confirmed that kefiran administration enhances bifidobacteria, however no changes were observed in Lactobacillus populations. The results of the analysis of bifidobacteria populations assessed on different sampling sites in a murine model support the use of this exopolysaccharide as a bifidogenic functional ingredient.

Functional genomic mRNA profiling of a large cancer data base demonstrates mesothelin overexpression in a broad range of tumor types.

PubMed

Lamberts, Laetitia E; de Groot, Derk Jan A; Bense, Rico D; de Vries, Elisabeth G E; Fehrmann, Rudolf S N

2015-09-29

The membrane bound glycoprotein mesothelin (MSLN) is a highly specific tumor marker, which is currently exploited as target for drugs. There are only limited data available on MSLN expression by human tumors. Therefore we determined overexpression of MSLN across different tumor types with Functional Genomic mRNA (FGM) profiling of a large cancer database. Results were compared with data in articles reporting immunohistochemical (IHC) MSLN tumor expression. FGM profiling is a technique that allows prediction of biologically relevant overexpression of proteins from a robust data set of mRNA microarrays. This technique was used in a database comprising 19,746 tumors to identify for 41 tumor types the percentage of samples with an overexpression of MSLN compared to a normal background. A literature search was performed to compare the FGM profiling data with studies reporting IHC MSLN tumor expression. FGM profiling showed MSLN overexpression in gastrointestinal (12-36%) and gynecological tumors (20-66%), non-small cell lung cancer (21%) and synovial sarcomas (30%). The overexpression found in thyroid cancers (5%) and renal cell cancers (10%) was not yet reported with IHC analyses. We observed that MSLN amplification rate within esophageal cancer depends on the histotype (31% for adenocarcinomas versus 3% for squamous-cell carcinomas). Subset analysis in breast cancer showed MSLN amplification rates of 28% in triple-negative breast cancer (TNBC) and 33% in basal-like breast cancer. Further subtype analysis of TNBCs showed the highest amplification rate (42%) in the basal-like 1 subtype and the lowest amplification rate (9%) in the luminal androgen receptor subtype.

The A and m coefficients in the Bruun/Dean equilibrium profile equation seen from the Arctic

USGS Publications Warehouse

Are, F.; Reimnitz, E.

2008-01-01

The Bruun/Dean relation between water depth and distance from the shore with a constant profile shape factor is widely used to describe shoreface profiles in temperate environments. However, it has been shown that the sediment scale parameter (A) and the profile shape factor (m) are interrelated variables. An analysis of 63 Arctic erosional shoreface profiles shows that both coefficients are highly variable. Relative frequency of the average m value is only 16% by the class width 0.1. No other m value frequency exceeds 21%. Therefore, there is insufficient reason to use average m to characterize Arctic shoreface profile shape. The shape of each profile has a definite combination of A and m values. Coefficients A and m show a distinct inverse relationship, as in temperate climate. A dependence of m values on coastal sediment grain size is seen, and m decreases with increasing grain size. With constant m = 0.67, parameter A obtains a dimension unit m1/3. But A equals the water depth in meters 1 m from the water edge. This fact and the variability of parameter m testify that the Bruun/Dean equation is essentially an empirical formula. There is no need to give any measurement unit to parameter A. But the International System of Units (SI) has to be used in applying the Bruun/Dean equation for shoreface profiles. A comparison of the shape of Arctic shoreface profiles with those of temperate environments shows surprising similarity. Therefore, the conclusions reached in this Arctic paper seem to apply also to temperate environments.

Comparison between Deflection and Vibration Characteristics of Rectangular and Trapezoidal profile Microcantilevers

PubMed Central

Ansari, Mohd. Zahid; Cho, Chongdu; Kim, Jooyong; Bang, Booun

2009-01-01

Arrays of microcantilevers are increasingly being used as physical, biological, and chemical sensors in various applications. To improve the sensitivity of microcantilever sensors, this study analyses and compares the deflection and vibration characteristics of rectangular and trapezoidal profile microcantilevers. Three models of each profile are investigated. The cantilevers are analyzed for maximum deflection, fundamental resonant frequency and maximum stress. The surface stress is modelled as in-plane tensile force applied on the top edge of the microcantilevers. A commercial finite element analysis software ANSYS is used to analyze the designs. Results show paddled trapezoidal profile microcantilevers have better sensitivity. PMID:22574041

Measuring discharge with ADCPs: Inferences from synthetic velocity profiles

USGS Publications Warehouse

Rehmann, C.R.; Mueller, D.S.; Oberg, K.A.

2009-01-01

Synthetic velocity profiles are used to determine guidelines for sampling discharge with acoustic Doppler current profilers (ADCPs). The analysis allows the effects of instrument characteristics, sampling parameters, and properties of the flow to be studied systematically. For mid-section measurements, the averaging time required for a single profile measurement always exceeded the 40 s usually recommended for velocity measurements, and it increased with increasing sample interval and increasing time scale of the large eddies. Similarly, simulations of transect measurements show that discharge error decreases as the number of large eddies sampled increases. The simulations allow sampling criteria that account for the physics of the flow to be developed. ?? 2009 ASCE.

Cognitive abilities in siblings of children with autism spectrum disorders.

PubMed

Gizzonio, Valentina; Avanzini, Pietro; Fabbri-Destro, Maddalena; Campi, Cristina; Rizzolatti, Giacomo

2014-07-01

The aim of the present study was to assess the cognitive profiles of children with autistic spectrum disorder and of their healthy siblings (Siblings). With the term cognitive profile, we indicate the relationship extant among the values of verbal and performance subtests of the Wechsler Intelligence Scale. The conducted statistical analyses indicated that, although siblings showed a normal intelligent quotient and did not differ in this aspect from typically developing group, their cognitive profile was amazingly similar to that of their relatives affected by autism. A k-means clustering analysis on the values of single subtests further confirmed this result, showing a clear separation between typically developing children on the one side, and autistics and their siblings on the other. We suggest that the common cognitive profile observed in autistic children and their siblings could represent a marker of liability to autism and, thus, a possible intermediate phenotype of this syndrome.

Upper mantle electrical conductivity for seven subcontinental regions of the Earth

USGS Publications Warehouse

Campbell, W.H.; Schiffmacher, E.R.

1988-01-01

Spherical harmonic analysis coefficients of the external and internal parts of the quiet-day geomagnetic field variations (Sq) separated for the 7 continental regions of the observatories have been used to determine conductivity profiles to depths of about 600 km by the Schmucker equivalent substitute conductor method. The profiles give evidence of increases in conductivity between about 150 and 350 km depth, then a general increase in conductivity thereafter. For South America we found a high conductivity at shallow depths. The European profile showed a highly conducting layer near 125 km. At the greater depths, Europe, Australia and South America had the lowest values of conductivity. North America and east Asia had intermediate values whereas the African and central Asian profiles both showed the conductivities rising rapidly beyond 450 km depth. The regional differences indicate that there may be considerable lateral heterogeneity of electrical conductivity in the Earth's upper mantle. -Authors

The effects of plant extracts on microbial community structure in a rumen-simulating continuous-culture system as revealed by molecular profiling.

PubMed

Ferme, D; Banjac, M; Calsamiglia, S; Busquet, M; Kamel, C; Avgustin, G

2004-01-01

An in vitro study in dual-flow continuous-culture fermentors was conducted with two different concentrations of monensin, cinnamaldehyde or garlic extract added to 1:1 forage-to-concentrate diet in order to determine their effects on selected rumen bacterial populations. Samples were subjected to total DNA extraction, restriction analysis of PCR amplified parts of 16S rRNA genes (ARDRA) and subsequent analysis of the restriction profiles by lab-on-chip technology with the Agilent's Bioanalyser 2100. Eub338-BacPre primer pair was used to select for the bacteria from the genera Bacteroides, Porphyromonas and Prevotella, especially the latter representing the dominant Gram-negative bacterial population in the rumen. Preliminary results of HaeIII restriction analysis show that the effects of monensin, cinnamaldehyde and garlic extract on the BacPre targeted ruminal bacteria are somewhat different in regard to targeted populations and to the nature of the effect. Garlic extract was found to trigger the most intensive changes in the structure of the BacPre targeted population. Comparison of the in silico restriction analysis of BacPre sequences deposited in different DNA databanks and of the results of performed amplified ribosomal DNA restriction analysis showed differences between the predicted and obtained HaeIII restriction profiles, and suggested the presence of novel, still unknown Prevotella populations in studied samples.

Comparative analysis of gene expression profiles of OPN signaling pathway in four kinds of liver diseases.

PubMed

Wang, Gaiping; Chen, Shasha; Zhao, Congcong; Li, Xiaofang; Zhao, Weiming; Yang, Jing; Chang, Cuifang; Xu, Cunshuan

2016-09-01

To explore the relevance of OPN signalling pathway to the occurrence and development of nonalcoholic fatty liver disease (NAFLD), liver cirrhosis (LC), hepatic cancer (HC) and acute hepatic failure (AHF) at transcriptional level, Rat Genome 230 2.0 Array was used to detect expression profiles of OPN signalling pathway-related genes in four kinds of liver diseases. The results showed that 23, 33, 59 and 74 genes were significantly changed in the above four kinds of liver diseases, respectively. H-clustering analysis showed that the expression profiles of OPN signalling-related genes were notably different in four kinds of liver diseases. Subsequently, a total of above-mentioned 147 genes were categorized into four clusters by k-means according to the similarity of gene expression, and expression analysis systematic explorer (EASE) functional enrichment analysis revealed that OPN signalling pathway-related genes were involved in cell adhesion and migration, cell proliferation, apoptosis, stress and inflammatory reaction, etc. Finally, ingenuity pathway analysis (IPA) software was used to predict the functions of OPN signalling-related genes, and the results indicated that the activities of ROS production, cell adhesion and migration, cell proliferation were remarkably increased, while that of apoptosis, stress and inflammatory reaction were reduced in four kinds of liver diseases. In summary, the above physiological activities changed more obviously in LC, HC and AHF than in NAFLD.

An error analysis of the recovery capability of the relative sea-surface profile over the Puerto Rican trench from multi-station and ship tracking of GEOS-2

NASA Technical Reports Server (NTRS)

Stanley, H. R.; Martin, C. F.; Roy, N. A.; Vetter, J. R.

1971-01-01

Error analyses were performed to examine the height error in a relative sea-surface profile as determined by a combination of land-based multistation C-band radars and optical lasers and one ship-based radar tracking the GEOS 2 satellite. It was shown that two relative profiles can be obtained: one using available south-to-north passes of the satellite and one using available north-to-south type passes. An analysis of multi-station tracking capability determined that only Antigua and Grand Turk radars are required to provide satisfactory orbits for south-to-north type satellite passes, while a combination of Merritt Island, Bermuda, and Wallops radars provide secondary orbits for north-to-south passes. Analysis of ship tracking capabilities shows that high elevation single pass range-only solutions are necessary to give only moderate sensitivity to systematic error effects.

Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling*

PubMed Central

Larance, Mark; Kirkwood, Kathryn J.; Tinti, Michele; Brenes Murillo, Alejandro; Ferguson, Michael A. J.; Lamond, Angus I.

2016-01-01

We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility during chromatographic separation. We show this efficiently detects both integral membrane and membrane-associated protein complexes,in addition to soluble complexes, allowing identification and analysis of complexes not accessible in native extracts. We compare the protein complexes detected by HPLC-MS protein correlation profiling in both native and formaldehyde crosslinked U2OS cell extracts. These proteome-wide data sets of both in vivo crosslinked and native protein complexes from U2OS cells are freely available via a searchable online database (www.peptracker.com/epd). Raw data are also available via ProteomeXchange (identifier PXD003754). PMID:27114452

Volatile profile, lipid oxidation and protein oxidation of irradiated ready-to-eat cured turkey meat products

NASA Astrophysics Data System (ADS)

Feng, Xi; Ahn, Dong Uk

2016-10-01

Irradiation had little effects on the thiobarbituric acid reactive substances (TBARS) values in ready-to-eat (RTE) turkey meat products, while it increased protein oxidation at 4.5 kGy. The volatile profile analyses indicated that the amount of sulfur compounds increased linearly as doses increased in RTE turkey meat products. By correlation analysis, a positive correlation was found between benzene/ benzene derivatives and alcohols with lipid oxidation, while aldehydes, ketones and alkane, alkenes and alkynes were positively correlated with protein oxidation. Principle component analysis showed that irradiated meat samples can be discriminated by two categories of volatile compounds: Strecker degradation products and radiolytic degradation products. The cluster analysis of volatile data demonstrated that low-dose irradiation had minor effects on the volatile profile of turkey sausages (<1.5 kGy). However, as the doses increased, the differences between the irradiated and non-irradiated cured turkey products became significant.

Genetic diversity reflects geographical origin of Ralstonia solanacearum strains isolated from plant and water sources in Spain.

PubMed

Caruso, Paola; Biosca, Elena G; Bertolini, Edson; Marco-Noales, Ester; Gorris, María Teresa; Licciardello, Concetta; López, María M

2017-12-01

The characterization and intraspecific diversity of a collection of 45 Ralstonia solanacearum strains isolated in Spain from different sources and geographical origins is reported. To test the influence of the site and the host on strain diversity, phenotypic and genotypic analysis were performed by a polyphasic approach. Biochemical and metabolic profiles were compared. Serological relationship was evaluated by Indirect-ELISA using polyclonal and monoclonal antibodies. For genotypic analysis, hrpB and egl DNA sequence analysis, repetitive sequences (rep-PCR), amplified fragment length polymorphism (AFLP) profiles and macrorestriction with XbaI followed by pulsed field gel electrophoresis (PFGE) were performed. The biochemical and metabolic characterization, serological tests, rep-PCR typing and phylogenetic analysis showed that all analysed strains belonged to phylotype II sequevar 1 and shared homogeneous profiles. However, interesting differences among strains were found by AFLP and macrorestriction with XbaI followed by PFGE techniques, some profiles being related to the geographical origin of the strains. Diversity results obtained offer new insights into the biogeography of this quarantine organism and its possible sources and reservoirs in Spain and Mediterranean countries. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Genome-wide analysis of soybean HD-Zip gene family and expression profiling under salinity and drought treatments.

PubMed

Chen, Xue; Chen, Zhu; Zhao, Hualin; Zhao, Yang; Cheng, Beijiu; Xiang, Yan

2014-01-01

Homeodomain-leucine zipper (HD-Zip) proteins, a group of homeobox transcription factors, participate in various aspects of normal plant growth and developmental processes as well as environmental responses. To date, no overall analysis or expression profiling of the HD-Zip gene family in soybean (Glycine max) has been reported. An investigation of the soybean genome revealed 88 putative HD-Zip genes. These genes were classified into four subfamilies, I to IV, based on phylogenetic analysis. In each subfamily, the constituent parts of gene structure and motif were relatively conserved. A total of 87 out of 88 genes were distributed unequally on 20 chromosomes with 36 segmental duplication events, indicating that segmental duplication is important for the expansion of the HD-Zip family. Analysis of the Ka/Ks ratios showed that the duplicated genes of the HD-Zip family basically underwent purifying selection with restrictive functional divergence after the duplication events. Analysis of expression profiles showed that 80 genes differentially expressed across 14 tissues, and 59 HD-Zip genes are differentially expressed under salinity and drought stress, with 20 paralogous pairs showing nearly identical expression patterns and three paralogous pairs diversifying significantly under drought stress. Quantitative real-time RT-PCR (qRT-PCR) analysis of six paralogous pairs of 12 selected soybean HD-Zip genes under both drought and salinity stress confirmed their stress-inducible expression patterns. This study presents a thorough overview of the soybean HD-Zip gene family and provides a new perspective on the evolution of this gene family. The results indicate that HD-Zip family genes may be involved in many plant responses to stress conditions. Additionally, this study provides a solid foundation for uncovering the biological roles of HD-Zip genes in soybean growth and development.

Prediction of functional profiles of gut microbiota from 16S rRNA metagenomic data provides a more robust evaluation of gut dysbiosis occurring in Japanese type 2 diabetic patients.

PubMed

Inoue, Ryo; Ohue-Kitano, Ryuji; Tsukahara, Takamitsu; Tanaka, Masashi; Masuda, Shinya; Inoue, Takayuki; Yamakage, Hajime; Kusakabe, Toru; Hasegawa, Koji; Shimatsu, Akira; Satoh-Asahara, Noriko

2017-11-01

We assessed whether gut microbial functional profiles predicted from 16S rRNA metagenomics differed in Japanese type 2 diabetic patients. A total of 22 Japanese subjects were recruited from our outpatient clinic in an observational study. Fecal samples were obtained from 12 control and 10 type 2 diabetic subjects. 16S rRNA metagenomic data were generated and functional profiles predicted using "Phylogenetic Investigation of Communities by Reconstruction of Unobserved States" software. We measured the parameters of glucose metabolism, gut bacterial taxonomy and functional profile, and examined the associations in a cross-sectional manner. Eleven of 288 "Kyoto Encyclopedia of Genes and Genomes" pathways were significantly enriched in diabetic patients compared with control subjects ( p <0.05, q<0.1). The relative abundance of almost all pathways, including the Insulin signaling pathway and Glycolysis/Gluconeogenesis , showed strong, positive correlations with hemoglobin A 1c (HbA 1c ) and fasting plasma glucose (FPG) levels. Bacterial taxonomic analysis showed that genus Blautia significantly differed between groups and had negative correlations with HbA 1c and FPG levels. Our findings suggest a novel pathophysiological relationship between gut microbial communities and diabetes, further highlighting the significance and utility of combining prediction of functional profiles with ordinal bacterial taxonomic analysis (UMIN Clinical Trails Registry number: UMIN000026592).

Isolation and analysis of linker histones across cellular compartments

PubMed Central

Harshman, Sean W.; Chen, Michael M.; Branson, Owen E.; Jacob, Naduparambil K.; Johnson, Amy J.; Byrd, John C.; Freitas, Michael A.

2013-01-01

Analysis of histones, especially histone H1, is severely limited by immunological reagent availability. This paper describes the application of cellular fractionation with LC-MS for profiling histones in the cytosol and upon chromatin. First, we show that linker histones enriched by cellular fractionation gives less nuclear contamination and higher histone content than when prepared by nuclei isolation. Second, we profiled the soluble linker histones throughout the cell cycle revealing phosphorylation increases as cells reach mitosis. Finally, we monitored histone H1.2–H1.5 translocation to the cytosol in response to the CDK inhibitor flavopiridol in primary CLL cells treated ex vivo. Data shows all H1 variants translocate in response to drug treatment with no specific order to their cytosolic appearance. The results illustrate the utility of cellular fractionation in conjunction with LC-MS for the analysis of histone H1 throughout the cell. PMID:24013129

Transient thermal analysis during friction stir welding between AA2014-T6 and pure copper

NASA Astrophysics Data System (ADS)

Gadhavi, A. R.; Ghetiya, N. D.; Patel, K. M.

2018-04-01

AA2xxx-Cu alloys showed larger applications in the defence sectors and in aerospace industries due to high strength to weight ratio and toughness. FSW in a butt joint configuration was carried out between AA2014-T6 and pure Copper placing AA2014 on AS and Cu on RS. Temperature profiles were observed by inserting K-type thermocouples in the mid-thickness at various locations of the plate. A sharp decrease in temperature profiles was observed on Copper side due to its higher thermal conductivity. A thermal numerical model was prepared in ANSYS to compare the simulated temperature profiles with the experimental temperature profiles and both the temperature profiles were found to be in good agreement.

Effects of Temperature and Air Density Profiles on Ozone Lidar Retrievals

NASA Astrophysics Data System (ADS)

Kirgis, G.; Langford, A. O.; Senff, C. J.; Alvarez, R. J. _II, II

2017-12-01

The recent reduction in the primary U.S. National Ambient Air Quality Standard (NAAQS) for ozone (O3) from 75 to 70 parts-per-billion by volume (ppbv) adds urgency to the need for better understanding of the processes that control ground-level concentrations in the United States. While ground-based in situ sensors are capable of measuring ozone levels, they don't give any insight into upper air transport and mixing. Differential absorption lidars such as the NOAA/ESRL Tunable Optical Profiler for Aerosol and oZone (TOPAZ) measure continuous vertical ozone profiles with high spatial and temporal resolution. However, the retrieved ozone mixing ratios depend on the temperature and air density profiles used in the analysis. This study analyzes the ozone concentrations for seven field campaigns from 2013 to 2016 to evaluate the impact of the assumed pressure and temperature profiles on the ozone mixing ratio retrieval. Pressure and temperature profiles from various spatial and temporal resolution models (Modern Era Retrospective-Analysis for Research and Applications, NCEP/NCAR Reanalysis, NCEP North American Regional Reanalysis, Rapid Refresh, and High-Resolution Rapid Refresh) are compared to reference ozone profiles created with pressure and temperature profiles from ozonesondes launched close to the TOPAZ measurement site. The results show significant biases with respect to time of day and season, altitude, and location of the model-extracted profiles. Limitations and advantages of all datasets used will also be discussed.

Microarray evaluation of gene expression profiles in inflamed and healthy human dental pulp: the role of IL1beta and CD40 in pulp inflammation.

PubMed

Gatta, V; Zizzari, V L; Dd ' Amico, V; Salini, L; D' Aurora, M; Franchi, S; Antonucci, I; Sberna, M T; Gherlone, E; Stuppia, L; Tetè, S

2012-01-01

Dental pulp undergoes a number of changes passing from healthy status to inflammation due to deep decay. These changes are regulated by several genes resulting differently expressed in inflamed and healthy dental pulp, and the knowledge of the processes underlying this differential expression is of great relevance in the identification of the pathogenesis of the disease. In this study, the gene expression profile of inflamed and healthy dental pulps were compared by microarray analysis, and data obtained were analyzed by Ingenuity Pathway Analysis (IPA) software. This analysis allows to focus on a variety of genes, typically expressed in inflamed tissues. The comparison analysis showed an increased expression of several genes in inflamed pulp, among which IL1β and CD40 resulted of particular interest. These results indicate that gene expression profile of human dental pulp in different physiological and pathological conditions may become an useful tool for improving our knowledge about processes regulating pulp inflammation.

LCMS analysis of fingerprints, the amino acid profile of 20 donors.

PubMed

de Puit, Marcel; Ismail, Mahado; Xu, Xiaoma

2014-03-01

The analysis of amino acids present in fingerprints has been studied several times. In this paper, we report a method for the analysis of amino acids using an fluorenylmethyloxycarbonyl chloride-derivatization for LC separation and MS detection. We have obtained good results with regard to the calibration curves and the limit of detection and LOQ for the target compounds. The extraction of the amino acids from the substrates used proved to be very efficient. Analysis of the derivatized amino acids enabled us to obtain full amino acid profiles for 20 donors. The intervariability is as expected rather large, with serine as the most abundant constituent, and when examining the total profile of the amino acids per donor, a characteristic pattern can be observed. Some amino acids were not detected in some donors, or fell out of the range of the calibration curve, where others showed a surprisingly high amount of material in the deposition analyses. Further investigations will have to address the intravariability of the amino acid profiles of the fingerprints from donors. By the development of the analytical method and the application to the analysis of fingerprints, we were able to gain insight in the variability of the constituents of fingerprints between the donors. © 2013 American Academy of Forensic Sciences.

Miscible gravitational instability of initially stable horizontal interface in a porous medium: Non-monotonic density profiles

NASA Astrophysics Data System (ADS)

Kim, Min Chan

2014-11-01

To simulate a CO2 sequestration process, some researchers employed a water/propylene glycol (PPG) system which shows a non-monotonic density profile. Motivated by this fact, the stability of the diffusion layer of two miscible fluids saturated in a porous medium is analyzed. For a non-monotonic density profile system, linear stability equations are derived in a global domain, and then transformed into a system of ordinary differential equations in an infinite domain. Initial growth rate analysis is conducted without the quasi-steady state approximation (QSSA) and shows that initially the system is unconditionally stable for the least stable disturbance. For the time evolving case, the ordinary differential equations are solved applying the eigen-analysis and numerical shooting scheme with and without the QSSA. To support these theoretical results, direct numerical simulations are conducted using the Fourier spectral method. The results of theoretical linear stability analyses and numerical simulations validate one another. The present linear and nonlinear analyses show that the water/PPG system is more unstable than the CO2/brine one, and the flow characteristics of these two systems are quite different from each other.

Scanning Electron Microscopy Investigation of a Sample Depth Profile Through the Martian Meteorite Nakhla

NASA Technical Reports Server (NTRS)

Toporski, Jan; Steele, Andrew; Westall, Frances; McKay, David S.

2000-01-01

The ongoing scientific debate as to whether or not the Martian meteorite ALH84001 contained evidence of possible biogenic activities showed the need to establish consistent methods to ascertain the origin of such evidence. To distinguish between terrestrial organic material/microbial contaminants and possible indigenous microbiota within meteorites is therefore crucial. With this in mind a depth profile consisting of four samples from a new sample allocation of Martian meteorite Nakhla was investigated using scanning electron microscopy (SEM) and energy dispersive X-ray analysis. SEM imaging of freshly broken fractured chips revealed structures strongly recent terrestrial microorganisms, in some cases showing evidence of active growth. This conclusion was supported by EDX analysis, which showed the presence of carbon associated with these structures, we concluded that these structures represent recent terrestrial contaminants rather than structures indigenous to the meteorite. Page

Subsurface profiling using integrated geophysical methods for 2D site response analysis in Bangalore city, India: a new approach

NASA Astrophysics Data System (ADS)

Chandran, Deepu; Anbazhagan, P.

2017-10-01

Recently, site response analysis has become a mandatory step for the design of important structures. Subsurface investigation is an essential step, from where the input parameters for the site response study like density, shear wave velocity (Vs), thickness and damping characteristics, etc, are obtained. Most site response studies at shallow bedrock sites are one-dimensional (1D) and are usually carried out by using Vs from multi-channel analysis of surface waves (MASW) or a standard penetration test (SPT) for N values with assumptions that soil layers are horizontal, uniform and homogeneous. These assumptions are not completely true in shallow bedrock regions as soil deposits are heterogeneous. The objective of this study is to generate the actual subsurface profiles in two-dimensions at shallow bedrock regions using integrated subsurface investigation testing. The study area selected for this work is Bangalore, India. Three survey lines were selected in Bangalore at two different locations; one at the Indian Institute of Science (IISc) Campus and the other at Whitefield. Geophysical surveys like ground penetrating radar (GPR) and 2D MASW were carried out at these survey lines. Geophysical test results are compared and validated with a conventional geotechnical SPT. At the IISc site, the soil profile is obtained from a trench excavated for a proposed pipeline used to compare the geophysical test results. Test results show that GPR is very useful to delineate subsurface layers, especially for shallow depths at both sites (IISc Campus and Whitefield). MASW survey results show variation of Vs values and layer thickness comparatively at deeper depths for both sites. They also show higher density soil strata with high Vs value obtained at the IISc Campus site, whereas at the Whitefield site weaker soil with low shear velocity is observed. Combining these two geophysical methods helped to generate representative 2D subsurface profiles. These subsurface profiles can be further used to understand the difference between 1D and 2D site response.

Genetic variability in MCF-7 sublines: evidence of rapid genomic and RNA expression profile modifications

PubMed Central

Nugoli, Mélanie; Chuchana, Paul; Vendrell, Julie; Orsetti, Béatrice; Ursule, Lisa; Nguyen, Catherine; Birnbaum, Daniel; Douzery, Emmanuel JP; Cohen, Pascale; Theillet, Charles

2003-01-01

Background Both phenotypic and cytogenetic variability have been reported for clones of breast carcinoma cell lines but have not been comprehensively studied. Despite this, cell lines such as MCF-7 cells are extensively used as model systems. Methods In this work we documented, using CGH and RNA expression profiles, the genetic variability at the genomic and RNA expression levels of MCF-7 cells of different origins. Eight MCF-7 sublines collected from different sources were studied as well as 3 subclones isolated from one of the sublines by limit dilution. Results MCF-7 sublines showed important differences in copy number alteration (CNA) profiles. Overall numbers of events ranged from 28 to 41. Involved chromosomal regions varied greatly from a subline to another. A total of 62 chromosomal regions were affected by either gains or losses in the 11 sublines studied. We performed a phylogenetic analysis of CGH profiles using maximum parsimony in order to reconstruct the putative filiation of the 11 MCF-7 sublines. The phylogenetic tree obtained showed that the MCF-7 clade was characterized by a restricted set of 8 CNAs and that the most divergent subline occupied the position closest to the common ancestor. Expression profiles of 8 MCF-7 sublines were analyzed along with those of 19 unrelated breast cancer cell lines using home made cDNA arrays comprising 720 genes. Hierarchical clustering analysis of the expression data showed that 7/8 MCF-7 sublines were grouped forming a cluster while the remaining subline clustered with unrelated breast cancer cell lines. These data thus showed that MCF-7 sublines differed at both the genomic and phenotypic levels. Conclusions The analysis of CGH profiles of the parent subline and its three subclones supported the heteroclonal nature of MCF-7 cells. This strongly suggested that the genetic plasticity of MCF-7 cells was related to their intrinsic capacity to generate clonal heterogeneity. We propose that MCF-7, and possibly the breast tumor it was derived from, evolved in a node like pattern, rather than according to a linear progression model. Due to their capacity to undergo rapid genetic changes MCF-7 cells could represent an interesting model for genetic evolution of breast tumors. PMID:12713671

Bully/Victim Profiles’ Differential Risk for Worsening Peer Acceptance: The Role of Friendship

PubMed Central

Kochel, Karen P.; Ladd, Gary W.; Bagwell, Catherine L.; Yabko, Brandon A.

2015-01-01

Study aims were to: (1) evaluate the association between bully/victim profiles, derived via latent profile analysis (LPA), and changes in peer acceptance from the fall to spring of 7th grade, and (2) investigate the likelihood of friendlessness, and the protective function of mutual friendship, among identified profiles. Participants were 2,587 7th graders; peer nomination and rating-scale data were collected in the fall and spring. Four profiles, including bullies, victims, bully-victims, and uninvolved adolescents, were identified at each time point. Findings showed that for victims, more so than for bullies and uninvolved profiles, acceptance scores worsened over time. Results further revealed that bully-victim and victim profiles included a greater proportion of friendless youth relative to the bully profile, which, in turn, contained a greater proportion of friendless adolescents than the uninvolved profile. Findings also provided evidence for the buffering role of friendship among all bully/victim profiles and among bully-victims especially. PMID:26309346

[Analysis of Time-to-onset of Interstitial Lung Disease after the Administration of Small Molecule Molecularly-targeted Drugs].

PubMed

Komada, Fusao

2018-01-01

　The aim of this study was to investigate the time-to-onset of drug-induced interstitial lung disease (DILD) following the administration of small molecule molecularly-targeted drugs via the use of the spontaneous adverse reaction reporting system of the Japanese Adverse Drug Event Report database. DILD datasets for afatinib, alectinib, bortezomib, crizotinib, dasatinib, erlotinib, everolimus, gefitinib, imatinib, lapatinib, nilotinib, osimertinib, sorafenib, sunitinib, temsirolimus, and tofacitinib were used to calculate the median onset times of DILD and the Weibull distribution parameters, and to perform the hierarchical cluster analysis. The median onset times of DILD for afatinib, bortezomib, crizotinib, erlotinib, gefitinib, and nilotinib were within one month. The median onset times of DILD for dasatinib, everolimus, lapatinib, osimertinib, and temsirolimus ranged from 1 to 2 months. The median onset times of the DILD for alectinib, imatinib, and tofacitinib ranged from 2 to 3 months. The median onset times of the DILD for sunitinib and sorafenib ranged from 8 to 9 months. Weibull distributions for these drugs when using the cluster analysis showed that there were 4 clusters. Cluster 1 described a subgroup with early to later onset DILD and early failure type profiles or a random failure type profile. Cluster 2 exhibited early failure type profiles or a random failure type profile with early onset DILD. Cluster 3 exhibited a random failure type profile or wear out failure type profiles with later onset DILD. Cluster 4 exhibited an early failure type profile or a random failure type profile with the latest onset DILD.

In vivo transcriptional profile analysis reveals RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis.

PubMed

Lim, Daniel A; Suárez-Fariñas, Mayte; Naef, Felix; Hacker, Coleen R; Menn, Benedicte; Takebayashi, Hirohide; Magnasco, Marcelo; Patil, Nila; Alvarez-Buylla, Arturo

2006-01-01

Neural stem cells and neurogenesis persist in the adult mammalian brain subventricular zone (SVZ). Cells born in the rodent SVZ migrate to the olfactory bulb (Ob) where they differentiate into interneurons. To determine the gene expression and functional profile of SVZ neurogenesis, we performed three complementary sets of transcriptional analysis experiments using Affymetrix GeneChips: (1) comparison of adult mouse SVZ and Ob gene expression profiles with those of the striatum, cerebral cortex, and hippocampus; (2) profiling of SVZ stem cells and ependyma isolated by fluorescent-activated cell sorting (FACS); and (3) analysis of gene expression changes during in vivo SVZ regeneration after anti-mitotic treatment. Gene Ontology (GO) analysis of data from these three separate approaches showed that in adult SVZ neurogenesis, RNA splicing and chromatin remodeling are biological processes as statistically significant as cell proliferation, transcription, and neurogenesis. In non-neurogenic brain regions, RNA splicing and chromatin remodeling were not prominent processes. Fourteen mRNA splicing factors including Sf3b1, Sfrs2, Lsm4, and Khdrbs1/Sam68 were detected along with 9 chromatin remodeling genes including Mll, Bmi1, Smarcad1, Baf53a, and Hat1. We validated the transcriptional profile data with Northern blot analysis and in situ hybridization. The data greatly expand the catalogue of cell cycle components, transcription factors, and migration genes for adult SVZ neurogenesis and reveal RNA splicing and chromatin remodeling as prominent biological processes for these germinal cells.

Growth, characterization and estimation of lattice strain and size in CdS nanoparticles: X-ray peak profile analysis

NASA Astrophysics Data System (ADS)

Solanki, Rekha Garg; Rajaram, Poolla; Bajpai, P. K.

2018-05-01

This work is based on the growth, characterization and estimation of lattice strain and crystallite size in CdS nanoparticles by X-ray peak profile analysis. The CdS nanoparticles were synthesized by a non-aqueous solvothermal method and were characterized by powder X-ray diffraction (XRD), transmission electron microscopy (TEM), Raman and UV-visible spectroscopy. XRD confirms that the CdS nanoparticles have the hexagonal structure. The Williamson-Hall (W-H) method was used to study the X-ray peak profile analysis. The strain-size plot (SSP) was used to study the individual contributions of crystallite size and lattice strain from the X-rays peaks. The physical parameters such as strain, stress and energy density values were calculated using various models namely, isotropic strain model, anisotropic strain model and uniform deformation energy density model. The particle size was estimated from the TEM images to be in the range of 20-40 nm. The Raman spectrum shows the characteristic optical 1LO and 2LO vibrational modes of CdS. UV-visible absorption studies show that the band gap of the CdS nanoparticles is 2.48 eV. The results show that the crystallite size estimated from Scherrer's formula, W-H plots, SSP and the particle size calculated by TEM images are approximately similar.

Effects of frying oils' fatty acids profile on the formation of polar lipids components and their retention in French fries over deep-frying process.

PubMed

Li, Xiaodan; Li, Jinwei; Wang, Yong; Cao, Peirang; Liu, Yuanfa

2017-12-15

The effects of frying oils' fatty acids profile on the formation of polar components and their retention in French fries and corresponding deep-fried oils were investigated in the present study, using oils with different fatty acids composition. Our analysis showed that the total polar compounds (TPCs) content in French fries was only slightly lower than that in deep-fried oils, indicating that there was no significant difference considering the amounts of TPCs in French fries and deep-fried oils. Our further analysis showed that different polar components in TPCs distributed differently in deep-fried oils and oils extracted from French fries. Specifically, the level of oligomeric and dimeric triacylglycerols was higher in French fries while oxidized triacylglycerols and diacylglycerols content was higher in deep-fried oils. The different retention of TPCs components in French fries may be explained by their interactions with carbohydrates, which are shown to enhance with the increase of hydrophobic property. Chemometric analysis showed that no correlation between the polar compounds level and saturated fatty acids profile was observed. Meanwhile, the polar compounds content was highly correlated with the formation of trans-C18:1, and a highly positive association between polar compounds and C18:2 content was also observed in palm oil. Copyright © 2017 Elsevier Ltd. All rights reserved.

Correlation between species-specific metabolite profiles and bioactivities of blueberries (Vaccinium spp.).

PubMed

Lee, Sarah; Jung, Eun Sung; Do, Seon-Gil; Jung, Ga-Young; Song, Gwanpil; Song, Jung-Min; Lee, Choong Hwan

2014-03-05

Metabolite profiling of three blueberry species (Vaccinium bracteatum Thunb., V. oldhamii Miquel., and V. corymbosum L.) was performed using gas chromatography-time-of-flight-mass spectrometry (GC-TOF-MS) and ultraperformance liquid chromatography-quadrupole-time-of-flight-mass spectrometry (UPLC-Q-TOF-MS) combined multivariate analysis. Partial least-squares discriminant analysis clearly showed metabolic differences among species. GC-TOF-MS analysis revealed significant differences in amino acids, organic acids, fatty acids, sugars, and phenolic acids among the three blueberry species. UPLC-Q-TOF-MS analysis indicated that anthocyanins were the major metabolites distinguishing V. bracteatum from V. oldhamii. The contents of anthocyanins such as glycosides of cyanidin were high in V. bracteatum, while glycosides of delphinidin, petunidin, and malvidin were high in V. oldhamii. Antioxidant activities assessed using ABTS and DPPH assays showed the greatest activity in V. oldhamii and revealed the highest correlation with total phenolic, total flavonoid, and total anthocyanin contents and their metabolites.

Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets.

PubMed

Amar, David; Hait, Tom; Izraeli, Shai; Shamir, Ron

2015-09-18

Genome-wide expression profiling has revolutionized biomedical research; vast amounts of expression data from numerous studies of many diseases are now available. Making the best use of this resource in order to better understand disease processes and treatment remains an open challenge. In particular, disease biomarkers detected in case-control studies suffer from low reliability and are only weakly reproducible. Here, we present a systematic integrative analysis methodology to overcome these shortcomings. We assembled and manually curated more than 14,000 expression profiles spanning 48 diseases and 18 expression platforms. We show that when studying a particular disease, judicious utilization of profiles from other diseases and information on disease hierarchy improves classification quality, avoids overoptimistic evaluation of that quality, and enhances disease-specific biomarker discovery. This approach yielded specific biomarkers for 24 of the analyzed diseases. We demonstrate how to combine these biomarkers with large-scale interaction, mutation and drug target data, forming a highly valuable disease summary that suggests novel directions in disease understanding and drug repurposing. Our analysis also estimates the number of samples required to reach a desired level of biomarker stability. This methodology can greatly improve the exploitation of the mountain of expression profiles for better disease analysis. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Network-Induced Classification Kernels for Gene Expression Profile Analysis

PubMed Central

Dror, Gideon; Shamir, Ron

2012-01-01

Abstract Computational classification of gene expression profiles into distinct disease phenotypes has been highly successful to date. Still, robustness, accuracy, and biological interpretation of the results have been limited, and it was suggested that use of protein interaction information jointly with the expression profiles can improve the results. Here, we study three aspects of this problem. First, we show that interactions are indeed relevant by showing that co-expressed genes tend to be closer in the network of interactions. Second, we show that the improved performance of one extant method utilizing expression and interactions is not really due to the biological information in the network, while in another method this is not the case. Finally, we develop a new kernel method—called NICK—that integrates network and expression data for SVM classification, and demonstrate that overall it achieves better results than extant methods while running two orders of magnitude faster. PMID:22697242

Low levels of serum serotonin and amino acids identified in migraine patients.

PubMed

Ren, Caixia; Liu, Jia; Zhou, Juntuo; Liang, Hui; Wang, Yayun; Sun, Yinping; Ma, Bin; Yin, Yuxin

2018-02-05

Migraine is a highly disabling primary headache associated with a high socioeconomic burden and a generally high prevalence. The clinical management of migraine remains a challenge. This study was undertaken to identify potential serum biomarkers of migraine. Using Liquid Chromatography coupled to Mass Spectrometry (LC-MS), the metabolomic profile of migraine was compared with healthy individuals. Principal component analysis (PCA) and Orthogonal partial least squares-discriminant analysis (orthoPLS-DA) showed the metabolomic profile of migraine is distinguishable from controls. Volcano plot analysis identified 10 serum metabolites significantly decreased during migraine. One of these was serotonin, and the other 9 were amino acids. Pathway analysis and enrichment analysis showed tryptophan metabolism (serotonin metabolism), arginine and proline metabolism, and aminoacyl-tRNA biosynthesis are the three most prominently altered pathways in migraine. ROC curve analysis indicated Glycyl-l-proline, N-Methyl-dl-Alanine and l-Methionine are potential sensitive and specific biomarkers for migraine. Our results show Glycyl-l-proline, N-Methyl-dl-Alanine and l-Methionine may be as specific or more specific for migraine than serotonin which is the traditional biomarker of migraine. We propose that therapeutic manipulation of these metabolites or metabolic pathways may be helpful in the prevention and treatment of migraine. Copyright © 2018 Elsevier Inc. All rights reserved.

The cognitive profile of behavioural variant FTD and its similarities with ALS: a systematic review and meta-analysis.

PubMed

Beeldman, Emma; Raaphorst, Joost; Klein Twennaar, Michelle; Govaarts, Rosanne; Pijnenburg, Yolande A L; de Haan, Rob J; de Visser, Marianne; Schmand, Ben A

2018-02-09

Approximately 30% of patients with amyotrophic lateral sclerosis (ALS) have cognitive impairment and 8%-14% fulfil the criteria for behavioural variant frontotemporal dementia (bv-FTD). The cognitive profiles of ALS and bv-FTD have been reported to be comparable, but this has never been systematically investigated. We aimed to determine the cognitive profile of bv-FTD and examine its similarities with that of ALS, to provide evidence for the existence of a cognitive disease continuum encompassing bv-FTD and ALS. We therefore systematically reviewed neuropsychological studies on bv-FTD patients and healthy volunteers. Neuropsychological tests were divided in 10 cognitive domains and effect sizes were calculated for all domains and compared with the cognitive profile of ALS by means of a visual comparison and a Pearson's r correlation coefficient. We included 120 studies, totalling 2425 bv-FTD patients and 2798 healthy controls. All cognitive domains showed substantial effect sizes, indicating cognitive impairment in bv-FTD patients compared to healthy controls. The cognitive domains with the largest effect sizes were social cognition, verbal memory and fluency (1.77-1.53). The cognitive profiles of bv-FTD and ALS (10 cognitive domains, 1287 patients) showed similarities on visual comparison and a moderate correlation 0.58 (p=0.13). When social cognition, verbal memory, fluency, executive functions, language and visuoperception were considered, i.e. the cognitive profile of ALS, Pearson's r was 0.73 (p=0.09), which raised to 0.92 (p=0.03), when language was excluded in this systematic analysis of patients with a non-language subtype of FTD. The cognitive profile of bv-FTD consists of deficits in social cognition, verbal memory, fluency and executive functions and shows similarities with the cognitive profile of ALS. These findings support a cognitive continuum encompassing ALS and bv-FTD. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling.

PubMed

Piro, Vitor C; Matschkowski, Marcel; Renard, Bernhard Y

2017-08-14

Many metagenome analysis tools are presently available to classify sequences and profile environmental samples. In particular, taxonomic profiling and binning methods are commonly used for such tasks. Tools available among these two categories make use of several techniques, e.g., read mapping, k-mer alignment, and composition analysis. Variations on the construction of the corresponding reference sequence databases are also common. In addition, different tools provide good results in different datasets and configurations. All this variation creates a complicated scenario to researchers to decide which methods to use. Installation, configuration and execution can also be difficult especially when dealing with multiple datasets and tools. We propose MetaMeta: a pipeline to execute and integrate results from metagenome analysis tools. MetaMeta provides an easy workflow to run multiple tools with multiple samples, producing a single enhanced output profile for each sample. MetaMeta includes a database generation, pre-processing, execution, and integration steps, allowing easy execution and parallelization. The integration relies on the co-occurrence of organisms from different methods as the main feature to improve community profiling while accounting for differences in their databases. In a controlled case with simulated and real data, we show that the integrated profiles of MetaMeta overcome the best single profile. Using the same input data, it provides more sensitive and reliable results with the presence of each organism being supported by several methods. MetaMeta uses Snakemake and has six pre-configured tools, all available at BioConda channel for easy installation (conda install -c bioconda metameta). The MetaMeta pipeline is open-source and can be downloaded at: https://gitlab.com/rki_bioinformatics .

Odor Profile of Different Varieties of Extra-Virgin Olive Oil During Deep Frying Using an Electronic Nose and SPME-GC-FID

NASA Astrophysics Data System (ADS)

Messina, Valeria; Biolatto, Andrea; Sancho, Ana; Descalzo, Adriana; Grigioni, Gabriela; de Reca, Noemí Walsöe

2011-09-01

The aim of the performed work was to evaluate with an electronic nose changes in odor profile of Arauco and Arbequina varieties of extra-virgin olive oil during deep-frying. Changes in odor were analyzed using an electronic nose composed of 16 sensors. Volatile compounds were analyzed by SPME-GC-FID. Principal Component Analysis was applied for electronic results. Arauco variety showed the highest response for sensors. Statistical analysis for volatile compounds indicated a significant (P<0.001) interaction between variety and time of frying processes. Arauco variety showed the highest production of volatile compounds at 60 min of deep frying. The two varieties presented distinct patterns of volatile products, being clearly identified with the electronic nose.

PCR-Restriction Fragment Length Polymorphism Analysis of the Phospholipase B (PLB1) Gene for Subtyping of Cryptococcus neoformans Isolates

PubMed Central

Latouche, G. Nicolas; Huynh, Matthew; Sorrell, Tania C.; Meyer, Wieland

2003-01-01

Cryptococcus neoformans is a pathogenic yeast that is currently divided into three varieties, five serotypes, and eight molecular types. The following report describes the use of PCR-restriction fragment length polymorphism (RFLP) analysis of the phospholipase B gene (PLB1) as a simple tool to differentiate between C. neoformans subgroups. A PLB1 fragment, 1,970 bp, was amplified and digested with either AvaI or HindIII. Both sets of profiles grouped the isolates into their respective varieties, but only the AvaI profiles allowed for the identification of the eight molecular types via the corresponding RFLP profiles A1 to A8. Digestion of the same fragments with HindIII resulted in RFLP profiles H1 to H5, which distinguished only between serotype A, AD, D, and B/C. Neither enzyme distinguished serotype B from serotype C. The serotype AD profile was a composite of the serotype A and D profiles. Further investigation showed that the serotype AD isolates used in this study are heterozygous, with one allele of PLB1 originating from a serotype A parent and the other from a serotype D parent. PMID:12676686

Passion and intrinsic motivation in digital gaming.

PubMed

Wang, Chee Keng John; Khoo, Angeline; Liu, Woon Chia; Divaharan, Shanti

2008-02-01

Digital gaming is fast becoming a favorite activity all over the world. Yet very few studies have examined the underlying motivational processes involved in digital gaming. One motivational force that receives little attention in psychology is passion, which could help us understand the motivation of gamers. The purpose of the present study was to identify subgroups of young people with distinctive passion profiles on self-determined regulations, flow dispositions, affect, and engagement time in gaming. One hundred fifty-five students from two secondary schools in Singapore participated in the survey. There were 134 males and 8 females (13 unspecified). The participants completed a questionnaire to measure harmonious passion (HP), obsessive passion (OP), perceived locus of causality, disposition flow, positive and negative affects, and engagement time in gaming. Cluster analysis found three clusters with distinct passion profiles. The first cluster had an average HP/OP profile, the second cluster had a low HP/OP profile, and the third cluster had a high HP/OP profile. The three clusters displayed different levels of cognitive, affective, and behavioral outcomes. Cluster analysis, as this study shows, is useful in identifying groups of gamers with different passion profiles. It has helped us gain a deeper understanding of motivation in digital gaming.

Integrated analysis of rice transcriptomic and metabolomic responses to elevated night temperatures identifies sensitivity- and tolerance-related profiles.

PubMed

Glaubitz, Ulrike; Li, Xia; Schaedel, Sandra; Erban, Alexander; Sulpice, Ronan; Kopka, Joachim; Hincha, Dirk K; Zuther, Ellen

2017-01-01

Transcript and metabolite profiling were performed on leaves from six rice cultivars under high night temperature (HNT) condition. Six genes were identified as central for HNT response encoding proteins involved in transcription regulation, signal transduction, protein-protein interactions, jasmonate response and the biosynthesis of secondary metabolites. Sensitive cultivars showed specific changes in transcript abundance including abiotic stress responses, changes of cell wall-related genes, of ABA signaling and secondary metabolism. Additionally, metabolite profiles revealed a highly activated TCA cycle under HNT and concomitantly increased levels in pathways branching off that could be corroborated by enzyme activity measurements. Integrated data analysis using clustering based on one-dimensional self-organizing maps identified two profiles highly correlated with HNT sensitivity. The sensitivity profile included genes of the functional bins abiotic stress, hormone metabolism, cell wall, signaling, redox state, transcription factors, secondary metabolites and defence genes. In the tolerance profile, similar bins were affected with slight differences in hormone metabolism and transcription factor responses. Metabolites of the two profiles revealed involvement of GABA signaling, thus providing a link to the TCA cycle status in sensitive cultivars and of myo-inositol as precursor for inositol phosphates linking jasmonate signaling to the HNT response specifically in tolerant cultivars. © 2016 John Wiley & Sons Ltd.

How are personality trait and profile agreement related?

PubMed Central

Allik, Jüri; Borkenau, Peter; Hřebíčková, Martina; Kuppens, Peter; Realo, Anu

2015-01-01

It is argued that if we compute self-other agreement on some personality traits then we possess no or very little information about the individuals who are the targets of this judgment. This idea is largely based on two separate ways of computing self-other agreement: trait agreement (rT) and profile agreement (rP), which are typically associated with two different trait-centered and person-centered approaches in personality research. Personality traits of 4115 targets from Czech, Belgian, Estonian, and German samples were rated by themselves and knowledgeable informants. We demonstrate that trait agreement can be partialled into individual contributions so that it is possible to show how much each individual pair of judges contributes to agreement on a particular trait. Similarly, it is possible to decompose agreement between two personality profiles into the individual contributions of traits from which these profiles are assembled. If normativeness is separated from distinctiveness of personality scores and individual profiles are ipsatized, then mean profile agreement rP becomes identical to mean trait agreement rT. The views that trait-by-trait analysis does not provide information regarding accuracy level of a particular pair of judges and profile analysis does not permit assessment of the relative contributions of traits to overall accuracy are not supported. PMID:26106356

Analysis of Human Plasma Metabolites across Different Liquid Chromatography - Mass Spectrometry Platforms: Cross-platform Transferable Chemical Signatures

PubMed Central

Telu, Kelly H.; Yan, Xinjian; Wallace, William E.; Stein, Stephen E.; Simón-Manso, Yamil

2016-01-01

RATIONALE The metabolite profiling of a NIST plasma Standard Reference Material (SRM 1950) on different LC-MS platforms showed significant differences. Although these findings suggest caution when interpreting metabolomics results, the degree of overlap of both profiles allowed us to use tandem mass spectral libraries of recurrent spectra to evaluate to what extent these results are transferable across platforms and to develop cross-platform chemical signatures. METHODS Non-targeted global metabolite profiles of SRM 1950 were obtained on different LC-MS platforms using reversed phase chromatography and different chromatographic scales (nano, conventional and UHPLC). The data processing and the metabolite differential analysis were carried out using publically available (XCMS), proprietary (Mass Profiler Professional) and in-house software (NIST pipeline). RESULTS Repeatability and intermediate precision showed that the non-targeted SRM 1950 profiling was highly reproducible when working on the same platform (RSD < 2%); however, substantial differences were found in the LC-MS patterns originating on different platforms or even using different chromatographic scales (conventional HPLC, UHPLC and nanoLC) on the same platform. A substantial degree of overlap (common molecular features) was also found. A procedure to generate consistent chemical signatures using tandem mass spectral libraries of recurrent spectra is proposed. CONLUSIONS Different platforms rendered significantly different metabolite profiles, but the results were highly reproducible when working within one platform. Tandem mass spectral libraries of recurrent spectra are proposed to evaluate the degree of transferability of chemical signatures generated on different platforms. Chemical signatures based on our procedure are most likely cross-platform transferable. PMID:26842580

Discrepancies between multicriteria decision analysis-based ranking and intuitive ranking for pharmaceutical benefit-risk profiles in a hypothetical setting.

PubMed

Hoshikawa, K; Ono, S

2017-02-01

Multicriteria decision analysis (MCDA) has been generally considered a promising decision-making methodology for the assessment of drug benefit-risk profiles. There have been many discussions in both public and private sectors on its feasibility and applicability, but it has not been employed in official decision-makings. For the purpose of examining to what extent MCDA would reflect the first-hand, intuitive preference of evaluators in practical pharmaceutical assessments, we conducted a questionnaire survey involving the participation of employees of pharmaceutical companies. Showing profiles of the efficacy and safety of four hypothetical drugs, each respondent was asked to rank them following the standard MCDA process and then to rank them intuitively (i.e. without applying any analytical framework). These two approaches resulted in substantially different ranking patterns from the same individuals, and the concordance rate was surprisingly low (17%). Although many respondents intuitively showed a preference for mild, balanced risk-benefit profiles over profiles with a conspicuous advantage in either risk or benefit, the ranking orders based on MCDA scores did not reflect the intuitive preference. Observed discrepancies between the rankings seemed to be primarily attributed to the structural characteristics of MCDA, which assumes that evaluation on each benefit and risk component should have monotonic impact on final scores. It would be difficult for MCDA to reflect commonly observed non-monotonic preferences for risk and benefit profiles. Possible drawbacks of MCDA should be further investigated prior to the real-world application of its benefit-risk assessment. © 2016 John Wiley & Sons Ltd.

Analysis of the Tikhonov regularization to retrieve thermal conductivity depth-profiles from infrared thermography data

NASA Astrophysics Data System (ADS)

Apiñaniz, Estibaliz; Mendioroz, Arantza; Salazar, Agustín; Celorrio, Ricardo

2010-09-01

We analyze the ability of the Tikhonov regularization to retrieve different shapes of in-depth thermal conductivity profiles, usually encountered in hardened materials, from surface temperature data. Exponential, oscillating, and sigmoidal profiles are studied. By performing theoretical experiments with added white noises, the influence of the order of the Tikhonov functional and of the parameters that need to be tuned to carry out the inversion are investigated. The analysis shows that the Tikhonov regularization is very well suited to reconstruct smooth profiles but fails when the conductivity exhibits steep slopes. We check a natural alternative regularization, the total variation functional, which gives much better results for sigmoidal profiles. Accordingly, a strategy to deal with real data is proposed in which we introduce this total variation regularization. This regularization is applied to the inversion of real data corresponding to a case hardened AISI1018 steel plate, giving much better anticorrelation of the retrieved conductivity with microindentation test data than the Tikhonov regularization. The results suggest that this is a promising way to improve the reliability of local inversion methods.

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

Aslan, Z.; Topcu, S.

A central objective of micrometeorological research is to establish fluxes from a knowledge of the mean temperature, humidity and wind speed profiles. The effect of time and spatial variations of surface heat and momentum fluxes is studied for various geographic regions. These analysis show the principal boundary conditions for micro and meso-scale analysis, air-sea interactions, weather forecasting air pollution, agrometeorology and climate changing models. The fluxes of heat and momentum can be obtained from observed profiles of wind speed and temperature using the similarity relations for the atmospheric surface layer. In recent years, harmonic analysis is a particularly useful toolmore » in studying annual patterns of some meteorological parameters at the field of micrometeorological studies.« less

Second-harmonic generation of practical Bessel beams

NASA Astrophysics Data System (ADS)

Huang, Jin H.; Ding, Desheng; Hsu, Yin-Sung

2009-11-01

A fast Gaussian expansion approach is used to investigate fundamental and second-harmonic generation in practical Bessel beams of finite aperture. The analysis is based on the integral solutions of the KZK equation under the quasilinear approximation. The influence of the medium's attenuation on the beam profile is considered. Analysis results show that the absorption parameter has a significant effect on the far-field beam profile of the second harmonic. Under certain circumstances, the second harmonic of a practical Bessel beam still has the main properties of an ideal Bessel beam of infinite aperture when it propagates within its depth of field.

Internalizing and externalizing personality and subjective effects in a sample of adolescent cannabis users.

PubMed

García-Sánchez, Sara; Matalí, Josep Lluís; Martín-Fernández, María; Pardo, Marta; Lleras, Maria; Castellano-Tejedor, Carmina; Haro, Josep Maria

2016-10-06

Cannabis is the illicit substance most widely used by adolescents. Certain personality traits such as impulsivity and sensation seeking, and the subjective effects experienced after substance use (e.g. euphoria or relaxation) have been identified as some of the main etiological factors of consumption. This study aims to categorize a sample of adolescent cannabis users based on their most dominant personality traits (internalizing and externalizing profile). Then, to make a comparison of both profiles considering a set of variables related to consumption, clinical severity and subjective effects experienced. From a cross-sectional design, 173 adolescents (104 men and 69 women) aged 13 to 18 asking for treatment for cannabis use disorder in an Addictive Behavior Unit (UCAD) from the hospital were recruited. For the assessment, an ad hoc protocol was employed to register consumption, the Millon Adolescent Clinical Inventory (MACI) and the Addiction Research Center Inventory (ARCI) 49-item short form were also administered. Factor analysis suggested a two-profile solution: Introverted, Inhibited, Doleful, Dramatizing (-), Egotistic (-), Self-demeaning and Borderline tendency scales composed the internalizing profile, and Submissive (-), Unruly, Forceful, Conforming (-) and Oppositional scales composed the externalizing profile. The comparative analysis showed that the internalizing profile has higher levels of clinical severity and more subjective effects reported than the externalizing profile. These results suggest the need to design specific intervention strategies for each profile.

Profiles of observed infant anger predict preschool behavior problems: Moderation by life stress

PubMed Central

Brooker, Rebecca J.; Buss, Kristin A.; Lemery-Chalfant, Kathryn; Aksan, Nazan; Davidson, Richard J.; Goldsmith, H. Hill

2014-01-01

Using both traditional composites and novel profiles of anger, we examined associations between infant anger and preschool behavior problems in a large, longitudinal data set (N = 966). We also tested the role of life stress as a moderator of the link between early anger and the development of behavior problems. Although traditional measures of anger were largely unrelated to later behavior problems, profiles of anger that dissociated typical from atypical development predicted behavior problems during preschool. Moreover, the relation between infant anger profiles and preschool behavior problems was moderated such that, when early life stress was low, infants with atypical profiles of early anger showed more preschool behavior problems than did infants with normative anger profiles. However, when early life stress was high, infants with atypical and normative profiles of infant anger did not differ in preschool behavior problems. We conclude that a discrete emotions approach including latent profile analysis is useful for elucidating biological and environmental developmental pathways to early problem behaviors. PMID:25151247

An Empirical Study on the Effect of Work/Life Commitment to Work-Life Conflict

NASA Astrophysics Data System (ADS)

Ma, Li; Yin, Jie-lin

This study examined the relation between work and life orientation and work interfere with personal life or personal life interfere with work of employees in China. Cluster analysis results showed that there are four profiles of orientation: work orientation, life orientation, integration and disengagement orientation. There are significant differences in work interfere personal life and personal life interfere work between different profiles.

Molecular profiling identifies prognostic markers of stage IA lung adenocarcinoma.

PubMed

Zhang, Jie; Shao, Jinchen; Zhu, Lei; Zhao, Ruiying; Xing, Jie; Wang, Jun; Guo, Xiaohui; Tu, Shichun; Han, Baohui; Yu, Keke

2017-09-26

We previously showed that different pathologic subtypes were associated with different prognostic values in patients with stage IA lung adenocarcinoma (AC). We hypothesize that differential gene expression profiles of different subtypes may be valuable factors for prognosis in stage IA lung adenocarcinoma. We performed microarray gene expression profiling on tumor tissues micro-dissected from patients with acinar and solid predominant subtypes of stage IA lung adenocarcinoma. These patients had undergone a lobectomy and mediastinal lymph node dissection at the Shanghai Chest Hospital, Shanghai, China in 2012. No patient had preoperative treatment. We performed the Gene Set Enrichment Analysis (GSEA) analysis to look for gene expression signatures associated with tumor subtypes. The histologic subtypes of all patients were classified according to the 2015 WHO lung Adenocarcinoma classification. We found that patients with the solid predominant subtype are enriched for genes involved in RNA polymerase activity as well as inactivation of the p53 pathway. Further, we identified a list of genes that may serve as prognostic markers for stage IA lung adenocarcinoma. Validation in the TCGA database shows that these genes are correlated with survival, suggesting that they are novel prognostic factors for stage IA lung adenocarcinoma. In conclusion, we have uncovered novel prognostic factors for stage IA lung adenocarcinoma using gene expression profiling in combination with histopathology subtyping.

Gene expression profiling of human mesenchymal stem cells derived from bone marrow during expansion and osteoblast differentiation.

PubMed

Kulterer, Birgit; Friedl, Gerald; Jandrositz, Anita; Sanchez-Cabo, Fatima; Prokesch, Andreas; Paar, Christine; Scheideler, Marcel; Windhager, Reinhard; Preisegger, Karl-Heinz; Trajanoski, Zlatko

2007-03-12

Human mesenchymal stem cells (MSC) with the capacity to differentiate into osteoblasts provide potential for the development of novel treatment strategies, such as improved healing of large bone defects. However, their low frequency in bone marrow necessitate ex vivo expansion for further clinical application. In this study we asked if MSC are developing in an aberrant or unwanted way during ex vivo long-term cultivation and if artificial cultivation conditions exert any influence on their stem cell maintenance. To address this question we first developed human oligonucleotide microarrays with 30.000 elements and then performed large-scale expression profiling of long-term expanded MSC and MSC during differentiation into osteoblasts. The results showed that MSC did not alter their osteogenic differentiation capacity, surface marker profile, and the expression profiles of MSC during expansion. Microarray analysis of MSC during osteogenic differentiation identified three candidate genes for further examination and functional analysis: ID4, CRYAB, and SORT1. Additionally, we were able to reconstruct the three developmental phases during osteoblast differentiation: proliferation, matrix maturation, and mineralization, and illustrate the activation of the SMAD signaling pathways by TGF-beta2 and BMPs. With a variety of assays we could show that MSC represent a cell population which can be expanded for therapeutic applications.

Dependence of Edge Profiles and Stability on Neutral Beam Power in NSTX

NASA Astrophysics Data System (ADS)

Travis, P.; Canal, G. P.; Osborne, T. H.; Maingi, R.; Sabbagh, S. A.; NSTX-U Team

2016-10-01

Studying the effect of neutral beam injected (NBI) power on edge plasma profiles and magnetohydrodynamic (MHD) stability is central to the understanding of edge-localized modes (ELMs). Higher heating power should quicken the development of pressure and current-driven peeling-ballooning modes. NSTX ELMy H-mode discharges with NBI power of 4, 5 and 6 MW were analyzed with a python-based set of analysis tools that fit plasma profiles, compute kinetic equilibria, and evaluate the MHD stability with the code ELITE. Electron density and temperature from Thomson scattering measurements, and ion density, temperature, and rotation from Charge Exchange Recombination Spectroscopy were inputs to the kinetic equilibrium fits. The power scan provides an opportunity to compare the stability calculations from the ELITE (ideal) and M3D-C1 (resistive) codes. Preliminary analysis shows that edge pressure profiles for the 5 and 6 MW discharges are comparable, suggesting they both reach a stability boundary. The 4 MW case shows lower edge pressure, which is likely limited by edge transport below the edge stability boundary. This work was supported in part by the U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists (WDTS) under the Science Undergraduate Laboratory Internship (SULI) program.

Molecular Docking and Pharmacological Investigations of Rivastigmine-Fluoxetine and Coumarin-Tacrine hybrids against Acetyl Choline Esterase.

PubMed

Babitha, Pallikkara Pulikkal; Sahila, Mohammed Marunnan; Bandaru, Srinivas; Nayarisseri, Anuraj; Sureshkumar, Sivanpillai

2015-01-01

The present AChE inhibitors have been successful in the treatment of Alzheimer׳s Diseases however suffers serious side effects. Therefore in this view, the present study was sought to identify compounds with appreciable pharmacological profile targeting AChE. Analogue of Rivastigmine and Fluoxetine hybrid synthesized by Toda et al, 2003 (dataset1), and Coumarin-Tacrine hybrids synthesized by Qi Sun et al (dataset2) formed the test compounds for the present pharmacological evaluation. p-cholorophenyl substituted Rivastigmine and Fluoxetine hybrid compound (26d) from dataset 1 and -OCH3 substitute Coumarin-Tacrine hybrids (1h) from dataset 2 demonstrated superior pharmacological profile. 26 d showed superior pharmacological profile comparison to the entire compounds in either dataset owing to its better electrostatic interactions and hydrogen bonding patterns. In order to identify still better compound with pharmacological profile than 26 d and 1h, virtual screening was performed. The best docked compound (PubCId: PubCid: 68874404) showed better affinity than its parent 26 d, however showed poor ADME profile and AMES toxicity. CHEMBL2391475 (PubCid: 71699632) similar to 1h had reduced affinity in comparison to its parent compound 1h. From, our extensive analysis involving binding affinity analysis, ADMET properties predictions and pharmacophoric mappings, we report p-cholorophenyl substituted rivastigmine and fluoxetine hybrid (26d) to be a potential candidate for AcHE inhibition which in addition can overcome narrow therapeutic window of present AChE inhibitors in clinical treatment of Alzheimer׳s disease. AD - Alzheimer׳s Disease, AChE - Acetyl Choline Estarase, OPLS - Optimized Potentials for Liquid Simulations, PDB - Protein Data Bank.

Effects of Histidine Supplementation on Global Serum and Urine 1H NMR-based Metabolomics and Serum Amino Acid Profiles in Obese Women from a Randomized Controlled Study.

PubMed

Du, Shanshan; Sun, Shuhong; Liu, Liyan; Zhang, Qiao; Guo, Fuchuan; Li, Chunlong; Feng, Rennan; Sun, Changhao

2017-06-02

The aim of current study was to investigate the metabolic changes associated with histidine supplementation in serum and urine metabolic signatures and serum amino acid (AA) profiles. Serum and urine 1 H NMR-based metabolomics and serum AA profiles were employed in 32 and 37 obese women with metabolic syndrome (MetS) intervened with placebo or histidine for 12 weeks. Multivariable statistical analysis were conducted to define characteristic metabolites. In serum 1 H NMR metabolic profiles, increases in histidine, glutamine, aspartate, glycine, choline, and trimethylamine-N-oxide (TMAO) were observed; meanwhile, decreases in cholesterol, triglycerides, fatty acids and unsaturated lipids, acetone, and α/β-glucose were exhibited after histidine supplement. In urine 1 H NMR metabolic profiles, citrate, creatinine/creatine, methylguanidine, and betaine + TMAO were higher, while hippurate was lower in histidine supplement group. In serum AA profiles, 10 AAs changed after histidine supplementation, including increased histidine, glycine, alanine, lysine, asparagine, and tyrosine and decreased leucine, isoleucine, ornithine, and citrulline. The study showed a systemic metabolic response in serum and urine metabolomics and AA profiles to histidine supplementation, showing significantly changed metabolism in AAs, lipid, and glucose in obese women with MetS.

Variability of nutrients intake, lipid profile and cardiovascular mortality among geographical areas in Spain: The DRECE study.

PubMed

Gómez de la Cámara, Agustín; De Andrés Esteban, Eva; Urrútia Cuchí, Gerard; Calderón Sandubete, Enrique; Rubio Herrera, Miguel Ángel; Menéndez Orenga, Miguel; Lora Pablos, David

2017-11-07

It has often been suggested that cardiovascular mortality and their geographical heterogeneity are associated with nutrients intake patterns and also lipid profile. The large Spanish study Dieta y Riesgo de Enfermedades Cardiovasculares en España (DRECE) investigated this theory from 1991 to 2010. Out of the 4,783 Spanish individuals making up the DRECE cohort, 220 subjects (148 men and 72 women) died (4.62%) during the course of the study. The mean age of patients who died from cardiovascular causes (32 in all) was 61.08 years 95% CI (57.47-64.69) and 70.91% of them were males. The consumption of nutrients and the lipid profile by geographical area, studied by geospatial models, showed that the east and southern area of the country had the highest fat intake coupled to a high rate of unhealthy lipid profile. It was concluded that the spatial geographical analysis showed a relationship between high fat intake, unhealthy lipid profile and cardiovascular mortality in the different geographical areas, with a high variability within the country.

Structure of n-alkyltrichlorosilane mono layers on Si(100)/SiO 2

DOE PAGES

H. -G. Steinruck; Ocko, B.; Will, J.; ...

2015-10-05

The structure of n-alkyltrichlorosilane self-assembled monolayers (SAMs) of alkyl chain lengths n = 12, 14, 18, and 22 formed on the amorphous native oxide of silicon (100) has been investigated via angstrom-resolution surface X-ray scattering techniques, with particular focus on the proliferation of lateral order along the molecules’ long axis. Grazing incidence diffraction shows that the monolayer is composed of hexagonally packed crystalline-like domains for n = 14, 18, and 22 with a lateral size of about 60 Å. However, Bragg rod analysis shows that ~12 of the CH 2 units are not included in the crystalline-like domains. We assignmore » this, and the limited lateral crystallites’ size, to strain induced by the size mismatch between the optimal chain–chain and headgroup–headgroup spacings. Lastly, analysis of X-ray reflectivity profiles for n = 12, 14, and 22 shows that the density profile used to successfully model n = 18 provides an excellent fit where the analysis-derived parameters provide complementary structural information to the grazing incidence results.« less

Quality, microstructure, biochemical and immunochemical characteristics of hypoallergenic pasta.

PubMed

Susanna, S; Prabhasankar, P

2012-08-01

Celiac disease is an immune-mediated enteropathy, characterized by lifelong intolerance to gluten in genetically susceptible individuals. This study aims to develop hypoallergenic pasta using blends of Triticum durum semolina, 40% of other non-wheat flours and additives. Formulated pasta samples were evaluated for product quality characteristics and also subjected to biochemical analysis. Results showed that cooking loss ranged from 6.9% to 7.4%, which were within the acceptable range of 8%. Color change was low and in vitro protein digestibility of the pasta was found to be insignificant. Pasting characteristics of the hypoallergenic flour showed the increased peak viscosity and decreased gelatinization temperature. The scanning electron microscopy results demonstrated less-affected microstructure of gluten network. Texture profile analysis and descriptive sensory analysis revealed that optimized hypoallergenic pasta with xanthan gum as additive was acceptable and comparable with control. SDS-PAGE pattern showed distinct protein profile and decreased intensity, which was supported by Dot-Blot. In conclusion, the hypoallergenic pasta prepared by replacing T durum flour by 40% of other non-gluten flours could be useful for celiac patients because of its low antigenic activity.

Literature-based compound profiling: application to toxicogenomics.

PubMed

Frijters, Raoul; Verhoeven, Stefan; Alkema, Wynand; van Schaik, René; Polman, Jan

2007-11-01

To reduce continuously increasing costs in drug development, adverse effects of drugs need to be detected as early as possible in the process. In recent years, compound-induced gene expression profiling methodologies have been developed to assess compound toxicity, including Gene Ontology term and pathway over-representation analyses. The objective of this study was to introduce an additional approach, in which literature information is used for compound profiling to evaluate compound toxicity and mode of toxicity. Gene annotations were built by text mining in Medline abstracts for retrieval of co-publications between genes, pathology terms, biological processes and pathways. This literature information was used to generate compound-specific keyword fingerprints, representing over-represented keywords calculated in a set of regulated genes after compound administration. To see whether keyword fingerprints can be used for assessment of compound toxicity, we analyzed microarray data sets of rat liver treated with 11 hepatotoxicants. Analysis of keyword fingerprints of two genotoxic carcinogens, two nongenotoxic carcinogens, two peroxisome proliferators and two randomly generated gene sets, showed that each compound produced a specific keyword fingerprint that correlated with the experimentally observed histopathological events induced by the individual compounds. By contrast, the random sets produced a flat aspecific keyword profile, indicating that the fingerprints induced by the compounds reflect biological events rather than random noise. A more detailed analysis of the keyword profiles of diethylhexylphthalate, dimethylnitrosamine and methapyrilene (MPy) showed that the differences in the keyword fingerprints of these three compounds are based upon known distinct modes of action. Visualization of MPy-linked keywords and MPy-induced genes in a literature network enabled us to construct a mode of toxicity proposal for MPy, which is in agreement with known effects of MPy in literature. Compound keyword fingerprinting based on information retrieved from literature is a powerful approach for compound profiling, allowing evaluation of compound toxicity and analysis of the mode of action.

Sm@C2v(3)-C80: site-hopping motion of endohedral Sm atom and metal-induced effect on redox profile

NASA Astrophysics Data System (ADS)

Xu, Wei; Niu, Ben; Shi, Zujin; Lian, Yongfu; Feng, Lai

2012-10-01

A new metallofullerene Sm@C2v(3)-C80 was synthesized and characterized. X-Ray analysis showed that the endohedral Sm atom undergoes a hopping motion between several off-center sites, even at low temperature. In addition, a comparative electrochemical study between Sm@C2v(3)-C80 and Yb@C2v(3)-C80 revealed their different redox potentials, suggesting a metal-induced effect on their redox profiles.A new metallofullerene Sm@C2v(3)-C80 was synthesized and characterized. X-Ray analysis showed that the endohedral Sm atom undergoes a hopping motion between several off-center sites, even at low temperature. In addition, a comparative electrochemical study between Sm@C2v(3)-C80 and Yb@C2v(3)-C80 revealed their different redox potentials, suggesting a metal-induced effect on their redox profiles. CCDC reference number 894168. For crystallographic data in CIF or other electronic format see DOI: 10.1039/c2nr32193a

Changes in Amino Acid Profile in Roots of Glyphosate Resistant and Susceptible Soybean (Glycine max) Induced by Foliar Glyphosate Application.

PubMed

Moldes, Carlos Alberto; Cantarelli, Miguel Angel; Camiña, José Manuel; Tsai, Siu Mui; Azevedo, Ricardo Antunes

2017-10-11

Amino acid profiles are useful to analyze the responses to glyphosate in susceptible and resistant soybean lines. Comparisons of profiles for 10 amino acids (Asp, Asn, Glu, Gln, Ser, His, Gly, Thr, Tyr, Leu) by HPLC in soybean roots were performed in two near isogenic pairs (four varieties). Foliar application of glyphosate was made to soybean plants after 5 weeks of seeding. Roots of four varieties were collected at 0 and 72 h after glyphosate application (AGA) for amino acid analysis by HPLC. Univariate analysis showed a significant increase of several amino acids in susceptible as well as resistant soybean lines; however, amino acids from the major pathways of carbon (C) and nitrogen (N) metabolism, such as Asp, Asn, Glu and Gln, and Ser, increased significantly in susceptible varieties at 72 h AGA. Multivariate analysis using principal component analysis (2D PCA and 3D PCA) allowed different groups to be identified and discriminated based on the soybean genetic origin, showing the amino acid responses on susceptible and resistant varieties. Based on the results, it is possible to infer that the increase of Asn, Asp, Glu, Gln, and Ser in susceptible varieties would be related to the deregulation of C and N metabolism, as well as changes in the growth mechanisms regulated by Ser.

A meta-analysis of the association of serum ischaemia-modified albumin levels with human hypothyroidism and hyperthyroidism.

PubMed

Reddy, Varikasuvu Seshadri; Bukke, Suman; Mahato, Khageshwar; Kumar, Vinod; Reddy, Netala Vasudeva; Munikumar, Manne; Vodelu, Bramahanapally

2017-02-28

Serum levels of ischaemia-modified albumin (IMA) have been studied as a novel and simple measure of oxidative stress (OXS) in different thyroid pathologies. However, results of available studies in the literature were not consistent. This meta-analysis was attempted to quantify the overall effect size for serum IMA levels in human hypothyroidism (HT) and hyperthyroidism (HYT) and to study its associations with the thyroid profile. Databases of PubMed/Medline, EMBASE, Google Scholar, Web of Science and Science Direct were searched for articles. Data on serum IMA levels in HT, HYT patients and euthyroid controls were extracted to compute standardized mean differences (SMD) by the random-effects model. The associations between IMA and thyroid profile were computed by the meta-analysis of correlation coefficients. IMA levels in HT patients (SMD=1.12; Z=2.76; P=0.006) and HYT patients (SMD=1.64; Z=2.57; P=0.01) were significantly higher than in euthyroid controls and the thyroid treatment showed a favourble effect on serum IMA levels. There were strong and significant correlations between IMA and hormonal status in HT and HYT groups. This meta-analysis showing increased IMA level in both HT and HYT patients and its association with thyroid profile suggests that serum IMA could be used as a simple measure of increased OXS in thyroid dysfunction. © 2017 The Author(s).

Analysis of pain behavior profiles and functional disability in outpatient physical therapy clinics.

PubMed

Hankin, H A; Spencer, T; Kegerreis, S; Worrell, T; Rice, J M

2001-02-01

Descriptive, ex post facto. To determine the proportion of physical therapy outpatients with pain who exhibit various pain behavior profiles, and to determine whether there are differences in functional disability across the profiles. Physical therapists treat many patients who have chronic pain. Research suggests that early identification and multidisciplinary treatment are effective and economical for these patients. The Multidimensional Pain Inventory (MPI) and the Pain Disability Index (PDI) are potential screening tools that could be used in physical therapy clinics to determine which patients should be referred for multidisciplinary treatment. MPI and PDI data were gathered on 57 physical therapy outpatients (mean age 44.3 +/- 14.5 years, 22 men and 35 women) with pain of 3 or more months duration. ANOVA was used to analyze differences in mean PDI scores across the MPI profiles. Of all patients, 42.1% fit the Adaptive Coper profile, 29.8% fit the Interpersonally Distressed profile, and 28.1% fit the Dysfunctional profile. There were significant differences in PDI scores among profile groups. Post hoc analysis showed that the PDI scores of the Adaptive Coper and Interpersonally Distressed groups were different from the Dysfunctional group, but that there was no difference between the Adaptive Coper and Interpersonally Distressed groups. Many patients in outpatient physical therapy settings exhibit behavioral, affective, and cognitive characteristics associated with chronic pain. Thirty-three patients (57.9%) had MPI profiles (interpersonally distressed and dysfunctional) that suggest they might benefit from multidisciplinary treatment.

A geochemical study of overbank sediments in an urban area (Madrid, Spain).

PubMed

Adánez Sanjuán, Paula; Llamas Borrajo, Juan F; Locutura Rupérez, Juan; García Cortés, Angel

2014-12-01

Overbank and stream sediments have been studied in the Community of Madrid. Four vertical profiles have been sampled corresponding to Guadarrama, Jarama, and finally Manzanares River, where two profiles have been studied upstream (El Pardo profile) and downstream (Rivas profile) Madrid city. Sieved samples (<63 µm) were subjected to total (ICP-MS/ICP-OES and INAA) and partial analysis (ICP-MS). AMS radiocarbon dating techniques revealed a young age (170 ± 40 years BP) at 2.40-2.65 m depth for Rivas profile. It has not been possible to detect pristine or pre-industrial overbank sediments, since in the rest of the studied profiles, anthropogenic wastes were found even in the lower levels. Three main sources of sediment have been detected in the area. Granitic and arkosic geology, located in the northern part of Madrid (U, Th, W, K, Na, or rare earth elements); clays located in the southeast of Madrid (Ni, Cr, or V), and finally an anthropogenic source has been identified (Au, Ag, Pb, Zn, or Sb) in Rivas profile. The influence of the anthropogenic activity has been established based on the contents distribution of contaminant elements in the profile. This can be associated to the growth of industrial activities and population in the city of Madrid during the last decades. The comparison of the profiles by a k-means cluster analysis showed some similarities for these samples that could have analogous sources (anthropogenic and geological).

Surface Composition of NiPd Alloys

NASA Technical Reports Server (NTRS)

Noebe, Ronald D.; Khalil, Joe; Bozzolo, Guillermo; Gray, Hugh R. (Technical Monitor)

2002-01-01

Surface segregation in Ni-Pd alloys has been studied using the BFS method for alloys. Not only does the method predict an oscillatory segregation profile but it also indicates that the number of Pd-enriched surface planes can vary as a function of orientation. The segregation profiles were computed as a function of temperature, crystal face, and composition. Pd enrichment of the first layer is observed in (111) and (100) surfaces, and enrichment of the top two layers occurs for (110) surfaces. In all cases, the segregation profile shows oscillations that are actually related to weak ordering tendencies in the bulk. An atom-by-atom analysis was performed to identify the competing mechanisms leading to the observed surface behaviors. Large-scale atomistic simulations were also performed to investigate the temperature dependence of the segregation profiles as well as for analysis of the bulk structures. Finally, the observed surface behaviors are discussed in relation to the bulk phase structure of Ni-Pd alloys, which exhibit a tendency to weakly order.

Existence of Inverted Profile in Chemically Responsive Molecular Pathways in the Zebrafish Liver

PubMed Central

Zhang, Xun; Li, Hu; Ma, Jing; Zhang, Louxin; Li, Baowen; Gong, Zhiyuan

2011-01-01

How a living organism maintains its healthy equilibrium in response to endless exposure of potentially harmful chemicals is an important question in current biology. By transcriptomic analysis of zebrafish livers treated by various chemicals, we defined hubs as molecular pathways that are frequently perturbed by chemicals and have high degree of functional connectivity to other pathways. Our network analysis revealed that these hubs were organized into two groups showing inverted functionality with each other. Intriguingly, the inverted activity profiles in these two groups of hubs were observed to associate only with toxicopathological states but not with physiological changes. Furthermore, these inverted profiles were also present in rat, mouse, and human under certain toxicopathological conditions. Thus, toxicopathological-associated anti-correlated profiles in hubs not only indicate their potential use in diagnosis but also development of systems-based therapeutics to modulate gene expression by chemical approach in order to rewire the deregulated activities of hubs back to normal physiology. PMID:22140468

Passion fruit juice with different sweeteners: sensory profile by descriptive analysis and acceptance.

PubMed

Rocha, Izabela Furtado de Oliveira; Bolini, Helena Maria André

2015-03-01

This study evaluated the effect of different sweeteners on the sensory profile, acceptance, and drivers of preference of passion fruit juice samples sweetened with sucrose, aspartame, sucralose, stevia, cyclamate/saccharin blend 2:1, and neotame. Sensory profiling was performed by 12 trained assessors using quantitative descriptive analysis (QDA). Acceptance tests (appearance, aroma, flavor, texture and overall impression) were performed with 124 consumers of tropical fruit juice. Samples with sucrose, aspartame and sucralose showed similar sensory profile (P < 0.05), without bitter taste, bitter aftertaste, and metallic taste, and samples with sucrose and sucralose did not differ from each other for the attribute sweet aftertaste. Passion fruit flavor affected positively and sweet aftertaste affected negatively the acceptance of the samples. Samples sweetened with aspartame, sucralose, and sucrose presented higher acceptance scores for the attributes flavor, texture, and overall impression, with no significant (P < 0.05) differences between them. Aspartame and sucralose can be good substitutes for sucrose in passion fruit juice.

Passion fruit juice with different sweeteners: sensory profile by descriptive analysis and acceptance

PubMed Central

Rocha, Izabela Furtado de Oliveira; Bolini, Helena Maria André

2015-01-01

This study evaluated the effect of different sweeteners on the sensory profile, acceptance, and drivers of preference of passion fruit juice samples sweetened with sucrose, aspartame, sucralose, stevia, cyclamate/saccharin blend 2:1, and neotame. Sensory profiling was performed by 12 trained assessors using quantitative descriptive analysis (QDA). Acceptance tests (appearance, aroma, flavor, texture and overall impression) were performed with 124 consumers of tropical fruit juice. Samples with sucrose, aspartame and sucralose showed similar sensory profile (P < 0.05), without bitter taste, bitter aftertaste, and metallic taste, and samples with sucrose and sucralose did not differ from each other for the attribute sweet aftertaste. Passion fruit flavor affected positively and sweet aftertaste affected negatively the acceptance of the samples. Samples sweetened with aspartame, sucralose, and sucrose presented higher acceptance scores for the attributes flavor, texture, and overall impression, with no significant (P < 0.05) differences between them. Aspartame and sucralose can be good substitutes for sucrose in passion fruit juice. PMID:25838891

Spiritual Development and Death Attitude in Female Patients With Type II Diabetes

PubMed Central

Nozari, Masoumeh; Khalilian, Alireza; Dousti, Yarali

2014-01-01

Objective: The present study aimed to investigate the differences regarding spiritual development dimensions and death attitude profiles, and also to determinate association between them, in patients suffering from type II diabetes. Methods: In a cross-sectional design study, 100 female outpatients who were suffering from type II diabetes were recruited in Imam Khomeini Hospital, Sari, Iran. Data were collected through two questionnaires including the Spiritual Assessment Inventory (SAI) and the Death Attitude Profile-Revised (DAPR). Analysis of the data involved analysis of covariance (ANCOVA) with the Fisher's Least Significant Difference (LSD) as post-hoc test plus the Pearson correlation. Results: There was a statistical significant difference in spiritual development dimensions and death attitude profile. The results showed that spiritual development were significantly associated with some items of death attitude profiles. Conclusion: Awareness of God was suitable in diabetic patients, but the quality of relationship with God indicated spiritually immature. It is necessary to provide instruction to improve patient's death attitude and following health behavior. PMID:25780376

Effects of Pump Pulsation on Hydrodynamic Properties and Dissolution Profiles in Flow-Through Dissolution Systems (USP 4).

PubMed

Yoshida, Hiroyuki; Kuwana, Akemi; Shibata, Hiroko; Izutsu, Ken-Ichi; Goda, Yukihiro

2016-06-01

To clarify the effects of pump pulsation and flow-through cell (FTC) dissolution system settings on the hydrodynamic properties and dissolution profiles of model formulations. Two FTC systems with different cell temperature control mechanisms were used. Particle image velocimetry (PIV) was used to analyze the hydrodynamic properties of test solutions in the flow-through dissolution test cell. Two pulsation pumps (semi-sine, full-sine) and a non-pulsatile pump were used to study the effects of varied flows on the dissolution profiles of United States Pharmacopeia standard tablets. PIV analysis showed periodic changes in the aligned upward fluid flow throughout the dissolution cell that was designed to reduce the temperature gradient during pump pulsation (0.5 s/pulse). The maximum instantaneous flow from the semi-sine pump was higher than that of the full-sine pump under all conditions. The flow from the semi-sine wave pump showed faster dissolution of salicylic acid and prednisone tablets than those from other pumps. The semi-sine wave pump flow showed similar dissolution profiles in the two FTC systems. Variations in instantaneous fluid flow caused by pump pulsation that meets the requirements of pharmacopoeias are a factor that affects the dissolution profiles of tablets in FTC systems.

Elemental depth profiling in transparent conducting oxide thin film by X-ray reflectivity and grazing incidence X-ray fluorescence combined analysis

NASA Astrophysics Data System (ADS)

Rotella, H.; Caby, B.; Ménesguen, Y.; Mazel, Y.; Valla, A.; Ingerle, D.; Detlefs, B.; Lépy, M.-C.; Novikova, A.; Rodriguez, G.; Streli, C.; Nolot, E.

2017-09-01

The optical and electrical properties of transparent conducting oxide (TCO) thin films are strongly linked with the structural and chemical properties such as elemental depth profile. In R&D environments, the development of non-destructive characterization techniques to probe the composition over the depth of deposited films is thus necessary. The combination of Grazing-Incidence X-ray Fluorescence (GIXRF) and X-ray reflectometry (XRR) is emerging as a fab-compatible solution for the measurement of thickness, density and elemental profile in complex stacks. Based on the same formalism, both techniques can be implemented on the same experimental set-up and the analysis can be combined in a single software in order to refine the sample model. While XRR is sensitive to the electronic density profile, GIXRF is sensitive to the atomic density (i. e. the elemental depth profile). The combination of both techniques allows to get simultaneous information about structural properties (thickness and roughness) as well as the chemical properties. In this study, we performed a XRR-GIXRF combined analysis on indium-free TCO thin films (Ga doped ZnO compound) in order to correlate the optical properties of the films with the elemental distribution of Ga dopant over the thickness. The variation of optical properties due to annealing process were probed by spectroscopic ellipsometry measurements. We studied the evolution of atomic profiles before and after annealing process. We show that the blue shift of the band gap in the optical absorption edge is linked to a homogenization of the atomic profiles of Ga and Zn over the layer after the annealing. This work demonstrates that the combination of the techniques gives insight into the material composition and makes the XRR-GIXRF combined analysis a promising technique for elemental depth profiling.

Auger analysis of a fiber/matrix interface in a ceramic matrix composite

NASA Technical Reports Server (NTRS)

Honecy, Frank S.; Pepper, Stephen V.

1988-01-01

Auger electron spectroscopy (AES) depth profiling was used to characterize the fiber/matrix interface of an SiC fiber, reaction bonded Si3N4 matrix composite. Depth profiles of the as received double coated fiber revealed concentration oscillations which disappeared after annealing the fiber in the environment used to fabricate the composite. After the composite was fractured, the Auger depth profiles showed that failure occurred in neither the Beta-SiC fiber body nor in the Si3N4 matrix but, concurrently, at the fiber coating/matrix interface and within the fiber coating itself.

In silico identification and comparative analysis of differentially expressed genes in human and mouse tissues

PubMed Central

Pao, Sheng-Ying; Lin, Win-Li; Hwang, Ming-Jing

2006-01-01

Background Screening for differentially expressed genes on the genomic scale and comparative analysis of the expression profiles of orthologous genes between species to study gene function and regulation are becoming increasingly feasible. Expressed sequence tags (ESTs) are an excellent source of data for such studies using bioinformatic approaches because of the rich libraries and tremendous amount of data now available in the public domain. However, any large-scale EST-based bioinformatics analysis must deal with the heterogeneous, and often ambiguous, tissue and organ terms used to describe EST libraries. Results To deal with the issue of tissue source, in this work, we carefully screened and organized more than 8 million human and mouse ESTs into 157 human and 108 mouse tissue/organ categories, to which we applied an established statistic test using different thresholds of the p value to identify genes differentially expressed in different tissues. Further analysis of the tissue distribution and level of expression of human and mouse orthologous genes showed that tissue-specific orthologs tended to have more similar expression patterns than those lacking significant tissue specificity. On the other hand, a number of orthologs were found to have significant disparity in their expression profiles, hinting at novel functions, divergent regulation, or new ortholog relationships. Conclusion Comprehensive statistics on the tissue-specific expression of human and mouse genes were obtained in this very large-scale, EST-based analysis. These statistical results have been organized into a database, freely accessible at our website , for easy searching of human and mouse tissue-specific genes and for investigating gene expression profiles in the context of comparative genomics. Comparative analysis showed that, although highly tissue-specific genes tend to exhibit similar expression profiles in human and mouse, there are significant exceptions, indicating that orthologous genes, while sharing basic genomic properties, could result in distinct phenotypes. PMID:16626500

The effect of safety factor profile on transport in steady-state, high-performance scenarios

DOE PAGES

Holcomb, C. T.; Ferron, J. R.; Luce, T. C.; ...

2012-03-09

In this study, an analysis of the dependence of transport on the safety factor profile in high-performance, steady-state scenario discharges is presented. This is based on experimental scans of q 95 and q min taken with fixed β N, toroidal field, double-null plasma shape, divertor pumping, and electron cyclotron current drive input. The temperature and thermal diffusivity profiles were found to vary considerably with the q-profile, and these variations were significantly different for electrons and ions. With fixed q 95, both temperature profiles increase and broaden as q min is increased and the magnetic shear becomes low or negative inmore » the inner half radius, but these temperature profile changes are stronger for the electrons. Power balance calculations show the peak in the ion thermal diffusivity (χ i) at ρ – 0.6 – 0.8 increases with q 95 or q min.« less

A metabolomics-based method for studying the effect of yfcC gene in Escherichia coli on metabolism.

PubMed

Wang, Xiyue; Xie, Yuping; Gao, Peng; Zhang, Sufang; Tan, Haidong; Yang, Fengxu; Lian, Rongwei; Tian, Jing; Xu, Guowang

2014-04-15

Metabolomics is a potent tool to assist in identifying the function of unknown genes through analysis of metabolite changes in the context of varied genetic backgrounds. However, the availability of a universal unbiased profiling analysis is still a big challenge. In this study, we report an optimized metabolic profiling method based on gas chromatography-mass spectrometry for Escherichia coli. It was found that physiological saline at -80°C could ensure satisfied metabolic quenching with less metabolite leakage. A solution of methanol/water (21:79, v/v) was proved to be efficient for intracellular metabolite extraction. This method was applied to investigate the metabolome difference among wild-type E. coli, its yfcC deletion, and overexpression mutants. Statistical and bioinformatic analysis of the metabolic profiling data indicated that the expression of yfcC potentially affected the metabolism of glyoxylate shunt. This finding was further validated by real-time quantitative polymerase chain reactions showing that expression of aceA and aceB, the key genes in glyoxylate shunt, was upregulated by yfcC. This study exemplifies the robustness of the proposed metabolic profiling analysis strategy and its potential roles in investigating unknown gene functions in view of metabolome difference. Copyright © 2014 Elsevier Inc. All rights reserved.

Targeted metabolomic profiling in rat tissues reveals sex differences.

PubMed

Ruoppolo, Margherita; Caterino, Marianna; Albano, Lucia; Pecce, Rita; Di Girolamo, Maria Grazia; Crisci, Daniela; Costanzo, Michele; Milella, Luigi; Franconi, Flavia; Campesi, Ilaria

2018-03-16

Sex differences affect several diseases and are organ-and parameter-specific. In humans and animals, sex differences also influence the metabolism and homeostasis of amino acids and fatty acids, which are linked to the onset of diseases. Thus, the use of targeted metabolite profiles in tissues represents a powerful approach to examine the intermediary metabolism and evidence for any sex differences. To clarify the sex-specific activities of liver, heart and kidney tissues, we used targeted metabolomics, linear discriminant analysis (LDA), principal component analysis (PCA), cluster analysis and linear correlation models to evaluate sex and organ-specific differences in amino acids, free carnitine and acylcarnitine levels in male and female Sprague-Dawley rats. Several intra-sex differences affect tissues, indicating that metabolite profiles in rat hearts, livers and kidneys are organ-dependent. Amino acids and carnitine levels in rat hearts, livers and kidneys are affected by sex: male and female hearts show the greatest sexual dimorphism, both qualitatively and quantitatively. Finally, multivariate analysis confirmed the influence of sex on the metabolomics profiling. Our data demonstrate that the metabolomics approach together with a multivariate approach can capture the dynamics of physiological and pathological states, which are essential for explaining the basis of the sex differences observed in physiological and pathological conditions.

An analysis of current source density profiles activated by local stimulation in the mouse auditory cortex in vitro.

PubMed

Yamamura, Daiki; Sano, Ayaka; Tateno, Takashi

2017-03-15

To examine local network properties of the mouse auditory cortex in vitro, we recorded extracellular spatiotemporal laminar profiles driven by short electric local stimulation on a planar multielectrode array substrate. The recorded local field potentials were subsequently evaluated using current source density (CSD) analysis to identify sources and sinks. Current sinks are thought to be an indicator of net synaptic current in the small volume of cortex surrounding the recording site. Thus, CSD analysis combined with multielectrode arrays enabled us to compare mean synaptic activity in response to small current stimuli on a layer-by-layer basis. We also used senescence-accelerated mice (SAM), some strains of which show earlier onset of age-related hearing loss, to examine the characteristic spatiotemporal CSD profiles stimulated by electrodes in specific cortical layers. Thus, the CSD patterns were classified into several clusters based on stimulation sites in the cortical layers. We also found some differences in CSD patterns between the two SAM strains in terms of aging according to principle component analysis with dimension reduction. For simultaneous two-site stimulation, we modeled the obtained CSD profiles as a linear superposition of the CSD profiles to individual single-site stimulation. The model analysis indicated the nonlinearity of spatiotemporal integration over stimulus-driven activity in a layer-specific manner. Finally, on the basis of these results, we discuss the auditory cortex local network properties and the effects of aging on these mouse strains. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of fingerprint samples, testing various conditions, for forensic DNA identification.

PubMed

Ostojic, Lana; Wurmbach, Elisa

2017-01-01

Fingerprints can be of tremendous value for forensic biology, since they can be collected from a wide variety of evident types, such as handles of weapons, tools collected in criminal cases, and objects with no apparent staining. DNA obtained from fingerprints varies greatly in quality and quantity, which ultimately affects the quality of the resulting STR profiles. Additional difficulties can arise when fingerprint samples show mixed STR profiles due to the handling of multiple persons. After applying a tested protocol for sample collection (swabbing with 5% Triton X-100), DNA extraction (using an enzyme that works at elevated temperatures), and PCR amplification (AmpFlSTR® Identifiler® using 31cycles) extensive analysis was performed to better understand the challenges inherent to fingerprint samples, with the ultimate goal of developing valuable profiles (≥50% complete). The impact of time on deposited fingerprints was investigated, revealing that while the quality of profiles deteriorated, full STR profiles could still be obtained from samples after 40days of storage at room temperature. By comparing the STR profiles from fingerprints of the dominant versus the non-dominant hand, we found a slightly better quality from the non-dominant hand, which was not always significant. Substrates seem to have greater effects on fingerprints. Tests on glass, plastic, paper and metal (US Quarter dollar, made of Cu and Ni), common substrates in offices and homes, showed best results for glass, followed by plastic and paper, while almost no profiles were obtained from a Quarter dollar. Important for forensic casework, we also assessed three-person mixtures of touched fingerprint samples. Unlike routinely used approaches for sampling evidence, the surface of an object (bottle) was sectioned into six equal parts and separate samples were taken from each section. The samples were processed separately for DNA extraction and STR amplification. The results included a few single source profiles and distinguishable two person mixtures. On average, this approach led to two profiles ≥50% complete per touched object. Some STR profiles were obtained more than once thereby increasing the confidence. Copyright © 2016 The Chartered Society of Forensic Sciences. Published by Elsevier Ireland Ltd. All rights reserved.

Proteome comparison for discrimination between honeydew and floral honeys from botanical species Mimosa scabrella Bentham by principal component analysis.

PubMed

Azevedo, Mônia Stremel; Valentim-Neto, Pedro Alexandre; Seraglio, Siluana Katia Tischer; da Luz, Cynthia Fernandes Pinto; Arisi, Ana Carolina Maisonnave; Costa, Ana Carolina Oliveira

2017-10-01

Due to the increasing valuation and appreciation of honeydew honey in many European countries and also to existing contamination among different types of honeys, authentication is an important aspect of quality control with regard to guaranteeing the origin in terms of source (honeydew or floral) and needs to be determined. Furthermore, proteins are minor components of the honey, despite the importance of their physiological effects, and can differ according to the source of the honey. In this context, the aims of this study were to carry out protein extraction from honeydew and floral honeys and to discriminate these honeys from the same botanical species, Mimosa scabrella Bentham, through proteome comparison using two-dimensional gel electrophoresis and principal component analysis. The results showed that the proteome profile and principal component analysis can be a useful tool for discrimination between these types of honey using matched proteins (45 matched spots). Also, the proteome profile showed 160 protein spots in honeydew honey and 84 spots in the floral honey. The protein profile can be a differential characteristic of this type of honey, in view of the importance of proteins as bioactive compounds in honey. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Transcription profile of brewery yeast under fermentation conditions.

PubMed

James, T C; Campbell, S; Donnelly, D; Bond, U

2003-01-01

Yeast strains, used in the brewing industry, experience distinctive physiological conditions. During a brewing fermentation, yeast are exposed to anaerobic conditions, high pressure, high specific gravity and low temperatures. The purpose of this study was to examine the global gene expression profile of yeast subjected to brewing stress. We have carried out a microarray analysis of a typical brewer's yeast during the course of an 8-day fermentation in 15 degrees P wort. We used the probes derived from Saccharomyces cerevisiae genomic DNA on the chip and RNA isolated from three stages of brewing. This analysis shows a high level of expression of genes involved in fatty acid and ergosterol biosynthesis early in fermentation. Furthermore, genes involved in respiration and mitochondrial protein synthesis also show higher levels of expression. Surprisingly, we observed a complete repression of many stress response genes and genes involved in protein synthesis throughout the 8-day period compared with that at the start of fermentation. This microarray data set provides an analysis of gene expression under brewing fermentation conditions. The data provide an insight into the various metabolic processes altered or activated by brewing conditions of growth. This study leads to future experiments whereby selective alterations in brewing conditions could be introduced to take advantage of the changing transcript profile to improve the quality of the brew.

Differential proteomic profiling of primary and recurrent chordomas.

PubMed

Chen, Su; Xu, Wei; Jiao, Jian; Jiang, Dongjie; Liu, Jian; Chen, Tenghui; Wan, Zongmiao; Xu, Leqin; Zhou, Zhenhua; Xiao, Jianru

2015-05-01

Chordomas are locally destructive tumors with high rates of recurrence and a poor prognosis. The mechanisms involved in chordoma recurrence remain largely unknown. In the present study, we examined the proteomic profile of a chordoma primary tumor (CSO) and a recurrent tumor (CSR) through mass spectrum in a chordoma patient who underwent surgery. Bioinformatic analysis of the profile showed that 359 proteins had a significant expression difference and 21 pathways had a striking alteration between the CSO and the CSR. The CSR showed a significant increase in carbohydrate metabolism. Immunohistochemistry (IHC) confirmed that the cancer stem cell marker activated leukocyte cell adhesion molecule (ALCAM or CD166) expression level was higher in the recurrent than that in the primary tumor. The present study analyzed the proteomic profile change between CSO and CSR and identified a new biomarker ALCAM in recurrent chordomas. This finding sheds light on unraveling the pathophysiology of chordoma recurrence and on exploring more effective prognostic biomarkers and targeted therapies against this devastating disease.

Active Brazilian crack cocaine users: nutritional, anthropometric, and drug use profiles.

PubMed

Escobar, Mariana; Scherer, Juliana N; Soares, Cassia M; Guimarães, Luciano S P; Hagen, Martine E; von Diemen, Lisia; Pechansky, Flavio

2018-02-15

To evaluate the nutritional status of crack users and to analyze its correlation with drug use profiles. Cross-sectional study with 108 crack users. Anthropometric data were assessed through body mass index (BMI) and bioimpedance (BIA) measurements. A blood test to analyze hematocrit, hemoglobin, glucose, and lipid profiles was also performed. Crack use was determined through a standardized interview. Based on BMI and BIA, most individuals were eutrophic (about 70%). Regarding hematological parameters, we found that hemoglobin and hematocrit levels were below normal for 32.4 and 30.6% of patients, respectively. Considering normal parameters, a large part of the sample (60.2%) had low levels of HDL cholesterol and high levels of triglycerides (38%). There were no significant correlations between drug profile and nutritional variables. This is a pioneering study that examines the nutritional status of crack users. Our results showed that most crack users present normal anthropometric findings and the prevalence of underweight is low. However, blood analysis showed changes and a specific type of malnutrition.

The risk typology of healthcare access and its association with unmet healthcare needs in Asian Americans.

PubMed

Jang, Yuri; Park, Nan Sook; Yoon, Hyunwoo; Huang, Ya-Ching; Rhee, Min-Kyoung; Chiriboga, David A; Kim, Miyong T

2018-01-01

Using data from the 2015 Asian American Quality of Life Survey (N = 2,609), latent profile analysis was conducted on general (health insurance, usual place for care and income) and immigrant-specific (nativity, length of stay in the U.S., English proficiency and acculturation) risk factors of healthcare access. Latent profile analysis identified a three-cluster model (low-risk, moderate-risk and high-risk groups). Compared with the low-risk group, the odds of having an unmet healthcare need was 1.52 times greater in the moderate-risk group and 2.24 times greater in the high-risk group. Challenging the myth of model minority, the present sample of Asian Americans demonstrates its vulnerability in access to healthcare. Findings also show the heterogeneity in healthcare access risk profiles. © 2017 John Wiley & Sons Ltd.

Asymmetric simple exclusion process with position-dependent hopping rates: Phase diagram from boundary-layer analysis.

PubMed

Mukherji, Sutapa

2018-03-01

In this paper, we study a one-dimensional totally asymmetric simple exclusion process with position-dependent hopping rates. Under open boundary conditions, this system exhibits boundary-induced phase transitions in the steady state. Similarly to totally asymmetric simple exclusion processes with uniform hopping, the phase diagram consists of low-density, high-density, and maximal-current phases. In various phases, the shape of the average particle density profile across the lattice including its boundary-layer parts changes significantly. Using the tools of boundary-layer analysis, we obtain explicit solutions for the density profile in different phases. A detailed analysis of these solutions under different boundary conditions helps us obtain the equations for various phase boundaries. Next, we show how the shape of the entire density profile including the location of the boundary layers can be predicted from the fixed points of the differential equation describing the boundary layers. We discuss this in detail through several examples of density profiles in various phases. The maximal-current phase appears to be an especially interesting phase where the boundary layer flows to a bifurcation point on the fixed-point diagram.

Asymmetric simple exclusion process with position-dependent hopping rates: Phase diagram from boundary-layer analysis

NASA Astrophysics Data System (ADS)

Mukherji, Sutapa

2018-03-01

In this paper, we study a one-dimensional totally asymmetric simple exclusion process with position-dependent hopping rates. Under open boundary conditions, this system exhibits boundary-induced phase transitions in the steady state. Similarly to totally asymmetric simple exclusion processes with uniform hopping, the phase diagram consists of low-density, high-density, and maximal-current phases. In various phases, the shape of the average particle density profile across the lattice including its boundary-layer parts changes significantly. Using the tools of boundary-layer analysis, we obtain explicit solutions for the density profile in different phases. A detailed analysis of these solutions under different boundary conditions helps us obtain the equations for various phase boundaries. Next, we show how the shape of the entire density profile including the location of the boundary layers can be predicted from the fixed points of the differential equation describing the boundary layers. We discuss this in detail through several examples of density profiles in various phases. The maximal-current phase appears to be an especially interesting phase where the boundary layer flows to a bifurcation point on the fixed-point diagram.

Analysis of alkylamides in Echinacea plant materials and dietary supplements by ultrafast liquid chromatography with diode array and mass spectrometric detection.

PubMed

Mudge, Elizabeth; Lopes-Lutz, Daise; Brown, Paula; Schieber, Andreas

2011-08-10

Alkylamides are a class of compounds present in plants of the genus Echinacea (Asteraceae), which have been shown to have high bioavailability and immunomodulatory effects. Fast analysis to identify these components in a variety of products is essential to profile products used in clinical trials and for quality control of these products. A method based on ultrafast liquid chromatography (UFLC) coupled with diode array detection and electrospray ionization mass spectrometry was developed for the analysis of alkylamides from the roots of Echinacea angustifolia (DC.) Hell., Echinacea purpurea (L.) Moench, and commercial dietary supplements. A total of 24 alkylamides were identified by LC-MS. The analysis time for these components is 15 min. Compared to the alkylamide profiles determined in the Echinacea root materials, the commercial products showed a more complex profile due to the blending of root and aerial parts of E. purpurea. This versatile method allows for the identification of alkylamides in a variety of Echinacea products and presents the most extensive characterization of alkylamides in E. angustifolia roots so far.

Chemotaxonomic Study of Citrus, Poncirus and Fortunella Genotypes Based on Peel Oil Volatile Compounds - Deciphering the Genetic Origin of Mangshanyegan (Citrus nobilis Lauriro)

PubMed Central

Liu, Cuihua; Jiang, Dong; Cheng, Yunjiang; Deng, Xiuxin; Chen, Feng; Fang, Liu; Ma, Zhaocheng; Xu, Juan

2013-01-01

Volatile profiles yielded from gas chromatography-mass spectrometry (GC-MS) analysis provide abundant information not only for metabolism-related research, but also for chemotaxonomy. To study the chemotaxonomy of Mangshanyegan, its volatile profiles of fruit and leaf and those of 29 other genotypes of Citrus, Poncirus, and Fortunella were subjected to phylogenetic analyses. Results showed that 145 identified (including 64 tentatively identified) and 15 unidentified volatile compounds were detected from their peel oils. The phylogenetic analysis of peel oils based on hierarchical cluster analysis (HCA) demonstrated a good agreement with the Swingle taxonomy system, in which the three genera of Citrus, Poncirus, and Fortunella were almost completely separated. As to Citrus, HCA indicated that Citrophorum, Cephalocitrus, and Sinocitrus fell into three subgroups, respectively. Also, it revealed that Mangshanyegan contain volatile compounds similar to those from pummelo, though it is genetically believed to be a mandarin. These results were further supported by the principal component analysis of the peel oils and the HCA results of volatile profiles of leaves in the study. PMID:23516475

Species differences in brain gene expression profiles associated with adult behavioral maturation in honey bees.

PubMed

Sen Sarma, Moushumi; Whitfield, Charles W; Robinson, Gene E

2007-06-29

Honey bees are known for several striking social behaviors, including a complex pattern of behavioral maturation that gives rise to an age-related colony division of labor and a symbolic dance language, by which successful foragers communicate the location of attractive food sources to their nestmates. Our understanding of honey bees is mostly based on studies of the Western honey bee, Apis mellifera, even though there are 9-10 other members of genus Apis, showing interesting variations in social behavior relative to A. mellifera. To facilitate future in-depth genomic and molecular level comparisons of behavior across the genus, we performed a microarray analysis of brain gene expression for A. mellifera and three key species found in Asia, A. cerana, A. florea and A. dorsata. For each species we compared brain gene expression patterns between foragers and adult one-day-old bees on an A. mellifera cDNA microarray and calculated within-species gene expression ratios to facilitate cross-species analysis. The number of cDNA spots showing hybridization fluorescence intensities above the experimental threshold was reduced by an average of 16% in the Asian species compared to A. mellifera, but an average of 71% of genes on the microarray were available for analysis. Brain gene expression profiles between foragers and one-day-olds showed differences that are consistent with a previous study on A. mellifera and were comparable across species. Although 1772 genes showed significant differences in expression between foragers and one-day-olds, only 218 genes showed differences in forager/one-day-old expression between species (p < 0.001). Principal Components Analysis revealed dominant patterns of expression that clearly distinguished between the four species but did not reflect known differences in behavior and ecology. There were species differences in brain expression profiles for functionally related groups of genes. We conclude that the A. mellifera cDNA microarray can be used effectively for cross-species comparisons within the genus. Our results indicate that there is a widespread conservation of the molecular processes in the honey bee brain underlying behavioral maturation. Species differences in brain expression profiles for functionally related groups of genes provide possible clues to the basis of behavioral variation in the genus.

Effects of oral contraceptives on metabolic profile in women with polycystic ovary syndrome: A meta-analysis comparing products containing cyproterone acetate with third generation progestins.

PubMed

Amiri, Mina; Ramezani Tehrani, Fahimeh; Nahidi, Fatemeh; Kabir, Ali; Azizi, Fereidoun; Carmina, Enrico

2017-08-01

Although oral contraceptives (OCs) are the most common treatment in women with polycystic ovary syndrome (PCOS), their effects and safety on the metabolic profiles of these patients are relatively unknown. In this meta-analysis the effects of the different durations (from 3months to 1year) of OC treatment using cyproterone acetate (CA) or third generation progestins on metabolic profile of patients with PCOS were assessed. PubMed, Scopus, Google Scholar and ScienceDirect databases (2001-2015) were searched to identify clinical trials investigating the effects of OC containing CA or third generation progestins on metabolic profiles of women with PCOS. Both fixed and random effect models were used. Subgroup analyses were performed based on the progestin compounds used and on duration of treatment. Oral contraceptive (OC) use was found to be associated with a worsening in lipid profiles but no changes were observed in other metabolic outcomes, including body mass index (BMI), fasting blood glucose (FBG), fasting insulin, homeostatic model for measuring insulin resistance (HOMA-IR) and in blood pressure (BP) values. All studied OCs showed similar effects on lipid profiles but with different timings, with products containing CA, requiring 6months to raise high density lipoprotein-cholesterol (HDL-C) levels and 12months to increase triglycerides (TG). On the contrary, products containing drospirenone (DRSP) or desogestrel (DSG) increased HDL-C after only 3months but determined elevations of TG after 6months. All OCs induced an increase in low density lipoprotein-cholesterol (LDL-C) after 12months of use. The study shows that, in women with PCOS, OC use is associated with significant changes in lipid profiles, including elevation not only in HDL-C but also in TG and LDL-C. All OCs studied showed similar effects but with different timings, with products containing CA generally requiring more prolonged use to increase serum lipids. Instead, OC use does not affect body weight, BP or glucose levels, with only some minor increase of fasting insulin levels. Copyright © 2017 Elsevier Inc. All rights reserved.

Evoked Emotions Predict Food Choice

PubMed Central

Dalenberg, Jelle R.; Gutjar, Swetlana; ter Horst, Gert J.; de Graaf, Kees; Renken, Remco J.; Jager, Gerry

2014-01-01

In the current study we show that non-verbal food-evoked emotion scores significantly improve food choice prediction over merely liking scores. Previous research has shown that liking measures correlate with choice. However, liking is no strong predictor for food choice in real life environments. Therefore, the focus within recent studies shifted towards using emotion-profiling methods that successfully can discriminate between products that are equally liked. However, it is unclear how well scores from emotion-profiling methods predict actual food choice and/or consumption. To test this, we proposed to decompose emotion scores into valence and arousal scores using Principal Component Analysis (PCA) and apply Multinomial Logit Models (MLM) to estimate food choice using liking, valence, and arousal as possible predictors. For this analysis, we used an existing data set comprised of liking and food-evoked emotions scores from 123 participants, who rated 7 unlabeled breakfast drinks. Liking scores were measured using a 100-mm visual analogue scale, while food-evoked emotions were measured using 2 existing emotion-profiling methods: a verbal and a non-verbal method (EsSense Profile and PrEmo, respectively). After 7 days, participants were asked to choose 1 breakfast drink from the experiment to consume during breakfast in a simulated restaurant environment. Cross validation showed that we were able to correctly predict individualized food choice (1 out of 7 products) for over 50% of the participants. This number increased to nearly 80% when looking at the top 2 candidates. Model comparisons showed that evoked emotions better predict food choice than perceived liking alone. However, the strongest predictive strength was achieved by the combination of evoked emotions and liking. Furthermore we showed that non-verbal food-evoked emotion scores more accurately predict food choice than verbal food-evoked emotions scores. PMID:25521352

Evoked emotions predict food choice.

PubMed

Dalenberg, Jelle R; Gutjar, Swetlana; Ter Horst, Gert J; de Graaf, Kees; Renken, Remco J; Jager, Gerry

2014-01-01

In the current study we show that non-verbal food-evoked emotion scores significantly improve food choice prediction over merely liking scores. Previous research has shown that liking measures correlate with choice. However, liking is no strong predictor for food choice in real life environments. Therefore, the focus within recent studies shifted towards using emotion-profiling methods that successfully can discriminate between products that are equally liked. However, it is unclear how well scores from emotion-profiling methods predict actual food choice and/or consumption. To test this, we proposed to decompose emotion scores into valence and arousal scores using Principal Component Analysis (PCA) and apply Multinomial Logit Models (MLM) to estimate food choice using liking, valence, and arousal as possible predictors. For this analysis, we used an existing data set comprised of liking and food-evoked emotions scores from 123 participants, who rated 7 unlabeled breakfast drinks. Liking scores were measured using a 100-mm visual analogue scale, while food-evoked emotions were measured using 2 existing emotion-profiling methods: a verbal and a non-verbal method (EsSense Profile and PrEmo, respectively). After 7 days, participants were asked to choose 1 breakfast drink from the experiment to consume during breakfast in a simulated restaurant environment. Cross validation showed that we were able to correctly predict individualized food choice (1 out of 7 products) for over 50% of the participants. This number increased to nearly 80% when looking at the top 2 candidates. Model comparisons showed that evoked emotions better predict food choice than perceived liking alone. However, the strongest predictive strength was achieved by the combination of evoked emotions and liking. Furthermore we showed that non-verbal food-evoked emotion scores more accurately predict food choice than verbal food-evoked emotions scores.

A comparison of instrumentation using Naviflex and Profile nickel-titanium engine-driven rotary instruments.

PubMed

Ottosen, S R; Nicholls, J I; Steiner, J C

1999-06-01

This study was designed to compare the changes in canal configuration resulting from instrumentation by either Profile or Naviflex instruments. Forty mesial canals in extracted human molar teeth were embedded and sectioned at two root levels. Reassembled teeth were instrumented with a modified crown-down technique as described in the Profile training video for Profile files and in a similar manner for Naviflex instruments. Superimposed pre- and postinstrumented cross-sectional root images were projected, traced, and scanned into a computer for analysis. Canal movement, in relation to the furca, and canal area change were recorded. The results showed no significant difference in canal center movement or canal area change between the Profile or Naviflex groups. The degree of canal curvature had no effect on canal center movement or canal area change.

Cored density profiles in the DARKexp model

NASA Astrophysics Data System (ADS)

Destri, Claudio

2018-05-01

The DARKexp model represents a novel and promising attempt to solve a long standing problem of statistical mechanics, that of explaining from first principles the quasi-stationary states at the end of the collisionless gravitational collapse. The model, which yields good fits to observation and simulation data on several scales, was originally conceived to provide a theoretical basis for the 1/r cusp of the Navarro-Frenk-White profile. In this note we show that it also allows for cored density profiles that, when viewed in three dimensions, in the r→0 limit have the conical shape characteristic of the Burkert profile. It remains to be established whether both cusps and cores, or only one of the two types, are allowed beyond the asymptotic analysis of this work.

Profiles of disruptive behavior across early childhood: Contributions of frustration reactivity, physiological regulation, and maternal behavior

PubMed Central

Degnan, Kathryn A.; Calkins, Susan D.; Keane, Susan P.; Hill-Soderlund, Ashley L.

2010-01-01

Disruptive behavior, including aggression, defiance, and temper tantrums, typically peaks in early toddlerhood and decreases by school entry; however, some children do not show this normative decline. The current study examined disruptive behavior in 318 boys and girls at 2, 4, and 5 years of age and frustration reactivity, physiological regulation, and maternal behavior in the laboratory at 2 years of age. A latent profile analysis (LPA) resulted in 4 longitudinal profiles of disruptive behavior, which were differentiated by interactions between reactivity, regulation, and maternal behavior. A high profile was associated with high reactivity combined with high maternal control or low regulation combined with low maternal control. Results are discussed from a developmental psychopathology perspective. PMID:18826530

Construction and application of EST library from Setaria italica in response to dehydration stress.

PubMed

Zhang, Jinpeng; Liu, Tingsong; Fu, Junjie; Zhu, Yun; Jia, Jinping; Zheng, Jun; Zhao, Yinhe; Zhang, Ying; Wang, Guoying

2007-07-01

Foxtail millet is a gramineous crop with low water requirement. Despite its high water use efficiency, less attention has been paid to the molecular genetics of foxtail millet. This article reports the construction of subtracted cDNA libraries from foxtail millet seedlings under dehydration stress and the expression profile analysis of 1947 UniESTs from the subtracted cDNA libraries by a cDNA microarray. The results showed that 95 and 57 ESTs were upregulated by dehydration stress, respectively, in roots and shoots of seedlings and that 10 and 27 ESTs were downregulated, respectively, in roots and shoots. The expression profile analysis showed that genes induced in foxtail millet roots were different from those in shoots during dehydration stress and that the early response to dehydration stress in foxtail millet roots was the activation of the glycolysis metabolism. Moreover, protein degradation pathway may also play a pivotal role in drought-tolerant responses of foxtail millet. Finally, Northern blot analysis validated well the cDNA microarray data.

Analysis of human plasma metabolites across different liquid chromatography/mass spectrometry platforms: Cross-platform transferable chemical signatures.

PubMed

Telu, Kelly H; Yan, Xinjian; Wallace, William E; Stein, Stephen E; Simón-Manso, Yamil

2016-03-15

The metabolite profiling of a NIST plasma Standard Reference Material (SRM 1950) on different liquid chromatography/mass spectrometry (LC/MS) platforms showed significant differences. Although these findings suggest caution when interpreting metabolomics results, the degree of overlap of both profiles allowed us to use tandem mass spectral libraries of recurrent spectra to evaluate to what extent these results are transferable across platforms and to develop cross-platform chemical signatures. Non-targeted global metabolite profiles of SRM 1950 were obtained on different LC/MS platforms using reversed-phase chromatography and different chromatographic scales (conventional HPLC, UHPLC and nanoLC). The data processing and the metabolite differential analysis were carried out using publically available (XCMS), proprietary (Mass Profiler Professional) and in-house software (NIST pipeline). Repeatability and intermediate precision showed that the non-targeted SRM 1950 profiling was highly reproducible when working on the same platform (relative standard deviation (RSD) <2%); however, substantial differences were found in the LC/MS patterns originating on different platforms or even using different chromatographic scales (conventional HPLC, UHPLC and nanoLC) on the same platform. A substantial degree of overlap (common molecular features) was also found. A procedure to generate consistent chemical signatures using tandem mass spectral libraries of recurrent spectra is proposed. Different platforms rendered significantly different metabolite profiles, but the results were highly reproducible when working within one platform. Tandem mass spectral libraries of recurrent spectra are proposed to evaluate the degree of transferability of chemical signatures generated on different platforms. Chemical signatures based on our procedure are most likely cross-platform transferable. Published in 2016. This article is a U.S. Government work and is in the public domain in the USA.

Analysis of proteome profile in germinating soybean seed, and its comparison with rice showing the styles of reserves mobilization in different crops.

PubMed

Han, Chao; Yin, Xiaojian; He, Dongli; Yang, Pingfang

2013-01-01

Seed germination is a complex physiological process during which mobilization of nutrient reserves happens. In different crops, this event might be mediated by different regulatory and metabolic pathways. Proteome profiling has been proved to be an efficient way that can help us to construct these pathways. However, no such studies have been performed in soybean germinating seeds up to date. Proteome profiling was conducted through one-dimensional gel electrophoresis followed by liquid chromatography and tandem mass spectrometry strategy in the germinating seeds of soybean (glycine max). Comprehensive comparisons were also carried out between rice and soybean germinating seeds. 764 proteins belonging to 14 functional groups were identified and metabolism related proteins were the largest group. Deep analyses of the proteins and pathways showed that lipids were degraded through lipoxygenase dependent pathway and proteins were degraded through both protease and 26S proteosome system, and the lipoxygenase could also help to remove the reactive oxygen species during the rapid mobilization of reserves of soybean germinating seeds. The differences between rice and soybean germinating seeds proteome profiles indicate that each crop species has distinct mechanism for reserves mobilization during germination. Different reserves could be converted into starches before they are totally utilized during the germination in different crops seeds. This study is the first comprehensive analysis of proteome profile in germinating soybean seeds to date. The data presented in this paper will improve our understanding of the physiological and biochemical status in the imbibed soybean seeds just prior to germination. Comparison of the protein profile with that of germinating rice seeds gives us new insights on mobilization of nutrient reserves during the germination of crops seeds.

Optimal Adherence to a Mediterranean Diet and High Muscular Fitness Are Associated with a Healthier Cardiometabolic Profile in Collegiate Students

PubMed Central

Correa-Bautista, Jorge Enrique; Ojeda-Pardo, Mónica Liliana; Sandoval-Cuellar, Carolina; González-Ruíz, Katherine; Prieto-Benavides, Daniel Humberto; Tordecilla-Sanders, Alejandra; Martinkėnas, Arvydas

2018-01-01

The aim of the study was to investigate the combined association of adherence to a Mediterranean diet (MedDiet) and muscular fitness (MF) with cardiometabolic health in collegiate students. The present cross-sectional analysis consisted of 1248 (714 females) healthy collegiate students (20.1 ± 2.7 years old). Adherence to a MedDiet was assessed by a KIDMED (Mediterranean Diet Quality Index) questionnaire. Standing broad jump, standing vertical jump, and isometric handgrip dynamometry were used as indicators of MF. The cardiometabolic profile was assessed using the following components: triglycerides, blood pressure, triglycerides, high-density lipoprotein (HDL)-cholesterol, glucose, and waist circumference. Analysis of covariance shows a significant difference in the cardiometabolic profile of both genders between the high MF/low MedDiet and high MF/optimal MedDiet groups, and the low MF/low MedDiet and low MF/optimal MedDiet groups (p < 0.001). No difference was found on cardiometabolic profile between high MF/optimal MedDiet and high MF/low MedDiet, both in males and females. Additionally, logistic regression shows that both female (odds ratio (OR) = 2.01; 95% confidence interval (CI): (1.8–3.7); p = 0.02) and male (OR = 3.38; 95% CI: (1.9–5.8); p < 0.001) participants in the optimal MedDiet/high MF group had the highest odds of expressing a healthier cardiometabolic profile as compared to those in the low MF/low MedDiet group. In conclusion, a combination of high MF levels and optimal adherence to a MedDiet is associated with a healthier cardiometabolic profile; however, high MF levels seem to circumvent the deleterious effects of having a low adherence to a MedDiet. PMID:29677099

Optimal Adherence to a Mediterranean Diet and High Muscular Fitness Are Associated with a Healthier Cardiometabolic Profile in Collegiate Students.

PubMed

Ramírez-Vélez, Robinson; Correa-Bautista, Jorge Enrique; Ojeda-Pardo, Mónica Liliana; Sandoval-Cuellar, Carolina; García-Hermoso, Antonio; Carrillo, Hugo Alejandro; González-Ruíz, Katherine; Prieto-Benavides, Daniel Humberto; Tordecilla-Sanders, Alejandra; Martinkėnas, Arvydas; Agostinis-Sobrinho, César

2018-04-20

The aim of the study was to investigate the combined association of adherence to a Mediterranean diet (MedDiet) and muscular fitness (MF) with cardiometabolic health in collegiate students. The present cross-sectional analysis consisted of 1248 (714 females) healthy collegiate students (20.1 ± 2.7 years old). Adherence to a MedDiet was assessed by a KIDMED (Mediterranean Diet Quality Index) questionnaire. Standing broad jump, standing vertical jump, and isometric handgrip dynamometry were used as indicators of MF. The cardiometabolic profile was assessed using the following components: triglycerides, blood pressure, triglycerides, high-density lipoprotein (HDL)-cholesterol, glucose, and waist circumference. Analysis of covariance shows a significant difference in the cardiometabolic profile of both genders between the high MF/low MedDiet and high MF/optimal MedDiet groups, and the low MF/low MedDiet and low MF/optimal MedDiet groups ( p < 0.001). No difference was found on cardiometabolic profile between high MF/optimal MedDiet and high MF/low MedDiet, both in males and females. Additionally, logistic regression shows that both female (odds ratio (OR) = 2.01; 95% confidence interval (CI): (1.8⁻3.7); p = 0.02) and male (OR = 3.38; 95% CI: (1.9⁻5.8); p < 0.001) participants in the optimal MedDiet/high MF group had the highest odds of expressing a healthier cardiometabolic profile as compared to those in the low MF/low MedDiet group. In conclusion, a combination of high MF levels and optimal adherence to a MedDiet is associated with a healthier cardiometabolic profile; however, high MF levels seem to circumvent the deleterious effects of having a low adherence to a MedDiet.

"Clinical brain profiling": a neuroscientific diagnostic approach for mental disorders.

PubMed

Peled, Abraham; Geva, Amir B

2014-10-01

Clinical brain profiling is an attempt to map a descriptive nosology in psychiatry to underlying constructs in neurobiology and brain dynamics. This paper briefly reviews the motivation behind clinical brain profiling (CBP) and presents some provisional validation using clinical assessments and meta-analyses of neuroscientific publications. The paper has four sections. In the first, we review the nature and motivation for clinical brain profiling. This involves a description of the key aspects of functional anatomy that can lead to psychopathology. These features constitute the dimensions or categories for a profile of brain disorders based upon pathophysiology. The second section describes a mapping or translation matrix that maps from symptoms and signs, of a descriptive sort, to the CBP dimensions that provide a more mechanistic explanation. We will describe how this mapping engenders archetypal diagnoses, referring readers to tables and figures. The third section addresses the construct validity of clinical brain profiling by establishing correlations between profiles based on clinical ratings of symptoms and signs under classical diagnostic categories with the corresponding profiles generated automatically using archetypal diagnoses. We then provide further validation by performing a cluster analysis on the symptoms and signs and showing how they correspond to the equivalent brain profiles based upon clinical and automatic diagnosis. In the fourth section, we address the construct validity of clinical brain profiling by looking for associations between pathophysiological mechanisms (such as connectivity and plasticity) and nosological diagnoses (such as schizophrenia and depression). Based upon the mechanistic perspective offered in the first section, we test some particular hypotheses about double dissociations using a meta-analysis of PubMed searches. The final section concludes with perspectives for the future and outstanding validation issues for clinical brain profiling. Copyright © 2014 Elsevier Ltd. All rights reserved.

Univariate and multivariate molecular spectral analyses of lipid related molecular structural components in relation to nutrient profile in feed and food mixtures

NASA Astrophysics Data System (ADS)

Abeysekara, Saman; Damiran, Daalkhaijav; Yu, Peiqiang

2013-02-01

The objectives of this study were (i) to determine lipid related molecular structures components (functional groups) in feed combination of cereal grain (barley, Hordeum vulgare) and wheat (Triticum aestivum) based dried distillers grain solubles (wheat DDGSs) from bioethanol processing at five different combination ratios using univariate and multivariate molecular spectral analyses with infrared Fourier transform molecular spectroscopy, and (ii) to correlate lipid-related molecular-functional structure spectral profile to nutrient profiles. The spectral intensity of (i) CH3 asymmetric, CH2 asymmetric, CH3 symmetric and CH2 symmetric groups, (ii) unsaturation (Cdbnd C) group, and (iii) carbonyl ester (Cdbnd O) group were determined. Spectral differences of functional groups were detected by hierarchical cluster analysis (HCA) and principal components analysis (PCA). The results showed that the combination treatments significantly inflicted modifications (P < 0.05) in nutrient profile and lipid related molecular spectral intensity (CH2 asymmetric stretching peak height, CH2 symmetric stretching peak height, ratio of CH2 to CH3 symmetric stretching peak intensity, and carbonyl peak area). Ratio of CH2 to CH3 symmetric stretching peak intensity, and carbonyl peak significantly correlated with nutrient profiles. Both PCA and HCA differentiated lipid-related spectrum. In conclusion, the changes of lipid molecular structure spectral profiles through feed combination could be detected using molecular spectroscopy. These changes were associated with nutrient profiles and functionality.

Characterization of monofloral honeys with multivariate analysis of their chemical profile and antioxidant activity.

PubMed

Sant'Ana, Luiza D'O; Sousa, Juliana P L M; Salgueiro, Fernanda B; Lorenzon, Maria Cristina Affonso; Castro, Rosane N

2012-01-01

Various bioactive chemical constituents were quantified for 21 honey samples obtained at Rio de Janeiro and Minas Gerais, Brazil. To evaluate their antioxidant activity, 3 different methods were used: the ferric reducing antioxidant power, the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity, and the 2,2'-azinobis (3-ethylbenzothiazolin)-6-sulfonate (ABTS) assays. Correlations between the parameters were statistically significant (-0.6684 ≤ r ≤-0.8410, P < 0.05). Principal component analysis showed that honey samples from the same floral origins had more similar profiles, which made it possible to group the eucalyptus, morrão de candeia, and cambara honey samples in 3 distinct areas, while cluster analysis could separate the artificial honey from the floral honeys. This research might aid in the discrimination of honey floral origin, by using simple analytical methods in association with multivariate analysis, which could also show a great difference among floral honeys and artificial honey, indicating a possible way to help with the identification of artificial honeys. © 2011 Institute of Food Technologists®

Motivational profiles in high school students: Differences in behavioural and emotional homework engagement and academic achievement.

PubMed

Regueiro, Bibiana; Núñez, José C; Valle, Antonio; Piñeiro, Isabel; Rodríguez, Susana; Rosário, Pedro

2016-12-12

This work examined whether combinations of academic and non-academic goals generated different motivational profiles in high school students. Besides, differences in homework behavioural engagement (i.e. amount of homework, time spent in homework, homework time management), homework emotional engagement (i.e. homework anxiety) and academic achievement were analysed. Participants were 714 high school students (43.4% boys and 56.6% girls). The study of potential motivational profiles was conducted by latent profile analysis, and the differences between the motivational profiles regarding homework variables and academic achievement were analysed using multivariate analysis. The results indicate the existence of five groups of motivational profiles: a group of students with multiple goals, a group of unmotivated students, two groups of students with a predominance of learning goals and, finally, a group comprising students with a high fear of failure. Both the group with multiple goals and the learning goals-oriented groups reported to do more homework, spending more time on homework, making better use of that time and having a higher academic achievement than counterparts. The avoidance-failure group and the group with multiple goals showed higher levels of homework anxiety. Globally, these results provide support for a person-centred approach. © 2016 International Union of Psychological Science.

Preliminary profiling of blood transcriptome in a rat model of hemorrhagic shock.

PubMed

Braga, D; Barcella, M; D'Avila, F; Lupoli, S; Tagliaferri, F; Santamaria, M H; DeLano, F A; Baselli, G; Schmid-Schönbein, G W; Kistler, E B; Aletti, F; Barlassina, C

2017-08-01

Hemorrhagic shock is a leading cause of morbidity and mortality worldwide. Significant blood loss may lead to decreased blood pressure and inadequate tissue perfusion with resultant organ failure and death, even after replacement of lost blood volume. One reason for this high acuity is that the fundamental mechanisms of shock are poorly understood. Proteomic and metabolomic approaches have been used to investigate the molecular events occurring in hemorrhagic shock but, to our knowledge, a systematic analysis of the transcriptomic profile is missing. Therefore, a pilot analysis using paired-end RNA sequencing was used to identify changes that occur in the blood transcriptome of rats subjected to hemorrhagic shock after blood reinfusion. Hemorrhagic shock was induced using a Wigger's shock model. The transcriptome of whole blood from shocked animals shows modulation of genes related to inflammation and immune response (Tlr13, Il1b, Ccl6, Lgals3), antioxidant functions (Mt2A, Mt1), tissue injury and repair pathways (Gpnmb, Trim72) and lipid mediators (Alox5ap, Ltb4r, Ptger2) compared with control animals. These findings are congruent with results obtained in hemorrhagic shock analysis by other authors using metabolomics and proteomics. The analysis of blood transcriptome may be a valuable tool to understand the biological changes occurring in hemorrhagic shock and a promising approach for the identification of novel biomarkers and therapeutic targets. Impact statement This study provides the first pilot analysis of the changes occurring in transcriptome expression of whole blood in hemorrhagic shock (HS) rats. We showed that the analysis of blood transcriptome is a useful approach to investigate pathways and functional alterations in this disease condition. This pilot study encourages the possible application of transcriptome analysis in the clinical setting, for the molecular profiling of whole blood in HS patients.

4U 1909+07: A Well-Hidden Pearl

NASA Technical Reports Server (NTRS)

Fuerst, F.; Kreykenbohm, I.; Barragan, L.; Wilms, J.; Rothschild, R. E.; Suchy, S.; Pottschmidt, K.

2009-01-01

We present the first detailed spectral and timing analysis of the High Mass X-ray Binary (HMXB) 4U 1909+07 with INTEGRAL and RXTE. 4U 1909+07 is detected with an average of 2.4 cps in ISGRI. but shows flares up to approx.50 cps. The system shows a pulse period of 605 s, but we found that the period changes erratically around this value. The pulse profile is extremely energy dependent: while it shows a double peaked structure at low energies, the secondary pulse decreases rapidly with increasing energy and above 20 ke V only the primary pulse is visible. This evolution is consistent between peA, HEXTE and ISGRI. We find that the phase averaged spectrum can be well fitted with a photo-absorbed power law with a cutoff at high energies and a blackbody component. To investigate the peculiar pulse profile, we performed phase resolved spectral analysis. We find that a change in the cutoff energy is required to fit the changing spectrum of the different pulse phases

Reproductive Status of Females in the Eusocial Wasp Polistes ferreri Saussure (Hymenoptera: Vespidae).

PubMed

Soares, E R P; Torres, V O; Antonialli-Junior, W F

2014-12-01

In the subfamily Polistinae, caste dimorphism is not pronounced and differences among females are primarily physiological and behavioral. We investigated factors that indicate the reproductive status in females of Polistes ferreri Saussure. We analyzed females from nine colonies and evaluated morphometric parameters, ovarian development, occurrence of insemination, relative age, and cuticular chemical profile. The colony females showed three kinds of ovarian development: type A, filamentous ovarioles; type B, ovarioles containing partially developed oocytes; and type C, long and well-developed ovarioles containing two or more mature oocytes. The stepwise discriminant analysis of the cuticular chemical profile showed that it was possible to distinguish the three groups of females: workers 1, workers 2, and queens. However, the stepwise discriminant analysis of the morphological differences did not show significant differences among these groups. The queens were among the older females in the colony and were always inseminated, while the age of the workers varied according to the stage of colony development.

Effects of various tool pin profiles on mechanical and metallurgical properties of friction stir welded joints of cryorolled AA2219 aluminium alloy

NASA Astrophysics Data System (ADS)

Kamal Babu, Karupannan; Panneerselvam, Kavan; Sathiya, Paulraj; Noorul Haq, Abdul Haq; Sundarrajan, Srinivasan; Mastanaiah, Potta; Srinivasa Murthy, Chunduri Venkata

2018-02-01

Friction stir welding (FSW) process was conducted on cryorolled (CR) AA2219 plate using different tool pin profiles such as cylindrical pin, threaded cylindrical pin, square pin and hexagonal pin profiles. The FSW was carried out with pairs of 6 mm thick CR aluminium plates with different tool pin profiles. The different tool pin profile weld portions' behaviors like mechanical (tensile strength, impact and hardness) and metallurgical characteristics were analyzed. The results of the mechanical analysis revealed that the joint made by the hexagonal pin tool had good strength compared to other pin profiles. This was due to the pulsating action and material flow of the tool resulting in dynamic recrystallization in the weld zone. This was confirmed by the ultra fine grain structure formation in Weld Nugget (WN) of hexagonal pin tool joint with a higher percentage of precipitate dissolution. The fractograph of the hexagonal tool pin weld portion confirmed the finer dimple structure morphology without having any interior defect compared to other tool pin profiles. The lowest weld joint strength was obtained from cylindrical pin profile weld joint due to insufficient material flow during welding. The Transmission Electron Microscope and EDX analysis showed the dissolution of the metastable θ″, θ' (Al2Cu) partial precipitates in the WN and proved the influence of metastable precipitates on enhancement of mechanical behavior of weld. The XRD results also confirmed the Al2Cu precipitation dissolution in the weld zone.

LIDAR Developments at Clermont-Ferrand—France for Atmospheric Observation

PubMed Central

Fréville, Patrick; Montoux, Nadège; Baray, Jean-Luc; Chauvigné, Aurélien; Réveret, François; Hervo, Maxime; Dionisi, Davide; Payen, Guillaume; Sellegri, Karine

2015-01-01

We present a Rayleigh-Mie-Raman LIDAR system in operation at Clermont-Ferrand (France) since 2008. The system provides continuous vertical tropospheric profiles of aerosols, cirrus optical properties and water vapour mixing ratio. Located in proximity to the high altitude Puy de Dôme station, labelled as the GAW global station PUY since August 2014, it is a useful tool to describe the boundary layer dynamics and hence interpret in situ measurements. This LIDAR has been upgraded with specific hardware/software developments and laboratory calibrations in order to improve the quality of the profiles, calibrate the depolarization ratio, and increase the automation of operation. As a result, we provide a climatological water vapour profile analysis for the 2009–2013 period, showing an annual cycle with a winter minimum and a summer maximum, consistent with in-situ observations at the PUY station. An overview of a preliminary climatology of cirrus clouds frequency shows that in 2014, more than 30% of days present cirrus events. Finally, the backscatter coefficient profile observed on 27 September 2014 shows the capacity of the system to detect cirrus clouds at 13 km altitude, in presence of aerosols below the 5 km altitude. PMID:25643059

Burnout in Health Professionals According to Their Self-Esteem, Social Support and Empathy Profile

PubMed Central

Molero Jurado, María del Mar; Pérez-Fuentes, María del Carmen; Gázquez Linares, José Jesús; Barragán Martín, Ana Belén

2018-01-01

Introduction: Professionals in the healthcare field are in situations that could be a source of stress and sometimes develop burnout syndrome. Self-esteem, social support, and empathy are variables which intervene and influence the appearance of this syndrome. Objective: Identify healthcare professional profiles based on self-esteem, empathy and perceived social support, and analyze the extent to which these profiles show differences in developing burnout. Method: The sample was made up of 719 healthcare professionals with a mean of 38.52 years of age. The Short Questionnaire of Burnout, the Rosenberg Self-Esteem Scale, the Perceived Social Support Questionnaire and the Basic Empathy Scale were used. Results: The results of a cluster analysis with self-esteem, empathy, and perceived social support showed four groups/profiles. Two of them, which included professionals with low self-esteem, differed in the rest of the characteristics. Furthermore, significant differences in burnout scores were found among the groups identified. Conclusion: The results show the need to study burnout with attention to individual and or social characteristics, where self-esteem is shown to be one of the explanatory variables making the main differences among the groups. PMID:29731725

Burnout in Health Professionals According to Their Self-Esteem, Social Support and Empathy Profile.

PubMed

Molero Jurado, María Del Mar; Pérez-Fuentes, María Del Carmen; Gázquez Linares, José Jesús; Barragán Martín, Ana Belén

2018-01-01

Introduction: Professionals in the healthcare field are in situations that could be a source of stress and sometimes develop burnout syndrome. Self-esteem, social support, and empathy are variables which intervene and influence the appearance of this syndrome. Objective: Identify healthcare professional profiles based on self-esteem, empathy and perceived social support, and analyze the extent to which these profiles show differences in developing burnout. Method: The sample was made up of 719 healthcare professionals with a mean of 38.52 years of age. The Short Questionnaire of Burnout, the Rosenberg Self-Esteem Scale, the Perceived Social Support Questionnaire and the Basic Empathy Scale were used. Results: The results of a cluster analysis with self-esteem, empathy, and perceived social support showed four groups/profiles. Two of them, which included professionals with low self-esteem, differed in the rest of the characteristics. Furthermore, significant differences in burnout scores were found among the groups identified. Conclusion: The results show the need to study burnout with attention to individual and or social characteristics, where self-esteem is shown to be one of the explanatory variables making the main differences among the groups.

Effects of Organic and Conventional Crop Nutrition on Profiles of Polar Metabolites in Grain of Wheat.

PubMed

Shewry, Peter; Rakszegi, Marianna; Lovegrove, Alison; Amos, Dominic; Corol, Delia-Irina; Tawfike, Ahmed; Mikó, Péter; Ward, Jane L

2018-05-30

The profiles of polar metabolites were determined in wholemeal flours of grain from the Broadbalk wheat experiment and from plants grown under organic and low-input systems to study the effects of nutrition on composition. The Broadbalk samples showed increased amino acids, acetate, and choline and decreased fructose and succinate with increasing nitrogen fertilization. Samples receiving farm yard manure had similar grain nitrogen to those receiving 96 kg of N/ha but had higher contents of amino acids, sugars, and organic acids. A comparison of the profiles of grain from organic and low-input systems showed only partial separation, with clear effects of climate and agronomy. However, supervised multivariate analysis showed that the low-input samples had higher contents of many amino acids, raffinose, glucose, organic acids, and choline and lower sucrose, fructose, and glycine. Consequently, although differences between organic and conventional grain occur, these cannot be used to confirm sample identity.

Associations of Streptococcus suis Serotype 2 Ribotype Profiles with Clinical Disease and Antimicrobial Resistance

PubMed Central

Rasmussen, S. R.; Aarestrup, F. M.; Jensen, N. E.; Jorsal, S. E.

1999-01-01

A total of 122 Streptococcus suis serotype 2 strains were characterized thoroughly by comparing clinical and pathological observations, ribotype profiles, and antimicrobial resistance. Twenty-one different ribotype profiles were found and compared by cluster analysis, resulting in the identification of three ribotype clusters. A total of 58% of all strains investigated were of two ribotypes belonging to different ribotype clusters. A remarkable relationship existed between the observed ribotype profiles and the clinical-pathological observations because strains of one of the two dominant ribotypes were almost exclusively isolated from pigs with meningitis, while strains of the other dominant ribotype were never associated with meningitis. This second ribotype was isolated only from pigs with pneumonia, endocarditis, pericarditis, or septicemia. Cluster analysis revealed that strains belonging to the same ribotype cluster as one of the dominant ribotypes came from pigs that showed clinical signs similar to those of pigs infected with strains with the respective dominant ribotype profiles. Furthermore, strains belonging to different ribotype clusters had totally different patterns of resistance to antibiotics because strains isolated from pigs with meningitis were resistant to sulfamethazoxazole and strains isolated from pigs with pneumonia, endocarditis, pericarditis, or septicemia were resistant to tetracycline. PMID:9889228

Effect of masticatory stimulation on the quantity and quality of saliva and the salivary metabolomic profile.

PubMed

Okuma, Nobuyuki; Saita, Makiko; Hoshi, Noriyuki; Soga, Tomoyoshi; Tomita, Masaru; Sugimoto, Masahiro; Kimoto, Katsuhiko

2017-01-01

This study characterized the changes in quality and quantity of saliva, and changes in the salivary metabolomic profile, to understand the effects of masticatory stimulation. Stimulated and unstimulated saliva samples were collected from 55 subjects and salivary hydrophilic metabolites were comprehensively quantified using capillary electrophoresis-time-of-flight mass spectrometry. In total, 137 metabolites were identified and quantified. The concentrations of 44 metabolites in stimulated saliva were significantly higher than those in unstimulated saliva. Pathway analysis identified the upregulation of the urea cycle and synthesis and degradation pathways of glycine, serine, cysteine and threonine in stimulated saliva. A principal component analysis revealed that the effect of masticatory stimulation on salivary metabolomic profiles was less dependent on sample population sex, age, and smoking. The concentrations of only 1 metabolite in unstimulated saliva, and of 3 metabolites stimulated saliva, showed significant correlation with salivary secretion volume, indicating that the salivary metabolomic profile and salivary secretion volume were independent factors. Masticatory stimulation affected not only salivary secretion volume, but also metabolite concentration patterns. A low correlation between the secretion volume and these patterns supports the conclusion that the salivary metabolomic profile may be a new indicator to characterize masticatory stimulation.

Genome-Wide Analysis of Soybean HD-Zip Gene Family and Expression Profiling under Salinity and Drought Treatments

PubMed Central

Chen, Xue; Chen, Zhu; Zhao, Hualin; Zhao, Yang; Cheng, Beijiu; Xiang, Yan

2014-01-01

Background Homeodomain-leucine zipper (HD-Zip) proteins, a group of homeobox transcription factors, participate in various aspects of normal plant growth and developmental processes as well as environmental responses. To date, no overall analysis or expression profiling of the HD-Zip gene family in soybean (Glycine max) has been reported. Methods and Findings An investigation of the soybean genome revealed 88 putative HD-Zip genes. These genes were classified into four subfamilies, I to IV, based on phylogenetic analysis. In each subfamily, the constituent parts of gene structure and motif were relatively conserved. A total of 87 out of 88 genes were distributed unequally on 20 chromosomes with 36 segmental duplication events, indicating that segmental duplication is important for the expansion of the HD-Zip family. Analysis of the Ka/Ks ratios showed that the duplicated genes of the HD-Zip family basically underwent purifying selection with restrictive functional divergence after the duplication events. Analysis of expression profiles showed that 80 genes differentially expressed across 14 tissues, and 59 HD-Zip genes are differentially expressed under salinity and drought stress, with 20 paralogous pairs showing nearly identical expression patterns and three paralogous pairs diversifying significantly under drought stress. Quantitative real-time RT-PCR (qRT-PCR) analysis of six paralogous pairs of 12 selected soybean HD-Zip genes under both drought and salinity stress confirmed their stress-inducible expression patterns. Conclusions This study presents a thorough overview of the soybean HD-Zip gene family and provides a new perspective on the evolution of this gene family. The results indicate that HD-Zip family genes may be involved in many plant responses to stress conditions. Additionally, this study provides a solid foundation for uncovering the biological roles of HD-Zip genes in soybean growth and development. PMID:24498296

Rheology, fatty acid profile and storage characteristics of cookies as influenced by flax seed (Linum usitatissimum).

PubMed

Rajiv, Jyotsna; Indrani, Dasappa; Prabhasankar, Pichan; Rao, G Venkateswara

2012-10-01

Flaxseed is a versatile functional ingredient owing to its unique nutrient profile. Studies on the effect of substitution of roasted and ground flaxseed (RGF) at 5, 10, 15 and 20% level on the wheat flour dough properties showed that amylograph peak viscosity, farinograph dough stability, extensograph resistance to extension and extensibility values decreased with the increase in the substitution of RGF from 0-20%. The cookie baking test showed a marginal decrease in spread ratio but beyond substitution of 15% RGF the texture and flavour of the cookies was adversely affected. The data on storage characteristics of control and cookies with 15% RGF showed no significant change with respect to acidity of extracted fat and peroxide values due to storage of cookies upto 90 days in metallised polyester pouches at ambient conditions. The gas chromatographic analysis of fatty acid profile indicated that the control cookies contained negligible linolenic acid and the flaxseed cookies contained 4.75 to 5.31% of linolenic acid which showed a marginal decrease over storage. Hence flaxseed could be used as a source of omega-3-fatty acid.

Attention profiles in autism spectrum disorder and subtypes of attention-deficit/hyperactivity disorder.

PubMed

Boxhoorn, Sara; Lopez, Eva; Schmidt, Catharina; Schulze, Diana; Hänig, Susann; Freitag, Christine M

2018-03-06

Attention problems are observed in attention-deficit/hyperactivity disorder (ADHD) and autism spectrum disorder (ASD). Most neuropsychological studies that compared both disorders focused on complex executive functions (EF), but missed to contrast basic attention functions, as well as ASD- and ADHD subtypes. The present study compared EF as well as basic attention functioning of children with the combined subtype (ADHD-C), the predominantly inattentive subtype (ADHD-I), and autism spectrum disorder without ADHD (ASD-) with typically developing controls (TD). Basic attention functions and EF profiles were analysed by testing the comprehensive attention function model of van Zomeren and Brouwer using profile analysis. Additionally, neurocognitive impairments in ASD- and ADHD were regressed on dimensional measures of attention- and hyperactive-impulsive symptoms across and within groups. ADHD-C revealed a strong impairment across measures of EF compared to ASD- and TD. The ADHD-C profile furthermore showed disorder specific impairments in interference control, whereas the ASD- profile showed a disorder specific impairment in basic attention component divided attention. Attention- and hyperactive-impulsive symptom severity did not predict neurocognitive impairments across- or within groups. Study findings thus support disorder and subtype specific attention/EF profiles, which refute the idea of a continuum of ADHD-I, ADHD-C, and ASD with increasing neurocognitive impairments.

A measurement system for vertical seawater profiles close to the air-sea interface

NASA Astrophysics Data System (ADS)

Sims, Richard P.; Schuster, Ute; Watson, Andrew J.; Yang, Ming Xi; Hopkins, Frances E.; Stephens, John; Bell, Thomas G.

2017-09-01

This paper describes a near-surface ocean profiler, which has been designed to precisely measure vertical gradients in the top 10 m of the ocean. Variations in the depth of seawater collection are minimized when using the profiler compared to conventional CTD/rosette deployments. The profiler consists of a remotely operated winch mounted on a tethered yet free-floating buoy, which is used to raise and lower a small frame housing sensors and inlet tubing. Seawater at the inlet depth is pumped back to the ship for analysis. The profiler can be used to make continuous vertical profiles or to target a series of discrete depths. The profiler has been successfully deployed during wind speeds up to 10 m s-1 and significant wave heights up to 2 m. We demonstrate the potential of the profiler by presenting measured vertical profiles of the trace gases carbon dioxide and dimethylsulfide. Trace gas measurements use an efficient microporous membrane equilibrator to minimize the system response time. The example profiles show vertical gradients in the upper 5 m for temperature, carbon dioxide and dimethylsulfide of 0.15 °C, 4 µatm and 0.4 nM respectively.

[Analysis of XRD spectral characteristics of soil clay mineral in two typical cultivated soils].

PubMed

Zhang, Zhi-Dan; Luo, Xiang-Li; Jiang, Hai-Chao; Li, Qiao; Shen, Cong-Ying; Liu, Hang; Zhou, Ya-Juan; Zhao, Lan-Po; Wang, Ji-Hong

2014-07-01

The present paper took black soil and chernozem, the typical cultivated soil in major grain producing area of Northeast, as the study object, and determinated the soil particle composition characteristics of two cultivated soils under the same climate and location. Then XRD was used to study the composition and difference of clay mineral in two kinds of soil and the evolutionary mechanism was explored. The results showed that the two kinds of soil particles were composed mainly of the sand, followed by clay and silt. When the particle accumulation rate reached 50%, the central particle size was in the 15-130 microm interval. Except for black soil profile of Shengli Xiang, the content of clay showed converse sequence to the central particle in two soils. Clay accumulated under upper layer (18.82%) in black soil profile while under caliche layer (17.41%) in chernozem profile. Clay content was the least in parent material horizon except in black profile of Quanyanling. Analysis of clay XRD atlas showed that the difference lied in not only the strength of diffraction peak, but also in the mineral composition. The main contents of black soil and chernozem were both 2 : 1 clay, the composition of black soil was smectite/illite mixed layer-illite-vermiculite and that of chernozem was S/I mixture-illite-montmorillonite, and both of them contained little kaolinite, chlorite, quartz and other primary mineral. This paper used XRD to determine the characteristics of clay minerals comprehensively, and analyzed two kinds of typical cultivated soil comparatively, and it was a new perspective of soil minerals study.

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

Sharma, Sanjeev, E-mail: sanjeevsharma145@gmail.com; Kumar, Rajendra, E-mail: khundrakpam-ss@yahoo.com; Singh, Kh. S., E-mail: khundrakpam-ss@yahoo.com

A simple design of broadband one dimensional dielectric/semiconductor multilayer structure having refractive index profile of exponentially graded material has been proposed. The theoretical analysis shows that the proposed structure works as a perfect mirror within a certain wavelength range (1550 nm). In order to calculate the reflection properties a transfer matrix method (TMM) has been used. This property shows that binary graded photonic crystal structures have widened omnidirectional reflector (ODR) bandgap. Hence a exponentially graded photonic crystal structure can be used as a broadband optical reflector and the range of reflection can be tuned to any wavelength region by varying themore » refractive index profile of exponentially graded photonic crystal structure.« less

Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes

PubMed Central

Li, Tongtong; Long, Meng; Li, Huan; Gatesoupe, François-Joël; Zhang, Xujie; Zhang, Qianqian; Feng, Dongyue; Li, Aihua

2017-01-01

Gut microbiota play key roles in host nutrition and metabolism. However, little is known about the relationship between host genetics, gut microbiota and metabolic profiles. Here, we used high-throughput sequencing and gas chromatography/mass spectrometry approaches to characterize the microbiota composition and the metabolite profiles in the gut of five cyprinid fish species with three different feeding habits raised under identical husbandry conditions. Our results showed that host species and feeding habits significantly affect not only gut microbiota composition but also metabolite profiles (ANOSIM, p ≤ 0.05). Mantel test demonstrated that host phylogeny, gut microbiota, and metabolite profiles were significantly related to each other (p ≤ 0.05). Additionally, the carps with the same feeding habits had more similarity in gut microbiota composition and metabolite profiles. Various metabolites were correlated positively with bacterial taxa involved in food degradation. Our results shed new light on the microbiome and metabolite profiles in the gut content of cyprinid fishes, and highlighted the correlations between host genotype, fish gut microbiome and putative functions, and gut metabolite profiles. PMID:28367147

Metabolic profiling of human lung cancer blood plasma using 1H NMR spectroscopy

NASA Astrophysics Data System (ADS)

Kokova, Daria; Dementeva, Natalia; Kotelnikov, Oleg; Ponomaryova, Anastasia; Cherdyntseva, Nadezhda; Kzhyshkowska, Juliya

2017-11-01

Lung cancer (both small cell and non-small cell) is the second most common cancer in both men and women. The article represents results of evaluating of the plasma metabolic profiles of 100 lung cancer patients and 100 controls to investigate significant metabolites using 400 MHz 1H NMR spectrometer. The results of multivariate statistical analysis show that a medium-field NMR spectrometer can obtain the data which are already sufficient for clinical metabolomics.

Cardioprotective and Metabolomic Profiling of Selected Medicinal Plants against Oxidative Stress

PubMed Central

Afsheen, Nadia; Jahan, Nazish; Ijaz, Misbah; Manzoor, Asad; Khan, Khalid Mahmood; Hina, Saman

2018-01-01

In this research work, the antioxidant and metabolomic profiling of seven selected medicinally important herbs including Rauvolfia serpentina, Terminalia arjuna, Coriandrum sativum, Elettaria cardamom, Piper nigrum, Allium sativum, and Crataegus oxyacantha was performed. The in vivo cardioprotective potential of these medicinal plants was evaluated against surgically induced oxidative stress through left anterior descending coronary artery ligation (LADCA) in dogs. The antioxidant profiling of these plants was done through DPPH and DNA protection assay. The C. oxyacantha and T. arjuna showed maximum antioxidant potential, while the E. cardamom showed poor antioxidative strength even at its high concentration. Different concentrations of extracts of the said plants exhibited the protection of plasmid DNA against H2O2 damage as compared to the plasmid DNA merely treated with H2O2. The metabolomic profiling through LC-MS analysis of these antioxidants revealed the presence of active secondary metabolites responsible for their antioxidant potential. During in vivo analysis, blood samples of all treatment groups were drawn at different time intervals to analyze the cardiac and hemodynamic parameters. The results depicted that the group pretreated with HC4 significantly sustained the level of CK-MB, SGOT, and LDH as well as hemodynamic parameters near to normal. The histopathological examination also confirmed the cardioprotective potential of HC4. Thus, the HC4 being safe and inexpensive cardioprotective herbal combination could be considered as an alternate of synthetic drugs. PMID:29576858

Patterns of stigma toward schizophrenia among the general population: a latent profile analysis.

PubMed

Loch, Alexandre A; Wang, Yuan-Pang; Guarniero, Francisco B; Lawson, Fabio L; Hengartner, Michael P; Rössler, Wulf; Gattaz, Wagner F

2014-09-01

Our purpose was to assess stigma toward schizophrenia in a representative sample of the Brazilian general population. The sample consisted of 1015 individuals interviewed by telephone. A vignette describing someone with schizophrenia was read, and four stigma aspects regarding this hypothetical individual were assessed: stereotypes, restrictions, perceived prejudice and social distance. Latent profile analysis searched for stigma profiles among the sample. Multinomial logistic regression was used to find correlates of each class. Four stigma profiles were found; 'no stigma' individuals (n = 251) mostly displayed positive opinions. 'Labelers' (n = 222) scored high on social distance; they more often had familial contact with mental illness and more often labeled the vignette's disorder as schizophrenia. 'Discriminators', the group with the majority of individuals (n = 302), showed high levels of stigmatizing beliefs in all dimensions; discriminators were significantly older. 'Unobtrusive stigma' individuals (n = 240) seemed to demonstrate uncertainty or low commitment since they mostly answered items with the middle/impartial option. Some findings from the international literature were replicated; however, familial contact increased stigma, possibly denoting a locally modulated determinant. Hereby, our study also adds important cross-cultural data by showing that stigma toward schizophrenia is high in a Latin-American setting. We highlight the importance of analyzing the general population as a heterogeneous group, aiming to better elaborate anti-stigma campaigns. © The Author(s) 2013.

Laboratory-based electrical conductivity at Martian mantle conditions

NASA Astrophysics Data System (ADS)

Verhoeven, Olivier; Vacher, Pierre

2016-12-01

Information on temperature and composition of planetary mantles can be obtained from electrical conductivity profiles derived from induced magnetic field analysis. This requires a modeling of the conductivity for each mineral phase at conditions relevant to planetary interiors. Interpretation of iron-rich Martian mantle conductivity profile therefore requires a careful modeling of the conductivity of iron-bearing minerals. In this paper, we show that conduction mechanism called small polaron is the dominant conduction mechanism at temperature, water and iron content conditions relevant to Mars mantle. We then review the different measurements performed on mineral phases with various iron content. We show that, for all measurements of mineral conductivity reported so far, the effect of iron content on the activation energy governing the exponential decrease in the Arrhenius law can be modeled as the cubic square root of the iron content. We recast all laboratory results on a common generalized Arrhenius law for iron-bearing minerals, anchored on Earth's mantle values. We then use this modeling to compute a new synthetic profile of Martian mantle electrical conductivity. This new profile matches perfectly, in the depth range [100,1000] km, the electrical conductivity profile recently derived from the study of Mars Global Surveyor magnetic field measurements.

Impact of Atmospheric Infrared Sounder (AIRS) Thermodynamic Profiles on Regional Weather Forecasting

NASA Technical Reports Server (NTRS)

Chou, Shih-Hung; Zavodsky, Bradley T.; Jedlovee, Gary J.

2010-01-01

In data sparse regions, remotely-sensed observations can be used to improve analyses and lead to better forecasts. One such source comes from the Atmospheric Infrared Sounder (AIRS), which together with the Advanced Microwave Sounding Unit (AMSU), provides temperature and moisture profiles with accuracy comparable to that of radiosondes. The purpose of this paper is to describe a procedure to assimilate AIRS thermodynamic profile data into a regional configuration of the Advanced Research Weather Research and Forecasting (WRF-ARW) model using its three-dimension variational (3DVAR) analysis component (WRF-Var). Quality indicators are used to select only the highest quality temperature and moisture profiles for assimilation in both clear and partly cloudy regions. Separate error characteristics for land and water profiles are also used in the assimilation process. Assimilation results indicate that AIRS profiles produce an analysis closer to in situ observations than the background field. Forecasts from a 37-day case study period in the winter of 2007 show that AIRS profile data can lead to improvements in 6-h cumulative precipitation forecasts due to instability added in the forecast soundings by the AIRS profiles. Additionally, in a convective heavy rainfall event from February 2007, assimilation of AIRS profiles produces a more unstable boundary layer resulting in enhanced updrafts in the model. These updrafts produce a squall line and precipitation totals that more closely reflect ground-based observations than a no AIRS control forecast. The location of available high-quality AIRS profiles ahead of approaching storm systems is found to be of paramount importance to the amount of impact the observations will have on the resulting forecasts.

Uplift history of the Sila Massif, southern Italy, deciphered from cosmogenic 10Be erosion rates and river longitudinal profile analysis

USGS Publications Warehouse

Olivetti, Valerio; Cyr, Andrew J.; Molin, Paola; Faccenna, Claudio; Granger, Darryl E.

2012-01-01

The Sila Massif in the Calabrian Arc (southern Italy) is a key site to study the response of a landscape to rock uplift. Here an uplift rate of ∼1 mm/yr has imparted a deep imprint on the Sila landscape recorded by a high-standing low-relief surface on top of the massif, deeply incised fluvial valleys along its flanks, and flights of marine terraces in the coastal belt. In this framework, we combined river longitudinal profile analysis with hillslope erosion rates calculated by 10Be content in modern fluvial sediments to reconstruct the long-term uplift history of the massif. Cosmogenic data show a large variation in erosion rates, marking two main domains. The samples collected in the high-standing low-relief surface atop Sila provide low erosion rates (from 0.09 ± 0.01 to 0.13 ± 0.01 mm/yr). Conversely, high values of erosion rate (up to 0.92 ± 0.08 mm/yr) characterize the incised fluvial valleys on the massif flanks. The analyzed river profiles exhibit a wide range of shapes diverging from the commonly accepted equilibrium concave-up form. Generally, the studied river profiles show two or, more frequently, three concave-up segments bounded by knickpoints and characterized by different values of concavity and steepness indices. The wide variation in cosmogenic erosion rates and the non-equilibrated river profiles indicate that the Sila landscape is in a transient state of disequilibrium in response to a strong and unsteady uplift not yet counterbalanced by erosion.

Nickel-Hydrogen Cell Testing Experience, NASA/Goddard Space Flight Center

NASA Technical Reports Server (NTRS)

Rao, Gopalakrishna M.

1999-01-01

The objectives of the project were to test the Nickel-Hydrogen Cell to: (1) verify the Aerospace Cell Flight Worthiness, (2) Elucidate the Aerospace Cell Thermal Behavior, (3) Develop the Aerospace Battery Assembly Design(s) and In-orbit Battery Management plan(s) and (4) Understand the Aerospace Cell Failure Mechanism. The tests included the LEO and GEO Life cycle tests, Calorimetric Analysis, Destructive Physical analysis, and special tests. Charts show the Mission Profile Cycling Data, Stress Cycling Data. The test data complies with the mission requirements, validating the flight worthiness of batteries. The nominal stress and mission profile cycling performance test shows the charge voltage as high as 1.60V and recharge ratio greater than 1.05. It is apparent that the electrochemical signatures alone do not provide conclusive proof for Nickel precharge. The researchers recommend a gas and positive plate analyses for further confirmation.

Indel analysis by droplet digital PCR: a sensitive method for DNA mixture detection and chimerism analysis.

PubMed

Santurtún, Ana; Riancho, José A; Arozamena, Jana; López-Duarte, Mónica; Zarrabeitia, María T

2017-01-01

Several methods have been developed to determinate genetic profiles from a mixed samples and chimerism analysis in transplanted patients. The aim of this study was to explore the effectiveness of using the droplet digital PCR (ddPCR) for mixed chimerism detection (a mixture of genetic profiles resulting after allogeneic hematopoietic stem cell transplantation (HSCT)). We analyzed 25 DNA samples from patients who had undergone HSCT and compared the performance of ddPCR and two established methods for chimerism detection, based upon the Indel and STRs analysis, respectively. Additionally, eight artificial mixture DNA samples were created to evaluate the sensibility of ddPCR. Our results show that the chimerism percentages estimated by the analysis of a single Indel using ddPCR were very similar to those calculated by the amplification of 15 STRs (r 2  = 0.970) and with the results obtained by the amplification of 38 Indels (r 2  = 0.975). Moreover, the amplification of a single Indel by ddPCR was sensitive enough to detect a minor DNA contributor comprising down to 0.5 % of the sample. We conclude that ddPCR can be a powerful tool for the determination of a genetic profile of forensic mixtures and clinical chimerism analysis when traditional techniques are not sensitive enough.

Derivative component analysis for mass spectral serum proteomic profiles.

PubMed

Han, Henry

2014-01-01

As a promising way to transform medicine, mass spectrometry based proteomics technologies have seen a great progress in identifying disease biomarkers for clinical diagnosis and prognosis. However, there is a lack of effective feature selection methods that are able to capture essential data behaviors to achieve clinical level disease diagnosis. Moreover, it faces a challenge from data reproducibility, which means that no two independent studies have been found to produce same proteomic patterns. Such reproducibility issue causes the identified biomarker patterns to lose repeatability and prevents it from real clinical usage. In this work, we propose a novel machine-learning algorithm: derivative component analysis (DCA) for high-dimensional mass spectral proteomic profiles. As an implicit feature selection algorithm, derivative component analysis examines input proteomics data in a multi-resolution approach by seeking its derivatives to capture latent data characteristics and conduct de-noising. We further demonstrate DCA's advantages in disease diagnosis by viewing input proteomics data as a profile biomarker via integrating it with support vector machines to tackle the reproducibility issue, besides comparing it with state-of-the-art peers. Our results show that high-dimensional proteomics data are actually linearly separable under proposed derivative component analysis (DCA). As a novel multi-resolution feature selection algorithm, DCA not only overcomes the weakness of the traditional methods in subtle data behavior discovery, but also suggests an effective resolution to overcoming proteomics data's reproducibility problem and provides new techniques and insights in translational bioinformatics and machine learning. The DCA-based profile biomarker diagnosis makes clinical level diagnostic performances reproducible across different proteomic data, which is more robust and systematic than the existing biomarker discovery based diagnosis. Our findings demonstrate the feasibility and power of the proposed DCA-based profile biomarker diagnosis in achieving high sensitivity and conquering the data reproducibility issue in serum proteomics. Furthermore, our proposed derivative component analysis suggests the subtle data characteristics gleaning and de-noising are essential in separating true signals from red herrings for high-dimensional proteomic profiles, which can be more important than the conventional feature selection or dimension reduction. In particular, our profile biomarker diagnosis can be generalized to other omics data for derivative component analysis (DCA)'s nature of generic data analysis.

Distinct Retinal Capillary Plexuses in Normal Eyes as Observed in Optical Coherence Tomography Angiography Axial Profile Analysis.

PubMed

Hirano, Takao; Chanwimol, Karntida; Weichsel, Julian; Tepelus, Tudor; Sadda, Srinivas

2018-06-20

Optical coherence tomography angiography (OCTA) allows the retinal microvasculature to be visualized at various retinal depths. Previous studies introduced OCTA axial profile analysis and showed regional variations in the number and location of axially distinct vascular retinal plexuses. OCTA acquisition and processing approaches, however, vary in terms of their resulting transverse and axial resolutions, and especially the latter could potentially influence the profile analysis results. Our study imaged normal eyes using the Spectralis OCT2 with a full-spectrum, probabilistic OCTA algorithm, that, in marked contrast to split-spectrum approaches, preserves the original high OCT axial resolution also within the resulting OCTA signal. En face OCTA images are generally created by averaging flow signals over a finite axial depth window. However, we assessed regional OCTA signal profiles at each depth position at full axial resolution. All regions had two sharp vessel density peaks near the inner and outer boundaries of the inner nuclear layer, indicating separate intermediate and deep capillary plexuses. The superficial vascular plexus (SVP) separated into two distinct peaks within the ganglion cell layer in the parafoveal zone. The nasal, superior, and inferior perifovea had a deeper SVP peak that was shifted anteriorly compared to the parafoveal zone. Axial vascular density analysis with high-resolution, full spectrum OCTA thus allows healthy retinal vasculature to be precisely reconstructed and may be useful for clinically assessing retinal pathology.

Mycotoxicological and palynological profiles of commercial brands of dried bee pollen.

PubMed

Deveza, Michele Valadares; Keller, Kelly Moura; Lorenzon, Maria Cristina Affonso; Nunes, Lucila Maria Teixeira; Sales, Érika Oliveira; Barth, Ortrud Monika

2015-01-01

Pollen is used in the human diet as a food supplement because of its high nutritional value; however, this product is prone to fungal contamination that could potentially generate toxins that are harmful to human health. This study aimed to verify the floral diversity of commercial brands of bee pollen and their mycotoxicological safety for human consumption. A total of 27 bee pollen samples were analyzed; these samples represented commercial brands, either showing an inspection seal or not, marketed in the State of Rio de Janeiro. The analyzed parameters included floral diversity through palynological analysis, water activity, fungal counts, identification and toxigenic profiles. The palynological analysis identified nine plant families, of which the Asteraceae was predominant. Analysis of hygienic quality based on fungal load showed that 92% of samples were reproved according to the commercial, sanitary, and food safety quality indicators. Aspergillus, Cladosporium and Penicillium were the most common genera. Toxigenic evaluation showed that 25% of the A. flavus strains produced aflatoxins. The high rate of contamination of products bearing an inspection seal emphasizes the need to monitor the entire procedure of bee pollen production, as well as to revise the current legislation to ensure safe commercialization of this product.

Aroma characterization based on aromatic series analysis in table grapes

PubMed Central

Wu, Yusen; Duan, Shuyan; Zhao, Liping; Gao, Zhen; Luo, Meng; Song, Shiren; Xu, Wenping; Zhang, Caixi; Ma, Chao; Wang, Shiping

2016-01-01

Aroma is an important part of quality in table grape, but the key aroma compounds and the aroma series of table grapes remains unknown. In this paper, we identified 67 aroma compounds in 20 table grape cultivars; 20 in pulp and 23 in skin were active compounds. C6 compounds were the basic background volatiles, but the aroma contents of pulp juice and skin depended mainly on the levels of esters and terpenes, respectively. Most obviously, ‘Kyoho’ grapevine series showed high contents of esters in pulp, while Muscat/floral cultivars showed abundant monoterpenes in skin. For the aroma series, table grapes were characterized mainly by herbaceous, floral, balsamic, sweet and fruity series. The simple and visualizable aroma profiles were established using aroma fingerprints based on the aromatic series. Hierarchical cluster analysis (HCA) and principal component analysis (PCA) showed that the aroma profiles of pulp juice, skin and whole berries could be classified into 5, 3, and 5 groups, respectively. Combined with sensory evaluation, we could conclude that fatty and balsamic series were the preferred aromatic series, and the contents of their contributors (β-ionone and octanal) may be useful as indicators for the improvement of breeding and cultivation measures for table grapes. PMID:27487935

Dating a tropical ice core by time-frequency analysis of ion concentration depth profiles

NASA Astrophysics Data System (ADS)

Gay, M.; De Angelis, M.; Lacoume, J.-L.

2014-09-01

Ice core dating is a key parameter for the interpretation of the ice archives. However, the relationship between ice depth and ice age generally cannot be easily established and requires the combination of numerous investigations and/or modelling efforts. This paper presents a new approach to ice core dating based on time-frequency analysis of chemical profiles at a site where seasonal patterns may be significantly distorted by sporadic events of regional importance, specifically at the summit area of Nevado Illimani (6350 m a.s.l.), located in the eastern Bolivian Andes (16°37' S, 67°46' W). We used ion concentration depth profiles collected along a 100 m deep ice core. The results of Fourier time-frequency and wavelet transforms were first compared. Both methods were applied to a nitrate concentration depth profile. The resulting chronologies were checked by comparison with the multi-proxy year-by-year dating published by de Angelis et al. (2003) and with volcanic tie points. With this first experiment, we demonstrated the efficiency of Fourier time-frequency analysis when tracking the nitrate natural variability. In addition, we were able to show spectrum aliasing due to under-sampling below 70 m. In this article, we propose a method of de-aliasing which significantly improves the core dating in comparison with annual layer manual counting. Fourier time-frequency analysis was applied to concentration depth profiles of seven other ions, providing information on the suitability of each of them for the dating of tropical Andean ice cores.

Integrative prescreening in analysis of multiple cancer genomic studies

PubMed Central

2012-01-01

Background In high throughput cancer genomic studies, results from the analysis of single datasets often suffer from a lack of reproducibility because of small sample sizes. Integrative analysis can effectively pool and analyze multiple datasets and provides a cost effective way to improve reproducibility. In integrative analysis, simultaneously analyzing all genes profiled may incur high computational cost. A computationally affordable remedy is prescreening, which fits marginal models, can be conducted in a parallel manner, and has low computational cost. Results An integrative prescreening approach is developed for the analysis of multiple cancer genomic datasets. Simulation shows that the proposed integrative prescreening has better performance than alternatives, particularly including prescreening with individual datasets, an intensity approach and meta-analysis. We also analyze multiple microarray gene profiling studies on liver and pancreatic cancers using the proposed approach. Conclusions The proposed integrative prescreening provides an effective way to reduce the dimensionality in cancer genomic studies. It can be coupled with existing analysis methods to identify cancer markers. PMID:22799431

Meta-Analysis of Tumor Stem-Like Breast Cancer Cells Using Gene Set and Network Analysis

PubMed Central

Lee, Won Jun; Kim, Sang Cheol; Yoon, Jung-Ho; Yoon, Sang Jun; Lim, Johan; Kim, You-Sun; Kwon, Sung Won; Park, Jeong Hill

2016-01-01

Generally, cancer stem cells have epithelial-to-mesenchymal-transition characteristics and other aggressive properties that cause metastasis. However, there have been no confident markers for the identification of cancer stem cells and comparative methods examining adherent and sphere cells are widely used to investigate mechanism underlying cancer stem cells, because sphere cells have been known to maintain cancer stem cell characteristics. In this study, we conducted a meta-analysis that combined gene expression profiles from several studies that utilized tumorsphere technology to investigate tumor stem-like breast cancer cells. We used our own gene expression profiles along with the three different gene expression profiles from the Gene Expression Omnibus, which we combined using the ComBat method, and obtained significant gene sets using the gene set analysis of our datasets and the combined dataset. This experiment focused on four gene sets such as cytokine-cytokine receptor interaction that demonstrated significance in both datasets. Our observations demonstrated that among the genes of four significant gene sets, six genes were consistently up-regulated and satisfied the p-value of < 0.05, and our network analysis showed high connectivity in five genes. From these results, we established CXCR4, CXCL1 and HMGCS1, the intersecting genes of the datasets with high connectivity and p-value of < 0.05, as significant genes in the identification of cancer stem cells. Additional experiment using quantitative reverse transcription-polymerase chain reaction showed significant up-regulation in MCF-7 derived sphere cells and confirmed the importance of these three genes. Taken together, using meta-analysis that combines gene set and network analysis, we suggested CXCR4, CXCL1 and HMGCS1 as candidates involved in tumor stem-like breast cancer cells. Distinct from other meta-analysis, by using gene set analysis, we selected possible markers which can explain the biological mechanisms and suggested network analysis as an additional criterion for selecting candidates. PMID:26870956

Daily chronomics of proteomic profile in aging and rotenone-induced Parkinson's disease model in male Wistar rat and its modulation by melatonin.

PubMed

Jagota, Anita; Mattam, Ushodaya

2017-08-01

Aging is associated with changes in several basic parameters of circadian timing system (CTS) in mammals leading to circadian dysfunction. We had reported earlier that upon aging and in rotenone induced Parkinson's disease (RIPD) rat model there were significant alterations in the core clock genes expression levels and daily pulses. To identify biomarkers of aging and PD chronomics of proteomic day-night profiles in suprachiasmatic nucleus (SCN), pineal and substantia nigra (SN) in 3 month (m), 12, 24 m and RIPD rat model were studied at two time points i.e. Zeitgeber Time (ZT)-6 (mid-day) and ZT-18 (mid-night). Proteome analysis was done by using two dimensional (2-D) electrophoresis and the spots showing robust day-night variations were identified by using MALDI TOF/TOF analysis. In 3 m rats the number of proteins showing day-night variations were relatively more than 12, 24 m and RIPD rat model in SCN and SN. But in pineal there was increase in number of protein spots showing day-night variations in 24 m. Mass spectroscopy of the protein spots showing robust day night variation in aging and RIPD rats were identified. As melatonin, a multitasking molecule, an endogenous synchronizer of rhythm, an antioxidant and an antiaging drug, declines with aging, the effects of melatonin administration on differential alterations in chronomics of 2-D protein profiles in aging and RIPD male Wistar rats were studied. We report here that the melatonin could be playing an important role in modulating the chronomics of 2-D protein profiles. Additionally, various proteins were identified for the first time in this study showing significant day night variation in SCN, pineal and SN may prove useful towards targeting novel treatments for circadian dysfunction, good health and longevity.

Modification of the background flow by roll vortices

NASA Technical Reports Server (NTRS)

Shirer, Hampton N.; Haack, Tracy

1990-01-01

Use of observed wind profiles, such as those obtained from ascent or descent aircraft soundings, for the identification of the expected roll modes is hindered by the fact that these modes are able to modify the wind profiles. When such modified wind profiles are utilized to estimate the critical values of the dynamic and thermodynamic forcing rates, large errors in the preferred orientation angles and aspect ratios of the rolls may result. Nonlinear analysis of a 14 coefficient spectral model of roll circulations shows that the primary modification of the background wind is the addition of a linear component. When the linear profile having the correct amount of shear is subtracted from the observed cross-roll winds, then the pre-roll wind profile can be estimated. A preliminary test of this hypothesis is given for a case in which cloud streets were observed during FIRE.

Quantitative Analysis of Gender Stereotypes and Information Aggregation in a National Election

PubMed Central

Tumminello, Michele; Miccichè, Salvatore; Varho, Jan; Piilo, Jyrki; Mantegna, Rosario N.

2013-01-01

By analyzing a database of a questionnaire answered by a large majority of candidates and elected in a parliamentary election, we quantitatively verify that (i) female candidates on average present political profiles which are more compassionate and more concerned with social welfare issues than male candidates and (ii) the voting procedure acts as a process of information aggregation. Our results show that information aggregation proceeds with at least two distinct paths. In the first case candidates characterize themselves with a political profile aiming to describe the profile of the majority of voters. This is typically the case of candidates of political parties which are competing for the center of the various political dimensions. In the second case, candidates choose a political profile manifesting a clear difference from opposite political profiles endorsed by candidates of a political party positioned at the opposite extreme of some political dimension. PMID:23555606

Surface analysis and depth profiling of corrosion products formed in lead pipes used to supply low alkalinity drinking water.

PubMed

Davidson, C M; Peters, N J; Britton, A; Brady, L; Gardiner, P H E; Lewis, B D

2004-01-01

Modern analytical techniques have been applied to investigate the nature of lead pipe corrosion products formed in pH adjusted, orthophosphate-treated, low alkalinity water, under supply conditions. Depth profiling and surface analysis have been carried out on pipe samples obtained from the water distribution system in Glasgow, Scotland, UK. X-ray diffraction spectrometry identified basic lead carbonate, lead oxide and lead phosphate as the principal components. Scanning electron microscopy/energy-dispersive x-ray spectrometry revealed the crystalline structure within the corrosion product and also showed spatial correlations existed between calcium, iron, lead, oxygen and phosphorus. Elemental profiling, conducted by means of secondary ion mass spectrometry (SIMS) and secondary neutrals mass spectrometry (SNMS) indicated that the corrosion product was not uniform with depth. However, no clear stratification was apparent. Indeed, counts obtained for carbonate, phosphate and oxide were well correlated within the depth range probed by SIMS. SNMS showed relationships existed between carbon, calcium, iron, and phosphorus within the bulk of the scale, as well as at the surface. SIMS imaging confirmed the relationship between calcium and lead and suggested there might also be an association between chloride and phosphorus.

Techniques, analysis, and noise in a Salt Lake Valley 4D gravity experiment

USGS Publications Warehouse

Gettings, P.; Chapman, D.S.; Allis, R.

2008-01-01

Repeated high-precision gravity measurements using an automated gravimeter and analysis of time series of 1-Hz samples allowed gravity measurements to be made with an accuracy of 5 ??Gal or better. Nonlinear instrument drift was removed using a new empirical staircase function built from multiple station loops. The new technique was developed between March 1999 and September 2000 in a pilot study conducted in the southern Salt Lake Valley along an east-west profile of eight stations from the Wasatch Mountains to the Jordan River. Gravity changes at eight profile stations were referenced to a set of five stations in the northern Salt Lake Valley, which showed residual signals of <10 ??Gal in amplitude, assuming a reference station near the Great Salt Lake to be stable. Referenced changes showed maximum amplitudes of -40 through +40 ??Gal at profile stations, with minima in summer 1999, maxima in winter 1999-2000, and some decrease through summer 2000. Gravity signals were likely a composite of production-induced changes monitored by well-water levels, elevation changes, precipitation-induced vadose-zone changes, and local irrigation effects for which magnitudes were estimated quantitatively. ?? 2008 Society of Exploration Geophysicists. All rights reserved.

Plasma metabolic profiling of dairy cows affected with clinical ketosis using LC/MS technology.

PubMed

Li, Y; Xu, C; Xia, C; Zhang, Hy; Sun, Lw; Gao, Y

2014-01-01

Ketosis in dairy cattle is an important metabolic disorder. Currently, the plasma metabolic profile of ketosis as determined using liquid chromatography-mass spectrometry (LC/MS) has not been reported. To investigate plasma metabolic profiles from cows with clinical ketosis in comparison to control cows. Twenty Holstein dairy cows were divided into two groups based on clinical signs and plasma β-hydroxybutyric acid and glucose concentrations 7-21 days postpartum: clinical ketosis and control cows. Plasma metabolic profiles were analyzed using LC/MS. Data were processed using principal component analysis and orthogonal partial least-squares discriminant analysis. Compared to control cows, the levels of valine, glycine, glycocholic, tetradecenoic acid, and palmitoleic acid increased significantly in clinical ketosis. On the other hand, the levels of arginine, aminobutyric acid, leucine/isoleucine, tryptophan, creatinine, lysine, norcotinine, and undecanoic acid decreased markedly. Our results showed that the metabolic changes in cows with clinical ketosis involve complex metabolic networks and signal transduction. These results are important for future studies elucidating the pathogenesis, diagnosis, and prevention of clinical ketosis in dairy cows.

A multivariate approach to the study of the composting process by means of analytical electrofocusing.

PubMed

Grigatti, Marco; Cavani, Luciano; Ciavatta, Claudio

2007-01-01

Three blends formed by: agro-industrial waste, wastewater sewage sludge, and their mixture, blended with tree pruning as bulking agent, were composted over a 3-month period. During the composting process the blends were monitored for the main physical and chemical characteristics. Electrofocusing (EF) was carried out on the extracted organic matter. The EF profiles were analyzed by principal component analysis (PCA) in order to assess the suitability of EF to evaluate the stabilisation level during the composting process. Throughout the process, the blends showed a general shifting of focused bands, from low to high pH, even though the compost origin affected the EF profiles. If the EF profile is analyzed by dividing it into pH regions, the interpretation of the results can be affected by the origin of compost. A good clustering of compost samples depending on the process time was obtained by analyzing the whole profile by PCA. Analysis of EF results with PCA represents a useful analytical technique to study the evolution and the stabilisation of composted organic matter.

Analysis of adolescent profiles by gender: strengths, attitudes toward violence and sexism.

PubMed

Ferragut, Marta; Blanca, Maria J; Ortiz-Tallo, Margarita

2014-02-20

The present study analyzes the profiles of boys and girls, considering gender, in the early stages of adolescence in the variables of character strengths, attitudes toward diversity and violence, and sexism. The aim is to explore the gender differences, whether the variables in each set differ from one another and whether these differences are maintained in profiles for boys and girls. The participants were 527 students (mean age = 12.21 and SD = 0.53) from the city of Málaga (Spain). Profile analysis was used to analyze data. The results, using an alpha of 0.0021 for each contrast, indicate that boys and girls differ in their character strengths, particularly in the case of girls, whose prominent strengths relate to pro-social behavior and peer relationships, where Cohen´s d are higher than .30. Moreover, boys justify attitudes of violence to a greater extent (Cohen´s d from .44 to .81) and show greater agreement with sexist beliefs (d = .63). The research suggests that it would be of interest to encourage advancement in character strengths at this age.

Microsatellite analysis of Fasciola spp. in Egypt.

PubMed

Dar, Yasser; Amer, Said; Courtioux, Bertrand; Dreyfuss, Gilles

2011-12-01

Recently, the topic of diversity in Fasciola population in Egypt is controversial. The present study was performed to study the genetic diversity of isolated flukes based on microsatellites markers. Fasciola worms were collected from different hosts and geographical locations in Egypt. Control samples of Fasciola hepatica from France as well as Fasciola gigantica from Cameroon were included in the study. Collected flukes were identified morphologically and subjected for analysis using four microsatellite markers. Results of microsatellite profile (FM1 and FM2) proved that both species of Fasciola are distributed in Egypt irrespective of geographical location and host. Nevertheless, the microsatellite profile of some analyzed loci (FM2 and FM3) proved that Egyptian flukes showed more alleles compared to the reference ones. Differences of microsatellite profile in Egyptian isolates than that of corresponding reference samples indicate the remarkable diversity of these isolates. The present results highlighted the utility of microsatellite profile to discriminate between Fasciola species and to elucidate the diversity within the species. To our knowledge, this is the first time to study microsatellite polymorphism in Fasciola populations in Egypt.

Analysis of asymmetric property with DC bias current on thin-film magnetoimpedance element

NASA Astrophysics Data System (ADS)

Kikuchi, Hiroaki; Sumida, Chihiro

2018-05-01

We theoretically analyzed the magnetoimpedance profile of a thin-film element with a DC bias current using the bias susceptibility theory and Maxwell's equations. Although the analysis model predicts that an element with a rectangular cross section shows symmetric impedance property with respect to the Z-axis with DC bias current, the experimental results showed asymmetric properties. Taking the shape imbalance and trapezoidal cross section of the element into account, we explained the asymmetric impedance properties qualitatively.

Clinical Profiles of Children with Disruptive Behaviors Based on the Severity of Their Conduct Problems, Callous-Unemotional Traits and Emotional Difficulties.

PubMed

Andrade, Brendan F; Sorge, Geoff B; Na, Jennifer Jiwon; Wharton-Shukster, Erika

2015-08-01

This study identified clinical profiles of referred children based on the severity of callous-unemotional (CU) traits, emotional difficulties, and conduct problems. Parents of 166 children (132 males) aged 6-12 years referred to a hospital clinic because of disruptive behavior completed measures to assess these key indicators, and person-centered analysis was used to identify profiles. Four distinct profiles were identified that include: (1) Children low in severity on the three domains, (2) Children high in severity on the three domains, (3) Children high in severity in conduct problems and CU traits with minimal emotional difficulties, and (4) Children high in severity in conduct problems and emotional difficulties with minimal CU traits. Profiles differed in degree of aggression and behavioral impairment. Findings show that clinic-referred children with disruptive behaviors can be grouped based on these important indicators into profiles that have important implications for assessment and treatment selection.

CP-ABE Based Privacy-Preserving User Profile Matching in Mobile Social Networks

PubMed Central

Cui, Weirong; Du, Chenglie; Chen, Jinchao

2016-01-01

Privacy-preserving profile matching, a challenging task in mobile social networks, is getting more attention in recent years. In this paper, we propose a novel scheme that is based on ciphertext-policy attribute-based encryption to tackle this problem. In our scheme, a user can submit a preference-profile and search for users with matching-profile in decentralized mobile social networks. In this process, no participant’s profile and the submitted preference-profile is exposed. Meanwhile, a secure communication channel can be established between the pair of successfully matched users. In contrast to existing related schemes which are mainly based on the secure multi-party computation, our scheme can provide verifiability (both the initiator and any unmatched user cannot cheat each other to pretend to be matched), and requires few interactions among users. We provide thorough security analysis and performance evaluation on our scheme, and show its advantages in terms of security, efficiency and usability over state-of-the-art schemes. PMID:27337001

CP-ABE Based Privacy-Preserving User Profile Matching in Mobile Social Networks.

PubMed

Cui, Weirong; Du, Chenglie; Chen, Jinchao

2016-01-01

Privacy-preserving profile matching, a challenging task in mobile social networks, is getting more attention in recent years. In this paper, we propose a novel scheme that is based on ciphertext-policy attribute-based encryption to tackle this problem. In our scheme, a user can submit a preference-profile and search for users with matching-profile in decentralized mobile social networks. In this process, no participant's profile and the submitted preference-profile is exposed. Meanwhile, a secure communication channel can be established between the pair of successfully matched users. In contrast to existing related schemes which are mainly based on the secure multi-party computation, our scheme can provide verifiability (both the initiator and any unmatched user cannot cheat each other to pretend to be matched), and requires few interactions among users. We provide thorough security analysis and performance evaluation on our scheme, and show its advantages in terms of security, efficiency and usability over state-of-the-art schemes.

Aging and well-being in French older adults regularly practicing physical activity: a self-determination perspective.

PubMed

Ferrand, Claude; Nasarre, Sandra; Hautier, Christophe; Bonnefoy, Marc

2012-04-01

The purpose of this study was to identify the motivational profiles of physically active older adults and to achieve a better understanding of their perceived motives to explain their regular physical activity behavior in relation to self-determination theory (SDT). To address these aims, this study used quantitative and qualitative approaches. Older adults (n = 92; M = 74.95, SD = 4.6) completed the French version of the Sport Motivational Scale. A cluster analysis showed two motivational profiles with differential motivational patterns. The first was named the high combined profile, with high scores on intrinsic motivation and introjected regulation and low levels of external regulation. The second profile was the low to moderate motivational profile, with low scores on intrinsic motivation and moderate scores on introjected regulation. The qualitative study's results demonstrate the usefulness of SDT in explaining the relationship between these motivational profiles and the intertwining of the three basic psychological needs.

Non-targeted metabolite profiling of citrus juices as a tool for variety discrimination and metabolite flow analysis.

PubMed

Arbona, Vicent; Iglesias, Domingo J; Gómez-Cadenas, Aurelio

2015-02-05

Genetic diversity of citrus includes intrageneric hybrids, cultivars arising from cross-pollination and/or somatic mutations with particular biochemical compounds such as sugar, acids and secondary metabolite composition. Secondary metabolite profiles of juices from 12 commercial varieties grouped into blonde and navel types, mandarins, lemons and grapefruits were analyzed by LC/ESI-QTOF-MS. HCA on metabolite profiling data revealed the existence of natural groups demarcating fruit types and varieties associated to specific composition patterns. The unbiased classification provided by HCA was used for PLS-DA to find the potential variables (mass chromatographic features) responsible for the classification. Abscisic acid and derivatives, several flavonoids and limonoids were identified by analysis of mass spectra. To facilitate interpretation, metabolites were represented as flow charts depicting biosynthetic pathways. Mandarins 'Fortune' and 'Hernandina' along with oranges showed higher ABA contents and ABA degradation products were present as glycosylated forms in oranges and certain mandarins. All orange and grapefruit varieties showed high limonin contents and its glycosylated form, that was only absent in lemons. The rest of identified limonoids were highly abundant in oranges. Particularly, Sucrenya cultivar showed a specific accumulation of obacunone and limonoate A-ring lactone. Polymethoxylated flavanones (tangeritin and isomers) were absolutely absent from lemons and grapefruits whereas kaempferol deoxyhexose hexose isomer #2, naringin and neohesperidin were only present in these cultivars. Analysis of relative metabolite build-up in closely-related genotypes allowed the efficient demarcation of cultivars and suggested the existence of genotype-specific regulatory mechanisms underlying the differential metabolite accumulation.

Distribution and health risk assessment of organochlorine pesticides (OCPs) in industrial site soils: a case study of urban renewal in Beijing, China.

PubMed

Yang, Wenrui; Wang, Rusong; Zhou, Chuanbin; Li, Feng

2009-01-01

Abstract A field survey was conducted in a contaminated industrial site of southern Beijing, China to investigate the contents and distribution of the organochlorine pesticides (alpha-, beta-, gamma-, delta-HCH, p,p'-DDT, p,p'-DDE, p,p'-DDD and o,p'-DDT) in the profiles of soil, and a health risk assessment was carried out with CalTOX multimedia exposure model. Results showed that mean concentrations of total hexachlorocyclohexane isomers (HCHs) and total dichlorodiphenyltrichloroethane isomers (DDXs) in soils were in the range of 13.20-148.71 mg/kg, and 3.02-67.43 mg/kg, respectively. Organochlorine pesticides (OCPs) content peaked in the surface and declined in soil profile with depth. The amounts of HCHs in three profiles of soil were larger than DDXs. Composition analysis indicated that there was a trend of degradation of OCPs in the site, but the mean of HCHs and DDXs concentration were over the state warning standard limit (HCHs, 0.50 mg/kg; DDXs, 0.50 mg/kg). According to current land use development, health risk assessment with CalTOX and Monte Carlo analysis showed that health risks mainly came from two exposure pathways: dermal uptake and inhalation, and the total risk values all exceeded the general acceptable health risk value (10-6). The sensitivity analysis indicated that five parameters significantly contributed to total risk.

Geomorphic effectiveness of long profile shape and role of inherent geological controls, Ganga River Basin, India

NASA Astrophysics Data System (ADS)

Sonam, Sonam; Jain, Vikrant

2017-04-01

River long profile is one of the fundamental geomorphic parameters which provides a platform to study interaction of geological and geomorphic processes at different time scales. Long profile shape is governed by geological processes at 10 ^ 5 - 10 ^ 6 years' time scale and it controls the modern day (10 ^ 0 - 10 ^ 1 years' time scale) fluvial processes by controlling the spatial variability of channel slope. Identification of an appropriate model for river long profile may provide a tool to analyse the quantitative relationship between basin geology, profile shape and its geomorphic effectiveness. A systematic analysis of long profiles has been carried for the Himalayan tributaries of the Ganga River basin. Long profile shape and stream power distribution pattern is derived using SRTM DEM data (90 m spatial resolution). Peak discharge data from 34 stations is used for hydrological analysis. Lithological variability and major thrusts are marked along the river long profile. The best fit of long profile is analysed for power, logarithmic and exponential function. Second order exponential function provides the best representation of long profiles. The second order exponential equation is Z = K1*exp(-β1*L) + K2*exp(-β2*L), where Z is elevation of channel long profile, L is the length, K and β are coefficients of the exponential function. K1 and K2 are the proportion of elevation change of the long profile represented by β1 (fast) and β2 (slow) decay coefficients of the river long profile. Different values of coefficients express the variability in long profile shapes and is related with the litho-tectonic variability of the study area. Channel slope of long profile is estimated taking the derivative of exponential function. Stream power distribution pattern along long profile is estimated by superimposing the discharge and long profile slope. Sensitivity analysis of stream power distribution with decay coefficients of the second order exponential equation is evaluated for a range of coefficient values. Our analysis suggests that the amplitude of stream power peak value is dependent on K1, the proportion of elevation change coming under the fast decay exponent and the location of stream power peak is dependent of the long profile decay coefficient (β1). Different long profile shapes owing to litho-tectonic variability across the Himalayas are responsible for spatial variability of stream power distribution pattern. Most of the stream power peaks lie in the Higher Himalaya. In general, eastern rivers have higher stream power in hinterland area and low stream power in the alluvial plains. This is responsible for, 1) higher erosion rate and sediment supply in hinterland of eastern rivers, 2) the incised and stable nature of channels in the western alluvial plains and 3) aggrading channels with dynamic nature in the eastern alluvial plains. Our study shows that the spatial variability of litho-units defines the coefficients of long profile function which in turn controls the position and magnitude of stream power maxima and hence the geomorphic variability in a fluvial system.

Transport simulation of EAST long-pulse H-mode discharge with integrated modeling

NASA Astrophysics Data System (ADS)

Wu, M. Q.; Li, G. Q.; Chen, J. L.; Du, H. F.; Gao, X.; Ren, Q. L.; Li, K.; Chan, Vincent; Pan, C. K.; Ding, S. Y.; Jian, X.; Zhu, X.; Lian, H.; Qian, J. P.; Gong, X. Z.; Zang, Q.; Duan, Y. M.; Liu, H. Q.; Lyu, B.

2018-04-01

In the 2017 EAST experimental campaign, a steady-state long-pulse H-mode discharge lasting longer than 100 s has been obtained using only radio frequency heating and current drive, and the confinement quality is slightly better than standard H-mode, H98y2 ~ 1.1, with stationary peaked electron temperature profiles. Integrated modeling of one long-pulse H-mode discharge in the 2016 EAST experimental campaign has been performed with equilibrium code EFIT, and transport codes TGYRO and ONETWO under integrated modeling framework OMFIT. The plasma current is fully-noninductively driven with a combination of ~2.2 MW LHW, ~0.3 MW ECH and ~1.1 MW ICRF. Time evolution of the predicted electron and ion temperature profiles through integrated modeling agree closely with that from measurements. The plasma current (I p ~ 0.45 MA) and electron density are kept constantly. A steady-state is achieved using integrated modeling, and the bootstrap current fraction is ~28%, the RF drive current fraction is ~72%. The predicted current density profile matches the experimental one well. Analysis shows that electron cyclotron heating (ECH) makes large contribution to the plasma confinement when heating in the core region while heating in large radius does smaller improvement, also a more peaked LHW driven current profile is got when heating in the core. Linear analysis shows that the high-k modes instability (electron temperature gradient driven modes) is suppressed in the core region where exists weak electron internal transport barriers. The trapped electron modes dominates in the low-k region, which is mainly responsible for driving the electron energy flux. It is found that the ECH heating effect is very local and not the main cause to sustained the good confinement, the peaked current density profile has the most important effect on plasma confinement improvement. Transport analysis of the long-pulse H-mode experiments on EAST will be helpful to build future experiments.

Dataset on growth factor levels and insulin use in patients with diabetes mellitus and incident breast cancer.

PubMed

Wintrob, Zachary A P; Hammel, Jeffrey P; Nimako, George K; Gaile, Dan P; Forrest, Alan; Ceacareanu, Alice C

2017-04-01

Growth factor profiles could be influenced by the utilization of exogenous insulin. The data presented shows the relationship between pre-existing use of injectable insulin in women diagnosed with breast cancer and type 2 diabetes mellitus, the growth factor profiles at the time of breast cancer diagnosis, and subsequent cancer outcomes. A Pearson correlation analysis evaluating the relationship between growth factors stratified by of insulin use and controls is also provided.

An Analysis of a Ray Trace Experiment on the Underwater Range at Dabob Bay

DTIC Science & Technology

1975-03-01

with a local oscil- lator havIng a frequency unique to that hyIrophone. ’The outputs of these oscillators are preamplified and fed to a multiplexer...conmpared with a Eeist value given by the reference gradient plus a designated change from 5 to 30%. When the computed gradient exceeds the test value...mid profile was also performed. This comparison was designed to show the effects of using a single profile to describe the environment when the actual

A maximum pseudo-profile likelihood estimator for the Cox model under length-biased sampling

PubMed Central

Huang, Chiung-Yu; Qin, Jing; Follmann, Dean A.

2012-01-01

This paper considers semiparametric estimation of the Cox proportional hazards model for right-censored and length-biased data arising from prevalent sampling. To exploit the special structure of length-biased sampling, we propose a maximum pseudo-profile likelihood estimator, which can handle time-dependent covariates and is consistent under covariate-dependent censoring. Simulation studies show that the proposed estimator is more efficient than its competitors. A data analysis illustrates the methods and theory. PMID:23843659

Efficacy and safety profile of xanthines in COPD: a network meta-analysis.

PubMed

Cazzola, Mario; Calzetta, Luigino; Barnes, Peter J; Criner, Gerard J; Martinez, Fernando J; Papi, Alberto; Gabriella Matera, Maria

2018-06-30

Theophylline can still have a role in the management of stable chronic obstructive pulmonary disease (COPD), but its use remains controversial, mainly due to its narrow therapeutic window. Doxofylline, another xanthine, is an effective bronchodilator and displays a better safety profile than theophylline. Therefore, we performed a quantitative synthesis to compare the efficacy and safety profile of different xanthines in COPD.The primary end-point of this meta-analysis was the impact of xanthines on lung function. In addition, we assessed the risk of adverse events by normalising data on safety as a function of person-weeks. Data obtained from 998 COPD patients were selected from 14 studies and meta-analysed using a network approach.The combined surface under the cumulative ranking curve (SUCRA) analysis of efficacy (change from baseline in forced expiratory volume in 1 s) and safety (risk of adverse events) showed that doxofylline was superior to aminophylline (comparable efficacy and significantly better safety), bamiphylline (significantly better efficacy and comparable safety), and theophylline (comparable efficacy and significantly better safety).Considering the overall efficacy/safety profile of the investigated agents, the results of this quantitative synthesis suggest that doxofylline seems to be the best xanthine for the treatment of COPD. Copyright ©ERS 2018.

Integrated genomic classification of melanocytic tumors of the central nervous system using mutation analysis, copy number alterations and DNA methylation profiling.

PubMed

Griewank, Klaus; Koelsche, Christian; van de Nes, Johannes A P; Schrimpf, Daniel; Gessi, Marco; Möller, Inga; Sucker, Antje; Scolyer, Richard A; Buckland, Michael E; Murali, Rajmohan; Pietsch, Torsten; von Deimling, Andreas; Schadendorf, Dirk

2018-06-11

In the central nervous system, distinguishing primary leptomeningeal melanocytic tumors from melanoma metastases and predicting their biological behavior solely using histopathologic criteria can be challenging. We aimed to assess the diagnostic and prognostic value of integrated molecular analysis. Targeted next-generation-sequencing, array-based genome-wide methylation analysis and BAP1 immunohistochemistry was performed on the largest cohort of central nervous system melanocytic tumors analyzed to date, incl. 47 primary tumors of the central nervous system, 16 uveal melanomas. 13 cutaneous melanoma metastasis and 2 blue nevus-like melanomas. Gene mutation, DNA-methylation and copy-number profiles were correlated with clinicopathological features. Combining mutation, copy-number and DNA-methylation profiles clearly distinguished cutaneous melanoma metastases from other melanocytic tumors. Primary leptomeningeal melanocytic tumors, uveal melanomas and blue nevus-like melanoma showed common DNA-methylation, copy-number alteration and gene mutation signatures. Notably, tumors demonstrating chromosome 3 monosomy and BAP1 alterations formed a homogeneous subset within this group. Integrated molecular profiling aids in distinguishing primary from metastatic melanocytic tumors of the central nervous system. Primary leptomeningeal melanocytic tumors, uveal melanoma and blue nevus-like melanoma share molecular similarity with chromosome 3 and BAP1 alterations markers of poor prognosis. Copyright ©2018, American Association for Cancer Research.

Research note: Molecular subtyping of Salmonella enterica serovar Tshiongwe recently isolated in Malaysia during 2001-2002.

PubMed

Thong, Kwai Lin; Bakeri, Shamsilawani Ahmad; Lai, Kin Seng; Koh, Yin Tee; Taib, Mohd Zainuldin; Lim, V K E; Yasin, Rohani Md

2004-03-01

Pulsed field gel electrophoresis (PFGE) and antimicrobial susceptibility analysis were undertaken on twenty-three strains of Salmonella enterica serovar Tshiongwe, an unusual serovar, which recently emerged in Malaysia. Antimicrobial susceptibility analysis showed that all the strains were sensitive to ampicilin, chloramphenicol, cotrimoxazole, and kanamycin. Twenty (87%) and 8 (3.5%) strains had resistance to tetracycline and streptomycin respectively. PFGE analysis subtyped 23 strains into 10 profiles (Dice coefficient of similarity, F = 0.7-1.0). The predominant profile, X1 was found in both clinical and environmental isolates and was widely distributed in different parts of Malaysia during the study period. In addition, isolates recovered from food, a hand-towel, apron and the surface of a table-top in one particular location had unique, indistinguishable profiles (X4/4a) and identical antibiograms. Similarly, isolates from cooked meat and a chopping board had PFGE profiles similar to some human isolates. These probably indicated cross-contamination and poor hygiene in food practices, hence contributing to Salmonellosis. Factors causing the emergence of this rare Salmonella serovar being responsible for food poisoning episodes during the study period remained unclear. The study reiterated the usefulness and versatility of PFGE in the molecular subtyping of this rare Salmonella serovar in Malaysia.

Multi-locus variable number tandem repeat analysis of 7th pandemic Vibrio cholerae

PubMed Central

2012-01-01

Background Seven pandemics of cholera have been recorded since 1817, with the current and ongoing pandemic affecting almost every continent. Cholera remains endemic in developing countries and is still a significant public health issue. In this study we use multilocus variable number of tandem repeats (VNTRs) analysis (MLVA) to discriminate between isolates of the 7th pandemic clone of Vibrio cholerae. Results MLVA of six VNTRs selected from previously published data distinguished 66 V. cholerae isolates collected between 1961–1999 into 60 unique MLVA profiles. Only 4 MLVA profiles consisted of more than 2 isolates. The discriminatory power was 0.995. Phylogenetic analysis showed that, except for the closely related profiles, the relationships derived from MLVA profiles were in conflict with that inferred from Single Nucleotide Polymorphism (SNP) typing. The six SNP groups share consensus VNTR patterns and two SNP groups contained isolates which differed by only one VNTR locus. Conclusions MLVA is highly discriminatory in differentiating 7th pandemic V. cholerae isolates and MLVA data was most useful in resolving the genetic relationships among isolates within groups previously defined by SNPs. Thus MLVA is best used in conjunction with SNP typing in order to best determine the evolutionary relationships among the 7th pandemic V. cholerae isolates and for longer term epidemiological typing. PMID:22624829

Social network utilization (Facebook) & e-Professionalism among medical students.

PubMed

Jawaid, Masood; Khan, Muhammad Hassaan; Bhutto, Shahzadi Nisar

2015-01-01

To find out the frequency and contents of online social networking (Facebook) among medical students of Dow University of Health Sciences. The sample of the study comprised of final year students of two medical colleges of Dow University of Health Sciences - Karachi. Systematic search for the face book profiles of the students was carried out with a new Facebook account. In the initial phase of search, it was determined whether each student had a Facebook account and the status of account as ''private'' ''intermediate'' or ''public'' was also sought. In the second phase of the study, objective information including gender, education, personal views, likes, tag pictures etc. were recorded for the publicly available accounts. An in depth qualitative content analysis of the public profiles of ten medical students, selected randomly with the help of random number generator technique was conducted. Social networking with Facebook is common among medical students with 66.9% having an account out of a total 535 students. One fifth of profiles 18.9% were publicly open, 36.6% profiles were private and 56.9% were identified to have an intermediate privacy setting, having customized settings for the profile information. In-depth analysis of some public profiles showed that potentially unprofessional material mostly related to violence and politics was posted by medical students. The usage of social network (Facebook) is very common among students of the university. Some unprofessional posts were also found on students' profiles mostly related to violence and politics.

Univariate and multivariate molecular spectral analyses of lipid related molecular structural components in relation to nutrient profile in feed and food mixtures.

PubMed

Abeysekara, Saman; Damiran, Daalkhaijav; Yu, Peiqiang

2013-02-01

The objectives of this study were (i) to determine lipid related molecular structures components (functional groups) in feed combination of cereal grain (barley, Hordeum vulgare) and wheat (Triticum aestivum) based dried distillers grain solubles (wheat DDGSs) from bioethanol processing at five different combination ratios using univariate and multivariate molecular spectral analyses with infrared Fourier transform molecular spectroscopy, and (ii) to correlate lipid-related molecular-functional structure spectral profile to nutrient profiles. The spectral intensity of (i) CH(3) asymmetric, CH(2) asymmetric, CH(3) symmetric and CH(2) symmetric groups, (ii) unsaturation (CC) group, and (iii) carbonyl ester (CO) group were determined. Spectral differences of functional groups were detected by hierarchical cluster analysis (HCA) and principal components analysis (PCA). The results showed that the combination treatments significantly inflicted modifications (P<0.05) in nutrient profile and lipid related molecular spectral intensity (CH(2) asymmetric stretching peak height, CH(2) symmetric stretching peak height, ratio of CH(2) to CH(3) symmetric stretching peak intensity, and carbonyl peak area). Ratio of CH(2) to CH(3) symmetric stretching peak intensity, and carbonyl peak significantly correlated with nutrient profiles. Both PCA and HCA differentiated lipid-related spectrum. In conclusion, the changes of lipid molecular structure spectral profiles through feed combination could be detected using molecular spectroscopy. These changes were associated with nutrient profiles and functionality. Copyright © 2012 Elsevier B.V. All rights reserved.

Monitoring of pistachio (Pistacia Vera) ripening by high field nuclear magnetic resonance spectroscopy.

PubMed

Sciubba, Fabio; Avanzato, Damiano; Vaccaro, Angela; Capuani, Giorgio; Spagnoli, Mariangela; Di Cocco, Maria Enrica; Tzareva, Irina Nikolova; Delfini, Maurizio

2017-04-01

The metabolic profiling of pistachio (Pistacia vera) aqueous extracts from two different cultivars, namely 'Bianca' and 'Gloria', was monitored over the months from May to September employing high field NMR spectroscopy. A large number of water-soluble metabolites were assigned by means of 1D and 2D NMR experiments. The change in the metabolic profiles monitored over time allowed the pistachio development to be investigated. Specific temporal trends of amino acids, sugars, organic acids and other metabolites were observed and analysed by multivariate Partial Least Squares (PLS) analysis. Statistical analysis showed that while in the period from May to September there were few differences between the two cultivars, the ripening rate was different.

A meta-analysis of differences in IQ profiles between individuals with Asperger's disorder and high-functioning autism.

PubMed

Chiang, Hsu-Min; Tsai, Luke Y; Cheung, Ying Kuen; Brown, Alice; Li, Huacheng

2014-07-01

A meta-analysis was performed to examine differences in IQ profiles between individuals with Asperger's disorder (AspD) and high-functioning autism (HFA). Fifty-two studies were included for this study. The results showed that (a) individuals with AspD had significantly higher full-scale IQ, verbal IQ (VIQ), and performance IQ (PIQ) than did individuals with HFA; (b) individuals with AspD had significantly higher VIQ than PIQ; and (c) VIQ was similar to PIQ in individuals with HFA. These findings seem to suggest that AspD and HFA are two different subtypes of Autism. The implications of the present findings to DSM-5 Autism Spectrum Disorder are discussed.

RASopathies are associated with a distinct personality profile.

PubMed

Bizaoui, Varoona; Gage, Jessica; Brar, Rita; Rauen, Katherine A; Weiss, Lauren A

2018-06-01

Personality is a complex, yet partially heritable, trait. Although some Mendelian diseases like Williams-Beuren syndrome are associated with a particular personality profile, studies have failed to assign the personality features to a single gene or pathway. As a family of monogenic disorders caused by mutations in the Ras/MAPK pathway known to influence social behavior, RASopathies are likely to provide insight into the genetic basis of personality. Eighty subjects diagnosed with cardiofaciocutaneous syndrome, Costello syndrome, neurofibromatosis type 1, and Noonan syndrome were assessed using a parent-report BFQ-C (Big Five Questionnaire for Children) evaluating agreeableness, extraversion, conscientiousness, intellect/openness, and neuroticism, along with 55 unaffected sibling controls. A short questionnaire was added to assess sense of humor. RASopathy subjects and sibling controls were compared for individual components of personality, multidimensional personality profiles, and individual questions using Student tests, analysis of variance, and principal component analysis. RASopathy subjects were given lower scores on average compared to sibling controls in agreeableness, extraversion, conscientiousness, openness, and sense of humor, and similar scores in neuroticism. When comparing the multidimensional personality profile between groups, RASopathies showed a distinct profile from unaffected siblings, but no difference in this global profile was found within RASopathies, revealing a common profile for the Ras/MAPK-related disorders. In addition, several syndrome-specific strengths or weaknesses were observed in individual domains. We describe for the first time an association between a single pathway and a specific personality profile, providing a better understanding of the genetics underlying personality, and new tools for tailoring educational and behavioral approaches for individuals with RASopathies. © 2018 Wiley Periodicals, Inc.

Influenza vaccine response profiles are affected by vaccine preparation and preexisting immunity, but not HIV infection.

PubMed

Berger, Christoph T; Greiff, Victor; Mehling, Matthias; Fritz, Stefanie; Meier, Marc A; Hoenger, Gideon; Conen, Anna; Recher, Mike; Battegay, Manuel; Reddy, Sai T; Hess, Christoph

2015-01-01

Vaccines dramatically reduce infection-related morbidity and mortality. Determining factors that modulate the host response is key to rational vaccine design and demands unsupervised analysis. To longitudinally resolve influenza-specific humoral immune response dynamics we constructed vaccine response profiles of influenza A- and B-specific IgM and IgG levels from 42 healthy and 31 HIV infected influenza-vaccinated individuals. Pre-vaccination antibody levels and levels at 3 predefined time points after vaccination were included in each profile. We performed hierarchical clustering on these profiles to study the extent to which HIV infection associated immune dysfunction, adaptive immune factors (pre-existing influenza-specific antibodies, T cell responses), an innate immune factor (Mannose Binding Lectin, MBL), demographic characteristics (gender, age), or the vaccine preparation (split vs. virosomal) impacted the immune response to influenza vaccination. Hierarchical clustering associated vaccine preparation and pre-existing IgG levels with the profiles of healthy individuals. In contrast to previous in vitro and animal data, MBL levels had no impact on the adaptive vaccine response. Importantly, while HIV infected subjects with low CD4 T cell counts showed a reduced magnitude of their vaccine response, their response profiles were indistinguishable from those of healthy controls, suggesting quantitative but not qualitative deficits. Unsupervised profile-based analysis ranks factors impacting the vaccine-response by relative importance, with substantial implications for comparing, designing and improving vaccine preparations and strategies. Profile similarity between HIV infected and HIV negative individuals suggests merely quantitative differences in the vaccine response in these individuals, offering a rationale for boosting strategies in the HIV infected population.

Spatial-phase-modulation-based study of polyvinyl-alcohol/acrylamide photopolymers in the low spatial frequency range.

PubMed

Gallego, Sergi; Márquez, André; Méndez, David; Marini, Stephan; Beléndez, Augusto; Pascual, Inmaculada

2009-08-01

Photopolymers are appealing materials for the fabrication of diffractive optical elements (DOEs). We evaluate the possibilities of polyvinyl-alcohol/acrylamide-based photopolymers to store diffractive elements with low spatial frequencies. We record gratings with different spatial frequencies in the material and analyze the material behavior measuring the transmitted and the reflected orders as a function of exposition. We study two different compositions for the photopolymer, with and without a cross-linker. The values of diffraction efficiency achieved for both compositions make the material suitable to record DOEs with long spatial periods. Assuming a Fermi-Dirac-function-based profile, we fitted the diffracted intensities (up to the eighth order) to obtain the phase profile of the recorded gratings. This analysis shows that it is possible to achieve a phase shift larger than 2pi rad with steep edges in the periodic phase profile. In the case of the measurements in reflection, we have obtained information dealing with the surface profile, which show that it has a smooth shape with an extremely large phase-modulation depth.

Comparative evaluation of rotary ProTaper, Profile, and conventional stepback technique on reduction in Enterococcus faecalis colony-forming units and vertical root fracture resistance of root canals.

PubMed

Singla, Mamta; Aggarwal, Vivek; Logani, Ajay; Shah, Naseem

2010-03-01

The purpose of this in vitro study was to evaluate the effect of various root canal instrumentation techniques with different instrument tapers on cleaning efficacy and resultant vertical root fracture (VRF) strength of the roots. Fifty human mandibular first premolar roots were enlarged to ISO size 20, inoculated with Enterococcus faecalis [ATCC2912] for 72 hours and divided into 5 groups: group I: prepared with .02 taper hand instruments ISO size 40; group II: Profile .04 taper size 40; group III: Profile .06 taper size 40; group IV: ProTaper size F4; and group V (control group) further divided into: Va: with bacterial inoculation and no mechanical instrumentation; and Group Vb: neither bacterial inoculation nor mechanical instrumentation. Cleaning efficacy was evaluated in terms of reduction of colony forming units (CFUs). The VRF strength was evaluated using D11 spreader as wedge in an Instron testing machine. Root canals instrumented with ProTaper and 6% Profile instruments showed maximum reduction in CFUs, with statistically insignificant difference between them. The VRF resistance decreased in all instrumented groups. The difference of VRF between 2% and 4% taper Profile groups was statistically insignificant (P = .195). One-way analysis of variance showed that canals instrumented with ProTaper F4 showed maximum reduction in VRF resistance compared with control uninstrumented group. Profile 6% taper instruments offer the advantage of maximum debridement without significant reduction in root fracture resistance. Copyright 2010 Mosby, Inc. All rights reserved.

Do recognizable lifetime eating disorder phenotypes naturally occur in a culturally asian population? A combined latent profile and taxometric approach.

PubMed

Thomas, Jennifer J; Eddy, Kamryn T; Ruscio, John; Ng, King Lam; Casale, Kristen E; Becker, Anne E; Lee, Sing

2015-05-01

We examined whether empirically derived eating disorder (ED) categories in Hong Kong Chinese patients (N = 454) would be consistent with recognizable lifetime ED phenotypes derived from latent structure models of European and American samples. We performed latent profile analysis (LPA) using indicator variables from data collected during routine assessment, and then applied taxometric analysis to determine whether latent classes were qualitatively versus quantitatively distinct. Latent profile analysis identified four classes: (i) binge/purge (47%); (ii) non-fat-phobic low-weight (34%); (iii) fat-phobic low-weight (12%); and (iv) overweight disordered eating (6%). Taxometric analysis identified qualitative (categorical) distinctions between the binge/purge and non-fat-phobic low-weight classes, and also between the fat-phobic and non-fat-phobic low-weight classes. Distinctions between the fat-phobic low-weight and binge/purge classes were indeterminate. Empirically derived categories in Hong Kong showed recognizable correspondence with recognizable lifetime ED phenotypes. Although taxometric findings support two distinct classes of low weight EDs, LPA findings also support heterogeneity among non-fat-phobic individuals. Copyright © 2015 John Wiley & Sons, Ltd and Eating Disorders Association.

Analysis of honeybush tea (Cyclopia spp.) volatiles by comprehensive two-dimensional gas chromatography using a single-stage thermal modulator.

PubMed

Ntlhokwe, Gaalebalwe; Tredoux, Andreas G J; Górecki, Tadeusz; Edwards, Matthew; Vestner, Jochen; Muller, Magdalena; Erasmus, Lené; Joubert, Elizabeth; Christel Cronje, J; de Villiers, André

2017-07-01

The applicability of comprehensive two-dimensional gas chromatography (GC×GC) using a single-stage thermal modulator was explored for the analysis of honeybush tea (Cyclopia spp.) volatile compounds. Headspace solid phase micro-extraction (HS-SPME) was used in combination with GC×GC separation on a non-polar × polar column set with flame ionisation (FID) detection for the analysis of fermented Cyclopia maculata, Cyclopia subternata and Cyclopia genistoides tea infusions of a single harvest season. Method optimisation entailed evaluation of the effects of several experimental parameters on the performance of the modulator, the choice of columns in both dimensions, as well as the HS-SPME extraction fibre. Eighty-four volatile compounds were identified by co-injection of reference standards. Principal component analysis (PCA) showed clear differentiation between the species based on their volatile profiles. Due to the highly reproducible separations obtained using the single-stage thermal modulator, multivariate data analysis was simplified. The results demonstrate both the complexity of honeybush volatile profiles and the potential of GC×GC separation in combination with suitable data analysis techniques for the investigation of the relationship between sensory properties and volatile composition of these products. The developed method therefore offers a fast and inexpensive methodology for the profiling of honeybush tea volatiles. Graphical abstract Surface plot obtained for the GC×GC-FID analysis of honeybush tea volatiles.

Chaperone expression profiles correlate with distinct physiological states of Plasmodium falciparum in malaria patients

PubMed Central

2010-01-01

Background Molecular chaperones have been shown to be important in the growth of the malaria parasite Plasmodium falciparum and inhibition of chaperone function by pharmacological agents has been shown to abrogate parasite growth. A recent study has demonstrated that clinical isolates of the parasite have distinct physiological states, one of which resembles environmental stress response showing up-regulation of specific molecular chaperones. Methods Chaperone networks operational in the distinct physiological clusters in clinical malaria parasites were constructed using cytoscape by utilizing their clinical expression profiles. Results Molecular chaperones show distinct profiles in the previously defined physiologically distinct states. Further, expression profiles of the chaperones from different cellular compartments correlate with specific patient clusters. While cluster 1 parasites, representing a starvation response, show up-regulation of organellar chaperones, cluster 2 parasites, which resemble active growth based on glycolysis, show up-regulation of cytoplasmic chaperones. Interestingly, cytoplasmic Hsp90 and its co-chaperones, previously implicated as drug targets in malaria, cluster in the same group. Detailed analysis of chaperone expression in the patient cluster 2 reveals up-regulation of the entire Hsp90-dependent pro-survival circuitries. In addition, cluster 2 also shows up-regulation of Plasmodium export element (PEXEL)-containing Hsp40s thought to have regulatory and host remodeling roles in the infected erythrocyte. Conclusion In all, this study demonstrates an intimate involvement of parasite-encoded chaperones, PfHsp90 in particular, in defining pathogenesis of malaria. PMID:20719001

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam

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

Chai, Juanjuan; Kora, Guruprasad; Ahn, Tae-Hyuk

2014-10-09

To supply some background, phylogenetic studies have provided detailed knowledge on the evolutionary mechanisms of genes and species in Bacteria and Archaea. However, the evolution of cellular functions, represented by metabolic pathways and biological processes, has not been systematically characterized. Many clades in the prokaryotic tree of life have now been covered by sequenced genomes in GenBank. This enables a large-scale functional phylogenomics study of many computationally inferred cellular functions across all sequenced prokaryotes. Our results show a total of 14,727 GenBank prokaryotic genomes were re-annotated using a new protein family database, UniFam, to obtain consistent functional annotations for accuratemore » comparison. The functional profile of a genome was represented by the biological process Gene Ontology (GO) terms in its annotation. The GO term enrichment analysis differentiated the functional profiles between selected archaeal taxa. 706 prokaryotic metabolic pathways were inferred from these genomes using Pathway Tools and MetaCyc. The consistency between the distribution of metabolic pathways in the genomes and the phylogenetic tree of the genomes was measured using parsimony scores and retention indices. The ancestral functional profiles at the internal nodes of the phylogenetic tree were reconstructed to track the gains and losses of metabolic pathways in evolutionary history. In conclusion, our functional phylogenomics analysis shows divergent functional profiles of taxa and clades. Such function-phylogeny correlation stems from a set of clade-specific cellular functions with low parsimony scores. On the other hand, many cellular functions are sparsely dispersed across many clades with high parsimony scores. These different types of cellular functions have distinct evolutionary patterns reconstructed from the prokaryotic tree.« less

Uncovering the molecular secrets of inflammatory breast cancer biology: an integrated analysis of three distinct affymetrix gene expression datasets.

PubMed

Van Laere, Steven J; Ueno, Naoto T; Finetti, Pascal; Vermeulen, Peter; Lucci, Anthony; Robertson, Fredika M; Marsan, Melike; Iwamoto, Takayuki; Krishnamurthy, Savitri; Masuda, Hiroko; van Dam, Peter; Woodward, Wendy A; Viens, Patrice; Cristofanilli, Massimo; Birnbaum, Daniel; Dirix, Luc; Reuben, James M; Bertucci, François

2013-09-01

Inflammatory breast cancer (IBC) is a poorly characterized form of breast cancer. So far, the results of expression profiling in IBC are inconclusive due to various reasons including limited sample size. Here, we present the integration of three Affymetrix expression datasets collected through the World IBC Consortium allowing us to interrogate the molecular profile of IBC using the largest series of IBC samples ever reported. Affymetrix profiles (HGU133-series) from 137 patients with IBC and 252 patients with non-IBC (nIBC) were analyzed using unsupervised and supervised techniques. Samples were classified according to the molecular subtypes using the PAM50-algorithm. Regression models were used to delineate IBC-specific and molecular subtype-independent changes in gene expression, pathway, and transcription factor activation. Four robust IBC-sample clusters were identified, associated with the different molecular subtypes (P<0.001), all of which were identified in IBC with a similar prevalence as in nIBC, except for the luminal A subtype (19% vs. 42%; P<0.001) and the HER2-enriched subtype (22% vs. 9%; P<0.001). Supervised analysis identified and validated an IBC-specific, molecular subtype-independent 79-gene signature, which held independent prognostic value in a series of 871 nIBCs. Functional analysis revealed attenuated TGF-β signaling in IBC. We show that IBC is transcriptionally heterogeneous and that all molecular subtypes described in nIBC are detectable in IBC, albeit with a different frequency. The molecular profile of IBC, bearing molecular traits of aggressive breast tumor biology, shows attenuation of TGF-β signaling, potentially explaining the metastatic potential of IBC tumor cells in an unexpected manner. ©2013 AACR.

Histological analysis and identification of spermatogenesis-related genes in 2-, 6-, and 12-month-old sheep testes

NASA Astrophysics Data System (ADS)

Bai, Man; Sun, Limin; Zhao, Jia; Xiang, Lujie; Cheng, Xiaoyin; Li, Jiarong; Jia, Chao; Jiang, Huaizhi

2017-10-01

Testis development and spermatogenesis are vital factors that influence male animal fertility. In order to identify spermatogenesis-related genes and further provide a theory basis for finding biomarkers related to male sheep fertility, 2-, 6-, and 12-month-old Small Tail Han Sheep testes were selected to investigate the dynamic changes of sheep testis development. Hematoxylin-eosin routine staining and RNA-Seq technique were used to perform histological and transcriptome analysis for these testes. The results showed that 630, 102, and 322 differentially expressed genes (DEGs) were identified in 2- vs 6-month-old, 6- vs 12-month-old, and 2- vs 12-month-old testes, respectively. GO and KEGG analysis showed the following: DEGs in 2- vs 6-month-old testes were mainly related to the GO terms of sexual maturation and the pathways of multiple metabolism and biosynthesis; in 6- vs 12-month-old testes, most of the GO terms that DEGs involved in were related to metabolism and translation processes; the most significantly enriched pathway is the ribosome pathway. The union of DEGs in 2- vs 6-month-old, 6- vs 12-month-old, and 2- vs 12-month-old testes was categorized into eight profiles by series cluster. Subsequently, the eight profiles were classified into four model profiles and four co-expression networks were constructed based on the DEGs in these model profiles. Finally, 29 key regulatory genes related to spermatogenesis were identified in the four co-expression networks. The expression of 13 DEGs (CA3, APOH, MYOC, CATSPER4, SYT6, SERPINA10, DAZL, ADIPOR2, RAB13, CEP41, SPAG4, ODF1, and FRG1) was validated by RT-PCR.

Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme▿†

PubMed Central

Pourcel, Christine; Minandri, Fabrizia; Hauck, Yolande; D'Arezzo, Silvia; Imperi, Francesco; Vergnaud, Gilles; Visca, Paolo

2011-01-01

Acinetobacter baumannii is an important opportunistic pathogen responsible for nosocomial outbreaks, mostly occurring in intensive care units. Due to the multiplicity of infection sources, reliable molecular fingerprinting techniques are needed to establish epidemiological correlations among A. baumannii isolates. Multiple-locus variable-number tandem-repeat analysis (MLVA) has proven to be a fast, reliable, and cost-effective typing method for several bacterial species. In this study, an MLVA assay compatible with simple PCR- and agarose gel-based electrophoresis steps as well as with high-throughput automated methods was developed for A. baumannii typing. Preliminarily, 10 potential polymorphic variable-number tandem repeats (VNTRs) were identified upon bioinformatic screening of six annotated genome sequences of A. baumannii. A collection of 7 reference strains plus 18 well-characterized isolates, including unique types and representatives of the three international A. baumannii lineages, was then evaluated in a two-center study aimed at validating the MLVA assay and comparing it with other genotyping assays, namely, macrorestriction analysis with pulsed-field gel electrophoresis (PFGE) and PCR-based sequence group (SG) profiling. The results showed that MLVA can discriminate between isolates with identical PFGE types and SG profiles. A panel of eight VNTR markers was selected, all showing the ability to be amplified and good amounts of polymorphism in the majority of strains. Independently generated MLVA profiles, composed of an ordered string of allele numbers corresponding to the number of repeats at each VNTR locus, were concordant between centers. Typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. A database containing information and MLVA profiles for several A. baumannii strains is available from http://mlva.u-psud.fr/. PMID:21147956

Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra.

PubMed

Mantini, Dante; Petrucci, Francesca; Del Boccio, Piero; Pieragostino, Damiana; Di Nicola, Marta; Lugaresi, Alessandra; Federici, Giorgio; Sacchetta, Paolo; Di Ilio, Carmine; Urbani, Andrea

2008-01-01

Independent component analysis (ICA) is a signal processing technique that can be utilized to recover independent signals from a set of their linear mixtures. We propose ICA for the analysis of signals obtained from large proteomics investigations such as clinical multi-subject studies based on MALDI-TOF MS profiling. The method is validated on simulated and experimental data for demonstrating its capability of correctly extracting protein profiles from MALDI-TOF mass spectra. The comparison on peak detection with an open-source and two commercial methods shows its superior reliability in reducing the false discovery rate of protein peak masses. Moreover, the integration of ICA and statistical tests for detecting the differences in peak intensities between experimental groups allows to identify protein peaks that could be indicators of a diseased state. This data-driven approach demonstrates to be a promising tool for biomarker-discovery studies based on MALDI-TOF MS technology. The MATLAB implementation of the method described in the article and both simulated and experimental data are freely available at http://www.unich.it/proteomica/bioinf/.

Size–strain separation in diffraction line profile analysis

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

Scardi, P.; Ermrich, M.; Fitch, A.

Separation of size and strain effects on diffraction line profiles has been studied in a round robin involving laboratory instruments and synchrotron radiation beamlines operating with different radiation, optics, detectors and experimental configurations. The studied sample, an extensively ball milled iron alloy powder, provides an ideal test case, as domain size broadening and strain broadening are of comparable size. The high energy available at some synchrotron radiation beamlines provides the best conditions for an accurate analysis of the line profiles, as the size–strain separation clearly benefits from a large number of Bragg peaks in the pattern; high counts, reliable intensitymore » values in low-absorption conditions, smooth background and data collection at different temperatures also support the possibility to include diffuse scattering in the analysis, for the most reliable assessment of the line broadening effect. However, results of the round robin show that good quality information on domain size distribution and microstrain can also be obtained using standard laboratory equipment, even when patterns include relatively few Bragg peaks, provided that the data are of good quality in terms of high counts and low and smooth background.« less

Joint small-angle X-ray and neutron scattering data analysis of asymmetric lipid vesicles

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

Eicher, Barbara; Heberle, Frederick A.; Marquardt, Drew T.

2017-02-28

Low- and high-resolution models describing the internal transbilayer structure of asymmetric lipid vesicles have been developed. These models can be used for the joint analysis of small-angle neutron and X-ray scattering data. The models describe the underlying scattering length density/electron density profiles either in terms of slabs or through the so-called scattering density profile, previously applied to symmetric lipid vesicles. Both models yield structural details of asymmetric membranes, such as the individual area per lipid, and the hydrocarbon thickness of the inner and outer bilayer leaflets. The scattering density profile model, however, comes at a cost of increased computational effortmore » but results in greater structural resolution, showing a slightly lower packing of lipids in the outer bilayer leaflet of ~120 nm diameter palmitoyloleoyl phosphatidylcholine (POPC) vesicles, compared to the inner leaflet. Here, analysis of asymmetric dipalmitoyl phosphatidylcholine/POPC vesicles did not reveal evidence of transbilayer coupling between the inner and outer leaflets at 323 K, i.e.above the melting transition temperature of the two lipids.« less

Size–strain separation in diffraction line profile analysis

DOE PAGES

Scardi, P.; Ermrich, M.; Fitch, A.; ...

2018-05-29

Separation of size and strain effects on diffraction line profiles has been studied in a round robin involving laboratory instruments and synchrotron radiation beamlines operating with different radiation, optics, detectors and experimental configurations. The studied sample, an extensively ball milled iron alloy powder, provides an ideal test case, as domain size broadening and strain broadening are of comparable size. The high energy available at some synchrotron radiation beamlines provides the best conditions for an accurate analysis of the line profiles, as the size–strain separation clearly benefits from a large number of Bragg peaks in the pattern; high counts, reliable intensitymore » values in low-absorption conditions, smooth background and data collection at different temperatures also support the possibility to include diffuse scattering in the analysis, for the most reliable assessment of the line broadening effect. However, results of the round robin show that good quality information on domain size distribution and microstrain can also be obtained using standard laboratory equipment, even when patterns include relatively few Bragg peaks, provided that the data are of good quality in terms of high counts and low and smooth background.« less

Global aphasia without hemiparesis: language profiles and lesion distribution

PubMed Central

Hanlon, R.; Lux, W.; Dromerick, A.

1999-01-01

OBJECTIVES—Global aphasia without hemiparesis (GAWH) is an uncommon stroke syndrome involving receptive and expressive language impairment, without the hemiparesis typically manifested by patients with global aphasia after large left perisylvian lesions. A few cases of GAWH have been reported with conflicting conclusions regarding pathogenesis, lesion localisation, and recovery. The current study was conducted to attempt to clarify these issues.
METHODS—Ten cases of GAWH were prospectively studied with language profiles and lesion analysis; five patients had multiple lesions, four patients had a single lesion, and one had a subarachnoid haemorrhage. Eight patients met criteria for cardioembolic ischaemic stroke.
RESULTS—Cluster analysis based on acute language profiles disclosed three subtypes of patients with GAWH; these clusters persisted on follow up language assessment. Each cluster evolved into a different aphasia subtype: persistent GAWH, Wernicke's aphasia, or transcortical motor aphasia (TCM). Composite lesion analysis showed that persistent GAWH was related to lesioning of the left superior temporal gyrus. Patients with acute GAWH who evolved into TCM type aphasia had common lesioning of the left inferior frontal gyrus and adjacent subcortical white matter. Patients with acute GAWH who evolved into Wernicke's type aphasia were characterised by lesioning of the left precentral and postcentral gyri. Recovery of language was poor in all but one patient.
CONCLUSIONS—Although patients with acute GAWH are similar on neurological examination, they are heterogeneous with respect to early aphasia profile, language recovery, and lesion profile.

 PMID:10084536

The Rotational Excitation Temperature of the 6614 DIB Carrier

NASA Technical Reports Server (NTRS)

Cami, J.; Salama, F.; Jimenez-Vicente, J.; Galazutdinov, G.; Krelowski, J.

2004-01-01

Analysis of high spectral resolution observations of the lambda6614 DIB line profile show systematic variations in the positions of the peaks in the substructure of the profile. These variations can only be understood in the framework of rotational contours of large molecules, where the variations are caused by changes in the rotational excitation temperature. We show that the rotational excitation temperature for the DIB carrier is of the order 10-40 K - much lower than the gas kinetic temperature - indicating that for this particular DIB carrier angular momentum buildup is not very efficient. The rotational constant indicates that the carrier of this DIB is smaller than previously assumed:7-22 C atoms, depending on the geometry.

A retrieval algorithm of hydrometer profile for submillimeter-wave radiometer

NASA Astrophysics Data System (ADS)

Liu, Yuli; Buehler, Stefan; Liu, Heguang

2017-04-01

Vertical profiles of particle microphysics perform vital functions for the estimation of climatic feedback. This paper proposes a new algorithm to retrieve the profile of the parameters of the hydrometeor(i.e., ice, snow, rain, liquid cloud, graupel) based on passive submillimeter-wave measurements. These parameters include water content and particle size. The first part of the algorithm builds the database and retrieves the integrated quantities. Database is built up by Atmospheric Radiative Transfer Simulator(ARTS), which uses atmosphere data to simulate the corresponding brightness temperature. Neural network, trained by the precalculated database, is developed to retrieve the water path for each type of particles. The second part of the algorithm analyses the statistical relationship between water path and vertical parameters profiles. Based on the strong dependence existing between vertical layers in the profiles, Principal Component Analysis(PCA) technique is applied. The third part of the algorithm uses the forward model explicitly to retrieve the hydrometeor profiles. Cost function is calculated in each iteration, and Differential Evolution(DE) algorithm is used to adjust the parameter values during the evolutionary process. The performance of this algorithm is planning to be verified for both simulation database and measurement data, by retrieving profiles in comparison with the initial one. Results show that this algorithm has the ability to retrieve the hydrometeor profiles efficiently. The combination of ARTS and optimization algorithm can get much better results than the commonly used database approach. Meanwhile, the concept that ARTS can be used explicitly in the retrieval process shows great potential in providing solution to other retrieval problems.

Thyroid tumors of uncertain malignant potential: morphologic and imunohistochemical analysis of 29 cases.

PubMed

Nechifor-Boila, Adela; Borda, Angela; Sassolas, Geneviève; Hafdi-Nejjari, Zakia; Cătană, Ramona; Borson-Chazot, Françoise; Berger, Nicole; Decaussin-Petrucci, Myriam

2015-04-01

Thyroid tumors of uncertain malignant potential (TT-UMP) include follicular and well-differentiated tumors of UMP (FT-UMP/WDT-UMP), as it refers to the presence of questionable capsular/vascular invasion or incompletely developed papillary thyroid carcinoma (PTC)-type nuclear changes. However, these tumors are difficult to diagnose in most cases. We aimed to investigate whether immunohistochemistry (HBME-1, cytokeratin-19, galectin-3, CD56 and p63) provides additional information concerning such lesions. We performed an immunohistochemical analysis on 29 TT-UMP cases (22 WDTs-UMP and 7 FTs-UMP) selected from the Rhone Alpes thyroid cancer registry and Departement of Pathology, Tîrgu-Mureş Emergency County Hospital database. The clinicopathological and follow-up data were obtained. In the WDT-UMP group, HBME-1 was positive in 9/22 (40.9%) cases. CD56, a marker whose expression is reduced or absent in thyroid carcinoma, showed a "malignant" profile (no expression) in 13/22 (59.1%) cases. 7/22 (31.9%) cases were both HBME-1+ and CD56-. One case showed the co-expression of HBME-1, CD56, galectin-3 and cytokeratin-19. In the FT-UMP group, two cases were positive for HBME-1, other two for both galectin-3 and CK19 and only one case revealed a "malignant" CD56 profile. The follow-up data showed no distant metastases or persistent disease. Our study demonstrated very heterogeneous immunohistochemical profiles for TTs-UMP, further supporting the borderline nature of these lesions. WDTs-UMP revealed a certain tendency toward a PTC profile, suggesting a possible pathogeneticlink between these two entities. However, immunohistochemistry is still to be regarded more as a supporting diagnostic tool, while morphological criteria should always prime in the diagnostic decision. Copyright © 2014 Elsevier GmbH. All rights reserved.

Characterization of potential plasma biomarkers related to cognitive impairment by untargeted profiling of phospholipids using the HILIC-ESI-IT-TOF-MS system.

PubMed

Song, Shuang; Cheong, Ling-Zhi; Man, Qing-Qing; Pang, Shao-Jie; Li, Yue-Qi; Ren, Biao; Zhang, Jian

2018-05-01

Early diagnosis of neural changes causing cognitive impairment is critical for development of preventive therapies for dementia. Biomarkers currently characterized cannot be extensively applied due to the invasive sampling of cerebrospinal fluid. The other imaging approaches are either expensive or require a high technique. Phospholipids (PLs), which are basic constituents of neurons, might be a key variable in the pathogenesis of cognitive impairment. Changes in plasma PL provide the possibility for development of novel biomarkers with minimal invasion and high patient acceptance. In this work, a HILIC-ESI-IT-TOF-MS system was introduced for untargeted profiling of plasma PLs to investigate the relationship between changes of plasma PL profiles and cognitive impairment. A total of 272 types of PL molecular structures were characterized in human plasma and quantified through the internal standard method. Univariate analysis shows 29 PLs were significantly different between the control (n = 41) and the cognitive impairment (CI) group (n = 41). Multivariate analysis (PCA and OPLS-DA) was conducted based on these 29 potential PL biomarkers. Both univariate and multivariate analyses show abnormality of PL metabolism in the CI group, and the downregulation of ethanolamine plasmalogen (pPE) supply, especially those with PUFAs, in the circulation system should be strongly associated with neurodegeneration. A discriminative model was established with satisfied fit (R2) and prediction (Q2) abilities, and the classification test showed better recognition of the CI group than the control group indicating that this model of PL biomarkers could be used as indicators for screening of CI. Graphical abstract Characterization of potential plasma biomarkers related to cognitive impairment by untargeted profiling of phospholipids.

Concentrations of carbonyl sulfide and hydrogen cyanide in the free upper troposphere and lower stratosphere deduced from ATMOS/Spacelab 3 infrared solar occultation spectra

NASA Technical Reports Server (NTRS)

Zander, R.; Rinsland, C. P.; Russell, J. M., III; Farmer, C. B.; Norton, R. H.

1988-01-01

This paper presents the results on the volume mixing ratio profiles of carbonyl sulfide and hydrogen cyanide, deduced from the spectroscopic analysis of IR solar absorption spectra obtained in the occultation mode with the Atmospheric Trace Molecule Spectroscopy (ATMOS) instrument during its mission aboard Spacelab 3. A comparison of the ATMOS measurements for both northern and southern latitudes with previous field investigations at low midlatitudes shows a relatively good agreement. Southern Hemisphere volume mixing ratio profiles for both molecules were obtained for the first time, as were the profiles for the Northern Hemisphere covering the upper troposphere and the lower stratosphere simultaneously.

Comparison of performance and quantitative descriptive analysis sensory profiling and its relationship to consumer liking between the artisanal cheese producers panel and the descriptive trained panel.

PubMed

Ramírez-Rivera, Emmanuel de Jesús; Díaz-Rivera, Pablo; Guadalupe Ramón-Canul, Lorena; Juárez-Barrientos, José Manuel; Rodríguez-Miranda, Jesús; Herman-Lara, Erasmo; Prinyawiwatkul, Witoon; Herrera-Corredor, José Andrés

2018-07-01

The aim of this research was to compare the performance and sensory profiling of a panel of artisanal cheese producers against a trained panel and their relationship to consumer liking (external preference mapping). Performance was analyzed statistically at an individual level using the Fisher's test (F) for discrimination, the mean square error for repeatability, and Manhattan plots for visualizing the intra-panel homogeneity. At group level, performance was evaluated using ANOVA. External preference mapping technique was applied to determine the efficiency of each sensory profile. Results showed that the producers panel was discriminant and repetitive with a performance similar to that of the trained panel. Manhattan plots showed that the performance of artisanal cheese producers was more homogeneous than trained panelists. The correlation between sensory profiles (Rv = 0.95) demonstrated similarities in the generation and use of sensory profiles. The external preference maps generated individually with the profiles of each panel were also similar. Recruiting individuals familiar with the production of artisanal cheeses as panelists is a viable strategy for sensory characterization of artisanal cheeses within their context of origin because their results were similar to those from the trained panel and can be correlated with consumer liking data. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Direct Analysis in Real Time by Mass Spectrometric Technique for Determining the Variation in Metabolite Profiles of Cinnamomum tamala Nees and Eberm Genotypes

PubMed Central

Singh, Vineeta; Gupta, Atul Kumar; Singh, S. P.; Kumar, Anil

2012-01-01

Cinnamomum tamala Nees & Eberm. is an important traditional medicinal plant, mentioned in various ancient literatures such as Ayurveda. Several of its medicinal properties have recently been proved. To characterize diversity in terms of metabolite profiles of Cinnamomum tamala Nees and Eberm genotypes, a newly emerging mass spectral ionization technique direct time in real time (DART) is very helpful. The DART ion source has been used to analyze an extremely wide range of phytochemicals present in leaves of Cinnamomum tamala. Ten genotypes were assessed for the presence of different phytochemicals. Phytochemical analysis showed the presence of mainly terpenes and phenols. These constituents vary in the different genotypes of Cinnamomum tamala. Principal component analysis has also been employed to analyze the DART data of these Cinnamomum genotypes. The result shows that the genotype of Cinnamomum tamala could be differentiated using DART MS data. The active components present in Cinnamomum tamala may be contributing significantly to high amount of antioxidant property of leaves and, in turn, conditional effects for diabetic patients. PMID:22701361

Characterization of volatile profile from ten different varieties of Chinese jujubes by HS-SPME/GC-MS coupled with E-nose.

PubMed

Chen, Qinqin; Song, Jianxin; Bi, Jinfeng; Meng, Xianjun; Wu, Xinye

2018-03-01

Volatile profile of ten different varieties of fresh jujubes was characterized by HS-SPME/GC-MS (headspace solid phase micro-extraction combined with gas chromatography-mass spectrometry) and E-nose (electronic nose). GC-MS results showed that a total of 51 aroma compounds were identified in jujubes, hexanoic acid, hexanal, (E)-2-hexenal, (Z)-2-heptenal, benzaldehyde and (E)-2-nonenal were the main aroma components with contributions that over 70%. Differentiation of jujube varieties was conducted by cluster analysis of GC-MS data and principal component analysis & linear discriminant analysis of E-nose data. Both results showed that jujubes could be mainly divided into two groups: group A (JZ, PDDZ, JSXZ and LWZZ) and group B (BZ, YZ, MZ, XZ and DZ). There were significant differences in contents of alcohols, acids and aromatic compounds between group A and B. GC-MS coupled with E-nose could be a fast and accurate method to identify the general flavor difference in different varieties of jujubes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effect of masticatory stimulation on the quantity and quality of saliva and the salivary metabolomic profile

PubMed Central

Hoshi, Noriyuki; Soga, Tomoyoshi; Tomita, Masaru; Sugimoto, Masahiro; Kimoto, Katsuhiko

2017-01-01

Background This study characterized the changes in quality and quantity of saliva, and changes in the salivary metabolomic profile, to understand the effects of masticatory stimulation. Methods Stimulated and unstimulated saliva samples were collected from 55 subjects and salivary hydrophilic metabolites were comprehensively quantified using capillary electrophoresis-time-of-flight mass spectrometry. Results In total, 137 metabolites were identified and quantified. The concentrations of 44 metabolites in stimulated saliva were significantly higher than those in unstimulated saliva. Pathway analysis identified the upregulation of the urea cycle and synthesis and degradation pathways of glycine, serine, cysteine and threonine in stimulated saliva. A principal component analysis revealed that the effect of masticatory stimulation on salivary metabolomic profiles was less dependent on sample population sex, age, and smoking. The concentrations of only 1 metabolite in unstimulated saliva, and of 3 metabolites stimulated saliva, showed significant correlation with salivary secretion volume, indicating that the salivary metabolomic profile and salivary secretion volume were independent factors. Conclusions Masticatory stimulation affected not only salivary secretion volume, but also metabolite concentration patterns. A low correlation between the secretion volume and these patterns supports the conclusion that the salivary metabolomic profile may be a new indicator to characterize masticatory stimulation. PMID:28813487

Multi-Component Profiling of Trace Volatiles in Blood by Gas Chromatography/Mass Spectrometry with Dynamic Headspace Extraction

PubMed Central

Kakuta, Shoji; Yamashita, Toshiyuki; Nishiumi, Shin; Yoshida, Masaru; Fukusaki, Eiichiro; Bamba, Takeshi

2015-01-01

A dynamic headspace extraction method (DHS) with high-pressure injection is described. This dynamic extraction method has superior sensitivity to solid phase micro extraction, SPME and is capable of extracting the entire gas phase by purging the headspace of a vial. Optimization of the DHS parameters resulted in a highly sensitive volatile profiling system with the ability to detect various volatile components including alcohols at nanogram levels. The average LOD for a standard volatile mixture was 0.50 ng mL−1, and the average LOD for alcohols was 0.66 ng mL−1. This method was used for the analysis of volatile components from biological samples and compared with acute and chronic inflammation models. The method permitted the identification of volatiles with the same profile pattern as in vitro oxidized lipid-derived volatiles. In addition, the concentration of alcohols and aldehydes from the acute inflammation model samples were significantly higher than that for the chronic inflammation model samples. The different profiles between these samples could also be identified by this method. Finally, it was possible to analyze alcohols and low-molecular-weight volatiles that are difficult to analyze by SPME in high sensitivity and to show volatile profiling based on multi-volatile simultaneous analysis. PMID:26819905

Multi-Component Profiling of Trace Volatiles in Blood by Gas Chromatography/Mass Spectrometry with Dynamic Headspace Extraction.

PubMed

Kakuta, Shoji; Yamashita, Toshiyuki; Nishiumi, Shin; Yoshida, Masaru; Fukusaki, Eiichiro; Bamba, Takeshi

2015-01-01

A dynamic headspace extraction method (DHS) with high-pressure injection is described. This dynamic extraction method has superior sensitivity to solid phase micro extraction, SPME and is capable of extracting the entire gas phase by purging the headspace of a vial. Optimization of the DHS parameters resulted in a highly sensitive volatile profiling system with the ability to detect various volatile components including alcohols at nanogram levels. The average LOD for a standard volatile mixture was 0.50 ng mL(-1), and the average LOD for alcohols was 0.66 ng mL(-1). This method was used for the analysis of volatile components from biological samples and compared with acute and chronic inflammation models. The method permitted the identification of volatiles with the same profile pattern as in vitro oxidized lipid-derived volatiles. In addition, the concentration of alcohols and aldehydes from the acute inflammation model samples were significantly higher than that for the chronic inflammation model samples. The different profiles between these samples could also be identified by this method. Finally, it was possible to analyze alcohols and low-molecular-weight volatiles that are difficult to analyze by SPME in high sensitivity and to show volatile profiling based on multi-volatile simultaneous analysis.

Profound Effect of Profiling Platform and Normalization Strategy on Detection of Differentially Expressed MicroRNAs – A Comparative Study

PubMed Central

Meyer, Swanhild U.; Kaiser, Sebastian; Wagner, Carola; Thirion, Christian; Pfaffl, Michael W.

2012-01-01

Background Adequate normalization minimizes the effects of systematic technical variations and is a prerequisite for getting meaningful biological changes. However, there is inconsistency about miRNA normalization performances and recommendations. Thus, we investigated the impact of seven different normalization methods (reference gene index, global geometric mean, quantile, invariant selection, loess, loessM, and generalized procrustes analysis) on intra- and inter-platform performance of two distinct and commonly used miRNA profiling platforms. Methodology/Principal Findings We included data from miRNA profiling analyses derived from a hybridization-based platform (Agilent Technologies) and an RT-qPCR platform (Applied Biosystems). Furthermore, we validated a subset of miRNAs by individual RT-qPCR assays. Our analyses incorporated data from the effect of differentiation and tumor necrosis factor alpha treatment on primary human skeletal muscle cells and a murine skeletal muscle cell line. Distinct normalization methods differed in their impact on (i) standard deviations, (ii) the area under the receiver operating characteristic (ROC) curve, (iii) the similarity of differential expression. Loess, loessM, and quantile analysis were most effective in minimizing standard deviations on the Agilent and TLDA platform. Moreover, loess, loessM, invariant selection and generalized procrustes analysis increased the area under the ROC curve, a measure for the statistical performance of a test. The Jaccard index revealed that inter-platform concordance of differential expression tended to be increased by loess, loessM, quantile, and GPA normalization of AGL and TLDA data as well as RGI normalization of TLDA data. Conclusions/Significance We recommend the application of loess, or loessM, and GPA normalization for miRNA Agilent arrays and qPCR cards as these normalization approaches showed to (i) effectively reduce standard deviations, (ii) increase sensitivity and accuracy of differential miRNA expression detection as well as (iii) increase inter-platform concordance. Results showed the successful adoption of loessM and generalized procrustes analysis to one-color miRNA profiling experiments. PMID:22723911

The Role of Vitamin D in the Transcriptional Program of Human Pregnancy

PubMed Central

Al-Garawi, Amal; Carey, Vincent J.; Chhabra, Divya; Morrow, Jarrett; Lasky-Su, Jessica; Qiu, Weiliang; Laranjo, Nancy; Litonjua, Augusto A.; Weiss, Scott T.

2016-01-01

Background Patterns of gene expression of human pregnancy are poorly understood. In a trial of vitamin D supplementation in pregnant women, peripheral blood transcriptomes were measured longitudinally on 30 women and used to characterize gene co-expression networks. Objective Studies suggest that increased maternal Vitamin D levels may reduce the risk of asthma in early life, yet the underlying mechanisms have not been examined. In this study, we used a network-based approach to examine changes in gene expression profiles during the course of normal pregnancy and evaluated their association with maternal Vitamin D levels. Design The VDAART study is a randomized clinical trial of vitamin D supplementation in pregnancy for reduction of pediatric asthma risk. The trial enrolled 881 women at 10–18 weeks of gestation. Longitudinal gene expression measures were obtained on thirty pregnant women, using RNA isolated from peripheral blood samples obtained in the first and third trimesters. Differentially expressed genes were identified using significance of analysis of microarrays (SAM), and clustered using a weighted gene co-expression network analysis (WGCNA). Gene-set enrichment was performed to identify major biological pathways. Results Comparison of transcriptional profiles between first and third trimesters of pregnancy identified 5839 significantly differentially expressed genes (FDR<0.05). Weighted gene co-expression network analysis clustered these transcripts into 14 co-expression modules of which two showed significant correlation with maternal vitamin D levels. Pathway analysis of these two modules revealed genes enriched in immune defense pathways and extracellular matrix reorganization as well as genes enriched in notch signaling and transcription factor networks. Conclusion Our data show that gene expression profiles of healthy pregnant women change during the course of pregnancy and suggest that maternal Vitamin D levels influence transcriptional profiles. These alterations of the maternal transcriptome may contribute to fetal immune imprinting and reduce allergic sensitization in early life. Trial Registration clinicaltrials.gov NCT00920621 PMID:27711190

GC-MS Profiling of Triterpenoid Saponins from 28 Quinoa Varieties (Chenopodium quinoa Willd.) Grown in Washington State.

PubMed

Medina-Meza, Ilce G; Aluwi, Nicole A; Saunders, Steven R; Ganjyal, Girish M

2016-11-16

Quinoa (Chenopodium quinoa Willd) contains 2 to 5% saponins in the form of oleanane-type triterpenoid glycosides or sapogenins found in the external layers of the seeds. These saponins confer an undesirable bitter flavor. This study maps the content and profile of glycoside-free sapogenins from 22 quinoa varieties and 6 original breeding lines grown in North America under similar agronomical conditions. Saponins were recovered using a novel extraction protocol and quantified by GC-MS. Oleanolic acid (OA), hederagenin (HD), serjanic acid (SA), and phytolaccagenic acid (PA) were identified by their mass spectra. Total saponin content ranged from 3.81 to 27.1 mg/g among the varieties studied. The most predominant sapogenin was phytolaccagenic acid with 16.72 mg/g followed by hederagenin at 4.22 mg/g representing the ∼70% and 30% of the total sapogenin content. Phytolaccagenic acid and the total sapogenin content had a positive correlation of r 2 = 0.88 (p < 0.05). Results showed that none of the varieties we studied can be classified as "sweet". Nine varieties were classified as "low-sapogenin". We recommend six of the varieties be subjected to saponin removal process before consumption. A multivariate analysis was conducted to evaluate and cluster the different genotypes according their sapogenin profile as a way of predicting the possible utility of separate quinoa in food products. The multivariate analysis showed no correlations between origin of seeds and saponin profile and/or content.

Metabolomic Profiling of Plasma from Melioidosis Patients Using UHPLC-QTOF MS Reveals Novel Biomarkers for Diagnosis.

PubMed

Lau, Susanna K P; Lee, Kim-Chung; Lo, George C S; Ding, Vanessa S Y; Chow, Wang-Ngai; Ke, Tony Y H; Curreem, Shirly O T; To, Kelvin K W; Ho, Deborah T Y; Sridhar, Siddharth; Wong, Sally C Y; Chan, Jasper F W; Hung, Ivan F N; Sze, Kong-Hung; Lam, Ching-Wan; Yuen, Kwok-Yung; Woo, Patrick C Y

2016-02-27

To identify potential biomarkers for improving diagnosis of melioidosis, we compared plasma metabolome profiles of melioidosis patients compared to patients with other bacteremia and controls without active infection, using ultra-high-performance liquid chromatography-electrospray ionization-quadruple time-of-flight mass spectrometry. Principal component analysis (PCA) showed that the metabolomic profiles of melioidosis patients are distinguishable from bacteremia patients and controls. Using multivariate and univariate analysis, 12 significant metabolites from four lipid classes, acylcarnitine (n = 6), lysophosphatidylethanolamine (LysoPE) (n = 3), sphingomyelins (SM) (n = 2) and phosphatidylcholine (PC) (n = 1), with significantly higher levels in melioidosis patients than bacteremia patients and controls, were identified. Ten of the 12 metabolites showed area-under-receiver operating characteristic curve (AUC) >0.80 when compared both between melioidosis and bacteremia patients, and between melioidosis patients and controls. SM(d18:2/16:0) possessed the largest AUC when compared, both between melioidosis and bacteremia patients (AUC 0.998, sensitivity 100% and specificity 91.7%), and between melioidosis patients and controls (AUC 1.000, sensitivity 96.7% and specificity 100%). Our results indicate that metabolome profiling might serve as a promising approach for diagnosis of melioidosis using patient plasma, with SM(d18:2/16:0) representing a potential biomarker. Since the 12 metabolites were related to various pathways for energy and lipid metabolism, further studies may reveal their possible role in the pathogenesis and host response in melioidosis.

Metabolomic Profiling of Plasma from Melioidosis Patients Using UHPLC-QTOF MS Reveals Novel Biomarkers for Diagnosis

PubMed Central

Lau, Susanna K. P.; Lee, Kim-Chung; Lo, George C. S.; Ding, Vanessa S. Y.; Chow, Wang-Ngai; Ke, Tony Y. H.; Curreem, Shirly O. T.; To, Kelvin K. W.; Ho, Deborah T. Y.; Sridhar, Siddharth; Wong, Sally C. Y.; Chan, Jasper F. W.; Hung, Ivan F. N.; Sze, Kong-Hung; Lam, Ching-Wan; Yuen, Kwok-Yung; Woo, Patrick C. Y.

2016-01-01

To identify potential biomarkers for improving diagnosis of melioidosis, we compared plasma metabolome profiles of melioidosis patients compared to patients with other bacteremia and controls without active infection, using ultra-high-performance liquid chromatography-electrospray ionization-quadruple time-of-flight mass spectrometry. Principal component analysis (PCA) showed that the metabolomic profiles of melioidosis patients are distinguishable from bacteremia patients and controls. Using multivariate and univariate analysis, 12 significant metabolites from four lipid classes, acylcarnitine (n = 6), lysophosphatidylethanolamine (LysoPE) (n = 3), sphingomyelins (SM) (n = 2) and phosphatidylcholine (PC) (n = 1), with significantly higher levels in melioidosis patients than bacteremia patients and controls, were identified. Ten of the 12 metabolites showed area-under-receiver operating characteristic curve (AUC) >0.80 when compared both between melioidosis and bacteremia patients, and between melioidosis patients and controls. SM(d18:2/16:0) possessed the largest AUC when compared, both between melioidosis and bacteremia patients (AUC 0.998, sensitivity 100% and specificity 91.7%), and between melioidosis patients and controls (AUC 1.000, sensitivity 96.7% and specificity 100%). Our results indicate that metabolome profiling might serve as a promising approach for diagnosis of melioidosis using patient plasma, with SM(d18:2/16:0) representing a potential biomarker. Since the 12 metabolites were related to various pathways for energy and lipid metabolism, further studies may reveal their possible role in the pathogenesis and host response in melioidosis. PMID:26927094

A Tool for Model-Based Generation of Scenario-driven Electric Power Load Profiles

NASA Technical Reports Server (NTRS)

Rozek, Matthew L.; Donahue, Kenneth M.; Ingham, Michel D.; Kaderka, Justin D.

2015-01-01

Power consumption during all phases of spacecraft flight is of great interest to the aerospace community. As a result, significant analysis effort is exerted to understand the rates of electrical energy generation and consumption under many operational scenarios of the system. Previously, no standard tool existed for creating and maintaining a power equipment list (PEL) of spacecraft components that consume power, and no standard tool existed for generating power load profiles based on this PEL information during mission design phases. This paper presents the Scenario Power Load Analysis Tool (SPLAT) as a model-based systems engineering tool aiming to solve those problems. SPLAT is a plugin for MagicDraw (No Magic, Inc.) that aids in creating and maintaining a PEL, and also generates a power and temporal variable constraint set, in Maple language syntax, based on specified operational scenarios. The constraint set can be solved in Maple to show electric load profiles (i.e. power consumption from loads over time). SPLAT creates these load profiles from three modeled inputs: 1) a list of system components and their respective power modes, 2) a decomposition hierarchy of the system into these components, and 3) the specification of at least one scenario, which consists of temporal constraints on component power modes. In order to demonstrate how this information is represented in a system model, a notional example of a spacecraft planetary flyby is introduced. This example is also used to explain the overall functionality of SPLAT, and how this is used to generate electric power load profiles. Lastly, a cursory review of the usage of SPLAT on the Cold Atom Laboratory project is presented to show how the tool was used in an actual space hardware design application.

Comparison of rapid descriptive sensory methodologies: Free-Choice Profiling, Flash Profile and modified Flash Profile.

PubMed

Liu, Jing; Bredie, Wender L P; Sherman, Emma; Harbertson, James F; Heymann, Hildegarde

2018-04-01

Rapid sensory methods have been developed as alternatives to traditional sensory descriptive analysis methods. Among them, Free-Choice Profiling (FCP) and Flash Profile (FP) are two that have been known for many years. The objectives of this work were to compare the rating-based FCP and ranking-based FP method; to evaluate the impact of adding adjustments to FP approach; to investigate the influence of the number of assessors on the outcome of modified FP. To achieve these aims, a conventional descriptive analysis (DA), FCP, FP and a modified version of FP were carried out. Red wines made by different grape maturity and ethanol concentration were used for sensory testing. This study showed that DA provided a more detailed and accurate information on products through a quantitative measure of the intensity of sensory attributes than FCP and FP. However, the panel hours for conducting DA were higher than that for rapid methods, and FP was even able to separate the samples to a higher degree than DA. When comparing FCP and FP, this study showed that the ranking-based FP provided a clearer separation of samples than rating-based FCP, but the latter was an easier task for most assessors. When restricting assessors on their use of attributes in FP, the sample space became clearer and the ranking task was simplified. The FP protocol with restricted attribute sets seems to be a promising approach for efficient screening of sensory properties in wine. When increasing the number of assessors from 10 to 20 for conducting the modified FP, the outcome tended to be slightly more stable, however, one should consider the degree of panel training when deciding the optimal number of assessors for conducting FP. Copyright © 2018 Elsevier Ltd. All rights reserved.

Analysis of differential secondary effects of novel rexinoids: select rexinoid X receptor ligands demonstrate differentiated side effect profiles

PubMed Central

Marshall, Pamela A; Jurutka, Peter W; Wagner, Carl E; van der Vaart, Arjan; Kaneko, Ichiro; Chavez, Pedro I; Ma, Ning; Bhogal, Jaskaran S; Shahani, Pritika; Swierski, Johnathon C; MacNeill, Mairi

2015-01-01

In order to determine the feasibility of utilizing novel rexinoids for chemotherapeutics and as potential treatments for neurological conditions, we undertook an assessment of the side effect profile of select rexinoid X receptor (RXR) analogs that we reported previously. We assessed pharmacokinetic profiles, lipid and thyroid-stimulating hormone (TSH) levels in rats, and cell culture activity of rexinoids in sterol regulatory element-binding protein (SREBP) induction and thyroid hormone inhibition assays. We also performed RNA sequencing of the brain tissues of rats that had been dosed with the compounds. We show here for the first time that potent rexinoid activity can be uncoupled from drastic lipid changes and thyroid axis variations, and we propose that rexinoids can be developed with improved side effect profiles than the parent compound, bexarotene (1). PMID:26038698

Targeted High Performance Liquid Chromatography Tandem Mass Spectrometry-based Metabolomics differentiates metabolic syndrome from obesity.

PubMed

Zhong, Fanyi; Xu, Mengyang; Bruno, Richard S; Ballard, Kevin D; Zhu, Jiangjiang

2017-04-01

Both obesity and the metabolic syndrome are risk factors for type 2 diabetes and cardiovascular disease. Identification of novel biomarkers are needed to distinguish metabolic syndrome from equally obese individuals in order to direct them to early interventions that reduce their risk of developing further health problems. We utilized mass spectrometry-based targeted metabolic profiling of 221 metabolites to evaluate the associations between metabolite profiles and established metabolic syndrome criteria (i.e. elevated waist circumference, hypertension, elevated fasting glucose, elevated triglycerides, and low high-density lipoprotein cholesterol) in plasma samples from obese men ( n = 29; BMI = 35.5 ± 5.2 kg/m 2 ) and women ( n = 40; 34.9 ± 6.7 kg/m 2 ), of which 26 met the criteria for metabolic syndrome (17 men and 9 women). Compared to obese individuals without metabolic syndrome, univariate statistical analysis and partial least squares discriminant analysis showed that a specific group of metabolites from multiple metabolic pathways (i.e. purine metabolism, valine, leucine and isoleucine degradation, and tryptophan metabolism) were associated with the presence of metabolic syndrome. Receiver operating characteristic curves generated based on the PLS-DA models showed excellent areas under the curve (0.85 and 0.96, for metabolites only model and enhanced metabolites model, respectively), high specificities (0.86 and 0.93), and good sensitivities (0.71 and 0.91). Moreover, principal component analysis revealed that metabolic profiles can be used to further differentiate metabolic syndrome with 3 versus 4-5 metabolic syndrome criteria. Collectively, these findings support targeted metabolomics approaches to distinguish metabolic syndrome from obesity alone, and to stratify metabolic syndrome status based on the number of criteria met. Impact statement We utilized mass spectrometry-based targeted metabolic profiling of 221 metabolites to evaluate the associations between metabolite profiles and established MetS criteria. To our best knowledge, the findings of this study provide the first evidence that metabolic profiles can be used to differentiate participants with MetS from similarly obese individuals who do not meet established criteria of MetS. Furthermore, the study demonstrated that within MetS participants, their unique metabolic profiles correlated to the number of criteria used for MetS determination. Taken together, this metabolic profiling approach can potentially serve as a novel tool for MetS detection and monitoring, and provide useful metabolic information for future interventions targeting obesity and MetS.

Profiles of Motivated Self-Regulation in College Computer Science Courses: Differences in Major versus Required Non-Major Courses

NASA Astrophysics Data System (ADS)

Shell, Duane F.; Soh, Leen-Kiat

2013-12-01

The goal of the present study was to utilize a profiling approach to understand differences in motivation and strategic self-regulation among post-secondary STEM students in major versus required non-major computer science courses. Participants were 233 students from required introductory computer science courses (194 men; 35 women; 4 unknown) at a large Midwestern state university. Cluster analysis identified five profiles: (1) a strategic profile of a highly motivated by-any-means good strategy user; (2) a knowledge-building profile of an intrinsically motivated autonomous, mastery-oriented student; (3) a surface learning profile of a utility motivated minimally engaged student; (4) an apathetic profile of an amotivational disengaged student; and (5) a learned helpless profile of a motivated but unable to effectively self-regulate student. Among CS majors and students in courses in their major field, the strategic and knowledge-building profiles were the most prevalent. Among non-CS majors and students in required non-major courses, the learned helpless, surface learning, and apathetic profiles were the most prevalent. Students in the strategic and knowledge-building profiles had significantly higher retention of computational thinking knowledge than students in other profiles. Students in the apathetic and surface learning profiles saw little instrumentality of the course for their future academic and career objectives. Findings show that students in STEM fields taking required computer science courses exhibit the same constellation of motivated strategic self-regulation profiles found in other post-secondary and K-12 settings.

Cutting efficiency of four different rotary nickel: Titanium instruments

PubMed Central

Cecchin, Doglas; de Sousa-Neto, Manoel Damião; Pécora, Jesus Djalma; Gariba-Silva, Ricardo

2011-01-01

Aim: The aim of this study was to evaluate the cutting efficiency of rotary nickel-titanium (NiTi) instruments K3, NiTi Tee, Profile, and Quantec with taper size 04/25. Materials and Methods: The number of samples was 10 for each group (n = 10). The cutting efficiency was measured by the mass loss from each acrylic resin block after instrumentation of a simulated canal using the Crown-down technique. Results: The analysis of variance (ANOVA) showed that there was a statistically significant difference among the studied groups. The Tukey's test showed that the acrylic resin blocks prepared with instruments K3 (0.00369 ± 0.00022), NiTi Tee (0.00368 ± 0.00023), and Profile (0.00351 ± 0.00026) presented the greatest mass loss, showing no statistically significant difference among them (P < 0.05). The lowest mass loss was found in the blocks prepared with Quantec instruments (0.00311 ± 0.0003) (P < 0.05). Conclusions: It could be concluded that the K3, NiTi Tee, and Profile instruments presented a greater cutting efficiency than the Quantec instruments. PMID:21814349

Study of the coumarate decarboxylase and vinylphenol reductase activities of Dekkera bruxellensis (anamorph Brettanomyces bruxellensis) isolates.

PubMed

Godoy, L; Garrido, D; Martínez, C; Saavedra, J; Combina, M; Ganga, M A

2009-04-01

To evaluate the coumarate descarboxylase (CD) and vinylphenol reductase (VR) activities in Dekkera bruxellensis isolates and study their relationship to the growth rate, protein profile and random amplified polymorphic DNA (RAPD) molecular pattern. CD and VR activities were quantified, as well, the growth rate, intracellular protein profile and molecular analysis (RAPD) were determined in 12 isolates of D. bruxellensis. All the isolates studied showed CD activity, but only some showed VR activity. Those isolates with the greatest growth rate did not present a different protein profile from the others. The FASC showed a relationship between RAPD molecular patterns and VR activity. CD activity is common to all of the D. bruxellensis isolates. This was not the case with VR activity, which was detected at a low percentage in the analysed micro-organisms. A correlation was observed between VR activity and the RAPD patterns. This is the first study that quantifies the CD and VR enzyme activities in D. bruxellensis, demonstrating that these activities are not present in all isolates of this yeast.

Robustness of Light-Transport Processes to Bending Deformations in Graded-Index Multimode Waveguides

NASA Astrophysics Data System (ADS)

Boonzajer Flaes, Dirk E.; Stopka, Jan; Turtaev, Sergey; de Boer, Johannes F.; Tyc, Tomáš; Čižmár, Tomáš

2018-06-01

Light transport through a multimode optical waveguide undergoes changes when subjected to bending deformations. We show that optical waveguides with a perfectly parabolic refractive index profile are almost immune to bending, conserving the structure of propagation-invariant modes. Moreover, we show that changes to the transmission matrix of parabolic-index fibers due to bending can be expressed with only two free parameters, regardless of how complex a particular deformation is. We provide detailed analysis of experimentally measured transmission matrices of a commercially available graded-index fiber as well as a gradient-index rod lens featuring a very faithful parabolic refractive index profile. Although parabolic-index fibers with a sufficiently precise refractive index profile are not within our reach, we show that imaging performance with standard commercially available graded-index fibers is significantly less influenced by bending deformations than step-index types under the same conditions. Our work thus predicts that the availability of ultraprecise parabolic-index fibers will make endoscopic applications with flexible probes feasible and free from extremely elaborate computational challenges.

Histological staining methods preparatory to laser capture microdissection significantly affect the integrity of the cellular RNA.

PubMed

Wang, Hongyang; Owens, James D; Shih, Joanna H; Li, Ming-Chung; Bonner, Robert F; Mushinski, J Frederic

2006-04-27

Gene expression profiling by microarray analysis of cells enriched by laser capture microdissection (LCM) faces several technical challenges. Frozen sections yield higher quality RNA than paraffin-imbedded sections, but even with frozen sections, the staining methods used for histological identification of cells of interest could still damage the mRNA in the cells. To study the contribution of staining methods to degradation of results from gene expression profiling of LCM samples, we subjected pellets of the mouse plasma cell tumor cell line TEPC 1165 to direct RNA extraction and to parallel frozen sectioning for LCM and subsequent RNA extraction. We used microarray hybridization analysis to compare gene expression profiles of RNA from cell pellets with gene expression profiles of RNA from frozen sections that had been stained with hematoxylin and eosin (H&E), Nissl Stain (NS), and for immunofluorescence (IF) as well as with the plasma cell-revealing methyl green pyronin (MGP) stain. All RNAs were amplified with two rounds of T7-based in vitro transcription and analyzed by two-color expression analysis on 10-K cDNA microarrays. The MGP-stained samples showed the least introduction of mRNA loss, followed by H&E and immunofluorescence. Nissl staining was significantly more detrimental to gene expression profiles, presumably owing to an aqueous step in which RNA may have been damaged by endogenous or exogenous RNAases. RNA damage can occur during the staining steps preparatory to laser capture microdissection, with the consequence of loss of representation of certain genes in microarray hybridization analysis. Inclusion of RNAase inhibitor in aqueous staining solutions appears to be important in protecting RNA from loss of gene transcripts.

Histological staining methods preparatory to laser capture microdissection significantly affect the integrity of the cellular RNA

PubMed Central

Wang, Hongyang; Owens, James D; Shih, Joanna H; Li, Ming-Chung; Bonner, Robert F; Mushinski, J Frederic

2006-01-01

Background Gene expression profiling by microarray analysis of cells enriched by laser capture microdissection (LCM) faces several technical challenges. Frozen sections yield higher quality RNA than paraffin-imbedded sections, but even with frozen sections, the staining methods used for histological identification of cells of interest could still damage the mRNA in the cells. To study the contribution of staining methods to degradation of results from gene expression profiling of LCM samples, we subjected pellets of the mouse plasma cell tumor cell line TEPC 1165 to direct RNA extraction and to parallel frozen sectioning for LCM and subsequent RNA extraction. We used microarray hybridization analysis to compare gene expression profiles of RNA from cell pellets with gene expression profiles of RNA from frozen sections that had been stained with hematoxylin and eosin (H&E), Nissl Stain (NS), and for immunofluorescence (IF) as well as with the plasma cell-revealing methyl green pyronin (MGP) stain. All RNAs were amplified with two rounds of T7-based in vitro transcription and analyzed by two-color expression analysis on 10-K cDNA microarrays. Results The MGP-stained samples showed the least introduction of mRNA loss, followed by H&E and immunofluorescence. Nissl staining was significantly more detrimental to gene expression profiles, presumably owing to an aqueous step in which RNA may have been damaged by endogenous or exogenous RNAases. Conclusion RNA damage can occur during the staining steps preparatory to laser capture microdissection, with the consequence of loss of representation of certain genes in microarray hybridization analysis. Inclusion of RNAase inhibitor in aqueous staining solutions appears to be important in protecting RNA from loss of gene transcripts. PMID:16643667

Further Examining Berry's Model: The Applicability of Latent Profile Analysis to Acculturation

ERIC Educational Resources Information Center

Fox, Rina S.; Merz, Erin L.; Solórzano, Martha T.; Roesch, Scott C.

2013-01-01

This study used latent profile analysis (LPA) to identify acculturation profiles. A three-profile solution fit the data best, and comparisons on demographic and psychosocial outcomes as a function of profile yielded expected results. The findings support using LPA as a parsimonious way to model acculturation without anticipating profiles in…

Chemical profiling of guarana seeds (Paullinia cupana) from different geographical origins using UPLC-QTOF-MS combined with chemometrics.

PubMed

da Silva, Givaldo Souza; Canuto, Kirley Marques; Ribeiro, Paulo Riceli Vasconcelos; de Brito, Edy Sousa; Nascimento, Madson Moreira; Zocolo, Guilherme Julião; Coutinho, Janclei Pereira; de Jesus, Raildo Mota

2017-12-01

Paullinia cupana, commonly known as guarana, is an Amazonian fruit whose seeds are used to produce the powdered guarana, which is rich in caffeine and consumed for its stimulating activity. The metabolic profile of guarana from the two largest producing regions was investigated using UPLC-MS combined with multivariate statistical analysis. The principal component analysis (PCA) showed significant differences between samples produced in the states of Bahia and Amazonas. The metabolites responsible for the differentiation were identified by orthogonal partial least squares discriminant analysis (OPLS-DA). Fourteen phenolic compounds were characterized in guarana powder samples, and catechin, epicatechin, B-type procyanidin dimer, A-type procyanidin trimer and A-type procyanidin dimer were the main compounds responsible for the geographical variation of the samples. Copyright © 2017. Published by Elsevier Ltd.

Phylogenetic Analysis of Enterohemorrhagic Escherichia coli O157, Germany, 1987–2008

PubMed Central

Jenke, Christian; Harmsen, Dag; Weniger, Thomas; Rothgänger, Jörg; Hyytiä-Trees, Eija; Bielaszewska, Martina; Karch, Helge

2010-01-01

Multilocus variable number tandem repeat analysis (MLVA) is a subtyping technique for characterizing human pathogenic bacteria such as enterohemorrhagic Escherichia coli (EHEC) O157. We determined the phylogeny of 202 epidemiologically unrelated EHEC O157:H7/H– clinical isolates through 8 MLVA loci obtained in Germany during 1987–2008. Biodiversity in the loci ranged from 0.66 to 0.90. Four of 8 loci showed null alleles and a frequency <44.1%. These loci were distributed among 48.5% of all strains. Overall, 141 MLVA profiles were identified. Phylogenetic analysis assigned 67.3% of the strains to 19 MLVA clusters. Specific MLVA profiles with an evolutionary persistence were identified, particularly within sorbitol-fermenting EHEC O157:H–.These pathogens belonged to the same MLVA cluster. Our findings indicate successful persistence of this clone. PMID:20350374

Phylogenetic analysis of enterohemorrhagic Escherichia coli O157, Germany, 1987-2008.

PubMed

Jenke, Christian; Harmsen, Dag; Weniger, Thomas; Rothganger, Jorg; Hyytia-Trees, Eija; Bielaszewska, Martina; Karch, Helge; Mellmann, Alexander

2010-04-01

Multilocus variable number tandem repeat analysis (MLVA) is a subtyping technique for characterizing human pathogenic bacteria such as enterohemorrhagic Escherichia coli (EHEC) O157. We determined the phylogeny of 202 epidemiologically unrelated EHEC O157:H7/H- clinical isolates through 8 MLVA loci obtained in Germany during 1987-2008. Biodiversity in the loci ranged from 0.66 to 0.90. Four of 8 loci showed null alleles and a frequency < or =44.1%. These loci were distributed among 48.5% of all strains. Overall, 141 MLVA profiles were identified. Phylogenetic analysis assigned 67.3% of the strains to 19 MLVA clusters. Specific MLVA profiles with an evolutionary persistence were identified, particularly within sorbitol-fermenting EHEC O157:H-.These pathogens belonged to the same MLVA cluster. Our findings indicate successful persistence of this clone.

Angular photogrammetric analysis of the soft-tissue facial profile of Indian adults.

PubMed

Pandian, K Saravana; Krishnan, Sindhuja; Kumar, S Aravind

2018-01-01

Soft-tissue analysis has become an important component of orthodontic diagnosis and treatment planning. Photographic evaluation of an orthodontic patient is a very close representation of the appearance of the person. The previously established norms for soft-tissue analysis will vary for different ethnic groups. Thus, there is a need to develop soft-tissue facial profile norms pertaining to Indian ethnic groups. The aim of this study is to establish the angular photogrammetric standards of soft-tissue facial profile for Indian males and females and also to compare sexual dimorphism present between them. The lateral profile photographs of 300 random participants (150 males and 150 females) between ages 18 and 25 years were taken and analyzed using FACAD tracing software. Inclusion criteria were angles Class I molar occlusion with acceptable crowding and proclination, normal growth and development with well-aligned dental arches, and full complements of permanent teeth irrespective of third molar status. This study was conducted in Indian population, and samples were taken from various cities across India. Descriptive statistical analysis was carried out, and sexual dimorphism was evaluated by Student's t-test between males and females. The results of the present study showed statistically significant (P < 0.05) gender difference in 5 parameters out of 12 parameters in Indian population. In the present study, soft-tissue facial measurements were established by means of photogrammetric analysis to facilitate orthodontists to carry out more quantitative evaluation and make disciplined decisions. The mean values obtained can be used for comparison with records of participants with the same characteristics by following this photogrammetric technique.

Muscle activation patterns in acceleration-based phases during reach-to-grasp movement.

PubMed

Tokuda, Keisuke; Lee, Bumsuk; Shiihara, Yasufumi; Takahashi, Kazuhiro; Wada, Naoki; Shirakura, Kenji; Watanabe, Hideomi

2016-11-01

[Purpose] An earlier study divided reaching activity into characteristic phases based on hand velocity profiles. By synchronizing muscle activities and the acceleration profile, a phasing approach for reaching movement, based on hand acceleration profiles, was attempted in order to elucidate the roles of individual muscle activities in the different phases of the acceleration profile in reaching movements. [Subjects and Methods] Ten healthy volunteer subjects participated in this study. The aim was to electromyographically evaluate muscles around the shoulder, the upper trapezius, the anterior deltoid, the biceps brachii, and the triceps brachii, most of which have been used to evaluate arm motion, as well as the acceleration of the upper limb during simple reaching movement in the reach-to-grasp task. [Results] Analysis showed the kinematic trajectories of the acceleration during a simple biphasic profile of the reaching movement could be divided into four phases: increasing acceleration (IA), decreasing acceleration (DA), increasing deceleration (ID), and decreasing deceleration (DD). Muscles around the shoulder showed different activity patterns, which were closely associated with these acceleration phases. [Conclusion] These results suggest the important role of the four phases, derived from the acceleration trajectory, in the elucidation of the muscular mechanisms which regulate and coordinate the muscles around the shoulder in reaching movements.

The Antagonistic Effect of Mycotoxins Deoxynivalenol and Zearalenone on Metabolic Profiling in Serum and Liver of Mice

PubMed Central

Ji, Jian; Zhu, Pei; Cui, Fangchao; Pi, Fuwei; Zhang, Yinzhi; Li, Yun; Wang, Jiasheng; Sun, Xiulan

2017-01-01

Metabolic profiling in liver and serum of mice was studied for the combined toxic effects of deoxynivalenol (DON) and zearalenone (ZEN), through gas chromatography mass spectrum. The spectrum of serum and liver sample of mice, treated with individual 2 mg/kg DON, 20 mg/kg ZEN, and the combined DON + ZEN with final concentration 2 mg/kg DON and 20 mg/kg ZEN for 21 days, were deconvoluted, aligned and identified with MS DIAL. The data matrix was processed with univariate analysis and multivariate analysis for selection of metabolites with variable importance for the projection (VIP) > 1, t-test p value < 0.05. The metabolic pathway analysis was performed with MetaMapp and drawn by CytoScape. Results show that the combined DON and ZEN treatment has an obvious “antagonistic effect” in serum and liver tissue metabolic profiling of mice. The blood biochemical indexes, like alkaline phosphatase, alanine transaminase, and albumin (ALB)/globulin (GLO), reveal a moderated trend in the combined DON + ZEN treatment group, which is consistent with histopathological examination. The metabolic pathway analysis demonstrated that the combined DON and ZEN treatment could down-regulate the valine, leucine and isoleucine biosynthesis, glycine, serine and threonine metabolism, and O-glycosyl compounds related glucose metabolism in liver tissue. The metabolic profiling in serum confirmed the finding that the combined DON and ZEN treatment has an “antagonistic effect” on liver metabolism of mice. PMID:28075412

Gait profile score and movement analysis profile in patients with Parkinson's disease during concurrent cognitive load

PubMed Central

Speciali, Danielli S.; Oliveira, Elaine M.; Cardoso, Jefferson R.; Correa, João C. F.; Baker, Richard; Lucareli, Paulo R. G.

2014-01-01

Background: Gait disorders are common in individuals with Parkinson's Disease (PD) and the concurrent performance of motor and cognitive tasks can have marked effects on gait. The Gait Profile Score (GPS) and the Movement Analysis Profile (MAP) were developed in order to summarize the data of kinematics and facilitate understanding of the results of gait analysis. Objective: To investigate the effectiveness of the GPS and MAP in the quantification of changes in gait during a concurrent cognitive load while walking in adults with and without PD. Method: Fourteen patients with idiopathic PD and nine healthy subjects participated in the study. All subjects performed single and dual walking tasks. The GPS/MAP was computed from three-dimensional gait analysis data. Results: Differences were found between tasks for GPS (P<0.05) and Gait Variable Score (GVS) (pelvic rotation, knee flexion-extension and ankle dorsiflexion-plantarflexion) (P<0.05) in the PD group. An interaction between task and group was observed for GPS (P<0.01) for the right side (Cohen's ¯d=0.99), left side (Cohen's ¯d=0.91), and overall (Cohen's ¯d=0.88). No interaction was observed only for hip internal-external rotation and foot internal-external progression GVS variables in the PD group. Conclusions: The results showed gait impairment during the dual task and suggest that GPS/MAP may be used to evaluate the effects of concurrent cognitive load while walking in patients with PD. PMID:25054382

Sagittal Thoracic and Lumbar Spine Profiles in Upright Standing and Lying Prone Positions Among Healthy Subjects: Influence of Various Biometric Features.

PubMed

Salem, Walid; Coomans, Ysaline; Brismée, Jean-Michel; Klein, Paul; Sobczak, Stéphane; Dugailly, Pierre-Michel

2015-08-01

A prospective study was performed on the assessment of both thoracic and lumbar spine sagittal profiles (from C7 to S1). To propose a new noninvasive method for measuring the spine curvatures in standing and lying prone positions and to analyze their relationship with various biometric characteristics. Modifications of spine curvatures (i.e. lordosis or kyphosis) are of importance in the development of spinal disorders. Studies have emphasized the development of new devices to measure the spine sagittal profiles using a noninvasive and low-cost method. To date, it has not been applied for analyzing both lumbar and thoracic alterations for various positioning. Seventy-five healthy subjects (mean 22.6 ± 4.3 yr) were recruited to participate in this study. Thoracic and lumbar sagittal profiles were assessed in standing and lying prone positions using a 3D digitizer. In addition, several biometric data were collected including maximal trunk isometric strength for flexion and extension movement. Statistical analysis consisted in data comparisons of spine profiles and a multivariate analysis including biometric features, to classify individuals considering low within- and high between-variability. Kyphosis and lordosis angles decreased significantly from standing to lying prone position by an average of 13.4° and 16.6°, respectively. Multivariate analysis showed a sample clustering of 3 homogenous subgroups. The first group displayed larger lordosis and flexibility, and had low data values for height, weight, and strength. The second group had lower values than the overall trend of the whole sample, whereas the third group had larger score values for the torques, height, weight, waist, body mass index, and kyphosis angle but a reduced flexibility. The present results demonstrate a significant effect of the positioning on both thoracic and lumbar spine sagittal profiles and highlight the use of cluster analysis to categorize subgroups after biometric characteristics including curvature measurement. N/A.

Development of DNA Microarrays for Metabolic Pathway and Bioprocess Monitoring

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

Gregory Stephanopoulos

Transcriptional profiling experiments utilizing DNA microarrays to study the intracellular accumulation of PHB in Synechocystis has proved difficult in large part because strains that show significant differences in PHB which would justify global analysis of gene expression have not been isolated.

Metabolomics Coupled with Multivariate Data and Pathway Analysis on Potential Biomarkers in Gastric Ulcer and Intervention Effects of Corydalis yanhusuo Alkaloid

PubMed Central

Shuai, Wang; Yongrui, Bao; Shanshan, Guan; Bo, Liu; Lu, Chen; Lei, Wang; Xiaorong, Ran

2014-01-01

Metabolomics, the systematic analysis of potential metabolites in a biological specimen, has been increasingly applied to discovering biomarkers, identifying perturbed pathways, measuring therapeutic targets, and discovering new drugs. By analyzing and verifying the significant difference in metabolic profiles and changes of metabolite biomarkers, metabolomics enables us to better understand substance metabolic pathways which can clarify the mechanism of Traditional Chinese Medicines (TCM). Corydalis yanhusuo alkaloid (CA) is a major component of Qizhiweitong (QZWT) prescription which has been used for treating gastric ulcer for centuries and its mechanism remains unclear completely. Metabolite profiling was performed by high-performance liquid chromatography combined with time-of-flight mass spectrometry (HPLC/ESI-TOF-MS) and in conjunction with multivariate data analysis and pathway analysis. The statistic software Mass Profiller Prossional (MPP) and statistic method including ANOVA and principal component analysis (PCA) were used for discovering novel potential biomarkers to clarify mechanism of CA in treating acid injected rats with gastric ulcer. The changes in metabolic profiling were restored to their base-line values after CA treatment according to the PCA score plots. Ten different potential biomarkers and seven key metabolic pathways contributing to the treatment of gastric ulcer were discovered and identified. Among the pathways, sphingophospholipid metabolism and fatty acid metabolism related network were acutely perturbed. Quantitative real time polymerase chain reaction (RT-PCR) analysis were performed to evaluate the expression of genes related to the two pathways for verifying the above results. The results show that changed biomarkers and pathways may provide evidence to insight into drug action mechanisms and enable us to increase research productivity toward metabolomics drug discovery. PMID:24454691

Integrative Analysis of Cancer Diagnosis Studies with Composite Penalization

PubMed Central

Liu, Jin; Huang, Jian; Ma, Shuangge

2013-01-01

Summary In cancer diagnosis studies, high-throughput gene profiling has been extensively conducted, searching for genes whose expressions may serve as markers. Data generated from such studies have the “large d, small n” feature, with the number of genes profiled much larger than the sample size. Penalization has been extensively adopted for simultaneous estimation and marker selection. Because of small sample sizes, markers identified from the analysis of single datasets can be unsatisfactory. A cost-effective remedy is to conduct integrative analysis of multiple heterogeneous datasets. In this article, we investigate composite penalization methods for estimation and marker selection in integrative analysis. The proposed methods use the minimax concave penalty (MCP) as the outer penalty. Under the homogeneity model, the ridge penalty is adopted as the inner penalty. Under the heterogeneity model, the Lasso penalty and MCP are adopted as the inner penalty. Effective computational algorithms based on coordinate descent are developed. Numerical studies, including simulation and analysis of practical cancer datasets, show satisfactory performance of the proposed methods. PMID:24578589

Pulsed-Field Gel Electrophoresis Analysis of Bordetella pertussis Isolates Circulating in Europe from 1998 to 2009

PubMed Central

Advani, Abdolreza; Hallander, Hans O.; Dalby, Tine; Krogfelt, Karen Angeliki; Guiso, Nicole; Njamkepo, Elisabeth; von Könnig, Carl Heinz Wirsing; Riffelmann, Marion; Mooi, Frits R.; Sandven, Per; Lutyńska, Anna; Fry, Norman K.; Mertsola, Jussi

2013-01-01

Between 1998 and 2009, Bordetella pertussis clinical isolates were collected during three periods, i.e., 1998 to 2001 (n = 102), 2004 to 2005 (n = 154), and 2007 to 2009 (n = 140), from nine countries with distinct vaccination programs, i.e., Denmark, Finland, France, Germany, The Netherlands, Norway, Poland, Sweden, and the United Kingdom. Pulsed-field gel electrophoresis (PFGE) analysis was performed according to standardized recommendations for epidemiological typing of B. pertussis. There were 81 different PFGE profiles, five of which (BpSR3, BpSR5, BpSR10, BpSR11, and BpSR12) were observed in 61% of the 396 isolates and shown to be predominant in almost all countries. The major profile, BpSR11, showed a decreasing trend from 25% to 30% in 1998 to 2005 to 13% in 2007 to 2009, and there were increases in BpSR3 and BpSR10 from 0% and 8% to 21% and 22%, respectively. One difference between these profiles is that BpSR11 contains isolates harboring the fim3-2 allele and BpSR3 and BpSR10 contain isolates harboring the fim3-1 allele. The total proportion of the five predominant profiles increased from 44% in 1998 to 2001 to 63% in 2004 to 2005 to 70% in 2007 to 2009. In conclusion, common PFGE profiles were identified in B. pertussis populations circulating in European countries with different vaccination programs and different vaccine coverages. These prevalent isolates contain the novel pertussis toxin promoter ptxP3 allele. However, there is evidence for diversifying selection between ptxP3 strains characterized by distinct PFGE profiles. This work shows that, even within a relatively short time span of 10 years, successful isolates which spread through Europe and cause large shifts in B. pertussis populations may emerge. PMID:23175253

The Premature Ejaculation Profile: validation of self-reported outcome measures for research and practice.

PubMed

Patrick, Donald L; Giuliano, François; Ho, Kai Fai; Gagnon, Dennis D; McNulty, Pauline; Rothman, Margaret

2009-02-01

To evaluate the reliability and validity of the Premature Ejaculation Profile (PEP), a self-reported outcome instrument for evaluating domains of PE and its treatment, comprised of four single-item measures, a profile, and an index score. Data were from men participating in observational studies in the USA (PE, 207 men; non-PE, 1380) and Europe (PE, 201; non-PE, 914) and from men with PE (1238) participating in a phase III randomized, placebo-controlled clinical trial of dapoxetine. The PEP contains four measures: perceived control over ejaculation, personal distress related to ejaculation, satisfaction with sexual intercourse, and interpersonal difficulty related to ejaculation, each assessed on five-point response scales. Test-retest reliability, known-groups validity, and ability to detect a patient-reported global impression of change (PGI) in condition were evaluated for the individual PEP measures and a PEP index score (the mean of all four measures). Profile analysis was conducted using multivariate analysis of variance. All PEP measures showed acceptable reliability (intraclass correlation coefficients ranged from 0.66 to 0.83) and mean scores for all measures differed significantly between PE and non-PE groups (P < 0.001). Men who reported a reduction in PE with treatment in the phase III trial had significantly greater scores on each of the four measures. The PEP profiles of men with and without PE differed significantly (P < 0.001) in both observational studies; higher levels of PGI were associated with higher PEP profiles (P < 0.001). The PEP index score also showed acceptable reliability and was significantly different between the PE and non-PE groups (P < 0.001). Men who reported an improvement in PE with treatment in the phase III trial had significantly greater PEP index scores. In the phase III trial, nausea was the most common adverse event with dapoxetine. The PEP provides a reliable, valid, and interpretable measure for use in monitoring outcomes of men with PE.

Stem cells isolated from adipose tissue of obese patients show changes in their transcriptomic profile that indicate loss in stemcellness and increased commitment to an adipocyte-like phenotype

PubMed Central

2013-01-01

Background The adipose tissue is an endocrine regulator and a risk factor for atherosclerosis and cardiovascular disease when by excessive accumulation induces obesity. Although the adipose tissue is also a reservoir for stem cells (ASC) their function and “stemcellness” has been questioned. Our aim was to investigate the mechanisms by which obesity affects subcutaneous white adipose tissue (WAT) stem cells. Results Transcriptomics, in silico analysis, real-time polymerase chain reaction (PCR) and western blots were performed on isolated stem cells from subcutaneous abdominal WAT of morbidly obese patients (ASCmo) and of non-obese individuals (ASCn). ASCmo and ASCn gene expression clustered separately from each other. ASCmo showed downregulation of “stemness” genes and upregulation of adipogenic and inflammatory genes with respect to ASCn. Moreover, the application of bioinformatics and Ingenuity Pathway Analysis (IPA) showed that the transcription factor Smad3 was tentatively affected in obese ASCmo. Validation of this target confirmed a significantly reduced Smad3 nuclear translocation in the isolated ASCmo. Conclusions The transcriptomic profile of the stem cells reservoir in obese subcutaneous WAT is highly modified with significant changes in genes regulating stemcellness, lineage commitment and inflammation. In addition to body mass index, cardiovascular risk factor clustering further affect the ASC transcriptomic profile inducing loss of multipotency and, hence, capacity for tissue repair. In summary, the stem cells in the subcutaneous WAT niche of obese patients are already committed to adipocyte differentiation and show an upregulated inflammatory gene expression associated to their loss of stemcellness. PMID:24040759

Estimation and Psychometric Analysis of Component Profile Scores via Multivariate Generalizability Theory

ERIC Educational Resources Information Center

Grochowalski, Joseph H.

2015-01-01

Component Universe Score Profile analysis (CUSP) is introduced in this paper as a psychometric alternative to multivariate profile analysis. The theoretical foundations of CUSP analysis are reviewed, which include multivariate generalizability theory and constrained principal components analysis. Because CUSP is a combination of generalizability…

Coparenting profiles in the context of Mexican-origin teen pregnancy: links to mother-daughter relationship quality and adjustment.

PubMed

Perez-Brena, Norma J; Updegraff, Kimberly A; Umaña-Taylor, Adriana J; Jahromi, Laudan; Guimond, Amy

2015-06-01

The current study explored the multifaceted nature of the mother-adolescent coparental relationship with data from 167 Mexican-origin adolescent mothers and their own mothers at 10 months post childbirth. Profiles of mother-adolescent coparenting were created with latent profile analysis using adolescents' reports of three dimensions of coparenting (communication, involvement, and conflict). Four profiles were identified: (a) Harmonious Coparents (equal involvement, high communication, low conflict); (b) Harmonious-Adolescent Primary (adolescent is more involved than mother, high communication, low conflict); (c) Conflictual Coparents (equal involvement, high communication, high conflict); and (d) Conflictual-Adolescent Primary (adolescent is more involved than mother, moderate communication, high conflict). Families characterized by high mother-daughter conflict and psychological control prior to childbirth were more likely to belong in the Conflictual Coparents profile. In addition, adolescents' and mothers' depressive symptoms and parenting efficacy after childbirth were linked to profile membership, such that the Harmonious-Adolescent Primary profile reported the most positive adjustment patterns, whereas profiles with high coparental conflict (i.e., Conflictual Coparenting and Conflictual-Adolescent Primary profiles) showed the least positive adjustment patterns. Discussion considers the applied implications of identifying precursors to healthy and problematic mother-daughter coparenting for families of adolescent mothers in the early years of parenting. © 2014 Family Process Institute.

Coparenting Profiles in the Context of Mexican-Origin Teen Pregnancy: Links to Mother-Daughter Relationship Quality and Adjustment

PubMed Central

Perez-Brena, Norma J.; Updegraff, Kimberly A.; Umaña-Taylor, Adriana J.; Jahromi, Laudan; Guimond, Amy

2015-01-01

The current study explored the multifaceted nature of the mother-adolescent coparental relationship with data from 167 Mexican-origin adolescent mothers and their own mothers at ten months post-childbirth. Profiles of mother-adolescent coparenting were created with latent profile analysis using adolescents’ reports of three dimensions of coparenting (communication, involvement and conflict). Four profiles were identified: (a) Harmonious Coparents (equal involvement, high communication, low conflict); (b) Harmonious-Adolescent Primary (adolescent is more involved than mother, high communication, low conflict); (c) Conflictual Coparents (equal involvement, high communication, high conflict); and (d) Conflictual-Adolescent Primary (adolescent is more involved than mother, moderate communication, high conflict). Families characterized by high mother-daughter conflict and psychological control prior to childbirth were more likely to belong in the Conflictual Coparents profile. In addition, adolescents’ and mothers’ depressive symptoms and parenting efficacy after childbirth were linked to profile membership, such that the Harmonious-Adolescent Primary profile reported the most positive adjustment patterns, whereas profiles with high coparental conflict (i.e., Conflictual Coparenting and Conflictual-Adolescent Primary profiles) showed the least positive adjustment patterns. Discussion considers the applied implications of identifying precursors to healthy and problematic mother-daughter coparenting for families of adolescent mothers in the early years of parenting. PMID:25438748

Evaluating the Invariance of Cognitive Profile Patterns Derived from Profile Analysis via Multidimensional Scaling (PAMS): A Bootstrapping Approach

ERIC Educational Resources Information Center

Kim, Se-Kang

2010-01-01

The aim of the current study is to validate the invariance of major profile patterns derived from multidimensional scaling (MDS) by bootstrapping. Profile Analysis via Multidimensional Scaling (PAMS) was employed to obtain profiles and bootstrapping was used to construct the sampling distributions of the profile coordinates and the empirical…

Intestinal microbial variation may predict early acute rejection after liver transplantation in rats.

PubMed

Ren, Zhigang; Jiang, Jianwen; Lu, Haifeng; Chen, Xinhua; He, Yong; Zhang, Hua; Xie, Haiyang; Wang, Weilin; Zheng, Shusen; Zhou, Lin

2014-10-27

Acute rejection (AR) remains a life-threatening complication after orthotopic liver transplantation (OLT) and there are few available diagnostic biomarkers clinically for AR. This study aims to identify intestinal microbial profile and explore potential application of microbial profile as a biomarker for AR after OLT. The OLT models in rats were established. Hepatic graft histology, ultrastructure, function, and intestinal barrier function were tested. Ileocecal contents were collected for intestinal microbial analysis. Hepatic graft suffered from the ischemia-reperfusion (I/R) injury on day 1, initial AR on day 3, and severe AR on day 7 after OLT. Real-time quantitative polymerase chain reaction results showed that genus Faecalibacterium prausnitzii and Lactobacillus were decreased, whereas Clostridium bolteae was increased during AR. Notably, cluster analysis of denaturing gradient gel electrophoresis (DGGE) profiles showed the 7AR and 3AR groups clustered together with 73.4% similarity, suggesting that intestinal microbiota was more sensitive than hepatic function in responding to AR. Microbial diversity and species richness were decreased during AR. Phylogenetic tree analysis showed that most of the decreased key bacteria belonged to phylum Firmicutes, whereas increased key bacteria belonged to phylum Bacteroidetes. Moreover, intestinal microvilli loss and tight junction damage were noted, and intestinal barrier dysfunction during AR presented a decrease of fecal secretory immunoglobulin A (sIgA) and increase of blood bacteremia, endotoxin, and tumor necrosis factor-α. We dynamically detail intestinal microbial characterization and find a high sensitivity of microbial change during AR after OLT, suggesting that intestinal microbial variation may predict AR in early phase and become an assistant therapeutic target to improve rejection after OLT.

Innovations in the development of healthier chicken sausages formulated with different lipid sources.

PubMed

Andrés, S C; Zaritzky, N E; Califano, A N

2009-08-01

Long-chain polyunsaturated n-3 fatty acids are critical nutrients for human health and the fortification of foods with these fatty acids is an important emerging area from the commercial and academic point of view. Development, characterization, and changes during refrigerated vacuum storage of low-fat chicken sausages formulated with preemulsified squid oil were examined and compared with those formulated with beef tallow. Physicochemical analysis and process yield after heat treatment were determined; the heat-treated sausages were evaluated by purge loss, color, texture, microstructure by SEM, microbial counts, fatty acid profile, lipid oxidation, and sensory analysis during refrigerated vacuum storage. Process yield of both formulations was higher than 97% and purge losses during storage were lower than 7%. Purge losses of oil-formulated sausages were lower than those with beef tallow. Sausages with squid oil resulted in higher lightness, lower redness and yellowness, and lower texture profile analysis parameters than the formulation prepared with beef tallow. Microstructure of both formulations was similar, except for the fat droplets that microscopic observations showed in the sausages made with beef tallow. Low lipid oxidation was detected in formulation with squid oil due to the the combination of ingredients and storage conditions. Microbial counts of both products were less than 5 log cfu/g at the end of 90 d of storage. The sausage formulated with squid oil presented more than 30 and 40 g/100 g of monounsaturated and polyunsaturated fatty acids, respectively. Docosahexaenoic acid was the predominant polyunsaturated fatty acid, followed by eicosapentaenoic acid and linoleic acid. Both products showed safe sanitary conditions, good sensory acceptability, and presented very good stability and quality attributes, but sausages formulated with squid oil showed a better fatty acid profile according to nutritional criteria.

Intestinal Microbial Variation May Predict Early Acute Rejection after Liver Transplantation in Rats

PubMed Central

Ren, Zhigang; Jiang, Jianwen; Lu, Haifeng; Chen, Xinhua; He, Yong; Zhang, Hua; Xie, Haiyang; Wang, Weilin; Zheng, Shusen; Zhou, Lin

2014-01-01

Background Acute rejection (AR) remains a life-threatening complication after orthotopic liver transplantation (OLT) and there are few available diagnostic biomarkers clinically for AR. This study aims to identify intestinal microbial profile and explore potential application of microbial profile as a biomarker for AR after OLT. Methods The OLT models in rats were established. Hepatic graft histology, ultrastructure, function, and intestinal barrier function were tested. Ileocecal contents were collected for intestinal microbial analysis. Results Hepatic graft suffered from the ischemia-reperfusion (I/R) injury on day 1, initial AR on day 3, and severe AR on day 7 after OLT. Real-time quantitative polymerase chain reaction results showed that genus Faecalibacterium prausnitzii and Lactobacillus were decreased, whereas Clostridium bolteae was increased during AR. Notably, cluster analysis of denaturing gradient gel electrophoresis (DGGE) profiles showed the 7AR and 3AR groups clustered together with 73.4% similarity, suggesting that intestinal microbiota was more sensitive than hepatic function in responding to AR. Microbial diversity and species richness were decreased during AR. Phylogenetic tree analysis showed that most of the decreased key bacteria belonged to phylum Firmicutes, whereas increased key bacteria belonged to phylum Bacteroidetes. Moreover, intestinal microvilli loss and tight junction damage were noted, and intestinal barrier dysfunction during AR presented a decrease of fecal secretory immunoglobulin A (sIgA) and increase of blood bacteremia, endotoxin, and tumor necrosis factor-α. Conclusion We dynamically detail intestinal microbial characterization and find a high sensitivity of microbial change during AR after OLT, suggesting that intestinal microbial variation may predict AR in early phase and become an assistant therapeutic target to improve rejection after OLT. PMID:25321166

Stratospheric column NO2 anomalies over Russia related to the 2011 Arctic ozone hole

NASA Astrophysics Data System (ADS)

Aheyeva, Viktoryia; Gruzdev, Aleksandr; Elokhov, Aleksandr; Grishaev, Mikhail; Salnikova, Natalia

2013-04-01

We analyze data of spectrometric measurements of stratospheric column NO2 contents at mid- and high-latitude stations of Zvenigorod (55.7°N, Moscow region), Tomsk (56.5°N, West Siberia), and Zhigansk (66.8°N, East Siberia). Measurements are done in visual spectral range with zenith-viewing spectrometers during morning and evening twilights. Alongside column NO2 contents, vertical profiles of NO2 are retrieved at the Zvenigorod station. Zvenigorod and Zhigansk are the measurement stations within the Network for the Detection of Atmospheric Composition Change (NDACC). For interpretation of results of analysis of NO2 data, data of Ozone Monitoring Instrument measurements of total column ozone and rawinsonde data are also analyzed and back trajectories calculated with the help of HYSPLIT trajectory model are used. Significant negative anomalies in stratospheric NO2 columns accompanied by episodes of significant cooling of the stratosphere and decrease in total ozone were observed at the three stations in the winter-spring period of 2011. Trajectory analysis shows that the anomalies were caused by the transport of stratospheric air from the region of the ozone hole observed that season in the Arctic. Although negative NO2 anomalies due to the transport from the Arctic were also observed in some other years, the anomalies in 2011 have had record magnitudes. Analysis of NO2 vertical profiles at Zvenigorod shows that the NO2 anomaly in 2011 compared to other years anomalies was additionally contributed by the denitrification of the Arctic lower stratosphere. NO2 profiles show that a certain degree of the denitrification probably survived even after the ozone hole.

The antimicrobial susceptibility, biofilm formation and genotypic profiles of Staphylococcus haemolyticus from bloodstream infections

PubMed Central

Silva, Patricia Vollú; Cruz, Raquel Souza; Keim, Luiz Sérgio; de Paula, Geraldo Renato; Carvalho, Bernadete Teixeira Ferreira; Coelho, Leonardo Rocchetto; Carvalho, Maria Cícera da Silva; da Rosa, Joel Mauricio Corrêa; Figueiredo, Agnes Marie Sá; Teixeira, Lenise Arneiro

2013-01-01

We analysed the antimicrobial susceptibility, biofilm formation and genotypic profiles of 27 isolates of Staphylococcus haemolyticus obtained from the blood of 19 patients admitted to a hospital in Rio de Janeiro, Brazil. Our analysis revealed a clinical significance of 36.8% and a multi-resistance rate of 92.6% among these isolates. All but one isolate carried the mecA gene. The staphylococcal cassette chromosome mec type I was the most prevalent mec element detected (67%). Nevertheless, the isolates showed clonal diversity based on pulsed-field gel electrophoresis analysis. The ability to form biofilms was detected in 66% of the isolates studied. Surprisingly, no icaAD genes were found among the biofilm-producing isolates. PMID:24037208

The antimicrobial susceptibility, biofilm formation and genotypic profiles of Staphylococcus haemolyticus from bloodstream infections.

PubMed

Silva, Patricia Vollú; Cruz, Raquel Souza; Keim, Luiz Sérgio; Paula, Geraldo Renato de; Carvalho, Bernadete Teixeira Ferreira; Coelho, Leonardo Rocchetto; Carvalho, Maria Cícera da Silva; Rosa, Joel Mauricio Corrêa da; Figueiredo, Agnes Marie Sá; Teixeira, Lenise Arneiro

2013-09-01

We analysed the antimicrobial susceptibility, biofilm formation and genotypic profiles of 27 isolates of Staphylococcus haemolyticus obtained from the blood of 19 patients admitted to a hospital in Rio de Janeiro, Brazil. Our analysis revealed a clinical significance of 36.8% and a multi-resistance rate of 92.6% among these isolates. All but one isolate carried the mecA gene. The staphylococcal cassette chromosome mec type I was the most prevalent mec element detected (67%). Nevertheless, the isolates showed clonal diversity based on pulsed-field gel electrophoresis analysis. The ability to form biofilms was detected in 66% of the isolates studied. Surprisingly, no icaAD genes were found among the biofilm-producing isolates.

Precision analysis for standard deviation measurements of immobile single fluorescent molecule images.

PubMed

DeSantis, Michael C; DeCenzo, Shawn H; Li, Je-Luen; Wang, Y M

2010-03-29

Standard deviation measurements of intensity profiles of stationary single fluorescent molecules are useful for studying axial localization, molecular orientation, and a fluorescence imaging system's spatial resolution. Here we report on the analysis of the precision of standard deviation measurements of intensity profiles of single fluorescent molecules imaged using an EMCCD camera.We have developed an analytical expression for the standard deviation measurement error of a single image which is a function of the total number of detected photons, the background photon noise, and the camera pixel size. The theoretical results agree well with the experimental, simulation, and numerical integration results. Using this expression, we show that single-molecule standard deviation measurements offer nanometer precision for a large range of experimental parameters.

Social network utilization (Facebook) & e-Professionalism among medical students

PubMed Central

Jawaid, Masood; Khan, Muhammad Hassaan; Bhutto, Shahzadi Nisar

2015-01-01

Objective: To find out the frequency and contents of online social networking (Facebook) among medical students of Dow University of Health Sciences. Methods: The sample of the study comprised of final year students of two medical colleges of Dow University of Health Sciences – Karachi. Systematic search for the face book profiles of the students was carried out with a new Facebook account. In the initial phase of search, it was determined whether each student had a Facebook account and the status of account as ‘‘private’’ ‘‘intermediate’’ or ‘‘public’’ was also sought. In the second phase of the study, objective information including gender, education, personal views, likes, tag pictures etc. were recorded for the publicly available accounts. An in depth qualitative content analysis of the public profiles of ten medical students, selected randomly with the help of random number generator technique was conducted. Results: Social networking with Facebook is common among medical students with 66.9% having an account out of a total 535 students. One fifth of profiles 18.9% were publicly open, 36.6% profiles were private and 56.9% were identified to have an intermediate privacy setting, having customized settings for the profile information. In-depth analysis of some public profiles showed that potentially unprofessional material mostly related to violence and politics was posted by medical students. Conclusion: The usage of social network (Facebook) is very common among students of the university. Some unprofessional posts were also found on students’ profiles mostly related to violence and politics. PMID:25878645

Measurements of fast ion spatial dynamics during magnetic activity in the RFP

NASA Astrophysics Data System (ADS)

Goetz, J. A.; Anderson, J. K.; Bonofiglo, P.; Kim, J.; McConnell, R.; Magee, R. M.

2017-10-01

Fast ions in the RFP are only weakly affected by a stochastic magnetic field and behave nearly classically in concentration too low to excite Alfvenic activity. At high fast ion concentration sourced by H-NBI in 300kA RFP discharges, a substantial drop in core-localized high pitch fast ions is observed during bursts of coupled EPM and IAE (magnetic island-induced Alfven eigenmode) activity (100-200kHz) through neutral particle analysis. Sourcing instead fast deuterium with NBI, the DD fusion products can measure the dynamics of the fast ion density profile. Both a collimated neutron detector and a new 3MeV fusion proton detector loaned by TriAlpha Energy measure the fast ion density profile with 5cm spatial resolution and 100 μs temporal resolution. In D-NBI, the bursting EPM is excited at slightly lower frequency and the IAE activity is nearly absent, likely due to an isotope effect and loss of wave-particle interaction. In these cases, neutral particle analysis shows little change in the core-localized high pitch fast ion content, and the fusion product profile indicates little change in the fast ion density profile, leaving unexplained the mechanism removing EPM drive. We measure a substantial redistribution of the fast ion profile due to strong lower-frequency ( 30kHz) MHD activity that accompanies the current profile relaxation in the RFP. Profile flattening is strongest in low bulk density discharges, which often occur with a total increase in global neutron flux from acceleration of the beam ions. Work supported by US DoE.

Preliminary profiling of blood transcriptome in a rat model of hemorrhagic shock

PubMed Central

Braga, D; Barcella, M; D’Avila, F; Lupoli, S; Tagliaferri, F; Santamaria, MH; DeLano, FA; Baselli, G; Schmid-Schönbein, GW; Kistler, EB; Aletti, F

2017-01-01

Hemorrhagic shock is a leading cause of morbidity and mortality worldwide. Significant blood loss may lead to decreased blood pressure and inadequate tissue perfusion with resultant organ failure and death, even after replacement of lost blood volume. One reason for this high acuity is that the fundamental mechanisms of shock are poorly understood. Proteomic and metabolomic approaches have been used to investigate the molecular events occurring in hemorrhagic shock but, to our knowledge, a systematic analysis of the transcriptomic profile is missing. Therefore, a pilot analysis using paired-end RNA sequencing was used to identify changes that occur in the blood transcriptome of rats subjected to hemorrhagic shock after blood reinfusion. Hemorrhagic shock was induced using a Wigger’s shock model. The transcriptome of whole blood from shocked animals shows modulation of genes related to inflammation and immune response (Tlr13, Il1b, Ccl6, Lgals3), antioxidant functions (Mt2A, Mt1), tissue injury and repair pathways (Gpnmb, Trim72) and lipid mediators (Alox5ap, Ltb4r, Ptger2) compared with control animals. These findings are congruent with results obtained in hemorrhagic shock analysis by other authors using metabolomics and proteomics. The analysis of blood transcriptome may be a valuable tool to understand the biological changes occurring in hemorrhagic shock and a promising approach for the identification of novel biomarkers and therapeutic targets. Impact statement This study provides the first pilot analysis of the changes occurring in transcriptome expression of whole blood in hemorrhagic shock (HS) rats. We showed that the analysis of blood transcriptome is a useful approach to investigate pathways and functional alterations in this disease condition. This pilot study encourages the possible application of transcriptome analysis in the clinical setting, for the molecular profiling of whole blood in HS patients. PMID:28661205

Interpersonal value profiles and analysis of adolescent academic performance and social thinking

PubMed Central

Gázquez, José J.; Sainz, Jorge; Pérez-Fuentes, María del C.; Molero, María del M.; Soler, Francisco J.

2015-01-01

The purposes of this study were to identify interpersonal value profiles and find out whether there were any differences in academic performance and social thinking. The study sample was 885 high school students of whom 49.8% (N = 441) were boys and 50.2% (N = 444) were girls. The results show that students with low Benevolence and Conformity levels showed higher prevalence of failures and repeated the year more often. Furthermore, students with a high level of Recognition and Leadership and low Conformity and Benevolence are socially incompetent students. Intervention programs should to achieve high levels of kindness and consideration, respect for rules and generosity, and diminish the perception of recognition by others and exertion of authority. Thus, this study shows the values that must be worked on to improve students’ Academic Performance and social competence. PMID:25999891

MicroRNA expression profiling in alveolar macrophages of indigenous Chinese Tongcheng pigs infected with PRRSV in vivo.

PubMed

Zhou, Xiang; Michal, Jennifer J; Jiang, Zhihua; Liu, Bang

2017-11-01

Porcine respiratory and reproductive syndrome (PRRS), caused by PRRS virus (PRRSV), is one of the most serious infectious diseases in the swine industry worldwide. Indigenous Chinese Tongcheng (TC) pigs reportedly show strong resistance to PRRSV infection. The miRNA expression profiles of porcine alveolar macrophages (PAMs) of control TC pigs and those infected with PRRSV in vivo were analyzed by high-throughput sequencing to explore changes induced by infection. A total of 182 known miRNAs including 101 miRNA-5p and 81 miRNA-3p were identified with 23 up-regulated differentially expressed miRNAs (DEmiRNAs) and 25 down-regulated DEmiRNAs. Gene Ontology analysis showed that predicted target genes for the DEmiRNAs were enriched in immune response, transcription regulation, and cell death. The integrative analysis of mRNA and miRNA expression revealed that down-regulated methylation-related genes (DNMT1 and DNMT3b) were targeted by five up-regulated DEmiRNAs. Furthermore, 35 pairs of miRNAs (70 miRNAs) were co-expressed after PRRSV infection and six pairs were co-expressed differently. Our results describe miRNA expression profiles of TC pigs in response to PRRSV infection and lay a strong foundation for developing novel therapies to control PRRS in pigs.

Genome-Wide Evolutionary Characterization and Expression Analyses of WRKY Family Genes in Brachypodium distachyon

PubMed Central

Wen, Feng; Zhu, Hong; Li, Peng; Jiang, Min; Mao, Wenqing; Ong, Chermaine; Chu, Zhaoqing

2014-01-01

Members of plant WRKY gene family are ancient transcription factors that function in plant growth and development and respond to biotic and abiotic stresses. In our present study, we have investigated WRKY family genes in Brachypodium distachyon, a new model plant of family Poaceae. We identified a total of 86 WRKY genes from B. distachyon and explored their chromosomal distribution and evolution, domain alignment, promoter cis-elements, and expression profiles. Combining the analysis of phylogenetic tree of BdWRKY genes and the result of expression profiling, results showed that most of clustered gene pairs had higher similarities in the WRKY domain, suggesting that they might be functionally redundant. Neighbour-joining analysis of 301 WRKY domains from Oryza sativa, Arabidopsis thaliana, and B. distachyon suggested that BdWRKY domains are evolutionarily more closely related to O. sativa WRKY domains than those of A. thaliana. Moreover, tissue-specific expression profile of BdWRKY genes and their responses to phytohormones and several biotic or abiotic stresses were analysed by quantitative real-time PCR. The results showed that the expression of BdWRKY genes was rapidly regulated by stresses and phytohormones, and there was a strong correlation between promoter cis-elements and the phytohormones-induced BdWRKY gene expression. PMID:24453041

Comprehensive analysis of the transcriptional profile of the Mediator complex across human cancer types.

PubMed

Syring, Isabella; Klümper, Niklas; Offermann, Anne; Braun, Martin; Deng, Mario; Boehm, Diana; Queisser, Angela; von Mässenhausen, Anne; Brägelmann, Johannes; Vogel, Wenzel; Schmidt, Doris; Majores, Michael; Schindler, Anne; Kristiansen, Glen; Müller, Stefan C; Ellinger, Jörg; Shaikhibrahim, Zaki; Perner, Sven

2016-04-26

The Mediator complex is a key regulator of gene transcription and several studies demonstrated altered expressions of particular subunits in diverse human diseases, especially cancer. However a systematic study deciphering the transcriptional expression of the Mediator across different cancer entities is still lacking.We therefore performed a comprehensive in silico cancer vs. benign analysis of the Mediator complex subunits (MEDs) for 20 tumor entities using Oncomine datasets. The transcriptional expression profiles across almost all cancer entities showed differentially expressed MEDs as compared to benign tissue. Differential expression of MED8 in renal cell carcinoma (RCC) and MED12 in lung cancer (LCa) were validated and further investigated by immunohistochemical staining on tissue microarrays containing large numbers of specimen. MED8 in clear cell RCC (ccRCC) associated with shorter survival and advanced TNM stage and showed higher expression in metastatic than primary tumors. In vitro, siRNA mediated MED8 knockdown significantly impaired proliferation and motility in ccRCC cell lines, hinting at a role for MED8 to serve as a novel therapeutic target in ccRCC. Taken together, our Mediator complex transcriptome proved to be a valid tool for identifying cancer-related shifts in Mediator complex composition, revealing that MEDs do exhibit cancer specific transcriptional expression profiles.

Entrainment at a sediment concentration interface in turbulent channel flow

NASA Astrophysics Data System (ADS)

Salinas, Jorge; Shringarpure, Mrugesh; Cantero, Mariano; Balachandar, S.

2016-11-01

In this work we address the role of turbulence on entrainment at a sediment concentration interface. This process can be conceived as the entrainment of sediment-free fluid into the bottom sediment-laden flow, or alternatively, as the entrainment of sediment into the top sediment-free flow. We have performed direct numerical simulations for fixed Reynolds and Schmidt numbers while varying the values of Richardson number and particle settling velocity. The analysis performed shows that the ability of the flow to pick up a given sediment size decreases with the distance from the bottom, and thus only fine enough sediment particles are entrained across the sediment concentration interface. For these cases, the concentration profiles evolve to a final steady state in good agreement with the well-known Rouse profile. The approach towards the Rouse profile happens through a transient self-similar state. Detailed analysis of the three dimensional structure of the sediment concentration interface shows the mechanisms by which sediment particles are lifted up by tongues of sediment-laden fluid with positive correlation between vertical velocity and sediment concentration. Finally, the mixing ability of the flow is addressed by monitoring the center of mass of the sediment-laden layer. With the support of ExxonMobil, NSF, ANPCyT, CONICET.

A Rocket Investigation of Mesospheric Eddy Diffusion Effects on Airglow and Oxygen Chemistry

NASA Technical Reports Server (NTRS)

Ulwick, James C.

2001-01-01

A Terrier Orion rocket was launched at 0750 Z on 02/25/98 about seven minutes after the Clemson University chemical release rocket. Measurements made of the electron density by a dc probe calibrated by a capacitance probe showed several layers of electron density on a rocket ascent in the altitude range from 90 to 110 km. Rocket descent results showed several but not all of the ascent structure. From power spectral analysis of the measured electron densities, turbulent parameters are derived Measurements were made on rocket ascent and descent by an infrared radiometer of the OH Meinel (3-1) band and O2 singlet delta emissions. Profiles of the emissions are presented and discussed on both rocket ascent and descent an enhancement of the OH emission monitored by the OH radiometer was observed above 90 km. The glow was not defected by the O2 radiometer and was significantly reduced on rocket descent. Using these data and a mechanistic analysis, a profile proportional to atomic oxygen is obtained. This profile is compared to one from the ATOX probe on the rocket. A one-dimensional (1-D) photochemical model that solves the time-dependent continuity equations is used with the rocket data to investigate the odd-oxygen concentration in the near equatorial mesosphere.

Targeted mutation analysis of endometrial clear cell carcinoma.

PubMed

Hoang, Lien N; McConechy, Melissa K; Meng, Bo; McIntyre, John B; Ewanowich, Carol; Gilks, Cyril Blake; Huntsman, David G; Köbel, Martin; Lee, Cheng-Han

2015-04-01

Endometrial clear cell carcinomas (CCC) constitute fewer than 5% of all carcinomas of the endometrium. Currently, little is known regarding the genetic basis of endometrial CCC. We performed genomic and immunohistochemical analyses on 14 rigorously reviewed pure endometrial CCC. The genomic analysis consisted of sequencing the coding regions of 26 genes implicated previously in endometrial carcinoma. Twelve of 14 tumours displayed a prototypical CCC immunophenotype [napsin A+, hepatocyte nuclear factor-1β (HNF1β(+) ) and oestrogen receptor(-) ] and all showed intact mismatch repair protein expression. We detected mutations in 11 of 14 tumours, and there was a predominance of mutations involving genes that are mutated more frequently in endometrial serous carcinomas than in endometrioid carcinomas. Two tumours displayed a prototypical serous carcinoma mutation profile (concurrent TP53 and PPP2R1A mutations, without PTEN, CTNNB1 or ARID1A mutation). No mutations in PTEN, CTNNB1 or POLE were identified. The overall mutation profile of this cohort of endometrial CCC appears to be more serous-like than endometrioid-like, with a minor subset in the TP53-mutated CCC showing serous carcinoma profile. These findings provide new insights into the molecular features of morphologically prototypical endometrial CCC, and underscore the need for further investigations into the oncogenesis of endometrial CCC. © 2014 John Wiley & Sons Ltd.

Variation of volatile compounds among wheat varieties and landraces.

PubMed

Starr, G; Petersen, M A; Jespersen, B M; Hansen, Å S

2015-05-01

Analysis of volatile compounds was performed on 81 wheat varieties and landraces, grown under controlled greenhouse conditions, in order to investigate the possibility of differentiating wheat varieties according to their volatile compound profiles. Volatile compounds from wheat samples were extracted by dynamic headspace extraction and analysed by gas chromatography-mass spectrometry. Seventy-two volatile compounds were identified in the wheat samples. Multivariate analysis of the data showed a large diversity in volatile profiles between samples. Differences occurred between samples from Austria compared to British, French and Danish varieties. Landraces were distinguishable from modern varieties and they were characterised by higher averaged peak areas for esters, alcohols, and some furans. Modern varieties were characterised by higher averaged peak areas for terpenes, pyrazines and straight-chained aldehydes. Differences in volatile profiles are demonstrated between wheat samples for the first time, based on variety. These results are significant to plant breeders and commercial users of wheat. Copyright © 2014 Elsevier Ltd. All rights reserved.

The deuterium depth profile in neutron-irradiated tungsten exposed to plasma

NASA Astrophysics Data System (ADS)

Shimada, Masashi; Cao, G.; Hatano, Y.; Oda, T.; Oya, Y.; Hara, M.; Calderoni, P.

2011-12-01

Tungsten samples (99.99% purity from A.L.M.T. Corp., 6 mm in diameter, 0.2 mm in thickness) were irradiated by high-flux neutrons at 50 °C to 0.025 dpa in the High Flux Isotope Reactor at Oak Ridge National Laboratory. Subsequently, the neutron-irradiated tungsten samples were exposed to high-flux deuterium plasmas (ion flux: 1021-1022 m-2 s-1, ion fluence: 1025-1026 m-2) in the Tritium Plasma Experiment at Idaho National Laboratory. This paper reports the results of deuterium depth profiling in neutron-irradiated tungsten exposed to plasmas at 100, 200 and 500 °C via nuclear reaction analysis (NRA). The NRA measurements show that a significant amount of deuterium (>0.1 at.% D/W) remains trapped in the bulk material (up to 5 μm) at 500 °C. Tritium Migration Analysis Program simulation results using the NRA profiles indicate that different trapping mechanisms exist for neutron-irradiated and unirradiated tungsten.

Methylation-sensitive amplified polymorphism-based genome-wide analysis of cytosine methylation profiles in Nicotiana tabacum cultivars.

PubMed

Jiao, J; Wu, J; Lv, Z; Sun, C; Gao, L; Yan, X; Cui, L; Tang, Z; Yan, B; Jia, Y

2015-11-26

This study aimed to investigate cytosine methylation profiles in different tobacco (Nicotiana tabacum) cultivars grown in China. Methylation-sensitive amplified polymorphism was used to analyze genome-wide global methylation profiles in four tobacco cultivars (Yunyan 85, NC89, K326, and Yunyan 87). Amplicons with methylated C motifs were cloned by reamplified polymerase chain reaction, sequenced, and analyzed. The results show that geographical location had a greater effect on methylation patterns in the tobacco genome than did sampling time. Analysis of the CG dinucleotide distribution in methylation-sensitive polymorphic restriction fragments suggested that a CpG dinucleotide cluster-enriched area is a possible site of cytosine methylation in the tobacco genome. The sequence alignments of the Nia1 gene (that encodes nitrate reductase) in Yunyan 87 in different regions indicate that a C-T transition might be responsible for the tobacco phenotype. T-C nucleotide replacement might also be responsible for the tobacco phenotype and may be influenced by geographical location.

Using cluster analysis to examine the combinations of motivation regulations of physical education students.

PubMed

Ullrich-French, Sarah; Cox, Anne

2009-06-01

According to self-determination theory, motivation is multidimensional, with motivation regulations lying along a continuum of self-determination (Ryan & Deci, 2007). Accounting for the different types of motivation in physical activity research presents a challenge. This study used cluster analysis to identify motivation regulation profiles and examined their utility by testing profile differences in relative levels of self-determination (i.e., self-determination index), and theoretical antecedents (i.e., competence, autonomy, relatedness) and consequences (i.e., enjoyment, worry, effort, value, physical activity) of physical education motivation. Students (N= 386) in 6th- through 8th-grade physical education classes completed questionnaires of the variables listed above. Five profiles emerged, including average (n = 81), motivated (n = 82), self-determined (n = 91), low motivation (n = 73), and external (n = 59). Group difference analyses showed that students with greater levels of self-determined forms of motivation, regardless of non-self-determined motivation levels, reported the most adaptive physical education experiences.

Genetic Relationships among Different Chemotypes of Lupinus sulphureus.

PubMed

Cook, Daniel; Mott, Ivan W; Larson, Steven R; Lee, Stephen T; Johnson, Robert; Stonecipher, Clinton A

2018-02-28

Lupines (Lupinus spp.) are a common plant legume species found on western U.S. rangelands. Lupinus spp. may contain quinolizidine and/or piperidine alkaloids that can be toxic and/or teratogenic to grazing livestock. Alkaloid profiles may vary between and within a species. The objectives of this study were to (1) further explore the characteristic alkaloid profiles of Lupinus sulphureus using field collections and (2) explore the phylogenetic relationship of the different populations and chemotypes of L. sulphureus using the amplified fragment length polymorphism method of DNA fingerprinting, thus providing possible explanations to the phenomena of multiple chemotypes within a species. A total of 49 accessions of L. sulphureus were classified into seven chemotypes. The DNA profiles showed that one L. sulphureus chemotype, chemotype A, is genetically divergent from the other chemotypes of L. sulphureus, suggesting that it represents an unresolved lupine taxon, possibly a new lupine species. Additionally, the different chemotypes of L. sulphureus represented different genetic groups, as shown by Bayesian cluster analysis and principle component analysis.

Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.

PubMed

Ceccarelli, Michele; Barthel, Floris P; Malta, Tathiane M; Sabedot, Thais S; Salama, Sofie R; Murray, Bradley A; Morozova, Olena; Newton, Yulia; Radenbaugh, Amie; Pagnotta, Stefano M; Anjum, Samreen; Wang, Jiguang; Manyam, Ganiraju; Zoppoli, Pietro; Ling, Shiyun; Rao, Arjun A; Grifford, Mia; Cherniack, Andrew D; Zhang, Hailei; Poisson, Laila; Carlotti, Carlos Gilberto; Tirapelli, Daniela Pretti da Cunha; Rao, Arvind; Mikkelsen, Tom; Lau, Ching C; Yung, W K Alfred; Rabadan, Raul; Huse, Jason; Brat, Daniel J; Lehman, Norman L; Barnholtz-Sloan, Jill S; Zheng, Siyuan; Hess, Kenneth; Rao, Ganesh; Meyerson, Matthew; Beroukhim, Rameen; Cooper, Lee; Akbani, Rehan; Wrensch, Margaret; Haussler, David; Aldape, Kenneth D; Laird, Peter W; Gutmann, David H; Noushmehr, Houtan; Iavarone, Antonio; Verhaak, Roel G W

2016-01-28

Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify molecular correlations, and provide insights into the progression from low- to high-grade disease. Whole-genome sequencing data analysis determined that ATRX but not TERT promoter mutations are associated with increased telomere length. Recent advances in glioma classification based on IDH mutation and 1p/19q co-deletion status were recapitulated through analysis of DNA methylation profiles, which identified clinically relevant molecular subsets. A subtype of IDH mutant glioma was associated with DNA demethylation and poor outcome; a group of IDH-wild-type diffuse glioma showed molecular similarity to pilocytic astrocytoma and relatively favorable survival. Understanding of cohesive disease groups may aid improved clinical outcomes. Copyright © 2016 Elsevier Inc. All rights reserved.

Influence of some packaging materials and of natural tocopherols on the sensory properties of breakfast cereals.

PubMed

Paradiso, Vito M; Caponio, Francesco; Summo, Carmine; Gomes, Tommaso

2014-04-01

The combined effect of natural antioxidants and packaging materials on the quality decay of breakfast cereals during storage was evaluated. Corn flakes were produced on industrial scale, using different packages and adding natural tocopherols to the ingredients, and stored for 1 year. The samples were then submitted to sensory analysis and HS-solid phase microextraction/gas chromatography/mass spectrometry (SPME/GC/MS) analysis. The packaging had a significant influence on the sensory profile of the aged product: metallized polypropylene gave the highest levels of oxidation compounds and sensory defects. The sensory profile was improved using polypropylene and especially high-density polyethylene. Natural tocopherols reduced the sensory decay of the flakes and the oxidative evolution of the volatile profile. They gave the most remarkable improvement in polypropylene (either metallized or not) packs. Polypropylene showed a barrier effect on the scalping of volatiles outside of the pack. This led to higher levels of oxidation volatiles and faster rates of the further oxidative processes involving the volatiles.

Uniform, optimal signal processing of mapped deep-sequencing data.

PubMed

Kumar, Vibhor; Muratani, Masafumi; Rayan, Nirmala Arul; Kraus, Petra; Lufkin, Thomas; Ng, Huck Hui; Prabhakar, Shyam

2013-07-01

Despite their apparent diversity, many problems in the analysis of high-throughput sequencing data are merely special cases of two general problems, signal detection and signal estimation. Here we adapt formally optimal solutions from signal processing theory to analyze signals of DNA sequence reads mapped to a genome. We describe DFilter, a detection algorithm that identifies regulatory features in ChIP-seq, DNase-seq and FAIRE-seq data more accurately than assay-specific algorithms. We also describe EFilter, an estimation algorithm that accurately predicts mRNA levels from as few as 1-2 histone profiles (R ∼0.9). Notably, the presence of regulatory motifs in promoters correlates more with histone modifications than with mRNA levels, suggesting that histone profiles are more predictive of cis-regulatory mechanisms. We show by applying DFilter and EFilter to embryonic forebrain ChIP-seq data that regulatory protein identification and functional annotation are feasible despite tissue heterogeneity. The mathematical formalism underlying our tools facilitates integrative analysis of data from virtually any sequencing-based functional profile.

A chronological expression profile of gene activity during embryonic mouse brain development.

PubMed

Goggolidou, P; Soneji, S; Powles-Glover, N; Williams, D; Sethi, S; Baban, D; Simon, M M; Ragoussis, I; Norris, D P

2013-12-01

The brain is a functionally complex organ, the patterning and development of which are key to adult health. To help elucidate the genetic networks underlying mammalian brain patterning, we conducted detailed transcriptional profiling during embryonic development of the mouse brain. A total of 2,400 genes were identified as showing differential expression between three developmental stages. Analysis of the data identified nine gene clusters to demonstrate analogous expression profiles. A significant group of novel genes of as yet undiscovered biological function were detected as being potentially relevant to brain development and function, in addition to genes that have previously identified roles in the brain. Furthermore, analysis for genes that display asymmetric expression between the left and right brain hemispheres during development revealed 35 genes as putatively asymmetric from a combined data set. Our data constitute a valuable new resource for neuroscience and neurodevelopment, exposing possible functional associations between genes, including novel loci, and encouraging their further investigation in human neurological and behavioural disorders.

Studying the MicroRNA role as a survival predictor and revealing its part in malignancy level determination in patients with supratentorial gliomas of brain

NASA Astrophysics Data System (ADS)

Stupak, E. V.; Veryaskina, Yu. A.; Titov, S. E.; Achmerova, L. G.; Stupak, V. V.; Dolzhenko, D. A.; Rabinovich, S. S.; Narodov, A. A.; Ivanov, M. K.; Zhimulev, I. F.; Kolesnikov, N. N.

2017-09-01

The numerous data show, that microRNA (miRNA) are direct participants of carcinogenesis. Also miRNA plays the role of a diagnostic and prognostic marker for different types of cancer, including gliomas. The aim of this research is to make the comparative analysis of 10 micro RNA (miR-124, -125b, -16, -181b, -191, -21, -221, -223, -31 and -451) expression profiles. The analysis was made for gliomas with different malignancy degree, then compared with the samples of the adjacent not changed tissues (n = 90). During the study the specific profiles of miRNA expression for various histotypes of tumors were revealed. It was determined, that miRNA acts as a predictor of patient survival in the cases with malignant supratentorial brain tumors. The diagnostic approaches based on miRNA expression profile were designed. It will help to determine the malignancy level and to predict the course of the disease.

Amino Acid profile as a feasible tool for determination of the authenticity of fruit juices.

PubMed

Asadpoor, Mostafa; Ansarin, Masoud; Nemati, Mahboob

2014-12-01

Fruit juice is a nutrient rich food product with a direct connection to public health. The purpose of this research was to determine the amino acid profile of juices and provide a quick and accurate indicator for determining their authenticity. The method of analysis was HPLC with fluorescence detector and pre-column derivatization by orthophtaldialdehyde (OPA). Sixty-six samples of fruit juices were analyzed, and fourteen amino acids were identified and determined in the sampled fruit juices. The fruit samples used for this analysis were apples, oranges, cherry, pineapple, mango, apricot, pomegranate, peach and grapes. The results showed that 32% of samples tested in this study had a lower concentrate percentage as compared to that of their labels and/or other possible authenticity problems in the manufacturing process. The following samples showed probable adulteration: four cherry juice samples, two pomegranate juice samples, one mango, three grape, four peach, seven orange, two apple and one apricot juice samples. In general, determining the amount of amino acids and comparing sample amino acids profiles with the standard values seems to be an indicator for quality control. This method can provide the regulatory agencies with a tool, to help produce a healthier juice. The aim of this study is the analytical control of the fruit juice composition is becoming an important issue, and HPLC can provide an important and essential tool for more accurate research as well as for routine analysis.

Quantitative Machine Learning Analysis of Brain MRI Morphology throughout Aging.

PubMed

Shamir, Lior; Long, Joe

2016-01-01

While cognition is clearly affected by aging, it is unclear whether the process of brain aging is driven solely by accumulation of environmental damage, or involves biological pathways. We applied quantitative image analysis to profile the alteration of brain tissues during aging. A dataset of 463 brain MRI images taken from a cohort of 416 subjects was analyzed using a large set of low-level numerical image content descriptors computed from the entire brain MRI images. The correlation between the numerical image content descriptors and the age was computed, and the alterations of the brain tissues during aging were quantified and profiled using machine learning. The comprehensive set of global image content descriptors provides high Pearson correlation of ~0.9822 with the chronological age, indicating that the machine learning analysis of global features is sensitive to the age of the subjects. Profiling of the predicted age shows several periods of mild changes, separated by shorter periods of more rapid alterations. The periods with the most rapid changes were around the age of 55, and around the age of 65. The results show that the process of brain aging of is not linear, and exhibit short periods of rapid aging separated by periods of milder change. These results are in agreement with patterns observed in cognitive decline, mental health status, and general human aging, suggesting that brain aging might not be driven solely by accumulation of environmental damage. Code and data used in the experiments are publicly available.

Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence.

PubMed

Sunkel, Benjamin; Wu, Dayong; Chen, Zhong; Wang, Chiou-Miin; Liu, Xiangtao; Ye, Zhenqing; Horning, Aaron M; Liu, Joseph; Mahalingam, Devalingam; Lopez-Nicora, Horacio; Lin, Chun-Lin; Goodfellow, Paul J; Clinton, Steven K; Jin, Victor X; Chen, Chun-Liang; Huang, Tim H-M; Wang, Qianben

2016-05-19

Identifying prostate cancer-driving transcription factors (TFs) in addition to the androgen receptor promises to improve our ability to effectively diagnose and treat this disease. We employed an integrative genomics analysis of master TFs CREB1 and FoxA1 in androgen-dependent prostate cancer (ADPC) and castration-resistant prostate cancer (CRPC) cell lines, primary prostate cancer tissues and circulating tumor cells (CTCs) to investigate their role in defining prostate cancer gene expression profiles. Combining genome-wide binding site and gene expression profiles we define CREB1 as a critical driver of pro-survival, cell cycle and metabolic transcription programs. We show that CREB1 and FoxA1 co-localize and mutually influence each other's binding to define disease-driving transcription profiles associated with advanced prostate cancer. Gene expression analysis in human prostate cancer samples found that CREB1/FoxA1 target gene panels predict prostate cancer recurrence. Finally, we showed that this signaling pathway is sensitive to compounds that inhibit the transcription co-regulatory factor MED1. These findings not only reveal a novel, global transcriptional co-regulatory function of CREB1 and FoxA1, but also suggest CREB1/FoxA1 signaling is a targetable driver of prostate cancer progression and serves as a biomarker of poor clinical outcomes. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Ice shelf structure from dispersion curve analysis of passive-source seismic data, Ross Ice Shelf, Antarctica

NASA Astrophysics Data System (ADS)

Diez, A.; Bromirski, P. D.; Gerstoft, P.; Stephen, R. A.; Anthony, R. E.; Aster, R. C.; Cai, C.; Nyblade, A.; Wiens, D.

2015-12-01

An L-shaped array of three-component short period seismic stations was deployed at the Ross Ice Shelf, Antarctica approximately 100 km south of the ice edge, near 180° longitude, from November 18 through 28, 2014. Polarization analysis of data from these stations clearly shows propagating waves from below the ice shelf for frequencies below 2 Hz. Energy above 2 Hz is dominated by Rayleigh and Love waves propagating from the north. Frequency-slowness plots were calculated using beamforming. Resulting Love and Rayleigh wave dispersion curves were inverted for the shear wave velocity profile, from which we derive a density profile. The derived shear wave velocity profiles differ within the firn for the inversions using Rayleigh and Love wave dispersion curves. This difference is attributed to an effective anisotropy due to fine layering. The layered structure of firn, ice, water, and ocean floor results in a characteristic dispersion curve pattern below 7 Hz. We investigate the observed structures in more detail by forward modeling of Rayleigh wave dispersion curves for representative firn, ice, water, sediment structures. Rayleigh waves are observed when wavelengths are long enough to span the distance from the ice shelf surface to the seafloor. Our results show that the analysis of high frequency Rayleigh waves on an ice shelf has the ability to resolve ice shelf thickness, water column thickness, and the physical properties of the underlying ocean floor using passive-source seismic data.

Wax ester profiling of seed oil by nano-electrospray ionization tandem mass spectrometry

PubMed Central

2013-01-01

Background Wax esters are highly hydrophobic neutral lipids that are major constituents of the cutin and suberin layer. Moreover they have favorable properties as a commodity for industrial applications. Through transgenic expression of wax ester biosynthetic genes in oilseed crops, it is possible to achieve high level accumulation of defined wax ester compositions within the seed oil to provide a sustainable source for such high value lipids. The fatty alcohol moiety of the wax esters is formed from plant-endogenous acyl-CoAs by the action of fatty acyl reductases (FAR). In a second step the fatty alcohol is condensed with acyl-CoA by a wax synthase (WS) to form a wax ester. In order to evaluate the specificity of wax ester biosynthesis, analytical methods are needed that provide detailed wax ester profiles from complex lipid extracts. Results We present a direct infusion ESI-tandem MS method that allows the semi-quantitative determination of wax ester compositions from complex lipid mixtures covering 784 even chain molecular species. The definition of calibration prototype groups that combine wax esters according to their fragmentation behavior enables fast quantitative analysis by applying multiple reaction monitoring. This provides a tool to analyze wax layer composition or determine whether seeds accumulate a desired wax ester profile. Besides the profiling method, we provide general information on wax ester analysis by the systematic definition of wax ester prototypes according to their collision-induced dissociation spectra. We applied the developed method for wax ester profiling of the well characterized jojoba seed oil and compared the profile with wax ester-accumulating Arabidopsis thaliana expressing the wax ester biosynthetic genes MaFAR and ScWS. Conclusions We developed a fast profiling method for wax ester analysis on the molecular species level. This method is suitable to screen large numbers of transgenic plants as well as other wax ester samples like cuticular lipid extracts to gain an overview on the molecular species composition. We confirm previous results from APCI-MS and GC-MS analysis, which showed that fragmentation patterns are highly dependent on the double bond distribution between the fatty alcohol and the fatty acid part of the wax ester. PMID:23829499

SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data

DOE PAGES

Silva, Genivaldo Gueiros Z.; Green, Kevin T.; Dutilh, Bas E.; ...

2015-10-09

Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reducedmore » reference database to report the subsystems present in metagenomic datasets and profile their abundances. We tested SUPER-FOCUS with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools.« less

Universal Profile of the Vortex Condensate in Two-Dimensional Turbulence

NASA Astrophysics Data System (ADS)

Laurie, Jason; Boffetta, Guido; Falkovich, Gregory; Kolokolov, Igor; Lebedev, Vladimir

2014-12-01

An inverse turbulent cascade in a restricted two-dimensional periodic domain creates a condensate—a pair of coherent system-size vortices. We perform extensive numerical simulations of this system and carry out theoretical analysis based on momentum and energy exchanges between the turbulence and the vortices. We show that the vortices have a universal internal structure independent of the type of small-scale dissipation, small-scale forcing, and boundary conditions. The theory predicts not only the vortex inner region profile, but also the amplitude, which both perfectly agree with the numerical data.

Diffusion profiling of tumor volumes using a histogram approach can predict proliferation and further microarchitectural features in medulloblastoma.

PubMed

Schob, Stefan; Beeskow, Anne; Dieckow, Julia; Meyer, Hans-Jonas; Krause, Matthias; Frydrychowicz, Clara; Hirsch, Franz-Wolfgang; Surov, Alexey

2018-05-31

Medulloblastomas are the most common central nervous system tumors in childhood. Treatment and prognosis strongly depend on histology and transcriptomic profiling. However, the proliferative potential also has prognostical value. Our study aimed to investigate correlations between histogram profiling of diffusion-weighted images and further microarchitectural features. Seven patients (age median 14.6 years, minimum 2 years, maximum 20 years; 5 male, 2 female) were included in this retrospective study. Using a Matlab-based analysis tool, histogram analysis of whole apparent diffusion coefficient (ADC) volumes was performed. ADC entropy revealed a strong inverse correlation with the expression of the proliferation marker Ki67 (r = - 0.962, p = 0.009) and with total nuclear area (r = - 0.888, p = 0.044). Furthermore, ADC percentiles, most of all ADCp90, showed significant correlations with Ki67 expression (r = 0.902, p = 0.036). Diffusion histogram profiling of medulloblastomas provides valuable in vivo information which potentially can be used for risk stratification and prognostication. First of all, entropy revealed to be the most promising imaging biomarker. However, further studies are warranted.

Profiling analysis of low molecular weight heparins by multiple heart-cutting two dimensional chromatography with quadruple time-of-flight mass spectrometry.

PubMed

Ouyang, Yilan; Zeng, Yangyang; Rong, Yinxiu; Song, Yue; Shi, Lv; Chen, Bo; Yang, Xinlei; Xu, Naiyu; Linhardt, Robert J; Zhang, Zhenqing

2015-09-01

Low molecular weight heparins (LMWHs) are polydisperse and microheterogenous mixtures of polysaccharides used as anticoagulant drugs. Profiling analysis is important for obtaining deeper insights into the structure of LMWHs. Previous oligosaccharide mapping methods are relatively low resolution and are unable to show an entire picture of the structural complexity of LMWHs. In the current study a profiling method was developed relying on multiple heart-cutting, two-dimensional, ultrahigh performance liquid chromatography with quadruple time-of-flight mass spectrometry. This represents an efficient, automated, and robust approach for profiling LMWHs. Using size-exclusion chromatography and ion-pairing reversed-phase chromatography in a two-dimensional separation, LMW components of different sizes and LMW components of the same size but with different charges and polarities can be resolved, providing a more complete picture of a LMWH. Structural information on each component was then obtained with quadrupole time-of-flight mass spectrometry. More than 80 and 120 oligosaccharides were observed and unambiguously assigned from the LMWHs, nadroparin and enoxaparin, respectively. This method might be useful for quality control of LMWHs and as a powerful tool for heparin-related glycomics.

New Insights on Developmental Dyslexia Subtypes: Heterogeneity of Mixed Reading Profiles

PubMed Central

Zoubrinetzky, Rachel; Bielle, Frédérique; Valdois, Sylviane

2014-01-01

We examined whether classifications based on reading performance are relevant to identify cognitively homogeneous subgroups of dyslexic children. Each of the 71 dyslexic participants was selected to have a mixed reading profile, i.e. poor irregular word and pseudo-word reading performance (accuracy and speed). Despite their homogeneous reading profile, the participants were found to split into four distinct cognitive subgroups, characterized by a single phonological disorder, a single visual attention span disorder, a double deficit or none of these disorders. The two subgroups characterized by single and contrasted cognitive disorders were found to exhibit a very similar reading pattern but more contrasted spelling performance (quantitative analysis). A qualitative analysis of the error types produced in reading and spelling provided some cues about the participants' underlying cognitive deficit. The overall findings disqualify subtyping based on reading profiles as a classification method to identify cognitively homogeneous subgroups of dyslexic children. They rather show an opaque relationship between the cognitive underpinnings of developmental dyslexia and their behavioral manifestations in reading and spelling. Future neuroimaging and genetic studies should take this issue into account since synthesizing over cognitively heterogeneous children would entail potential pitfalls. PMID:24918441

DNA Methylation Profiles of Selected Pro-Inflammatory Cytokines in Alzheimer Disease.

PubMed

Nicolia, Vincenzina; Cavallaro, Rosaria A; López-González, Irene; Maccarrone, Mauro; Scarpa, Sigfrido; Ferrer, Isidre; Fuso, Andrea

2017-01-01

By means of functional genomics analysis, we recently described the mRNA expression profiles of various genes involved in the neuroinflammatory response in the brains of subjects with late-onset Alzheimer Disease (LOAD). Some of these genes, namely interleukin (IL)-1β and IL-6, showed distinct expression profiles with peak expression during the first stages of the disease and control-like levels at later stages. IL-1β and IL-6 genes are modulated by DNA methylation in different chronic and degenerative diseases; it is also well known that LOAD may have an epigenetic basis. Indeed, we and others have previously reported gene-specific DNA methylation alterations in LOAD and in related animal models. Based on these data, we studied the DNA methylation profiles, at single cytosine resolution, of IL-1β and IL-6 5'-flanking region by bisulphite modification in the cortex of healthy controls and LOAD patients at 2 different disease stages: Braak I-II/A and Braak V-VI/C. Our analysis provides evidence that neuroinflammation in LOAD is associated with (and possibly mediated by) epigenetic modifications. © 2017 American Association of Neuropathologists, Inc. All rights reserved.

Random whole metagenomic sequencing for forensic discrimination of soils.

PubMed

Khodakova, Anastasia S; Smith, Renee J; Burgoyne, Leigh; Abarno, Damien; Linacre, Adrian

2014-01-01

Here we assess the ability of random whole metagenomic sequencing approaches to discriminate between similar soils from two geographically distinct urban sites for application in forensic science. Repeat samples from two parklands in residential areas separated by approximately 3 km were collected and the DNA was extracted. Shotgun, whole genome amplification (WGA) and single arbitrarily primed DNA amplification (AP-PCR) based sequencing techniques were then used to generate soil metagenomic profiles. Full and subsampled metagenomic datasets were then annotated against M5NR/M5RNA (taxonomic classification) and SEED Subsystems (metabolic classification) databases. Further comparative analyses were performed using a number of statistical tools including: hierarchical agglomerative clustering (CLUSTER); similarity profile analysis (SIMPROF); non-metric multidimensional scaling (NMDS); and canonical analysis of principal coordinates (CAP) at all major levels of taxonomic and metabolic classification. Our data showed that shotgun and WGA-based approaches generated highly similar metagenomic profiles for the soil samples such that the soil samples could not be distinguished accurately. An AP-PCR based approach was shown to be successful at obtaining reproducible site-specific metagenomic DNA profiles, which in turn were employed for successful discrimination of visually similar soil samples collected from two different locations.

Effects of age, sex, and genotype on high-sensitivity metabolomic profiles in the fruit fly, Drosophila melanogaster

PubMed Central

Hoffman, Jessica M; Soltow, Quinlyn A; Li, Shuzhao; Sidik, Alfire; Jones, Dean P; Promislow, Daniel E L

2014-01-01

Researchers have used whole-genome sequencing and gene expression profiling to identify genes associated with age, in the hope of understanding the underlying mechanisms of senescence. But there is a substantial gap from variation in gene sequences and expression levels to variation in age or life expectancy. In an attempt to bridge this gap, here we describe the effects of age, sex, genotype, and their interactions on high-sensitivity metabolomic profiles in the fruit fly, Drosophila melanogaster. Among the 6800 features analyzed, we found that over one-quarter of all metabolites were significantly associated with age, sex, genotype, or their interactions, and multivariate analysis shows that individual metabolomic profiles are highly predictive of these traits. Using a metabolomic equivalent of gene set enrichment analysis, we identified numerous metabolic pathways that were enriched among metabolites associated with age, sex, and genotype, including pathways involving sugar and glycerophospholipid metabolism, neurotransmitters, amino acids, and the carnitine shuttle. Our results suggest that high-sensitivity metabolomic studies have excellent potential not only to reveal mechanisms that lead to senescence, but also to help us understand differences in patterns of aging among genotypes and between males and females. PMID:24636523

Profiles of equilibrium constants for self-association of aromatic molecules

NASA Astrophysics Data System (ADS)

Beshnova, Daria A.; Lantushenko, Anastasia O.; Davies, David B.; Evstigneev, Maxim P.

2009-04-01

Analysis of the noncovalent, noncooperative self-association of identical aromatic molecules assumes that the equilibrium self-association constants are either independent of the number of molecules (the EK-model) or change progressively with increasing aggregation (the AK-model). The dependence of the self-association constant on the number of molecules in the aggregate (i.e., the profile of the equilibrium constant) was empirically derived in the AK-model but, in order to provide some physical understanding of the profile, it is proposed that the sources for attenuation of the equilibrium constant are the loss of translational and rotational degrees of freedom, the ordering of molecules in the aggregates and the electrostatic contribution (for charged units). Expressions are derived for the profiles of the equilibrium constants for both neutral and charged molecules. Although the EK-model has been widely used in the analysis of experimental data, it is shown in this work that the derived equilibrium constant, KEK, depends on the concentration range used and hence, on the experimental method employed. The relationship has also been demonstrated between the equilibrium constant KEK and the real dimerization constant, KD, which shows that the value of KEK is always lower than KD.

Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level

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

Farajzadeh, Leila; Hornshøj, Henrik; Momeni, Jamal

Highlights: •Transcriptome sequencing yielded 223 mill porcine RNA-seq reads, and 59,000 transcribed locations. •Establishment of unique transcription profiles for ten porcine tissues including four brain tissues. •Comparison of transcription profiles at gene, isoform, promoter and transcription start site level. •Highlights a high level of regulation of neuro-related genes at both gene, isoform, and TSS level. •Our results emphasize the pig as a valuable animal model with respect to human biological issues. -- Abstract: The transcriptome is the absolute set of transcripts in a tissue or cell at the time of sampling. In this study RNA-Seq is employed to enable themore » differential analysis of the transcriptome profile for ten porcine tissues in order to evaluate differences between the tissues at the gene and isoform expression level, together with an analysis of variation in transcription start sites, promoter usage, and splicing. Totally, 223 million RNA fragments were sequenced leading to the identification of 59,930 transcribed gene locations and 290,936 transcript variants using Cufflinks with similarity to approximately 13,899 annotated human genes. Pairwise analysis of tissues for differential expression at the gene level showed that the smallest differences were between tissues originating from the porcine brain. Interestingly, the relative level of differential expression at the isoform level did generally not vary between tissue contrasts. Furthermore, analysis of differential promoter usage between tissues, revealed a proportionally higher variation between cerebellum (CBE) versus frontal cortex and cerebellum versus hypothalamus (HYP) than in the remaining comparisons. In addition, the comparison of differential transcription start sites showed that the number of these sites is generally increased in comparisons including hypothalamus in contrast to other pairwise assessments. A comprehensive analysis of one of the tissue contrasts, i.e. cerebellum versus heart for differential variation at the gene, isoform, and transcription start site (TSS), and promoter level showed that several of the genes differed at all four levels. Interestingly, these genes were mainly annotated to the “electron transport chain” and neuronal differentiation, emphasizing that “tissue important” genes are regulated at several levels. Furthermore, our analysis shows that the “across tissue approach” has a promising potential when screening for possible explanations for variations, such as those observed at the gene expression levels.« less

Linking of Microorganisms to Phenanthrene Metabolism in Soil by Analysis of 13C-Labeled Cell Lipids

PubMed Central

Johnsen, Anders R.; Winding, Anne; Karlson, Ulrich; Roslev, Peter

2002-01-01

Phenanthrene-metabolizing soil microbial communities were characterized by examining mineralization of [14C]phenanthrene, by most-probable-number (MPN) counting, by 16S-23S spacer DNA analysis of the numerically dominant, culturable phenanthrene-degrading isolates, and by examining incorporation of [13C]phenanthrene-derived carbon into sterols and polar lipid fatty acids (PLFAs). An unpolluted agricultural soil, a roadside soil diffusely polluted with polycyclic aromatic hydrocarbons (PAHs), and two highly PAH-polluted soils from industrial sites were analyzed. Microbial phenanthrene degraders were not detected by MPN counting in the agricultural soil and the roadside soil. In the industrial soils, phenanthrene degraders constituted 0.04 and 3.6% of the total number of CFU. 16S-23S spacer DNA analysis followed by partial 16S DNA sequencing of representative isolates from one of the industrial soils showed that one-half of the isolates belonged to the genus Sphingomonas and the other half were closely related to an unclassified beta-proteobacterium. The 13C-PLFA profiles of the two industrial soils were relatively similar and resembled the profiles of phenanthrene-degrading Sphingomonas reference strains and unclassified beta-proteobacterium isolates but did not match the profiles of Pseudomonas, Mycobacterium, or Nocardia reference strains. The 13C-PLFA profiles of phenanthrene degraders in the agricultural soil and the roadside soil were different from each other and different from the profiles of the highly polluted industrial soils. Only in the roadside soil were 10me/12me18:0 PLFAs enriched in 13C, suggesting that actinomycetes metabolized phenanthrene in this soil. The 13C-PLFA profiles of the unpolluted agricultural soil did not resemble the profiles of any of the reference strains. In all of the soils investigated, no excess 13C was recovered in the 18:2ω6,9 PLFA, suggesting that fungi did not contribute significantly to assimilation of [13C]phenanthrene. PMID:12450834

How Patient-Pharmacist Communication Using the Drug Profile Book Relates to Patient's Behavior regarding Its Use.

PubMed

Shoji, Masaki; Iwade, Kentaro; Fujii, Keiko; Hirota, Miyuki; Kanou, Akira; Moriya, Mami; Ishii, Masaki; Shimoji, Shizuka; Onda, Mitsuko; Arakawa, Yukio

2016-01-01

 This survey aimed to examine how patient-pharmacist communication using the drug profile book relates patient's behavior regarding its use. Among patients who visited one of the five pharmacies during the 4 months between July and October of 2013, 245 patients who had been prescribed antihypertensives were asked to complete a questionnaire. Items included patient attributes, whether the patient thought the drug profile book was useful to them ("sense of utility"), whether the patient has ever been questioned by a pharmacist while showing the drug profile book ("experience of being questioned by a pharmacist while showing the drug profile book"), and whether the patient has ever shown the drug profile book to the physician ("experience of showing the drug profile book to the physician"). In addition, pharmacists counted the frequency of patients bringing the drug profile book, and if so, the frequency of the sticker affix during the last 5 visits. 34.3% of responding patients answered that they had the "experience of being questioned while showing the drug profile book". Response rates of "frequency of bringing the drug profile book", "sense of utility", and "experience of showing the drug profile book to the physician" in the group with "experience of being questioned while showing the drug profile book" were significantly higher than those in the group without such experience. This survey indicated that experience of being questioned by a pharmacist while showing the drug profile book related patient's behavior regarding its use.

Understanding developmental and adaptive cues in pine through metabolite profiling and co-expression network analysis

PubMed Central

Cañas, Rafael A.; Canales, Javier; Muñoz-Hernández, Carmen; Granados, Jose M.; Ávila, Concepción; García-Martín, María L.; Cánovas, Francisco M.

2015-01-01

Conifers include long-lived evergreen trees of great economic and ecological importance, including pines and spruces. During their long lives conifers must respond to seasonal environmental changes, adapt to unpredictable environmental stresses, and co-ordinate their adaptive adjustments with internal developmental programmes. To gain insights into these responses, we examined metabolite and transcriptomic profiles of needles from naturally growing 25-year-old maritime pine (Pinus pinaster L. Aiton) trees over a year. The effect of environmental parameters such as temperature and rain on needle development were studied. Our results show that seasonal changes in the metabolite profiles were mainly affected by the needles’ age and acclimation for winter, but changes in transcript profiles were mainly dependent on climatic factors. The relative abundance of most transcripts correlated well with temperature, particularly for genes involved in photosynthesis or winter acclimation. Gene network analysis revealed relationships between 14 co-expressed gene modules and development and adaptation to environmental stimuli. Novel Myb transcription factors were identified as candidate regulators during needle development. Our systems-based analysis provides integrated data of the seasonal regulation of maritime pine growth, opening new perspectives for understanding the complex regulatory mechanisms underlying conifers’ adaptive responses. Taken together, our results suggest that the environment regulates the transcriptome for fine tuning of the metabolome during development. PMID:25873654

Country analysis briefs: 1994. Profiles of major world energy producers, consumers, and transport centers

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

NONE

1995-05-01

Country Analysis Briefs: 1994 is a compilation of country profiles prepared by the Energy Markets and Contingency Information Division (EMCID) of the Office of Energy Markets and End Use. EMCID maintains Country Analysis Briefs (CABs) for specific countries or geographical areas that are important to world energy markets. As a general rule, CABs are prepared for all members of the Organization of Petroleum Exporting Countries (OPEC), major non-OPEC oil producers (i.e., the North Sea, Russia), major energy transit areas (i.e., Ukraine), and other areas of current interest to energy analysts and policy makers. As of January 1995, EMCID maintained overmore » 40 CABs, updated on an annual schedule and subject to revision as events warrant. This report includes 25 CABs updated during 1994. All CABs contain a profile section, a map showing the country`s location, and a narrative section. The profile section includes outlines of the country`s economy, energy sector, and environment. The narrative provides further information and discussion of these topics. Some CABs also include a detailed map displaying locations of major oil and gas fields, pipelines, ports, etc. These maps were created as a result of special individual requests and so are not typically a standard feature of the CABs. They are presented here wherever available as a supplement to the information contained in the CABs.« less

Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl−/− retinal transcriptomes

PubMed Central

Brooks, Matthew J.; Rajasimha, Harsha K.; Roger, Jerome E.

2011-01-01

Purpose Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods Retinal mRNA profiles of 21-day-old wild-type (WT) and neural retina leucine zipper knockout (Nrl−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Results Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm9) and identified 16,014 transcripts in the retinas of WT and Nrl−/− mice with BWA workflow and 34,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. PMID:22162623

Bioinformatics identification and transcript profile analysis of the mitogen-activated protein kinase gene family in the diploid woodland strawberry Fragaria vesca

PubMed Central

Wei, Wei; Chai, Zhuangzhuang; Xie, Yinge; Gao, Kuan; Cui, Mengyuan; Jiang, Ying

2017-01-01

Mitogen-activated protein kinases (MAPKs) play essential roles in mediating biotic and abiotic stress responses in plants. However, the MAPK gene family in strawberry has not been systematically characterized. Here, we performed a genome-wide survey and identified 12 MAPK genes in the Fragaria vesca genome. Protein domain analysis indicated that all FvMAPKs have typical protein kinase domains. Sequence alignments and phylogenetic analysis classified the FvMAPK genes into four different groups. Conserved motif and exon-intron organization supported the evolutionary relationships inferred from the phylogenetic analysis. Analysis of the stress-related cis-regulatory element in the promoters and subcellular localization predictions of FvMAPKs were also performed. Gene transcript profile analysis showed that the majority of the FvMAPK genes were ubiquitously transcribed in strawberry leaves after Podosphaera aphanis inoculation and after treatment with cold, heat, drought, salt and the exogenous hormones abscisic acid, ethephon, methyl jasmonate, and salicylic acid. RT-qPCR showed that six selected FvMAPK genes comprehensively responded to various stimuli. Additionally, interaction networks revealed that the crucial signaling transduction controlled by FvMAPKs may be involved in the biotic and abiotic stress responses. Our results may provide useful information for future research on the function of the MAPK gene family and the genetic improvement of strawberry resistance to environmental stresses. PMID:28562633

DNA Identification of Skeletal Remains from World War II Mass Graves Uncovered in Slovenia

PubMed Central

Marjanović, Damir; Durmić-Pašić, Adaleta; Bakal, Narcisa; Haverić, Sanin; Kalamujić, Belma; Kovačević, Lejla; Ramić, Jasmin; Pojskić, Naris; Škaro, Vedrana; Projić, Petar; Bajrović, Kasim; Hadžiselimović, Rifat; Drobnič, Katja; Huffine, Ed; Davoren, Jon; Primorac, Dragan

2007-01-01

Aim To present the joint effort of three institutions in the identification of human remains from the World War II found in two mass graves in the area of Škofja Loka, Slovenia. Methods The remains of 27 individuals were found in two small and closely located mass graves. The DNA was isolated from bone and teeth samples using either standard phenol/chloroform alcohol extraction or optimized Qiagen DNA extraction procedure. Some recovered samples required the employment of additional DNA purification methods, such as N-buthanol treatment. QuantifilerTM Human DNA Quantification Kit was used for DNA quantification. PowerPlex 16 kit was used to simultaneously amplify 15 short tandem repeat (STR) loci. Matching probabilities were estimated using the DNA View program. Results Out of all processed samples, 15 remains were fully profiled at all 15 STR loci. The other 12 profiles were partial. The least successful profile included 13 loci. Also, 69 referent samples (buccal swabs) from potential living relatives were collected and profiled. Comparison of victims' profile against referent samples database resulted in 4 strong matches. In addition, 5 other profiles were matched to certain referent samples with lower probability. Conclusion Our results show that more than 6 decades after the end of the World War II, DNA analysis may significantly contribute to the identification of the remains from that period. Additional analysis of Y-STRs and mitochondrial DNA (mtDNA) markers will be performed in the second phase of the identification project. PMID:17696306

Disorder profile of nebulin encodes a vernierlike position sensor for the sliding thin and thick filaments of the skeletal muscle sarcomere

NASA Astrophysics Data System (ADS)

Wu, Ming-Chya; Forbes, Jeffrey G.; Wang, Kuan

2016-06-01

Nebulin is an about 1 μ m long intrinsically disordered scaffold for the thin filaments of skeletal muscle sarcomere. It is a multifunctional elastic protein that wraps around actin filament, stabilizes thin filaments, and regulates Ca-dependent actomyosin interactions. This study investigates whether the disorder profile of nebulin might encode guidelines for thin and thick filament interactions in the sarcomere of the skeletal muscle. The question was addressed computationally by analyzing the predicted disorder profile of human nebulin (6669 residues, ˜200 actin-binding repeats) by pondr and the periodicity of the A-band stripes (reflecting the locations of myosin-associated proteins) in the electron micrographs of the sarcomere. Using the detrended fluctuation analysis, a scale factor for the A-band stripe image data with respect to the nebulin disorder profile was determined to make the thin and thick filaments aligned to have maximum correlation. The empirical mode decomposition method was then applied to identify hidden periodicities in both the nebulin disorder profile and the rescaled A-band data. The decomposition reveals three characteristic length scales (45 nm, 100 nm, and 200 nm) that are relevant for correlational analysis. The dynamical cross-correlation analyses with moving windows at various sarcomere lengths depict a vernierlike design for both periodicities, thus enabling nebulin to sense position and fine tune sarcomere overlap. This shows that the disorder profile of scaffolding proteins may encode a guideline for cellular architecture.

Benefit of the Use of GCxGC/MS Profiles for 1D GC/MS Data Treatment Illustrated by the Analysis of Pyrolysis Products from East Asian Handmade Papers

NASA Astrophysics Data System (ADS)

Han, Bin; Lob, Silvia; Sablier, Michel

2018-06-01

In this study, we report the use of pyrolysis-GCxGC/MS profiles for an optimized treatment of data issued from pyrolysis-GC/MS combined with the automatic deconvolution software Automated Mass Spectral Deconvolution and Identification System (AMDIS). The method was illustrated by the characterization of marker compounds of East Asian handmade papers through the examination of pyrolysis-GCxGC/MS data to get information which was used for manually identifying low concentrated and co-eluting compounds in 1D GC/MS data. The results showed that the merits of a higher separation power for co-eluting compounds and a better sensitivity for low concentration compounds offered by a GCxGC system can be used effectively for AMDIS 1D GC/MS data treatment: (i) the compound distribution in pyrolysis-GCxGC/MS profiles can be used as "peak finder" for manual check of low concentration and co-eluting compound identification in 1D GC/MS data, and (ii) pyrolysis-GCxGC/MS profiles can provide better quality mass spectra with observed higher match factors in the AMDIS automatic match process. The combination of 2D profile with AMDIS was shown to contribute efficiently to a better characterization of compound profiles in the chromatograms obtained by 1D analysis in focusing on the mass spectral identification. [Figure not available: see fulltext.

Clinical signs and bacterial communities of deciduous necrotic root canals detected by PCR-DGGE analysis: research association.

PubMed

de Paula, Viviane Andrade Cancio; de Carvalho Ferreira, Dennis; Cavalcante, Fernanda Sampaio; do Carmo, Flávia Lima; Rosado, Alexandre Soares; Primo, Laura Guimarães; dos Santos, Kátia Regina Netto

2014-08-01

This study sought to investigate the possible association between clinical and radiographic data of the patients with the bacterial community profiles involved in cases of necrosis in primary root canals. Microbial community profiles for 25 samples from necrotic deciduous root canals were analyzed using the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting approach. These results were related to the clinical and radiographic data of these patients. The analysis showed a large diversity of microbial communities in necrotic deciduous root canals. The statistical results pointed out that posterior and anterior teeth were associated with <20 bands and >20 bands in PCR-DGGE method, respectively. A relationship was verified between ages >4 years old and posterior teeth and, ages ≤4 years old and anterior teeth. The data showed a polymicrobial community and pointed out the association of age with necrosis in anterior and posterior teeth. Copyright © 2014 Elsevier Ltd. All rights reserved.

Identification and Characterization of Diploid and Tetraploid in Platycodon grandiflorum.

PubMed

Shin, Jeoung-Hwa; Ahn, Yun Gyong; Jung, Ju-Hee; Woo, Sun-Hee; Kim, Hag-Hyun; Gorinstein, Shela; Boo, Hee-Ock

2017-03-01

Platycodon grandiflorum (PG), a species of herbaceous flowering perennial plant of the family Campanulaceae, has been used as a traditional oriental medicine for bronchitis, asthma, pulmonary tuberculosis, diabetes, hepatic fibrosis, bone disorders and many others similar diseases and as a food supplement. For the primary profiling of PG gas chromatography coupled with high resolution - time of flight mass spectrometry (GC/HR-TOF MS) was used as an analytical tool. A comparison of optimal extraction of metabolites was carried out with a number of solvents [hexane, methylene chloride, methanol, ethanol, methanol: ethanol (70:30, v:v)]. In extracts with methanol: ethanol (70:30 v:v) were detected higher amounts of metabolites than with other solvents. Principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) plots showed significant differences between the diploid and tetraploid metabolite profiles. Extracts of tetraploid showed higher amounts of amino acids, while extracts of diploid contained more organic acids and sugars. Graphical Abstract ᅟ.

The Frontal Behavioural Inventory (Italian version) differentiates frontotemporal lobar degeneration variants from Alzheimer's disease.

PubMed

Alberici, A; Geroldi, C; Cotelli, M; Adorni, A; Calabria, M; Rossi, G; Borroni, B; Padovani, A; Zanetti, O; Kertesz, A

2007-04-01

The objective was to evaluate the construct validity of the Italian version of the Frontal Behavioural Inventory (FBI) and its usefulness in the differential diagnosis of dementias. Standard criteria were used in the clinical diagnosis of dementias in 83 patients and 33 agematched healthy volunteers. The FBI scale was translated from English into Italian language and back-translated. Cronbach's alpha, inter-rater and test-retest reliability, FBI convergent validity and discriminant analysis were calculated. FBI profile was compared between patients affected by frontotemporal lobar degeneration (FTLD) and Alzheimer's disease (AD). The FBI showed a high internal consistency and inter-rater reliability and it distinguished normal behavioural conditions from those presented in FTLD or AD. An 86.8% diagnostic accuracy was calculated by the discriminant analysis, selecting only age at disease onset and FBI, and particularly distinguishing behavioural variants within the FTLD spectrum. FTLD patients showed a characteristic behavioural profile. The FBI might be a reliable and useful diagnostic tool for dementias in clinical practice.

Predominant yeasts in Chinese traditional sourdough and their influence on aroma formation in Chinese steamed bread.

PubMed

Liu, Tongjie; Li, Yang; Sadiq, Faizan A; Yang, Huanyi; Gu, Jingsi; Yuan, Lei; Lee, Yuan Kun; He, Guoqing

2018-03-01

A total of 105 yeast isolates was obtained from 15 sourdough samples collected from different regions in China and subjected to random amplified polymorphic DNA (RAPD) analysis. Six species were identified including Pichia membranifaciens, which has not previously been reported in Chinese sourdoughs. Different species of yeast were used in single-culture fermentation to make Chinese steamed bread (CSB). The volatiles of the CSB were captured by solid-phase microextraction method, separated and identified by gas chromatography-mass spectrometry. In total, 41 volatile compounds were found in all the steamed breads. All CSBs showed a similar volatile profile; however, significant differences in the quantity of some volatile compounds were seen among the CSB fermented by different yeast species. A partial least squares discriminant analysis showed that the CSBs could be separated by their characteristic volatile profiles. The study suggested that the aromatic properties of CSB are determined by the yeast used. Copyright © 2017 Elsevier Ltd. All rights reserved.

FRAPCON analysis of cladding performance during dry storage operations

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

Richmond, David J.; Geelhood, Kenneth J.

There is an increasing need in the U.S. and around the world to move used nuclear fuel from wet storage in fuel pools to dry storage in casks stored at independent spent fuel storage installations (ISFSI) or interim storage sites. The NRC limits cladding temperature to 400°C while maintaining cladding hoop stress below 90 MPa in an effort to avoid radial hydride reorientation. An analysis was conducted with FRAPCON-4.0 on three modern fuel designs with three representative used nuclear fuel storage temperature profiles that peaked at 400 °C. Results were representative of the majority of U.S. LWR fuel. They conservativelymore » showed that hoop stress remains below 90 MPa at the licensing temperature limit. Results also show that the limiting case for hoop stress may not be at the highest rod internal pressure in all cases but will be related to the axial temperature and oxidation profiles of the rods at the end of life and in storage.« less

Grapevine-shoot stilbene extract as a preservative in red wine.

PubMed

Raposo, Rafaela; Ruiz-Moreno, María José; Garde-Cerdán, Teresa; Puertas, Belén; Moreno-Rojas, José Manuel; Gonzalo-Diago, Ana; Guerrero, Raúl; Ortíz, Víctor; Cantos-Villar, Emma

2016-04-15

This paper reports the use of a grapevine-shoot stilbene extract (Vineatrol®) as a preservative in red wine. Its effectiveness to preserve red wine quality under two different winemaking systems (traditional and Ganimede) was studied at bottling and after twelve months of storage in bottle. Enological parameters, color related parameters, volatile composition, sensory analysis and olfactometric profile were evaluated. At bottling wines treated with Vineatrol showed higher color related parameters and higher score in sensory analysis than those treated with SO2. The use of SO2 increased ester and alcohol volatile compounds in relation to the use of Vineatrol. Wine olfactometric profile was modified by Vineatrol addition. Two new odorant zones with high modified frequency appeared in wines treated with Vineatrol. After 12months of storage in bottle, wines treated with Vineatrol showed parameters related to oxidation. The weak point of the process seemed to be the evolution during the storage in bottle. Copyright © 2015 Elsevier Ltd. All rights reserved.

Flupyradifurone: a brief profile of a new butenolide insecticide

PubMed Central

Nauen, Ralf; Jeschke, Peter; Velten, Robert; Beck, Michael E; Ebbinghaus-Kintscher, Ulrich; Thielert, Wolfgang; Wölfel, Katharina; Haas, Matthias; Kunz, Klaus; Raupach, Georg

2015-01-01

BACKGROUND The development and commercialisation of new chemical classes of insecticides for efficient crop protection measures against destructive invertebrate pests is of utmost importance to overcome resistance issues and to secure sustainable crop yields. Flupyradifurone introduced here is the first representative of the novel butenolide class of insecticides active against various sucking pests and showing an excellent safety profile. RESULTS The discovery of flupyradifurone was inspired by the butenolide scaffold in naturally occurring stemofoline. Flupyradifurone acts reversibly as an agonist on insect nicotinic acetylcholine receptors but is structurally different from known agonists, as shown by chemical similarity analysis. It shows a fast action on a broad range of sucking pests, as demonstrated in laboratory bioassays, and exhibits excellent field efficacy on a number of crops with different application methods, including foliar, soil, seed treatment and drip irrigation. It is readily taken up by plants and translocated in the xylem, as demonstrated by phosphor imaging analysis. Flupyradifurone is active on resistant pests, including cotton whiteflies, and is not metabolised by recombinantly expressed CYP6CM1, a cytochrome P450 conferring metabolic resistance to neonicotinoids and pymetrozine. CONCLUSION The novel butenolide insecticide flupyradifurone shows unique properties and will become a new tool for integrated pest management around the globe, as demonstrated by its insecticidal, ecotoxicological and safety profile. © 2014 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. PMID:25351824

Time evolution of fine structures in the solar chromosphere.

NASA Astrophysics Data System (ADS)

Tsiropoula, G.; Alissandrakis, C. E.; Schmieder, B.

1994-10-01

We have studied the temporal evolution of two quiet chromospheric regions, one with a typical rosette and another with chains of mottles at the junction of three supergranules. The observations were obtained during 15 minutes with the Multichannel Subtractive Double Pass spectrograph (MSDP) operating in Hα at the Pic du Midi Observatory. We derived intensity maps and Doppler shift velocities at different wavelengths along the Hα profile over a two dimensional field of view. The observed contrast profiles were matched with theoretical contrast profiles using Beckers' cloud model for a more accurate determination of the line of sight velocity. A statistical analysis with cross correlation functions showed that the fine structures were stable in intensity over the observation period (15 min), but the line of sight velocity showed important changes within a few minutes. A detailed analysis of the velocities along the axes of dark mottles showed that the predominant pattern of bulk motion is that of downflow at their footpoints and alternating phases of upflow and downflow at their tops. This motion is consistent with Pikel'ner's model for spicules, which attributes this pattern to the reconnection of opposite magnetic filed lines. This picture is also consistent with the velocity reversals with time observed in spicules and may be associated to the systematic downflows observed in the transition region. Doppler shift velocities in dark mottles are too low compared to those derived with the cloud model; the latter are comparable to those reported for spicules, strengthening the view that these structures are identical.

Sensory evaluation and electronic tongue for sensing flavored mineral water taste attributes.

PubMed

Sipos, László; Gere, Attila; Szöllősi, Dániel; Kovács, Zoltán; Kókai, Zoltán; Fekete, András

2013-10-01

In this article a trained sensory panel evaluated 6 flavored mineral water samples. The samples consisted of 3 different brands, each with 2 flavors (pear-lemon grass and josta berry). The applied sensory method was profile analysis. Our aim was to analyze the sensory profiles and to investigate the similarities between the sensitivity of the trained human panel and an electronic tongue device. Another objective was to demonstrate the possibilities for the prediction of sensory attributes from electronic tongue measurements using a multivariate statistical method (Partial Least Squares regression [PLS]). The results showed that the products manufactured under different brand name but with the same aromas had very similar sensory profiles. The panel performance evaluation showed that it is appropriate (discrimination ability, repeatability, and panel consensus) to compare the panel's results with the results of the electronic tongue. The samples can be discriminated by the electronic tongue and an accurate classification model can be built. Principal Component Analysis BiPlot diagrams showed that Brand A and B were similar because the manufacturers use the same aroma brands for their products. It can be concluded that Brand C was quite different compared to the other samples independently of the aroma content. Based on the electronic tongue results good prediction models can be obtained with high correlation coefficient (r(2) > 0.81) and low prediction error (RMSEP < 13.71 on the scale of the sensory evaluation from 0 to 100). © 2013 Institute of Food Technologists®

Drinking Patterns and Victimization among Male and Female Students in Mexico

PubMed Central

Strunin, Lee; Díaz-Martínez, L. Rosa; Díaz-Martínez, Alejandro; Heeren, Timothy; Winter, Michael; Kuranz, Seth; Hernández–Ávila, Carlos A.; Fernández-Varela, Héctor; Solís-Torres, Cuauhtémoc

2015-01-01

Aims: The purpose of this study is to estimate the prevalence of alcohol use and alcohol-related consequences, identify drinking profiles using latent profile analysis (LPA), and investigate associations between profiles and violent victimization among young people in Mexico. Methods: LPA identified profiles of drinking behavior in a survey of entering first year university students. Multinomial and logistic regression examined associations between drinking patterns, socio-demographic variables and violent victimization. Results: The LPA identified five profiles of behaviors and consequences among the 22,224 current, former and never drinkers: Non/Infrequent-No Consequences, Occasional-Few Consequences, Regular-Some Consequences, Heavy-Many Consequences and Excessive-Many Consequences drinkers. The Occasional-Few Consequences profile comprised the largest, and the Excessive-Many Consequences profile the smallest, group of drinkers. Multinomial regression showed males and older students more likely to be Heavy or Excessive-Many Consequences drinkers. Living alone was associated with higher odds, and higher maternal education with lower odds, of being a Non/Infrequent-No Consequences drinker. Heavier drinking profiles were more likely to experience violent victimization adverse consequences. Logistic regression showed male and female Heavy and Excessive-Many Consequences drinkers had the highest odds, and Non/Infrequent drinkers the lowest odds, of experiencing any victimization. Conclusion: Findings suggest changes in male and female drinking behavior and a continuation of the established pattern of infrequent but high consumption among Mexican youths. Both male and female Heavy and Excessive-Many Consequences drinkers were at elevated risk for experiencing victimization. Identifying cultural gender norms about drinking including drinker expectations and drinking context that contribute to these patterns can inform prevention efforts. PMID:25534933

A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification.

PubMed

Xie, Xin-Ping; Xie, Yu-Feng; Wang, Hong-Qiang

2017-08-23

Large-scale accumulation of omics data poses a pressing challenge of integrative analysis of multiple data sets in bioinformatics. An open question of such integrative analysis is how to pinpoint consistent but subtle gene activity patterns across studies. Study heterogeneity needs to be addressed carefully for this goal. This paper proposes a regulation probability model-based meta-analysis, jGRP, for identifying differentially expressed genes (DEGs). The method integrates multiple transcriptomics data sets in a gene regulatory space instead of in a gene expression space, which makes it easy to capture and manage data heterogeneity across studies from different laboratories or platforms. Specifically, we transform gene expression profiles into a united gene regulation profile across studies by mathematically defining two gene regulation events between two conditions and estimating their occurring probabilities in a sample. Finally, a novel differential expression statistic is established based on the gene regulation profiles, realizing accurate and flexible identification of DEGs in gene regulation space. We evaluated the proposed method on simulation data and real-world cancer datasets and showed the effectiveness and efficiency of jGRP in identifying DEGs identification in the context of meta-analysis. Data heterogeneity largely influences the performance of meta-analysis of DEGs identification. Existing different meta-analysis methods were revealed to exhibit very different degrees of sensitivity to study heterogeneity. The proposed method, jGRP, can be a standalone tool due to its united framework and controllable way to deal with study heterogeneity.

Delving deeper into technological innovations to understand differences in rice quality.

PubMed

Calingacion, Mariafe; Fang, Lu; Quiatchon-Baeza, Lenie; Mumm, Roland; Riedel, Arthur; Hall, Robert D; Fitzgerald, Melissa

2015-12-01

Increasing demand for better quality rice varieties, which are also more suited to growth under sub-optimal cultivation conditions, is driving innovation in rice research. Here we have used a multi-disciplinary approach, involving SNP-based genotyping together with phenotyping based on yield analysis, metabolomic analysis of grain volatiles, and sensory panel analysis to determine differences between two contrasting rice varieties, Apo and IR64. Plants were grown under standard and drought-induced conditions. Results revealed important differences between the volatile profiles of the two rice varieties and we relate these differences to those perceived by the sensory panel. Apo, which is the more drought tolerant variety, was less affected by the drought condition concerning both sensory profile and yield; IR64, which has higher quality but is drought sensitive, showed greater differences in these characteristics in response to the two growth conditions. Metabolomics analyses using GCxGC-MS, followed by multivariate statistical analyses of the data, revealed a number of discriminatory compounds between the varieties, but also effects of the difference in cultivation conditions. Results indicate the complexity of rice volatile profile, even of non-aromatic varieties, and how metabolomics can be used to help link changes in aroma profile with the sensory phenotype. Our outcomes also suggest valuable multi-disciplinary approaches which can be used to help define the aroma profile in rice, and its underlying genetic background, in order to support breeders in the generation of improved rice varieties combining high yield with high quality, and tolerance of both these traits to climate change.

Evaluation of facial attractiveness in black people according to the subjective facial analysis criteria.

PubMed

Melo, Andréa Reis de; Conti, Ana Cláudia de Castro Ferreira; Almeida-Pedrin, Renata Rodrigues; Didier, Victor; Valarelli, Danilo Pinelli; Capelozza Filho, Leopoldino

2017-02-01

The objective of this study was to evaluate the facial attractiveness in 30 black individuals, according to the Subjective Facial Analysis criteria. Frontal and profile view photographs of 30 black individuals were evaluated for facial attractiveness and classified as esthetically unpleasant, acceptable, or pleasant by 50 evaluators: the 30 individuals from the sample, 10 orthodontists, and 10 laymen. Besides assessing the facial attractiveness, the evaluators had to identify the structures responsible for the classification as unpleasant and pleasant. Intraexaminer agreement was assessed by using Spearman's correlation, correlation within each category using Kendall concordance coefficient, and correlation between the 3 categories using chi-square test and proportions. Most of the frontal (53. 5%) and profile view (54. 9%) photographs were classified as esthetically acceptable. The structures most identified as esthetically unpleasant were the mouth, lips, and face, in the frontal view; and nose and chin in the profile view. The structures most identified as esthetically pleasant were harmony, face, and mouth, in the frontal view; and harmony and nose in the profile view. The ratings by the examiners in the sample and laymen groups showed statistically significant correlation in both views. The orthodontists agreed with the laymen on the evaluation of the frontal view and disagreed on profile view, especially regarding whether the images were esthetically unpleasant or acceptable. Based on these results, the evaluation of facial attractiveness according to the Subjective Facial Analysis criteria proved to be applicable and to have a subjective influence; therefore, it is suggested that the patient's opinion regarding the facial esthetics should be considered in orthodontic treatmentplanning.

Combined LC/MS-platform for analysis of all major stratum corneum lipids, and the profiling of skin substitutes.

PubMed

van Smeden, Jeroen; Boiten, Walter A; Hankemeier, Thomas; Rissmann, Robert; Bouwstra, Joke A; Vreeken, Rob J

2014-01-01

Ceramides (CERs), cholesterol, and free fatty acids (FFAs) are the main lipid classes in human stratum corneum (SC, outermost skin layer), but no studies report on the detailed analysis of these classes in a single platform. The primary aims of this study were to 1) develop an LC/MS method for (semi-)quantitative analysis of all main lipid classes present in human SC; and 2) use this method to study in detail the lipid profiles of human skin substitutes and compare them to human SC lipids. By applying two injections of 10μl, the developed method detects all major SC lipids using RPLC and negative ion mode APCI-MS for detection of FFAs, and NPLC using positive ion mode APCI-MS to analyze CERs and cholesterol. Validation showed this lipid platform to be robust, reproducible, sensitive, and fast. The method was successfully applied on ex vivo human SC, human SC obtained from tape strips and human skin substitutes (porcine SC and human skin equivalents). In conjunction with FFA profiles, clear differences in CER profiles were observed between these different SC sources. Human skin equivalents more closely mimic the lipid composition of human stratum corneum than porcine skin does, although noticeable differences are still present. These differences gave biologically relevant information on some of the enzymes that are probably involved in SC lipid processing. For future research, this provides an excellent method for (semi-)quantitative, 'high-throughput' profiling of SC lipids and can be used to advance the understanding of skin lipids and the biological processes involved. © 2013.

Surface Glycosylation Profiles of Urine Extracellular Vesicles

PubMed Central

Gerlach, Jared Q.; Krüger, Anja; Gallogly, Susan; Hanley, Shirley A.; Hogan, Marie C.; Ward, Christopher J.

2013-01-01

Urinary extracellular vesicles (uEVs) are released by cells throughout the nephron and contain biomolecules from their cells of origin. Although uEV-associated proteins and RNA have been studied in detail, little information exists regarding uEV glycosylation characteristics. Surface glycosylation profiling by flow cytometry and lectin microarray was applied to uEVs enriched from urine of healthy adults by ultracentrifugation and centrifugal filtration. The carbohydrate specificity of lectin microarray profiles was confirmed by competitive sugar inhibition and carbohydrate-specific enzyme hydrolysis. Glycosylation profiles of uEVs and purified Tamm Horsfall protein were compared. In both flow cytometry and lectin microarray assays, uEVs demonstrated surface binding, at low to moderate intensities, of a broad range of lectins whether prepared by ultracentrifugation or centrifugal filtration. In general, ultracentrifugation-prepared uEVs demonstrated higher lectin binding intensities than centrifugal filtration-prepared uEVs consistent with lesser amounts of co-purified non-vesicular proteins. The surface glycosylation profiles of uEVs showed little inter-individual variation and were distinct from those of Tamm Horsfall protein, which bound a limited number of lectins. In a pilot study, lectin microarray was used to compare uEVs from individuals with autosomal dominant polycystic kidney disease to those of age-matched controls. The lectin microarray profiles of polycystic kidney disease and healthy uEVs showed differences in binding intensity of 6/43 lectins. Our results reveal a complex surface glycosylation profile of uEVs that is accessible to lectin-based analysis following multiple uEV enrichment techniques, is distinct from co-purified Tamm Horsfall protein and may demonstrate disease-specific modifications. PMID:24069349

Kozeny-Carman permeability relationship with disintegration process predicted from early dissolution profiles of immediate release tablets.

PubMed

Kumari, Parveen; Rathi, Pooja; Kumar, Virender; Lal, Jatin; Kaur, Harmeet; Singh, Jasbir

2017-07-01

This study was oriented toward the disintegration profiling of the diclofenac sodium (DS) immediate-release (IR) tablets and development of its relationship with medium permeability k perm based on Kozeny-Carman equation. Batches (L1-L9) of DS IR tablets with different porosities and specific surface area were prepared at different compression forces and evaluated for porosity, in vitro dissolution and particle-size analysis of the disintegrated mass. The k perm was calculated from porosities and specific surface area, and disintegration profiles were predicted from the dissolution profiles of IR tablets by stripping/residual method. The disintegration profiles were subjected to exponential regression to find out the respective disintegration equations and rate constants k d . Batches L1 and L2 showed the fastest disintegration rates as evident from their bi-exponential equations while the rest of the batches L3-L9 exhibited the first order or mono-exponential disintegration kinetics. The 95% confidence interval (CI 95% ) revealed significant differences between k d values of different batches except L4 and L6. Similar results were also spotted for dissolution profiles of IR tablets by similarity (f 2 ) test. The final relationship between k d and k perm was found to be hyperbolic, signifying the initial effect of k perm on the disintegration rate. The results showed that disintegration profiling is possible because a relationship exists between k d and k perm . The later being relatable with porosity and specific surface area can be determined by nondestructive tests.

Gene Expression Profiling Predicts the Development of Oral Cancer

PubMed Central

Saintigny, Pierre; Zhang, Li; Fan, You-Hong; El-Naggar, Adel K.; Papadimitrakopoulou, Vali; Feng, Lei; Lee, J. Jack; Kim, Edward S.; Hong, Waun Ki; Mao, Li

2011-01-01

Patients with oral preneoplastic lesion (OPL) have high risk of developing oral cancer. Although certain risk factors such as smoking status and histology are known, our ability to predict oral cancer risk remains poor. The study objective was to determine the value of gene expression profiling in predicting oral cancer development. Gene expression profile was measured in 86 of 162 OPL patients who were enrolled in a clinical chemoprevention trial that used the incidence of oral cancer development as a prespecified endpoint. The median follow-up time was 6.08 years and 35 of the 86 patients developed oral cancer over the course. Gene expression profiles were associated with oral cancer-free survival and used to develope multivariate predictive models for oral cancer prediction. We developed a 29-transcript predictive model which showed marked improvement in terms of prediction accuracy (with 8% predicting error rate) over the models using previously known clinico-pathological risk factors. Based on the gene expression profile data, we also identified 2182 transcripts significantly associated with oral cancer risk associated genes (P-value<0.01, single variate Cox proportional hazards model). Functional pathway analysis revealed proteasome machinery, MYC, and ribosomes components as the top gene sets associated with oral cancer risk. In multiple independent datasets, the expression profiles of the genes can differentiate head and neck cancer from normal mucosa. Our results show that gene expression profiles may improve the prediction of oral cancer risk in OPL patients and the significant genes identified may serve as potential targets for oral cancer chemoprevention. PMID:21292635

A comparison of honeybee (Apis mellifera) queen, worker and drone larvae by RNA-Seq.

PubMed

He, Xu-Jiang; Jiang, Wu-Jun; Zhou, Mi; Barron, Andrew B; Zeng, Zhi-Jiang

2017-11-06

Honeybees (Apis mellifera) have haplodiploid sex determination: males develop from unfertilized eggs and females develop from fertilized ones. The differences in larval food also determine the development of females. Here we compared the total somatic gene expression profiles of 2-day and 4-day-old drone, queen and worker larvae by RNA-Seq. The results from a co-expression network analysis on all expressed genes showed that 2-day-old drone and worker larvae were closer in gene expression profiles than 2-day-old queen larvae. This indicated that for young larvae (2-day-old) environmental factors such as larval diet have a greater effect on gene expression profiles than ploidy or sex determination. Drones had the most distinct gene expression profiles at the 4-day larval stage, suggesting that haploidy, or sex dramatically affects the gene expression of honeybee larvae. Drone larvae showed fewer differences in gene expression profiles at the 2-day and 4-day time points than the worker and queen larval comparisons (598 against 1190 and 1181), suggesting a different pattern of gene expression regulation during the larval development of haploid males compared to diploid females. This study indicates that early in development the queen caste has the most distinct gene expression profile, perhaps reflecting the very rapid growth and morphological specialization of this caste compared to workers and drones. Later in development the haploid male drones have the most distinct gene expression profile, perhaps reflecting the influence of ploidy or sex determination on gene expression. © 2017 Institute of Zoology, Chinese Academy of Sciences.

From loquacious to reticent: understanding patient health information communication to guide consumer health IT design.

PubMed

Valdez, Rupa S; Guterbock, Thomas M; Fitzgibbon, Kara; Williams, Ishan C; Wellbeloved-Stone, Claire A; Bears, Jaime E; Menefee, Hannah K

2017-07-01

It is increasingly recognized that some patients self-manage in the context of social networks rather than alone. Consumer health information technology (IT) designed to support socially embedded self-management must be responsive to patients' everyday communication practices. There is an opportunity to improve consumer health IT design by explicating how patients currently leverage social media to support health information communication. The objective of this study was to determine types of health information communication patterns that typify Facebook users with chronic health conditions to guide consumer health IT design. Seven hundred participants with type 2 diabetes were recruited through a commercial survey access panel. Cluster analysis was used to identify distinct approaches to health information communication both on and off Facebook. Analysis of variance (ANOVA) methods were used to identify demographic and behavioral differences among profiles. Secondary analysis of qualitative interviews ( n  = 25) and analysis of open-ended survey questions were conducted to understand participant rationales for each profile. Our analysis yielded 7 distinct health information communication profiles. Five of 7 profiles had consistent patterns both on and off Facebook, while the remaining 2 demonstrated distinct practices, with no health information communication on Facebook but some off Facebook. One profile was distinct from all others in both health information communication practices and demographic composition. Rationales for following specific health information communication practices were categorized under 6 themes: altruism, instrumental support, social support, privacy and stigma, convenience, and Facebook knowledge. Facebook has been widely adopted for health information communication; This study demonstrates that Facebook has been widely adopted for health information communication. It also shows that the ways in which patients communicate health information on and off Facebook are diverse. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Outer-disk reddening and gas-phase metallicities: The CALIFA connection

NASA Astrophysics Data System (ADS)

Marino, R. A.; Gil de Paz, A.; Sánchez, S. F.; Sánchez-Blázquez, P.; Cardiel, N.; Castillo-Morales, A.; Pascual, S.; Vílchez, J.; Kehrig, C.; Mollá, M.; Mendez-Abreu, J.; Catalán-Torrecilla, C.; Florido, E.; Perez, I.; Ruiz-Lara, T.; Ellis, S.; López-Sánchez, A. R.; González Delgado, R. M.; de Lorenzo-Cáceres, A.; García-Benito, R.; Galbany, L.; Zibetti, S.; Cortijo, C.; Kalinova, V.; Mast, D.; Iglesias-Páramo, J.; Papaderos, P.; Walcher, C. J.; Bland-Hawthorn, J.

2016-01-01

We study, for the first time in a statistically significant and well-defined sample, the relation between the outer-disk ionized-gas metallicity gradients and the presence of breaks in the surface brightness profiles of disk galaxies. Sloan Digital Sky Survey (SDSS) g'- and r'-band surface brightness, (g' - r') color, and ionized-gasoxygen abundance profiles for 324 galaxies within the Calar Alto Legacy Integral Field Area (CALIFA) survey are used for this purpose. We perform a detailed light-profile classification, finding that 84% of our disks show down- or up-bending profiles (Type II and Type III, respectively), while the remaining 16% are well fitted by one single exponential (Type I). The analysis of the color gradients at both sides of this break shows a U-shaped profile for most Type II galaxies with an average minimum (g' - r') color of ~0.5 mag and an ionized-gas metallicity flattening associated with it only in the case of low-mass galaxies. Comparatively, more massive systems show a rather uniform negative metallicity gradient. The correlation between metallicity flattening and stellar mass for these systems results in p-values as low as 0.01. Independent of the mechanism having shaped the outer light profiles of these galaxies, stellar migration or a previous episode of star formation in a shrinking star-forming disk, it is clear that the imprint in their ionized-gas metallicity was different for low- and high-mass Type II galaxies. In the case of Type III disks, a positive correlation between the change in color and abundance gradient is found (the null hypothesis is ruled out with a p-value of 0.02), with the outer disks of Type III galaxies with masses ≤1010 M⊙ showing a weak color reddening or even a bluing. This is interpreted as primarily due to a mass downsizing effect on the population of Type III galaxies that recently experienced an enhanced inside-out growth.

Profile 1999 : softwood sawmills in the United States and Canada

Treesearch

Henry. Spelter; Tim. McKeever

More than 1,200 sawmills produce the bulk of U.S. and Canadian softwood lumber. The maps and tables in this report show the location and size of these mills by State and Province. Analysis of timber inventories in relation to use shows a close correspondence between pricing and use intensity. In some Southern States, the intensity of use is approaching recent growth...

Ribosome A and P sites revealed by length analysis of ribosome profiling data

PubMed Central

Martens, Andrew T.; Taylor, James; Hilser, Vincent J.

2015-01-01

The high-throughput sequencing of nuclease-protected mRNA fragments bound to ribosomes, a technique known as ribosome profiling, quantifies the relative frequencies with which different regions of transcripts are translated. This technique has revealed novel translation initiation sites with unprecedented scope and has furthered investigations into the connections between codon biases and translation rates. Yet the location of the codon being decoded in ribosome footprints is still unknown, and has been complicated by the recent observation of footprints with non-canonical lengths. Here we show how taking into account the variations in ribosome footprint lengths can reveal the ribosome aminoacyl (A) and peptidyl (P) site locations. These location assignments are in agreement with the proposed mechanisms for various ribosome pauses and further enhance the resolution of the profiling data. We also show that GC-rich motifs at the 5′ ends of footprints are found in yeast, calling into question the anti-Shine-Dalgarno effect's role in ribosome pausing. PMID:25805170

Antitrypanosomal lead discovery: Identification of a ligand-efficient inhibitor of Trypanosoma cruzi CYP51 and parasite growth

PubMed Central

Andriani, Grasiella; Amata, Emanuele; Beatty, Joel; Clements, Zeke; Coffey, Brian J.; Courtemanche, Gilles; Devine, William; Erath, Jessey; Juda, Cristin E.; Wawrzak, Zdzislaw; Wood, JodiAnne T.; Lepesheva, Galina I.; Rodriguez, Ana; Pollastri, Michael P.

2013-01-01

Chagas disease is caused by the intracellular protozoan parasite Trypanosomal cruzi, and current drugs are lacking in terms of desired safety and efficacy profiles. Following on a recently reported high-throughput screening campaign, we have explored initial structure-activity relationships around a class of imidazole-based compounds. This profiling has uncovered compounds 4c (NEU321) and 4j (NEU704), which are potent against in vitro cultures of T. cruzi and are greater than 160-fold selective over host cells. We report in vitro drug metabolism and properties profiling of 4c and show that this chemotype inhibits the T cruzi CYP51 enzyme, an observation confirmed by X-ray crystallographic analysis. We compare the binding orientation of 4c to that of other, previously reported inhibitors. We show that 4c displays a significantly better ligand efficiency and a shorter synthetic route over previously disclosed CYP51 inhibitors, and should therefore be considered a promising lead compound for further optimization. PMID:23448316

Vanillin Inhibits Translation and Induces Messenger Ribonucleoprotein (mRNP) Granule Formation in Saccharomyces cerevisiae: Application and Validation of High-Content, Image-Based Profiling

PubMed Central

Suga, Yohei; Izawa, Shingo; Ohya, Yoshikazu

2013-01-01

Vanillin, generated by acid hydrolysis of lignocellulose, acts as a potent inhibitor of the growth of the yeast Saccharomyces cerevisiae. Here, we investigated the cellular processes affected by vanillin using high-content, image-based profiling. Among 4,718 non-essential yeast deletion mutants, the morphology of those defective in the large ribosomal subunit showed significant similarity to that of vanillin-treated cells. The defects in these mutants were clustered in three domains of the ribosome: the mRNA tunnel entrance, exit and backbone required for small subunit attachment. To confirm that vanillin inhibited ribosomal function, we assessed polysome and messenger ribonucleoprotein granule formation after treatment with vanillin. Analysis of polysome profiles showed disassembly of the polysomes in the presence of vanillin. Processing bodies and stress granules, which are composed of non-translating mRNAs and various proteins, were formed after treatment with vanillin. These results suggest that vanillin represses translation in yeast cells. PMID:23637899

Shock drive capabilities of a 30-Joule laser at the matter in extreme conditions hutch of the Linac Coherent Light Source

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

Brown, Shaughnessy Brennan; Hashim, Akel; Gleason, Arianna

In this paper, we measure the shock drive capabilities of a 30 J, nanosecond, 527 nm laser system at the matter in extreme conditions hutch of the Linac Coherent Light Source. Using a velocity interferometer system for any reflector, we ascertain the maximum instantaneous ablation pressure and characterize its dependence on a drive laser spot size, spatial profile, and temporal profile. We also examine the effects of these parameters on shock spatial and temporal uniformity. Our analysis shows the drive laser capable of generating instantaneous ablation pressures exceeding 160 GPa while maintaining a 1D shock profile. We find that slopemore » pulses provide higher instantaneous ablation pressures than plateau pulses. Our results show instantaneous ablation pressures comparable to those measured at the Omega Laser Facility in Rochester, NY under similar optical drive parameters. In conclusion, we analyze how optical laser ablation pressures are compare with known scaling relations, accounting for variable laser wavelengths.« less

Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.

PubMed

Hurst, Travis; Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2018-05-10

The selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) method probes RNA local structural and dynamic information at single nucleotide resolution. To gain quantitative insights into the relationship between nucleotide flexibility, RNA 3D structure, and SHAPE reactivity, we develop a 3D Structure-SHAPE Relationship model (3DSSR) to rebuild SHAPE profiles from 3D structures. The model starts from RNA structures and combines nucleotide interaction strength and conformational propensity, ligand (SHAPE reagent) accessibility, and base-pairing pattern through a composite function to quantify the correlation between SHAPE reactivity and nucleotide conformational stability. The 3DSSR model shows the relationship between SHAPE reactivity and RNA structure and energetics. Comparisons between the 3DSSR-predicted SHAPE profile and the experimental SHAPE data show correlation, suggesting that the extracted analytical function may have captured the key factors that determine the SHAPE reactivity profile. Furthermore, the theory offers an effective method to sieve RNA 3D models and exclude models that are incompatible with experimental SHAPE data.

Shock drive capabilities of a 30-Joule laser at the matter in extreme conditions hutch of the Linac Coherent Light Source

DOE PAGES

Brown, Shaughnessy Brennan; Hashim, Akel; Gleason, Arianna; ...

2017-10-23

In this paper, we measure the shock drive capabilities of a 30 J, nanosecond, 527 nm laser system at the matter in extreme conditions hutch of the Linac Coherent Light Source. Using a velocity interferometer system for any reflector, we ascertain the maximum instantaneous ablation pressure and characterize its dependence on a drive laser spot size, spatial profile, and temporal profile. We also examine the effects of these parameters on shock spatial and temporal uniformity. Our analysis shows the drive laser capable of generating instantaneous ablation pressures exceeding 160 GPa while maintaining a 1D shock profile. We find that slopemore » pulses provide higher instantaneous ablation pressures than plateau pulses. Our results show instantaneous ablation pressures comparable to those measured at the Omega Laser Facility in Rochester, NY under similar optical drive parameters. In conclusion, we analyze how optical laser ablation pressures are compare with known scaling relations, accounting for variable laser wavelengths.« less

CLASH: Weak-lensing shear-and-magnification analysis of 20 galaxy clusters

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

Umetsu, Keiichi; Czakon, Nicole; Medezinski, Elinor

2014-11-10

We present a joint shear-and-magnification weak-lensing analysis of a sample of 16 X-ray-regular and 4 high-magnification galaxy clusters at 0.19 ≲ z ≲ 0.69 selected from the Cluster Lensing And Supernova survey with Hubble (CLASH). Our analysis uses wide-field multi-color imaging, taken primarily with Suprime-Cam on the Subaru Telescope. From a stacked-shear-only analysis of the X-ray-selected subsample, we detect the ensemble-averaged lensing signal with a total signal-to-noise ratio of ≅ 25 in the radial range of 200-3500 kpc h {sup –1}, providing integrated constraints on the halo profile shape and concentration-mass relation. The stacked tangential-shear signal is well described bymore » a family of standard density profiles predicted for dark-matter-dominated halos in gravitational equilibrium, namely, the Navarro-Frenk-White (NFW), truncated variants of NFW, and Einasto models. For the NFW model, we measure a mean concentration of c{sub 200c}=4.01{sub −0.32}{sup +0.35} at an effective halo mass of M{sub 200c}=1.34{sub −0.09}{sup +0.10}×10{sup 15} M{sub ⊙}. We show that this is in excellent agreement with Λ cold dark matter (ΛCDM) predictions when the CLASH X-ray selection function and projection effects are taken into account. The best-fit Einasto shape parameter is α{sub E}=0.191{sub −0.068}{sup +0.071}, which is consistent with the NFW-equivalent Einasto parameter of ∼0.18. We reconstruct projected mass density profiles of all CLASH clusters from a joint likelihood analysis of shear-and-magnification data and measure cluster masses at several characteristic radii assuming an NFW density profile. We also derive an ensemble-averaged total projected mass profile of the X-ray-selected subsample by stacking their individual mass profiles. The stacked total mass profile, constrained by the shear+magnification data, is shown to be consistent with our shear-based halo-model predictions, including the effects of surrounding large-scale structure as a two-halo term, establishing further consistency in the context of the ΛCDM model.« less

Insight into Genes Regulating Postharvest Aflatoxin Contamination of Tetraploid Peanut from Transcriptional Profiling.

PubMed

Korani, Walid; Chu, Ye; Holbrook, C Corley; Ozias-Akins, Peggy

2018-05-01

Postharvest aflatoxin contamination is a challenging issue that affects peanut quality. Aflatoxin is produced by fungi belonging to the Aspergilli group, and is known as an acutely toxic, carcinogenic, and immune-suppressing class of mycotoxins. Evidence for several host genetic factors that may impact aflatoxin contamination has been reported, e.g. , genes for lipoxygenase (PnLOX1 and PnLOX2/PnLOX3 that showed either positive or negative regulation with Aspergillus infection), reactive oxygen species, and WRKY (highly associated with or differentially expressed upon infection of maize with Aspergillus flavus ); however, their roles remain unclear. Therefore, we conducted an RNA-sequencing experiment to differentiate gene response to the infection by A. flavus between resistant (ICG 1471) and susceptible (Florida-07) cultivated peanut genotypes. The gene expression profiling analysis was designed to reveal differentially expressed genes in response to the infection (infected vs. mock-treated seeds). In addition, the differential expression of the fungal genes was profiled. The study revealed the complexity of the interaction between the fungus and peanut seeds as the expression of a large number of genes was altered, including some in the process of plant defense to aflatoxin accumulation. Analysis of the experimental data with "keggseq," a novel designed tool for Kyoto Encyclopedia of Genes and Genomes enrichment analysis, showed the importance of α-linolenic acid metabolism, protein processing in the endoplasmic reticulum, spliceosome, and carbon fixation and metabolism pathways in conditioning resistance to aflatoxin accumulation. In addition, coexpression network analysis was carried out to reveal the correlation of gene expression among peanut and fungal genes. The results showed the importance of WRKY, toll/Interleukin1 receptor-nucleotide binding site leucine-rich repeat (TIR-NBS-LRR), ethylene, and heat shock proteins in the resistance mechanism. Copyright © 2018 by the Genetics Society of America.

Heat and mass transport during microwave heating of mashed potato in domestic oven--model development, validation, and sensitivity analysis.

PubMed

Chen, Jiajia; Pitchai, Krishnamoorthy; Birla, Sohan; Negahban, Mehrdad; Jones, David; Subbiah, Jeyamkondan

2014-10-01

A 3-dimensional finite-element model coupling electromagnetics and heat and mass transfer was developed to understand the interactions between the microwaves and fresh mashed potato in a 500 mL tray. The model was validated by performing heating of mashed potato from 25 °C on a rotating turntable in a microwave oven, rated at 1200 W, for 3 min. The simulated spatial temperature profiles on the top and bottom layer of the mashed potato showed similar hot and cold spots when compared to the thermal images acquired by an infrared camera. Transient temperature profiles at 6 locations collected by fiber-optic sensors showed good agreement with predicted results, with the root mean square error ranging from 1.6 to 11.7 °C. The predicted total moisture loss matched well with the observed result. Several input parameters, such as the evaporation rate constant, the intrinsic permeability of water and gas, and the diffusion coefficient of water and gas, are not readily available for mashed potato, and they cannot be easily measured experimentally. Reported values for raw potato were used as baseline values. A sensitivity analysis of these input parameters on the temperature profiles and the total moisture loss was evaluated by changing the baseline values to their 10% and 1000%. The sensitivity analysis showed that the gas diffusion coefficient, intrinsic water permeability, and the evaporation rate constant greatly influenced the predicted temperature and total moisture loss, while the intrinsic gas permeability and the water diffusion coefficient had little influence. This model can be used by the food product developers to understand microwave heating of food products spatially and temporally. This tool will allow food product developers to design food package systems that would heat more uniformly in various microwave ovens. The sensitivity analysis of this study will help us determine the most significant parameters that need to be measured accurately for reliable model prediction. © 2014 Institute of Food Technologists®

Gas chromatography-mass spectrometry-based metabolic profiling of cerebrospinal fluid from epileptic dogs.

PubMed

Hasegawa, Tetsuya; Sumita, Maho; Horitani, Yusuke; Tamai, Reo; Tanaka, Katsuhiro; Komori, Masayuki; Takenaka, Shigeo

2014-04-01

Epilepsy is a common neurological disorder with seizures, but diagnostic approaches in veterinary clinics remain limited. Cerebrospinal fluid (CSF) is a body fluid used for diagnosis in veterinary medicine. In this study, we explored canine epilepsy diagnostic biomarkers using gas chromatography-mass spectrometry (GC-MS)-based metabolic profiling of CSF and multivariate data analysis. Profiles for subjects with idiopathic epilepsy differed significantly from those of healthy controls and subjects with symptomatic epilepsy. Among 60 identified metabolites, the levels of 20 differed significantly among the three groups. Glutamic acid was significantly increased in idiopathic epilepsy, and some metabolites including ascorbic acid were changed in both forms of epilepsy. These findings show that metabolic profiles of CSF differ between idiopathic and symptomatic epilepsy and that metabolites including glutamic acid and ascorbic acid in CSF may be useful for diagnosis of canine epilepsy.

Variation of D-region nitric-oxide density with solar activity and season at the dip equator

NASA Technical Reports Server (NTRS)

Chakrabarty, D. K.; Pakhomov, S. V.; Beig, G.

1989-01-01

To study the solar control on electron density (N sub e) in the equatorial D region, a program was initiated with Soviet collaboration in 1979. A total of 31 rockets were launched during the high solar activity period, and 47 rockets during the low solar activity period, from Thumba to measure the N sub e profiles. Analysis of the data shows that the average values of N sub e for the high solar activity period are higher by a factor of about 2 to 3 compared to the low solar activity values. It was found that a single nitric oxide density, (NO), profile cannot reproduce all the observed N sub e profiles. An attempt was made to reproduce theoretically the observed N sub e profiles by introducing variation in (NO) for the different solar activity periods and seasons.

Social Disadvantage, Severe Child Abuse, and Biological Profiles in Adulthood.

PubMed

Lee, Chioun; Coe, Christopher L; Ryff, Carol D

2017-09-01

Guided by the stress process model and the life course perspective, we hypothesize: (1) that childhood abuse is concentrated, in terms of type and intensity, among socially disadvantaged individuals, and (2) that experiencing serious abuse contributes to poor biological profiles in multiple body systems in adulthood. Data came from the Biomarker subsample of Midlife in the United States (2004-2006). We used latent class analysis to identify distinct profiles of childhood abuse, each reflecting a combination of type and severity. Results indicate that disadvantaged groups, women, and those from disadvantaged families are at greater risk of experiencing more severe and multiple types of abuse. Those with more severe and multifaceted childhood abuse show greater physiological dysregulation. Childhood abuse experiences partially accounted for the social status differences in physiological profiles. Our findings underscore that differential exposure to serious childhood stressors plays a significant role in gender and class inequalities in adult health.

Derivation of atmospheric extinction profiles and wind speed over the ocean from a satellite-borne lidar.

PubMed

Weinman, J A

1988-10-01

A simulated analysis is presented that shows that returns from a single-frequency space-borne lidar can be combined with data from conventional visible satellite imagery to yield profiles of aerosol extinction coefficients and the wind speed at the ocean surface. The optical thickness of the aerosols in the atmosphere can be derived from visible imagery. That measurement of the total optical thickness can constrain the solution to the lidar equation to yield a robust estimate of the extinction profile. The specular reflection of the lidar beam from the ocean can be used to determine the wind speed at the sea surface once the transmission of the atmosphere is known. The impact on the retrieved aerosol profiles and surface wind speed produced by errors in the input parameters and noise in the lidar measurements is also considered.

Motivational profile of astronauts at the International Space Station

NASA Astrophysics Data System (ADS)

Brcic, Jelena

2010-11-01

Research has demonstrated that the motive triad of needs for achievement, power, and affiliation can predict variables such as occupational success and satisfaction, innovation, aggressiveness, susceptibility to illness, cooperation, conformity, and many others. The present study documents the motivational profiles of astronauts at three stages of their expedition. Thematic content analysis was employed for references to Winter's well-established motive markers in narratives (media interviews, journals, and oral histories) of 46 astronauts participating in International Space Station (ISS) expeditions. Significant pre-flight differences were found in relation to home agency and job status. NASA astronauts, compared with those from the Russian Space Agency, are motivated by higher need for power, as are commanders in comparison to flight engineers. The need for affiliation motive showed a significant change from pre-flight to in-flight stages. The implications of the relationship between the motivational profile of astronauts and the established behavioural correlates of such profiles are discussed.

Elemental profiling of laser cladded multilayer coatings by laser induced breakdown spectroscopy and energy dispersive X-ray spectroscopy

NASA Astrophysics Data System (ADS)

Lednev, V. N.; Sdvizhenskii, P. A.; Filippov, M. N.; Grishin, M. Ya.; Filichkina, V. A.; Stavertiy, A. Ya.; Tretyakov, R. S.; Bunkin, A. F.; Pershin, S. M.

2017-09-01

Multilayer tungsten carbide wear resistant coatings were analyzed by laser induced breakdown spectroscopy (LIBS) and energy dispersive X-ray (EDX) spectroscopy. Coaxial laser cladding technique was utilized to produce tungsten carbide coating deposited on low alloy steel substrate with additional inconel 625 interlayer. EDX and LIBS techniques were used for elemental profiling of major components (Ni, W, C, Fe, etc.) in the coating. A good correlation between EDX and LIBS data was observed while LIBS provided additional information on light element distribution (carbon). A non-uniform distribution of tungsten carbide grains along coating depth was detected by both LIBS and EDX. In contrast, horizontal elemental profiling showed a uniform tungsten carbide particles distribution. Depth elemental profiling by layer-by-layer LIBS analysis was demonstrated to be an effective method for studying tungsten carbide grains distribution in wear resistant coating without any sample preparation.

1H NMR Spectroscopy and MVA Analysis of Diplodus sargus Eating the Exotic Pest Caulerpa cylindracea.

PubMed

De Pascali, Sandra A; Del Coco, Laura; Felline, Serena; Mollo, Ernesto; Terlizzi, Antonio; Fanizzi, Francesco P

2015-06-05

The green alga Caulerpa cylindracea is a non-autochthonous and invasive species that is severely affecting the native communities in the Mediterranean Sea. Recent researches show that the native edible fish Diplodus sargus actively feeds on this alga and cellular and physiological alterations have been related to the novel alimentary habits. The complex effects of such a trophic exposure to the invasive pest are still poorly understood. Here we report on the metabolic profiles of plasma from D. sargus individuals exposed to C. cylindracea along the southern Italian coast, using 1H NMR spectroscopy and multivariate analysis (Principal Component Analysis, PCA, Orthogonal Partial Least Square, PLS, and Orthogonal Partial Least Square Discriminant Analysis, OPLS-DA). Fish were sampled in two seasonal periods from three different locations, each characterized by a different degree of algal abundance. The levels of the algal bisindole alkaloid caulerpin, which is accumulated in the fish tissues, was used as an indicator of the trophic exposure to the seaweed and related to the plasma metabolic profiles. The profiles appeared clearly influenced by the sampling period beside the content of caulerpin, while the analyses also supported a moderate alteration of lipid and choline metabolism related to the Caulerpa-based diet.

Saponin Profile of Wild Asparagus Species.

PubMed

Jaramillo-Carmona, Sara; Rodriguez-Arcos, Rocío; Jiménez-Araujo, Ana; López, Sergio; Gil, Juan; Moreno, Roberto; Guillén-Bejarano, Rafael

2017-03-01

The aim of this work was to study the saponin profiles from spears of different wild asparagus species in the context of its genetic diversity aside from geographical seed origin. They included Asparagus pseudoscaber Grecescu, Asparagus maritimus (L.) Mill., Asparagus brachiphyllus Turcz., Asparagus prostrates Dumort., and Asparagus officinalis L. The saponin analysis by LC-MS has shown that saponin profile from wild asparagus is similar to that previously described for triguero asparagus from Huétor-Tájar landrace (triguero HT), which had not ever been reported in the edible part of asparagus. All the samples, except A. officinalis, were characterized for having saponins distinct to protodioscin and the total saponin contents were 10-fold higher than those described for commercial hybrids of green asparagus. In particular, A. maritimus from different origins were rich in saponins previously found in triguero HT. These findings supported previous suggestion, based on genetic analysis, about A. maritimus being the origin of triguero HT. Multivariate statistics including principal component analysis and hierarchical clustering analysis were used to define both similarities and differences among samples. The results showed that the greatest variance of the tested wild asparagus could be attributed to differences in the concentration of particular saponins and this knowledge could be a tool for identifying similar species. © 2017 Institute of Food Technologists®.

The emotional impact of bullying and cyberbullying on victims: a European cross-national study.

PubMed

Ortega, Rosario; Elipe, Paz; Mora-Merchán, Joaquin A; Genta, M Luisa; Brighi, Antonella; Guarini, Annalisa; Smith, Peter K; Thompson, Fran; Tippett, Neil

2012-01-01

Past research has demonstrated the effects of bullying can be severe and long term for the individuals involved. The main aim of this study is to analyze the emotional impact on victims of traditional bullying, both direct and indirect forms, and of cyberbullying through mobile phones and the Internet. A sample of 5,862 adolescents from three different countries, Italy (N = 1,964), Spain (N = 1,671), and England (N = 2,227), responded to a questionnaire that asked if they had experience of various forms of bullying, and the consequent emotional impact. The results show that both traditional bullying and cyberbullying have a significant prevalence in the samples. Emotional responses are linked to types of bullying. Analysis of answers identified specific emotional profiles for the different types of bullying and cyberbullying. Direct bullying and cyberbullying via mobile phone showed similar profiles, and also indirect bullying and cyberbullying using the Internet. Similarities and differences between profiles are discussed and some hypotheses are presented to explain the results. In addition, school grade, gender, country, and severity of bullying episodes were related to the specific emotional profiles of each type of bullying. © 2012 Wiley Periodicals, Inc.

Unbiased Metabolite Profiling of Schizophrenia Fibroblasts under Stressful Perturbations Reveals Dysregulation of Plasmalogens and Phosphatidylcholines.

PubMed

Huang, Joanne H; Park, Hyoungjun; Iaconelli, Jonathan; Berkovitch, Shaunna S; Watmuff, Bradley; McPhie, Donna; Öngür, Dost; Cohen, Bruce M; Clish, Clary B; Karmacharya, Rakesh

2017-02-03

We undertook an unbiased metabolite profiling of fibroblasts from schizophrenia patients and healthy controls to identify metabolites and pathways that are dysregulated in disease, seeking to gain new insights into the disease biology of schizophrenia and to discover potential disease-related biomarkers. We measured polar and nonpolar metabolites in the fibroblasts under normal conditions and under two stressful physiological perturbations: growth in low-glucose media and exposure to the steroid hormone dexamethasone. We found that metabolites that were significantly different between schizophrenia and control subjects showed separation of the two groups by partial least-squares discriminant analysis methods. This separation between schizophrenia and healthy controls was more robust with metabolites identified under the perturbation conditions. The most significant individual metabolite differences were also found in the perturbation experiments. Metabolites that were significantly different between schizophrenia and healthy controls included a number of plasmalogens and phosphatidylcholines. We present these results in the context of previous reports of metabolic profiling of brain tissue and plasma in schizophrenia. These results show the applicability of metabolite profiling under stressful perturbations to reveal cellular pathways that may be involved in disease biology.

Immune-spaying as an alternative to surgical spaying in Iberian x Duroc females: Effect on the sensory traits and volatile organic compound profile of dry-cured shoulders and dry-cured loins.

PubMed

Gamero-Negrón, Rafael; García, Carmen; Reina, Raquel; Sánchez Del Pulgar, José

2018-09-01

The aim of this study was to assess the effect of immune-spaying on sensory characteristics and the volatile organic compound (VOC) profile of dry-cured shoulders and loins by comparing Iberian × Duroc surgically spayed females, immune-spayed females and entire females. VOC profile of dry-cured shoulders was not significantly affected by the reproductive status, probably due to the large heterogeneity of dry-cured shoulders as a product. Correspondingly, dry-cured shoulders showed little differences among treatment groups, with better scores for marbling, hardness and chewiness attributes in the immune-spayed females. Dry-cured loin sensory traits such as brightness, marbling, chewiness and juiciness, presented better scores in immune-spayed females. Moreover, dry-cured loins showed a higher homogeneity that allowed the effects of spaying to be observed, thus the Principal Component Analysis performed on VOC profile data indicated a better separation of samples among treatment groups. Consequently, immune-spaying could be a viable alternative to surgical spaying from the point of view of meat quality. Copyright © 2018 Elsevier Ltd. All rights reserved.

Nutritional composition and antinutritional properties of maize ogi cofermented with pigeon pea.

PubMed

Okafor, Uchechukwu I; Omemu, Adebunkola M; Obadina, Adewale O; Bankole, Mobolaji O; Adeyeye, Samuel A O

2018-03-01

Maize was cofermented with pigeon pea for ogi production and evaluated for nutritional (proximate composition, minerals, vitamins, and amino acid profile analyses) and antinutritional (phytate, tannin, and trypsin inhibitor activity analyses) qualities. White maize and pigeon pea were mixed at ratios of 90:10, 80:20, 70:30, 60:40, and 50:50, respectively, with 100:0 serving as the control. Mixtures were cofermented for 96 hr at 27°C ± 2°C and nutritional, mineral, and antinutritional qualities were analyzed using analysis of variance. Results of proximate analysis showed that the values were significantly difference at p  ≤   .05. Maize cofermented with pigeon pea at a ratio of 60:40 had the highest protein (22.79 mg/100 g), fat (19.27 mg/100 g), ash (2.98 mg/100 g), crude fiber (0.73 mg/100 g), and lowest moisture (1.98 mg/100 g) content, and was significantly ( p  ≤   .05) different from the other ratios. Of all the mixtures analyzed, 60:40 was significantly ( p  ≤   .05) different and had the highest Vitamin B 1 , B 2 , and B 3 contents. Amino acid profile results showed that maize cofermented with pigeon pea at a ratio of 60:40 showed the highest contents of lysine (93.95 mg/g), tryptophan (20.38 mg/g), isoleucine (54.78 mg/g), phenylalanine (86.23 mg/g), leucine (109.55 mg/g), and valine (68.29 mg/g), respectively, and was significantly ( p  ≤   .05) different from the other ratios. Results of antinutritional analysis showed low phytate, tannin, and trypsin inhibitor values in maize cofermented with pigeon pea at a ratio of 60:40 when compared with other ratios. The cofermented maize-pigeon pea product 60:40 had high amino acid profile than the others.

Antimicrobial Resistance Profiles and Diversity in Salmonella from Humans and Cattle, 2004-2011.

PubMed

Afema, J A; Mather, A E; Sischo, W M

2015-11-01

Analysis of long-term anti-microbial resistance (AMR) data is useful to understand source and transmission dynamics of AMR. We analysed 5124 human clinical isolates from Washington State Department of Health, 391 cattle clinical isolates from the Washington Animal Disease Diagnostic Laboratory and 1864 non-clinical isolates from foodborne disease research on dairies in the Pacific Northwest. Isolates were assigned profiles based on phenotypic resistance to 11 anti-microbials belonging to eight classes. Salmonella Typhimurium (ST), Salmonella Newport (SN) and Salmonella Montevideo (SM) were the most common serovars in both humans and cattle. Multinomial logistic regression showed ST and SN from cattle had greater probability of resistance to multiple classes of anti-microbials than ST and SN from humans (P < 0.0001). While these findings could be consistent with the belief that cattle are a source of resistant ST and SN for people, occurrence of profiles unique to cattle and not observed in temporally related human isolates indicates these profiles are circulating in cattle only. We used various measures to assess AMR diversity, conditional on the weighting of rare versus abundant profiles. AMR profile richness was greater in the common serovars from humans, although both source data sets were dominated by relatively few profiles. The greater profile richness in human Salmonella may be due to greater diversity of sources entering the human population compared to cattle or due to continuous evolution in the human environment. Also, AMR diversity was greater in clinical compared to non-clinical cattle Salmonella, and this could be due to anti-microbial selection pressure in diseased cattle that received treatment. The use of bootstrapping techniques showed that although there were shared profiles between humans and cattle, the expected and observed number of profiles was different, suggesting Salmonella and associated resistance from humans and cattle may not be wholly derived from a common population. © 2014 The Authors. Zoonoses and Public Health Published by Blackwell Verlag GmbH.

Molecular Analysis of Mixed Endometrial Carcinomas Shows Clonality in Most Cases.

PubMed

Köbel, Martin; Meng, Bo; Hoang, Lien N; Almadani, Noorah; Li, Xiaodong; Soslow, Robert A; Gilks, C Blake; Lee, Cheng-Han

2016-02-01

Mixed endometrial carcinoma refers to a tumor that comprises 2 or more distinct histotypes. We studied 18 mixed-type endometrial carcinomas-11 mixed serous and low-grade endometrioid carcinomas (SC/EC), 5 mixed clear cell and low-grade ECs (CCC/EC), and 2 mixed CCC and SCs (CCC/SC), using targeted next-generation sequencing and immunohistochemistry to compare the molecular profiles of the different histotypes present in each case. In 16 of 18 cases there was molecular evidence that both components shared a clonal origin. Eight cases (6 EC/SC, 1 EC/CCC, and 1 SC/CCC) showed an SC molecular profile that was the same in both components. Five cases (3 CCC/EC and 2 SC/EC) showed a shared endometrioid molecular profile and identical mismatch-repair protein deficiency in both components. A single SC/EC case harbored the same POLE exonuclease domain mutation in both components. One SC/CCC and 1 EC/CCC case showed both shared and unique molecular features in the 2 histotype components, suggesting early molecular divergence from a common clonal origin. In 2 cases, there were no shared molecular features, and these appear to be biologically unrelated synchronous tumors. Overall, these results show that the different histologic components in mixed endometrial carcinomas typically share the same molecular aberrations. Mixed endometrial carcinomas most commonly occur through morphologic mimicry, whereby tumors with serous-type molecular profile show morphologic features of EC or CCC, or through underlying deficiency in DNA nucleotide repair, with resulting rapid accrual of mutations and intratumoral phenotypic heterogeneity. Less commonly, mixed endometrial carcinomas are the result of early molecular divergence from a common progenitor clone or are synchronous biologically unrelated tumors (collision tumors).

Molecular analysis of mixed endometrial carcinomas shows clonality in most cases

PubMed Central

Hoang, Lien N.; Almadani, Noorah; Li, Xiaodong; Soslow, Robert A; Gilks, C. Blake; Lee, Cheng-Han

2016-01-01

Mixed endometrial carcinoma refers to a tumor that is comprised of two or more distinct histotypes. We studied 18 mixed-type endometrial carcinomas - 11 mixed serous and low-grade endometrioid carcinomas (SC/EC), 5 mixed clear cell and low-grade endometrioid carcinomas (CCC/EC), and 2 mixed clear cell and serous carcinoma (CCC/SC), using targeted next generation sequencing and immunohistochemistry to compare the molecular profiles of the different histotypes present in each case. In 16 of 18 cases there was molecular evidence that both components shared a clonal origin. Eight cases (6 EC/SC, 1 EC/CCC and 1 SC/CCC) showed a serous carcinoma molecular profile that was the same in both components. Five cases (3 CCC/EC and 2 SC/EC) showed a shared endometrioid molecular profile and identical mismatch repair protein (MMR) deficiency in both components. A single SC/EC case harbored the same POLE exonuclease domain mutation in both components. One SC/CCC and one EC/CCC case showed both shared and unique molecular features in the two histotype components, suggesting early molecular divergence from a common clonal origin. In two cases, there were no shared molecular features and these appear to be biologically unrelated synchronous tumors. Overall, these results show that the different histologic components in mixed endometrial carcinomas typically share the same molecular aberrations. Mixed endometrial carcinomas most commonly occur through morphological mimicry, whereby tumors with serous-type molecular profile show morphological features of endometrioid or clear cell carcinoma, or through underlying deficiency in DNA nucleotide repair, with resulting rapid accrual of mutations and intratumoral phenotypic heterogeneity. Less commonly, mixed endometrial carcinomas are the result of early molecular divergence from a common progenitor clone or are synchronous biologically unrelated tumors (collision tumors). PMID:26492180

Monitoring the ripening process of Cheddar cheese based on hydrophilic component profiling using gas chromatography-mass spectrometry.

PubMed

Ochi, H; Sakai, Y; Koishihara, H; Abe, F; Bamba, T; Fukusaki, E

2013-01-01

We proposed an application methodology that combines metabolic profiling with multiple appropriate multivariate analyses and verified it on the industrial scale of the ripening process of Cheddar cheese to make practical use of hydrophilic low-molecular-weight compound profiling using gas chromatography-mass spectrometry to design optimal conditions and quality monitoring of the cheese ripening process. Principal components analysis provided an overview of the effect of sodium chloride content and kind of lactic acid bacteria starter on the metabolic profile in the ripening process of Cheddar cheese and orthogonal partial least squares-discriminant analysis unveiled the difference in characteristic metabolites. When the sodium chloride contents were different (1.6 and 0.2%) but the same lactic acid bacteria starter was used, the 2 cheeses were classified by orthogonal partial least squares-discriminant analysis from their metabolic profiles, but were not given perfect discrimination. Not much difference existed in the metabolic profile between the 2 cheeses. Compounds including lactose, galactose, lactic acid, 4-aminobutyric acid, and phosphate were identified as contents that differed between the 2 cheeses. On the other hand, in the case of the same salt content of 1.6%, but different kinds of lactic acid bacteria starter, an excellent distinctive discrimination model was obtained, which showed that the difference of lactic acid bacteria starter caused an obvious difference in metabolic profiles. Compounds including lactic acid, lactose, urea, 4-aminobutyric acid, galactose, phosphate, proline, isoleucine, glycine, alanine, lysine, leucine, valine, and pyroglutamic acid were identified as contents that differed between the 2 cheeses. Then, a good sensory prediction model for "rich flavor," which was defined as "thick and rich, including umami taste and soy sauce-like flavor," was constructed based on the metabolic profile during ripening using partial least squares regression analysis. The amino acids proline, leucine, valine, isoleucine, pyroglutamic acid, alanine, glutamic acid, glycine, lysine, tyrosine, serine, phenylalanine, methionine, aspartic acid, and ornithine were extracted as ripening process markers. The present study is not limited to Cheddar cheese and can be applied to various maturation-type natural cheeses. This study provides the technical platform for designing optimal conditions and quality monitoring of the cheese ripening process. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Profiling elements in Puerh tea from Yunnan province, China.

PubMed

Zhang, Jianyang; Ma, Guicen; Chen, Liyan; Liu, Ting; Liu, Xin; Lu, Chengyin

2017-09-01

Puerh tea, as the most representative Chinese dark tea, has attracted global interest in recent years. Profiling the levels of metal elements in Puerh tea is very important since its presence is related to human health. In this study, 41 elements in 98 Puerh tea samples from Yunnan province, China including Puerh raw tea and Puerh ripe tea were evaluated by microwave digestion combined with inductively coupled plasma mass spectrometry . The content of toxic elements, essential elements and rare earth elements of Puerh tea from different regions was discussed in detail. The concentrations of Ba, Cr, As, Pb, Bi, Fe, Zn, V, Mn, Be, Ag and Tl showed significant differences (p < 0.05) by ANOVA analysis. Principal component analysis and linear discriminant analysis were used to describe the relationship of Puerh tea from different regions. This study provided a comprehensive database for Puerh tea quality control and intake risk assessment.

Efficient design and verification of diagnostics for impurity transport experiments.

PubMed

Chilenski, M A; Greenwald, M J; Marzouk, Y M; Rice, J E; White, A E

2018-01-01

Recent attempts to measure impurity transport in Alcator C-Mod using an x-ray imaging crystal spectrometer and laser blow-off impurity injector have failed to yield unique reconstructions of the transport coefficient profiles. This paper presents a fast, linearized model which was constructed to estimate diagnostic requirements for impurity transport experiments. The analysis shows that the spectroscopic diagnostics on Alcator C-Mod should be capable of inferring simple profiles of impurity diffusion D Z and convection V Z accurate to better than ±10% uncertainty, suggesting that the failure to infer unique D Z and V Z from experimental data is attributable to an inadequate analysis procedure rather than the result of insufficient diagnostics. Furthermore, the analysis reveals that even a modest spatial resolution can overcome a low time resolution. This approach can be adapted to design and verify diagnostics for transport experiments on any magnetic confinement device.

Taste characteristics of Chinese bayberry juice characterized by sensory evaluation, chromatography analysis, and an electronic tongue.

PubMed

Yu, Haiyan; Zhang, Yan; Zhao, Jie; Tian, Huaixiang

2018-05-01

To evaluate the taste characteristics of Chinese bayberry juice, four types of bayberry juice sourced from different origins and varieties were analysed using sensory evaluation, chromatography, spectroscopy analysis and an electronic tongue (E-tongue). Nine organic acids and three sugars were assessed using high performance liquid chromatography. Total polyphenols were measured by spectrophotometry. The overall taste profile was collected using the E-tongue. The four types of bayberry juice differed in the sensory attributes of sour, sweet, bitter, and astringent. The E-tongue responses combined with discriminant analysis were able to characterise the taste profiles of the juices. The relationships between the taste compounds and the sensory panel scores established by partial least squares showed that total polyphenols, quininic acid, maleic acid, fructose, citric acid, lactic acid, succinic acid and sucrose made significant contributions to the taste characteristics of the Chinese bayberry juice.

Genome-Wide Investigation and Expression Profiling of HD-Zip Transcription Factors in Foxtail Millet (Setaria italica L.).

PubMed

Chai, Wenbo; Si, Weina; Ji, Wei; Qin, Qianqian; Zhao, Manli; Jiang, Haiyang

2018-01-01

HD-Zip proteins represent the major transcription factors in higher plants, playing essential roles in plant development and stress responses. Foxtail millet is a crop to investigate the systems biology of millet and biofuel grasses and the HD-Zip gene family has not been studied in foxtail millet. For further investigation of the expression profile of the HD-Zip gene family in foxtail millet, a comprehensive genome-wide expression analysis was conducted in this study. We found 47 protein-encoding genes in foxtail millet using BLAST search tools; the putative proteins were classified into four subfamilies, namely, subfamilies I, II, III, and IV. Gene structure and motif analysis indicate that the genes in one subfamily were conserved. Promotor analysis showed that HD-Zip gene was involved in abiotic stress. Duplication analysis revealed that 8 (~17%) hdz genes were tandemly duplicated and 28 (58%) were segmentally duplicated; purifying duplication plays important roles in gene expansion. Microsynteny analysis revealed the maximum relationship in foxtail millet-sorghum and foxtail millet-rice. Expression profiling upon the abiotic stresses of drought and high salinity and the biotic stress of ABA revealed that some genes regulated responses to drought and salinity stresses via an ABA-dependent process, especially sihdz29 and sihdz45. Our study provides new insight into evolutionary and functional analyses of HD-Zip genes involved in environmental stress responses in foxtail millet.

Meta-Analysis of Postoperative Outcome Parameters Comparing Descemet Membrane Endothelial Keratoplasty Versus Descemet Stripping Automated Endothelial Keratoplasty.

PubMed

Pavlovic, Ivana; Shajari, Mehdi; Herrmann, Eva; Schmack, Ingo; Lencova, Anna; Kohnen, Thomas

2017-12-01

This meta-analysis compares Descemet membrane endothelial keratoplasty (DMEK) with Descemet stripping automated endothelial keratoplasty (DSAEK) to evaluate their strength and weakness profiles. Meta-analysis. We performed a meta-analysis and searched the peer-reviewed literature in PubMed, Cochrane Library, Web of Science, and Embase following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Prospective and retrospective trials performing and comparing DMEK and DSAEK were included. Effects were calculated as odds ratios or standardized mean differences. A total of 11 studies with a total of 723 eyes (350 DMEK and 373 DSAEK) were included. No significant difference was found regarding the total detachment rate, graft failure, and rejection. One of 340 eyes undergoing DMEK showed total detachment and 5 of 363 eyes undergoing DSAEK showed total detachment (P = 0.28). Six of 280 eyes undergoing DMEK showed graft failure; 1 of 313 eyes undergoing DSAEK developed this complication (P = 0.18). No rejection was observed in 158 eyes undergoing DMEK; 4 cases of rejection occurred in 196 eyes undergoing DSAEK (P = 0.37). No significant difference was found regarding endothelial cell loss (P = 0.48). There was a significantly higher partial detachment rate with DMEK: 88 of 340 eyes undergoing DMEK showed partial detachment; 16 of 363 eyes undergoing DSAEK showed this complication (P < 0.00001). DMEK was superior in best-corrected visual acuity after 6 months (P < 0.001), subjective evaluation of visual acuity (P = 0.001), patient satisfaction (P < 0.001), and was the method preferred by patients (P = 0.001). DMEK and DSAEK have a similar complication profile. However, the superiority in the visual outcome and patient satisfaction makes DMEK the preferred option for most patients.

Microbial analysis in primary and persistent endodontic infections by using pyrosequencing.

PubMed

Hong, Bo-Young; Lee, Tae-Kwon; Lim, Sang-Min; Chang, Seok Woo; Park, Joonhong; Han, Seung Hyun; Zhu, Qiang; Safavi, Kamran E; Fouad, Ashraf F; Kum, Kee Yeon

2013-09-01

The aim of this study was to investigate the bacterial community profile of intracanal microbiota in primary and persistent endodontic infections associated with asymptomatic chronic apical periodontitis by using GS-FLX Titanium pyrosequencing. The null hypothesis was that there is no difference in diversity of overall bacterial community profiles between primary and persistent infections. Pyrosequencing analysis from 10 untreated and 8 root-filled samples was conducted. Analysis from 18 samples yielded total of 124,767 16S rRNA gene sequences (with a mean of 6932 reads per sample) that were taxonomically assigned into 803 operational taxonomic units (3% distinction), 148 genera, and 10 phyla including unclassified. Bacteroidetes was the most abundant phylum in both primary and persistent infections. There were no significant differences in bacterial diversity between the 2 infection groups (P > .05). The bacterial community profile that was based on dendrogram showed that bacterial population in both infections was not significantly different in their structure and composition (P > .05). The present pyrosequencing study demonstrates that persistent infections have as diverse bacterial community as primary infections. Copyright © 2013 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

The effects of personality traits on academic burnout in Korean medical students.

PubMed

Lee, Soo Jin; Choi, Young Jun; Chae, Han

2017-06-01

Previous studies suggest that personality traits play an important role in academic burnout. The aim of this study was to investigate how Cloninger's temperament and character traits explain academic burnout in a highly competitive environment of medical school. A total of 184 Korean medical students participated in the survey. The Cloninger's Temperament and Character Inventory was measured around the beginning of the semester and Maslach Burnout Inventory-Student Survey at the end of the semester. The correlations and stepwise regression analysis were conducted to explain the association between personality traits and academic burnout. In addition, latent profile analysis and profile analysis were employed to distinguish and explain differences of personality traits among latent academic burnout subgroups. The higher harm avoidance of temperament and lower self-directedness and cooperativeness of character predicted the subscales of academic burnout in medical students. The Temperament and Character Inventory personality profile of high, middle, and low latent burnout subgroups were significantly different. This study showed that personality might account for the burnout level in medical education. The importance of character dimension for modulating the effects of temperament traits on academic burnout was discussed for future research.

The Predictive Effects of Early Pregnancy Lipid Profiles and Fasting Glucose on the Risk of Gestational Diabetes Mellitus Stratified by Body Mass Index.

PubMed

Wang, Chen; Zhu, Weiwei; Wei, Yumei; Su, Rina; Feng, Hui; Lin, Li; Yang, Huixia

2016-01-01

This study aimed at evaluating the predictive effects of early pregnancy lipid profiles and fasting glucose on the risk of gestational diabetes mellitus (GDM) in patients stratified by prepregnancy body mass index (p-BMI) and to determine the optimal cut-off values of each indicator for different p-BMI ranges. A retrospective system cluster sampling survey was conducted in Beijing during 2013 and a total of 5,265 singleton pregnancies without prepregnancy diabetes were included. The information for each participant was collected individually using questionnaires and medical records. Logistic regression analysis and receiver operator characteristics analysis were used in the analysis. Outcomes showed that potential markers for the prediction of GDM include early pregnancy lipid profiles (cholesterol, triacylglycerols, low-density lipoprotein cholesterol/high-density lipoprotein cholesterol ratios [LDL-C/HDL-C], and triglyceride to high-density lipoprotein cholesterol ratios [TG/HDL-C]) and fasting glucose, of which fasting glucose level was the most accurate indicator. Furthermore, the predictive effects and cut-off values for these factors varied according to p-BMI. Thus, p-BMI should be a consideration for the risk assessment of pregnant patients for GDM development.

Influence of Tooth Spacing Error on Gears With and Without Profile Modifications

NASA Technical Reports Server (NTRS)

Padmasolala, Giri; Lin, Hsiang H.; Oswald, Fred B.

2000-01-01

A computer simulation was conducted to investigate the effectiveness of profile modification for reducing dynamic loads in gears with different tooth spacing errors. The simulation examined varying amplitudes of spacing error and differences in the span of teeth over which the error occurs. The modification considered included both linear and parabolic tip relief. The analysis considered spacing error that varies around most of the gear circumference (similar to a typical sinusoidal error pattern) as well as a shorter span of spacing errors that occurs on only a few teeth. The dynamic analysis was performed using a revised version of a NASA gear dynamics code, modified to add tooth spacing errors to the analysis. Results obtained from the investigation show that linear tip relief is more effective in reducing dynamic loads on gears with small spacing errors but parabolic tip relief becomes more effective as the amplitude of spacing error increases. In addition, the parabolic modification is more effective for the more severe error case where the error is spread over a longer span of teeth. The findings of this study can be used to design robust tooth profile modification for improving dynamic performance of gear sets with different tooth spacing errors.

Pharmacokinetics and pharmacodynamics of SCT800, a new recombinant FVIII, in hemophilia A mice

PubMed Central

Gu, Ruo-lan; Liu, Liang; Xie, Liang-zhi; Gai, Wen-lin; Cao, Si-shuo; Meng, Zhi-yun; Gan, Hui; Wu, Zhuo-na; Li, Jian; Zheng, Ying; Zhu, Xiao-xia; Dou, Gui-fang

2016-01-01

Aim: SCT800 is a new third-generation recombinant FVIII agent that is undergoing promising preclinical study. This study aimed to investigate the pharmacokinetic and pharmacodynamic profiles of SCT800 in hemophilia A mice. Methods: After hemophilia A mice were intravenously injected with single dose of SCT800 (80, 180, and 280 IU/kg) or the commercially available product Xyntha (280 IU/kg), pharmacokinetics profiles were evaluated based on measuring plasma FVIII: C. For pharmacodynamics study, dose-response curves of SCT800 and Xyntha (1–200 IU/kg) were constructed using a tail bleeding model monitoring both bleeding time and blood loss. Results: Pharmacokinetics profile analysis showed a dose independency of SCT800 ranging from 80 to 280 IU/kg and comparable pharmacokinetic profiles between SCT800 and Xyntha at the doses tested. Pharmacodynamics study revealed comparable ED50 values of SCT800 and Xyntha in the tail bleeding model: 14.78 and 15.81 IU/kg for bleeding time, respectively; 13.50 and 13.58 IU/kg for blood loss, respectively. Moreover, at the doses tested, the accompanying dose-related safety evaluation in the tail bleeding model showed lower hypercoagulable tendency and wider dosage range potential for SCT800 than Xyntha. Conclusion: In hemophilia A mice, SCT800 shows comparable pharmacokinetics and pharmacodynamics to Xyntha at the doses tested, and possibly with better safety properties. PMID:26806305

The personality context of relational aggression: A Five-Factor Model profile analysis.

PubMed

Reardon, Kathleen W; Tackett, Jennifer L; Lynam, Don

2018-05-01

Relational aggression (RAgg) is a form of behavior intended to damage the victim's social status or interpersonal relationships through the use of purposeful interpersonal manipulation or social exclusion (Archer & Coyne, 2005). RAgg is impairing, stable, and largely defined by dysfunctional patterns of interpersonal interactions-all of which invokes comparisons to personality and, more specifically, personality pathology. Leveraging research using the Five Factor Model (FFM) in personality disorder (PD) work, the present study aims to understand the personality context of RAgg by applying this FFM profile approach in 2 ways: (a) by compiling a personality profile of RAgg based on a thorough review of the relevant literature and (b) by compiling a personality profile of RAgg based on expert ratings (N = 19). We then compared these profiles to each other and to existing personality profiles of Cluster B PDs to examine how RAgg fits into the personality space represented by Cluster B PDs. These analyses indicate that both FFM profiles of RAgg show substantial overlap with the FFM profile of narcissistic PD. The present study has important implications for bridging disjointed domains of research on personality pathology and RAgg and underscores the relevance of RAgg for early emergence of PD characteristics. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Comparison of Global Transcriptional Responses of Chicken Following Primary and Secondary Eimeria acervulina Infections

USDA-ARS?s Scientific Manuscript database

In the current study, we compared chicken gene transcriptional profiles following primary and secondary infections with Eimeria acervulina using a 9.6K avian intestinal intraepithelial lymphocyte cDNA microarray (AVIELA). Gene Ontology analysis showed that primary infection significantly modulated ...

Inorganic material profiling using Arn+ cluster: Can we achieve high quality profiles?

NASA Astrophysics Data System (ADS)

Conard, T.; Fleischmann, C.; Havelund, R.; Franquet, A.; Poleunis, C.; Delcorte, A.; Vandervorst, W.

2018-06-01

Retrieving molecular information by sputtering of organic systems has been concretized in the last years due to the introduction of sputtering by large gas clusters which drastically eliminated the compound degradation during the analysis and has led to strong improvements in depth resolution. Rapidly however, a limitation was observed for heterogeneous systems where inorganic layers or structures needed to be profiled concurrently. As opposed to organic material, erosion of the inorganic layer appears very difficult and prone to many artefacts. To shed some light on these problems we investigated a simple system consisting of aluminum delta layer(s) buried in a silicon matrix in order to define the most favorable beam conditions for practical analysis. We show that counterintuitive to the small energy/atom used and unlike monoatomic ion sputtering, the information depth obtained with large cluster ions is typically very large (∼10 nm) and that this can be caused both by a large roughness development at early stages of the sputtering process and by a large mixing zone. As a consequence, a large deformation of the Al intensity profile is observed. Using sample rotation during profiling significantly improves the depth resolution while sample temperature has no significant effect. The determining parameter for high depth resolution still remains the total energy of the cluster instead of the energy per atom in the cluster.

Metabolic Profiling in Patients with Pneumonia on Intensive Care.

PubMed

Antcliffe, David; Jiménez, Beatriz; Veselkov, Kirill; Holmes, Elaine; Gordon, Anthony C

2017-04-01

Clinical features and investigations lack predictive value when diagnosing pneumonia, especially when patients are ventilated and when patients develop ventilator associated pneumonia (VAP). New tools to aid diagnosis are important to improve outcomes. This pilot study examines the potential for metabolic profiling to aid the diagnosis in critical care. In this prospective observational study ventilated patients with brain injuries or pneumonia were recruited in the intensive care unit and serum samples were collected soon after the start of ventilation. Metabolic profiles were produced using 1D 1 H NMR spectra. Metabolic data were compared using multivariate statistical techniques including Principal Component Analysis (PCA) and Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA). We recruited 15 patients with pneumonia and 26 with brain injuries, seven of whom went on to develop VAP. Comparison of metabolic profiles using OPLS-DA differentiated those with pneumonia from those with brain injuries (R 2 Y=0.91, Q 2 Y=0.28, p=0.02) and those with VAP from those without (R 2 Y=0.94, Q 2 Y=0.27, p=0.05). Metabolites that differentiated patients with pneumonia included lipid species, amino acids and glycoproteins. Metabolic profiling shows promise to aid in the diagnosis of pneumonia in ventilated patients and may allow a more timely diagnosis and better use of antibiotics. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Investigation of Salmonella Enteritidis outbreaks in South Africa using multi-locus variable-number tandem-repeats analysis, 2013-2015.

PubMed

Muvhali, Munyadziwa; Smith, Anthony Marius; Rakgantso, Andronica Moipone; Keddy, Karen Helena

2017-10-02

Salmonella enterica serovar Enteritidis (Salmonella Enteritidis) has become a significant pathogen in South Africa, and the need for improved molecular surveillance of this pathogen has become important. Over the years, multi-locus variable-number tandem-repeats analysis (MLVA) has become a valuable molecular subtyping technique for Salmonella, particularly for highly homogenic serotypes such as Salmonella Enteritidis. This study describes the use of MLVA in the molecular epidemiological investigation of outbreak isolates in South Africa. Between the years 2013 and 2015, the Centre for Enteric Diseases (CED) received 39 Salmonella Enteritidis isolates from seven foodborne illness outbreaks, which occurred in six provinces. MLVA was performed on all isolates. Three MLVA profiles (MLVA profiles 21, 22 and 28) were identified among the 39 isolates. MLVA profile 28 accounted for 77% (30/39) of the isolates. Isolates from a single outbreak were grouped into a single MLVA profile. A minimum spanning tree (MST) created from the MLVA data showed a close relationship between MLVA profiles 21, 22 and 28, with a single VNTR locus difference between them. MLVA has proven to be a reliable method for the molecular epidemiological investigation of Salmonella Enteritidis outbreaks in South Africa. These foodborne outbreaks emphasize the importance of the One Health approach as an essential component for combating the spread of zoonotic pathogens such as Salmonella Enteritidis.

Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis

PubMed Central

Alamgir, Md; Eroukova, Veronika; Jessulat, Matthew; Xu, Jianhua; Golshani, Ashkan

2008-01-01

Background Functional genomics has received considerable attention in the post-genomic era, as it aims to identify function(s) for different genes. One way to study gene function is to investigate the alterations in the responses of deletion mutants to different stimuli. Here we investigate the genetic profile of yeast non-essential gene deletion array (yGDA, ~4700 strains) for increased sensitivity to paromomycin, which targets the process of protein synthesis. Results As expected, our analysis indicated that the majority of deletion strains (134) with increased sensitivity to paromomycin, are involved in protein biosynthesis. The remaining strains can be divided into smaller functional categories: metabolism (45), cellular component biogenesis and organization (28), DNA maintenance (21), transport (20), others (38) and unknown (39). These may represent minor cellular target sites (side-effects) for paromomycin. They may also represent novel links to protein synthesis. One of these strains carries a deletion for a previously uncharacterized ORF, YBR261C, that we term TAE1 for Translation Associated Element 1. Our focused follow-up experiments indicated that deletion of TAE1 alters the ribosomal profile of the mutant cells. Also, gene deletion strain for TAE1 has defects in both translation efficiency and fidelity. Miniaturized synthetic genetic array analysis further indicates that TAE1 genetically interacts with 16 ribosomal protein genes. Phenotypic suppression analysis using TAE1 overexpression also links TAE1 to protein synthesis. Conclusion We show that a previously uncharacterized ORF, YBR261C, affects the process of protein synthesis and reaffirm that large-scale genetic profile analysis can be a useful tool to study novel gene function(s). PMID:19055778

Chemical-genetic profile analysis in yeast suggests that a previously uncharacterized open reading frame, YBR261C, affects protein synthesis.

PubMed

Alamgir, Md; Eroukova, Veronika; Jessulat, Matthew; Xu, Jianhua; Golshani, Ashkan

2008-12-03

Functional genomics has received considerable attention in the post-genomic era, as it aims to identify function(s) for different genes. One way to study gene function is to investigate the alterations in the responses of deletion mutants to different stimuli. Here we investigate the genetic profile of yeast non-essential gene deletion array (yGDA, approximately 4700 strains) for increased sensitivity to paromomycin, which targets the process of protein synthesis. As expected, our analysis indicated that the majority of deletion strains (134) with increased sensitivity to paromomycin, are involved in protein biosynthesis. The remaining strains can be divided into smaller functional categories: metabolism (45), cellular component biogenesis and organization (28), DNA maintenance (21), transport (20), others (38) and unknown (39). These may represent minor cellular target sites (side-effects) for paromomycin. They may also represent novel links to protein synthesis. One of these strains carries a deletion for a previously uncharacterized ORF, YBR261C, that we term TAE1 for Translation Associated Element 1. Our focused follow-up experiments indicated that deletion of TAE1 alters the ribosomal profile of the mutant cells. Also, gene deletion strain for TAE1 has defects in both translation efficiency and fidelity. Miniaturized synthetic genetic array analysis further indicates that TAE1 genetically interacts with 16 ribosomal protein genes. Phenotypic suppression analysis using TAE1 overexpression also links TAE1 to protein synthesis. We show that a previously uncharacterized ORF, YBR261C, affects the process of protein synthesis and reaffirm that large-scale genetic profile analysis can be a useful tool to study novel gene function(s).

Nephron Toxicity Profiling via Untargeted Metabolome Analysis Employing a High Performance Liquid Chromatography-Mass Spectrometry-based Experimental and Computational Pipeline*

PubMed Central

Ranninger, Christina; Rurik, Marc; Limonciel, Alice; Ruzek, Silke; Reischl, Roland; Wilmes, Anja; Jennings, Paul; Hewitt, Philip; Dekant, Wolfgang; Kohlbacher, Oliver; Huber, Christian G.

2015-01-01

Untargeted metabolomics has the potential to improve the predictivity of in vitro toxicity models and therefore may aid the replacement of expensive and laborious animal models. Here we describe a long term repeat dose nephrotoxicity study conducted on the human renal proximal tubular epithelial cell line, RPTEC/TERT1, treated with 10 and 35 μmol·liter−1 of chloroacetaldehyde, a metabolite of the anti-cancer drug ifosfamide. Our study outlines the establishment of an automated and easy to use untargeted metabolomics workflow for HPLC-high resolution mass spectrometry data. Automated data analysis workflows based on open source software (OpenMS, KNIME) enabled a comprehensive and reproducible analysis of the complex and voluminous metabolomics data produced by the profiling approach. Time- and concentration-dependent responses were clearly evident in the metabolomic profiles. To obtain a more comprehensive picture of the mode of action, transcriptomics and proteomics data were also integrated. For toxicity profiling of chloroacetaldehyde, 428 and 317 metabolite features were detectable in positive and negative modes, respectively, after stringent removal of chemical noise and unstable signals. Changes upon treatment were explored using principal component analysis, and statistically significant differences were identified using linear models for microarray assays. The analysis revealed toxic effects only for the treatment with 35 μmol·liter−1 for 3 and 14 days. The most regulated metabolites were glutathione and metabolites related to the oxidative stress response of the cells. These findings are corroborated by proteomics and transcriptomics data, which show, among other things, an activation of the Nrf2 and ATF4 pathways. PMID:26055719

Phenotypic and genetic characterization of Vibrio cholerae O1 clinical isolates collected through national antimicrobial resistance surveillance network in Nepal.

PubMed

Shakya, Geeta; Kim, Dong Wook; Clemens, John D; Malla, Sarala; Upadhyaya, Bishnu Prasad; Dumre, Shyam Prakash; Shrestha, Sirjana Devi; Adhikari, Shailaja; Sharma, Supriya; Rijal, Nisha; Shrestha, Sanjaya K; Mason, Carl; Kansakar, Palpasa

2012-08-01

Cholera occurs in sporadic cases and outbreaks in Nepal each year. Vibrio cholerae O1 (n = 522) isolated during 2007-2010 from diarrheal patients at 10 different hospital laboratories in Nepal were characterized. Biochemical and serologic identifications showed that all the isolates belonged to serogroup O1, El Tor biotype. Except 72 isolates of Inaba serotype isolated in the year 2007, all the remaining isolates were of Ogawa serotype. All isolates were resistant to nalidixic acid and furazolidone. Resistance to tetracycline, ciprofloxacin, erythromycin and co-trimoxazole were 21, 4, 16 and 90 % respectively. Seventy-seven of these isolates were selected for further characterization for ctxB gene and MLVA typing. Two different variants of classical type cholera toxin were observed. Ogawa strains from 2007 and 2010-Western Nepal outbreak harbored CTX-3 type cholera toxin, whereas Inaba serotypes in 2007 and the remaining Ogawa serotypes in 2008-2010 harbored CTX 3b-type toxin. MLVA analysis showed circulation of four different groups of altered V. cholerae O1 El Tor strains. Two different profiles were seen among 2007 Inaba (9, 3, 6, x, x) and Ogawa (10, 7, 6, x, x) isolates. The MLVA profile of 2008 and 2009 Ogawa isolates were similar to those of Inaba strains of 2007. Isolates from 2010 also showed three different MLVA profiles; profile 9, 3, 6, x, x in 3 isolates, 11, 7, 6, x, x among 2010 Western Nepal outbreak strains and profile 8, 3, 6, x, x among isolates from Butwal and Kathmandu.

Gene expression profiling of whole blood: Comparison of target preparation methods for accurate and reproducible microarray analysis

PubMed Central

Vartanian, Kristina; Slottke, Rachel; Johnstone, Timothy; Casale, Amanda; Planck, Stephen R; Choi, Dongseok; Smith, Justine R; Rosenbaum, James T; Harrington, Christina A

2009-01-01

Background Peripheral blood is an accessible and informative source of transcriptomal information for many human disease and pharmacogenomic studies. While there can be significant advantages to analyzing RNA isolated from whole blood, particularly in clinical studies, the preparation of samples for microarray analysis is complicated by the need to minimize artifacts associated with highly abundant globin RNA transcripts. The impact of globin RNA transcripts on expression profiling data can potentially be reduced by using RNA preparation and labeling methods that remove or block globin RNA during the microarray assay. We compared four different methods for preparing microarray hybridization targets from human whole blood collected in PAXGene tubes. Three of the methods utilized the Affymetrix one-cycle cDNA synthesis/in vitro transcription protocol but varied treatment of input RNA as follows: i. no treatment; ii. treatment with GLOBINclear; or iii. treatment with globin PNA oligos. In the fourth method cDNA targets were prepared with the Ovation amplification and labeling system. Results We find that microarray targets generated with labeling methods that reduce globin mRNA levels or minimize the impact of globin transcripts during hybridization detect more transcripts in the microarray assay compared with the standard Affymetrix method. Comparison of microarray results with quantitative PCR analysis of a panel of genes from the NF-kappa B pathway shows good correlation of transcript measurements produced with all four target preparation methods, although method-specific differences in overall correlation were observed. The impact of freezing blood collected in PAXGene tubes on data reproducibility was also examined. Expression profiles show little or no difference when RNA is extracted from either fresh or frozen blood samples. Conclusion RNA preparation and labeling methods designed to reduce the impact of globin mRNA transcripts can significantly improve the sensitivity of the DNA microarray expression profiling assay for whole blood samples. While blockage of globin transcripts during first strand cDNA synthesis with globin PNAs resulted in the best overall performance in this study, we conclude that selection of a protocol for expression profiling studies in blood should depend on several factors, including implementation requirements of the method and study design. RNA isolated from either freshly collected or frozen blood samples stored in PAXGene tubes can be used without altering gene expression profiles. PMID:19123946

Fatty acid methyl ester analysis to identify sources of soil in surface water.

PubMed

Banowetz, Gary M; Whittaker, Gerald W; Dierksen, Karen P; Azevedo, Mark D; Kennedy, Ann C; Griffith, Stephen M; Steiner, Jeffrey J

2006-01-01

Efforts to improve land-use practices to prevent contamination of surface waters with soil are limited by an inability to identify the primary sources of soil present in these waters. We evaluated the utility of fatty acid methyl ester (FAME) profiles of dry reference soils for multivariate statistical classification of soils collected from surface waters adjacent to agricultural production fields and a wooded riparian zone. Trials that compared approaches to concentrate soil from surface water showed that aluminum sulfate precipitation provided comparable yields to that obtained by vacuum filtration and was more suitable for handling large numbers of samples. Fatty acid methyl ester profiles were developed from reference soils collected from contrasting land uses in different seasons to determine whether specific fatty acids would consistently serve as variables in multivariate statistical analyses to permit reliable classification of soils. We used a Bayesian method and an independent iterative process to select appropriate fatty acids and found that variable selection was strongly impacted by the season during which soil was collected. The apparent seasonal variation in the occurrence of marker fatty acids in FAME profiles from reference soils prevented preparation of a standardized set of variables. Nevertheless, accurate classification of soil in surface water was achieved utilizing fatty acid variables identified in seasonally matched reference soils. Correlation analysis of entire chromatograms and subsequent discriminant analyses utilizing a restricted number of fatty acid variables showed that FAME profiles of soils exposed to the aquatic environment still had utility for classification at least 1 wk after submersion.

Untargeted UPLC-MS Profiling Pipeline to Expand Tissue Metabolome Coverage: Application to Cardiovascular Disease

PubMed Central

2015-01-01

Metabolic profiling studies aim to achieve broad metabolome coverage in specific biological samples. However, wide metabolome coverage has proven difficult to achieve, mostly because of the diverse physicochemical properties of small molecules, obligating analysts to seek multiplatform and multimethod approaches. Challenges are even greater when it comes to applications to tissue samples, where tissue lysis and metabolite extraction can induce significant systematic variation in composition. We have developed a pipeline for obtaining the aqueous and organic compounds from diseased arterial tissue using two consecutive extractions, followed by a different untargeted UPLC-MS analysis method for each extract. Methods were rationally chosen and optimized to address the different physicochemical properties of each extract: hydrophilic interaction liquid chromatography (HILIC) for the aqueous extract and reversed-phase chromatography for the organic. This pipeline can be generic for tissue analysis as demonstrated by applications to different tissue types. The experimental setup and fast turnaround time of the two methods contributed toward obtaining highly reproducible features with exceptional chromatographic performance (CV % < 0.5%), making this pipeline suitable for metabolic profiling applications. We structurally assigned 226 metabolites from a range of chemical classes (e.g., carnitines, α-amino acids, purines, pyrimidines, phospholipids, sphingolipids, free fatty acids, and glycerolipids) which were mapped to their corresponding pathways, biological functions and known disease mechanisms. The combination of the two untargeted UPLC-MS methods showed high metabolite complementarity. We demonstrate the application of this pipeline to cardiovascular disease, where we show that the analyzed diseased groups (n = 120) of arterial tissue could be distinguished based on their metabolic profiles. PMID:25664760

Blood lipids profile and lung cancer risk in a meta-analysis of prospective cohort studies.

PubMed

Lin, Xiaojing; Lu, Lei; Liu, Lingli; Wei, Siyu; He, Yunyun; Chang, Jing; Lian, Xuemei

Emerging evidence has connected lipid metabolism disturbance with lung diseases, but the relationship between blood lipid profile and lung cancer risk is controversial and inconclusive. We conducted a meta-analysis of prospective cohort studies to evaluate the relationship between blood lipids profile and lung cancer incidence. Relevant studies were identified by searching PubMed, Cochrane Library, Web of Science, EBSCO, Ovid, CNKI, VIP, and WANGFANG MED through August 2016. Nine prospective cohort studies were included in the meta-analysis, and fixed or random effects model was used to calculate pooled relative risk (RRs). The RR was calculated using either highest vs lowest categories, or upper quantile vs lowest quantile. The thresholds were determined by the authors of each original publication, based on either predefined cut-offs or the distributions within their study population. Analysis of 18,111 lung cancer cases among 1,832,880 participants showed that serum total cholesterol levels were inverse associated with lung cancer risk (RR = 0.93, 95% confidence interval [CI]: 0.85-1.03). Further analysis considered the lag time and excluded the effects of preclinical cancer, with totally 1,239,948 participants and 14,052 lung cancer cases, found a significantly inverse association between total cholesterol and lung cancer risk (RR = 0.89, 95% CI: 0.83-0.94). Analysis of 3067 lung cancer cases among 59,242 participants found that the high-density lipoprotein cholesterol levels (RR = 0.76, 95% CI: 0.59-0.97) was negatively associated with lung cancer risk and 4673 lung cancer cases among 685,852 participants showed that the total triglyceride (RR = 1.68, 95% CI: 1.44-1.96) was positively associated with lung cancer risk. Cholesterol and fatty acid metabolism might present different and specific mechanism on lung cancer etiology and needs further elucidation. Copyright © 2017 National Lipid Association. Published by Elsevier Inc. All rights reserved.

Forensic DNA methylation profiling from minimal traces: How low can we go?

PubMed

Naue, Jana; Hoefsloot, Huub C J; Kloosterman, Ate D; Verschure, Pernette J

2018-03-01

Analysis of human DNA methylation (DNAm) can provide additional investigative leads in crime cases, e.g. the type of tissue or body fluid, the chronological age of an individual, and differentiation between identical twins. In contrast to the genetic profile, the DNAm level is not the same in every cell. At the single cell level, DNAm represents a binary event at a defined CpG site (methylated versus non-methylated). The DNAm level from a DNA extract however represents the average level of methylation of the CpG of interest of all molecules in the forensic sample. The variance of DNAm levels between replicates is often attributed to technological issues, i.e. degradation of DNA due to bisulfite treatment, preferential amplification of DNA, and amplification failure. On the other hand, we show that stochastic variations can lead to gross fluctuation in the analysis of methylation levels in samples with low DNA levels. This stochasticity in DNAm results is relevant since low DNA amounts (1pg - 1ng) is rather the norm than the exception when analyzing forensic DNA samples. This study describes a conceptual analysis of DNAm profiling and its dependence on the amount of input DNA. We took a close look at the variation of DNAm analysis due to DNA input and its consequences for different DNAm-based forensic applications. As can be expected, the 95%-confidence interval of measured DNAm becomes narrower with increasing amounts of DNA. We compared this aspect for two different DNAm-based forensic applications: body fluid identification and chronological age determination. Our study shows that DNA amount should be well considered when using DNAm for forensic applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural analysis of star-forming blue early-type galaxies. Merger-driven star formation in elliptical galaxies

NASA Astrophysics Data System (ADS)

George, Koshy

2017-02-01

Context. Star-forming blue early-type galaxies at low redshift can give insight to the stellar mass growth of L⋆ elliptical galaxies in the local Universe. Aims: We wish to understand the reason for star formation in these otherwise passively evolving red and dead stellar systems. The fuel for star formation can be acquired through recent accretion events such as mergers or flyby. The signatures of such events should be evident from a structural analysis of the galaxy image. Methods: We carried out structural analysis on SDSS r-band imaging data of 55 star-forming blue elliptical galaxies, derived the structural parameters, analysed the residuals from best-fit to surface brightness distribution, and constructed the galaxy scaling relations. Results: We found that star-forming blue early-type galaxies are bulge-dominated systems with axial ratio >0.5 and surface brightness profiles fitted by Sérsic profiles with index (n) mostly >2. Twenty-three galaxies are found to have n< 2; these could be hosting a disc component. The residual images of the 32 galaxy surface brightness profile fits show structural features indicative of recent interactions. The star-forming blue elliptical galaxies follow the Kormendy relation and show the characteristics of normal elliptical galaxies as far as structural analysis is concerned. There is a general trend for high-luminosity galaxies to display interaction signatures and high star formation rates. Conclusions: The star-forming population of blue early-type galaxies at low redshifts could be normal ellipticals that might have undergone a recent gas-rich minor merger event. The star formation in these galaxies will shut down once the recently acquired fuel is consumed, following which the galaxy will evolve to a normal early-type galaxy.

Non-invasive intraoperative optical coherence tomography of the resection cavity during surgery of intrinsic brain tumors

NASA Astrophysics Data System (ADS)

Giese, A.; Böhringer, H. J.; Leppert, J.; Kantelhardt, S. R.; Lankenau, E.; Koch, P.; Birngruber, R.; Hüttmann, G.

2006-02-01

Optical coherence tomography (OCT) is a non-invasive imaging technique with a micrometer resolution. It allows non-contact / non-invasive analysis of central nervous system tissues with a penetration depth of 1-3,5 mm reaching a spatial resolution of approximately 4-15 μm. We have adapted spectral-domain OCT (SD-OCT) and time-domain OCT (TD-OCT) for intraoperative detection of residual tumor during brain tumor surgery. Human brain tumor tissue and areas of the resection cavity were analyzed during the resection of gliomas using this new technology. The site of analysis was registered using a neuronavigation system and biopsies were taken and submitted to routine histology. We have used post image acquisition processing to compensate for movements of the brain and to realign A-scan images for calculation of a light attenuation factor. OCT imaging of normal cortex and white matter showed a typical light attenuation profile. Tumor tissue depending on the cellularity of the specimen showed a loss of the normal light attenuation profile resulting in altered light attenuation coefficients compared to normal brain. Based on this parameter and the microstructure of the tumor tissue, which was entirely absent in normal tissue, OCT analysis allowed the discrimination of normal brain tissue, invaded brain, solid tumor tissue, and necrosis. Following macroscopically complete resections OCT analysis of the resection cavity displayed the typical microstructure and light attenuation profile of tumor tissue in some specimens, which in routine histology contained microscopic residual tumor tissue. We have demonstrated that this technology may be applied to the intraoperative detection of residual tumor during resection of human gliomas.

Isolation and genetic analysis of pure cells from forensic biological mixtures: The precision of a digital approach.

PubMed

Fontana, F; Rapone, C; Bregola, G; Aversa, R; de Meo, A; Signorini, G; Sergio, M; Ferrarini, A; Lanzellotto, R; Medoro, G; Giorgini, G; Manaresi, N; Berti, A

2017-07-01

Latest genotyping technologies allow to achieve a reliable genetic profile for the offender identification even from extremely minute biological evidence. The ultimate challenge occurs when genetic profiles need to be retrieved from a mixture, which is composed of biological material from two or more individuals. In this case, DNA profiling will often result in a complex genetic profile, which is then subject matter for statistical analysis. In principle, when more individuals contribute to a mixture with different biological fluids, their single genetic profiles can be obtained by separating the distinct cell types (e.g. epithelial cells, blood cells, sperm), prior to genotyping. Different approaches have been investigated for this purpose, such as fluorescent-activated cell sorting (FACS) or laser capture microdissection (LCM), but currently none of these methods can guarantee the complete separation of different type of cells present in a mixture. In other fields of application, such as oncology, DEPArray™ technology, an image-based, microfluidic digital sorter, has been widely proven to enable the separation of pure cells, with single-cell precision. This study investigates the applicability of DEPArray™ technology to forensic samples analysis, focusing on the resolution of the forensic mixture problem. For the first time, we report here the development of an application-specific DEPArray™ workflow enabling the detection and recovery of pure homogeneous cell pools from simulated blood/saliva and semen/saliva mixtures, providing full genetic match with genetic profiles of corresponding donors. In addition, we assess the performance of standard forensic methods for DNA quantitation and genotyping on low-count, DEPArray™-isolated cells, showing that pure, almost complete profiles can be obtained from as few as ten haploid cells. Finally, we explore the applicability in real casework samples, demonstrating that the described approach provides complete separation of cells with outstanding precision. In all examined cases, DEPArray™ technology proves to be a groundbreaking technology for the resolution of forensic biological mixtures, through the precise isolation of pure cells for an incontrovertible attribution of the obtained genetic profiles. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Differential gene expression profiling of endometrium during the mid-luteal phase of the estrous cycle between a repeat breeder (RB) and non-RB cows.

PubMed

Hayashi, Ken-Go; Hosoe, Misa; Kizaki, Keiichiro; Fujii, Shiori; Kanahara, Hiroko; Takahashi, Toru; Sakumoto, Ryosuke

2017-03-23

Repeat breeding directly affects reproductive efficiency in cattle due to an increase in services per conception and calving interval. This study aimed to investigate whether changes in endometrial gene expression profile are involved in repeat breeding in cows. Differential gene expression profiles of the endometrium were investigated during the mid-luteal phase of the estrous cycle between repeat breeder (RB) and non-RB cows using microarray analysis. The caruncular (CAR) and intercaruncular (ICAR) endometrium of both ipsilateral and contralateral uterine horns to the corpus luteum were collected from RB (inseminated at least three times but not pregnant) and non-RB cows on Day 15 of the estrous cycle (4 cows/group). Global gene expression profiles of these endometrial samples were analyzed with a 15 K custom-made oligo-microarray for cattle. Immunohistochemistry was performed to investigate the cellular localization of proteins of three identified transcripts in the endometrium. Microarray analysis revealed that 405 and 397 genes were differentially expressed in the CAR and ICAR of the ipsilateral uterine horn of RB, respectively when compared with non-RB cows. In the contralateral uterine horn, 443 and 257 differentially expressed genes were identified in the CAR and ICAR of RB, respectively when compared with non-RB cows. Gene ontology analysis revealed that genes involved in development and morphogenesis were mainly up-regulated in the CAR of RB cows. In the ICAR of both the ipsilateral and contralateral uterine horns, genes related to the metabolic process were predominantly enriched in the RB cows when compared with non-RB cows. In the analysis of the whole uterus (combining the data above four endometrial compartments), RB cows showed up-regulation of 37 genes including PRSS2, GSTA3 and PIPOX and down-regulation of 39 genes including CHGA, KRT35 and THBS4 when compared with non-RB cows. Immunohistochemistry revealed that CHGA, GSTA3 and PRSS2 proteins were localized in luminal and glandular epithelial cells and stroma of the endometrium. The present study showed that endometrial gene expression profiles are different between RB and non-RB cows. The identified candidate endometrial genes and functions in each endometrial compartment may contribute to bovine reproductive performance.

An Improved Version of the NASA-Lockheed Multielement Airfoil Analysis Computer Program

NASA Technical Reports Server (NTRS)

Brune, G. W.; Manke, J. W.

1978-01-01

An improved version of the NASA-Lockheed computer program for the analysis of multielement airfoils is described. The predictions of the program are evaluated by comparison with recent experimental high lift data including lift, pitching moment, profile drag, and detailed distributions of surface pressures and boundary layer parameters. The results of the evaluation show that the contract objectives of improving program reliability and accuracy have been met.

Thermomechanical properties of polymeric materials and related stresses

NASA Technical Reports Server (NTRS)

Lee, Sheng Yen

1990-01-01

The thermomechanical properties of a number of widely used polymeric materials were determined by thermomechanical analysis and dynamic mechanical analysis. A combined profile of the coefficient of thermal expansion and the modulus change over a wide temperature range obtained by the analyses shows clearly the drastic effect of the glass transition on both the CTE and the modulus of a polymer, and the damaging potential due to such effect.

Viscoelasticity of Axisymmetric Composite Structures: Analysis and Experimental Validation

DTIC Science & Technology

2013-02-01

compressive stress at the interface between the composite and steel prior to the sheath’s cut-off. Accordingly, the viscoelastic analysis is used...The hoop-stress profile in figure 6 shows the steel region is in compression , resulting from the winding tension of composite overwrap. The stress...mechanical and thermal loads. Experimental validation of the model is conducted using a high- tensioned composite overwrapped on a steel cylinder. The creep

Cloning and expression profile of ionotropic receptors in the parasitoid wasp Microplitis mediator (Hymenoptera: Braconidae).

PubMed

Wang, Shan-Ning; Peng, Yong; Lu, Zi-Yun; Dhiloo, Khalid Hussain; Zheng, Yao; Shan, Shuang; Li, Rui-Jun; Zhang, Yong-Jun; Guo, Yu-Yuan

2016-07-01

Ionotropic receptors (IRs) mainly detect the acids and amines having great importance in many insect species, representing an ancient olfactory receptor family in insects. In the present work, we performed RNAseq of Microplitis mediator antennae and identified seventeen IRs. Full-length MmedIRs were cloned and sequenced. Phylogenetic analysis of the Hymenoptera IRs revealed that ten MmedIR genes encoded "antennal IRs" and seven encoded "divergent IRs". Among the IR25a orthologous groups, two genes, MmedIR25a.1 and MmedIR25a.2, were found in M. mediator. Gene structure analysis of MmedIR25a revealed a tandem duplication of IR25a in M. mediator. The tissue distribution and development specific expression of the MmedIR genes suggested that these genes showed a broad expression profile. Quantitative gene expression analysis showed that most of the genes are highly enriched in adult antennae, indicating the candidate chemosensory function of this family in parasitic wasps. Using immunocytochemistry, we confirmed that one co-receptor, MmedIR8a, was expressed in the olfactory sensory neurons. Our data will supply fundamental information for functional analysis of the IRs in parasitoid wasp chemoreception. Copyright © 2016 Elsevier Ltd. All rights reserved.

Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks.

PubMed

Pellacani, Davide; Bilenky, Misha; Kannan, Nagarajan; Heravi-Moussavi, Alireza; Knapp, David J H F; Gakkhar, Sitanshu; Moksa, Michelle; Carles, Annaick; Moore, Richard; Mungall, Andrew J; Marra, Marco A; Jones, Steven J M; Aparicio, Samuel; Hirst, Martin; Eaves, Connie J

2016-11-15

The normal adult human mammary gland is a continuous bilayered epithelial system. Bipotent and myoepithelial progenitors are prominent and unique components of the outer (basal) layer. The inner (luminal) layer includes both luminal-restricted progenitors and a phenotypically separable fraction that lacks progenitor activity. We now report an epigenomic comparison of these three subsets with one another, with their associated stromal cells, and with three immortalized, non-tumorigenic human mammary cell lines. Each genome-wide analysis contains profiles for six histone marks, methylated DNA, and RNA transcripts. Analysis of these datasets shows that each cell type has unique features, primarily within genomic regulatory regions, and that the cell lines group together. Analyses of the promoter and enhancer profiles place the luminal progenitors in between the basal cells and the non-progenitor luminal subset. Integrative analysis reveals networks of subset-specific transcription factors. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Differentiation of Brazilian Peppertree (Schinus terebinthifolius Raddi) and Peruvian Peppertree (Schinus molle L.) Fruits by UHPLC-UV-MS Analysis of Their Anthocyanin and Biflavonoid Profiles.

PubMed

Feuereisen, Michelle M; Zimmermann, Benno F; Schulze-Kaysers, Nadine; Schieber, Andreas

2017-07-05

The objectives of this work were to determine the phenolic profile of Schinus terebinthifolius and Schinus molle fruits and to develop a reliable method for the differentiation of these two similar spices both known as pink pepper. Anthocyanins, biflavonoids and gallotannins, some of which are reported for the first time in these species, were identified by UHPLC-UV/vis-MS/MS. Consideration of the relative and absolute amounts of phenolics as well as indicator compounds from 18 samples revealed that the relative amounts of anthocyanins and biflavonoids are the most trustworthy parameters. Principal component analysis and cluster analysis (CA) allowed a grouping of the samples according to their species, showing that the anthocyanins are most important for the identification of species. As a result, authentication of the two Schinus species can be accomplished by UHPLC analysis of the relative amounts of anthocyanins combined with CA.

Uniformity analysis for a direct-drive laser fusion reactor

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

Lund, L.D.; Skupsky, S.; Goldman, L.M.

1983-01-01

We show the results of an analysis of the uniformity for a direct-drive reactor using 20, 32, 60, or 96 beams. Several of these options achieve less than the 1% nonuniformity that is required. These options are considered for the cases where the solid angle fraction of the beam ports is 2% and 8%. The analysis is facilitated by separating the contributions due to the geometrical effects related to the number and orientation of the beams from those due to the spatial profile of the individual beams. Emphasis is placed on the wavelength of the nonuniformities, as the shorter wavelengthmore » nonuniformities are more easily smoothed by thermal conduction within the target. The analysis demonstrates that the longer wavelengths can be minimized by suitable choices of geometry and by maintaining beam balance, whereas the shorter wavelength nonuniformities can be reduced by optimizing parameters such as the focal position and the spatial intensity profile of each beam. The tolerances required for beam-to-beam energy balance will be discussed.« less

LC-QTOF-MS Analysis and Activity Profiles of Popular Antioxidant Dietary Supplements in Terms of Quality Control

PubMed Central

Baj, Tomasz; Sawicki, Rafal; Wanat, Aleksandra; Wojtanowski, Krzysztof Kamil; Ginalska, Grazyna; Zgorka, Grazyna; Szymanska, Jolanta

2017-01-01

The dietary supplements with claimed antioxidant activity constitute a substantial part of the dietary supplement market. In this study, we performed the LC-QTOF-MS analysis and investigated the activity profiles of popular antioxidant dietary supplements from different chemical groups in terms of quality control. The commonly used antioxidant tests and statistical analysis revealed that substantial part of the results was comparable if 1 g sample was considered, but while comparing single and daily doses, significant differences in antioxidant values were noticed in all assays. The best antioxidant activity was obtained in ORAC assay (from 142 to 13814 μM of Trolox equivalents per 1 g of sample), and the strongest correlation occurred between TPC and ORAC. The LC-QTOF-MS analysis revealed that catechins were present in samples having the best antioxidant activity and that dietary supplements showing the weakest activity contained very small amount of any chemical constituents. PMID:28642814

Self-similarity of temperature profiles in distant galaxy clusters: the quest for a universal law

NASA Astrophysics Data System (ADS)

Baldi, A.; Ettori, S.; Molendi, S.; Gastaldello, F.

2012-09-01

Context. We present the XMM-Newton temperature profiles of 12 bright (LX > 4 × 1044 erg s-1) clusters of galaxies at 0.4 < z < 0.9, having an average temperature in the range 5 ≲ kT ≲ 11 keV. Aims: The main goal of this paper is to study for the first time the temperature profiles of a sample of high-redshift clusters, to investigate their properties, and to define a universal law to describe the temperature radial profiles in galaxy clusters as a function of both cosmic time and their state of relaxation. Methods: We performed a spatially resolved spectral analysis, using Cash statistics, to measure the temperature in the intracluster medium at different radii. Results: We extracted temperature profiles for the clusters in our sample, finding that all profiles are declining toward larger radii. The normalized temperature profiles (normalized by the mean temperature T500) are found to be generally self-similar. The sample was subdivided into five cool-core (CC) and seven non cool-core (NCC) clusters by introducing a pseudo-entropy ratio σ = (TIN/TOUT) × (EMIN/EMOUT)-1/3 and defining the objects with σ < 0.6 as CC clusters and those with σ ≥ 0.6 as NCC clusters. The profiles of CC and NCC clusters differ mainly in the central regions, with the latter exhibiting a slightly flatter central profile. A significant dependence of the temperature profiles on the pseudo-entropy ratio σ is detected by fitting a function of r and σ, showing an indication that the outer part of the profiles becomes steeper for higher values of σ (i.e. transitioning toward the NCC clusters). No significant evidence of redshift evolution could be found within the redshift range sampled by our clusters (0.4 < z < 0.9). A comparison of our high-z sample with intermediate clusters at 0.1 < z < 0.3 showed how the CC and NCC cluster temperature profiles have experienced some sort of evolution. This can happen because higher z clusters are at a less advanced stage of their formation and did not have enough time to create a relaxed structure, which is characterized by a central temperature dip in CC clusters and by flatter profiles in NCC clusters. Conclusions: This is the first time that a systematic study of the temperature profiles of galaxy clusters at z > 0.4 has been attempted. We were able to define the closest possible relation to a universal law for the temperature profiles of galaxy clusters at 0.1 < z < 0.9, showing a dependence on both the relaxation state of the clusters and the redshift. Appendix A is only available in electronic form at http://www.aanda.org

Qualitative Profiling and Quantification of Neonicotinoid Metabolites in Human Urine by Liquid Chromatography Coupled with Mass Spectrometry

PubMed Central

Taira, Kumiko; Fujioka, Kazutoshi; Aoyama, Yoshiko

2013-01-01

Neonicotinoid pesticides have been widely applied for the production of fruits and vegetables, and occasionally detected in conventionally grown produce. Thus oral exposure to neonicotinoid pesticides may exist in the general population; however, neonicotinoid metabolites in human body fluids have not been investigated comprehensively. The purpose of this study is the qualitative profiling and quantitative analysis of neonicotinoid metabolites in the human spot urine by liquid chromatography coupled with mass spectrometry (LC/MS). Human urine samples were collected from three patients suspected of subacute exposure to neonicotinoid pesticides. A qualitative profiling of urinary metabolites was performed using liquid chromatography/time-of-flight mass spectrometry (LC/TOFMS) with a database of nominal molecular weights of 57 known metabolites of three neonicotinoid pesticides (acetamiprid, Imidacloprid, and clothianidin), as well as the parent compounds. Then a quantitative analysis of selected urinary metabolites was performed using liquid chromatography/tandem mass spectrometry (LC/MS/MS) with a standard pesticide and metabolite, which were detected by the qualitative profiling. The result of qualitative profiling showed that seven metabolites, i.e. an acetamiprid metabolite, N-desmethyl-acetamiprid; three Imidacloprid metabolites, 5-hydroxy-Imidacloprid, 4,5-dihydroxy-imidacloprid, 4,5-dehydro-Imidacloprid; a common metabolite of acetamiprid and Imidacloprid, N-(6-chloronicotinoyl)-glycine; and two clothianidin metabolites, N-desmethyl-clothianidin, N-(2-(methylsulfanyl)thiazole-5-carboxyl)-glycine, as well as acetamiprid, were detected in the urine of three cases. The result of the quantitative analysis showed N-desmethyl-acetamiprid was determined in the urine of one case, which had been collected on the first visit, at a concentration of 3.2 ng/mL. This is the first report on the qualitative and quantitative detection of N-desmethyl-acetamiprid in the human urine. The results suggest that the one case with detection of N-desmethyl-acetamiprid was exposed to acetamiprid through the consumption of contaminated foods. Urinary N-desmethyl-acetamiprid, as well as 5-hydroxy-Imidacloprid and N-desmethyl-clothianidin, may be a good biomarker for neonicotinoid exposure in humans and warrants further investigation. PMID:24265808

Differentiation of South American crack and domestic (US) crack cocaine via headspace-gas chromatography/mass spectrometry.

PubMed

Colley, Valerie L; Casale, John F

2015-03-01

South American 'crack' cocaine, produced directly from coca leaf, can be distinguished from US domestically produced crack on the basis of occluded solvent profiles. In addition, analysis of domestically produced crack indicates the solvents that were used for cocaine hydrochloride (HCl) processing in South America. Samples of cocaine base (N=3) from South America and cocaine from the USA (N=157 base, N=88 HCl) were analyzed by headspace-gas chromatography-mass spectrometry (HS-GC-MS) to determine their solvent profiles. Each cocaine HCl sample was then converted to crack cocaine using the traditional crack production method and re-examined by HS-GC-MS. The resulting occluded solvent profiles were then compared to their original HCl solvent profiles. Analysis of the corresponding crack samples confirmed the same primary processing solvents found in the original HCl samples, but at reduced levels. Domestically seized crack samples also contained reduced levels of base-to-HCl conversion solvents. In contrast, analysis of South American crack samples confirmed the presence of low to high boiling hydrocarbons and no base-to-HCl conversion solvents. The presented study showed analysis of crack cocaine samples provides data on which processing solvents were originally utilized in the production of cocaine HCl in South America, prior to conversion to crack cocaine. Determination of processing solvents provides valuable information to the counter-drug intelligence community and assists the law enforcement community in determining cocaine distribution and trafficking routes throughout the world. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Protein profiles associated with survival in lung adenocarcinoma

PubMed Central

Chen, Guoan; Gharib, Tarek G; Wang, Hong; Huang, Chiang-Ching; Kuick, Rork; Thomas, Dafydd G.; Shedden, Kerby A.; Misek, David E.; Taylor, Jeremy M. G.; Giordano, Thomas J.; Kardia, Sharon L. R.; Iannettoni, Mark D.; Yee, John; Hogg, Philip J.; Orringer, Mark B.; Hanash, Samir M.; Beer, David G.

2003-01-01

Morphologic assessment of lung tumors is informative but insufficient to adequately predict patient outcome. We previously identified transcriptional profiles that predict patient survival, and here we identify proteins associated with patient survival in lung adenocarcinoma. A total of 682 individual protein spots were quantified in 90 lung adenocarcinomas by using quantitative two-dimensional polyacrylamide gel electrophoresis analysis. A leave-one-out cross-validation procedure using the top 20 survival-associated proteins identified by Cox modeling indicated that protein profiles as a whole can predict survival in stage I tumor patients (P = 0.01). Thirty-three of 46 survival-associated proteins were identified by using mass spectrometry. Expression of 12 candidate proteins was confirmed as tumor-derived with immunohistochemical analysis and tissue microarrays. Oligonucleotide microarray results from both the same tumors and from an independent study showed mRNAs associated with survival for 11 of 27 encoded genes. Combined analysis of protein and mRNA data revealed 11 components of the glycolysis pathway as associated with poor survival. Among these candidates, phosphoglycerate kinase 1 was associated with survival in the protein study, in both mRNA studies and in an independent validation set of 117 adenocarcinomas and squamous lung tumors using tissue microarrays. Elevated levels of phosphoglycerate kinase 1 in the serum were also significantly correlated with poor outcome in a validation set of 107 patients with lung adenocarcinomas using ELISA analysis. These studies identify new prognostic biomarkers and indicate that protein expression profiles can predict the outcome of patients with early-stage lung cancer. PMID:14573703

Investigation of Chemical and Physical Changes to Bioapatite During Fossilization Using Trace Element Geochemistry, Infrared Spectroscopy and Stable Isotopes

NASA Astrophysics Data System (ADS)

Suarez, C. A.; Kohn, M. J.

2013-12-01

Bioapatite in the form of vertebrate bone can be used for a wide variety of paleo-proxies, from determination of ancient diet to the isotopic composition of meteoric water. Bioapatite alteration during diagenesis is a constant barrier to the use of fossil bone as a paleo-proxy. To elucidate the physical and chemical alteration of bone apatite during fossilization, we analyzed an assortment of fossil bones of different ages for trace elements, using LA-ICP-MS, stable isotopes, and reflected IR spectroscopy. One set of fossil bones from the Pleistocene of Idaho show a diffusion recrystallization profile, however, rare earth element (REE) profiles indicate diffusion adsorption. This suggests that REE diffusion is controlled by changing (namely decreasing) boundary conditions (i.e. decreasing concentration of REE in surrounding pore fluids). Reflected IR analysis along this concentration profile reveal that areas high in U have lost type A carbonate from the crystal structure in addition to water and organics. Stable isotopic analysis of carbon and oxygen will determine what, if any, change in the isotopic composition of the carbonate component of apatite has occurred do to the diffusion and recrystallization process. Analysis of much older bone from the Cretaceous of China reveal shallow REE and U concentration profiles and very uniform reflected IR spectra with a significant loss of type A carbonate throughout the entire bone cortex. Analysis of stable isotopes through the bone cortex will be compared to the stable isotopes collected from the Pleistocene of Idaho.

Sensory Characterization of Odors in Used Disposable Absorbent Incontinence Products

PubMed Central

Widén, Heléne; Forsgren-Brusk, Ulla; Hall, Gunnar

2017-01-01

PURPOSE: The objectives of this study were to characterize the odors of used incontinence products by descriptive analysis and to define attributes to be used in the analysis. A further objective was to investigate to what extent the odor profiles of used incontinence products differed from each other and, if possible, to group these profiles into classes. SUBJECTS AND SETTING: Used incontinence products were collected from 14 residents with urinary incontinence living in geriatric nursing homes in the Gothenburg area, Sweden. METHODS: Pieces were cut from the wet area of used incontinence products. They were placed in glass bottles and kept frozen until odor analysis was completed. A trained panel consisting of 8 judges experienced in this area of investigation defined terminology for odor attributes. The intensities of these attributes in the used products were determined by descriptive odor analysis. Data were analyzed both by analysis of variance (ANOVA) followed by the Tukey post hoc test and by principal component analysis and cluster analysis. RESULTS: An odor wheel, with 10 descriptive attributes, was developed. The total odor intensity, and the intensities of the attributes, varied considerably between different, used incontinence products. The typical odors varied from “sweetish” to “urinal,” “ammonia,” and “smoked.” Cluster analysis showed that the used products, based on the quantitative odor data, could be divided into 5 odor classes with different profiles. CONCLUSIONS: The used products varied considerably in odor character and intensity. Findings suggest that odors in used absorptive products are caused by different types of compounds that may vary in concentration. PMID:28328646

River profile response to normal fault growth and linkage: an example from the Hellenic forearc of south-central Crete, Greece

NASA Astrophysics Data System (ADS)

Gallen, Sean F.; Wegmann, Karl W.

2017-02-01

Topography is a reflection of the tectonic and geodynamic processes that act to uplift the Earth's surface and the erosional processes that work to return it to base level. Numerous studies have shown that topography is a sensitive recorder of tectonic signals. A quasi-physical understanding of the relationship between river incision and rock uplift has made the analysis of fluvial topography a popular technique for deciphering relative, and some argue absolute, histories of rock uplift. Here we present results from a study of the fluvial topography from south-central Crete, demonstrating that river longitudinal profiles indeed record the relative history of uplift, but several other processes make it difficult to recover quantitative uplift histories. Prior research demonstrates that the south-central coastline of Crete is bound by a large ( ˜ 100 km long) E-W striking composite normal fault system. Marine terraces reveal that it is uplifting between 0.1 and 1.0 mm yr-1. These studies suggest that two normal fault systems, the offshore Ptolemy and onshore South-Central Crete faults, linked together in the recent geologic past (ca. 0.4-1 My BP). Fault mechanics predict that when adjacent faults link into a single fault the uplift rate in footwalls of the linkage zone will increase rapidly. We use this natural experiment to assess the response of river profiles to a temporal jump in uplift rate and to assess the applicability of the stream power incision model to this setting. Using river profile analysis we show that rivers in south-central Crete record the relative uplift history of fault growth and linkage as theory predicts that they should. Calibration of the commonly used stream power incision model shows that the slope exponent, n, is ˜ 0.5, contrary to most studies that find n ≥ 1. Analysis of fluvial knickpoints shows that migration distances are not proportional to upstream contributing drainage area, as predicted by the stream power incision model. Maps of the transformed stream distance variable, χ, indicate that drainage basin instability, drainage divide migration, and river capture events complicate river profile analysis in south-central Crete. Waterfalls are observed in southern Crete and appear to operate under less efficient and different incision mechanics than assumed by the stream power incision model. Drainage area exchange and waterfall formation are argued to obscure linkages between empirically derived metrics and quasi-physical descriptions of river incision, making it difficult to quantitatively interpret rock uplift histories from river profiles in this setting. Karst hydrology, break down of assumed drainage area discharge scaling, and chemical weathering might also contribute to the failure of the stream power incision model to adequately predict the behavior of the fluvial system in south-central Crete.

Partial Characterization of Venom from the Colombian Spider Phoneutria Boliviensis (Aranae:Ctenidae)

PubMed Central

Estrada-Gomez, Sebastian; Vargas Muñoz, Leidy Johana; Lanchero, Paula; Segura Latorre, Cesar

2015-01-01

We report on the first studies on the characterization of venom from Phoneutria boliviensis (Aranae:Ctenidae) (F. O. Pickard-Cambridge, 1897), done with Colombian species. After the electrostimulation extraction process, the venom showed physicochemical properties corresponding to a colorless and water-soluble liquid with a density of 0.86 mg/mL and 87% aqueous content. P. boliviensis venom and RP-HPLC fractions showed hemolytic activity and hydrolyzed the synthetic substrate 4-nitro-3-octanoyloxy-benzoic acid, indicating the presence of phospholipases A2 enzymes. The electrophoretic profile showed an important protein content with molecular masses below 14 kDa, and differences between male and female protein content were also revealed. The RP-HPLC venom profile exposes differences between males and female content consistent with the electrophoretic profile. Five fractions collected from the RP-HPLC displayed significant larvicidal activity. Mass analysis indicates the presence of peptides ranging from 1047.71 to 3278.07 Da. Two peptides, Ctenitoxin-Pb48 and Ctenitoxin-Pb53, were partially identified using HPLC-nESI-MS/MS, which showed a high homology with other Ctenitoxins (family Tx3) from Phoneutria nigriventer, Phoneutria keyserlingi and Phoneutria reidyi affecting voltage-gated calcium receptors (Cav 1, 2.1, 2.2 and 2.3) and NMDA-glutamate receptors. PMID:26264023

“His” and “Her” Marriage? The Role of Positive and Negative Marital Characteristics in Global Marital Satisfaction Among Older Adults

PubMed Central

Jopp, Daniela S.; Carr, Deborah; Sosinsky, Laura; Kim, Se-Kang

2014-01-01

Objectives. We explore gender differences in older adults’ appraisals of positive and negative aspects of their marriages, examine how these appraisals relate to global marital satisfaction, and identify distinctive marital profiles associated with global satisfaction in men and women. Method. Data are from the Changing Lives of Older Couples Study (n = 1,110). We used a variant of principal components analysis to generate marital quality profiles, based on one’s endorsement of positive and negative marital characteristics. OLS regression was used to detect associations between marital profiles and global marital satisfaction. Results. Men offered more positive marital assessments than women, particularly on items reflecting positive treatment by one’s wife. Three marital quality profiles emerged: Positive, Positive–Negative, and Negative. Although marital satisfaction was best explained by positive appraisals in both genders, they were less important for men than for women. The negative profile showed a tendency for a stronger prediction in men. Discussion. Prior studies show small differences in men’s and women’s global marital satisfaction. Our work provides evidence that the presence and magnitude of such gender differences may vary based on the specific marital component considered. We discuss ways that gender shapes marital interactions, expectations, and perceptions, and the implications of our results for the well-being of married older adults. PMID:24742399

An insight into nutritional profile of selected Pleurotus species.

PubMed

Irshad, A; Sharif, S; Riaz, M; Anjum, F

2018-01-01

The global demand for good quality food indicates that consumers are more concerned about a particular diet associated with good health and lower risk for certain ailments. Mushrooms are widely used as healthy nutritious food. In the present study, the nutritional composition of four different Pleurotus sp. was determined. Prior to extraction, all the selected mushrooms were subjected for proximate composition analysis. The protein, fat, ash, total carbohydrate, fiber and energy contents were in the range of (16.07- 25.15%), (0.64-2.02%), (2.1-9.14%), (65.66-82.47%), (6.21-54.12%) and (342.20-394.30Kcal/100g), respectively. The spectrophotometric analysis showed that the concentration of protein was in the range of 45.78-33.47 mg/g in all Pleurotus sp. High performance liquid chromatographic analysis of sugars showed six different mono and disaccharides in all the selected mushrooms. The fatty acid profile by gas chromatography-mass spectrometry revealed that the main fatty acids in selected mushrooms were present in the order linoliec acid> oleic acid> palmitic acid. The results suggested that all the Pleurotus sp. could be considered as a rich source of nutrients.

The Case for Optically Thick High-Velocity Broad-Line Region Gas in Active Galactic Nuclei

NASA Astrophysics Data System (ADS)

Snedden, Stephanie A.; Gaskell, C. Martin

2007-11-01

A combined analysis of the profiles of the main broad quasar emission lines in both Hubble Space Telescope and optical spectra shows that while the profiles of the strong UV lines are quite similar, there is frequently a strong increase in the Lyα/Hα ratio in the high-velocity gas. We show that the suggestion that the high-velocity gas is optically thin presents many problems. We show that the relative strengths of the high-velocity wings arise naturally in an optically thick BLR component. An optically thick model successfully explains the equivalent widths of the lines, the Lyα/Hα ratios and flatter Balmer decrements in the line wings, the strengths of C III] and the λ1400 blend, and the strong variability in flux of high-velocity, high-ionization lines (especially He II and He I).

Global simulation of edge pedestal micro-instabilities

NASA Astrophysics Data System (ADS)

Wan, Weigang; Parker, Scott; Chen, Yang

2011-10-01

We study micro turbulence of the tokamak edge pedestal with global gyrokinetic particle simulations. The simulation code GEM is an electromagnetic δf code. Two sets of DIII-D experimental profiles, shot #131997 and shot #136051 are used. The dominant instabilities appear to be two kinds of modes both propagating in the electron diamagnetic direction, with comparable linear growth rates. The low n mode is at the Alfven frequency range and driven by density and ion temperature gradients. The high n mode is driven by electron temperature gradient and has a low real frequency. A β scan shows that the low n mode is electromagnetic. Frequency analysis shows that the high n mode is sometimes mixed with an ion instability. Experimental radial electric field is applied and its effects studied. We will also show some preliminary nonlinear results. We thank R. Groebner, P. Snyder and Y. Zheng for providing experimental profiles and helpful discussions.

Fano resonance in anodic aluminum oxide based photonic crystals.

PubMed

Shang, Guo Liang; Fei, Guang Tao; Zhang, Yao; Yan, Peng; Xu, Shao Hui; Ouyang, Hao Miao; Zhang, Li De

2014-01-08

Anodic aluminum oxide based photonic crystals with periodic porous structure have been prepared using voltage compensation method. The as-prepared sample showed an ultra-narrow photonic bandgap. Asymmetric line-shape profiles of the photonic bandgaps have been observed, which is attributed to Fano resonance between the photonic bandgap state of photonic crystal and continuum scattering state of porous structure. And the exhibited Fano resonance shows more clearly when the sample is saturated ethanol gas than air-filled. Further theoretical analysis by transfer matrix method verified these results. These findings provide a better understanding on the nature of photonic bandgaps of photonic crystals made up of porous materials, in which the porous structures not only exist as layers of effective-refractive-index material providing Bragg scattering, but also provide a continuum light scattering state to interact with Bragg scattering state to show an asymmetric line-shape profile.

Technical player profiles related to the physical fitness of young female volleyball players predict team performance.

PubMed

Dávila-Romero, C; Hernández-Mocholí, M A; García-Hermoso, A

2015-03-01

This study is divided into three sequential stages: identification of fitness and game performance profiles (individual player performance), an assessment of the relationship between these profiles, and an assessment of the relationship between individual player profiles and team performance during play (in championship performance). The overall study sample comprised 525 (19 teams) female volleyball players aged 12-16 years and a subsample (N.=43) used to examine study aims one and two was selected from overall sample. Anthropometric, fitness and individual player performance (actual game) data were collected in the subsample. These data were analyzed through clustering methods, ANOVA and independence chi-square test. Then, we investigated whether the proportion of players with the highest individual player performance profile might predict a team's results in the championship. Cluster analysis identified three volleyball fitness profiles (high, medium, and low) and two individual player performance profiles (high and low). The results showed a relationship between both types of profile (fitness and individual player performance). Then, linear regression revealed a moderate relationship between the number of players with a high volleyball fitness profile and a team's results in the championship (R2=0.23). The current study findings may enable coaches and trainers to manage training programs more efficiently in order to obtain tailor-made training, identify volleyball-specific physical fitness training requirements and reach better results during competitions.

Efficient three-dimensional resist profile-driven source mask optimization optical proximity correction based on Abbe-principal component analysis and Sylvester equation

NASA Astrophysics Data System (ADS)

Lin, Pei-Chun; Yu, Chun-Chang; Chen, Charlie Chung-Ping

2015-01-01

As one of the critical stages of a very large scale integration fabrication process, postexposure bake (PEB) plays a crucial role in determining the final three-dimensional (3-D) profiles and lessening the standing wave effects. However, the full 3-D chemically amplified resist simulation is not widely adopted during the postlayout optimization due to the long run-time and huge memory usage. An efficient simulation method is proposed to simulate the PEB while considering standing wave effects and resolution enhancement techniques, such as source mask optimization and subresolution assist features based on the Sylvester equation and Abbe-principal component analysis method. Simulation results show that our algorithm is 20× faster than the conventional Gaussian convolution method.

Elastic-Plastic Thermal Stress Analysis of a High-Pressure Cryogenic Storage Tank

NASA Technical Reports Server (NTRS)

Barker, J. Mark; Field, Robert E. (Technical Monitor)

2003-01-01

The thermal stresses on a cryogenic storage tank contribute strongly to the state of stress of the tank material and its ability to withstand operational stresses. These thermal stresses also affect the growth of any surface damage that might occur in the tank walls. These stresses are particularly of concern during the initial cooldown period for a new tank placed into service, and during any subsequent thermal cycles. A previous preliminary elastic analysis showed that the thermal stress on the inner wall would reach approximately 1,000MPa (145,000 psi). This stress far exceeds the ASTM specified room temperature values for both yield (170MPa) and ultimate (485 MPa) strength for 304L stainless steel. The present analysis determines the thermal stresses using an elastic-plastic model. The commercial software application ANSYS was used to determine the transient spatial temperature profile and the associated spatial thermal stress profiles in a segment of a thick-walled vessel during a typical cooldown process. A strictly elastic analysis using standard material properties for 304L stainless steel showed that the maximum thermal stress on the inner and outer walls was approximately 960 MPa (tensile) and - 270 MPa (compressive) respectively. These values occurred early in the cooldown process, but at different times, An elastic-plastic analysis showed significantly reducing stress, as expected due to the plastic deformation of the material. The maximum stress for the inner wall was approximately 225 MPa (tensile), while the maximum stress for the outer wall was approximately - 130 MPa (compressive).

Coping profiles, perceived stress and health-related behaviors: a cluster analysis approach.

PubMed

Doron, Julie; Trouillet, Raphael; Maneveau, Anaïs; Ninot, Grégory; Neveu, Dorine

2015-03-01

Using cluster analytical procedure, this study aimed (i) to determine whether people could be differentiated on the basis of coping profiles (or unique combinations of coping strategies); and (ii) to examine the relationships between these profiles and perceived stress and health-related behaviors. A sample of 578 French students (345 females, 233 males; M(age)= 21.78, SD(age)= 2.21) completed the Perceived Stress Scale-14 ( Bruchon-Schweitzer, 2002), the Brief COPE ( Muller and Spitz, 2003) and a series of items measuring health-related behaviors. A two-phased cluster analytic procedure (i.e. hierarchical and non-hierarchical-k-means) was employed to derive clusters of coping strategy profiles. The results yielded four distinctive coping profiles: High Copers, Adaptive Copers, Avoidant Copers and Low Copers. The results showed that clusters differed significantly in perceived stress and health-related behaviors. High Copers and Avoidant Copers displayed higher levels of perceived stress and engaged more in unhealthy behavior, compared with Adaptive Copers and Low Copers who reported lower levels of stress and engaged more in healthy behaviors. These findings suggested that individuals' relative reliance on some strategies and de-emphasis on others may be a more advantageous way of understanding the manner in which individuals cope with stress. Therefore, cluster analysis approach may provide an advantage over more traditional statistical techniques by identifying distinct coping profiles that might best benefit from interventions. Future research should consider coping profiles to provide a deeper understanding of the relationships between coping strategies and health outcomes and to identify risk groups. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Comparative Geostatistical Analysis of Flowmeter and Direct-Push Hydraulic Conductivity Profiles at the MADE Site

NASA Astrophysics Data System (ADS)

Bohling, G.; Liu, G.; Knobbe, S. J.; Reboulet, E. C.; Hyndman, D. W.; Dietrich, P.; Butler, J. J.

2010-12-01

Spatial variations in hydraulic conductivity (K) are a critical control on subsurface solute transport. Characterization of such variations at the resolution (cm to dm) required for transport investigations, however, has proven to be a formidable challenge. A new generation of direct-push (DP) tools has now been developed for the characterization of vertical K variations at this resolution. These tools, which can be run in high- (0.015-m) and low- (0.4 m) resolution modes, were recently applied to the extensively studied and highly heterogeneous MADE site. Results from a geostatistical analysis of 64 DP K profiles compare favorably with the flowmeter K data that have served as the primary basis for previous MADE studies. The global statistics of the low-resolution DP and flowmeter K data are in excellent agreement. The correlation structures for the high-resolution DP data show excellent agreement with those computed from the flowmeter data. However, the geometric mean DP K value for high-resolution profiling is roughly one order of magnitude lower than the geometric mean flowmeter K value, possibly as a result of the biases inherent in each approach compounded with differences in the areal distribution of flowmeter and DP profile locations. A DP profile through the MADE aquifer to a depth of 12 m can be completed as rapidly as 1.5-2 hours, a small fraction of the time required to obtain a single flowmeter profile when well drilling, installation, and development are considered. The results of this study demonstrate that DP profiling is a practically feasible approach for characterization of spatial variations in K at the resolution required for transport investigations in highly heterogeneous systems.

Dislocation, crystallite size distribution and lattice strain of magnesium oxide nanoparticles

NASA Astrophysics Data System (ADS)

Sutapa, I. W.; Wahid Wahab, Abdul; Taba, P.; Nafie, N. L.

2018-03-01

The oxide of magnesium nanoparticles synthesized using sol-gel method and analysis of the structural properties was conducted. The functional groups of nanoparticles has been analysed by Fourier Transform Infrared Spectroscopy (FT-IR). Dislocations, average size of crystal, strain, stress, the energy density of crystal, crystallite size distribution and morphologies of the crystals were determined based on X-ray diffraction profile analysis. The morphological of the crystal was analysed based on the image resulted from SEM analysis. The crystallite size distribution was calculated with the contention that the particle size has a normal logarithmic form. The most orientations of crystal were determined based on the textural crystal from diffraction data of X-ray diffraction profile analysis. FT-IR results showed the stretching vibration mode of the Mg-O-Mg in the range of 400.11-525 cm-1 as a broad band. The average size crystal of nanoparticles resulted is 9.21 mm with dislocation value of crystal is 0.012 nm-2. The strains, stress, the energy density of crystal are 1.5 x 10-4 37.31 MPa; 0.72 MPa respectively. The highest texture coefficient value of the crystal is 0.98. This result is supported by morphological analysis using SEM which shows most of the regular cubic-shaped crystals. The synthesis method is suitable for simple and cost-effective synthesis model of MgO nanoparticles.

Modeling the reflection of Photosynthetically active radiation in a monodominant floodable forest in the Pantanal of Mato Grosso State using multivariate statistics and neural networks.

PubMed

Curado, Leone F A; Musis, Carlo R DE; Cunha, Cristiano R DA; Rodrigues, Thiago R; Pereira, Vinicius M R; Nogueira, José S; Sanches, Luciana

2016-09-01

The study of radiation entrance and exit dynamics and energy consumption in a system is important for understanding the environmental processes that rule the biosphere-atmosphere interactions of all ecosystems. This study provides an analysis of the interaction of energy in the form of photosynthetically active radiation (PAR) in the Pantanal, a Brazilian wetland forest, by studying the variation of PAR reflectance and its interaction with local rainfall. The study site is located in Private Reserve of Natural Heritage, Mato Grosso State, Brazil, where the vegetation is a monodominant forest of Vochysia divergens Phol. The results showed a high correlation between the reflection of visible radiation and rainfall; however, the behavior was not the same at the three heights studied. An analysis of the hourly variation of the reflected waves also showed the seasonality of these phenomena in relation to the dry and rainy seasons. A predictive model for PAR was developed with a neural network that has a hidden layer, and it showed a determination coefficient of 0.938. This model showed that the Julian day and time of measurements had an inverse association with the wind profile and a direct association with the relative humidity profile.

Turbulent heat fluxes by profile and inertial dissipation methods: analysis of the atmospheric surface layer from shipboard measurements during the SOFIA/ASTEX and SEMAPHORE experiments

NASA Astrophysics Data System (ADS)

Dupuis, Hélène; Weill, Alain; Katsaros, Kristina; Taylor, Peter K.

1995-10-01

Heat flux estimates obtained using the inertial dissipation method, and the profile method applied to radiosonde soundings, are assessed with emphasis on the parameterization of the roughness lengths for temperature and specific humidity. Results from the inertial dissipation method show a decrease of the temperature and humidity roughness lengths for increasing neutral wind speed, in agreement with previous studies. The sensible heat flux estimates were obtained using the temperature estimated from the speed of sound determined by a sonic anemometer. This method seems very attractive for estimating heat fluxes over the ocean. However allowance must be made in the inertial dissipation method for non-neutral stratification. The SOFIA/ASTEX and SEMAPHORE results show that, in unstable stratification, a term due to the transport terms in the turbulent kinetic energy budget, has to be included in order to determine the friction velocity with better accuracy. Using the profile method with radiosonde data, the roughness length values showed large scatter. A reliable estimate of the temperature roughness length could not be obtained. The humidity roughness length values were compatible with those found using the inertial dissipation method.

Heterogeneity of Systemic Oxidative Stress Profiles in COPD: A Potential Role of Gender.

PubMed

Maury, Jonathan; Gouzi, Farés; De Rigal, Philippe; Heraud, Nelly; Pincemail, Joël; Molinari, Nicolas; Pomiès, Pascal; Laoudj-Chenivesse, Dalila; Mercier, Jacques; Préfaut, Christian; Hayot, Maurice

2015-01-01

Oxidative stress (OS) plays a key role in the muscle impairment and exercise capacity of COPD patients. However, the literature reveals that systemic OS markers show great heterogeneity, which may hinder the prescription of effective antioxidant supplementation. This study therefore aimed to identify OS markers imbalance of COPD patients, relative to validated normal reference values, and to investigate the possibility of systemic OS profiles. We measured systemic enzymatic/nonenzymatic antioxidant and lipid peroxidation (LP) levels in 54 stable COPD patients referred for a rehabilitation program. The main systemic antioxidant deficits in these patients concerned vitamins and trace elements. Fully 89% of the COPD patients showed a systemic antioxidant imbalance which may have caused the elevated systemic LP levels in 69% of them. Interestingly, two patient profiles (clusters 3 and 4) had a more elevated increase in LP combined with increased copper and/or decreased vitamin C, GSH, and GPx. Further analysis revealed that the systemic LP level was higher in COPD women and associated with exercise capacity. Our present data therefore support future supplementations with antioxidant vitamins and trace elements to improve exercise capacity, but COPD patients will probably show different positive responses.

Brief and precarious lives: infant mortality in contrasting sites from medieval and post-medieval England (AD 850-1859).

PubMed

Lewis, Mary E; Gowland, Rebecca

2007-09-01

This study compares the infant mortality profiles of 128 infants from two urban and two rural cemetery sites in medieval England. The aim of this paper is to assess the impact of urbanization and industrialization in terms of endogenous or exogenous causes of death. In order to undertake this analysis, two different methods of estimating gestational age from long bone lengths were used: a traditional regression method and a Bayesian method. The regression method tended to produce more marked peaks at 38 weeks, while the Bayesian method produced a broader range of ages and were more comparable with the expected "natural" mortality profiles.At all the sites, neonatal mortality (28-40 weeks) outweighed post-neonatal mortality (41-48 weeks) with rural Raunds Furnells in Northamptonshire, showing the highest number of neonatal deaths and post-medieval Spitalfields, London, showing a greater proportion of deaths due to exogenous or environmental factors. Of the four sites under study, Wharram Percy in Yorkshire showed the most convincing "natural" infant mortality profile, suggesting the inclusion of all births at the site (i.e., stillbirths and unbaptised infants). (c) 2007 Wiley-Liss, Inc.

Workplace Learning in Malaysia: The Learner's Perspective

ERIC Educational Resources Information Center

Muhamad, Mazanah; Idris, Khairuddin

2005-01-01

This paper offers a scenario of workplace learning as practiced in Malaysia. Based on survey research, the article describes learner profiles, learning provision and pattern. The analysis shows that Malaysians participate in formal workplace learning as part of their employment activities. Workplace learning in Malaysia is contextual, promoted by…

Sensory Correlations in Autism

ERIC Educational Resources Information Center

Kern, Janet K.; Trivedi, Madhukar H.; Grannemann, Bruce D.; Garver, Carolyn R.; Johnson, Danny G.; Andrews, Alonzo A.; Savla, Jayshree S.; Mehta, Jyutika A.; Schroeder, Jennifer L.

2007-01-01

This study examined the relationship between auditory, visual, touch, and oral sensory dysfunction in autism and their relationship to multisensory dysfunction and severity of autism. The Sensory Profile was completed on 104 persons with a diagnosis of autism, 3 to 56 years of age. Analysis showed a significant correlation between the different…

Oxygen microprofile in the prepared sediments and its implication for the sediment oxygen consuming process in a heavily polluted river of China.

PubMed

Wang, Chao; Zhai, Wanying; Shan, Baoqing

2016-05-01

Dissolved oxygen (DO) microprofiles of prepared sediments from 24 sampling sites in the Fuyang River were measured using a gold amalgam microelectrode in this study. The measured microprofiles can be divided into four types. In type I profiles, DO kept constant in the overlying water and decreased smoothly in the pore water; in type II profile, DO showed fluctuation in the pore water; in type III profiles, DO showed peak in the SWI; in type IV profiles, DO decreased obviously in the overlying water. Type I profiles indicated the absence of benthic organisms and thus the degradation of the sediment habitat. Type II and III profiles indicated the activity of benthic animal and epipelic algae, which is common in the healthy aquatic sediment. Type IV profiles indicated that the excessive accumulation of pollutants in the sediment and thus the serious sediment pollution. There are nine sites showing type I profile, three sites showing type II profile, nine sites showing type III profile, and three sites showing type IV profile in the Fuyang River. The dominance of type I and appearance of type IV indicated that sediment oxygen consumption processes in the Fuyang River were strongly influenced by the sediment pollutants release and the vanish of benthic organisms. The pharmacy, metallurgy, and curriery industries may contribute to the sediment deterioration and thus to the occurrence of type I and type IV oxygen profiles in the Fuyang River.

The Non-linear Trajectory of Change in Play Profiles of Three Children in Psychodynamic Play Therapy.

PubMed

Halfon, Sibel; Çavdar, Alev; Orsucci, Franco; Schiepek, Gunter K; Andreassi, Silvia; Giuliani, Alessandro; de Felice, Giulio

2016-01-01

Aim: Even though there is substantial evidence that play based therapies produce significant change, the specific play processes in treatment remain unexamined. For that purpose, processes of change in long-term psychodynamic play therapy are assessed through a repeated systematic assessment of three children's "play profiles," which reflect patterns of organization among play variables that contribute to play activity in therapy, indicative of the children's coping strategies, and an expression of their internal world. The main aims of the study are to investigate the kinds of play profiles expressed in treatment, and to test whether there is emergence of new and more adaptive play profiles using dynamic systems theory as a methodological framework. Methods and Procedures: Each session from the long-term psychodynamic treatment (mean number of sessions = 55) of three 6-year-old good outcome cases presenting with Separation Anxiety were recorded, transcribed and coded using items from the Children's Play Therapy Instrument (CPTI), created to assess the play activity of children in psychotherapy, generating discrete and measurable units of play activity arranged along a continuum of four play profiles: "Adaptive," "Inhibited," "Impulsive," and "Disorganized." The play profiles were clustered through K -means Algorithm, generating seven discrete states characterizing the course of treatment and the transitions between these states were analyzed by Markov Transition Matrix, Recurrence Quantification Analysis (RQA) and odds ratios comparing the first and second halves of psychotherapy. Results: The Markov Transitions between the states scaled almost perfectly and also showed the ergodicity of the system, meaning that the child can reach any state or shift to another one in play. The RQA and odds ratios showed two trends of change, first concerning the decrease in the use of "less adaptive" strategies, second regarding the reduction of play interruptions. Conclusion: The results support that these children express different psychic states in play, which can be captured through the lens of play profiles, and begin to modify less dysfunctional profiles over the course of treatment. The methodology employed showed the productivity of treating psychodynamic play therapy as a complex system, taking advantage of non-linear methods to study psychotherapeutic play activity.

Investigating the Role of Gravity Wave on Equatorial Ionospheric Irregularities using SABER and C/NOFS Satellites Observations

NASA Astrophysics Data System (ADS)

Nigussie, M.; Damtie, B.; Moldwin, M.; Yizengaw, E.; Tesema, F.; Tebabal, A.

2017-12-01

Theoretical simulations have shown that gravity wave (GW) seeded perturbations amplified by Rayleigh-Taylor Instability (RTI) results in ESF (equatorial spread F); however, there have been limited observational studies using simultaneous observations of GW and ionospheric parameters. In this paper, for the fist time, simultaneous atmospheric temperature perturbation profiles that are due to GWs obtained from Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) on-board the TIMED satellite and equatorial in -situ ion density and vertical plasma drift velocity observations with and without ESF activity obtained from C/NOFS satellites are used to investigate the effect of GW on the generation of ESF. The horizontal and vertical wavelengths of ionospheric oscillations and GWs respectively have been estimated applying wavelet transforms. Cross wavelet analysis has also been applied between two closely observed profiles of temperature perturbations to estimate the horizontal wavelength of the GWs. Moreover, vertically propagating GWs that dissipate energy at the upper atmosphere have been investigated using spectral analysis compared with theoretical results. The analysis show that when the ion density shows strong post sunset irregularity between 20 and 24 LT, vertically upward drift velocities increase between 17 and 19 LT, but it becomes vertically downward when the ion density shows smooth variation. The horizontal wavelengths estimated from C/NOFS and SABER observations show excellent agreement when ion density observations show strong fluctuations; otherwise, they have poor agreement. It is also found that altitude profiles of potential energy of GW increases up to 90 km and then decreases significantly. It is found that the vertical wavelength of GW, corresponding to the dominant spectral power, ranges from about 7 km to 20 km regardless of the situation of the ionosphere; however, GWs with vertical wavelengths between 100 m to 1 km are found to be saturated between 90 and 110 km whether the ionosphere exhibits irregularity or not. The above results imply that ESF is due to the amplification of perturbations as a result of energy dissipation from GW with vertical wavelength 100 m to 1 km by the RTI that is mainly controlled by Pre-Reversal Enhancement of the zonal electric field.

A Module for Assimilating Hyperspectral Infrared Retrieved Profiles into the Gridpoint Statistical Interpolation System for Unique Forecasting Applications

NASA Technical Reports Server (NTRS)

Berndt, Emily; Zavodsky, Bradley; Srikishen, Jayanthi; Blankenship, Clay

2015-01-01

Hyperspectral infrared sounder radiance data are assimilated into operational modeling systems however the process is computationally expensive and only approximately 1% of available data are assimilated due to data thinning as well as the fact that radiances are restricted to cloud-free fields of view. In contrast, the number of hyperspectral infrared profiles assimilated is much higher since the retrieved profiles can be assimilated in some partly cloudy scenes due to profile coupling other data, such as microwave or neural networks, as first guesses to the retrieval process. As the operational data assimilation community attempts to assimilate cloud-affected radiances, it is possible that the use of retrieved profiles might offer an alternative methodology that is less complex and more computationally efficient to solve this problem. The NASA Short-term Prediction Research and Transition (SPoRT) Center has assimilated hyperspectral infrared retrieved profiles into Weather Research and Forecasting Model (WRF) simulations using the Gridpoint Statistical Interpolation (GSI) System. Early research at SPoRT demonstrated improved initial conditions when assimilating Atmospheric Infrared Sounder (AIRS) thermodynamic profiles into WRF (using WRF-Var and assigning more appropriate error weighting to the profiles) to improve regional analysis and heavy precipitation forecasts. Successful early work has led to more recent research utilizing WRF and GSI for applications including the assimilation of AIRS profiles to improve WRF forecasts of atmospheric rivers and assimilation of AIRS, Cross-track Infrared and Microwave Sounding Suite (CrIMSS), and Infrared Atmospheric Sounding Interferometer (IASI) profiles to improve model representation of tropopause folds and associated non-convective wind events. Although more hyperspectral infrared retrieved profiles can be assimilated into model forecasts, one disadvantage is the retrieved profiles have traditionally been assigned the same error values as the rawinsonde observations when assimilated with GSI. Typically, satellitederived profile errors are larger and more difficult to quantify than traditional rawinsonde observations (especially in the boundary layer), so it is important to appropriately assign observation errors within GSI to eliminate potential spurious innovations and analysis increments that can sometimes arise when using retrieved profiles. The goal of this study is to describe modifications to the GSI source code to more appropriately assimilate hyperspectral infrared retrieved profiles and outline preliminary results that show the differences between a model simulation that assimilated the profiles as rawinsonde observations and one that assimilated the profiles in a module with the appropriate error values.

Preliminary study of inphase gusts and moment force wind loads over the first 150 meters at KSC, Florida

NASA Technical Reports Server (NTRS)

Kaufman, J. W.

1985-01-01

A mathematical/statistical analysis of inphase gusts and wind velocity moment forces over the first 150 m at the Kennedy Space Center (KSC) is presented. The wind velocity profile data were acquired at the KSC 150 m ground wind tower. The results show that planetary boundary layer (PBL) winds can sustain near peak speeds for periods up to 60 sec and longer. This is proven from calculating the autocorrelation functions of moment forces for several 10 min cases of wind profile data. The results show that lower atmospheric planetary boundary layer winds have periodic variations for long periods of time. This flow characteristic is valuable as aerospace vehicle engineering and design criteria where wind loading must be determined.

Measuring health-promoting behaviors: cross-cultural validation of the Health-Promoting Lifestyle Profile-II.

PubMed

Sousa, Pedro; Gaspar, Pedro; Vaz, Daniela C; Gonzaga, Sílvia; Dixe, M Anjos

2015-04-01

Individual lifestyles have emerged as valuable health constructs. This study aims to psychometrically test the Portuguese (European) version of the Health-Promoting Lifestyle Profile-II. After an adequate linguistic and cultural adaptation of the Health-Promoting Lifestyle Profile-II scale, their psychometric properties were assessed (N = 889) by Cronbach's alpha and confirmatory factor analysis. Results showed an adequate fit to a 52-item, six-factor structure. A global alpha of .925 was obtained. The Portuguese version demonstrated good validity and reliability in a wide adult sample, and can thus be applied to the Portuguese population. This instrument is useful as an evaluation tool for health-promoting lifestyles and as an instrument for testing the effectiveness of health-promoting programs. © 2014 NANDA International, Inc.

Do students with dyslexia have a different personality profile as measured with the big five?

PubMed

Tops, Wim; Verguts, Ellen; Callens, Maaike; Brysbaert, Marc

2013-01-01

Few studies are available about the personality profile of higher education students with dyslexia and to which extent this could be any different from their non-dyslexic peers. AIMS AND SAMPLES: To obtain empirical evidence, we compared the personality profile of a group of 100 Dutch-speaking students with dyslexia with that of a control group of 100 students without learning disabilities. The NEO-PI-R based on the Big Five in personality research was used. Our study showed no differences in the personality between both groups. This agrees with a recent meta-analysis of English findings (Swanson & Hsieh, 2009), suggesting that students with dyslexia do not perceive themselves differently than their non-dyslexic peers. Practical implications and directions for future research are considered.

[A DNA study of rat liver oligonucleosomes enriched by transcriptionally active genes during induction due to the administration of an amino acid mixture].

PubMed

Vardevanian, P O; Davtian, A M; Tiratsuian, S G; Vardevanian, A O

1990-01-01

A highly active fraction of rat liver oligonucleosome DNA has been isolated and studied by means of thermal denaturation after induction by amino acid mixture or hydrocortisone. A considerable redistribution of DNA content has been shown in sucrose gradient fractions during these forms of induction. The changes are revealed in melting temperature, differential melting profile of DNA, isolated from actively transcribed chromatine fractions. Analysis of melting profiles shows changes of GC content of oligonucleosome DNA, suggesting that there are differences in activation during two studied forms of induction.

OBSERVATIONS AND SIMULATIONS OF THE Na i D{sub 1} LINE PROFILES IN AN M-CLASS SOLAR FLARE

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

Kuridze, D.; Mathioudakis, M.; Jess, D. B.

2016-12-01

We study the temporal evolution of the Na i D{sub 1} line profiles in the M3.9 flare SOL2014-06-11T21:03 UT, using observations at high spectral resolution obtained with the Interferometric Bidimensional Spectrometer instrument on the Dunn Solar Telescope combined with radiative hydrodynamic simulations. Our results show a significant increase in the intensities of the line core and wings during the flare. The analysis of the line profiles from the flare ribbons reveals that the Na i D{sub 1} line has a central reversal with excess emission in the blue wing (blue asymmetry). We combine RADYN and RH simulations to synthesize Na imore » D{sub 1} line profiles of the flaring atmosphere and find good agreement with the observations. Heating with a beam of electrons modifies the radiation field in the flaring atmosphere and excites electrons from the ground state 3s {sup 2}S to the first excited state 3p {sup 2}P, which in turn modifies the relative population of the two states. The change in temperature and the population density of the energy states make the sodium line profile revert from absorption into emission. Furthermore, the rapid changes in temperature break the pressure balance between the different layers of the lower atmosphere, generating upflow/downflow patterns. Analysis of the simulated spectra reveals that the asymmetries of the Na i D{sub 1} flare profile are produced by the velocity gradients in the lower solar atmosphere.« less

Complex and region-specific changes in astroglial markers in the aging brain.

PubMed

Rodríguez, José J; Yeh, Chia-Yu; Terzieva, Slavica; Olabarria, Markel; Kulijewicz-Nawrot, Magdalena; Verkhratsky, Alexei

2014-01-01

Morphological aging of astrocytes was investigated in entorhinal cortex (EC), dentate gyrus (DG), and cornu ammonis 1 (CA1) regions of hippocampus of male SV129/C57BL6 mice of different age groups (3, 9, 18, and 24 months). Astroglial profiles were visualized by immunohistochemistry by using glial fibrillary acidic protein (GFAP), glutamine synthetase (GS), and s100β staining; these profiles were imaged using confocal or light microscopy for subsequent morphometric analysis. GFAP-positive profiles in the DG and the CA1 of the hippocampus showed progressive age-dependent hypertrophy, as indicated by an increase in surface, volume, and somata volume at 24 months of age compared with 3-month-old mice. In contrast with the hippocampal regions, aging induced a decrease in GFAP-positive astroglial profiles in the EC: the surface, volume, and cell body volume of astroglial cells at 24 months of age were decreased significantly compared with the 3-month group. The GS-positive astrocytes displayed smaller cellular surface areas at 24 months compared with 3-month-old animals in both areas of hippocampus, whereas GS-positive profiles remained unchanged in the EC of old mice. The morphometry of s100β-immunoreactive profiles revealed substantial increase in the EC, more moderate increase in the DG, and no changes in the CA1 area. Based on the morphological analysis of 3 astroglial markers, we conclude that astrocytes undergo a complex age-dependent remodeling in a brain region-specific manner. Copyright © 2014. Published by Elsevier Inc.

Use of fatty acid methyl ester profiles for discrimination of Bacillus cereus T-strain spores grown on different media.

PubMed

Ehrhardt, Christopher J; Chu, Vivian; Brown, TeeCie; Simmons, Terrie L; Swan, Brandon K; Bannan, Jason; Robertson, James M

2010-03-01

The goal of this study was to determine if cellular fatty acid methyl ester (FAME) profiling could be used to distinguish among spore samples from a single species (Bacillus cereus T strain) that were prepared on 10 different medium formulations. To analyze profile differences and identify FAME biomarkers diagnostic for the chemical constituents in each sporulation medium, a variety of statistical techniques were used, including nonmetric multidimensional scaling (nMDS), analysis of similarities (ANOSIM), and discriminant function analysis (DFA). The results showed that one FAME biomarker, oleic acid (18:1 omega9c), was exclusively associated with spores grown on Columbia agar supplemented with sheep blood and was indicative of blood supplements that were present in the sporulation medium. For spores grown in other formulations, multivariate comparisons across several FAME biomarkers were required to discern profile differences. Clustering patterns in nMDS plots and R values from ANOSIM revealed that dissimilarities among FAME profiles were most pronounced when spores grown with disparate sources of complex additives or protein supplements were compared (R > 0.8), although other factors also contributed to FAME differences. DFA indicated that differentiation could be maximized with a targeted subset of FAME variables, and the relative contributions of branched FAME biomarkers to group dissimilarities changed when different media were compared. When taken together, these analyses indicate that B. cereus spore samples grown in different media can be resolved with FAME profiling and that this may be a useful technique for providing intelligence about the production methods of Bacillus organisms in a forensic investigation.

Motivational Cluster Profiles of Adolescent Athletes: An Examination of Differences in Physical-Self Perception

PubMed Central

Çağlar, Emine; Aşçı, F. Hülya

2010-01-01

The primary purpose of the present study was to identify motivational profiles of adolescent athletes using cluster analysis in non-Western culture. A second purpose was to examine relationships between physical self-perception differences of adolescent athletes and motivational profiles. One hundred and thirty six male (Mage = 17.46, SD = 1.25 years) and 80 female adolescent athletes (Mage = 17.61, SD = 1.19 years) from a variety of team sports including basketball, soccer, volleyball, and handball volunteered to participate in this study. The Sport Motivation Scale (SMS) and Physical Self-Perception Profile (PSPP) were administered to all participants. Hierarchical cluster analysis revealed a four-cluster solution for this sample: amotivated, low motivated, moderate motivated, and highly motivated. A 4 x 5 (Cluster x PSPP Subscales) MANOVA revealed no significant main effect of motivational clusters on physical self-perception levels (p > 0.05). As a result, findings of the present study showed that motivational types of the adolescent athletes constituted four different motivational clusters. Highly and moderate motivated athletes consistently scored higher than amotivated athletes on the perceived sport competence, physical condition, and physical self-worth subscales of PSPP. This study identified motivational profiles of competitive youth-sport participants. Key points Highly motivated athletes have a tendency to perceive themselves competent in psychomotor domains as compared to the amotivated athletes As the athletes feel more competent in psychomotor domain, they are more intrinsically motivated. The information about motivational profiles of adolescent athletes could be used for developing strategies and interventions designed to improve the strength and quality of sport participants’ motivation. PMID:24149690

The Micro-Pulse Lidar Network (MPLNET): A Federated Network of Micro-pulse Lidars and AERONET Sunphotometers

NASA Technical Reports Server (NTRS)

Welton, Ellsworth J.; Campbell, James R.; Spinhirne, James D.; Berkoff, Timothy A.; Holben, Brent; Tsay, Si-Chee

2004-01-01

We present the formation of a new global-ground based eye-safe lidar network, the NASA Micro-Pulse Lidar Network (MPLNET). The aim of MPLNET is to acquire long- term observations of aerosol and cloud vertical profiles at unique geographic sites within the NASA Aerosol Robotic Network (AERONET). MPLNET utilizes standard instrumentation and data processing algorithms for efficient network operations and direct comparison of data between each site. The micro-pulse lidar is eye-safe, compact, and commercially available, and most easily allows growth of the network without sacrificing standardized instrumentation goals. Network growth follows a federated approach, pioneered by AERONET, wherein independent research groups may join MPLNET with their own instrument and site. MPLNET sites produce not only vertical profile data, but also column-averaged products already available from AERONET (aerosol optical depth, sky radiance, size distributions). Algorithms are presented for each MPLNET data product. Real-time Level 1 data products (next-day) include daily lidar signal images from the surface to -2Okm, and Level 1.5 aerosol extinction profiles at times co-incident with AERONET observations. Quality assured Level 2 aerosol extinction profiles are generated after screening the Level 1.5 results and removing bad data. Level 3 products include continuous day/night aerosol extinction profiles, and are produced using Level 2 calibration data. Rigorous uncertainty calculations are presented for all data products. Analysis of MPLNET data show the MPL and our analysis routines are capable of successfully retrieving aerosol profiles, with the strenuous accounting of uncertainty necessary for accurate interpretation of the results.

Use of Fatty Acid Methyl Ester Profiles for Discrimination of Bacillus cereus T-Strain Spores Grown on Different Media▿

PubMed Central

Ehrhardt, Christopher J.; Chu, Vivian; Brown, TeeCie; Simmons, Terrie L.; Swan, Brandon K.; Bannan, Jason; Robertson, James M.

2010-01-01

The goal of this study was to determine if cellular fatty acid methyl ester (FAME) profiling could be used to distinguish among spore samples from a single species (Bacillus cereus T strain) that were prepared on 10 different medium formulations. To analyze profile differences and identify FAME biomarkers diagnostic for the chemical constituents in each sporulation medium, a variety of statistical techniques were used, including nonmetric multidimensional scaling (nMDS), analysis of similarities (ANOSIM), and discriminant function analysis (DFA). The results showed that one FAME biomarker, oleic acid (18:1 ω9c), was exclusively associated with spores grown on Columbia agar supplemented with sheep blood and was indicative of blood supplements that were present in the sporulation medium. For spores grown in other formulations, multivariate comparisons across several FAME biomarkers were required to discern profile differences. Clustering patterns in nMDS plots and R values from ANOSIM revealed that dissimilarities among FAME profiles were most pronounced when spores grown with disparate sources of complex additives or protein supplements were compared (R > 0.8), although other factors also contributed to FAME differences. DFA indicated that differentiation could be maximized with a targeted subset of FAME variables, and the relative contributions of branched FAME biomarkers to group dissimilarities changed when different media were compared. When taken together, these analyses indicate that B. cereus spore samples grown in different media can be resolved with FAME profiling and that this may be a useful technique for providing intelligence about the production methods of Bacillus organisms in a forensic investigation. PMID:20097814

Vertically resolved characteristics of air pollution during two severe winter haze episodes in urban Beijing, China

NASA Astrophysics Data System (ADS)

Wang, Qingqing; Sun, Yele; Xu, Weiqi; Du, Wei; Zhou, Libo; Tang, Guiqian; Chen, Chen; Cheng, Xueling; Zhao, Xiujuan; Ji, Dongsheng; Han, Tingting; Wang, Zhe; Li, Jie; Wang, Zifa

2018-02-01

We conducted the first real-time continuous vertical measurements of particle extinction (bext), gaseous NO2, and black carbon (BC) from ground level to 260 m during two severe winter haze episodes at an urban site in Beijing, China. Our results illustrated four distinct types of vertical profiles: (1) uniform vertical distributions (37 % of the time) with vertical differences less than 5 %, (2) higher values at lower altitudes (29 %), (3) higher values at higher altitudes (16 %), and (4) significant decreases at the heights of ˜ 100-150 m (14 %). Further analysis demonstrated that vertical convection as indicated by mixing layer height, temperature inversion, and local emissions are three major factors affecting the changes in vertical profiles. Particularly, the formation of type 4 was strongly associated with the stratified layer that was formed due to the interactions of different air masses and temperature inversions. Aerosol composition was substantially different below and above the transition heights with ˜ 20-30 % higher contributions of local sources (e.g., biomass burning and cooking) at lower altitudes. A more detailed evolution of vertical profiles and their relationship with the changes in source emissions, mixing layer height, and aerosol chemistry was illustrated by a case study. BC showed overall similar vertical profiles as those of bext (R2 = 0.92 and 0.69 in November and January, respectively). While NO2 was correlated with bext for most of the time, the vertical profiles of bext / NO2 varied differently for different profiles, indicating the impact of chemical transformation on vertical profiles. Our results also showed that more comprehensive vertical measurements (e.g., more aerosol and gaseous species) at higher altitudes in the megacities are needed for a better understanding of the formation mechanisms and evolution of severe haze episodes in China.

Molecular Typing and Virulence Gene Profiles of Enterotoxin Gene Cluster (egc)-Positive Staphylococcus aureus Isolates Obtained from Various Food and Clinical Specimens.

PubMed

Song, Minghui; Shi, Chunlei; Xu, Xuebing; Shi, Xianming

2016-11-01

The enterotoxin gene cluster (egc) has been proposed to contribute to the Staphylococcus aureus colonization, which highlights the need to evaluate genetic diversity and virulence gene profiles of the egc-positive population. Here, a total of 43 egc-positive isolates (16.2%) were identified from 266 S. aureus isolates that were obtained from various food and clinical specimens in Shanghai. Seven different egc profiles were found based on the polymerase chain reaction (PCR) result for egc genes. Then, these 43 egc-positive isolates were further typed by multilocus sequence typing, pulsed-field gel electrophoresis (PFGE), multiple-locus variable-number tandem-repeat analysis (MLVA), and accessory gene regulatory (agr) typing. It showed that the 43 egc-positive isolates displayed 17 sequence types, 28 PFGE patterns, 29 MLVA types, and 4 agr types, respectively. Among them, the dominant clonal lineage was CC5-agr II (48.84%). Thirty toxin and 20 adhesion-associated genes were detected by PCR in egc-positive isolates. Notably, invasive toxin genes showed a high prevalence, such as 76.7% for Panton-Valentine leukocidin encoding genes, 27.9% for sec, and 23.3% for tsst-1. Most of the examined adhesion-associated genes were found to be conserved (76.7-100%), whereas the fnbB gene was only found in 8 (18.6%) isolates. In addition, 33 toxin gene profiles and 13 adhesion gene profiles were identified, respectively. Our results imply that isolates belonging to the same clonal lineage harbored similar adhesion gene profiles but diverse toxin gene profiles. Overall, the high prevalence of invasive virulence genes increases the potential risk of egc-positive isolates in S. aureus infection.

Further Evidence that Severe Scores in the Aggression/Anxiety-Depression/Attention Subscales of Child Behavior Checklist (Severe Dysregulation Profile) Can Screen for Bipolar Disorder Symptomatology: A Conditional Probability Analysis

PubMed Central

Uchida, Mai; Faraone, Stephen V; Martelon, MaryKate; Kenworthy, Tara; Woodworth, K Yvonne; Spencer, Thomas; Wozniak, Janet; Biederman, Joseph

2014-01-01

Background Previous work shows that children with high scores (2 SD, combined score ≥ 210) on the Attention Problems, Aggressive Behavior, and Anxious-Depressed (A-A-A) subscales of the Child Behavior Checklist (CBCL) are more likely than other children to meet criteria for bipolar (BP)-I disorder. However, the utility of this profile as a screening tool has remained unclear. Methods We compared 140 patients with pediatric BP-I disorder, 83 with attention deficit hyperactivity disorder (ADHD), and 114 control subjects. We defined the CBCL-Severe Dysregulation profile as an aggregate cutoff score of ≥ 210 on the A-A-A scales. Patients were assessed with structured diagnostic interviews and functional measures. Results Patients with BP-I disorder were significantly more likely than both control subjects (Odds Ratio [OR]: 173.2; 95% Confidence Interval [CI], 21.2 to 1413.8; P < 0.001) and those with ADHD (OR: 14.6; 95% CI, 6.2 to 34.3; P < 0.001) to have a positive CBCL-Severe Dysregulation profile. Receiver Operating Characteristics analyses showed that the area under the curve for this profile comparing children with BP-I disorder against control subjects and those with ADHD was 99% and 85%, respectively. The corresponding positive predictive values for this profile were 99% and 92% with false positive rates of < 0.2% and 8% for the comparisons with control subjects and patients with ADHD, respectively. Limitations Non-clinician raters administered structured diagnostic interviews, and the sample was referred and largely Caucasian. Conclusions The CBCL-Severe Dysregulation profile can be useful as a screen for BP-I disorder in children in clinical practice. PMID:24882182

Circulating tumor DNA profiling reveals clonal evolution and real-time disease progression in advanced hepatocellular carcinoma.

PubMed

Cai, Zhi-Xiong; Chen, Geng; Zeng, Yong-Yi; Dong, Xiu-Qing; Lin, Min-Jie; Huang, Xin-Hui; Zhang, Da; Liu, Xiao-Long; Liu, Jing-Feng

2017-09-01

Circulating tumor DNA (ctDNA) provides a potential non-invasive biomarker for cancer diagnosis and prognosis, but whether it could reflect tumor heterogeneity and monitor therapeutic responses in hepatocellular carcinoma (HCC) is unclear. Focusing on 574 cancer genes known to harbor actionable mutations, we identified the mutation repertoire of HCC tissues, and monitored the corresponding ctDNA features in blood samples to evaluate its clinical significance. Analysis of 3 HCC patients' mutation profiles revealed that ctDNA could overcome tumor heterogeneity and provide information of tumor burden and prognosis. Further analysis was conducted on the 4th HCC case with multiple lesion samples and sequential plasma samples. We identified 160 subclonal SNVs in tumor tissues as well as matched peritumor tissues with PBMC as control. 96.9% of this patient's tissue mutations could be also detected in plasma samples. These subclonal SNVs were grouped into 9 clusters according to their trends of cellular prevalence shift in tumor tissues. Two clusters constituted of tumor stem somatic mutations showed circulating levels relating with cancer progression. Analysis of tumor somatic mutations revealed that circulating level of such tumor stem somatic mutations could reflect tumor burden and even predict prognosis earlier than traditional strategies. Furthermore, HCK (p.V174M), identified as a recurrent/metastatic related mutation site, could promote migration and invasion of HCC cells. Taken together, study of mutation profiles in biopsy and plasma samples in HCC patients showed that ctDNA could overcome tumor heterogeneity and real-time track the therapeutic responses in the longitudinal monitoring. © 2017 UICC.

Gene expression profiles of fin regeneration in loach (Paramisgurnus dabryanu).

PubMed

Li, Li; He, Jingya; Wang, Linlin; Chen, Weihua; Chang, Zhongjie

2017-11-01

Teleost fins can regenerate accurate position-matched structure and function after amputation. However, we still lack systematic transcriptional profiling and methodologies to understand the molecular basis of fin regeneration. After histological analysis, we established a suppression subtraction hybridization library containing 418 distinct sequences expressed differentially during the process of blastema formation and differentiation in caudal fin regeneration. Genome ontology and comparative analysis of differential distribution of our data and the reference zebrafish genome showed notable subcategories, including multi-organism processes, response to stimuli, extracellular matrix, antioxidant activity, and cell junction function. KEGG pathway analysis allowed the effective identification of relevant genes in those pathways involved in tissue morphogenesis and regeneration, including tight junction, cell adhesion molecules, mTOR and Jak-STAT signaling pathway. From relevant function subcategories and signaling pathways, 78 clones were examined for further Southern-blot hybridization. Then, 17 genes were chosen and characterized using semi-quantitative PCR. Then 4 candidate genes were identified, including F11r, Mmp9, Agr2 and one without a match to any database. After real-time quantitative PCR, the results showed obvious expression changes in different periods of caudal fin regeneration. We can assume that the 4 candidates, likely valuable genes associated with fin regeneration, deserve additional attention. Thus, our study demonstrated how to investigate the transcript profiles with an emphasis on bioinformatics intervention and how to identify potential genes related to fin regeneration processes. The results also provide a foundation or knowledge for further research into genes and molecular mechanisms of fin regeneration. Copyright © 2017 Elsevier B.V. All rights reserved.