Quantitative descriptions of generalized arousal, an elementary function of the vertebrate brain

PubMed Central

Quinkert, Amy Wells; Vimal, Vivek; Weil, Zachary M.; Reeke, George N.; Schiff, Nicholas D.; Banavar, Jayanth R.; Pfaff, Donald W.

2011-01-01

We review a concept of the most primitive, fundamental function of the vertebrate CNS, generalized arousal (GA). Three independent lines of evidence indicate the existence of GA: statistical, genetic, and mechanistic. Here we ask, is this concept amenable to quantitative analysis? Answering in the affirmative, four quantitative approaches have proven useful: (i) factor analysis, (ii) information theory, (iii) deterministic chaos, and (iv) application of a Gaussian equation. It strikes us that, to date, not just one but at least four different quantitative approaches seem necessary for describing different aspects of scientific work on GA. PMID:21555568

40 CFR 799.9780 - TSCA immunotoxicity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... quantitative analysis of the effects of a chemical on the numbers of cells in major lymphocyte populations and..., and the research sample shall be stored under conditions that maintain its purity and stability. Prior... type of effect. (ii) All observed results, quantitative and incidental, shall be evaluated by an...

40 CFR 799.9780 - TSCA immunotoxicity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... quantitative analysis of the effects of a chemical on the numbers of cells in major lymphocyte populations and..., and the research sample shall be stored under conditions that maintain its purity and stability. Prior... type of effect. (ii) All observed results, quantitative and incidental, shall be evaluated by an...

40 CFR 799.9780 - TSCA immunotoxicity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... quantitative analysis of the effects of a chemical on the numbers of cells in major lymphocyte populations and..., and the research sample shall be stored under conditions that maintain its purity and stability. Prior... type of effect. (ii) All observed results, quantitative and incidental, shall be evaluated by an...

40 CFR 799.9780 - TSCA immunotoxicity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... quantitative analysis of the effects of a chemical on the numbers of cells in major lymphocyte populations and..., and the research sample shall be stored under conditions that maintain its purity and stability. Prior... type of effect. (ii) All observed results, quantitative and incidental, shall be evaluated by an...

40 CFR 799.9780 - TSCA immunotoxicity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... quantitative analysis of the effects of a chemical on the numbers of cells in major lymphocyte populations and..., and the research sample shall be stored under conditions that maintain its purity and stability. Prior... type of effect. (ii) All observed results, quantitative and incidental, shall be evaluated by an...

Application of sequential extraction analysis to Pb(II) recovery by zerovalent iron-based particles.

PubMed

Zhu, Neng-Min; Xu, Yan-Sheng; Dai, Lichun; Zhang, Yun-Fei; Hu, Guo-Quan

2018-06-05

Zerovalent iron (ZVI) is an environmental-friendly reactive reagent for recovering heavy metals. However, the detailed recovery mechanism remains unclear due to a lack of quantitative analysis of recovery products. Herein, microscale ZVI, nanoscale ZVI and Ni/Fe nanoparticles were used to recover Pb(II) in aqueous solution and a sequential extraction procedure (SEP) was applied to determine the formed lead species quantitatively. At high initial Pb(II) concentration (500 mg L -1 ), more than 99.5% of Pb(II) was immobilized by Ni/Fe and n-ZVI, whereas m-ZVI caused inferior recovery efficiency (<25%). XRD and XPS results revealed that Pb(II) was reduced to Pb 0 prior to the formation of metal hydroxides as the external shell of ZVI. SEP results showed that the fraction bound to carbonates (PbO), fraction bound to iron oxides and exchangeable fraction were the main lead species conducted by Ni/Fe, n-ZVI and m-ZVI, respectively. Consequently, (co-)precipitation and specific adsorption dominated Pb(II) recovery by Ni/Fe and n-ZVI, whereas m-ZVI conducted Pb(II) recovery mainly via weak adsorption. The reactivity of ZVI toward Pb(II) followed the increasing order of m-ZVI < n-ZVI ≤ Ni/Fe. The detailed mechanisms of Pb(II) recovery conducted by different ZVI were proposed. Copyright © 2018 Elsevier B.V. All rights reserved.

The Tongue and Quill

DTIC Science & Technology

2004-08-01

ethnography , phenomenological study , grounded theory study and content analysis. THE HISTORICAL METHOD Methods I. Qualitative Research Methods ... Phenomenological Study 4. Grounded Theory Study 5. Content Analysis II. Quantitative Research Methods A...A. The Historical Method B. General Qualitative

Putting tools in the toolbox: Development of a free, open-source toolbox for quantitative image analysis of porous media.

NASA Astrophysics Data System (ADS)

Iltis, G.; Caswell, T. A.; Dill, E.; Wilkins, S.; Lee, W. K.

2014-12-01

X-ray tomographic imaging of porous media has proven to be a valuable tool for investigating and characterizing the physical structure and state of both natural and synthetic porous materials, including glass bead packs, ceramics, soil and rock. Given that most synchrotron facilities have user programs which grant academic researchers access to facilities and x-ray imaging equipment free of charge, a key limitation or hindrance for small research groups interested in conducting x-ray imaging experiments is the financial cost associated with post-experiment data analysis. While the cost of high performance computing hardware continues to decrease, expenses associated with licensing commercial software packages for quantitative image analysis continue to increase, with current prices being as high as $24,000 USD, for a single user license. As construction of the Nation's newest synchrotron accelerator nears completion, a significant effort is being made here at the National Synchrotron Light Source II (NSLS-II), Brookhaven National Laboratory (BNL), to provide an open-source, experiment-to-publication toolbox that reduces the financial and technical 'activation energy' required for performing sophisticated quantitative analysis of multidimensional porous media data sets, collected using cutting-edge x-ray imaging techniques. Implementation focuses on leveraging existing open-source projects and developing additional tools for quantitative analysis. We will present an overview of the software suite that is in development here at BNL including major design decisions, a demonstration of several test cases illustrating currently available quantitative tools for analysis and characterization of multidimensional porous media image data sets and plans for their future development.

Quantitative chromatin pattern description in Feulgen-stained nuclei as a diagnostic tool to characterize the oligodendroglial and astroglial components in mixed oligo-astrocytomas.

PubMed

Decaestecker, C; Lopes, B S; Gordower, L; Camby, I; Cras, P; Martin, J J; Kiss, R; VandenBerg, S R; Salmon, I

1997-04-01

The oligoastrocytoma, as a mixed glioma, represents a nosologic dilemma with respect to precisely defining the oligodendroglial and astroglial phenotypes that constitute the neoplastic cell lineages of these tumors. In this study, cell image analysis with Feulgen-stained nuclei was used to distinguish between oligodendroglial and astrocytic phenotypes in oligodendrogliomas and astrocytomas and then applied to mixed oligoastrocytomas. Quantitative features with respect to chromatin pattern (30 variables) and DNA ploidy (8 variables) were evaluated on Feulgen-stained nuclei in a series of 71 gliomas using computer-assisted microscopy. These included 32 oligodendrogliomas (OLG group: 24 grade II and 8 grade III tumors according to the WHO classification), 32 astrocytomas (AST group: 13 grade II and 19 grade III tumors), and 7 oligoastrocytomas (OLGAST group). Initially, image analysis with multivariate statistical analyses (Discriminant Analysis) could identify each glial tumor group. Highly significant statistical differences were obtained distinguishing the morphonuclear features of oligodendrogliomas from those of astrocytomas, regardless of their histological grade. When compared with the 7 mixed oligoastrocytomas under study, 5 exhibited DNA ploidy and chromatin pattern characteristics similar to grade II oligodendrogliomas, I to grade III oligodendrogliomas, and I to grade II astrocytomas. Using multifactorial statistical analyses (Discriminant Analysis combined with Principal Component Analysis). It was possible to quantify the proportion of "typical" glial cell phenotypes that compose grade II and III oligodendrogliomas and grade II and III astrocytomas in each mixed glioma. Cytometric image analysis may be an important adjunct to routine histopathology for the reproducible identification of neoplasms containing a mixture of oligodendroglial and astrocytic phenotypes.

Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes*

PubMed Central

Mosley, Amber L.; Sardiu, Mihaela E.; Pattenden, Samantha G.; Workman, Jerry L.; Florens, Laurence; Washburn, Michael P.

2011-01-01

The use of quantitative proteomics methods to study protein complexes has the potential to provide in-depth information on the abundance of different protein components as well as their modification state in various cellular conditions. To interrogate protein complex quantitation using shotgun proteomic methods, we have focused on the analysis of protein complexes using label-free multidimensional protein identification technology and studied the reproducibility of biological replicates. For these studies, we focused on three highly related and essential multi-protein enzymes, RNA polymerase I, II, and III from Saccharomyces cerevisiae. We found that label-free quantitation using spectral counting is highly reproducible at the protein and peptide level when analyzing RNA polymerase I, II, and III. In addition, we show that peptide sampling does not follow a random sampling model, and we show the need for advanced computational models to predict peptide detection probabilities. In order to address these issues, we used the APEX protocol to model the expected peptide detectability based on whole cell lysate acquired using the same multidimensional protein identification technology analysis used for the protein complexes. Neither method was able to predict the peptide sampling levels that we observed using replicate multidimensional protein identification technology analyses. In addition to the analysis of the RNA polymerase complexes, our analysis provides quantitative information about several RNAP associated proteins including the RNAPII elongation factor complexes DSIF and TFIIF. Our data shows that DSIF and TFIIF are the most highly enriched RNAP accessory factors in Rpb3-TAP purifications and demonstrate our ability to measure low level associated protein abundance across biological replicates. In addition, our quantitative data supports a model in which DSIF and TFIIF interact with RNAPII in a dynamic fashion in agreement with previously published reports. PMID:21048197

Defining the Pathophysiological Role of Tau in Experimental TBI

DTIC Science & Technology

2017-10-01

clinically a blood test for improving the diagnosis of TBI-induced chronic neurodegenerative disease in the long-term post -injury time period. The...we will complete the quantitative analysis of perforant pathway synapse integrity in all 63 long-term post -injury cases. Our results thus far support...substantiated by quantitative analysis of NeuN-positive neuronal density in lateral entorhinal cortex layer II at 4 months post -injury (Table 1). At

Characterization of breast lesion using T1-perfusion magnetic resonance imaging: Qualitative vs. quantitative analysis.

PubMed

Thakran, S; Gupta, P K; Kabra, V; Saha, I; Jain, P; Gupta, R K; Singh, A

2018-06-14

The objective of this study was to quantify the hemodynamic parameters using first pass analysis of T 1 -perfusion magnetic resonance imaging (MRI) data of human breast and to compare these parameters with the existing tracer kinetic parameters, semi-quantitative and qualitative T 1 -perfusion analysis in terms of lesion characterization. MRI of the breast was performed in 50 women (mean age, 44±11 [SD] years; range: 26-75) years with a total of 15 benign and 35 malignant breast lesions. After pre-processing, T 1 -perfusion MRI data was analyzed using qualitative approach by two radiologists (visual inspection of the kinetic curve into types I, II or III), semi-quantitative (characterization of kinetic curve types using empirical parameters), generalized-tracer-kinetic-model (tracer kinetic parameters) and first pass analysis (hemodynamic-parameters). Chi-squared test, t-test, one-way analysis-of-variance (ANOVA) using Bonferroni post-hoc test and receiver-operating-characteristic (ROC) curve were used for statistical analysis. All quantitative parameters except leakage volume (Ve), qualitative (type-I and III) and semi-quantitative curves (type-I and III) provided significant differences (P<0.05) between benign and malignant lesions. Kinetic parameters, particularly volume transfer coefficient (K trans ) provided a significant difference (P<0.05) between all grades except grade-II vs III. The hemodynamic parameter (relative-leakage-corrected-breast-blood-volume [rBBVcorr) provided a statistically significant difference (P<0.05) between all grades. It also provided highest sensitivity and specificity among all parameters in differentiation between different grades of malignant breast lesions. Quantitative parameters, particularly rBBVcorr and K trans provided similar sensitivity and specificity in differentiating benign from malignant breast lesions for this cohort. Moreover, rBBVcorr provided better differentiation between different grades of malignant breast lesions among all the parameters. Copyright © 2018. Published by Elsevier Masson SAS.

TOXNET: Toxicology Data Network

MedlinePlus

... 4. Supporting Data for Carcinogenicity Expand II.B. Quantitative Estimate of Carcinogenic Risk from Oral Exposure II. ... of Confidence (Carcinogenicity, Oral Exposure) Expand II.C. Quantitative Estimate of Carcinogenic Risk from Inhalation Exposure II. ...

Problem-based learning on quantitative analytical chemistry course

NASA Astrophysics Data System (ADS)

Fitri, Noor

2017-12-01

This research applies problem-based learning method on chemical quantitative analytical chemistry, so called as "Analytical Chemistry II" course, especially related to essential oil analysis. The learning outcomes of this course include aspects of understanding of lectures, the skills of applying course materials, and the ability to identify, formulate and solve chemical analysis problems. The role of study groups is quite important in improving students' learning ability and in completing independent tasks and group tasks. Thus, students are not only aware of the basic concepts of Analytical Chemistry II, but also able to understand and apply analytical concepts that have been studied to solve given analytical chemistry problems, and have the attitude and ability to work together to solve the problems. Based on the learning outcome, it can be concluded that the problem-based learning method in Analytical Chemistry II course has been proven to improve students' knowledge, skill, ability and attitude. Students are not only skilled at solving problems in analytical chemistry especially in essential oil analysis in accordance with local genius of Chemistry Department, Universitas Islam Indonesia, but also have skilled work with computer program and able to understand material and problem in English.

Quantitative Phosphoproteomics Dissection of Seven-transmembrane Receptor Signaling Using Full and Biased Agonists*

PubMed Central

Christensen, Gitte L.; Kelstrup, Christian D.; Lyngsø, Christina; Sarwar, Uzma; Bøgebo, Rikke; Sheikh, Søren P.; Gammeltoft, Steen; Olsen, Jesper V.; Hansen, Jakob L.

2010-01-01

Seven-transmembrane receptors (7TMRs) signal through the well described heterotrimeric G proteins but can also activate G protein-independent signaling pathways of which the impact and complexity are less understood. The angiotensin II type 1 receptor (AT1R) is a prototypical 7TMR and an important drug target in cardiovascular diseases. “Biased agonists” with intrinsic “functional selectivity” that simultaneously blocks Gαq protein activity and activates G protein-independent pathways of the AT1R confer important perspectives in treatment of cardiovascular diseases. In this study, we performed a global quantitative phosphoproteomics analysis of the AT1R signaling network. We analyzed ligand-stimulated SILAC (stable isotope labeling by amino acids in cell culture) cells by high resolution (LTQ-Orbitrap) MS and compared the phosphoproteomes of the AT1R agonist angiotensin II and the biased agonist [Sar1,Ile4,Ile8]angiotensin II (SII angiotensin II), which only activates the Gαq protein-independent signaling. We quantified more than 10,000 phosphorylation sites of which 1183 were regulated by angiotensin II or its analogue SII angiotensin II. 36% of the AT1R-regulated phosphorylations were regulated by SII angiotensin II. Analysis of phosphorylation site patterns showed a striking distinction between protein kinases activated by Gαq protein-dependent and -independent mechanisms, and we now place protein kinase D as a key protein involved in both Gαq-dependent and -independent AT1R signaling. This study provides substantial novel insight into angiotensin II signal transduction and is the first study dissecting the differences between a full agonist and a biased agonist from a 7TMR on a systems-wide scale. Importantly, it reveals a previously unappreciated diversity and quantity of Gαq protein-independent signaling and uncovers novel signaling pathways. We foresee that the amount and diversity of G protein-independent signaling may be more pronounced than previously recognized for other 7TMRs as well. Quantitative mass spectrometry is a promising tool for evaluation of the signaling properties of biased agonists to other receptors in the future. PMID:20363803

In situ immobilization on the silica gel surface and adsorption capacity of polymer-based azobenzene on toxic metal ions

NASA Astrophysics Data System (ADS)

Savchenko, Irina; Yanovska, Elina; Sternik, Dariusz; Kychkyruk, Olga; Ol'khovik, Lidiya; Polonska, Yana

2018-03-01

In situ immobilization of poly[(4-methacryloyloxy-(4'-carboxy)azobenzene] on silica gel surface has been performed by radical polymerization of monomer. The fact of polymer immobilization is confirmed by IR spectroscopy. TG and DSC-MS analysis showed that the mass of the immobilized polymer was 10.61%. The SEM-microphotograph-synthesized composite analysis showed that the immobilized polymer on the silica gel surface is placed in the form of fibers. It has been found that the synthesized composite exhibits the sorption ability in terms of microquantities of Cu(II), Cd(II), Pb(II), Mn(II) and Fe(III) ions in a neutral aqueous medium. The quantitative sorption of microquantities of Pb(II) and Fe(III) ions has been recorded. It has been found that immobilization of the silica gel surface leads to an increase in its sorption capacitance for Fe(III), Cu(II) and Pb(II) ions by half.

Quantitative analysis of dinuclear manganese(II) EPR spectra

NASA Astrophysics Data System (ADS)

Golombek, Adina P.; Hendrich, Michael P.

2003-11-01

A quantitative method for the analysis of EPR spectra from dinuclear Mn(II) complexes is presented. The complex [(Me 3TACN) 2Mn(II) 2(μ-OAc) 3]BPh 4 ( 1) (Me 3TACN= N, N', N''-trimethyl-1,4,7-triazacyclononane; OAc=acetate 1-; BPh 4=tetraphenylborate 1-) was studied with EPR spectroscopy at X- and Q-band frequencies, for both perpendicular and parallel polarizations of the microwave field, and with variable temperature (2-50 K). Complex 1 is an antiferromagnetically coupled dimer which shows signals from all excited spin manifolds, S=1 to 5. The spectra were simulated with diagonalization of the full spin Hamiltonian which includes the Zeeman and zero-field splittings of the individual manganese sites within the dimer, the exchange and dipolar coupling between the two manganese sites of the dimer, and the nuclear hyperfine coupling for each manganese ion. All possible transitions for all spin manifolds were simulated, with the intensities determined from the calculated probability of each transition. In addition, the non-uniform broadening of all resonances was quantitatively predicted using a lineshape model based on D- and r-strain. As the temperature is increased from 2 K, an 11-line hyperfine pattern characteristic of dinuclear Mn(II) is first observed from the S=3 manifold. D- and r-strain are the dominate broadening effects that determine where the hyperfine pattern will be resolved. A single unique parameter set was found to simulate all spectra arising for all temperatures, microwave frequencies, and microwave modes. The simulations are quantitative, allowing for the first time the determination of species concentrations directly from EPR spectra. Thus, this work describes the first method for the quantitative characterization of EPR spectra of dinuclear manganese centers in model complexes and proteins. The exchange coupling parameter J for complex 1 was determined ( J=-1.5±0.3 cm-1; H ex=-2J S1· S2) and found to be in agreement with a previous determination from magnetization. The phenomenon of exchange striction was found to be insignificant for 1.

Final Report for Dynamic Models for Causal Analysis of Panel Data. Models for Change in Quantitative Variables, Part III: Estimation from Panel Data. Part II, Chapter 5.

ERIC Educational Resources Information Center

Hannan, Michael T.

This document is part of a series of chapters described in SO 011 759. Addressing the problems of studying change and the change process, the report argues that sociologists should study coupled changes in qualitative and quantitative outcomes (e.g., marital status and earnings). The author presents a model for sociological studies of change in…

Usefulness of the admission electrocardiogram to predict long-term outcomes after non-ST-elevation acute coronary syndrome (from the FRISC II, ICTUS, and RITA-3 [FIR] Trials).

PubMed

Damman, Peter; Holmvang, Lene; Tijssen, Jan G P; Lagerqvist, Bo; Clayton, Tim C; Pocock, Stuart J; Windhausen, Fons; Hirsch, Alexander; Fox, Keith A A; Wallentin, Lars; de Winter, Robbert J

2012-01-01

The aim of this study was to evaluate the independent prognostic value of qualitative and quantitative admission electrocardiographic (ECG) analysis regarding long-term outcomes after non-ST-segment elevation acute coronary syndromes (NSTE-ACS). From the Fragmin and Fast Revascularization During Instability in Coronary Artery Disease (FRISC II), Invasive Versus Conservative Treatment in Unstable Coronary Syndromes (ICTUS), and Randomized Intervention Trial of Unstable Angina 3 (RITA-3) patient-pooled database, 5,420 patients with NSTE-ACS with qualitative ECG data, of whom 2,901 had quantitative data, were included in this analysis. The main outcome was 5-year cardiovascular death or myocardial infarction. Hazard ratios (HRs) were calculated with Cox regression models, and adjustments were made for established outcome predictors. The additional discriminative value was assessed with the category-less net reclassification improvement and integrated discrimination improvement indexes. In the 5,420 patients, the presence of ST-segment depression (≥1 mm; adjusted HR 1.43, 95% confidence interval [CI] 1.25 to 1.63) and left bundle branch block (adjusted HR 1.64, 95% CI 1.18 to 2.28) were independently associated with long-term cardiovascular death or myocardial infarction. Risk increases were short and long term. On quantitative ECG analysis, cumulative ST-segment depression (≥5 mm; adjusted HR 1.34, 95% CI 1.05 to 1.70), the presence of left bundle branch block (adjusted HR 2.15, 95% CI 1.36 to 3.40) or ≥6 leads with inverse T waves (adjusted HR 1.22, 95% CI 0.97 to 1.55) was independently associated with long-term outcomes. No interaction was observed with treatment strategy. No improvements in net reclassification improvement and integrated discrimination improvement were observed after the addition of quantitative characteristics to a model including qualitative characteristics. In conclusion, in the FRISC II, ICTUS, and RITA-3 NSTE-ACS patient-pooled data set, admission ECG characteristics provided long-term prognostic value for cardiovascular death or myocardial infarction. Quantitative ECG characteristics provided no incremental discrimination compared to qualitative data. Copyright © 2012 Elsevier Inc. All rights reserved.

ANALYSIS OF PERFLUORINATED CARBOXYLIC ACIDS IN SOILS II: OPTIMIZATION OF CHROMATOGRAPHY AND EXTRACTION

EPA Science Inventory

With the objective of detecting and quantitating low concentrations of perfluorinated carboxylic acids (PFCAs), including perfluorinated octanoic acid (PFOA), in soils, we compared the analytical suitability of liquid chromatography columns containing three different stationary p...

Identification and quantitation of semi-crystalline microplastics using image analysis and differential scanning calorimetry.

PubMed

Rodríguez Chialanza, Mauricio; Sierra, Ignacio; Pérez Parada, Andrés; Fornaro, Laura

2018-06-01

There are several techniques used to analyze microplastics. These are often based on a combination of visual and spectroscopic techniques. Here we introduce an alternative workflow for identification and mass quantitation through a combination of optical microscopy with image analysis (IA) and differential scanning calorimetry (DSC). We studied four synthetic polymers with environmental concern: low and high density polyethylene (LDPE and HDPE, respectively), polypropylene (PP), and polyethylene terephthalate (PET). Selected experiments were conducted to investigate (i) particle characterization and counting procedures based on image analysis with open-source software, (ii) chemical identification of microplastics based on DSC signal processing, (iii) dependence of particle size on DSC signal, and (iv) quantitation of microplastics mass based on DSC signal. We describe the potential and limitations of these techniques to increase reliability for microplastic analysis. Particle size demonstrated to have particular incidence in the qualitative and quantitative performance of DSC signals. Both, identification (based on characteristic onset temperature) and mass quantitation (based on heat flow) showed to be affected by particle size. As a result, a proper sample treatment which includes sieving of suspended particles is particularly required for this analytical approach.

Near infrared spectroscopy combined with multivariate analysis for monitoring the ethanol precipitation process of fraction I + II + III supernatant in human albumin separation

NASA Astrophysics Data System (ADS)

Li, Can; Wang, Fei; Zang, Lixuan; Zang, Hengchang; Alcalà, Manel; Nie, Lei; Wang, Mingyu; Li, Lian

2017-03-01

Nowadays, as a powerful process analytical tool, near infrared spectroscopy (NIRS) has been widely applied in process monitoring. In present work, NIRS combined with multivariate analysis was used to monitor the ethanol precipitation process of fraction I + II + III (FI + II + III) supernatant in human albumin (HA) separation to achieve qualitative and quantitative monitoring at the same time and assure the product's quality. First, a qualitative model was established by using principal component analysis (PCA) with 6 of 8 normal batches samples, and evaluated by the remaining 2 normal batches and 3 abnormal batches. The results showed that the first principal component (PC1) score chart could be successfully used for fault detection and diagnosis. Then, two quantitative models were built with 6 of 8 normal batches to determine the content of the total protein (TP) and HA separately by using partial least squares regression (PLS-R) strategy, and the models were validated by 2 remaining normal batches. The determination coefficient of validation (Rp2), root mean square error of cross validation (RMSECV), root mean square error of prediction (RMSEP) and ratio of performance deviation (RPD) were 0.975, 0.501 g/L, 0.465 g/L and 5.57 for TP, and 0.969, 0.530 g/L, 0.341 g/L and 5.47 for HA, respectively. The results showed that the established models could give a rapid and accurate measurement of the content of TP and HA. The results of this study indicated that NIRS is an effective tool and could be successfully used for qualitative and quantitative monitoring the ethanol precipitation process of FI + II + III supernatant simultaneously. This research has significant reference value for assuring the quality and improving the recovery ratio of HA in industrialization scale by using NIRS.

Near infrared spectroscopy combined with multivariate analysis for monitoring the ethanol precipitation process of fraction I+II+III supernatant in human albumin separation.

PubMed

Li, Can; Wang, Fei; Zang, Lixuan; Zang, Hengchang; Alcalà, Manel; Nie, Lei; Wang, Mingyu; Li, Lian

2017-03-15

Nowadays, as a powerful process analytical tool, near infrared spectroscopy (NIRS) has been widely applied in process monitoring. In present work, NIRS combined with multivariate analysis was used to monitor the ethanol precipitation process of fraction I+II+III (FI+II+III) supernatant in human albumin (HA) separation to achieve qualitative and quantitative monitoring at the same time and assure the product's quality. First, a qualitative model was established by using principal component analysis (PCA) with 6 of 8 normal batches samples, and evaluated by the remaining 2 normal batches and 3 abnormal batches. The results showed that the first principal component (PC1) score chart could be successfully used for fault detection and diagnosis. Then, two quantitative models were built with 6 of 8 normal batches to determine the content of the total protein (TP) and HA separately by using partial least squares regression (PLS-R) strategy, and the models were validated by 2 remaining normal batches. The determination coefficient of validation (R p 2 ), root mean square error of cross validation (RMSECV), root mean square error of prediction (RMSEP) and ratio of performance deviation (RPD) were 0.975, 0.501g/L, 0.465g/L and 5.57 for TP, and 0.969, 0.530g/L, 0.341g/L and 5.47 for HA, respectively. The results showed that the established models could give a rapid and accurate measurement of the content of TP and HA. The results of this study indicated that NIRS is an effective tool and could be successfully used for qualitative and quantitative monitoring the ethanol precipitation process of FI+II+III supernatant simultaneously. This research has significant reference value for assuring the quality and improving the recovery ratio of HA in industrialization scale by using NIRS. Copyright © 2016 Elsevier B.V. All rights reserved.

An Overview of ACRL"Metrics", Part II: Using NCES and IPEDs Data

ERIC Educational Resources Information Center

Stewart, Christopher

2012-01-01

This report is the second in a two-part analysis of ACRL"Metrics", an online service that provides access to a range of quantitative data for academic libraries. In this analysis, ACRL"Metrics"' inclusion of data from the National Center for Educational Statistics' Academic Libraries Survey and the Integrated Postsecondary Education Data System is…

An analysis of radio frequency surveillance systems for air traffic control volume II: appendixes

DOT National Transportation Integrated Search

1976-02-01

Performance criteria that afford quantitative evaluation of a variety of current and proposed configurations of the Air Traffic Control Radar Beacon System (ATCRBS) are described in detail. Two analytic system models are developed to allow applicatio...

Adduct simplification in the analysis of cyanobacterial toxins by matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Howard, Karen L; Boyer, Gregory L

2007-01-01

A novel method for simplifying adduct patterns to improve the detection and identification of peptide toxins using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry is presented. Addition of 200 microM zinc sulfate heptahydrate (ZnSO(4) . 7H(2)O) to samples prior to spotting on the target enhances detection of the protonated molecule while suppressing competing adducts. This produces a highly simplified spectrum with the potential to enhance quantitative analysis, particularly for complex samples. The resulting improvement in total signal strength and reduction in the coefficient of variation (from 31.1% to 5.2% for microcystin-LR) further enhance the potential for sensitive and accurate quantitation. Other potential additives tested, including 18-crown-6 ether, alkali metal salts (lithium chloride, sodium chloride, potassium chloride), and other transition metal salts (silver chloride, silver nitrate, copper(II) nitrate, copper(II) sulfate, zinc acetate), were unable to achieve comparable results. Application of this technique to the analysis of several microcystins, potent peptide hepatotoxins from cyanobacteria, is illustrated. Copyright (c) 2007 John Wiley & Sons, Ltd.

qSR: a quantitative super-resolution analysis tool reveals the cell-cycle dependent organization of RNA Polymerase I in live human cells.

PubMed

Andrews, J O; Conway, W; Cho, W -K; Narayanan, A; Spille, J -H; Jayanth, N; Inoue, T; Mullen, S; Thaler, J; Cissé, I I

2018-05-09

We present qSR, an analytical tool for the quantitative analysis of single molecule based super-resolution data. The software is created as an open-source platform integrating multiple algorithms for rigorous spatial and temporal characterizations of protein clusters in super-resolution data of living cells. First, we illustrate qSR using a sample live cell data of RNA Polymerase II (Pol II) as an example of highly dynamic sub-diffractive clusters. Then we utilize qSR to investigate the organization and dynamics of endogenous RNA Polymerase I (Pol I) in live human cells, throughout the cell cycle. Our analysis reveals a previously uncharacterized transient clustering of Pol I. Both stable and transient populations of Pol I clusters co-exist in individual living cells, and their relative fraction vary during cell cycle, in a manner correlating with global gene expression. Thus, qSR serves to facilitate the study of protein organization and dynamics with very high spatial and temporal resolutions directly in live cell.

Qualitative and quantitative assessment of collagen and elastin in annulus fibrosus of the physiologic and scoliotic intervertebral discs.

PubMed

Kobielarz, Magdalena; Szotek, Sylwia; Głowacki, Maciej; Dawidowicz, Joanna; Pezowicz, Celina

2016-09-01

The biophysical properties of the annulus fibrosus of the intervertebral disc are determined by collagen and elastin fibres. The progression of scoliosis is accompanied by a number of pathological changes concerning these structural proteins. This is a major cause of dysfunction of the intervertebral disc. The object of the study were annulus fibrosus samples excised from intervertebral discs of healthy subjects and patients treated surgically for scoliosis in the thoracolumbar or lumbar spine. The research material was subjected to structural analysis by light microscopy and quantitative analysis of the content of collagen types I, II, III and IV as well as elastin by immunoenzymatic test (ELISA). A statistical analysis was conducted to assess the impact of the sampling site (Mann-Whitney test, α=0.05) and scoliosis (Wilcoxon matched pairs test, α=0.05) on the obtained results. The microscopic studies conducted on scoliotic annulus fibrosus showed a significant architectural distortion of collagen and elastin fibres. Quantitative biochemical assays demonstrated region-dependent distribution of only collagen types I and II in the case of healthy intervertebral discs whereas in the case of scoliotic discs region-dependent distribution concerned all examined proteins of the extracellular matrix. Comparison of scoliotic and healthy annulus fibrosus revealed a significant decrease in the content of collagen type I and elastin as well as a slight increase in the proportion of collagen types III and IV. The content of collagen type II did not differ significantly between both groups. The observed anomalies are a manifestation of degenerative changes affecting annulus fibrosus of the intervertebral disc in patients suffering from scoliosis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Unlocking Barriers to DNA Vaccine Immunogenicity: A Cross-Species Analysis of Cytosolic DNA Sensing in Skeletal Muscle Myocytes

DTIC Science & Technology

2017-10-01

CRISPR Subtask 1A: i) design and produce mammalian expression plasmids encoding the Cas9 protein and specially...duration in SOW: 2017 Q4 – 2018 Q1 Subtask 2A: i) produce mouse myocyte cell lines that have undergone gene disruption via a technique named CRISPR ii...named CRISPR ii) confirm gene disruption and GFP expression iii) select multiple individual clones characterized with quantitative gene

Supramolecular assembly affording a ratiometric two-photon fluorescent nanoprobe for quantitative detection and bioimaging.

PubMed

Wang, Peng; Zhang, Cheng; Liu, Hong-Wen; Xiong, Mengyi; Yin, Sheng-Yan; Yang, Yue; Hu, Xiao-Xiao; Yin, Xia; Zhang, Xiao-Bing; Tan, Weihong

2017-12-01

Fluorescence quantitative analyses for vital biomolecules are in great demand in biomedical science owing to their unique detection advantages with rapid, sensitive, non-damaging and specific identification. However, available fluorescence strategies for quantitative detection are usually hard to design and achieve. Inspired by supramolecular chemistry, a two-photon-excited fluorescent supramolecular nanoplatform ( TPSNP ) was designed for quantitative analysis with three parts: host molecules (β-CD polymers), a guest fluorophore of sensing probes (Np-Ad) and a guest internal reference (NpRh-Ad). In this strategy, the TPSNP possesses the merits of (i) improved water-solubility and biocompatibility; (ii) increased tissue penetration depth for bioimaging by two-photon excitation; (iii) quantitative and tunable assembly of functional guest molecules to obtain optimized detection conditions; (iv) a common approach to avoid the limitation of complicated design by adjustment of sensing probes; and (v) accurate quantitative analysis by virtue of reference molecules. As a proof-of-concept, we utilized the two-photon fluorescent probe NHS-Ad-based TPSNP-1 to realize accurate quantitative analysis of hydrogen sulfide (H 2 S), with high sensitivity and good selectivity in live cells, deep tissues and ex vivo -dissected organs, suggesting that the TPSNP is an ideal quantitative indicator for clinical samples. What's more, TPSNP will pave the way for designing and preparing advanced supramolecular sensors for biosensing and biomedicine.

A relative quantitative Methylation-Sensitive Amplified Polymorphism (MSAP) method for the analysis of abiotic stress.

PubMed

Bednarek, Piotr T; Orłowska, Renata; Niedziela, Agnieszka

2017-04-21

We present a new methylation-sensitive amplified polymorphism (MSAP) approach for the evaluation of relative quantitative characteristics such as demethylation, de novo methylation, and preservation of methylation status of CCGG sequences, which are recognized by the isoschizomers HpaII and MspI. We applied the technique to analyze aluminum (Al)-tolerant and non-tolerant control and Al-stressed inbred triticale lines. The approach is based on detailed analysis of events affecting HpaII and MspI restriction sites in control and stressed samples, and takes advantage of molecular marker profiles generated by EcoRI/HpaII and EcoRI/MspI MSAP platforms. Five Al-tolerant and five non-tolerant triticale lines were exposed to aluminum stress using the physiologicaltest. Total genomic DNA was isolated from root tips of all tolerant and non-tolerant lines before and after Al stress following metAFLP and MSAP approaches. Based on codes reflecting events affecting cytosines within a given restriction site recognized by HpaII and MspI in control and stressed samples demethylation (DM), de novo methylation (DNM), preservation of methylated sites (MSP), and preservation of nonmethylatedsites (NMSP) were evaluated. MSAP profiles were used for Agglomerative hierarchicalclustering (AHC) based on Squared Euclidean distance and Ward's Agglomeration method whereas MSAP characteristics for ANOVA. Relative quantitative MSAP analysis revealed that both Al-tolerant and non-tolerant triticale lines subjected to Al stress underwent demethylation, with demethylation of CG predominating over CHG. The rate of de novo methylation in the CG context was ~3-fold lower than demethylation, whereas de novo methylation of CHG was observed only in Al-tolerant lines. Our relative quantitative MSAP approach, based on methylation events affecting cytosines within HpaII-MspI recognition sequences, was capable of quantifying de novo methylation, demethylation, methylation, and non-methylated status in control and stressed Al-tolerant and non-tolerant triticale inbred lines. The method could also be used to analyze methylation events affecting CG and CHG contexts, which were differentially methylated under Al stress. We cannot exclude that the methylation changes revealed among lines as well as between Al-tolerant and non-tolerant groups of lines were due to some experimental errors or that the number of lines was too small for ANOVA to prove the influence of Al stress. Nevertheless, we suspect that Al tolerance in triticale could be partly regulated by epigenetic factors acting at the level of DNA methylation. This method provides a valuable tool for studies of abiotic stresses in plants.

Golgi-type I and Golgi-type II neurons in the ventral anterior thalamic nucleus of the adult human: morphological features and quantitative analysis.

PubMed

Al-Hussain Bani Hani, Saleh M; El-Dwairi, Qasim A; Bataineh, Ziad M; Al-Haidari, Mohammad S; Al-Alami, Jamil

2008-05-01

The morphological and quantitative features of neurons in the adult human ventral anterior thalamic nucleus were studied in Golgi preparations. Two neuronal types were found and their quantitative features were studied. Golgi-type I neurons were medium to large cells with dense dendritic trees and dendritic protrusions and short hair-like appendages. They have somatic mean diameter of 30.8 microm (+/-9.4, n = 85). They have an average 100.3 dendritic branches, 48.97 dendritic branching points, and 58.85 dendritic tips. The mean diameters of their primary, secondary, and tertiary dendrites were 3.1 microm (+/-1, n = 80), 1.85 microm (+/-0.8, n = 145), and 1.5 microm (+/-0.4, n = 160), respectively. Golgi-type II neurons were small to medium cells with few sparsely branching dendrites and dendritic stalked appendages with or without terminal swellings. They have somatic mean diameters of 22.2 microm (+/-5.8, n = 120). They have an average 33.76 dendritic branches, 16.49 dendritic branching points, and 21.97 dendritic tips. The mean diameters of their primary, secondary, and tertiary dendrites were 1.6 microm (+/-0.86, n = 70), 1.15 microm (+/-0.55, n = 118), and 1 microm (+/-0.70, n = 95), respectively. These quantitative data may form the basis for further quantitative studies involving aging or some degenerative diseases that may affect cell bodies and/or dendritic trees of the Golgi-type I and/or Golgi-type II thalamic neurons.

Changes in content and synthesis of collagen types and proteoglycans in osteoarthritis of the knee joint and comparison of quantitative analysis with Photoshop-based image analysis.

PubMed

Lahm, Andreas; Mrosek, Eike; Spank, Heiko; Erggelet, Christoph; Kasch, Richard; Esser, Jan; Merk, Harry

2010-04-01

The different cartilage layers vary in synthesis of proteoglycan and of the distinct types of collagen with the predominant collagen Type II with its associated collagens, e.g. types IX and XI, produced by normal chondrocytes. It was demonstrated that proteoglycan decreases in degenerative tissue and a switch from collagen type II to type I occurs. The aim of this study was to evaluate the correlation of real-time (RT)-PCR and Photoshop-based image analysis in detecting such lesions and find new aspects about their distribution. We performed immunohistochemistry and histology with cartilage tissue samples from 20 patients suffering from osteoarthritis compared with 20 healthy biopsies. Furthermore, we quantified our results on the gene expression of collagen type I and II and aggrecan with the help of real-time (RT)-PCR. Proteoglycan content was measured colorimetrically. Using Adobe Photoshop the digitized images of histology and immunohistochemistry stains of collagen type I and II were stored on an external data storage device. The area occupied by any specific colour range can be specified and compared in a relative manner directly from the histogram using the "magic wand tool" in the select similar menu. In the image grow menu gray levels or luminosity (colour) of all pixels within the selected area, including mean, median and standard deviation, etc. are depicted. Statistical Analysis was performed using the t test. With the help of immunohistochemistry, RT-PCR and quantitative RT- PCR we found that not only collagen type II, but also collagen type I is synthesized by the cells of the diseased cartilage tissue, shown by increasing amounts of collagen type I mRNA especially in the later stages of osteoarthritis. A decrease of collagen type II is visible especially in the upper fibrillated area of the advanced osteoarthritic samples, which leads to an overall decrease. Analysis of proteoglycan showed a loss of the overall content and a quite uniform staining in the different zones compared to the healthy cartilage with a classical zonal formation. Correlation analysis of the proteoglycan Photoshop measurements with the RT-PCR using Spearman correlation analysis revealed strong correlation for Safranin O and collagen type I, medium for collagen type II and glycoprotein but weak correlation between PCR aggrecan results. Photoshop-based image analysis might become a valuable supplement for well known histopathological grading systems of lesioned articular cartilage.

Dispersive liquid-liquid microextraction of lead(II) as 5-(4-dimethylaminobenzylidene) rhodanine chelates from food and water samples.

PubMed

Alothman, Zeid A; Al-Shaalan, Nora H; Habila, Mohamed A; Unsal, Yunus E; Tuzen, Mustafa; Soylak, Mustafa

2015-02-01

A dispersive liquid-liquid microextraction procedure for lead(II) as its 5-(4-dimethylaminobenzylidene) rhodanine complex has been established prior to its microsampling flame atomic absorption spectrometric determination. The influences of various analytical parameters including pH, solvent type and volume, dispersive solvent type and volume, 5-(4-dimethylaminobenzylidene) rhodanine amount, salt effect, and centrifugation time and speed were investigated. The effects of certain alkali, alkaline earth, and transition metal ions on the quantitative extraction of lead(II) were also studied. Quantitative recoveries were obtained at pH 6. The enrichment factor was calculated as 125. The detection limit for lead is 1.1 μg/L. The accuracy of the method was tested with the additions recovery test and analysis of the standard reference materials (SPS-WW2 waste water, NIST SRM 1515 apple leaves, and TMDA-51.3 fortified water). Applications of the present procedure were tested by analyzing water and food samples.

Histopathological image analysis of chemical-induced hepatocellular hypertrophy in mice.

PubMed

Asaoka, Yoshiji; Togashi, Yuko; Mutsuga, Mayu; Imura, Naoko; Miyoshi, Tomoya; Miyamoto, Yohei

2016-04-01

Chemical-induced hepatocellular hypertrophy is frequently observed in rodents, and is mostly caused by the induction of phase I and phase II drug metabolic enzymes and peroxisomal lipid metabolic enzymes. Liver weight is a sensitive and commonly used marker for detecting hepatocellular hypertrophy, but is also increased by a number of other factors. Histopathological observations subjectively detect changes such as hepatocellular hypertrophy based on the size of a hepatocyte. Therefore, quantitative microscopic observations are required to evaluate histopathological alterations objectively. In the present study, we developed a novel quantitative method for an image analysis of hepatocellular hypertrophy using liver sections stained with hematoxylin and eosin, and demonstrated its usefulness for evaluating hepatocellular hypertrophy induced by phenobarbital (a phase I and phase II enzyme inducer) and clofibrate (a peroxisomal enzyme inducer) in mice. The algorithm of this imaging analysis was designed to recognize an individual hepatocyte through a combination of pixel-based and object-based analyses. Hepatocellular nuclei and the surrounding non-hepatocellular cells were recognized by the pixel-based analysis, while the areas of the recognized hepatocellular nuclei were then expanded until they ran against their expanding neighboring hepatocytes and surrounding non-hepatocellular cells by the object-based analysis. The expanded area of each hepatocellular nucleus was regarded as the size of an individual hepatocyte. The results of this imaging analysis showed that changes in the sizes of hepatocytes corresponded with histopathological observations in phenobarbital and clofibrate-treated mice, and revealed a correlation between hepatocyte size and liver weight. In conclusion, our novel image analysis method is very useful for quantitative evaluations of chemical-induced hepatocellular hypertrophy. Copyright © 2015 Elsevier GmbH. All rights reserved.

The life sciences mass spectrometry research unit.

PubMed

Hopfgartner, Gérard; Varesio, Emmanuel

2012-01-01

The Life Sciences Mass Spectrometry (LSMS) research unit focuses on the development of novel analytical workflows based on innovative mass spectrometric and software tools for the analysis of low molecular weight compounds, peptides and proteins in complex biological matrices. The present article summarizes some of the recent work of the unit: i) the application of matrix-assisted laser desorption/ionization (MALDI) for mass spectrometry imaging (MSI) of drug of abuse in hair, ii) the use of high resolution mass spectrometry for simultaneous qualitative/quantitative analysis in drug metabolism and metabolomics, and iii) the absolute quantitation of proteins by mass spectrometry using the selected reaction monitoring mode.

Fast Potentiometric Analysis of Lead in Aqueous Medium under Competitive Conditions Using an Acridono-Crown Ether Neutral Ionophore.

PubMed

Golcs, Ádám; Horváth, Viola; Huszthy, Péter; Tóth, Tünde

2018-05-03

Lead is a particularly toxic heavy metal that is present above acceptable levels in the water of many countries. This article describes a quick detection method of lead(II) ions using a polyvinyl chloride (PVC)-based ion-selective membrane electrode containing an acridono-crown ether ionophore by potentiometry. The electrochemical cell exhibits a Nernstian response for lead(II) ions between the concentration range of 10 −4 to 10 −2 M, and can be used in the pH range of 4⁻7. The applicability of this sensor was verified by measuring a multicomponent aqueous sample. Under the given conditions, this electrode is suitable for the selective quantitative analysis of lead(II) ions in the presence of many additional metal ions.

Ultrastructural and mechanical changes in tubular epithelial cells by angiotensin II and aldosterone as observed with atomic force microscopy.

PubMed

Quan, Fu-Shi; Jeong, Kyung Hwan; Lee, Gi-Ja

2018-07-01

Tubular epithelial cells (TECs) play an important pathophysiological role in the promotion of renal fibrosis. Quantitative analysis of the mechanical changes in TECs may be helpful in evaluating novel pharmacological strategies. Atomic force microscopy (AFM) is a common nanotechnology tool used for imaging and measuring interaction forces in biological systems. In this study, we used AFM to study ultrastructural and mechanical changes in TECs mediated by the renin-angiotensin-aldosterone system. We quantitatively analyzed changes in the mechanical properties of TECs using three extrinsic factors, namely, chemical fixation, angiotensin II (AT II), and aldosterone (AD). Fixed TECs were 11 times stiffer at the cell body and 3 times stiffer at the cell-cell junction compared to live TECs. After stimulation with AT II, live TECs were four times stiffer at the junctional area than at the cell body, while fixed TECs after AT II stimulation were approximately two times stiffer at the both cell body and cell-cell junction compared to fixed unstimulated TECs. Fixed TECs also reflected changes in the mechanical properties of TECs at the cell body region after AD stimulation. Together, our results suggest that cell stiffness at the cell body region may serve as an effective index for evaluating drugs and stimulation, regardless of whether the cells are live or fixed at the time of analysis. In addition, studying the changes to the intrinsic mechanical property of TECs after application of external stimuli may be useful for investigating pathophysiologic mechanisms and effective therapeutic strategies for renal injury. Copyright © 2018 Elsevier Ltd. All rights reserved.

Synthesis, characterization and analytical applications of Ni(II)-ion imprinted polymer

NASA Astrophysics Data System (ADS)

Singh, D. K.; Mishra, Shraddha

2010-10-01

Ion recognition-based separation techniques have received much attention because of their high selectivity for target ions. In this study, we have prepared a novel ion imprinted polymer (IIP) to remove nickel ions with high selectivity. The imprinted polymer was prepared by copolymerization of 2-hydroxy ethyl methacrylate (HEMA) with nickel vinylbenzoate complex in the presence of ethylene glycol dimethacrylate (EGDMA) as a crosslinker. The polymerization was carried out in bulk with free radical initiation using 2-methoxy ethanol as a solvent and porogen. The adsorbed nickel was completely eluted with 15 mL of 1 M HCl. Control polymer was also prepared by similar experimental conditions without using imprint ion. The above synthesized polymers were characterized by surface area measurements, FT-IR, microanalysis and SEM analysis. The adsorption capacity of IIP and CP was found to be 1.51 and 0.65 mmol g -1, respectively. The optimal pH for quantitative enrichment was 6.5. Nature of eluent, eluent concentration and eluent volume were also studied. The relative selectivity factor ( αr) values of Ni(II)/Zn(II), Ni(II)/Cu(II) and Ni(II)/Co(II) were 78.6, 111.1 and 91.6, respectively. Five replicate determinations of 30 μg L -1 of Ni(II) gave a mean absorbance of 0.067 with a relative standard deviation of 1.06%. The lowest concentration determined by GTA-AAS below which the recovery becomes non-quantitative is 6 μg L -1. IIP was tested for removal of Ni(II) from sea water sample.

Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy.

PubMed

Zhao, Ziqing W; Roy, Rahul; Gebhardt, J Christof M; Suter, David M; Chapman, Alec R; Xie, X Sunney

2014-01-14

Superresolution microscopy based on single-molecule centroid determination has been widely applied to cellular imaging in recent years. However, quantitative imaging of the mammalian nucleus has been challenging due to the lack of 3D optical sectioning methods for normal-sized cells, as well as the inability to accurately count the absolute copy numbers of biomolecules in highly dense structures. Here we report a reflected light-sheet superresolution microscopy method capable of imaging inside the mammalian nucleus with superior signal-to-background ratio as well as molecular counting with single-copy accuracy. Using reflected light-sheet superresolution microscopy, we probed the spatial organization of transcription by RNA polymerase II (RNAP II) molecules and quantified their global extent of clustering inside the mammalian nucleus. Spatiotemporal clustering analysis that leverages on the blinking photophysics of specific organic dyes showed that the majority (>70%) of the transcription foci originate from single RNAP II molecules, and no significant clustering between RNAP II molecules was detected within the length scale of the reported diameter of "transcription factories." Colocalization measurements of RNAP II molecules equally labeled by two spectrally distinct dyes confirmed the primarily unclustered distribution, arguing against a prevalent existence of transcription factories in the mammalian nucleus as previously proposed. The methods developed in our study pave the way for quantitative mapping and stoichiometric characterization of key biomolecular species deep inside mammalian cells.

Experimental and theoretical analysis of a rare nitrato bridged 3d-4f complex containing LaZn2 core synthesized from a Zn(II) metalloligand

NASA Astrophysics Data System (ADS)

Sreejith, S. S.; Mohan, Nithya; Kurup, M. R. Prathapachandra

2018-02-01

A trinulcear Zn2La Schiff base complex was synthesized using slow-solvent evaporation technique from a Zn(II) mononuclear metalloligand by 2:1 addition with La(NO3)3 salt. Single crystal XRD analysis revealed a rare nitrato bridged trinuclear entity which is seldom seen in these class of ligand systems. Qualitative and quantitative analysis of intermolecular interactions/short contacts were done using Hirshfeld surface and 2D finger print analysis. The thermally stable, blue luminescent compound exhibits internal heavy atom effect thereby quenching the emission intensity of the ligand. DFT calculations were performed on the compound to analyze frontier orbitals and also ESP plots were used to monitor nucleophilic/electrophilic regions on the compound and its implications on hydrogen bonding. A comparison of the bond orders and atomic charges on the trinuclear compound and the Zn(II) metalloligand precursor was performed to substantiate the formation of the trinuclear product through ligand exchange.

Quantitative option analysis for implementation and management of landfills.

PubMed

Kerestecioğlu, Merih

2016-09-01

The selection of the most feasible strategy for implementation of landfills is a challenging step. Potential implementation options of landfills cover a wide range, from conventional construction contracts to the concessions. Montenegro, seeking to improve the efficiency of the public services while maintaining affordability, was considering privatisation as a way to reduce public spending on service provision. In this study, to determine the most feasible model for construction and operation of a regional landfill, a quantitative risk analysis was implemented with four steps: (i) development of a global risk matrix; (ii) assignment of qualitative probabilities of occurrences and magnitude of impacts; (iii) determination of the risks to be mitigated, monitored, controlled or ignored; (iv) reduction of the main risk elements; and (v) incorporation of quantitative estimates of probability of occurrence and expected impact for each risk element in the reduced risk matrix. The evaluated scenarios were: (i) construction and operation of the regional landfill by the public sector; (ii) construction and operation of the landfill by private sector and transfer of the ownership to the public sector after a pre-defined period; and (iii) operation of the landfill by the private sector, without ownership. The quantitative risk assessment concluded that introduction of a public private partnership is not the most feasible option, unlike the common belief in several public institutions in developing countries. A management contract for the first years of operation was advised to be implemented, after which, a long term operating contract may follow. © The Author(s) 2016.

Matching Microscopic and Macroscopic Responses in Glasses.

PubMed

Baity-Jesi, M; Calore, E; Cruz, A; Fernandez, L A; Gil-Narvion, J M; Gordillo-Guerrero, A; Iñiguez, D; Maiorano, A; Marinari, E; Martin-Mayor, V; Monforte-Garcia, J; Muñoz-Sudupe, A; Navarro, D; Parisi, G; Perez-Gaviro, S; Ricci-Tersenghi, F; Ruiz-Lorenzo, J J; Schifano, S F; Seoane, B; Tarancon, A; Tripiccione, R; Yllanes, D

2017-04-14

We first reproduce on the Janus and Janus II computers a milestone experiment that measures the spin-glass coherence length through the lowering of free-energy barriers induced by the Zeeman effect. Secondly, we determine the scaling behavior that allows a quantitative analysis of a new experiment reported in the companion Letter [S. Guchhait and R. Orbach, Phys. Rev. Lett. 118, 157203 (2017)].PRLTAO0031-900710.1103/PhysRevLett.118.157203 The value of the coherence length estimated through the analysis of microscopic correlation functions turns out to be quantitatively consistent with its measurement through macroscopic response functions. Further, nonlinear susceptibilities, recently measured in glass-forming liquids, scale as powers of the same microscopic length.

Biosorption of Microelements by Spirulina: Towards Technology of Mineral Feed Supplements

PubMed Central

Chojnacka, Katarzyna

2014-01-01

Surface characterization and metal ion adsorption properties of Spirulina sp. and Spirulina maxima were verified by various instrumental techniques. FTIR spectroscopy and potentiometric titration were used for qualitative and quantitative determination of metal ion-binding groups. Comparative FTIR spectra of natural and Cu(II)-treated biomass proved involvement of both phosphoryl and sulfone groups in metal ions sorption. The potentiometric titration data analysis provided the best fit with the model assuming the presence of three types of surface functional groups and the carboxyl group as the major binding site. The mechanism of metal ions biosorption was investigated by comparing the results from multielemental analyses by ICP-OES and SEM-EDX. Biosorption of Cu(II), Mn(II), Zn(II), and Co(II) ions by lyophilized Spirulina sp. was performed to determine the metal affinity relationships for single- and multicomponent systems. Obtained results showed the replacement of naturally bound ions: Na(I), K(I), or Ca(II) with sorbed metal ions in a descending order of Mn(II) > Cu(II) > Zn(II) > Co(II) for single- and Cu(II) > Mn(II) > Co(II) > Zn(II) for multicomponent systems, respectively. Surface elemental composition of natural and metal-loaded material was determined both by ICP-OES and SEM-EDX analysis, showing relatively high value of correlation coefficient between the concentration of Na(I) ions in algal biomass. PMID:25386594

21 CFR 514.1 - Applications.

Code of Federal Regulations, 2011 CFR

2011-04-01

... post office address of, and must be countersigned by, an authorized attorney, agent, or official... pharmacologically related drugs. (c) Description of dosage form and quantitative composition. (ii) Scientific... quantitative statement of composition. Reasonable alternatives for any listed component may be specified. (ii...

21 CFR 514.1 - Applications.

Code of Federal Regulations, 2010 CFR

2010-04-01

... post office address of, and must be countersigned by, an authorized attorney, agent, or official... pharmacologically related drugs. (c) Description of dosage form and quantitative composition. (ii) Scientific... quantitative statement of composition. Reasonable alternatives for any listed component may be specified. (ii...

21 CFR 514.1 - Applications.

Code of Federal Regulations, 2012 CFR

2012-04-01

... post office address of, and must be countersigned by, an authorized attorney, agent, or official... pharmacologically related drugs. (c) Description of dosage form and quantitative composition. (ii) Scientific... quantitative statement of composition. Reasonable alternatives for any listed component may be specified. (ii...

21 CFR 514.1 - Applications.

Code of Federal Regulations, 2014 CFR

2014-04-01

... post office address of, and must be countersigned by, an authorized attorney, agent, or official... pharmacologically related drugs. (c) Description of dosage form and quantitative composition. (ii) Scientific... quantitative statement of composition. Reasonable alternatives for any listed component may be specified. (ii...

21 CFR 514.1 - Applications.

Code of Federal Regulations, 2013 CFR

2013-04-01

... post office address of, and must be countersigned by, an authorized attorney, agent, or official... pharmacologically related drugs. (c) Description of dosage form and quantitative composition. (ii) Scientific... quantitative statement of composition. Reasonable alternatives for any listed component may be specified. (ii...

Multispectral colour analysis for quantitative evaluation of pseudoisochromatic color deficiency tests

NASA Astrophysics Data System (ADS)

Ozolinsh, Maris; Fomins, Sergejs

2010-11-01

Multispectral color analysis was used for spectral scanning of Ishihara and Rabkin color deficiency test book images. It was done using tunable liquid-crystal LC filters built in the Nuance II analyzer. Multispectral analysis keeps both, information on spatial content of tests and on spectral content. Images were taken in the range of 420-720nm with a 10nm step. We calculated retina neural activity charts taking into account cone sensitivity functions, and processed charts in order to find the visibility of latent symbols in color deficiency plates using cross-correlation technique. In such way the quantitative measure is found for each of diagnostics plate for three different color deficiency carrier types - protanopes, deutanopes and tritanopes. Multispectral color analysis allows to determine the CIE xyz color coordinates of pseudoisochromatic plate design elements and to perform statistical analysis of these data to compare the color quality of available color deficiency test books.

AGE-RELATED DIFFERENCES IN SUSCEPTIBILITY TO CARCINOGENESIS II, APPROACHES FOR APPLICATION AND UNCERTAINTY ANALYSES FOR INDIVIDUAL GENETICALLY ACTING CARCINOGENS

EPA Science Inventory

An earlier paper (Hattis et al., 2003) developed a quantitative likelihood-based statistical analysis of the differences in apparent sensitivity of rodents to mutagenic carcinogens across three life stages (fetal, birth-weaning, and weaning-60 days) relative to exposures in adult...

Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy

PubMed Central

Zhao, Ziqing W.; Roy, Rahul; Gebhardt, J. Christof M.; Suter, David M.; Chapman, Alec R.; Xie, X. Sunney

2014-01-01

Superresolution microscopy based on single-molecule centroid determination has been widely applied to cellular imaging in recent years. However, quantitative imaging of the mammalian nucleus has been challenging due to the lack of 3D optical sectioning methods for normal-sized cells, as well as the inability to accurately count the absolute copy numbers of biomolecules in highly dense structures. Here we report a reflected light-sheet superresolution microscopy method capable of imaging inside the mammalian nucleus with superior signal-to-background ratio as well as molecular counting with single-copy accuracy. Using reflected light-sheet superresolution microscopy, we probed the spatial organization of transcription by RNA polymerase II (RNAP II) molecules and quantified their global extent of clustering inside the mammalian nucleus. Spatiotemporal clustering analysis that leverages on the blinking photophysics of specific organic dyes showed that the majority (>70%) of the transcription foci originate from single RNAP II molecules, and no significant clustering between RNAP II molecules was detected within the length scale of the reported diameter of “transcription factories.” Colocalization measurements of RNAP II molecules equally labeled by two spectrally distinct dyes confirmed the primarily unclustered distribution, arguing against a prevalent existence of transcription factories in the mammalian nucleus as previously proposed. The methods developed in our study pave the way for quantitative mapping and stoichiometric characterization of key biomolecular species deep inside mammalian cells. PMID:24379392

Qualitative and quantitative interpretation of SEM image using digital image processing.

PubMed

Saladra, Dawid; Kopernik, Magdalena

2016-10-01

The aim of the this study is improvement of qualitative and quantitative analysis of scanning electron microscope micrographs by development of computer program, which enables automatic crack analysis of scanning electron microscopy (SEM) micrographs. Micromechanical tests of pneumatic ventricular assist devices result in a large number of micrographs. Therefore, the analysis must be automatic. Tests for athrombogenic titanium nitride/gold coatings deposited on polymeric substrates (Bionate II) are performed. These tests include microshear, microtension and fatigue analysis. Anisotropic surface defects observed in the SEM micrographs require support for qualitative and quantitative interpretation. Improvement of qualitative analysis of scanning electron microscope images was achieved by a set of computational tools that includes binarization, simplified expanding, expanding, simple image statistic thresholding, the filters Laplacian 1, and Laplacian 2, Otsu and reverse binarization. Several modifications of the known image processing techniques and combinations of the selected image processing techniques were applied. The introduced quantitative analysis of digital scanning electron microscope images enables computation of stereological parameters such as area, crack angle, crack length, and total crack length per unit area. This study also compares the functionality of the developed computer program of digital image processing with existing applications. The described pre- and postprocessing may be helpful in scanning electron microscopy and transmission electron microscopy surface investigations. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Quantitative analysis of pulmonary pathophysiology using postmortem computed tomography with regard to the cause of death.

PubMed

Michiue, Tomomi; Sakurai, Terumi; Ishikawa, Takaki; Oritani, Shigeki; Maeda, Hitoshi

2012-07-10

Radiological lung transparency depends on the air contents involved in respiratory function. The present study quantitatively investigated postmortem lung air distribution in forensic autopsy cases (n=135) using computed tomography (CT) to analyze cardiopulmonary pathophysiology in the death process, involving emphysema, congestion and edema. Combined analyses of the CT morphology and attenuation value (Hounsfield unit, HU) of the bilateral lungs, with reference to histopathology, could categorize CT findings (10-90 percentile mode/mean HU values) with regard to the causes of death as follows: (I) hyperaeration (mode/mean HU below -760/-560: emphysema) for obstructive pulmonary disease, starvation and hypothermia (cold exposure); (II) mostly normal aeration with partial ground glass opacification (mode/mean HU, -850 to -360/-700 to -380: partial congestion and edema), consisting of subtype II-a with peri-bronchial/-vascular opacity for mechanical asphyxia, drowning and fire fatality, and subtype II-b with decreased vascularity for gunshot head injury, cerebrovascular disease and hemopericardium; (III) hypoaeration to airless with predominant hypostatic ground glass opacification (mode/mean HU, -870 to 0/-720 to -200: mottled hypostatic congestion and edema) for blunt head/neck injury, intoxication, hyperthermia (heat stroke) and congestive heart failure; (IV) hypoaeration to airless with predominant hypostatic consolidation (mode/mean HU, -790 to 0/-520 to -70: intense hypostatic congestion with edema) for acute ischemic heart disease; and (V) airless to consolidated (mode/mean HU over -420/-370: segmental or multiple patchy consolidations with edema) for pneumonia. Mode HU represents the major alveolar status, while the mean HU reflects the whole lung air contents. CT data analysis is useful for quantitative evaluation of pulmonary pathology as a supplementary procedure. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

DNA-protein crosslinking by trans-platinum(II)diamminedichloride in mammalian cells, a new method of analysis.

PubMed

Kohn, K W; Ewig, R A

1979-03-28

DNA-protien crosslinks produced in mouse leukemia L1210 cells by trans-Pt(II)diamminedichloride were quantitated using the technique of DNA alkaline elution. DNA single-strand segments that were or were not linked to protein were separable into distinct components by alkaline elution after exposure of the cells to 2--15 kR of X-ray. Protein-linked DNA strands were separated on the basis of their retention of filters at pH 12 while free DNA strands of the size generated by 2--15 kR of X-ray passed rapidly through the filters. The retention of protein-linked DNA strands was attributable to adsorption of protein to the filter under the conditions of alkaline elution. The results obeyed a simple quantitative model according to which the frequency of DNA-protein crosslinks could be calculated.

Linkage study of the low-density lipoprotein-receptor gene and cholesterol levels in an Afrikaner family. Quantitative genetics and identification of a minor founder effect.

PubMed

Brink, P A; Brink, L T; Torrington, M; Bester, A J

1990-03-17

Overlap of clinical and biochemical characteristics between hypercholesterolaemia in members of the general population and familial hypercholesterolaemic (FH) individuals may lead to misdiagnosis. Quantitative analysis of family data may circumvent this problem. A way of looking for an association between plasma cholesterol levels and restriction fragment length polymorphism markers (RFLP) on the low-density lipoprotein (LDL) receptor gene by using reference cholesterol distributions was explored. Linkage, with a logarithm of the odds (LOD) score of 6.8 at theta 0, was detected between cholesterol levels and the LDL receptor in an extended Afrikaner family. Two RFLP-haplotypes, one previously found in a majority of Afrikaner FH homozygotes, and a second, Stu I-, BstE II+, Pvu II+, Nco I+, were associated with high cholesterol levels in this pedigree.

The onset of Wolf-Rayet wind outflow and the nature of the hot component in the symbiotic nova PU Vulpecula

NASA Technical Reports Server (NTRS)

Sion, Edward M.; Shore, Steven N.; Ready, Christian J.; Scheible, Maureen P.

1993-01-01

We have analyzed temporal variations in the far ultraviolet He II (1640), Si IV (1393, 1402), and C IV (1548, 1550) line profiles in eight high dispersion, International Ultraviolet Explorer Short Wavelength Prime spectra of the symbiotic nova PU Vul by comparatively examining these profiles on a common velocity scale. We see clear evidence of the onset of a Wolf-Rayet-like wind outflow from the bloated, contracting white dwarf hot component with terminal velocity of approximately equals -550 to -600 km/s. We have quantitatively analyzed the complicated He II (1640) emission region for the first time and show that the discrete absorption features seen in the He II region occur at precisely the same velocites in each spectrum, thus demonstrating that the absorbing source is steady and not affected by any orbital motion. We demonstrate that there is an underlying He II wind emission feature whose true shape is hidden by superposed absorption due to the foreground red giant wind flowing in front of the white dwarf and abscuring the white dwarf's wind outflow. We present synthetic spectra of He II emission behind an absorbing slab with u = 20 km/s, T = 5000 K, and column densities in the range N = 1 x 10(exp 22) and 1 x 10(exp 23)/sq cm which explain these absorptions. Our analysis of the Si IV and C IV resonance doublets, in velocity space, reveal temporal variations in the profile between 1987 and 1991 with the emergence of clear P Cygni profiles in Si IV by 1990. A nebular emission feature in C III 1909 also appears in the most recent spectra (e.g., SW42538H) while it was absent or extremely weak in the earliest spectra (e.g., SW36332H), thus strengthening evidence that the nebular emission, as seen in permitted and semiforbidden lines, intensities in step with the onset of the hot, fast, wind outflow. We also report the first detection of narrow interstellar (circumbinary shell?) absorption lines near -1 km/s, most strongly in Al III (1854, 1862) and Si IV (1392, 1402). We have carried out a rough quantitative analysis of the He II wind emission by using the theoretical He II Wolf-Rayet profiles of Hamann & Schmutz (1987). We obtain a lower limit to the He II net emission equivalent width of approximately 1 A, a hot component temperature in the range 25,000 to 35,000 K, a hot component radius in the range 5 solar radius to 30 solar radius, a maximum wind velocity of approximately equals -600 km/s and a rough upper limit to the mass-loss rate of less than 1 x 10(exp -5) solar mass/yr. To our knowledge, this is the first quantitative wind analysis, albeit crude, to be carried out for the hot component of a symbiotic nova or symbiotic variable.

The effects of Wechsler Intelligence Scale for Children-Fourth Edition cognitive abilities on math achievement.

PubMed

Parkin, Jason R; Beaujean, A Alexander

2012-02-01

This study used structural equation modeling to examine the effect of Stratum III (i.e., general intelligence) and Stratum II (i.e., Comprehension-Knowledge, Fluid Reasoning, Short-Term Memory, Processing Speed, and Visual Processing) factors of the Cattell-Horn-Carroll (CHC) cognitive abilities, as operationalized by the Wechsler Intelligence Scale for Children, Fourth Edition (WISC-IV; Wechsler, 2003a) subtests, on Quantitative Knowledge, as operationalized by the Wechsler Individual Achievement Test, Second Edition (WIAT-II; Wechsler, 2002) subtests. Participants came from the WISC-IV/WIAT-II linking sample (n=550). We compared models that predicted Quantitative Knowledge using only Stratum III factors, only Stratum II factors, and both Stratum III and Stratum II factors. Results indicated that the model with only the Stratum III factor predicting Quantitative Knowledge best fit the data. Copyright © 2011 Society for the Study of School Psychology. Published by Elsevier Ltd. All rights reserved.

Measuring social interaction in music ensembles

PubMed Central

D'Ausilio, Alessandro; Badino, Leonardo; Camurri, Antonio; Fadiga, Luciano

2016-01-01

Music ensembles are an ideal test-bed for quantitative analysis of social interaction. Music is an inherently social activity, and music ensembles offer a broad variety of scenarios which are particularly suitable for investigation. Small ensembles, such as string quartets, are deemed a significant example of self-managed teams, where all musicians contribute equally to a task. In bigger ensembles, such as orchestras, the relationship between a leader (the conductor) and a group of followers (the musicians) clearly emerges. This paper presents an overview of recent research on social interaction in music ensembles with a particular focus on (i) studies from cognitive neuroscience; and (ii) studies adopting a computational approach for carrying out automatic quantitative analysis of ensemble music performances. PMID:27069054

Measuring social interaction in music ensembles.

PubMed

Volpe, Gualtiero; D'Ausilio, Alessandro; Badino, Leonardo; Camurri, Antonio; Fadiga, Luciano

2016-05-05

Music ensembles are an ideal test-bed for quantitative analysis of social interaction. Music is an inherently social activity, and music ensembles offer a broad variety of scenarios which are particularly suitable for investigation. Small ensembles, such as string quartets, are deemed a significant example of self-managed teams, where all musicians contribute equally to a task. In bigger ensembles, such as orchestras, the relationship between a leader (the conductor) and a group of followers (the musicians) clearly emerges. This paper presents an overview of recent research on social interaction in music ensembles with a particular focus on (i) studies from cognitive neuroscience; and (ii) studies adopting a computational approach for carrying out automatic quantitative analysis of ensemble music performances. © 2016 The Author(s).

Estimating weak ratiometric signals in imaging data. II. Meta-analysis with multiple, dual-channel datasets.

PubMed

Sornborger, Andrew; Broder, Josef; Majumder, Anirban; Srinivasamoorthy, Ganesh; Porter, Erika; Reagin, Sean S; Keith, Charles; Lauderdale, James D

2008-09-01

Ratiometric fluorescent indicators are used for making quantitative measurements of a variety of physiological variables. Their utility is often limited by noise. This is the second in a series of papers describing statistical methods for denoising ratiometric data with the aim of obtaining improved quantitative estimates of variables of interest. Here, we outline a statistical optimization method that is designed for the analysis of ratiometric imaging data in which multiple measurements have been taken of systems responding to the same stimulation protocol. This method takes advantage of correlated information across multiple datasets for objectively detecting and estimating ratiometric signals. We demonstrate our method by showing results of its application on multiple, ratiometric calcium imaging experiments.

Bovine serum albumin-Cu(II) hybrid nanoflowers: An effective adsorbent for solid phase extraction and slurry sampling flame atomic absorption spectrometric analysis of cadmium and lead in water, hair, food and cigarette samples.

PubMed

Yilmaz, Erkan; Ocsoy, Ismail; Ozdemir, Nalan; Soylak, Mustafa

2016-02-04

Herein, the synthesis of bovine serum albumin-Cu(II) hybrid nanoflowers (BSA-NFs) through the building blocks of bovine serum albumin (BSA) and copper(II) ions in phosphate buffered saline (PBS) and their use as adsorbent for cadmium and lead ions are reported. The BSA-NFs, for the first time, were efficiently utilized as novel adsorbent for solid phase extraction (SPE) of cadmium and lead ions in water, food, cigarette and hair samples. The method is based on the separation and pre-concentration of Cd(II) and Pb(II) by BSA-NFs prior to determination by slurry analysis via flame atomic absorption spectrometry (FAAS). The analytes were adsorbed on BSA-NFs under the vortex mixing and then the ion-loaded slurry was separated and directly introduced into the flame AAS nebulizer by using a hand-made micro sample introduction system to eliminate a number of drawbacks. The effects of analytical key parameters, such as pH, amount of BSA-NFs, vortexing time, sample volume, and matrix effect of foreign ions on adsorbing of Cd(II) and Pb(II) were systematically investigated and optimized. The limits of detection (LODs) for Cd(II) and Pb(II) were calculated as 0.37 μg L(-)(1) and 8.8 μg L(-)(1), respectively. The relative standard deviation percentages (RSDs) (N = 5) for Cd(II) and Pb(II) were 7.2%, and 5.0%, respectively. The accuracy of the developed procedure was validated by the analysis of certified reference materials (TMDA-53.3 Fortified Water, TMDA-70 Fortified Water, SPS-WW2 Waste Water, NCSDC-73349 Bush Branches and Leaves) and by addition/recovery analysis. The quantitative recoveries were obtained for the analysis of certified reference materials and addition/recovery tests. The method was successfully applied to the analysis of cadmium and lead in water, food, cigarette and hair samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Simultaneous determination of bifonazole and tinctures of calendula flower in pharmaceutical creams by reversed-phase liquid chromatography.

PubMed

Ferreyra, Carola F; Ortiz, Cristina S

2005-01-01

The aim of this research was to develop and validate a sensitive, rapid, easy, and precise reversed-phase liquid chromatography (LC) method for stability studies of bifonazole (I) formulated with tinctures of calendula flower (II). The method was especially developed for the analysis and quantitative determination of I and II in pure and combined forms in cream pharmaceutical formulations without using gradient elution and at room temperature. The influence on the stability of compound I of temperature, artificial radiation, and drug II used for the new pharmaceutical design was evaluated. The LC separation was carried out using a Supelcosil LC-18 column (25 cm x 4.6 mm id, 5 microm particle size); the mobile phase was composed of methanol-0.1 M ammonium acetate buffer (85 + 15, v/v) pumped isocratically at a flow rate of 1 mL/min; and ultraviolet detection was at 254 nm. The analysis time was less than 10 min. Calibration graphs were found to be linear in the 0.125-0.375 mg/mL (rI = 0.9991) and 0.639-1.916 mg/mL (rII = 0.9995) ranges for I and II, respectively. The linearity, precision, recovery, and limits of detection and quantification were satisfactory for I and II. The results obtained suggested that the developed LC method is selective and specific for the analysis of I and II in pharmaceutical products, and that it can be applied to stability studies.

Exploring the interactome: microfluidic isolation of proteins and interacting partners for quantitative analysis by electron microscopy.

PubMed

Giss, Dominic; Kemmerling, Simon; Dandey, Venkata; Stahlberg, Henning; Braun, Thomas

2014-05-20

Multimolecular protein complexes are important for many cellular processes. However, the stochastic nature of the cellular interactome makes the experimental detection of complex protein assemblies difficult and quantitative analysis at the single molecule level essential. Here, we present a fast and simple microfluidic method for (i) the quantitative isolation of endogenous levels of untagged protein complexes from minute volumes of cell lysates under close to physiological conditions and (ii) the labeling of specific components constituting these complexes. The method presented uses specific antibodies that are conjugated via a photocleavable linker to magnetic beads that are trapped in microcapillaries to immobilize the target proteins. Proteins are released by photocleavage, eluted, and subsequently analyzed by quantitative transmission electron microscopy at the single molecule level. Additionally, before photocleavage, immunogold can be employed to label proteins that interact with the primary target protein. Thus, the presented method provides a new way to study the interactome and, in combination with single molecule transmission electron microscopy, to structurally characterize the large, dynamic, heterogeneous multimolecular protein complexes formed.

Development and psychometric properties of a new social support scale for self-care in middle-aged patients with type II diabetes (S4-MAD)

PubMed Central

2012-01-01

Background Social support has proved to be one of the most effective factors on the success of diabetic self-care. This study aimed to develop a scale for evaluating social support for self-care in middle-aged patients (30–60 years old) with type II diabetes. Methods This was a two-phase qualitative and quantitative study. The study was conducted during 2009 to 2011 in Tehran, Iran. In the qualitative part, a sample of diabetic patients participated in four focus group discussions in order to develop a preliminary item pool. Consequently, content and face validity were performed to provide a pre-final version of the questionnaire. Then, in a quantitative study, reliability (internal consistency and test-retest analysis), validity and factor analysis (both exploratory and confirmatory) were performed to assess psychometric properties of the scale. Results A 38-item questionnaire was developed through the qualitative phase. It was reduced to a 33-item after content validity. Exploratory factor analysis loaded a 30-item with a five-factor solution (nutrition, physical activity, self monitoring of blood glucose, foot care and smoking) that jointly accounted for 72.3% of observed variance. The confirmatory factor analysis indicated a good fit to the data. The Cronbach’s alpha coefficient showed excellent internal consistency (alpha=0.94), and test-retest of the scale with 2-weeks intervals indicated an appropriate stability for the scale (ICC=0.87). Conclusion The findings showed that the designed questionnaire was a valid and reliable instrument for measuring social support for self-care in middle-aged patients with type II diabetes. It is an easy to use questionnaire and contains the most significant diabetes related behaviors that need continuous support for self-care. PMID:23190685

PyXRF: Python-based X-ray fluorescence analysis package

NASA Astrophysics Data System (ADS)

Li, Li; Yan, Hanfei; Xu, Wei; Yu, Dantong; Heroux, Annie; Lee, Wah-Keat; Campbell, Stuart I.; Chu, Yong S.

2017-09-01

We developed a python-based fluorescence analysis package (PyXRF) at the National Synchrotron Light Source II (NSLS-II) for the X-ray fluorescence-microscopy beamlines, including Hard X-ray Nanoprobe (HXN), and Submicron Resolution X-ray Spectroscopy (SRX). This package contains a high-level fitting engine, a comprehensive commandline/ GUI design, rigorous physics calculations, and a visualization interface. PyXRF offers a method of automatically finding elements, so that users do not need to spend extra time selecting elements manually. Moreover, PyXRF provides a convenient and interactive way of adjusting fitting parameters with physical constraints. This will help us perform quantitative analysis, and find an appropriate initial guess for fitting. Furthermore, we also create an advanced mode for expert users to construct their own fitting strategies with a full control of each fitting parameter. PyXRF runs single-pixel fitting at a fast speed, which opens up the possibilities of viewing the results of fitting in real time during experiments. A convenient I/O interface was designed to obtain data directly from NSLS-II's experimental database. PyXRF is under open-source development and designed to be an integral part of NSLS-II's scientific computation library.

The FAQUIRE Approach: FAst, QUantitative, hIghly Resolved and sEnsitivity Enhanced 1H, 13C Data.

PubMed

Farjon, Jonathan; Milande, Clément; Martineau, Estelle; Akoka, Serge; Giraudeau, Patrick

2018-02-06

The targeted analysis of metabolites in complex mixtures is a challenging issue. NMR is one of the major tools in this field, but there is a strong need for more sensitive, better-resolved, and faster quantitative methods. In this framework, we introduce the concept of FAst, QUantitative, hIghly Resolved and sEnsitivity enhanced (FAQUIRE) NMR to push forward the limits of metabolite NMR analysis. 2D 1 H, 13 C 2D quantitative maps are promising alternatives for enhancing the spectral resolution but are highly time-consuming because of (i) the intrinsic nature of 2D, (ii) the longer recycling times required for quantitative conditions, and (iii) the higher number of scans needed to reduce the level of detection/quantification to access low concentrated metabolites. To reach this aim, speeding up the recently developed QUantItative Perfected and pUre shifted HSQC (QUIPU HSQC) is an interesting attempt to develop the FAQUIRE concept. Thanks to the combination of spectral aliasing, nonuniform sampling, and variable repetition time, the acquisition time of 2D quantitative maps is reduced by a factor 6 to 9, while conserving a high spectral resolution thanks to a pure shift approach. The analytical potential of the new Quick QUIPU HSQC (Q QUIPU HSQC) is evaluated on a model metabolite sample, and its potential is shown on breast-cell extracts embedding metabolites at millimolar to submillimolar concentrations.

Opportunism or aquatic specialization? Evidence of freshwater fish exploitation at Ohalo II- A waterlogged Upper Paleolithic site

PubMed Central

Dayan, Tamar; Goren, Menachem; Nadel, Dani; Hershkovitz, Israel

2018-01-01

Analysis of ca. 17,000 fish remains recovered from the late Upper Paleolithic/early Epi-Paleolithic (LGM; 23,000 BP) waterlogged site of Ohalo II (Rift Valley, Israel) provides new insights into the role of wetland habitats and the fish inhabiting them during the evolution of economic strategies prior to the agricultural evolution. Of the current 19 native fish species in Lake Kinneret (Sea of Galilee), eight species were identified at Ohalo II, belonging to two freshwater families: Cyprinidae (carps) and Cichlidae (St. Peter fish). Employing a large set of quantitative and qualitative criteria (NISP, species richness, diversity, skeletal element representation, fragmentation, color, spatial distribution, etc.), we demonstrate that the inhabitants of Ohalo II used their knowledge of the breeding behavior of different species of fish, for year-round intensive exploitation. PMID:29912923

Opportunism or aquatic specialization? Evidence of freshwater fish exploitation at Ohalo II- A waterlogged Upper Paleolithic site.

PubMed

Zohar, Irit; Dayan, Tamar; Goren, Menachem; Nadel, Dani; Hershkovitz, Israel

2018-01-01

Analysis of ca. 17,000 fish remains recovered from the late Upper Paleolithic/early Epi-Paleolithic (LGM; 23,000 BP) waterlogged site of Ohalo II (Rift Valley, Israel) provides new insights into the role of wetland habitats and the fish inhabiting them during the evolution of economic strategies prior to the agricultural evolution. Of the current 19 native fish species in Lake Kinneret (Sea of Galilee), eight species were identified at Ohalo II, belonging to two freshwater families: Cyprinidae (carps) and Cichlidae (St. Peter fish). Employing a large set of quantitative and qualitative criteria (NISP, species richness, diversity, skeletal element representation, fragmentation, color, spatial distribution, etc.), we demonstrate that the inhabitants of Ohalo II used their knowledge of the breeding behavior of different species of fish, for year-round intensive exploitation.

Real-time PCR to determine transgene copy number and to quantitate the biolocalization of adoptively transferred cells from EGFP-transgenic mice.

PubMed

Joshi, Molishree; Keith Pittman, H; Haisch, Carl; Verbanac, Kathryn

2008-09-01

Quantitative real-time PCR (qPCR) is a sensitive technique for the detection and quantitation of specific DNA sequences. Here we describe a Taqman qPCR assay for quantification of tissue-localized, adoptively transferred enhanced green fluorescent protein (EGFP)-transgenic cells. A standard curve constructed from serial dilutions of a plasmid containing the EGFP transgene was (i) highly reproducible, (ii) detected as few as two copies, and (iii) was included in each qPCR assay. qPCR analysis of genomic DNA was used to determine transgene copy number in several mouse strains. Fluorescent microscopy of tissue sections showed that adoptively transferred vascular endothelial cells (VEC) from EGFP-transgenic mice specifically localized to tissue with metastatic tumors in syngeneic recipients. VEC microscopic enumeration of liver metastases strongly correlated with qPCR analysis of identical sections (Pearson correlation 0.81). EGFP was undetectable in tissue from control mice by qPCR. In another study using intra-tumor EGFP-VEC delivery to subcutaneous tumors, manual cell count and qPCR analysis of alternating sections also strongly correlated (Pearson correlation 0.82). Confocal microscopy of the subcutaneous tumor sections determined that visual fluorescent signals were frequently tissue artifacts. This qPCR methodology offers specific, objective, and rapid quantitation, uncomplicated by tissue autofluorescence, and should be readily transferable to other in vivo models to quantitate the biolocalization of transplanted cells.

Correlation of quantitative sensorimotor tractography with clinical grade of cerebral palsy.

PubMed

Trivedi, Richa; Agarwal, Shruti; Shah, Vipul; Goyel, Puneet; Paliwal, Vimal K; Rathore, Ram K S; Gupta, Rakesh K

2010-08-01

The purpose of this study was to determine whether tract-specific diffusion tensor imaging measures in somatosensory and motor pathways correlate with clinical grades as defined using the Gross Motor Function Classification System (GMFCS) in cerebral palsy (CP) children. Quantitative diffusion tensor tractography was performed on 39 patients with spastic quadriparesis (mean age = 8 years) and 14 age/sex-matched controls. All patients were graded on the basis of GMFCS scale into grade II (n = 12), grade IV (n = 22), and grade V (n = 5) CP and quantitative analysis reconstruction of somatosensory and motor tracts performed. Significant inverse correlation between clinical grade and fractional anisotropy (FA) was observed in both right and left motor and sensory tracts. A significant direct correlation of mean diffusivity values from both motor and sensory tracts was also observed with clinical grades. Successive decrease in FA values was observed in all tracts except for left motor tracts moving from age/sex-matched controls to grade V through grades II and IV. We conclude that white matter tracts from both the somatosensory and the motor cortex play an important role in the pathophysiology of motor disability in patients with CP.

Symposium II: Mechanochemistry in Materials Science, MRS Fall Meeting, Nov 30-Dec 4, 2009, Boston, MA

DTIC Science & Technology

2010-09-02

Dynamic Mechanical Analysis (DMA). The fracture behavior of the mechanophore-linked polymer is also examined through the Double Cleavage Drilled ...multinary complex structures. Structural, microstructural, and chemical characterizations were explored by metrological tools to support this...simple hydrocarbons in order to quantitatively define structure-property relationships for reacting materials under shock compression. Embedded gauge

A Local Vision on Soil Hydrology (John Dalton Medal Lecture)

NASA Astrophysics Data System (ADS)

Roth, K.

2012-04-01

After shortly looking back to some research trails of the past decades, and touching on the role of soils in our environmental machinery, a vision on the future of soil hydrology is offered. It is local in the sense of being based on limited experience as well as in the sense of focussing on local spatial scales, from 1 m to 1 km. Cornerstones of this vision are (i) rapid developments of quantitative observation technology, illustrated with the example of ground-penetrating radar (GPR), and (ii) the availability of ever more powerful compute facilities which allow to simulate increasingly complicated model representations in unprecedented detail. Together, they open a powerful and flexible approach to the quantitative understanding of soil hydrology where two lines are fitted: (i) potentially diverse measurements of the system of interest and their analysis and (ii) a comprehensive model representation, including architecture, material properties, forcings, and potentially unknown aspects, together with the same analysis as for (i). This approach pushes traditional inversion to operate on analyses, not on the underlying state variables, and to become flexible with respect to architecture and unknown aspects. The approach will be demonstrated for simple situations at test sites.

Quantitative T2 Magnetic Resonance Imaging Compared to Morphological Grading of the Early Cervical Intervertebral Disc Degeneration: An Evaluation Approach in Asymptomatic Young Adults

PubMed Central

Han, Zhihua; Shao, Lixin; Xie, Yan; Wu, Jianhong; Zhang, Yan; Xin, Hongkui; Ren, Aijun; Guo, Yong; Wang, Deli; He, Qing; Ruan, Dike

2014-01-01

Objective The objective of this study was to evaluate the efficacy of quantitative T2 magnetic resonance imaging (MRI) for quantifying early cervical intervertebral disc (IVD) degeneration in asymptomatic young adults by correlating the T2 value with Pfirrmann grade, sex, and anatomic level. Methods Seventy asymptomatic young subjects (34 men and 36 women; mean age, 22.80±2.11 yr; range, 18–25 years) underwent 3.0-T MRI to obtain morphological data (one T1-fast spin echo (FSE) and three-plane T2-FSE, used to assign a Pfirrmann grade (I–V)) and for T2 mapping (multi-echo spin echo). T2 values in the nucleus pulposus (NP, n = 350) and anulus fibrosus (AF, n = 700) were obtained. Differences in T2 values between sexes and anatomic level were evaluated, and linear correlation analysis of T2 values versus degenerative grade was conducted. Findings Cervical IVDs of healthy young adults were commonly determined to be at Pfirrmann grades I and II. T2 values of NPs were significantly higher than those of AF at all anatomic levels (P<0.000). The NP, anterior AF and posterior AF values did not differ significantly between genders at the same anatomic level (P>0.05). T2 values decreased linearly with degenerative grade. Linear correlation analysis revealed a strong negative association between the Pfirrmann grade and the T2 values of the NP (P = 0.000) but not the T2 values of the AF (P = 0.854). However, non-degenerated discs (Pfirrmann grades I and II) showed a wide range of T2 relaxation time. T2 values according to disc degeneration level classification were as follows: grade I (>62.03 ms), grade II (54.60–62.03 ms), grade III (<54.60 ms). Conclusions T2 quantitation provides a more sensitive and robust approach for detecting and characterizing the early stage of cervical IVD degeneration and to create a reliable quantitative in healthy young adults. PMID:24498384

Quantitative T2 magnetic resonance imaging compared to morphological grading of the early cervical intervertebral disc degeneration: an evaluation approach in asymptomatic young adults.

PubMed

Chen, Chun; Huang, Minghua; Han, Zhihua; Shao, Lixin; Xie, Yan; Wu, Jianhong; Zhang, Yan; Xin, Hongkui; Ren, Aijun; Guo, Yong; Wang, Deli; He, Qing; Ruan, Dike

2014-01-01

The objective of this study was to evaluate the efficacy of quantitative T2 magnetic resonance imaging (MRI) for quantifying early cervical intervertebral disc (IVD) degeneration in asymptomatic young adults by correlating the T2 value with Pfirrmann grade, sex, and anatomic level. Seventy asymptomatic young subjects (34 men and 36 women; mean age, 22.80±2.11 yr; range, 18-25 years) underwent 3.0-T MRI to obtain morphological data (one T1-fast spin echo (FSE) and three-plane T2-FSE, used to assign a Pfirrmann grade (I-V)) and for T2 mapping (multi-echo spin echo). T2 values in the nucleus pulposus (NP, n = 350) and anulus fibrosus (AF, n = 700) were obtained. Differences in T2 values between sexes and anatomic level were evaluated, and linear correlation analysis of T2 values versus degenerative grade was conducted. Cervical IVDs of healthy young adults were commonly determined to be at Pfirrmann grades I and II. T2 values of NPs were significantly higher than those of AF at all anatomic levels (P<0.000). The NP, anterior AF and posterior AF values did not differ significantly between genders at the same anatomic level (P>0.05). T2 values decreased linearly with degenerative grade. Linear correlation analysis revealed a strong negative association between the Pfirrmann grade and the T2 values of the NP (P = 0.000) but not the T2 values of the AF (P = 0.854). However, non-degenerated discs (Pfirrmann grades I and II) showed a wide range of T2 relaxation time. T2 values according to disc degeneration level classification were as follows: grade I (>62.03 ms), grade II (54.60-62.03 ms), grade III (<54.60 ms). T2 quantitation provides a more sensitive and robust approach for detecting and characterizing the early stage of cervical IVD degeneration and to create a reliable quantitative in healthy young adults.

Evaluating the association of common APOA2 variants with type 2 diabetes

PubMed Central

Duesing, Konsta; Charpentier, Guillaume; Marre, Michel; Tichet, Jean; Hercberg, Serge; Balkau, Beverley; Froguel, Philippe; Gibson, Fernando

2009-01-01

Background APOA2 is a positional and biological candidate gene for type 2 diabetes at the chromosome 1q21-q24 susceptibility locus. The aim of this study was to examine if HapMap phase II tag SNPs in APOA2 are associated with type 2 diabetes and quantitative traits in French Caucasian subjects. Methods We genotyped the three HapMap phase II tagging SNPs (rs6413453, rs5085 and rs5082) required to capture the common variation spanning the APOA2 locus in our type 2 diabetes case-control cohort comprising 3,093 French Caucasian subjects. The association between these variants and quantitative traits was also examined in the normoglycaemic adults of the control cohort. In addition, meta-analysis of publicly available whole genome association data was performed. Results None of the APOA2 tag SNPs were associated with type 2 diabetes in the French Caucasian case-control cohort (rs6413453, P = 0.619; rs5085, P = 0.245; rs5082, P = 0.591). However, rs5082 was marginally associated with total cholesterol levels (P = 0.026) and waist-to-hip ratio (P = 0.029). The meta-analysis of data from 12,387 subjects confirmed our finding that common variation at the APOA2 locus is not associated with type 2 diabetes. Conclusion The available data does not support a role for common variants in APOA2 on type 2 diabetes susceptibility or related quantitative traits in Northern Europeans. PMID:19216768

Evaluating the association of common APOA2 variants with type 2 diabetes.

PubMed

Duesing, Konsta; Charpentier, Guillaume; Marre, Michel; Tichet, Jean; Hercberg, Serge; Balkau, Beverley; Froguel, Philippe; Gibson, Fernando

2009-02-13

APOA2 is a positional and biological candidate gene for type 2 diabetes at the chromosome 1q21-q24 susceptibility locus. The aim of this study was to examine if HapMap phase II tag SNPs in APOA2 are associated with type 2 diabetes and quantitative traits in French Caucasian subjects. We genotyped the three HapMap phase II tagging SNPs (rs6413453, rs5085 and rs5082) required to capture the common variation spanning the APOA2 locus in our type 2 diabetes case-control cohort comprising 3,093 French Caucasian subjects. The association between these variants and quantitative traits was also examined in the normoglycaemic adults of the control cohort. In addition, meta-analysis of publicly available whole genome association data was performed. None of the APOA2 tag SNPs were associated with type 2 diabetes in the French Caucasian case-control cohort (rs6413453, P = 0.619; rs5085, P = 0.245; rs5082, P = 0.591). However, rs5082 was marginally associated with total cholesterol levels (P = 0.026) and waist-to-hip ratio (P = 0.029). The meta-analysis of data from 12,387 subjects confirmed our finding that common variation at the APOA2 locus is not associated with type 2 diabetes. The available data does not support a role for common variants in APOA2 on type 2 diabetes susceptibility or related quantitative traits in Northern Europeans.

Waveguide analysis of heat-drawn and chemically etched probe tips for scanning near-field optical microscopy.

PubMed

Moar, Peter N; Love, John D; Ladouceur, François; Cahill, Laurence W

2006-09-01

We analyze two basic aspects of a scanning near-field optical microscope (SNOM) probe's operation: (i) spot-size evolution of the electric field along the probe with and without a metal layer, and (ii) a modal analysis of the SNOM probe, particularly in close proximity to the aperture. A slab waveguide model is utilized to minimize the analytical complexity, yet provides useful quantitative results--including losses associated with the metal coating--which can then be used as design rules.

CALIPSO: an interactive image analysis software package for desktop PACS workstations

NASA Astrophysics Data System (ADS)

Ratib, Osman M.; Huang, H. K.

1990-07-01

The purpose of this project is to develop a low cost workstation for quantitative analysis of multimodality images using a Macintosh II personal computer. In the current configuration the Macintosh operates as a stand alone workstation where images are imported either from a central PACS server through a standard Ethernet network or recorded through video digitizer board. The CALIPSO software developed contains a large variety ofbasic image display and manipulation tools. We focused our effort however on the design and implementation ofquantitative analysis methods that can be applied to images from different imaging modalities. Analysis modules currently implemented include geometric and densitometric volumes and ejection fraction calculation from radionuclide and cine-angiograms Fourier analysis ofcardiac wall motion vascular stenosis measurement color coded parametric display of regional flow distribution from dynamic coronary angiograms automatic analysis ofmyocardial distribution ofradiolabelled tracers from tomoscintigraphic images. Several of these analysis tools were selected because they use similar color coded andparametric display methods to communicate quantitative data extracted from the images. 1. Rationale and objectives of the project Developments of Picture Archiving and Communication Systems (PACS) in clinical environment allow physicians and radiologists to assess radiographic images directly through imaging workstations (''). This convenient access to the images is often limited by the number of workstations available due in part to their high cost. There is also an increasing need for quantitative analysis ofthe images. During thepast decade

Cancer imaging phenomics toolkit: quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.

PubMed

Davatzikos, Christos; Rathore, Saima; Bakas, Spyridon; Pati, Sarthak; Bergman, Mark; Kalarot, Ratheesh; Sridharan, Patmaa; Gastounioti, Aimilia; Jahani, Nariman; Cohen, Eric; Akbari, Hamed; Tunc, Birkan; Doshi, Jimit; Parker, Drew; Hsieh, Michael; Sotiras, Aristeidis; Li, Hongming; Ou, Yangming; Doot, Robert K; Bilello, Michel; Fan, Yong; Shinohara, Russell T; Yushkevich, Paul; Verma, Ragini; Kontos, Despina

2018-01-01

The growth of multiparametric imaging protocols has paved the way for quantitative imaging phenotypes that predict treatment response and clinical outcome, reflect underlying cancer molecular characteristics and spatiotemporal heterogeneity, and can guide personalized treatment planning. This growth has underlined the need for efficient quantitative analytics to derive high-dimensional imaging signatures of diagnostic and predictive value in this emerging era of integrated precision diagnostics. This paper presents cancer imaging phenomics toolkit (CaPTk), a new and dynamically growing software platform for analysis of radiographic images of cancer, currently focusing on brain, breast, and lung cancer. CaPTk leverages the value of quantitative imaging analytics along with machine learning to derive phenotypic imaging signatures, based on two-level functionality. First, image analysis algorithms are used to extract comprehensive panels of diverse and complementary features, such as multiparametric intensity histogram distributions, texture, shape, kinetics, connectomics, and spatial patterns. At the second level, these quantitative imaging signatures are fed into multivariate machine learning models to produce diagnostic, prognostic, and predictive biomarkers. Results from clinical studies in three areas are shown: (i) computational neuro-oncology of brain gliomas for precision diagnostics, prediction of outcome, and treatment planning; (ii) prediction of treatment response for breast and lung cancer, and (iii) risk assessment for breast cancer.

Quantitative structure activity relationship studies of sulfamide derivatives as carbonic anhydrase inhibitor: as antiglaucoma agents.

PubMed

Kumar, Surendra; Singh, Vineet; Tiwari, Meena

2007-07-01

Selective inhibition of ciliary process enzyme i.e. Carbonic Anhydrase-II is an excellent approach in reducing elevated intraocular pressure, thus treating glaucoma. Due to characteristic physicochemical properties of sulphonamide (Inhibition of Carbonic Anhydrase), they are clinically effective against glaucoma. But the non-specificity of sulphonamide derivatives to isozyme, leads to a range of side effects. Presently, the absence of comparative studies related to the binding of the sulphonamides as inhibitors to CA isozymes limits their use. In this paper we have represented "Three Dimensional Quantitative Structure Activity Relationship" study to characterize structural features of Sulfamide derivative [RR'NSO(2)NH(2)] as inhibitors, that are required for selective binding of carbonic anhydrase isozymes (CAI and CAII). In the analysis, stepwise multiple linear regression was performed using physiochemical parameters as independent variable and CA-I and CA-II inhibitory activity as dependent variable, respectively. The best multiparametric QSAR model obtained for CA-I inhibitory activity shows good statistical significance (r= 0.9714) and predictability (Q(2)=0.8921), involving the Electronic descriptors viz. Highest Occupied Molecular Orbital, Lowest Unoccupied Molecular Orbital and Steric descriptors viz. Principal moment of Inertia at X axis. Similarly, CA-II inhibitory activity also shows good statistical significance (r=0.9644) and predictability (Q(2)=0.8699) involving aforementioned descriptors. The predictive power of the model was successfully tested externally using a set of six compounds as test set for CA-I inhibitory activity and a set of seven compounds in case of CA-II inhibitory activity with good predictive squared correlation coefficient, r(2)(pred)=0.6016 and 0.7662, respectively. Overview of analysis favours substituents with high electronegativity and less bulk at R and R' positions of the parent nucleus, provides a basis to design new Sulfamide derivatives possessing potent and selective carbonic anhydrase-II inhibitory activity.

New Methods for Analysis of Spatial Distribution and Coaggregation of Microbial Populations in Complex Biofilms

PubMed Central

Almstrand, Robert; Daims, Holger; Persson, Frank; Sörensson, Fred

2013-01-01

In biofilms, microbial activities form gradients of substrates and electron acceptors, creating a complex landscape of microhabitats, often resulting in structured localization of the microbial populations present. To understand the dynamic interplay between and within these populations, quantitative measurements and statistical analysis of their localization patterns within the biofilms are necessary, and adequate automated tools for such analyses are needed. We have designed and applied new methods for fluorescence in situ hybridization (FISH) and digital image analysis of directionally dependent (anisotropic) multispecies biofilms. A sequential-FISH approach allowed multiple populations to be detected in a biofilm sample. This was combined with an automated tool for vertical-distribution analysis by generating in silico biofilm slices and the recently developed Inflate algorithm for coaggregation analysis of microbial populations in anisotropic biofilms. As a proof of principle, we show distinct stratification patterns of the ammonia oxidizers Nitrosomonas oligotropha subclusters I and II and the nitrite oxidizer Nitrospira sublineage I in three different types of wastewater biofilms, suggesting niche differentiation between the N. oligotropha subclusters, which could explain their coexistence in the same biofilms. Coaggregation analysis showed that N. oligotropha subcluster II aggregated closer to Nitrospira than did N. oligotropha subcluster I in a pilot plant nitrifying trickling filter (NTF) and a moving-bed biofilm reactor (MBBR), but not in a full-scale NTF, indicating important ecophysiological differences between these phylogenetically closely related subclusters. By using high-resolution quantitative methods applicable to any multispecies biofilm in general, the ecological interactions of these complex ecosystems can be understood in more detail. PMID:23892743

[Prognostic value of chosen parameters of mechanical and bioelectrical uterine activity in prediction of threatening preterm labour].

PubMed

Zietek, Jerzy; Sikora, Jerzy; Horoba, Krzysztof; Matonia, Adam; Jezewski, Janusz; Magnucki, Jacek; Kobielska, Lucyna

2009-03-01

To record and analyse bioelectrical activity of the uterine muscle in the course of physiological pregnancy, labour and threatening premature labour; to define which parameters from the analysis of both electrohysterogram and mechanical activity signal allow us to predict threatening premature labour. Material comprised 62 pregnant women: Group I--27 patients in their first physiological pregnancy, Group II--21 patients in their first pregnancy with symptoms of threatening premature labour, and Group III--14 patients in the first labour period. The on-line analysis of the mechanical (TOCO) and electrical (EHG) contraction activity relied on determination of quantitative parameters of detected uterine contractions. The obtained statistical results demonstrated a possibility to differentiate between Group I and II through the amplitude and contraction area for EHG signal, and only the contraction amplitude for TOCO signal. Additionally, significant differentiating parameters for electrohysterogram are: contraction power and its median frequency. Analyzing Group I and III, significant differences were noted for contraction amplitude and area obtained both from EHG and TOCO signals. Similarly, the contraction power (from EHG) enables us to assign the contractions either to records from Group I or to labour type. There was no significant difference noted between Group II and III. Identification of pregnant women at risk of premature labour should lead to their inclusion in rigorous perinatal surveillance. This requires novel, more sensitive methods that are able to detect early symptoms of the uterine contraction activity increase. Electrohysterography provides complete information on principles of bioelectrical uterine activity. Quantitative parameters of EHG analysis enable the detection of records (contractions) with the symptoms of premature uterine contraction activity.

Quality-by-Design II: Application of Quantitative Risk Analysis to the Formulation of Ciprofloxacin Tablets.

PubMed

Claycamp, H Gregg; Kona, Ravikanth; Fahmy, Raafat; Hoag, Stephen W

2016-04-01

Qualitative risk assessment methods are often used as the first step to determining design space boundaries; however, quantitative assessments of risk with respect to the design space, i.e., calculating the probability of failure for a given severity, are needed to fully characterize design space boundaries. Quantitative risk assessment methods in design and operational spaces are a significant aid to evaluating proposed design space boundaries. The goal of this paper is to demonstrate a relatively simple strategy for design space definition using a simplified Bayesian Monte Carlo simulation. This paper builds on a previous paper that used failure mode and effects analysis (FMEA) qualitative risk assessment and Plackett-Burman design of experiments to identity the critical quality attributes. The results show that the sequential use of qualitative and quantitative risk assessments can focus the design of experiments on a reduced set of critical material and process parameters that determine a robust design space under conditions of limited laboratory experimentation. This approach provides a strategy by which the degree of risk associated with each known parameter can be calculated and allocates resources in a manner that manages risk to an acceptable level.

42 CFR 431.424 - Evaluation requirements.

Code of Federal Regulations, 2012 CFR

2012-10-01

... evaluations. Demonstration evaluations will include the following: (1) Quantitative research methods. (i... of appropriate evaluation strategies (including experimental and other quantitative and qualitative... demonstration. (ii) CMS will consider alternative evaluation designs when quantitative designs are technically...

42 CFR 431.424 - Evaluation requirements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... evaluations. Demonstration evaluations will include the following: (1) Quantitative research methods. (i... of appropriate evaluation strategies (including experimental and other quantitative and qualitative... demonstration. (ii) CMS will consider alternative evaluation designs when quantitative designs are technically...

42 CFR 431.424 - Evaluation requirements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... evaluations. Demonstration evaluations will include the following: (1) Quantitative research methods. (i... of appropriate evaluation strategies (including experimental and other quantitative and qualitative... demonstration. (ii) CMS will consider alternative evaluation designs when quantitative designs are technically...

Speciation of Mn(II), Mn(VII) and total manganese in water and food samples by coprecipitation-atomic absorption spectrometry combination.

PubMed

Citak, Demirhan; Tuzen, Mustafa; Soylak, Mustafa

2010-01-15

A speciation procedure based on the coprecipitation of manganese(II) with zirconium(IV) hydroxide has been developed for the investigation of levels of manganese species. The determination of manganese levels was performed by flame atomic absorption spectrometry (FAAS). Total manganese was determined after the reduction of Mn(VII) to Mn(II) by ascorbic acid. The analytical parameters including pH, amount of zirconium(IV), sample volume, etc., were investigated for the quantitative recoveries of manganese(II). The effects of matrix ions were also examined. The recoveries for manganese(II) were in the range of 95-98%. Preconcentration factor was calculated as 50. The detection limit for the analyte ions based on 3 sigma (n=21) was 0.75 microg L(-1) for Mn(II). The relative standard deviation was found to be lower than 7%. The validation of the presented procedure was performed by analysis of certified reference material having different matrices, NIST SRM 1515 (Apple Leaves) and NIST SRM 1568a (Rice Flour). The procedure was successfully applied to natural waters and food samples.

Immunohistochemichal Assessment of the CrkII Proto-oncogene Expression in Common Malignant Salivary Gland Tumors and Pleomorphic Adenoma.

PubMed

Askari, Mitra; Darabi, Masoud; Jahanzad, Esa; Mostakhdemian Hosseini, Zahra; Musavi Chavoshi, Marjan; Darabi, Maryam

2015-01-01

Background and aims. Various morphologies are seen in different salivary gland tumorsor within an individual tumor, and the lesions show divers biological behaviors. Experimental results support the hypothesis that increased CrkII proto-oncogene is associated with cytokine-induced tumor initiation and progression by altering cell motility signaling pathway. The aim of this study was to assess the CrkII expression in common malignant salivary gland tumors and pleomorphic ade-noma. Materials and methods. Immunohistochemical analysis of CrkII expression was performed on paraffin blocks of 64 car-cinomas of salivary glands, 10 pleomorphic adenomas, and 10 normal salivary glands. Biopsies were subjected to immu-nostaining with EnVision detection system using monoclonal anti-CrkII. Evaluation of immunoreactivity of CrkII was based on the immunoreaction intensity and percentage of stained tumor cells which were scored semi-quantitatively on a scale with four grades 0 to 3. Kruskal-wallis test and additional Mann-Whitney statistical test were used for analysis of CrkII expression levels. Results. Increased expression of CrkII was seen (P=0.005) in malignant tumors including: mucoepidermoid carcinoma, adenoid cystic carcinoma, and carcinoma ex pleomorphic adenoma, but CrkII expression in acinic cell carcinoma was weak. CrkII expression in pleomorphic adenoma was weak or negative. A weak staining was sparsely seen in normal acinar serous cell. Conclusion. Increased expression of CrkII and its higher intensity of staining in tumors with more aggressive biologic behavior in carcinomas of salivary gland is consistent with a role for this proto-oncogene in salivary gland tumorigenesis and cancer progression.

75 FR 9488 - Basel Comprehensive Quantitative Impact Study

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-02

... DEPARTMENT OF THE TREASURY Office of Thrift Supervision Basel Comprehensive Quantitative Impact... Quantitative Impact Study. OMB Number: 1550-0NEW. Form Numbers: N/A. Regulation requirement: 12 CFR Part 567... Basel II Capital Accord, the Basel Committee will conduct a quantitative impact study (QIS) to assess...

Advances in the detection of as in environmental samples using low energy X-ray fluorescence in a scanning transmission X-ray microscope: arsenic immobilization by an Fe(II)-oxidizing freshwater bacteria.

PubMed

Hitchcock, A P; Obst, M; Wang, J; Lu, Y S; Tyliszczak, T

2012-03-06

Speciation and quantitative mapping of elements, organic and inorganic compounds, and mineral phases in environmental samples at high spatial resolution is needed in many areas of geobiochemistry and environmental science. Scanning transmission X-ray microscopes (STXMs) provide a focused beam which can interrogate samples at a fine spatial scale. Quantitative chemical information can be extracted using the transmitted and energy-resolved X-ray fluorescence channels simultaneously. Here we compare the relative merits of transmission and low-energy X-ray fluorescence detection of X-ray absorption for speciation and quantitative analysis of the spatial distribution of arsenic(V) within cell-mineral aggregates formed by Acidovorax sp. strain BoFeN1, an anaerobic nitrate-reducing Fe(II)-oxidizing β-proteobacteria isolated from the sediments of Lake Constance. This species is noted to be highly tolerant to high levels of As(V). Related, As-tolerant Acidovorax-strains have been found in As-contaminated groundwater wells in Bangladesh and Cambodia wherein they might influence the mobility of As by providing sorption sites which might have different properties as compared to chemically formed Fe-minerals. In addition to demonstrating the lower detection limits that are achieved with X-ray fluorescence relative to transmission detection in STXM, this study helps to gain insights into the mechanisms of As immobilization by biogenic Fe-mineral formation and to further the understanding of As-resistance of anaerobic Fe(II)-oxidizing bacteria.

In-depth quantitative analysis of the microstructures produced by Surface Mechanical Attrition Treatment (SMAT)

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

Samih, Y., E-mail: youssef.samih@univ-lorraine.fr; Université de Lorraine, Laboratory of Excellence on Design of Alloy Metals for low-mAss Structures; Beausir, B.

2013-09-15

Electron BackScattered Diffraction (EBSD) maps are used to characterize quantitatively the graded microstructure formed by Surface Mechanical Attrition Treatment (SMAT) and applied here to the 316L stainless steel. In particular, the analysis of GNDs – coupled with relevant and reliable criteria – was used to depict the thickness of each zone identified in the SMAT-affected layers: (i) the “ultrafine grain” (UFG) zone present at the extreme top surface, (ii), the “transition zone” where grains were fragmented under the heavy plastic deformation and, finally, (iii) the “deformed zone” where initial grains are simply deformed. The interest of this procedure is illustratedmore » through the comparative analysis of the effect of some SMAT processing parameters (amplitude of vibration and treatment duration). The UFG and transition zones are more significantly modified than the overall affected thickness under our tested conditions. - Highlights: • EBSD maps are used to characterize quantitatively the microstructure of SMAT treated samples. • Calculation of the GND density to quantify strain gradients • A new method to depict the different zone thicknesses in the SMAT affected layer • Effects of SMAT processing parameters on the surface microstructure evolution.« less

Quantitative Analysis of Ca, Mg, and K in the Roots of Angelica pubescens f. biserrata by Laser-Induced Breakdown Spectroscopy Combined with Artificial Neural Networks

NASA Astrophysics Data System (ADS)

Wang, J.; Shi, M.; Zheng, P.; Xue, Sh.; Peng, R.

2018-03-01

Laser-induced breakdown spectroscopy has been applied for the quantitative analysis of Ca, Mg, and K in the roots of Angelica pubescens Maxim. f. biserrata Shan et Yuan used in traditional Chinese medicine. Ca II 317.993 nm, Mg I 517.268 nm, and K I 769.896 nm spectral lines have been chosen to set up calibration models for the analysis using the external standard and artificial neural network methods. The linear correlation coefficients of the predicted concentrations versus the standard concentrations of six samples determined by the artificial neural network method are 0.9896, 0.9945, and 0.9911 for Ca, Mg, and K, respectively, which are better than for the external standard method. The artificial neural network method also gives better performance comparing with the external standard method for the average and maximum relative errors, average relative standard deviations, and most maximum relative standard deviations of the predicted concentrations of Ca, Mg, and K in the six samples. Finally, it is proved that the artificial neural network method gives better performance compared to the external standard method for the quantitative analysis of Ca, Mg, and K in the roots of Angelica pubescens.

WHERE HAVE OUR PEOPLE GONE SEQUESTRATION’S EFFECTS ON DOD HUMAN CAPITAL

DTIC Science & Technology

2017-06-01

the research will only add to the discussion on how any future budget cuts will be applied in the future. QUANTITATIVE ANALYSIS & DISCUSSION ON...Kevin T. Boutwell, GS-13, USAF A Research Report Submitted to the Faculty In Partial Fulfillment of the Graduation Requirements...ii Disclaimer The views expressed in this academic research paper are those of the author and do not reflect

1H, 13C, 15N NMR analysis of sildenafil base and citrate (Viagra) in solution, solid state and pharmaceutical dosage forms.

PubMed

Wawer, Iwona; Pisklak, Maciej; Chilmonczyk, Zdzisław

2005-08-10

Sildenafil citrate (SC) (Viagra) and sildenafil base in pure form are easily and unequivocally characterized by multinuclear NMR spectroscopy. Analysis of chemical shifts indicates that: (i) N6-H forms intramolecular hydrogen bonds, (ii) N25 is protonated in the salt and (iii) intermolecular OH...N hydrogen bonds involving N2 and N4 are present in the solid sildenafil citrate. 13C CPMAS NMR method has been proposed for the identification and quantitation of Viagra in its pharmaceutical formulations.

Use of the pH sensitive fluorescence probe pyranine to monitor internal pH changes in Escherichia coli membrane vesicles.

PubMed

Damiano, E; Bassilana, M; Rigaud, J L; Leblanc, G

1984-01-23

Measurements of the fluorescent properties of 8-hydroxy-1,3,6-pyrenetrisulfonate (pyranine) enclosed within the internal space of Escherichia coli membrane vesicles enable recordings and quantitative analysis of: (i) changes in intravesicular pH taking place during oxidation of electron donors by the membrane respiratory chain; (ii) transient alkalization of the internal aqueous space resulting from the creation of outwardly directed acetate diffusion gradients across the vesicular membrane. Quantitation of the fluorescence variations recorded during the creation of transmembrane acetate gradients shows a close correspondence between the measured shifts in internal pH value and those expected from the amplitude of the imposed acetate gradients.

Spatiotemporal changes of seismic attenuation caused by injected CO2 at the Frio-II pilot site, Dayton, TX, USA

NASA Astrophysics Data System (ADS)

Zhu, Tieyuan; Ajo-Franklin, Jonathan B.; Daley, Thomas M.

2017-09-01

A continuous active source seismic monitoring data set was collected with crosswell geometry during CO2 injection at the Frio-II brine pilot, near Liberty, TX. Previous studies have shown that spatiotemporal changes in the P wave first arrival time reveal the movement of the injected CO2 plume in the storage zone. To further constrain the CO2 saturation, particularly at higher saturation levels, we investigate spatial-temporal changes in the seismic attenuation of the first arrivals. The attenuation changes over the injection period are estimated by the amount of the centroid frequency shift computed by local time-frequency analysis. We observe that (1) at receivers above the injection zone seismic attenuation does not change in a physical trend; (2) at receivers in the injection zone attenuation sharply increases following injection and peaks at specific points varying with distributed receivers, which is consistent with observations from time delays of first arrivals; then, (3) attenuation decreases over the injection time. The attenuation change exhibits a bell-shaped pattern during CO2 injection. Under Frio-II field reservoir conditions, White's patchy saturation model can quantitatively explain both the P wave velocity and attenuation response observed. We have combined the velocity and attenuation change data in a crossplot format that is useful for model-data comparison and determining patch size. Our analysis suggests that spatial-temporal attenuation change is not only an indicator of the movement and saturation of CO2 plumes, even at large saturations, but also can quantitatively constrain CO2 plume saturation when used jointly with seismic velocity.

A quantitative benefit-risk assessment approach to improve decision making in drug development: Application of a multicriteria decision analysis model in the development of combination therapy for overactive bladder.

PubMed

de Greef-van der Sandt, I; Newgreen, D; Schaddelee, M; Dorrepaal, C; Martina, R; Ridder, A; van Maanen, R

2016-04-01

A multicriteria decision analysis (MCDA) approach was developed and used to estimate the benefit-risk of solifenacin and mirabegron and their combination in the treatment of overactive bladder (OAB). The objectives were 1) to develop an MCDA tool to compare drug effects in OAB quantitatively, 2) to establish transparency in the evaluation of the benefit-risk profile of various dose combinations, and 3) to quantify the added value of combination use compared to monotherapies. The MCDA model was developed using efficacy, safety, and tolerability attributes and the results of a phase II factorial design combination study were evaluated. Combinations of solifenacin 5 mg and mirabegron 25 mg and mirabegron 50 (5+25 and 5+50) scored the highest clinical utility and supported combination therapy development of solifenacin and mirabegron for phase III clinical development at these dose regimens. This case study underlines the benefit of using a quantitative approach in clinical drug development programs. © 2015 The American Society for Clinical Pharmacology and Therapeutics.

TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization.

PubMed

Ollion, Jean; Cochennec, Julien; Loll, François; Escudé, Christophe; Boudier, Thomas

2013-07-15

The cell nucleus is a highly organized cellular organelle that contains the genetic material. The study of nuclear architecture has become an important field of cellular biology. Extracting quantitative data from 3D fluorescence imaging helps understand the functions of different nuclear compartments. However, such approaches are limited by the requirement for processing and analyzing large sets of images. Here, we describe Tools for Analysis of Nuclear Genome Organization (TANGO), an image analysis tool dedicated to the study of nuclear architecture. TANGO is a coherent framework allowing biologists to perform the complete analysis process of 3D fluorescence images by combining two environments: ImageJ (http://imagej.nih.gov/ij/) for image processing and quantitative analysis and R (http://cran.r-project.org) for statistical processing of measurement results. It includes an intuitive user interface providing the means to precisely build a segmentation procedure and set-up analyses, without possessing programming skills. TANGO is a versatile tool able to process large sets of images, allowing quantitative study of nuclear organization. TANGO is composed of two programs: (i) an ImageJ plug-in and (ii) a package (rtango) for R. They are both free and open source, available (http://biophysique.mnhn.fr/tango) for Linux, Microsoft Windows and Macintosh OSX. Distribution is under the GPL v.2 licence. thomas.boudier@snv.jussieu.fr Supplementary data are available at Bioinformatics online.

Quantitative impact of aerosols on numerical weather prediction. Part II: Impacts to IR radiance assimilation

NASA Astrophysics Data System (ADS)

Marquis, J. W.; Campbell, J. R.; Oyola, M. I.; Ruston, B. C.; Zhang, J.

2017-12-01

This is part II of a two-part series examining the impacts of aerosol particles on weather forecasts. In this study, the aerosol indirect effects on weather forecasts are explored by examining the temperature and moisture analysis associated with assimilating dust contaminated hyperspectral infrared radiances. The dust induced temperature and moisture biases are quantified for different aerosol vertical distribution and loading scenarios. The overall impacts of dust contamination on temperature and moisture forecasts are quantified over the west coast of Africa, with the assistance of aerosol retrievals from AERONET, MPL, and CALIOP. At last, methods for improving hyperspectral infrared data assimilation in dust contaminated regions are proposed.

Imidazole derivatives as angiotensin II AT1 receptor blockers: Benchmarks, drug-like calculations and quantitative structure-activity relationships modeling

NASA Astrophysics Data System (ADS)

Alloui, Mebarka; Belaidi, Salah; Othmani, Hasna; Jaidane, Nejm-Eddine; Hochlaf, Majdi

2018-03-01

We performed benchmark studies on the molecular geometry, electron properties and vibrational analysis of imidazole using semi-empirical, density functional theory and post Hartree-Fock methods. These studies validated the use of AM1 for the treatment of larger systems. Then, we treated the structural, physical and chemical relationships for a series of imidazole derivatives acting as angiotensin II AT1 receptor blockers using AM1. QSAR studies were done for these imidazole derivatives using a combination of various physicochemical descriptors. A multiple linear regression procedure was used to design the relationships between molecular descriptor and the activity of imidazole derivatives. Results validate the derived QSAR model.

[Phenotypic and genetic analysis of a patient presented with Tietz/Waardenburg type II a syndrome].

PubMed

Wang, Huanhuan; Tang, Lifang; Zhang, Jingmin; Hu, Qin; Chen, Yingwei; Xiao, Bing

2015-08-01

To determine the genetic cause for a patient featuring decreased pigmentation of the skin and iris, hearing loss and multiple congenital anomalies. Routine chromosomal banding was performed to analyze the karyotype of the patient and his parents. Single nucleotide polymorphism array (SNP array) was employed to identify cryptic chromosome aberrations, and quantitative real-time PCR was used to confirm the results. Karyotype analysis has revealed no obvious anomaly for the patient and his parents. SNP array analysis of the patient has demonstrated a 3.9 Mb deletion encompassing 3p13p14.1, which caused loss of entire MITF gene. The deletion was confirmed by quantitative real-time PCR. Clinical features of the patient have included severe bilateral hearing loss, decreased pigmentation of the skin and iris and multiple congenital anomalies. The patient, carrying a 3p13p14.1 deletion, has features of Tietz syndrome/Waardenburg syndrome type IIa. This case may provide additional data for the study of genotype-phenotype correlation of this disease.

Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity: in silico bioinformatic step-by-step guide using quantitative structure-activity relationships.

PubMed

Hattotuwagama, Channa K; Doytchinova, Irini A; Flower, Darren R

2007-01-01

Quantitative structure-activity relationship (QSAR) analysis is a cornerstone of modern informatics. Predictive computational models of peptide-major histocompatibility complex (MHC)-binding affinity based on QSAR technology have now become important components of modern computational immunovaccinology. Historically, such approaches have been built around semiqualitative, classification methods, but these are now giving way to quantitative regression methods. We review three methods--a 2D-QSAR additive-partial least squares (PLS) and a 3D-QSAR comparative molecular similarity index analysis (CoMSIA) method--which can identify the sequence dependence of peptide-binding specificity for various class I MHC alleles from the reported binding affinities (IC50) of peptide sets. The third method is an iterative self-consistent (ISC) PLS-based additive method, which is a recently developed extension to the additive method for the affinity prediction of class II peptides. The QSAR methods presented here have established themselves as immunoinformatic techniques complementary to existing methodology, useful in the quantitative prediction of binding affinity: current methods for the in silico identification of T-cell epitopes (which form the basis of many vaccines, diagnostics, and reagents) rely on the accurate computational prediction of peptide-MHC affinity. We have reviewed various human and mouse class I and class II allele models. Studied alleles comprise HLA-A*0101, HLA-A*0201, HLA-A*0202, HLA-A*0203, HLA-A*0206, HLA-A*0301, HLA-A*1101, HLA-A*3101, HLA-A*6801, HLA-A*6802, HLA-B*3501, H2-K(k), H2-K(b), H2-D(b) HLA-DRB1*0101, HLA-DRB1*0401, HLA-DRB1*0701, I-A(b), I-A(d), I-A(k), I-A(S), I-E(d), and I-E(k). In this chapter we show a step-by-step guide into predicting the reliability and the resulting models to represent an advance on existing methods. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made are freely available online at the URL http://www.jenner.ac.uk/MHCPred.

40 CFR 795.225 - Dermal pharmacokinetics of DGBE and DGBA.

Code of Federal Regulations, 2010 CFR

2010-07-01

... this section because they will facilitate the work and improve the reliability of quantitative... for this purpose. (ii) Biotransformation after dermal dosing. Appropriate qualitative and quantitative... tabular form. (2) Evaluation of results. All observed results, quantitative or incidental, shall be...

Conformational heterogeneity in the C-terminal zinc fingers of human MTF-1: an NMR and zinc-binding study.

PubMed

Giedroc, D P; Chen, X; Pennella, M A; LiWang, A C

2001-11-09

The human metalloregulatory transcription factor, metal-response element (MRE)-binding transcription factor-1 (MTF-1), contains six TFIIIA-type Cys(2)-His(2) motifs, each of which was projected to form well-structured betabetaalpha domains upon Zn(II) binding. In this report, the structure and backbone dynamics of a fragment containing the unusual C-terminal fingers F4-F6 has been investigated. (15)N heteronuclear single quantum coherence (HSQC) spectra of uniformly (15)N-labeled hMTF-zf46 show that Zn(II) induces the folding of hMTF-zf46. Analysis of the secondary structure of Zn(3) hMTF-zf46 determined by (13)Calpha chemical shift indexing and the magnitude of (3)J(Halpha-HN) clearly reveal that zinc fingers F4 and F6 adopt typical betabetaalpha structures. An analysis of the heteronuclear backbone (15)N relaxation dynamics behavior is consistent with this picture and further reveals independent tumbling of the finger domains in solution. Titration of apo-MTF-zf46 with Zn(II) reveals that the F4 domain binds Zn(II) significantly more tightly than do the other two finger domains. In contrast to fingers F4 and F6, the betabetaalpha fold of finger F5 is unstable and only partially populated at substoichiometric Zn(II); a slight molar excess of zinc results in severe conformational exchange broadening of all F5 NH cross-peaks. Finally, although Cd(II) binds to apo-hMTF-zf46 as revealed by intense S(-)-->Cd(II) absorption, a non-native structure results; addition of stoichiometric Zn(II) to the Cd(II) complex results in quantitative refolding of the betabetaalpha structure in F4 and F6. The functional implications of these results are discussed.

1996 PAMS hydrocarbon QA studies in EPA Region II: Part II. Trends and insights

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

Teitz, A.; Kantz, M.

1997-12-31

Comparison of ambient air samples between EPA Region II and the PAMS monitoring organizations within the Region, and comparisons among EPA Regions I, II, and III, revealed the following analytical trends: (1) Agreement between laboratories was typically between 10-20% for many of the PAMS analytes found at higher concentrations, i.e., butane, isopentane, benzene, toluene, and m/p-xylene; (2) Nafion dryer systems tended to underestimate the amount of acetylene by 35-50%; (3) Isobutylene co-elution with 1-butene proved difficult to resolve unless a 100 meter DB-1 or a regular length PLOT GC column was used; (4) Organizations that monitor for polar compounds foundmore » that co-elution of ethanol/acetone can interfere with the analysis of 1-pentene; (5) Analytical systems capable of polar analyses can have co-elution and/or misidentification of these aldehydes, typically in the styrene/heptanal/o-xylene regions of the chromatogram; and (6) Tetrachloroethylene was found to interfere with octane quantitation in some analyses.« less

The influence of ligand field effects on the magnetic exchange of high-spin Co(II)-semiquinonate complexes.

PubMed

Bencini, Alessandro; Beni, Alessandra; Costantino, Ferdinando; Dei, Andrea; Gatteschi, Dante; Sorace, Lorenzo

2006-02-07

[Co(Me(4)cyclam)(tropolonate)](PF(6)) was synthesised and structurally characterised. Its electronic and W-band EPR spectra have been analysed by means of the angular overlap calculation of the Spin Hamiltonian parameters that provided also a satisfactory reproduction of the temperature dependence of the magnetic susceptibility. The present results can be interpreted assuming a pseudo-octahedral character for the Co(II) center. This prompted us to reconsider the model formerly used for the analysis of the magnetic coupling between hs-Co(II) and the paramagnetic o-semiquinonate ligand in the corresponding derivatives [Co(Me(4)cyclam)(PhenSQ)](PF(6)) and [Co(Me(4)cyclam)(DTBSQ)](PF(6)). These results indicate that the effect of the magnetic coupling is active only below 50 K and that a more refined model of exchange coupling between Co(II) and semiquinonato ligands is needed to quantitatively analyze the magnetic behaviour of this class of systems.

Chromium(IV)–Peroxo Complex Formation and Its Nitric Oxide Dioxygenase Reactivity

PubMed Central

Yokoyama, Atsutoshi; Han, Jung Eun; Cho, Jaeheung; Kubo, Minoru; Ogura, Takashi; Siegler, Maxime A.; Karlin, Kenneth D.; Nam, Wonwoo

2012-01-01

The O2 and NO reactivity of a Cr(II) complex bearing a 12-membered tetraazamacrocyclic TMC ligand, [CrII(12-TMC)(Cl)]+ (1), and the NO reactivity of its peroxo derivative, [CrIV(12-TMC)(O2)(Cl)]+ (2), are described. By contrast to the previously reported Cr(III)-superoxo complex, [CrIII(14-TMC)(O2)(Cl)]+, a Cr(IV)-peroxo complex (2) is formed in the reaction of 1 and O2. Full spectroscopic and X-ray analysis reveals that 2 possesses a side-on η2-peroxo ligation. A quantitative reaction of 2 with NO affords a reduction in Cr oxidation state and production of a Cr(III)-nitrato complex, [CrIII(12-TMC)(NO3)(Cl)]+ (3). The latter is suggested to form via a Cr(III)-peroxynitrite intermediate. A Cr(II)-nitrosyl complex, [CrII(12-TMC)(NO)(Cl)]+ (4), derived from 1 andNO could also be synthesized; however, it does not react with O2. PMID:22950528

Observation of the time-course for peptidoglycan lipid intermediate II polymerization by Staphylococcus aureus monofunctional transglycosylase.

PubMed

Braddick, Darren; Sandhu, Sandeep; Roper, David I; Chappell, Michael J; Bugg, Timothy D H

2014-08-01

The polymerization of lipid intermediate II by the transglycosylase activity of penicillin-binding proteins (PBPs) represents an important target for antibacterial action, but limited methods are available for quantitative assay of this reaction, or screening potential inhibitors. A new labelling method for lipid II polymerization products using Sanger's reagent (fluoro-2,4-dinitrobenzene), followed by gel permeation HPLC analysis, has permitted the observation of intermediate polymerization products for Staphylococcus aureus monofunctional transglycosylase MGT. Peak formation is inhibited by 6 µM ramoplanin or enduracidin. Characterization by mass spectrometry indicates the formation of tetrasaccharide and octasaccharide intermediates, but not a hexasaccharide intermediate, suggesting a dimerization of a lipid-linked tetrasaccharide. Numerical modelling of the time-course data supports a kinetic model involving addition to lipid-linked tetrasaccharide of either lipid II or lipid-linked tetrasaccharide. Observation of free octasaccharide suggests that hydrolysis of the undecaprenyl diphosphate lipid carrier occurs at this stage in peptidoglycan transglycosylation. © 2014 The Authors.

The protein expression landscape of mitosis and meiosis in diploid budding yeast.

PubMed

Becker, Emmanuelle; Com, Emmanuelle; Lavigne, Régis; Guilleux, Marie-Hélène; Evrard, Bertrand; Pineau, Charles; Primig, Michael

2017-03-06

Saccharomyces cerevisiae is an established model organism for the molecular analysis of fundamental biological processes. The genomes of numerous strains have been sequenced, and the transcriptome and proteome ofmajor phases during the haploid and diploid yeast life cycle have been determined. However, much less is known about dynamic changes of the proteome when cells switch from mitotic growth to meiotic development. We report a quantitative protein profiling analysis of yeast cell division and differentiation based on mass spectrometry. Information about protein levels was integrated with strand-specific tiling array expression data. We identified a total of 2366 proteins in at least one condition, including 175 proteins showing a statistically significant>5-fold change across the sample set, and 136 proteins detectable in sporulating but not respiring cells. We correlate protein expression patterns with biological processes and molecular function by Gene Ontology term enrichment, chemoprofiling, transcription interference and the formation of double stranded RNAs by overlapping sense/antisense transcripts. Our work provides initial quantitative insight into protein expression in diploid respiring and differentiating yeast cells. Critically, it associates developmentally regulated induction of antisense long noncoding RNAs and double stranded RNAs with fluctuating protein concentrations during growth and development. This integrated genomics analysis helps better understand how the transcriptome and the proteome correlate in diploid yeast cells undergoing mitotic growth in the presence of acetate (respiration) versus meiotic differentiation (Meiosis I and II). The study (i) provides quantitative expression data for 2366 proteins and their cognate mRNAs in at least one sample, (ii) shows strongly fluctuating protein levels during growth and differentiation for 175 cases, and (iii) identifies 136 proteins absent in mitotic but present in meiotic yeast cells. We have integrated protein profiling data using mass spectrometry with tiling array RNA profiling data and information on double-stranded RNAs (dsRNAs) by overlapping sense/antisense transcripts from an RNA-Sequencing experiment. This work therefore provides quantitative insight into protein expression during cell division and development and associates changing protein levels with developmental stage specific induction of antisense transcripts and the formation of dsRNAs. Copyright © 2017 Elsevier B.V. All rights reserved.

A simple two-stage design for quantitative responses with application to a study in diabetic neuropathic pain.

PubMed

Whitehead, John; Valdés-Márquez, Elsa; Lissmats, Agneta

2009-01-01

Two-stage designs offer substantial advantages for early phase II studies. The interim analysis following the first stage allows the study to be stopped for futility, or more positively, it might lead to early progression to the trials needed for late phase II and phase III. If the study is to continue to its second stage, then there is an opportunity for a revision of the total sample size. Two-stage designs have been implemented widely in oncology studies in which there is a single treatment arm and patient responses are binary. In this paper the case of two-arm comparative studies in which responses are quantitative is considered. This setting is common in therapeutic areas other than oncology. It will be assumed that observations are normally distributed, but that there is some doubt concerning their standard deviation, motivating the need for sample size review. The work reported has been motivated by a study in diabetic neuropathic pain, and the development of the design for that trial is described in detail. Copyright 2008 John Wiley & Sons, Ltd.

Review of Department of Defense Education Activity (DODEA) Schools. Volume II: Quantitative Analysis of Educational Quality

DTIC Science & Technology

2000-10-01

most enlightening sources found on how to approach the problem were as follows: 1. Eric A. Hanushek and Others, Making Schools Work, Improving... Hanushek traces the history of educational inputs and outputs in the United States. Since the 1950s, test scores have not increased, while...important inputs see Eric A. Hanushek and Others, Making Schools Work: Improving Performance and Controlling Costs, The Brookings Institution, 1994 and

Final Report for Dynamic Models for Causal Analysis of Panel Data. Models for Change in Quantitative Variables, Part I Deterministic Models. Part II, Chapter 3.

ERIC Educational Resources Information Center

Hannan, Michael T.

This document is part of a series of chapters described in SO 011 759. Addressing the question of effective models to measure change and the change process, the author suggests that linear structural equation systems may be viewed as steady state outcomes of continuous-change models and have rich sociological grounding. Two interpretations of the…

Structural Basis for Certain Naturally Occurring Bioflavonoids to Function as Reducing Co-Substrates of Cyclooxygenase I and II

PubMed Central

Zhu, Bao Ting

2010-01-01

Background Recent studies showed that some of the dietary bioflavonoids can strongly stimulate the catalytic activity of cyclooxygenase (COX) I and II in vitro and in vivo, presumably by facilitating enzyme re-activation. In this study, we sought to understand the structural basis of COX activation by these dietary compounds. Methodology/Principal Findings A combination of molecular modeling studies, biochemical analysis and site-directed mutagenesis assay was used as research tools. Three-dimensional quantitative structure-activity relationship analysis (QSAR/CoMFA) predicted that the ability of bioflavonoids to activate COX I and II depends heavily on their B-ring structure, a moiety known to be associated with strong antioxidant ability. Using the homology modeling and docking approaches, we identified the peroxidase active site of COX I and II as the binding site for bioflavonoids. Upon binding to this site, bioflavonoid can directly interact with hematin of the COX enzyme and facilitate the electron transfer from bioflavonoid to hematin. The docking results were verified by biochemical analysis, which reveals that when the cyclooxygenase activity of COXs is inhibited by covalent modification, myricetin can still stimulate the conversion of PGG2 to PGE2, a reaction selectively catalyzed by the peroxidase activity. Using the site-directed mutagenesis analysis, we confirmed that Q189 at the peroxidase site of COX II is essential for bioflavonoids to bind and re-activate its catalytic activity. Conclusions/Significance These findings provide the structural basis for bioflavonoids to function as high-affinity reducing co-substrates of COXs through binding to the peroxidase active site, facilitating electron transfer and enzyme re-activation. PMID:20808785

Problems and solutions of polyethylene glycol co-injection method in multiresidue pesticide analysis by gas chromatography-mass spectrometry: evaluation of instability phenomenon in type II pyrethroids and its suppression by novel analyte protectants.

PubMed

Akutsu, Kazuhiko; Kitagawa, Yoko; Yoshimitsu, Masato; Takatori, Satoshi; Fukui, Naoki; Osakada, Masakazu; Uchida, Kotaro; Azuma, Emiko; Kajimura, Keiji

2018-05-01

Polyethylene glycol 300 is commonly used as a base material for "analyte protection" in multiresidue pesticide analysis via gas chromatography-mass spectrometry. However, the disadvantage of the co-injection method using polyethylene glycol 300 is that it causes peak instability in α-cyano pyrethroids (type II pyrethroids) such as fluvalinate. In this study, we confirmed the instability phenomenon in type II pyrethroids and developed novel analyte protectants for acetone/n-hexane mixture solution to suppress the phenomenon. Our findings revealed that among the examined additive compounds, three lipophilic ascorbic acid derivatives, 3-O-ethyl-L-ascorbic acid, 6-O-palmitoyl-L-ascorbic acid, and 6-O-stearoyl-L-ascorbic acid, could effectively stabilize the type II pyrethroids in the presence of polyethylene glycol 300. A mixture of the three ascorbic acid derivatives and polyethylene glycol 300 proved to be an effective analyte protectant for multiresidue pesticide analysis. Further, we designed and evaluated a new combination of analyte protectant compounds without using polyethylene glycol or the troublesome hydrophilic compounds. Consequently, we obtained a set of 10 medium- and long-chain saturated fatty acids as an effective analyte protectant suitable for acetone/n-hexane solution that did not cause peak instability in type II pyrethroids. These analyte protectants will be useful in multiresidue pesticide analysis by gas chromatography-mass spectrometry in terms of ruggedness and reliable quantitativeness. Graphical abstract Comparison of effectiveness of the addition of lipophilic derivatives of ascorbic acid in controlling the instability phenomenon of fluvalinate with polyethylene glycol 300.

No association between ACTN3 R577X and ACE I/D polymorphisms and endurance running times in 698 Caucasian athletes.

PubMed

Papadimitriou, Ioannis D; Lockey, Sarah J; Voisin, Sarah; Herbert, Adam J; Garton, Fleur; Houweling, Peter J; Cieszczyk, Pawel; Maciejewska-Skrendo, Agnieszka; Sawczuk, Marek; Massidda, Myosotis; Calò, Carla Maria; Astratenkova, Irina V; Kouvatsi, Anastasia; Druzhevskaya, Anastasiya M; Jacques, Macsue; Ahmetov, Ildus I; Stebbings, Georgina K; Heffernan, Shane; Day, Stephen H; Erskine, Robert; Pedlar, Charles; Kipps, Courtney; North, Kathryn N; Williams, Alun G; Eynon, Nir

2018-01-03

Studies investigating associations between ACTN3 R577X and ACE I/D genotypes and endurance athletic status have been limited by small sample sizes from mixed sport disciplines and lack quantitative measures of performance. To examine the association between ACTN3 R577X and ACE I/D genotypes and best personal running times in a large homogeneous cohort of endurance runners. We collected a total of 1064 personal best 1500, 3000, 5000 m and marathon running times of 698 male and female Caucasian endurance athletes from six countries (Australia, Greece, Italy, Poland, Russia and UK). Athletes were genotyped for ACTN3 R577X and ACE ID variants. There was no association between ACTN3 R577X or ACE I/D genotype and running performance at any distance in men or women. Mean (SD) marathon times (in s) were for men: ACTN3 RR 9149 (593), RX 9221 (582), XX 9129 (582) p = 0.94; ACE DD 9182 (665), ID 9214 (549), II 9155 (492) p = 0.85; for women: ACTN3 RR 10796 (818), RX 10667 (695), XX 10675 (553) p = 0.36; ACE DD 10604 (561), ID 10766 (740), II 10771 (708) p = 0.21. Furthermore, there were no associations between these variants and running time for any distance in a sub-analysis of athletes with personal records within 20% of world records. Thus, consistent with most case-control studies, this multi-cohort quantitative analysis demonstrates it is unlikely that ACTN3 XX genotype provides an advantage in competitive endurance running performance. For ACE II genotype, some prior studies show an association but others do not. Our data indicate it is also unlikely that ACE II genotype provides an advantage in endurance running.

Final Report: Molecular mechanisms and kinetics of microbial anaerobic nitrate-dependent U(IV) and Fe(II) oxidation

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

O'Day, Peggy A.; Asta, Maria P.; Kanematsu, Masakazu

2015-02-27

In this project, we combined molecular genetic, spectroscopic, and microscopic techniques with kinetic and reactive transport studies to describe and quantify biotic and abiotic mechanisms underlying anaerobic, nitrate-dependent U(IV) and Fe(II) oxidation, which influences the long-term efficacy of in situ reductive immobilization of uranium at DOE sites. In these studies, Thiobacillus denitrificans, an autotrophic bacterium that catalyzes anaerobic U(IV) and Fe(II) oxidation, was used to examine coupled oxidation-reduction processes under either biotic (enzymatic) or abiotic conditions in batch and column experiments with biogenically produced UIVO2(s). Synthesis and quantitative analysis of coupled chemical and transport processes were done with the reactivemore » transport modeling code Crunchflow. Research focused on identifying the primary redox proteins that catalyze metal oxidation, environmental factors that influence protein expression, and molecular-scale geochemical factors that control the rates of biotic and abiotic oxidation.« less

Susceptibility to fraud in systematic reviews: lessons from the Reuben case.

PubMed

Marret, Emmanuel; Elia, Nadia; Dahl, Jørgen B; McQuay, Henry J; Møiniche, Steen; Moore, R Andrew; Straube, Sebastian; Tramèr, Martin R

2009-12-01

Dr. Scott Reuben allegedly fabricated data. The authors of the current article examined the impact of Reuben reports on conclusions of systematic reviews. The authors searched in ISI Web of Knowledge systematic reviews citing Reuben reports. Systematic reviews were grouped into one of three categories: I, only cited but did not include Reuben reports; II, retrieved and considered, but eventually excluded Reuben reports; III, included Reuben reports. For quantitative systematic reviews (i.e., meta-analyses), a relevant difference was defined as a significant result becoming nonsignificant (or vice versa) by excluding Reuben reports. For qualitative systematic reviews, each author decided independently whether noninclusion of Reuben reports would have changed conclusions. Twenty-five systematic reviews (5 category I, 6 category II, 14 category III) cited 27 Reuben reports (published 1994-2007). Most tested analgesics in surgical patients. One of 6 quantitative category III reviews would have reached different conclusions without Reuben reports. In all 6 (30 subgroup analyses involving Reuben reports), exclusion of Reuben reports never made any difference when the number of patients from Reuben reports was less than 30% of all patients included in the analysis. Of 8 qualitative category III reviews, all authors agreed that one would certainly have reached different conclusions without Reuben reports. For another 4, the authors' judgment was not unanimous. Carefully performed systematic reviews proved robust against the impact of Reuben reports. Quantitative systematic reviews were vulnerable if the fraudulent data were more than 30% of the total. Qualitative systematic reviews seemed at greater risk than quantitative.

Removal and recovery of mercury(II) from hazardous wastes using 1-(2-thiazolylazo)-2-naphthol functionalized activated carbon as solid phase extractant.

PubMed

Starvin, A M; Rao, T Prasada

2004-09-10

As a part of removal of toxic heavy metals from hazardous wastes, solid phase extraction (SPE) of mercury(II) at trace and ultra trace levels was studied using 1-(2-thiazolylazo)-2-naphthol (TAN) functionalized activated carbon (AC). The SPE material removes traces of mercury(II) quantitatively in the pH range 6.0 +/- 0.2. Other parameters that influence quantitative recovery of mercury(II), viz. percent concentration of TAN in AC, amount of TAN-AC, preconcentration time and volume of aqueous phase were varied and optimized. The possible means of removal of Hg(II) from other metal ions that are likely to be present in the wastes of the chloroalkali industry is discussed. The potential of TAN-functionalized AC SPE material for decontaminating mercury from the brine sludge and cell house effluent of a chloralkali plant has been evaluated.

Improvement of ion chromatography with ultraviolet photometric detection and comparison with conductivity detection for the determination of serum cations.

PubMed

Shintani, H

1985-05-31

Studies were made of the analytical conditions required for indirect photometric ion chromatography using ultraviolet photometric detection (UV method) for the determination of serum cations following a previously developed serum pre-treatment. The sensitivities of the conductivity detection (CD) and UV methods and the amounts of serum cations determined by both methods were compared. Attempts to improve the sensitivity of the conventional UV method are reported. It was found that the mobile phase previously reported by Small and Miller showed no quantitative response when more than 4 mM copper(II) sulphate pentahydrate was used. As a result, there was no significant difference in the amounts of serum cations shown by the CD and UV methods. However, by adding 0.5-5 mM cobalt(II) sulphate heptahydrate, nickel(II) sulphate hexahydrate, zinc(II) sulphate heptahydrate or cobalt(II) diammonium sulphate hexahydrate to 0.5-1.5 mM copper(II) sulphate pentahydrate, higher sensitivity and a quantitative response were attained.

Evaluation of different strategies for quantitative depth profile analysis of Cu/NiCu layers and multilayers via pulsed glow discharge - Time of flight mass spectrometry

NASA Astrophysics Data System (ADS)

Muñiz, Rocío; Lobo, Lara; Németh, Katalin; Péter, László; Pereiro, Rosario

2017-09-01

There is still a lack of approaches for quantitative depth-profiling when dealing with glow discharges (GD) coupled to mass spectrometric detection. The purpose of this work is to develop quantification procedures using pulsed GD (PGD) - time of flight mass spectrometry. In particular, research was focused towards the depth profile analysis of Cu/NiCu nanolayers and multilayers electrodeposited on Si wafers. PGDs are characterized by three different regions due to the temporal application of power: prepeak, plateau and afterglow. This last region is the most sensitive and so it is convenient for quantitative analysis of minor components; however, major elements are often saturated, even at 30 W of applied radiofrequency power for these particular samples. For such cases, we have investigated two strategies based on a multimatrix calibration procedure: (i) using the afterglow region for all the sample components except for the major element (Cu) that was analyzed in the plateau, and (ii) using the afterglow region for all the elements measuring the ArCu signal instead of Cu. Seven homogeneous certified reference materials containing Si, Cr, Fe, Co, Ni and Cu have been used for quantification. Quantitative depth profiles obtained with these two strategies for samples containing 3 or 6 multilayers (of a few tens of nanometers each layer) were in agreement with the expected values, both in terms of thickness and composition of the layers.

A mixed method exploration of survivorship among Chinese American and non-Hispanic White breast cancer survivors: the role of socioeconomic well-being.

PubMed

Wang, Judy Huei-yu; Adams, Inez F; Tucker-Seeley, Reginald; Gomez, Scarlett Lin; Allen, Laura; Huang, Ellen; Wang, Yiru; Pasick, Rena J

2013-12-01

Cancer-related stress is heavily influenced by culture. This study explored similarities and differences in survivorship care concerns among Chinese American and non-Hispanic White (NHW) breast cancer survivors. A sequential, mixed-method design (inductive/qualitative research-phase I and deductive/quantitative research-phase II) was employed. Eligible women identified from the Greater Bay Area Cancer Registry were age ≥21, diagnosed with stage 0-IIa breast cancer between 2006 and 2011, and had no recurrence or other cancers. In phase I, we conducted 4 Chinese (n = 19) and 4 NHW (n = 22) focus groups, and 31 individual telephone interviews (18 Chinese immigrants, 7 Chinese US-born, and 6 NHW). Content analysis was conducted to examine qualitative data. In phase II, another 296 survivors (148 NHW age-matched to 148 Chinese cases) completed a cross-sectional survey. Descriptive statistics and linear regression analysis were conducted to examine quantitative data. Qualitative data revealed "socioeconomic well-being" (SWB) as a dominant survivorship concern, which was operationalized as a cancer survivor's perceived economic and social resources available to access care. Quantitative data showed that low-acculturated Chinese immigrants reported the poorest SWB, controlling for covariates. Highly acculturated Chinese immigrants and the US-born Chinese/NHW group reported similar SWB. Women who had low-income levels or chemotherapy had poorer SWB. SWB emerged as an important aspect of breast cancer survivorship. Immigration stress, cancer care costs, and cultural values all contributed to immigrants' socioeconomic distress. Immigrant and US-born breast cancer survivors experienced different socioeconomic circumstances and well-being following treatment. Our findings warrant further investigation of socioeconomic distress and survivorship outcomes.

A Mixed Method Exploration of Survivorship among Chinese American and Non-Hispanic White Breast Cancer Survivors: The Role of Socioeconomic Well-Being

PubMed Central

Wang, Judy Huei-yu; Adams, Inez F.; Tucker-Seeley, Reginald; Gomez, Scarlett Lin; Allen, Laura; Huang, Ellen; Wang, Yiru; Pasick, Rena J.

2013-01-01

Purpose Cancer-related stress is heavily influenced by culture. This study explored similarities and differences in survivorship care concerns among Chinese American and Non-Hispanic White (NHW) breast cancer survivors. Methods A sequential, mixed-method design (inductive/qualitative research-phase I and deductive/quantitative research-phase II) was employed. Eligible women identified from the Greater Bay Area Cancer Registry were age ≥21, diagnosed with stage 0-IIa breast cancer between 2006–2011, and had no recurrence or other cancers. In phase I, we conducted 4 Chinese (n=19) and 4 NHW (n=22) focus groups, and 31 individual telephone interviews (18 Chinese immigrants, 7 Chinese US-born, and 6 NHW). Content analysis was conducted to examine qualitative data. In phase II, another 296 survivors (148 NHW age-matched to 148 Chinese cases) completed a cross-sectional survey. Descriptive statistics and linear regression analysis were conducted to examine quantitative data. Results Qualitative data revealed “socioeconomic wellbeing” (SWB) as a dominant survivorship concern, which was operationalized as a cancer survivor’s perceived economic and social resources available to access care. Quantitative data showed that low-acculturated Chinese immigrants reported the poorest SWB, controlling for covariates. Highly-acculturated Chinese immigrants and the US-born Chinese/NHW group reported similar SWB. Women who had low income levels or chemotherapy had poorer SWB. Conclusions SWB emerged as an important aspect of breast cancer survivorship. Immigration stress, cancer care costs, and cultural values all contributed to immigrants’ socioeconomic distress. Immigrant and US-born breast cancer survivors experienced different socioeconomic circumstances and well-being following treatment. Our findings warrant further investigation of socioeconomic distress and survivorship outcomes. PMID:23591710

Carnitine palmitoyltransferase II deficiency

PubMed Central

Roe, C R.; Yang, B-Z; Brunengraber, H; Roe, D S.; Wallace, M; Garritson, B K.

2008-01-01

Background: Carnitine palmitoyltransferase II (CPT II) deficiency is an important cause of recurrent rhabdomyolysis in children and adults. Current treatment includes dietary fat restriction, with increased carbohydrate intake and exercise restriction to avoid muscle pain and rhabdomyolysis. Methods: CPT II enzyme assay, DNA mutation analysis, quantitative analysis of acylcarnitines in blood and cultured fibroblasts, urinary organic acids, the standardized 36-item Short-Form Health Status survey (SF-36) version 2, and bioelectric impedance for body fat composition. Diet treatment with triheptanoin at 30% to 35% of total daily caloric intake was used for all patients. Results: Seven patients with CPT II deficiency were studied from 7 to 61 months on the triheptanoin (anaplerotic) diet. Five had previous episodes of rhabdomyolysis requiring hospitalizations and muscle pain on exertion prior to the diet (two younger patients had not had rhabdomyolysis). While on the diet, only two patients experienced mild muscle pain with exercise. During short periods of noncompliance, two patients experienced rhabdomyolysis with exercise. None experienced rhabdomyolysis or hospitalizations while on the diet. All patients returned to normal physical activities including strenuous sports. Exercise restriction was eliminated. Previously abnormal SF-36 physical composite scores returned to normal levels that persisted for the duration of the therapy in all five symptomatic patients. Conclusions: The triheptanoin diet seems to be an effective therapy for adult-onset carnitine palmitoyltransferase II deficiency. GLOSSARY ALT = alanine aminotransferase; AST = aspartate aminotransferase; ATP = adenosine triphosphate; BHP = β-hydroxypentanoate; BKP = β-ketopentanoate; BKP-CoA = β-ketopentanoyl–coenzyme A; BUN = blood urea nitrogen; CAC = citric acid cycle; CoA = coenzyme A; CPK = creatine phosphokinase; CPT II = carnitine palmitoyltransferase II; LDL = low-density lipoprotein; MCT = medium-chain triglyceride; PCS = physical composite score; SF-36 = 36-item Short-Form Health Status survey. PMID:18645163

Expression of the alpha and beta subunits of Ca2+/calmodulin kinase II in the cerebellum of jaundiced Gunn rats during development: a quantitative light microscopic analysis.

PubMed

Conlee, J W; Shapiro, S M; Churn, S B

2000-04-01

The homozygous (jj) jaundiced Gunn rat model for hyperbilirubinemia displays pronounced cerebellar hypoplasia. To examine the cellular mechanisms involved in bilirubin toxicity, this study focused on the effect of hyperbilirubinemia on calcium/calmodulin-dependent kinase II (CaM kinase II). CaM kinase II is a neuronally enriched enzyme which performs several important functions. Immunohistochemical analysis of alternating serial sections were performed using monoclonal antibodies for the alpha and beta subunits of CaM kinase II. Measurements were made of the total numbers of stained cells in each of the deep cerebellar nuclei and of Purkinje and granule cell densities in cerebellar lobules II, VI, and IX. The beta subunit was present in Purkinje cells and deep cerebellar nuclei of both groups at all ages, but only granule cells which had migrated through the Purkinje cell layer showed staining for beta subunit; external granule cells were completely negative. Many Purkinje cells had degenerated in the older animals, and the percent of granule cells stained for beta subunit was significantly reduced. The alpha subunit was found exclusively in Purkinje cells, although its appearance was delayed in the jaundiced animals. Sulfadimethoxine was administered to some jj rats 24 h or 15 days prior to sacrifice to increase brain bilirubin concentration. Results showed that bilirubin exposure modulated both alpha and beta CaM kinase II subunit expression in selective neuronal populations, but sulfadimethoxine had no acute effect on enzyme immunoreactivity. Thus, developmental expression of the alpha and beta subunits of CaM kinase II was affected by chronic bilirubin exposure during early postnatal development of jaundiced Gunn rats.

Genome-wide identification and expression analysis of the ClTCP transcription factors in Citrullus lanatus.

PubMed

Shi, Pibiao; Guy, Kateta Malangisha; Wu, Weifang; Fang, Bingsheng; Yang, Jinghua; Zhang, Mingfang; Hu, Zhongyuan

2016-04-12

The plant-specific TCP transcription factor family, which is involved in the regulation of cell growth and proliferation, performs diverse functions in multiple aspects of plant growth and development. However, no comprehensive analysis of the TCP family in watermelon (Citrullus lanatus) has been undertaken previously. A total of 27 watermelon TCP encoding genes distributed on nine chromosomes were identified. Phylogenetic analysis clustered the genes into 11 distinct subgroups. Furthermore, phylogenetic and structural analyses distinguished two homology classes within the ClTCP family, designated Class I and Class II. The Class II genes were differentiated into two subclasses, the CIN subclass and the CYC/TB1 subclass. The expression patterns of all members were determined by semi-quantitative PCR. The functions of two ClTCP genes, ClTCP14a and ClTCP15, in regulating plant height were confirmed by ectopic expression in Arabidopsis wild-type and ortholog mutants. This study represents the first genome-wide analysis of the watermelon TCP gene family, which provides valuable information for understanding the classification and functions of the TCP genes in watermelon.

Structurally related hydrazone-based metal complexes with different antitumor activities variably induce apoptotic cell death.

PubMed

Megger, Dominik A; Rosowski, Kristin; Radunsky, Christian; Kösters, Jutta; Sitek, Barbara; Müller, Jens

2017-04-05

Three new complexes bearing the tridentate hydrazone-based ligand 2-(2-(1-(pyridin-2-yl)ethylidene)hydrazinyl)pyridine (L) were synthesized and structurally characterized. Biological tests indicate that the Zn(ii) complex [ZnCl 2 (L)] is of low cytotoxicity against the hepatocellular carcinoma cell line HepG2. In contrast, the Cu(ii) and Mn(ii) complexes [CuCl 2 (L)] and [MnCl 2 (L)] are highly cytotoxic with EC 50 values of 1.25 ± 0.01 μM and 20 ± 1 μM, respectively. A quantitative proteome analysis reveals that treatment of the cells with the Cu(ii) complex leads to a significantly altered abundance of 102 apoptosis-related proteins, whereas 38 proteins were up- or down-regulated by the Mn(ii) complex. A closer inspection of those proteins regulated only by the Cu(ii) complex suggests that the superior cytotoxic activity of this complex is likely to be related to an initiation of the caspase-independent cell death (CICD). In addition, an increased generation of reactive oxygen species (ROS) and a strong up-regulation of proteins responsive to oxidative stress suggest that alterations of the cellular redox metabolism likely contribute to the cytotoxicity of the Cu(ii) complex.

Volumetric neuroimaging in Usher syndrome: evidence of global involvement.

PubMed

Schaefer, G B; Bodensteiner, J B; Thompson, J N; Kimberling, W J; Craft, J M

1998-08-27

Usher syndrome is a group of genetic disorders consisting of congenital sensorineural hearing loss and retinitis pigmentosa of variable onset and severity depending on the genetic type. It was suggested that the psychosis of Usher syndrome might be secondary to a metabolic degeneration involving the brain more diffusely. There have been reports of focal and diffuse atrophic changes in the supratentorial brain as well as atrophy of some of the structures of the posterior fossa. We previously performed quantitative analysis of magnetic resonance imaging studies of 19 Usher syndrome patients (12 with type I and 7 with type II) looking at the cerebellum and various cerebellar components. We found atrophy of the cerebellum in both types and sparing of cerebellar vermis lobules I-V in type II Usher syndrome patients only. We now have studied another group of 19 patients (with some overlap in the patients studied from the previous report) with Usher syndrome (8 with type I, 11 with type II). We performed quantitative volumetric measurements of various brain structures compared to age- and sex-matched controls. We found a significant decrease in intracranial volume and in size of the brain and cerebellum with a trend toward an increase in the size of the subarachnoid spaces. These data suggest that the disease process in Usher syndrome involves the entire brain and is not limited to the posterior fossa or auditory and visual systems.

Efficient Algorithm for Fuzzy Linear Programming with Multiple Objectives.

DTIC Science & Technology

1984-12-01

constraint). Because of other reasons at least 6 of the smallest trucks were wanted in the fleet. The management wanted to use quantitative analysis and...to the price Ki. For each share the values of the criteria are multiplied by a weight gi : (66) gi = 100/ki This percentage transformation is useful in...could be useful for a repeated and promising analysis . II 92 cL ) C7 C, CJ o4-- S- 00 L C) C 4.) 0n -’ I. - 4s , 4.4- C)C) 4-) ’,0 LC) C unS. - a

AP2/ERF Transcription Factor, Ii049, Positively Regulates Lignan Biosynthesis in Isatis indigotica through Activating Salicylic Acid Signaling and Lignan/Lignin Pathway Genes

PubMed Central

Ma, Ruifang; Xiao, Ying; Lv, Zongyou; Tan, Hexin; Chen, Ruibing; Li, Qing; Chen, Junfeng; Wang, Yun; Yin, Jun; Zhang, Lei; Chen, Wansheng

2017-01-01

Lignans, such as lariciresinol and its derivatives, have been identified as effective antiviral ingredients in Isatis indigotica. Evidence suggests that the APETALA2/ethylene response factor (AP2/ERF) family might be related to the biosynthesis of lignans in I. indigotica. However, the special role played by the AP2/ERF family in the metabolism and its underlying putative mechanism still need to be elucidated. One novel AP2/ERF gene, named Ii049, was isolated and characterized from I. indigotica in this study. The quantitative real-time PCR analysis revealed that Ii049 was expressed highest in the root and responded to methyl jasmonate, salicylic acid (SA) and abscisic acid treatments to various degrees. Subcellular localization analysis indicated that Ii049 protein was localized in the nucleus. Knocking-down the expression of Ii049 caused a remarkable reduction of lignan/lignin contents and transcript levels of genes involved in the lignan/lignin biosynthetic pathway. Ii049 bound to the coupled element 1, RAV1AAT and CRTAREHVCBF2 motifs of genes IiPAL and IiCCR, the key structural genes in the lignan/lignin pathway. Furthermore, Ii049 was also essential for SA biosynthesis, and SA induced lignan accumulation in I. indigotica. Notably, the transgenic I. indigotica hairy roots overexpressing Ii049 showed high expression levels of lignan/lignin biosynthetic genes and SA content, resulting in significant accumulation of lignan/lignin. The best-engineered line (OVX049-10) produced 425.60 μg·g−1 lariciresinol, an 8.3-fold increase compared with the wild type production. This study revealed the function of Ii049 in regulating lignan/lignin biosynthesis, which had the potential to increase the content of valuable lignan/lignin in economically significant medicinal plants. PMID:28824690

Molecular Dynamics Simulations of Protein-Ligand Complexes in Near Physiological Conditions

NASA Astrophysics Data System (ADS)

Wambo, Thierry Oscar

Proteins are important molecules for their key functions. However, under certain circumstances, the function of these proteins needs to be regulated to keep us healthy. Ligands are small molecules often used to modulate the function of proteins. The binding affinity is a quantitative measure of how strong the ligand will modulate the function of the protein: a strong binding affinity will highly impact the performance of the protein. It becomes clear that it is critical to have appropriate techniques to accurately compute the binding affinity. The most difficult task in computer simulations is how to efficiently sample the space spanned by the ligand during the binding process. In this work, we have developed some schemes to compute the binding affinity of a ligand to a protein, and of a metal ion to a protein. Application of these techniques to some complexes yield results in agreement with experimental values. These methods are a brute force approach and make no assumption other than that the complexes are governed by the force field used. Specifically, we computed the free energy of binding between (1) human carbonic anhydrase II and the drug acetazolamide (hcaII-AZM), (2) human carbonic anhydrase II and the zinc ion (hcaII-Zinc), and (3) beta-lactoglobulin and five fatty acids complexes (BLG-FAs). We found the following free energies of binding in unit of kcal/mol: -12.96 +/-2.44 (-15.74) for hcaII-Zinc complex, -5.76+/-0.76 (-5.57) for BLG-OCA , -4.44+/-1.08 (-5.22) for BLG-DKA,-6.89+/-1.25 (-7.24) for BLG-DAO, -8.57+/-0.82 (-8.14) for BLG-MYR, -8.99+/-0.87 (-8.72) for BLG-PLM, and -11.87+/-1.8 (-10.8) for hcaII-AZM. The values inside the parentheses are experimental results. The simulations and quantitative analysis of each system provide interesting insights into the interactions between each entity and helps us to better understand the dynamics of these systems.

STEM_CELL: a software tool for electron microscopy: part 2--analysis of crystalline materials.

PubMed

Grillo, Vincenzo; Rossi, Francesca

2013-02-01

A new graphical software (STEM_CELL) for analysis of HRTEM and STEM-HAADF images is here introduced in detail. The advantage of the software, beyond its graphic interface, is to put together different analysis algorithms and simulation (described in an associated article) to produce novel analysis methodologies. Different implementations and improvements to state of the art approach are reported in the image analysis, filtering, normalization, background subtraction. In particular two important methodological results are here highlighted: (i) the definition of a procedure for atomic scale quantitative analysis of HAADF images, (ii) the extension of geometric phase analysis to large regions up to potentially 1μm through the use of under sampled images with aliasing effects. Copyright © 2012 Elsevier B.V. All rights reserved.

Multivariate approach in popcorn genotypes using the Ward-MLM strategy: morpho-agronomic analysis and incidence of Fusarium spp.

PubMed

Kurosawa, R N F; do Amaral Junior, A T; Silva, F H L; Dos Santos, A; Vivas, M; Kamphorst, S H; Pena, G F

2017-02-08

The multivariate analyses are useful tools to estimate the genetic variability between accessions. In the breeding programs, the Ward-Modified Location Model (MLM) multivariate method has been a powerful strategy to quantify variability using quantitative and qualitative variables simultaneously. The present study was proposed in view of the dearth of information about popcorn breeding programs under a multivariate approach using the Ward-MLM methodology. The objective of this study was thus to estimate the genetic diversity among 37 genotypes of popcorn aiming to identify divergent groups associated with morpho-agronomic traits and traits related to resistance to Fusarium spp. To this end, 7 qualitative and 17 quantitative variables were analyzed. The experiment was conducted in 2014, at Universidade Estadual do Norte Fluminense, located in Campos dos Goytacazes, RJ, Brazil. The Ward-MLM strategy allowed the identification of four groups as follows: Group I with 10 genotypes, Group II with 11 genotypes, Group III with 9 genotypes, and Group IV with 7 genotypes. Group IV was distant in relation to the other groups, while groups I, II, and III were near. The crosses between genotypes from the other groups with those of group IV allow an exploitation of heterosis. The Ward-MLM strategy provided an appropriate grouping of genotypes; ear weight, ear diameter, and grain yield were the traits that most contributed to the analysis of genetic diversity.

Quantitative proteomics reveals the mechanism and consequence of gliotoxin-mediated dysregulation of the methionine cycle in Aspergillus niger.

PubMed

Manzanares-Miralles, Lara; Sarikaya-Bayram, Özlem; Smith, Elizabeth B; Dolan, Stephen K; Bayram, Özgür; Jones, Gary W; Doyle, Sean

2016-01-10

Gliotoxin (GT) is a redox-active metabolite, produced by Aspergillus fumigatus, which inhibits the growth of other fungi. Here we demonstrate how Aspergillus niger responds to GT exposure. Quantitative proteomics revealed that GT dysregulated the abundance of 378 proteins including those involved in methionine metabolism and induced de novo abundance of two S-adenosylmethionine (SAM)-dependent methyltransferases. Increased abundance of enzymes S-adenosylhomocysteinase (p=0.0018) required for homocysteine generation from S-adenosylhomocysteine (SAH), and spermidine synthase (p=0.0068), involved in the recycling of Met, was observed. Analysis of Met-related metabolites revealed significant increases in the levels of Met and adenosine, in correlation with proteomic data. Methyltransferase MT-II is responsible for bisthiobis(methylthio)gliotoxin (BmGT) formation, deletion of MT-II abolished BmGT formation and led to increased GT sensitivity in A. niger. Proteomic analysis also revealed that GT exposure also significantly (p<0.05) increased hydrolytic enzyme abundance, including glycoside hydrolases (n=22) and peptidases (n=16). We reveal that in an attempt to protect against the detrimental affects of GT, methyltransferase-mediated GT thiomethylation alters cellular pathways involving Met and SAM, with consequential dysregulation of hydrolytic enzyme abundance in A. niger. Thus, it provides new opportunities to exploit the response of GT-naïve fungi to GT. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantification of febuxostat polymorphs using powder X-ray diffraction technique.

PubMed

Qiu, Jing-bo; Li, Gang; Sheng, Yue; Zhu, Mu-rong

2015-03-25

Febuxostat is a pharmaceutical compound with more than 20 polymorphs of which form A is most widely used and usually exists in a mixed polymorphic form with form G. In the present study, a quantification method for polymorphic form A and form G of febuxostat (FEB) has been developed using powder X-ray diffraction (PXRD). Prior to development of a quantification method, pure polymorphic form A and form G are characterized. A continuous scan with a scan rate of 3° min(-1) over an angular range of 3-40° 2θ is applied for the construction of the calibration curve using the characteristic peaks of form A at 12.78° 2θ (I/I0100%) and form G at 11.72° 2θ (I/I0100%). The linear regression analysis data for the calibration plots shows good linear relationship with R(2)=0.9985 with respect to peak area in the concentration range 10-60 wt.%. The method is validated for precision, recovery and ruggedness. The limits of detection and quantitation are 1.5% and 4.6%, respectively. The obtained results prove that the method is repeatable, sensitive and accurate. The proposed developed PXRD method can be applied for the quantitative analysis of mixtures of febuxostat polymorphs (forms A and G). Copyright © 2015 Elsevier B.V. All rights reserved.

Performance evaluation of dispersion parameterization schemes in the plume simulation of FFT-07 diffusion experiment

NASA Astrophysics Data System (ADS)

Pandey, Gavendra; Sharan, Maithili

2018-01-01

Application of atmospheric dispersion models in air quality analysis requires a proper representation of the vertical and horizontal growth of the plume. For this purpose, various schemes for the parameterization of dispersion parameters σ‧s are described in both stable and unstable conditions. These schemes differ on the use of (i) extent of availability of on-site measurements (ii) formulations developed for other sites and (iii) empirical relations. The performance of these schemes is evaluated in an earlier developed IIT (Indian Institute of Technology) dispersion model with the data set in single and multiple releases conducted at Fusion Field Trials, Dugway Proving Ground, Utah 2007. Qualitative and quantitative evaluation of the relative performance of all the schemes is carried out in both stable and unstable conditions in the light of (i) peak/maximum concentrations, and (ii) overall concentration distribution. The blocked bootstrap resampling technique is adopted to investigate the statistical significance of the differences in performances of each of the schemes by computing 95% confidence limits on the parameters FB and NMSE. The various analysis based on some selected statistical measures indicated consistency in the qualitative and quantitative performances of σ schemes. The scheme which is based on standard deviation of wind velocity fluctuations and Lagrangian time scales exhibits a relatively better performance in predicting the peak as well as the lateral spread.

Security Events and Vulnerability Data for Cybersecurity Risk Estimation.

PubMed

Allodi, Luca; Massacci, Fabio

2017-08-01

Current industry standards for estimating cybersecurity risk are based on qualitative risk matrices as opposed to quantitative risk estimates. In contrast, risk assessment in most other industry sectors aims at deriving quantitative risk estimations (e.g., Basel II in Finance). This article presents a model and methodology to leverage on the large amount of data available from the IT infrastructure of an organization's security operation center to quantitatively estimate the probability of attack. Our methodology specifically addresses untargeted attacks delivered by automatic tools that make up the vast majority of attacks in the wild against users and organizations. We consider two-stage attacks whereby the attacker first breaches an Internet-facing system, and then escalates the attack to internal systems by exploiting local vulnerabilities in the target. Our methodology factors in the power of the attacker as the number of "weaponized" vulnerabilities he/she can exploit, and can be adjusted to match the risk appetite of the organization. We illustrate our methodology by using data from a large financial institution, and discuss the significant mismatch between traditional qualitative risk assessments and our quantitative approach. © 2017 Society for Risk Analysis.

Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.

PubMed

Sreedharan, Vipin T; Schultheiss, Sebastian J; Jean, Géraldine; Kahles, André; Bohnert, Regina; Drewe, Philipp; Mudrakarta, Pramod; Görnitz, Nico; Zeller, Georg; Rätsch, Gunnar

2014-05-01

We present Oqtans, an open-source workbench for quantitative transcriptome analysis, that is integrated in Galaxy. Its distinguishing features include customizable computational workflows and a modular pipeline architecture that facilitates comparative assessment of tool and data quality. Oqtans integrates an assortment of machine learning-powered tools into Galaxy, which show superior or equal performance to state-of-the-art tools. Implemented tools comprise a complete transcriptome analysis workflow: short-read alignment, transcript identification/quantification and differential expression analysis. Oqtans and Galaxy facilitate persistent storage, data exchange and documentation of intermediate results and analysis workflows. We illustrate how Oqtans aids the interpretation of data from different experiments in easy to understand use cases. Users can easily create their own workflows and extend Oqtans by integrating specific tools. Oqtans is available as (i) a cloud machine image with a demo instance at cloud.oqtans.org, (ii) a public Galaxy instance at galaxy.cbio.mskcc.org, (iii) a git repository containing all installed software (oqtans.org/git); most of which is also available from (iv) the Galaxy Toolshed and (v) a share string to use along with Galaxy CloudMan.

Evaluation of metal biouptake from the analysis of bulk metal depletion kinetics at various cell concentrations: theory and application.

PubMed

Rotureau, Elise; Billard, Patrick; Duval, Jérôme F L

2015-01-20

Bioavailability of trace metals is a key parameter for assessment of toxicity on living organisms. Proper evaluation of metal bioavailability requires monitoring the various interfacial processes that control metal partitioning dynamics at the biointerface, which includes metal transport from solution to cell membrane, adsorption at the biosurface, internalization, and possible excretion. In this work, a methodology is proposed to quantitatively describe the dynamics of Cd(II) uptake by Pseudomonas putida. The analysis is based on the kinetic measurement of Cd(II) depletion from bulk solution at various initial cell concentrations using electroanalytical probes. On the basis of a recent formalism on the dynamics of metal uptake by complex biointerphases, the cell concentration-dependent depletion time scales and plateau values reached by metal concentrations at long exposure times (>3 h) are successfully rationalized in terms of limiting metal uptake flux, rate of excretion, and metal affinity to internalization sites. The analysis shows the limits of approximate depletion models valid in the extremes of high and weak metal affinities. The contribution of conductive diffusion transfer of metals from the solution to the cell membrane in governing the rate of Cd(II) uptake is further discussed on the basis of estimated resistances for metal membrane transfer and extracellular mass transport.

Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities

PubMed Central

Tomasso, Maria E.; Tarver, Micheal J.; Devarajan, Deepa; Whitten, Steven T.

2016-01-01

The properties of disordered proteins are thought to depend on intrinsic conformational propensities for polyproline II (PP II) structure. While intrinsic PP II propensities have been measured for the common biological amino acids in short peptides, the ability of these experimentally determined propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs) has not been established. Presented here are results from molecular simulations of disordered proteins showing that the hydrodynamic radius (R h) can be predicted from experimental PP II propensities with good agreement, even when charge-based considerations are omitted. The simulations demonstrate that R h and chain propensity for PP II structure are linked via a simple power-law scaling relationship, which was tested using the experimental R h of 22 IDPs covering a wide range of peptide lengths, net charge, and sequence composition. Charge effects on R h were found to be generally weak when compared to PP II effects on R h. Results from this study indicate that the hydrodynamic dimensions of IDPs are evidence of considerable sequence-dependent backbone propensities for PP II structure that qualitatively, if not quantitatively, match conformational propensities measured in peptides. PMID:26727467

26 CFR 1.6045B-1 - Returns relating to actions affecting basis of securities.

Code of Federal Regulations, 2012 CFR

2012-04-01

... measured for the action. (v) Effect of the action. The quantitative effect of the organizational action on... issuer may file the return before the organizational action if the quantitative effect on basis is determinable beforehand. (ii) Reasonable assumptions. To report the quantitative effect on basis by the due...

75 FR 18571 - Agency Information Collection Activities: Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-12

... Comprehensive Quantitative Impact Study.'' The OCC has also given notice that it has sent this collection to OMB... following new information collection: Title: Basel Comprehensive Quantitative Impact Study. OMB Control No... the Basel II Capital Accord, the Basel Committee will conduct a quantitative impact study (QIS) to...

26 CFR 1.6045B-1 - Returns relating to actions affecting basis of securities.

Code of Federal Regulations, 2011 CFR

2011-04-01

... measured for the action. (v) Effect of the action. The quantitative effect of the organizational action on... issuer may file the return before the organizational action if the quantitative effect on basis is determinable beforehand. (ii) Reasonable assumptions. To report the quantitative effect on basis by the due...

26 CFR 1.6045B-1 - Returns relating to actions affecting basis of securities.

Code of Federal Regulations, 2013 CFR

2013-04-01

... measured for the action. (v) Effect of the action. The quantitative effect of the organizational action on... issuer may file the return before the organizational action if the quantitative effect on basis is determinable beforehand. (ii) Reasonable assumptions. To report the quantitative effect on basis by the due...

Feasibility of atmospheric pressure desorption/ionization on silicon mass spectrometry in analysis of drugs.

PubMed

Huikko, K; Ostman, P; Sauber, C; Mandel, F; Grigoras, K; Franssila, S; Kotiaho, T; Kostiainen, R

2003-01-01

The feasibility of atmospheric pressure desorption/ionization on silicon mass spectrometry (AP-DIOS-MS) for drug analysis was investigated. It was observed that only compounds with relative high proton affinity are efficiently ionized under AP-DIOS conditions. The limits of detection (LODs) achieved in MS mode with midazolam, propranolol, and angiotensin II were 80 fmol, 20 pmol, and 1 pmol, respectively. In MS/MS mode the LODs for midazolam and propranolol were 10 fmol and 5 pmol, respectively. The good linearity (r(2) > 0.991), linear dynamic range of 3 orders of magnitude, and reasonable repeatability showed that the method is suitable for quantitative analysis. Copyright 2003 John Wiley & Sons, Ltd.

Quantitative proteome analysis of barley seeds using ruthenium(II)-tris-(bathophenanthroline-disulphonate) staining.

PubMed

Witzel, Katja; Surabhi, Giridara-Kumar; Jyothsnakumari, Gottimukkala; Sudhakar, Chinta; Matros, Andrea; Mock, Hans-Peter

2007-04-01

This paper describes the application of the recently introduced fluorescence stain Ruthenium(II)-tris-(bathophenanthroline-disulphonate) (RuBP) on a comparative proteome analysis of two phenotypically different barley lines. We carried out an analysis of protein patterns from 2-D gels of the parental lines of the Oregon Wolfe Barley mapping population DOM and REC and stained with either the conventional colloidal Coomassie Brilliant Blue (cCBB) or with the novel RuBP solution. We wished to experimentally verify the usefulness of such a stain in evaluating the complex pattern of a seed proteome, in comparison to the previously used cCBB staining technique. To validate the efficiency of visualization by both stains, we first compared the overall number of detected protein spots. On average, 790 spots were visible by cCBB staining and 1200 spots by RuBP staining. Then, the intensity of a set of spots was assessed, and changes in relative abundance were determined using image analysis software. As expected, staining with RuBP performed better in quantitation in terms of sensitivity and dynamic range. Furthermore, spots from a cultivar-specific region in the protein map were chosen for identification to asses the gain of biological information due to the staining procedure. From this particular region, eight spots were visualized exclusively by RuBP and identification was successful for all spots, proving the ability to identify even very low abundant proteins. Performance in MS analysis was comparable for both protein stains. Proteins were identified by MALDI-TOF MS peptide mass fingerprinting. This approach was not successful for all spots, due to the restricted entry number for barley in the database. Therefore, we subsequently used LC-ESI-Q-TOF MS/MS and de novo sequencing for identification. Because only an insufficient number of proteins from barley is annotated, an EST-based identification strategy was chosen for our experiment. We wished to test whether under these limitations the application of a more sensitive stain would lead to a more advanced proteome approach. In summary, we demonstrate here that the application of RuBP as an economical but reliable and sensitive fluorescence stain is highly suitable for quantitative proteome analysis of plant seeds.

Diagnostic value of succinate ubiquinone reductase activity in the identification of patients with mitochondrial DNA depletion.

PubMed

Hargreaves, P; Rahman, S; Guthrie, P; Taanman, J W; Leonard, J V; Land, J M; Heales, S J R

2002-02-01

Mitochondrial DNA (mtDNA) depletion syndrome (McKusick 251880) is characterized by a progressive quantitative loss of mtDNA resulting in severe mitochondrial dysfunction. A diagnosis of mtDNA depletion can only be confirmed after Southern blot analysis of affected tissue. Only a limited number of centres have the facilities to offer this service, and this is frequently on an irregular basis. There is therefore a need for a test that can refine sample selection as well as complementing the molecular analysis. In this study we compared the activities of the nuclear-encoded succinate ubiquinone reductase (complex II) to the activities of the combined mitochondrial and nuclear-encoded mitochondrial electron transport chain (ETC) complexes; NADH:ubiquinone reductase (complex I), ubiquinol-cytochrome-c reductase (complex III), and cytochrome-c oxidase (complex IV), in skeletal muscle biopsies from 7 patients with confirmed mtDNA depletion. In one patient there was no evidence of an ETC defect. However, the remaining 6 patients exhibited reduced complex I and IV activities. Five of these patients also displayed reduced complex II-III (succinate:cytochrome-c reductase) activity. Individual measurement of complex II and complex III activities demonstrated normal levels of complex II activity compared to complex III, which was reduced in the 5 biopsies assayed. These findings suggest a possible diagnostic value for the detection of normal levels of complex II activity in conjunction with reduced complex I, III and IV activity in the identification of likely candidates for mtDNA depletion syndrome

Speciation analysis of Mn(II)/Mn(VII) using Fe3O4@ionic liquids-β-cyclodextrin polymer magnetic solid phase extraction coupled with ICP-OES.

PubMed

Chen, Songqing; Qin, Xingxiu; Gu, Weixi; Zhu, Xiashi

2016-12-01

Ionic liquids-β-cyclodextrin polymer (ILs-β-CDCP) was attached on Fe 3 O 4 nanoparticles to prepare magnetic solid phase extraction agent (Fe 3 O 4 @ILs-β-CDCP). The properties and morphology of Fe 3 O 4 @ILs-β-CDCP were characterized by Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction(XRD), size distribution and magnetic analysis. A new method of magnetic solid phase extraction (MSPE) coupled to ICP-OES for the speciation of Mn(II)/Mn(VII) in water samples was established. The results showed that Mn(VII) and total manganese [Mn(II)+Mn(VII)] were quantitatively extracted after adjusting aqueous sample solution to pH 6.0 and 10.0, respectively. Mn(II) was calculated by subtraction of Mn(VII) from total manganese. Fe 3 O 4 @ILs-β-CDCP showed a higher adsorption capacity toward Mn(II) and Mn(VII). Several factors, such as the pH value, extraction temperature and sample volume, were optimized to achieve the best extraction efficiency. Moreover, the adsorption ability of Fe 3 O 4 @ILs-β-CDCP would not be significantly lower after reusing of 10 times. The accuracy of the developed method was confirmed by analyzing certified reference materials (GSB 07-1189-2000), and by spiking spring water, city water and lake water samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Selective flotation-spectrophotometric determination of trace copper(II) in natural waters, human blood and drug samples using phenanthraquinone monophenylthiosemicarbazone.

PubMed

Khalifa, M E; Akl, M A; Ghazy, S E

2001-06-01

Copper(II) forms 1:1 and 1:2 intense red complexes with phenanthraquinone monophenylthiosemicarbazone (PPT) at pH 3-3.5 and > or =6.5, respectively. These complexes exhibit maximal absorbance at 545 and 517 nm, the molar absorptivity being 2.3 x 10(4) and 4.8 x 10(4) l mol(-1) cm(-1), respectively. However, the 1:1 complex was quantitatively floated with oleic acid (HOL) surfactant in the pH range 4.5-5.5, providing a highly selective and sensitive procedure for the spectrophotometric determination of CuII. The molar absorptivity of the floated Cu-PPT complex was 1.5 x 10(5) l mol)(-1) cm(-1). Beer's law was obeyed over the range 3-400 ppb at 545 nm. The analytical parameters affecting the flotation process and hence the determination of copper traces were reported. Also, the structure of the isolated solid complex and the mechanism of flotation were suggested. Moreover, the procedure was successfully applied to the analysis of CuII in natural waters, serum blood and some drug samples.

Using bio-dispersive solution of chitosan for green dispersive liquid-liquid microextraction of trace amounts of Cu(II) in edible oils prior to analysis by ICP-OES.

PubMed

Limchoowong, Nunticha; Sricharoen, Phitchan; Techawongstien, Suchila; Chanthai, Saksit

2017-09-01

A green approach using chitosan solution as a novel bio-dispersive agent for the dispersive liquid-liquid microextraction (DLLME) of trace amounts of Cu(II) in edible oils is presented. An emulsion was formed by mixing the oil sample with 300µL of 0.25% (w/v) chitosan solution containing 200µL of 6molL -1 HCl. Deionized water was used to induce emulsion breaking without centrifugation. The centrifuged Cu(II) extract was collected and analyzed using an inductively coupled plasma-optical emission spectrometer. The detection and quantitation limits were 2.1 and 6.8µgL -1 , respectively. Trace amounts of Cu(II) in six edible oil samples were tested under optimum conditions for DLLME, with a recovery ranging from 90.3% to 109.3%. Therefore, the new dispersive agent in DLLME offers superior performance owing to the non-toxic nature of the solvent, short extraction time, high sensitivity, and easy operation. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Relation Between Inflation in Type-I and Type-II Error Rate and Population Divergence in Genome-Wide Association Analysis of Multi-Ethnic Populations.

PubMed

Derks, E M; Zwinderman, A H; Gamazon, E R

2017-05-01

Population divergence impacts the degree of population stratification in Genome Wide Association Studies. We aim to: (i) investigate type-I error rate as a function of population divergence (F ST ) in multi-ethnic (admixed) populations; (ii) evaluate the statistical power and effect size estimates; and (iii) investigate the impact of population stratification on the results of gene-based analyses. Quantitative phenotypes were simulated. Type-I error rate was investigated for Single Nucleotide Polymorphisms (SNPs) with varying levels of F ST between the ancestral European and African populations. Type-II error rate was investigated for a SNP characterized by a high value of F ST . In all tests, genomic MDS components were included to correct for population stratification. Type-I and type-II error rate was adequately controlled in a population that included two distinct ethnic populations but not in admixed samples. Statistical power was reduced in the admixed samples. Gene-based tests showed no residual inflation in type-I error rate.

Development of a particle-trap preconcentration-soft ionization mass spectrometric technique for the quantification of mercury halides in air.

PubMed

Deeds, Daniel A; Ghoshdastidar, Avik; Raofie, Farhad; Guérette, Élise-Andrée; Tessier, Alain; Ariya, Parisa A

2015-01-01

Measurement of oxidized mercury, Hg(II), in the atmosphere poses a significant analytical challenge as Hg(II) is present at ultra-trace concentrations (picograms per cubic meter air). Current technologies are sufficiently sensitive to measure the total Hg present as Hg(II) but cannot determine the chemical speciation of Hg(II). We detail here the development of a soft ionization mass spectrometric technique coupled with preconcentration onto nano- or microparticle-based traps prior to analysis for the measurement of mercury halides in air. The current methodology has comparable detection limits (4-11 pg m(-3)) to previously developed techniques for the measurement of total inorganic mercury in air while allowing for the identification of HgX2 in collected samples. Both mercury chloride and mercury bromide have been sporadically detected in Montreal urban and indoor air using atmospheric pressure chemical ionization-mass spectrometry (APCI-MS). We discuss limitations and advantages of the current technique and discuss potential avenues for future research including quantitative trace measurements of a larger range of mercury compounds.

A magnesium-induced triplex pre-organizes the SAM-II riboswitch

PubMed Central

Roy, Susmita; Lammert, Heiko; Dayie, T. Kwaku; Sanbonmatsu, Karissa Y.

2017-01-01

Our 13C- and 1H-chemical exchange saturation transfer (CEST) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, all-atom structure-based molecular simulations, with the electrostatic effects of Manning counter-ion condensation and explicit magnesium ions are employed to calculate the folding free energy landscape of the SAM-II riboswitch. We use this analysis to predict that magnesium ions remodel the landscape, shifting the equilibrium away from the extended, partially unfolded state towards a compact, pre-organized conformation that resembles the ligand-bound state. Our CEST and SAXS experiments, at different magnesium ion concentrations, quantitatively confirm our simulation results, demonstrating that magnesium ions induce collapse and pre-organization. Agreement between theory and experiment bolsters microscopic interpretation of our simulations, which shows that triplex formation between helix P2b and loop L1 is highly sensitive to magnesium and plays a key role in pre-organization. Pre-organization of the SAM-II riboswitch allows rapid detection of ligand with high selectivity, which is important for biological function. PMID:28248966

Is Weapon System Cost Growth Increasing? A Quantitative Assessment of Completed and Ongoing Programs

DTIC Science & Technology

2007-01-01

analysis of the point at five years past MS B may be prudent. 49 APPENDIX A Completed Programs Aircraft A-7D Corsair II Data are from September 1969...rocket vehicle used to deploy satellites to higher orbits from the space shuttle payload bay or atop the Titan IV booster. SARs report that quantities...Cost Growth Increasing? Other Common Strategic Rotary Launcher This program designed and built mechanisms housed within bomb bays to accommodate the

POWTEX Neutron Diffractometer at FRM II - New Perspectives in Rock Deformation and Recrystallisation Analysis

NASA Astrophysics Data System (ADS)

Walter, J. M.; Stipp, M.; Ullemeyer, K.; Klein, H.; Leiss, B.; Hansen, B.; Kuhs, W. F.

2011-12-01

Neutron diffraction has become a routine method in Geoscience for the quantitative analysis of crystallographic preferred orientations (CPOs) and for (experimental) powder diffraction. Quantitative texture analysis is a common tool for the investigation of fabric development in mono- and polyphase rocks, their deformation histories and kinematics. Furthermore the quantitative characterization of anisotropic physical properties by bulk texture measurements can be achieved due to the high penetration capabilities of neutrons. To cope with increasing needs for beam time at neutron diffraction facilities with the corresponding technical characteristics and equipment, POWTEX (POWder and TEXture Diffractometer) is designed as a high-intensity diffractometer at the neutron research reactor FRM II in Garching, Germany by groups from the RWTH Aachen, Forschungszentrum Jülich and the University of Göttingen. Complementary to existing neutron diffractometers (SKAT at Dubna, Russia; GEM at ISIS, UK; HIPPO at Los Alamos, USA; D20 at ILL, France; and the local STRESS-SPEC and SPODI at FRM II) the layout of POWTEX is focused on fast (texture) measurements for either time-resolved experiments or the measurement of larger sample series as necessary for the study of large scale geological structures. By utilizing a range of neutron wavelengths simultaneously (TOF-technique), a high flux (~1 x 107 n/cm2s) and a high detector coverage ( 9.8 sr) effective texture measurements without sample tilting and rotation are possible. Furthermore the instrument and the angular detector resolution is sufficient for strong recrystallisation textures as well as weak textures of polyphase rocks. Thereby large sample environments will be implemented at POWTEX allowing in-situ time-resolved texture measurements during deformation experiments on rocksalt, ice and other materials. Furthermore a furnace for 3D-recrystallisation analysis of single grains will be realized complementary to the furnace that already exists for fine grained materials at the synchrotron beamline BW5 at HASYLAB, Germany (e.g. Klein et al. 2009). The in-situ triaxial deformation apparatus is operated by a uniaxial spindle drive with a maximum axial load of 200 kN, which will be redesigned to minimize shadowing effects on the detector. The HT experiments will be carried out in uniaxial compression or extension and an upgrade to triaxial deformation conditions is envisaged. The load frame can alternatively be used for ice deformation by inserting a cryostat cell for temperatures down to 77 K with a triaxial apparatus allowing also simple shear experiments on ice. Strain rates range between 10-8 and 10-3 s-1 reaching to at least 50 % axial strain. The furnace for the recrystallization analysis will be a mirror furnace with temperatures up to 1500° C, which will be rotatable around a vertical axis to obtain the required stereologic orientation information.

A proof for substitution of endogenous iron (II) in lipoxygenase by exogenous Cu2+.

PubMed

Cai, Yan; Xu, Hong; Xia, Yongmei; Su, Yafen; Fang, Yun

2010-10-01

Soybean lipoxygenase (LOX) contains endogenous iron (II) at the active site, which is important for the enzyme activity. The activity of LOX can be accelerated by some exogenous metal ions including Cu2+. However, the mechanism of the activity improvement caused by exogenous metal ions remains unclear, not only for LOX but for most other metalloenzymes. Meanwhile, the possibility that exogenous metal ions can displace endogenous iron (II) is still in discussion for a lack of a direct and quantitative proof. In this paper, a quantitative proof of replacing iron (II) inside LOX by exogenous Cu2+ was provided, simply using UV-Vis spectrometry with two indicators p-carboxylantipyrylazo and 9-(4-carboxyphenyl)-2,3,7-trihydroxyl-6-fluorine. A 0.56 microM free iron (II) was observed in the bulk solution after incubating 9.45 microM Cu2+ with 16.10 microM LOX at 20 degrees C for 5 min, which is in coincidence with the decrement of Cu2+ in the bulk solution (0.53 microM), implying that iron (II) was replaced by Cu2+.

The expression ratio of Map7/B2M is prognostic for survival in patients with stage II colon cancer.

PubMed

Blum, Craig; Graham, Amanda; Yousefzadeh, Matt; Shrout, Jessica; Benjamin, Katie; Krishna, Murli; Hoda, Raza; Hoda, Rana; Cole, David J; Garrett-Mayer, Elizabeth; Reed, Carolyn; Wallace, Michael; Mitas, Michael

2008-09-01

Colorectal cancer (CRC) is the second most frequent cause of cancer-related death in the United States. To determine whether certain molecular markers might be prognostic for survival, we measured by quantitative real-time RT-PCR the expression levels of 15 previously studied genes that are known to be up-regulated or down-regulated in the progression of epithelial cancers. The tumor samples were extracted from formalin-fixed paraffin-embedded primary tissues derived from patients with Stage II CRC who developed disease recurrence within two years (n=10), or were disease-free for at least 4 years (n=12). We were able to determine, by AUC curve analysis, that the ratio of microtubule associated protein 7 (Map7)/B2M was predictive of outcome in our sample set. Further, using Kaplan-Meier survival analysis, we observed significantly different curves as a function of marker positivity for the Map7/B2M (p=0.0001; HR=11) expression ratio. This suggests that the expression ratio of Map7/B2M may serve as a valuable prognostic marker in patients with Stage II colon cancer, and potentially guide therapeutic decision making.

The expression ratio of Map7/B2M is prognostic for survival in patients with stage II colon cancer

PubMed Central

BLUM, CRAIG; GRAHAM, AMANDA; YOUSEFZADEH, MATT; SHROUT, JESSICA; BENJAMIN, KATIE; KRISHNA, MURLI; HODA, RAZA; HODA, RANA; COLE, DAVID J.; GARRETT-MAYER, ELIZABETH; REED, CAROLYN; WALLACE, MICHAEL; MITAS, MICHAEL

2012-01-01

Colorectal cancer (CRC) is the second most frequent cause of cancer-related death in the United States. To determine whether certain molecular markers might be prognostic for survival, we measured by quantitative real-time RT-PCR the expression levels of 15 previously studied genes that are known to be up-regulated or down-regulated in the progression of epithelial cancers. The tumor samples were extracted from formalin-fixed paraffin-embedded primary tissues derived from patients with Stage II CRC who developed disease recurrence within two years (n=10), or were disease-free for at least 4 years (n=12). We were able to determine, by AUC curve analysis, that the ratio of microtubule associated protein 7 (Map7)/B2M was predictive of outcome in our sample set. Further, using Kaplan-Meier survival analysis, we observed significantly different curves as a function of marker positivity for the Map7/B2M (p=0.0001; HR=11) expression ratio. This suggests that the expression ratio of Map7/B2M may serve as a valuable prognostic marker in patients with Stage II colon cancer, and potentially guide therapeutic decision making. PMID:18695889

Effect of sample preparation method on quantification of polymorphs using PXRD.

PubMed

Alam, Shahnwaz; Patel, Sarsvatkumar; Bansal, Arvind Kumar

2010-01-01

The purpose of this study was to improve the sensitivity and accuracy of quantitative analysis of polymorphic mixtures. Various techniques such as hand grinding and mixing (in mortar and pestle), air jet milling and ball milling for micronization of particle and mixing were used to prepare binary mixtures. Using these techniques, mixtures of form I and form II of clopidogrel bisulphate were prepared in various proportions from 0-5% w/w of form I in form II and subjected to x-ray powder diffraction analysis. In order to obtain good resolution in minimum time, step time and step size were varied to optimize scan rate. Among the six combinations, step size of 0.05 degrees with step time of 5 s demonstrated identification of maximum characteristic peaks of form I in form II. Data obtained from samples prepared using both grinding and mixing in ball mill showed good analytical sensitivity and accuracy compared to other methods. Powder x-ray diffraction method was reproducible, precise with LOD of 0.29% and LOQ of 0.91%. Validation results showed excellent correlation between actual and predicted concentration with R2 > 0.9999.

Molecular Cloning and Expression Analysis of Eight PgWRKY Genes in Panax ginseng Responsive to Salt and Hormones.

PubMed

Xiu, Hao; Nuruzzaman, Mohammed; Guo, Xiangqian; Cao, Hongzhe; Huang, Jingjia; Chen, Xianghui; Wu, Kunlu; Zhang, Ru; Huang, Yuzhao; Luo, Junli; Luo, Zhiyong

2016-03-04

Despite the importance of WRKY genes in plant physiological processes, little is known about their roles in Panax ginseng C.A. Meyer. Forty-eight unigenes on this species were previously reported as WRKY transcripts using the next-generation sequencing (NGS) technology. Subsequently, one gene that encodes PgWRKY1 protein belonging to subgroup II-d was cloned and functionally characterized. In this study, eight WRKY genes from the NGS-based transcriptome sequencing dataset designated as PgWRKY2-9 have been cloned and characterized. The genes encoding WRKY proteins were assigned to WRKY Group II (one subgroup II-c, four subgroup II-d, and three subgroup II-e) based on phylogenetic analysis. The cDNAs of the cloned PgWRKYs encode putative proteins ranging from 194 to 358 amino acid residues, each of which includes one WRKYGQK sequence motif and one C₂H₂-type zinc-finger motif. Quantitative real-time PCR (qRT-PCR) analysis demonstrated that the eight analyzed PgWRKY genes were expressed at different levels in various organs including leaves, roots, adventitious roots, stems, and seeds. Importantly, the transcription responses of these PgWRKYs to methyl jasmonate (MeJA) showed that PgWRKY2, PgWRKY3, PgWRKY4, PgWRKY5, PgWRKY6, and PgWRKY7 were downregulated by MeJA treatment, while PgWRKY8 and PgWRKY9 were upregulated to varying degrees. Moreover, the PgWRKY genes increased or decreased by salicylic acid (SA), abscisic acid (ABA), and NaCl treatments. The results suggest that the PgWRKYs may be multiple stress-inducible genes responding to both salt and hormones.

Portable paper-based device for quantitative colorimetric assays relying on light reflectance principle.

PubMed

Li, Bowei; Fu, Longwen; Zhang, Wei; Feng, Weiwei; Chen, Lingxin

2014-04-01

This paper presents a novel paper-based analytical device based on the colorimetric paper assays through its light reflectance. The device is portable, low cost (<20 dollars), and lightweight (only 176 g) that is available to assess the cost-effectiveness and appropriateness of the original health care or on-site detection information. Based on the light reflectance principle, the signal can be obtained directly, stably and user-friendly in our device. We demonstrated the utility and broad applicability of this technique with measurements of different biological and pollution target samples (BSA, glucose, Fe, and nitrite). Moreover, the real samples of Fe (II) and nitrite in the local tap water were successfully analyzed, and compared with the standard UV absorption method, the quantitative results showed good performance, reproducibility, and reliability. This device could provide quantitative information very conveniently and show great potential to broad fields of resource-limited analysis, medical diagnostics, and on-site environmental detection. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multifractal spectrum and lacunarity as measures of complexity of osseointegration.

PubMed

de Souza Santos, Daniel; Dos Santos, Leonardo Cavalcanti Bezerra; de Albuquerque Tavares Carvalho, Alessandra; Leão, Jair Carneiro; Delrieux, Claudio; Stosic, Tatijana; Stosic, Borko

2016-07-01

The goal of this study is to contribute to a better quantitative description of the early stages of osseointegration, by application of fractal, multifractal, and lacunarity analysis. Fractal, multifractal, and lacunarity analysis are performed on scanning electron microscopy (SEM) images of titanium implants that were first subjected to different treatment combinations of i) sand blasting, ii) acid etching, and iii) exposition to calcium phosphate, and were then submersed in a simulated body fluid (SBF) for 30 days. All the three numerical techniques are applied to the implant SEM images before and after SBF immersion, in order to provide a comprehensive set of common quantitative descriptors. It is found that implants subjected to different physicochemical treatments before submersion in SBF exhibit a rather similar level of complexity, while the great variety of crystal forms after SBF submersion reveals rather different quantitative measures (reflecting complexity), for different treatments. In particular, it is found that acid treatment, in most combinations with the other considered treatments, leads to a higher fractal dimension (more uniform distribution of crystals), lower lacunarity (lesser variation in gap sizes), and narrowing of the multifractal spectrum (smaller fluctuations on different scales). The current quantitative description has shown the capacity to capture the main features of complex images of implant surfaces, for several different treatments. Such quantitative description should provide a fundamental tool for future large scale systematic studies, considering the large variety of possible implant treatments and their combinations. Quantitative description of early stages of osseointegration on titanium implants with different treatments should help develop a better understanding of this phenomenon, in general, and provide basis for further systematic experimental studies. Clinical practice should benefit from such studies in the long term, by more ready access to implants of higher quality.

Quantitative determination and evaluation of Paris polyphylla var. yunnanensis with different harvesting times using UPLC-UV-MS and FT-IR spectroscopy in combination with partial least squares discriminant analysis.

PubMed

Yang, Yuan-Gui; Zhang, Ji; Zhao, Yan-Li; Zhang, Jin-Yu; Wang, Yuan-Zhong

2017-07-01

A rapid method was developed and validated by ultra-performance liquid chromatography-triple quadrupole mass spectroscopy with ultraviolet detection (UPLC-UV-MS) for simultaneous determination of paris saponin I, paris saponin II, paris saponin VI and paris saponin VII. Partial least squares discriminant analysis (PLS-DA) based on UPLC and Fourier transform infrared (FT-IR) spectroscopy was employed to evaluate Paris polyphylla var. yunnanensis (PPY) at different harvesting times. Quantitative determination implied that the various contents of bioactive compounds with different harvesting times may lead to different pharmacological effects; the average content of total saponins for PPY harvested at 8 years was higher than that from other samples. The PLS-DA of FT-IR spectra had a better performance than that of UPLC for discrimination of PPY from different harvesting times. Copyright © 2016 John Wiley & Sons, Ltd.

Recovering the dynamics of root growth and development using novel image acquisition and analysis methods

PubMed Central

Wells, Darren M.; French, Andrew P.; Naeem, Asad; Ishaq, Omer; Traini, Richard; Hijazi, Hussein; Bennett, Malcolm J.; Pridmore, Tony P.

2012-01-01

Roots are highly responsive to environmental signals encountered in the rhizosphere, such as nutrients, mechanical resistance and gravity. As a result, root growth and development is very plastic. If this complex and vital process is to be understood, methods and tools are required to capture the dynamics of root responses. Tools are needed which are high-throughput, supporting large-scale experimental work, and provide accurate, high-resolution, quantitative data. We describe and demonstrate the efficacy of the high-throughput and high-resolution root imaging systems recently developed within the Centre for Plant Integrative Biology (CPIB). This toolset includes (i) robotic imaging hardware to generate time-lapse datasets from standard cameras under infrared illumination and (ii) automated image analysis methods and software to extract quantitative information about root growth and development both from these images and via high-resolution light microscopy. These methods are demonstrated using data gathered during an experimental study of the gravitropic response of Arabidopsis thaliana. PMID:22527394

Statistical methodology: II. Reliability and validity assessment in study design, Part B.

PubMed

Karras, D J

1997-02-01

Validity measures the correspondence between a test and other purported measures of the same or similar qualities. When a reference standard exists, a criterion-based validity coefficient can be calculated. If no such standard is available, the concepts of content and construct validity may be used, but quantitative analysis may not be possible. The Pearson and Spearman tests of correlation are often used to assess the correspondence between tests, but do not account for measurement biases and may yield misleading results. Techniques that measure interest differences may be more meaningful in validity assessment, and the kappa statistic is useful for analyzing categorical variables. Questionnaires often can be designed to allow quantitative assessment of reliability and validity, although this may be difficult. Inclusion of homogeneous questions is necessary to assess reliability. Analysis is enhanced by using Likert scales or similar techniques that yield ordinal data. Validity assessment of questionnaires requires careful definition of the scope of the test and comparison with previously validated tools.

Recovering the dynamics of root growth and development using novel image acquisition and analysis methods.

PubMed

Wells, Darren M; French, Andrew P; Naeem, Asad; Ishaq, Omer; Traini, Richard; Hijazi, Hussein I; Hijazi, Hussein; Bennett, Malcolm J; Pridmore, Tony P

2012-06-05

Roots are highly responsive to environmental signals encountered in the rhizosphere, such as nutrients, mechanical resistance and gravity. As a result, root growth and development is very plastic. If this complex and vital process is to be understood, methods and tools are required to capture the dynamics of root responses. Tools are needed which are high-throughput, supporting large-scale experimental work, and provide accurate, high-resolution, quantitative data. We describe and demonstrate the efficacy of the high-throughput and high-resolution root imaging systems recently developed within the Centre for Plant Integrative Biology (CPIB). This toolset includes (i) robotic imaging hardware to generate time-lapse datasets from standard cameras under infrared illumination and (ii) automated image analysis methods and software to extract quantitative information about root growth and development both from these images and via high-resolution light microscopy. These methods are demonstrated using data gathered during an experimental study of the gravitropic response of Arabidopsis thaliana.

Quantitative T2 mapping evaluation for articular cartilage lesions in a rabbit model of anterior cruciate ligament transection osteoarthritis.

PubMed

Wei, Zheng-mao; Du, Xiang-ke; Huo, Tian-long; Li, Xu-bin; Quan, Guang-nan; Li, Tian-ran; Cheng, Jin; Zhang, Wei-tao

2012-03-01

Quantitative T2 mapping has been a widely used method for the evaluation of pathological cartilage properties, and the histological assessment system of osteoarthritis in the rabbit has been published recently. The aim of the study was to investigate the effectiveness of quantitative T2 mapping evaluation for articular cartilage lesions of a rabbit model of anterior cruciate ligament transection (ACLT) osteoarthritis. Twenty New Zealand White (NZW) rabbits were divided into ACLT surgical group and sham operated group equally. The anterior cruciate ligaments of the rabbits in ACLT group were transected, while the joints were closed intactly in sham operated group. Magnetic resonance (MR) examinations were performed on 3.0T MR unit at week 0, week 6, and week 12. T2 values were computed on GE ADW4.3 workstation. All rabbits were killed at week 13, and left knees were stained with Haematoxylin and Eosin. Semiquantitative histological grading was obtained according to the osteoarthritis cartilage histopathology assessment system. Computerized image analysis was performed to quantitate the immunostained collagen type II. The average MR T2 value of whole left knee cartilage in ACLT surgical group ((29.05±12.01) ms) was significantly higher than that in sham operated group ((24.52±7.97) ms) (P=0.024) at week 6. The average T2 value increased to (32.18±12.79) ms in ACLT group at week 12, but remained near the baseline level ((27.66±8.08) ms) in the sham operated group (P=0.03). The cartilage lesion level of left knee in ACLT group was significantly increased at week 6 (P=0.005) and week 12 (P<0.001). T2 values had positive correlation with histological grading scores, but inverse correlation with optical densities (OD) of type II collagen. This study demonstrated the reliability and practicability of quantitative T2 mapping for the cartilage injury of rabbit ACLT osteoarthritis model.

Near-Infrared II Fluorescence for Imaging Hindlimb Vessel Regeneration with Dynamic Tissue Perfusion Measurement

PubMed Central

Hong, Guosong; Lee, Jerry C.; Jha, Arshi; Diao, Shuo; Nakayama, Karina H.; Hou, Luqia; Doyle, Timothy C.; Robinson, Joshua T.; Antaris, Alexander L.; Dai, Hongjie; Cooke, John P.; Huang, Ngan F.

2014-01-01

Background Real-time vascular imaging that provides both anatomic and hemodynamic information could greatly facilitate the diagnosis of vascular diseases and provide accurate assessment of therapeutic effects. Here we have developed a novel fluorescence-based all-optical method, named near-infrared II (NIR-II) fluorescence imaging, to image murine hindlimb vasculature and blood flow in an experimental model of peripheral arterial disease, by exploiting fluorescence in the NIR-II region (1000–1400 nm) of photon wavelengths. Methods and Results Owing to the reduced photon scattering of NIR-II fluorescence compared to traditional NIR fluorescence imaging and thus much deeper penetration depth into the body, we demonstrated that the mouse hindlimb vasculature could be imaged with higher spatial resolution than in vivo microCT. Furthermore, imaging over 26 days revealed a significant increase in hindlimb microvascular density in response to experimentally induced ischemia within the first 8 days of the surgery (P < 0.005), which was confirmed by histological analysis of microvascular density. Moreover, the tissue perfusion in the ischemic hindlimb could be quantitatively measured by the dynamic NIR-II method, revealing the temporal kinetics of blood flow recovery that resembled microbead-based blood flowmetry and laser Doppler blood spectroscopy. Conclusions The penetration depth of millimeters, high spatial resolution and fast acquisition rate of NIR-II imaging makes it a useful imaging tool for murine models of vascular disease. PMID:24657826

Near-infrared II fluorescence for imaging hindlimb vessel regeneration with dynamic tissue perfusion measurement.

PubMed

Hong, Guosong; Lee, Jerry C; Jha, Arshi; Diao, Shuo; Nakayama, Karina H; Hou, Luqia; Doyle, Timothy C; Robinson, Joshua T; Antaris, Alexander L; Dai, Hongjie; Cooke, John P; Huang, Ngan F

2014-05-01

Real-time vascular imaging that provides both anatomic and hemodynamic information could greatly facilitate the diagnosis of vascular diseases and provide accurate assessment of therapeutic effects. Here, we have developed a novel fluorescence-based all-optical method, named near-infrared II (NIR-II) fluorescence imaging, to image murine hindlimb vasculature and blood flow in an experimental model of peripheral arterial disease, by exploiting fluorescence in the NIR-II region (1000-1400 nm) of photon wavelengths. Because of the reduced photon scattering of NIR-II fluorescence compared with traditional NIR fluorescence imaging and thus much deeper penetration depth into the body, we demonstrated that the mouse hindlimb vasculature could be imaged with higher spatial resolution than in vivo microscopic computed tomography. Furthermore, imaging during 26 days revealed a significant increase in hindlimb microvascular density in response to experimentally induced ischemia within the first 8 days of the surgery (P<0.005), which was confirmed by histological analysis of microvascular density. Moreover, the tissue perfusion in the ischemic hindlimb could be quantitatively measured by the dynamic NIR-II method, revealing the temporal kinetics of blood flow recovery that resembled microbead-based blood flowmetry and laser Doppler blood spectroscopy. The penetration depth of millimeters, high spatial resolution, and fast acquisition rate of NIR-II imaging make it a useful imaging tool for murine models of vascular disease. © 2014 American Heart Association, Inc.

Solid Phase Extraction of Trace Elements in Waterand Tissue Samples on a Mini Column with Diphenylcarbazone Impregnated Nano-TiO2 and Their Determination by Inductively Coupled Plasma Optical Emission Spectrometry

PubMed Central

Baytak, Sıtkı; Arslan, Zikri

2015-01-01

This study presents a simple, robust and environmentally friendly solid phase preconcentration procedure for multielement determination by inductively coupled plasma optical emission spectrometry (ICP-OES) using diphenylcarbazone (DPC) impregnated TiO2 nanopowder (n-TiO2). DPC was successfully impregnated onto n-TiO2 in colloidal solution. A number of elements, including Co(II), Cr(III), Cu(II), Fe(III), Mn(II) and Zn(II) were quantitatively preconcentrated from aqueous solutions between pH 8 and 8.5 at a flow rate of 2 mL min−1, and then eluted with 2 mL of 5% (v/v) HNO3. A mini-column packed with 0.12 g DPC impregnated n-TiO2 retained all elements quantitatively from up to 250 mL multielement solution (2.5 μg per analyte) affording an enrichment factor of 125. The limits of detection (LOD) for preconcentration of 50 mL blank solutions (n = 12) were 0.28, 0.15, 0.25, 0.22, 0.12, and 0.10 μg L−1 for Co, Cr, Cu, Fe, Mn, and Zn, respectively. The relative standard deviation (RSD) for five replicate determinations was 0.8, 3.4, 2.6, 2.2, 1.2 and 3.3% for Co, Cr, Cu, Fe, Mn and Zn, respectively, at 5 μg L−1 level. The method was validated with analysis of Freshwater (SRM 1643e) and Lobster hepatopancreas (TORT-2) certified reference materials, and then applied to the determination of the elements from tap water and lake water samples by ICP-OES. PMID:26236403

The Quantitative Analysis of bFGF and VEGF by ELISA in Human Meningiomas

PubMed Central

Denizot, Yves; De Armas, Rafael; Caire, François; Moreau, Jean Jacques; Pommepuy, Isabelle; Truffinet, Véronique; Labrousse, François

2006-01-01

The quantitative analysis of VEGF using ELISA in various subtypes of grade I meningiomas reported higher VEGF contents in meningothelial (2.38 ± 0.62 pg/μg protein, n = 7), transitional (1.08 ± 0.21 pg/μg protein, n = 13), and microcystic meningiomas (1.98 ± 0.87 pg/μg protein, n = 5) as compared with fibrous ones (0.36 ± 0.09 pg/μg protein, n = 5). In contrast to VEGF, no difference in the concentrations of bFGF was detected. VEGF levels did not correlate with meningioma grade (1.47 ± 0.23 pg/μg versus 2.29 ± 0.58 pg/μg for 32 and 16 grade I and II, resp), vascularisation (1.53 ± 0.41 pg/μg versus 1.96 ± 0.28 pg/μg for 24 low and 24 high vascularisated tumours, resp), and brain invasion (2.32 ± 0.59 pg/μg versus 1.46 ± 0.27 pg/μg for 7 and 41 patients with and without invasion, resp). The ELISA procedure is, thus, an interesting tool to ensure VEGF and bFGF levels in meningiomas and to test putative correlations with clinical parameters. It is, thus, tempting to speculate that ELISA would also be valuable for the quantitative analysis of other angiogenic growth factors and cytokines in intracranial tumours. PMID:17392584

Information Management of a Structured Admissions Interview Process in a Medical College with an Apple II System

PubMed Central

O'Reilly, Robert; Fedorko, Steve; Nicholson, Nigel

1983-01-01

This paper describes a structured interview process for medical school admissions supported by an Apple II computer system which provides feedback to interviewers and the College admissions committee. Presented are the rationale for the system, the preliminary results of analysis of some of the interview data, and a brief description of the computer program and output. The present data show that the structured interview yields very high interrater reliability coefficients, is acceptable to the medical school faculty, and results in quantitative data useful in the admission process. The system continues in development at this time, a second year of data will be shortly available, and further refinements are being made to the computer program to enhance its utilization and exportability.

Collagen type IX from human cartilage: a structural profile of intermolecular cross-linking sites.

PubMed Central

Diab, M; Wu, J J; Eyre, D R

1996-01-01

Type IX collagen, a quantitatively minor collagenous component of cartilage, is known to be associated with and covalently cross-linked to type II collagen fibrils in chick and bovine cartilage. Type IX collagen molecules have also been shown to form covalent cross-links with each other in bovine cartilage. In the present study we demonstrate by structural analysis and location of cross-linking sites that, in human cartilage, type IX collagen is covalently cross-linked to type II collagen and to other molecules of type IX collagen. We also present evidence that, if the proteoglycan form of type IX collagen is present in human cartilage, it can only be a minor component of the matrix, similar to findings with bovine cartilage. PMID:8660302

Type II Modic Changes May not Always Represent Fat Degeneration: A Study Using MR Fat Suppression Sequence.

PubMed

Feng, Zhiyun; Liu, Yuanhao; Wei, Wei; Hu, Shengping; Wang, Yue

2016-08-15

A radiological study of type II Modic changes (MCs). The aim of this study was to determine the characteristics of type II MCs on fat suppression (FS) magnetic resonance (MR) images and its association with radiological disc degeneration. Type II MCs are common endplate signal changes on MR images. On the basis of limited histological samples, type II MCs are thought to be stable fat degeneration. FS technique on MR, which can quantify fat content, may be an alternative to explore the pathology of MCs. To date, however, the characteristics of type II MCs on FS sequence have not been studied. Lumbar MR images conducted in a single hospital during a defined period were reviewed to include those with type II MCs and FS images. On FS images, signal status of type II MCs was visually classified as suppressed or not-suppressed. Signal intensity of vertebral regions with and without MCs was measured quantitatively on T2-weighted (T2W) and FS images to calculate fat content index and validate the visual classification. Using image analysis program Osirix, MCs size and adjacent disc degeneration were measured quantitatively. Paired t-tests and logistic regressions were used to determine the associations studied. Sixty-four lumbar MRIs were included and 150 endplates with type II MCs were studied. Although signal of 37 (24.7%) type II MCs was suppressed on FS images, that of 113 (75.3%) was not suppressed. The discs adjacent to type II MCs had lower signal intensity (0.13 ± 0.003 vs. 0.14 ± 0.004, P < 0.001), lesser disc height (9.73 ± 1.97 vs. 11.07 ± 1.99, P < 0.001) and greater bulging area (80.0 ± 31.4 vs. 61.3 ± 27.5 for anterior bulging, 33.72 ± 21.24 vs. 27.93 ± 12.79 for posterior bulging, and 113.7 ± 39.9 vs. 89.2 ± 35.2 for total bulging, P < 0.05) than normal controls. Type II MCs that were not suppressed on FS image were associated with greater age [odds ratio (OR) = 1.11, P < 0.001], lower height (OR = 0.94, P < 0.05), and greater posterior bulging (OR = 1.05, P < 0.001) at the adjacent disc. Signal of most type II MCs was not suppressed on FS MR images, suggesting that there are ongoing complicated pathologies. Type II MCs may not merely represent fat replacement. 3.

The Role of Angiotensin II/AT1 Receptor Signaling in Regulating Retinal Microglial Activation.

PubMed

Phipps, Joanna A; Vessey, Kirstan A; Brandli, Alice; Nag, Nupur; Tran, Mai X; Jobling, Andrew I; Fletcher, Erica L

2018-01-01

This study explored whether the proangiogenic factor Angiotensin II (AngII) had a direct effect on the activation state of microglia via the Angiotensin type 1 receptor (AT1-R). Microglial dynamic activity was investigated in live retinal flatmounts from adult Cx3Cr1+/GFP mice under control, AngII (5 μM) or AngII (5 μM) + candesartan (0.227 μM) conditions. The effects of intravitreal administration of AngII (10 mM) were also investigated at 24 hours, with retinae processed for immunocytochemistry, flow cytometry, or inflammatory quantitative PCR arrays. We found FACS isolated retinal microglia expressed AT1-R. In retinal flatmounts, microglia showed characteristic movement of processes under control conditions. Perfusion of AngII induced an immediate change in process length (-42%, P < 0.05) and activation state of microglia that was ameliorated by AT1-R blockade, suggesting a direct effect of AngII on microglia via the AT1-R. Intravitreal injection of AngII induced microglial activation after 24 hours, which was characterized by increased soma size (23%, P < 0.001) and decreased process length (20%, P < 0.05). Further analysis indicated a significant decrease in the number of microglial contacts with retinal neurons (saline 15.6 ± 2.31 versus AngII 7.8 ± 1.06, P < 0.05). Retinal cytokine and chemokine expression was modulated, indicative of an inflammatory retinal phenotype. We show that retinal microglia express AT1-R and their activation state is significantly altered by the angiogenic factor, AngII. Specifically, AngII may directly activate AT1-Rs on microglia and contribute to retinal inflammation. This may have implications for diseases like diabetic retinopathy where increases in AngII and inflammation have been shown to play an important role.

Magnetic susceptibility of alkali-tetracyanoquinodimethane salts and extended Hubbard models with bond order and charge density wave phases

NASA Astrophysics Data System (ADS)

Kumar, Manoranjan; Topham, Benjamin J.; Yu, RuiHui; Ha, Quoc Binh Dang; Soos, Zoltán G.

2011-06-01

The molar spin susceptibilities χ(T) of Na-tetracyanoquinodimethane (TCNQ), K-TCNQ, and Rb-TCNQ(II) are fit quantitatively to 450 K in terms of half-filled bands of three one-dimensional Hubbard models with extended interactions using exact results for finite systems. All three models have bond order wave (BOW) and charge density wave (CDW) phases with boundary V = Vc(U) for nearest-neighbor interaction V and on-site repulsion U. At high T, all three salts have regular stacks of TCNQ^- anion radicals. The χ(T) fits place Na and K in the CDW phase and Rb(II) in the BOW phase with V ≈ Vc. The Na and K salts have dimerized stacks at T < Td while Rb(II) has regular stacks at 100 K. The χ(T) analysis extends to dimerized stacks and to dimerization fluctuations in Rb(II). The three models yield consistent values of U, V, and transfer integrals t for closely related TCNQ^- stacks. Model parameters based on χ(T) are smaller than those from optical data that in turn are considerably reduced by electronic polarization from quantum chemical calculation of U, V, and t of adjacent TCNQ^- ions. The χ(T) analysis shows that fully relaxed states have reduced model parameters compared to optical or vibration spectra of dimerized or regular TCNQ^- stacks.

Differential substrate behaviour of phenol and aniline derivatives during oxidation by horseradish peroxidase: kinetic evidence for a two-step mechanism.

PubMed

Gilabert, María Angeles; Hiner, Alexander N P; García-Ruiz, Pedro Antonio; Tudela, José; García-Molina, Francisco; Acosta, Manuel; García-Cánovas, Francisco; Rodríguez-López, José Neptuno

2004-06-01

The catalytic constant (k(cat)) and the second-order association constant of compound II with reducing substrate (k(5)) of horseradish peroxidase C (HRPC) acting on phenols and anilines have been determined from studies of the steady-state reaction velocities (V(0) vs. [S(0)]). Since k(cat)=k(2)k(6)/k(2)+k(6), and k(2) (the first-order rate constant for heterolytic cleavage of the oxygen-oxygen bond of hydrogen peroxide during compound I formation) is known, it has been possible to calculate the first-order rate constant for the transformation of each phenol or aniline by HRPC compound II (k(6)). The values of k(6) are quantitatively correlated to the sigma values (Hammett equation) and can be rationalized by an aromatic substrate oxidation mechanism in which the substrate donates an electron to the oxyferryl group in HRPC compound II, accompanied by two proton additions to the ferryl oxygen atom, one from the substrate and the other the protein or solvent. k(6) is also quantitatively correlated to the experimentally determined (13)C-NMR chemical shifts (delta(1)) and the calculated ionization potentials, E (HOMO), of the substrates. Similar dependencies were observed for k(cat) and k(5). From the kinetic analysis, the absolute values of the Michaelis constants for hydrogen peroxide and the reducing substrates (K(M)(H(2)O(2)) and K(M)(S)), respectively, were obtained.

Surface complexation and precipitate geometry for aqueous Zn(II) sorption on ferrihydrite: II. XANES analysis and simulation

USGS Publications Warehouse

Waychunas, G.A.; Fuller, C.C.; Davis, J.A.; Rehr, J.J.

2003-01-01

X-ray absorption near-edge spectroscopy (XANES) analysis of sorption complexes has the advantages of high sensitivity (10- to 20-fold greater than extended X-ray absorption fine structure [EXAFS] analysis) and relative ease and speed of data collection (because of the short k-space range). It is thus a potentially powerful tool for characterization of environmentally significant surface complexes and precipitates at very low surface coverages. However, quantitative analysis has been limited largely to "fingerprint" comparison with model spectra because of the difficulty of obtaining accurate multiple-scattering amplitudes for small clusters with high confidence. In the present work, calculations of the XANES for 50- to 200-atom clusters of structure from Zn model compounds using the full multiple-scattering code Feff 8.0 accurately replicate experimental spectra and display features characteristic of specific first-neighbor anion coordination geometry and second-neighbor cation geometry and number. Analogous calculations of the XANES for small molecular clusters indicative of precipitation and sorption geometries for aqueous Zn on ferrihydrite, and suggested by EXAFS analysis, are in good agreement with observed spectral trends with sample composition, with Zn-oxygen coordination and with changes in second-neighbor cation coordination as a function of sorption coverage. Empirical analysis of experimental XANES features further verifies the validity of the calculations. The findings agree well with a complete EXAFS analysis previously reported for the same sample set, namely, that octahedrally coordinated aqueous Zn2+ species sorb as a tetrahedral complex on ferrihydrite with varying local geometry depending on sorption density. At significantly higher densities but below those at which Zn hydroxide is expected to precipitate, a mainly octahedral coordinated Zn2+ precipitate is observed. An analysis of the multiple scattering paths contributing to the XANES demonstrates the importance of scattering paths involving the anion sublattice. We also describe the specific advantages of complementary quantitative XANES and EXAFS analysis and estimate limits on the extent of structural information obtainable from XANES analysis. ?? 2003 Elsevier Science Ltd.

Quantification of fossil organic matter in contaminated sediments from an industrial watershed: validation of the quantitative multimolecular approach by radiocarbon analysis.

PubMed

Jeanneau, Laurent; Faure, Pierre

2010-09-01

The quantitative multimolecular approach (QMA) based on an exhaustive identification and quantification of molecules from the extractable organic matter (EOM) has been recently developed in order to investigate organic contamination in sediments by a more complete method than the restrictive quantification of target contaminants. Such an approach allows (i) the comparison between natural and anthropogenic inputs, (ii) between modern and fossil organic matter and (iii) the differentiation between several anthropogenic sources. However QMA is based on the quantification of molecules recovered by organic solvent and then analyzed by gas chromatography-mass spectrometry, which represent a small fraction of sedimentary organic matter (SOM). In order to extend the conclusions of QMA to SOM, radiocarbon analyses have been performed on organic extracts and decarbonated sediments. This analysis allows (i) the differentiation between modern biomass (contemporary (14)C) and fossil organic matter ((14)C-free) and (ii) the calculation of the modern carbon percentage (PMC). At the confluence between Fensch and Moselle Rivers, a catchment highly contaminated by both industrial activities and urbanization, PMC values in decarbonated sediments are well correlated with the percentage of natural molecular markers determined by QMA. It highlights that, for this type of contamination by fossil organic matter inputs, the conclusions of QMA can be scaled up to SOM. QMA is an efficient environmental diagnostic tool that leads to a more realistic quantification of fossil organic matter in sediments. Copyright 2010 Elsevier B.V. All rights reserved.

Improving multisensor estimation of heavy-to-extreme precipitation via conditional bias-penalized optimal estimation

NASA Astrophysics Data System (ADS)

Kim, Beomgeun; Seo, Dong-Jun; Noh, Seong Jin; Prat, Olivier P.; Nelson, Brian R.

2018-01-01

A new technique for merging radar precipitation estimates and rain gauge data is developed and evaluated to improve multisensor quantitative precipitation estimation (QPE), in particular, of heavy-to-extreme precipitation. Unlike the conventional cokriging methods which are susceptible to conditional bias (CB), the proposed technique, referred to herein as conditional bias-penalized cokriging (CBPCK), explicitly minimizes Type-II CB for improved quantitative estimation of heavy-to-extreme precipitation. CBPCK is a bivariate version of extended conditional bias-penalized kriging (ECBPK) developed for gauge-only analysis. To evaluate CBPCK, cross validation and visual examination are carried out using multi-year hourly radar and gauge data in the North Central Texas region in which CBPCK is compared with the variant of the ordinary cokriging (OCK) algorithm used operationally in the National Weather Service Multisensor Precipitation Estimator. The results show that CBPCK significantly reduces Type-II CB for estimation of heavy-to-extreme precipitation, and that the margin of improvement over OCK is larger in areas of higher fractional coverage (FC) of precipitation. When FC > 0.9 and hourly gauge precipitation is > 60 mm, the reduction in root mean squared error (RMSE) by CBPCK over radar-only (RO) is about 12 mm while the reduction in RMSE by OCK over RO is about 7 mm. CBPCK may be used in real-time analysis or in reanalysis of multisensor precipitation for which accurate estimation of heavy-to-extreme precipitation is of particular importance.

Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data.

PubMed

Tu, Chengjian; Li, Jun; Sheng, Quanhu; Zhang, Ming; Qu, Jun

2014-04-04

Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R(2) > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery.

Systematic Assessment of Survey Scan and MS2-Based Abundance Strategies for Label-Free Quantitative Proteomics Using High-Resolution MS Data

PubMed Central

2015-01-01

Survey-scan-based label-free method have shown no compelling benefit over fragment ion (MS2)-based approaches when low-resolution mass spectrometry (MS) was used, the growing prevalence of high-resolution analyzers may have changed the game. This necessitates an updated, comparative investigation of these approaches for data acquired by high-resolution MS. Here, we compared survey scan-based (ion current, IC) and MS2-based abundance features including spectral-count (SpC) and MS2 total-ion-current (MS2-TIC), for quantitative analysis using various high-resolution LC/MS data sets. Key discoveries include: (i) study with seven different biological data sets revealed only IC achieved high reproducibility for lower-abundance proteins; (ii) evaluation with 5-replicate analyses of a yeast sample showed IC provided much higher quantitative precision and lower missing data; (iii) IC, SpC, and MS2-TIC all showed good quantitative linearity (R2 > 0.99) over a >1000-fold concentration range; (iv) both MS2-TIC and IC showed good linear response to various protein loading amounts but not SpC; (v) quantification using a well-characterized CPTAC data set showed that IC exhibited markedly higher quantitative accuracy, higher sensitivity, and lower false-positives/false-negatives than both SpC and MS2-TIC. Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery. PMID:24635752

Stochastic Simulation of Isotopic Exchange Mechanisms for Fe(II)-Catalyzed Recrystallization of Goethite.

PubMed

Zarzycki, Piotr; Rosso, Kevin M

2017-07-05

Understanding Fe(II)-catalyzed transformations of Fe(III)-(oxyhydr)oxides is critical for correctly interpreting stable isotopic distributions and for predicting the fate of metal ions in the environment. Recent Fe isotopic tracer experiments have shown that goethite undergoes rapid recrystallization without phase change when exposed to aqueous Fe(II). The proposed explanation is oxidation of sorbed Fe(II) and reductive Fe(II) release coupled 1:1 by electron conduction through crystallites. Given the availability of two tracer exchange data sets that explore pH and particle size effects (e.g., Handler et al. Environ. Sci. Technol. 2014 , 48 , 11302 - 11311 ; Joshi and Gorski Environ. Sci. Technol. 2016 , 50 , 7315 - 7324 ), we developed a stochastic simulation that exactly mimics these experiments, while imposing the 1:1 constraint. We find that all data can be represented by this model, and unifying mechanistic information emerges. At pH 7.5 a rapid initial exchange is followed by slower exchange, consistent with mixed surface- and diffusion-limited kinetics arising from prominent particle aggregation. At pH 5.0 where aggregation and net Fe(II) sorption are minimal, that exchange is quantitatively proportional to available particle surface area and the density of sorbed Fe(II) is more readily evident. Our analysis reveals a fundamental atom exchange rate of ∼10 -5 Fe nm -2 s -1 , commensurate with some of the reported reductive dissolution rates of goethite, suggesting Fe(II) release is the rate-limiting step in the conduction mechanism during recrystallization.

Adsorption studies of Cd(II) onto Al 2O 3/Nb 2O 5 mixed oxide dispersed on silica matrix and its on-line preconcentration and determination by flame atomic absorption spectrometry

NASA Astrophysics Data System (ADS)

Mendonça Costa, Lucimara; Ribeiro, Emerson Schwingel; Segatelli, Mariana Gava; do Nascimento, Danielle Raphael; de Oliveira, Fernanda Midori; Tarley, César Ricardo Teixeira

2011-05-01

The present study describes the adsorption characteristic of Cd(II) onto Nb 2O 5/Al 2O 3 mixed oxide dispersed on silica matrix. The characterization of the adsorbent has been carried out by infrared spectroscopy (IR), scanning electronic microscopy (SEM), energy dispersive spectroscopy (EDS), energy dispersive X-ray fluorescence analysis (EDXRF) and specific surface area ( SBET). From batch experiments, adsorption kinetic of Cd(II) was described by a pseudo-second-order kinetic model. The Langmuir linear isotherm fitted to the experimental adsorption isotherm very well, and the maximum adsorption capacity was found to be 17.88 mg g -1. Using the effective material, a method for Cd(II) preconcentration at trace level was developed. The method was based on on-line adsorption of Cd(II) onto SiO 2/Al 2O 3/Nb 2O 5 at pH 8.64, in which the quantitative desorption occurs with 1.0 mol L -1 hydrochloric acid towards FAAS detector. The experimental parameters related to the system were studied by means of multivariate analysis, using 2 4 full factorial design and Doehlert matrix. The effect of SO 42-, Cu 2+, Zn 2+ and Ni 2+ foreign ions showed no interference at 1:100 analyte:interferent proportion. Under the most favorable experimental conditions, the preconcentration system provided a preconcentration factor of 18.4 times, consumption index of 1.08 mL, sample throughput of 14 h -1, concentration efficiency of 4.35 min -1, linear range from 5.0 up to 35.0 μg L -1 and limits of detection and quantification of 0.19 and 0.65 μg L -1 respectively. The feasibility of the proposed method for Cd(II) determination was assessed by analysis of water samples, cigarette sample and certified reference materials TORT-2 (Lobster hepatopancreas) and DOLT-4 (Dogfish liver).

Model-based Analysis of Mixed Uranium(VI) Reduction by Biotic and Abiotic Pathways During in Situ Bioremediation

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

Zhao, Jiao; Scheibe, Timothy D.; Mahadevan, Radhakrishnan

2013-10-24

Uranium bioremediation has emerged as a potential strategy of cleanup of radionuclear contamination worldwide. An integrated geochemical & microbial community model is a promising approach to predict and provide insights into the bioremediation of a complicated natural subsurface. In this study, an integrated column-scale model of uranium bioremediation was developed, taking into account long-term interactions between biotic and abiotic processes. It is also combined with a comprehensive thermodynamic analysis to track the fate and cycling of biogenic species. As compared with other bioremediation models, the model increases the resolution of the connection of microbial community to geochemistry and establishes directmore » quantitative correlation between overall community evolution and geochemical variation, thereby accurately predicting the community dynamics under different sedimentary conditions. The thermodynamic analysis examined a recently identified homogeneous reduction of U(VI) by Fe(II) under dynamic sedimentary conditions across time and space. It shows that the biogenic Fe(II) from Geobacter metabolism can be removed rapidly by the biogenic sulphide from sulfate reducer metabolism, hence constituting one of the reasons that make the abiotic U(VI) reduction thermodynamically infeasible in the subsurface. Further analysis indicates that much higher influent concentrations of both Fe(II) and U(VI) than normal are required to for abiotic U(VI) reduction to be thermodynamically feasible, suggesting that the abiotic reduction cannot be an alternative to the biotic reduction in the remediation of uranium contaminated groundwater.« less

(99m)Tc-Annexin A5 quantification of apoptotic tumor response: a systematic review and meta-analysis of clinical imaging trials.

PubMed

Belhocine, Tarik Z; Blankenberg, Francis G; Kartachova, Marina S; Stitt, Larry W; Vanderheyden, Jean-Luc; Hoebers, Frank J P; Van de Wiele, Christophe

2015-12-01

(99m)Tc-Annexin A5 has been used as a molecular imaging probe for the visualization, characterization and measurement of apoptosis. In an effort to define the quantitative (99m)Tc-annexin A5 uptake criteria that best predict tumor response to treatment, we performed a systematic review and meta-analysis of the results of all clinical imaging trials found in the literature or publicly available databases. Included in this review were 17 clinical trials investigating quantitative (99m)Tc-annexin A5 (qAnx5) imaging using different parameters in cancer patients before and after the first course of chemotherapy and/or radiation therapy. Qualitative assessment of the clinical studies for diagnostic accuracy was performed using the QUADAS-2 criteria. Of these studies, five prospective single-center clinical trials (92 patients in total) were included in the meta-analysis after exclusion of one multicenter clinical trial due to heterogeneity. Pooled positive predictive values (PPV) and pooled negative predictive values (NPV) (with 95% CI) were calculated using Meta-Disc software version 1.4. Absolute quantification and/or relative quantification of (99m)Tc-annexin A5 uptake were performed at baseline and after the start of treatment. Various quantitative parameters have been used for the calculation of (99m)Tc-annexin A5 tumor uptake and delta (Δ) tumor changes post-treatment compared to baseline including: tumor-to-background ratio (TBR), ΔTBR, tumor-to-noise ratio, relative tumor ratio (TR), ΔTR, standardized tumor uptake ratio (STU), ΔSTU, maximum count per pixel within the tumor volume (Cmax), Cmax%, absolute ΔU and percentage (ΔU%), maximum ΔU counts, semiquantitative visual scoring, percent injected dose (%ID) and %ID/cm(3). Clinical trials investigating qAnx5 imaging have included patients with lung cancer, lymphoma, breast cancer, head and neck cancer and other less common tumor types. In two phase I/II single-center clinical trials, an increase of ≥25% in uptake following treatment was considered a significant threshold for an apoptotic tumor response (partial response, complete response). In three other phase I/II clinical trials, increases of ≥28%, ≥42% and ≥47% in uptake following treatment were found to be the mean cut-off levels in responders. In a phase II/III multicenter clinical trial, an increase of ≥23% in uptake following treatment was found to be the minimum cut-off level for a tumor response. In one clinical trial, no significant difference in (99m)Tc-annexin A5 uptake in terms of %ID was found in healthy tissues after chemotherapy compared to baseline. In two other clinical trials, intraobserver and interobserver measurements of (99m)Tc-annexin A5 tumor uptake were found to be reproducible (mean difference <5%, kappa =  0.90 and 0.82, respectively) and to be highly correlated with treatment outcome (Spearman r = 0.99, p < 0.0001). The meta-analysis demonstrated a pooled positive PPV of 100% (95% CI 92 - 100%) and a pooled NPV of 70% (95% CI 55 - 82%) for prediction of a tumor response after the first course of chemotherapy and/or radiotherapy in terms of ΔU%. In a symmetric sROC analysis, the AUC was 0.919 and the Q* index was 85.21 %. Quantitative (99m)Tc-annexin A5 imaging has been investigated in clinical trials for the assessment of apoptotic tumor responses. This meta-analysis showed a high pooled PPV and a moderate pooled NPV with ΔU cut-off values ranging between 20% and 30%. Standardization of quantification and harmonization of results are required for high-quality clinical research. A standardized uptake value score (SUV, ΔSUV) using quantitative SPECT/CT imaging may be a promising approach to the simple, reproducible and semiquantitative assessment of apoptotic tumor changes.

Linking agent-based models and stochastic models of financial markets

PubMed Central

Feng, Ling; Li, Baowen; Podobnik, Boris; Preis, Tobias; Stanley, H. Eugene

2012-01-01

It is well-known that financial asset returns exhibit fat-tailed distributions and long-term memory. These empirical features are the main objectives of modeling efforts using (i) stochastic processes to quantitatively reproduce these features and (ii) agent-based simulations to understand the underlying microscopic interactions. After reviewing selected empirical and theoretical evidence documenting the behavior of traders, we construct an agent-based model to quantitatively demonstrate that “fat” tails in return distributions arise when traders share similar technical trading strategies and decisions. Extending our behavioral model to a stochastic model, we derive and explain a set of quantitative scaling relations of long-term memory from the empirical behavior of individual market participants. Our analysis provides a behavioral interpretation of the long-term memory of absolute and squared price returns: They are directly linked to the way investors evaluate their investments by applying technical strategies at different investment horizons, and this quantitative relationship is in agreement with empirical findings. Our approach provides a possible behavioral explanation for stochastic models for financial systems in general and provides a method to parameterize such models from market data rather than from statistical fitting. PMID:22586086

Quantitative trait loci and metabolic pathways

PubMed Central

McMullen, M. D.; Byrne, P. F.; Snook, M. E.; Wiseman, B. R.; Lee, E. A.; Widstrom, N. W.; Coe, E. H.

1998-01-01

The interpretation of quantitative trait locus (QTL) studies is limited by the lack of information on metabolic pathways leading to most economic traits. Inferences about the roles of the underlying genes with a pathway or the nature of their interaction with other loci are generally not possible. An exception is resistance to the corn earworm Helicoverpa zea (Boddie) in maize (Zea mays L.) because of maysin, a C-glycosyl flavone synthesized in silks via a branch of the well characterized flavonoid pathway. Our results using flavone synthesis as a model QTL system indicate: (i) the importance of regulatory loci as QTLs, (ii) the importance of interconnecting biochemical pathways on product levels, (iii) evidence for “channeling” of intermediates, allowing independent synthesis of related compounds, (iv) the utility of QTL analysis in clarifying the role of specific genes in a biochemical pathway, and (v) identification of a previously unknown locus on chromosome 9S affecting flavone level. A greater understanding of the genetic basis of maysin synthesis and associated corn earworm resistance should lead to improved breeding strategies. More broadly, the insights gained in relating a defined genetic and biochemical pathway affecting a quantitative trait should enhance interpretation of the biological basis of variation for other quantitative traits. PMID:9482823

Linking agent-based models and stochastic models of financial markets.

PubMed

Feng, Ling; Li, Baowen; Podobnik, Boris; Preis, Tobias; Stanley, H Eugene

2012-05-29

It is well-known that financial asset returns exhibit fat-tailed distributions and long-term memory. These empirical features are the main objectives of modeling efforts using (i) stochastic processes to quantitatively reproduce these features and (ii) agent-based simulations to understand the underlying microscopic interactions. After reviewing selected empirical and theoretical evidence documenting the behavior of traders, we construct an agent-based model to quantitatively demonstrate that "fat" tails in return distributions arise when traders share similar technical trading strategies and decisions. Extending our behavioral model to a stochastic model, we derive and explain a set of quantitative scaling relations of long-term memory from the empirical behavior of individual market participants. Our analysis provides a behavioral interpretation of the long-term memory of absolute and squared price returns: They are directly linked to the way investors evaluate their investments by applying technical strategies at different investment horizons, and this quantitative relationship is in agreement with empirical findings. Our approach provides a possible behavioral explanation for stochastic models for financial systems in general and provides a method to parameterize such models from market data rather than from statistical fitting.

POWTEX Neutron Diffractometer at FRM II - New Perspectives for In-Situ Rock Deformation Analysis

NASA Astrophysics Data System (ADS)

Walter, J. M.; Stipp, M.; Ullemeyer, K.; Klein, H.; Leiss, B.; Hansen, B. T.; Kuhs, W. F.

2012-04-01

In Geoscience quantitative texture analysis here defined as the quantitative analysis of the crystallographic preferred orientation (CPO), is a common tool for the investigation of fabric development in mono- and polyphase rocks, their deformation histories and kinematics. Bulk texture measurements also allow the quantitative characterisation of the anisotropic physical properties of rock materials. A routine tool to measure bulk sample volumes is neutron texture diffraction, as neutrons have large penetration capabilities of several cm in geological sample materials. The new POWTEX (POWder and TEXture) Diffractometer at the neutron research reactor FRM II in Garching, Germany is designed as a high-intensity diffractometer by groups from the RWTH Aachen, Forschungszentrum Jülich and the University of Göttingen. Complementary to existing neutron diffractometers (SKAT at Dubna, Russia; GEM at ISIS, UK; HIPPO at Los Alamos, USA; D20 at ILL, France; and the local STRESS-SPEC and SPODI at FRM II) the layout of POWTEX is focused on fast time-resolved experiments and the measurement of larger sample series as necessary for the study of large scale geological structures. POWTEX is a dedicated beam line for geoscientific research. Effective texture measurements without sample tilting and rotation are possible firstly by utilizing a range of neutron wavelengths simultaneously (Time-of-Flight technique) and secondly by the high detector coverage (9.8 sr) and a high flux (~1 - 107 n/cm2s) at the sample. Furthermore the instrument and the angular detector resolution is designed also for strong recrystallisation textures as well as for weak textures of polyphase rocks. These instrument characteristics allow in-situ time-resolved texture measurements during deformation experiments on rocksalt, ice and other materials as large sample environments will be implemented at POWTEX. The in-situ deformation apparatus is operated by a uniaxial spindle drive with a maximum axial load of 250 kN, which will be redesigned to minimize shadowing effects inside the cylindrical detector. The HT deformatione experiments will be carried out in uniaxial compression or extension and an upgrade to triaxial deformation conditions is envisaged. The load frame can alternatively be used for ice deformation by inserting a cryostat cell for temperatures down to 77 K with a triaxial apparatus allowing also simple shear experiments on ice. Strain rates range between 10-8 and 10-3 s-1 reaching to at least 50 % axial strain. The deformation apparatus is designed for continuous long-term deformation experiments and can be exchanged between in-situ and ex-situ placements during continuous operation inside and outside the neutron detector.

Sampling of illicit drugs for quantitative analysis--part II. Study of particle size and its influence on mass reduction.

PubMed

Bovens, M; Csesztregi, T; Franc, A; Nagy, J; Dujourdy, L

2014-01-01

The basic goal in sampling for the quantitative analysis of illicit drugs is to maintain the average concentration of the drug in the material from its original seized state (the primary sample) all the way through to the analytical sample, where the effect of particle size is most critical. The size of the largest particles of different authentic illicit drug materials, in their original state and after homogenisation, using manual or mechanical procedures, was measured using a microscope with a camera attachment. The comminution methods employed included pestle and mortar (manual) and various ball and knife mills (mechanical). The drugs investigated were amphetamine, heroin, cocaine and herbal cannabis. It was shown that comminution of illicit drug materials using these techniques reduces the nominal particle size from approximately 600 μm down to between 200 and 300 μm. It was demonstrated that the choice of 1 g increments for the primary samples of powdered drugs and cannabis resin, which were used in the heterogeneity part of our study (Part I) was correct for the routine quantitative analysis of illicit seized drugs. For herbal cannabis we found that the appropriate increment size was larger. Based on the results of this study we can generally state that: An analytical sample weight of between 20 and 35 mg of an illicit powdered drug, with an assumed purity of 5% or higher, would be considered appropriate and would generate an RSDsampling in the same region as the RSDanalysis for a typical quantitative method of analysis for the most common, powdered, illicit drugs. For herbal cannabis, with an assumed purity of 1% THC (tetrahydrocannabinol) or higher, an analytical sample weight of approximately 200 mg would be appropriate. In Part III we will pull together our homogeneity studies and particle size investigations and use them to devise sampling plans and sample preparations suitable for the quantitative instrumental analysis of the most common illicit drugs. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Rigorous quantitative elemental microanalysis by scanning electron microscopy/energy dispersive x-ray spectrometry (SEM/EDS) with spectrum processing by NIST DTSA-II

NASA Astrophysics Data System (ADS)

Newbury, Dale E.; Ritchie, Nicholas W. M.

2014-09-01

Quantitative electron-excited x-ray microanalysis by scanning electron microscopy/silicon drift detector energy dispersive x-ray spectrometry (SEM/SDD-EDS) is capable of achieving high accuracy and high precision equivalent to that of the high spectral resolution wavelength dispersive x-ray spectrometer even when severe peak interference occurs. The throughput of the SDD-EDS enables high count spectra to be measured that are stable in calibration and resolution (peak shape) across the full deadtime range. With this high spectral stability, multiple linear least squares peak fitting is successful for separating overlapping peaks and spectral background. Careful specimen preparation is necessary to remove topography on unknowns and standards. The standards-based matrix correction procedure embedded in the NIST DTSA-II software engine returns quantitative results supported by a complete error budget, including estimates of the uncertainties from measurement statistics and from the physical basis of the matrix corrections. NIST DTSA-II is available free for Java-platforms at: http://www.cstl.nist.gov/div837/837.02/epq/dtsa2/index.html).

The quantitation of buffering action II. Applications of the formal & general approach.

PubMed

Schmitt, Bernhard M

2005-03-16

The paradigm of "buffering" originated in acid-base physiology, but was subsequently extended to other fields and is now used for a wide and diverse set of phenomena. In the preceding article, we have presented a formal and general approach to the quantitation of buffering action. Here, we use that buffering concept for a systematic treatment of selected classical and other buffering phenomena. H+ buffering by weak acids and "self-buffering" in pure water represent "conservative buffered systems" whose analysis reveals buffering properties that contrast in important aspects from classical textbook descriptions. The buffering of organ perfusion in the face of variable perfusion pressure (also termed "autoregulation") can be treated in terms of "non-conservative buffered systems", the general form of the concept. For the analysis of cytoplasmic Ca++ concentration transients (also termed "muffling"), we develop a related unit that is able to faithfully reflect the time-dependent quantitative aspect of buffering during the pre-steady state period. Steady-state buffering is shown to represent the limiting case of time-dependent muffling, namely for infinitely long time intervals and infinitely small perturbations. Finally, our buffering concept provides a stringent definition of "buffering" on the level of systems and control theory, resulting in four absolute ratio scales for control performance that are suited to measure disturbance rejection and setpoint tracking, and both their static and dynamic aspects. Our concept of buffering provides a powerful mathematical tool for the quantitation of buffering action in all its appearances.

A Bispidol Chelator with a Phosphonate Pendant Arm: Synthesis, Cu(II) Complexation, and 64Cu Labeling.

PubMed

Gillet, Raphaël; Roux, Amandine; Brandel, Jérémy; Huclier-Markai, Sandrine; Camerel, Franck; Jeannin, Olivier; Nonat, Aline M; Charbonnière, Loïc J

2017-10-02

Here we present the synthesis and characterization of a new bispidine (3,7-diazabicyclo[3.3.1]nonane) ligand with N-methanephosphonate substituents (L 2 ). Its physicochemical properties in water, as well as those of the corresponding Cu(II) and Zn(II) complexes, have been evaluated by using UV-visible absorption spectroscopy, potentiometry, 1 H and 31 P NMR, and cyclic voltammetry. Radiolabeling experiments with 64 Cu II have been carried out, showing excellent radiolabeling properties. Quantitative complexation was achieved within 60 min under stoichiometric conditions, at room temperature and in the nanomolar concentration range. It was also demonstrated that the complexation occurred below pH 2. Properties have been compared to those of the analogue bispidol bearing a N-methanecarboxylate substituent (L 1 ). Although both systems meet the required criteria to be used as new chelator for 64/67 Cu in terms of the kinetics of formation, thermodynamic stability, selectivity for Cu(II), and kinetic inertness regarding redox- or acid-assisted decomplexation processes, substitution of the carboxylic acid function by the phosphonic moiety is responsible for a significant increase in the thermodynamic stability of the Cu(II) complex (+2 log units for pCu) and also leads to an increase in the radiochemical yields with 64 Cu II which is quantitative for L 2 .

Actualizing system benefits--Part II.

PubMed

Zinn, T K; DiGiulio, L W

1988-05-01

Do benefits impact the psychology of the information system buying decision? Is system success tied to achieving "promoted" benefits? Part II of this series reveals responses from a survey of some 3,000 executives about the importance of qualitative and quantitative benefits in the "buying process."

Heavy metal contents of play dough, face and finger paint samples sold in turkish markets.

PubMed

Erbas, Zeliha; Karatepe, Aslihan; Soylak, Mustafa

2017-08-01

Lead, cadmium, nickel, manganese, cobalt and copper contents of some play dough, face and finger paint samples were determined by using a new solid phase extraction method which has been developed by using multi-walled carbon nanotube with patent blue (V) sodium salt to selectively separate and preconcentrate these metal ions. Flame atomic absorption spectrometry was used to determine the metal ions. Analytical parameters affecting the complex formation and solid phase extraction performance such as pH, the amount of ligand and volume of sample solution were investigated. The recoveries of the studied metal ions were not affected by the foreign ions. Analytes were recovered quantitatively at pH 5.5 and with a nitric acid of 2molL -1 as eluent. Analysis of a certified reference material was performed to validate the method before applying it to determine the metal ions in the real samples. Detection limits were found to be as Pb(II): 7.71μgL -1 , Cu(II): 1.43μgL -1 , Cd(III): 0.21μgL -1 , Mn(II): 0.47μgL -1 , Ni(II): 3.52μgL -1 and Co(II): 1.96μgL -1 . Copyright © 2017 Elsevier B.V. All rights reserved.

The Human Respiratory Syncytial Virus Nonstructural Protein 1 Regulates Type I and Type II Interferon Pathways*

PubMed Central

Hastie, Marcus L.; Headlam, Madeleine J.; Patel, Nirav B.; Bukreyev, Alexander A.; Buchholz, Ursula J.; Dave, Keyur A.; Norris, Emma L.; Wright, Cassandra L.; Spann, Kirsten M.; Collins, Peter L.; Gorman, Jeffrey J.

2012-01-01

Respiratory syncytial viruses encode a nonstructural protein (NS1) that interferes with type I and III interferon and other antiviral responses. Proteomic studies were conducted on human A549 type II alveolar epithelial cells and type I interferon-deficient Vero cells (African green monkey kidney cells) infected with wild-type and NS1-deficient clones of human respiratory syncytial virus to identify other potential pathway and molecular targets of NS1 interference. These analyses included two-dimensional differential gel electrophoresis and quantitative Western blotting. Surprisingly, NS1 was found to suppress the induction of manganese superoxide dismutase (SOD2) expression in A549 cells and to a much lesser degree Vero cells in response to infection. Because SOD2 is not directly inducible by type I interferons, it served as a marker to probe the impact of NS1 on signaling of other cytokines known to induce SOD2 expression and/or indirect effects of type I interferon signaling. Deductive analysis of results obtained from cell infection and cytokine stimulation studies indicated that interferon-γ signaling was a potential target of NS1, possibly as a result of modulation of STAT1 levels. However, this was not sufficient to explain the magnitude of the impact of NS1 on SOD2 induction in A549 cells. Vero cell infection experiments indicated that NS1 targeted a component of the type I interferon response that does not directly induce SOD2 expression but is required to induce another initiator of SOD2 expression. STAT2 was ruled out as a target of NS1 interference using quantitative Western blot analysis of infected A549 cells, but data were obtained to indicate that STAT1 was one of a number of potential targets of NS1. A label-free mass spectrometry-based quantitative approach is proposed as a means of more definitive identification of NS1 targets. PMID:22322095

Evaluation of a method based on liquid chromatography-diode array detector-tandem mass spectrometry for a rapid and comprehensive characterization of the fat-soluble vitamin and carotenoid profile of selected plant foods.

PubMed

Gentili, Alessandra; Caretti, Fulvia

2011-02-04

The feasibility of using reversed-phase liquid chromatography/diode array/tandem mass spectrometry (LC-DAD-MS/MS) for a rapid and comprehensive profiling of fat soluble vitamins and pigments in some foods of plant origin (maize flour, green and golden kiwi) was evaluated. The instrumental approach was planned for obtaining two main outcomes within the same chromatographic run: (i) the quantitative analysis of ten target analytes, whose standards are commercially available; (ii) the screening of pigments occurring in the selected matrices. The quantitative analysis was performed simultaneously for four carotenoids (lutein, zeaxanthin, β-cryptoxanthin, and β-carotene) and six compounds with fat-soluble activity (α-tocopherol, δ-tocopherol, γ-tocopherol, ergocalciferol, phylloquinone and menaquinone-4), separated on a C30 reversed-phase column and detected by atmospheric pressure chemical ionization (APCI) tandem mass spectrometry, operating in Selected Reaction Monitoring (SRM) mode. Extraction procedure was based on matrix solid-phase dispersion with recoveries of all compounds under study exceeding 78 and 60% from maize flour and kiwi, respectively. The method intra-day precision ranged between 3 and 7%, while the inter-day one was below 12%. The mild isolation conditions precluded artefacts creation, such as cis-isomerization phenomena for carotenoids. During the quantitative LC-SRM determination of the ten target analytes, the identification power of the diode array detector joined to that of the triple quadrupole (QqQ) allowed the tentatively identification of several pigments (chlorophylls and carotenoids), without the aid of standards, on the basis of: (i) the UV-vis spectra recorded in the range of 200-700nm; (ii) the expected retention time; (iii) the two SRM transitions, chosen for the target carotenoids but also common to many of isomeric carotenoids occurring in the selected foods. Copyright © 2010 Elsevier B.V. All rights reserved.

The Commissioning of the Arcetri Near-Infrared Camera ARNICA: II. Broadband Astronomical Performance

NASA Astrophysics Data System (ADS)

Hunt, L.; Maioíino, R.; Moriondo, G.; Testi, L.

1994-11-01

This report is the second of a series that describes the data analysis and the quantitative results obtained with ARNICA. Our original intention was to limit this report to a description of ARNICA's performance during the commissioning of the camera at the TIRGO (November 1992 - June 1993). Various considerations have since induced us to also include a discussion of results obtained during an observing run in December, 1993, at the William Herschel Telescope (WHT, La Palma, Canary Islands), and during a subsequent observing run at the TIRGO (February, 1994).

How Do We Turn This Thing Off? A Study to Determine an Approach for Making Curtailment of Service and Closure Decisions in Health Care Facilities.

DTIC Science & Technology

1979-04-09

22a. NAME OF RESPONSIBLE INDIVIDUAL 22b TELEPHONE (Include Area Code) 22c. OFFICE SYMBOL Lawrence M. Leahy, MAJ, MS (512) 221-6345 HSHA-IHC DO Form...Facilities. Germantown, MD.: Aspen Systems Corporation, 1976. Bierman, Harold Jr., Charles R. Bonini and Warren H. Hausman . Quantitative Analysis for Business...Assessment," Topics in Health Care Financing II, No. 4 ( Summer , 1976), 109-121. Drake, David F. and Kozak, David M. "A Primer on Antitrust and Hospital

Osteoinductive effects of glyceollins on adult mesenchymal stromal/stem cells from adipose tissue and bone marrow.

PubMed

Bateman, Marjorie E; Strong, Amy L; Hunter, Ryan S; Bratton, Melyssa R; Komati, Rajesh; Sridhar, Jayalakshmi; Riley, Kevin E; Wang, Guangdi; Hayes, Daniel J; Boue, Stephen M; Burow, Matthew E; Bunnell, Bruce A

2017-04-15

While current therapies for osteoporosis focus on reducing bone resorption, the development of therapies to regenerate bone may also be beneficial. Promising anabolic therapy candidates include phytoestrogens, such as daidzein, which effectively induce osteogenesis of adipose-derived stromal cells (ASCs) and bone marrow stromal cells (BMSCs). To investigate the effects of glyceollins, structural derivatives of daidzein, on osteogenesis of ASCs and BMSCs. Herein, the osteoinductive effects of glyceollin I and glyceollin II were assessed and compared to estradiol in ASCs and BMSCs. The mechanism by which glyceollin II induces osteogenesis was further examined. The ability of glyceollins to promote osteogenesis of ASCs and BMSCs was evaluated in adherent and scaffold cultures. Relative deposition of calcium was analyzed using Alizarin Red staining, Bichinchoninic acid Protein Assay, and Alamar Blue Assay. To further explore the mechanism by which glyceollin II exerts its osteoinductive effects, docking studies of glyceollin II, RNA isolation, cDNA synthesis, and quantitative RT-PCR (qPCR) were performed. In adherent cultures, ASCs and BMSCs treated with estradiol, glyceollin I, or glyceollin II demonstrated increased calcium deposition relative to vehicle-treated cells. During evaluation on PLGA scaffolds seeded with ASCs and BMSCs, glyceollin II was the most efficacious in inducing ASC and BMSC osteogenesis compared to estradiol and glyceollin I. Dose-response analysis in ASCs and BMSCs revealed that glyceollin II has the highest potency at 10nM in adherent cultures and 1µM in tissue scaffold cultures. At all doses, osteoinductive effects were attenuated by fulvestrant, suggesting that glyceollin II acts at least in part through estrogen receptor-mediated pathways to induce osteogenesis. Analysis of gene expression demonstrated that, similar to estradiol, glyceollin II induces upregulation of genes involved in osteogenic differentiation. The ability of glyceollin II to induce osteogenic differentiation in ASCs and BMSCs indicates that glyceollins hold the potential for the development of pharmacological interventions to improve clinical outcomes of patients with osteoporosis. Copyright © 2017 Elsevier GmbH. All rights reserved.

Position-specific binding of FUS to nascent RNA regulates mRNA length

PubMed Central

Masuda, Akio; Takeda, Jun-ichi; Okuno, Tatsuya; Okamoto, Takaaki; Ohkawara, Bisei; Ito, Mikako; Ishigaki, Shinsuke; Sobue, Gen

2015-01-01

More than half of all human genes produce prematurely terminated polyadenylated short mRNAs. However, the underlying mechanisms remain largely elusive. CLIP-seq (cross-linking immunoprecipitation [CLIP] combined with deep sequencing) of FUS (fused in sarcoma) in neuronal cells showed that FUS is frequently clustered around an alternative polyadenylation (APA) site of nascent RNA. ChIP-seq (chromatin immunoprecipitation [ChIP] combined with deep sequencing) of RNA polymerase II (RNAP II) demonstrated that FUS stalls RNAP II and prematurely terminates transcription. When an APA site is located upstream of an FUS cluster, FUS enhances polyadenylation by recruiting CPSF160 and up-regulates the alternative short transcript. In contrast, when an APA site is located downstream from an FUS cluster, polyadenylation is not activated, and the RNAP II-suppressing effect of FUS leads to down-regulation of the alternative short transcript. CAGE-seq (cap analysis of gene expression [CAGE] combined with deep sequencing) and PolyA-seq (a strand-specific and quantitative method for high-throughput sequencing of 3' ends of polyadenylated transcripts) revealed that position-specific regulation of mRNA lengths by FUS is operational in two-thirds of transcripts in neuronal cells, with enrichment in genes involved in synaptic activities. PMID:25995189

Synthesis of tin (II) oxide from tin (II) oxohydroxide

NASA Astrophysics Data System (ADS)

Kuznetsova, Svetlana; Lisitsa, Konstantin

2017-11-01

Sufficiently limited use of tin (II) oxide is associated with the difficulties of its preparation without impurities of tin (IV) oxide. Understanding the cause of the oxidation process will make it possible to develop methods for obtaining SnO without impurities. The influence of ammonium chloride concentration in the suspension on the oxide composition was investigated. The temperature of oxidation (400 °C) on the air and temperature decomposition in the argon (350 °C) of Sn6O4(OH)4 in the solid phase were determined by the thermal analysis method. The decomposition temperature of the oxyhydroxide in the suspension of ammonium chloride does not exceed 100 °C. An increase in the content of ammonium chloride in an aqueous solution leads to an increase i n the solubility of oxohydroxide and leads to an increase in pH. The suspensions of Sn6O4(OH)4 were subjected to heat treatment on a sand bath and under microwave irradiation. Samples of tin oxide were obtained. The quantitative composition of the mixture of tin oxides was determined. The research also highlights emphasizes that the oxidation of tin (II) to tin (IV) is associated with the dissolved oxygen content in the suspension.

Evidence for the possible involvement of Selenomonas ruminantium in rumen fiber digestion.

PubMed

Sawanon, Suriya; Koike, Satoshi; Kobayashi, Yasuo

2011-12-01

Selenomonas ruminantium strains were isolated from sheep rumen, and their significance for fiber digestion was evaluated. Based on the phylogenetic classification, two clades of S. ruminantium (clades I and II) were proposed. Clade II is newly found, as it comprised only new isolates that were phylogenetically distant from the type strain, while all of the known isolates were grouped in the major clade I. More than half of clade I isolates displayed CMCase activity with no relation to the degree of bacterial adherence to fibers. Although none of the isolates digested fiber in monoculture, they stimulated fiber digestion when co-cultured with Fibrobacter succinogenes, and there was an enhancement of propionate production. The extent of such synergy depended on the clade, with higher digestion observed by co-culture of clade I isolates with F. succinogenes than by co-culture with clade II isolates. Quantitative PCR analysis showed that bacterial abundance in the rumen was higher for clade I than for clade II. These results suggest that S. ruminantium, in particular the major clade I, is involved in rumen fiber digestion by cooperating with F. succinogenes. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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

Zarzycki, Piotr; Rosso, Kevin M.

Understanding Fe(II)-catalyzed transformations of Fe(III)- (oxyhydr)oxides is critical for correctly interpreting stable isotopic distributions and for predicting the fate of metal ions in the environment. Recent Fe isotopic tracer experiments have shown that goethite undergoes rapid recrystallization without phase change when exposed to aqueous Fe(II). The proposed explanation is oxidation of sorbed Fe(II) and reductive Fe(II) release coupled 1:1 by electron conduction through crystallites. Given the availability of two tracer exchange data sets that explore pH and particle size effects (e.g., Handler et al. Environ. Sci. Technol. 2014, 48, 11302-11311; Joshi and Gorski Environ. Sci. Technol. 2016, 50, 7315-7324), wemore » developed a stochastic simulation that exactly mimics these experiments, while imposing the 1:1 constraint. We find that all data can be represented by this model, and unifying mechanistic information emerges. At pH 7.5 a rapid initial exchange is followed by slower exchange, consistent with mixed surface- and diffusion-limited kinetics arising from prominent particle aggregation. At pH 5.0 where aggregation and net Fe(II) sorption are minimal, that exchange is quantitatively proportional to available particle surface area and the density of sorbed Fe(II) is more readily evident. Our analysis reveals a fundamental atom exchange rate of ~10-5 Fe nm-2 s-1, commensurate with some of the reported reductive dissolution rates of goethite, suggesting Fe(II) release is the rate-limiting step in the conduction mechanism during recrystallization.« less

Modern Scientific Visualization is more than Just Pretty Pictures

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

Bethel, E Wes; Rubel, Oliver; Wu, Kesheng

2008-12-05

While the primary product of scientific visualization is images and movies, its primary objective is really scientific insight. Too often, the focus of visualization research is on the product, not the mission. This paper presents two case studies, both that appear in previous publications, that focus on using visualization technology to produce insight. The first applies"Query-Driven Visualization" concepts to laser wakefield simulation data to help identify and analyze the process of beam formation. The second uses topological analysis to provide a quantitative basis for (i) understanding the mixing process in hydrodynamic simulations, and (ii) performing comparative analysis of data frommore » two different types of simulations that model hydrodynamic instability.« less

40 CFR 125.95 - As an owner or operator of a Phase II existing facility, what must I collect and submit when I...

Code of Federal Regulations, 2010 CFR

2010-07-01

... appropriate for a quantitative survey and include consideration of the methods used in other studies performed... basis for any assumptions and quantitative estimates. If you plan to use an entrainment survival rate...

40 CFR 125.95 - As an owner or operator of a Phase II existing facility, what must I collect and submit when I...

Code of Federal Regulations, 2013 CFR

2013-07-01

... appropriate for a quantitative survey and include consideration of the methods used in other studies performed... basis for any assumptions and quantitative estimates. If you plan to use an entrainment survival rate...

40 CFR 125.95 - As an owner or operator of a Phase II existing facility, what must I collect and submit when I...

Code of Federal Regulations, 2014 CFR

2014-07-01

... appropriate for a quantitative survey and include consideration of the methods used in other studies performed... basis for any assumptions and quantitative estimates. If you plan to use an entrainment survival rate...

40 CFR 125.95 - As an owner or operator of a Phase II existing facility, what must I collect and submit when I...

Code of Federal Regulations, 2011 CFR

2011-07-01

... appropriate for a quantitative survey and include consideration of the methods used in other studies performed... basis for any assumptions and quantitative estimates. If you plan to use an entrainment survival rate...

40 CFR 125.95 - As an owner or operator of a Phase II existing facility, what must I collect and submit when I...

Code of Federal Regulations, 2012 CFR

2012-07-01

... appropriate for a quantitative survey and include consideration of the methods used in other studies performed... basis for any assumptions and quantitative estimates. If you plan to use an entrainment survival rate...

Behavioral responses of juvenile Daphnia magna after exposure to glyphosate and glyphosate-copper complexes.

PubMed

Hansen, Lone Rykær; Roslev, Peter

2016-10-01

Glyphosate (N-(phosphonomethyl)glycine) is the active ingredient in a range of popular broad-spectrum herbicide formulations. Glyphosate is a chelating agent that can form stable complexes with divalent metal ions including Cu(II). Little is known about the bioavailability and ecotoxicity of glyphosate-Cu(II) complexes to aquatic organisms. In this study, we used video tracking and behavior analysis to investigate sublethal effects of binary mixtures of glyphosate and Cu(II) to juvenile D. magna. Behavioral responses were quantified for individual D. magna after 24h and 48h exposure to glyphosate and glyhosate-Cu(II) mixtures. Sublethal concentrations resulted in decreases in swimming velocity, acceleration speed, and distance moved whereas inactive time of D. magna increased. Distance moved and inactive time were the most responsive parameters to glyphosate and glyphosate-Cu(II) exposure. On a molar basis, glyphosate-Cu(II) complexes appeared more toxic to D. magna than glyphosate alone. The 48h EC50 for glyphosate and glyphosate-Cu(II) determined from swimming distance were 75.2μM and 8.4μM, respectively. In comparison, traditional visual observation of mobility resulted in 48h EC50 values of 52.8μM and 25.5μM for glyphosate and glyphosate-Cu(II), respectively. The behavioral responses indicated that exposure of D. magna to mixtures of glyphosate and Cu(II) attenuated acute metal toxicity but increased apparent glyphosate toxicity due to complexation with Cu(II). The study suggests that glyphosate is a likely mediator of aquatic metal toxicity, and that video tracking provides an opportunity for quantitative studies of sublethal effects of pesticide complexes. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of intradermal dilutional testing, skin prick testing, and modified quantitative testing for common allergens.

PubMed

Peltier, Jacques; Ryan, Matthew W

2007-08-01

To compare and correlate wheal size using the Multi-Test II applicator with the endpoint obtained by intradermal dilutional testing (IDT) for 5 common allergens. To examine the safety of modified quantitative testing (MQT) for determining immunotherapy starting doses. Prospective comparative clinical study. A total of 134 subjects were simultaneously skin tested for immediate hypersensitivity using the Multi-Test II device and IDT. There was a 77% concordance between results from IDT and results from MQT. When there was a difference, MQT predicted a safer endpoint for starting immunotherapy in all but 2 cases. Wheal size by SPT is predictive of endpoint by IDT. MQT is nearly as effective as formal IDT in determining endpoint. Modified quantitative testing appears to be a safe alternative to IDT for determining starting doses for immunotherapy.

Mycoplasma pneumoniae Protein P30 Is Required for Cytadherence and Associated with Proper Cell Development

PubMed Central

Romero-Arroyo, Cynthia E.; Jordan, Jarrat; Peacock, Susan J.; Willby, Melisa J.; Farmer, Mark A.; Krause, Duncan C.

1999-01-01

The attachment organelle of Mycoplasma pneumoniae is a polar, tapered cell extension containing an intracytoplasmic, electron-dense core. This terminal structure is the leading end in gliding motility, and its duplication is thought to precede cell division, raising the possibility that mutations affecting cytadherence also confer a defect in motility or cell development. Mycoplasma surface protein P30 is associated with the attachment organelle, and P30 mutants II-3 and II-7 do not cytadhere. In this study, the recombinant wild-type but not the mutant II-3 p30 allele restored cytadherence when transformed into P30 mutants by recombinant transposon delivery. The mutations associated with loss of P30 in mutant II-3 and reacquisition of P30 in cytadhering revertants thereof were identified by nucleotide sequencing of the p30 gene. Morphological abnormalities that included ovoid or multilobed cells having a poorly defined tip structure were associated with loss of P30. Digital image analysis confirmed quantitatively the morphological differences noted visually. Transformation of the P30 mutants with the wild-type p30 allele restored a normal morphology, as determined both visually and by digital image analysis, suggesting that P30 plays a role in mycoplasma cell development. Finally, the P30 mutants localized the adhesin protein P1 to the terminal organelle, indicating that P30 is not involved in P1 trafficking but may be required for its receptor-binding function. PMID:9973332

Development and validation of a questionnaire assessing the perceived control in health care among older adults with care needs in the Netherlands.

PubMed

Claassens, L; Terwee, C B; Deeg, D J H; Broese van Groenou, M I; Widdershoven, G A M; Huisman, M

2016-04-01

In response to the increased emphasis placed on older people's self-reliance in many welfare societies, we aimed to develop and validate a measurement instrument, assessing perceived control in health care among older adults with care needs. The target group consists of older people who live (semi-)independently and use professional health care, with or without informal care. Phase I (development) of the study consisted of the construction of the instrument based on the input from a variety of stakeholders. Phase II (validation) entailed a quantitative study in a sample of 247 respondents selected from the Longitudinal Aging Study Amsterdam, to assess the instrument's construct validity (structural validity and hypotheses testing) and reliability (internal consistency). The questionnaire consists of 29 items, related to organizing professional care, communication with care professionals, health management in the home situation, planning (more) complex care in the future, and perceived support from the social network. Based on a factor analysis, we identified three subscales: (I.) 'perceived personal control in health care'; (II.) 'anticipated personal control regarding future health care'; and (III.) 'perceived support from the social network,' with internal consistencies varying from Cronbach's α = .71 to .90. Factor I was associated with mastery, self-efficacy, self-esteem (r = .31-.35) and factor III with social loneliness (r = -.42). Factor II correlated less strongly with mastery, self-efficacy, and self-esteem (r < .30). Our questionnaire revealed sufficient construct validity and internal consistency. The instrument provides a basis for further quantitative research regarding control, especially in relation to health care-related outcomes.

Kinetics of Cd(ii) adsorption and desorption on ferrihydrite: experiments and modeling.

PubMed

Liang, Yuzhen; Tian, Lei; Lu, Yang; Peng, Lanfang; Wang, Pei; Lin, Jingyi; Cheng, Tao; Dang, Zhi; Shi, Zhenqing

2018-05-15

The kinetics of Cd(ii) adsorption/desorption on ferrihydrite is an important process affecting the fate, transport, and bioavailability of Cd(ii) in the environment, which was rarely systematically studied and understood at quantitative levels. In this work, a combination of stirred-flow kinetic experiments, batch adsorption equilibrium experiments, high-resolution transmission electron microscopy (HR-TEM), and mechanistic kinetic modeling were used to study the kinetic behaviors of Cd(ii) adsorption/desorption on ferrihydrite. HR-TEM images showed the open, loose, and sponge-like structure of ferrihydrite. The batch adsorption equilibrium experiments revealed that higher pH and initial metal concentration increased Cd(ii) adsorption on ferrihydrite. The stirred-flow kinetic results demonstrated the increased adsorption rate and capacity as a result of the increased pH, influent concentration, and ferrihydrite concentration. The mechanistic kinetic model successfully described the kinetic behaviors of Cd(ii) during the adsorption and desorption stages under various chemistry conditions. The model calculations showed that the adsorption rate coefficients varied as a function of solution chemistry, and the relative contributions of the weak and strong ferrihydrite sites for Cd(ii) binding varied with time at different pH and initial metal concentrations. Our model is able to quantitatively assess the contributions of each individual ferrihydrite binding site to the overall Cd(ii) adsorption/desorption kinetics. This study provided insights into the dynamic behavior of Cd(ii) and a predictive modeling tool for Cd(ii) adsorption/desorption kinetics when ferrihydrite is present, which may be helpful for the risk assessment and management of Cd contaminated sites.

An empirical investigation into health sector absenteeism.

PubMed

Walker, Vivienne; Bamford, David

2011-08-01

The purpose of this research was to consider why absenteeism in Health and Social Care is so high and to suggest proactive changes in organization activity to address this. The research took a multimethod approach with a quantitative emphasis; there were three parts: (i) quantitative survey questionnaire; (ii) analysis of absenteeism and related secondary data; and (iii) qualitative data from other questions in survey and discussion groups. The quantitative emphasis in the research is appropriate, given the gap identified in the literature. Perceived limitations are that the study considers just one part of the overall system. The research indicates that managers underestimate staff absence levels and almost half believe absenteeism cannot reduce. Professional managers were more negative and over half of nurse managers believed that absence could not reduce. Unless there is a systematic systemic change in organizations, which changes managers' attitudes and understanding of absence with a consequent change in activity across the absence continuum, there is no prospect of a sustained reduction in absence levels. Manager impact and role in absence management are poorly covered in research, so this research helps inform those gaps.

Molecular classification of patients with grade II/III glioma using quantitative MRI characteristics.

PubMed

Bahrami, Naeim; Hartman, Stephen J; Chang, Yu-Hsuan; Delfanti, Rachel; White, Nathan S; Karunamuni, Roshan; Seibert, Tyler M; Dale, Anders M; Hattangadi-Gluth, Jona A; Piccioni, David; Farid, Nikdokht; McDonald, Carrie R

2018-06-02

Molecular markers of WHO grade II/III glioma are known to have important prognostic and predictive implications and may be associated with unique imaging phenotypes. The purpose of this study is to determine whether three clinically relevant molecular markers identified in gliomas-IDH, 1p/19q, and MGMT status-show distinct quantitative MRI characteristics on FLAIR imaging. Sixty-one patients with grade II/III gliomas who had molecular data and MRI available prior to radiation were included. Quantitative MRI features were extracted that measured tissue heterogeneity (homogeneity and pixel correlation) and FLAIR border distinctiveness (edge contrast; EC). T-tests were conducted to determine whether patients with different genotypes differ across the features. Logistic regression with LASSO regularization was used to determine the optimal combination of MRI and clinical features for predicting molecular subtypes. Patients with IDH wildtype tumors showed greater signal heterogeneity (p = 0.001) and lower EC (p = 0.008) within the FLAIR region compared to IDH mutant tumors. Among patients with IDH mutant tumors, 1p/19q co-deleted tumors had greater signal heterogeneity (p = 0.002) and lower EC (p = 0.005) compared to 1p/19q intact tumors. MGMT methylated tumors showed lower EC (p = 0.03) compared to the unmethylated group. The combination of FLAIR border distinctness, heterogeneity, and pixel correlation optimally classified tumors by IDH status. Quantitative imaging characteristics of FLAIR heterogeneity and border pattern in grade II/III gliomas may provide unique information for determining molecular status at time of initial diagnostic imaging, which may then guide subsequent surgical and medical management.

Tool development in threat assessment: syntax regularization and correlative analysis. Final report Task I and Task II, November 21, 1977-May 21, 1978. [Linguistic analysis

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

Miron, M.S.; Christopher, C.; Hirshfield, S.

1978-05-01

Psycholinguistics provides crisis managers in nuclear threat incidents with a quantitative methodology which can aid in the determination of threat credibility, authorship identification and perpetrator apprehension. The objective of this contract is to improve and enhance present psycholinguistic software systems by means of newly-developed, computer-automated techniques which significantly extend the technology of automated content and stylistic analysis of nuclear threat. In accordance with this overall objective, the first two contract Tasks have been completed and are reported on in this document. The first Task specifies the development of software support for the purpose of syntax regularization of vocabulary to rootmore » form. The second calls for the exploration and development of alternative approaches to correlative analysis of vocabulary usage.« less

21 CFR 170.35 - Affirmation of generally recognized as safe (GRAS) status.

Code of Federal Regulations, 2010 CFR

2010-04-01

... as provided in § 170.30(e), except those subject to the NAS/NRC GRAS list survey (36 FR 20546...) Quantitative compositions. (h) Manufacturing process (excluding any trade secrets). (ii) Use of the substance... the substance in food, including: (a) References to qualitative and quantitative methods for...

21 CFR 170.35 - Affirmation of generally recognized as safe (GRAS) status.

Code of Federal Regulations, 2012 CFR

2012-04-01

... as provided in § 170.30(e), except those subject to the NAS/NRC GRAS list survey (36 FR 20546...) Quantitative compositions. (h) Manufacturing process (excluding any trade secrets). (ii) Use of the substance... the substance in food, including: (a) References to qualitative and quantitative methods for...

21 CFR 170.35 - Affirmation of generally recognized as safe (GRAS) status.

Code of Federal Regulations, 2011 CFR

2011-04-01

... as provided in § 170.30(e), except those subject to the NAS/NRC GRAS list survey (36 FR 20546...) Quantitative compositions. (h) Manufacturing process (excluding any trade secrets). (ii) Use of the substance... the substance in food, including: (a) References to qualitative and quantitative methods for...

21 CFR 170.35 - Affirmation of generally recognized as safe (GRAS) status.

Code of Federal Regulations, 2013 CFR

2013-04-01

... as provided in § 170.30(e), except those subject to the NAS/NRC GRAS list survey (36 FR 20546...) Quantitative compositions. (h) Manufacturing process (excluding any trade secrets). (ii) Use of the substance... the substance in food, including: (a) References to qualitative and quantitative methods for...

76 FR 37620 - Risk-Based Capital Standards: Advanced Capital Adequacy Framework-Basel II; Establishment of a...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-28

... systems. E. Quantitative Methods for Comparing Capital Frameworks The NPR sought comment on how the... industry while assessing levels of capital. This commenter points out maintaining reliable comparative data over time could make quantitative methods for this purpose difficult. For example, evaluating asset...

Framework for a Quantitative Systemic Toxicity Model (FutureToxII)

EPA Science Inventory

EPA’s ToxCast program profiles the bioactivity of chemicals in a diverse set of ~700 high throughput screening (HTS) assays. In collaboration with L’Oreal, a quantitative model of systemic toxicity was developed using no effect levels (NEL) from ToxRefDB for 633 chemicals with HT...

An analysis of the impact of LHC Run I proton-lead data on nuclear parton densities.

PubMed

Armesto, Néstor; Paukkunen, Hannu; Penín, José Manuel; Salgado, Carlos A; Zurita, Pía

2016-01-01

We report on an analysis of the impact of available experimental data on hard processes in proton-lead collisions during Run I at the large hadron collider on nuclear modifications of parton distribution functions. Our analysis is restricted to the EPS09 and DSSZ global fits. The measurements that we consider comprise production of massive gauge bosons, jets, charged hadrons and pions. This is the first time a study of nuclear PDFs includes this number of different observables. The goal of the paper is twofold: (i) checking the description of the data by nPDFs, as well as the relevance of these nuclear effects, in a quantitative manner; (ii) testing the constraining power of these data in eventual global fits, for which we use the Bayesian reweighting technique. We find an overall good, even too good, description of the data, indicating that more constraining power would require a better control over the systematic uncertainties and/or the proper proton-proton reference from LHC Run II. Some of the observables, however, show sizeable tension with specific choices of proton and nuclear PDFs. We also comment on the corresponding improvements as regards the theoretical treatment.

Characterization and quantification of flavonoids and saponins in adzuki bean (Vigna angularis L.) by HPLC-DAD-ESI-MSn analysis.

PubMed

Liu, Rui; Cai, Zongwei; Xu, Baojun

2017-09-22

Bioactive activities of adzuki bean have been widely reported, however, the phytochemical information of adzuki bean is incomplete. The aim of this study was to characterize and quantify flavonoids and saponins in adzuki bean. High performance liquid chromatography with diode array detection and electro spray ionization-tandem multi-stage mass spectrometry (HPLC-DAD-ESI-MS n ) were applied to do qualitative and quantitative analyses. A total of 15 compounds from adzuki bean were identified by HPLC-DAD-ESI-MS n . Among 15 compounds identified, four flavonoids (catechin, vitexin-4″-O-glucoside, quercetin-3-O-glucoside, and quercetin-3-O-rutinoside) and six saponins (azukisaponin I, II, III, IV, V, and VI) in adzuki bean were further quantified by external calibration method using HPLC-MS with the program of time segment and extract ion chromatogram (EIC) analysis. Current qualitative and quantitative method based on HPLC and MS technique provides a scientific basis for in vitro and in vivo pharmacological study in the future. Graphical abstract Isolation and characterization of flavonoids and saponins from adzuki bean.

Single-case synthesis tools II: Comparing quantitative outcome measures.

PubMed

Zimmerman, Kathleen N; Pustejovsky, James E; Ledford, Jennifer R; Barton, Erin E; Severini, Katherine E; Lloyd, Blair P

2018-03-07

Varying methods for evaluating the outcomes of single case research designs (SCD) are currently used in reviews and meta-analyses of interventions. Quantitative effect size measures are often presented alongside visual analysis conclusions. Six measures across two classes-overlap measures (percentage non-overlapping data, improvement rate difference, and Tau) and parametric within-case effect sizes (standardized mean difference and log response ratio [increasing and decreasing])-were compared to determine if choice of synthesis method within and across classes impacts conclusions regarding effectiveness. The effectiveness of sensory-based interventions (SBI), a commonly used class of treatments for young children, was evaluated. Separately from evaluations of rigor and quality, authors evaluated behavior change between baseline and SBI conditions. SBI were unlikely to result in positive behavior change across all measures except IRD. However, subgroup analyses resulted in variable conclusions, indicating that the choice of measures for SCD meta-analyses can impact conclusions. Suggestions for using the log response ratio in SCD meta-analyses and considerations for understanding variability in SCD meta-analysis conclusions are discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

Quantitative T2 evaluation at 3.0T compared to morphological grading of the lumbar intervertebral disc: a standardized evaluation approach in patients with low back pain.

PubMed

Stelzeneder, David; Welsch, Goetz Hannes; Kovács, Balázs Krisztián; Goed, Sabine; Paternostro-Sluga, Tatjana; Vlychou, Marianna; Friedrich, Klaus; Mamisch, Tallal Charles; Trattnig, Siegfried

2012-02-01

The purpose of our investigation was to compare quantitative T2 relaxation time measurement evaluation of lumbar intervertebral discs with morphological grading in young to middle-aged patients with low back pain, using a standardized region-of-interest evaluation approach. Three hundred thirty lumbar discs from 66 patients (mean age, 39 years) with low back pain were examined on a 3.0T MR unit. Sagittal T1-FSE, sagittal, coronal, and axial T2-weighted FSE for morphological MRI, as well as a multi-echo spin-echo sequence for T2 mapping, were performed. Morphologically, all discs were classified according to Pfirrmann et al. Equally sized rectangular regions of interest (ROIs) for the annulus fibrosus were selected anteriorly and posteriorly in the outermost 20% of the disc. The space between was defined as the nucleus pulposus. To assess the reproducibility of this evaluation, inter- and intraobserver statistics were performed. The Pfirrmann scoring of 330 discs showed the following results: grade I: six discs (1.8%); grade II: 189 (57.3%); grade III: 96 (29.1%); grade IV: 38 (11.5%); and grade V: one (0.3%). The mean T2 values (in milliseconds) for the anterior and the posterior annulus, and the nucleus pulposus for the respective Pfirrmann groups were: I: 57/30/239; II: 44/67/129; III: 42/51/82; and IV: 42/44/56. The nucleus pulposus T2 values showed a stepwise decrease from Pfirrmann grade I to IV. The posterior annulus showed the highest T2 values in Pfirrmann group II, while the anterior annulus showed relatively constant T2 values in all Pfirrmann groups. The inter- and intraobserver analysis yielded intraclass correlation coefficients (ICC) for average measures in a range from 0.82 (anterior annulus) to 0.99 (nucleus). Our standardized method of region-specific quantitative T2 relaxation time evaluation seems to be able to characterize different degrees of disc degeneration quantitatively. The reproducibility of our ROI measurements is sufficient to encourage the use of this method in future investigations, particularly for longitudinal studies. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

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

Novel atomic absorption spectrometric and rapid spectrophotometric methods for the quantitation of paracetamol in saliva: application to pharmacokinetic studies.

PubMed

Issa, M M; Nejem, R M; El-Abadla, N S; Al-Kholy, M; Saleh, Akila A

2008-01-01

A novel atomic absorption spectrometric method and two highly sensitive spectrophotometric methods were developed for the determination of paracetamol. These techniques based on the oxidation of paracetamol by iron (III) (method I); oxidation of p-aminophenol after the hydrolysis of paracetamol (method II). Iron (II) then reacts with potassium ferricyanide to form Prussian blue color with a maximum absorbance at 700 nm. The atomic absorption method was accomplished by extracting the excess iron (III) in method II and aspirates the aqueous layer into air-acetylene flame to measure the absorbance of iron (II) at 302.1 nm. The reactions have been spectrometrically evaluated to attain optimum experimental conditions. Linear responses were exhibited over the ranges 1.0-10, 0.2-2.0 and 0.1-1.0 mug/ml for method I, method II and atomic absorption spectrometric method, respectively. A high sensitivity is recorded for the proposed methods I and II and atomic absorption spectrometric method value indicate: 0.05, 0.022 and 0.012 mug/ml, respectively. The limit of quantitation of paracetamol by method II and atomic absorption spectrometric method were 0.20 and 0.10 mug/ml. Method II and the atomic absorption spectrometric method were applied to demonstrate a pharmacokinetic study by means of salivary samples in normal volunteers who received 1.0 g paracetamol. Intra and inter-day precision did not exceed 6.9%.

Novel Atomic Absorption Spectrometric and Rapid Spectrophotometric Methods for the Quantitation of Paracetamol in Saliva: Application to Pharmacokinetic Studies

PubMed Central

Issa, M. M.; Nejem, R. M.; El-Abadla, N. S.; Al-Kholy, M.; Saleh, Akila. A.

2008-01-01

A novel atomic absorption spectrometric method and two highly sensitive spectrophotometric methods were developed for the determination of paracetamol. These techniques based on the oxidation of paracetamol by iron (III) (method I); oxidation of p-aminophenol after the hydrolysis of paracetamol (method II). Iron (II) then reacts with potassium ferricyanide to form Prussian blue color with a maximum absorbance at 700 nm. The atomic absorption method was accomplished by extracting the excess iron (III) in method II and aspirates the aqueous layer into air-acetylene flame to measure the absorbance of iron (II) at 302.1 nm. The reactions have been spectrometrically evaluated to attain optimum experimental conditions. Linear responses were exhibited over the ranges 1.0-10, 0.2-2.0 and 0.1-1.0 μg/ml for method I, method II and atomic absorption spectrometric method, respectively. A high sensitivity is recorded for the proposed methods I and II and atomic absorption spectrometric method value indicate: 0.05, 0.022 and 0.012 μg/ml, respectively. The limit of quantitation of paracetamol by method II and atomic absorption spectrometric method were 0.20 and 0.10 μg/ml. Method II and the atomic absorption spectrometric method were applied to demonstrate a pharmacokinetic study by means of salivary samples in normal volunteers who received 1.0 g paracetamol. Intra and inter-day precision did not exceed 6.9%. PMID:20046743

Comparative scanning electron microscope analysis of diode laser and desensitizing toothpastes for evaluation of efficacy of dentinal tubular occlusion.

PubMed

Reddy, Guntakala Vikram; Akula, Sushma; Malgikar, Suryakanth; Babu, Palaparthy Raja; Reddy, Gooty Jagadish; Josephin, Johnson Juliet

2017-01-01

The present study aims to evaluate the efficacy of diode laser alone and in combination with desensitizing toothpastes in occluding dentinal tubules (both partially occluded and completely occluded tubules) by scanning electron microscope (SEM). Fifty human teeth were extracted, cervical cavities were prepared and etched with 17% ethylenediaminetetraacetic acid, and smear layer was removed to expose the tubules. The teeth were divided into five groups: Group I - Application of NovaMin-formulated toothpaste, Group II - Application of Pro-Argin ™ -formulated toothpaste, Group III - Application of diode laser in noncontact mode, Group IV - NovaMin-formulated toothpaste followed by laser irradiation, and Group V - Pro-Argin ™ -formulated toothpaste followed by laser irradiation. After treatment, quantitative analysis of occluded dentinal tubules was done by SEM analysis. The mean values of percentages of total occlusion of dentinal tubules in Groups I, II, III, IV, and V were 92.73% ± 1.38, 90.67% ± 1.86, 96.57% ± 0.64, 97.3% ± 0.68, and 96.9% ± 6.08, respectively. Addition of diode laser (Groups III, IV, and V) yielded a significant occlusion of the dentinal tubules when compared to desensitizing toothpastes alone (Groups I and II). Diode laser (Group III) has shown more efficacy in occluding dentinal tubules when compared with desensitizing toothpastes which was statistically significant ( P < 0.05). Among the five groups, NovaMin + diode laser (Group IV) showed the highest percentage of occluded dentinal tubules.

Multiple internal standard normalization for improving HS-SPME-GC-MS quantitation in virgin olive oil volatile organic compounds (VOO-VOCs) profile.

PubMed

Fortini, Martina; Migliorini, Marzia; Cherubini, Chiara; Cecchi, Lorenzo; Calamai, Luca

2017-04-01

The commercial value of virgin olive oils (VOOs) strongly depends on their classification, also based on the aroma of the oils, usually evaluated by a panel test. Nowadays, a reliable analytical method is still needed to evaluate the volatile organic compounds (VOCs) and support the standard panel test method. To date, the use of HS-SPME sampling coupled to GC-MS is generally accepted for the analysis of VOCs in VOOs. However, VOO is a challenging matrix due to the simultaneous presence of: i) compounds at ppm and ppb concentrations; ii) molecules belonging to different chemical classes and iii) analytes with a wide range of molecular mass. Therefore, HS-SPME-GC-MS quantitation based upon the use of external standard method or of only a single internal standard (ISTD) for data normalization in an internal standard method, may be troublesome. In this work a multiple internal standard normalization is proposed to overcome these problems and improving quantitation of VOO-VOCs. As many as 11 ISTDs were used for quantitation of 71 VOCs. For each of them the most suitable ISTD was selected and a good linearity in a wide range of calibration was obtained. Except for E-2-hexenal, without ISTD or with an unsuitable ISTD, the linear range of calibration was narrower with respect to that obtained by a suitable ISTD, confirming the usefulness of multiple internal standard normalization for the correct quantitation of VOCs profile in VOOs. The method was validated for 71 VOCs, and then applied to a series of lampante virgin olive oils and extra virgin olive oils. In light of our results, we propose the application of this analytical approach for routine quantitative analyses and to support sensorial analysis for the evaluation of positive and negative VOOs attributes. Copyright © 2017 Elsevier B.V. All rights reserved.

Robust Linear Models for Cis-eQTL Analysis.

PubMed

Rantalainen, Mattias; Lindgren, Cecilia M; Holmes, Christopher C

2015-01-01

Expression Quantitative Trait Loci (eQTL) analysis enables characterisation of functional genetic variation influencing expression levels of individual genes. In outbread populations, including humans, eQTLs are commonly analysed using the conventional linear model, adjusting for relevant covariates, assuming an allelic dosage model and a Gaussian error term. However, gene expression data generally have noise that induces heavy-tailed errors relative to the Gaussian distribution and often include atypical observations, or outliers. Such departures from modelling assumptions can lead to an increased rate of type II errors (false negatives), and to some extent also type I errors (false positives). Careful model checking can reduce the risk of type-I errors but often not type II errors, since it is generally too time-consuming to carefully check all models with a non-significant effect in large-scale and genome-wide studies. Here we propose the application of a robust linear model for eQTL analysis to reduce adverse effects of deviations from the assumption of Gaussian residuals. We present results from a simulation study as well as results from the analysis of real eQTL data sets. Our findings suggest that in many situations robust models have the potential to provide more reliable eQTL results compared to conventional linear models, particularly in respect to reducing type II errors due to non-Gaussian noise. Post-genomic data, such as that generated in genome-wide eQTL studies, are often noisy and frequently contain atypical observations. Robust statistical models have the potential to provide more reliable results and increased statistical power under non-Gaussian conditions. The results presented here suggest that robust models should be considered routinely alongside other commonly used methodologies for eQTL analysis.

Effects of copper on the abundance and diversity of ammonia oxidizers during dairy cattle manure composting.

PubMed

Yin, Yanan; Song, Wen; Gu, Jie; Zhang, Kaiyu; Qian, Xun; Zhang, Xin; Zhang, Yajun; Li, Yang; Wang, Xiaojuan

2016-12-01

This study investigated the effects of adding Cu(II) at two exposure levels (50 and 500mgkg -1 , i.e., Cu50 and Cu500 treatments, respectively) on the activity of ammonia-oxidizing microorganisms during dairy cattle manure composting. The results showed that the pH, NH 4 + -N, NO 3 - -N, and potential ammonia oxidation values were inhibited significantly by the addition of Cu(II). Furthermore, the abundances of the ammonia-oxidizing archaea (AOA) amoA gene and ammonia-oxidizing bacteria (AOB) amoA gene were determined by quantitative PCR, and their compositions were evaluated by denaturing gradient gel electrophoresis (DGGE). AOA was the dominant ammonia oxidizing microorganism, of which the abundance was much higher than AOB during composting. Cu50 and Cu500 had significant inhibitory effects on the abundance of the amoA gene. The DGGE profile and statistical analysis showed that Cu(II) changed the AOA and AOB community structure and diversity, where Nitrosomonas and Crenarchaeota dominated throughout the composting process. Copyright © 2016. Published by Elsevier Ltd.

Using laser capture microdissection to study fiber specific signaling in locomotor muscle in COPD: A pilot study.

PubMed

Mohan, Divya; Lewis, Amy; Patel, Mehul S; Curtis, Katrina J; Lee, Jen Y; Hopkinson, Nicholas S; Wilkinson, Ian B; Kemp, Paul R; Polkey, Michael I

2017-06-01

Quadriceps dysfunction is important in chronic obstructive pulmonary disease (COPD), with an associated increased proportion of type II fibers. Investigation of protein synthesis and degradation has yielded conflicting results, possibly due to study of whole biopsy samples, whereas signaling may be fiber-specific. Our objective was to develop a method for fiber-specific gene expression analysis. 12 COPD and 6 healthy subjects underwent quadriceps biopsy. Cryosections were immunostained for type II fibers, which were separated using laser capture microdissection (LCM). Whole muscle and different fiber populations were subject to quantitative polymerase chain reaction. Levels of muscle-RING-finger-protein-1 and Atrogin-1 were lower in type II fibers of COPD versus healthy subjects (P = 0.02 and P = 0.03, respectively), but differences were not apparent in whole muscle or type I fibers. We describe a novel method for studying fiber-specific gene expression in optimum cutting temperature compound-embedded muscle specimens. LCM offers a more sensitive way to identify molecular changes in COPD muscle. Muscle Nerve 55: 902-912, 2017. © 2016 Wiley Periodicals, Inc.

Simulation of water solutions of Ni 2+ at infinite dilution

NASA Astrophysics Data System (ADS)

Natália, M.; Cordeiro, D. S.; Ignaczak, Anna; Gomes, José A. N. F.

1993-10-01

A new ab initio pair potential is developed to describe the nickel—water interactions in Ni(II) aqueous solutions. Results of Monte Carlo simulations for the Ni(II)(H 2O) 200 system are presented for this pair potential with and without three-body classical polarization terms (the water—water interaction is described by the ab initio MCY potential). The structure of the solution around Ni(II) is discussed in terms of radial distribution functions, coordination numbers and thermal ellipsoids. The results show that the three-body terms have a non-negligible effect on the simulated solution. In fact, the experimental coordination number of six is reproduced with the full potential while a higher value is predicted when the simple pairwise-additive potential is used. The equilibrium NiO distance for the first hydration shell is also dependent on the use of the three-body terms. Comparison of our distribution functions with those obtained by neutron-diffraction experiments shows a reasonable quantitative agreement. Statistical pattern recognition analysis has also been applied to our simulations in order to better understand the local thermal motion of the water molecules around the metal ion. In this way, thermal ellipsoids have been computed (and graphically displayed) for each atom of the water molecules belonging to the Ni(II) first hydration shell. This analysis revealed that the twisting and bending motions are greater than the radial motion, and that the hydrogens have a higher mobility than the oxygens. In addition, a thermodynamic perturbation method has been incorporated in our Monte Carlo procedure in order to compute the free energy of hydration for the Ni(II) ion. Agreement between these results and the experimental ones is also sufficiently reasonable to demonstrate the feasibility of this new potential for the nickel—water interactions.

Endogenous angiotensinergic system in neurons of rat and human trigeminal ganglia

PubMed Central

Imboden, Hans; Patil, Jaspal; Nussberger, Juerg; Nicoud, Françoise; Hess, Benno; Ahmed, Nermin; Schaffner, Thomas; Wellner, Maren; Müller, Dominik; Inagami, Tadashi; Senbonmatsu, Takaaki; Pavel, Jaroslav; Saavedra, Juan M.

2009-01-01

To clarify the role of Angiotensin II (Ang II) in the sensory system and especially in the trigeminal ganglia, we studied the expression of angiotensinogen (Ang-N)-, renin-, angiotensin converting enzyme (ACE)- and cathepsin D-mRNA, and the presence of Ang II and substance P in the rat and human trigeminal ganglia. The rat trigeminal ganglia expressed substantial amounts of Ang-N- and ACE mRNA as determined by quantitative real time PCR. Renin mRNA was untraceable in rat samples. Cathepsin D was detected in the rat trigeminal ganglia indicating the possibility of existence of pathways alternative to renin for Ang I formation. In situ hybridization in rat trigeminal ganglia revealed expression of Ang-N mRNA in the cytoplasm of numerous neurons. By using immunocytochemistry, a number of neurons and their processes in both the rat and human trigeminal ganglia were stained for Ang II. Post in situ hybridization immunocytochemistry reveals that in the rat trigeminal ganglia some, but not all Ang-N mRNA-positive neurons marked for Ang II. In some neurons Substance P was found colocalized with Ang II. Angiotensins from rat trigeminal ganglia were quantitated by radioimmunoassay with and without prior separation by high performance liquid chromatography. Immunoreactive angiotensin II (ir-Ang II) was consistently present and the sum of true Ang II (1-8) octapeptide and its specifically measured metabolites were found to account for it. Radioimmunological and immunocytochemical evidence of ir-Ang II in neuronal tissue is compatible with Ang II as a neurotransmitter. In conclusion, these results suggest that Ang II could be produced locally in the neurons of rat trigeminal ganglia. The localization and colocalization of neuronal Ang II with Substance P in the trigeminal ganglia neurons may be the basis for a participation and function of Ang II in the regulation of nociception and migraine pathology. PMID:19323983

Development of Individuality in Children's Handwriting.

PubMed

Srihari, Sargur N; Meng, Lu; Hanson, Lisa

2016-09-01

Handwriting of children in early grades is studied from the viewpoint of quantitatively measuring the development of handwriting individuality. Handwriting samples of children, in grades 2-4, writing a paragraph of text in both handprinted and cursive, collected over a period of 3 years, were analyzed using two different approaches: (i) characteristics of the word "and" and (ii) entire paragraphs using an automated system. In the first approach, word characteristics were analyzed using statistical measures. In the second approach, pairs of paragraphs were compared. Both types of analysis, single word and complete writing, led to the same conclusions: (i) handwriting of each child remains relatively similar when handwriting has been just learnt and becomes markedly different from grades 3 to 4 and (ii) handwriting of different children becomes progressively more different from grades 2 to 4. The results provide strong support that handwriting becomes more individualistic with child development. © 2016 American Academy of Forensic Sciences.

Quantitative Raman spectroscopy as a tool to study the kinetics and formation mechanism of carbonates.

PubMed

Bonales, L J; Muñoz-Iglesias, V; Santamaría-Pérez, D; Caceres, M; Fernandez-Remolar, D; Prieto-Ballesteros, O

2013-12-01

We have carried out a systematic study of abiotic precipitation at different temperatures of several Mg and Ca carbonates (calcite, nesquehonite, hydrocalcite) present in carbonaceous chondrites. This study highlights the capability of Raman spectroscopy as a primary tool for performing full mineralogical analysis. The precipitation reaction and the structure of the resulting carbonates were monitored and identified with Raman spectroscopy. Raman spectroscopy enabled us to confirm that the precipitation reaction is very fast (minutes) when Ca(II) is present in the solution, whereas for Mg(II) such reactions developed at rather slow rates (weeks). We also observed that both the composition and the reaction mechanisms depended on temperature, which might help to clarify several issues in the fields of planetology and geology, because of the environmental implications of these carbonates on both terrestrial and extraterrestrial objects. Copyright © 2013 Elsevier B.V. All rights reserved.

Rapid determination of ions by combined solid-phase extraction--diffuse reflectance spectroscopy

NASA Technical Reports Server (NTRS)

Fritz, James S.; Arena, Matteo P.; Steiner, Steven A.; Porter, Marc D.

2003-01-01

We introduce colorimetric solid-phase extraction (C-SPE) for the rapid determination of selected ions. This new technique links the exhaustive concentration of an analyte by SPE onto a membrane disk surface for quantitative measurement with a hand-held diffuse reflectance spectrometer. The concentration/measurement procedure is complete in approximately 1 min and can be performed almost anywhere. This method has been used to monitor iodine and iodide in spacecraft water in the 0.1-5.0 ppm range and silver(I) in the range of 5.0-1000 microg/l. Applications to the trace analysis of copper(II), nickel(II), iron(III) and chromium(VI) are described. Studies on the mechanism of extraction showed that impregnation of the disk with a surfactant as well as a complexing reagent results in uptake of additional water, which markedly improves the extraction efficiency.

Solid-phase extraction of heavy metal ions on bucky tubes disc in natural water and herbal plant samples.

PubMed

Soylak, Mustafa; Unsal, Yunus Emre

2011-10-01

A preconcentration-separation procedure has been established based on solid-phase extraction of Fe(III) and Pb(II) on bucky tubes (BTs) disc. Fe(III) and Pb(II) ions were quantitatively recovered at pH 6. The influences of the analytical parameters like sample volume, flow rates on the recoveries of analytes on BT disc were investigated. The effects of co-existing ions on the recoveries were also studied. The detection limits for iron and lead were found 1.6 and 4.9 μg L⁻¹, respectively. The validation of the presented method was checked by the analysis of TMDA-51.3 fortified water certified reference material. The presented procedure was successfully applied to the separation-preconcentration and determination of iron and lead content of some natural water and herbal plant samples from Kayseri, Turkey.

Numerical modelling in biosciences using delay differential equations

NASA Astrophysics Data System (ADS)

Bocharov, Gennadii A.; Rihan, Fathalla A.

2000-12-01

Our principal purposes here are (i) to consider, from the perspective of applied mathematics, models of phenomena in the biosciences that are based on delay differential equations and for which numerical approaches are a major tool in understanding their dynamics, (ii) to review the application of numerical techniques to investigate these models. We show that there are prima facie reasons for using such models: (i) they have a richer mathematical framework (compared with ordinary differential equations) for the analysis of biosystem dynamics, (ii) they display better consistency with the nature of certain biological processes and predictive results. We analyze both the qualitative and quantitative role that delays play in basic time-lag models proposed in population dynamics, epidemiology, physiology, immunology, neural networks and cell kinetics. We then indicate suitable computational techniques for the numerical treatment of mathematical problems emerging in the biosciences, comparing them with those implemented by the bio-modellers.

Weld pool development during GTA and laser beam welding of Type 304 stainless steel; Part II-experimental correlation

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

Zacharia, T.; David, S.A.; Vitek, J.M.

1989-12-01

In part I of the paper, the results of the heat flow and the fluid flow analysis were presented. Here, in Part II of the paper, predictions of the computational model are verified by comparing the numerically predicted and experimentally observed fusion zone size and shape. Stationary gas tungsten arc and laser beam welds were made on Type 304 stainless steel for different times to provide a variety of solidification conditions such as cooling rate and temperature gradient. Calculated temperatures and cooling rates are correlated with the experimentally observed fusion zone structure. In addition, the effect of sulfur on GTAmore » weld penetration was quantitatively evaluated by considering two heats of 304 stainless steel containing 90 and 240 ppm sulfur. Sulfur, as expected, increased the depth/width ratio by altering the surface tension gradient driven flow in the weld pool.« less

Secular trends of infectious disease mortality in The Netherlands, 1911-1978: quantitative estimates of changes coinciding with the introduction of antibiotics.

PubMed

Mackenbach, J P; Looman, C W

1988-09-01

Secular trends of mortality from 21 infectious diseases in the Netherlands were studied by inspection of age/sex-standardized mortality curves and by log-linear regression analysis. An attempt was made to obtain quantitative estimates for changes coinciding with the introduction of antibiotics. Two possible types of effect were considered: a sharp reduction of mortality at the moment of the introduction of antibiotics, and a longer lasting (acceleration of) mortality decline after the introduction. Changes resembling the first type of effect were possibly present for many infectious diseases, but were difficult to measure exactly, due to late effects on mortality of World War II. Changes resembling the second type of effect were present in 16 infectious diseases and were sometimes quite large. For example, estimated differences in per cent per annum mortality change were 10% or larger for puerperal fever, scarlet fever, rheumatic fever, erysipelas, otitis media, tuberculosis, and bacillary dysentery. No acceleration of mortality decline after the introduction of antibiotics was present in mortality from 'all other diseases'. Although the exact contribution of antibiotics to the observed changes cannot be inferred from this time trend analysis, the quantitative estimates of the changes show that even a partial contribution would represent a substantial effect of antibiotics on mortality from infectious diseases in the Netherlands.

Research Quality: Critique of Quantitative Articles in the "Journal of Counseling & Development"

ERIC Educational Resources Information Center

Wester, Kelly L.; Borders, L. DiAnne; Boul, Steven; Horton, Evette

2013-01-01

The purpose of this study was to examine the quality of quantitative articles published in the "Journal of Counseling & Development." Quality concerns arose in regard to omissions of psychometric information of instruments, effect sizes, and statistical power. Type VI and II errors were found. Strengths included stated research…

The NIR Ca ii triplet at low metallicity. Searching for extremely low-metallicity stars in classical dwarf galaxies

NASA Astrophysics Data System (ADS)

Starkenburg, E.; Hill, V.; Tolstoy, E.; González Hernández, J. I.; Irwin, M.; Helmi, A.; Battaglia, G.; Jablonka, P.; Tafelmeyer, M.; Shetrone, M.; Venn, K.; de Boer, T.

2010-04-01

The NIR Ca ii triplet absorption lines have proven to be an important tool for quantitative spectroscopy of individual red giant branch stars in the Local Group, providing a better understanding of metallicities of stars in the Milky Way and dwarf galaxies and thereby an opportunity to constrain their chemical evolution processes. An interesting puzzle in this field is the significant lack of extremely metal-poor stars, below [Fe/H] = -3, found in classical dwarf galaxies around the Milky Way using this technique. The question arises whether these stars are really absent, or if the empirical Ca ii triplet method used to study these systems is biased in the low-metallicity regime. Here we present results of synthetic spectral analysis of the Ca ii triplet, that is focused on a better understanding of spectroscopic measurements of low-metallicity giant stars. Our results start to deviate strongly from the widely-used and linear empirical calibrations at [Fe/H] < -2. We provide a new calibration for Ca ii triplet studies which is valid for -0.5 ≥ [Fe/H] ≥ -4. We subsequently apply this new calibration to current data sets and suggest that the classical dwarf galaxies are not so devoid of extremely low-metallicity stars as was previously thought. Using observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere, Chile proposal 171.B-0588.

Functional condition of masseters muscles of patients with class ?? subdivision.

PubMed

Kuroyedova, Vera D; Makarova, Alexandra N; Chicor, Tatyana A

Main functional characteristics of masticator muscles in patients with class ?? malocclusions is activity dominance of m. temporalis in comparison with m. ?asseter. We have not found datum about functional status of the masticators in patients with class II subdivision. The purpose of our study was to investigate the functional characteristics of m. ?asseter, m. temporalis in adult patients with class II subdivision malocclusion. There have been carried out the surface electromyographic study of m. masseter, m. temporalis in 17 adult patients with class II subdivision. It was realized quantitative analysis of 271 electromyogram, it was determined the average bioelectric activity, index activity, symmetry and torsion index. It was observed predominance of the bioelectrical activity of m. temporales on m. masseter for all persons with class II subdivision. Bioelectrical activity for m. masseter was bigger on side of distal ratio and for m. temporales on side of neutral ratio. In class ?? subdivision right, the mandible was deviated to the left side and in class ?? subdivision left is deviated to the right side. Thus, rotational moment generated during compression of the jaws, causes deviation of the lower jaw to the side, with a neutral molar ratio. During voluntary chewing bioelectrical activity of m. masseter and m. temporalis was higher in the right side. In accordance with the functional condition of the masticatory muscles of class II subdivision is characterized with functional features of distal occlusion.

VBA: A Probabilistic Treatment of Nonlinear Models for Neurobiological and Behavioural Data

PubMed Central

Daunizeau, Jean; Adam, Vincent; Rigoux, Lionel

2014-01-01

This work is in line with an on-going effort tending toward a computational (quantitative and refutable) understanding of human neuro-cognitive processes. Many sophisticated models for behavioural and neurobiological data have flourished during the past decade. Most of these models are partly unspecified (i.e. they have unknown parameters) and nonlinear. This makes them difficult to peer with a formal statistical data analysis framework. In turn, this compromises the reproducibility of model-based empirical studies. This work exposes a software toolbox that provides generic, efficient and robust probabilistic solutions to the three problems of model-based analysis of empirical data: (i) data simulation, (ii) parameter estimation/model selection, and (iii) experimental design optimization. PMID:24465198

Research progress in Asia on methods of processing laser-induced breakdown spectroscopy data

NASA Astrophysics Data System (ADS)

Guo, Yang-Min; Guo, Lian-Bo; Li, Jia-Ming; Liu, Hong-Di; Zhu, Zhi-Hao; Li, Xiang-You; Lu, Yong-Feng; Zeng, Xiao-Yan

2016-10-01

Laser-induced breakdown spectroscopy (LIBS) has attracted much attention in terms of both scientific research and industrial application. An important branch of LIBS research in Asia, the development of data processing methods for LIBS, is reviewed. First, the basic principle of LIBS and the characteristics of spectral data are briefly introduced. Next, two aspects of research on and problems with data processing methods are described: i) the basic principles of data preprocessing methods are elaborated in detail on the basis of the characteristics of spectral data; ii) the performance of data analysis methods in qualitative and quantitative analysis of LIBS is described. Finally, a direction for future development of data processing methods for LIBS is also proposed.

Probing the Interaction of Ionic Liquids with CO2: A Raman Spectroscopy and Ab Initio Study

DTIC Science & Technology

2008-05-05

called physisorption. Regardless of the sorption mechanism, a few quantitative parameters can be used to describe a gas-liquid interaction at a...Controllers (I and II) I II 22 and tube fittings, 0.062 inch perfluoroalkoxy ( PFA ) tubing, Tylan General Model FC-128 Flow Controllers

PacRIM II: A review of AirSAR operations and system performance

NASA Technical Reports Server (NTRS)

Moller, D.; Chu, A.; Lou, Y.; Miller, T.; O'Leary, E.

2001-01-01

In this paper we briefly review the AirSAR system, its expected performance, and quality of data obtained during that mission. We discuss the system hardware calibration methodologies, and present quantitative performance values of radar backscatter and interferometric height errors (random and systematic) from PACRIM II calibration data.

A multiplex real-time polymerase chain reaction assay differentiates between Bolbphorus damnificus and Bolbophorus type II sp

USDA-ARS?s Scientific Manuscript database

A duplex quantitative real-time polymerase chain reaction (qPCR) assay was developed to differentiate between Bolbophorus damnificus and Bolbophorus type II species cercariae. Both trematode species are prevalent throughout the commercial catfish industry,.as both infect the ram’s horn snail, Plano...

Uncertainty Analysis of Radar and Gauge Rainfall Estimates in the Russian River Basin

NASA Astrophysics Data System (ADS)

Cifelli, R.; Chen, H.; Willie, D.; Reynolds, D.; Campbell, C.; Sukovich, E.

2013-12-01

Radar Quantitative Precipitation Estimation (QPE) has been a very important application of weather radar since it was introduced and made widely available after World War II. Although great progress has been made over the last two decades, it is still a challenging process especially in regions of complex terrain such as the western U.S. It is also extremely difficult to make direct use of radar precipitation data in quantitative hydrologic forecasting models. To improve the understanding of rainfall estimation and distributions in the NOAA Hydrometeorology Testbed in northern California (HMT-West), extensive evaluation of radar and gauge QPE products has been performed using a set of independent rain gauge data. This study focuses on the rainfall evaluation in the Russian River Basin. The statistical properties of the different gridded QPE products will be compared quantitatively. The main emphasis of this study will be on the analysis of uncertainties of the radar and gauge rainfall products that are subject to various sources of error. The spatial variation analysis of the radar estimates is performed by measuring the statistical distribution of the radar base data such as reflectivity and by the comparison with a rain gauge cluster. The application of mean field bias values to the radar rainfall data will also be described. The uncertainty analysis of the gauge rainfall will be focused on the comparison of traditional kriging and conditional bias penalized kriging (Seo 2012) methods. This comparison is performed with the retrospective Multisensor Precipitation Estimator (MPE) system installed at the NOAA Earth System Research Laboratory. The independent gauge set will again be used as the verification tool for the newly generated rainfall products.

Qualitative and quantitative analysis of palmar dermatoglyphics among smokeless tobacco users.

PubMed

Vijayaraghavan, Athreya; Aswath, Nalini

2015-01-01

Palm prints formed once does not change throughout life and is not influenced by environment. Palmar Dermatoglyphics can indicate the development of potentially malignant and malignant lesions and help in identifying persons at high risk of developing Oral submucous fibrosis (OSMF) and Oral squamous cell carcinoma (OSSC). To analyze the qualitative [finger ridge pattern and presence or absence of hypothenar pattern] and quantitative [mean ATD angle and total AB ridge count] variations in Palmar Dermatoglyphics in patients suffering from OSMF and OSCC. A prospective comparative study among 40 patients (Group I--10 samples of smokeless tobacco users with OSMF, Group II--10 samples of smokeless tobacco users with OSCC, Group III--10 samples of smokeless tobacco users without OSMF or OSCC and Group IV--10 samples without smokeless tobacco habit without OSMF and OSCC as controls) were selected. The palm prints were recorded using an HP inkjet scanner. The patients were asked to place the palm gently on the scanner with the fingers wide apart from each other. The images of the palm prints were edited and qualitative and quantitative analysis were done. Statistical analysis such as Kruskal Wallis, Post Hoc and Analysis of Varience were done. A highly significant difference among the finger ridge, hypothenar pattern and mean ATD angle (P<0.001) and total AB ridge count (P=0.005) in OSMF and OSCC patients were obtained. There is predominance of arches and loops, presence of hypothenar pattern, decrease in mean ATD angle and total AB ridge count in OSMF and Oral Cancer patients. Palmar Dermatoglyphics can predict the probable occurrence of OSMF and OSCC in smokelees tobacco users.

The Motivational Effects of Gender, Residency, Worldview, and Acculturation Towards Science Study at American Institutes of Higher Education

NASA Astrophysics Data System (ADS)

Doppke, Max George

This non-experimental, quantitative exploratory study examined the relationship between genders, student residency status, acculturation, worldviews, and the motivation towards science education for a group of 291 undergraduate students in the United States. As all demographic variables were nominal, and all survey variables were ordinal, associations and differences utilized non-parametric statistical procedures. The overall design was descriptive, comparative, and correlational. Spearman's rho signified that there was a moderate positive correlation between the total scores on the Worldview Analysis Scale (WAS) and the total scores on the Science Motivation Questionnaire-II (SMQ-II; rs = .393, *p< .01, two-tailed). A Goodman and Kruskal's Gamma was conducted to determine the association between the seven subscales of the Worldview Assessment Survey (WAS) and the five subscales of the Science Motivation Questionnaire -II (SMQ-II). The results showed a moderate to strongly moderate, positive association between WAS Communalism (WASCOM) and the SMQ-II subscales of intrinsic motivation (SMQINTR; G = .322, p<.0005); self-efficacy (SMQSELF; G = .350, p< .0005); career motivation (SMQCAR; G = .307, p< .0005); and self-determination (SMQSELFDET; G = .364, p< .0005). A Mann-Whitney U test was run on the Worldview Analysis Scale (WAS) and the Science Motivation Questionnaire-II (SMQ-II) to determine if differences in score were based on gender. The WAS score was statistically significantly higher in males (Median = 180.00) than in females ( Median = 164.00, U = 8521.500, z = -2.840, p = .005). . The SMQ-II score was statistically insignificantly higher in males (Median = 152.56) than in females (Median = 140.08, U = 9652.500, z = -1.263, p = .207). In following the fundamental dictates of social research, this study offered a thorough description of a situation that ultimately provokes various possible explanations as necessary conclusions to intellectually stimulating thought, without the burden of propagating dubious inferences through unwarranted deterministic or probabilistic causality. Recommendations for future work include mixed-method studies with interviews, longitudinal studies, instructor-student studies, and gender vs. sexual orientation studies.

Quantitative Analysis of Proteome Modulations in Alveolar Epithelial Type II Cells in Response to Pulmonary Aspergillus fumigatus Infection.

PubMed

Seddigh, Pegah; Bracht, Thilo; Molinier-Frenkel, Válerie; Castellano, Flavia; Kniemeyer, Olaf; Schuster, Marc; Weski, Juliane; Hasenberg, Anja; Kraus, Andreas; Poschet, Gernot; Hager, Thomas; Theegarten, Dirk; Opitz, Christiane A; Brakhage, Axel A; Sitek, Barbara; Hasenberg, Mike; Gunzer, Matthias

2017-12-01

The ubiquitous mold Aspergillus fumigatus threatens immunosuppressed patients as inducer of lethal invasive aspergillosis. A. fumigatus conidia are airborne and reach the alveoli, where they encounter alveolar epithelial cells (AEC). Previous studies reported the importance of the surfactant-producing AEC II during A. fumigatus infection via in vitro experiments using cell lines. We established a negative isolation protocol yielding untouched primary murine AEC II with a purity >90%, allowing ex vivo analyses of the cells, which encountered the mold in vivo By label-free proteome analysis of AEC II isolated from mice 24h after A. fumigatus or mock infection we quantified 2256 proteins and found 154 proteins to be significantly differentially abundant between both groups (ANOVA p value ≤ 0.01, ratio of means ≥1.5 or ≤0.67, quantified with ≥2 peptides). Most of these proteins were higher abundant in the infected condition and reflected a comprehensive activation of AEC II on interaction with A. fumigatus This was especially represented by proteins related to oxidative phosphorylation, hence energy production. However, the most strongly induced protein was the l-amino acid oxidase (LAAO) Interleukin 4 induced 1 (IL4I1) with a 42.9 fold higher abundance (ANOVA p value 2.91 -10 ). IL4I1 has previously been found in B cells, macrophages, dendritic cells and rare neurons. Increased IL4I1 abundance in AEC II was confirmed by qPCR, Western blot and immunohistology. Furthermore, A. fumigatus infected lungs showed high levels of IL4I1 metabolic products. Importantly, higher IL4I1 abundance was also confirmed in lung tissue from human aspergilloma. Because LAAO are key enzymes for bactericidal product generation, AEC II might actively participate in pathogen defense. We provide insights into proteome changes of primary AEC II thereby opening new avenues to analyze the molecular changes of this central lung cell on infectious threats. Data are available via ProteomeXchange with identifier PXD005834. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Biochemical evaluation of articular cartilage in patients with osteochondrosis dissecans by means of quantitative T2- and T2-mapping at 3T MRI: a feasibility study.

PubMed

Marik, W; Apprich, S; Welsch, G H; Mamisch, T C; Trattnig, S

2012-05-01

To perform an in vivo evaluation comparing overlying articular cartilage in patients suffering from osteochondrosis dissecans (OCD) in the talocrural joint and healthy volunteers using quantitative T2 mapping at 3.0 T. Ten patients with OCD of Grade II or lower and 9 healthy age matched volunteers were examined at a 3.0 T whole body MR scanner using a flexible multi-element coil. In all investigated persons MRI included proton-density (PD)-FSE and 3D GRE (TrueFisp) sequences for morphological diagnosis and location of anatomical site and quantitative T2 and T2 maps. Region of interest (ROI) analysis was performed for the cartilage layer above the OCD and for a morphologically healthy graded cartilage layer. Mean T2 and T2 values were then statistically analysed. The cartilage layer of healthy volunteers showed mean T2 and T2 values of 29.4 ms (SD 4.9) and 11.8 ms (SD 2.7), respectively. In patients with OCD of grade I and II lesions mean T2 values were 40.9 ms (SD 6.6), 48.7 ms (SD 11.2) and mean T2 values were 16.1 ms (SD 3.2), 16.2 ms (SD 4.8). Therefore statistically significantly higher mean T2 and T2 values were found in patients suffering from OCD compared to healthy volunteers. T2 and T2 mapping can help assess the microstructural composition of cartilage overlying osteochondral lesions. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Multi-component determination and chemometric analysis of Paris polyphylla by ultra high performance liquid chromatography with photodiode array detection.

PubMed

Chen, Pei; Jin, Hong-Yu; Sun, Lei; Ma, Shuang-Cheng

2016-09-01

Multi-source analysis of traditional Chinese medicine is key to ensuring its safety and efficacy. Compared with traditional experimental differentiation, chemometric analysis is a simpler strategy to identify traditional Chinese medicines. Multi-component analysis plays an increasingly vital role in the quality control of traditional Chinese medicines. A novel strategy, based on chemometric analysis and quantitative analysis of multiple components, was proposed to easily and effectively control the quality of traditional Chinese medicines such as Chonglou. Ultra high performance liquid chromatography was more convenient and efficient. Five species of Chonglou were distinguished by chemometric analysis and nine saponins, including Chonglou saponins I, II, V, VI, VII, D, and H, as well as dioscin and gracillin, were determined in 18 min. The method is feasible and credible, and enables to improve quality control of traditional Chinese medicines and natural products. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Metallothionein from Wild Populations of the African Catfish Clarias gariepinus: From Sequence, Protein Expression and Metal Binding Properties to Transcriptional Biomarker of Metal Pollution.

PubMed

M'kandawire, Ethel; Mierek-Adamska, Agnieszka; Stürzenbaum, Stephen R; Choongo, Kennedy; Yabe, John; Mwase, Maxwell; Saasa, Ngonda; Blindauer, Claudia A

2017-07-18

Anthropogenic pollution with heavy metals is an on-going concern throughout the world, and methods to monitor release and impact of heavy metals are of high importance. With a view to probe its suitability as molecular biomarker of metal pollution, this study has determined a coding sequence for metallothionein of the African sharptooth catfish Clarias gariepinus . The gene product was recombinantly expressed in Escherichia coli in presence of Zn(II), Cd(II), or Cu, and characterised by Electrospray Ionisation Mass Spectrometry and elemental analysis. C. gariepinus MT displays typical features of fish MTs, including 20 conserved cysteines, and seven bound divalent cations (Zn(II) or Cd(II)) when saturated. Livers from wild C. gariepinus fish collected in all three seasons from four different sites on the Kafue River of Zambia were analysed for their metal contents and for MT expression levels by quantitative PCR. Significant correlations were found between Zn and Cu levels and MT expression in livers, with MT expression clearly highest at the most polluted site, Chililabombwe, which is situated in the Copperbelt region. Based on our findings, hepatic expression of MT from C. gariepinus may be further developed as a major molecular biomarker of heavy metal pollution resulting from mining activities in this region.

Experimental parameters optimization of instrumental neutron activation analysis in order to determine selected elements in some industrial soils in Turkey

NASA Astrophysics Data System (ADS)

Haciyakupoglu, Sevilay; Nur Esen, Ayse; Erenturk, Sema

2014-08-01

The purpose of this study is optimization of the experimental parameters for analysis of soil matrix by instrumental neutron activation analysis and quantitative determination of barium, cerium, lanthanum, rubidium, scandium and thorium in soil samples collected from industrialized urban areas near Istanbul. Samples were irradiated in TRIGA MARK II Research Reactor of Istanbul Technical University. Two types of reference materials were used to check the accuracy of the applied method. The achieved results were found to be in compliance with certified values of the reference materials. The calculated En numbers for mentioned elements were found to be less than 1. The presented data of element concentrations in soil samples will help to trace the pollution as an impact of urbanization and industrialization, as well as providing database for future studies.

Sensitive determination of trace mercury by UV-visible diffuse reflectance spectroscopy after complexation and membrane filtration-enrichment.

PubMed

Yin, Changhai; Iqbal, Jibran; Hu, Huilian; Liu, Bingxiang; Zhang, Lei; Zhu, Bilin; Du, Yiping

2012-09-30

A simple, sensitive and selective solid phase reflectometry method is proposed for the determination of trace mercury in aqueous samples. The complexation reagent dithizone was firstly injected into the properly buffered solution with vigorous stirring, which started a simultaneous formation of nanoparticles suspension of dithizone and its complexation reaction with the mercury(II) ions to make Hg-dithizone nanoparticles. After a definite time, the mixture was filtered with membrane, and then quantified directly on the surface of the membrane by using integrating sphere accessory of the UV-visible spectrophotometer. The quantitative analysis was carried out at a wavelength of 485 nm since it yielded the largest difference in diffuse reflectance spectra before and after reaction with mercury(II).A good linear correlation in the range of 0.2-4.0 μg/L with a squared correlation coefficient (R(2)) of 0.9944 and a detection limit of 0.12 μg/L were obtained. The accuracy of the method was evaluated by the analysis of spiked mercury(II) concentrations determined using this method along with those determined by the atomic fluorescence mercury vapourmeter and the results obtained were in good agreement. The proposed method was applied to the determination of mercury in tap water and river water samples with the recovery in an acceptable range (95.7-105.3%). Copyright © 2012 Elsevier B.V. All rights reserved.

Capsular Outcomes After Pediatric Cataract Surgery Without Intraocular Lens Implantation: Qualitative Classification and Quantitative Measurement.

PubMed

Tan, Xuhua; Lin, Haotian; Lin, Zhuoling; Chen, Jingjing; Tang, Xiangchen; Luo, Lixia; Chen, Weirong; Liu, Yizhi

2016-03-01

The objective of this study was to investigate capsular outcomes 12 months after pediatric cataract surgery without intraocular lens implantation via qualitative classification and quantitative measurement.This study is a cross-sectional study that was approved by the institutional review board of Zhongshan Ophthalmic Center of Sun Yat-sen University in Guangzhou, China.Digital coaxial retro-illumination photographs of 329 aphakic pediatric eyes were obtained 12 months after pediatric cataract surgery without intraocular lens implantation. Capsule digital coaxial retro-illumination photographs were divided as follows: anterior capsule opening area (ACOA), posterior capsule opening area (PCOA), and posterior capsule opening opacity (PCOO). Capsular outcomes were qualitatively classified into 3 types based on the PCOO: Type I-capsule with mild opacification but no invasion into the capsule opening; Type II-capsule with moderate opacification accompanied by contraction of the ACOA and invasion to the occluding part of the PCOA; and Type III-capsule with severe opacification accompanied by total occlusion of the PCOA. Software was developed to quantitatively measure the ACOA, PCOA, and PCOO using standardized DCRPs. The relationships between the accurate intraoperative anterior and posterior capsulorhexis sizes and the qualitative capsular types were statistically analyzed.The DCRPs of 315 aphakic eyes (95.8%) of 191 children were included. Capsular outcomes were classified into 3 types: Type I-120 eyes (38.1%); Type II-157 eyes (49.8%); Type III-38 eyes (12.1%). The scores of the capsular outcomes were negatively correlated with intraoperative anterior capsulorhexis size (R = -0.572, P < 0.001), but no significant correlation with intraoperative posterior capsulorhexis size (R = -0.16, P = 0.122) was observed. The ACOA significantly decreased from Type I to Type II to Type III, the PCOA increased in size from Type I to Type II, and the PCOO increased from Type II to Type III (all P < 0.05).Capsular outcomes after pediatric cataract surgery can be qualitatively classified and quantitatively measured by acquisition, division, definition, and user-friendly software analyses of high-quality digital coaxial retro-illumination photographs.

Separation and Determination of Fe(III) and Fe(II) in Natural and Waste Waters Using Silica Gel Sequentially Modified with Polyhexamethylene Guanidine and Tiron

PubMed Central

Maksimov, Nikolay; Trofimchuk, Anatoly; Zaporogets, Olga

2017-01-01

Silica gel, sequentially modified with polyhexamethylene guanidine and pyrocatechin-3,5-disulfonic acid (Tiron), was suggested for sorption separation and determination of Fe(III) and Fe(II). It was found that quantitative extraction of Fe(III) and its separation from Fe(II) were attained at pH 2.5–4.0, while quantitative extraction of Fe(II) was observed at pH 6.0–7.5. An intensive signal with g = 4.27, which is characteristic for Fe(III), appeared in EPR spectra of the sorbents after Fe(II) and Fe(III) sorption. During interaction between Fe(II) and Tiron, fixed on the sorbent surface, its oxidation up to Fe(III) occurred. Red-lilac complexes of the composition FeL3 were formed on the sorbent surface during sorption regardless of initial oxidation level of iron. Diffuse reflectance spectrum of surface complexes exhibited wide band with slightly expressed maxima at 480 and 510 nm. Procedures for separation and photometric determination of Fe(III) and Fe(II) at the joint presence and total Fe content determination as Fe(II) in waste and natural waters was developed. The limit of detection for iron was 0.05 μg per 0.100 g of the sorbent. The calibration graph was linear up to 20.0 μg of Fe per 0.100 g of the sorbent. The RSD in the determination of more than 0.2 μg of Fe was less than 0.06. PMID:29214095

Biologic determinants of tumor recurrence in stage II colon cancer: validation study of the 12-gene recurrence score in cancer and leukemia group B (CALGB) 9581.

PubMed

Venook, Alan P; Niedzwiecki, Donna; Lopatin, Margarita; Ye, Xing; Lee, Mark; Friedman, Paula N; Frankel, Wendy; Clark-Langone, Kim; Millward, Carl; Shak, Steven; Goldberg, Richard M; Mahmoud, Najjia N; Warren, Robert S; Schilsky, Richard L; Bertagnolli, Monica M

2013-05-10

A greater understanding of the biology of tumor recurrence should improve adjuvant treatment decision making. We conducted a validation study of the 12-gene recurrence score (RS), a quantitative assay integrating stromal response and cell cycle gene expression, in tumor specimens from patients enrolled onto Cancer and Leukemia Group B (CALGB) 9581. CALGB 9581 randomly assigned 1,713 patients with stage II colon cancer to treatment with edrecolomab or observation and found no survival difference. The analysis reported here included all patients with available tissue and recurrence (n = 162) and a random (approximately 1:3) selection of nonrecurring patients. RS was assessed in 690 formalin-fixed paraffin-embedded tumor samples with quantitative reverse transcriptase polymerase chain reaction by using prespecified genes and a previously validated algorithm. Association of RS and recurrence was analyzed by weighted Cox proportional hazards regression. Continuous RS was significantly associated with risk of recurrence (P = .013) as was mismatch repair (MMR) gene deficiency (P = .044). In multivariate analyses, RS was the strongest predictor of recurrence (P = .004), independent of T stage, MMR, number of nodes examined, grade, and lymphovascular invasion. In T3 MMR-intact (MMR-I) patients, prespecified low and high RS groups had average 5-year recurrence risks of 13% (95% CI, 10% to 16%) and 21% (95% CI, 16% to 26%), respectively. The 12-gene RS predicts recurrence in stage II colon cancer in CALGB 9581. This is consistent with the importance of stromal response and cell cycle gene expression in colon tumor recurrence. RS appears to be most discerning for patients with T3 MMR-I tumors, although markers such as grade and lymphovascular invasion did not add value in this subset of patients.

Why Are Men Satisfied or Dissatisfied with Penile Implants? A Mixed Method Study on Satisfaction with Penile Prosthesis Implantation.

PubMed

Carvalheira, Ana; Santana, Rita; Pereira, Nuno M

2015-12-01

Studies have demonstrated high levels of satisfaction with penile prosthesis implantation (PPI). However, qualitative research exploring the experience of PPI through men's narratives is scarce. The main goals were to analyze (i) the level of sexual satisfaction (quantitatively), and (ii) the reasons for satisfaction and/or dissatisfaction with PPI (qualitatively). Participants were 47 men with erectile dysfunction who underwent surgery between 2003 and 2012, placed by a single surgeon. Structured telephone interviews were carried out. Satisfaction with PPI was a qualitative and quantitative measure assessed through the following four items: (i) "Would you repeat the PPI surgery?"; (ii) "Would you recommend the PPI surgery?"; (iii) "How satisfied are you with the PP?"; and (iv) "Could you explain the motives of your satisfaction/dissatisfaction?". The majority of men (79%) reported to be satisfied with PPI. Content analysis revealed four main themes for men's satisfaction with the PPI: (i) psychological factors were reported 54 times (n = 54) and included positive emotions, self-esteem, confidence, enhancement of male identity, major live change, and self-image; (ii) improvement of sexual function was reported 54 times (n = 54) and referred to achievement of vaginal penetration, increase of sexual desire, sexual satisfaction, penis size, and improvement of erectile function; (iii) relationship factors were reported 11 times (n = 11) and referred to relationship improvement and the possibility of giving pleasure to the partner; and (iv) improvement in urinary function (n = 3). The level of satisfaction with the implementation of penile prostheses is very high, therefore constituting a treatment for erectile dysfunction with a positive impact on the experience of men at sexual, psychological and relational level. © 2015 International Society for Sexual Medicine.

Theoretical foundations for a quantitative approach to paleogenetics. I, II.

NASA Technical Reports Server (NTRS)

Holmquist, R.

1972-01-01

It is shown that by neglecting the phenomena of multiple hits, back mutation, and chance coincidence errors larger than 100% can be introduced in the calculated value of the average number of nucleotide base differences to be expected between two homologous polynucleotides. Mathematical formulas are derived to correct quantitatively for these effects. It is pointed out that the effects change materially the quantitative aspects of phylogenics, such as the length of the legs of the trees. A number of problems are solved without approximation.-

Proteomic identification of potential biomarkers for cervical squamous cell carcinoma and human papillomavirus infection.

PubMed

Qing, Song; Tulake, Wuniqiemu; Ru, Mingfang; Li, Xiaohong; Yuemaier, Reziwanguli; Lidifu, Dilare; Rouzibilali, Aierken; Hasimu, Axiangu; Yang, Yun; Rouziahong, Reziya; Upur, Halmurat; Abudula, Abulizi

2017-04-01

It is known that high-risk human papillomavirus infection is the main etiological factor in cervical carcinogenesis. However, human papillomavirus screening is not sufficient for early diagnosis. In this study, we aimed to identify potential biomarkers common to cervical carcinoma and human papillomavirus infection by proteomics for human papillomavirus-based early diagnosis and prognosis. To this end, we collected 76 cases of fresh cervical tissues and 116 cases of paraffin-embedded tissue slices, diagnosed as cervical squamous cell carcinoma, cervical intraepithelial neoplasia II-III, or normal cervix from ethnic Uighur and Han women. Human papillomavirus infection by eight oncogenic human papillomavirus types was detected in tissue DNA samples using a quantitative polymerase chain reaction. The protein profile of cervical specimens from human papillomavirus 16-positive squamous cell carcinoma and human papillomavirus-negative normal controls was analyzed by proteomics and bioinformatics. The expression of candidate proteins was further determined by quantitative reverse transcriptase-polymerase chain reaction and immunohistochemistry. We identified 67 proteins that were differentially expressed in human papillomavirus 16-positive squamous cell carcinoma compared to normal cervix. The quantitative reverse transcriptase-polymerase chain reaction analysis verified the upregulation of ASAH1, PCBP2, DDX5, MCM5, TAGLN2, hnRNPA1, ENO1, TYPH, CYC, and MCM4 in squamous cell carcinoma compared to normal cervix ( p < 0.05). In addition, the transcription of PCBP2, MCM5, hnRNPA1, TYPH, and CYC was also significantly increased in cervical intraepithelial neoplasia II-III compared to normal cervix. Immunohistochemistry staining further confirmed the overexpression of PCBP2, hnRNPA1, ASAH1, and DDX5 in squamous cell carcinoma and cervical intraepithelial neoplasia II-III compared to normal controls ( p < 0.05). Our data suggest that the expression of ASAH1, PCBP2, DDX5, and hnRNPA1, and possibly MCM4, MCM5, CYC, ENO1, and TYPH, is upregulated during cervical carcinogenesis and potentially associated with human papillomavirus infection. Further validation studies of the profile will contribute to establishing auxiliary diagnostic markers for human papillomavirus-based cancer prognosis.

An In-Vitro Evaluation and Comparison of Apical Sealing Ability of Three Different Obturation Technique - Lateral Condensation, Obtura II, and Thermafil.

PubMed

Emmanuel, Samson; Shantaram, Kulkarni; Sushil, Kumar C; Manoj, Likhitkar

2013-04-01

Success of non-surgical root canal treatment is predicted by meticulous cleaning and shaping of the root canal system, three-dimensional obturation and a well-fitting "leakage-free" coronal restoration. The techniques of obturation that are available have their own relative position in the historical development of filling techniques. Over the years, pitfalls with one technique have often led to the development of newer methods of obturation, along with the recognition that no one method of obturation may satisfy all clinical cases. A total of 120 extracted human permanent anterior maxillary and mandibular single rooted teeth were selected for the present study and divided into 3 groups based on the method of obturation technique. Following the preparation the patency at the apical foramen was confirmed by passing a file #15. After obturation of all three groups, teeth were immersed in 1% of aqueous methylene blue dye for a period of two weeks and then samples were subjected to spectrophotometric analysis. The present study was conducted to evaluate in vitro the spectrophotometric analysis to quantitatively analyze relative amount of dye penetration using lateral condensation (Group I), Obtura II (Group II ), Thermafil obturating technique (Group III) with ZOE sealer used in all groups. Teeth obturated with lateral condensation (Group I) shows mean value of 0.0243 and standard deviation of 0.0056. The Group II thermoplasticized injectable moulded Guttapercha (Obtura II) showed 0.0239 mean and standard deviation value of 0.0045 and Group III Thermafil obturation technique shows 0.0189 as mean value and 0.0035 standard deviation values. Following conclusion was drawn from the present study. Group III i.e., Thermafil obturating technique shows minimum mean apical dye penetration compared to Group II (ObturaII) and Group I (lateral condensation).Lateral condensation shows maximum mean apical dye penetration in all three groups.There is no significant difference between the apical dye penetration of lateral condensation and Obtura II. Obturation, lateral condensation, Obtura II, Thermafil, Spectrophotometer, dye penetration. How to cite this article: Samson E, Kulkarni S, Sushil K C, Likhitkar M. An In-Vitro Evaluation and Comparison of Apical Sealing Ability of Three Different Obturation Technique - Lateral Condensation, Obtura II, and Thermafil. J Int Oral Health 2013; 5(2):35-43.

Multispectral Imaging Broadens Cellular Analysis

NASA Technical Reports Server (NTRS)

2007-01-01

Amnis Corporation, a Seattle-based biotechnology company, developed ImageStream to produce sensitive fluorescence images of cells in flow. The company responded to an SBIR solicitation from Ames Research Center, and proposed to evaluate several methods of extending the depth of field for its ImageStream system and implement the best as an upgrade to its commercial products. This would allow users to view whole cells at the same time, rather than just one section of each cell. Through Phase I and II SBIR contracts, Ames provided Amnis the funding the company needed to develop this extended functionality. For NASA, the resulting high-speed image flow cytometry process made its way into Medusa, a life-detection instrument built to collect, store, and analyze sample organisms from erupting hydrothermal vents, and has the potential to benefit space flight health monitoring. On the commercial end, Amnis has implemented the process in ImageStream, combining high-resolution microscopy and flow cytometry in a single instrument, giving researchers the power to conduct quantitative analyses of individual cells and cell populations at the same time, in the same experiment. ImageStream is also built for many other applications, including cell signaling and pathway analysis; classification and characterization of peripheral blood mononuclear cell populations; quantitative morphology; apoptosis (cell death) assays; gene expression analysis; analysis of cell conjugates; molecular distribution; and receptor mapping and distribution.

Analysis of small carbohydrates in several bioactive botanicals by gas chromatography with mass spectrometry and liquid chromatography with tandem mass spectrometry.

PubMed

Moldoveanu, Serban; Scott, Wayne; Zhu, Jeff

2015-11-01

Bioactive botanicals contain natural compounds with specific biological activity, such as antibacterial, antioxidant, immune stimulating, and taste improving. A full characterization of the chemical composition of these botanicals is frequently necessary. A study of small carbohydrates from the plant materials of 18 bioactive botanicals is further described. The study presents the identification of the carbohydrate using a gas chromatographic-mass spectrometric analysis that allows detection of molecules as large as maltotetraose, after changing them into trimethylsilyl derivatives. A number of carbohydrates in the plant (fructose, glucose, mannose, sucrose, maltose, xylose, sorbitol, and myo-, chiro-, and scyllo-inositols) were quantitated using a novel liquid chromatography with tandem mass spectrometric technique. Both techniques involved new method developments. The gas chromatography with mass spectrometric analysis involved derivatization and separation on a Rxi(®)-5Sil MS column with H2 as a carrier gas. The liquid chromatographic separation was obtained using a hydrophilic interaction type column, YMC-PAC Polyamine II. The tandem mass spectrometer used an electrospray ionization source in multiple reaction monitoring positive ion mode with the detection of the adducts of the carbohydrates with Cs(+) ions. The validated quantitative procedure showed excellent precision and accuracy allowing the analysis in a wide range of concentrations of the analytes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genome-wide association study of perioperative myocardial infarction after coronary artery bypass surgery.

PubMed

Kertai, Miklos D; Li, Yi-Ju; Li, Yen-Wei; Ji, Yunqi; Alexander, John; Newman, Mark F; Smith, Peter K; Joseph, Diane; Mathew, Joseph P; Podgoreanu, Mihai V

2015-05-06

Identification of patient subpopulations susceptible to develop myocardial infarction (MI) or, conversely, those displaying either intrinsic cardioprotective phenotypes or highly responsive to protective interventions remain high-priority knowledge gaps. We sought to identify novel common genetic variants associated with perioperative MI in patients undergoing coronary artery bypass grafting using genome-wide association methodology. 107 secondary and tertiary cardiac surgery centres across the USA. We conducted a stage I genome-wide association study (GWAS) in 1433 ethnically diverse patients of both genders (112 cases/1321 controls) from the Genetics of Myocardial Adverse Outcomes and Graft Failure (GeneMAGIC) study, and a stage II analysis in an expanded population of 2055 patients (225 cases/1830 controls) combined from the GeneMAGIC and Duke Perioperative Genetics and Safety Outcomes (PEGASUS) studies. Patients undergoing primary non-emergent coronary bypass grafting were included. The primary outcome variable was perioperative MI, defined as creatine kinase MB isoenzyme (CK-MB) values ≥10× upper limit of normal during the first postoperative day, and not attributable to preoperative MI. Secondary outcomes included postoperative CK-MB as a quantitative trait, or a dichotomised phenotype based on extreme quartiles of the CK-MB distribution. Following quality control and adjustment for clinical covariates, we identified 521 single nucleotide polymorphisms in the stage I GWAS analysis. Among these, 8 common variants in 3 genes or intergenic regions met p<10(-5) in stage II. A secondary analysis using CK-MB as a quantitative trait (minimum p=1.26×10(-3) for rs609418), or a dichotomised phenotype based on extreme CK-MB values (minimum p=7.72×10(-6) for rs4834703) supported these findings. Pathway analysis revealed that genes harbouring top-scoring variants cluster in pathways of biological relevance to extracellular matrix remodelling, endoplasmic reticulum-to-Golgi transport and inflammation. Using a two-stage GWAS and pathway analysis, we identified and prioritised several potential susceptibility loci for perioperative MI. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Quantitative assessment of the association between the angiotensin-converting enzyme gene insertion/deletion polymorphism and digestive system cancer risk.

PubMed

Wang, J; Yang, S; Guo, F H; Mao, X; Zhou, H; Dong, Y Q; Wang, Z M; Luo, F

2015-11-13

The angiotensin-converting enzyme (ACE) gene insertion/deletion (I/D) polymorphism has been reported to be associated with digestive system cancer; however, the results from previous studies have been conflicting. The present study aimed to investigate the association between the ACE I/D polymorphism and the risk of digestive system cancer using a meta-analysis of previously published studies. Databases were systematically searched to identify relevant studies published prior to December 2014. We estimated the pooled OR with its 95%CI to assess the association. The meta-analysis consisted of thirteen case-control studies that included 2557 patients and 4356 healthy controls. Meta-analysis results based on all the studies showed no significant association between the ACE I/D polymorphism and the risk of digestive system cancer (DD vs II: OR = 0.85, 95%CI = 0.59-1.24; DI vs II: OR = 0.94, 95%CI = 0.78-1.15; dominant model: OR = 0.96, 95%CI = 0.81- 1.15; recessive model: OR = 1.06, 95%CI = 0.76-1.48). Subgroup analyses by race and cancer type did not detect an association between the ACE I/D polymorphism and digestive system cancer risk. However, when the analyses were restricted to smaller studies (N < 500 patients), the summary OR of DI vs II was 0.80 (95%CI = 0.66-0.97). Our analyses detected a possibility of publication bias with a misestimate of the true association by smaller studies. Overall, meta-analysis results suggest the ACE I/D polymorphism might not be associated with susceptibility to digestive system cancer. Further large and well-designed studies are needed to confirm these conclusions.

DNA Microarray Analysis Identifies CKS2 and LEPR as Potential Markers of Meningioma Recurrence

PubMed Central

Menghi, Francesca; Orzan, Francesca N.; Eoli, Marica; Farinotti, Mariangela; Maderna, Emanuela; Pisati, Federica; Bianchessi, Donatella; Valletta, Lorella; Lodrini, Sandro; Galli, Giuseppe; Anghileri, Elena; Pellegatta, Serena; Pollo, Bianca

2011-01-01

Meningiomas are the most frequent intracranial tumors. Surgery can be curative, but recurrences are possible. We performed gene expression analyses and loss of heterozygosity (LOH) studies looking for new markers predicting the recurrence risk. We analyzed expression profiles of 23 meningiomas (10 grade I, 10 grade II, and 3 grade III) and validated the data using quantitative polymerase chain reaction (qPCR). We performed LOH analysis on 40 meningiomas, investigating chromosomal regions on 1p, 9p, 10q, 14q, and 22q. We found 233 and 268 probe sets to be significantly down- and upregulated, respectively, in grade II or III meningiomas. Genes downregulated in high-grade meningiomas were overrepresented on chromosomes 1, 6, 9, 10, and 14. Based on functional enrichment analysis, we selected LIM domain and actin binding 1 (LIMA1), tissue inhibitor of metalloproteinases 3 (TIMP3), cyclin-dependent kinases regulatory subunit 2 (CKS2), leptin receptor (LEPR), and baculoviral inhibitor of apoptosis repeat-containing 5 (BIRC5) for validation using qPCR and confirmed their differential expression in the two groups of tumors. We calculated ΔCt values of CKS2 and LEPR and found that their differential expression (C-L index) was significantly higher in grade I than in grade II or III meningiomas (p < .0001). Interestingly, the C-L index of nine grade I meningiomas from patients who relapsed in <5 years was significantly lower than in grade I meningiomas from patients who did not relapse. These findings indicate that the C-L index may be relevant to define the progression risk in meningioma patients, helping guide their clinical management. A prospective analysis on a larger number of cases is warranted. PMID:21948653

DNA microarray analysis identifies CKS2 and LEPR as potential markers of meningioma recurrence.

PubMed

Menghi, Francesca; Orzan, Francesca N; Eoli, Marica; Farinotti, Mariangela; Maderna, Emanuela; Pisati, Federica; Bianchessi, Donatella; Valletta, Lorella; Lodrini, Sandro; Galli, Giuseppe; Anghileri, Elena; Pellegatta, Serena; Pollo, Bianca; Finocchiaro, Gaetano

2011-01-01

Meningiomas are the most frequent intracranial tumors. Surgery can be curative, but recurrences are possible. We performed gene expression analyses and loss of heterozygosity (LOH) studies looking for new markers predicting the recurrence risk. We analyzed expression profiles of 23 meningiomas (10 grade I, 10 grade II, and 3 grade III) and validated the data using quantitative polymerase chain reaction (qPCR). We performed LOH analysis on 40 meningiomas, investigating chromosomal regions on 1p, 9p, 10q, 14q, and 22q. We found 233 and 268 probe sets to be significantly down- and upregulated, respectively, in grade II or III meningiomas. Genes downregulated in high-grade meningiomas were overrepresented on chromosomes 1, 6, 9, 10, and 14. Based on functional enrichment analysis, we selected LIM domain and actin binding 1 (LIMA1), tissue inhibitor of metalloproteinases 3 (TIMP3), cyclin-dependent kinases regulatory subunit 2 (CKS2), leptin receptor (LEPR), and baculoviral inhibitor of apoptosis repeat-containing 5 (BIRC5) for validation using qPCR and confirmed their differential expression in the two groups of tumors. We calculated ΔCt values of CKS2 and LEPR and found that their differential expression (C-L index) was significantly higher in grade I than in grade II or III meningiomas (p < .0001). Interestingly, the C-L index of nine grade I meningiomas from patients who relapsed in <5 years was significantly lower than in grade I meningiomas from patients who did not relapse. These findings indicate that the C-L index may be relevant to define the progression risk in meningioma patients, helping guide their clinical management. A prospective analysis on a larger number of cases is warranted.

Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation

PubMed Central

Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

2015-01-01

Mapping expression quantitative trait loci (eQTLs) has been shown as a powerful tool to uncover the genetic underpinnings of many complex traits at molecular level. In this paper, we present an integrative analysis approach that leverages eQTL data collected from multiple population groups. In particular, our approach effectively identifies multiple independent cis-eQTL signals that are consistent across populations, accounting for population heterogeneity in allele frequencies and linkage disequilibrium patterns. Furthermore, by integrating genomic annotations, our analysis framework enables high-resolution functional analysis of eQTLs. We applied our statistical approach to analyze the GEUVADIS data consisting of samples from five population groups. From this analysis, we concluded that i) jointly analysis across population groups greatly improves the power of eQTL discovery and the resolution of fine mapping of causal eQTL ii) many genes harbor multiple independent eQTLs in their cis regions iii) genetic variants that disrupt transcription factor binding are significantly enriched in eQTLs (p-value = 4.93 × 10-22). PMID:25906321

Quantitative petrographic analysis of Desmoinesian sandstones from Oklahoma

USGS Publications Warehouse

Dyman, Thaddeus S.

1989-01-01

Desmoinesian sandstones from the northern Oklahoma platform and the Anadarko, Arkoma, and Ardmore basins record a complex interaction between mid-Pennsylvanian source-area tectonism and cyclic sedimentation patterns associated with numerous transgressions and regressions. Framework-grain summaries for 50 thin sections from sandstones of the Krebs, Cabaniss, and Marmaton Groups and their surface and subsurface equivalents were subjected to multivariate statistical analyses to establish regional compositional trends for provenance analysis. R-mode cluster and correspondence analyses were used to determine the contributing effect (total variance) of key framework grains. Fragments of monocrystalline and polycrystalline quartz; potassium and plagioclase feldspar; chert; and metamorphic, limestone, and mudstone-sandstone rock fragments contribute most to the variation in the grain population. Q-mode cluster and correspondence analyses were used to identify four petrofacies and establish the range of compositional variation in Desmoinesian sandstones. Petrofacies I is rich in monocrystalline quartz (78-98%); mica and rock fragments are rare. Petrofacies II is also rich in monocrystalline quartz (60-84%) and averages 12% total rock fragments. Petrofacies III and IV are compositionally heterogeneous and contain variable percentages of monocrystalline and polycrystalline quartz, potassium feldspar, mica, chert, and metamorphic and sedimentary rock fragments. Quantitative analyses indicate that Desmoinesian sandstones were derived from sedimentary, igneous, and metamorphic source areas. Sandstones of petrofacies I and II occur mostly in the lower Desmoinesian and are widely distributed, although they are most abundant in eastern and central Oklahoma; sandstones of petrofacies III and IV are widely distributed and occur primarily in the middle and upper Desmoinesian. The range of compositional variation and the distribution of petrofacies are related to paleotectonics and basin development, sediment recycling, and varying depositional environments.

Quantitative analysis of H2O and CO2 in cordierite using polarized FTIR spectroscopy

NASA Astrophysics Data System (ADS)

Della Ventura, Giancarlo; Radica, Francesco; Bellatreccia, Fabio; Cavallo, Andrea; Capitelli, Francesco; Harley, Simon

2012-11-01

We report a FTIR (Fourier transform infrared) study of a set of cordierite samples from different occurrence and with different H2O/CO2 content. The specimens were fully characterized by a combination of techniques including optical microscopy, single-crystal X-ray diffraction, EMPA (electron microprobe analysis), SIMS (secondary ion mass spectrometry), and FTIR spectroscopy. All cordierites are orthorhombic Ccmm. According to the EMPA data, the Si/Al ratio is always close to 5:4; X Mg ranges from 76.31 to 96.63, and additional octahedral constituents occur in very small amounts. Extraframework K and Ca are negligible, while Na reaches the values up to 0.84 apfu. SIMS shows H2O up to 1.52 and CO2 up to 1.11 wt%. Optically transparent single crystals were oriented using the spindle stage and examined by FTIR micro-spectroscopy under polarized light. On the basis of the polarizing behaviour, the observed bands were assigned to water molecules in two different orientations and to CO2 molecules in the structural channels. The IR spectra also show the presence of small amounts of CO in the samples. Refined integrated molar absorption coefficients were calibrated for the quantitative microanalysis of both H2O and CO2 in cordierite based on single-crystal polarized-light FTIR spectroscopy. For H2O the integrated molar coefficients for type I and type II water molecules (ν3 modes) were calculated separately and are [I]ɛ = 5,200 ± 700 l mol-1 cm-2 and [II]ɛ = 13,000 ± 3,000 l mol-1 cm-2, respectively. For CO2 the integrated coefficient is \\varepsilon_{{{{CO}}_{ 2} }} = 19,000 ± 2,000 l mol-1 cm-2.

Integrated identification, qualification and quantification strategy for pharmacokinetic profile study of Guizhi Fuling capsule in healthy volunteers

PubMed Central

Zhong, Yun-Xi; Jin, Xiao-Liang; Gu, Shi-Yin; Peng, Ying; Zhang, Ke-Rong; Ou-Yang, Bing-Chen; Wang, Yu; Xiao, Wei; Wang, Zhen-Zhong; Aa, Ji-Ye; Wang, Guang-Ji; Sun, Jian-Guo

2016-01-01

Guizhi Fuling capsule (GZFL), a traditional Chinese medicine formulation, is widely used in China to relieve pain from dysmenorrhea and is now in a Phase II clinical trial in the USA. Due to the low exposure of the five main medicative ingredients (amygdalin, cinnamic acid, gallic acid, paeoniflorin and paeonol) of GZFL in human, a strategy was built to qualitatively and quantitatively identify the possible metabolites of GZFL and to describe the pharmacokinetic profiles of GZFL in human. In this strategy, LC-Q-TOF/MS was used to identify and structurally elucidate the possible metabolites of GZFL in vivo; and a time-based metabolite-confirming step (TBMCs) was used to confirm uncertain metabolites. The simultaneously quantitation results by LC-MS/MS showed low exposure of the five medicative ingredients. According to the strategy we built, a total of 36 metabolites were found and structurally elucidated. The simultaneously semi-quantitative analysis by LC-MS/MS showed that obvious time-concentration curves could be established for 12 of the metabolites, and most of them showed a relatively higher exposure. This study provides a better understanding of the metabolic processes of GZFL in human. PMID:27527657

Integrated identification, qualification and quantification strategy for pharmacokinetic profile study of Guizhi Fuling capsule in healthy volunteers.

PubMed

Zhong, Yun-Xi; Jin, Xiao-Liang; Gu, Shi-Yin; Peng, Ying; Zhang, Ke-Rong; Ou-Yang, Bing-Chen; Wang, Yu; Xiao, Wei; Wang, Zhen-Zhong; Aa, Ji-Ye; Wang, Guang-Ji; Sun, Jian-Guo

2016-08-16

Guizhi Fuling capsule (GZFL), a traditional Chinese medicine formulation, is widely used in China to relieve pain from dysmenorrhea and is now in a Phase II clinical trial in the USA. Due to the low exposure of the five main medicative ingredients (amygdalin, cinnamic acid, gallic acid, paeoniflorin and paeonol) of GZFL in human, a strategy was built to qualitatively and quantitatively identify the possible metabolites of GZFL and to describe the pharmacokinetic profiles of GZFL in human. In this strategy, LC-Q-TOF/MS was used to identify and structurally elucidate the possible metabolites of GZFL in vivo; and a time-based metabolite-confirming step (TBMCs) was used to confirm uncertain metabolites. The simultaneously quantitation results by LC-MS/MS showed low exposure of the five medicative ingredients. According to the strategy we built, a total of 36 metabolites were found and structurally elucidated. The simultaneously semi-quantitative analysis by LC-MS/MS showed that obvious time-concentration curves could be established for 12 of the metabolites, and most of them showed a relatively higher exposure. This study provides a better understanding of the metabolic processes of GZFL in human.

Automated Software Analysis of Fetal Movement Recorded during a Pregnant Woman's Sleep at Home.

PubMed

Nishihara, Kyoko; Ohki, Noboru; Kamata, Hideo; Ryo, Eiji; Horiuchi, Shigeko

2015-01-01

Fetal movement is an important biological index of fetal well-being. Since 2008, we have been developing an original capacitive acceleration sensor and device that a pregnant woman can easily use to record fetal movement by herself at home during sleep. In this study, we report a newly developed automated software system for analyzing recorded fetal movement. This study will introduce the system and compare its results to those of a manual analysis of the same fetal movement signals (Experiment I). We will also demonstrate an appropriate way to use the system (Experiment II). In Experiment I, fetal movement data reported previously for six pregnant women at 28-38 gestational weeks were used. We evaluated the agreement of the manual and automated analyses for the same 10-sec epochs using prevalence-adjusted bias-adjusted kappa (PABAK) including quantitative indicators for prevalence and bias. The mean PABAK value was 0.83, which can be considered almost perfect. In Experiment II, twelve pregnant women at 24-36 gestational weeks recorded fetal movement at night once every four weeks. Overall, mean fetal movement counts per hour during maternal sleep significantly decreased along with gestational weeks, though individual differences in fetal development were noted. This newly developed automated analysis system can provide important data throughout late pregnancy.

Automated Software Analysis of Fetal Movement Recorded during a Pregnant Woman’s Sleep at Home

PubMed Central

Nishihara, Kyoko; Ohki, Noboru; Kamata, Hideo; Ryo, Eiji; Horiuchi, Shigeko

2015-01-01

Fetal movement is an important biological index of fetal well-being. Since 2008, we have been developing an original capacitive acceleration sensor and device that a pregnant woman can easily use to record fetal movement by herself at home during sleep. In this study, we report a newly developed automated software system for analyzing recorded fetal movement. This study will introduce the system and compare its results to those of a manual analysis of the same fetal movement signals (Experiment I). We will also demonstrate an appropriate way to use the system (Experiment II). In Experiment I, fetal movement data reported previously for six pregnant women at 28-38 gestational weeks were used. We evaluated the agreement of the manual and automated analyses for the same 10-sec epochs using prevalence-adjusted bias-adjusted kappa (PABAK) including quantitative indicators for prevalence and bias. The mean PABAK value was 0.83, which can be considered almost perfect. In Experiment II, twelve pregnant women at 24-36 gestational weeks recorded fetal movement at night once every four weeks. Overall, mean fetal movement counts per hour during maternal sleep significantly decreased along with gestational weeks, though individual differences in fetal development were noted. This newly developed automated analysis system can provide important data throughout late pregnancy. PMID:26083422

Least-Squares Regression and Spectral Residual Augmented Classical Least-Squares Chemometric Models for Stability-Indicating Analysis of Agomelatine and Its Degradation Products: A Comparative Study.

PubMed

Naguib, Ibrahim A; Abdelrahman, Maha M; El Ghobashy, Mohamed R; Ali, Nesma A

2016-01-01

Two accurate, sensitive, and selective stability-indicating methods are developed and validated for simultaneous quantitative determination of agomelatine (AGM) and its forced degradation products (Deg I and Deg II), whether in pure forms or in pharmaceutical formulations. Partial least-squares regression (PLSR) and spectral residual augmented classical least-squares (SRACLS) are two chemometric models that are being subjected to a comparative study through handling UV spectral data in range (215-350 nm). For proper analysis, a three-factor, four-level experimental design was established, resulting in a training set consisting of 16 mixtures containing different ratios of interfering species. An independent test set consisting of eight mixtures was used to validate the prediction ability of the suggested models. The results presented indicate the ability of mentioned multivariate calibration models to analyze AGM, Deg I, and Deg II with high selectivity and accuracy. The analysis results of the pharmaceutical formulations were statistically compared to the reference HPLC method, with no significant differences observed regarding accuracy and precision. The SRACLS model gives comparable results to the PLSR model; however, it keeps the qualitative spectral information of the classical least-squares algorithm for analyzed components.

Comparative scanning electron microscope analysis of diode laser and desensitizing toothpastes for evaluation of efficacy of dentinal tubular occlusion

PubMed Central

Reddy, Guntakala Vikram; Akula, Sushma; Malgikar, Suryakanth; Babu, Palaparthy Raja; Reddy, Gooty Jagadish; Josephin, Johnson Juliet

2017-01-01

Background: The present study aims to evaluate the efficacy of diode laser alone and in combination with desensitizing toothpastes in occluding dentinal tubules (both partially occluded and completely occluded tubules) by scanning electron microscope (SEM). Materials and Methods: Fifty human teeth were extracted, cervical cavities were prepared and etched with 17% ethylenediaminetetraacetic acid, and smear layer was removed to expose the tubules. The teeth were divided into five groups: Group I – Application of NovaMin-formulated toothpaste, Group II – Application of Pro-Argin™-formulated toothpaste, Group III – Application of diode laser in noncontact mode, Group IV – NovaMin-formulated toothpaste followed by laser irradiation, and Group V – Pro-Argin™-formulated toothpaste followed by laser irradiation. After treatment, quantitative analysis of occluded dentinal tubules was done by SEM analysis. Results: The mean values of percentages of total occlusion of dentinal tubules in Groups I, II, III, IV, and V were 92.73% ± 1.38, 90.67% ± 1.86, 96.57% ± 0.64, 97.3% ± 0.68, and 96.9% ± 6.08, respectively. Addition of diode laser (Groups III, IV, and V) yielded a significant occlusion of the dentinal tubules when compared to desensitizing toothpastes alone (Groups I and II). Conclusion: Diode laser (Group III) has shown more efficacy in occluding dentinal tubules when compared with desensitizing toothpastes which was statistically significant (P < 0.05). Among the five groups, NovaMin + diode laser (Group IV) showed the highest percentage of occluded dentinal tubules. PMID:29398853

The Miniaturized Mossbauer Spectrometer MIMOS II for the Asteroid Redirect Mission (ARM): Quantitative Iron Mineralogy and Oxidation States

NASA Technical Reports Server (NTRS)

Schroder, Christian; Klingelhofer, Gostar; Morris, Richard V.; Yen, Albert S.; Renz, Franz; Graff, Trevor G.

2016-01-01

The miniaturized Mossbauer spectrometer MIMOS II is an off-the-shelf instrument, which has been successfully deployed during NASA's Mars Exploration Rover (MER) mission and was on-board the ESA/UK Beagle 2 Mars lander and the Russian Phobos-Grunt sample return mission. We propose to use a fully-qualified flight-spare MIMOS II instrument available from these missions for in situ asteroid characterization with the Asteroid Redirect Robotic Mission (ARRM).

Mechanism of 1,4,5,8-naphthalene tetracarboxylic acid dianhydride hydrolysis and formation in aqueous solution.

PubMed

Barros, T C; Cuccovia, I M; Farah, J P S; Masini, J C; Chaimovich, H; Politi, M J

2006-01-07

The study of highly conjugated, carbonyl-containing molecules such as 1,4,5,8-naphthalene tetracarboxylic dianhydride, III, is of interest since reactivity differences and transmission of electronic effects through the conjugated framework can be evidenced. The kinetics of hydrolysis of III in aqueous solution were determined from 5 M acid to pH 10. In basic solution hydrolysis of III yields, sequentially, 1,4,5,8-naphthalene diacid monoanhydride, II, and 1,4,5,8-naphthalene tetracarboxylic acid, I. The second order rate constant for alkaline hydrolysis is 200 fold higher for the first ring opening. The water-catalyzed hydrolysis of III yields a pH-dependent mixture of ionic forms of I and II. The rate constant for water-catalyzed hydrolysis of III is 25 fold higher than that for II. In concentrated acid the rates for reaching equilibrium (I, II and III) increase and III is the major product. The pK(a)s of I (3.24, 5.13 and 6.25) and II (3.05, 5.90) were determined by potentiometric, fluorescence and UV spectroscopy titrations and by quantitative fit of the kinetic and equilibrium data. The apparent, pH-dependent, equilibrium constants, K(EqII), for anhydride formation between I and II were obtained from the UV spectra. The quantitative fit of kinetic and equilibrium data are consistent with the assumption that anhydride formation only proceeds with the fully protonated species for both I and II and permitted the estimation of the equilibrium constants for anhydride formation, K(EqII). The value of K(EqII) (I <==> II) between pH 1 and 6 was ca. 5. Geometry optimization calculations in the gas phase of the reactions of III in alkaline, neutral and acid conditions, at the DFT level of theory, gave electronic distributions that were qualitatively consistent with the experimental results.

Pharmacometabolomics Informs Quantitative Radiomics for Glioblastoma Diagnostic Innovation.

PubMed

Katsila, Theodora; Matsoukas, Minos-Timotheos; Patrinos, George P; Kardamakis, Dimitrios

2017-08-01

Applications of omics systems biology technologies have enormous promise for radiology and diagnostics in surgical fields. In this context, the emerging fields of radiomics (a systems scale approach to radiology using a host of technologies, including omics) and pharmacometabolomics (use of metabolomics for patient and disease stratification and guiding precision medicine) offer much synergy for diagnostic innovation in surgery, particularly in neurosurgery. This synthesis of omics fields and applications is timely because diagnostic accuracy in central nervous system tumors still challenges decision-making. Considering the vast heterogeneity in brain tumors, disease phenotypes, and interindividual variability in surgical and chemotherapy outcomes, we believe that diagnostic accuracy can be markedly improved by quantitative radiomics coupled to pharmacometabolomics and related health information technologies while optimizing economic costs of traditional diagnostics. In this expert review, we present an innovation analysis on a systems-level multi-omics approach toward diagnostic accuracy in central nervous system tumors. For this, we suggest that glioblastomas serve as a useful application paradigm. We performed a literature search on PubMed for articles published in English between 2006 and 2016. We used the search terms "radiomics," "glioblastoma," "biomarkers," "pharmacogenomics," "pharmacometabolomics," "pharmacometabonomics/pharmacometabolomics," "collaborative informatics," and "precision medicine." A list of the top 4 insights we derived from this literature analysis is presented in this study. For example, we found that (i) tumor grading needs to be better refined, (ii) diagnostic precision should be improved, (iii) standardization in radiomics is lacking, and (iv) quantitative radiomics needs to prove clinical implementation. We conclude with an interdisciplinary call to the metabolomics, pharmacy/pharmacology, radiology, and surgery communities that pharmacometabolomics coupled to information technologies (chemoinformatics tools, databases, collaborative systems) can inform quantitative radiomics, thus translating Big Data and information growth to knowledge growth, rational drug development and diagnostics innovation for glioblastomas, and possibly in other brain tumors.

Effect of vision, touch and stance on cerebellar vermian-related sway and tremor: a quantitative physiological and MRI study.

PubMed

Sullivan, Edith V; Rose, Jessica; Pfefferbaum, Adolf

2006-08-01

Postural balance is impaired in individuals with pathology of the anterior superior vermis of the cerebellum. Chronic alcoholism, with its known vermian pathology, provides a viable model for studying the relationship between cerebellar pathology and postural stability. Decades of separate study of recovering alcoholics and post-mortem neuroanatomical analysis have demonstrated vermian pathology but few studies have used quantitative posturography, acquired concurrently with quantitative neuroimaging, to establish whether this brain structure-function relationship is selective in vivo. Here, 30 healthy men and 39 chronic alcoholic men, abstinent from alcohol for several months, underwent MRI for volumetric quantitation of the cerebellar vermis and three comparison brain regions, the cerebellar hemispheres, supratentorial cortex and corpus callosum. All subjects also participated in an experiment involving a force platform that measured sway path length and tremor during static standing balance under four sensory conditions and two stance conditions. Three novel findings emerged: (i) sway path length, a physiological index of postural control, was selectively related to volume of the cerebellar vermis and not to any comparison brain region in the alcoholics; (ii) spectral analysis revealed sway prominence in the 2-5 Hz band, another physiological sign of vermian lesions and also selectively related to vermian volume in the alcoholics; and (iii) despite substantial postural sway in the patients, they successfully used vision, touch and stance to normalize sway and reduce tremor. The selective relationship of sway path to vermian but not lateral cerebellar volume provides correlational evidence for functional differentiation of these cerebellar regions. Improvement to virtual normal levels in balance and reduction in sway and tremor with changes in vision, touch and stance provide evidence that adaptive mechanisms recruiting sensorimotor integration can be invoked to compensate for underlying cerebellar vermian-related dysfunction.

IWGT report on quantitative approaches to genotoxicity risk assessment II. Use of point-of-departure (PoD) metrics in defining acceptable exposure limits and assessing human risk

EPA Science Inventory

This is the second of two reports from the International Workshops on Genotoxicity Testing (IWGT) Working Group on Quantitative Approaches to Genetic Toxicology Risk Assessment (the QWG). The first report summarized the discussions and recommendations of the QWG related to the ne...

Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir.II. Spring and fall cold-hardiness

Treesearch

K.D. Jermstad; D.L. Bassoni; N.C. Wheeler; T.S. Anekonda; S.N. Aitken; W.T. Adams; D.B. Neale

2001-01-01

Abstract Quantitative trait loci (QTLs) affecting fall and spring cold-hardiness were identified in a three-generation outbred pedigree of coastal Douglas-fir [Pseudotsuga meniziesii (Mirb.) Franco var. menziesii]. Eleven QTLs controlling fall cold-hardiness were detected on four linkage groups, and 15 QTLs controlling spring cold-hardiness were detected on four...

[Medical and ecological assessment of climate effects on urolithiasis morbidity in population of Primorsky territory].

PubMed

Koval'chuk, V K

2004-01-01

The article presents medicoecological estimation of quantitative relations between monsoon climate and urolithiasis primary morbidity in the Primorsky Territory. Quantitative estimation of the climate was performed by V. I. Rusanov (1973) who calculated daily meteorological data for 1 p.m. throughout 1991-1999. Primary urolithiasis morbidity for this period of time was provided by regional health department. The data were processed by methods of medical mapping and paired correlation analysis. In the Territory, mapping revealed the same location of the zones with high frequency of discomfortable weather of class V and VI causing chilblain in positive air temperatures and zones with elevated primary urolithiasis morbidity in children and adults. Correlation analysis confirmed mapping results and determined significant negative correlations between frequency of relatively comfortable moment weather classes II-IV and morbidity of children and adults, positive correlation between frequency of discomfortable class VI and adult morbidity. Thus, high frequency of days per year with discomfortable classes of moment weather in low positive air temperatures may be one of the factors of urolithiasis risk in population of the Primorsky Territory. Climatic factors should be taken into consideration in planning primary prophylaxis of this disease in the Primorsky Territory.

Characterization of specimens obtained by different sampling methods for evaluation of periodontal bacteria.

PubMed

Okada, Ayako; Sogabe, Kaoru; Takeuchi, Hiroaki; Okamoto, Masaaki; Nomura, Yoshiaki; Hanada, Nobuhiro

2017-12-27

Quantitative analysis of periodontal bacteria is considered useful for clinical diagnosis, evaluation and assessment of the risk of periodontal disease. The purpose of this study was to compare the effectiveness of sampling of saliva, supragingival and subgingival plaque for evaluation of periodontal bacteria. From each of 12 subjects, i) subgingival plaque was collected from the deepest pocket using a sterile paper point, ii) stimulated whole saliva was collected after chewing gum, and iii) supragingival plaque was collected using a tooth brush. These samples were sent to the medical examination laboratory for quantitative analysis of the counts of three periodontal bacterial species: Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia. The proportions of these bacteria in subgingival plaque were higher than those in saliva or supragingival plaque, but lower in subgingival plaque than in saliva or supragingival plaque. In several cases, periodontal bacteria were below the levels of detection in subgingival plaque. We concluded that samples taken from subgingival plaque may be more useful for evaluating the proportion of periodontal bacteria in deep pockets than is the case for other samples. Therefore, for evaluation of periodontal bacteria, clinicians should consider the characteristics of the specimens obtained using different sampling methods.

Screening key candidate genes and pathways involved in insulinoma by microarray analysis.

PubMed

Zhou, Wuhua; Gong, Li; Li, Xuefeng; Wan, Yunyan; Wang, Xiangfei; Li, Huili; Jiang, Bin

2018-06-01

Insulinoma is a rare type tumor and its genetic features remain largely unknown. This study aimed to search for potential key genes and relevant enriched pathways of insulinoma.The gene expression data from GSE73338 were downloaded from Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified between insulinoma tissues and normal pancreas tissues, followed by pathway enrichment analysis, protein-protein interaction (PPI) network construction, and module analysis. The expressions of candidate key genes were validated by quantitative real-time polymerase chain reaction (RT-PCR) in insulinoma tissues.A total of 1632 DEGs were obtained, including 1117 upregulated genes and 514 downregulated genes. Pathway enrichment results showed that upregulated DEGs were significantly implicated in insulin secretion, and downregulated DEGs were mainly enriched in pancreatic secretion. PPI network analysis revealed 7 hub genes with degrees more than 10, including GCG (glucagon), GCGR (glucagon receptor), PLCB1 (phospholipase C, beta 1), CASR (calcium sensing receptor), F2R (coagulation factor II thrombin receptor), GRM1 (glutamate metabotropic receptor 1), and GRM5 (glutamate metabotropic receptor 5). DEGs involved in the significant modules were enriched in calcium signaling pathway, protein ubiquitination, and platelet degranulation. Quantitative RT-PCR data confirmed that the expression trends of these hub genes were similar to the results of bioinformatic analysis.The present study demonstrated that candidate DEGs and enriched pathways were the potential critical molecule events involved in the development of insulinoma, and these findings were useful for better understanding of insulinoma genesis.

Effects of RNAi-Mediated Knockdown of Histone Methyltransferases on the Sex-Specific mRNA Expression of Imp in the Silkworm Bombyx mori

PubMed Central

Suzuki, Masataka G.; Ito, Haruka; Aoki, Fugaku

2014-01-01

Sexual differentiation in Bombyx mori is controlled by sex-specific splicing of Bmdsx, which results in the omission of exons 3 and 4 in a male-specific manner. In B. mori, insulin-like growth factor II mRNA-binding protein (Imp) is a male-specific factor involved in male-specific splicing of Bmdsx. Male-specific Imp mRNA results from the male-specific inclusion of exon 8. To verify the link between histone methylation and alternative RNA processing in Imp, we examined the effects of RNAi-mediated knockdown of several histone methyltransferases on the sex-specific mRNA expression of Imp. As a result, male-specific expression of Imp mRNA was completely abolished when expression of the H3K79 methyltransferase DOT1L was repressed to <10% of that in control males. Chromatin immunoprecipitation-quantitative PCR analysis revealed a higher distribution of H3K79me2 in normal males than in normal females across Imp. RNA polymerase II (RNAP II) processivity assays indicated that RNAi knockdown of DOT1L in males caused a twofold decrease in RNAP II processivity compared to that in control males, with almost equivalent levels to those observed in normal females. Inhibition of RNAP II-mediated elongation in male cells repressed the male-specific splicing of Imp. Our data suggest the possibility that H3K79me2 accumulation along Imp is associated with the male-specific alternative processing of Imp mRNA that results from increased RNAP II processivity. PMID:24758924

Ionised gas kinematics in bipolar H II regions

NASA Astrophysics Data System (ADS)

Dalgleish, Hannah S.; Longmore, Steven N.; Peters, Thomas; Henshaw, Jonathan D.; Veitch-Michaelis, Joshua L.; Urquhart, James S.

2018-05-01

Stellar feedback plays a fundamental role in shaping the evolution of galaxies. Here we explore the use of ionised gas kinematics in young, bipolar H II regions as a probe of early feedback in these star-forming environments. We have undertaken a multi-wavelength study of a young, bipolar H II region in the Galactic disc, G316.81-0.06, which lies at the centre of a massive (˜103 M⊙) infrared-dark cloud filament. It is still accreting molecular gas as well as driving a ˜0.2 pc ionised gas outflow perpendicular to the filament. Intriguingly, we observe a large velocity gradient (47.81 ± 3.21 km s-1 pc-1) across the ionised gas in a direction perpendicular to the outflow. This kinematic signature of the ionised gas shows a reasonable correspondence with the simulations of young H II regions. Based on a qualitative comparison between our observations and these simulations, we put forward a possible explanation for the velocity gradients observed in G316.81-0.06. If the velocity gradient perpendicular to the outflow is caused by rotation of the ionised gas, then we infer that this rotation is a direct result of the initial net angular momentum in the natal molecular cloud. If this explanation is correct, this kinematic signature should be common in other young (bipolar) H II regions. We suggest that further quantitative analysis of the ionised gas kinematics of young H II regions, combined with additional simulations, should improve our understanding of feedback at these early stages.

Effects of DNA extraction and purification methods on real-time quantitative PCR analysis of Roundup Ready soybean.

PubMed

Demeke, Tigst; Ratnayaka, Indira; Phan, Anh

2009-01-01

The quality of DNA affects the accuracy and repeatability of quantitative PCR results. Different DNA extraction and purification methods were compared for quantification of Roundup Ready (RR) soybean (event 40-3-2) by real-time PCR. DNA was extracted using cetylmethylammonium bromide (CTAB), DNeasy Plant Mini Kit, and Wizard Magnetic DNA purification system for food. CTAB-extracted DNA was also purified using the Zymo (DNA Clean & Concentrator 25 kit), Qtip 100 (Qiagen Genomic-Tip 100/G), and QIAEX II Gel Extraction Kit. The CTAB extraction method provided the largest amount of DNA, and the Zymo purification kit resulted in the highest percentage of DNA recovery. The Abs260/280 and Abs260/230 ratios were less than the expected values for some of the DNA extraction and purification methods used, indicating the presence of substances that could inhibit PCR reactions. Real-time quantitative PCR results were affected by the DNA extraction and purification methods used. Further purification or dilution of the CTAB DNA was required for successful quantification of RR soybean. Less variability of quantitative PCR results was observed among experiments and replications for DNA extracted and/or purified by CTAB, CTAB+Zymo, CTAB+Qtip 100, and DNeasy methods. Correct and repeatable results for real-time PCR quantification of RR soybean were achieved using CTAB DNA purified with Zymo and Qtip 100 methods.

The glycosylated IgII extracellular domain of EMMPRIN is implicated in the induction of MMP-2.

PubMed

Papadimitropoulou, Adriana; Mamalaki, Avgi

2013-07-01

EMMPRIN is a widely expressed transmembrane glycoprotein that plays important roles in many physiological and pathological processes, such as tumor invasion and metastasis. It stimulates the production of matrix metalloproteinase (MMPs) by tumor-associated fibroblasts. In the present study, our aim was to (a) to investigate if the IgII loop domain of the extracellular domain (ECD) of EMMPRIN contributes to the MMP production by fibroblasts and (b) to evaluate the significance of glycosylation in this process. For this purpose, we expressed the ECD, IgI, or IgII domains of EMMPRIN, in their glycosylated and non-glycosylated forms, in the heterologous expression systems of P. pastoris and E. coli, respectively. Dermal fibroblasts were treated with purified recombinant domains and proteins from cell extracts and supernatants were analyzed by Western blot and zymography assays. Fibroblasts treated with ECD-, IgI-, and IgII-glycosylated domains of EMMPRIN significantly stimulated the gelatinolytic activity of MMP-2, compared to untreated fibroblasts, whereas no significant effect was observed after treatment with the non-glycosylated ECD, IgI, and IgII domains. Western blot analysis from cell extracts and supernatants revealed that only the glycosylated forms were able to stimulate MMP-2 production and secretion, respectively. Quantitative PCR revealed that this effect was not attributed to transcriptional alterations. This study showed that N-glycosylation was a prerequisite for efficient MMP-2 production, with the IgII loop domain contributing significantly to this process. Perturbation of the function of IgII-EMMPRIN loop could have potential therapeutic value in the inhibition of MMP-2-dependent cancer cell invasion and metastasis.

[Pharmacogenetic approaches to predicting the efficiency and safety of amlodipine in patients with arterial hypertension].

PubMed

Sychev, D A; Shih, N V; Kalle, E G; Ryzhikova, K A; Morozova, T E

2017-10-01

An open, non-comparative, prospective clinical study was conducted to evaluate the antihypertensive efficacy and tolerability of amlodipine, a calcium antagonist, in patients with arterial hypertension (AH) I-II stages, depending on the genotype for the polymorphic marker C3435T of the ABCB1 gene. The study included 100 patients with AH I-II stages, aged from 45 to 58 years. The initial dose of amlodipine was 5 mg, duration of treatment was 12 weeks. General clinical examination methods, office measurement and daily blood pressure monitoring, tolerance evaluation, and genotyping using the ABCB1 polymorphic marker C3435T by the PCR-RFLP method (polymerase chain reaction and restriction fragment length polymorphism) were used. The statistical analysis of results was carried out using the Mann-Whitney U test for quantitative variables, Kruskal-Wallis one-way analysis of variance (ANOVA) for three independent groups of quantitative data. Excellent antihypertensive efficacy with the CC genotype was found in 11.8% patients, with CT - 33.9%, with TT - 43.3%; good - 35.3%, 32.1%, and 33.3% respectively, satisfactory - 52.9%, 34,0% and 23.4% respectively. Six patients with the CT genotype and nine patients with the CC genotype required the increase in the dose to 10 mg. The number of patients with Adverse drug reactions (ADR) were found in 35.3% of patients with the CC genotype, 6.7% with the TT genotype and 11.3% with the CT genotype. The Kruskal-Wallis test revealed significant differences between CC and TT genotypes in the degree of decrease in SBP (p=0.02), antihypertensive efficacy parameter (p=0.02), an increase in dose requirements (p = 0.04) and the incidence of ADR(p=0.05). In AH patients (I-II stage) with the TT genotype of the C3435T gene polymorphism one can expect higher rates of antihypertensive efficacy of amlodipine in combination with a good safety profile and the lowest ADR percentage, while patients with the CC genotype more likely to develop ADR and lower antihypertensive responsiveness.

An open-source method to analyze optokinetic reflex responses in larval zebrafish.

PubMed

Scheetz, Seth D; Shao, Enhua; Zhou, Yangzhong; Cario, Clinton L; Bai, Qing; Burton, Edward A

2018-01-01

Optokinetic reflex (OKR) responses provide a convenient means to evaluate oculomotor, integrative and afferent visual function in larval zebrafish models, which are commonly used to elucidate molecular mechanisms underlying development, disease and repair of the vertebrate nervous system. We developed an open-source MATLAB-based solution for automated quantitative analysis of OKR responses in larval zebrafish. The package includes applications to: (i) generate sinusoidally-transformed animated grating patterns suitable for projection onto a cylindrical screen to elicit the OKR; (ii) determine and record the angular orientations of the eyes in each frame of a video recording showing the OKR response; and (iii) analyze angular orientation data from the tracking program to yield a set of parameters that quantify essential elements of the OKR. The method can be employed without modification using the operating manual provided. In addition, annotated source code is included, allowing users to modify or adapt the software for other applications. We validated the algorithms and measured OKR responses in normal larval zebrafish, showing good agreement with published quantitative data, where available. We provide the first open-source method to elicit and analyze the OKR in larval zebrafish. The wide range of parameters that are automatically quantified by our algorithms significantly expands the scope of quantitative analysis previously reported. Our method for quantifying OKR responses will be useful for numerous applications in neuroscience using the genetically- and chemically-tractable zebrafish model. Published by Elsevier B.V.

Faults and foibles of quantitative scanning electron microscopy/energy dispersive x-ray spectrometry (SEM/EDS)

NASA Astrophysics Data System (ADS)

Newbury, Dale E.; Ritchie, Nicholas W. M.

2012-06-01

Scanning electron microscopy with energy dispersive x-ray spectrometry (SEM/EDS) is a powerful and flexible elemental analysis method that can identify and quantify elements with atomic numbers > 4 (Be) present as major constituents (where the concentration C > 0.1 mass fraction, or 10 weight percent), minor (0.01<= C <= 0.1) and trace (C < 0.01, with a minimum detectable limit of ~+/- 0.0005 - 0.001 under routine measurement conditions, a level which is analyte and matrix dependent ). SEM/EDS can select specimen volumes with linear dimensions from ~ 500 nm to 5 μm depending on composition (masses ranging from ~ 10 pg to 100 pg) and can provide compositional maps that depict lateral elemental distributions. Despite the maturity of SEM/EDS, which has a history of more than 40 years, and the sophistication of modern analytical software, the method is vulnerable to serious shortcomings that can lead to incorrect elemental identifications and quantification errors that significantly exceed reasonable expectations. This paper will describe shortcomings in peak identification procedures, limitations on the accuracy of quantitative analysis due to specimen topography or failures in physical models for matrix corrections, and quantitative artifacts encountered in xray elemental mapping. Effective solutions to these problems are based on understanding the causes and then establishing appropriate measurement science protocols. NIST DTSA II and Lispix are open source analytical software available free at www.nist.gov that can aid the analyst in overcoming significant limitations to SEM/EDS.

Development of a novel MWCNTs-triazene-modified carbon paste electrode for potentiometric assessment of Hg(II) in the aquatic environments.

PubMed

Mashhadizadeh, Mohammad Hossein; Ramezani, Soleyman; Rofouei, Mohammad Kazem

2015-02-01

In this approach, a new chemically modified carbon paste electrode was assembled for potentiometric assay of mercury(II) ion in the aqueous environments. Hereby, MWCNTs were used in the carbon paste composition to meliorate the electrical conductivity and sensitivity of the carbon paste owing to its exceptional physicochemical characteristics. Likewise, participation of the BEPT as a super-selective ionophore in the carbon paste composition boosted significantly the selectivity of the modified electrode towards Hg(II) ions over a wide concentration range of 4.0 × 10(-9)-2.2 × 10(-3) mol L(-1) with a lower detection limit of 3.1 × 10(-9) mol L(-1). Besides, Nernstian slope of the proposed sensor was 28.9(± 0.4)mV/decade over a pH range of 3.0-5.2 with potentiometric short response time of 10s. In the interim, by storing in the dark and cool dry place during non-usage period, the electrode can be used for at least 30 days without any momentous divergence of the potentiometric response. Eventually, to judge about its practical efficiency, the arranged sensor was utilized successfully as an indicator electrode for potentiometric titration of mercury(II) with standard solution of EDTA. As well, the quantitative analysis of mercury(II) ions in some aqueous samples with sensible accuracy and precision was satisfactorily performed. Copyright © 2014 Elsevier B.V. All rights reserved.

Biosorption of Pb (II) from aqueous solution by extracellular polymeric substances extracted from Klebsiella sp. J1: Adsorption behavior and mechanism assessment

NASA Astrophysics Data System (ADS)

Wei, Wei; Wang, Qilin; Li, Ang; Yang, Jixian; Ma, Fang; Pi, Shanshan; Wu, Dan

2016-08-01

The adsorption performance and mechanism of extracellular polymeric substances (EPS) extracted from Klebsiella sp. J1 for soluble Pb (II) were investigated. The maximum biosorption capacity of EPS for Pb (II) was found to be 99.5 mg g-1 at pH 6.0 and EPS concentration of 0.2 g/L. The data for adsorption process satisfactorily fitted to both Langmuir isotherm and pseudo-second order kinetic model. The mean free energy E and activation energy Ea were determined at 8.22- 8.98 kJ mol-1 and 42.46 kJ mol-1, respectively. The liquid-film diffusion step might be the rate-limiting step. The thermodynamic parameters (ΔGo, ΔHo and ΔSo) revealed that the adsorption process was spontaneous and exothermic under natural conditions. The interactions between EPS system and Pb (II) ions were investigated by qualitative analysis methods (i.e Zeta potential, FT-IR and EDAX). Based on the strong experimental evidence from the mass balance of the related elements participating in the sorption process, an ion exchange process was identified quantitatively as the major mechanism responsible for Pb (II) adsorption by EPS. Molar equivalents of both K+ and Mg2+ could be exchanged with Pb2+ molar equivalents in the process and the contribution rate of ion exchange to adsorption accounted for 85.72% (Δmequiv = -0.000541).

Biosorption of Pb (II) from aqueous solution by extracellular polymeric substances extracted from Klebsiella sp. J1: Adsorption behavior and mechanism assessment

PubMed Central

Wei, Wei; Wang, Qilin; Li, Ang; Yang, Jixian; Ma, Fang; Pi, Shanshan; Wu, Dan

2016-01-01

The adsorption performance and mechanism of extracellular polymeric substances (EPS) extracted from Klebsiella sp. J1 for soluble Pb (II) were investigated. The maximum biosorption capacity of EPS for Pb (II) was found to be 99.5 mg g−1 at pH 6.0 and EPS concentration of 0.2 g/L. The data for adsorption process satisfactorily fitted to both Langmuir isotherm and pseudo-second order kinetic model. The mean free energy E and activation energy Ea were determined at 8.22– 8.98 kJ mol−1 and 42.46 kJ mol−1, respectively. The liquid-film diffusion step might be the rate-limiting step. The thermodynamic parameters (ΔGo, ΔHo and ΔSo) revealed that the adsorption process was spontaneous and exothermic under natural conditions. The interactions between EPS system and Pb (II) ions were investigated by qualitative analysis methods (i.e Zeta potential, FT-IR and EDAX). Based on the strong experimental evidence from the mass balance of the related elements participating in the sorption process, an ion exchange process was identified quantitatively as the major mechanism responsible for Pb (II) adsorption by EPS. Molar equivalents of both K+ and Mg2+ could be exchanged with Pb2+ molar equivalents in the process and the contribution rate of ion exchange to adsorption accounted for 85.72% (Δmequiv = −0.000541). PMID:27514493

48 CFR 15.305 - Proposal evaluation.

Code of Federal Regulations, 2011 CFR

2011-10-01

... comparative assessment of past performance information is separate from the responsibility determination... requirements; and (ii) A summary, matrix, or quantitative ranking, along with appropriate supporting narrative...

48 CFR 15.305 - Proposal evaluation.

Code of Federal Regulations, 2010 CFR

2010-10-01

... comparative assessment of past performance information is separate from the responsibility determination... requirements; and (ii) A summary, matrix, or quantitative ranking, along with appropriate supporting narrative...

48 CFR 15.305 - Proposal evaluation.

Code of Federal Regulations, 2014 CFR

2014-10-01

... comparative assessment of past performance information is separate from the responsibility determination... requirements; and (ii) A summary, matrix, or quantitative ranking, along with appropriate supporting narrative...

48 CFR 15.305 - Proposal evaluation.

Code of Federal Regulations, 2012 CFR

2012-10-01

... comparative assessment of past performance information is separate from the responsibility determination... requirements; and (ii) A summary, matrix, or quantitative ranking, along with appropriate supporting narrative...

48 CFR 15.305 - Proposal evaluation.

Code of Federal Regulations, 2013 CFR

2013-10-01

... comparative assessment of past performance information is separate from the responsibility determination... requirements; and (ii) A summary, matrix, or quantitative ranking, along with appropriate supporting narrative...

A quantitative structure–function relationship for the Photosystem II reaction center: Supermolecular behavior in natural photosynthesis

PubMed Central

Barter, Laura M. C.; Durrant, James R.; Klug, David R.

2003-01-01

Light-induced charge separation is the primary photochemical event of photosynthesis. Efficient charge separation in photosynthetic reaction centers requires the balancing of electron and excitation energy transfer processes, and in Photosystem II (PSII), these processes are particularly closely entangled. Calculations that treat the cofactors of the PSII reaction center as a supermolecular complex allow energy and electron transfer reactions to be described in a unified way. This calculational approach is shown to be in good agreement with experimentally observed energy and electron transfer dynamics. This supermolecular view also correctly predicts the effect of changing the redox potentials of cofactors by site-directed mutagenesis, thus providing a unified and quantitative structure–function relationship for the PSII reaction center. PMID:12538865

Selective solid-phase extraction using oxidized activated carbon modified with triethylenetetramine for preconcentration of metal ions

NASA Astrophysics Data System (ADS)

Zhang, Li; Chang, Xijun; Li, Zhenhua; He, Qun

2010-02-01

A new selective solid-phase extractant using activated carbon as matrix which was purified, oxidized and modified by triethylenetetramine (AC-TETA) was prepared and characterized by FT-IR spectroscopy. At pH 4, quantitative extraction of trace Cr(III), Fe(III) and Pb(II) was obtained and determined by inductively coupled plasma optical emission spectrometry (ICP-OES). Complete elution of the adsorbed metal ions from the sorbent surface was carried out using 0.5 mol L -1 HCl. The maximum static adsorption capacity of sorbent for Cr(III), Fe(III) and Pb(II) was 34.6, 36.5 and 51.9 mg g -1, respectively. The time of quantitative adsorption was less than 2 min. The detection limits of the method was found to be 0.71, 0.35 and 0.45 ng mL -1 for Cr(III), Fe(III) and Pb(II), and the relative standard deviation (RSD) was 3.7%, 2.2% and 2.5%, respectively. Moreover, the method was free from interference with common coexiting ions. The method was also successfully applied to the preconcentration of trace Cr(III), Fe(III) and Pb(II) in synthetic samples and a real sample with satisfactory results.

Serine Proteases-Like Genes in the Asian Rice Gall Midge Show Differential Expression in Compatible and Incompatible Interactions with Rice

PubMed Central

Sinha, Deepak Kumar; Lakshmi, Mulagondla; Anuradha, Ghanta; Rahman, Shaik J.; Siddiq, Ebrahimali A.; Bentur, Jagadish S.; Nair, Suresh

2011-01-01

The Asian rice gall midge, Orseolia oryzae (Wood-Mason), is a serious pest of rice. Investigations into the gall midge-rice interaction will unveil the underlying molecular mechanisms which, in turn, can be used as a tool to assist in developing suitable integrated pest management strategies. The insect gut is known to be involved in various physiological and biological processes including digestion, detoxification and interaction with the host. We have cloned and identified two genes, OoprotI and OoprotII, homologous to serine proteases with the conserved His87, Asp136 and Ser241 residues. OoProtI shared 52.26% identity with mosquito-type trypsin from Hessian fly whereas OoProtII showed 52.49% identity to complement component activated C1s from the Hessian fly. Quantitative real time PCR analysis revealed that both the genes were significantly upregulated in larvae feeding on resistant cultivar than in those feeding on susceptible cultivar. These results provide an opportunity to understand the gut physiology of the insect under compatible or incompatible interactions with the host. Phylogenetic analysis grouped these genes in the clade containing proteases of phytophagous insects away from hematophagous insects. PMID:21686154

Application of computerized exercise ECG digitization. Interpretation in large clinical trials.

PubMed

Caralis, D G; Shaw, L; Bilgere, B; Younis, L; Stocke, K; Wiens, R D; Chaitman, B R

1992-04-01

The authors report on a semiautomated program that incorporates both visual identification of fiducial points and digital determination of the ST-segment at 60 ms and 80 ms from the J point, ST slope, changes in R wave, and baseline drift. The off-line program can enhance the accuracy of detecting electrocardiographic (ECG) changes, as well as reproducibility of the exercise and postexercise ECG, as a marker of myocardial ischemia. The analysis program is written in Microsoft QuickBASIC 2.0 for an IBM personal computer interfaced to a Summagraphics mm1201 microgrid II digitizer. The program consists of the following components: (1) alphanumeric data entry, (2) ECG wave form digitization, (2) calculation of test results, (4) physician overread, and (5) editor function for remeasurements. This computerized exercise ECG digitization-interpretation program is accurate and reproducible for the quantitative assessment of ST changes and requires minimal time allotment for physician overread. The program is suitable for analysis and interpretation of large volumes of exercise tests in multicenter clinical trials and is currently utilized in the TIMI II, TIMI III, and BARI studies sponsored by the National Institutes of Health.

Reduction of precursor decay anomaly in single crystal lithium fluoride

NASA Astrophysics Data System (ADS)

Sano, Yukio

2000-08-01

The purpose of this study is to reveal that the precursor decay anomaly in single crystal lithium fluoride is reduced by Sano's decay curve [Y. Sano, J. Appl. Phys. 85, 7616 (1999)], which is much smaller in slope than Asay's decay curve [J. R. Asay, G. R. Fowles, G. E. Duvall, M. H. Miles, and R. F. Tinder, J. Appl. Phys. 43, 2132 (1972)]. To this end, strain, particle, velocity, and stress in a precursor and near the leading edge of the follower changing with time along Sano's decay curve are first analyzed quantitatively. The analysis verified the existence of degenerate contraction waves I and II and a subrarefaction wave R', and the decay process [Y. Sano, J. Appl. Phys. 77, 3746 (1995)] caused in sequence by evolving followers C, I, II, R', Rb. Next, inequalities relating decay rates qualitatively to plastic strain rates at the leading edge of the follower, which are derived using the properties of the followers, are incorporated into the analysis. Calculation results showed that the plastic strain rates were reduced by low decay rates. This indicates that the precursor decay anomaly might be greatly reduced by Sano's decay curve.

Proteomic analysis of Herbaspirillum seropedicae reveals ammonium-induced AmtB-dependent membrane sequestration of PII proteins.

PubMed

Huergo, Luciano F; Noindorf, Lilian; Gimenes, Camila; Lemgruber, Renato S P; Cordellini, Daniela F; Falarz, Lucas J; Cruz, Leonardo M; Monteiro, Rose A; Pedrosa, Fábio O; Chubatsu, Leda S; Souza, Emanuel M; Steffens, Maria B R

2010-07-01

This study was aimed at describing the spectrum and dynamics of proteins associated with the membrane in the nitrogen-fixing bacterium Herbaspirillum seropedicae according to the availability of fixed nitrogen. Using two-dimensional electrophoresis we identified 79 protein spots representing 45 different proteins in the membrane fraction of H. seropedicae. Quantitative analysis of gel images of membrane extracts indicated two spots with increased levels when cells were grown under nitrogen limitation in comparison with nitrogen sufficiency; these spots were identified as the GlnK protein and as a conserved noncytoplasmic protein of unknown function which was encoded in an operon together with GlnK and AmtB. Comparison of gel images of membrane extracts from cells grown under nitrogen limitation or under the same regime but collected after an ammonium shock revealed two proteins, GlnB and GlnK, with increased levels after the shock. The P(II) proteins were not present in the membrane fraction of an amtB mutant. The results reported here suggest that changes in the cellular localization of P(II) might play a role in the control of nitrogen metabolism in H. seropedicae.

Qualitative research methods in renal medicine: an introduction.

PubMed

Bristowe, Katherine; Selman, Lucy; Murtagh, Fliss E M

2015-09-01

Qualitative methodologies are becoming increasingly widely used in health research. However, within some specialties, including renal medicine, qualitative approaches remain under-represented in the high-impact factor journals. Qualitative research can be undertaken: (i) as a stand-alone research method, addressing specific research questions; (ii) as part of a mixed methods approach alongside quantitative approaches or (iii) embedded in clinical trials, or during the development of complex interventions. The aim of this paper is to introduce qualitative research, including the rationale for choosing qualitative approaches, and guidance for ensuring quality when undertaking and reporting qualitative research. In addition, we introduce types of qualitative data (observation, interviews and focus groups) as well as some of the most commonly encountered methodological approaches (case studies, ethnography, phenomenology, grounded theory, thematic analysis, framework analysis and content analysis). © The Author 2015. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

FRET excited ratiometric oxygen sensing in living tissue

PubMed Central

Ingram, Justin M.; Zhang, Chunfeng; Xu, Jian; Schiff, Steven J.

2013-01-01

Dynamic analysis of oxygen (O2) has been limited by the lack of a real-time, quantitative, and biocompatible sensor. To address these demands, we designed a ratiometric optode matrix consisting of the phosphorescence quenching dye platinum (II) octaethylporphine ketone (PtOEPK) and nanocystal quantum dots (NQDs), which when embedded within an inert polymer matrix allows long-term pre-designed excitation through fluorescence resonance energy transfer (FRET). Depositing this matrix on various glass substrates allowed the development of a series of optical sensors able to measure interstitial oxygen concentration [O2] with several hundred millisecond temporal resolution in varying biological microdomains of active brain tissue. PMID:23333398

Analysing neutron scattering data using McStas virtual experiments

NASA Astrophysics Data System (ADS)

Udby, L.; Willendrup, P. K.; Knudsen, E.; Niedermayer, Ch.; Filges, U.; Christensen, N. B.; Farhi, E.; Wells, B. O.; Lefmann, K.

2011-04-01

With the intention of developing a new data analysis method using virtual experiments we have built a detailed virtual model of the cold triple-axis spectrometer RITA-II at PSI, Switzerland, using the McStas neutron ray-tracing package. The parameters characterising the virtual instrument were carefully tuned against real experiments. In the present paper we show that virtual experiments reproduce experimentally observed linewidths within 1-3% for a variety of samples. Furthermore we show that the detailed knowledge of the instrumental resolution found from virtual experiments, including sample mosaicity, can be used for quantitative estimates of linewidth broadening resulting from, e.g., finite domain sizes in single-crystal samples.

Electrophysiological evidence during episodic prospection implicates medial prefrontal and bilateral middle temporal gyrus.

PubMed

Hsu, Chia-Fen; Sonuga-Barke, Edmund J S

2016-08-01

fMRI studies have implicated the medial prefrontal cortex and medial temporal lobe, components of the default mode network (DMN), in episodic prospection. This study compared quantitative EEG localized to these DMN regions during prospection and during resting and while waiting for rewards. EEG was recorded in twenty-two adults while they were asked to (i) envision future monetary episodes; (ii) wait for rewards and (iii) rest. Activation sources were localized to core DMN regions. EEG power and phase coherence were compared across conditions. Prospection, compared to resting and waiting, was associated with reduced power in the medial prefrontal gyrus and increased power in the bilateral medial temporal gyrus across frequency bands as well as greater phase synchrony between these regions in the delta band. The current quantitative EEG analysis confirms prior fMRI research suggesting that medial prefrontal and medial temporal gyrus interactions are central to the capacity for episodic prospection. Copyright © 2016 Elsevier B.V. All rights reserved.

Absolute Quantitation of Water and Metabolites in the Human Brain. II. Metabolite Concentrations

NASA Astrophysics Data System (ADS)

Kreis, R.; Ernst, T.; Ross, B. D.

A method for determining absolute metabolite concentrations with in vivo1H magnetic resonance spectroscopy is presented. Using the compartmentation model introduced in the preceding paper of this series ( J. Magn. Reson. B102, 1, 1993), it is possible to express NMR results in terms of most commonly used concentration units. The proposed scheme, involving the measurement of an external standard as well as of the localized water signal, is verified on cerebral spectra obtained from 22 subjects. Besides concentrations, longitudinal and transverse relaxation times are determined for parietal white and occipital gray matter. The determination of these quantities crucially depends on the analysis of the T2 signal decay as a function of echo time. The in vivo concentrations of the four metabolites N-acetyl aspartate, creatine plus phosphocreatine, choline, and myo-inositol are in good agreement with biochemical determinations performed in vitro. Two clinical examples emphasize the relevance of absolute quantitation in the investigation of human neuropathology and normal development.

A pre-edge analysis of Mn K-edge XANES spectra to help determine the speciation of manganese in minerals and glasses

NASA Astrophysics Data System (ADS)

Chalmin, E.; Farges, F.; Brown, G. E.

2009-01-01

High-resolution manganese K-edge X-ray absorption near edge structure spectra were collected on a set of 40 Mn-bearing minerals. The pre-edge feature information (position, area) was investigated to extract as much as possible quantitative valence and symmetry information for manganese in various “test” and “unknown” minerals and glasses. The samples present a range of manganese symmetry environments (tetrahedral, square planar, octahedral, and cubic) and valences (II to VII). The extraction of the pre-edge information is based on a previous multiple scattering and multiplet calculations for model compounds. Using the method described in this study, a robust estimation of the manganese valence could be obtained from the pre-edge region at 5% accuracy level. This method applied to 20 “test” compounds (such as hausmannite and rancieite) and to 15 “unknown” compounds (such as axinite and birnessite) provides a quantitative estimate of the average valence of manganese in complex minerals and silicate glasses.

Harnessing cell-to-cell variations to probe bacterial structure and biophysics

NASA Astrophysics Data System (ADS)

Cass, Julie A.

Advances in microscopy and biotechnology have given us novel insights into cellular biology and physics. While bacteria were long considered to be relatively unstructured, the development of fluorescence microscopy techniques, and spatially and temporally resolved high-throughput quantitative studies, have uncovered that the bacterial cell is highly organized, and its structure rigorously maintained. In this thesis I will describe our gateTool software, designed to harness cell-to-cell variations to probe bacterial structure, and discuss two exciting aspects of structure that we have employed gateTool to investigate: (i) chromosome organization and the cellular mechanisms for controlling DNA dynamics, and (ii) the study of cell wall synthesis, and how the genes in the synthesis pathway impact cellular shape. In the first project, we develop a spatial and temporal mapping of cell-cycle-dependent chromosomal organization, and use this quantitative map to discover that chromosomal loci segregate from midcell with universal dynamics. In the second project, I describe preliminary time- lapse and snapshot imaging analysis suggesting phentoypical coherence across peptidoglycan synthesis pathways.

Standardization approaches in absolute quantitative proteomics with mass spectrometry.

PubMed

Calderón-Celis, Francisco; Encinar, Jorge Ruiz; Sanz-Medel, Alfredo

2017-07-31

Mass spectrometry-based approaches have enabled important breakthroughs in quantitative proteomics in the last decades. This development is reflected in the better quantitative assessment of protein levels as well as to understand post-translational modifications and protein complexes and networks. Nowadays, the focus of quantitative proteomics shifted from the relative determination of proteins (ie, differential expression between two or more cellular states) to absolute quantity determination, required for a more-thorough characterization of biological models and comprehension of the proteome dynamism, as well as for the search and validation of novel protein biomarkers. However, the physico-chemical environment of the analyte species affects strongly the ionization efficiency in most mass spectrometry (MS) types, which thereby require the use of specially designed standardization approaches to provide absolute quantifications. Most common of such approaches nowadays include (i) the use of stable isotope-labeled peptide standards, isotopologues to the target proteotypic peptides expected after tryptic digestion of the target protein; (ii) use of stable isotope-labeled protein standards to compensate for sample preparation, sample loss, and proteolysis steps; (iii) isobaric reagents, which after fragmentation in the MS/MS analysis provide a final detectable mass shift, can be used to tag both analyte and standard samples; (iv) label-free approaches in which the absolute quantitative data are not obtained through the use of any kind of labeling, but from computational normalization of the raw data and adequate standards; (v) elemental mass spectrometry-based workflows able to provide directly absolute quantification of peptides/proteins that contain an ICP-detectable element. A critical insight from the Analytical Chemistry perspective of the different standardization approaches and their combinations used so far for absolute quantitative MS-based (molecular and elemental) proteomics is provided in this review. © 2017 Wiley Periodicals, Inc.

Copper(II)-rubeanic acid coprecipitation system for separation-preconcentration of trace metal ions in environmental samples for their flame atomic absorption spectrometric determinations.

PubMed

Soylak, Mustafa; Erdogan, Nilgun D

2006-09-21

A simple and facile preconcentration procedure based on the coprecipitation of trace heavy metal ions with copper(II)-rubeanic acid complex has been developed. The analytical parameters including pH, amounts of rubeanic acid, sample volume, etc. was investigated for the quantitative recoveries of Pb(II), Fe(III), Cd(II), Au(III), Pd(II) and Ni(II). No interferic effects were observed from the concomitant ions. The detection limits for analyte ions by 3 sigma were in the range of 0.14 microg/l for iron-3.4 microg/l for lead. The proposed coprecipitation method was successfully applied to water samples from Palas Lake-Kayseri, soil and sediment samples from Kayseri and Yozgat-Turkey.

Apolipoproteins regulate the kinetics of endothelial lipase-mediated hydrolysis of phospholipids in reconstituted high-density lipoproteins.

PubMed

Caiazza, Daniela; Jahangiri, Anisa; Rader, Daniel J; Marchadier, Dawn; Rye, Kerry-Anne

2004-09-21

Endothelial lipase (EL) is a newly identified member of the triglyceride lipase gene family that hydrolyzes high-density lipoprotein (HDL) phospholipids. This study investigates the ability of the major apolipoproteins of rHDL to regulate the kinetics of EL-mediated phospholipid hydrolysis in well-characterized, homogeneous preparations of spherical rHDL. The rHDL contained either apoA-I as the only apolipoprotein, (A-I)rHDL, apoA-II as the only apolipoprotein, (A-II)rHDL, or apoA-I as well as apoA-II, (A-I/A-II)rHDL. The rHDL were comparable in terms of size and lipid composition and contained cholesteryl esters (CE) as their sole core lipid. Phospholipid hydrolysis was quantitated as the mass of nonesterified fatty acids (NEFA) released from the rHDL during incubation with EL. The V(max) of phospholipid hydrolysis for (A-I/A-II)rHDL [391.9 +/- 12.9 nmol of NEFA formed (mL of EL)(-1) h(-1)] was greater than (A-I)rHDL [152.8 +/- 4.7 nmol of NEFA formed (mL of EL)(-1) h(-1)]. The energy of activation (E(a)) for the hydrolysis reactions was calculated to be 52.1 and 34.8 kJ mol(-1) for (A-I)rHDL and (A-I/A-II)rHDL, respectively. Minimal phospholipid hydrolysis was observed for the (A-II)rHDL. Kinetic analysis showed that EL has a higher affinity for the phospholipids in (A-I)rHDL [K(m)(app) = 0.10 +/- 0.01 mM] than in (A-I/A-II)rHDL [K(m)(app) = 0.27 +/- 0.03 mM]. Furthermore, (A-I)rHDL is a competitive inhibitor of the EL-mediated phospholipid hydrolysis of (A-I/A-II)rHDL. These results establish that apolipoproteins are major determinants of the kinetics of EL-mediated phospholipid hydrolysis in rHDL.

[Comparative analysis of real-time quantitative PCR-Sanger sequencing method and TaqMan probe method for detection of KRAS/BRAF mutation in colorectal carcinomas].

PubMed

Zhang, Xun; Wang, Yuehua; Gao, Ning; Wang, Jinfen

2014-02-01

To compare the application values of real-time quantitative PCR-Sanger sequencing and TaqMan probe method in the detection of KRAS and BRAF mutations, and to correlate KRAS/BRAF mutations with the clinicopathological characteristics in colorectal carcinomas. Genomic DNA of the tumor cells was extracted from formalin fixed paraffin embedded (FFPE) tissue samples of 344 colorectal carcinomas by microdissection. Real-time quantitative PCR-Sanger sequencing and TaqMan probe method were performed to detect the KRAS/BRAF mutations. The frequency and types of KRAS/BRAF mutations, clinicopathological characteristics and survival time were analyzed. KRAS mutations were detected in 39.8% (137/344) and 38.7% (133/344) of 344 colorectal carcinomas by using real-time quantitative PCR-Sanger sequencing and TaqMan probe method, respectively. BRAF mutation was detected in 4.7% (16/344) and 4.1% (14/344), respectively. There was no significant correlation between the two methods. The frequency of the KRAS mutation in female was higher than that in male (P < 0.05). The frequency of the BRAF mutation in colon was higher than that in rectum. The frequency of the BRAF mutation in stage III-IV cases was higher than that in stageI-II cases. The frequency of the BRAF mutation in signet ring cell carcinoma was higher than that in mucinous carcinoma and nonspecific adenocarcinoma had the lowest mutation rate. The frequency of the BRAF mutation in grade III cases was higher than that in grade II cases (P < 0.05). The overall concordance for the two methods of KRAS/BRAF mutation detection was 98.8% (kappa = 0.976). There was statistic significance between BRAF and KRAS mutations for the survival time of colorectal carcinomas (P = 0.039). There were no statistic significance between BRAF mutation type and BRAF/KRAS wild type (P = 0.058). (1) Compared with real-time quantitative PCR-Sanger sequencing, TaqMan probe method is better with regard to handling time, efficiency, repeatability, cost and equipment. (2) The frequency of the KRAS mutation is correlated with gender. BRAF mutation is correlated with primary tumor site, TNM stage, histological types and histological grades.(3) BRAF gene mutation is an independent prognostic marker for colorectal carcinomas.

Segmentation and Quantitative Analysis of Apoptosis of Chinese Hamster Ovary Cells from Fluorescence Microscopy Images.

PubMed

Du, Yuncheng; Budman, Hector M; Duever, Thomas A

2017-06-01

Accurate and fast quantitative analysis of living cells from fluorescence microscopy images is useful for evaluating experimental outcomes and cell culture protocols. An algorithm is developed in this work to automatically segment and distinguish apoptotic cells from normal cells. The algorithm involves three steps consisting of two segmentation steps and a classification step. The segmentation steps are: (i) a coarse segmentation, combining a range filter with a marching square method, is used as a prefiltering step to provide the approximate positions of cells within a two-dimensional matrix used to store cells' images and the count of the number of cells for a given image; and (ii) a fine segmentation step using the Active Contours Without Edges method is applied to the boundaries of cells identified in the coarse segmentation step. Although this basic two-step approach provides accurate edges when the cells in a given image are sparsely distributed, the occurrence of clusters of cells in high cell density samples requires further processing. Hence, a novel algorithm for clusters is developed to identify the edges of cells within clusters and to approximate their morphological features. Based on the segmentation results, a support vector machine classifier that uses three morphological features: the mean value of pixel intensities in the cellular regions, the variance of pixel intensities in the vicinity of cell boundaries, and the lengths of the boundaries, is developed for distinguishing apoptotic cells from normal cells. The algorithm is shown to be efficient in terms of computational time, quantitative analysis, and differentiation accuracy, as compared with the use of the active contours method without the proposed preliminary coarse segmentation step.

Fracture Energy-Based Brittleness Index Development and Brittleness Quantification by Pre-peak Strength Parameters in Rock Uniaxial Compression

NASA Astrophysics Data System (ADS)

Munoz, H.; Taheri, A.; Chanda, E. K.

2016-12-01

Brittleness is a fundamental mechanical rock property critical to many civil engineering works, mining development projects and mineral exploration operations. However, rock brittleness is a concept yet to be investigated as there is not any unique criterion available, widely accepted by rock engineering community able to describe rock brittleness quantitatively. In this study, new brittleness indices were developed based on fracture strain energy quantities obtained from the complete stress-strain characteristics of rocks. In doing so, different rocks having unconfined compressive strength values ranging from 7 to 215 MPa were examined in a series of quasi-static uniaxial compression tests after properly implementing lateral-strain control in a closed-loop system to apply axial load to rock specimen. This testing method was essential to capture post-peak regime of the rocks since a combination of class I-II or class II behaviour featured post-peak stress-strain behaviour. Further analysis on the post-peak strain localisation, stress-strain characteristics and the fracture pattern causing class I-II and class II behaviour were undertaken by analysing the development of field of strains in the rocks via three-dimensional digital image correlation. Analysis of the results demonstrated that pre-peak stress-strain brittleness indices proposed solely based on pre-peak stress-strain behaviour do not show any correlation with any of pre-peak rock mechanical parameters. On the other hand, the proposed brittleness indices based on pre-peak and post-peak stress-strain relations were found to competently describe an unambiguous brittleness scale against rock deformation and strength parameters such as the elastic modulus, the crack damage stress and the peak stress relevant to represent failure process.

Human and rat liver phenol sulfotransferase: structure-activity relationships for phenolic substrates.

PubMed

Campbell, N R; Van Loon, J A; Sundaram, R S; Ames, M M; Hansch, C; Weinshilboum, R

1987-12-01

Phenol sulfotransferase (PST) catalyzes the sulfate conjugation of many phenolic drugs. Human liver contains thermostable (TS) and thermolabile forms of PST. Ion exchange chromatography shows that two isozymes of TS PST (peaks I and II) are present in human liver preparations. Rat liver contains four forms of PST that can be separated by ion exchange chromatography. Quantitative structure-activity relationship (QSAR) analysis was used to study phenolic substrates for both human and rat liver PST. Thirty-six substituted phenols were tested as substrates for partially purified human liver TS PST peak I. QSAR analysis resulted in derivation of the following equation: log 1/Km = 0.92 (+/- 0.18)log P - 1.48 (+/- 0.38)MR'4 - 0.64 (+/- 0.41)MR3 + 1.04 (+/- 0.63)MR2 + 0.67(+/- 0.44) sigma- + 4.03 (+/- 0.42). In this equation Km is the Michaelis constant, P is the octanol-water partition coefficient, MR is the molar refractivity of substituents at the 2-, 3-, and 4-positions, and sigma- is the Hammett constant. Values of log 1/Km calculated with this equation were highly correlated with log 1/Km values (r = 0.950) that were observed experimentally. Nine phenols were also tested as substrates for partially purified human liver TS PST peak II. Log 1/Km values for these compounds were significantly correlated for the two isozymes of TS PST (r = 0.992, p less than 0.001). QSAR analysis was also used to derive equations that described the behavior of phenolic substrates for rat liver PST forms I and II. These equations differed substantially from the equation derived for compounds tested with human liver TS PST peak I. Therefore, the characteristics of the active sites of human liver TS PST peak I and rat liver PST forms I and II appear to differ. Application of these equations may make it possible to predict Km values of phenolic substrates for human liver TS PST and for rat liver PST forms I and II.

Determination of the main solid-state form of albendazole in bulk drug, employing Raman spectroscopy coupled to multivariate analysis.

PubMed

Calvo, Natalia L; Arias, Juan M; Altabef, Aída Ben; Maggio, Rubén M; Kaufman, Teodoro S

2016-09-10

Albendazole (ALB) is a broad-spectrum anthelmintic, which exhibits two solid-state forms (Forms I and II). The Form I is the metastable crystal at room temperature, while Form II is the stable one. Because the drug has poor aqueous solubility and Form II is less soluble than Form I, it is desirable to have a method to assess the solid-state form of the drug employed for manufacturing purposes. Therefore, a Partial Least Squares (PLS) model was developed for the determination of Form I of ALB in its mixtures with Form II. For model development, both solid-state forms of ALB were prepared and characterized by microscopic (optical and with normal and polarized light), thermal (DSC) and spectroscopic (ATR-FTIR, Raman) techniques. Mixtures of solids in different ratios were prepared by weighing and mechanical mixing of the components. Their Raman spectra were acquired, and subjected to peak smoothing, normalization, standard normal variate correction and de-trending, before performing the PLS calculations. The optimal spectral region (1396-1280cm(-1)) and number of latent variables (LV=3) were obtained employing a moving window of variable size strategy. The method was internally validated by means of the leave one out procedure, providing satisfactory statistics (r(2)=0.9729 and RMSD=5.6%) and figures of merit (LOD=9.4% and MDDC=1.4). Furthermore, the method's performance was also evaluated by analysis of two validation sets. Validation set I was used for assessment of linearity and range and Validation set II, to demonstrate accuracy and precision (Recovery=101.4% and RSD=2.8%). Additionally, a third set of spiked commercial samples was evaluated, exhibiting excellent recoveries (94.2±6.4%). The results suggest that the combination of Raman spectroscopy with multivariate analysis could be applied to the assessment of the main crystal form and its quantitation in samples of ALB bulk drug, in the routine quality control laboratory. Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of toxic metals and chemicals on biofilm and biocorrosion.

PubMed

Fang, Herbert H P; Xu, Li-Chong; Chan, Kwong-Yu

2002-11-01

Microbes in marine biofilms aggregated into clusters and increased the production of extracellular polymeric substances (EPS), by over 100% in some cases, when the seawater media containing toxic metals and chemicals, such as Cd(II), Cu(II), Pb(II), Zn(II), AI(III), Cr(III), glutaraldehyde, and phenol. The formation of microbial cluster and the increased production of EPS, which contained 84-92% proteins and 8-16% polysaccharides, accelerated the corrosion of the mild steel. However, there was no quantitative relationship between the degree of increased corrosion and the toxicity of metals/chemicals towards sulfate-reducing bacteria, or the increased EPS production.

Metallothionein from Wild Populations of the African Catfish Clarias gariepinus: From Sequence, Protein Expression and Metal Binding Properties to Transcriptional Biomarker of Metal Pollution

PubMed Central

M’kandawire, Ethel; Mierek-Adamska, Agnieszka; Stürzenbaum, Stephen R.; Choongo, Kennedy; Yabe, John; Mwase, Maxwell; Saasa, Ngonda; Blindauer, Claudia A.

2017-01-01

Anthropogenic pollution with heavy metals is an on-going concern throughout the world, and methods to monitor release and impact of heavy metals are of high importance. With a view to probe its suitability as molecular biomarker of metal pollution, this study has determined a coding sequence for metallothionein of the African sharptooth catfish Clarias gariepinus. The gene product was recombinantly expressed in Escherichia coli in presence of Zn(II), Cd(II), or Cu, and characterised by Electrospray Ionisation Mass Spectrometry and elemental analysis. C. gariepinus MT displays typical features of fish MTs, including 20 conserved cysteines, and seven bound divalent cations (Zn(II) or Cd(II)) when saturated. Livers from wild C. gariepinus fish collected in all three seasons from four different sites on the Kafue River of Zambia were analysed for their metal contents and for MT expression levels by quantitative PCR. Significant correlations were found between Zn and Cu levels and MT expression in livers, with MT expression clearly highest at the most polluted site, Chililabombwe, which is situated in the Copperbelt region. Based on our findings, hepatic expression of MT from C. gariepinus may be further developed as a major molecular biomarker of heavy metal pollution resulting from mining activities in this region. PMID:28718783

Interfacial charge separation and photovoltaic efficiency in Fe(ii)-carbene sensitized solar cells.

PubMed

Pastore, Mariachiara; Duchanois, Thibaut; Liu, Li; Monari, Antonio; Assfeld, Xavier; Haacke, Stefan; Gros, Philippe C

2016-10-12

The first combined theoretical and photovoltaic characterization of both homoleptic and heteroleptic Fe(ii)-carbene sensitized photoanodes in working dye sensitized solar cells (DSSCs) has been performed. Three new heteroleptic Fe(ii)-NHC dye sensitizers have been synthesized, characterized and tested. Despite an improved interfacial charge separation in comparison to the homoleptic compounds, the heteroleptic complexes did not show boosted photovoltaic performances. The ab initio quantitative analysis of the interfacial electron and hole transfers and the measured photovoltaic data clearly evidenced fast recombination reactions for heteroleptics, even associated with un unfavorable directional electron flow, and hence slower injection rates, in the case of homoleptics. Notably, quantum mechanics calculations revealed that deprotonation of the not anchored carboxylic function in the homoleptic complex can effectively accelerate the electron injection rate and completely suppress the electron recombination to the oxidized dye. This result suggests that introduction of strong electron-donating substituents on the not-anchored carbene ligand in heteroleptic complexes, in such a way of mimicking the electronic effects of the carboxylate functionality, should yield markedly improved interfacial charge generation properties. The present results, providing for the first time a detailed understanding of the interfacial electron transfers and photovoltaic characterization in Fe(ii)-carbene sensitized solar cells, open the way to a rational molecular engineering of efficient iron-based dyes for photoelectrochemical applications.

Goethite surface reactivity: a macroscopic investigation unifying proton, chromate, carbonate, and lead(II) adsorption.

PubMed

Villalobos, Mario; Pérez-Gallegos, Ayax

2008-10-15

The goethite surface structure has been extensively studied, but no convincing quantitative description of its highly variable surface reactivity as inversely related to its specific surface area (SSA) has been found. The present study adds experimental evidence and provides a unified macroscopic explanation to this anomalous behavior from differences in average adsorption capacities, and not in average adsorption affinities. We investigated the chromate anion and lead(II) cation adsorption behavior onto three different goethites with SSA varying from 50 to 94 m(2)/g, and analyzed an extensive set of published anion adsorption and proton charging data for variable SSA goethites. Maximum chromate adsorption was found to occupy on average from 3.1 to 9.7 sites/nm(2), inversely related to SSA. Congruency of oxyanion and Pb(II) adsorption behavior based on fractional site occupancy using these values, and a site density analysis suggest that: (i) ion binding occurs to singly and doubly coordinated sites, (ii) proton binding occurs to singly and triply coordinated sites (ranging from 6.2 to 8 total sites/nm(2), in most cases), and (iii) a predominance of (210) and/or (010) faces explains the high reactivity of low SSA goethites. The results imply that the macroscopic goethite adsorption behavior may be predicted without a need to investigate extensive structural details of each specific goethite of interest.

A Century of Progress in Molecular Mass Spectrometry

NASA Astrophysics Data System (ADS)

McLafferty, Fred W.

2011-07-01

The first mass spectrum of a molecule was measured by J.J. Thomson in 1910. Mass spectrometry (MS) soon became crucial to the study of isotopes and atomic weights and to the development of atomic weapons for World War II. Its notable applications to molecules began with the quantitative analysis of light hydrocarbons during World War II. When I joined the Dow Chemical Company in 1950, MS was not favored by organic chemists. This situation improved only with an increased understanding of gaseous ion chemistry, which was obtained through the use of extensive reference data. Gas chromatography-MS was developed in 1956, and tandem MS was first used a decade later. In neutralization-reionization MS, an unusual, unstable species is prepared by ion-beam neutralization and characterized by reionization. Electrospray ionization of a protein mixture produces its corresponding ionized molecules. In top-down proteomics, ions from an individual component can be mass separated and subjected to collision-activated and electron-capture dissociation to provide extensive sequence information.

Improved assessment of accuracy and performance using a rotational paper-based device for multiplexed detection of heavy metals.

PubMed

Sun, Xiange; Li, Bowei; Qi, Anjin; Tian, Chongguo; Han, Jinglong; Shi, Yajun; Lin, Bingcheng; Chen, Lingxin

2018-02-01

In this work, a novel rotational microfluidic paper-based device was developed to improve the accuracy and performance of the multiplexed colorimetric detection by effectively avoiding the diffusion of colorimetric reagent on the detection zone. The integrated paper-based rotational valves were used to control the connection or disconnection between detection zones and fluid channels. Based on the manipulation of the rotational valves, this rotational paper-based device could prevent the random diffusion of colorimetric reagent and reduce the error of quantitative analysis considerably. The multiplexed colorimetric detection of heavy metals Ni(II), Cu(II) and Cr(VI) were implemented on the rotational device and the detection limits could be found to be 4.8, 1.6, and 0.18mg/L, respectively. The developed rotational device showed the great advantage in improving the detection accuracy and was expected to be a low-cost, portable analytical platform for the on-site detection. Copyright © 2017 Elsevier B.V. All rights reserved.

Metabolic studies of an orally active platinum anticancer drug by liquid chromatography-electrospray ionization mass spectrometry.

PubMed

Poon, G K; Raynaud, F I; Mistry, P; Odell, D E; Kelland, L R; Harrap, K R; Barnard, C F; Murrer, B A

1995-09-29

Bis(acetato)amminedichloro(cyclohexylamine) platinum(IV) (JM216) is a new orally administered platinum complex with antitumor properties, and is currently undergoing phase II clinical trials. When JM216 was incubated with human plasma ultrafiltrate, 93% of the platinum species were protein-bound and 7% were unbound. The unbound platinum complexes in the ultrafiltrates of human plasma were analysed using a liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) method. Apart from the parent drug, four metabolites were identified and characterised. These include JM118 [amminedichloro(cyclohexylamine) platinum(II)], JM383 [bis(acetato)ammine(cyclohexylamine)dihydroxo platinum(IV)] and the two isomers JM559 and JM518 [bis(acetato)amminechloro(cyclohexylamine) hydroxo platinum(IV)]. Their elemental compositions were determined by accurate mass measurement during the LC analysis, to confirm their identities. Quantitation of these metabolites by off-line LC atomic absorption spectroscopy demonstrated that JM118 is the major metabolite in plasma from patients receiving JM216 treatment.

Evaluation of calcium alginate beads for Ce, La and Nd preconcentration from groundwater prior to ICP OES analysis.

PubMed

Arantes de Carvalho, Gabriel G; Kondaveeti, Stalin; Petri, Denise F S; Fioroto, Alexandre M; Albuquerque, Luiza G R; Oliveira, Pedro V

2016-12-01

Analytical methods for the determination of rare earth elements (REE) in natural waters by plasma spectrochemical techniques often require sample preparation procedures for analytes preconcentration as well as for removing matrix constituents, that may interfere on the analytical measurements. In the present work, calcium alginate (CA) beads were used for the first time aiming at Ce, La and Nd preconcentration from groundwater samples for further determination by inductively coupled plasma optical emission spectrometry (ICP OES). Test samples were analyzed in batch mode by transferring a 40mL test portion (pH=5±0.2) into a 50mL polyethylene flask containing 125mg CA beads. After 15min contact, the analytes were quantitatively extracted from the loaded CA beads with 2.0mL of 1.0molL -1 HCl solution for further determination by ICP OES, using Ce (II) 456.236, La (II) 379.478 and Nd (II) 430.358nm emission lines. The proposed approach is a reliable alternative for REE single-stage preconcentration from aqueous samples, as it provided accurate results based on the addition and recovery analysis of groundwater. The results obtained by the proposed method were also compared with those from reference method based on inductively coupled plasma mass spectrometry (ICP-MS) and no significant differences were observed after applying the Student's t-test at 95% confidence level. Copyright © 2016 Elsevier B.V. All rights reserved.

Accuracy of commercially available c-reactive protein rapid tests in the context of undifferentiated fevers in rural Laos.

PubMed

Phommasone, Koukeo; Althaus, Thomas; Souvanthong, Phonesavanh; Phakhounthong, Khansoudaphone; Soyvienvong, Laxoy; Malapheth, Phatthaphone; Mayxay, Mayfong; Pavlicek, Rebecca L; Paris, Daniel H; Dance, David; Newton, Paul; Lubell, Yoel

2016-02-04

C-Reactive Protein (CRP) has been shown to be an accurate biomarker for discriminating bacterial from viral infections in febrile patients in Southeast Asia. Here we investigate the accuracy of existing rapid qualitative and semi-quantitative tests as compared with a quantitative reference test to assess their potential for use in remote tropical settings. Blood samples were obtained from consecutive patients recruited to a prospective fever study at three sites in rural Laos. At each site, one of three rapid qualitative or semi-quantitative tests was performed, as well as a corresponding quantitative NycoCard Reader II as a reference test. We estimate the sensitivity and specificity of the three tests against a threshold of 10 mg/L and kappa values for the agreement of the two semi-quantitative tests with the results of the reference test. All three tests showed high sensitivity, specificity and kappa values as compared with the NycoCard Reader II. With a threshold of 10 mg/L the sensitivity of the tests ranged from 87-98 % and the specificity from 91-98 %. The weighted kappa values for the semi-quantitative tests were 0.7 and 0.8. The use of CRP rapid tests could offer an inexpensive and effective approach to improve the targeting of antibiotics in remote settings where health facilities are basic and laboratories are absent. This study demonstrates that accurate CRP rapid tests are commercially available; evaluations of their clinical impact and cost-effectiveness at point of care is warranted.

Field Ionization Mass Spectrometric Rapid Diagnosis of Infectious Diseases

DTIC Science & Technology

1975-10-01

microorganisms following extraction. We also planned to examine artificial growth media.for changes in chemical composition following short periods of...patients suffering from infectious diseases, particularly, infec- tious hepatitis and mononucleosis . LI. 4 ’V iiN II. Carry out the same type of...analytical chemi- stry determines quantitatively one constituent at a time. When applied I to clinical diagnosis of metabolic disorders, from hormone

Terminal oxidase diversity and function in "Metallosphaera yellowstonensis": gene expression and protein modeling suggest mechanisms of Fe(II) oxidation in the sulfolobales.

PubMed

Kozubal, M A; Dlakic, M; Macur, R E; Inskeep, W P

2011-03-01

"Metallosphaera yellowstonensis" is a thermoacidophilic archaeon isolated from Yellowstone National Park that is capable of autotrophic growth using Fe(II), elemental S, or pyrite as electron donors. Analysis of the draft genome sequence from M. yellowstonensis strain MK1 revealed seven different copies of heme copper oxidases (subunit I) in a total of five different terminal oxidase complexes, including doxBCEF, foxABCDEFGHIJ, soxABC, and the soxM supercomplex, as well as a novel hypothetical two-protein doxB-like polyferredoxin complex. Other genes found in M. yellowstonensis with possible roles in S and or Fe cycling include a thiosulfate oxidase (tqoAB), a sulfite oxidase (som), a cbsA cytochrome b(558/566), several small blue copper proteins, and a novel gene sequence coding for a putative multicopper oxidase (Mco). Results from gene expression studies, including reverse transcriptase (RT) quantitative PCR (qPCR) of cultures grown autotrophically on either Fe(II), pyrite, or elemental S showed that the fox gene cluster and mco are highly expressed under conditions where Fe(II) is an electron donor. Metagenome sequence and gene expression studies of Fe-oxide mats confirmed the importance of fox genes (e.g., foxA and foxC) and mco under Fe(II)-oxidizing conditions. Protein modeling of FoxC suggests a novel lysine-lysine or lysine-arginine heme B binding domain, indicating that it is likely the cytochrome component of a heterodimer complex with foxG as a ferredoxin subunit. Analysis of mco shows that it encodes a novel multicopper blue protein with two plastocyanin type I copper domains that may play a role in the transfer of electrons within the Fox protein complex. An understanding of metabolic pathways involved in aerobic iron and sulfur oxidation in Sulfolobales has broad implications for understanding the evolution and niche diversification of these thermophiles as well as practical applications in fields such as bioleaching of trace metals from pyritic ores.

Quantitative Proteomic Analysis of Mouse Embryonic Fibroblasts and Induced Pluripotent Stem Cells Using 16O /18O labeling

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

Huang, Xin; Tian, Changhai; Liu, Miao

2012-04-06

Induced pluripotent stem cells (iPSC) hold great promise for regenerative medicine as well as for investigations into the pathogenesis and treatment of various diseases. Understanding of key intracellular signaling pathways and protein targets that control development of iPSC from somatic cells is essential for designing new approaches to improve reprogramming efficiency. Here we report the development and application of an integrated quantitative proteomics platform for investigating differences in protein expressions between mouse embryonic fibroblasts (MEF) and MEF-derived iPSC. This platform consists of 16O/18O labeling, multidimensional peptide separation coupled with tandem mass spectrometry, and data analysis with UNiquant software. Using thismore » platform a total of 2,481 proteins were identified and quantified from the 16O/18O-labeled MEF-iPSC proteome mixtures with a false discovery rate of 0.01. Among them, 218 proteins were significantly upregulated, while 247 proteins were significantly downregulated in iPSC compared to MEF. Many nuclear proteins, including Hdac1, Dnmt1, Pcna, Ccnd1, Smarcc1, and subunits in DNA replication and RNA polymerase II complex were found to be enhanced in iPSC. Protein network analysis revealed that Pcna functions as a hub orchestrating complicated mechanisms including DNA replication, epigenetic inheritance (Dnmt1) and chromatin remodeling (Smarcc1) to reprogram MEF and maintain stemness of iPSC.« less

Conditional symbolic analysis detects nonlinear influences of respiration on cardiovascular control in humans

PubMed Central

Porta, Alberto; Marchi, Andrea; Bari, Vlasta; Heusser, Karsten; Tank, Jens; Jordan, Jens; Barbic, Franca; Furlan, Raffaello

2015-01-01

We propose a symbolic analysis framework for the quantitative characterization of complex dynamical systems. It allows the description of the time course of a single variable, the assessment of joint interactions and an analysis triggered by a conditioning input. The framework was applied to spontaneous variability of heart period (HP), systolic arterial pressure (SAP) and integrated muscle sympathetic nerve activity (MSNA) with the aim of characterizing cardiovascular control and nonlinear influences of respiration at rest in supine position, during orthostatic challenge induced by 80° head-up tilt (TILT) and about 3 min before evoked pre-syncope signs (PRESY). The approach detected (i) the exaggerated sympathetic modulation and vagal withdrawal from HP variability and the increased presence of fast MSNA variability components during PRESY compared with TILT; (ii) the increase of the SAP–HP coordination occurring at slow temporal scales and a decrease of that occurring at faster time scales during PRESY compared with TILT; (iii) the reduction of the coordination between fast MSNA and SAP patterns during TILT and PRESY; (iv) the nonlinear influences of respiration leading to an increased likelihood to observe the abovementioned findings during expiration compared with inspiration one. The framework provided simple, quantitative indexes able to distinguish experimental conditions characterized by different states of the autonomic nervous system and to detect the early signs of a life threatening situation such as postural syncope. PMID:25548269

Multivariate linear regression analysis to identify general factors for quantitative predictions of implant stability quotient values

PubMed Central

Huang, Hairong; Xu, Zanzan; Shao, Xianhong; Wismeijer, Daniel; Sun, Ping; Wang, Jingxiao

2017-01-01

Objectives This study identified potential general influencing factors for a mathematical prediction of implant stability quotient (ISQ) values in clinical practice. Methods We collected the ISQ values of 557 implants from 2 different brands (SICace and Osstem) placed by 2 surgeons in 336 patients. Surgeon 1 placed 329 SICace implants, and surgeon 2 placed 113 SICace implants and 115 Osstem implants. ISQ measurements were taken at T1 (immediately after implant placement) and T2 (before dental restoration). A multivariate linear regression model was used to analyze the influence of the following 11 candidate factors for stability prediction: sex, age, maxillary/mandibular location, bone type, immediate/delayed implantation, bone grafting, insertion torque, I-stage or II-stage healing pattern, implant diameter, implant length and T1-T2 time interval. Results The need for bone grafting as a predictor significantly influenced ISQ values in all three groups at T1 (weight coefficients ranging from -4 to -5). In contrast, implant diameter consistently influenced the ISQ values in all three groups at T2 (weight coefficients ranging from 3.4 to 4.2). Other factors, such as sex, age, I/II-stage implantation and bone type, did not significantly influence ISQ values at T2, and implant length did not significantly influence ISQ values at T1 or T2. Conclusions These findings provide a rational basis for mathematical models to quantitatively predict the ISQ values of implants in clinical practice. PMID:29084260

Quantitative determination of copper in a glass matrix using double pulse laser induced breakdown and electron paramagnetic resonance spectroscopic techniques.

PubMed

Khalil, Ahmed A I; Morsy, Mohamed A

2016-07-01

A series of lithium-lead-borate glasses of a variable copper oxide loading were quantitatively analyzed in this work using two distinct spectroscopic techniques, namely double pulse laser induced breakdown spectroscopy (DP-LIBS) and electron paramagnetic resonance (EPR). DP-LIBS results measured upon a combined nanosecond lasers irradiation running at 266nm and 1064nm pulses of a collinear configuration directed to the surface of borate glass samples with a known composition. This arrangement was employed to predict the electron's temperature (Te) and density (Ne) of the excited plasma from the recorded spectra. The intensity of elements' responses using this scheme is higher than that of single-pulse laser induced breakdown spectroscopy (SP-LIBS) setup under the same experimental conditions. On the other hand, the EPR data shows typical Cu (II) EPR-signals in the borate glass system that is networked at a distorted tetragonal Borate-arrangement. The signal intensity of the Cu (II) peak at g⊥=2.0596 has been used to quantify the Cu-content accurately in the glass matrix. Both techniques produced linear calibration curves of Cu-metals in glasses with excellent linear regression coefficient (R(2)) values. This study establishes a good correlation between DP-LIBS analysis of glass and the results obtained using EPR spectroscopy. The proposed protocols prove the great advantage of DP-LIBS system for the detection of a trace copper on the surface of glasses. Copyright © 2016 Elsevier B.V. All rights reserved.

Solid Phase Extraction of Trace Al(III), Fe(II), Co(II), Cu(II), Cd(II) and Pb(II) Ions in Beverages on Functionalized Polymer Microspheres Prior to Flame Atomic Absorption Spectrometric Determinations.

PubMed

Berber, Hale; Alpdogan, Güzin

2017-01-01

In this study, poly(glycidyl methacrylate-methyl methacrylate-divinylbenzene) was synthesized in the form of microspheres, and then functionalized by 2-aminobenzothiazole ligand. The sorption properties of these functionalized microspheres were investigated for separation, preconcentration and determination of Al(III), Fe(II), Co(II), Cu(II), Cd(II) and Pb(II) ions using flame atomic absorption spectrometry. The optimum pH values for quantitative sorption were 2 - 4, 5 - 8, 6 - 8, 4 - 6, 2 - 6 and 2 - 3 for Al(III), Fe(II), Co(II), Cu(II), Cd(II) and Pb(II), respectively, and also the highest sorption capacity of the functionalized microspheres was found to be for Cu(II) with the value of 1.87 mmol g -1 . The detection limits (3σ; N = 6) obtained for the studied metals in the optimal conditions were observed in the range of 0.26 - 2.20 μg L -1 . The proposed method was successfully applied to different beverage samples for the determination of Al(III), Fe(II), Co(II), Cu(II), Cd(II) and Pb(II) ions, with the relative standard deviation of <3.7%.

Classification of the medicinal plants of the genus Atractylodes using high-performance liquid chromatography with diode array and tandem mass spectrometry detection combined with multivariate statistical analysis.

PubMed

Cho, Hyun-Deok; Kim, Unyong; Suh, Joon Hyuk; Eom, Han Young; Kim, Junghyun; Lee, Seul Gi; Choi, Yong Seok; Han, Sang Beom

2016-04-01

Analytical methods using high-performance liquid chromatography with diode array and tandem mass spectrometry detection were developed for the discrimination of the rhizomes of four Atractylodes medicinal plants: A. japonica, A. macrocephala, A. chinensis, and A. lancea. A quantitative study was performed, selecting five bioactive components, including atractylenolide I, II, III, eudesma-4(14),7(11)-dien-8-one and atractylodin, on twenty-six Atractylodes samples of various origins. Sample extraction was optimized to sonication with 80% methanol for 40 min at room temperature. High-performance liquid chromatography with diode array detection was established using a C18 column with a water/acetonitrile gradient system at a flow rate of 1.0 mL/min, and the detection wavelength was set at 236 nm. Liquid chromatography with tandem mass spectrometry was applied to certify the reliability of the quantitative results. The developed methods were validated by ensuring specificity, linearity, limit of quantification, accuracy, precision, recovery, robustness, and stability. Results showed that cangzhu contained higher amounts of atractylenolide I and atractylodin than baizhu, and especially atractylodin contents showed the greatest variation between baizhu and cangzhu. Multivariate statistical analysis, such as principal component analysis and hierarchical cluster analysis, were also employed for further classification of the Atractylodes plants. The established method was suitable for quality control of the Atractylodes plants. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

12 CFR 944.6 - Bank community support programs.

Code of Federal Regulations, 2010 CFR

2010-01-01

... modification, which shall require the Bank to: (i) Conduct market research in the Bank's district; (ii... and implementing its Targeted Community Lending Plan; and (iv) Establish quantitative targeted...

Demonstration of a viable quantitative theory for interplanetary type II radio bursts

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

Schmidt, J. M., E-mail: jschmidt@physics.usyd.edu.au; Cairns, Iver H.

Between 29 November and 1 December 2013 the two widely separated spacecraft STEREO A and B observed a long lasting, intermittent, type II radio burst for the extended frequency range ≈ 4 MHz to 30 kHz, including an intensification when the shock wave of the associated coronal mass ejection (CME) reached STEREO A. We demonstrate for the first time our ability to quantitatively and accurately simulate the fundamental (F) and harmonic (H) emission of type II bursts from the higher corona (near 11 solar radii) to 1 AU. Our modeling requires the combination of data-driven three-dimensional magnetohydrodynamic simulations for the CME andmore » plasma background, carried out with the BATS-R-US code, with an analytic quantitative kinetic model for both F and H radio emission, including the electron reflection at the shock, growth of Langmuir waves and radio waves, and the radiations propagation to an arbitrary observer. The intensities and frequencies of the observed radio emissions vary hugely by factors ≈ 10{sup 6} and ≈ 10{sup 3}, respectively; the theoretical predictions are impressively accurate, being typically in error by less than a factor of 10 and 20 %, for both STEREO A and B. We also obtain accurate predictions for the timing and characteristics of the shock and local radio onsets at STEREO A, the lack of such onsets at STEREO B, and the z-component of the magnetic field at STEREO A ahead of the shock, and in the sheath. Very strong support is provided by these multiple agreements for the theory, the efficacy of the BATS-R-US code, and the vision of using type IIs and associated data-theory iterations to predict whether a CME will impact Earth’s magnetosphere and drive space weather events.« less

Demonstration of a viable quantitative theory for interplanetary type II radio bursts

NASA Astrophysics Data System (ADS)

Schmidt, J. M.; Cairns, Iver H.

2016-03-01

Between 29 November and 1 December 2013 the two widely separated spacecraft STEREO A and B observed a long lasting, intermittent, type II radio burst for the extended frequency range ≈ 4 MHz to 30 kHz, including an intensification when the shock wave of the associated coronal mass ejection (CME) reached STEREO A. We demonstrate for the first time our ability to quantitatively and accurately simulate the fundamental (F) and harmonic (H) emission of type II bursts from the higher corona (near 11 solar radii) to 1 AU. Our modeling requires the combination of data-driven three-dimensional magnetohydrodynamic simulations for the CME and plasma background, carried out with the BATS-R-US code, with an analytic quantitative kinetic model for both F and H radio emission, including the electron reflection at the shock, growth of Langmuir waves and radio waves, and the radiations propagation to an arbitrary observer. The intensities and frequencies of the observed radio emissions vary hugely by factors ≈ 106 and ≈ 103, respectively; the theoretical predictions are impressively accurate, being typically in error by less than a factor of 10 and 20 %, for both STEREO A and B. We also obtain accurate predictions for the timing and characteristics of the shock and local radio onsets at STEREO A, the lack of such onsets at STEREO B, and the z-component of the magnetic field at STEREO A ahead of the shock, and in the sheath. Very strong support is provided by these multiple agreements for the theory, the efficacy of the BATS-R-US code, and the vision of using type IIs and associated data-theory iterations to predict whether a CME will impact Earth's magnetosphere and drive space weather events.

A novel quantitative electrochemical method to monitor DNA double-strand breaks caused by a DNA cleavage agent at a DNA sensor.

PubMed

Banasiak, Anna; Cassidy, John; Colleran, John

2018-06-01

To date, DNA cleavage, caused by cleavage agents, has been monitored mainly by gel and capillary electrophoresis. However, these techniques are time-consuming, non-quantitative and require gel stains. In this work, a novel, simple and, importantly, a quantitative method for monitoring the DNA nuclease activity of potential anti-cancer drugs, at a DNA electrochemical sensor, is presented. The DNA sensors were prepared using thiol-modified oligonucleotides that self-assembled to create a DNA monolayer at gold electrode surfaces. The quantification of DNA double-strand breaks is based on calculating the DNA surface coverage, before and after exposure to a DNA cleavage agent. The nuclease properties of a model DNA cleavage agent, copper bis-phenanthroline ([Cu II (phen) 2 ] 2+ ), that can cleave DNA in a Fenton-type reaction, were quantified electrochemically. The DNA surface coverage decreased on average by 21% after subjecting the DNA sensor to a nuclease assay containing [Cu II (phen) 2 ] 2+ , a reductant and an oxidant. This percentage indicates that 6 base pairs were cleaved in the nuclease assay from the immobilised 30 base pair strands. The DNA cleavage can be also induced electrochemically in the absence of a chemical reductant. [Cu II (phen) 2 ] 2+ intercalates between DNA base pairs and, on application of a suitable potential, can be reduced to [Cu I (phen) 2 ] + , with dissolved oxygen acting as the required oxidant. This reduction process is facilitated through DNA strands via long-range electron transfer, resulting in DNA cleavage of 23%. The control measurements for both chemically and electrochemically induced cleavage revealed that DNA strand breaks did not occur under experimental conditions in the absence of [Cu II (phen) 2 ] 2+ . Copyright © 2018 Elsevier B.V. All rights reserved.

Evaluation of the performance of high temperature conversion reactors for compound-specific oxygen stable isotope analysis.

PubMed

Hitzfeld, Kristina L; Gehre, Matthias; Richnow, Hans-Hermann

2017-05-01

In this study conversion conditions for oxygen gas chromatography high temperature conversion (HTC) isotope ratio mass spectrometry (IRMS) are characterised using qualitative mass spectrometry (IonTrap). It is shown that physical and chemical properties of a given reactor design impact HTC and thus the ability to accurately measure oxygen isotope ratios. Commercially available and custom-built tube-in-tube reactors were used to elucidate (i) by-product formation (carbon dioxide, water, small organic molecules), (ii) 2nd sources of oxygen (leakage, metal oxides, ceramic material), and (iii) required reactor conditions (conditioning, reduction, stability). The suitability of the available HTC approach for compound-specific isotope analysis of oxygen in volatile organic molecules like methyl tert-butyl ether is assessed. Main problems impeding accurate analysis are non-quantitative HTC and significant carbon dioxide by-product formation. An evaluation strategy combining mass spectrometric analysis of HTC products and IRMS 18 O/ 16 O monitoring for future method development is proposed.

Hierarchical Cluster Analysis of Three-Dimensional Reconstructions of Unbiased Sampled Microglia Shows not Continuous Morphological Changes from Stage 1 to 2 after Multiple Dengue Infections in Callithrix penicillata

PubMed Central

Diniz, Daniel G.; Silva, Geane O.; Naves, Thaís B.; Fernandes, Taiany N.; Araújo, Sanderson C.; Diniz, José A. P.; de Farias, Luis H. S.; Sosthenes, Marcia C. K.; Diniz, Cristovam G.; Anthony, Daniel C.; da Costa Vasconcelos, Pedro F.; Picanço Diniz, Cristovam W.

2016-01-01

It is known that microglial morphology and function are related, but few studies have explored the subtleties of microglial morphological changes in response to specific pathogens. In the present report we quantitated microglia morphological changes in a monkey model of dengue disease with virus CNS invasion. To mimic multiple infections that usually occur in endemic areas, where higher dengue infection incidence and abundant mosquito vectors carrying different serotypes coexist, subjects received once a week subcutaneous injections of DENV3 (genotype III)-infected culture supernatant followed 24 h later by an injection of anti-DENV2 antibody. Control animals received either weekly anti-DENV2 antibodies, or no injections. Brain sections were immunolabeled for DENV3 antigens and IBA-1. Random and systematic microglial samples were taken from the polymorphic layer of dentate gyrus for 3-D reconstructions, where we found intense immunostaining for TNFα and DENV3 virus antigens. We submitted all bi- or multimodal morphological parameters of microglia to hierarchical cluster analysis and found two major morphological phenotypes designated types I and II. Compared to type I (stage 1), type II microglia were more complex; displaying higher number of nodes, processes and trees and larger surface area and volumes (stage 2). Type II microglia were found only in infected monkeys, whereas type I microglia was found in both control and infected subjects. Hierarchical cluster analysis of morphological parameters of 3-D reconstructions of random and systematic selected samples in control and ADE dengue infected monkeys suggests that microglia morphological changes from stage 1 to stage 2 may not be continuous. PMID:27047345

Hierarchical Cluster Analysis of Three-Dimensional Reconstructions of Unbiased Sampled Microglia Shows not Continuous Morphological Changes from Stage 1 to 2 after Multiple Dengue Infections in Callithrix penicillata.

PubMed

Diniz, Daniel G; Silva, Geane O; Naves, Thaís B; Fernandes, Taiany N; Araújo, Sanderson C; Diniz, José A P; de Farias, Luis H S; Sosthenes, Marcia C K; Diniz, Cristovam G; Anthony, Daniel C; da Costa Vasconcelos, Pedro F; Picanço Diniz, Cristovam W

2016-01-01

It is known that microglial morphology and function are related, but few studies have explored the subtleties of microglial morphological changes in response to specific pathogens. In the present report we quantitated microglia morphological changes in a monkey model of dengue disease with virus CNS invasion. To mimic multiple infections that usually occur in endemic areas, where higher dengue infection incidence and abundant mosquito vectors carrying different serotypes coexist, subjects received once a week subcutaneous injections of DENV3 (genotype III)-infected culture supernatant followed 24 h later by an injection of anti-DENV2 antibody. Control animals received either weekly anti-DENV2 antibodies, or no injections. Brain sections were immunolabeled for DENV3 antigens and IBA-1. Random and systematic microglial samples were taken from the polymorphic layer of dentate gyrus for 3-D reconstructions, where we found intense immunostaining for TNFα and DENV3 virus antigens. We submitted all bi- or multimodal morphological parameters of microglia to hierarchical cluster analysis and found two major morphological phenotypes designated types I and II. Compared to type I (stage 1), type II microglia were more complex; displaying higher number of nodes, processes and trees and larger surface area and volumes (stage 2). Type II microglia were found only in infected monkeys, whereas type I microglia was found in both control and infected subjects. Hierarchical cluster analysis of morphological parameters of 3-D reconstructions of random and systematic selected samples in control and ADE dengue infected monkeys suggests that microglia morphological changes from stage 1 to stage 2 may not be continuous.

Melanie II--a third-generation software package for analysis of two-dimensional electrophoresis images: I. Features and user interface.

PubMed

Appel, R D; Palagi, P M; Walther, D; Vargas, J R; Sanchez, J C; Ravier, F; Pasquali, C; Hochstrasser, D F

1997-12-01

Although two-dimensional electrophoresis (2-DE) computer analysis software packages have existed ever since 2-DE technology was developed, it is only now that the hardware and software technology allows large-scale studies to be performed on low-cost personal computers or workstations, and that setting up a 2-DE computer analysis system in a small laboratory is no longer considered a luxury. After a first attempt in the seventies and early eighties to develop 2-DE analysis software systems on hardware that had poor or even no graphical capabilities, followed in the late eighties by a wave of innovative software developments that were possible thanks to new graphical interface standards such as XWindows, a third generation of 2-DE analysis software packages has now come to maturity. It can be run on a variety of low-cost, general-purpose personal computers, thus making the purchase of a 2-DE analysis system easily attainable for even the smallest laboratory that is involved in proteome research. Melanie II 2-D PAGE, developed at the University Hospital of Geneva, is such a third-generation software system for 2-DE analysis. Based on unique image processing algorithms, this user-friendly object-oriented software package runs on multiple platforms, including Unix, MS-Windows 95 and NT, and Power Macintosh. It provides efficient spot detection and quantitation, state-of-the-art image comparison, statistical data analysis facilities, and is Internet-ready. Linked to proteome databases such as those available on the World Wide Web, it represents a valuable tool for the "Virtual Lab" of the post-genome area.

Correlation of DNA content and nucleomorphometric features with World Health Organization grading of meningiomas.

PubMed

Grunewald, J P; Röhl, F W; Kirches, E; Dietzmann, K

1998-02-01

Many studies dealing with extracranial cancer showed a strong correlation of DNA ploidy to a poor clinical outcome, recurrence, or malignancy. In brain tumors, analysis of DNA content did not always provided significant diagnostic information. In this study, DNA density and karyometric parameters of 50 meningiomas (26 Grade I, 10 Grade II, 14 Grade III) were quantitatively evaluated by digital cell image analyses of Feulgen-stained nuclei. In particular, the densitometric parameter SEXT, which describes nuclear DNA content, as well as the morphometric values LENG (a computer-assisted measurement of nuclear circumference), AREA (a computer-assisted measurement of nuclear area), FCON (a parameter that describes nuclear roundness), and CONC (a describing nuclear contour), evaluated with the software IMAGE C, were correlated to World Health Organization (WHO) grading using univariate and multivariate methods. AREA and LENG values showed significant differences between tumors of Grades I and III. FCON values were unable to distinguish WHO Grade III from Grade I/II but were useful in clearly separating Grade II from Grade I tumors. CONC values detected differences between WHO Grades II and I/III tumors but not between the latter. SEXT values clearly distinguished Grade III from Grade I/II tumors. The 1c, 2c, 2.5c, and 5c exceeding rates showed no predictive values. Only the 6c exceeding rate showed a significant difference between Grades I and III. These results outline the characteristic features of the atypical (Grade II) meningiomas, which make them a recognizable tumor entity distinct from benign and anaplastic meningiomas. The combination of DNA densitometric and morphometric findings seems to be a powerful addition to the histopathologic classification of meningiomas, as suggested by the WHO.

Investigation on Quantitative Structure Activity Relationships and Pharmacophore Modeling of a Series of mGluR2 Antagonists

PubMed Central

Zhang, Meng-Qi; Zhang, Xiao-Le; Li, Yan; Fan, Wen-Jia; Wang, Yong-Hua; Hao, Ming; Zhang, Shu-Wei; Ai, Chun-Zhi

2011-01-01

MGluR2 is G protein-coupled receptor that is targeted for diseases like anxiety, depression, Parkinson’s disease and schizophrenia. Herein, we report the three-dimensional quantitative structure–activity relationship (3D-QSAR) studies of a series of 1,3-dihydrobenzo[ b][1,4]diazepin-2-one derivatives as mGluR2 antagonists. Two series of models using two different activities of the antagonists against rat mGluR2, which has been shown to be very similar to the human mGluR2, (activity I: inhibition of [3H]-LY354740; activity II: mGluR2 (1S,3R)-ACPD inhibition of forskolin stimulated cAMP.) were derived from datasets composed of 137 and 69 molecules respectively. For activity I study, the best predictive model obtained from CoMFA analysis yielded a Q2 of 0.513, R2 ncv of 0.868, R2 pred = 0.876, while the CoMSIA model yielded a Q2 of 0.450, R2 ncv = 0.899, R2 pred = 0.735. For activity II study, CoMFA model yielded statistics of Q2 = 0.5, R2 ncv = 0.715, R2 pred = 0.723. These results prove the high predictability of the models. Furthermore, a combined analysis between the CoMFA, CoMSIA contour maps shows that: (1) Bulky substituents in R7, R3 and position A benefit activity I of the antagonists, but decrease it when projected in R8 and position B; (2) Hydrophilic groups at position A and B increase both antagonistic activity I and II; (3) Electrostatic field plays an essential rule in the variance of activity II. In search for more potent mGluR2 antagonists, two pharmacophore models were developed separately for the two activities. The first model reveals six pharmacophoric features, namely an aromatic center, two hydrophobic centers, an H-donor atom, an H-acceptor atom and an H-donor site. The second model shares all features of the first one and has an additional acceptor site, a positive N and an aromatic center. These models can be used as guidance for the development of new mGluR2 antagonists of high activity and selectivity. This work is the first report on 3D-QSAR modeling of these mGluR2 antagonists. All the conclusions may lead to a better understanding of the mechanism of antagonism and be helpful in the design of new potent mGluR2 antagonists. PMID:22016641

Investigation on quantitative structure activity relationships and pharmacophore modeling of a series of mGluR2 antagonists.

PubMed

Zhang, Meng-Qi; Zhang, Xiao-Le; Li, Yan; Fan, Wen-Jia; Wang, Yong-Hua; Hao, Ming; Zhang, Shu-Wei; Ai, Chun-Zhi

2011-01-01

MGluR2 is G protein-coupled receptor that is targeted for diseases like anxiety, depression, Parkinson's disease and schizophrenia. Herein, we report the three-dimensional quantitative structure-activity relationship (3D-QSAR) studies of a series of 1,3-dihydrobenzo[ b][1,4]diazepin-2-one derivatives as mGluR2 antagonists. Two series of models using two different activities of the antagonists against rat mGluR2, which has been shown to be very similar to the human mGluR2, (activity I: inhibition of [(3)H]-LY354740; activity II: mGluR2 (1S,3R)-ACPD inhibition of forskolin stimulated cAMP.) were derived from datasets composed of 137 and 69 molecules respectively. For activity I study, the best predictive model obtained from CoMFA analysis yielded a Q(2) of 0.513, R(2) (ncv) of 0.868, R(2) (pred) = 0.876, while the CoMSIA model yielded a Q(2) of 0.450, R(2) (ncv) = 0.899, R(2) (pred) = 0.735. For activity II study, CoMFA model yielded statistics of Q(2) = 0.5, R(2) (ncv) = 0.715, R(2) (pred) = 0.723. These results prove the high predictability of the models. Furthermore, a combined analysis between the CoMFA, CoMSIA contour maps shows that: (1) Bulky substituents in R(7), R(3) and position A benefit activity I of the antagonists, but decrease it when projected in R(8) and position B; (2) Hydrophilic groups at position A and B increase both antagonistic activity I and II; (3) Electrostatic field plays an essential rule in the variance of activity II. In search for more potent mGluR2 antagonists, two pharmacophore models were developed separately for the two activities. The first model reveals six pharmacophoric features, namely an aromatic center, two hydrophobic centers, an H-donor atom, an H-acceptor atom and an H-donor site. The second model shares all features of the first one and has an additional acceptor site, a positive N and an aromatic center. These models can be used as guidance for the development of new mGluR2 antagonists of high activity and selectivity. This work is the first report on 3D-QSAR modeling of these mGluR2 antagonists. All the conclusions may lead to a better understanding of the mechanism of antagonism and be helpful in the design of new potent mGluR2 antagonists.

Fluorescent probe based subcellular distribution of Cu(II) ions in living electrotrophs isolated from Cu(II)-reduced biocathodes of microbial fuel cells.

PubMed

Tao, Ye; Xue, Hua; Huang, Liping; Zhou, Peng; Yang, Wei; Quan, Xie; Yuan, Jinxiu

2017-02-01

Based on the four indigenous electrotrophs (Stenotrophomonas maltophilia JY1, Citrobacter sp. JY3, Pseudomonas aeruginosa JY5 and Stenotrophomonas sp. JY6) isolated from well adapted Cu(II)-reduced biocathodes of microbial fuel cells (MFCs), a rhodamine based Cu(II) fluorescent probe was used to imaginably and quantitatively track subcellular Cu(II) ions in these electrotrophs. Cathodic electrons led to more Cu(II) ions (14.3-30.1%) in the intracellular sites at operation time of 2-3h with Cu(II) removal rates of 2.90-3.64mg/Lh whereas the absence of cathodic electrons prolonged the appearance of more Cu(II) ions (16.6-22.5%) to 5h with Cu(II) removal rates of 1.96-2.28mg/Lh. This study illustrates that cathodic electrons directed more Cu(II) ions for quicker entrance into the electrotrophic cytoplasm, and gives an alternative approach for developing imaging and functionally tracking Cu(II) ions in the electrotrophs of MFCs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mars Global Surveyor Data Analysis Program. Origins of Small Volcanic Cones: Eruption Mechanisms and Implications for Water on Mars

NASA Technical Reports Server (NTRS)

Fagents, Sarah A.; Greeley, Ronald; Thordarson, Thorvaldur

2002-01-01

The goal of the proposed work was to determine the origins of small volcanic cones observed in Mars Global Surveyor (MGS) data, and their implications for regolith ice stores and magma volatile contents. For this 1-year study, our approach involved a combination of: Quantitative morphologic analysis and interpretation of Mars Orbiter Camera (MOC) and Mars Orbiter Laser Altimeter (MOLA) data; Numerical modeling of eruption processes responsible for producing the observed features; Fieldwork on terrestrial analogs in Iceland. Following this approach, this study succeeded in furthering our understanding of (i) the spatial and temporal distribution of near-surface water ice, as defined by the distribution and sizes of rootless volcanic cones ("pseudocraters"), and (ii) the properties, eruption conditions, and volatile contents of magmas producing primary vent cones.

Novel glioblastoma markers with diagnostic and prognostic value identified through transcriptome analysis.

PubMed

Reddy, Sreekanth P; Britto, Ramona; Vinnakota, Katyayni; Aparna, Hebbar; Sreepathi, Hari Kishore; Thota, Balaram; Kumari, Arpana; Shilpa, B M; Vrinda, M; Umesh, Srikantha; Samuel, Cini; Shetty, Mitesh; Tandon, Ashwani; Pandey, Paritosh; Hegde, Sridevi; Hegde, A S; Balasubramaniam, Anandh; Chandramouli, B A; Santosh, Vani; Kondaiah, Paturu; Somasundaram, Kumaravel; Rao, M R Satyanarayana

2008-05-15

Current methods of classification of astrocytoma based on histopathologic methods are often subjective and less accurate. Although patients with glioblastoma have grave prognosis, significant variability in patient outcome is observed. Therefore, the aim of this study was to identify glioblastoma diagnostic and prognostic markers through microarray analysis. We carried out transcriptome analysis of 25 diffusely infiltrating astrocytoma samples [WHO grade II--diffuse astrocytoma, grade III--anaplastic astrocytoma, and grade IV--glioblastoma (GBM)] using cDNA microarrays containing 18,981 genes. Several of the markers identified were also validated by real-time reverse transcription quantitative PCR and immunohistochemical analysis on an independent set of tumor samples (n = 100). Survival analysis was carried out for two markers on another independent set of retrospective cases (n = 51). We identified several differentially regulated grade-specific genes. Independent validation by real-time reverse transcription quantitative PCR analysis found growth arrest and DNA-damage-inducible alpha (GADD45alpha) and follistatin-like 1 (FSTL1) to be up-regulated in most GBMs (both primary and secondary), whereas superoxide dismutase 2 and adipocyte enhancer binding protein 1 were up-regulated in the majority of primary GBM. Further, identification of the grade-specific expression of GADD45alpha and FSTL1 by immunohistochemical staining reinforced our findings. Analysis of retrospective GBM cases with known survival data revealed that cytoplasmic overexpression of GADD45alpha conferred better survival while the coexpression of FSTL1 with p53 was associated with poor survival. Our study reveals that GADD45alpha and FSTLI are GBM-specific whereas superoxide dismutase 2 and adipocyte enhancer binding protein 1 are primary GBM-specific diagnostic markers. Whereas GADD45alpha overexpression confers a favorable prognosis, FSTL1 overexpression is a hallmark of poor prognosis in GBM patients.

Atomic Force Microscopy of Photosystem II and Its Unit Cell Clustering Quantitatively Delineate the Mesoscale Variability in Arabidopsis Thylakoids

PubMed Central

Onoa, Bibiana; Schneider, Anna R.; Brooks, Matthew D.; Grob, Patricia; Nogales, Eva; Geissler, Phillip L.; Niyogi, Krishna K.; Bustamante, Carlos

2014-01-01

Photoautotrophic organisms efficiently regulate absorption of light energy to sustain photochemistry while promoting photoprotection. Photoprotection is achieved in part by triggering a series of dissipative processes termed non-photochemical quenching (NPQ), which depend on the re-organization of photosystem (PS) II supercomplexes in thylakoid membranes. Using atomic force microscopy, we characterized the structural attributes of grana thylakoids from Arabidopsis thaliana to correlate differences in PSII organization with the role of SOQ1, a recently discovered thylakoid protein that prevents formation of a slowly reversible NPQ state. We developed a statistical image analysis suite to discriminate disordered from crystalline particles and classify crystalline arrays according to their unit cell properties. Through detailed analysis of the local organization of PSII supercomplexes in ordered and disordered phases, we found evidence that interactions among light-harvesting antenna complexes are weakened in the absence of SOQ1, inducing protein rearrangements that favor larger separations between PSII complexes in the majority (disordered) phase and reshaping the PSII crystallization landscape. The features we observe are distinct from known protein rearrangements associated with NPQ, providing further support for a role of SOQ1 in a novel NPQ pathway. The particle clustering and unit cell methodology developed here is generalizable to multiple types of microscopy and will enable unbiased analysis and comparison of large data sets. PMID:25007326

Bisoprolol for the treatment of chronic heart failure: a meta-analysis on individual data of two placebo-controlled studies--CIBIS and CIBIS II. Cardiac Insufficiency Bisoprolol Study.

PubMed

Leizorovicz, Alain; Lechat, Philippe; Cucherat, Michel; Bugnard, Françoise

2002-02-01

Despite the available evidence from randomized clinical trials, beta-blockers are often not used optimally in patients with congestive heart failure (CHF). This meta-analysis aims at providing a precise and quantitative estimate of the benefit and risks of long-term bisoprolol on major clinical events in patients with CHF, both overall and in selected subgroups. This may help clinicians in their decisions as to whether to prescribe bisoprolol for their individual patients. Meta-analysis was performed of results from the 2 randomized, controlled clinical studies in which bisoprolol was compared with placebo (Cardiac Insufficiency Bisoprolol Study [CIBIS and CIBIS II]), which included 3288 patients with proven CHF. The main outcomes were total death, cardiovascular death, sudden death, hospitalization for heart failure, and myocardial infarction. A highly significant 29.3% relative reduction of death (17%, 40%; P =.00003) was observed, as well as significant risk reduction in cardiovascular death and sudden death in favor of bisoprolol. Also, a highly significant relative reduction of 18.4% (25%, 11%; P =.00001) in hospital admission or death was observed. A similar relative reduction of death was consistently observed in selected subgroups of patients. Bisoprolol prevents major cardiovascular events in patients with CHF with a high benefit-to-risk ratio and can be recommended for these patients.

Atomic Force Microscopy of Photosystem II and Its Unit Cell Clustering Quantitatively Delineate the Mesoscale Variability in Arabidopsis Thylakoids

DOE PAGES

Onoa, Bibiana; Schneider, Anna R.; Brooks, Matthew D.; ...

2014-07-09

Photoautotrophic organisms efficiently regulate absorption of light energy to sustain photochemistry while promoting photoprotection. Photoprotection is achieved in part by triggering a series of dissipative processes termed non-photochemical quenching (NPQ), which depend on the re-organization of photosystem (PS) II supercomplexes in thylakoid membranes. Using atomic force microscopy, we characterized the structural attributes of grana thylakoids from Arabidopsis thaliana to correlate differences in PSII organization with the role of SOQ1, a recently discovered thylakoid protein that prevents formation of a slowly reversible NPQ state. We developed a statistical image analysis suite to discriminate disordered from crystalline particles and classify crystalline arraysmore » according to their unit cell properties. Through detailed analysis of the local organization of PSII supercomplexes in ordered and disordered phases, we found evidence that interactions among light-harvesting antenna complexes are weakened in the absence of SOQ1, inducing protein rearrangements that favor larger separations between PSII complexes in the majority (disordered) phase and reshaping the PSII crystallization landscape. The features we observe are distinct from known protein rearrangements associated with NPQ, providing further support for a role of SOQ1 in a novel NPQ pathway. The particle clustering and unit cell methodology developed here is generalizable to multiple types of microscopy and will enable unbiased analysis and comparison of large data sets.« less

Identification of potential impacts of climate change and anthropogenic activities on streamflow alterations in the Tarim River Basin, China.

PubMed

Xue, Lianqing; Yang, Fan; Yang, Changbing; Chen, Xinfang; Zhang, Luochen; Chi, Yixia; Yang, Guang

2017-08-15

Understanding contributions of climate change and human activities to changes in streamflow is important for sustainable management of water resources in an arid area. This study presents quantitative analysis of climatic and anthropogenic factors to streamflow alteration in the Tarim River Basin (TRB) using the double mass curve method (DMC) and the Budyko methods. The time series (1960~2015) are divided into three periods: the prior impacted period (1960~1972) and the two post impacted periods, 1973~1986 and 1987~2015 with trend analysis. Our results suggest that human activities played a dominant role in deduction in the streamflow in TRB with contribution of 144.6% to 120.68% during the post impacted period I and 228.68% to 140.38% during the post impacted period II. Climatic variables accounted for 20.68%~44.6% of the decrease during the post impacted period I and 40.38% ~128.68% during the post impacted period II. Sensitivity analysis indicates that the streamflow alteration was most sensitive to changes in landscape parameters. The aridity index and all the elasticities showed an obvious increasing trend from the upstream to the downstream in the TRB. Our study suggests that it is important to take effective measures for sustainable development of eco-hydrological and socio-economic systems in the TRB.

Recombinant plasmid-based quantitative Real-Time PCR analysis of Salmonella enterica serotypes and its application to milk samples.

PubMed

Gokduman, Kurtulus; Avsaroglu, M Dilek; Cakiris, Aris; Ustek, Duran; Gurakan, G Candan

2016-03-01

The aim of the current study was to develop, a new, rapid, sensitive and quantitative Salmonella detection method using a Real-Time PCR technique based on an inexpensive, easy to produce, convenient and standardized recombinant plasmid positive control. To achieve this, two recombinant plasmids were constructed as reference molecules by cloning the two most commonly used Salmonella-specific target gene regions, invA and ttrRSBC. The more rapid detection enabled by the developed method (21 h) compared to the traditional culture method (90 h) allows the quantitative evaluation of Salmonella (quantification limits of 10(1)CFU/ml and 10(0)CFU/ml for the invA target and the ttrRSBC target, respectively), as illustrated using milk samples. Three advantages illustrated by the current study demonstrate the potential of the newly developed method to be used in routine analyses in the medical, veterinary, food and water/environmental sectors: I--The method provides fast analyses including the simultaneous detection and determination of correct pathogen counts; II--The method is applicable to challenging samples, such as milk; III--The method's positive controls (recombinant plasmids) are reproducible in large quantities without the need to construct new calibration curves. Copyright © 2016 Elsevier B.V. All rights reserved.

Genetic dissection of MHC-associated susceptibility to Lepeophtheirus salmonis in Atlantic salmon

PubMed Central

Gharbi, Karim; Glover, Kevin A; Stone, Louise C; MacDonald, Elizabeth S; Matthews, Louise; Grimholt, Unni; Stear, Michael J

2009-01-01

Background Genetic variation has been shown to play a significant role in determining susceptibility to the salmon louse, Lepeophtheirus salmonis. However, the mechanisms involved in differential response to infection remain poorly understood. Recent findings in Atlantic salmon (Salmo salar) have provided evidence for a potential link between marker variation at the major histocompatibility complex (MHC) and differences in lice abundance among infected siblings, suggesting that MHC genes can modulate susceptibility to the parasite. In this study, we used quantitative trait locus (QTL) analysis to test the effect of genomic regions linked to MHC class I and II on linkage groups (LG) 15 and 6, respectively. Results Significant QTL effects were detected on both LG 6 and LG 15 in sire-based analysis but the QTL regions remained unresolved due to a lack of recombination between markers. In dam-based analysis, a significant QTL was identified on LG 6, which accounted for 12.9% of within-family variance in lice abundance. However, the QTL was located at the opposite end of DAA, with no significant overlap with the MHC class II region. Interestingly, QTL modelling also revealed evidence of sex-linked differences in lice abundance, indicating that males and females may have different susceptibility to infection. Conclusion Overall, QTL analysis provided relatively weak support for a proximal effect of classical MHC regions on lice abundance, which can partly be explained by linkage to other genes controlling susceptibility to L. salmonis on the same chromosome. PMID:19397823

[Quantitative surface analysis of Pt-Co, Cu-Au and Cu-Ag alloy films by XPS and AES].

PubMed

Li, Lian-Zhong; Zhuo, Shang-Jun; Shen, Ru-Xiang; Qian, Rong; Gao, Jie

2013-11-01

In order to improve the quantitative analysis accuracy of AES, We associated XPS with AES and studied the method to reduce the error of AES quantitative analysis, selected Pt-Co, Cu-Au and Cu-Ag binary alloy thin-films as the samples, used XPS to correct AES quantitative analysis results by changing the auger sensitivity factors to make their quantitative analysis results more similar. Then we verified the accuracy of the quantitative analysis of AES when using the revised sensitivity factors by other samples with different composition ratio, and the results showed that the corrected relative sensitivity factors can reduce the error in quantitative analysis of AES to less than 10%. Peak defining is difficult in the form of the integral spectrum of AES analysis since choosing the starting point and ending point when determining the characteristic auger peak intensity area with great uncertainty, and to make analysis easier, we also processed data in the form of the differential spectrum, made quantitative analysis on the basis of peak to peak height instead of peak area, corrected the relative sensitivity factors, and verified the accuracy of quantitative analysis by the other samples with different composition ratio. The result showed that the analytical error in quantitative analysis of AES reduced to less than 9%. It showed that the accuracy of AES quantitative analysis can be highly improved by the way of associating XPS with AES to correct the auger sensitivity factors since the matrix effects are taken into account. Good consistency was presented, proving the feasibility of this method.

[Microbiota of lower urine tract and genital organs of healthy men and in infertility].

PubMed

Naboka, Iu L; Kogan, M I; Gudima, I A; Ibishev, Kh S; Pasechnik, D G; Logvinov, A K; Ilmdarov, Sh B

2015-01-01

Study microflora of urine, ejaculate, urethra scrape in normal state and infertility. 2 groups of men were examined: I (28)--control, conditionally healthy men (20 - 25 years of age), II (26)--infertile patients (25 - 35 years of age). Middle portion of morning urine, ejaculate, urethra scrape were studied in group I, in II--ejaculate. Bacteriologic study of urine and ejaculate was carried out in an extended kit of nutrient media (HiMedia) for facultative- anaerobic (FAB) and non-clostridia anaerobic bacteria (NAB). Urethra scrape and ejaculate were studied by PCR in group I. In urethra scrape and ejaculate a wide spectrum of FAB and NAB was detected in group I. Corynebacterium spp. and coagulase-negative staphylococci (67.9% each) were the dominant cluster of FAB. Eubacterium spp.--in NAB. Bacteriologic study of ejaculate corresponded in PCR with similar results of dominating bacteria. Among FAB the same clusters dominated during bacteriologic study of ejaculate from group II patients, among NAB--Propionibacterium spp., Peptococcus spp. and Peptostreptococcus spp. Quantitative characteristics of ejaculate of group I and II differed insignificantly. The frequency of detection of certain genera of FAB and NAB was significantly higher in patients with infertility than in conditionally healthy men, however quantitative parameters of the isolated microorganisms practically did not differ between groups.

12 CFR 1290.6 - Bank community support programs.

Code of Federal Regulations, 2011 CFR

2011-01-01

... modification, which shall require the Bank to—(i) Conduct market research in the Bank's district; (ii) Describe... implementing its Targeted Community Lending Plan; and (iv) Establish quantitative targeted community lending...

12 CFR 1290.6 - Bank community support programs.

Code of Federal Regulations, 2013 CFR

2013-01-01

... modification, which shall require the Bank to—(i) Conduct market research in the Bank's district; (ii) Describe... implementing its Targeted Community Lending Plan; and (iv) Establish quantitative targeted community lending...

12 CFR 1290.6 - Bank community support programs.

Code of Federal Regulations, 2012 CFR

2012-01-01

... modification, which shall require the Bank to—(i) Conduct market research in the Bank's district; (ii) Describe... implementing its Targeted Community Lending Plan; and (iv) Establish quantitative targeted community lending...

Tandem transmission/reflection mode XRD instrument including XRF for in situ measurement of Martian rocks and soils

NASA Astrophysics Data System (ADS)

Delhez, Robert; Van der Gaast, S. J.; Wielders, Arno; de Boer, J. L.; Helmholdt, R. B.; van Mechelen, J.; Reiss, C.; Woning, L.; Schenk, H.

2003-02-01

The mineralogy of the surface material of Mars is the key to disclose its present and past life and climates. Clay mineral species, carbonates, and ice (water and CO2) are and/or contain their witnesses. X-ray powder diffraction (XRPD) is the most powerful analytical method to identify and quantitatively characterize minerals in complex mixtures. This paper discusses the development of a working model of an instrument consisting of a reflection mode diffractometer and a transmission mode CCD-XRPD instrument, combined with an XRF module. The CCD-XRD/XRF instrument is analogous to the instrument for Mars missions developed by Sarrazin et al. (1998). This part of the tandem instrument enables "quick and dirty" analysis of powdered (!) matter to monitor semi-quantitatively the presence of clay minerals as a group, carbonates, and ices and yields semi-quantitative chemical information from X-ray fluorescence (XRF). The reflection mode instrument (i) enables in-situ measurements of rocks and soils and quantitative information on the compounds identified, (ii) has a high resolution and reveals large spacings for accurate identification, in particular of clay mineral species, and (iii) the shape of the line profiles observed reveals the kind and approximate amounts of lattice imperfections present. It will be shown that the information obtained with the reflection mode diffractometer is crucial for finding signs of life and changes in the climate on Mars. Obviously this instrument can also be used for other extra-terrestrial research.

A quantitative strategy to detect changes in accessibility of protein regions to chemical modification on heterodimerization

PubMed Central

Dreger, Mathias; Leung, Bo Wah; Brownlee, George G; Deng, Tao

2009-01-01

We describe a method for studying quantitative changes in accessibility of surface lysine residues of the PB1 subunit of the influenza RNA polymerase as a result of association with the PA subunit to form a PB1-PA heterodimer. Our method combines two established methods: (i) the chemical modification of surface lysine residues of native proteins by N-hydroxysuccinimidobiotin (NHS-biotin) and (ii) the stable isotope labeling of amino acids in cell culture (SILAC) followed by tryptic digestion and mass spectrometry. By linking the chemical modification with the SILAC methodology for the first time, we obtain quantitative data on chemical modification allowing subtle changes in accessibility to be described. Five regions in the PB1 monomer showed altered reactivity to NHS-biotin when compared with the [PB1-PA] heterodimer. Mutational analysis of residues in two such regions—at K265 and K481 of PB1, which were about three- and twofold, respectively, less accessible to biotinylation in the PB1-PA heterodimer compared with the PB1 monomer, demonstrated that both K265 and K481 were crucial for polymerase function. This novel assay of quantitative profiling of biotinylation patterns (Q-POP assay) highlights likely conformational changes at important functional sites, as observed here for PB1, and may provide information on protein–protein interaction interfaces. The Q-POP assay should be a generally applicable approach and may detect novel functional sites suitable for targeting by drugs. PMID:19517532

Hologram quantitative structure-activity relationship and comparative molecular field analysis studies within a series of tricyclic phthalimide HIV-1 integrase inhibitors.

PubMed

Magalhães, Uiaran de Oliveira; Souza, Alessandra Mendonça Teles de; Albuquerque, Magaly Girão; Brito, Monique Araújo de; Bello, Murilo Lamim; Cabral, Lucio Mendes; Rodrigues, Carlos Rangel

2013-01-01

Acquired immunodeficiency syndrome is a public health problem worldwide caused by the Human immunodeficiency virus (HIV). Treatment with antiretroviral drugs is the best option for viral suppression, reducing morbidity and mortality. However, viral resistance in HIV-1 therapy has been reported. HIV-1 integrase (IN) is an essential enzyme for effective viral replication and an attractive target for the development of new inhibitors. In the study reported here, two- and three-dimensional quantitative structure-activity relationship (2D/3D-QSAR) studies, applying hologram quantitative structure-activity relationship (HQSAR) and comparative molecular field analysis (CoMFA) methods, respectively, were performed on a series of tricyclic phthalimide HIV-1 IN inhibitors. The best HQSAR model (q (2) = 0.802, r (2) = 0.972) was obtained using atoms, bonds, and connectivity as the fragment distinction, a fragment size of 2-5 atoms, hologram length of 61 bins, and six components. The best CoMFA model (q (2) = 0.748, r (2) = 0.974) was obtained with alignment of all atoms of the tricyclic phthalimide moiety (alignment II). The HQSAR contribution map identified that the carbonyl-hydroxy-aromatic nitrogen motif made a positive contribution to the activity of the compounds. Furthermore, CoMFA contour maps suggested that bulky groups in meta and para positions in the phenyl ring would increase the biological activity of this class. The conclusions of this work may lead to a better understanding of HIV-1 IN inhibition and contribute to the design of new and more potent derivatives.

Highly hydrogen-sensitive thermal desorption spectroscopy system for quantitative analysis of low hydrogen concentration (˜1 × 1016 atoms/cm3) in thin-film samples

NASA Astrophysics Data System (ADS)

Hanna, Taku; Hiramatsu, Hidenori; Sakaguchi, Isao; Hosono, Hideo

2017-05-01

We developed a highly hydrogen-sensitive thermal desorption spectroscopy (HHS-TDS) system to detect and quantitatively analyze low hydrogen concentrations in thin films. The system was connected to an in situ sample-transfer chamber system, manipulators, and an rf magnetron sputtering thin-film deposition chamber under an ultra-high-vacuum (UHV) atmosphere of ˜10-8 Pa. The following key requirements were proposed in developing the HHS-TDS: (i) a low hydrogen residual partial pressure, (ii) a low hydrogen exhaust velocity, and (iii) minimization of hydrogen thermal desorption except from the bulk region of the thin films. To satisfy these requirements, appropriate materials and components were selected, and the system was constructed to extract the maximum performance from each component. Consequently, ˜2000 times higher sensitivity to hydrogen than that of a commercially available UHV-TDS system was achieved using H+-implanted Si samples. Quantitative analysis of an amorphous oxide semiconductor InGaZnO4 thin film (1 cm × 1 cm × 1 μm thickness, hydrogen concentration of 4.5 × 1017 atoms/cm3) was demonstrated using the HHS-TDS system. This concentration level cannot be detected using UHV-TDS or secondary ion mass spectroscopy (SIMS) systems. The hydrogen detection limit of the HHS-TDS system was estimated to be ˜1 × 1016 atoms/cm3, which implies ˜2 orders of magnitude higher sensitivity than that of SIMS and resonance nuclear reaction systems (˜1018 atoms/cm3).

Quantitative Profiling of Major Neutral Lipid Classes in Human Meibum by Direct Infusion Electrospray Ionization Mass Spectrometry

PubMed Central

Chen, Jianzhong; Green, Kari B.; Nichols, Kelly K.

2013-01-01

Purpose. The purpose of this investigation was to better understand lipid composition in human meibum. Methods. Intact lipids in meibum samples were detected by direct infusion electrospray ionization mass spectrometry (ESI-MS) analysis in positive detection mode using sodium iodide (NaI) as an additive. The peak intensities of all major types of lipid species, that is, wax esters (WEs), cholesteryl esters (CEs), and diesters (DEs) were corrected for peak overlapping and isotopic distribution; an additional ionization efficiency correction was performed for WEs and CEs, which was simplified by the observation that the corresponding ionization efficiency was primarily dependent on the specific lipid class and saturation degree of the lipids while independent of the carbon chain length. A set of WE and CE standards was spiked in meibum samples for ionization efficiency determination and absolute quantitation. Results. The absolute amount (μmol/mg) for each of 51 WEs and 31 CEs in meibum samples was determined. The summed masses for 51 WEs and 31 CEs accounted for 48 ± 4% and 40 ± 2%, respectively, of the total meibum lipids. The mass percentages of saturated and unsaturated species were determined to be 75 ± 2% and 25 ± 1% for CEs and 14 ± 1% and 86 ± 1% for WEs. The profiles for two types of DEs were also obtained, which include 42 α,ω Type II DEs, and 21 ω Type I-St DEs. Conclusions. Major neutral lipid classes in meibum samples were quantitatively profiled by ESI-MS analysis with NaI additive. PMID:23847307

Hologram quantitative structure–activity relationship and comparative molecular field analysis studies within a series of tricyclic phthalimide HIV-1 integrase inhibitors

PubMed Central

de Oliveira Magalhães, Uiaran; de Souza, Alessandra Mendonça Teles; Albuquerque, Magaly Girão; de Brito, Monique Araújo; Bello, Murilo Lamim; Cabral, Lucio Mendes; Rodrigues, Carlos Rangel

2013-01-01

Acquired immunodeficiency syndrome is a public health problem worldwide caused by the Human immunodeficiency virus (HIV). Treatment with antiretroviral drugs is the best option for viral suppression, reducing morbidity and mortality. However, viral resistance in HIV-1 therapy has been reported. HIV-1 integrase (IN) is an essential enzyme for effective viral replication and an attractive target for the development of new inhibitors. In the study reported here, two- and three-dimensional quantitative structure–activity relationship (2D/3D-QSAR) studies, applying hologram quantitative structure–activity relationship (HQSAR) and comparative molecular field analysis (CoMFA) methods, respectively, were performed on a series of tricyclic phthalimide HIV-1 IN inhibitors. The best HQSAR model (q2 = 0.802, r2 = 0.972) was obtained using atoms, bonds, and connectivity as the fragment distinction, a fragment size of 2–5 atoms, hologram length of 61 bins, and six components. The best CoMFA model (q2 = 0.748, r2 = 0.974) was obtained with alignment of all atoms of the tricyclic phthalimide moiety (alignment II). The HQSAR contribution map identified that the carbonyl-hydroxy-aromatic nitrogen motif made a positive contribution to the activity of the compounds. Furthermore, CoMFA contour maps suggested that bulky groups in meta and para positions in the phenyl ring would increase the biological activity of this class. The conclusions of this work may lead to a better understanding of HIV-1 IN inhibition and contribute to the design of new and more potent derivatives. PMID:24039405

Predicting MHC-II binding affinity using multiple instance regression

PubMed Central

EL-Manzalawy, Yasser; Dobbs, Drena; Honavar, Vasant

2011-01-01

Reliably predicting the ability of antigen peptides to bind to major histocompatibility complex class II (MHC-II) molecules is an essential step in developing new vaccines. Uncovering the amino acid sequence correlates of the binding affinity of MHC-II binding peptides is important for understanding pathogenesis and immune response. The task of predicting MHC-II binding peptides is complicated by the significant variability in their length. Most existing computational methods for predicting MHC-II binding peptides focus on identifying a nine amino acids core region in each binding peptide. We formulate the problems of qualitatively and quantitatively predicting flexible length MHC-II peptides as multiple instance learning and multiple instance regression problems, respectively. Based on this formulation, we introduce MHCMIR, a novel method for predicting MHC-II binding affinity using multiple instance regression. We present results of experiments using several benchmark datasets that show that MHCMIR is competitive with the state-of-the-art methods for predicting MHC-II binding peptides. An online web server that implements the MHCMIR method for MHC-II binding affinity prediction is freely accessible at http://ailab.cs.iastate.edu/mhcmir. PMID:20855923

Selection and Validation of Appropriate Reference Genes for qRT-PCR Analysis in Isatis indigotica Fort.

PubMed Central

Li, Tao; Wang, Jing; Lu, Miao; Zhang, Tianyi; Qu, Xinyun; Wang, Zhezhi

2017-01-01

Due to its sensitivity and specificity, real-time quantitative PCR (qRT-PCR) is a popular technique for investigating gene expression levels in plants. Based on the Minimum Information for Publication of Real-Time Quantitative PCR Experiments (MIQE) guidelines, it is necessary to select and validate putative appropriate reference genes for qRT-PCR normalization. In the current study, three algorithms, geNorm, NormFinder, and BestKeeper, were applied to assess the expression stability of 10 candidate reference genes across five different tissues and three different abiotic stresses in Isatis indigotica Fort. Additionally, the IiYUC6 gene associated with IAA biosynthesis was applied to validate the candidate reference genes. The analysis results of the geNorm, NormFinder, and BestKeeper algorithms indicated certain differences for the different sample sets and different experiment conditions. Considering all of the algorithms, PP2A-4 and TUB4 were recommended as the most stable reference genes for total and different tissue samples, respectively. Moreover, RPL15 and PP2A-4 were considered to be the most suitable reference genes for abiotic stress treatments. The obtained experimental results might contribute to improved accuracy and credibility for the expression levels of target genes by qRT-PCR normalization in I. indigotica. PMID:28702046

Application of micro-TLC to the total antioxidant potential (TAP) measurement.

PubMed

Głód, Bronisław K; Wantusiak, Paweł M; Piszcz, Paweł; Lewczuk, Elwira; Zarzycki, Paweł K

2015-04-15

DPPH is commonly applied for estimation of antioxidant capacity of single and complex biological samples, and changes colour from purple to yellow during reduction to DPPH-H. Importantly, for some samples, for example coloured foods, such reaction cannot be used because of interference from pigments. Therefore, the number of reported quantitative protocols involving off- or on-line sample reaction with DPPH are based on chromatographic separation of target components. In typical planar chromatographic assay, developed plates are sprayed with DPPH solution for antioxidant screening. Such approach enables simple visualisation of separated spots exhibiting antioxidant activities, but unfortunately, such procedure may also give the misleading signal for coloured spots. In the present communication we examined a new approach for measuring antioxidant capacity using quantitative analysis of DPPH and DPPH-H molecules after reaction with the sample, and then separated from the interfering compounds by micro-thin-layer chromatography. Particularly, the antioxidant capacities of coloured food samples (such as herbs and meads) were determined and the results compared with those obtained using the classical photometric assay. The main advantages of the new micro-TLC assay are (i) low cost, (ii) multiple measurements, (iii) short analysis time, (iv) simplification of sample preparation and (v) effective separation of DPPH signal from interfering compounds. Copyright © 2014 Elsevier Ltd. All rights reserved.

Superclustering in the explosion scenario. II - Prolate spheroidal shells from superconducting cosmic strings

NASA Technical Reports Server (NTRS)

Borden, David; Ostriker, Jeremiah P.; Weinberg, David H.

1989-01-01

If galaxies form on shells, then clusters of galaxies should form at the vertices where three shells intersect. Weinberg, Ostriker, and Dekel (WOD, 1989) studied this picture quantitatively and found that an intersecting spherical shell model reproduces many of the properties of the observed distribution of galaxy clusters, but that too much superclustering is produced. In this paper, the WOD analysis is repeated with prolate spheroids that could be created by superconducting cosmic strings. It is found that most of the attractive features of the WOD model are maintained in the more general case and there is slight improvement in some aspects, but that the overall problem of excessive superclustering is not really alleviated.

Linear canonical transformations of coherent and squeezed states in the Wigner phase space. II - Quantitative analysis

NASA Technical Reports Server (NTRS)

Han, D.; Kim, Y. S.; Noz, Marilyn E.

1989-01-01

It is possible to calculate expectation values and transition probabilities from the Wigner phase-space distribution function. Based on the canonical transformation properties of the Wigner function, an algorithm is developed for calculating these quantities in quantum optics for coherent and squeezed states. It is shown that the expectation value of a dynamical variable can be written in terms of its vacuum expectation value of the canonically transformed variable. Parallel-axis theorems are established for the photon number and its variant. It is also shown that the transition probability between two squeezed states can be reduced to that of the transition from one squeezed state to vacuum.

Overexpression of Multiple Detoxification Genes in Deltamethrin Resistant Laodelphax striatellus (Hemiptera: Delphacidae) in China

PubMed Central

Xu, Lu; Wu, Min; Han, Zhaojun

2013-01-01

Background The small brown planthopper (SBPH), Laodelphax striatellus (Fallén), is one of the major rice pests in Asia and has developed resistance to multiple classes of insecticides. Understanding resistance mechanisms is essential to the management of this pest. Biochemical and molecular assays were performed in this study to systematically characterize deltamethrin resistance mechanisms with laboratory-selected resistant and susceptible strains of SBPH. Methodology/Principal Findings Deltamethrin resistant strains of SBPH (JH-del) were derived from a field population by continuously selections (up to 30 generations) in the laboratory, while a susceptible strain (JHS) was obtained from the same population by removing insecticide pressure for 30 generations. The role of detoxification enzymes in the resistance was investigated using synergism and enzyme activity assays with strains of different resistant levels. Furthermore, 71 cytochrome P450, 93 esterases and 12 glutathione-S-transferases cDNAs were cloned based on transcriptome data of a field collected population. Semi-quantitative RT-PCR screening analysis of 176 identified detoxification genes demonstrated that multiple P450 and esterase genes were overexpressed (>2-fold) in JH-del strains (G4 and G30) when compared to that in JHS, and the results of quantitative PCR coincided with the semi-quantitative RT-PCR results. Target mutation at IIS3–IIS6 regions encoded by the voltage-gated sodium channel gene was ruled out for conferring the observed resistance. Conclusion/Significance As the first attempt to discover genes potentially involved in SBPH pyrethroid resistance, this study putatively identified several candidate genes of detoxification enzymes that were significantly overexpressed in the resistant strain, which matched the synergism and enzyme activity testing. The biochemical and molecular evidences suggest that the high level pyrethroid resistance in L. striatellus could be due to enhanced detoxification rather than target insensitivity. The findings lay a solid ground for further resistance mechanism elucidation studies. PMID:24324548

A systematic review of relations between neighborhoods and mental health.

PubMed

Truong, Khoa D; Ma, Sai

2006-09-01

The relationship between neighborhood characteristics and resident mental health has been widely investigated in individual studies in recent years, but this literature is not adequately reviewed. To systematically review relevant individual research of the relation between neighborhoods and adult mental health by identifying and synthesizing all relevant studies in this literature. We conducted an electronic search with PubMed and PsycINFO, and manual reference-checking, resulting in 8,562 screened studies of which 29 were selected. Studies were included in the main synthesis if they (i) were published in English in peer reviewed journals; (ii) had relevant definitions and measures of neighborhood characteristics; (iii) utilized standardized measures of adult mental health; (iv) controlled for individual characteristics; (v) reported quantitative results; and, (vi) studied a population in a developed country. We focused on two key areas within this literature: the methodologies utilized to study neighborhood effects and quantitative results. With regard to the former, we examined five major issues: (i) definitions and measures of neighborhoods; (ii) definitions and measures of mental health; (iii) controls for individual level characteristics; (iv) conceptual models; and (v) analytical models. As for quantitative results, the relation was reviewed by types of neighborhood characteristics. We summarized general quantitative findings and drew common conclusions across groups of studies. 27/29 studies found statistically significant association between mental health and at least one measure of neighborhood characteristics, after adjusting for individual factors. This association was evident for all types of neighborhood features, varying from sociodemographic characteristics to physical environment, and from objective to subjective measures. Neighborhood effects were weakened when adding individual-level characteristics into the regression models, and were generally modest relative to individual effects. Although the evidence is highly consistent across studies, detailed evaluation of each individual study reveals a complex reality. The included studies used various study designs and measures of mental health and neighborhoods, making generalization of their relationships less meaningful. It is not possible to conclude that studies with weaker controls for individual characteristics found stronger association between neighborhoods and mental health and vice versa. As only two studies used randomized and controlled trials, causal effects must be interpreted with caution. Formal meta-analysis techniques cannot be used due to large heterogeneity across the included studies. Efficient methods for quantitative analysis remain a great challenge. The current evidence suggests that efforts to improve mental health may be limited if only individual-level interventions are implemented. The calculation of the costs and benefits of neighborhood-level interventions deserves more attention. Moreover, policy makers may want to incorporate mental health as a measure for evaluating neighborhood improvement programs. There are not enough replicated or comparable studies in this literature to make more precise quantitative conclusions of this relation. Key aspects of study design and analyses could be improved to better understand the true nature of causal relationships. The data resolution of neighborhood characteristics needs to better match with the scale of neighborhood definition that is hypothesized to affect the residents' mental health. As experimental designs are rare in this area, thoughtful use of panel data, instrumental variable (IV) techniques, and other non-experimental approaches deserves further exploration.

N-butylamine functionalized graphene oxide for detection of iron(III) by photoluminescence quenching.

PubMed

Gholami, Javad; Manteghian, Mehrdad; Badiei, Alireza; Ueda, Hiroshi; Javanbakht, Mehran

2016-02-01

An N-butylamine functionalized graphene oxide nanolayer was synthesized and characterized by ultraviolet (UV)-visible spectrometry, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and transmission electron microscopy. Detection of iron(III) based on photoluminescence spectroscopy was investigated. The N-butylamine functionalized graphene oxide was shown to specifically interact with iron (III), compared with other cationic trace elements including potassium (I), sodium (I), calcium (II), chromium (III), zinc (II), cobalt (II), copper (II), magnesium (II), manganese (II), and molybdenum (VI). The quenching effect of iron (III) on the luminescence emission of N-butylamine functionalized graphene oxide layer was used to detect iron (III). The limit of detection (2.8 × 10(-6)  M) and limit of quantitation (2.9 × 10(-5)  M) were obtained under optimal conditions. Copyright © 2015 John Wiley & Sons, Ltd.

SP70-alpha-benzoin oxime chelating resin for preconcentration-separation of Pb(II), Cd(II), Co(II) and Cr(III) in environmental samples.

PubMed

Narin, Ibrahim; Surme, Yavuz; Bercin, Erdogan; Soylak, Mustafa

2007-06-25

In the presented work, alpha-benzoin oxime immobilized SP70 chelating resin was synthesized for separation and preconcentration of Pb(II), Cd(II), Co(II) and Cr(III). The optimization procedure for analytical parameters including pH, eluent type, flow rate, etc. was examined in order to gain quantitative recoveries of analyte ions. The effects of foreign ions on the recoveries of studied metal ions were also investigated. The detection limits (3sigma) were found to be 16.0, 4.2, 1.3, 2.4microgL(-1) for Pb, Cd, Co and Cr, respectively. The preconcentration factor was 75 for Pb, 100 for Cd, Co and Cr. The optimized method was validated with certified reference materials and successfully applied to the waters, crops and pharmaceutical samples with good results (recoveries greater than 95%, R.S.D. lower than 10%).

Relationship Between Tumor Gene Expression and Recurrence in Four Independent Studies of Patients With Stage II/III Colon Cancer Treated With Surgery Alone or Surgery Plus Adjuvant Fluorouracil Plus Leucovorin

PubMed Central

O'Connell, Michael J.; Lavery, Ian; Yothers, Greg; Paik, Soonmyung; Clark-Langone, Kim M.; Lopatin, Margarita; Watson, Drew; Baehner, Frederick L.; Shak, Steven; Baker, Joffre; Cowens, J. Wayne; Wolmark, Norman

2010-01-01

Purpose These studies were conducted to determine the relationship between quantitative tumor gene expression and risk of cancer recurrence in patients with stage II or III colon cancer treated with surgery alone or surgery plus fluorouracil (FU) and leucovorin (LV) to develop multigene algorithms to quantify the risk of recurrence as well as the likelihood of differential treatment benefit of FU/LV adjuvant chemotherapy for individual patients. Patients and Methods We performed quantitative reverse transcription polymerase chain reaction (RT-qPCR) on RNA extracted from fixed, paraffin-embedded (FPE) tumor blocks from patients with stage II or III colon cancer who were treated with surgery alone (n = 270 from National Surgical Adjuvant Breast and Bowel Project [NSABP] C-01/C-02 and n = 765 from Cleveland Clinic [CC]) or surgery plus FU/LV (n = 308 from NSABP C-04 and n = 508 from NSABP C-06). Overall, 761 candidate genes were studied in C-01/C-02 and C-04, and a subset of 375 genes was studied in CC/C-06. Results A combined analysis of the four studies identified 48 genes significantly associated with risk of recurrence and 66 genes significantly associated with FU/LV benefit (with four genes in common). Seven recurrence-risk genes, six FU/LV-benefit genes, and five reference genes were selected, and algorithms were developed to identify groups of patients with low, intermediate, and high likelihood of recurrence and benefit from FU/LV. Conclusion RT-qPCR of FPE colon cancer tissue applied to four large independent populations has been used to develop multigene algorithms for estimating recurrence risk and benefit from FU/LV. These algorithms are being independently validated, and their clinical utility is being evaluated in the Quick and Simple and Reliable (QUASAR) study. PMID:20679606

Biologic Determinants of Tumor Recurrence in Stage II Colon Cancer: Validation Study of the 12-Gene Recurrence Score in Cancer and Leukemia Group B (CALGB) 9581

PubMed Central

Venook, Alan P.; Niedzwiecki, Donna; Lopatin, Margarita; Ye, Xing; Lee, Mark; Friedman, Paula N.; Frankel, Wendy; Clark-Langone, Kim; Millward, Carl; Shak, Steven; Goldberg, Richard M.; Mahmoud, Najjia N.; Warren, Robert S.; Schilsky, Richard L.; Bertagnolli, Monica M.

2013-01-01

Purpose A greater understanding of the biology of tumor recurrence should improve adjuvant treatment decision making. We conducted a validation study of the 12-gene recurrence score (RS), a quantitative assay integrating stromal response and cell cycle gene expression, in tumor specimens from patients enrolled onto Cancer and Leukemia Group B (CALGB) 9581. Patients and Methods CALGB 9581 randomly assigned 1,713 patients with stage II colon cancer to treatment with edrecolomab or observation and found no survival difference. The analysis reported here included all patients with available tissue and recurrence (n = 162) and a random (approximately 1:3) selection of nonrecurring patients. RS was assessed in 690 formalin-fixed paraffin-embedded tumor samples with quantitative reverse transcriptase polymerase chain reaction by using prespecified genes and a previously validated algorithm. Association of RS and recurrence was analyzed by weighted Cox proportional hazards regression. Results Continuous RS was significantly associated with risk of recurrence (P = .013) as was mismatch repair (MMR) gene deficiency (P = .044). In multivariate analyses, RS was the strongest predictor of recurrence (P = .004), independent of T stage, MMR, number of nodes examined, grade, and lymphovascular invasion. In T3 MMR-intact (MMR-I) patients, prespecified low and high RS groups had average 5-year recurrence risks of 13% (95% CI, 10% to 16%) and 21% (95% CI, 16% to 26%), respectively. Conclusion The 12-gene RS predicts recurrence in stage II colon cancer in CALGB 9581. This is consistent with the importance of stromal response and cell cycle gene expression in colon tumor recurrence. RS appears to be most discerning for patients with T3 MMR-I tumors, although markers such as grade and lymphovascular invasion did not add value in this subset of patients. PMID:23530100

Relationship between tumor gene expression and recurrence in four independent studies of patients with stage II/III colon cancer treated with surgery alone or surgery plus adjuvant fluorouracil plus leucovorin.

PubMed

O'Connell, Michael J; Lavery, Ian; Yothers, Greg; Paik, Soonmyung; Clark-Langone, Kim M; Lopatin, Margarita; Watson, Drew; Baehner, Frederick L; Shak, Steven; Baker, Joffre; Cowens, J Wayne; Wolmark, Norman

2010-09-01

These studies were conducted to determine the relationship between quantitative tumor gene expression and risk of cancer recurrence in patients with stage II or III colon cancer treated with surgery alone or surgery plus fluorouracil (FU) and leucovorin (LV) to develop multigene algorithms to quantify the risk of recurrence as well as the likelihood of differential treatment benefit of FU/LV adjuvant chemotherapy for individual patients. We performed quantitative reverse transcription polymerase chain reaction (RT-qPCR) on RNA extracted from fixed, paraffin-embedded (FPE) tumor blocks from patients with stage II or III colon cancer who were treated with surgery alone (n = 270 from National Surgical Adjuvant Breast and Bowel Project [NSABP] C-01/C-02 and n = 765 from Cleveland Clinic [CC]) or surgery plus FU/LV (n = 308 from NSABP C-04 and n = 508 from NSABP C-06). Overall, 761 candidate genes were studied in C-01/C-02 and C-04, and a subset of 375 genes was studied in CC/C-06. A combined analysis of the four studies identified 48 genes significantly associated with risk of recurrence and 66 genes significantly associated with FU/LV benefit (with four genes in common). Seven recurrence-risk genes, six FU/LV-benefit genes, and five reference genes were selected, and algorithms were developed to identify groups of patients with low, intermediate, and high likelihood of recurrence and benefit from FU/LV. RT-qPCR of FPE colon cancer tissue applied to four large independent populations has been used to develop multigene algorithms for estimating recurrence risk and benefit from FU/LV. These algorithms are being independently validated, and their clinical utility is being evaluated in the Quick and Simple and Reliable (QUASAR) study.

[Analysis on 2011 quality control results on aerobic plate count of microbiology laboratories in China].

PubMed

Han, Haihong; Li, Ning; Li, Yepeng; Fu, Ping; Yu, Dongmin; Li Zhigang; Du, Chunming; Guo, Yunchang

2015-01-01

To test the aerobic plate count examining capability of microbiology laboratories, to ensure the accuracy and comparability of quantitative bacteria examination results, and to improve the quality of monitoring. The 4 different concentration aerobic plate count piece samples were prepared and noted as I, II, III and IV. After homogeneity and stability tests, the samples were delivered to monitoring institutions. The results of I, II, III samples were logarithmic transformed, and evaluated with Z-score method using the robust average and standard deviation. The results of IV samples were evaluated as "satisfactory" when reported as < 10 CFU/piece or as "not satisfactory" otherwise. Pearson χ2 test was used to analyze the ratio results. 309 monitoring institutions, which was 99.04% of the total number, reported their results. 271 institutions reported a satisfactory result, and the satisfactory rate was 87.70%. There was no statistical difference in satisfactory rates of I, II and III samples which were 81.52%, 88.30% and 91.40% respectively. The satisfactory rate of IV samples was 93.33%. There was no statistical difference in satisfactory rates between provincial and municipal CDC. The quality control program has provided scientific data that the aerobic plate count capability of the laboratories meets the requirements of monitoring tasks.

Comparative evaluation of serum C-reactive protein levels in chronic and aggressive periodontitis patients and association with periodontal disease severity.

PubMed

Goyal, Lata; Bey, Afshan; Gupta, N D; Sharma, Vivek Kumar

2014-10-01

C-reactive protein (CRP) is an acute-phase reactant and has been proved to be a significant predictor of future cardiovascular events. Recent studies have demonstrated a correlation between periodontitis and elevated CRP levels. However, most of the studies have focused on chronic periodontitis and very few studies are done in patients with aggressive periodontitis. The aim of this study was to determine and compare the relative levels of serum CRP in aggressive and chronic periodontitis patients. A total of 75 systemically healthy subjects were divided into three groups: Group I, nonperiodontitis subjects; group II, chronic generalized periodontitis patients and group III, generalized aggressive periodontitis patients. All participants were subjected to quantitative CRP analysis using enzyme-linked immunosorbent assay. Mean CRP levels were significantly greater in both group II and III as compared to group I and group III having greater level than group II. Furthermore, CRP levels positively correlated with the amount of periodontal destruction as measured by probing depth and clinical attachment loss. The present study indicates a positive correlation between CRP and periodontal disease severity with particular concern in younger individuals that could be a possible underlying pathway in the association between periodontal disease and the observed higher risk for cardiovascular disease in periodontitis patients.

Improved Reagents for Newborn Screening of Mucopolysaccharidosis Types I, II, and VI by Tandem Mass Spectrometry

PubMed Central

2015-01-01

Tandem mass spectrometry for the multiplex and quantitative analysis of enzyme activities in dried blood spots on newborn screening cards has emerged as a powerful technique for early assessment of lysosomal storage diseases. Here we report the design and process-scale synthesis of substrates for the enzymes α-l-iduronidase, iduronate-2-sulfatase, and N-acetylgalactosamine-4-sulfatase that are used for newborn screening of mucopolysaccharidosis types I, II, and VI. The products contain a bisamide unit that is hypothesized to readily protonate in the gas phase, which improves detection sensitivity by tandem mass spectrometry. The products contain a benzoyl group, which provides a useful site for inexpensive deuteration, thus facilitating the preparation of internal standards for the accurate quantification of enzymatic products. Finally, the reagents are designed with ease of synthesis in mind, thus permitting scale-up preparation to support worldwide newborn screening of lysosomal storage diseases. The new reagents provide the most sensitive assay for the three lysosomal enzymes reported to date as shown by their performance in reactions using dried blood spots as the enzyme source. Also, the ratio of assay signal to that measured in the absence of blood (background) is superior to all previously reported mucopolysaccharidosis types I, II, and VI assays. PMID:24694010

Intratumor partitioning and texture analysis of dynamic contrast-enhanced (DCE)-MRI identifies relevant tumor subregions to predict pathological response of breast cancer to neoadjuvant chemotherapy.

PubMed

Wu, Jia; Gong, Guanghua; Cui, Yi; Li, Ruijiang

2016-11-01

To predict pathological response of breast cancer to neoadjuvant chemotherapy (NAC) based on quantitative, multiregion analysis of dynamic contrast enhancement magnetic resonance imaging (DCE-MRI). In this Institutional Review Board-approved study, 35 patients diagnosed with stage II/III breast cancer were retrospectively investigated using 3T DCE-MR images acquired before and after the first cycle of NAC. First, principal component analysis (PCA) was used to reduce the dimensionality of the DCE-MRI data with high temporal resolution. We then partitioned the whole tumor into multiple subregions using k-means clustering based on the PCA-defined eigenmaps. Within each tumor subregion, we extracted four quantitative Haralick texture features based on the gray-level co-occurrence matrix (GLCM). The change in texture features in each tumor subregion between pre- and during-NAC was used to predict pathological complete response after NAC. Three tumor subregions were identified through clustering, each with distinct enhancement characteristics. In univariate analysis, all imaging predictors except one extracted from the tumor subregion associated with fast washout were statistically significant (P < 0.05) after correcting for multiple testing, with area under the receiver operating characteristic (ROC) curve (AUC) or AUCs between 0.75 and 0.80. In multivariate analysis, the proposed imaging predictors achieved an AUC of 0.79 (P = 0.002) in leave-one-out cross-validation. This improved upon conventional imaging predictors such as tumor volume (AUC = 0.53) and texture features based on whole-tumor analysis (AUC = 0.65). The heterogeneity of the tumor subregion associated with fast washout on DCE-MRI predicted pathological response to NAC in breast cancer. J. Magn. Reson. Imaging 2016;44:1107-1115. © 2016 International Society for Magnetic Resonance in Medicine.

[ICF-Checklist to Evaluate Inclusion of Elderlies with Intellectual Disability - Psychometric Properties].

PubMed

Queri, Silvia; Eggart, Michael; Wendel, Maren; Peter, Ulrike

2017-11-28

Background An instrument should have been developed to measure participation as one possible criterion to evaluate inclusion of elderly people with intellectual disability. The ICF was utilized, because participation is one part of health related functioning, respectively disability. Furthermore ICF includes environmental factors (contextual factors) and attaches them an essentially influence on health related functioning, in particular on participation. Thus ICF Checklist additionally identifies environmental barriers for elimination. Methodology A linking process with VINELAND-II yielded 138 ICF items for the Checklist. The sample consists of 50 persons with a light or moderate intellectual disability. Two-thirds are female and the average age is 68. They were directly asked about their perceived quality of life. Additionally, proxy interviews were carried out with responsible staff members concerning necessary support and behavioral deviances. The ICF Checklist was administered twice, once (t2) the current staff member should rate health related functioning at the given time and in addition, a staff member who knows the person at least 10 years before (t1) should rate the former functioning. Content validity was investigated with factor analysis and criterion validity with correlational analysis related to supports need, behavioral deviances and perceived quality of life. Quantitative analysis was validated by qualitative content analysis of patient documentation. Results Factor analysis shows logical variable clusters across the extracted factors but neither interpretable factors. The Checklist is reliable, valid related to the chosen criterions and shows the expected age-related shifts. Qualitative analysis corresponds with quantitative data. Consequences/Conclusion ICF Checklist is appropriate to manage and evaluate patient-centered care. © Georg Thieme Verlag KG Stuttgart · New York.

Compound Specific Hydrogen Isotope Composition of Type II and III Kerogen Extracted by Pyrolysis-GC-MS-IRMS

NASA Technical Reports Server (NTRS)

Socki, Richard A.; Pernia, Denet; Evans, Michael; Fu, Qi; Bissada, Kadry K.; Curiale, Joseph A.; Niles, Paul B.

2013-01-01

The use of Hydrogen (H) isotopes in understanding oil and gas resource plays is in its infancy. Described here is a technique for H isotope analysis of organic compounds pyrolyzed from oil and gas shale-derived kerogen. Application of this technique will progress our understanding. This work complements that of Pernia et al. (2013, this meeting) by providing a novel method for the H isotope analysis of specific compounds in the characterization of kerogen extracted by analytically diverse techniques. Hydrogen isotope analyses were carried out entirely "on-line" utilizing a CDS 5000 Pyroprobe connected to a Thermo Trace GC Ultra interfaced with a Thermo MAT 253 IRMS. Also, a split of GC-separated products was sent to a DSQ II quadrupole MS to make semi-quantitative compositional measurements of the extracted compounds. Kerogen samples from five different basins (type II and III) were dehydrated (heated to 80 C overnight in vacuum) and analyzed for their H isotope compositions by Pyrolysis-GC-MS-TC-IRMS. This technique takes pyrolysis products separated via GC and reacts them in a high temperature conversion furnace (1450 C) which quantitatively forms H2, following a modified method of Burgoyne and Hayes, (1998, Anal. Chem., 70, 5136-5141). Samples ranging from approximately 0.5 to 1.0mg in size, were pyrolyzed at 800 C for 30s. Compounds were separated on a Poraplot Q GC column. Hydrogen isotope data from all kerogen samples typically show enrichment in D from low to high molecular weight compounds. Water (H2O) average deltaD = -215.2 (V-SMOW), ranging from -271.8 for the Marcellus Shale to -51.9 for the Polish Shale. Higher molecular weight compounds like toluene (C7H8) have an average deltaD of -89.7 0/00, ranging from -156.0 for the Barnett Shale to -50.0 for the Monterey Shale. We interpret these data as representative of potential H isotope exchange between hydrocarbons and sediment pore water during formation within each basin. Since hydrocarbon H isotopes readily exchange with water, these data may provide some useful information on gas-water or oil-water interaction in resource plays, and further as a possible indicator of paleo-environmental conditions. Alternatively, our data may be an indication of H isotope exchange with water and/or acid during the kerogen isolation process. Either of these interpretations will prove useful when deciphering H isotope data derived from kerogen analysis. More experiments are planned to discern these two or other possible scenarios.

Determination of Serotonin and Dopamine Metabolites in Human Brain Microdialysis and Cerebrospinal Fluid Samples by UPLC-MS/MS: Discovery of Intact Glucuronide and Sulfate Conjugates

PubMed Central

Suominen, Tina; Uutela, Päivi; Ketola, Raimo A.; Bergquist, Jonas; Hillered, Lars; Finel, Moshe; Zhang, Hongbo; Laakso, Aki; Kostiainen, Risto

2013-01-01

An UPLC-MS/MS method was developed for the determination of serotonin (5-HT), dopamine (DA), their phase I metabolites 5-HIAA, DOPAC and HVA, and their sulfate and glucuronide conjugates in human brain microdialysis samples obtained from two patients with acute brain injuries, ventricular cerebrospinal fluid (CSF) samples obtained from four patients with obstructive hydrocephalus, and a lumbar CSF sample pooled mainly from patients undergoing spinal anesthesia in preparation for orthopedic surgery. The method was validated by determining the limits of detection and quantification, linearity, repeatability and specificity. The direct method enabled the analysis of the intact phase II metabolites of 5-HT and DA, without hydrolysis of the conjugates. The method also enabled the analysis of the regioisomers of the conjugates, and several intact glucuronide and sulfate conjugates were identified and quantified for the first time in the human brain microdialysis and CSF samples. We were able to show the presence of 5-HIAA sulfate, and that dopamine-3-O-sulfate predominates over dopamine-4-O-sulfate in the human brain. The quantitative results suggest that sulfonation is a more important phase II metabolism pathway than glucuronidation in the human brain. PMID:23826355

Impact of Depression, Fatigue, and Global Measure of Cortical Volume on Cognitive Impairment in Multiple Sclerosis

PubMed Central

De Cola, Maria Cristina; D'Aleo, Giangaetano; Sessa, Edoardo; Marino, Silvia

2015-01-01

Objective. To investigate the influence of demographic and clinical variables, such as depression, fatigue, and quantitative MRI marker on cognitive performances in a sample of patients affected by multiple sclerosis (MS). Methods. 60 MS patients (52 relapsing remitting and 8 primary progressive) underwent neuropsychological assessments using Rao's Brief Repeatable Battery of Neuropsychological Tests (BRB-N), the Beck Depression Inventory-second edition (BDI-II), and the Fatigue Severity Scale (FSS). We performed magnetic resonance imaging to all subjects using a 3 T scanner and obtained tissue-specific volumes (normalized brain volume and cortical brain volume). We used Student's t-test to compare depressed and nondepressed MS patients. Finally, we performed a multivariate regression analysis in order to assess possible predictors of patients' cognitive outcome among demographic and clinical variables. Results. 27.12% of the sample (16/59) was cognitively impaired, especially in tasks requiring attention and information processing speed. From between group comparison, we find that depressed patients had worse performances on BRB-N score, greater disability and disease duration, and brain volume decrease. According to multiple regression analysis, the BDI-II score was a significant predictor for most of the neuropsychological tests. Conclusions. Our findings suggest that the presence of depressive symptoms is an important determinant of cognitive performance in MS patients. PMID:25861633

Prevalence of overweight and obesity among children and adolescents with intellectual disabilities: a systematic review and meta-analysis.

PubMed

Maïano, C; Hue, O; Morin, A J S; Moullec, G

2016-07-01

Although there have been numerous studies examining the prevalence of overweight and obesity among children and adolescents with intellectual disabilities, they have not yet been integrated and synthesized through a systematic quantitative review process. The purpose of this systematic review and meta-analysis was to determine: (i) the prevalence of overweight/obesity among children and adolescents with intellectual disabilities; (ii) the sources of heterogeneity in studies reporting the prevalence of overweight/obesity in this population; and (iii) the risk of overweight/obesity in this population compared with their typically developing peers. A systematic literature search was performed and 16 studies, published between 1985 and 2015, met the inclusion criteria. The resulting pooled prevalence estimates for overweight, overweight-obesity and obesity were respectively: (i) 15%, 30%, and 13%, in children; and (ii) 18%, 33%, and 15% in adolescents. Subgroup analyses showed significant variations in the pooled prevalence estimates as a function of geographical region, recruitment setting, additional diagnoses, and norms used to define overweight or obesity. The findings also showed adolescents with intellectual disabilities to be respectively 1.54 and 1.80 times more at risk of overweight-obesity and obesity than typically developing adolescents. Unfortunately, no such comparison is available for children. © 2016 World Obesity. © 2016 World Obesity.

Selection of reference genes for expression studies with fish myogenic cell cultures.

PubMed

Bower, Neil I; Johnston, Ian A

2009-08-10

Relatively few studies have used cell culture systems to investigate gene expression and the regulation of myogenesis in fish. To produce robust data from quantitative real-time PCR mRNA levels need to be normalised using internal reference genes which have stable expression across all experimental samples. We have investigated the expression of eight candidate genes to identify suitable reference genes for use in primary myogenic cell cultures from Atlantic salmon (Salmo salar L.). The software analysis packages geNorm, Normfinder and Best keeper were used to rank genes according to their stability across 42 samples during the course of myogenic differentiation. Initial results showed several of the candidate genes exhibited stable expression throughout myogenic culture while Sdha was identified as the least stable gene. Further analysis with geNorm, Normfinder and Bestkeeper identified Ef1alpha, Hprt1, Ppia and RNApolII as stably expressed. Comparison of data normalised with the geometric average obtained from combinations of any three of these genes showed no significant differences, indicating that any combination of these genes is valid. The geometric average of any three of Hprt1, Ef1alpha, Ppia and RNApolII is suitable for normalisation of gene expression data in primary myogenic cultures from Atlantic salmon.

Gender differences in temporomandibular disorders in adult populational studies: a systematic review and meta-analysis.

PubMed

Bueno, Caroline H; Pereira, Duziene D; Pattussi, Marcos P; Grossi, Patrícia K; Grossi, Márcio L

2018-05-31

The objective of this study was to systematically evaluate gender differences in the prevalence of TMD.A systematic review was performed in PUBMED,EMBASE,WEB OF SCIENCE and LILACS in duplicate by two independent reviewers. The inclusion criteria were cross-sectional studies that reported the prevalence of TMD for men and women and that used the RDC/TMD Axis I group diagnostic criteria:(group I=muscle disorders; group II=disc displacements; group III=arthralgias/arthritis/arthrosis).To be eligible for inclusion, studies must include adult individuals (>18 years) from a non-clinical population (i.e.,without pre-diagnosis of TMD);in other words, from population-based studies.There were no restrictions on the year and language of publication. The quality of the articles was assessed by an adapted version of the Newcastle-Ottawa Scale(NOS), and the publication bias was assessed by a funnel plot graph. Data were quantitatively analyzed by meta-analysis using odds ratio (OR) as the measure effect. The electronic search retrieved a total of 6,104 articles, of which 112 articles were selected for full-text reading according to the eligibility criteria. By means of manual search, one study was retrieved. Five articles were selected for meta-analysis with a combined sample of 2,518 subjects.Women had higher prevalence of TMD in all RDC/TMD diagnostic groups. The meta-analysis yielded the following results:a) OR=2.24 for global TMD (groups I, II and III combined), b) OR=2.09 for group I, c) OR=1.6 for group II,and d) OR=2.08 for group III. The importance of gender in the development of TMD has been demonstrated,with a two-times greater risk for women to develop it as compared to men. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Methylation of WNT target genes AXIN2 and DKK1 as robust biomarkers for recurrence prediction in stage II colon cancer

PubMed Central

Kandimalla, R; Linnekamp, J F; van Hooff, S; Castells, A; Llor, X; Andreu, M; Jover, R; Goel, A; Medema, J P

2017-01-01

Stage II colon cancer (CC) still remains a clinical challenge with patient stratification for adjuvant therapy (AT) largely relying on clinical parameters. Prognostic biomarkers are urgently needed for better stratification. Previously, we have shown that WNT target genes AXIN2, DKK1, APCDD1, ASCL2 and LGR5 are silenced by DNA methylation and could serve as prognostic markers in stage II CC patients using methylation-specific PCR. Here, we have extended our discovery cohort AMC90-AJCC-II (N=65) and methylation was analyzed by quantitative pyrosequencing. Subsequently, we validated the results in an independent EPICOLON1 CC cohort (N=79). Methylation of WNT target genes is negatively correlated to mRNA expression. A combination of AXIN2 and DKK1 methylation significantly predicted recurrences in univariate (area under the curve (AUC)=0.83, confidence interval (CI): 0.72–0.94, P<0.0001) analysis in stage II microsatellite stable (MSS) CC patients. This two marker combination showed an AUC of 0.80 (CI: 0.68–0.91, P<0.0001) in the EPICOLON1 validation cohort. Multivariate analysis in the Academic Medical Center (AMC) cohort revealed that both WNT target gene methylation and consensus molecular subtype 4 (CMS4) are significantly associated with poor recurrence-free survival (hazard ratio (HR)methylation: 3.84, 95% CI: 1.14–12.43; HRCMS4: 3.73, 95% CI: 1.22–11.48). CMS4 subtype tumors with WNT target methylation showed worse prognosis. Combining WNT target gene methylation and CMS4 subtype lead to an AUC of 0.89 (0.791–0.982, P<0.0001) for recurrence prediction. Notably, we observed that methylation of DKK1 is high in BRAF mutant and CIMP (CpG island methylator phenotype)-positive cancers, whereas AXIN2 methylation appears to be associated with CMS4. Methylation of AXIN2 and DKK1 were found to be robust markers for recurrence prediction in stage II MSS CC patients. Further validation of these findings in a randomized and prospective manner could pave a way to identify poor prognosis patients of stage II CC for AT. PMID:28368388

Influence of Axisymmetrically Deformed Explosions in Type II Supernovae on the Reproduction of the Solar System Abundances

NASA Astrophysics Data System (ADS)

Nagataki, Shigehiro

1999-01-01

We have tried to reproduce the solar system abundances using the nucleosynthesis products of Type Ia and Type II supernovae. In particular, we examined the effects of axisymmetrically deformed explosions in Type II supernovae. 44Ca and 47,48Ti are enhanced considerably in axisymmetrically deformed explosion models because of the active alpha-rich freezeout. The enhancement of nuclei around A=45 is a welcome result since it solves the problem of the nuclei shortage. Moreover, 59Co, 63,65Cu, and 66Zn are enhanced enough to reproduce the solar system abundances. The enhancement of Cu and Zn means the possibility that these nuclei, which have been said to be produced by the slow process, can be synthesized fairly well during the explosive nucleosynthesis. To discuss their origin quantitatively, the position of the mass cut is a very important parameter that is very difficult to determine numerically at present. We also stress that an axisymmetrically deformed explosion of Type II supernovae of the degree that is considered in this analysis is not excluded by the results of calculations of explosive nucleosynthesis, that is, the nucleosynthesis products are not extremely disturbed and the solar system abundances can be reproduced fairly well by the axisymmetrically deformed explosion models. This conclusion will be good for the theory of core collapse including the rotation of an iron core, magnetic field, and axisymmetrically modified neutrino radiation from a rotating protoneutron star, which possibly can cause an axisymmetrically deformed explosion.

Clathrochelates meet phosphorus. New thio- and phosphorylation reactions of an iron(II) dichloroclathrochelate precursor and preparation of its first phosphorus(III)-containing macrobicyclic derivative.

PubMed

Artyushin, Oleg I; Matveeva, Ekaterina V; Vologzhanina, Anna V; Voloshin, Yan Z

2016-03-28

Phosphorylation reactions of an iron(II) dichloroclathrochelate FeBd2(Cl2Gm)(BF)2 (where Bd(2-) and Cl2Gm(2-) are α-benzildioxime and dichloroglyoxime dianions, respectively) with diphenylphosphine oxide and diethyl thiophosphite were performed under phase-transfer conditions. In the case of diethyl thiophosphite as a P-nucleophile, the best yields were obtained in the dichloromethane-50% NaOH aqueous solution-5 mol% triethylbenzylammonium chloride (TEBAC) system. The use of different molar ratios of a macrobicycle precursor and this thiophosphorylating agent allowed us to obtain both the mono- and the diphosphorylated cage complexes. Nucleophilic substitution with diphenylphosphine oxide was performed in the K2CO3-acetonitrile-5 mol% TEBAC system, giving only the corresponding monophosphorylated iron(II) complex in high yield even in the presence of an excess of this P-nucleophile. The phosphorus(v)-containing clathrochelate product was reduced with an excess of silicoform to give an iron(II) macrobicycle with an inherent diphenylphosphine group in an almost quantitative yield, which was then characterized by (31)P{(1)H} NMR and single-crystal X-ray diffraction; it easily undergoes re-oxidation to the initial clathrochelate. The synthesized phosphorus(v)-containing cage complexes were characterized using elemental analysis, MALDI-TOF mass, IR, UV-Vis, (1)H, (11)B, (13)C{(1)H}, (19)F{(1)H} and (31)P{(1)H} NMR spectra, and by single-crystal X-ray diffraction.

The mechanism of opiorphin-induced experimental priapism in rats involves activation of the polyamine synthetic pathway.

PubMed

Kanika, Nirmala Devi; Tar, Moses; Tong, Yuehong; Kuppam, Dwaraka Srinivasa Rao; Melman, Arnold; Davies, Kelvin Paul

2009-10-01

Intracorporal injection of plasmids encoding opiorphins into retired breeder rats can result in animals developing a priapic-like condition. Microarray analysis demonstrated that following intracorporal gene transfer of plasmids expressing opiorphins the most significantly upregulated gene in corporal tissue was the ornithine decarboxylase gene (ODC). Quantitative RT-PCR confirmed the upregulation of ODC, as well as other genes involved in polyamine synthesis, such as arginase-I and -II, polyamine oxidase, spermidine synthase, spermidine acetyltransferase (SAT), and S-adenosylmethionine decarboxylase. Western blot analysis demonstrated upregulation of arginase-I and -II, ODC, and SAT at the protein level. Levels of the polyamine putrescine were upregulated in animals treated with opiorphin-expressing plasmids compared with controls. A direct role for the upregulation of polyamine synthesis in the development of the priapic-like condition was supported by the observation that the ODC inhibitor 1,3-diaminopropane, when added to the drinking water of animals treated with plasmids expressing opiorphins, prevented experimental priapism. We also demonstrate that in sickle cell mice, another model of priapism, there is increased expression of the mouse opiorphin homologue in corporal tissue compared with the background strain at a life stage prior to evidence of priapism. At a life stage when there is onset of priapism, there is increased expression of the enzymes involved in polyamine synthesis (ODC and arginase-I and -II). Our results suggest that the upregulation of enzymes involved in the polyamine synthetic pathway may play a role in the development of experimental priapism and represent a target for the prevention of priapism.

The mechanism of opiorphin-induced experimental priapism in rats involves activation of the polyamine synthetic pathway

PubMed Central

Kanika, Nirmala Devi; Tar, Moses; Tong, Yuehong; Kuppam, Dwaraka Srinivasa Rao; Melman, Arnold

2009-01-01

Intracorporal injection of plasmids encoding opiorphins into retired breeder rats can result in animals developing a priapic-like condition. Microarray analysis demonstrated that following intracorporal gene transfer of plasmids expressing opiorphins the most significantly upregulated gene in corporal tissue was the ornithine decarboxylase gene (ODC). Quantitative RT-PCR confirmed the upregulation of ODC, as well as other genes involved in polyamine synthesis, such as arginase-I and -II, polyamine oxidase, spermidine synthase, spermidine acetyltransferase (SAT), and S-adenosylmethionine decarboxylase. Western blot analysis demonstrated upregulation of arginase-I and -II, ODC, and SAT at the protein level. Levels of the polyamine putrescine were upregulated in animals treated with opiorphin-expressing plasmids compared with controls. A direct role for the upregulation of polyamine synthesis in the development of the priapic-like condition was supported by the observation that the ODC inhibitor 1,3-diaminopropane, when added to the drinking water of animals treated with plasmids expressing opiorphins, prevented experimental priapism. We also demonstrate that in sickle cell mice, another model of priapism, there is increased expression of the mouse opiorphin homologue in corporal tissue compared with the background strain at a life stage prior to evidence of priapism. At a life stage when there is onset of priapism, there is increased expression of the enzymes involved in polyamine synthesis (ODC and arginase-I and -II). Our results suggest that the upregulation of enzymes involved in the polyamine synthetic pathway may play a role in the development of experimental priapism and represent a target for the prevention of priapism. PMID:19657052

Common Distribution Patterns of Marsupials Related to Physiographical Diversity in Venezuela

PubMed Central

Ventura, Jacint; Bagaria, Guillem; Sans-Fuentes, Maria Assumpció; Pérez-Hernández, Roger

2014-01-01

The aim of this study is to identify significant biotic regions (groups of areas with similar biotas) and biotic elements (groups of taxa with similar distributions) for the marsupial fauna in a part of northern South America using physiographical areas as Operational Geographical Units (OGUs). We considered Venezuela a good model to elucidate this issue because of its high diversity in landscapes and the relatively vast amount of information available on the geographical distribution of marsupial species. Based on the presence-absence of 33 species in 15 physiographical sub-regions (OGUs) we identified Operational Biogeographical Units (OBUs) and chorotypes using a quantitative analysis that tested statistical significance of the resulting groups. Altitudinal and/or climatic trends in the OBUs and chorotypes were studied using a redundancy analysis. The classification method revealed four OBUs. Strong biotic boundaries separated: i) the xerophytic zone of the Continental coast (OBU I); ii) the sub-regions north of the Orinoco River (OBU III and IV); and those south to the river (OBU II). Eleven chorotypes were identified, four of which included a single species with a restricted geographic distribution. As for the other chorotypes, three main common distribution patterns have been inferred: i) species from the Llanos and/or distributed south of the Orinoco River; ii) species exclusively from the Andes; and iii) species that either occur exclusively north of the Orinoco River or that show a wide distribution throughout Venezuela. Mean altitude, evapotranspiration and precipitation of the driest month, and temperature range allowed us to characterize environmentally most of the OBUs and chorotypes obtained. PMID:24806452

Evaluation of the internal and external biofidelity of current rear impact ATDs to response targets developed from moderate-speed rear impacts of PMHS.

PubMed

Moorhouse, Kevin; Donnelly, Bruce; Kang, Yun-Seok; Bolte, John H; Herriott, Rodney

2012-10-01

The goal of this study is to evaluate both the internal and external biofidelity of existing rear impact anthropomorphic test devices (BioRID II, RID3D, Hybrid III 50th) in two moderate-speed rear impact sled test conditions (8.5g, 17 km/h; 10.5g, 24 km/h) by quantitatively comparing the ATD responses to biomechanical response targets developed from PMHS testing in a corresponding study. The ATDs and PMHS were tested in an experimental seat system that is capable of simulating the dynamic seat back rotation response of production seats. The experimental seat contains a total of fourteen load cells installed such that external loads from the ATDs and PMHS can be measured to evaluate external biofidelity. The PMHS were instrumented to correspond to the instrumentation contained in the ATDs so that direct comparison between ATDs and PMHS could be made to evaluate internal biofidelity. The NHTSA Biofidelity Ranking system was used to quantitatively evaluate the biofidelity of the ATDs and an additional tool was introduced and utilized which allows for the biofidelity score to be partitioned into components of amplitude, phase, and shape. For internal biofidelity, the BioRID II and RID3D were more biofidelic than the Hybrid III in the 17 km/h test, and the BioRID II was most biofidelic in the 24 km/h test. For external biofidelity, the BioRID II was most biofidelic in the 17 km/h test, while both the BioRID II and the RID3D were more biofidelic than the Hybrid III in the 24 km/h test. Overall, the BioRID II demonstrated the best biofidelity in both the 17 km/h and 24 km/h tests.

Quasi-aromatic Möbius Metal Chelates.

PubMed

Mahmoudi, Ghodrat; Afkhami, Farhad A; Castiñeiras, Alfonso; García-Santos, Isabel; Gurbanov, Atash; Zubkov, Fedor I; Mitoraj, Mariusz P; Kukułka, Mercedes; Sagan, Filip; Szczepanik, Dariusz W; Konyaeva, Irina A; Safin, Damir A

2018-04-16

We report the design as well as structural and spectroscopic characterizations of two new coordination compounds obtained from Cd(NO 3 ) 2 ·4H 2 O and polydentate ligands, benzilbis(pyridin-2-yl)methylidenehydrazone (L I ) and benzilbis(acetylpyridin-2-yl)methylidenehydrazone (L II ), in a mixture with two equivalents of NH 4 NCS in MeOH, namely [Cd(SCN)(NCS)(L I )(MeOH)] (1) and [Cd(NCS) 2 (L II )(MeOH)] (2). Both L I and L II are bound via two pyridyl-imine units yielding a tetradentate coordination mode giving rise to the 12 π electron chelate ring. It has been determined for the first time (qualitatively and quantitatively), using the EDDB electron population-based method, the HOMA index, and the ETS-NOCV charge and energy decomposition scheme, that the chelate ring containing Cd II can be classified as a quasi-aromatic Möbius motif. Notably, using the methyl-containing ligand L II controls the exclusive presence of the NCS - connected with the Cd II atom (structure 2), while applying L I allows us to simultaneously coordinate NCS - and SCN - ligands (structure 1). Both systems are stabilized mostly by hydrogen bonding, C-H···π interactions, aromatic π···π stacking, and dihydrogen C-H···H-C bonds. The optical properties have been investigated by diffused reflectance spectroscopy as well as molecular and periodic DFT/TD-DFT calculations. The DFT-based ETS-NOCV analysis as well as periodic calculations led us to conclude that the monomers which constitute the obtained chelates are extremely strongly bonded to each other, and the calculated interaction energies are found to be in the regime of strong covalent connections. Intramolecular van der Waals dispersion forces, due to the large size of L I and L II , appeared to significantly stabilize these systems as well as amplify the aromaticity phenomenon.

Comprehensive Genomic Analysis and Expression Profiling of the NOX Gene Families under Abiotic Stresses and Hormones in Plants.

PubMed

Chang, Yan-Li; Li, Wen-Yan; Miao, Hai; Yang, Shuai-Qi; Li, Ri; Wang, Xiang; Li, Wen-Qiang; Chen, Kun-Ming

2016-02-23

Plasma membrane NADPH oxidases (NOXs) are key producers of reactive oxygen species under both normal and stress conditions in plants and they form functional subfamilies. Studies of these subfamilies indicated that they show considerable evolutionary selection. We performed a comparative genomic analysis that identified 50 ferric reduction oxidases (FRO) and 77 NOX gene homologs from 20 species representing the eight major plant lineages within the supergroup Plantae: glaucophytes, rhodophytes, chlorophytes, bryophytes, lycophytes, gymnosperms, monocots, and eudicots. Phylogenetic and structural analysis classified these FRO and NOX genes into four well-conserved groups represented as NOX, FRO I, FRO II, and FRO III. Further analysis of NOXs of phylogenetic and exon/intron structures showed that single intron loss and gain had occurred, yielding the diversified gene structures during the evolution of NOXs family genes and which were classified into four conserved subfamilies which are represented as Sub.I, Sub.II, Sub.III, and Sub.IV. Additionally, both available global microarray data analysis and quantitative real-time PCR experiments revealed that the NOX genes in Arabidopsis and rice (Oryza sativa) have different expression patterns in different developmental stages, various abiotic stresses and hormone treatments. Finally, coexpression network analysis of NOX genes in Arabidopsis and rice revealed that NOXs have significantly correlated expression profiles with genes which are involved in plants metabolic and resistance progresses. All these results suggest that NOX family underscores the functional diversity and divergence in plants. This finding will facilitate further studies of the NOX family and provide valuable information for functional validation of this family in plants. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Quantitative methylene blue decolourisation assays as rapid screening tools for assessing the efficiency of catalytic reactions.

PubMed

Kruid, Jan; Fogel, Ronen; Limson, Janice Leigh

2017-05-01

Identifying the most efficient oxidation process to achieve maximum removal of a target pollutant compound forms the subject of much research. There exists a need to develop rapid screening tools to support research in this area. In this work we report on the development of a quantitative assay as a means for identifying catalysts capable of decolourising methylene blue through the generation of oxidising species from hydrogen peroxide. Here, a previously described methylene blue test strip method was repurposed as a quantitative, aqueous-based spectrophotometric assay. From amongst a selection of metal salts and metallophthalocyanine complexes, monitoring of the decolourisation of the cationic dye methylene blue (via Fenton-like and non-Fenton oxidation reactions) by the assay identified the following to be suitable oxidation catalysts: CuSO 4 (a Fenton-like catalyst), iron(II)phthalocyanine (a non-Fenton oxidation catalyst), as well as manganese(II) phthalocyanine. The applicability of the method was examined for the removal of bisphenol A (BPA), as measured by HPLC, during parallel oxidation experiments. The order of catalytic activity was identified as FePc > MnPc > CuSO 4 for both BPA and MB. The quantitative MB decolourisation assay may offer a rapid method for screening a wide range of potential catalysts for oxidation processes. Copyright © 2017 Elsevier Ltd. All rights reserved.

PROTICdb: a web-based application to store, track, query, and compare plant proteome data.

PubMed

Ferry-Dumazet, Hélène; Houel, Gwenn; Montalent, Pierre; Moreau, Luc; Langella, Olivier; Negroni, Luc; Vincent, Delphine; Lalanne, Céline; de Daruvar, Antoine; Plomion, Christophe; Zivy, Michel; Joets, Johann

2005-05-01

PROTICdb is a web-based application, mainly designed to store and analyze plant proteome data obtained by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and mass spectrometry (MS). The purposes of PROTICdb are (i) to store, track, and query information related to proteomic experiments, i.e., from tissue sampling to protein identification and quantitative measurements, and (ii) to integrate information from the user's own expertise and other sources into a knowledge base, used to support data interpretation (e.g., for the determination of allelic variants or products of post-translational modifications). Data insertion into the relational database of PROTICdb is achieved either by uploading outputs of image analysis and MS identification software, or by filling web forms. 2-D PAGE annotated maps can be displayed, queried, and compared through a graphical interface. Links to external databases are also available. Quantitative data can be easily exported in a tabulated format for statistical analyses. PROTICdb is based on the Oracle or the PostgreSQL Database Management System and is freely available upon request at the following URL: http://moulon.inra.fr/ bioinfo/PROTICdb.

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA

PubMed Central

2010-01-01

Background In recent years, the number of available RNA structures has rapidly grown reflecting the increased interest on RNA biology. Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in RNA. Results Here we introduce an all-against-all sequence- and three-dimensional (3D) structure-based comparison of a representative set of RNA structures, which have allowed us to quantitatively confirm that: (i) there is a measurable relationship between sequence and structure conservation that weakens for alignments resulting in below 60% sequence identity, (ii) evolution tends to conserve more RNA structure than sequence, and (iii) there is a twilight zone for RNA homology detection. Discussion The computational analysis here presented quantitatively describes the relationship between sequence and structure for RNA molecules and defines a twilight zone region for detecting RNA homology. Our work could represent the theoretical basis and limitations for future developments in comparative RNA 3D structure prediction. PMID:20550657

Quantitative analysis of chromosome condensation in fission yeast.

PubMed

Petrova, Boryana; Dehler, Sascha; Kruitwagen, Tom; Hériché, Jean-Karim; Miura, Kota; Haering, Christian H

2013-03-01

Chromosomes undergo extensive conformational rearrangements in preparation for their segregation during cell divisions. Insights into the molecular mechanisms behind this still poorly understood condensation process require the development of new approaches to quantitatively assess chromosome formation in vivo. In this study, we present a live-cell microscopy-based chromosome condensation assay in the fission yeast Schizosaccharomyces pombe. By automatically tracking the three-dimensional distance changes between fluorescently marked chromosome loci at high temporal and spatial resolution, we analyze chromosome condensation during mitosis and meiosis and deduct defined parameters to describe condensation dynamics. We demonstrate that this method can determine the contributions of condensin, topoisomerase II, and Aurora kinase to mitotic chromosome condensation. We furthermore show that the assay can identify proteins required for mitotic chromosome formation de novo by isolating mutants in condensin, DNA polymerase ε, and F-box DNA helicase I that are specifically defective in pro-/metaphase condensation. Thus, the chromosome condensation assay provides a direct and sensitive system for the discovery and characterization of components of the chromosome condensation machinery in a genetically tractable eukaryote.

Quantitative Analysis of Chromosome Condensation in Fission Yeast

PubMed Central

Petrova, Boryana; Dehler, Sascha; Kruitwagen, Tom; Hériché, Jean-Karim; Miura, Kota

2013-01-01

Chromosomes undergo extensive conformational rearrangements in preparation for their segregation during cell divisions. Insights into the molecular mechanisms behind this still poorly understood condensation process require the development of new approaches to quantitatively assess chromosome formation in vivo. In this study, we present a live-cell microscopy-based chromosome condensation assay in the fission yeast Schizosaccharomyces pombe. By automatically tracking the three-dimensional distance changes between fluorescently marked chromosome loci at high temporal and spatial resolution, we analyze chromosome condensation during mitosis and meiosis and deduct defined parameters to describe condensation dynamics. We demonstrate that this method can determine the contributions of condensin, topoisomerase II, and Aurora kinase to mitotic chromosome condensation. We furthermore show that the assay can identify proteins required for mitotic chromosome formation de novo by isolating mutants in condensin, DNA polymerase ε, and F-box DNA helicase I that are specifically defective in pro-/metaphase condensation. Thus, the chromosome condensation assay provides a direct and sensitive system for the discovery and characterization of components of the chromosome condensation machinery in a genetically tractable eukaryote. PMID:23263988

Full magnetization process of 3d-4f hard magnetic materials in ultrahigh magnetic fields (an example: RFe11Ti)

NASA Astrophysics Data System (ADS)

Kuz'min, M. D.; Zvezdin, A. K.

1998-03-01

The prospects of using the free-powder high-field magnetization method for a quantitative study of inter-sublattice exchange interaction in 3d-4f hard magnetic materials are analyzed. Such analysis is stimulated by the availability of pulsed magnetic fields ˜103 T generated by implosion. Particular attention is paid to effects due to magnetic anisotropy, essential for these materials. The 3d-4f ferrimagnets where both sublattices contribute positively to the easy-axis anisotropy are shown to be suitable objects of study by the free-powder method, because (i) anomalies in their low-temperature magnetizatization curves are sharp and (ii) anisotropic effects can be allowed for without quantitative knowledge of the anisotropy constants. Moreover, these "good" hard magnetic materials can be brought into metamagnetic regime by diluting the rare earth sublattice with nonmagnetic yttrium; then, regardless of the anisotropy constants, the magnetization curve at low temperatures has just one steplike anomaly, the threshold field being equal exactly to the molecular field acting on the rare earth.

Novel spinal instrumentation to enhance osteogenesis and fusion: a preliminary study.

PubMed

MacEwan, Matthew R; Talcott, Michael R; Moran, Daniel W; Leuthardt, Eric C

2016-09-01

OBJECTIVE Instrumented spinal fusion continues to exhibit high failure rates in patients undergoing multilevel lumbar fusion or pseudarthrosis revision; with Grade II or higher spondylolisthesis; or in those possessing risk factors such as obesity, tobacco use, or metabolic disorders. Direct current (DC) electrical stimulation of bone growth represents a unique surgical adjunct in vertebral fusion procedures, yet existing spinal fusion stimulators are not optimized to enhance interbody fusion. To develop an advanced method of applying DC electrical stimulation to promote interbody fusion, a novel osteogenic spinal system capable of routing DC through rigid instrumentation and into the vertebral bodies was fabricated. A pilot study was designed to assess the feasibility of osteogenic instrumentation and compare the ability of osteogenic instrumentation to promote successful interbody fusion in vivo to standard spinal instrumentation with autograft. METHODS Instrumented, single-level, posterior lumbar interbody fusion (PLIF) with autologous graft was performed at L4-5 in adult Toggenburg/Alpine goats, using both osteogenic spinal instrumentation (plus electrical stimulation) and standard spinal instrumentation (no electrical stimulation). At terminal time points (3 months, 6 months), animals were killed and lumbar spines were explanted for radiographic analysis using a SOMATOM Dual Source Definition CT Scanner and high-resolution Microcat II CT Scanner. Trabecular continuity, radiodensity within the fusion mass, and regional bone formation were examined to determine successful spinal fusion. RESULTS Quantitative analysis of average bone density in pedicle screw beds confirmed that electroactive pedicle screws used in the osteogenic spinal system focally enhanced bone density in instrumented vertebral bodies. Qualitative and quantitative analysis of high-resolution CT scans of explanted lumbar spines further demonstrated that the osteogenic spinal system induced solid bony fusion across the L4-5 disc space as early as 6 weeks postoperatively. In comparison, inactive spinal instrumentation with autograft was unable to promote successful interbody fusion by 6 months postoperatively. CONCLUSIONS Results of this study demonstrate that novel osteogenic spinal instrumentation supports interbody fusion through the focal delivery of DC electrical stimulation. With further technical development and scientific/clinical validation, osteogenic spinal instrumentation may offer a unique alternative to biological scaffolds and pharmaceutical adjuncts used in spinal fusion procedures.

Analysis of organic compounds in aqueous samples of former ammunition plants

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

Levsen, K.; Preiss, A.; Berger-Preiss, E.

1995-12-31

In Germany, a large number of sites exist where ammunition was produced before and in particular during World War II. These former production sites represent a particular threat to the environment because these plants were constructed and operated under war conditions, where production was far more important than protection of the health of the (in general forced) workers and the environment. New approaches are presented for the extraction and analysis of explosives and related compounds in aqueous samples from former ammunition production sites. Quantitative extraction of nitro aromatics but also of the polar nitroamines such as RDX and HMX ismore » achieved by solid phase extraction with styrene-divinylbenzene polymers (Lichrolut EN). Proton nuclear magnetic resonance ({sup 1}H-NMR) has been used to identify and quantify unknowns in ammunition waste water. Finally, automated multiple development (AMD) high performance thin layer chromatography was applied for the first time to the analysis of this compound class.« less

An Investigation of Wave Propagations in Discontinuous Galerkin Method

NASA Technical Reports Server (NTRS)

Hu, Fang Q.

2004-01-01

Analysis of the discontinuous Galerkin method has been carried out for one- and two-dimensional system of hyperbolic equations. Analytical, as well as numerical, properties of wave propagation in a DGM scheme are derived and verified with direct numerical simulations. In addition to a systematic examination of the dissipation and dispersion errors, behaviours of a DG scheme at an interface of two different grid topologies are also studied. Under the same framework, a quantitative discrete analysis of various artificial boundary conditions is also conducted. Progress has been made in numerical boundary condition treatment that is closely related to the application of DGM in aeroacoustics problems. Finally, Fourier analysis of DGM for the Convective diffusion equation has also be studied in connection with the application of DG schemes for the Navier-Stokes equations. This research has resulted in five(5) publications, plus one additional manuscript in preparation, four(4) conference presentations, and three(3) departmental seminars, as summarized in part II. Abstracts of papers are given in part 111 of this report.

Approaches to Observe Anthropogenic Aerosol-Cloud Interactions.

PubMed

Quaas, Johannes

Anthropogenic aerosol particles exert an-quantitatively very uncertain-effective radiative forcing due to aerosol-cloud interactions via an immediate altering of cloud albedo on the one hand and via rapid adjustments by alteration of cloud processes and by changes in thermodynamic profiles on the other hand. Large variability in cloud cover and properties and the therefore low signal-to-noise ratio for aerosol-induced perturbations hamper the identification of effects in observations. Six approaches are discussed as a means to isolate the impact of anthropogenic aerosol on clouds from natural cloud variability to estimate or constrain the effective forcing. These are (i) intentional cloud modification, (ii) ship tracks, (iii) differences between the hemispheres, (iv) trace gases, (v) weekly cycles and (vi) trends. Ship track analysis is recommendable for detailed process understanding, and the analysis of weekly cycles and long-term trends is most promising to derive estimates or constraints on the effective radiative forcing.

Comparative analysis of qualitative dermatoglyphic traits of Albanian and Turkish populations living in the area of Dukagjin Valley in Kosovo.

PubMed

Temaj, Gazmend; Krajacić, Petra; Milicić, Jasna; Jurić, Tatjana Skarić; Behluli, Ibrahim; Narancić, Nina Smolej; Hadziselimović, Rifat; Nefić, Hilda; Sopi, Ramadan; Belegu, Mazllan; Jakupi, Muharrem; Rudan, Pavao

2011-09-01

Dermatoglyphic prints were collected from 800 inhabitants of Dukagjin valley in Kosovo. The sample consisted of two ethnically different sub-populations who refer themselves as Albanians (N = 400) and Turks (N = 400). Qualitative analysis of prints concerned the frequency of the patterns on fingers (arch, ulnar and radial loop, whorl, accidental whorl) and on palms (Thenar and I, II, III, and IV interdigital area and the hypothenar, main line index, and the axial "t" triradius position). As was expected due to previous study of quantitative dermatoglyphic traits, in the same population the Alba-nians and Turks showed to be significantly different in most explored qualitative dermatoglyphic variables. Found differences indicated that the reproductive isolation between the Albanian and Turkish population in Kosovo is substantial, despite the fact that those two ethnic sub-populations live in the close vicinity through several centuries.

Signal and noise modeling in confocal laser scanning fluorescence microscopy.

PubMed

Herberich, Gerlind; Windoffer, Reinhard; Leube, Rudolf E; Aach, Til

2012-01-01

Fluorescence confocal laser scanning microscopy (CLSM) has revolutionized imaging of subcellular structures in biomedical research by enabling the acquisition of 3D time-series of fluorescently-tagged proteins in living cells, hence forming the basis for an automated quantification of their morphological and dynamic characteristics. Due to the inherently weak fluorescence, CLSM images exhibit a low SNR. We present a novel model for the transfer of signal and noise in CLSM that is both theoretically sound as well as corroborated by a rigorous analysis of the pixel intensity statistics via measurement of the 3D noise power spectra, signal-dependence and distribution. Our model provides a better fit to the data than previously proposed models. Further, it forms the basis for (i) the simulation of the CLSM imaging process indispensable for the quantitative evaluation of CLSM image analysis algorithms, (ii) the application of Poisson denoising algorithms and (iii) the reconstruction of the fluorescence signal.

Second Harmonic Generation Guided Raman Spectroscopy for Sensitive Detection of Polymorph Transitions

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

Chowdhury, Azhad U.; Ye, Dong Hye; Song, Zhengtian

Second harmonic generation (SHG) was integrated with Raman spectroscopy for the analysis of pharmaceutical materials. Particulate formulations of clopidogrel bisulfate were prepared in two crystal forms (Form I and Form II). Image analysis approaches enable automated identification of particles by bright field imaging, followed by classification by SHG. Quantitative SHG microscopy enabled discrimination of crystal form on a per particle basis with 99.95% confidence in a total measurement time of ~10 ms per particle. Complementary measurements by Raman and synchrotron XRD are in excellent agreement with the classifications made by SHG, with measurement times of ~1 min and several secondsmore » per particle, respectively. Coupling these capabilities with at-line monitoring may enable real-time feedback for reaction monitoring during pharmaceutical production to favor the more bioavailable but metastable Form I with limits of detection in the ppm regime.« less

System of polarization correlometry of polycrystalline layers of urine in the differentiation stage of diabetes

NASA Astrophysics Data System (ADS)

Ushenko, Yu. O.; Pashkovskaya, N. V.; Marchuk, Y. F.; Dubolazov, O. V.; Savich, V. O.

2015-08-01

The work consists of investigation results of diagnostic efficiency of a new azimuthally stable Muellermatrix method of analysis of laser autofluorescence coordinate distributions of biological liquid layers. A new model of generalized optical anisotropy of biological tissues protein networks is proposed in order to define the processes of laser autofluorescence. The influence of complex mechanisms of both phase anisotropy (linear birefringence and optical activity) and linear (circular) dichroism is taken into account. The interconnections between the azimuthally stable Mueller-matrix elements characterizing laser autofluorescence and different mechanisms of optical anisotropy are determined. The statistic analysis of coordinate distributions of such Mueller-matrix rotation invariants is proposed. Thereupon the quantitative criteria (statistic moments of the 1st to the 4th order) of differentiation of human urine polycrystalline layers for the sake of diagnosing and differentiating cholelithiasis with underlying chronic cholecystitis (group 1) and diabetes mellitus of degree II (group 2) are estimated.

Population and Star Formation Histories from the Outer Limits Survey

NASA Astrophysics Data System (ADS)

Brondel, Brian Joseph; Saha, Abhijit; Olszewski, Edward

2015-08-01

The Outer Limits Survey (OLS) is a deep survey of selected fields in the outlying areas of the Magellanic Clouds based on the MOSAIC-II instrument on the Blanco 4-meter Telescope at CTIO. OLS is designed to probe the outer disk and halo structures of Magellanic System. The survey comprises ~50 fields obtained in Landolt R, I and Washington C, M and DDO51 filters, extending to a depth of about 24th magnitude in I. While qualitative examination of the resulting data has yielded interesting published results, we report here on quantitative analysis through matching of Hess diagrams to theoretical isochrones. We present analysis based on techniques developed by Dolphin (e.g., 2002, MNRAS, 332, 91) for fields observed by OLS. Our results broadly match those found by qualitative examination of the CMDs, but interesting details emerge from isochrone fitting.

Radiometric and geometric analysis of hyperspectral imagery acquired from an unmanned aerial vehicle

DOE PAGES

Hruska, Ryan; Mitchell, Jessica; Anderson, Matthew; ...

2012-09-17

During the summer of 2010, an Unmanned Aerial Vehicle (UAV) hyperspectral in-flight calibration and characterization experiment of the Resonon PIKA II imaging spectrometer was conducted at the U.S. Department of Energy’s Idaho National Laboratory (INL) UAV Research Park. The purpose of the experiment was to validate the radiometric calibration of the spectrometer and determine the georegistration accuracy achievable from the on-board global positioning system (GPS) and inertial navigation sensors (INS) under operational conditions. In order for low-cost hyperspectral systems to compete with larger systems flown on manned aircraft, they must be able to collect data suitable for quantitative scientific analysis.more » The results of the in-flight calibration experiment indicate an absolute average agreement of 96.3%, 93.7% and 85.7% for calibration tarps of 56%, 24%, and 2.5% reflectivity, respectively. The achieved planimetric accuracy was 4.6 meters (based on RMSE).« less

Enzymatic production of single-molecule FISH and RNA capture probes.

PubMed

Gaspar, Imre; Wippich, Frank; Ephrussi, Anne

2017-10-01

Arrays of singly labeled short oligonucleotides that hybridize to a specific target revolutionized RNA biology, enabling quantitative, single-molecule microscopy analysis and high-efficiency RNA/RNP capture. Here, we describe a simple and efficient method that allows flexible functionalization of inexpensive DNA oligonucleotides by different fluorescent dyes or biotin using terminal deoxynucleotidyl transferase and custom-made functional group conjugated dideoxy-UTP. We show that (i) all steps of the oligonucleotide labeling-including conjugation, enzymatic synthesis, and product purification-can be performed in a standard biology laboratory, (ii) the process yields >90%, often >95% labeled product with minimal carryover of impurities, and (iii) the oligonucleotides can be labeled with different dyes or biotin, allowing single-molecule FISH, RNA affinity purification, and Northern blot analysis to be performed. © 2017 Gaspar et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Behavior, sensitivity, and power of activation likelihood estimation characterized by massive empirical simulation.

PubMed

Eickhoff, Simon B; Nichols, Thomas E; Laird, Angela R; Hoffstaedter, Felix; Amunts, Katrin; Fox, Peter T; Bzdok, Danilo; Eickhoff, Claudia R

2016-08-15

Given the increasing number of neuroimaging publications, the automated knowledge extraction on brain-behavior associations by quantitative meta-analyses has become a highly important and rapidly growing field of research. Among several methods to perform coordinate-based neuroimaging meta-analyses, Activation Likelihood Estimation (ALE) has been widely adopted. In this paper, we addressed two pressing questions related to ALE meta-analysis: i) Which thresholding method is most appropriate to perform statistical inference? ii) Which sample size, i.e., number of experiments, is needed to perform robust meta-analyses? We provided quantitative answers to these questions by simulating more than 120,000 meta-analysis datasets using empirical parameters (i.e., number of subjects, number of reported foci, distribution of activation foci) derived from the BrainMap database. This allowed to characterize the behavior of ALE analyses, to derive first power estimates for neuroimaging meta-analyses, and to thus formulate recommendations for future ALE studies. We could show as a first consequence that cluster-level family-wise error (FWE) correction represents the most appropriate method for statistical inference, while voxel-level FWE correction is valid but more conservative. In contrast, uncorrected inference and false-discovery rate correction should be avoided. As a second consequence, researchers should aim to include at least 20 experiments into an ALE meta-analysis to achieve sufficient power for moderate effects. We would like to note, though, that these calculations and recommendations are specific to ALE and may not be extrapolated to other approaches for (neuroimaging) meta-analysis. Copyright © 2016 Elsevier Inc. All rights reserved.

Combined Falling Drop/Open Port Sampling Interface System for Automated Flow Injection Mass Spectrometry

DOE PAGES

Van Berkel, Gary J.; Kertesz, Vilmos; Orcutt, Matt; ...

2017-11-07

The aim of this work was to demonstrate and to evaluate the analytical performance of a combined falling drop/open port sampling interface (OPSI) system as a simple noncontact, no-carryover, automated system for flow injection analysis with mass spectrometry. The falling sample drops were introduced into the OPSI using a widely available autosampler platform utilizing low cost disposable pipet tips and conventional disposable microtiter well plates. The volume of the drops that fell onto the OPSI was in the 7–15 μL range with an injected sample volume of several hundred nanoliters. Sample drop height, positioning of the internal capillary on themore » sampling end of the probe, and carrier solvent flow rate were optimized for maximum signal. Sample throughput, signal reproducibility, matrix effects, and quantitative analysis capability of the system were established using the drug molecule propranolol and its isotope labeled internal standard in water, unprocessed river water and two commercially available buffer matrices. A sample-to-sample throughput of ~45 s with a ~4.5 s base-to-base flow injection peak profile was obtained in these experiments. In addition, quantitation with minimally processed rat plasma samples was demonstrated with three different statin drugs (atorvastatin, rosuvastatin, and fluvastatin). Direct characterization capability of unprocessed samples was demonstrated by the analysis of neat vegetable oils. Employing the autosampler system for spatially resolved liquid extraction surface sampling exemplified by the analysis of propranolol and its hydroxypropranolol glucuronide phase II metabolites from a rat thin tissue section was also illustrated.« less

Combined Falling Drop/Open Port Sampling Interface System for Automated Flow Injection Mass Spectrometry

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

Van Berkel, Gary J.; Kertesz, Vilmos; Orcutt, Matt

The aim of this work was to demonstrate and to evaluate the analytical performance of a combined falling drop/open port sampling interface (OPSI) system as a simple noncontact, no-carryover, automated system for flow injection analysis with mass spectrometry. The falling sample drops were introduced into the OPSI using a widely available autosampler platform utilizing low cost disposable pipet tips and conventional disposable microtiter well plates. The volume of the drops that fell onto the OPSI was in the 7–15 μL range with an injected sample volume of several hundred nanoliters. Sample drop height, positioning of the internal capillary on themore » sampling end of the probe, and carrier solvent flow rate were optimized for maximum signal. Sample throughput, signal reproducibility, matrix effects, and quantitative analysis capability of the system were established using the drug molecule propranolol and its isotope labeled internal standard in water, unprocessed river water and two commercially available buffer matrices. A sample-to-sample throughput of ~45 s with a ~4.5 s base-to-base flow injection peak profile was obtained in these experiments. In addition, quantitation with minimally processed rat plasma samples was demonstrated with three different statin drugs (atorvastatin, rosuvastatin, and fluvastatin). Direct characterization capability of unprocessed samples was demonstrated by the analysis of neat vegetable oils. Employing the autosampler system for spatially resolved liquid extraction surface sampling exemplified by the analysis of propranolol and its hydroxypropranolol glucuronide phase II metabolites from a rat thin tissue section was also illustrated.« less

Behavior, Sensitivity, and power of activation likelihood estimation characterized by massive empirical simulation

PubMed Central

Eickhoff, Simon B.; Nichols, Thomas E.; Laird, Angela R.; Hoffstaedter, Felix; Amunts, Katrin; Fox, Peter T.

2016-01-01

Given the increasing number of neuroimaging publications, the automated knowledge extraction on brain-behavior associations by quantitative meta-analyses has become a highly important and rapidly growing field of research. Among several methods to perform coordinate-based neuroimaging meta-analyses, Activation Likelihood Estimation (ALE) has been widely adopted. In this paper, we addressed two pressing questions related to ALE meta-analysis: i) Which thresholding method is most appropriate to perform statistical inference? ii) Which sample size, i.e., number of experiments, is needed to perform robust meta-analyses? We provided quantitative answers to these questions by simulating more than 120,000 meta-analysis datasets using empirical parameters (i.e., number of subjects, number of reported foci, distribution of activation foci) derived from the BrainMap database. This allowed to characterize the behavior of ALE analyses, to derive first power estimates for neuroimaging meta-analyses, and to thus formulate recommendations for future ALE studies. We could show as a first consequence that cluster-level family-wise error (FWE) correction represents the most appropriate method for statistical inference, while voxel-level FWE correction is valid but more conservative. In contrast, uncorrected inference and false-discovery rate correction should be avoided. As a second consequence, researchers should aim to include at least 20 experiments into an ALE meta-analysis to achieve sufficient power for moderate effects. We would like to note, though, that these calculations and recommendations are specific to ALE and may not be extrapolated to other approaches for (neuroimaging) meta-analysis. PMID:27179606

Junior high school students' cognitive process in solving the developed algebraic problems based on information processing taxonomy model

NASA Astrophysics Data System (ADS)

Purwoko, Saad, Noor Shah; Tajudin, Nor'ain Mohd

2017-05-01

This study aims to: i) develop problem solving questions of Linear Equations System of Two Variables (LESTV) based on levels of IPT Model, ii) explain the level of students' skill of information processing in solving LESTV problems; iii) explain students' skill in information processing in solving LESTV problems; and iv) explain students' cognitive process in solving LESTV problems. This study involves three phases: i) development of LESTV problem questions based on Tessmer Model; ii) quantitative survey method on analyzing students' skill level of information processing; and iii) qualitative case study method on analyzing students' cognitive process. The population of the study was 545 eighth grade students represented by a sample of 170 students of five Junior High Schools in Hilir Barat Zone, Palembang (Indonesia) that were chosen using cluster sampling. Fifteen students among them were drawn as a sample for the interview session with saturated information obtained. The data were collected using the LESTV problem solving test and the interview protocol. The quantitative data were analyzed using descriptive statistics, while the qualitative data were analyzed using the content analysis. The finding of this study indicated that students' cognitive process was just at the step of indentifying external source and doing algorithm in short-term memory fluently. Only 15.29% students could retrieve type A information and 5.88% students could retrieve type B information from long-term memory. The implication was the development problems of LESTV had validated IPT Model in modelling students' assessment by different level of hierarchy.

Metabolic pathway profiling of mitochondrial respiratory chain mutants in C. elegans

PubMed Central

MJ, Falk; Z, Zhang; Rosenjack; Nissim; E, Daikhin; Nissim; MM, Sedensky; M, Yudkoff; PG, Morgan

2008-01-01

C. elegans affords a model of primary mitochondrial dysfunction that provides insight into cellular adaptations which accompany mutations in nuclear gene that encode mitochondrial proteins. To this end, we characterized genome-wide expression profiles of C. elegans strains with mutations in nuclear-encoded subunits of respiratory chain complexes. Our goal was to detect concordant changes among clusters of genes that comprise defined metabolic pathways. Results indicate that respiratory chain mutants significantly upregulate a variety of basic cellular metabolic pathways involved in carbohydrate, amino acid, and fatty acid metabolism, as well as cellular defense pathways such as the metabolism of P450 and glutathione. To further confirm and extend expression analysis findings, quantitation of whole worm free amino acid levels was performed in C. elegans mitochondrial mutants for subunits of complexes I, II, and III. Significant differences were seen for 13 of 16 amino acid levels in complex I mutants compared with controls, as well as overarching similarities among profiles of complex I, II, and III mutants compared with controls. The specific pattern of amino acid alterations observed provides novel evidence to suggest that an increase in glutamate-linked transamination reactions caused by the failure of NAD+ dependent oxidation of ketoacids occurs in primary mitochondrial respiratory chain mutants. Recognition of consistent alterations among patterns of nuclear gene expression for multiple biochemical pathways and in quantitative amino acid profiles in a translational genetic model of mitochondrial dysfunction allows insight into the complex pathogenesis underlying primary mitochondrial disease. Such knowledge may enable the development of a metabolomic profiling diagnostic tool applicable to human mitochondrial disease. PMID:18178500

Fatigue crack growth in an aluminum alloy-fractographic study

NASA Astrophysics Data System (ADS)

Salam, I.; Muhammad, W.; Ejaz, N.

2016-08-01

A two-fold approach was adopted to understand the fatigue crack growth process in an Aluminum alloy; fatigue crack growth test of samples and analysis of fractured surfaces. Fatigue crack growth tests were conducted on middle tension M(T) samples prepared from an Aluminum alloy cylinder. The tests were conducted under constant amplitude loading at R ratio 0.1. The stress applied was from 20,30 and 40 per cent of the yield stress of the material. The fatigue crack growth data was recorded. After fatigue testing, the samples were subjected to detailed scanning electron microscopic (SEM) analysis. The resulting fracture surfaces were subjected to qualitative and quantitative fractographic examinations. Quantitative fracture analysis included an estimation of crack growth rate (CGR) in different regions. The effect of the microstructural features on fatigue crack growth was examined. It was observed that in stage II (crack growth region), the failure mode changes from intergranular to transgranular as the stress level increases. In the region of intergranular failure the localized brittle failure was observed and fatigue striations are difficult to reveal. However, in the region of transgranular failure the crack path is independent of the microstructural features. In this region, localized ductile failure mode was observed and well defined fatigue striations were present in the wake of fatigue crack. The effect of interaction of growing fatigue crack with microstructural features was not substantial. The final fracture (stage III) was ductile in all the cases.

LC-DAD-MS (ESI+) analysis and antioxidant capacity of crocus sativus petal extracts.

PubMed

Termentzi, Aikaterini; Kokkalou, Eugene

2008-04-01

In this study, various fractions isolated from the petals of Crocus sativus were assessed at first for their phenolic content both qualitatively and quantitatively and secondly for their antioxidant activity. The phytochemical analysis was carried out by LC-DAD-MS (ESI (+)) whereas the antioxidant potential was evaluated by applying two methodologies, the DPPH. radical scavenging activity test and the Co(II)-induced luminol chemiluminescence procedure. According to data obtained from these antioxidant tests, the diethyl ether, ethyl acetate and aqueous fractions demonstrated the strongest antioxidant capacity. Interestingly, the major constituents identified in these fractions correspond to kaempferol, quercetin, naringenin and some flavanone and flavanol derivatives glycosylated and esterified with phenylpropanoic acids. In addition, the presence of some nitrogen-containing substances, as well as other phenolics and phenylpropanoic derivatives was also traced. The identification and structural elucidation of all substances isolated in this study was achieved by both comparing available literature data and by proposed fragmentation mechanisms based on evaluating the LC-DAD-MS (ESI (+)) experimental data. The quantitative analysis data obtained thus far have shown that Crocus sativus petals are a rich source of flavonoids. Such a fact suggests that the good antioxidant capacity detected in the various fractions of Crocus sativus petals could be attributed to the presence of flavonoids, since it is already known that these molecules exert antioxidant capability. The latter, along with the use of Crocus sativus in food and pharmaceutical industry is discussed.

Implementation of a polling protocol for predicting celiac disease in videocapsule analysis.

PubMed

Ciaccio, Edward J; Tennyson, Christina A; Bhagat, Govind; Lewis, Suzanne K; Green, Peter H

2013-07-16

To investigate the presence of small intestinal villous atrophy in celiac disease patients from quantitative analysis of videocapsule image sequences. Nine celiac patient data with biopsy-proven villous atrophy and seven control patient data lacking villous atrophy were used for analysis. Celiacs had biopsy-proven disease with scores of Marsh II-IIIC except in the case of one hemophiliac patient. At four small intestinal levels (duodenal bulb, distal duodenum, jejunum, and ileum), video clips of length 200 frames (100 s) were analyzed. Twenty-four measurements were used for image characterization. These measurements were determined by quantitatively processing the videocapsule images via techniques for texture analysis, motility estimation, volumetric reconstruction using shape-from-shading principles, and image transformation. Each automated measurement method, or automaton, was polled as to whether or not villous atrophy was present in the small intestine, indicating celiac disease. Each automaton's vote was determined based upon an optimized parameter threshold level, with the threshold levels being determined from prior data. A prediction of villous atrophy was made if it received the majority of votes (≥ 13), while no prediction was made for tie votes (12-12). Thus each set of images was classified as being from either a celiac disease patient or from a control patient. Separated by intestinal level, the overall sensitivity of automata polling for predicting villous atrophy and hence celiac disease was 83.9%, while the specificity was 92.9%, and the overall accuracy of automata-based polling was 88.1%. The method of image transformation yielded the highest sensitivity at 93.8%, while the method of texture analysis using subbands had the highest specificity at 76.0%. Similar results of prediction were observed at all four small intestinal locations, but there were more tie votes at location 4 (ileum). Incorrect prediction which reduced sensitivity occurred for two celiac patients with Marsh type II pattern, which is characterized by crypt hyperplasia, but normal villous architecture. Pooled from all levels, there was a mean of 14.31 ± 3.28 automaton votes for celiac vs 9.67 ± 3.31 automaton votes for control when celiac patient data was analyzed (P < 0.001). Pooled from all levels, there was a mean of 9.71 ± 2.8128 automaton votes for celiac vs 14.32 ± 2.7931 automaton votes for control when control patient data was analyzed (P < 0.001). Automata-based polling may be useful to indicate presence of mucosal atrophy, indicative of celiac disease, across the entire small bowel, though this must be confirmed in a larger patient set. Since the method is quantitative and automated, it can potentially eliminate observer bias and enable the detection of subtle abnormality in patients lacking a clear diagnosis. Our paradigm was found to be more efficacious at proximal small intestinal locations, which may suggest a greater presence and severity of villous atrophy at proximal as compared with distal locations.

Implementation of a polling protocol for predicting celiac disease in videocapsule analysis

PubMed Central

Ciaccio, Edward J; Tennyson, Christina A; Bhagat, Govind; Lewis, Suzanne K; Green, Peter H

2013-01-01

AIM: To investigate the presence of small intestinal villous atrophy in celiac disease patients from quantitative analysis of videocapsule image sequences. METHODS: Nine celiac patient data with biopsy-proven villous atrophy and seven control patient data lacking villous atrophy were used for analysis. Celiacs had biopsy-proven disease with scores of Marsh II-IIIC except in the case of one hemophiliac patient. At four small intestinal levels (duodenal bulb, distal duodenum, jejunum, and ileum), video clips of length 200 frames (100 s) were analyzed. Twenty-four measurements were used for image characterization. These measurements were determined by quantitatively processing the videocapsule images via techniques for texture analysis, motility estimation, volumetric reconstruction using shape-from-shading principles, and image transformation. Each automated measurement method, or automaton, was polled as to whether or not villous atrophy was present in the small intestine, indicating celiac disease. Each automaton’s vote was determined based upon an optimized parameter threshold level, with the threshold levels being determined from prior data. A prediction of villous atrophy was made if it received the majority of votes (≥ 13), while no prediction was made for tie votes (12-12). Thus each set of images was classified as being from either a celiac disease patient or from a control patient. RESULTS: Separated by intestinal level, the overall sensitivity of automata polling for predicting villous atrophy and hence celiac disease was 83.9%, while the specificity was 92.9%, and the overall accuracy of automata-based polling was 88.1%. The method of image transformation yielded the highest sensitivity at 93.8%, while the method of texture analysis using subbands had the highest specificity at 76.0%. Similar results of prediction were observed at all four small intestinal locations, but there were more tie votes at location 4 (ileum). Incorrect prediction which reduced sensitivity occurred for two celiac patients with Marsh type II pattern, which is characterized by crypt hyperplasia, but normal villous architecture. Pooled from all levels, there was a mean of 14.31 ± 3.28 automaton votes for celiac vs 9.67 ± 3.31 automaton votes for control when celiac patient data was analyzed (P < 0.001). Pooled from all levels, there was a mean of 9.71 ± 2.8128 automaton votes for celiac vs 14.32 ± 2.7931 automaton votes for control when control patient data was analyzed (P < 0.001). CONCLUSION: Automata-based polling may be useful to indicate presence of mucosal atrophy, indicative of celiac disease, across the entire small bowel, though this must be confirmed in a larger patient set. Since the method is quantitative and automated, it can potentially eliminate observer bias and enable the detection of subtle abnormality in patients lacking a clear diagnosis. Our paradigm was found to be more efficacious at proximal small intestinal locations, which may suggest a greater presence and severity of villous atrophy at proximal as compared with distal locations. PMID:23858375

Transfer Hydro-dehalogenation of Organic Halides Catalyzed by Ruthenium(II) Complex.

PubMed

You, Tingjie; Wang, Zhenrong; Chen, Jiajia; Xia, Yuanzhi

2017-02-03

A simple and efficient Ru(II)-catalyzed transfer hydro-dehalogenation of organic halides using 2-propanol solvent as the hydride source was reported. This methodology is applicable for hydro-dehalogenation of a variety of aromatic halides and α-haloesters and amides without additional ligand, and quantitative yields were achieved in many cases. The potential synthetic application of this method was demonstrated by efficient gram-scale transformation with catalyst loading as low as 0.5 mol %.

42 CFR 495.316 - State monitoring and reporting regarding activities required to receive an incentive payment.

Code of Federal Regulations, 2010 CFR

2010-10-01

... quality measures data; and (v) A description and quantitative data on how its incentive payment program... for quality improvement, reduction of disparities, research or outreach. (ii) Capability to submit...

42 CFR 495.316 - State monitoring and reporting regarding activities required to receive an incentive payment.

Code of Federal Regulations, 2011 CFR

2011-10-01

... quality measures data; and (v) A description and quantitative data on how its incentive payment program... for quality improvement, reduction of disparities, research or outreach. (ii) Capability to submit...

Occurrence and prevalence of antibiotic resistance in landfill leachate.

PubMed

Wang, Yangqing; Tang, Wei; Qiao, Jing; Song, Liyan

2015-08-01

Antibiotic resistance (AR) is extensively present in various environments, posing emerging threat to public and environmental health. Landfill receives unused and unwanted antibiotics through household waste and AR within waste (e.g., activated sludge and illegal clinical waste) and is supposed to serve as an important AR reservoir. In this study, we used culture-dependent methods and quantitative molecular techniques to detect and quantify antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in 12 landfill leachate samples from six geographic different landfills, China. Five tested ARGs (tetO, tetW, bla(TEM), sulI, and sulII) and seven kinds of antibiotic-resistant heterotrophic ARB were extensively detected in all samples, demonstrating their occurrence in landfill. The detected high ratio (10(-2) to 10(-5)) of ARGs to 16S ribosomal RNA (rRNA) gene copies implied that ARGs are prevalent in landfill. Correlation analysis showed that ARGs (tetO, tetW, sulI, and sulII) significantly correlated to ambient bacterial 16S rRNA gene copies, suggesting that the abundance of bacteria in landfill leachate may play an important role in the horizontal spread of ARGs.

Analysis of the unusual wavelength dependence of the first hyperpolarizability of porphyrin derivatives

NASA Astrophysics Data System (ADS)

De Mey, K.; Clays, K.; Therien, Michael J.; Beratan, David N.; Asselberghs, Inge

2010-08-01

Successfully predicting the frequency dispersion of electronic hyperpolarizabilities is an unresolved challenge in materials science and electronic structure theory. It has been shown1 that the generalized Thomas-Kuhn sum rules combined with linear absorption data and measured hyperpolarizabilities at one or two frequencies, may be used to predict the entire frequency-dependent electronic hyperpolarizability spectrum. This treatment includes two- and threelevel contributions that arise from the lowest two or three excited state manifolds, enabling us to describe the unusual observed frequency dispersion of the dynamic hyperpolarizability in high oscillator strength M-PZn chromophores, where (porphinato)zinc(II) (PZn) and metal(II)polypyridyl (M) units are connected via an ethyne unit that aligns the high oscillator strength transition dipoles of these components in a head-to-tail arrangement. Importantly, this approach provides a quantitative scheme to use linear optical absorption spectra and very few individual hyperpolarizability values to predict the entire frequency-dependent nonlinear optical response. In addition we provide here experimental dynamic hyperpolarizability values determined by hyper-Rayleigh scattering that underscore the validity of our approach.

Primary role of the electrostatic contributions in a rational growth of hysteresis loop in spin-crossover Fe(II) complexes.

PubMed

Kepenekian, Mikaël; Le Guennic, Boris; Robert, Vincent

2009-08-19

We report a comprehensive analysis of the hysteresis behavior in a series of well-characterized spin-crossover Fe(II) materials. On the basis of the available X-ray data and multireference CASSCF (complete active space self-consistent field) calculations, we show that the growth of the hysteresis loop is controlled by electrostatic contributions. These environment effects turn out to be deeply modified as the crystal structure changes along the spin transition. Our theoretical inspection demonstrates the synergy between weak bonds and electrostatic interactions in the growth of hysteresis behavior. Quantitatively, it is suggested that the electrostatic contributions significantly enhance the cooperativity factor while weak bonds are determinant in the structuration of the 3D networks. Our picture does not rely on any parametrization but uses the microscopic information to derive an expression for the cooperativity parameter. The calculated values are in very good agreement with the experimental observations. Such inspection can thus be carried out to anticipate the hysteresis behavior of this intriguing class of materials.

New software for cervical vertebral geometry assessment and its relationship to skeletal maturation—a pilot study

PubMed Central

Cunha, A R; Júnior, G C; Fernandes, N; Campos, M J S; Costa, L F M; Vitral, R W F; Bolognese, A M

2014-01-01

Objectives: In the present study, we developed new software for quantitative analysis of cervical vertebrae maturation, and we evaluated its applicability through a multinomial logistic regression model (MLRM). Methods: Digitized images of the bodies of the second (C2), third (C3) and fourth (C4) cervical vertebrae were analysed in cephalometric radiographs of 236 subjects (116 boys and 120 girls) by using a software developed for digitized vertebrae analysis. The sample was initially distributed into 11 categories according to the Fishman's skeletal maturity indicators and were then grouped into four stages for quantitative cervical maturational changes (QCMC) analysis (QCMC I, II, III and IV). Seven variables of interest were measured and analysed to identify morphologic alterations of the vertebral bodies in each QCMC category. Results: Statistically significant differences (p < 0.05) were observed among all QCMC categories for the variables analysed. The MLRM used to calculate the probability that an individual belonged to each of the four cervical vertebrae maturation categories was constructed by taking into account gender, chronological age and four variables determined by digitized vertebrae analysis (Ang_C3, MP_C3, MP_C4 and SP_C4). The MLRM presented a predictability of 81.4%. The weighted κ test showed almost perfect agreement (κ = 0.832) between the categories defined initially by the method of Fishman and those allocated by the MLRM. Conclusions: Significant alterations in the morphologies of the C2, C3 and C4 vertebral bodies that were analysed through the digitized vertebrae analysis software occur during the different stages of skeletal maturation. The model that combines the four parameters measured on the vertebral bodies, the age and the gender showed an excellent prediction. PMID:24319125

The Strategic Environment Assessment bibliographic network: A quantitative literature review analysis

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

Caschili, Simone, E-mail: s.caschili@ucl.ac.uk; De Montis, Andrea; Ganciu, Amedeo

2014-07-01

Academic literature has been continuously growing at such a pace that it can be difficult to follow the progression of scientific achievements; hence, the need to dispose of quantitative knowledge support systems to analyze the literature of a subject. In this article we utilize network analysis tools to build a literature review of scientific documents published in the multidisciplinary field of Strategic Environment Assessment (SEA). The proposed approach helps researchers to build unbiased and comprehensive literature reviews. We collect information on 7662 SEA publications and build the SEA Bibliographic Network (SEABN) employing the basic idea that two publications are interconnectedmore » if one cites the other. We apply network analysis at macroscopic (network architecture), mesoscopic (sub graph) and microscopic levels (node) in order to i) verify what network structure characterizes the SEA literature, ii) identify the authors, disciplines and journals that are contributing to the international discussion on SEA, and iii) scrutinize the most cited and important publications in the field. Results show that the SEA is a multidisciplinary subject; the SEABN belongs to the class of real small world networks with a dominance of publications in Environmental studies over a total of 12 scientific sectors. Christopher Wood, Olivia Bina, Matthew Cashmore, and Andrew Jordan are found to be the leading authors while Environmental Impact Assessment Review is by far the scientific journal with the highest number of publications in SEA studies. - Highlights: • We utilize network analysis to analyze scientific documents in the SEA field. • We build the SEA Bibliographic Network (SEABN) of 7662 publications. • We apply network analysis at macroscopic, mesoscopic and microscopic network levels. • We identify SEABN architecture, relevant publications, authors, subjects and journals.« less

New software for cervical vertebral geometry assessment and its relationship to skeletal maturation--a pilot study.

PubMed

Santiago, R C; Cunha, A R; Júnior, G C; Fernandes, N; Campos, M J S; Costa, L F M; Vitral, R W F; Bolognese, A M

2014-01-01

In the present study, we developed new software for quantitative analysis of cervical vertebrae maturation, and we evaluated its applicability through a multinomial logistic regression model (MLRM). Digitized images of the bodies of the second (C2), third (C3) and fourth (C4) cervical vertebrae were analysed in cephalometric radiographs of 236 subjects (116 boys and 120 girls) by using a software developed for digitized vertebrae analysis. The sample was initially distributed into 11 categories according to the Fishman's skeletal maturity indicators and were then grouped into four stages for quantitative cervical maturational changes (QCMC) analysis (QCMC I, II, III and IV). Seven variables of interest were measured and analysed to identify morphologic alterations of the vertebral bodies in each QCMC category. Statistically significant differences (p < 0.05) were observed among all QCMC categories for the variables analysed. The MLRM used to calculate the probability that an individual belonged to each of the four cervical vertebrae maturation categories was constructed by taking into account gender, chronological age and four variables determined by digitized vertebrae analysis (Ang_C3, MP_C3, MP_C4 and SP_C4). The MLRM presented a predictability of 81.4%. The weighted κ test showed almost perfect agreement (κ = 0.832) between the categories defined initially by the method of Fishman and those allocated by the MLRM. Significant alterations in the morphologies of the C2, C3 and C4 vertebral bodies that were analysed through the digitized vertebrae analysis software occur during the different stages of skeletal maturation. The model that combines the four parameters measured on the vertebral bodies, the age and the gender showed an excellent prediction.

Microstructural effects on fracture toughness of polycrystalline ceramics in combined mode I and mode II loading

NASA Technical Reports Server (NTRS)

Singh, D.; Shetty, D. K.

1988-01-01

Fracture toughness of polycrystalline alumina and ceria partially-stabilized tetragonal zirconia (CeO2-TZP) ceramics were assessed in combined mode I and mode II loading using precracked disk specimens in diametral compression. Stress states ranging from pure mode I, combined mode I and mode II, and pure mode II were obtained by aligning the center crack at specific angles relative to the loading diameter. The resulting mixed-mode fracture toughness envelope showed significant deviation to higher fracture toughness in mode II relative to the predictions of the linear elastic fracture mechanics theory. Critical comparison with corresponding results on soda-lime glass and fracture surface observations showed that crack surface resistance arising from grain interlocking and abrasion was the main source of the increased fracture toughness in mode II loading of the polycrystalline ceramics. The normalized fracture toughness for pure mode II loading, (KII/KIc), increased with increasing grain size for the CeO2-TZP ceramics. Quantitative fractography confirmed an increased percentage of transgranular fracture of the grains in mode II loading.

Interactions between meniscal cells and a self assembled biomimetic surface composed of hyaluronic acid, chitosan and meniscal extracellular matrix molecules.

PubMed

Tan, Guak-Kim; Dinnes, Donna L M; Butler, Lauren N; Cooper-White, Justin J

2010-08-01

Menisci are one of the most commonly injured parts of the knee with a limited healing potential. This study focuses on fabrication and characterization of biomimetic surfaces for meniscal tissue engineering. To achieve this, a combination of hyaluronic acid/chitosan (HA/CH) mutilayers with covalently immobilized major extracellular matrix (ECM) components of native meniscus, namely collagen I/II (COL.I/II) and chondroitin-6-sulfate (C6S) was employed. Adsorption of the biomolecules was monitored using a quartz crystal microbalance with dissipation (QCM-D) and fourier transform-surface plasmon resonance (FT-SPR). Immobilization of the biomolecules onto HA/CH mutilayers was achieved by sequential adsorption, with optimum binding at a molar ratio of 1.4:1 (COL.I/II: C6S). After adding COL.I/II, the layers became relatively more rigid and large aggregates were evident. The effects of the modified surfaces on cell proliferation, gene expression and proteoglycan production of rat meniscal cells were examined. Quantitative real-time reverse transcriptase polymerase chain reaction (RT-qPCR) analysis showed that primary meniscal cells dedifferentiated rapidly after one passage in monolayer culture. This process could be reversed by culturing the cells on C6S surfaces, as indicated by increases in both collagen II and aggrecan gene expression, as well as proteoglycan production. Cells with abundant lipid vacuoles were evident on all the surfaces over an extended culture period. The results demonstrate the feasibility of C6S surfaces to avoid the dedifferentiation that normally occurs during monolayer expansion of meniscal cells. Crown Copyright 2010. Published by Elsevier Ltd. All rights reserved.

Preintervention lesion remodelling affects operative mechanisms of balloon optimised directional coronary atherectomy procedures: a volumetric study with three dimensional intravascular ultrasound

PubMed Central

von Birgelen, C; Mintz, G; de Vrey, E A; Serruys, P; Kimura, T; Nobuyoshi, M; Popma, J; Leon, M; Erbel, R; de Feyter, P J

2000-01-01

AIMS—To classify atherosclerotic coronary lesions on the basis of adequate or inadequate compensatory vascular enlargement, and to examine changes in lumen, plaque, and vessel volumes during balloon optimised directional coronary atherectomy procedures in relation to the state of adaptive remodelling before the intervention.
DESIGN—29 lesion segments in 29 patients were examined with intravascular ultrasound before and after successful balloon optimised directional coronary atherectomy procedures, and a validated volumetric intravascular ultrasound analysis was performed off-line to assess the atherosclerotic lesion remodelling and changes in plaque and vessel volumes that occurred during the intervention. Based on the intravascular ultrasound data, lesions were classified according to whether there was inadequate (group I) or adequate (group II) compensatory enlargement.
RESULTS—There was no significant difference in patient and lesion characteristics between groups I and II (n = 10 and 19), including lesion length and details of the intervention. Quantitative coronary angiographic data were similar for both groups. However, plaque and vessel volumes were significantly smaller in group I than in II. In group I, 9 (4)% (mean (SD)) of the plaque volume was ablated, while in group II 16 (11)% was ablated (p = 0.01). This difference was reflected in a lower lumen volume gain in group I than in group II (46 (18) mm3 v 80 (49) mm3 (p < 0.02)).
CONCLUSIONS—Preintervention lesion remodelling has an impact on the operative mechanisms of balloon optimised directional coronary atherectomy procedures. Plaque ablation was found to be particularly low in lesions with inadequate compensatory vascular enlargement.


Keywords: intravascular ultrasound; ultrasonics; remodelling; coronary artery disease; atherectomy PMID:10648496

Tibiofemoral contact stress and stress distribution evaluation of total knee arthroplasties.

PubMed

Szivek, J A; Cutignola, L; Volz, R G

1995-08-01

The Fuji film (Itochu, Los Angeles, CA) area analysis technique demonstrates that a more accurate assessment of tibiofemoral contact stresses is possible when the film is used at 37 degrees C and at the upper end of its sensitivity range (in this case, a 2,000-N load). An AMK with a regular and Hylamer-M insert (DePuy, Warsaw, IN), an MG II (Zimmer, Warsaw, IN), an Omnifit (Osteonics, Allendale, NJ), an Ortholoc III (Dow Corning Wright, Midland, MI), a PCA II (Howmedica, Rutherford, NJ), and a PFC (Johnson & Johnson Orthopaedics, Raynham, MA) had average contact stresses that varied only 12% at 60 degrees flexion. At 0 degrees, 15 degrees and 60 degrees flexion, stresses ranged from 13 to 25 MPa. Contact area distribution ratios, which were smaller at 37 degrees C than at 24 degrees C, provide a quantitative means of grouping implants according to the shape of the tibiofemoral contact area. The Omnifit, MG II, PCA II, and PFC had small ratios (symmetric areas). The AMK and Ortholoc III had large ratios (asymmetric contact areas). If the impression is reflective of wear, it would be expected to be focal in knees with small ratios and contact areas, and uniform in knees with large ratios and contact areas, whereas large ratios and small areas would imply a linear wear pattern. Calibrated electrical resistance contact stress measurements indicated that the Fuji film measurements underestimated the magnitude of contact stresses. They also provided a means of quantifying the rate of area increase during initial loading of the knees, with the highest area increase noted for the knee with the roughest insert (Ortholoc III) and the lowest area increase for the knee with the smoothest insert (PCA II).

NABOS-II Observational Program in the Arctic Ocean: New Perspectives and New Challenges

NASA Astrophysics Data System (ADS)

Ivanov, V.; Polyakov, I.; Ashik, I. M.; Pnyushkov, A.; Alkire, M. B.; Repina, I.; Alexeev, V. A.; Waddington, I.; Kanzow, T.; Goszczko, I.; Rember, R.; Artamonov, A.

2016-02-01

NABOS-II observational program was launched in 2013 on the basis of new knowledge obtained during NABOS (=Nansen and Amundsen Basins Observations System) project back in 2000s. Up to now two large scale expeditions in the Eurasian sector of the Arctic Ocean were carried out in framework of NABOS-II: in 2013 and in 2015. These field studies were conducted by International Arctic Research Center (IARC) University of Alaska Fairbanks, USA in partnership with Arctic and Antarctic Research Institute (AARI) St.Petersburg Russia. The main goal of the NABOS-II project is to provide quantitative assessment of circulation and water mass transformation along the principal pathways transporting water from the Nordic Seas to the Arctic Basin under conditions of substantially reduced summer ice cover. Reduced sea ice causes changes in the water column and in the overlying atmosphere. Documenting of these changes was the main target of the NABOS-II cruises. The scope of this goal and the opportunities of extended scientific research in the Arctic, provided during NABOS expeditions, encouraged scientific institutions from the USA, Europe and Asia to raise funds, contribute to the cruise program and to send their personnel to expeditions, thus giving them a true multidisciplinary status. The ambitious mission of collecting a two year long time series of hydrographic data at 6 moorings along 126E meridian from the upper slope (250 m depth) to the deep basin (3900 m depth) in the Laptev Sea was successfully accomplished in 2015. The collected data are truly unique, since they shed new light on the structure and spatio-temporal variability of water properties and transports in the Lapev Sea, which is the key region for understanding of interaction between Atlantic water branches. This presentation describes preliminary results of performed analysis.

NABOS-II Observational Program in the Arctic Ocean: New Perspectives and new Challenges

NASA Astrophysics Data System (ADS)

Ivanov, Vladimir; Polyakov, Igor; Ashik, Igor; Pnyushkov, Andrey; Alkire, Matthew; Repina, Irina; Alexeev, Vladimir; Waddington, Ian; Kanzow, Torsten; Rember, Robert; Artamonov, Alexander; Goszczko, Ilona

2016-04-01

NABOS-II observational program was launched in 2013 on the basis of new knowledge obtained during NABOS (=Nansen and Amundsen Basins Observations System) project back in 2000s. Up to now two large scale expeditions in the Eurasian sector of the Arctic Ocean were carried out in framework of NABOS-II: in 2013 and in 2015. These field studies were conducted by International Arctic Research Center (IARC) University of Alaska Fairbanks, USA in partnership with Arctic and Antarctic Research Institute (AARI) St.Petersburg Russia. The main goal of the NABOS-II project is to provide quantitative assessment of circulation and water mass transformation along the principal pathways transporting water from the Nordic Seas to the Arctic Basin under conditions of substantially reduced summer ice cover. Reduced sea ice causes changes in the water column and in the overlying atmosphere. Documenting of these changes was the main target of the NABOS-II cruises. The scope of this goal and the opportunities of extended scientific research in the Arctic, provided during NABOS expeditions, encouraged scientific institutions from the USA, Europe and Asia to raise funds, contribute to the cruise program and to send their personnel to expeditions, thus giving them a true multidisciplinary status. The ambitious mission of collecting a two year long time series of hydrographic data at 6 moorings along 126E meridian from the upper slope (250 m depth) to the deep basin (3900 m depth) in the Laptev Sea was successfully accomplished in 2015. The collected data are truly unique, since they shed new light on the structure and spatio-temporal variability of water properties and transports in the Lapev Sea, which is the key region for understanding of interaction between Atlantic water branches. This presentation describes preliminary results of performed analysis.

An apparatus for generation and quantitative measurement of homogeneous isotropic turbulence in He ii

NASA Astrophysics Data System (ADS)

Mastracci, Brian; Guo, Wei

2018-01-01

The superfluid phase of helium-4, known as He ii, exhibits extremely small kinematic viscosity and may be a useful tool for economically producing and studying high Reynolds number turbulent flow. Such applications are not currently possible because a comprehensive understanding of the complex two-fluid behavior of He ii is lacking. This situation could be remedied by a systematic investigation of simple, well controlled turbulence that can be directly compared with theoretical models. To this end, we have developed a new apparatus that combines flow visualization with second sound attenuation to study turbulence in the wake of a mesh grid towed through a He ii filled channel. One of three mesh grids (mesh number M = 3, 3.75, or 5 mm) can be pulled at speeds between 0.1 and 60 cm/s through a cast acrylic flow channel which has a 16 mm × 16 mm cross section and measures 330 mm long. The motion of solidified deuterium tracer particles, with diameter of the order 1 μm, in the resulting flow is captured by a high speed camera, and a particle tracking velocimetry algorithm resolves the Lagrangian particle trajectories through the turbulent flow field. A pair of oscillating superleak second sound transducers installed in the channel allows complementary measurement of vortex line density in the superfluid throughout the turbulent decay process. Success in early experiments demonstrates the effectiveness of both probes, and preliminary analysis of the data shows that both measurements strongly correlate with each other. Further investigations will provide comprehensive information that can be used to address open questions about turbulence in He ii and move toward the application of this fluid to high Reynolds number fluid research.

Both qualitative and quantitative genetic variation of MHC class II molecules may influence susceptibility to autoimmune diseases: the case of endemic pemphigus foliaceus.

PubMed

Piovezan, Bruno Zagonel; Petzl-Erler, Maria Luiza

2013-09-01

The MHC class II transactivator (CIITA) is a key regulator in expression of the HLA class II genes. It is well known that HLA-DRB1 genotypes have a strong influence on the risk of multifactorial autoimmune diseases, but the effect of CIITA genotypes remains controversial. We tested in a case-control study whether CIITA polymorphisms influence the risk of developing endemic pemphigus foliaceus (EPF) and whether CIITA and HLA-DRB1 interact as regards susceptibility to the disease. The rs4774 SNP is not associated to EPF, while rs3087456 in the CIITA gene promoter is associated with susceptibility [odds ratio (OR) = 2.6, p < 0.001 and OR = 2.0 p = 0.003 for genotypes G/G and G/A, respectively]. We suggest that the associations result from the effect of genetically controlled levels of CIITA on expression of the susceptible and protective HLA class II molecules. Remarkably, the interaction between CIITA and HLA-DRB1 genotypes is strong and additive. The OR for individuals having two susceptible HLA-DRB1 alleles is 14.1 in presence of the susceptible CIITA G/G or G/A genotypes and much lower (2.2) in presence of the protective CIITA A/A genotype. We conclude that quantitative as well as qualitative variation of HLA class II molecules have an effect on the risk of an individual developing EPF. Copyright © 2013 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Aggravated phosphorus limitation on biomass production under increasing nitrogen loading: a meta-analysis.

PubMed

Li, Yong; Niu, Shuli; Yu, Guirui

2016-02-01

Nitrogen (N) and phosphorus (P), either individually or in combination, have been demonstrated to limit biomass production in terrestrial ecosystems. Field studies have been extensively synthesized to assess global patterns of N impacts on terrestrial ecosystem processes. However, to our knowledge, no synthesis has been done so far to reveal global patterns of P impacts on terrestrial ecosystems, especially under different nitrogen (N) levels. Here, we conducted a meta-analysis of impacts of P addition, either alone or with N addition, on aboveground (AGB) and belowground biomass production (BGB), plant and soil P concentrations, and N : P ratio in terrestrial ecosystems. Overall, our meta-analysis quantitatively confirmed existing notions: (i) colimitation of N and P on biomass production and (ii) more P limitation in tropical forest than other ecosystems. More importantly, our analysis revealed new findings: (i) P limitation on biomass production was aggravated by N enrichment and (ii) plant P concentration was a better indicator of P limitation than soil P availability. Specifically, P addition increased AGB and BGB by 34% and 13%, respectively. The effect size of P addition on biomass production was larger in tropical forest than grassland, wetland, and tundra and varied with P fertilizer forms, P addition rates, or experimental durations. The P-induced increase in biomass production and plant P concentration was larger under elevated than ambient N. Our findings suggest that the global limitation of P on biomass production will become severer under increasing N fertilizer and deposition in the future. © 2015 John Wiley & Sons Ltd.

Family members' narratives of lifespace: Mapping changes before and after a brain injury causing driving disruption.

PubMed

Liang, Phyllis; Liddle, Jacki; Fleming, Jennifer; Gustafsson, Louise

2016-06-01

Family members of a person with an acquired brain injury often provide transport assistance during driving disruption with potential impacts on their own travel and participation within the community. The geographic area in which people travel and conduct their activities is known as lifespace. This study aimed to describe the quantitative changes in family members' lifespace after brain injury and understand their subjective experiences through interacting with maps during narratives. Mapping was embedded within in-depth semi-structured interviews with 15 family members. Two sets of maps were generated per participant showing the number of travel locations before and after brain injury. In the interviews, participants reflected on the perceived meaning of lifespace change. Qualitative data were analysed using a narrative approach. Quantitative data from the mapping revealed an increase in travel locations for nine participants, a decrease for five, and no change for one participant. Data analysis revealed four typologies which complemented and enriched the quantitative data: (i) I will do everything for him or her; (ii) Trying to fit all in; (iii) We spend all our time together now; (iv) I need to also care for myself. The findings describe the change in family members' lifespace after taking on the driver role following acquired brain injury. This study highlights the importance of understanding both quantitative and qualitative aspects of lifespace. The subjective experiences and consequences of lifespace changes are different from the impact on individuals with health conditions. Mapping in an interview as a tool has potential clinical utility. © 2016 Occupational Therapy Australia.

Data Driven Performance Evaluation of Wireless Sensor Networks

PubMed Central

Frery, Alejandro C.; Ramos, Heitor S.; Alencar-Neto, José; Nakamura, Eduardo; Loureiro, Antonio A. F.

2010-01-01

Wireless Sensor Networks are presented as devices for signal sampling and reconstruction. Within this framework, the qualitative and quantitative influence of (i) signal granularity, (ii) spatial distribution of sensors, (iii) sensors clustering, and (iv) signal reconstruction procedure are assessed. This is done by defining an error metric and performing a Monte Carlo experiment. It is shown that all these factors have significant impact on the quality of the reconstructed signal. The extent of such impact is quantitatively assessed. PMID:22294920

Ratiometric pH Imaging with a CoII2 MRI Probe via CEST Effects of Opposing pH Dependences (Postprint)

DTIC Science & Technology

2017-10-13

7b08574 14. ABSTRACT (Maximum 200 words) We report a Co2-based magnetic resonance (MR) probe that enables the ratiometric quantitation and imaging of...ratios of CEST peak intensities at 104 and 64 ppm are correlated with solution pH in the physiological range 6.5−7.6 to construct a linear calibration...magnetic resonance (MR); ratiometric quantitation ; chemical exchange saturation transfer (CEST); carboxamide; hydroxyl-substituted bisphosphonate

Detecting stellar-wind bubbles through infrared arcs in H II regions

NASA Astrophysics Data System (ADS)

Mackey, Jonathan; Haworth, Thomas J.; Gvaramadze, Vasilii V.; Mohamed, Shazrene; Langer, Norbert; Harries, Tim J.

2016-02-01

Mid-infrared arcs of dust emission are often seen near ionizing stars within H II regions. A possible explanations for these arcs is that they could show the outer edges of asymmetric stellar wind bubbles. We use two-dimensional, radiation-hydrodynamics simulations of wind bubbles within H II regions around individual stars to predict the infrared emission properties of the dust within the H II region. We assume that dust and gas are dynamically well-coupled and that dust properties (composition, size distribution) are the same in the H II region as outside it, and that the wind bubble contains no dust. We post-process the simulations to make synthetic intensity maps at infrared wavebands using the torus code. We find that the outer edge of a wind bubble emits brightly at 24 μm through starlight absorbed by dust grains and re-radiated thermally in the infrared. This produces a bright arc of emission for slowly moving stars that have asymmetric wind bubbles, even for cases where there is no bow shock or any corresponding feature in tracers of gas emission. The 24 μm intensity decreases exponentially from the arc with increasing distance from the star because the dust temperature decreases with distance. The size distribution and composition of the dust grains has quantitative but not qualitative effects on our results. Despite the simplifications of our model, we find good qualitative agreement with observations of the H II region RCW 120, and can provide physical explanations for any quantitative differences. Our model produces an infrared arc with the same shape and size as the arc around CD -38°11636 in RCW 120, and with comparable brightness. This suggests that infrared arcs around O stars in H II regions may be revealing the extent of stellar wind bubbles, although we have not excluded other explanations.

Arsenic upregulates the expression of angiotensin II Type I receptor in mouse aortic endothelial cells.

PubMed

Hossain, Ekhtear; Ota, Akinobu; Takahashi, Miyuki; Karnan, Sivasundaram; Damdindorj, Lkhagvasuren; Konishi, Yuko; Konishi, Hiroyuki; Hosokawa, Yoshitaka

2013-06-20

Although chronic arsenic exposure is a well-known risk for cardiovascular disease and has a strong correlation with hypertension, the molecular pathogenesis underlying arsenic exposure-induced hypertension remains poorly understood. To delineate the pathogenesis, we examined changes in the mRNA levels of 2 angiotensin II Type I receptor (AT1R) subtypes, AT1AR and AT1BR, in a mouse aortic endothelial cell line, END-D. Quantitative real-time PCR analysis revealed significant increases in the mRNA levels of 2 AT1R subtypes, AT1AR and AT1BR following sodium arsenite (SA) treatment. Flow cytometry analysis revealed that SA increases the generation of reactive oxygen species (ROS) in a dose-dependent manner. In addition, western blot analysis revealed that SA enhances the phosphorylations of c-Jun N-terminal kinases (JNK) and activated protein 1 (AP-1). These phosphorylations were inhibited by N-acetylcysteine (NAC), an anti-oxidant. Finally, SA-induced AT1R expression was found to be prevented both by NAC and specific JNK inhibitor, SP6001325, strongly indicating that AT1R upregulation is a result of the ROS-mediated activation of the JNK signaling pathway. Taken together, our results indicate that arsenic indeed upregulates the AT1R expression, thus highlighting a role of arsenic-induced aberrant AT1R signaling in the pathogenesis of hypertension. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Solid phase selective separation and preconcentration of Cu(II) by Cu(II)-imprinted polymethacrylic microbeads.

PubMed

Dakova, Ivanka; Karadjova, Irina; Ivanov, Ivo; Georgieva, Ventsislava; Evtimova, Bisera; Georgiev, George

2007-02-12

Ion-imprinted polymer (IIP) particles are prepared by copolymerization of methacrylic acid as monomer, trimethylolpropane trimethacrylate as crosslinking agent and 2,2'-azo-bis-isobutyronitrile as initiator in the presence of Cu(II), a Cu(II)-4-(2-pyridylazo)resorcinol (Cu(II)-PAR) complex, and PAR only. A batch procedure is used for the determination of the characteristics of the Cu(II) solid phase extraction from the IIP produced. The results obtained show that the Cu(II)-PAR IIP has the greatest adsorption capacity (37.4 micromol g(-1) of dry copolymer) among the IIPs investigated. The optimal pH value for the quantitative preconcentration is 7, and full desorption is achieved by 1 M HNO(3). The selectivity coefficients (S(Cu/Me)) for Me=Ni(II), Co(II) are 45.0 and 38.5, respectively. It is established that Cu(II)-PAR IIPs can be used repeatedly without a considerable adsorption capacity loss. The determination of Cu(II) ions in seawater shows that the interfering matrix does not influence the preconcentration and selectivity values of the Cu(II)-PAR IIPs. The detection and quantification limits are 0.001 micromol L(-1) (3sigma) and 0.003 micromol L(-1) (6sigma), respectively.

Chemically modified activated carbon with 1-acylthiosemicarbazide for selective solid-phase extraction and preconcentration of trace Cu(II), Hg(II) and Pb(II) from water samples.

PubMed

Gao, Ru; Hu, Zheng; Chang, Xijun; He, Qun; Zhang, Lijun; Tu, Zhifeng; Shi, Jianping

2009-12-15

A new sorbent 1-acylthiosemicarbazide-modified activated carbon (AC-ATSC) was prepared as a solid-phase extractant and applied for removing of trace Cu(II), Hg(II) and Pb(II) prior to their determination by inductively coupled plasma optical emission spectrometry (ICP-OES). The separation/preconcentration conditions of analytes were investigated, including effects of pH, the shaking time, the sample flow rate and volume, the elution condition and the interfering ions. At pH 3, the maximum static adsorption capacity of Cu(II), Hg(II) and Pb(II) onto the AC-ATSC were 78.20, 67.80 and 48.56 mg g(-1), respectively. The adsorbed metal ions were quantitatively eluted by 3.0 mL of 2% CS(NH2)2 and 2.0 mol L(-1) HCl solution. Common coexisting ions did not interfere with the separation. According to the definition of IUPAC, the detection limits (3sigma) of this method for Cu(II), Hg(II) and Pb(II) were 0.20, 0.12 and 0.45 ng mL(-1), respectively. The relative standard deviation under optimum conditions is less than 4.0% (n=8). The prepared sorbent was applied for the preconcentration of trace Cu(II), Hg(II) and Pb(II) in certified and water samples with satisfactory results.

Mapping sites of aspirin-induced acetylations in live cells by quantitative acid-cleavable activity-based protein profiling (QA-ABPP)

PubMed Central

Wang, Jigang; Zhang, Chong-Jing; Zhang, Jianbin; He, Yingke; Lee, Yew Mun; Chen, Songbi; Lim, Teck Kwang; Ng, Shukie; Shen, Han-Ming; Lin, Qingsong

2015-01-01

Target-identification and understanding of mechanism-of-action (MOA) are challenging for development of small-molecule probes and their application in biology and drug discovery. For example, although aspirin has been widely used for more than 100 years, its molecular targets have not been fully characterized. To cope with this challenge, we developed a novel technique called quantitative acid-cleavable activity-based protein profiling (QA-ABPP) with combination of the following two parts: (i) activity-based protein profiling (ABPP) and iTRAQ™ quantitative proteomics for identification of target proteins and (ii) acid-cleavable linker-based ABPP for identification of peptides with specific binding sites. It is known that reaction of aspirin with its target proteins leads to acetylation. We thus applied the above technique using aspirin-based probes in human cancer HCT116 cells. We identified 1110 target proteins and 2775 peptides with exact acetylation sites. By correlating these two sets of data, 523 proteins were identified as targets of aspirin. We used various biological assays to validate the effects of aspirin on inhibition of protein synthesis and induction of autophagy which were elicited from the pathway analysis of Aspirin target profile. This technique is widely applicable for target identification in the field of drug discovery and biology, especially for the covalent drugs. PMID:25600173

Spectral Interferences Manganese (Mn) - Europium (Eu) Lines in X-Ray Fluorescence Spectrometry Spectrum

NASA Astrophysics Data System (ADS)

Tanc, Beril; Kaya, Mustafa; Gumus, Lokman; Kumral, Mustafa

2016-04-01

X-ray fluorescence (XRF) spectrometry is widely used for quantitative and semi quantitative analysis of many major, minor and trace elements in geological samples. Some advantages of the XRF method are; non-destructive sample preparation, applicability for powder, solid, paste and liquid samples and simple spectrum that are independent from chemical state. On the other hand, there are some disadvantages of the XRF methods such as poor sensitivity for low atomic number elements, matrix effect (physical matrix effects, such as fine versus course grain materials, may impact XRF performance) and interference effect (the spectral lines of elements may overlap distorting results for one or more elements). Especially, spectral interferences are very significant factors for accurate results. In this study, semi-quantitative analyzed manganese (II) oxide (MnO, 99.99%) was examined. Samples were pelleted and analyzed with XRF spectrometry (Bruker S8 Tiger). Unexpected peaks were obtained at the side of the major Mn peaks. Although sample does not contain Eu element, in results 0,3% Eu2O3 was observed. These result can occur high concentration of MnO and proximity of Mn and Eu lines. It can be eliminated by using correction equation or Mn concentration can confirm with other methods (such as Atomic absorption spectroscopy). Keywords: Spectral Interferences; Manganese (Mn); Europium (Eu); X-Ray Fluorescence Spectrometry Spectrum.

Hydrogen (H) Isotope Composition of Type II Kerogen Extracted by Pyrolysis-GC-MS-IRMS: Terrestrial Shale Deposits as Martian Analogs

NASA Technical Reports Server (NTRS)

Socki, Richard A.; Pernia, Denet; Evans, Michael; Fu, Qi; Bissada, Kadry K.; Curiale, Joseph A.; Niles, Paul B.

2014-01-01

Described here is a technique for H isotope analysis of organic compounds pyrolyzed from kerogens isolated from gas- and liquids-rich shales. Application of this technique will progress the understanding of the use of H isotopes not only in potential kerogen occurrences on Mars, but also in terrestrial oil and gas resource plays. H isotope extraction and analyses were carried out utilizing a CDS 5000 Pyroprobe connected to a Thermo Trace GC interfaced with a Thermo MAT 253 IRMS. Also, a split of GC-separated products was sent to a DSQ II quadrupole MS to make qualitative and semi-quantitative compositional measurements of these products. Kerogen samples from five different basins (type II and II-S) were dehydrated (heated to 80 C overnight under vacuum) and analyzed for their H isotope compositions by Pyrolysis-GC-MS-TC-IRMS. This technique takes pyrolysis products separated via GC and reacts them in a high temperature conversion furnace (1450 C), which quantitatively forms H2. Samples ranging from 0.5 to 1.0mg in size, were pyrolyzed at 800 C for 30s. and separated on a Poraplot Q GC column. H isotope data from all kerogen samples typically show enrichment in D from low to high molecular weight. H2O average delta D = -215.2 per mille (V-SMOW), ranging from - 271.8 per mille for the Marcellus Shale to -51.9 per mille for a Polish shale. Higher molecular weight compounds like toluene (C7H8) have an average delta D of -89.7 per mille, ranging from -156.0 per mille for the Barnett Shale to -50.0 per mille for the Monterey Shale. We interpret these data as representative of potential H isotope exchange between hydrocarbons and sediment pore water during basin formation. Since hydrocarbon H isotopes readily exchange with water, these data may provide some useful information on gas-water or oil-water interaction in resource plays, and further as a possible indicator of paleoenvironmental conditions. Alternatively, our data may be an indication of H isotope exchange with water and/or acid during the kerogen isolation process. Either of these interpretations will prove useful when deciphering H isotope data derived from kerogen analyses. Understanding the role that these H-bearing compounds play in terrestrial shale paleo-environmental reconstruction may also prove useful as analogs for understanding the interactions of water and potential kerogen/organic compounds on the planet Mars.

Quantitative analysis of collagen network structure and fibril dimensions in cartilage repair with autologous chondrocyte transplantation.

PubMed

Långsjö, Teemu K; Vasara, Anna I; Hyttinen, Mika M; Lammi, Mikko J; Kaukinen, Antti; Helminen, Heikki J; Kiviranta, Ilkka

2010-01-01

The aim of this study was to undertake a stereological analysis to quantify the dimensions of the collagen network in the repair tissue of porcine joints after they had been subjected to autologous chondrocyte transplantation (ACT). ACT was used to repair cartilage lesions in knee joints of pigs. Electron-microscopic stereology, immunostaining for type II collagen, and quantitative polarized-light microscopy were utilized to study the collagen fibrils in the repair tissue 3 and 12 months after the operation. The collagen volume density (V(V)) was lower in the repair tissue than in normal cartilage at 3 months (20.4 vs. 23.7%) after the operation. The collagen surface density (S(V), 1.5·10(-2) vs. 3.1·10(-2) nm(2)/nm(3)) and V(V) increased with time in the repair tissue (20.4 vs. 44.7%). Quantitative polarized-light microscopy detected a higher degree of collagen parallelism in the repair tissue at 3 months after the operation (55.7 vs. 49.7%). In contrast, 1 year after the operation, fibril parallelism was lower in the repair tissue than in the control cartilage (47.5 vs. 69.8%). Following ACT, V(V) and S(V) increased in the repair tissue with time, reflecting maturation of the tissue. One year after the operation, there was a lower level of fibril organization in the repair tissue than in the control cartilage. Thus, the newly synthesized collagen fibrils in the repair tissue appeared to form a denser network than in the control cartilage, but the fibrils remained more randomly oriented. Copyright © 2010 S. Karger AG, Basel.

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.

PubMed

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. This database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.

Quantitative DNA methylation analyses reveal stage dependent DNA methylation and association to clinico-pathological factors in breast tumors.

PubMed

Klajic, Jovana; Fleischer, Thomas; Dejeux, Emelyne; Edvardsen, Hege; Warnberg, Fredrik; Bukholm, Ida; Lønning, Per Eystein; Solvang, Hiroko; Børresen-Dale, Anne-Lise; Tost, Jörg; Kristensen, Vessela N

2013-10-05

Aberrant DNA methylation of regulatory genes has frequently been found in human breast cancers and correlated to clinical outcome. In the present study we investigate stage specific changes in the DNA methylation patterns in order to identify valuable markers to understand how these changes affect breast cancer progression. Quantitative DNA methylation analyses of 12 candidate genes ABCB1, BRCCA1, CDKN2A, ESR1, GSTP1, IGF2, MGMT, HMLH1, PPP2R2B, PTEN, RASSF1A and FOXC1 was performed by pyrosequencing a series of 238 breast cancer tissue samples from DCIS to invasive tumors stage I to IV. Significant differences in methylation levels between the DCIS and invasive stage II tumors were observed for six genes RASSF1A, CDKN2A, MGMT, ABCB1, GSTP1 and FOXC1. RASSF1A, ABCB1 and GSTP1 showed significantly higher methylation levels in late stage compared to the early stage breast carcinoma. Z-score analysis revealed significantly lower methylation levels in DCIS and stage I tumors compared with stage II, III and IV tumors. Methylation levels of PTEN, PPP2R2B, FOXC1, ABCB1 and BRCA1 were lower in tumors harboring TP53 mutations then in tumors with wild type TP53. Z-score analysis showed that TP53 mutated tumors had significantly lower overall methylation levels compared to tumors with wild type TP53. Methylation levels of RASSF1A, PPP2R2B, GSTP1 and FOXC1 were higher in ER positive vs. ER negative tumors and methylation levels of PTEN and CDKN2A were higher in HER2 positive vs. HER2 negative tumors. Z-score analysis also showed that HER2 positive tumors had significantly higher z-scores of methylation compared to the HER2 negative tumors. Univariate survival analysis identifies methylation status of PPP2R2B as significant predictor of overall survival and breast cancer specific survival. In the present study we report that the level of aberrant DNA methylation is higher in late stage compared with early stage of invasive breast cancers and DCIS for genes mentioned above.

Preparing Colorful Astronomical Images II

NASA Astrophysics Data System (ADS)

Levay, Z. G.; Frattare, L. M.

2002-12-01

We present additional techniques for using mainstream graphics software (Adobe Photoshop and Illustrator) to produce composite color images and illustrations from astronomical data. These techniques have been used on numerous images from the Hubble Space Telescope to produce photographic, print and web-based products for news, education and public presentation as well as illustrations for technical publication. We expand on a previous paper to present more detail and additional techniques, taking advantage of new or improved features available in the latest software versions. While Photoshop is not intended for quantitative analysis of full dynamic range data (as are IRAF or IDL, for example), we have had much success applying Photoshop's numerous, versatile tools to work with scaled images, masks, text and graphics in multiple semi-transparent layers and channels.

Preparation and quantification of radioactive particles for tracking hydrodynamic behavior in multiphase reactors.

PubMed

Yunos, Mohd Amirul Syafiq Mohd; Hussain, Siti Aslina; Yusoff, Hamdan Mohamed; Abdullah, Jaafar

2014-09-01

Radioactive particle tracking (RPT) has emerged as a promising and versatile technique that can provide rich information about a variety of multiphase flow systems. However, RPT is not an off-the-shelf technique, and thus, users must customize RPT for their applications. This paper presents a simple procedure for preparing radioactive tracer particles created via irradiation with neutrons from the TRIGA Mark II research reactor. The present study focuses on the performance evaluation of encapsulated gold and scandium particles for applications as individual radioactive tracer particles using qualitative and quantitative neutron activation analysis (NAA) and an X-ray microcomputed tomography (X-ray Micro-CT) scanner installed at the Malaysian Nuclear Agency. Copyright © 2014 Elsevier Ltd. All rights reserved.

Curve of Spee and its relationship to vertical eruption of teeth among different malocclusion groups.

PubMed

Veli, Ilknur; Ozturk, Mehmet Ali; Uysal, Tancan

2015-03-01

Our objectives were to assess the depth of the curve of Spee (COS) in different malocclusion groups, to relate this to the eruption of anterior or posterior teeth quantitatively, and to determine whether the depth of the COS is affected by the vertical eruption of anterior or posterior teeth. Two hundred conventional lateral cephalograms and 3-dimensional models of untreated patients (70 boys, mean age: 16.4 ± 1.4 years; 130 young women, mean age: 18.1 ± 1.8 years) were included and assigned to 4 malocclusion groups as Class I, Class II Division 1, Class II Division 2, and Class III. The depth of the COS, overjet, and overbite were measured on 3-dimensional models. The perpendicular distance between the incisal tip of the mandibular central incisor (L1-MP), the deepest point of the COS (S-MP), and the distobuccal cusp tip of the mandibular second molar (L7-MP) to the mandibular plane were calculated and proportioned with each other. The Pearson correlation coefficient was calculated, and multiple linear regression analysis was carried out. Also, multivariate analysis of variance was performed at the P <0.05 level. The mesiobuccal cusp of the first molar was the deepest part of the COS in all groups, with a maximum depth of 2.44 ± 0.73 mm in the Class II Division 1 subjects and a minimum depth of 1.76 ± 0.94 in the Class III subjects. The depth of the COS changed as follows: Class II Division 1 > Class II Division 2 > Class I > Class III malocclusion groups. Statistically significant positive correlations were found between the depth of the COS and L1-MP/S-MP (r = 0.541) and L7-MP/S-MP (r = 0.269) in the Class I and Class III subjects, and between the depth of the COS and overjet (r = 0.483) and L7-MP/S-MP (r = 0.289) in the Class II Division 1 subjects. All variables except overjet had positive correlations with the depth of the COS in Class II Division 2 subjects. The multivariate analysis of variance showed statistically significant differences in overjet, overbite, L1-MP/S-MP, L7-MP/S-MP, and the depth of the COS (P <0.001) among the groups. Although the overjet differed, vertical eruption of the anterior teeth did not differ among the different malocclusion groups and had a significant contribution to the depth of the COS in subjects with Class I and Class III malocclusions. Copyright © 2015 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

Development of a structured sensory honey analysis: application to artisanal Madrid honeys.

PubMed

González, M M; de Lorenzo, C; Pérez, R A

2010-02-01

In this work a methodology to evaluate the sensory properties of honeys has been developed. The sensory analysis was carried out by means of a quantitative descriptive analysis (QDA) method, based on several reference scales, for the coverage of the designed range for each descriptor. The peculiarity of this sensory analysis is that the reference scales have been constituted by common foodstuffs agreed upon by consensus of the panel. The main sensory attributes evaluated in the analyses were: adhesiveness, viscosity, bitterness, aroma, sweetness, acidity, color and granularity. Both the intensity and persistence of honey aromas have also been estimated, together with the classification of the identified aromatic attributes into different groups. The method was applied to 55 artisanal honeys from Madrid (Spain) with the following results: (i) the developed sensory profile sheet allowed a satisfactory description of Madrid honeys; (ii) correlations between sensory attributes of three broad groups of Madrid honeys were obtained and (iii) aroma persistence, sweetness, bitterness, color and granularity appeared as the main sensorial characteristics of honey with discrimination power between floral and honeydew honeys.

75 FR 54117 - Building Energy Standards Program: Preliminary Determination Regarding Energy Efficiency...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-03

... Response to Comments on Previous Analysis C. Summary of the Comparative Analysis 1. Quantitative Analysis 2... preliminary quantitative analysis are specific building designs, in most cases with specific spaces defined... preliminary determination. C. Summary of the Comparative Analysis DOE carried out both a broad quantitative...

Stability of polymorphic forms of ranitidine hydrochloride.

PubMed

Wu, V; Rades, T; Saville, D J

2000-07-01

Ranitidine-HCl can exist in two different polymorphic forms: form I (m.p. 134-140 degrees C) and form II (m.p. 140-144 degrees C). In the present study the stability of form I of ranitidine-HCl to a selection of powder pretreatments, to reflect conditions which might occur in manufacturing procedures, and also to a limited range of storage conditions was investigated. The original samples of form I and form II used were characterised by X-ray powder diffraction (XRPD), hot stage microscopy (HSM) and differential scanning calorimetry (DSC). A quantitative XRPD method for determining the fraction of form II in the presence of form I was used. XRPD data were analysed using regression techniques and artificial neural networks (ANN). The quantitative XRPD technique was then used to monitor the relative proportion of form II in each treated sample. Pretreatments of form I included (i) mixing with form II or with common excipients (ii) compression and grinding (iii) contact with solvents (followed by drying) before storage. Storage conditions involved three temperatures (20 degrees C, 30 degrees C, 42 degrees C) and three relative humidities (45% RH; 55% RH; 75% RH). Samples were stored for a period of 6 months. A limited factorial design was used. No increase in the form II:form I ratio was observed in the following pretreatment processes: introduction of form II nuclei into form I; introduction of excipients to form I; compression of form I powder at 5 and 15 tons; normal mixing and grinding processes; addition of isopropanol (IPA) or water/IPA mix followed by drying. In the pretreatment process where water was added to form I powder (with most or all of the powder dissolving), drying of the liquefied mass led to a mix of form I and form II. On storage at room temperature (20-30 degrees C), low relative humidity (45-55% RH), and in an air-tight container there was no increase in the form II:form I ratio. Storage of form I/form II mixes, particularly at high humidity, resulted in a preferential loss of form II (compared to form I). Loss was greater at 30 degrees C/75% RH than at 20 degrees C/75% RH. Form II was also preferentially lost under low humidity conditions created by a saturated solution of potassium carbonate (45% RH) at the elevated temperature of 42 degrees C. This environment was shown to be acidic.

MicroRNA-297 promotes cardiomyocyte hypertrophy via targeting sigma-1 receptor.

PubMed

Bao, Qinxue; Zhao, Mingyue; Chen, Li; Wang, Yu; Wu, Siyuan; Wu, Wenchao; Liu, Xiaojing

2017-04-15

Sigma-1 receptor (Sig-1R) is a ligand-regulated endoplasmic reticulum (ER) chaperone involved in cardiac hypertrophy, but it is not known whether Sig-1R is regulated by microRNAs (miRNAs). According to bioinformatic analysis, miR-297 was suggested as a potential target miRNA for Sig-1R. Therefore, we verified whether miR-297 could target Sig-1R and investigated the possible mechanisms underlying the role of miR-297 in cardiac hypertrophy. Bioinformatic analysis combined with laboratory experiments, including quantitative RT-PCR, Western blotting, and luciferase assay, were performed to identify the target miRNA of Sig-1R. Transverse aortic constriction (TAC) model and neonatal rat cardiomyocytes (NCMs) stimulated with angiotensin II (AngII) were used to explore the relationship between miR-297 and Sig-1R. Additionally, the function of miR-297 in cardiomyocyte hypertrophy and ER stress/unfolded protein response (UPR) signaling pathway was investigated by transfecting miR-297 mimics/inhibitor. miR-297 levels were increased in both TAC-induced hypertrophic heart tissue and AngII-induced cardiomyocyte hypertrophy. Up-regulation of miR-297 by specific mimics exacerbated AngII-induced cardiomyocyte hypertrophy, whereas inhibition of miR-297 suppressed the process. During cardiomyocyte hypertrophy, Sig-1R expression, which was negatively regulated by miR-297 by directly targeting its 3'untranslated region (UTR), was decreased. Furthermore, attenuation of miR-297 inhibited the activation of X-box binding protein 1 (Xbp1) and activating transcriptional factor 4 (ATF4) signaling pathways in NCMs. Our data demonstrate that miR-297 promotes cardiomyocyte hypertrophy by inhibiting the expression of Sig-1R and activation of ER stress signaling, which provides a novel interpretation for cardiac hypertrophy. Copyright © 2017 Elsevier Inc. All rights reserved.

Physiotherapy rehabilitation for whiplash associated disorder II: a systematic review and meta-analysis of randomised controlled trials

PubMed Central

Wright, Chris; Heneghan, Nicola; Eveleigh, Gillian; Calvert, Melanie; Freemantle, Nick

2011-01-01

Objective To evaluate effectiveness of physiotherapy management in patients experiencing whiplash associated disorder II, on clinically relevant outcomes in the short and longer term. Design Systematic review and meta-analysis. Two reviewers independently searched information sources, assessed studies for inclusion, evaluated risk of bias and extracted data. A third reviewer mediated disagreement. Assessment of risk of bias was tabulated across included trials. Quantitative synthesis was conducted on comparable outcomes across trials with similar interventions. Meta-analyses compared effect sizes, with random effects as primary analyses. Data sources Predefined terms were employed to search electronic databases. Additional studies were identified from key journals, reference lists, authors and experts. Eligibility criteria for selecting studies Randomised controlled trials (RCTs) published in English before 31 December 2010 evaluating physiotherapy management of patients (>16 years), experiencing whiplash associated disorder II. Any physiotherapy intervention was included, when compared with other types of management, placebo/sham, or no intervention. Measurements reported on ≥1 outcome from the domains within the international classification of function, disability and health, were included. Results 21 RCTs (2126 participants, 9 countries) were included. Interventions were categorised as active physiotherapy or a specific physiotherapy intervention. 20/21 trials were evaluated as high risk of bias and one as unclear. 1395 participants were incorporated in the meta-analyses on 12 trials. In evaluating short term outcome in the acute/sub-acute stage, there was some evidence that active physiotherapy intervention reduces pain and improves range of movement, and that a specific physiotherapy intervention may reduce pain. However, moderate/considerable heterogeneity suggested that treatments may differ in nature or effect in different trial patients. Differences between participants, interventions and trial designs limited potential meta-analyses. Conclusions Inconclusive evidence exists for the effectiveness of physiotherapy management for whiplash associated disorder II. There is potential benefit for improving range of movement and pain short term through active physiotherapy, and for improving pain through a specific physiotherapy intervention. PMID:22102642

THE ORION H ii REGION AND THE ORION BAR IN THE MID-INFRARED

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

Salgado, F.; Tielens, A. G. G. M.; Berné, O.

2016-10-20

We present mid-infrared photometry of the Orion bar obtained with the Faint Object infraRed Camera for the SOFIA Telescope (FORCAST) on board SOFIA at 6.4, 6.6, 7.7, 19.7, 31.5, and 37.1 μ m. By complementing this observation with archival FORCAST and Herschel /PACS images, we are able to construct a complete infrared spectral energy distribution of the Huygens region in the Orion nebula. Comparing the infrared images with gas tracers, we find that PACS maps trace the molecular cloud, while the FORCAST data trace the photodissociation region (PDR) and the H ii region. Analysis of the energetics of the regionmore » reveal that the PDR extends for 0.28 pc along the line of sight and that the bar is inclined at an angle of 4°. The infrared and submillimeter images reveal that the Orion bar represents a swept-up shell with a thickness of 0.1 pc. The mass of the shell implies a shock velocity of ≃3 km s{sup −1} and an age of ≃10{sup 5} years for the H ii region. Our analysis shows that the UV and infrared dust opacities in the H ii region and the PDR are a factor 5 to 10 lower than in the diffuse interstellar medium. In the ionized gas, Ly α photons are a major source of dust heating at distances larger than ≃0.06 pc from θ {sup 1} Ori C. Dust temperatures can be explained if the size of the grains is between 0.1 and 1 μ m. We derive the photoelectric heating efficiency of the atomic gas in the Orion bar. The results are in good qualitative agreement with models and the quantitative differences indicate a decreased polycyclic aromatic hydrocarbon abundance in this region.« less

Application of Standards-Based Quantitative SEM-EDS Analysis to Oxide Minerals

NASA Astrophysics Data System (ADS)

Mengason, M. J.; Ritchie, N. W.; Newbury, D. E.

2016-12-01

SEM and EPMA analysis are powerful tools for documenting and evaluating the relationships between minerals in thin sections and for determining chemical compositions in-situ. The time and costs associated with determining major, minor, and some trace element concentrations in geologic materials can be reduced due to advances in EDS spectrometer performance and the availability of software tools such as NIST DTSA II to perform multiple linear least squares (MLLS) fitting of energy spectra from standards to the spectra from samples recorded under the same analytical conditions. MLLS fitting is able to overcome spectral peak overlaps among the transition-metal elements that commonly occur in oxide minerals, which had previously been seen as too difficult for EDS analysis, allowing for rapid and accurate determination of concentrations. The quantitative use of EDS is demonstrated in the chemical analysis of magnetite (NMNH 114887) and ilmenite (NMNH 96189) from the Smithsonian Natural History Museum Microbeam Standards Collection. Average concentrations from nine total spots over three grains are given in mass % listed as (recommended; measured concentration ± one standard deviation). Spectra were collected for sixty seconds live time at 15 kV and 10 nA over a 12 micrometer wide scan area. Analysis of magnetite yielded Magnesium (0.03; 0.04 ± 0.01), Aluminum (none given; 0.040 ± 0.006), Titanium (0.10; 0.11 ± 0.02), Vanadium (none given; 0.16 ± 0.01), Chromium (0.17; 0.14 ± 0.02), and Iron (70.71, 71.4 ± 0.2). Analysis of ilmenite yielded Magnesium (0.19; 0.183 ± 0.008), Aluminum (none given; 0.04 ± 0.02), Titanium (27.4, 28.1 ± 0.1), Chromium (none given; 0.04 ± 0.01), Manganese (3.69; 3.73 ± 0.03), Iron (36.18; 35.8 ± 0.1), and Niobium (0.64; 0.68 ± 0.03). The analysis of geologic materials by standards-based quantitative EDS can be further illustrated with chemical analyses of oxides from ocean island basalts representing several locations globally to illustrate the suitability of the method to the goal of evaluating trends in major and minor element concentrations and variability among locations. The shorter collection times of EDS, compared to WDS, allow greater sampling of the populations of oxides present as fine-grained quench products in addition to sampling larger inclusions hosted by silicate minerals.

Generalized whole-body Patlak parametric imaging for enhanced quantification in clinical PET.

PubMed

Karakatsanis, Nicolas A; Zhou, Yun; Lodge, Martin A; Casey, Michael E; Wahl, Richard L; Zaidi, Habib; Rahmim, Arman

2015-11-21

We recently developed a dynamic multi-bed PET data acquisition framework to translate the quantitative benefits of Patlak voxel-wise analysis to the domain of routine clinical whole-body (WB) imaging. The standard Patlak (sPatlak) linear graphical analysis assumes irreversible PET tracer uptake, ignoring the effect of FDG dephosphorylation, which has been suggested by a number of PET studies. In this work: (i) a non-linear generalized Patlak (gPatlak) model is utilized, including a net efflux rate constant kloss, and (ii) a hybrid (s/g)Patlak (hPatlak) imaging technique is introduced to enhance contrast to noise ratios (CNRs) of uptake rate Ki images. Representative set of kinetic parameter values and the XCAT phantom were employed to generate realistic 4D simulation PET data, and the proposed methods were additionally evaluated on 11 WB dynamic PET patient studies. Quantitative analysis on the simulated Ki images over 2 groups of regions-of-interest (ROIs), with low (ROI A) or high (ROI B) true kloss relative to Ki, suggested superior accuracy for gPatlak. Bias of sPatlak was found to be 16-18% and 20-40% poorer than gPatlak for ROIs A and B, respectively. By contrast, gPatlak exhibited, on average, 10% higher noise than sPatlak. Meanwhile, the bias and noise levels for hPatlak always ranged between the other two methods. In general, hPatlak was seen to outperform all methods in terms of target-to-background ratio (TBR) and CNR for all ROIs. Validation on patient datasets demonstrated clinical feasibility for all Patlak methods, while TBR and CNR evaluations confirmed our simulation findings, and suggested presence of non-negligible kloss reversibility in clinical data. As such, we recommend gPatlak for highly quantitative imaging tasks, while, for tasks emphasizing lesion detectability (e.g. TBR, CNR) over quantification, or for high levels of noise, hPatlak is instead preferred. Finally, gPatlak and hPatlak CNR was systematically higher compared to routine SUV values.