Quantitative imaging of rhizosphere pH and CO2 dynamics with planar optodes.

PubMed

Blossfeld, Stephan; Schreiber, Christina Maria; Liebsch, Gregor; Kuhn, Arnd Jürgen; Hinsinger, Philippe

2013-07-01

Live imaging methods have become extremely important for the exploration of biological processes. In particular, non-invasive measurement techniques are key to unravelling organism-environment interactions in close-to-natural set-ups, e.g. in the highly heterogeneous and difficult-to-probe environment of plant roots: the rhizosphere. pH and CO2 concentration are the main drivers of rhizosphere processes. Being able to monitor these parameters at high spatio-temporal resolution is of utmost importance for relevant interpretation of the underlying processes, especially in the complex environment of non-sterile plant-soil systems. This study introduces the application of easy-to-use planar optode systems in different set-ups to quantify plant root-soil interactions. pH- and recently developed CO2-sensors were applied to rhizobox systems to investigate roots with different functional traits, highlighting the potential of these tools. Continuous and highly resolved real-time measurements were made of the pH dynamics around Triticum turgidum durum (durum wheat) roots, Cicer arietinum (chickpea) roots and nodules, and CO2 dynamics in the rhizosphere of Viminaria juncea. Wheat root tips acidified slightly, while their root hair zone alkalized their rhizosphere by more than 1 pH unit and the effect of irrigation on soil pH could be visualized as well. Chickpea roots and nodules acidified the surrounding soil during N2 fixation and showed diurnal changes in acidification activity. A growing root of V. juncea exhibited a large zone of influence (mm) on soil CO2 content and therefore on its biogeochemical surrounding, all contributing to the extreme complexity of the root-soil interactions. This technique provides a unique tool for future root research applications and overcomes limitations of previous systems by creating quantitative maps without, for example, interpolation and time delays between single data points.

Mapping Soil pH Buffering Capacity of Selected Fields

NASA Technical Reports Server (NTRS)

Weaver, A. R.; Kissel, D. E.; Chen, F.; West, L. T.; Adkins, W.; Rickman, D.; Luvall, J. C.

2003-01-01

Soil pH buffering capacity, since it varies spatially within crop production fields, may be used to define sampling zones to assess lime requirement, or for modeling changes in soil pH when acid forming fertilizers or manures are added to a field. Our objective was to develop a procedure to map this soil property. One hundred thirty six soil samples (0 to 15 cm depth) from three Georgia Coastal Plain fields were titrated with calcium hydroxide to characterize differences in pH buffering capacity of the soils. Since the relationship between soil pH and added calcium hydroxide was approximately linear for all samples up to pH 6.5, the slope values of these linear relationships for all soils were regressed on the organic C and clay contents of the 136 soil samples using multiple linear regression. The equation that fit the data best was b (slope of pH vs. lime added) = 0.00029 - 0.00003 * % clay + 0.00135 * % O/C, r(exp 2) = 0.68. This equation was applied within geographic information system (GIS) software to create maps of soil pH buffering capacity for the three fields. When the mapped values of the pH buffering capacity were compared with measured values for a total of 18 locations in the three fields, there was good general agreement. A regression of directly measured pH buffering capacities on mapped pH buffering capacities at the field locations for these samples gave an r(exp 2) of 0.88 with a slope of 1.04 for a group of soils that varied approximately tenfold in their pH buffering capacities.

Quantitative susceptibility mapping of human brain at 3T: a multisite reproducibility study.

PubMed

Lin, P-Y; Chao, T-C; Wu, M-L

2015-03-01

Quantitative susceptibility mapping of the human brain has demonstrated strong potential in examining iron deposition, which may help in investigating possible brain pathology. This study assesses the reproducibility of quantitative susceptibility mapping across different imaging sites. In this study, the susceptibility values of 5 regions of interest in the human brain were measured on 9 healthy subjects following calibration by using phantom experiments. Each of the subjects was imaged 5 times on 1 scanner with the same procedure repeated on 3 different 3T systems so that both within-site and cross-site quantitative susceptibility mapping precision levels could be assessed. Two quantitative susceptibility mapping algorithms, similar in principle, one by using iterative regularization (iterative quantitative susceptibility mapping) and the other with analytic optimal solutions (deterministic quantitative susceptibility mapping), were implemented, and their performances were compared. Results show that while deterministic quantitative susceptibility mapping had nearly 700 times faster computation speed, residual streaking artifacts seem to be more prominent compared with iterative quantitative susceptibility mapping. With quantitative susceptibility mapping, the putamen, globus pallidus, and caudate nucleus showed smaller imprecision on the order of 0.005 ppm, whereas the red nucleus and substantia nigra, closer to the skull base, had a somewhat larger imprecision of approximately 0.01 ppm. Cross-site errors were not significantly larger than within-site errors. Possible sources of estimation errors are discussed. The reproducibility of quantitative susceptibility mapping in the human brain in vivo is regionally dependent, and the precision levels achieved with quantitative susceptibility mapping should allow longitudinal and multisite studies such as aging-related changes in brain tissue magnetic susceptibility. © 2015 by American Journal of Neuroradiology.

Quantitative characterization of all single amino acid variants of a viral capsid-based drug delivery vehicle.

PubMed

Hartman, Emily C; Jakobson, Christopher M; Favor, Andrew H; Lobba, Marco J; Álvarez-Benedicto, Ester; Francis, Matthew B; Tullman-Ercek, Danielle

2018-04-11

Self-assembling proteins are critical to biological systems and industrial technologies, but predicting how mutations affect self-assembly remains a significant challenge. Here, we report a technique, termed SyMAPS (Systematic Mutation and Assembled Particle Selection), that can be used to characterize the assembly competency of all single amino acid variants of a self-assembling viral structural protein. SyMAPS studies on the MS2 bacteriophage coat protein revealed a high-resolution fitness landscape that challenges some conventional assumptions of protein engineering. An additional round of selection identified a previously unknown variant (CP[T71H]) that is stable at neutral pH but less tolerant to acidic conditions than the wild-type coat protein. The capsids formed by this variant could be more amenable to disassembly in late endosomes or early lysosomes-a feature that is advantageous for delivery applications. In addition to providing a mutability blueprint for virus-like particles, SyMAPS can be readily applied to other self-assembling proteins.

High-resolution melt analysis to identify and map sequence-tagged site anchor points onto linkage maps: a white lupin (Lupinus albus) map as an exemplar.

PubMed

Croxford, Adam E; Rogers, Tom; Caligari, Peter D S; Wilkinson, Michael J

2008-01-01

* The provision of sequence-tagged site (STS) anchor points allows meaningful comparisons between mapping studies but can be a time-consuming process for nonmodel species or orphan crops. * Here, the first use of high-resolution melt analysis (HRM) to generate STS markers for use in linkage mapping is described. This strategy is rapid and low-cost, and circumvents the need for labelled primers or amplicon fractionation. * Using white lupin (Lupinus albus, x = 25) as a case study, HRM analysis was applied to identify 91 polymorphic markers from expressed sequence tag (EST)-derived and genomic libraries. Of these, 77 generated STS anchor points in the first fully resolved linkage map of the species. The map also included 230 amplified fragment length polymorphisms (AFLP) loci, spanned 1916 cM (84.2% coverage) and divided into the expected 25 linkage groups. * Quantitative trait loci (QTL) analyses performed on the population revealed genomic regions associated with several traits, including the agronomically important time to flowering (tf), alkaloid synthesis and stem height (Ph). Use of HRM-STS markers also allowed us to make direct comparisons between our map and that of the related crop, Lupinus angustifolius, based on the conversion of RFLP, microsatellite and single nucleotide polymorphism (SNP) markers into HRM markers.

Group additivity-Pourbaix diagrams advocate thermodynamically stable nanoscale clusters in aqueous environments

PubMed Central

Wills, Lindsay A.; Qu, Xiaohui; Chang, I-Ya; Mustard, Thomas J. L.; Keszler, Douglas A.; Persson, Kristin A.; Cheong, Paul Ha-Yeon

2017-01-01

The characterization of water-based corrosion, geochemical, environmental and catalytic processes rely on the accurate depiction of stable phases in a water environment. The process is aided by Pourbaix diagrams, which map the equilibrium solid and solution phases under varying conditions of pH and electrochemical potential. Recently, metastable or possibly stable nanometric aqueous clusters have been proposed as intermediate species in non-classical nucleation processes. Herein, we describe a Group Additivity approach to obtain Pourbaix diagrams with full consideration of multimeric cluster speciation from computations. Comparisons with existing titration results from experiments yield excellent agreement. Applying this Group Additivity-Pourbaix approach to Group 13 elements, we arrive at a quantitative evaluation of cluster stability, as a function of pH and concentration, and present compelling support for not only metastable but also thermodynamically stable multimeric clusters in aqueous solutions. PMID:28643782

Group additivity-Pourbaix diagrams advocate thermodynamically stable nanoscale clusters in aqueous environments

NASA Astrophysics Data System (ADS)

Wills, Lindsay A.; Qu, Xiaohui; Chang, I.-Ya; Mustard, Thomas J. L.; Keszler, Douglas A.; Persson, Kristin A.; Cheong, Paul Ha-Yeon

2017-06-01

The characterization of water-based corrosion, geochemical, environmental and catalytic processes rely on the accurate depiction of stable phases in a water environment. The process is aided by Pourbaix diagrams, which map the equilibrium solid and solution phases under varying conditions of pH and electrochemical potential. Recently, metastable or possibly stable nanometric aqueous clusters have been proposed as intermediate species in non-classical nucleation processes. Herein, we describe a Group Additivity approach to obtain Pourbaix diagrams with full consideration of multimeric cluster speciation from computations. Comparisons with existing titration results from experiments yield excellent agreement. Applying this Group Additivity-Pourbaix approach to Group 13 elements, we arrive at a quantitative evaluation of cluster stability, as a function of pH and concentration, and present compelling support for not only metastable but also thermodynamically stable multimeric clusters in aqueous solutions.

Usefulness of quantitative susceptibility mapping for the diagnosis of Parkinson disease.

PubMed

Murakami, Y; Kakeda, S; Watanabe, K; Ueda, I; Ogasawara, A; Moriya, J; Ide, S; Futatsuya, K; Sato, T; Okada, K; Uozumi, T; Tsuji, S; Liu, T; Wang, Y; Korogi, Y

2015-06-01

Quantitative susceptibility mapping allows overcoming several nonlocal restrictions of susceptibility-weighted and phase imaging and enables quantification of magnetic susceptibility. We compared the diagnostic accuracy of quantitative susceptibility mapping and R2* (1/T2*) mapping to discriminate between patients with Parkinson disease and controls. For 21 patients with Parkinson disease and 21 age- and sex-matched controls, 2 radiologists measured the quantitative susceptibility mapping values and R2* values in 6 brain structures (the thalamus, putamen, caudate nucleus, pallidum, substantia nigra, and red nucleus). The quantitative susceptibility mapping values and R2* values of the substantia nigra were significantly higher in patients with Parkinson disease (P < .01); measurements in other brain regions did not differ significantly between patients and controls. For the discrimination of patients with Parkinson disease from controls, receiver operating characteristic analysis suggested that the optimal cutoff values for the substantia nigra, based on the Youden Index, were >0.210 for quantitative susceptibility mapping and >28.8 for R2*. The sensitivity, specificity, and accuracy of quantitative susceptibility mapping were 90% (19 of 21), 86% (18 of 21), and 88% (37 of 42), respectively; for R2* mapping, they were 81% (17 of 21), 52% (11 of 21), and 67% (28 of 42). Pair-wise comparisons showed that the areas under the receiver operating characteristic curves were significantly larger for quantitative susceptibility mapping than for R2* mapping (0.91 versus 0.69, P < .05). Quantitative susceptibility mapping showed higher diagnostic performance than R2* mapping for the discrimination between patients with Parkinson disease and controls. © 2015 by American Journal of Neuroradiology.

Establishment of a high-resolution 2-D reference map of human spermatozoal proteins from 12 fertile sperm-bank donors.

PubMed

Li, Ling-Wei; Fan, Li-Qing; Zhu, Wen-Bing; Nien, Hong-Chuan; Sun, Bo-Lan; Luo, Ke-Li; Liao, Ting-Ting; Tang, Le; Lu, Guang-Xiu

2007-05-01

To extend the analysis of the proteome of human spermatozoa and establish a 2-D gel electrophoresis (2-DE) reference map of human spermatozoal proteins in a pH range of 3.5-9.0. In order to reveal more protein spots, immobilized pH gradient strips (24 cm) of broad range of pH 3-10 and the narrower range of pH 6-9, as well as different overlapping narrow range pH immobilized pH gradient (IPG) strips, including 3.5-4.5, 4.0-5.0, 4.5-5.5, 5.0-6.0 and 5.5-6.7, were used. After 2-DE, several visually identical spots between the different pH range 2-D gel pairs were cut from the gels and confirmed by mass spectrometry and used as landmarks for computer analysis. The 2-D reference map with pH value from 3.5 to 9.0 was synthesized by using the ImageMaster analysis software. The overlapping spots were excluded, so that every spot was counted only once. A total of 3872 different protein spots were identified from the reference map, an approximately 3-fold increase compared to the broad range pH 3-10 IPG strip (1306 spots). The present 2-D pattern is a high resolution 2-D reference map for human fertile spermatozoal protein spots. A comprehensive knowledge of the protein composition of human spermatozoa is very meaningful in studying dysregulation of male fertility.

What Is a Doctorate? A Concept-Mapped Analysis of Process versus Product in the Supervision of Lab-Based PhDs

ERIC Educational Resources Information Center

Kandiko, Camille B.; Kinchin, Ian M.

2012-01-01

Background: Concept-mapping and interview techniques are used to track knowledge and understanding over the duration of PhD study amongst four students and their supervisors in the course of full-time research towards their PhDs. This work is in contrast to much PhD supervision research and policy research that focuses on supervisory styles and…

pH imaging of mouse kidneys in vivo using a frequency-dependent paraCEST agent

PubMed Central

Wu, Yunkou; Zhang, Shanrong; Soesbe, Todd C.; Yu, Jing; Vinogradov, Elena; Lenkinski, Robert E.; Sherry, A. Dean

2015-01-01

Purpose This study explored the feasibility of using a pH responsive paraCEST agent to image the pH gradient in kidneys of healthy mice. Methods CEST signals were acquired on an Agilent 9.4 T small animal MRI system using a steady-state gradient echo pulse sequence after a bolus injection of agent. The magnetic field inhomogeneity across each kidney was corrected using the WASSR method and pH maps were calculated by measuring the frequency of water exchange signal arising from the agent. Results Dynamic CEST studies demonstrated that the agent was readily detectable in kidneys only between 4 to 12 min post-injection. The CEST images showed a higher signal intensity in the pelvis and calyx regions and lower signal intensity in the medulla and cortex regions. The pH maps reflected tissue pH values spanning from 6.0 to 7.5 in kidneys of healthy mice. Conclusion This study demonstrated that pH maps of the kidney can be imaged in vivo by measuring the pH-dependent chemical shift of a single water exchange CEST peak without prior knowledge of the agent concentration in vivo. The results demonstrate the potential of using a simple frequency-dependent paraCEST agent for mapping tissue pH in vivo. PMID:26173637

Toward shrimp consumption without chemicals: Combined effects of freezing and modified atmosphere packaging (MAP) on some quality characteristics of Giant Red Shrimp (Aristaeomorpha foliacea) during storage.

PubMed

Bono, Gioacchino; Okpala, Charles Odilichukwu R; Alberio, Giuseppina R A; Messina, Concetta M; Santulli, Andrea; Giacalone, Gabriele; Spagna, Giovanni

2016-04-15

The combined effects of freezing and modified atmosphere packaging (MAP) (100% N2 and 50% N2+50% CO2) on some quality characteristics of Giant Red Shrimp (GRS) (Aristaeomorpha foliacea) was studied during 12-month storage. In particular, the quality characteristics determined proximal and gas compositions, melanosis scores, pH, total volatile basic-nitrogen (TVB-N), thiobarbituric acid (TBA) as well as free amino acid (FAA). In addition, the emergent data were compared to those subject to vacuum packaging as well as conventional preservative method of sulphite treatment (SUL). Most determined qualities exhibited quantitative differences with storage. By comparisons, while pH and TVB-N statistically varied between treatments (P<0.05) and TBA that ranged between ∼0.15 and 0.30 mg MDA/kg appeared least at end of storage for 100% N2 treated-group, the latter having decreased melanosis scores showed such treatments with high promise to keep the colour of GRS sample hence, potential replacement for SUL group. By comparisons also, while some individual FAA values showed increases especially at the 100% N2-treated group, the total FAAs statistically differed with storage (P<0.05). The combination of freezing and MAP treatments as preservative treatment method shows high promise to influence some quality characteristics of GRS samples of this study. Copyright © 2015 Elsevier Ltd. All rights reserved.

A tunable ratiometric pH sensor based on carbon nanodots for the quantitative measurement of the intracellular pH of whole cells.

PubMed

Shi, Wen; Li, Xiaohua; Ma, Huimin

2012-06-25

The whole picture: Carbon nanodots labeled with two fluorescent dyes have been developed as a tunable ratiometric pH sensor to measure intracellular pH. The nanosensor shows good biocompatibility and cellular dispersibility. Quantitative determinations on intact HeLa cells and pH fluctuations associated with oxidative stress were performed. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Flexible pH-Sensing Hydrogel Fibers for Epidermal Applications.

PubMed

Tamayol, Ali; Akbari, Mohsen; Zilberman, Yael; Comotto, Mattia; Lesha, Emal; Serex, Ludovic; Bagherifard, Sara; Chen, Yu; Fu, Guoqing; Ameri, Shideh Kabiri; Ruan, Weitong; Miller, Eric L; Dokmeci, Mehmet R; Sonkusale, Sameer; Khademhosseini, Ali

2016-03-01

Epidermal pH is an indication of the skin's physiological condition. For example, pH of wound can be correlated to angiogenesis, protease activity, bacterial infection, etc. Chronic nonhealing wounds are known to have an elevated alkaline environment, while healing process occurs more readily in an acidic environment. Thus, dermal patches capable of continuous pH measurement can be used as point-of-care systems for monitoring skin disorder and the wound healing process. Here, pH-responsive hydrogel fibers are presented that can be used for long-term monitoring of epidermal wound condition. pH-responsive dyes are loaded into mesoporous microparticles and incorporated into hydrogel fibers using a microfluidic spinning system. The fabricated pH-responsive microfibers are flexible and can create conformal contact with skin. The response of pH-sensitive fibers with different compositions and thicknesses are characterized. The suggested technique is scalable and can be used to fabricate hydrogel-based wound dressings with clinically relevant dimensions. Images of the pH-sensing fibers during real-time pH measurement can be captured with a smart phone camera for convenient readout on-site. Through image processing, a quantitative pH map of the hydrogel fibers and the underlying tissue can be extracted. The developed skin dressing can act as a point-of-care device for monitoring the wound healing process. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Determine precipitation rates from visible and infrared satellite images of clouds by pattern recognition technique. Progress Report, 1 Jul. 1985 - 31 Mar. 1987 Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Weinman, James A.; Garan, Louis

1987-01-01

A more advanced cloud pattern analysis algorithm was subsequently developed to take the shape and brightness of the various clouds into account in a manner that is more consistent with the human analyst's perception of GOES cloud imagery. The results of that classification scheme were compared with precipitation probabilities observed from ships of opportunity off the U.S. east coast to derive empirical regressions between cloud types and precipitation probability. The cloud morphology was then quantitatively and objectively used to map precipitation probabilities during two winter months during which severe cold air outbreaks were observed over the northwest Atlantic. Precipitation probabilities associated with various cloud types are summarized. Maps of precipitation probability derived from the cloud morphology analysis program for two months and the precipitation probability derived from thirty years of ship observation were observed.

xQTL workbench: a scalable web environment for multi-level QTL analysis.

PubMed

Arends, Danny; van der Velde, K Joeri; Prins, Pjotr; Broman, Karl W; Möller, Steffen; Jansen, Ritsert C; Swertz, Morris A

2012-04-01

xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator. xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org. m.a.swertz@rug.nl.

xQTL workbench: a scalable web environment for multi-level QTL analysis

PubMed Central

Arends, Danny; van der Velde, K. Joeri; Prins, Pjotr; Broman, Karl W.; Möller, Steffen; Jansen, Ritsert C.; Swertz, Morris A.

2012-01-01

Summary: xQTL workbench is a scalable web platform for the mapping of quantitative trait loci (QTLs) at multiple levels: for example gene expression (eQTL), protein abundance (pQTL), metabolite abundance (mQTL) and phenotype (phQTL) data. Popular QTL mapping methods for model organism and human populations are accessible via the web user interface. Large calculations scale easily on to multi-core computers, clusters and Cloud. All data involved can be uploaded and queried online: markers, genotypes, microarrays, NGS, LC-MS, GC-MS, NMR, etc. When new data types come available, xQTL workbench is quickly customized using the Molgenis software generator. Availability: xQTL workbench runs on all common platforms, including Linux, Mac OS X and Windows. An online demo system, installation guide, tutorials, software and source code are available under the LGPL3 license from http://www.xqtl.org. Contact: m.a.swertz@rug.nl PMID:22308096

pH imaging of mouse kidneys in vivo using a frequency-dependent paraCEST agent.

PubMed

Wu, Yunkou; Zhang, Shanrong; Soesbe, Todd C; Yu, Jing; Vinogradov, Elena; Lenkinski, Robert E; Sherry, A Dean

2016-06-01

This study explored the feasibility of using a pH responsive paramagnetic chemical exchange saturation transfer (paraCEST) agent to image the pH gradient in kidneys of healthy mice. CEST signals were acquired on an Agilent 9.4 Tesla small animal MRI system using a steady-state gradient echo pulse sequence after a bolus injection of agent. The magnetic field inhomogeneity across each kidney was corrected using the WASSR method and pH maps were calculated by measuring the frequency of water exchange signal arising from the agent. Dynamic CEST studies demonstrated that the agent was readily detectable in kidneys only between 4 to 12 min postinjection. The CEST images showed a higher signal intensity in the pelvis and calyx regions and lower signal intensity in the medulla and cortex regions. The pH maps reflected tissue pH values spanning from 6.0 to 7.5 in kidneys of healthy mice. This study demonstrated that pH maps of the kidney can be imaged in vivo by measuring the pH-dependent chemical shift of a single water exchange CEST peak without prior knowledge of the agent concentration in vivo. The results demonstrate the potential of using a simple frequency-dependent paraCEST agent for mapping tissue pH in vivo. Magn Reson Med 75:2432-2441, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Doctoral training in statistics, measurement, and methodology in psychology: replication and extension of Aiken, West, Sechrest, and Reno's (1990) survey of PhD programs in North America.

PubMed

Aiken, Leona S; West, Stephen G; Millsap, Roger E

2008-01-01

In a survey of all PhD programs in psychology in the United States and Canada, the authors documented the quantitative methodology curriculum (statistics, measurement, and research design) to examine the extent to which innovations in quantitative methodology have diffused into the training of PhDs in psychology. In all, 201 psychology PhD programs (86%) participated. This survey replicated and extended a previous survey (L. S. Aiken, S. G. West, L. B. Sechrest, & R. R. Reno, 1990), permitting examination of curriculum development. Most training supported laboratory and not field research. The median of 1.6 years of training in statistics and measurement was mainly devoted to the modally 1-year introductory statistics course, leaving little room for advanced study. Curricular enhancements were noted in statistics and to a minor degree in measurement. Additional coverage of both fundamental and innovative quantitative methodology is needed. The research design curriculum has largely stagnated, a cause for great concern. Elite programs showed no overall advantage in quantitative training. Forces that support curricular innovation are characterized. Human capital challenges to quantitative training, including recruiting and supporting young quantitative faculty, are discussed. Steps must be taken to bring innovations in quantitative methodology into the curriculum of PhD programs in psychology. PsycINFO Database Record (c) 2008 APA, all rights reserved.

Doctoral Training in Statistics, Measurement, and Methodology in Psychology: Replication and Extension of Aiken, West, Sechrest, and Reno's (1990) Survey of PhD Programs in North America

ERIC Educational Resources Information Center

Aiken, Leona S.; West, Stephen G.; Millsap, Roger E.

2008-01-01

In a survey of all PhD programs in psychology in the United States and Canada, the authors documented the quantitative methodology curriculum (statistics, measurement, and research design) to examine the extent to which innovations in quantitative methodology have diffused into the training of PhDs in psychology. In all, 201 psychology PhD…

EVALUATION OF STACHYBOTRYS CHARTARUM IN THE HOUSE OF AN INFANT WITH PULMONARY HEMORRHAGE: QUANTITATIVE ASSESSMENT BEFORE, DURING, AND AFTER REMEDIATION

EPA Science Inventory

Stachybotrys chartarum is an indoor mold that has been associated with pulmonary hemorrhage (PH) cases in the Cleveland, Ohio area. This study applied two new quantitative measurements to air samples from a home where an infant developed PH. Quantitative polymerase chain reacti...

Structural analysis of chromosomal rearrangements associated with the developmental mutations Ph, W19H, and Rw on mouse chromosome 5.

PubMed Central

Nagle, D L; Martin-DeLeon, P; Hough, R B; Bućan, M

1994-01-01

We are studying the chromosomal structure of three developmental mutations, dominant spotting (W), patch (Ph), and rump white (Rw) on mouse chromosome 5. These mutations are clustered in a region containing three genes encoding tyrosine kinase receptors (Kit, Pdgfra, and Flk1). Using probes for these genes and for a closely linked locus, D5Mn125, we established a high-resolution physical map covering approximately 2.8 Mb. The entire chromosomal segment mapped in this study is deleted in the W19H mutation. The map indicates the position of the Ph deletion, which encompasses not more than 400 kb around and including the Pdgfra gene. The map also places the distal breakpoint of the Rw inversion to a limited chromosomal segment between Kit and Pdgfra. In light of the structure of the Ph-W-Rw region, we interpret the previously published complementation analyses as indicating that the pigmentation defect in Rw/+ heterozygotes could be due to the disruption of Kit and/or Pdgfra regulatory sequences, whereas the gene(s) responsible for the recessive lethality of Rw/Rw embryos is not closely linked to the Ph and W loci and maps proximally to the W19H deletion. The structural analysis of chromosomal rearrangements associated with W19H, Ph, and Rw combined with the high-resolution physical mapping points the way toward the definition of these mutations in molecular terms and isolation of homologous genes on human chromosome 4. Images PMID:8041773

Quantitative X-ray mapping, scatter diagrams and the generation of correction maps to obtain more information about your material

NASA Astrophysics Data System (ADS)

Wuhrer, R.; Moran, K.

2014-03-01

Quantitative X-ray mapping with silicon drift detectors and multi-EDS detector systems have become an invaluable analysis technique and one of the most useful methods of X-ray microanalysis today. The time to perform an X-ray map has reduced considerably with the ability to map minor and trace elements very accurately due to the larger detector area and higher count rate detectors. Live X-ray imaging can now be performed with a significant amount of data collected in a matter of minutes. A great deal of information can be obtained from X-ray maps. This includes; elemental relationship or scatter diagram creation, elemental ratio mapping, chemical phase mapping (CPM) and quantitative X-ray maps. In obtaining quantitative x-ray maps, we are able to easily generate atomic number (Z), absorption (A), fluorescence (F), theoretical back scatter coefficient (η), and quantitative total maps from each pixel in the image. This allows us to generate an image corresponding to each factor (for each element present). These images allow the user to predict and verify where they are likely to have problems in our images, and are especially helpful to look at possible interface artefacts. The post-processing techniques to improve the quantitation of X-ray map data and the development of post processing techniques for improved characterisation are covered in this paper.

Accurate Quantitative Sensing of Intracellular pH based on Self-ratiometric Upconversion Luminescent Nanoprobe.

PubMed

Li, Cuixia; Zuo, Jing; Zhang, Li; Chang, Yulei; Zhang, Youlin; Tu, Langping; Liu, Xiaomin; Xue, Bin; Li, Qiqing; Zhao, Huiying; Zhang, Hong; Kong, Xianggui

2016-12-09

Accurate quantitation of intracellular pH (pH i ) is of great importance in revealing the cellular activities and early warning of diseases. A series of fluorescence-based nano-bioprobes composed of different nanoparticles or/and dye pairs have already been developed for pH i sensing. Till now, biological auto-fluorescence background upon UV-Vis excitation and severe photo-bleaching of dyes are the two main factors impeding the accurate quantitative detection of pH i . Herein, we have developed a self-ratiometric luminescence nanoprobe based on förster resonant energy transfer (FRET) for probing pH i , in which pH-sensitive fluorescein isothiocyanate (FITC) and upconversion nanoparticles (UCNPs) were served as energy acceptor and donor, respectively. Under 980 nm excitation, upconversion emission bands at 475 nm and 645 nm of NaYF 4 :Yb 3+ , Tm 3+ UCNPs were used as pH i response and self-ratiometric reference signal, respectively. This direct quantitative sensing approach has circumvented the traditional software-based subsequent processing of images which may lead to relatively large uncertainty of the results. Due to efficient FRET and fluorescence background free, a highly-sensitive and accurate sensing has been achieved, featured by 3.56 per unit change in pH i value 3.0-7.0 with deviation less than 0.43. This approach shall facilitate the researches in pH i related areas and development of the intracellular drug delivery systems.

In Situ Cross-Linking of Stimuli-Responsive Hemicellulose Microgels during Spray Drying

PubMed Central

2015-01-01

Chemical cross-linking during spray drying offers the potential for green fabrication of microgels with a rapid stimuli response and good blood compatibility and provides a platform for stimuli-responsive hemicellulose microgels (SRHMGs). The cross-linking reaction occurs rapidly in situ at elevated temperature during spray drying, enabling the production of microgels in a large scale within a few minutes. The SRHMGs with an average size range of ∼1–4 μm contain O-acetyl-galactoglucomannan as a matrix and poly(acrylic acid), aniline pentamer (AP), and iron as functional additives, which are responsive to external changes in pH, electrochemical stimuli, magnetic field, or dual-stimuli. The surface morphologies, chemical compositions, charge, pH, and mechanical properties of these smart microgels were evaluated using scanning electron microscopy, IR, zeta potential measurements, pH evaluation, and quantitative nanomechanical mapping, respectively. Different oxidation states were observed when AP was introduced, as confirmed by UV spectroscopy and cyclic voltammetry. Systematic blood compatibility evaluations revealed that the SRHMGs have good blood compatibility. This bottom-up strategy to synthesize SRHMGs enables a new route to the production of smart microgels for biomedical applications. PMID:25630464

In situ cross-linking of stimuli-responsive hemicellulose microgels during spray drying.

PubMed

Zhao, Weifeng; Nugroho, Robertus Wahyu N; Odelius, Karin; Edlund, Ulrica; Zhao, Changsheng; Albertsson, Ann-Christine

2015-02-25

Chemical cross-linking during spray drying offers the potential for green fabrication of microgels with a rapid stimuli response and good blood compatibility and provides a platform for stimuli-responsive hemicellulose microgels (SRHMGs). The cross-linking reaction occurs rapidly in situ at elevated temperature during spray drying, enabling the production of microgels in a large scale within a few minutes. The SRHMGs with an average size range of ∼ 1-4 μm contain O-acetyl-galactoglucomannan as a matrix and poly(acrylic acid), aniline pentamer (AP), and iron as functional additives, which are responsive to external changes in pH, electrochemical stimuli, magnetic field, or dual-stimuli. The surface morphologies, chemical compositions, charge, pH, and mechanical properties of these smart microgels were evaluated using scanning electron microscopy, IR, zeta potential measurements, pH evaluation, and quantitative nanomechanical mapping, respectively. Different oxidation states were observed when AP was introduced, as confirmed by UV spectroscopy and cyclic voltammetry. Systematic blood compatibility evaluations revealed that the SRHMGs have good blood compatibility. This bottom-up strategy to synthesize SRHMGs enables a new route to the production of smart microgels for biomedical applications.

Mapcurves: a quantitative method for comparing categorical maps.

Treesearch

William W. Hargrove; M. Hoffman Forrest; Paul F. Hessburg

2006-01-01

We present Mapcurves, a quantitative goodness-of-fit (GOF) method that unambiguously shows the degree of spatial concordance between two or more categorical maps. Mapcurves graphically and quantitatively evaluate the degree of fit among any number of maps and quantify a GOF for each polygon, as well as the entire map. The Mapcurve method indicates a perfect fit even if...

Failure Maps for Rectangular 17-4PH Stainless Steel Sandwiched Foam Panels

NASA Technical Reports Server (NTRS)

Raj, S. V.; Ghosn, L. J.

2007-01-01

A new and innovative concept is proposed for designing lightweight fan blades for aircraft engines using commercially available 17-4PH precipitation hardened stainless steel. Rotating fan blades in aircraft engines experience a complex loading state consisting of combinations of centrifugal, distributed pressure and torsional loads. Theoretical failure plastic collapse maps, showing plots of the foam relative density versus face sheet thickness, t, normalized by the fan blade span length, L, have been generated for rectangular 17-4PH sandwiched foam panels under these three loading modes assuming three failure plastic collapse modes. These maps show that the 17-4PH sandwiched foam panels can fail by either the yielding of the face sheets, yielding of the foam core or wrinkling of the face sheets depending on foam relative density, the magnitude of t/L and the loading mode. The design envelop of a generic fan blade is superimposed on the maps to provide valuable insights on the probable failure modes in a sandwiched foam fan blade.

Determination of bromhexine in plasma by reversed-phase liquid chromatography. Interference of lipoproteins on extraction.

PubMed

Johansson, M; Lenngren, S

1988-11-18

Extraction of the hydrophobic tertiary amine bromhexine from plasma using cyclohexane-heptafluorobutanol (99.5:0.5, v/v) was studied at different pH values. The extraction yield from buffer solutions was quantitative at pH greater than 4.1, but from plasma the extraction yield decreased with increasing pH. Furthermore, at pH 8.4 the extraction yield varied greatly (56-99%) in different human plasma. The addition of lipoproteins to phosphate buffer, at pH 8.1, decreased the extraction yields considerably. Quantitative extraction from plasma was obtained by using a very long extraction time at pH 8.4 or by decreasing the pH to 5.4. The chromatographic system consisted of a reversed-phase column (Nucleosil C18, 5 microns) with an acidic mobile phase (methanol-phosphate buffer, pH 2) containing an aliphatic tertiary amine. UV detection at 308 or 254 nm was used. The limit of quantitation was 5 ng/ml using 3.00 ml of plasma and detection at 254 nm. The intra-assay precision for bromhexine was better than 3.6% at 5 ng/ml.

Expression of the mucus adhesion genes Mub and MapA, adhesion-like factor EF-Tu and bacteriocin gene plaA of Lactobacillus plantarum 423, monitored with real-time PCR.

PubMed

Ramiah, K; van Reenen, C A; Dicks, L M T

2007-05-30

Expression of the mucus adhesion genes Mub and MapA, adhesion-like factor EF-Tu and bacteriocin gene plaA by Lactobacillus plantarum 423, grown in the presence of bile, pancreatin and at low pH, was studied by real-time PCR. Mub, MapA and EF-Tu were up-regulated in the presence of mucus, proportional to increasing concentrations. Expression of MapA was up-regulated in the presence of 3.0 g/l bile and 3.0 g/l pancreatin at pH 6.5. Similar results were recorded in the presence of 10.0 g/l bile and 10.0 g/l pancreatin at pH 6.5. Expression of Mub was down-regulated in the presence of bile and pancreatin, whilst the expression of EF-Tu and plaA remained unchanged. Expression of Mub and MapA remained unchanged at pH 4.0, whilst expression of EF-Tu and plaA were up-regulated. Expression of MapA was down-regulated in the presence of 1.0 g/l l-cysteine HCl, suggesting that the gene is regulated by transcription attenuation that involves cysteine.

Updated sesame genome assembly and fine mapping of plant height and seed coat color QTLs using a new high-density genetic map.

PubMed

Wang, Linhai; Xia, Qiuju; Zhang, Yanxin; Zhu, Xiaodong; Zhu, Xiaofeng; Li, Donghua; Ni, Xuemei; Gao, Yuan; Xiang, Haitao; Wei, Xin; Yu, Jingyin; Quan, Zhiwu; Zhang, Xiurong

2016-01-05

Sesame is an important high-quality oil seed crop. The sesame genome was de novo sequenced and assembled in 2014 (version 1.0); however, the number of anchored pseudomolecules was higher than the chromosome number (2n = 2x = 26) due to the lack of a high-density genetic map with 13 linkage groups. We resequenced a permanent population consisting of 430 recombinant inbred lines and constructed a genetic map to improve the sesame genome assembly. We successfully anchored 327 scaffolds onto 13 pseudomolecules. The new genome assembly (version 2.0) included 97.5 % of the scaffolds greater than 150 kb in size present in assembly version 1.0 and increased the total pseudomolecule length from 233.7 to 258.4 Mb with 94.3 % of the genome assembled and 97.2 % of the predicted gene models anchored. Based on the new genome assembly, a bin map including 1,522 bins spanning 1090.99 cM was generated and used to identified 41 quantitative trait loci (QTLs) for sesame plant height and 9 for seed coat color. The plant height-related QTLs explained 3-24 % the phenotypic variation (mean value, 8 %), and 29 of them were detected in at least two field trials. Two major loci (qPH-8.2 and qPH-3.3) that contributed 23 and 18 % of the plant height were located in 350 and 928-kb spaces on Chr8 and Chr3, respectively. qPH-3.3, is predicted to be responsible for the semi-dwarf sesame plant phenotype and contains 102 candidate genes. This is the first report of a sesame semi-dwarf locus and provides an interesting opportunity for a plant architecture study of the sesame. For the sesame seed coat color, the QTLs of the color spaces L*, a*, and b* were detected with contribution rates of 3-46 %. qSCb-4.1 contributed approximately 39 % of the b* value and was located on Chr4 in a 199.9-kb space. A list of 32 candidate genes for the locus, including a predicted black seed coat-related gene, was determined by screening the newly anchored genome. This study offers a high-density genetic map and an improved assembly of the sesame genome. The number of linkage groups and pseudomolecules in this assembly equals the number of sesame chromosomes for the first time. The map and updated genome assembly are expected to serve as a platform for future comparative genomics and genetic studies.

Dissection of genetic architecture of rice plant height and heading date by multiple-strategy-based association studies

PubMed Central

Zhou, Liyuan; Liu, Shouye; Wu, Weixun; Chen, Daibo; Zhan, Xiaodeng; Zhu, Aike; Zhang, Yingxin; Cheng, Shihua; Cao, Liyong; Lou, Xiangyang; Xu, Haiming

2016-01-01

Xieyou9308 is a certified super hybrid rice cultivar with a high grain yield. To investigate its underlying genetic basis of high yield potential, a recombinant inbred line (RIL) population derived from the cross between the maintainer line XieqingzaoB (XQZB) and the restorer line Zhonghui9308 (ZH9308) was constructed for identification of quantitative trait SNPs (QTSs) associated with two important agronomic traits, plant height (PH) and heading date (HD). By re-sequencing of 138 recombinant inbred lines (RILs), a total of ~0.7 million SNPs were identified for the association studies on the PH and HD. Three association mapping strategies (including hypothesis-free genome-wide association and its two complementary hypothesis-engaged ones, QTL-based association and gene-based association) were adopted for data analysis. Using a saturated mixed linear model including epistasis and environmental interaction, we identified a total of 31 QTSs associated with either the PH or the HD. The total estimated heritability across three analyses ranged from 37.22% to 45.63% and from 37.53% to 55.96% for the PH and HD, respectively. In this study we examined the feasibility of association studies in an experimental population (RIL) and identified several common loci through multiple strategies which could be preferred candidates for further research. PMID:27406081

Mechanical properties of amyloid-like fibrils defined by secondary structures

NASA Astrophysics Data System (ADS)

Bortolini, C.; Jones, N. C.; Hoffmann, S. V.; Wang, C.; Besenbacher, F.; Dong, M.

2015-04-01

Amyloid and amyloid-like fibrils represent a generic class of highly ordered nanostructures that are implicated in some of the most fatal neurodegenerative diseases. On the other hand, amyloids, by possessing outstanding mechanical robustness, have also been successfully employed as functional biomaterials. For these reasons, physical and chemical factors driving fibril self-assembly and morphology are extensively studied - among these parameters, the secondary structures and the pH have been revealed to be crucial, since a variation in pH changes the fibril morphology and net chirality during protein aggregation. It is important to quantify the mechanical properties of these fibrils in order to help the design of effective strategies for treating diseases related to the presence of amyloid fibrils. In this work, we show that by changing pH the mechanical properties of amyloid-like fibrils vary as well. In particular, we reveal that these mechanical properties are strongly related to the content of secondary structures. We analysed and estimated the Young's modulus (E) by comparing the persistence length (Lp) - measured from the observation of TEM images by using statistical mechanics arguments - with the mechanical information provided by peak force quantitative nanomechanical property mapping (PF-QNM). The secondary structure content and the chirality are investigated by means of synchrotron radiation circular dichroism (SR-CD). Results arising from this study could be fruitfully used as a protocol to investigate other medical or engineering relevant peptide fibrils.Amyloid and amyloid-like fibrils represent a generic class of highly ordered nanostructures that are implicated in some of the most fatal neurodegenerative diseases. On the other hand, amyloids, by possessing outstanding mechanical robustness, have also been successfully employed as functional biomaterials. For these reasons, physical and chemical factors driving fibril self-assembly and morphology are extensively studied - among these parameters, the secondary structures and the pH have been revealed to be crucial, since a variation in pH changes the fibril morphology and net chirality during protein aggregation. It is important to quantify the mechanical properties of these fibrils in order to help the design of effective strategies for treating diseases related to the presence of amyloid fibrils. In this work, we show that by changing pH the mechanical properties of amyloid-like fibrils vary as well. In particular, we reveal that these mechanical properties are strongly related to the content of secondary structures. We analysed and estimated the Young's modulus (E) by comparing the persistence length (Lp) - measured from the observation of TEM images by using statistical mechanics arguments - with the mechanical information provided by peak force quantitative nanomechanical property mapping (PF-QNM). The secondary structure content and the chirality are investigated by means of synchrotron radiation circular dichroism (SR-CD). Results arising from this study could be fruitfully used as a protocol to investigate other medical or engineering relevant peptide fibrils. Electronic supplementary information (ESI) available: A molecular model for the peptide studied and the charge chart associated to it. In addition, an AFM image of pH 4 fibrils is presented. See DOI: 10.1039/c4nr05109b

Developing and applying quantitative skills maps for STEM curricula, with a focus on different modes of learning

NASA Astrophysics Data System (ADS)

Reid, Jackie; Wilkes, Janelle

2016-08-01

Mapping quantitative skills across the science, technology, engineering and mathematics (STEM) curricula will help educators identify gaps and duplication in the teaching, practice and assessment of the necessary skills. This paper describes the development and implementation of quantitative skills mapping tools for courses in STEM at a regional university that offers both on-campus and distance modes of study. Key elements of the mapping project included the identification of key graduate quantitative skills, the development of curriculum mapping tools to record in which unit(s) and at what level of attainment each quantitative skill is taught, practised and assessed, and identification of differences in the way quantitative skills are developed for on-campus and distance students. Particular attention is given to the differences that are associated with intensive schools, which consist of concentrated periods of face-to-face learning over a three-four day period, and are available to distance education students enrolled in STEM units. The detailed quantitative skills mapping process has had an impact on the review of first-year mathematics units, resulted in crucial changes to the curriculum in a number of courses, and contributed to a more integrated approach, and a collective responsibility, to the development of students' quantitative skills for both face-to-face and online modes of learning.

Quantitative Susceptibility Mapping and R2* Measured Changes during White Matter Lesion Development in Multiple Sclerosis: Myelin Breakdown, Myelin Debris Degradation and Removal, and Iron Accumulation.

PubMed

Zhang, Y; Gauthier, S A; Gupta, A; Chen, W; Comunale, J; Chiang, G C-Y; Zhou, D; Askin, G; Zhu, W; Pitt, D; Wang, Y

2016-09-01

Quantitative susceptibility mapping and R2* are sensitive to myelin and iron changes in multiple sclerosis lesions. This study was designed to characterize lesion changes on quantitative susceptibility mapping and R2* at various gadolinium-enhancement stages. This study included 64 patients with MS with different enhancing patterns in white matter lesions: nodular, shell-like, nonenhancing < 1 year old, and nonenhancing 1-3 years old. These represent acute, late acute, early chronic, and late chronic lesions, respectively. Susceptibility values measured on quantitative susceptibility mapping and R2* values were compared among the 4 lesion types. Their differences were assessed with a generalized estimating equation, controlling for Expanded Disability Status Scale score, age, and disease duration. We analyzed 203 lesions: 80 were nodular-enhancing, of which 77 (96.2%) were isointense on quantitative susceptibility mapping; 33 were shell-enhancing, of which 30 (90.9%) were hyperintense on quantitative susceptibility mapping; and 49 were nonenhancing lesions < 1 year old and 41 were nonenhancing lesions 1-3 years old, all of which were hyperintense on quantitative susceptibility mapping. Their relative susceptibility/R2* values were 0.5 ± 4.4 parts per billion/-5.6 ± 2.9 Hz, 10.2 ± 5.4 parts per billion/-8.0 ± 2.6 Hz, 20.2 ± 7.8 parts per billion/-3.1 ± 2.3 Hz, and 33.2 ± 8.2 parts per billion/-2.0 ± 2.6 Hz, respectively, and were significantly different (P < .005). Early active MS lesions with nodular enhancement show R2* decrease but no quantitative susceptibility mapping change, reflecting myelin breakdown; late active lesions with peripheral enhancement show R2* decrease and quantitative susceptibility mapping increase in the lesion center, reflecting further degradation and removal of myelin debris; and early or late chronic nonenhancing lesions show both quantitative susceptibility mapping and R2* increase, reflecting iron accumulation. © 2016 by American Journal of Neuroradiology.

High-Resolution Maps of Mouse Reference Populations

PubMed Central

Simecek, Petr; Forejt, Jiri; Williams, Robert W.; Shiroishi, Toshihiko; Takada, Toyoyuki; Lu, Lu; Johnson, Thomas E.; Bennett, Beth; Deschepper, Christian F.; Scott-Boyer, Marie-Pier; Pardo-Manuel de Villena, Fernando; Churchill, Gary A.

2017-01-01

Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, and C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA. PMID:28839117

High-Resolution Maps of Mouse Reference Populations.

PubMed

Simecek, Petr; Forejt, Jiri; Williams, Robert W; Shiroishi, Toshihiko; Takada, Toyoyuki; Lu, Lu; Johnson, Thomas E; Bennett, Beth; Deschepper, Christian F; Scott-Boyer, Marie-Pier; Pardo-Manuel de Villena, Fernando; Churchill, Gary A

2017-10-05

Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, and C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA. Copyright © 2017 Simecek et al.

Preoperative Cerebral Oxygen Extraction Fraction Imaging Generated from 7T MR Quantitative Susceptibility Mapping Predicts Development of Cerebral Hyperperfusion following Carotid Endarterectomy.

PubMed

Nomura, J-I; Uwano, I; Sasaki, M; Kudo, K; Yamashita, F; Ito, K; Fujiwara, S; Kobayashi, M; Ogasawara, K

2017-12-01

Preoperative hemodynamic impairment in the affected cerebral hemisphere is associated with the development of cerebral hyperperfusion following carotid endarterectomy. Cerebral oxygen extraction fraction images generated from 7T MR quantitative susceptibility mapping correlate with oxygen extraction fraction images on positron-emission tomography. The present study aimed to determine whether preoperative oxygen extraction fraction imaging generated from 7T MR quantitative susceptibility mapping could identify patients at risk for cerebral hyperperfusion following carotid endarterectomy. Seventy-seven patients with unilateral internal carotid artery stenosis (≥70%) underwent preoperative 3D T2*-weighted imaging using a multiple dipole-inversion algorithm with a 7T MR imager. Quantitative susceptibility mapping images were then obtained, and oxygen extraction fraction maps were generated. Quantitative brain perfusion single-photon emission CT was also performed before and immediately after carotid endarterectomy. ROIs were automatically placed in the bilateral middle cerebral artery territories in all images using a 3D stereotactic ROI template, and affected-to-contralateral ratios in the ROIs were calculated on quantitative susceptibility mapping-oxygen extraction fraction images. Ten patients (13%) showed post-carotid endarterectomy hyperperfusion (cerebral blood flow increases of ≥100% compared with preoperative values in the ROIs on brain perfusion SPECT). Multivariate analysis showed that a high quantitative susceptibility mapping-oxygen extraction fraction ratio was significantly associated with the development of post-carotid endarterectomy hyperperfusion (95% confidence interval, 33.5-249.7; P = .002). Sensitivity, specificity, and positive- and negative-predictive values of the quantitative susceptibility mapping-oxygen extraction fraction ratio for the prediction of the development of post-carotid endarterectomy hyperperfusion were 90%, 84%, 45%, and 98%, respectively. Preoperative oxygen extraction fraction imaging generated from 7T MR quantitative susceptibility mapping identifies patients at risk for cerebral hyperperfusion following carotid endarterectomy. © 2017 by American Journal of Neuroradiology.

Identification of minor effect QTLs for plant architecture related traits using super high density genotyping and large recombinant inbred population in maize (Zea mays).

PubMed

Wang, Baobao; Liu, Han; Liu, Zhipeng; Dong, Xiaomei; Guo, Jinjie; Li, Wei; Chen, Jing; Gao, Chi; Zhu, Yanbin; Zheng, Xinmei; Chen, Zongliang; Chen, Jian; Song, Weibin; Hauck, Andrew; Lai, Jinsheng

2018-01-18

Plant Architecture Related Traits (PATs) are of great importance for maize breeding, and mainly controlled by minor effect quantitative trait loci (QTLs). However, cloning or even fine-mapping of minor effect QTLs is very difficult in maize. Theoretically, large population and high density genetic map can be helpful for increasing QTL mapping resolution and accuracy, but such a possibility have not been actually tested. Here, we employed a genotyping-by-sequencing (GBS) strategy to construct a linkage map with 16,769 marker bins for 1021 recombinant inbred lines (RILs). Accurately mapping of well studied genes P1, pl1 and r1 underlying silk color demonstrated the map quality. After QTL analysis, a total of 51 loci were mapped for six PATs. Although all of them belong to minor effect alleles, the lengths of the QTL intervals, with a minimum and median of 1.03 and 3.40 Mb respectively, were remarkably reduced as compared with previous reports using smaller size of population or small number of markers. Several genes with known function in maize were shown to be overlapping with or close neighboring to these QTL peaks, including na1, td1, d3 for plant height, ra1 for tassel branch number, and zfl2 for tassel length. To further confirm our mapping results, a plant height QTL, qPH1a, was verified by an introgression lines (ILs). We demonstrated a method for high resolution mapping of minor effect QTLs in maize, and the resulted comprehensive QTLs for PATs are valuable for maize molecular breeding in the future.

A Quantitative Review and Meta-Models of the Variability and Factors Affecting Oral Drug Absorption-Part I: Gastrointestinal pH.

PubMed

Abuhelwa, Ahmad Y; Foster, David J R; Upton, Richard N

2016-09-01

This study aimed to conduct a quantitative meta-analysis for the values of, and variability in, gastrointestinal (GI) pH in the different GI segments; characterize the effect of food on the values and variability in these parameters; and present quantitative meta-models of distributions of GI pH to help inform models of oral drug absorption. The literature was systemically reviewed for the values of, and the variability in, GI pH under fed and fasted conditions. The GI tract was categorized into the following 10 distinct regions: stomach (proximal, mid-distal), duodenum (proximal, mid-distal), jejunum and ileum (proximal, mid, and distal small intestine), and colon (ascending, transverse, and descending colon). Meta-analysis used the "metafor" package of the R language. The time course of postprandial stomach pH was modeled using NONMEM. Food significantly influenced the estimated meta-mean stomach and duodenal pH but had no significant influence on small intestinal and colonic pH. The time course of postprandial pH was described using an exponential model. Increased meal caloric content increased the extent and duration of postprandial gastric pH buffering. The different parts of the small intestine had significantly different pH. Colonic pH was significantly different for descending but not for ascending and transverse colon. Knowledge of GI pH is important for the formulation design of the pH-dependent dosage forms and in understanding the dissolution and absorption of orally administered drugs. The meta-models of GI pH may also be used as part of semi-physiological pharmacokinetic models to characterize the effect of GI pH on the in vivo drug release and pharmacokinetics.

Developing and Applying Quantitative Skills Maps for STEM Curricula, with a Focus on Different Modes of Learning

ERIC Educational Resources Information Center

Reid, Jackie; Wilkes, Janelle

2016-01-01

Mapping quantitative skills across the science, technology, engineering and mathematics (STEM) curricula will help educators identify gaps and duplication in the teaching, practice and assessment of the necessary skills. This paper describes the development and implementation of quantitative skills mapping tools for courses in STEM at a regional…

Early warning smartphone diagnostics for water security and analysis using real-time pH mapping

NASA Astrophysics Data System (ADS)

Hossain, Md. Arafat; Canning, John; Ast, Sandra; Rutledge, Peter J.; Jamalipour, Abbas

2015-12-01

Early detection of environmental disruption, unintentional or otherwise, is increasingly desired to ensure hazard minimization in many settings. Here, using a field-portable, smartphone fluorimeter to assess water quality based on the pH response of a designer probe, a map of pH of public tap water sites has been obtained. A custom designed Android application digitally processed and mapped the results utilizing the global positioning system (GPS) service of the smartphone. The map generated indicates no disruption in pH for all sites measured, and all the data are assessed to fall inside the upper limit of local government regulations, consistent with authority reported measurements. This implementation demonstrates a new security concept: network environmental forensics utilizing the potential of novel smartgrid analysis with wireless sensors for the detection of potential disruption to water quality at any point in the city. This concept is applicable across all smartgrid strategies within the next generation of the Internet of Things and can be extended on national and global scales to address a range of target analytes, both chemical and biological.

Design and validation of a new ratiometric intracellular pH imaging probe using lanthanide-doped upconverting nanoparticles.

PubMed

Du, Shuoren; Hernández-Gil, Javier; Dong, Hao; Zheng, Xiaoyu; Lyu, Guangming; Bañobre-López, Manuel; Gallo, Juan; Sun, Ling-Dong; Yan, Chun-Hua; Long, Nicholas J

2017-10-17

pH homeostasis is strictly controlled at a subcellular level. A deregulation of the intra/extra/subcellular pH environment is associated with a number of diseases and as such, the monitoring of the pH state of cells and tissues is a valuable diagnostic tool. To date, only a few tools have been developed to measure the pH in living cells with the spatial resolution needed for intracellular imaging. Among the techniques available, only optical imaging offers enough resolution and biocompatibility to be proposed for subcellular pH monitoring. We present herein a ratiometric probe based on upconversion nanoparticles modified with a pH sensitive moiety for the quantitative imaging of pH at the subcellular level in living cells. This system provides the properties required for live cell quantitative imaging i.e. positive cellular uptake, biocompatibility, long wavelength excitation, sensitive response to pH within a biologically relevant range, and self-referenced signal.

Combining Quantitative Susceptibility Mapping with Automatic Zero Reference (QSM0) and Myelin Water Fraction Imaging to Quantify Iron-Related Myelin Damage in Chronic Active MS Lesions.

PubMed

Yao, Y; Nguyen, T D; Pandya, S; Zhang, Y; Hurtado Rúa, S; Kovanlikaya, I; Kuceyeski, A; Liu, Z; Wang, Y; Gauthier, S A

2018-02-01

A hyperintense rim on susceptibility in chronic MS lesions is consistent with iron deposition, and the purpose of this study was to quantify iron-related myelin damage within these lesions as compared with those without rim. Forty-six patients had 2 longitudinal quantitative susceptibility mapping with automatic zero reference scans with a mean interval of 28.9 ± 11.4 months. Myelin water fraction mapping by using fast acquisition with spiral trajectory and T2 prep was obtained at the second time point to measure myelin damage. Mixed-effects models were used to assess lesion quantitative susceptibility mapping and myelin water fraction values. Quantitative susceptibility mapping scans were on average 6.8 parts per billion higher in 116 rim-positive lesions compared with 441 rim-negative lesions ( P < .001). All rim-positive lesions retained a hyperintense rim over time, with increasing quantitative susceptibility mapping values of both the rim and core regions ( P < .001). Quantitative susceptibility mapping scans and myelin water fraction in rim-positive lesions decreased from rim to core, which is consistent with rim iron deposition. Whole lesion myelin water fractions for rim-positive and rim-negative lesions were 0.055 ± 0.07 and 0.066 ± 0.04, respectively. In the mixed-effects model, rim-positive lesions had on average 0.01 lower myelin water fraction compared with rim-negative lesions ( P < .001). The volume of the rim at the initial quantitative susceptibility mapping scan was negatively associated with follow-up myelin water fraction ( P < .01). Quantitative susceptibility mapping rim-positive lesions maintained a hyperintense rim, increased in susceptibility, and had more myelin damage compared with rim-negative lesions. Our results are consistent with the identification of chronic active MS lesions and may provide a target for therapeutic interventions to reduce myelin damage. © 2018 by American Journal of Neuroradiology.

Soil pH Mapping with an On-The-Go Sensor

PubMed Central

Schirrmann, Michael; Gebbers, Robin; Kramer, Eckart; Seidel, Jan

2011-01-01

Soil pH is a key parameter for crop productivity, therefore, its spatial variation should be adequately addressed to improve precision management decisions. Recently, the Veris pH Manager™, a sensor for high-resolution mapping of soil pH at the field scale, has been made commercially available in the US. While driving over the field, soil pH is measured on-the-go directly within the soil by ion selective antimony electrodes. The aim of this study was to evaluate the Veris pH Manager™ under farming conditions in Germany. Sensor readings were compared with data obtained by standard protocols of soil pH assessment. Experiments took place under different scenarios: (a) controlled tests in the lab, (b) semicontrolled test on transects in a stop-and-go mode, and (c) tests under practical conditions in the field with the sensor working in its typical on-the-go mode. Accuracy issues, problems, options, and potential benefits of the Veris pH Manager™ were addressed. The tests demonstrated a high degree of linearity between standard laboratory values and sensor readings. Under practical conditions in the field (scenario c), the measure of fit (r2) for the regression between the on-the-go measurements and the reference data was 0.71, 0.63, and 0.84, respectively. Field-specific calibration was necessary to reduce systematic errors. Accuracy of the on-the-go maps was considerably higher compared with the pH maps obtained by following the standard protocols, and the error in calculating lime requirements was reduced by about one half. However, the system showed some weaknesses due to blockage by residual straw and weed roots. If these problems were solved, the on-the-go sensor investigated here could be an efficient alternative to standard sampling protocols as a basis for liming in Germany. PMID:22346591

Soil pH mapping with an on-the-go sensor.

PubMed

Schirrmann, Michael; Gebbers, Robin; Kramer, Eckart; Seidel, Jan

2011-01-01

Soil pH is a key parameter for crop productivity, therefore, its spatial variation should be adequately addressed to improve precision management decisions. Recently, the Veris pH Manager™, a sensor for high-resolution mapping of soil pH at the field scale, has been made commercially available in the US. While driving over the field, soil pH is measured on-the-go directly within the soil by ion selective antimony electrodes. The aim of this study was to evaluate the Veris pH Manager™ under farming conditions in Germany. Sensor readings were compared with data obtained by standard protocols of soil pH assessment. Experiments took place under different scenarios: (a) controlled tests in the lab, (b) semicontrolled test on transects in a stop-and-go mode, and (c) tests under practical conditions in the field with the sensor working in its typical on-the-go mode. Accuracy issues, problems, options, and potential benefits of the Veris pH Manager™ were addressed. The tests demonstrated a high degree of linearity between standard laboratory values and sensor readings. Under practical conditions in the field (scenario c), the measure of fit (r(2)) for the regression between the on-the-go measurements and the reference data was 0.71, 0.63, and 0.84, respectively. Field-specific calibration was necessary to reduce systematic errors. Accuracy of the on-the-go maps was considerably higher compared with the pH maps obtained by following the standard protocols, and the error in calculating lime requirements was reduced by about one half. However, the system showed some weaknesses due to blockage by residual straw and weed roots. If these problems were solved, the on-the-go sensor investigated here could be an efficient alternative to standard sampling protocols as a basis for liming in Germany.

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

Potential of on-line visible and near infrared spectroscopy for measurement of pH for deriving variable rate lime recommendations.

PubMed

Tekin, Yücel; Kuang, Boyan; Mouazen, Abdul M

2013-08-08

This paper aims at exploring the potential of visible and near infrared (vis-NIR) spectroscopy for on-line measurement of soil pH, with the intention to produce variable rate lime recommendation maps. An on-line vis-NIR soil sensor set up to a frame was used in this study. Lime application maps, based on pH predicted by vis-NIR techniques, were compared with maps based on traditional lab-measured pH. The validation of the calibration model using off-line spectra provided excellent prediction accuracy of pH (R2 = 0.85, RMSEP = 0.18 and RPD = 2.52), as compared to very good accuracy obtained with the on-line measured spectra (R2 = 0.81, RMSEP = 0.20 and RPD = 2.14). On-line predicted pH of all points (e.g., 2,160) resulted in the largest overall field virtual lime requirement (1.404 t), as compared to those obtained with 16 validation points off-line prediction (0.28 t), on-line prediction (0.14 t) and laboratory reference measurement (0.48 t). The conclusion is that the vis-NIR spectroscopy can be successfully used for the prediction of soil pH and for deriving lime recommendations. The advantage of the on-line sensor over sampling with limited number of samples is that more detailed information about pH can be obtained, which is the reason for a higher but precise calculated lime recommendation rate.

Potential of On-Line Visible and Near Infrared Spectroscopy for Measurement of pH for Deriving Variable Rate Lime Recommendations

PubMed Central

Tekin, Yücel; Kuang, Boyan; Mouazen, Abdul M.

2013-01-01

This paper aims at exploring the potential of visible and near infrared (vis-NIR) spectroscopy for on-line measurement of soil pH, with the intention to produce variable rate lime recommendation maps. An on-line vis-NIR soil sensor set up to a frame was used in this study. Lime application maps, based on pH predicted by vis-NIR techniques, were compared with maps based on traditional lab-measured pH. The validation of the calibration model using off-line spectra provided excellent prediction accuracy of pH (R2 = 0.85, RMSEP = 0.18 and RPD = 2.52), as compared to very good accuracy obtained with the on-line measured spectra (R2 = 0.81, RMSEP = 0.20 and RPD = 2.14). On-line predicted pH of all points (e.g., 2,160) resulted in the largest overall field virtual lime requirement (1.404 t), as compared to those obtained with 16 validation points off-line prediction (0.28 t), on-line prediction (0.14 t) and laboratory reference measurement (0.48 t). The conclusion is that the vis-NIR spectroscopy can be successfully used for the prediction of soil pH and for deriving lime recommendations. The advantage of the on-line sensor over sampling with limited number of samples is that more detailed information about pH can be obtained, which is the reason for a higher but precise calculated lime recommendation rate. PMID:23966186

Essential Public Health Competencies for Medical Students: Establishing a Consensus in Family Medicine.

PubMed

Morley, Christopher P; Rosas, Scott R; Mishori, Ranit; Jordan, William; Jarris, Yumi Shitama; Competencies Work Group, Family Medicine/Public Health; Prunuske, Jacob

2017-01-01

Phenomenon: The integration of public health (PH) competency training into medical education, and further integration of PH and primary care, has been urged by the U.S. Institute of Medicine. However, PH competencies are numerous, and no consensus exists over which competencies are most important for adoption by current trainees. Our objective was to conduct a group concept mapping exercise with stakeholders identifying the most important and feasible PH skills to incorporate in medical and residency curricula. We utilized a group concept mapping technique via the Concept System Global Max ( http://www.conceptsystems.com ), where family medicine educators and PH professionals completed the phrase, "A key Public Health competency for physicians-in-training to learn is …" with 1-10 statements. The statement list was edited for duplication and other issues; stakeholders then sorted the statements and rated them for importance and feasibility of integration. Multidimensional scaling and cluster analysis were used to create a two-dimensional point map of domains of PH training, allowing visual comparison of groupings of related ideas and relative importance of these ideas. There were 116 nonduplicative statements (225 total) suggested by 120 participants. Three metacategories of competencies emerged: Clinic, Community & Culture, Health System Understanding, and Population Health Science & Data. Insights: We identified and organized a set of topics that serve as a foundation for the integration of family medicine and PH education. Incorporating these topics into medical education is viewed as important and feasible by family medicine educators and PH professions.

MapX An In Situ, Full-frame X-Ray Spectroscopic Imager for Planetary Science and Astrobiology

NASA Technical Reports Server (NTRS)

Blake, David; Sarrazin, Philippe; Thompson, Kathleen; Bristow, Thomas

2017-01-01

Microbial life exploits micron-scale disequilibria at boundaries where valence, chemical potential, pH, Eh, etc. vary on a length scale commensurate with the organisms - 10's to 100's of microns. The detection of accumulations of the biogenic elements C,N,O,P,S at appropriate concentrations on or in a mineral/ice substrate would constitute permissive evidence of extant life, but context is also required. Does the putative biosignature exist under habitable conditions? Under what conditions of P, T, and chemical potential was the host mineralogy formed? MapX is an in situ robotic spacecraft instrument that images the biogenic elements C, N, O, P, S, as well as the cations of the rock-forming minerals (Na, Mg, Al, Si, K, Ca, Ti, Cr, Mn, Fe) and important anions such as Cl, Fl. MapX provides element maps with less than or equal to100 microns resolution over a 2.5 cm X 2.5 cm area, as well as quantitative XRF spectra from ground- or instrument-selected Regions of Interest (ROI). XRF spectra are converted to mineralogies using ground- or instrument-based algorithms. Either X-ray tube or radioisotope sources such as 244Cm (Alpha-particle and gamma- ray fluorescence) can be used. Fluoresced sample Xrays are imaged onto an X-ray sensitive CCD through an X-ray MicroPore Optic (MPO). The MapX design as well as baseline performance requirements for a MapX instrument intended for life detection / identification of habitable environments will be presented.

Targeted nanosensor aided three-dimensional pH mapping in tumor spheroids using two-photon microscopy

NASA Astrophysics Data System (ADS)

Ray, Aniruddha; Lee, Yong-Eun Koo; Elbez, Remy; Kopelman, Raoul

2012-03-01

Tumors are generally characterized by a pH lower than the surrounding tissues. The mapping of tumor pH is of great importance as it plays a critical role in drug delivery and its effectiveness. Here we present a pH mapping technique in tumor spheroids, using targeted, ratiometric, fluorescent, pH nano-sensor that is based on two-photon excitation. Spheroids are micro-tumors that are widely used as an in-vitro three dimensional tumor model to study the different properties of the tumor for the purpose of drug delivery, therapy etc. The nanosensor consists of 8-Hydroxypyrene- 1,3,6-trisulfonic acid (HPTS), a pH sensitive dye, encapsulated in polyacrylamide hydrogel nanoparticle matrix and F3 peptide, conjugated to the nanoparticle's surface. The nanosensor has an average size of 68nm and contains approximately 0.5% dye by weight. The fluorescence intensity ratio, at the two-photon excitation wavelengths of 900nm and 750nm, increases linearly in the pH range from 6.0 to 8.0 and is used to determine the pH of the local environment. Our study reveals the pH distribution inside human cervix cancer spheroids (of different sizes) during the various stages of their formation. This information can be used to develop more efficient drug delivery mechanisms. The two-photon excitation used for this purpose is especially useful as it drastically minimizes both photobleaching and autofluorescence, thus leading to an increase in the signal-to-noise ratio. It also enables deep tissue imaging due to higher photon penetration depth.

Hematocrit Measurement with R2* and Quantitative Susceptibility Mapping in Postmortem Brain.

PubMed

Walsh, A J; Sun, H; Emery, D J; Wilman, A H

2018-05-24

Noninvasive venous oxygenation quantification with MR imaging will improve the neurophysiologic investigation and the understanding of the pathophysiology in neurologic diseases. Available MR imaging methods are limited by sensitivity to flow and often require assumptions of the hematocrit level. In situ postmortem imaging enables evaluation of methods in a fully deoxygenated environment without flow artifacts, allowing direct calculation of hematocrit. This study compares 2 venous oxygenation quantification methods in in situ postmortem subjects. Transverse relaxation (R2*) mapping and quantitative susceptibility mapping were performed on a whole-body 4.7T MR imaging system. Intravenous measurements in major draining intracranial veins were compared between the 2 methods in 3 postmortem subjects. The quantitative susceptibility mapping technique was also applied in 10 healthy control subjects and compared with reference venous oxygenation values. In 2 early postmortem subjects, R2* mapping and quantitative susceptibility mapping measurements within intracranial veins had a significant and strong correlation ( R 2 = 0.805, P = .004 and R 2 = 0.836, P = .02). Higher R2* and susceptibility values were consistently demonstrated within gravitationally dependent venous segments during the early postmortem period. Hematocrit ranged from 0.102 to 0.580 in postmortem subjects, with R2* and susceptibility as large as 291 seconds -1 and 1.75 ppm, respectively. Measurements of R2* and quantitative susceptibility mapping within large intracranial draining veins have a high correlation in early postmortem subjects. This study supports the use of quantitative susceptibility mapping for evaluation of in vivo venous oxygenation and postmortem hematocrit concentrations. © 2018 by American Journal of Neuroradiology.

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.

The effects of AVIRIS atmospheric calibration methodology on identification and quantitative mapping of surface mineralogy, Drum Mountains, Utah

NASA Technical Reports Server (NTRS)

Kruse, Fred A.; Dwyer, John L.

1993-01-01

The Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) measures reflected light in 224 contiguous spectra bands in the 0.4 to 2.45 micron region of the electromagnetic spectrum. Numerous studies have used these data for mineralogic identification and mapping based on the presence of diagnostic spectral features. Quantitative mapping requires conversion of the AVIRIS data to physical units (usually reflectance) so that analysis results can be compared and validated with field and laboratory measurements. This study evaluated two different AVIRIS calibration techniques to ground reflectance: an empirically-based method and an atmospheric model based method to determine their effects on quantitative scientific analyses. Expert system analysis and linear spectral unmixing were applied to both calibrated data sets to determine the effect of the calibration on the mineral identification and quantitative mapping results. Comparison of the image-map results and image reflectance spectra indicate that the model-based calibrated data can be used with automated mapping techniques to produce accurate maps showing the spatial distribution and abundance of surface mineralogy. This has positive implications for future operational mapping using AVIRIS or similar imaging spectrometer data sets without requiring a priori knowledge.

Mapping quantitative trait loci for traits defined as ratios.

PubMed

Yang, Runqing; Li, Jiahan; Xu, Shizhong

2008-03-01

Many traits are defined as ratios of two quantitative traits. Methods of QTL mapping for regular quantitative traits are not optimal when applied to ratios due to lack of normality for traits defined as ratios. We develop a new method of QTL mapping for traits defined as ratios. The new method uses a special linear combination of the two component traits, and thus takes advantage of the normal property of the new variable. Simulation study shows that the new method can substantially increase the statistical power of QTL detection relative to the method which treats ratios as regular quantitative traits. The new method also outperforms the method that uses Box-Cox transformed ratio as the phenotype. A real example of QTL mapping for relative growth rate in soybean demonstrates that the new method can detect more QTL than existing methods of QTL mapping for traits defined as ratios.

MapX: An In Situ, Full-Frame X-Ray Spectroscopic Imager for the Biogenic Elements

NASA Technical Reports Server (NTRS)

Blake, David; Sarrazin, Philippe; Thompson, Kathy; Bristow, Thomas

2016-01-01

Microbial life exploits microscale disequilibria at boundaries where valence, chemical potential, pH, Eh, etc. vary on a length scale commensurate with the organisms themselves - tens to hundreds of micrometers. These disequilibria can exist within cracks or veins in rocks and ice, at inter- or intra-crystalline boundaries, at sediment/water or sediment/atmosphere interfaces, or even within fluid inclusions trapped inside minerals. The detection of accumulations of the biogenic elements C,N,O,P,S at appropriate concentrations on or in a mineral/ice substrate would constitute permissive evidence of extant life, but context is also required. Does the putative biosignature exist in a habitable environment? Under what conditions of P, T, and chemical potential was the host mineralogy formed? MapX is an arm-deployed contact instrument that directly images the biogenic elements C, N, O, P, S, as well as the cations of the rock-forming minerals (Na, Mg, Al, Si, K, Ca, Ti, Cr, Mn, Fe) and important anions such as Cl, Fl. The instrument provides element images having =100 micron lateral spatial resolution over a 2.5 cm X 2.5 cm area, as well as quantitative XRF spectra from ground-selected or instrument-selected Regions of Interest (ROI) on the sample. Quantitative XRF spectra from ROI can be translated into mineralogies using ground- or instrument-based algorithms. Either an X-ray tube source (X-ray fluorescence) or a radioisotope source such as 244-Cm (alpha-particle and gamma-ray fluorescence) can be used, and characteristic X-rays emitted from the sample are imaged onto an X-ray sensitive CCD through an X-ray MicroPore Optic (MPO). As a fluorescent source, 244-Cm is highly desirable in a MapX instrument intended for life detection since high-energy alpha-particles are unrivaled in fluorescence yield for the low-Z elements. The MapX design as well as baseline performance requirements for a MapX instrument intended for life detection/identification of habitable environments will be presented.

Self-Assembled Fluorescent Bovine Serum Albumin Nanoprobes for Ratiometric pH Measurement inside Living Cells.

PubMed

Yang, Qiaoyu; Ye, Zhongju; Zhong, Meile; Chen, Bo; Chen, Jian; Zeng, Rongjin; Wei, Lin; Li, Hung-wing; Xiao, Lehui

2016-04-20

In this work, we demonstrated a new ratiometric method for the quantitative analysis of pH inside living cells. The structure of the nanosensor comprises a biofriendly fluorescent bovine serum albumin (BSA) matrix, acting as a pH probe, and pH-insensitive reference dye Alexa 594 enabling ratiometric quantitative pH measurement. The fluorescent BSA matrix was synthesized by cross-linking of the denatured BSA proteins in ethanol with glutaraldehyde. The size of the as-synthesized BSA nanoparticles can be readily manipulated from 30 to 90 nm, which exhibit decent fluorescence at the peak wavelength of 535 nm with a pH response range of 6-8. The potential of this pH sensor for intracellular pH monitoring was demonstrated inside living HeLa cells, whereby a significant change in fluorescence ratio was observed when the pH of the cell was switched from normal to acidic with anticancer drug treatment. The fast response of the nanosensor makes it a very powerful tool in monitoring the processes occurring within the cytosol.

Parameterization of hyperpolarized (13)C-bicarbonate-dissolution dynamic nuclear polarization.

PubMed

Scholz, David Johannes; Otto, Angela M; Hintermair, Josef; Schilling, Franz; Frank, Annette; Köllisch, Ulrich; Janich, Martin A; Schulte, Rolf F; Schwaiger, Markus; Haase, Axel; Menzel, Marion I

2015-12-01

(13)C metabolic MRI using hyperpolarized (13)C-bicarbonate enables preclinical detection of pH. To improve signal-to-noise ratio, experimental procedures were refined, and the influence of pH, buffer capacity, temperature, and field strength were investigated. Bicarbonate preparation was investigated. Bicarbonate was prepared and applied in spectroscopy at 1, 3, 14 T using pure dissolution, culture medium, and MCF-7 cell spheroids. Healthy rats were imaged by spectral-spatial spiral acquisition for spatial and temporal bicarbonate distribution, pH mapping, and signal decay analysis. An optimized preparation technique for maximum solubility of 6 mol/L and polarization levels of 19-21% is presented; T1 and SNR dependency on field strength, buffer capacity, and pH was investigated. pH mapping in vivo is demonstrated. An optimized bicarbonate preparation and experimental procedure provided improved T1 and SNR values, allowing in vitro and in vivo applications.

Monitoring of pyrocatechol indoor air pollution

NASA Astrophysics Data System (ADS)

Eškinja, I.; Grabarić, Z.; Grabarić, B. S.

Spectrophotometric and electrochemical methods for monitoring of pyrocatechol (PC) indoor air pollution have been investigated. Spectrophotometric determination was performed using Fe(III) and iodine methods. The adherence to Beer's law was found in the concentration range between 0 and 12 μg ml - for iodine method at pH = 5.7 measuring absorbance at 725 nm, and in the range 0-30 μg ml - for Fe(III) method at pH = 9.5 measuring absorbance at 510 nm. The former method showed greater sensitivity than the latter one. Differential pulse voltammetry (DPV) and chronoamperometric (CA) detection in flow injection analysis (FIA) using carbon paste electrode in phosphate buffer solution of pH = 6.5 was also used for pyrocatechol determination. The electrochemical methods allowed pyrocatechol quantitation in submicromolar concentration level with an overall reproducibility of ± 1%. The efficiency of pyrocatechol sampling collection was investigated at two temperatures (27 and 40°C) in water, 0.1 M NaOH and 0.1 M HCl solutions. Solution of 0.1 M HCl gave the best collection efficiency (95.5-98.5%). A chamber testing simulating the indoor pollution has been performed. In order to check the reliability of the proposed methods for monitoring of the indoor pyrocatechol pollution, the air in working premises with pyrocatechol released from meteorological charts during mapping and paper drying was analyzed using proposed methods. The concentration of pyrocatechol in the air during mapping was found to be 1.8 mg m -3 which is below the hygienic standard of permissible exposure of 20 mg m -3 (≈ 5 ppm). The release of pyrocatechol from the paper impregnated with pyrocatechol standing at room temperature during one year was also measured. The proposed methods can be used for indoor pyrocatechol pollution monitoring in working premises of photographic, rubber, oil and dye industries, fur and furniture dyeing and cosmetic or pharmaceutical premises where pyrocatechol and related compounds are in use.

Quantitative use of multiincidence-angle SAR for geologic mapping

NASA Technical Reports Server (NTRS)

Farr, T. G.; Albee, A. L.; Evans, D. L.; Solomon, J. E.; Daily, M. I.; Labotka, T. C.; Smith, M. O.

1984-01-01

It is proposed that techniques be developed and used for quantitative interpretation of shuttle imaging radar-B (SIR-B) data for lithologic identification and mapping. The use of backscatter versus incidence angle signatures derived from SIR-B images is to be investigated. The use of SIR-B with other sensors for geologic mapping is also to be considered. Anticipated results are discussed in terms of geologic mapping.

Development of a quantitative pachytene chromosome map and its unification with somatic chromosome and linkage maps of rice (Oryza sativa L.).

PubMed

Ohmido, Nobuko; Iwata, Aiko; Kato, Seiji; Wako, Toshiyuki; Fukui, Kiichi

2018-01-01

A quantitative pachytene chromosome map of rice (Oryza sativa L.) was developed using imaging methods. The map depicts not only distribution patterns of chromomeres specific to pachytene chromosomes, but also the higher order information of chromosomal structures, such as heterochromatin (condensed regions), euchromatin (decondensed regions), the primary constrictions (centromeres), and the secondary constriction (nucleolar organizing regions, NOR). These features were image analyzed and quantitatively mapped onto the map by Chromosome Image Analyzing System ver. 4.0 (CHIAS IV). Correlation between H3K9me2, an epigenetic marker and formation and/or maintenance of heterochromatin, thus was, clearly visualized. Then the pachytene chromosome map was unified with the existing somatic chromosome and linkage maps by physically mapping common DNA markers among them, such as a rice A genome specific tandem repeat sequence (TrsA), 5S and 45S ribosomal RNA genes, five bacterial artificial chromosome (BAC) clones, four P1 bacteriophage artificial chromosome (PAC) clones using multicolor fluorescence in situ hybridization (FISH). Detailed comparison between the locations of the DNA probes on the pachytene chromosomes using multicolor FISH, and the linkage map enabled determination of the chromosome number and short/long arms of individual pachytene chromosomes using the chromosome number and arm assignment designated for the linkage map. As a result, the quantitative pachytene chromosome map was unified with two other major rice chromosome maps representing somatic prometaphase chromosomes and genetic linkages. In conclusion, the unification of the three rice maps serves as an indispensable basic information, not only for an in-depth comparison between genetic and chromosomal data, but also for practical breeding programs.

Quantitative Chemical Exchange Saturation Transfer MRI of Intervertebral Disc in a Porcine Model

PubMed Central

Zhou, Zhengwei; Bez, Maxim; Tawackoli, Wafa; Giaconi, Joseph; Sheyn, Dmitriy; de Mel, Sandra; Maya, Marcel M.; Pressman, Barry D.; Gazit, Zulma; Pelled, Gadi; Gazit, Dan; Li, Debiao

2017-01-01

Purpose Previous studies have associated low pH in interver-tebral discs (IVDs) with discogenic back pain. The purpose of this study was to determine whether quantitative CEST (qCEST) MRI can be used to detect pH changes in IVDs in vivo. Methods The exchange rate ksw between glycosaminoglycan (GAG) protons and water protons was determined from qCEST analysis. Its dependence on pH value was investigated in GAG phantoms with varying pH and concentrations. The relationship between ksw and pH was studied further in vivo in a porcine model on a 3T MR scanner and validated using a pH meter. Sodium lactate was injected into the IVDs to induce various pH values within the discs ranging from 5 to 7. Results Phantom and animal results revealed that ksw measured using qCEST MRI is highly correlated with pH level. In the animal studies, the relationship can be described as ksw =9.2 × 106 × 10−pH + 196.9, R2 = 0.7883. Conclusion The exchange rate between GAG and water protons determined from qCEST MRI is closely correlated with pH value. This technique has the potential to noninvasively measure pH in the IVDs of patients with discogenic pain. PMID:27670140

Spatial distribution of pH and organic matter in urban soils and its implications on site-specific land uses in Xuzhou, China.

PubMed

Mao, Yingming; Sang, Shuxun; Liu, Shiqi; Jia, Jinlong

2014-05-01

The spatial variation of soil pH and soil organic matter (SOM) in the urban area of Xuzhou, China, was investigated in this study. Conventional statistics, geostatistics, and a geographical information system (GIS) were used to produce spatial distribution maps and to provide information about land use types. A total of 172 soil samples were collected based on grid method in the study area. Soil pH ranged from 6.47 to 8.48, with an average of 7.62. SOM content was very variable, ranging from 3.51 g/kg to 17.12 g/kg, with an average of 8.26 g/kg. Soil pH followed a normal distribution, while SOM followed a log-normal distribution. The results of semi-variograms indicated that soil pH and SOM had strong (21%) and moderate (44%) spatial dependence, respectively. The variogram model was spherical for soil pH and exponential for SOM. The spatial distribution maps were achieved using kriging interpolation. The high pH and high SOM tended to occur in the mixed forest land cover areas such as those in the southwestern part of the urban area, while the low values were found in the eastern and the northern parts, probably due to the effect of industrial and human activities. In the central urban area, the soil pH was low, but the SOM content was high, which is mainly attributed to the disturbance of regional resident activities and urban transportation. Furthermore, anthropogenic organic particles are possible sources of organic matter after entering the soil ecosystem in urban areas. These maps provide useful information for urban planning and environmental management. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

Skin thickness effects on in vivo LXRF

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

Preiss, I.L.; Washington, W. II

The analysis of lead concentration in bone utilizing LXRF can be adversely effected by overlying issue. A quantitative measure of the attenuation of the 10.5 keV Pb L a x-ray signal by skin and skin equivalent plastic has been conducted. Concentration ranges in plaster of Paris and goat bone from 7 to 90 ppm with attenuators of Lucite{reg_sign} and pig skin were examined. It is concluded that no quantitative or semi quantitative analysis can be achieved if overlying sue thickness exceeds 3 mm for Ph concentrations of less than 30 porn Ph in bone.

Effect of packaging technology on microbiological and sensory quality of a cooked blood sausage, Morcela de Arroz, from Monchique region of Portugal.

PubMed

Pereira, J A; Dionísio, L; Patarata, L; Matos, T J S

2015-03-01

Morcela de Arroz (MA), a popular Portuguese blood sausage, with high pH and water activity (aw), is traditionally commercialized without preservatives and unpacked. This study evaluated the best packaging solution to extend MA shelf life stored at 4±1°C for 44days: without packaging (WP), vacuum (VP) and modified atmosphere packaging (MAP) (80% CO2; 20% N2). Mesophilic (MTVC), psychrotrophic (PTVC), lactic acid bacteria (LAB), pseudomonads, molds and yeasts, Enterobacteriaceae, Listeria monocytogenes, Salmonella spp., Bacillus cereus, Clostridium perfringens, sensory properties, pH, moisture and aw were studied. Moisture and aw decreased (p<0.05) in WP. pH decreased in WP and MAP during storage. MTVC and PTVC counts increased to values around 7logCFU/g at 44days of storage. LAB and Enterobacteriaceae counts were higher (p<0.05) in VP. Pseudomonads were inhibited (p<0.05) by MAP after 8days of storage. Sensory parameters were affected (p<0.05) by packaging and storage time. Globally, MAP performed better. Copyright © 2014 Elsevier Ltd. All rights reserved.

Use of single nucleotide polymorphisms (SNP) to fine-map quantitative trait loci (QTL) in swine

USDA-ARS?s Scientific Manuscript database

Mapping quantitative trait loci (QTL) in swine at the US Meat Animal Research Center has relied heavily on linkage mapping in either F2 or Backcross families. QTL identified in the initial scans typically have very broad confidence intervals and further refinement of the QTL’s position is needed bef...

Influence of levels of information as presented by different technologies on students' understanding of acid, base, and ph concepts

NASA Astrophysics Data System (ADS)

Nakhleh, Mary B.; Krajcik, Joseph S.

We investigated how different levels of information presented by various technologies affected secondary students' understanding of acid, base, and pH concepts. Secondary students who were selected for the study had just completed their study of acid-base chemistry. No attempt was made to provide further instruction. We analyzed changes in the understanding of individual students by constructing concept maps from the propositions that the students used in interviews conducted before and after a series of acid-base titrations. After the initial interview, students were divided into three groups. Within each group, students individually performed the same set of titrations using different technologies: chemical indicators, pH meters, and microcomputer-based laboratories (MBL). After the titrations were completed, all students were interviewed again. We found that students using MBL exhibited a larger positive shift in their concept map scores, which indicates a greater differentiation and integration of their knowledge of acids and bases. The chemical indicator students exhibited a more moderate positive shift in their concept map scores, and the pH meter students exhibited a smaller positive shift. We also found that the MBL students constructed more inappropriate links in their concept maps than the chemical indicator or pH meter students. However, we speculate that this increased number of inappropriate links indicates a high level of involvement with the technology. We therefore argue that the level of information offered by the technology affected students' understanding of the chemical concepts.Received: 24 February 1993; Revised: 21 February 1994;

Developing Discourses of Knowledge and Understanding: Longitudinal Studies of Ph.D. Supervision

ERIC Educational Resources Information Center

Kandiko, Camille B.; Kinchin, Ian M.

2013-01-01

Competing notions of what a Ph.D. has been, is and should be are undercurrents in doctoral education. A longitudinal study of Ph.D. supervision based on interviews and concept mapping was used to surface understandings of the purpose of a Ph.D. This research tracks change over time for both the student and the supervisor. The data were analysed…

Deficiency mapping of quantitative trait loci affecting longevity in Drosophila melanogaster.

PubMed Central

Pasyukova, E G; Vieira, C; Mackay, T F

2000-01-01

In a previous study, sex-specific quantitative trait loci (QTL) affecting adult longevity were mapped by linkage to polymorphic roo transposable element markers, in a population of recombinant inbred lines derived from the Oregon and 2b strains of Drosophila melanogaster. Two life span QTL were each located on chromosomes 2 and 3, within sections 33E-46C and 65D-85F on the cytological map, respectively. We used quantitative deficiency complementation mapping to further resolve the locations of life span QTL within these regions. The Oregon and 2b strains were each crossed to 47 deficiencies spanning cytological regions 32F-44E and 64C-76B, and quantitative failure of the QTL alleles to complement the deficiencies was assessed. We initially detected a minimum of five and four QTL in the chromosome 2 and 3 regions, respectively, illustrating that multiple linked factors contribute to each QTL detected by recombination mapping. The QTL locations inferred from deficiency mapping did not generally correspond to those of candidate genes affecting oxidative and thermal stress or glucose metabolism. The chromosome 2 QTL in the 35B-E region was further resolved to a minimum of three tightly linked QTL, containing six genetically defined loci, 24 genes, and predicted genes that are positional candidates corresponding to life span QTL. This region was also associated with quantitative variation in life span in a sample of 10 genotypes collected from nature. Quantitative deficiency complementation is an efficient method for fine-scale QTL mapping in Drosophila and can be further improved by controlling the background genotype of the strains to be tested. PMID:11063689

Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.).

PubMed

Zhang, Zhen; Shang, Haihong; Shi, Yuzhen; Huang, Long; Li, Junwen; Ge, Qun; Gong, Juwu; Liu, Aiying; Chen, Tingting; Wang, Dan; Wang, Yanling; Palanga, Koffi Kibalou; Muhammad, Jamshed; Li, Weijie; Lu, Quanwei; Deng, Xiaoying; Tan, Yunna; Song, Weiwu; Cai, Juan; Li, Pengtao; Rashid, Harun or; Gong, Wankui; Yuan, Youlu

2016-04-11

Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0-153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15-16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection.

Spatial variability of soil carbon, pH, available phosphorous and potassium in organic farm located in Mediterranean Croatia

NASA Astrophysics Data System (ADS)

Bogunović, Igor; Pereira, Paulo; Šeput, Miranda

2016-04-01

Soil organic carbon (SOC), pH, available phosphorus (P), and potassium (K) are some of the most important factors to soil fertility. These soil parameters are highly variable in space and time, with implications to crop production. The aim of this work is study the spatial variability of SOC, pH, P and K in an organic farm located in river Rasa valley (Croatia). A regular grid (100 x 100 m) was designed and 182 samples were collected on Silty Clay Loam soil. P, K and SOC showed moderate heterogeneity with coefficient of variation (CV) of 21.6%, 32.8% and 51.9%, respectively. Soil pH record low spatial variability with CV of 1.5%. Soil pH, P and SOC did not follow normal distribution. Only after a Box-Cox transformation, data respected the normality requirements. Directional exponential models were the best fitted and used to describe spatial autocorrelation. Soil pH, P and SOC showed strong spatial dependence with nugget to sill ratio with 13.78%, 0.00% and 20.29%, respectively. Only K recorded moderate spatial dependence. Semivariogram ranges indicate that future sampling interval could be 150 - 200 m in order to reduce sampling costs. Fourteen different interpolation models for mapping soil properties were tested. The method with lowest Root Mean Square Error was the most appropriated to map the variable. The results showed that radial basis function models (Spline with Tension and Completely Regularized Spline) for P and K were the best predictors, while Thin Plate Spline and inverse distance weighting models were the least accurate. The best interpolator for pH and SOC was the local polynomial with the power of 1, while the least accurate were Thin Plate Spline. According to soil nutrient maps investigated area record very rich supply with K while P supply was insufficient on largest part of area. Soil pH maps showed mostly neutral reaction while individual parts of alkaline soil indicate the possibility of penetration of seawater and salt accumulation in the soil profile. Future research should focus on spatial patterns on soil pH, electrical conductivity and sodium adsorption ratio. Keywords: geostatistics, semivariogram, interpolation models, soil chemical properties

A quantitative analysis of IRAS maps of molecular clouds

NASA Technical Reports Server (NTRS)

Wiseman, Jennifer J.; Adams, Fred C.

1994-01-01

We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

Colorimetric Determination of pH.

ERIC Educational Resources Information Center

Tucker, Sheryl; And Others

1989-01-01

Presented is an activity in which the pH of a solution can be quantitatively measured using a spectrophotometer. The theory, experimental details, sample preparation and selection, instrumentation, and results are discussed. (CW)

Left Ventricular End-Systolic Eccentricity Index for Assessment of Pulmonary Hypertension in Infants.

PubMed

Abraham, Sharon; Weismann, Constance G

2016-06-01

Pulmonary hypertension (PH) is a common problem in the neonatal intensive care unit and is associated with significant morbidity and mortality. The aim of this study was to identify a quantitative echocardiographic marker of septal curvature that can be used to accurately identify PH in NICU infants with concern for PH. Echocardiograms of infants who were prematurely born and infants with persistent pulmonary hypertension of the newborn were performed using a defined protocol for evaluation of PH. Qualitative assessment by a single pediatric cardiologist was used as a reference standard. Qualitative and quantitative parameters of right ventricular (RV) size, pressure, and function were documented. Left ventricular end-systolic eccentricity index (EI) was defined as the ratio of the anterior-inferior and septal-posterolateral cavity dimensions at the mid-ventricular level. A total of 216 infants at risk for PH were included in this study. One hundred forty-three (66%) had an interpretable tricuspid regurgitation jet velocity. While systolic septal flattening was recognized at EIs ≥ 1.15, more than half-systemic RV pressure became apparent at EIs ≥ 1.3. Unlike qualitative assessment of septal flattening, there was high inter-observer agreement for EIs. Quantitative parameters of RV systolic function were impaired only at EIs ≥ 1.3. We suggest that EIs should be incorporated into routine protocols when there is a concern for PH in neonates. This may lead to a more reliable assessment of PH and may reduce inter-observer variability. Correlation of EIs with invasive hemodynamic data is needed to validate our results. © 2016, Wiley Periodicals, Inc.

Quantitative Susceptibility Mapping after Sports-Related Concussion.

PubMed

Koch, K M; Meier, T B; Karr, R; Nencka, A S; Muftuler, L T; McCrea, M

2018-06-07

Quantitative susceptibility mapping using MR imaging can assess changes in brain tissue structure and composition. This report presents preliminary results demonstrating changes in tissue magnetic susceptibility after sports-related concussion. Longitudinal quantitative susceptibility mapping metrics were produced from imaging data acquired from cohorts of concussed and control football athletes. One hundred thirty-six quantitative susceptibility mapping datasets were analyzed across 3 separate visits (24 hours after injury, 8 days postinjury, and 6 months postinjury). Longitudinal quantitative susceptibility mapping group analyses were performed on stability-thresholded brain tissue compartments and selected subregions. Clinical concussion metrics were also measured longitudinally in both cohorts and compared with the measured quantitative susceptibility mapping. Statistically significant increases in white matter susceptibility were identified in the concussed athlete group during the acute (24 hour) and subacute (day 8) period. These effects were most prominent at the 8-day visit but recovered and showed no significant difference from controls at the 6-month visit. The subcortical gray matter showed no statistically significant group differences. Observed susceptibility changes after concussion appeared to outlast self-reported clinical recovery metrics at a group level. At an individual subject level, susceptibility increases within the white matter showed statistically significant correlations with return-to-play durations. The results of this preliminary investigation suggest that sports-related concussion can induce physiologic changes to brain tissue that can be detected using MR imaging-based magnetic susceptibility estimates. In group analyses, the observed tissue changes appear to persist beyond those detected on clinical outcome assessments and were associated with return-to-play duration after sports-related concussion. © 2018 by American Journal of Neuroradiology.

Imaging Cerebral Microhemorrhages in Military Service Members with Chronic Traumatic Brain Injury.

PubMed

Liu, Wei; Soderlund, Karl; Senseney, Justin S; Joy, David; Yeh, Ping-Hong; Ollinger, John; Sham, Elyssa B; Liu, Tian; Wang, Yi; Oakes, Terrence R; Riedy, Gerard

2016-02-01

To detect cerebral microhemorrhages in military service members with chronic traumatic brain injury by using susceptibility-weighted magnetic resonance (MR) imaging. The longitudinal evolution of microhemorrhages was monitored in a subset of patients by using quantitative susceptibility mapping. The study was approved by the Walter Reed National Military Medical Center institutional review board and is compliant with HIPAA guidelines. All participants underwent two-dimensional conventional gradient-recalled-echo MR imaging and three-dimensional flow-compensated multiecho gradient-recalled-echo MR imaging (processed to generate susceptibility-weighted images and quantitative susceptibility maps), and a subset of patients underwent follow-up imaging. Microhemorrhages were identified by two radiologists independently. Comparisons of microhemorrhage number, size, and magnetic susceptibility derived from quantitative susceptibility maps between baseline and follow-up imaging examinations were performed by using the paired t test. Among the 603 patients, cerebral microhemorrhages were identified in 43 patients, with six excluded for further analysis owing to artifacts. Seventy-seven percent (451 of 585) of the microhemorrhages on susceptibility-weighted images had a more conspicuous appearance than on gradient-recalled-echo images. Thirteen of the 37 patients underwent follow-up imaging examinations. In these patients, a smaller number of microhemorrhages were identified at follow-up imaging compared with baseline on quantitative susceptibility maps (mean ± standard deviation, 9.8 microhemorrhages ± 12.8 vs 13.7 microhemorrhages ± 16.6; P = .019). Quantitative susceptibility mapping-derived quantitative measures of microhemorrhages also decreased over time: -0.85 mm(3) per day ± 1.59 for total volume (P = .039) and -0.10 parts per billion per day ± 0.14 for mean magnetic susceptibility (P = .016). The number of microhemorrhages and quantitative susceptibility mapping-derived quantitative measures of microhemorrhages all decreased over time, suggesting that hemosiderin products undergo continued, subtle evolution in the chronic stage. © RSNA, 2015.

Quantitative trait locus analysis of heterosis for plant height and ear height in an elite maize hybrid zhengdan 958 by design III.

PubMed

Li, Hongjian; Yang, Qingsong; Fan, Nannan; Zhang, Ming; Zhai, Huijie; Ni, Zhongfu; Zhang, Yirong

2017-04-17

Plant height (PH) and ear height (EH) are two important agronomic traits in maize selection breeding. F 1 hybrid exhibit significant heterosis for PH and EH as compared to their parental inbred lines. To understand the genetic basis of heterosis controlling PH and EH, we conducted quantitative trait locus (QTL) analysis using a recombinant inbreed line (RIL) based design III population derived from the elite maize hybrid Zhengdan 958 in five environments. A total of 14 environmentally stable QTLs were identified, and the number of QTLs for Z 1 and Z 2 populations was six and eight, respectively. Notably, all the eight environmentally stable QTLs for Z 2 were characterized by overdominance effect (OD), suggesting that overdominant QTLs were the most important contributors to heterosis for PH and EH. Furthermore, 14 environmentally stable QTLs were anchored on six genomic regions, among which four are trait-specific QTLs, suggesting that the genetic basis for PH and EH is partially different. Additionally, qPH.A-1.3, modifying about 10 centimeters of PH, was further validated in backcross populations. The genetic basis for PH and EH is partially different, and overdominant QTLs are important factors for heterosis of PH and EH. A major QTL qPH.A-1.3 may be a desired target for genetic improvement of maize plant height.

Mapping, fine mapping, and molecular dissection of quantitative trait Loci in domestic animals.

PubMed

Georges, Michel

2007-01-01

Artificial selection has created myriad breeds of domestic animals, each characterized by unique phenotypes pertaining to behavior, morphology, physiology, and disease. Most domestic animal populations share features with isolated founder populations, making them well suited for positional cloning. Genome sequences are now available for most domestic species, and with them a panoply of tools including high-density single-nucleotide polymorphism panels. As a result, domestic animal populations are becoming invaluable resources for studying the molecular architecture of complex traits and of adaptation. Here we review recent progress and issues in the positional identification of genes underlying complex traits in domestic animals. As many phenotypes studied in animals are quantitative, we focus on mapping, fine mapping, and cloning of quantitative trait loci.

Mapping bark pH to better understand the cortisphere

NASA Astrophysics Data System (ADS)

Levia, D. F., Jr.; Köhler, S.; Jungkunst, H. F.; Gerold, G.

2016-12-01

The biogeochemistry of the cortisphere is poorly understood, despite the fact that a large variety of microbes, epiphytes, and insects live on, within, and just beneath corticular surfaces. Bark pH is a critical parameter that partially controls the chemodynamics of the cortisphere and its habitability by bark dwelling organisms as well as the chemistry of throughfall and stemflow. This presentation articulates, tests, and validates a method to accurately determine bark pH in situ. We employed agar-agar panels, embedded with a pH marker, to determine the spatiality of bark pH on cacao trees in Indonesia. In contrast to existing ex situ methods, we were able to record spatial differences in bark pH. In particular, bark pH was observed to fluctuate in relation to both morphological features on the bark, possibly corresponding to preferential flowpaths of stemflow, and epiphytic coverage. Due to its simplicity and economical nature, our method may be attractive to a variety of researchers interested in bark pH, its spatial variability, influence on stemflow chemistry, and its effect on organisms dwelling in the cortipshere. Publication note: This presentation is based on the following article: Köhler, S., Levia, D.F., Jungkunst, H.F. and Gerold, G. 2015. An in situ method to measure and map bark pH. Journal of Wood Chemistry and Technology 35(6): 438-449. [DOI: 10.1080/02773813.2015.1025285

Deep Learning for Magnetic Resonance Fingerprinting: A New Approach for Predicting Quantitative Parameter Values from Time Series.

PubMed

Hoppe, Elisabeth; Körzdörfer, Gregor; Würfl, Tobias; Wetzl, Jens; Lugauer, Felix; Pfeuffer, Josef; Maier, Andreas

2017-01-01

The purpose of this work is to evaluate methods from deep learning for application to Magnetic Resonance Fingerprinting (MRF). MRF is a recently proposed measurement technique for generating quantitative parameter maps. In MRF a non-steady state signal is generated by a pseudo-random excitation pattern. A comparison of the measured signal in each voxel with the physical model yields quantitative parameter maps. Currently, the comparison is done by matching a dictionary of simulated signals to the acquired signals. To accelerate the computation of quantitative maps we train a Convolutional Neural Network (CNN) on simulated dictionary data. As a proof of principle we show that the neural network implicitly encodes the dictionary and can replace the matching process.

Structural Bioinformatics-Based Prediction of Exceptional Selectivity of p38 MAP Kinase Inhibitor PH-797804

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

Xing, Li; Shieh, Huey S.; Selness, Shaun R.

2009-07-24

PH-797804 is a diarylpyridinone inhibitor of p38{alpha} mitogen-activated protein (MAP) kinase derived from a racemic mixture as the more potent atropisomer (aS), first proposed by molecular modeling and subsequently confirmed by experiments. On the basis of structural comparison with a different biaryl pyrazole template and supported by dozens of high-resolution crystal structures of p38{alpha} inhibitor complexes, PH-797804 is predicted to possess a high level of specificity across the broad human kinase genome. We used a structural bioinformatics approach to identify two selectivity elements encoded by the TXXXG sequence motif on the p38{alpha} kinase hinge: (i) Thr106 that serves as themore » gatekeeper to the buried hydrophobic pocket occupied by 2,4-difluorophenyl of PH-797804 and (ii) the bidentate hydrogen bonds formed by the pyridinone moiety with the kinase hinge requiring an induced 180{sup o} rotation of the Met109-Gly110 peptide bond. The peptide flip occurs in p38{alpha} kinase due to the critical glycine residue marked by its conformational flexibility. Kinome-wide sequence mining revealed rare presentation of the selectivity motif. Corroboratively, PH-797804 exhibited exceptionally high specificity against MAP kinases and the related kinases. No cross-reactivity was observed in large panels of kinase screens (selectivity ratio of >500-fold). In cellular assays, PH-797804 demonstrated superior potency and selectivity consistent with the biochemical measurements. PH-797804 has met safety criteria in human phase I studies and is under clinical development for several inflammatory conditions. Understanding the rationale for selectivity at the molecular level helps elucidate the biological function and design of specific p38{alpha} kinase inhibitors.« less

EM Algorithm for Mapping Quantitative Trait Loci in Multivalent Tetraploids

USDA-ARS?s Scientific Manuscript database

Multivalent tetraploids that include many plant species, such as potato, sugarcane and rose, are of paramount importance to agricultural production and biological research. Quantitative trait locus (QTL) mapping in multivalent tetraploids is challenged by their unique cytogenetic properties, such ...

Differential plating medium for quantitative detection of histamine-producing bacteria.

PubMed Central

Niven, C F; Jeffrey, M B; Corlett, D A

1981-01-01

A histidine-containing agar medium has been devised for quantitative detection of histamine-producing bacteria that are alleged to be associated with scombroid fish poisoning outbreaks. The responsible bacteria produce a marked pH change in the agar, with attendant color change of pH indicator adjacent to the colonies, thus facilitating their recognition. Proteus morganii and Klebsiella pneumoniae were the two most common histidine-decarboxylating species isolated from scombroid fish and mahi mahi. PMID:7013698

Establishment of the Ph. Eur. erythropoietin chemical reference substance batch 1.

PubMed

Burns, C; Bristow, A F; Buchheit, K H; Daas, A; Wierer, M; Costanzo, A

2015-01-01

The Erythropoietin (EPO) European Pharmacopoeia (Ph. Eur.) Biological Reference Preparation (BRP) batch 3 was calibrated in 2006 by in vivo bioassay and was used as a reference preparation for these assays as well as for the physicochemical methods in the Ph. Eur. monograph Erythropoietin concentrated solution (1316). In order to avoid the frequent replacement of this standard and thus reduce the use of animals, a new EPO Chemical Reference Substance (CRS) was established to be used solely for the physicochemical methods. Here we report the outcome of a collaborative study aimed at demonstrating the suitability of the candidate CRS (cCRS) as a reference for the physicochemical methods in the Ph. Eur. monograph. Results from the study demonstrated that for the physicochemical methods currently required in the monograph (capillary zone electrophoresis (CZE), polyacrylamide gel electrophoresis (PAGE)/immunoblotting and peptide mapping), the cCRS is essentially identical to the existing BRP. However, data also indicated that, for the physicochemical methods under consideration for inclusion in a revised monograph (test for oxidised forms and glycan mapping), the suitability of the cCRS as a reference needs to be confirmed with additional work. Further to completion of the study, the Ph. Eur. Commission adopted the cCRS as "Erythropoietin for physicochemical tests CRS batch 1" to be used for CZE, PAGE/immunoblotting and peptide mapping.

A journey from a SSR-based low density map to a SNP-based high density map for identification of disease resistance quantitative trait loci in peanut

USDA-ARS?s Scientific Manuscript database

Mapping and identification of quantitative trait loci (QTLs) are important for efficient marker-assisted breeding. Diseases such as leaf spots and Tomato spotted wilt virus (TSWV) cause significant loses to peanut growers. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to...

Summertime sea surface temperature fronts associated with upwelling around the Taiwan Bank

NASA Astrophysics Data System (ADS)

Lan, Kuo-Wei; Kawamura, Hiroshi; Lee, Ming-An; Chang, Yi; Chan, Jui-Wen; Liao, Cheng-Hsin

2009-04-01

It is well known that upwelling of subsurface water is dominant around the Taiwan Bank (TB) and the Penghu (PH) Islands in the southern Taiwan Strait in summertime. Sea surface temperature (SST) frontal features and related phenomena around the TB upwelling and the PH upwelling were investigated using long-term AVHRR (1996-2005) and SeaWiFS (1998-2005) data received at the station of National Taiwan Ocean University. SST and chlorophyll-a (Chl-a) images with a spatial resolution of 0.01° were generated and used for the monthly SST and Chl-a maps. SST fronts were extracted from each SST images and gradient magnitudes (GMs); the orientations were derived for the SST fronts. Monthly maps of cold fronts where the cooler SSTs were over a shallower bottom were produced from the orientation. Areas with high GMs (0.1-0.2 °C/km) with characteristic shapes appeared at geographically fixed positions around the TB/PH upwelling region where SSTs were lower than the surrounding waters. The well-shaped high GMs corresponded to cold fronts. Two areas with high Chl-a were found around the TB and PH Islands. The southern border of the high-Chl-a area in the TB upwelling area was outlined by the high-GM area. Shipboard measurements of snapshot vertical sections of temperature (T) and salinity (S) along the PH Channel showed a dome structure east of PH Islands, over which low SST and high GM in the maps of the corresponding month were present. Clear evidence of upwelling (vertically uniform distributions of T and S) was indicated at the TB edge in the T and S sections close to TB upwelling. This case of upwelling may be caused by bottom currents ascending the TB slope as pointed out by previous studies. The position of low SSTs in the monthly maps matched the upwelling area, and the high GMs corresponded to the area of eastern surface fronts in the T/S sections.

Global, quantitative and dynamic mapping of protein subcellular localization.

PubMed

Itzhak, Daniel N; Tyanova, Stefka; Cox, Jürgen; Borner, Georg Hh

2016-06-09

Subcellular localization critically influences protein function, and cells control protein localization to regulate biological processes. We have developed and applied Dynamic Organellar Maps, a proteomic method that allows global mapping of protein translocation events. We initially used maps statically to generate a database with localization and absolute copy number information for over 8700 proteins from HeLa cells, approaching comprehensive coverage. All major organelles were resolved, with exceptional prediction accuracy (estimated at >92%). Combining spatial and abundance information yielded an unprecedented quantitative view of HeLa cell anatomy and organellar composition, at the protein level. We subsequently demonstrated the dynamic capabilities of the approach by capturing translocation events following EGF stimulation, which we integrated into a quantitative model. Dynamic Organellar Maps enable the proteome-wide analysis of physiological protein movements, without requiring any reagents specific to the investigated process, and will thus be widely applicable in cell biology.

Separation of thorium from lanthanides by solvent extraction with ionizable crown ethers.

PubMed

Du, H S; Wood, D J; Elshani, S; Wai, C M

1993-02-01

Thorium and the lanthanides are extracted by alpha-(sym-dibenzo-16-crown-5-oxy)acetic acid and its analogues in different pH ranges. At pH 4.5, Th is quantitatively extracted by the crown ether carboxylic acids into chloroform whereas the extraction of the lanthanides is negligible. Separation of Th from the lanthanides can be achieved by solvent extraction under this condition. The extraction does not require specific counteranions and is reversible with respect to pH. Trace amounts of Th in water can be quantitatively recovered using this extraction system for neutron activation analysis. The nature of the extracted Th complex and the mechanism of extraction are discussed.

Precision Sensing by Two Opposing Gradient Sensors: How Does Escherichia coli Find its Preferred pH Level?

PubMed Central

Hu, Bo; Tu, Yuhai

2013-01-01

It is essential for bacteria to find optimal conditions for their growth and survival. The optimal levels of certain environmental factors (such as pH and temperature) often correspond to some intermediate points of the respective gradients. This requires the ability of bacteria to navigate from both directions toward the optimum location and is distinct from the conventional unidirectional chemotactic strategy. Remarkably, Escherichia coli cells can perform such a precision sensing task in pH taxis by using the same chemotaxis machinery, but with opposite pH responses from two different chemoreceptors (Tar and Tsr). To understand bacterial pH sensing, we developed an Ising-type model for a mixed cluster of opposing receptors based on the push-pull mechanism. Our model can quantitatively explain experimental observations in pH taxis for various mutants and wild-type cells. We show how the preferred pH level depends on the relative abundance of the competing sensors and how the sensory activity regulates the behavioral response. Our model allows us to make quantitative predictions on signal integration of pH and chemoattractant stimuli. Our study reveals two general conditions and a robust push-pull scheme for precision sensing, which should be applicable in other adaptive sensory systems with opposing gradient sensors. PMID:23823247

Quantitative measurement and real-time tracking of high intensity focused ultrasound using phase-sensitive optical coherence tomography: Feasibility study.

PubMed

Le, Nhan; Song, ShaoZhen; Nabi, Ghulam; Wang, Ruikang; Huang, Zhihong

2016-09-01

Phase-sensitive optical coherence tomography (PhS-OCT) is proposed, as a new high intensity focused ultrasound (HIFU) imaging guidance to detect and track HIFU focus inside 1% agar samples in this work. The experiments studied the effect of varying HIFU power on the induction of shear wave, which can be implemented as a new technique to monitor focused ultrasound surgery (FUS). A miniature HIFU transducer (1.02 MHz, 20 mm aperture diameter, 15 mm radius of curvature) was produced in-house, pressure-field mapped, and calibrated. The transducer was then embedded inside a 1% agar phantom, which was placed under PhS-OCT for observation, under various HIFU power settings (acoustic power, and number of cycles per pulse). Shear wave was induced on the sample surface by HIFU and was captured in full under PhS-OCT. The lowest HIFU acoustic power output for the detection of shear wave was found to be 0.36 W (1.02 MHz, 100 cycles/pulse), or with the number of cycles/pulse as low as 20 (1.02 MHz, 0.98 W acoustic power output). A linear relationship between acoustic power output and the maximum shear wave displacement was found in the first study. The second study explores a non-linear correlation between the (HIFU) numbers of cycles per pulse, and the maximum shear wave displacement. PhS-OCT demonstrates excellent tracking and detection of HIFU-induced shear wave. The results could benefit other imaging techniques in tracking and guiding HIFU focus. Further studies will explore the relationship between the physical transducer characteristics and the HIFU-induced shear wave.

Cerebral Metabolic Rate of Oxygen (CMRO2 ) Mapping by Combining Quantitative Susceptibility Mapping (QSM) and Quantitative Blood Oxygenation Level-Dependent Imaging (qBOLD).

PubMed

Cho, Junghun; Kee, Youngwook; Spincemaille, Pascal; Nguyen, Thanh D; Zhang, Jingwei; Gupta, Ajay; Zhang, Shun; Wang, Yi

2018-03-07

To map the cerebral metabolic rate of oxygen (CMRO 2 ) by estimating the oxygen extraction fraction (OEF) from gradient echo imaging (GRE) using phase and magnitude of the GRE data. 3D multi-echo gradient echo imaging and perfusion imaging with arterial spin labeling were performed in 11 healthy subjects. CMRO 2 and OEF maps were reconstructed by joint quantitative susceptibility mapping (QSM) to process GRE phases and quantitative blood oxygen level-dependent (qBOLD) modeling to process GRE magnitudes. Comparisons with QSM and qBOLD alone were performed using ROI analysis, paired t-tests, and Bland-Altman plot. The average CMRO 2 value in cortical gray matter across subjects were 140.4 ± 14.9, 134.1 ± 12.5, and 184.6 ± 17.9 μmol/100 g/min, with corresponding OEFs of 30.9 ± 3.4%, 30.0 ± 1.8%, and 40.9 ± 2.4% for methods based on QSM, qBOLD, and QSM+qBOLD, respectively. QSM+qBOLD provided the highest CMRO 2 contrast between gray and white matter, more uniform OEF than QSM, and less noisy OEF than qBOLD. Quantitative CMRO 2 mapping that fits the entire complex GRE data is feasible by combining QSM analysis of phase and qBOLD analysis of magnitude. © 2018 International Society for Magnetic Resonance in Medicine.

Colorectal carcinoma: Ex vivo evaluation using 3-T high-spatial-resolution quantitative T2 mapping and its correlation with histopathologic findings.

PubMed

Yamada, Ichiro; Yoshino, Norio; Hikishima, Keigo; Miyasaka, Naoyuki; Yamauchi, Shinichi; Uetake, Hiroyuki; Yasuno, Masamichi; Saida, Yukihisa; Tateishi, Ukihide; Kobayashi, Daisuke; Eishi, Yoshinobu

2017-05-01

In this study, we aimed to evaluate the feasibility of determining the mural invasion depths of colorectal carcinomas using high-spatial-resolution (HSR) quantitative T2 mapping on a 3-T magnetic resonance (MR) scanner. Twenty colorectal specimens containing adenocarcinomas were imaged on a 3-T MR system equipped with a 4-channel phased-array surface coil. HSR quantitative T2 maps were acquired using a spin-echo sequence with a repetition time/echo time of 7650/22.6-361.6ms (16 echoes), 87×43.5-mm field of view, 2-mm section thickness, 448×224 matrix, and average of 1. HSR fast-spin-echo T2-weighted images were also acquired. Differences between the T2 values (ms) of the tumor tissue, colorectal wall layers, and fibrosis were measured, and the MR images and histopathologic findings were compared. In all specimens (20/20, 100%), the HSR quantitative T2 maps clearly depicted an 8-layer normal colorectal wall in which the T2 values of each layer differed from those of the adjacent layer(s) (P<0.001). Using this technique, fibrosis (73.6±9.4ms) and tumor tissue (104.2±6.4ms) could also be clearly differentiated (P<0.001). In 19 samples (95%), the HSR quantitative T2 maps and histopathologic data yielded the same findings regarding the tumor invasion depth. Our results indicate that 3-T HSR quantitative T2 mapping is useful for distinguishing colorectal wall layers and differentiating tumor and fibrotic tissues. Accordingly, this technique could be used to determine mural invasion by colorectal carcinomas with a high level of accuracy. Copyright © 2017 Elsevier Inc. All rights reserved.

Lateral Asymmetry and Spatial Difference of Iron Deposition in the Substantia Nigra of Patients with Parkinson Disease Measured with Quantitative Susceptibility Mapping.

PubMed

Azuma, M; Hirai, T; Yamada, K; Yamashita, S; Ando, Y; Tateishi, M; Iryo, Y; Yoneda, T; Kitajima, M; Wang, Y; Yamashita, Y

2016-05-01

Quantitative susceptibility mapping is useful for assessing iron deposition in the substantia nigra of patients with Parkinson disease. We aimed to determine whether quantitative susceptibility mapping is useful for assessing the lateral asymmetry and spatial difference in iron deposits in the substantia nigra of patients with Parkinson disease. Our study population comprised 24 patients with Parkinson disease and 24 age- and sex-matched healthy controls. They underwent 3T MR imaging by using a 3D multiecho gradient-echo sequence. On reconstructed quantitative susceptibility mapping, we measured the susceptibility values in the anterior, middle, and posterior parts of the substantia nigra, the whole substantia nigra, and other deep gray matter structures in both hemibrains. To identify the more and less affected hemibrains in patients with Parkinson disease, we assessed the severity of movement symptoms for each hemibrain by using the Unified Parkinson's Disease Rating Scale. In the posterior substantia nigra of patients with Parkinson disease, the mean susceptibility value was significantly higher in the more than the less affected hemibrain substantia nigra (P < .05). This value was significantly higher in both the more and less affected hemibrains of patients with Parkinson disease than in controls (P < .05). Asymmetry of the mean susceptibility values was significantly greater for patients than controls (P < .05). Receiver operating characteristic analysis showed that quantitative susceptibility mapping of the posterior substantia nigra in the more affected hemibrain provided the highest power for discriminating patients with Parkinson disease from the controls. Quantitative susceptibility mapping is useful for assessing the lateral asymmetry and spatial difference of iron deposition in the substantia nigra of patients with Parkinson disease. © 2016 by American Journal of Neuroradiology.

Quantitative structure-permeability relationships at various pH values for acidic and basic drugs and drug-like compounds.

PubMed

Oja, M; Maran, U

2015-01-01

Absorption in gastrointestinal tract compartments varies and is largely influenced by pH. Therefore, considering pH in studies and analyses of membrane permeability provides an opportunity to gain a better understanding of the behaviour of compounds and to obtain good permeability estimates for prediction purposes. This study concentrates on relationships between the chemical structure and membrane permeability of acidic and basic drugs and drug-like compounds. The membrane permeability of 36 acidic and 61 basic compounds was measured using the parallel artificial membrane permeability assay (PAMPA) at pH 3, 5, 7.4 and 9. Descriptive and/or predictive single-parameter quantitative structure-permeability relationships were derived for all pH values. For acidic compounds, membrane permeability is mainly influenced by hydrogen bond donor properties, as revealed by models with r(2) > 0.8 for pH 3 and pH 5. For basic compounds, the best (r(2) > 0.7) structure-permeability relationships are obtained with the octanol-water distribution coefficient for pH 7.4 and pH 9, indicating the importance of partition properties. In addition to the validation set, the prediction quality of the developed models was tested with folic acid and astemizole, showing good matches between experimental and calculated membrane permeabilities at key pHs. Selected QSAR models are available at the QsarDB repository ( http://dx.doi.org/10.15152/QDB.166 ).

Intracellular pH measurements made simple by fluorescent protein probes and the phasor approach to fluorescence lifetime imaging†

PubMed Central

Digman, Michelle A.; Gratton, Enrico; Storti, Barbara; Beltram, Fabio

2013-01-01

A versatile pH-dependent fluorescent protein was applied to intracellular pH measurements by means of the phasor approach to fluorescence lifetime imaging. By this fit-less method we obtain intracellular pH maps under resting or altered physiological conditions by single-photon confocal or two-photon microscopy. PMID:22517076

Candida tropicalis biofilm and human epithelium invasion is highly influenced by environmental pH.

PubMed

Ferreira, Carina; Gonçalves, Bruna; Vilas Boas, Diana; Oliveira, Hugo; Henriques, Mariana; Azeredo, Joana; Silva, Sónia

2016-11-01

The main goal of this study was to investigate the role of pH on Candida tropicalis virulence determinants, namely the ability to form biofilms and to colonize/invade reconstituted human vaginal epithelia. Biofilm formation was evaluated by enumeration of cultivable cells, total biomass quantification and structural analysis by scanning electron microscopy and confocal laser scanning microscopy. Candida tropicalis human vaginal epithelium colonization and invasiveness were examined qualitatively by epifluorescence microscopy and quantitatively by a novel quantitative real-time PCR protocol for Candida quantification in tissues. The results revealed that environmental pH influences C. tropicalis biofilm formation as well as the colonization and potential to invade human epithelium with intensification at neutral and alkaline conditions compared to acidic conditions. For the first time, we have demonstrated that C. tropicalis biofilm formation and invasion is highly influenced by environmental pH. © Crown copyright 2016.

Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in U.S. strawberry (Fragaria×ananassa) breeding populations using pedigree-based QTL analysis

PubMed Central

Verma, Sujeet; Zurn, Jason D; Salinas, Natalia; Mathey, Megan M; Denoyes, Beatrice; Hancock, James F; Finn, Chad E; Bassil, Nahla V; Whitaker, Vance M

2017-01-01

The cultivated strawberry (Fragaria×ananassa) is consumed worldwide for its flavor and nutritional benefits. Genetic analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this species. Although several quantitative trait loci (QTL) have been previously detected for fruit quality and flowering traits using low-density genetic maps, clarity on the sub-genomic locations of these QTLs was missing. Recent discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism (SNP) array, enabling high-density genetic maps and finer resolution QTL analysis. In this study, breeder-specified traits were evaluated in the Eastern (Michigan) and Western (Oregon) United States for a common set of breeding populations during 2 years. Several QTLs were validated for soluble solids content (SSC), fruit weight (FWT), pH and titratable acidity (TA) using a pedigree-based QTL analysis approach. For fruit quality, a QTL for SSC on linkage group (LG) 6A, a QTL for FWT on LG 2BII, a QTL for pH on LG 4CII and two QTLs for TA on LGs 2A and 5B were detected. In addition, a large-effect QTL for flowering was detected at the distal end of LG 4A, coinciding with the FaPFRU locus. Marker haplotype analysis in the FaPFRU region indicated that the homozygous recessive genotype was highly predictive of seasonal flowering. SNP probes in the FaPFRU region may help facilitate marker-assisted selection for this trait. PMID:29138689

Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in U.S. strawberry (Fragaria×ananassa) breeding populations using pedigree-based QTL analysis.

PubMed

Verma, Sujeet; Zurn, Jason D; Salinas, Natalia; Mathey, Megan M; Denoyes, Beatrice; Hancock, James F; Finn, Chad E; Bassil, Nahla V; Whitaker, Vance M

2017-01-01

The cultivated strawberry ( Fragaria × ananassa ) is consumed worldwide for its flavor and nutritional benefits. Genetic analysis of commercially important traits in strawberry are important for the development of breeding methods and tools for this species. Although several quantitative trait loci (QTL) have been previously detected for fruit quality and flowering traits using low-density genetic maps, clarity on the sub-genomic locations of these QTLs was missing. Recent discoveries in allo-octoploid strawberry genomics led to the development of the IStraw90 single-nucleotide polymorphism (SNP) array, enabling high-density genetic maps and finer resolution QTL analysis. In this study, breeder-specified traits were evaluated in the Eastern (Michigan) and Western (Oregon) United States for a common set of breeding populations during 2 years. Several QTLs were validated for soluble solids content (SSC), fruit weight (FWT), pH and titratable acidity (TA) using a pedigree-based QTL analysis approach. For fruit quality, a QTL for SSC on linkage group (LG) 6A, a QTL for FWT on LG 2BII, a QTL for pH on LG 4CII and two QTLs for TA on LGs 2A and 5B were detected. In addition, a large-effect QTL for flowering was detected at the distal end of LG 4A, coinciding with the FaPFRU locus. Marker haplotype analysis in the FaPFRU region indicated that the homozygous recessive genotype was highly predictive of seasonal flowering. SNP probes in the FaPFRU region may help facilitate marker-assisted selection for this trait.

Healthmap | NIH MedlinePlus the Magazine

MedlinePlus

... P.H., and Brownstein, Ph.D., of Boston Children's Informatics Program. Their report was published online by JAMA Pediatrics . "HealthMap can also bring together outbreak data from informal sources, such as social media, with formal sources like the Centers for Disease ...

Quantitative Oxygenation Venography from MRI Phase

PubMed Central

Fan, Audrey P.; Bilgic, Berkin; Gagnon, Louis; Witzel, Thomas; Bhat, Himanshu; Rosen, Bruce R.; Adalsteinsson, Elfar

2014-01-01

Purpose To demonstrate acquisition and processing methods for quantitative oxygenation venograms that map in vivo oxygen saturation (SvO2) along cerebral venous vasculature. Methods Regularized quantitative susceptibility mapping (QSM) is used to reconstruct susceptibility values and estimate SvO2 in veins. QSM with ℓ1 and ℓ2 regularization are compared in numerical simulations of vessel structures with known magnetic susceptibility. Dual-echo, flow-compensated phase images are collected in three healthy volunteers to create QSM images. Bright veins in the susceptibility maps are vectorized and used to form a three-dimensional vascular mesh, or venogram, along which to display SvO2 values from QSM. Results Quantitative oxygenation venograms that map SvO2 along brain vessels of arbitrary orientation and geometry are shown in vivo. SvO2 values in major cerebral veins lie within the normal physiological range reported by 15O positron emission tomography. SvO2 from QSM is consistent with previous MR susceptometry methods for vessel segments oriented parallel to the main magnetic field. In vessel simulations, ℓ1 regularization results in less than 10% SvO2 absolute error across all vessel tilt orientations and provides more accurate SvO2 estimation than ℓ2 regularization. Conclusion The proposed analysis of susceptibility images enables reliable mapping of quantitative SvO2 along venograms and may facilitate clinical use of venous oxygenation imaging. PMID:24006229

Biobased, Internally pH-Sensitive Materials: Immobilized Yellow Fluorescent Protein as an Optical Sensor for Spatiotemporal Mapping of pH Inside Porous Matrices.

PubMed

Consolati, Tanja; Bolivar, Juan M; Petrasek, Zdenek; Berenguer, Jose; Hidalgo, Aurelio; Guisán, Jose M; Nidetzky, Bernd

2018-02-28

The pH is fundamental to biological function and its measurement therefore crucial across all biosciences. Unlike homogenous bulk solution, solids often feature internal pH gradients due to partition effects and confined biochemical reactions. Thus, a full spatiotemporal mapping for pH characterization in solid materials with biological systems embedded in them is essential. In here, therefore, a fully biocompatible methodology for real-time optical sensing of pH within porous materials is presented. A genetically encoded ratiometric pH sensor, the enhanced superfolder yellow fluorescent protein (sYFP), is used to functionalize the internal surface of different materials, including natural and synthetic organic polymers as well as silica frameworks. By using controlled, tailor-made immobilization, sYFP is homogenously distributed within these materials and so enables, via self-referenced imaging analysis, pH measurements in high accuracy and with useful spatiotemporal resolution. Evolution of internal pH is monitored in consequence of a proton-releasing enzymatic reaction, the hydrolysis of penicillin by a penicillin acylase, taking place in solution or confined to the solid surface of the porous matrix. Unlike optochemical pH sensors, which often interfere with biological function, labeling with sYFP enables pH sensing without altering the immobilized enzyme's properties in any of the materials used. Fast response of sYFP to pH change permits evaluation of biochemical kinetics within the solid materials. Thus, pH sensing based on immobilized sYFP represents a broadly applicable technique to the study of biology confined to the internally heterogeneous environment of solid matrices.

A hemicyanine based ratiometric fluorescence probe for mapping lysosomal pH during heat stroke in living cells.

PubMed

Wu, Luling; Wang, Yang; James, Tony D; Jia, Nengqin; Huang, Chusen

2018-05-29

Heat stroke is a lethal condition which can cause dysfunction in the central nervous system, multi-organ damage and even death. However, there is still limited knowledge of the detailed mechanism about the roles of lysosomes in heat stroke due to lack of effective tools. Herein, we introduce our previously developed hemicyanine with a large D-π-A structure as the key fluorophore to develop a new fluorescent probe (CPY) for ratiometric mapping of lysosomal pH changes in live cells under a heat shock stimulus.

OdorMapComparer: an application for quantitative analyses and comparisons of fMRI brain odor maps.

PubMed

Liu, Nian; Xu, Fuqiang; Miller, Perry L; Shepherd, Gordon M

2007-01-01

Brain odor maps are reconstructed flat images that describe the spatial activity patterns in the glomerular layer of the olfactory bulbs in animals exposed to different odor stimuli. We have developed a software application, OdorMapComparer, to carry out quantitative analyses and comparisons of the fMRI odor maps. This application is an open-source window program that first loads two odor map images being compared. It allows image transformations including scaling, flipping, rotating, and warping so that the two images can be appropriately aligned to each other. It performs simple subtraction, addition, and average of signals in the two images. It also provides comparative statistics including the normalized correlation (NC) and spatial correlation coefficient. Experimental studies showed that the rodent fMRI odor maps for aliphatic aldehydes displayed spatial activity patterns that are similar in gross outlines but somewhat different in specific subregions. Analyses with OdorMapComparer indicate that the similarity between odor maps decreases with increasing difference in the length of carbon chains. For example, the map of butanal is more closely related to that of pentanal (with a NC = 0.617) than to that of octanal (NC = 0.082), which is consistent with animal behavioral studies. The study also indicates that fMRI odor maps are statistically odor-specific and repeatable across both the intra- and intersubject trials. OdorMapComparer thus provides a tool for quantitative, statistical analyses and comparisons of fMRI odor maps in a fashion that is integrated with the overall odor mapping techniques.

Human brain atlas for automated region of interest selection in quantitative susceptibility mapping: application to determine iron content in deep gray matter structures.

PubMed

Lim, Issel Anne L; Faria, Andreia V; Li, Xu; Hsu, Johnny T C; Airan, Raag D; Mori, Susumu; van Zijl, Peter C M

2013-11-15

The purpose of this paper is to extend the single-subject Eve atlas from Johns Hopkins University, which currently contains diffusion tensor and T1-weighted anatomical maps, by including contrast based on quantitative susceptibility mapping. The new atlas combines a "deep gray matter parcellation map" (DGMPM) derived from a single-subject quantitative susceptibility map with the previously established "white matter parcellation map" (WMPM) from the same subject's T1-weighted and diffusion tensor imaging data into an MNI coordinate map named the "Everything Parcellation Map in Eve Space," also known as the "EvePM." It allows automated segmentation of gray matter and white matter structures. Quantitative susceptibility maps from five healthy male volunteers (30 to 33 years of age) were coregistered to the Eve Atlas with AIR and Large Deformation Diffeomorphic Metric Mapping (LDDMM), and the transformation matrices were applied to the EvePM to produce automated parcellation in subject space. Parcellation accuracy was measured with a kappa analysis for the left and right structures of six deep gray matter regions. For multi-orientation QSM images, the Kappa statistic was 0.85 between automated and manual segmentation, with the inter-rater reproducibility Kappa being 0.89 for the human raters, suggesting "almost perfect" agreement between all segmentation methods. Segmentation seemed slightly more difficult for human raters on single-orientation QSM images, with the Kappa statistic being 0.88 between automated and manual segmentation, and 0.85 and 0.86 between human raters. Overall, this atlas provides a time-efficient tool for automated coregistration and segmentation of quantitative susceptibility data to analyze many regions of interest. These data were used to establish a baseline for normal magnetic susceptibility measurements for over 60 brain structures of 30- to 33-year-old males. Correlating the average susceptibility with age-based iron concentrations in gray matter structures measured by Hallgren and Sourander (1958) allowed interpolation of the average iron concentration of several deep gray matter regions delineated in the EvePM. Copyright © 2013 Elsevier Inc. All rights reserved.

Correlation of quantitative dual-energy computed tomography iodine maps and abdominal computed tomography perfusion measurements: are single-acquisition dual-energy computed tomography iodine maps more than a reduced-dose surrogate of conventional computed tomography perfusion?

PubMed

Stiller, Wolfram; Skornitzke, Stephan; Fritz, Franziska; Klauss, Miriam; Hansen, Jens; Pahn, Gregor; Grenacher, Lars; Kauczor, Hans-Ulrich

2015-10-01

Study objectives were the quantitative evaluation of whether conventional abdominal computed tomography (CT) perfusion measurements mathematically correlate with quantitative single-acquisition dual-energy CT (DECT) iodine concentration maps, the determination of the optimum time of acquisition for achieving maximum correlation, and the estimation of the potential for radiation exposure reduction when replacing conventional CT perfusion by single-acquisition DECT iodine concentration maps. Dual-energy CT perfusion sequences were dynamically acquired over 51 seconds (34 acquisitions every 1.5 seconds) in 24 patients with histologically verified pancreatic carcinoma using dual-source DECT at tube potentials of 80 kVp and 140 kVp. Using software developed in-house, perfusion maps were calculated from 80-kVp image series using the maximum slope model after deformable motion correction. In addition, quantitative iodine maps were calculated for each of the 34 DECT acquisitions per patient. Within a manual segmentation of the pancreas, voxel-by-voxel correlation between the perfusion map and each of the iodine maps was calculated for each patient to determine the optimum time of acquisition topt defined as the acquisition time of the iodine map with the highest correlation coefficient. Subsequently, regions of interest were placed inside the tumor and inside healthy pancreatic tissue, and correlation between mean perfusion values and mean iodine concentrations within these regions of interest at topt was calculated for the patient sample. The mean (SD) topt was 31.7 (5.4) seconds after the start of contrast agent injection. The mean (SD) perfusion values for healthy pancreatic and tumor tissues were 67.8 (26.7) mL per 100 mL/min and 43.7 (32.2) mL per 100 mL/min, respectively. At topt, the mean (SD) iodine concentrations were 2.07 (0.71) mg/mL in healthy pancreatic and 1.69 (0.98) mg/mL in tumor tissue, respectively. Overall, the correlation between perfusion values and iodine concentrations was high (0.77), with correlation of 0.89 in tumor and of 0.56 in healthy pancreatic tissue at topt. Comparing radiation exposure associated with a single DECT acquisition at topt (0.18 mSv) to that of an 80 kVp CT perfusion sequence (2.96 mSv) indicates that an average reduction of Deff by 94% could be achieved by replacing conventional CT perfusion with a single-acquisition DECT iodine concentration map. Quantitative iodine concentration maps obtained with DECT correlate well with conventional abdominal CT perfusion measurements, suggesting that quantitative iodine maps calculated from a single DECT acquisition at an organ-specific and patient-specific optimum time of acquisition might be able to replace conventional abdominal CT perfusion measurements if the time of acquisition is carefully calibrated. This could lead to large reductions of radiation exposure to the patients while offering quantitative perfusion data for diagnosis.

Evaluation and Quantitative trait loci mapping of resistance to powdery mildew in lettuce

USDA-ARS?s Scientific Manuscript database

Lettuce (Lactuca sativa L.) is the major leafy vegetable that is susceptible to powdery mildew disease under greenhouse and field conditions. We mapped quantitative trait loci (QTLs) for resistance to powdery mildew under greenhouse conditions in an interspecific population derived from a cross betw...

Quantifying Qualitative Data Using Cognitive Maps

ERIC Educational Resources Information Center

Scherp, Hans-Ake

2013-01-01

The aim of the article is to show how substantial qualitative material consisting of graphic cognitive maps can be analysed by using digital CmapTools, Excel and SPSS. Evidence is provided of how qualitative and quantitative methods can be combined in educational research by transforming qualitative data into quantitative data to facilitate…

Quantitative maps of genetic interactions in yeast - comparative evaluation and integrative analysis.

PubMed

Lindén, Rolf O; Eronen, Ville-Pekka; Aittokallio, Tero

2011-03-24

High-throughput genetic screening approaches have enabled systematic means to study how interactions among gene mutations contribute to quantitative fitness phenotypes, with the aim of providing insights into the functional wiring diagrams of genetic interaction networks on a global scale. However, it is poorly known how well these quantitative interaction measurements agree across the screening approaches, which hinders their integrated use toward improving the coverage and quality of the genetic interaction maps in yeast and other organisms. Using large-scale data matrices from epistatic miniarray profiling (E-MAP), genetic interaction mapping (GIM), and synthetic genetic array (SGA) approaches, we carried out here a systematic comparative evaluation among these quantitative maps of genetic interactions in yeast. The relatively low association between the original interaction measurements or their customized scores could be improved using a matrix-based modelling framework, which enables the use of single- and double-mutant fitness estimates and measurements, respectively, when scoring genetic interactions. Toward an integrative analysis, we show how the detections from the different screening approaches can be combined to suggest novel positive and negative interactions which are complementary to those obtained using any single screening approach alone. The matrix approximation procedure has been made available to support the design and analysis of the future screening studies. We have shown here that even if the correlation between the currently available quantitative genetic interaction maps in yeast is relatively low, their comparability can be improved by means of our computational matrix approximation procedure, which will enable integrative analysis and detection of a wider spectrum of genetic interactions using data from the complementary screening approaches.

Validity of the Medical College Admission Test for Predicting MD-PhD Student Outcomes

ERIC Educational Resources Information Center

Bills, James L.; VanHouten, Jacob; Grundy, Michelle M.; Chalkley, Roger; Dermody, Terence S.

2016-01-01

The Medical College Admission Test (MCAT) is a quantitative metric used by MD and MD-PhD programs to evaluate applicants for admission. This study assessed the validity of the MCAT in predicting training performance measures and career outcomes for MD-PhD students at a single institution. The study population consisted of 153 graduates of the…

The Benefits of Publishing Systematic Quantitative Literature Reviews for PhD Candidates and Other Early-Career Researchers

ERIC Educational Resources Information Center

Pickering, Catherine; Byrne, Jason

2014-01-01

Universities increasingly expect students to publish during a PhD candidature because it benefits the candidate, supervisor, institution, and wider community. Here, we describe a method successfully used by early-career researchers including PhD candidates to undertake and publish literature reviews--a challenge for researchers new to a field. Our…

Precision sensing by two opposing gradient sensors: how does Escherichia coli find its preferred pH level?

PubMed

Hu, Bo; Tu, Yuhai

2013-07-02

It is essential for bacteria to find optimal conditions for their growth and survival. The optimal levels of certain environmental factors (such as pH and temperature) often correspond to some intermediate points of the respective gradients. This requires the ability of bacteria to navigate from both directions toward the optimum location and is distinct from the conventional unidirectional chemotactic strategy. Remarkably, Escherichia coli cells can perform such a precision sensing task in pH taxis by using the same chemotaxis machinery, but with opposite pH responses from two different chemoreceptors (Tar and Tsr). To understand bacterial pH sensing, we developed an Ising-type model for a mixed cluster of opposing receptors based on the push-pull mechanism. Our model can quantitatively explain experimental observations in pH taxis for various mutants and wild-type cells. We show how the preferred pH level depends on the relative abundance of the competing sensors and how the sensory activity regulates the behavioral response. Our model allows us to make quantitative predictions on signal integration of pH and chemoattractant stimuli. Our study reveals two general conditions and a robust push-pull scheme for precision sensing, which should be applicable in other adaptive sensory systems with opposing gradient sensors. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Uncertainties in ecosystem service maps: a comparison on the European scale.

PubMed

Schulp, Catharina J E; Burkhard, Benjamin; Maes, Joachim; Van Vliet, Jasper; Verburg, Peter H

2014-01-01

Safeguarding the benefits that ecosystems provide to society is increasingly included as a target in international policies. To support such policies, ecosystem service maps are made. However, there is little attention for the accuracy of these maps. We made a systematic review and quantitative comparison of ecosystem service maps on the European scale to generate insights in the uncertainty of ecosystem service maps and discuss the possibilities for quantitative validation. Maps of climate regulation and recreation were reasonably similar while large uncertainties among maps of erosion protection and flood regulation were observed. Pollination maps had a moderate similarity. Differences among the maps were caused by differences in indicator definition, level of process understanding, mapping aim, data sources and methodology. Absence of suitable observed data on ecosystem services provisioning hampers independent validation of the maps. Consequently, there are, so far, no accurate measures for ecosystem service map quality. Policy makers and other users need to be cautious when applying ecosystem service maps for decision-making. The results illustrate the need for better process understanding and data acquisition to advance ecosystem service mapping, modelling and validation.

The Quantitative Evaluation of the Clinical and Translational Science Awards (CTSA) Program Based on Science Mapping and Scientometric Analysis

PubMed Central

Zhang, Yin; Wang, Lei

2013-01-01

Abstract The Clinical and Translational Science Awards (CTSA) program is one of the most important initiatives in translational medical funding. The quantitative evaluation of the efficiency and performance of the CTSA program has a significant referential meaning for the decision making of global translational medical funding. Using science mapping and scientometric analytic tools, this study quantitatively analyzed the scientific articles funded by the CTSA program. The results of the study showed that the quantitative productivities of the CTSA program had a stable increase since 2008. In addition, the emerging trends of the research funded by the CTSA program covered clinical and basic medical research fields. The academic benefits from the CTSA program were assisting its members to build a robust academic home for the Clinical and Translational Science and to attract other financial support. This study provided a quantitative evaluation of the CTSA program based on science mapping and scientometric analysis. Further research is required to compare and optimize other quantitative methods and to integrate various research results. PMID:24330689

The quantitative evaluation of the Clinical and Translational Science Awards (CTSA) program based on science mapping and scientometric analysis.

PubMed

Zhang, Yin; Wang, Lei; Diao, Tianxi

2013-12-01

The Clinical and Translational Science Awards (CTSA) program is one of the most important initiatives in translational medical funding. The quantitative evaluation of the efficiency and performance of the CTSA program has a significant referential meaning for the decision making of global translational medical funding. Using science mapping and scientometric analytic tools, this study quantitatively analyzed the scientific articles funded by the CTSA program. The results of the study showed that the quantitative productivities of the CTSA program had a stable increase since 2008. In addition, the emerging trends of the research funded by the CTSA program covered clinical and basic medical research fields. The academic benefits from the CTSA program were assisting its members to build a robust academic home for the Clinical and Translational Science and to attract other financial support. This study provided a quantitative evaluation of the CTSA program based on science mapping and scientometric analysis. Further research is required to compare and optimize other quantitative methods and to integrate various research results. © 2013 Wiley Periodicals, Inc.

Global, quantitative and dynamic mapping of protein subcellular localization

PubMed Central

Itzhak, Daniel N; Tyanova, Stefka; Cox, Jürgen; Borner, Georg HH

2016-01-01

Subcellular localization critically influences protein function, and cells control protein localization to regulate biological processes. We have developed and applied Dynamic Organellar Maps, a proteomic method that allows global mapping of protein translocation events. We initially used maps statically to generate a database with localization and absolute copy number information for over 8700 proteins from HeLa cells, approaching comprehensive coverage. All major organelles were resolved, with exceptional prediction accuracy (estimated at >92%). Combining spatial and abundance information yielded an unprecedented quantitative view of HeLa cell anatomy and organellar composition, at the protein level. We subsequently demonstrated the dynamic capabilities of the approach by capturing translocation events following EGF stimulation, which we integrated into a quantitative model. Dynamic Organellar Maps enable the proteome-wide analysis of physiological protein movements, without requiring any reagents specific to the investigated process, and will thus be widely applicable in cell biology. DOI: http://dx.doi.org/10.7554/eLife.16950.001 PMID:27278775

Quantitative Susceptibility Mapping: Contrast Mechanisms and Clinical Applications

PubMed Central

Liu, Chunlei; Wei, Hongjiang; Gong, Nan-Jie; Cronin, Matthew; Dibb, Russel; Decker, Kyle

2016-01-01

Quantitative susceptibility mapping (QSM) is a recently developed MRI technique for quantifying the spatial distribution of magnetic susceptibility within biological tissues. It first uses the frequency shift in the MRI signal to map the magnetic field profile within the tissue. The resulting field map is then used to determine the spatial distribution of the underlying magnetic susceptibility by solving an inverse problem. The solution is achieved by deconvolving the field map with a dipole field, under the assumption that the magnetic field is a result of the superposition of the dipole fields generated by all voxels and that each voxel has its unique magnetic susceptibility. QSM provides improved contrast to noise ratio for certain tissues and structures compared to its magnitude counterpart. More importantly, magnetic susceptibility is a direct reflection of the molecular composition and cellular architecture of the tissue. Consequently, by quantifying magnetic susceptibility, QSM is becoming a quantitative imaging approach for characterizing normal and pathological tissue properties. This article reviews the mechanism generating susceptibility contrast within tissues and some associated applications. PMID:26844301

Novel cardiac magnetic resonance biomarkers: native T1 and extracellular volume myocardial mapping.

PubMed

Cannaò, Paola Maria; Altabella, Luisa; Petrini, Marcello; Alì, Marco; Secchi, Francesco; Sardanelli, Francesco

2016-04-28

Cardiac magnetic resonance (CMR) is a non-invasive diagnostic tool playing a key role in the assessment of cardiac morphology and function as well as in tissue characterization. Late gadolinium enhancement is a fundamental CMR technique for detecting focal or regional abnormalities such as scar tissue, replacement fibrosis, or inflammation using qualitative, semi-quantitative, or quantitative methods, but not allowing for evaluating the whole myocardium in the presence of diffuse disease. The novel T1 mapping approach permits a quantitative assessment of the entire myocardium providing a voxel-by-voxel map of native T1 relaxation time, obtained before the intravenous administration of gadolinium-based contrast material. Combining T1 data obtained before and after contrast injection, it is also possible to calculate the voxel-by-voxel extracellular volume (ECV), resulting in another myocardial parametric map. This article describes technical challenges and clinical perspectives of these two novel CMR biomarkers: myocardial native T1 and ECV mapping.

Potentiometric and Relaxometric Properties of a Gadolinium-based MRI Contrast Agent for Sensing Tissue pH

PubMed Central

Kálmán, Ferenc K.; Woods, Mark; Caravan, Peter; Jurek, Paul; Spiller, Marga; Tircsó, Gyula; Király, Róbert; Brücher, Ernő; Sherry, A. Dean

2008-01-01

The pH sensitive contrast agent, GdDOTA-4AmP (Gd1) has been successfully used to map tissue pH by MRI. Further studies now demonstrate that two distinct chemical forms of the complex can be prepared depending upon the pH at which Gd3+ is mixed with ligand 1. The desired pH sensitive form of this complex, referred to here as a Type II complex, is obtained as the exclusive product only when the complexation reaction is performed above pH 8. At lower pH values, a second complex is formed that, by analogy with an intermediate formed during preparation of GdDOTA, we tentatively assign this to a Type I complex where the Gd3+ is coordinated only by the appended side-chain arms of 1. The proportion of Type I complex formed is largely determined by the pH of the complexation reaction. The magnitude of pH dependent change in relaxivity of Gd1 was found to be less than earlier reported (S. Zhang, K. Wu, and A. D. Sherry, Angew. Chem., Int. Ed., 1999, 38, 3192), likely due to contamination of the earlier sample by an unknown amount of Type I complex. Examination of the NMRD and relaxivity temperature profiles, coupled with information from potentiometric titrations, shows that the amphoteric character of the phosphonate side-chains enables rapid prototropic exchange between the single bound water of the complex with those of the bulk water thereby giving Gd1 a unique pH dependent relaxivity that is quite useful for pH mapping of tissues by MRI. PMID:17539632

Precipitation of molybdenum(V) as the hydroxide and its separation from rhenium.

PubMed

Yatirajam, V; Ahuja, U; Kakkar, L R

1975-03-01

A study of the conditions for precipitation of molybdenum(V) hydroxide shows that for Mo concentration 1 mg ml about 97.5% of the Mo can be precipitated between pH 5 and 5.8. Lower concentrations of molybdenum(V) or molybdenum(VI) can be precipitated quantitatively by using 20 times the amount of zirconium as collector, at the same pH. On this basis, a simple method is given for quantitative separation of rhenium from large amounts of molybdenum and is attested by analysis of synthetic and molybdenite samples.

Comparative evaluation of two quantitative test methods for determining the efficacy of liquid sporicides and sterilants on a hard surface: a precollaborative study.

PubMed

Tomasino, Stephen F; Hamilton, Martin A

2007-01-01

Two quantitative carrier-based test methods for determining the efficacy of liquid sporicides and sterilants on a hard surface, the Standard Quantitative Carrier Test Method-ASTM E 2111-00 and an adaptation of a quantitative micro-method as reported by Sagripanti and Bonifacino, were compared in this study. The methods were selected based on their desirable characteristics (e.g., well-developed protocol, previous use with spores, fully quantitative, and use of readily available equipment) for testing liquid sporicides and sterilants on a hard surface. In this paper, the Sagripanti-Bonifacino procedure is referred to as the Three Step Method (TSM). AOAC Official Method 966.04 was included in this study as a reference method. Three laboratories participated in the evaluation. Three chemical treatments were tested: (1) 3000 ppm sodium hypochlorite with pH adjusted to 7.0, (2) a hydrogen peroxide/peroxyacetic acid product, and (3) 3000 ppm sodium hypochlorite with pH unadjusted (pH of approximately 10.0). A fourth treatment, 6000 ppm sodium hypochlorite solution with pH adjusted to 7.0, was included only for Method 966.04 as a positive control (high level of efficacy). The contact time was 10 min for all chemical treatments except the 6000 ppm sodium hypochlorite treatment which was tested at 30 min. Each chemical treatment was tested 3 times using each of the methods. Only 2 of the laboratories performed the AOAC method. Method performance was assessed by the within-laboratory variance, between-laboratory variance, and total variance associated with the log reduction (LR) estimates generated by each quantitative method. The quantitative methods performed similarly, and the LR values generated by each method were not statistically different for the 3 treatments evaluated. Based on feedback from the participating laboratories, compared to the TSM, ASTM E 2111-00 was more resource demanding and required more set-up time. The logistical and resource concerns identified for ASTM E 2111-00 were largely associated with the filtration process and counting bacterial colonies on filters. Thus, the TSM was determined to be the most suitable method.

Detection of elevated right ventricular extracellular volume in pulmonary hypertension using Accelerated and Navigator-Gated Look-Locker Imaging for Cardiac T1 Estimation (ANGIE) cardiovascular magnetic resonance.

PubMed

Mehta, Bhairav B; Auger, Daniel A; Gonzalez, Jorge A; Workman, Virginia; Chen, Xiao; Chow, Kelvin; Stump, Claire J; Mazimba, Sula; Kennedy, Jamie L W; Gay, Elizabeth; Salerno, Michael; Kramer, Christopher M; Epstein, Frederick H; Bilchick, Kenneth C

2015-12-21

Assessment of diffuse right ventricular (RV) fibrosis is of particular interest in pulmonary hypertension (PH) and heart failure (HF). Current cardiovascular magnetic resonance (CMR) T1 mapping techniques such as Modified Look-Locker inversion recovery (MOLLI) imaging have limited resolution, but accelerated and navigator-gated Look-Locker imaging for cardiac T1 estimation (ANGIE) is a novel CMR sequence with spatial resolution suitable for T1 mapping of the RV. We tested the hypothesis that patients with PH would have significantly more RV fibrosis detected with MRI ANGIE compared with normal volunteers and patients having HF with reduced (LV) ejection fraction (HFrEF) without co-existing PH, independent of RV dilitation and dysfunction. Patients with World Health Organization group 1 or group 4 PH, patients with HFrEF without PH, and normal volunteers were recruited to undergo contrast-enhanced CMR. RV and LV extracellular volume fractions (RV-ECV and LV-ECV) were determined using pre-contrast and post-contrast T1 mapping using ANGIE (RV and LV) and MOLLI (LV only). Thirty-two participants (53.1% female, median age 52 years, IQR 26-65 years) were enrolled, including n = 12 with PH, n = 10 having HFrEF without co-existing PH, and n = 10 normal volunteers. ANGIE ECV imaging was of high quality, and ANGIE measurements of LV-ECV were highly correlated with those of MOLLI (r = 0.91; p < 0.001). The RV-ECV in PH patients was 27.2% greater than the RV-ECV in normal volunteers (0.341 v. 0.268; p < 0.0001) and 18.9% greater than the RV-ECV in HFrEF patients without PH (0.341 v. 0.287; p < 0.0001). RV-ECV was greater than LV-ECV in PH (RV-LV difference = 0.04), but RV-ECV was nearly equivalent to LV-ECV in normal volunteers (RV-LV difference = 0.002) (p < 0.0001 for RV-LV difference in PH versus normal volunteers). RV-ECV was linearly associated with both increasing RVEDVI (p = 0.049) and decreasing RVEF (p = 0.04) in a multivariable linear model, but PH was still associated with greater RV-ECV even after adjustment for RVEDVI and RVEF. Pre- and post-contrast ANGIE imaging provides high-resolution ECV determination for the RV. PH is independently associated with increased RV-ECV even after adjustment for RV dilatation and dysfunction, consistent with an independent effect of PH on fibrosis. ANGIE RV imaging merits further clinical evaluation in PH.

Improving training in methodology enriches the science of psychology.

PubMed

Aiken, Leona S; West, Stephen G; Millsap, Roger E

2009-01-01

Replies to the comment Ramifications of increased training in quantitative methodology by Herbet Zimiles on the current authors original article "Doctoral training in statistics, measurement, and methodology in psychology: Replication and extension of Aiken, West, Sechrest, and Reno's (1990) survey of PhD programs in North America". The current authors state that in their recent article, they reported the results of an extensive survey of quantitative training in all PhD programs in North America. They compared these results with those of a similar survey conducted 12 years earlier (Aiken, West, Sechrest, & Reno, 1990), and raised issues for the future methodological training of substantive and quantitative researchers in psychology. The authors then respond to Zimiles three questions. PsycINFO Database Record 2009 APA.

Mapping of quantitative trait loci associated with partial resistance to phytophthora sojae and flooding tolerance in soybean

USDA-ARS?s Scientific Manuscript database

Phytophthora root rot (PRR) caused by Phytophthora sojae Kaufm. & Gerd. and flooding can limit growth and productivity, of soybean [Glycine max (L.) Merr.], especially on poorly drained soils. The primary objective of this research project was to map quantitative trait loci (QTL) associated with f...

Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. III

Treesearch

Kathleen D. Jermstad; Daniel L. Bassoni; Keith S. Jech; Gary A. Ritchie; Nicholas C. Wheeler; David B. Neale

2003-01-01

Quantitative trait loci (QTL) were mapped in the woody perennial Douglas fir (Pseudotsuga menziesii var. menziesii [Mirb.] Franco) for complex traits controlling the timing of growth initiation and growth cessation. QTL were estimated under controlled environmental conditions to identify QTL interactions with photoperiod, moisture stress, winter chilling, and spring...

Quantitative evaluation of malignant gliomas damage induced by photoactivation of IR700 dye

NASA Astrophysics Data System (ADS)

Sakuma, Morito; Kita, Sayaka; Higuchi, Hideo

2016-01-01

The processes involved in malignant gliomas damage were quantitatively evaluated by microscopy. The near-infrared fluorescent dye IR700 that is conjugated to an anti-CD133 antibody (IR700-CD133) specifically targets malignant gliomas (U87MG) and stem cells (BT142) and is endocytosed into the cells. The gliomas are then photodamaged by the release of reactive oxygen species (ROS) and the heat induced by illumination of IR700 by a red laser, and the motility of the vesicles within these cells is altered as a result of cellular damage. To investigate these changes in motility, we developed a new method that measures fluctuations in the intensity of phase-contrast images obtained from small areas within cells. The intensity fluctuation in U87MG cells gradually decreased as cell damage progressed, whereas the fluctuation in BT142 cells increased. The endocytosed IR700 dye was co-localized in acidic organelles such as endosomes and lysosomes. The pH in U87MG cells, as monitored by a pH indicator, was decreased and then gradually increased by the illumination of IR700, while the pH in BT142 cells increased monotonically. In these experiments, the processes of cell damage were quantitatively evaluated according to the motility of vesicles and changes in pH.

In Vivo Proton–Electron Double-Resonance Imaging of Extracellular Tumor pH Using an Advanced Nitroxide Probe

PubMed Central

Samouilov, Alexandre; Efimova, Olga V.; Bobko, Andrey A.; Sun, Ziqi; Petryakov, Sergey; Eubank, Timothy D.; Trofimov, Dmitrii G.; Kirilyuk, Igor A.; Grigor’ev, Igor A.; Takahashi, Wataru; Zweier, Jay L.; Khramtsov, Valery V.

2014-01-01

A variable radio frequency proton–electron double-resonance imaging (VRF PEDRI) approach for pH mapping of aqueous samples has been recently developed (Efimova et al. J. Magn. Reson. 2011, 209, 227–232). A pH map is extracted from two PEDRI acquisitions performed at electron paramagnetic resonance (EPR) frequencies of protonated and unprotonated forms of a pH-sensitive probe. To translate VRF PEDRI to an in vivo setting, an advanced pH probe was synthesized. Probe deuteration resulted in a narrow spectral line of 1.2 G compared to a nondeuterated analogue line width of 2.1 G allowing for an increase of Overhauser enhancements and reduction in rf power deposition. Binding of the probe to the cell-impermeable tripeptide, glutathione (GSH), allows for targeting to extracellular tissue space for monitoring extracellular tumor acidosis, a prognostic factor in tumor pathophysiology. The probe demonstrated pH sensitivity in the 5.8–7.8 range, optimum for measurement of acidic extracellular tumor pH (pHe). In vivo VRF PEDRI was performed on Met-1 tumor-bearing mice. Compared to normal mammary glands with a neutral mean pHe (7.1 ± 0.1), we observed broader pH distribution with acidic mean pHe (6.8 ± 0.1) in tumor tissue. In summary, VRF PEDRI in combination with a newly developed pH probe provides an analytical approach for spatially resolved noninvasive pHe monitoring, in vivo. PMID:24372284

Trends in Ph.D. Productivity and Diversity in Top-50 U.S. Chemistry Departments: An Institutional Analysis

ERIC Educational Resources Information Center

Laursen, Sandra L.; Weston, Timothy J.

2014-01-01

The education of doctoral chemists contributes to the chemical research enterprise and thus to innovation as an engine of the economy. This quantitative analysis describes trends in the production and diversity of chemistry Ph.D. degrees in the top-50 U.S. Ph.D.-granting departments in the past two decades. Time series data for individual…

Mapping montane vegetation in Southern California from color infrared imagery

NASA Technical Reports Server (NTRS)

Minnich, R. A.; Bowden, L. W.; Pease, R. W.

1969-01-01

Mapping a large area in California like the San Bernardino Mountains, demonstrated that color infrared photography is suitable for detailed mapping and offers potential for quantitative mapping. The level of information presented is comparable or superior to the most detailed mapping by ground survey.

Phenotypic assessments of peanut nested association mapping (NAM) populations

USDA-ARS?s Scientific Manuscript database

Nested association mapping (NAM) is a valuable innovation and multi-parental mapping population strategy in peanut genetics which increases the power to map quantitative trait loci and assists in extending the gene pool of elite peanut lines. In the peanut research community, two structured mapping ...

Techniques in Linear and Nonlinear Partial Differential Equations

DTIC Science & Technology

1991-10-21

theory. J. Grotowski (a student) studied the heat flow approach to harmonic maps betv:een manifolds: between spheres. and from the ball B’ in R 3 into...T. Yau; S. Kichenessamy: F. H. Lin. L. Sadun: Wu. Sigue; Yi. Fang. Also these graduate students: Li, Cong Ming, received Ph.D. in 1989. J. Grotowski . received Ph.D. in 1990. I. Birindelli, working on Ph.D. thesis. 5

Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy

PubMed Central

Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

2016-01-01

Local surface charge density of lipid membranes influences membrane–protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values. PMID:27561322

Quantitative Trait Loci Controlling Vegetative Growth Rate in the Edible Basidiomycete Pleurotus ostreatus

PubMed Central

Larraya, Luis M.; Idareta, Eneko; Arana, Dani; Ritter, Enrique; Pisabarro, Antonio G.; Ramírez, Lucia

2002-01-01

Mycelium growth rate is a quantitative characteristic that exhibits continuous variation. This trait has applied interest, as growth rate is correlated with production yield and increased advantage against competitors. In this work, we studied growth rate variation in the edible basidiomycete Pleurotus ostreatus growing as monokaryotic or dikaryotic mycelium on Eger medium or on wheat straw. Our analysis resulted in identification of several genomic regions (quantitative trait loci [QTLs]) involved in the control of growth rate that can be mapped on the genetic linkage map of this fungus. In some cases monokaryotic and dikaryotic QTLs clustered at the same map position, indicating that there are principal genomic areas responsible for growth rate control. The availability of this linkage map of growth rate QTLs can help in the design of rational strain breeding programs based on genomic information. PMID:11872457

Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy

NASA Astrophysics Data System (ADS)

Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

2016-08-01

Local surface charge density of lipid membranes influences membrane-protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values.

Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy.

PubMed

Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

2016-08-26

Local surface charge density of lipid membranes influences membrane-protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values.

pH optimization for a reliable quantification of brain tumor cell and tissue extracts with (1)H NMR: focus on choline-containing compounds and taurine.

PubMed

Robert, O; Sabatier, J; Desoubzdanne, D; Lalande, J; Balayssac, S; Gilard, V; Martino, R; Malet-Martino, M

2011-01-01

The aim of this study was to define the optimal pH for (1)H nuclear magnetic resonance (NMR) spectroscopy analysis of perchloric acid or methanol-chloroform-water extracts from brain tumor cells and tissues. The systematic study of the proton chemical shift variations as a function of pH of 13 brain metabolites in model solutions demonstrated that recording (1)H NMR spectra at pH 10 allowed resolving resonances that are overlapped at pH 7, especially in the 3.2-3.3 ppm choline-containing-compounds region. (1)H NMR analysis of extracts at pH 7 or 10 showed that quantitative measurements of lactate, alanine, glutamate, glutamine (Gln), creatine + phosphocreatine and myo-inositol (m-Ino) can be readily performed at both pHs. The concentrations of glycerophosphocholine, phosphocholine and choline that are crucial metabolites for tumor brain malignancy grading were accurately measured at pH 10 only. Indeed, the resonances of their trimethylammonium moieties are cleared of any overlapping signal, especially those of taurine (Tau) and phosphoethanolamine. The four non-ionizable Tau protons resonating as a singlet in a non-congested spectral region permits an easier and more accurate quantitation of this apoptosis marker at pH 10 than at pH 7 where the triplet at 3.43 ppm can be overlapped with the signals of glucose or have an intensity too low to be measured. Glycine concentration was determined indirectly at both pHs after subtracting the contribution of the overlapped signals of m-Ino at pH 7 or Gln at pH 10.

Geometrical Calibration of the Photo-Spectral System and Digital Maps Retrieval

NASA Astrophysics Data System (ADS)

Bruchkouskaya, S.; Skachkova, A.; Katkovski, L.; Martinov, A.

2013-12-01

Imaging systems for remote sensing of the Earth are required to demonstrate high metric accuracy of the picture which can be provided through preliminary geometrical calibration of optical systems. Being defined as a result of the geometrical calibration, parameters of internal and external orientation of the cameras are needed while solving such problems of image processing, as orthotransformation, geometrical correction, geographical coordinate fixing, scale adjustment and image registration from various channels and cameras, creation of image mosaics of filmed territories, and determination of geometrical characteristics of objects in the images. The geometrical calibration also helps to eliminate image deformations arising due to manufacturing defects and errors in installation of camera elements and photo receiving matrices as well as those resulted from lens distortions. A Photo-Spectral System (PhSS), which is intended for registering reflected radiation spectra of underlying surfaces in a wavelength range from 350 nm to 1050 nm and recording images of high spatial resolution, has been developed at the A.N. Sevchenko Research Institute of Applied Physical Problems of the Belarusian State University. The PhSS has undergone flight tests over the territory of Belarus onboard the Antonov AN-2 aircraft with the aim to obtain visible range images of the underlying surface. Then we performed the geometrical calibration of the PhSS and carried out the correction of images obtained during the flight tests. Furthermore, we have plotted digital maps of the terrain using the stereo pairs of images acquired from the PhSS and evaluated the accuracy of the created maps. Having obtained the calibration parameters, we apply them for correction of the images from another identical PhSS device, which is located at the Russian Orbital Segment of the International Space Station (ROS ISS), aiming to retrieve digital maps of the terrain with higher accuracy.

Quantitative Susceptibility Mapping of the Midbrain in Parkinson’s Disease

PubMed Central

Du, Guangwei; Liu, Tian; Lewis, Mechelle M.; Kong, Lan; Wang, Yi; Connor, James; Mailman, Richard B.; Huang, Xuemei

2017-01-01

Background Parkinson’s disease (PD) is marked pathologically by dopamine neuron loss and iron overload in the substantia nigra pars compacta. Midbrain iron content is reported to be increased in PD based on magnetic resonance imaging (MRI) R2* changes. Because quantitative susceptibility mapping is a novel MRI approach to measure iron content, we compared it with R2* for assessing midbrain changes in PD. Methods Quantitative susceptibility mapping and R2* maps were obtained from 47 PD patients and 47 healthy controls. Midbrain susceptibility and R2* values were analyzed by using both voxel-based and region-of-interest approaches in normalized space, and analyzed along with clinical data, including disease duration, Unified Parkinson’s Disease Rating Scale (UPDRS) I, II, and III sub-scores, and levodopa-equivalent daily dosage. All studies were done while PD patients were “on drug.” Results Compared with controls, PD patients showed significantly increased susceptibility values in both right (cluster size = 106 mm3) and left (164 mm3) midbrain, located ventrolateral to the red nucleus that corresponded to the substantia nigra pars compacta. Susceptibility values in this region were correlated significantly with disease duration, UPDRS II, and levodopa-equivalent daily dosage. Conversely, R2* was increased significantly only in a much smaller region (62 mm3) of the left lateral substantia nigra pars compacta and was not significantly correlated with clinical parameters. Conclusion The use of quantitative susceptibility mapping demonstrated marked nigral changes that correlated with clinical PD status more sensitively than R2*. These data suggest that quantitative susceptibility mapping may be a superior imaging biomarker to R2* for estimating brain iron levels in PD. PMID:26362242

QACD: A method for the quantitative assessment of compositional distribution in geologic materials

NASA Astrophysics Data System (ADS)

Loocke, M. P.; Lissenberg, J. C. J.; MacLeod, C. J.

2017-12-01

In order to fully understand the petrogenetic history of a rock, it is critical to obtain a thorough characterization of the chemical and textural relationships of its mineral constituents. Element mapping combines the microanalytical techniques that allow for the analysis of major- and minor elements at high spatial resolutions (e.g., electron microbeam analysis) with 2D mapping of samples in order to provide unprecedented detail regarding the growth histories and compositional distributions of minerals within a sample. We present a method for the acquisition and processing of large area X-ray element maps obtained by energy-dispersive X-ray spectrometer (EDS) to produce a quantitative assessment of compositional distribution (QACD) of mineral populations within geologic materials. By optimizing the conditions at which the EDS X-ray element maps are acquired, we are able to obtain full thin section quantitative element maps for most major elements in relatively short amounts of time. Such maps can be used to not only accurately identify all phases and calculate mineral modes for a sample (e.g., a petrographic thin section), but, critically, enable a complete quantitative assessment of their compositions. The QACD method has been incorporated into a python-based, easy-to-use graphical user interface (GUI) called Quack. The Quack software facilitates the generation of mineral modes, element and molar ratio maps and the quantification of full-sample compositional distributions. The open-source nature of the Quack software provides a versatile platform which can be easily adapted and modified to suit the needs of the user.

Proposal for a study of computer mapping of terrain using multispectral data from ERTS-A for the Yellowstone National Park test site

NASA Technical Reports Server (NTRS)

Smedes, H. W. (Principal Investigator); Root, R. R.; Roller, N. E. G.; Despain, D.

1978-01-01

The author has identified the following significant results. A terrain map of Yellowstone National Park showed plant community types and other classes of ground cover in what is basically a wild land. The map comprised 12 classes, six of which were mapped with accuracies of 70 to 95%. The remaining six classes had spectral reflectances that overlapped appreciably, and hence, those were mapped less accurately. Techniques were devised for quantitatively comparing the recognition map of the park with control data acquired from ground inspection and from analysis of sidelooking radar images, a thermal IR mosaic, and IR aerial photos of several scales. Quantitative analyses were made in ten 40 sq km test areas. Comparison mechanics were performed by computer with the final results displayed on line printer output. Forested areas were mapped by computer using ERTS data for less than 1/4 the cost of the conventional forest mapping technique for topographic base maps.

Quantitative analysis of autophagic flux by confocal pH-imaging of autophagic intermediates

PubMed Central

Maulucci, Giuseppe; Chiarpotto, Michela; Papi, Massimiliano; Samengo, Daniela; Pani, Giovambattista; De Spirito, Marco

2015-01-01

Although numerous techniques have been developed to monitor autophagy and to probe its cellular functions, these methods cannot evaluate in sufficient detail the autophagy process, and suffer limitations from complex experimental setups and/or systematic errors. Here we developed a method to image, contextually, the number and pH of autophagic intermediates by using the probe mRFP-GFP-LC3B as a ratiometric pH sensor. This information is expressed functionally by AIPD, the pH distribution of the number of autophagic intermediates per cell. AIPD analysis reveals how intermediates are characterized by a continuous pH distribution, in the range 4.5–6.5, and therefore can be described by a more complex set of states rather than the usual biphasic one (autophagosomes and autolysosomes). AIPD shape and amplitude are sensitive to alterations in the autophagy pathway induced by drugs or environmental states, and allow a quantitative estimation of autophagic flux by retrieving the concentrations of autophagic intermediates. PMID:26506895

Rapid quantitative chemical mapping of surfaces with sub-2 nm resolution

NASA Astrophysics Data System (ADS)

Lai, Chia-Yun; Perri, Saverio; Santos, Sergio; Garcia, Ricardo; Chiesa, Matteo

2016-05-01

We present a theory that exploits four observables in bimodal atomic force microscopy to produce maps of the Hamaker constant H. The quantitative H maps may be employed by the broader community to directly interpret the high resolution of standard bimodal AFM images as chemical maps while simultaneously quantifying chemistry in the non-contact regime. We further provide a simple methodology to optimize a range of operational parameters for which H is in the closest agreement with the Lifshitz theory in order to (1) simplify data acquisition and (2) generalize the methodology to any set of cantilever-sample systems.We present a theory that exploits four observables in bimodal atomic force microscopy to produce maps of the Hamaker constant H. The quantitative H maps may be employed by the broader community to directly interpret the high resolution of standard bimodal AFM images as chemical maps while simultaneously quantifying chemistry in the non-contact regime. We further provide a simple methodology to optimize a range of operational parameters for which H is in the closest agreement with the Lifshitz theory in order to (1) simplify data acquisition and (2) generalize the methodology to any set of cantilever-sample systems. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr00496b

Educational Software for Mapping Quantitative Trait Loci (QTL)

ERIC Educational Resources Information Center

Helms, T. C.; Doetkott, C.

2007-01-01

This educational software was developed to aid teachers and students in their understanding of how the process of identifying the most likely quantitative trait loci (QTL) position is determined between two flanking DNA markers. The objective of the software that we developed was to: (1) show how a QTL is mapped to a position on a chromosome using…

Mapping and validation of quantitative trait loci associated with concentrations of 16 elements in unmilled rice grain

USDA-ARS?s Scientific Manuscript database

In this study, quantitative trait loci (QTLs) affecting the concentrations of 16 elements in whole, unmilled rice (Oryza sativa L.) grain were identified. Two rice mapping populations, the ‘Lemont’ x ‘TeQing’ recombinant inbred lines (LT-RILs), and the TeQing-into-Lemont backcross introgression lin...

Refining Landsat classification results using digital terrain data

USGS Publications Warehouse

Miller, Wayne A.; Shasby, Mark

1982-01-01

 Scientists at the U.S. Geological Survey's Earth Resources Observation systems (EROS) Data Center have recently completed two land-cover mapping projects in which digital terrain data were used to refine Landsat classification results. Digital ter rain data were incorporated into the Landsat classification process using two different procedures that required developing decision criteria either subjectively or quantitatively. The subjective procedure was used in a vegetation mapping project in Arizona, and the quantitative procedure was used in a forest-fuels mapping project in Montana. By incorporating digital terrain data into the Landsat classification process, more spatially accurate landcover maps were produced for both projects.

Quantitative genetic-interaction mapping in mammalian cells

PubMed Central

Roguev, Assen; Talbot, Dale; Negri, Gian Luca; Shales, Michael; Cagney, Gerard; Bandyopadhyay, Sourav; Panning, Barbara; Krogan, Nevan J

2013-01-01

Mapping genetic interactions (GIs) by simultaneously perturbing pairs of genes is a powerful tool for understanding complex biological phenomena. Here we describe an experimental platform for generating quantitative GI maps in mammalian cells using a combinatorial RNA interference strategy. We performed ~11,000 pairwise knockdowns in mouse fibroblasts, focusing on 130 factors involved in chromatin regulation to create a GI map. Comparison of the GI and protein-protein interaction (PPI) data revealed that pairs of genes exhibiting positive GIs and/or similar genetic profiles were predictive of the corresponding proteins being physically associated. The mammalian GI map identified pathways and complexes but also resolved functionally distinct submodules within larger protein complexes. By integrating GI and PPI data, we created a functional map of chromatin complexes in mouse fibroblasts, revealing that the PAF complex is a central player in the mammalian chromatin landscape. PMID:23407553

Quantitative Phase Fraction Detection in Organic Photovoltaic Materials through EELS Imaging

DOE PAGES

Dyck, Ondrej; Hu, Sheng; Das, Sanjib; ...

2015-11-24

Organic photovoltaic materials have recently seen intense interest from the research community. Improvements in device performance are occurring at an impressive rate; however, visualization of the active layer phase separation still remains a challenge. Our paper outlines the application of two electron energy-loss spectroscopic (EELS) imaging techniques that can complement and enhance current phase detection techniques. Specifically, the bulk plasmon peak position, often used to produce contrast between phases in energy filtered transmission electron microscopy (EFTEM), is quantitatively mapped across a sample cross section. One complementary spectrum image capturing the carbon and sulfur core loss edges is compared with themore » plasmon peak map and found to agree quite well, indicating that carbon and sulfur density differences between the two phases also allows phase discrimination. Additionally, an analytical technique for determining absolute atomic areal density is used to produce an absolute carbon and sulfur areal density map. We also show how these maps may be re-interpreted as a phase ratio map, giving quantitative information about the purity of the phases within the junction.« less

Quantitative determination of p-aminosalicylic acid and its degradation product m-aminophenol in pellets by ion-pair high-performance liquid chromatography applying the monolithic Chromolith Speedrod RP-18e column.

PubMed

Vasbinder, E; Van der Weken, G; Vander Heyden, Y; Baeyens, W R G; Debunne, A; Remon, J P; García-Campaña, A M

2004-01-01

An ion-pair high performance liquid chromatographic method was developed for the simultaneous determination of p-aminosalicylic acid (PAS) and its degradation product m-aminophenol (MAP) in a newly developed multiparticular drug delivery system. Owing to the concentration differences of PAS and MAP, acetanilide and sulfanilic acid were used as internal standards, respectively. The separation was performed on a Chromolith SpeedROD RP-18e column, a new packing material consisting of monolithic rods of highly porous silica. The mobile phase composition was of 20 mm phosphate buffer, 20 mm tetrabutylammonium hydrogen sulphate and 16% (v/v) methanol adjusted to pH 6.8, at a flow-rate of 1.0 mL/min, resulting in a run-time of about 6 min. Detection was by UV at 233 nm. The method was validated and proved to be useful for stability testing of the new dosage form. Separation efficiency was compared between the new packing material Chromolith SpeedROD RP-18e and the conventional reversed-phase cartridge LiChroCART 125-4 (5 microm). A robustness test was carried out on both columns and different separation parameters (retention, resolution, run time, temperature) were determined. Copyright 2004 John Wiley & Sons, Ltd.

Human brain atlas for automated region of interest selection in quantitative susceptibility mapping: application to determine iron content in deep gray matter structures

PubMed Central

Lim, Issel Anne L.; Faria, Andreia V.; Li, Xu; Hsu, Johnny T.C.; Airan, Raag D.; Mori, Susumu; van Zijl, Peter C. M.

2013-01-01

The purpose of this paper is to extend the single-subject Eve atlas from Johns Hopkins University, which currently contains diffusion tensor and T1-weighted anatomical maps, by including contrast based on quantitative susceptibility mapping. The new atlas combines a “deep gray matter parcellation map” (DGMPM) derived from a single-subject quantitative susceptibility map with the previously established “white matter parcellation map” (WMPM) from the same subject’s T1-weighted and diffusion tensor imaging data into an MNI coordinate map named the “Everything Parcellation Map in Eve Space,” also known as the “EvePM.” It allows automated segmentation of gray matter and white matter structures. Quantitative susceptibility maps from five healthy male volunteers (30 to 33 years of age) were coregistered to the Eve Atlas with AIR and Large Deformation Diffeomorphic Metric Mapping (LDDMM), and the transformation matrices were applied to the EvePM to produce automated parcellation in subject space. Parcellation accuracy was measured with a kappa analysis for the left and right structures of six deep gray matter regions. For multi-orientation QSM images, the Kappa statistic was 0.85 between automated and manual segmentation, with the inter-rater reproducibility Kappa being 0.89 for the human raters, suggesting “almost perfect” agreement between all segmentation methods. Segmentation seemed slightly more difficult for human raters on single-orientation QSM images, with the Kappa statistic being 0.88 between automated and manual segmentation, and 0.85 and 0.86 between human raters. Overall, this atlas provides a time-efficient tool for automated coregistration and segmentation of quantitative susceptibility data to analyze many regions of interest. These data were used to establish a baseline for normal magnetic susceptibility measurements for over 60 brain structures of 30- to 33-year-old males. Correlating the average susceptibility with age-based iron concentrations in gray matter structures measured by Hallgren and Sourander (1958) allowed interpolation of the average iron concentration of several deep gray matter regions delineated in the EvePM. PMID:23769915

Effects of three kinds of organic acids on phosphorus recovery by magnesium ammonium phosphate (MAP) crystallization from synthetic swine wastewater.

PubMed

Song, Yonghui; Dai, Yunrong; Hu, Qiong; Yu, Xiaohua; Qian, Feng

2014-04-01

P recovery from swine wastewater has become a great concern as a result of the high demand for P resources and its potential eutrophication effects on water ecosystems. The method of magnesium ammonium phosphate (MAP) crystallization was used to recover P from simulated swine wastewater, and the effects of three organic acids (citric acid, succinic acid and acetic acid) on P removal efficiency and rate at different pH values were investigated. The results indicated that the P removal efficiency was worst affected by citric acid in the optimal pH range of 9.0-10.5, followed by succinic acid and acetic acid, and the influencing extent of organic acids decreased with the increasing pH value. Due to the complexation between organic acid and Mg(2+)/NH4(+), all of three organic acids could inhibit the P removal rate at the beginning of the reaction, which showed positive correlation between the inhibition effects and the concentration of organic acids. The high concentration of citric acid could completely suppress the MAP crystallization reaction. Moreover, citric acid and succinic acid brought obvious effects on the morphology of the crystallized products. The experimental results also demonstrated that MAP crystals could be obtained in the presence of different kinds and concentrations of organic acids. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bacterially produced Pt-GFP as ratiometric dual-excitation sensor for in planta mapping of leaf apoplastic pH in intact Avena sativa and Vicia faba.

PubMed

Geilfus, Christoph-Martin; Mühling, Karl H; Kaiser, Hartmut; Plieth, Christoph

2014-01-01

Ratiometric analysis with H(+)-sensitive fluorescent sensors is a suitable approach for monitoring apoplastic pH dynamics. For the acidic range, the acidotropic dual-excitation dye Oregon Green 488 is an excellent pH sensor. Long lasting (hours) recordings of apoplastic pH in the near neutral range, however, are more problematic because suitable pH indicators that combine a good pH responsiveness at a near neutral pH with a high photostability are lacking. The fluorescent pH reporter protein from Ptilosarcus gurneyi (Pt-GFP) comprises both properties. But, as a genetically encoded indicator and expressed by the plant itself, it can be used almost exclusively in readily transformed plants. In this study we present a novel approach and use purified recombinant indicators for measuring ion concentrations in the apoplast of crop plants such as Vicia faba L. and Avena sativa L. Pt-GFP was purified using a bacterial expression system and subsequently loaded through stomata into the leaf apoplast of intact plants. Imaging verified the apoplastic localization of Pt-GFP and excluded its presence in the symplast. The pH-dependent emission signal stood out clearly from the background. PtGFP is highly photostable, allowing ratiometric measurements over hours. By using this approach, a chloride-induced alkalinizations of the apoplast was demonstrated for the first in oat. Pt-GFP appears to be an excellent sensor for the quantification of leaf apoplastic pH in the neutral range. The presented approach encourages to also use other genetically encoded biosensors for spatiotemporal mapping of apoplastic ion dynamics.

pH & Rate of Enzymatic Reactions.

ERIC Educational Resources Information Center

Clariana, Roy B.

1991-01-01

A quantitative and inexpensive way to measure the rate of enzymatic reaction is provided. The effects of different pH levels on the reaction rate of an enzyme from yeast are investigated and the results graphed. Background information, a list of needed materials, directions for preparing solutions, procedure, and results and discussion are…

Quantitative evaluation of dual-flip-angle T1 mapping on DCE-MRI kinetic parameter estimation in head and neck

PubMed Central

Chow, Steven Kwok Keung; Yeung, David Ka Wai; Ahuja, Anil T; King, Ann D

2012-01-01

Purpose To quantitatively evaluate the kinetic parameter estimation for head and neck (HN) dynamic contrast-enhanced (DCE) MRI with dual-flip-angle (DFA) T1 mapping. Materials and methods Clinical DCE-MRI datasets of 23 patients with HN tumors were included in this study. T1 maps were generated based on multiple-flip-angle (MFA) method and different DFA combinations. Tofts model parameter maps of kep, Ktrans and vp based on MFA and DFAs were calculated and compared. Fitted parameter by MFA and DFAs were quantitatively evaluated in primary tumor, salivary gland and muscle. Results T1 mapping deviations by DFAs produced remarkable kinetic parameter estimation deviations in head and neck tissues. In particular, the DFA of [2º, 7º] overestimated, while [7º, 12º] and [7º, 15º] underestimated Ktrans and vp, significantly (P<0.01). [2º, 15º] achieved the smallest but still statistically significant overestimation for Ktrans and vp in primary tumors, 32.1% and 16.2% respectively. kep fitting results by DFAs were relatively close to the MFA reference compared to Ktrans and vp. Conclusions T1 deviations induced by DFA could result in significant errors in kinetic parameter estimation, particularly Ktrans and vp, through Tofts model fitting. MFA method should be more reliable and robust for accurate quantitative pharmacokinetic analysis in head and neck. PMID:23289084

Assessing mine drainage pH from the color and spectral reflectance of chemical precipitates

USGS Publications Warehouse

Williams, D.J.; Bigham, J.M.; Cravotta, C.A.; Traina, S.J.; Anderson, J.E.; Lyon, J.G.

2002-01-01

The pH of mine impacted waters was estimated from the spectral reflectance of resident sediments composed mostly of chemical precipitates. Mine drainage sediments were collected from sites in the Anthracite Region of eastern Pennsylvania, representing acid to near neutral pH. Sediments occurring in acidic waters contained primarily schwertmannite and goethite while near neutral waters produced ferrihydrite. The minerals comprising the sediments occurring at each pH mode were spectrally separable. Spectral angle difference mapping was used to correlate sediment color with stream water pH (r2=0.76). Band-center and band-depth analysis of spectral absorption features were also used to discriminate ferrihydrite and goethite and/or schwertmannite by analyzing the 4T1??? 6A1 crystal field transition (900-1000 nm). The presence of these minerals accurately predicted stream water pH (r2=0.87) and provided a qualitative estimate of dissolved SO4 concentrations. Spectral analysis results were used to analyze airborne digital multispectral video (DMSV) imagery for several sites in the region. The high spatial resolution of the DMSV sensor allowed for precise mapping of the mine drainage sediments. The results from this study indicate that airborne and space-borne imaging spectrometers may be used to accurately classify streams impacted by acid vs. neutral-to-alkaline mine drainage after appropriate spectral libraries are developed.

A Road Map Towards High pH Adaptability: Phenomic and Genomic Approaches to Azalea Breeding (Rhododendron sp.)

USDA-ARS?s Scientific Manuscript database

A research grant from the Azalea Society of America has enabled us to collect and begin evaluating diverse Rhododendron viscosum germplasm to identify genetic and phenotypic variation for pH adaptability. During the Spring of 2014, we developed novel, in vitro screening methods for Rhododendron to ...

Enamel demineralization and remineralization under plaque fluid-like conditions: a quantitative light-induced fluorescence study.

PubMed

Lippert, F; Butler, A; Lynch, R J M

2011-01-01

The present study investigated de- and remineralization in enamel lesions under plaque fluid (PF)-like conditions using quantitative light-induced fluorescence (QLF). Preformed lesions were exposed to partially saturated lactic acid solutions, varying in pH and fluoride concentration ([F]) based on a 5 × 3 factorial study design (0/0.1/0.5/1.5/4 ppm F; pH 4.9/5.2/5.5). Average fluorescence loss (ΔF) was monitored for 11 days. Subsequently, lesions were demineralized in a partially saturated acetic acid solution for two 24-hour periods. Data were analyzed using repeated measures analysis of covariance. Lesions exposed to PF at 4 ppm F and pH 5.5 showed not only the most remineralization (ΔΔF = 28.2 ± 14.0%) for all groups after 11 days, but also the most demineralization (ΔΔF = -19.3 ± 13.5%) after subsequent acetic acid exposure. Increased [F] resulted in more remineralization, regardless of pH. Higher pH values resulted in more remineralization. No remineralization was observed in lesions exposed to F-free solutions, regardless of pH. Remineralization was noticeable under the following conditions: pH 4.9 - [F] = 4 ppm, pH 5.2 - [F] ≥ 1.5 ppm, and pH 5.5 - [F] ≥ 0.5 ppm. Overall, [F] had a stronger effect on remineralization than pH. Subsequent demineralization showed that little protection was offered by PF-like solutions, and further demineralization compared with baseline was observed on lesions not remineralized initially. [F] had a stronger effect on net mineral change than pH. The present study has shown that QLF is a valuable tool in studying lesion de- and remineralization under PF-like conditions, where [F] was shown to be more important than pH. Copyright © 2011 S. Karger AG, Basel.

Knowledge base and functionality of concepts of some Filipino biology teachers in five biology topics

NASA Astrophysics Data System (ADS)

Barquilla, Manuel B.

2018-01-01

This mixed research, is a snapshot of some Filipino Biology teachers' knowledge structure and how their concepts of the five topics in Biology (Photosynthesis, Cellular Respiration, human reproductive system, Mendelian genetics and NonMendelian genetics) functions and develops inside a biology classroom. The study focuses on the six biology teachers and a total of 222 students in their respective classes. Of the Six (6) teachers, three (3) are under the Science curriculum and the other three (3) are under regular curriculum in both public and private schools in Iligan city and Lanao del Norte, Philippines. The study utilized classroom discourses, concept maps, interpretative case-study method, bracketing method, and concept analysis for qualitative part; the quantitative part uses a nonparametric statistical tool, Kendall's tau Coefficient for determining relationship and congruency while measures of central tendencies and dispersion (mean, and standard deviation) for concept maps scores interpretation. Knowledge Base of Biology teachers were evaluated by experts in field of specialization having a doctorate program (e.g. PhD in Genetics) and PhD Biology candidates. The data collection entailed seven (7) months immersion: one (1) month for preliminary phase for the researcher to gain teachers' and students' confidence and the succeeding six (6) months for main observation and data collection. The evaluation of teachers' knowledge base by experts indicated that teachers' knowledge of (65%) is lower than the minimum (75%) recommended by ABD-el-Khalick and Boujaoude (1997). Thus, the experts believe that content knowledge of the teachers is hardly adequate for their teaching assignment. Moreover, the teachers in this study do not systematically use reallife situation to apply the concepts they teach. They can identify concepts too abstract for their student; however, they seldom use innovative ways to bring the discussion to their students' level of readiness and capacity to learn. Kendall's Tau Coefficient of agreement indicated that there is an agreement of the rating by experts and PhD (Biology) candidates. As for recommended level for teaching based on the respondent content knowledge structure, the experts and the PhD (Biology) candidates agree that the content knowledge of the teachers is at the borderline (rating of 6) between elementary and high school. These results imply that biology teachers need in-service training to upgrade their content knowledge in the subject. At the same time, the pre-service curriculum for biology teachers needs upgrading.

A Quantitative Chemotherapy Genetic Interaction Map Reveals Factors Associated with PARP Inhibitor Resistance.

PubMed

Hu, Hsien-Ming; Zhao, Xin; Kaushik, Swati; Robillard, Lilliane; Barthelet, Antoine; Lin, Kevin K; Shah, Khyati N; Simmons, Andy D; Raponi, Mitch; Harding, Thomas C; Bandyopadhyay, Sourav

2018-04-17

Chemotherapy is used to treat most cancer patients, yet our understanding of factors that dictate response and resistance to such drugs remains limited. We report the generation of a quantitative chemical-genetic interaction map in human mammary epithelial cells charting the impact of the knockdown of 625 genes related to cancer and DNA repair on sensitivity to 29 drugs, covering all classes of chemotherapy. This quantitative map is predictive of interactions maintained in other cell lines, identifies DNA-repair factors, predicts cancer cell line responses to therapy, and prioritizes synergistic drug combinations. We identify that ARID1A loss confers resistance to PARP inhibitors in cells and ovarian cancer patients and that loss of GPBP1 causes resistance to cisplatin and PARP inhibitors through the regulation of genes involved in homologous recombination. This map helps navigate patient genomic data and optimize chemotherapeutic regimens by delineating factors involved in the response to specific types of DNA damage. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Quantitative x-ray phase-contrast imaging using a single grating of comparable pitch to sample feature size.

PubMed

Morgan, Kaye S; Paganin, David M; Siu, Karen K W

2011-01-01

The ability to quantitatively retrieve transverse phase maps during imaging by using coherent x rays often requires a precise grating or analyzer-crystal-based setup. Imaging of live animals presents further challenges when these methods require multiple exposures for image reconstruction. We present a simple method of single-exposure, single-grating quantitative phase contrast for a regime in which the grating period is much greater than the effective pixel size. A grating is used to create a high-visibility reference pattern incident on the sample, which is distorted according to the complex refractive index and thickness of the sample. The resolution, along a line parallel to the grating, is not restricted by the grating spacing, and the detector resolution becomes the primary determinant of the spatial resolution. We present a method of analysis that maps the displacement of interrogation windows in order to retrieve a quantitative phase map. Application of this analysis to the imaging of known phantoms shows excellent correspondence.

In vivo pH monitoring using boron doped diamond microelectrode and silver needles: Application to stomach disorder diagnosis

NASA Astrophysics Data System (ADS)

Fierro, Stéphane; Seishima, Ryo; Nagano, Osamu; Saya, Hideyuki; Einaga, Yasuaki

2013-11-01

This study presents the in vivo electrochemical monitoring of pH using boron doped diamond (BDD) microelectrode and silver needles for potential application in medical diagnosis. Accurate calibration curve for pH determination were obtained through in vitro electrochemical measurements. The increase induced in stomach pH by treatment with pantoprazole was used to demonstrate that it is possible to monitor the pH in vivo using the simple and noninvasive system proposed herein. Using the results of the in vivo and in vitro experiments, a quantitative analysis of the increase in stomach pH is also presented. It is proposed that the catheter-free pH monitoring system presented in this study could be potentially employed in any biological environment.

In vivo pH monitoring using boron doped diamond microelectrode and silver needles: application to stomach disorder diagnosis.

PubMed

Fierro, Stéphane; Seishima, Ryo; Nagano, Osamu; Saya, Hideyuki; Einaga, Yasuaki

2013-11-19

This study presents the in vivo electrochemical monitoring of pH using boron doped diamond (BDD) microelectrode and silver needles for potential application in medical diagnosis. Accurate calibration curve for pH determination were obtained through in vitro electrochemical measurements. The increase induced in stomach pH by treatment with pantoprazole was used to demonstrate that it is possible to monitor the pH in vivo using the simple and noninvasive system proposed herein. Using the results of the in vivo and in vitro experiments, a quantitative analysis of the increase in stomach pH is also presented. It is proposed that the catheter-free pH monitoring system presented in this study could be potentially employed in any biological environment.

Quantitative DNA fiber mapping

DOEpatents

Gray, Joe W.; Weier, Heinz-Ulrich G.

1998-01-01

The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.

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.

Noninvasive Assessment of Biochemical and Mechanical Properties of Lumbar Discs Through Quantitative Magnetic Resonance Imaging in Asymptomatic Volunteers.

PubMed

Foltz, Mary H; Kage, Craig C; Johnson, Casey P; Ellingson, Arin M

2017-11-01

Intervertebral disc degeneration is a prevalent phenomenon associated with back pain. It is of critical clinical interest to discriminate disc health and identify early stages of degeneration. Traditional clinical T2-weighted magnetic resonance imaging (MRI), assessed using the Pfirrmann classification system, is subjective and fails to adequately capture initial degenerative changes. Emerging quantitative MRI techniques offer a solution. Specifically, T2* mapping images water mobility in the macromolecular network, and our preliminary ex vivo work shows high predictability of the disc's glycosaminoglycan content (s-GAG) and residual mechanics. The present study expands upon this work to predict the biochemical and biomechanical properties in vivo and assess their relationship with both age and Pfirrmann grade. Eleven asymptomatic subjects (range: 18-62 yrs) were enrolled and imaged using a 3T MRI scanner. T2-weighted images (Pfirrmann grade) and quantitative T2* maps (predict s-GAG and residual stress) were acquired. Surface maps based on the distribution of these properties were generated and integrated to quantify the surface volume. Correlational analyses were conducted to establish the relationship between each metric of disc health derived from the quantitative T2* maps with both age and Pfirrmann grade, where an inverse trend was observed. Furthermore, the nucleus pulposus (NP) signal in conjunction with volumetric surface maps provided the ability to discern differences during initial stages of disc degeneration. This study highlights the ability of T2* mapping to noninvasively assess the s-GAG content, residual stress, and distributions throughout the entire disc, which may provide a powerful diagnostic tool for disc health assessment.

Optical measurement of acidification of human dental plaque in vitro

NASA Astrophysics Data System (ADS)

Graham, Jasmine Y.; Nelson, Leonard Y.; Seibel, Eric J.

2018-02-01

A pH measurement of oral biofilms is helpful for monitoring the impact of acidogenic bacteria in the caries process. Demineralization of dental enamel is closely related to the time dependent pH of human plaque. Therefore, providing a means to easily measure the local pH of biofilms is a useful clinical diagnostic in the arsenal of caries prevention tools. Optical measurement methods of plaque metabolism can use intrinsic fluorescence or extrinsic fluorescence from added dyes. Autofluorescence spectral features of human oral biofilms at green (500 nm) and red (634 nm) fluorescence wavelengths using 405 nm excitation did not demonstrate a spectral or intensity shift between neutral and acidic conditions. Chlorin e6, an ingredient in chlorophyllin food supplement, exhibited a spectral and intensity shift of fluorescence emission in buffered solutions, but this quantitative pH-dependence was not transferable to a human plaque environment. Finally, a ratiometric quantitative pH measure was achieved by exciting (405 nm laser) a mixture of two dyes, fluorescein and rhodamine B. This two-dye mixture produced two strong fluorescent bands centered at 515 nm (fluorescein) and 580 nm (rhodamine B), where the 515 nm band was pH sensitive and the 580 nm band served as a pH insensitive reference. This dual-dye fluorescence ratio exhibited a linear response over pH 7 to 5 in human oral biofilms during a sugar challenge. We have explored methods to use non-contact, optical measures of local acidity levels in difficult to access dental locations such as occlusal fissures using various pH sensitive fluorescent dye systems.

Identification of Novel Associations of Candidate Genes with Resistance to Late Blight in Solanum tuberosum Group Phureja

PubMed Central

Álvarez, María F.; Angarita, Myrian; Delgado, María C.; García, Celsa; Jiménez-Gomez, José; Gebhardt, Christiane; Mosquera, Teresa

2017-01-01

The genetic basis of quantitative disease resistance has been studied in crops for several decades as an alternative to R gene mediated resistance. The most important disease in the potato crop is late blight, caused by the oomycete Phytophthora infestans. Quantitative disease resistance (QDR), as any other quantitative trait in plants, can be genetically mapped to understand the genetic architecture. Association mapping using DNA-based markers has been implemented in many crops to dissect quantitative traits. We used an association mapping approach with candidate genes to identify the first genes associated with quantitative resistance to late blight in Solanum tuberosum Group Phureja. Twenty-nine candidate genes were selected from a set of genes that were differentially expressed during the resistance response to late blight in tetraploid European potato cultivars. The 29 genes were amplified and sequenced in 104 accessions of S. tuberosum Group Phureja from Latin America. We identified 238 SNPs in the selected genes and tested them for association with resistance to late blight. The phenotypic data were obtained under field conditions by determining the area under disease progress curve (AUDPC) in two seasons and in two locations. Two genes were associated with QDR to late blight, a potato homolog of thylakoid lumen 15 kDa protein (StTL15A) and a stem 28 kDa glycoprotein (StGP28). Key message: A first association mapping experiment was conducted in Solanum tuberosum Group Phureja germplasm, which identified among 29 candidates two genes associated with quantitative resistance to late blight. PMID:28674545

Identification of Novel Associations of Candidate Genes with Resistance to Late Blight in Solanum tuberosum Group Phureja.

PubMed

Álvarez, María F; Angarita, Myrian; Delgado, María C; García, Celsa; Jiménez-Gomez, José; Gebhardt, Christiane; Mosquera, Teresa

2017-01-01

The genetic basis of quantitative disease resistance has been studied in crops for several decades as an alternative to R gene mediated resistance. The most important disease in the potato crop is late blight, caused by the oomycete Phytophthora infestans. Quantitative disease resistance (QDR), as any other quantitative trait in plants, can be genetically mapped to understand the genetic architecture. Association mapping using DNA-based markers has been implemented in many crops to dissect quantitative traits. We used an association mapping approach with candidate genes to identify the first genes associated with quantitative resistance to late blight in Solanum tuberosum Group Phureja. Twenty-nine candidate genes were selected from a set of genes that were differentially expressed during the resistance response to late blight in tetraploid European potato cultivars. The 29 genes were amplified and sequenced in 104 accessions of S. tuberosum Group Phureja from Latin America. We identified 238 SNPs in the selected genes and tested them for association with resistance to late blight. The phenotypic data were obtained under field conditions by determining the area under disease progress curve (AUDPC) in two seasons and in two locations. Two genes were associated with QDR to late blight, a potato homolog of thylakoid lumen 15 kDa protein ( StTL15A ) and a stem 28 kDa glycoprotein ( StGP28 ). Key message : A first association mapping experiment was conducted in Solanum tuberosum Group Phureja germplasm, which identified among 29 candidates two genes associated with quantitative resistance to late blight.

pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism.

PubMed

Mangan, Niall M; Flamholz, Avi; Hood, Rachel D; Milo, Ron; Savage, David F

2016-09-06

Many carbon-fixing bacteria rely on a CO2 concentrating mechanism (CCM) to elevate the CO2 concentration around the carboxylating enzyme ribulose bisphosphate carboxylase/oxygenase (RuBisCO). The CCM is postulated to simultaneously enhance the rate of carboxylation and minimize oxygenation, a competitive reaction with O2 also catalyzed by RuBisCO. To achieve this effect, the CCM combines two features: active transport of inorganic carbon into the cell and colocalization of carbonic anhydrase and RuBisCO inside proteinaceous microcompartments called carboxysomes. Understanding the significance of the various CCM components requires reconciling biochemical intuition with a quantitative description of the system. To this end, we have developed a mathematical model of the CCM to analyze its energetic costs and the inherent intertwining of physiology and pH. We find that intracellular pH greatly affects the cost of inorganic carbon accumulation. At low pH the inorganic carbon pool contains more of the highly cell-permeable H2CO3, necessitating a substantial expenditure of energy on transport to maintain internal inorganic carbon levels. An intracellular pH ≈8 reduces leakage, making the CCM significantly more energetically efficient. This pH prediction coincides well with our measurement of intracellular pH in a model cyanobacterium. We also demonstrate that CO2 retention in the carboxysome is necessary, whereas selective uptake of HCO3 (-) into the carboxysome would not appreciably enhance energetic efficiency. Altogether, integration of pH produces a model that is quantitatively consistent with cyanobacterial physiology, emphasizing that pH cannot be neglected when describing biological systems interacting with inorganic carbon pools.

pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism

PubMed Central

Flamholz, Avi; Hood, Rachel D.; Milo, Ron

2016-01-01

Many carbon-fixing bacteria rely on a CO2 concentrating mechanism (CCM) to elevate the CO2 concentration around the carboxylating enzyme ribulose bisphosphate carboxylase/oxygenase (RuBisCO). The CCM is postulated to simultaneously enhance the rate of carboxylation and minimize oxygenation, a competitive reaction with O2 also catalyzed by RuBisCO. To achieve this effect, the CCM combines two features: active transport of inorganic carbon into the cell and colocalization of carbonic anhydrase and RuBisCO inside proteinaceous microcompartments called carboxysomes. Understanding the significance of the various CCM components requires reconciling biochemical intuition with a quantitative description of the system. To this end, we have developed a mathematical model of the CCM to analyze its energetic costs and the inherent intertwining of physiology and pH. We find that intracellular pH greatly affects the cost of inorganic carbon accumulation. At low pH the inorganic carbon pool contains more of the highly cell-permeable H2CO3, necessitating a substantial expenditure of energy on transport to maintain internal inorganic carbon levels. An intracellular pH ≈8 reduces leakage, making the CCM significantly more energetically efficient. This pH prediction coincides well with our measurement of intracellular pH in a model cyanobacterium. We also demonstrate that CO2 retention in the carboxysome is necessary, whereas selective uptake of HCO3− into the carboxysome would not appreciably enhance energetic efficiency. Altogether, integration of pH produces a model that is quantitatively consistent with cyanobacterial physiology, emphasizing that pH cannot be neglected when describing biological systems interacting with inorganic carbon pools. PMID:27551079

Mapping quantitative trait loci controlling early growth in a (longleaf pine × slash pine) × slash pine BC1 family

Treesearch

C. Weng; Thomas L. Kubisiak; C. Dana Nelson; M. Stine

2002-01-01

Random amplified polymorphic DNA (RAPD) markers were employed to map the genome and quantitative trait loci controlling the early growth of a pine hybrid F1 tree (Pinus palustris Mill. × P. elliottii Engl.) and a recurrent slash pine tree (P. ellottii Engl.) in a (longleaf pine × slash pine...

Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. I. Timing of vegetative bud flush.

Treesearch

K.D. Jermstad; D.L. Bassoni; K.S. Jech; N.C. Wheeler; D.B. Neale

2001-01-01

Abstract Thirty three unique quantitative trait loci (QTLs) affecting the timing of spring bud flush have been identified in an intraspecific mapping population of coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii]. Both terminal and lateral bud flush were measured over a 4-year period on clonal replicates at two test sites, allowing for the...

Sensitive detection of strong acidic condition by a novel rhodamine-based fluorescent pH chemosensor.

PubMed

Tan, Jia-Lian; Yang, Ting-Ting; Liu, Yu; Zhang, Xue; Cheng, Shu-Jin; Zuo, Hua; He, Huawei

2016-05-01

A novel rhodamine-based fluorescent pH probe responding to extremely low pH values has been synthesized and characterized. This probe showed an excellent photophysical response to pH on the basis that the colorless spirocyclic structure under basic conditions opened to a colored and highly fluorescent form under extreme acidity. The quantitative relationship between fluorescence intensity and pH value (1.75-2.62) was consistent with the equilibrium equation pH = pKa + log[(Imax - I)/(I - Imin)]. This sensitive pH probe was also characterized with good reversibility and no interaction with interfering metal ions, and was successfully applied to image Escherichia coli under strong acidity. Copyright © 2015 John Wiley & Sons, Ltd.

Geoscience data visualization and analysis using GeoMapApp

NASA Astrophysics Data System (ADS)

Ferrini, Vicki; Carbotte, Suzanne; Ryan, William; Chan, Samantha

2013-04-01

Increased availability of geoscience data resources has resulted in new opportunities for developing visualization and analysis tools that not only promote data integration and synthesis, but also facilitate quantitative cross-disciplinary access to data. Interdisciplinary investigations, in particular, frequently require visualizations and quantitative access to specialized data resources across disciplines, which has historically required specialist knowledge of data formats and software tools. GeoMapApp (www.geomapapp.org) is a free online data visualization and analysis tool that provides direct quantitative access to a wide variety of geoscience data for a broad international interdisciplinary user community. While GeoMapApp provides access to online data resources, it can also be packaged to work offline through the deployment of a small portable hard drive. This mode of operation can be particularly useful during field programs to provide functionality and direct access to data when a network connection is not possible. Hundreds of data sets from a variety of repositories are directly accessible in GeoMapApp, without the need for the user to understand the specifics of file formats or data reduction procedures. Available data include global and regional gridded data, images, as well as tabular and vector datasets. In addition to basic visualization and data discovery functionality, users are provided with simple tools for creating customized maps and visualizations and to quantitatively interrogate data. Specialized data portals with advanced functionality are also provided for power users to further analyze data resources and access underlying component datasets. Users may import and analyze their own geospatial datasets by loading local versions of geospatial data and can access content made available through Web Feature Services (WFS) and Web Map Services (WMS). Once data are loaded in GeoMapApp, a variety options are provided to export data and/or 2D/3D visualizations into common formats including grids, images, text files, spreadsheets, etc. Examples of interdisciplinary investigations that make use of GeoMapApp visualization and analysis functionality will be provided.

Spatial access priority mapping (SAPM) with fishers: a quantitative GIS method for participatory planning.

PubMed

Yates, Katherine L; Schoeman, David S

2013-01-01

Spatial management tools, such as marine spatial planning and marine protected areas, are playing an increasingly important role in attempts to improve marine management and accommodate conflicting needs. Robust data are needed to inform decisions among different planning options, and early inclusion of stakeholder involvement is widely regarded as vital for success. One of the biggest stakeholder groups, and the most likely to be adversely impacted by spatial restrictions, is the fishing community. In order to take their priorities into account, planners need to understand spatial variation in their perceived value of the sea. Here a readily accessible, novel method for quantitatively mapping fishers' spatial access priorities is presented. Spatial access priority mapping, or SAPM, uses only basic functions of standard spreadsheet and GIS software. Unlike the use of remote-sensing data, SAPM actively engages fishers in participatory mapping, documenting rather than inferring their priorities. By so doing, SAPM also facilitates the gathering of other useful data, such as local ecological knowledge. The method was tested and validated in Northern Ireland, where over 100 fishers participated in a semi-structured questionnaire and mapping exercise. The response rate was excellent, 97%, demonstrating fishers' willingness to be involved. The resultant maps are easily accessible and instantly informative, providing a very clear visual indication of which areas are most important for the fishers. The maps also provide quantitative data, which can be used to analyse the relative impact of different management options on the fishing industry and can be incorporated into planning software, such as MARXAN, to ensure that conservation goals can be met at minimum negative impact to the industry. This research shows how spatial access priority mapping can facilitate the early engagement of fishers and the ready incorporation of their priorities into the decision-making process in a transparent, quantitative way.

Evaluation of prognostic and predictive value of microtubule associated protein tau in two independent cohorts.

PubMed

Baquero, Maria T; Lostritto, Karen; Gustavson, Mark D; Bassi, Kimberly A; Appia, Franck; Camp, Robert L; Molinaro, Annette M; Harris, Lyndsay N; Rimm, David L

2011-11-02

Microtubule associated proteins (MAPs) endogenously regulate microtubule stabilization and have been reported as prognostic and predictive markers for taxane response. The microtubule stabilizer, MAP-tau, has shown conflicting results. We quantitatively assessed MAP-tau expression in two independent breast cancer cohorts to determine prognostic and predictive value of this biomarker. MAP-tau expression was evaluated in the retrospective Yale University breast cancer cohort (n = 651) using tissue microarrays and also in the TAX 307 cohort, a clinical trial randomized for TAC versus FAC chemotherapy (n = 140), using conventional whole tissue sections. Expression was measured using the AQUA method for quantitative immunofluorescence. Scores were correlated with clinicopathologic variables, survival, and response to therapy. Assessment of the Yale cohort using Cox univariate analysis indicated an improved overall survival (OS) in tumors with a positive correlation between high MAP-tau expression and overall survival (OS) (HR = 0.691, 95% CI = 0.489-0.974; P = 0.004). Kaplan Meier analysis showed 10-year survival for 65% of patients with high MAP-tau expression compared to 52% with low expression (P = .006). In TAX 307, high expression was associated with significantly longer median time to tumor progression (TTP) regardless of treatment arm (33.0 versus 23.4 months, P = 0.010) with mean TTP of 31.2 months. Response rates did not differ by MAP-tau expression (P = 0.518) or by treatment arm (P = 0.584). Quantitative measurement of MAP-tau expression has prognostic value in both cohorts, with high expression associated with longer TTP and OS. Differences by treatment arm or response rate in low versus high MAP-tau groups were not observed, indicating that MAP-tau is not associated with response to taxanes and is not a useful predictive marker for taxane-based chemotherapy.

Quantitative and simultaneous detection of four foodborne bacterial pathogens with a multi-channel SPR sensor.

PubMed

Taylor, Allen D; Ladd, Jon; Yu, Qiuming; Chen, Shengfu; Homola, Jirí; Jiang, Shaoyi

2006-12-15

We report the quantitative and simultaneous detection of four species of bacteria, Escherichia coli O157:H7, Salmonella choleraesuis serotype typhimurium, Listeria monocytogenes, and Campylobacter jejuni, using an eight-channel surface plasmon resonance (SPR) sensor based on wavelength division multiplexing. Detection curves showing SPR response versus analyte concentration were established for each species of bacteria in buffer at pH 7.4, apple juice at native pH 3.7, and apple juice at an adjusted pH of 7.4, as well as for a mixture containing all four species of bacteria in buffer. Control experiments were performed to show the non-fouling characteristics of the sensor surface as well as the specificity of the amplification antibodies used in this study. The limit of detection (LOD) for each of the four species of bacteria in the tested matrices ranges from 3.4 x 10(3) to 1.2 x 10(5) cfu/ml. Detection curves in buffer of an individual species of bacteria in a mixture of all four species of bacteria correlated well with detection curves of the individual species of bacteria alone. SPR responses were higher for bacteria in apple juice at pH 7.4 than in apple juice at pH 3.7. This difference in sensor response could be partly attributed to the pH dependence of antibody-antigen binding.

Imaging Cerebral Microhemorrhages in Military Service Members with Chronic Traumatic Brain Injury

PubMed Central

Liu, Wei; Soderlund, Karl; Senseney, Justin S.; Joy, David; Yeh, Ping-Hong; Ollinger, John; Sham, Elyssa B.; Liu, Tian; Wang, Yi; Oakes, Terrence R.; Riedy, Gerard

2017-01-01

Purpose To detect cerebral microhemorrhages in military service members with chronic traumatic brain injury by using susceptibility-weighted magnetic resonance (MR) imaging. The longitudinal evolution of microhemorrhages was monitored in a subset of patients by using quantitative susceptibility mapping. Materials and Methods The study was approved by the Walter Reed National Military Medical Center institutional review board and is compliant with HIPAA guidelines. All participants underwent two-dimensional conventional gradient-recalled-echo MR imaging and three-dimensional flow-compensated multi-echo gradient-recalled-echo MR imaging (processed to generate susceptibility-weighted images and quantitative susceptibility maps), and a subset of patients underwent follow-up imaging. Microhemorrhages were identified by two radiologists independently. Comparisons of microhemorrhage number, size, and magnetic susceptibility derived from quantitative susceptibility maps between baseline and follow-up imaging examinations were performed by using the paired t test. Results Among the 603 patients, cerebral microhemorrhages were identified in 43 patients, with six excluded for further analysis owing to artifacts. Seventy-seven percent (451 of 585) of the microhemorrhages on susceptibility-weighted images had a more conspicuous appearance than on gradient-recalled-echo images. Thirteen of the 37 patients underwent follow-up imaging examinations. In these patients, a smaller number of microhemorrhages were identified at follow-up imaging compared with baseline on quantitative susceptibility maps (mean ± standard deviation, 9.8 microhemorrhages ± 12.8 vs 13.7 microhemorrhages ± 16.6; P = .019). Quantitative susceptibility mapping–derived quantitative measures of microhemorrhages also decreased over time: −0.85 mm3 per day ± 1.59 for total volume (P = .039) and −0.10 parts per billion per day ± 0.14 for mean magnetic susceptibility (P = .016). Conclusion The number of microhemorrhages and quantitative susceptibility mapping–derived quantitative measures of microhemorrhages all decreased over time, suggesting that hemosiderin products undergo continued, subtle evolution in the chronic stage. PMID:26371749

Validation of a method for the quantitation of ghrelin and unacylated ghrelin by HPLC.

PubMed

Staes, Edith; Rozet, Eric; Ucakar, Bernard; Hubert, Philippe; Préat, Véronique

2010-02-05

An HPLC/UV method was first optimized for the separation and quantitation of human acylated and unacylated (or des-acyl) ghrelin from aqueous solutions. This method was validated by an original approach using accuracy profiles based on tolerance intervals for the total error measurement. The concentration range that achieved adequate accuracy extended from 1.85 to 59.30microM and 1.93 to 61.60microM for acylated and unacylated ghrelin, respectively. Then, optimal temperature, pH and buffer for sample storage were determined. Unacylated ghrelin was found to be stable in all conditions tested. At 37 degrees C acylated ghrelin was stable at pH 4 but unstable at pH 7.4, the main degradation product was unacylated ghrelin. Finally, this validated HPLC/UV method was used to evaluate the binding of acylated and unacylated ghrelin to liposomes.

Educational Training and Careers of Ph.D. Holders: An Exploratory Empirical Study. Planning Paper 27.

ERIC Educational Resources Information Center

Morris, Jeffrey

This study analyzes the occupational mobility of individuals who hold the Ph.D. degree. Drawing upon data contained in the National Register of Scientific and Technical Personnel compiled by the National Science Foundation, this paper presents the quantitative relationships between educational background, occupational mobility, and salaries. Based…

Phosphorus Imaging as a Tool for Studying the pH Metabolism in Living Insects

NASA Astrophysics Data System (ADS)

Skibbe, U.; Christeller, J. T.; Eccles, C. D.; Laing, W. A.; Callaghan, P. T.

1995-09-01

Comparative 31P NMR and 1H NMR imaging experiments at submillimeter pixel resolution were carried out, using a specially constructed solenoidal RF coil. Chemical-shift imaging is used to provide pH maps from the midgut of a Lepidopteran larvae and to demonstrate physiological dependence in the resulting images, The titration curve of pH versus chemical shift for inorganic phosphate is extended beyond the "normal" biological range to the strong alkaline limit.

The effect of respiratory induced density variations on non-TOF PET quantitation in the lung.

PubMed

Holman, Beverley F; Cuplov, Vesna; Hutton, Brian F; Groves, Ashley M; Thielemans, Kris

2016-04-21

Accurate PET quantitation requires a matched attenuation map. Obtaining matched CT attenuation maps in the thorax is difficult due to the respiratory cycle which causes both motion and density changes. Unlike with motion, little attention has been given to the effects of density changes in the lung on PET quantitation. This work aims to explore the extent of the errors caused by pulmonary density attenuation map mismatch on dynamic and static parameter estimates. Dynamic XCAT phantoms were utilised using clinically relevant (18)F-FDG and (18)F-FMISO time activity curves for all organs within the thorax to estimate the expected parameter errors. The simulations were then validated with PET data from 5 patients suffering from idiopathic pulmonary fibrosis who underwent PET/Cine-CT. The PET data were reconstructed with three gates obtained from the Cine-CT and the average Cine-CT. The lung TACs clearly displayed differences between true and measured curves with error depending on global activity distribution at the time of measurement. The density errors from using a mismatched attenuation map were found to have a considerable impact on PET quantitative accuracy. Maximum errors due to density mismatch were found to be as high as 25% in the XCAT simulation. Differences in patient derived kinetic parameter estimates and static concentration between the extreme gates were found to be as high as 31% and 14%, respectively. Overall our results show that respiratory associated density errors in the attenuation map affect quantitation throughout the lung, not just regions near boundaries. The extent of this error is dependent on the activity distribution in the thorax and hence on the tracer and time of acquisition. Consequently there may be a significant impact on estimated kinetic parameters throughout the lung.

Quantitative T2 mapping of recurrent glioblastoma under bevacizumab improves monitoring for non-enhancing tumor progression and predicts overall survival

PubMed Central

Hattingen, Elke; Jurcoane, Alina; Daneshvar, Keivan; Pilatus, Ulrich; Mittelbronn, Michel; Steinbach, Joachim P.; Bähr, Oliver

2013-01-01

Background Anti-angiogenic treatment in recurrent glioblastoma patients suppresses contrast enhancement and reduces vasogenic edema while non-enhancing tumor progression is common. Thus, the importance of T2-weighted imaging is increasing. We therefore quantified T2 relaxation times, which are the basis for the image contrast on T2-weighted images. Methods Conventional and quantitative MRI procedures were performed on 18 patients with recurrent glioblastoma before treatment with bevacizumab and every 8 weeks thereafter until further tumor progression. We segmented the tumor on conventional MRI into 3 subvolumes: enhancing tumor, non-enhancing tumor, and edema. Using coregistered quantitative maps, we followed changes in T2 relaxation time in each subvolume. Moreover, we generated differential T2 maps by a voxelwise subtraction using the first T2 map under bevacizumab as reference. Results Visually segmented areas of tumor and edema did not differ in T2 relaxation times. Non-enhancing tumor volume did not decrease after commencement of bevacizumab treatment but strikingly increased at progression. Differential T2 maps clearly showed non-enhancing tumor progression in previously normal brain. T2 relaxation times decreased under bevacizumab without re-increasing at tumor progression. A decrease of <26 ms in the enhancing tumor following exposure to bevacizumab was associated with longer overall survival. Conclusions Combining quantitative MRI and tumor segmentation improves monitoring of glioblastoma patients under bevacizumab. The degree of change in T2 relaxation time under bevacizumab may be an early response parameter predictive of overall survival. The sustained decrease in T2 relaxation times toward values of healthy tissue masks progressive tumor on conventional T2-weighted images. Therefore, quantitative T2 relaxation times may detect non-enhancing progression better than conventional T2-weighted imaging. PMID:23925453

The effect of respiratory induced density variations on non-TOF PET quantitation in the lung

NASA Astrophysics Data System (ADS)

Holman, Beverley F.; Cuplov, Vesna; Hutton, Brian F.; Groves, Ashley M.; Thielemans, Kris

2016-04-01

Accurate PET quantitation requires a matched attenuation map. Obtaining matched CT attenuation maps in the thorax is difficult due to the respiratory cycle which causes both motion and density changes. Unlike with motion, little attention has been given to the effects of density changes in the lung on PET quantitation. This work aims to explore the extent of the errors caused by pulmonary density attenuation map mismatch on dynamic and static parameter estimates. Dynamic XCAT phantoms were utilised using clinically relevant 18F-FDG and 18F-FMISO time activity curves for all organs within the thorax to estimate the expected parameter errors. The simulations were then validated with PET data from 5 patients suffering from idiopathic pulmonary fibrosis who underwent PET/Cine-CT. The PET data were reconstructed with three gates obtained from the Cine-CT and the average Cine-CT. The lung TACs clearly displayed differences between true and measured curves with error depending on global activity distribution at the time of measurement. The density errors from using a mismatched attenuation map were found to have a considerable impact on PET quantitative accuracy. Maximum errors due to density mismatch were found to be as high as 25% in the XCAT simulation. Differences in patient derived kinetic parameter estimates and static concentration between the extreme gates were found to be as high as 31% and 14%, respectively. Overall our results show that respiratory associated density errors in the attenuation map affect quantitation throughout the lung, not just regions near boundaries. The extent of this error is dependent on the activity distribution in the thorax and hence on the tracer and time of acquisition. Consequently there may be a significant impact on estimated kinetic parameters throughout the lung.

Cognitive Implications of Deep Gray Matter Iron in Multiple Sclerosis.

PubMed

Fujiwara, E; Kmech, J A; Cobzas, D; Sun, H; Seres, P; Blevins, G; Wilman, A H

2017-05-01

Deep gray matter iron accumulation is increasingly recognized in association with multiple sclerosis and can be measured in vivo with MR imaging. The cognitive implications of this pathology are not well-understood, especially vis-à-vis deep gray matter atrophy. Our aim was to investigate the relationships between cognition and deep gray matter iron in MS by using 2 MR imaging-based iron-susceptibility measures. Forty patients with multiple sclerosis (relapsing-remitting, n = 16; progressive, n = 24) and 27 healthy controls were imaged at 4.7T by using the transverse relaxation rate and quantitative susceptibility mapping. The transverse relaxation rate and quantitative susceptibility mapping values and volumes (atrophy) of the caudate, putamen, globus pallidus, and thalamus were determined by multiatlas segmentation. Cognition was assessed with the Brief Repeatable Battery of Neuropsychological Tests. Relationships between cognition and deep gray matter iron were examined by hierarchic regressions. Compared with controls, patients showed reduced memory ( P < .001) and processing speed ( P = .02) and smaller putamen ( P < .001), globus pallidus ( P = .002), and thalamic volumes ( P < .001). Quantitative susceptibility mapping values were increased in patients compared with controls in the putamen ( P = .003) and globus pallidus ( P = .003). In patients only, thalamus ( P < .001) and putamen ( P = .04) volumes were related to cognitive performance. After we controlled for volume effects, quantitative susceptibility mapping values in the globus pallidus ( P = .03; trend for transverse relaxation rate, P = .10) were still related to cognition. Quantitative susceptibility mapping was more sensitive compared with the transverse relaxation rate in detecting deep gray matter iron accumulation in the current multiple sclerosis cohort. Atrophy and iron accumulation in deep gray matter both have negative but separable relationships to cognition in multiple sclerosis. © 2017 by American Journal of Neuroradiology.

Hyperspectral Imaging for Predicting the Internal Quality of Kiwifruits Based on Variable Selection Algorithms and Chemometric Models.

PubMed

Zhu, Hongyan; Chu, Bingquan; Fan, Yangyang; Tao, Xiaoya; Yin, Wenxin; He, Yong

2017-08-10

We investigated the feasibility and potentiality of determining firmness, soluble solids content (SSC), and pH in kiwifruits using hyperspectral imaging, combined with variable selection methods and calibration models. The images were acquired by a push-broom hyperspectral reflectance imaging system covering two spectral ranges. Weighted regression coefficients (BW), successive projections algorithm (SPA) and genetic algorithm-partial least square (GAPLS) were compared and evaluated for the selection of effective wavelengths. Moreover, multiple linear regression (MLR), partial least squares regression and least squares support vector machine (LS-SVM) were developed to predict quality attributes quantitatively using effective wavelengths. The established models, particularly SPA-MLR, SPA-LS-SVM and GAPLS-LS-SVM, performed well. The SPA-MLR models for firmness (R pre  = 0.9812, RPD = 5.17) and SSC (R pre  = 0.9523, RPD = 3.26) at 380-1023 nm showed excellent performance, whereas GAPLS-LS-SVM was the optimal model at 874-1734 nm for predicting pH (R pre  = 0.9070, RPD = 2.60). Image processing algorithms were developed to transfer the predictive model in every pixel to generate prediction maps that visualize the spatial distribution of firmness and SSC. Hence, the results clearly demonstrated that hyperspectral imaging has the potential as a fast and non-invasive method to predict the quality attributes of kiwifruits.

Pore-Scale Transport of Strontium During Dynamic Water Content Changes in the Unsaturated Zone

NASA Astrophysics Data System (ADS)

Weaver, W.; Kibbey, T. C. G.; Papelis, C.

2016-12-01

Dynamic water content changes in the unsaturated zone caused by natural and manmade processes, such as evaporation, rainfall, and irrigation, have an effect on contaminant mobility. In general, in the unsaturated zone, evaporation causes an increase in contaminant concentrations, potentially leading to sorption of contaminants on aquifer materials or precipitation of crystalline or amorphous phases. On the other hand, increase of water content may result in dissolution of precipitated phases and increased mobility of contaminants. The objective of this study was to develop a quantitative model for the transport of strontium through sand under dynamic water content conditions, as a function of strontium concentration, pH, and ionic strength. Strontium was selected as a surrogate for strontium-90, a by-product of nuclear reactions. The dynamic water content was determined using an automated device for rapidly measuring the hysteretic capillary pressure—saturation relationship, followed by ambient air evaporation, and gravimetric water content measurement. Strontium concentrations were measured using inductively coupled plasma mass spectrometry (ICP-MS). Flow interruption experiments were conducted to determine whether equilibrium conditions existed for a given flowrate. Scanning electron microscopy (SEM) was used to visualize the treated quartz sand particles and the distribution of strontium on sand grains was determined using elemental maps created by energy-dispersive x-ray spectroscopy (EDX). Strontium behavior appears to be pH dependent as well as ionic strength dependent under these conditions.

TheCellMap.org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network

PubMed Central

Usaj, Matej; Tan, Yizhao; Wang, Wen; VanderSluis, Benjamin; Zou, Albert; Myers, Chad L.; Costanzo, Michael; Andrews, Brenda; Boone, Charles

2017-01-01

Providing access to quantitative genomic data is key to ensure large-scale data validation and promote new discoveries. TheCellMap.org serves as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) experiments with the budding yeast Saccharomyces cerevisiae. In particular, TheCellMap.org allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize subnetworks, using data-driven network layouts in an intuitive and interactive manner. PMID:28325812

TheCellMap.org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network.

PubMed

Usaj, Matej; Tan, Yizhao; Wang, Wen; VanderSluis, Benjamin; Zou, Albert; Myers, Chad L; Costanzo, Michael; Andrews, Brenda; Boone, Charles

2017-05-05

Providing access to quantitative genomic data is key to ensure large-scale data validation and promote new discoveries. TheCellMap.org serves as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) experiments with the budding yeast Saccharomyces cerevisiae In particular, TheCellMap.org allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize subnetworks, using data-driven network layouts in an intuitive and interactive manner. Copyright © 2017 Usaj et al.

Qualitative and quantitative mass spectrometry imaging of drugs and metabolites in tissue at therapeutic levels.

PubMed

Sun, Na; Walch, Axel

2013-08-01

Mass spectrometry imaging (MSI) is a rapidly evolving technology that yields qualitative and quantitative distribution maps of small pharmaceutical-active molecules and their metabolites in tissue sections in situ. The simplicity, high sensitivity and ability to provide comprehensive spatial distribution maps of different classes of biomolecules make MSI a valuable tool to complement histopathology for diagnostics and biomarker discovery. In this review, qualitative and quantitative MSI of drugs and metabolites in tissue at therapeutic levels are discussed and the impact of this technique in drug discovery and clinical research is highlighted.

Preliminary Mapping of the Western Corn Rootworm (Diabrotica virgifera virgifera) Genome and Quantitative Trait Locus (QTL) Interval Mapping for Growth

USDA-ARS?s Scientific Manuscript database

Preliminary investigations into the organization of the western corn rootworm (Diabrotica virgifera virgifera; WCR) genome have resulted in low to moderate density gender-specific maps constructed from progeny of a backcrossed, short-diapause WCR family. Maps were based upon variation at microsatel...

Highly resolved imaging at the soil - plant root interface: A combination of fluorescence imaging and neutron radiography

NASA Astrophysics Data System (ADS)

Rudolph, N.; Oswald, S. E.; Lehmann, E.

2012-12-01

This study represents a novel experimental set up to non-invasivley map the gradients of biogeochemical parameters at the soil -root interface of plants in situ. The patterns of oxygen, pH and the soil water content distribution were mapped in high resolution with a combination of fluorescence imaging and neutron radiography. Measuring the real-time distribution of water, pH and oxygen concentration would enable us to locate the active parts of the roots in respect to water uptake, exudation and respiration. Roots performance itself is variable as a function of age and development stage and is interrelated with local soil conditions such as water and oxygen availability or nutrients and pH buffering capacity in soil. Non-destructive imaging methods such as fluorescence and neutron imaging have provided a unique opportunity to unravel some of these complex processes. Thin glass containers (inner size 10cm x 10cm x 1.5 cm) were filled with 2 different sandy soils. Sensor foil for O2 and pH were installed on the inner-sides of the containers. We grew lupine plants in the container under controlled conditions until the root system was developed. Growing plants at different stages prior to the imaging experiment, we took neutron radiographs and fluorescence images of 10-day old and 30-day old root systems of lupine plants over a range of soil water contents, and therefore a range of root activities and oxygen changes. We observed the oxygen consumption pattern, the pH changes, and the root water uptake of lupine plants over the course of several days. We observed a higher respiration activity around the lateral roots than for the tap root. The oxygen depletion zones around the roots extended to farther distances after each rewatering of the samples. Root systems of the plants were mapped from the neutron radiograps. Close association of the roots distribution and the the location of oxygen depletion patterns provided evidence that this effect was caused by roots. The oxygen deficit pattern intensified with increasing root age. Due to the high soil water content after rewatering, the aeration from atmosphere was limited. pH dynamic was closely related to the root age. Initially, the soil pH strongly decreased around the young growing tap root. This pattern changed with time to an increased pH around the tap root but a strong acidification in the vicinity of lateral roots. After each rewatering, the pH increased which might be due to the dilution of H+ in high soil water contents. With our coupled imaging set up we were able to monitor the dynamics of oxygen, pH and water content around the roots of plant with high spatial and temporal resolutions over day and night at a wide range of soil water contents. Our experimental set up provides the opportunity to simultaneousely map the dynamics of these vital parameters in the root zone of plants.

The effect of antioxidants on quantitative changes of lysine and methionine in linoleic acid emulsions at different pH conditions.

PubMed

Hęś, Marzanna; Gliszczyńska-Świgło, Anna; Gramza-Michałowska, Anna

2017-01-01

Plants are an important source of phenolic compounds. The antioxidant capacities of green tea, thyme and rosemary extracts that contain these compounds have been reported earlier. However, there is a lack of accessible information about their activity against lipid oxidation in emulsions and inhibit the interaction of lipid oxidation products with amino acids. Therefore, the influence of green tea, thyme and rosemary extracts and BHT (butylated hydroxytoluene) on quantitative changes in lysine and methionine in linoleic acid emulsions at a pH of isoelectric point and a pH lower than the isoelectric point of amino acids was investigated. Total phenolic contents in plant extracts were determined spectrophotometrically by using Folin-Ciocalteu's reagent, and individual phenols by using HPLC. The level of oxidation of emulsion was determined using the measurement of peroxides and TBARS (thiobarbituric acid reactive substances). Methionine and lysine in the system were reacted with sodium nitroprusside and trinitrobenzenesulphonic acid respectively, and the absorbance of the complexes was measured. Extract of green tea had the highest total polyphenol content. The system containing antioxidants and amino acid protected linoleic acid more efficiently than by the addition of antioxidants only. Lysine and methionine losses in samples without the addition of antioxidants were lower in their isoelectric points than below these points. Antioxidants decrease the loss of amino acids. The protective properties of antioxidants towards methionine were higher in a pH of isoelectric point whereas towards lysine in pH below this point. Green tea, thyme and rosemary extracts exhibit antioxidant activity in linoleic acid emulsions. Moreover, they can be utilized to inhibit quantitative changes in amino acids in lipid emulsions. However, the antioxidant efficiency of these extracts seems to depend on pH conditions. Further investigations should be carried out to clarify this issue.

Imaging Performance of Quantitative Transmission Ultrasound

PubMed Central

Lenox, Mark W.; Wiskin, James; Lewis, Matthew A.; Darrouzet, Stephen; Borup, David; Hsieh, Scott

2015-01-01

Quantitative Transmission Ultrasound (QTUS) is a tomographic transmission ultrasound modality that is capable of generating 3D speed-of-sound maps of objects in the field of view. It performs this measurement by propagating a plane wave through the medium from a transmitter on one side of a water tank to a high resolution receiver on the opposite side. This information is then used via inverse scattering to compute a speed map. In addition, the presence of reflection transducers allows the creation of a high resolution, spatially compounded reflection map that is natively coregistered to the speed map. A prototype QTUS system was evaluated for measurement and geometric accuracy as well as for the ability to correctly determine speed of sound. PMID:26604918

Lunar terrain mapping and relative-roughness analysis

NASA Technical Reports Server (NTRS)

Rowan, L. C.; Mccauley, J. F.; Holm, E. A.

1971-01-01

Terrain maps of the equatorial zone were prepared at scales of 1:2,000,000 and 1:1,000,000 to classify lunar terrain with respect to roughness and to provide a basis for selecting sites for Surveyor and Apollo landings, as well as for Ranger and Lunar Orbiter photographs. Lunar terrain was described by qualitative and quantitative methods and divided into four fundamental classes: maria, terrae, craters, and linear features. Some 35 subdivisions were defined and mapped throughout the equatorial zone, and, in addition, most of the map units were illustrated by photographs. The terrain types were analyzed quantitatively to characterize and order their relative roughness characteristics. For some morphologically homogeneous mare areas, relative roughness can be extrapolated to the large scales from measurements at small scales.

Note: In vivo pH imaging system using luminescent indicator and color camera

NASA Astrophysics Data System (ADS)

Sakaue, Hirotaka; Dan, Risako; Shimizu, Megumi; Kazama, Haruko

2012-07-01

Microscopic in vivo pH imaging system is developed that can capture the luminescent- and color-imaging. The former gives a quantitative measurement of a pH distribution in vivo. The latter captures the structural information that can be overlaid to the pH distribution for correlating the structure of a specimen and its pH distribution. By using a digital color camera, a luminescent image as well as a color image is obtained. The system uses HPTS (8-hydroxypyrene-1,3,6-trisulfonate) as a luminescent pH indicator for the luminescent imaging. Filter units are mounted in the microscope, which extract two luminescent images for using the excitation-ratio method. A ratio of the two images is converted to a pH distribution through a priori pH calibration. An application of the system to epidermal cells of Lactuca Sativa L is shown.

Calibration of diatom-pH-alkalinity methodology for the interpretation of the sedimentary record in Emerald Lake Integrated watershed study. Final report, 6 May 1985-10 October 1986

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

Holmes, R.W.

1986-10-10

The present study was designed to establish quantitative relationships between lake air-equilibrated pH, alkalinity, and diatoms occurring in the surface sediments in high-elevation Sierra Nevada Lakes. These relationships provided the necessary information to develop predictive equations relating lake pH to the composition of surface-sediment diatom assemblages in 27 study lakes. Using the Hustedt diatom pH classification system, Index B of Renberg and Hellberg, and multiple linear regression analysis, two equations were developed which predict lake pH from the relative abundance of sediment diatoms occurring in each of four diatom pH groupings.

The Geographic Information System applied to study schistosomiasis in Pernambuco

PubMed Central

Barbosa, Verônica Santos; Loyo, Rodrigo Moraes; Guimarães, Ricardo José de Paula Souza e; Barbosa, Constança Simões

2017-01-01

ABSTRACT OBJECTIVE Diagnose risk environments for schistosomiasis in coastal localities of Pernambuco using geoprocessing techniques. METHODS A coproscopic and malacological survey were carried out in the Forte Orange and Serrambi areas. Environmental variables (temperature, salinity, pH, total dissolved solids and water fecal coliform dosage) were collected from Biomphalaria breeding sites or foci. The spatial analysis was performed using ArcGis 10.1 software, applying the kernel estimator, elevation map, and distance map. RESULTS In Forte Orange, 4.3% of the population had S. mansoni and were found two B. glabrata and 26 B. straminea breeding sites. The breeding sites had temperatures of 25ºC to 41ºC, pH of 6.9 to 11.1, total dissolved solids between 148 and 661, and salinity of 1,000 d. In Serrambi, 4.4% of the population had S. mansoni and were found seven B. straminea and seven B. glabrata breeding sites. Breeding sites had temperatures of 24ºC to 36ºC, pH of 7.1 to 9.8, total dissolved solids between 116 and 855, and salinity of 1,000 d. The kernel estimator shows the clusters of positive patients and foci of Biomphalaria, and the digital elevation map indicates areas of rainwater concentration. The distance map shows the proximity of the snail foci with schools and health facilities. CONCLUSIONS Geoprocessing techniques prove to be a competent tool for locating and scaling the risk areas for schistosomiasis, and can subsidize the health services control actions. PMID:29166439

Quantitative inference of population response properties across eccentricity from motion-induced maps in macaque V1

PubMed Central

Chen, Ming; Wu, Si; Lu, Haidong D.; Roe, Anna W.

2013-01-01

Interpreting population responses in the primary visual cortex (V1) remains a challenge especially with the advent of techniques measuring activations of large cortical areas simultaneously with high precision. For successful interpretation, a quantitatively precise model prediction is of great importance. In this study, we investigate how accurate a spatiotemporal filter (STF) model predicts average response profiles to coherently drifting random dot motion obtained by optical imaging of intrinsic signals in V1 of anesthetized macaques. We establish that orientation difference maps, obtained by subtracting orthogonal axis-of-motion, invert with increasing drift speeds, consistent with the motion streak effect. Consistent with perception, the speed at which the map inverts (the critical speed) depends on cortical eccentricity and systematically increases from foveal to parafoveal. We report that critical speeds and response maps to drifting motion are excellently reproduced by the STF model. Our study thus suggests that the STF model is quantitatively accurate enough to be used as a first model of choice for interpreting responses obtained with intrinsic imaging methods in V1. We show further that this good quantitative correspondence opens the possibility to infer otherwise not easily accessible population receptive field properties from responses to complex stimuli, such as drifting random dot motions. PMID:23197457

Toward uniform implementation of parametric map Digital Imaging and Communication in Medicine standard in multisite quantitative diffusion imaging studies.

PubMed

Malyarenko, Dariya; Fedorov, Andriy; Bell, Laura; Prah, Melissa; Hectors, Stefanie; Arlinghaus, Lori; Muzi, Mark; Solaiyappan, Meiyappan; Jacobs, Michael; Fung, Maggie; Shukla-Dave, Amita; McManus, Kevin; Boss, Michael; Taouli, Bachir; Yankeelov, Thomas E; Quarles, Christopher Chad; Schmainda, Kathleen; Chenevert, Thomas L; Newitt, David C

2018-01-01

This paper reports on results of a multisite collaborative project launched by the MRI subgroup of Quantitative Imaging Network to assess current capability and provide future guidelines for generating a standard parametric diffusion map Digital Imaging and Communication in Medicine (DICOM) in clinical trials that utilize quantitative diffusion-weighted imaging (DWI). Participating sites used a multivendor DWI DICOM dataset of a single phantom to generate parametric maps (PMs) of the apparent diffusion coefficient (ADC) based on two models. The results were evaluated for numerical consistency among models and true phantom ADC values, as well as for consistency of metadata with attributes required by the DICOM standards. This analysis identified missing metadata descriptive of the sources for detected numerical discrepancies among ADC models. Instead of the DICOM PM object, all sites stored ADC maps as DICOM MR objects, generally lacking designated attributes and coded terms for quantitative DWI modeling. Source-image reference, model parameters, ADC units and scale, deemed important for numerical consistency, were either missing or stored using nonstandard conventions. Guided by the identified limitations, the DICOM PM standard has been amended to include coded terms for the relevant diffusion models. Open-source software has been developed to support conversion of site-specific formats into the standard representation.

Vacuolar Localization of Endoproteinases EP(1) and EP(2) in Barley Mesophyll Cells.

PubMed

Thayer, S S; Huffaker, R C

1984-05-01

The localization of two previously characterized endoproteinases (EP(1) and EP(2)) that comprise more than 95% of the protease activity in primary Hordeum vulgare L. var Numar leaves was determined. Intact vacuoles released from washed mesophyll protoplasts by gentle osmotic shock and increase in pH, were purified by flotation through a four-step Ficoll gradient. These vacuoles contained endoproteinases that rapidly degraded purified barley ribulose-1,5-bisphosphate carboxylase (RuBPCase) substrate. Breakdown products and extent of digestion of RuBPCase were determined using 12% polyacrylamide-sodium dodecyl sulfate gels. Coomassie brilliant blue- or silver-stained gels were scanned, and the peaks were integrated to provide quantitative information. The characteristics of the vacuolar endoproteinases (e.g. sensitivity to various inhibitors and activators, and the molecular weights of the breakdown products, i.e. peptide maps) closely resembled those of purified EP(1) and partially purified EP(2). It is therefore concluded that EP(1) and EP(2) are localized in the vacuoles of mesophyll cells.

In situ chemical sensing for hydrothermal plume mapping and modeling

NASA Astrophysics Data System (ADS)

Fukuba, T.; Kusunoki, T.; Maeda, Y.; Shitashima, K.; Kyo, M.; Fujii, T.; Noguchi, T.; Sunamura, M.

2012-12-01

Detection, monitoring, and mapping of biogeochemical anomalies in seawater such as temperature, salinity, turbidity, oxidation-reduction potential, and pH are essential missions to explore undiscovered hydrothermal sites and to understand distribution and behavior of hydrothermal plumes. Utilization of reliable and useful in situ sensors has been widely accepted as a promised approach to realize a spatiotemporally resolved mapping of anomalies without water sampling operations. Due to remarkable progresses of sensor technologies and its relatives, a number of highly miniaturized and robust chemical sensors have been proposed and developed. We have been developed, evaluated, and operated a compact ISFET (Ion-Sensitive Field-Effect Transistor)-based chemical sensors for ocean environmental sensing purposes. An ISFET has advantages against conventional glass-based electrodes on its faster response, robustness, and potential on miniaturization, and thus variety of chemical sensors has been already on the market. In this study, ISFET-based standalone pH sensors with a solid-state Cl-ISE as a reference electrode were mounted on various platforms and operated to monitor the pH anomalies in deep-sea environment at the Kairei, Edmond, and surrounding hydrothermal sites in the southern Central Indian Ridge area during KH10-06 scientific cruise (Nov. 2010), supported by project TAIGA (Trans-crustal Advection and In situ biogeochemical processes of Global sub-seafloor Aquifer). Up to three pH sensors were mounted on a wire-lined CTD/RMS (Rosette Multiple Sampler), dredge sampler, a series of MTD plankton nets, and VMPS (Vertical Multiple-operating Plankton Sampler). A standalone temperature sensor was bundled and operated with the pH sensor when they were mounted on the dredge sampler, MTD plankton nets, and VMPS. An AUV equipped with the pH sensor was also operated for hydrothermal activity survey operations. As a result of Tow-Yo intersect operations of the CTD/RMS, distribution of pH anomalies were successfully visualized at the Kairei site. During the operations with the dredge sampler, MTD nets, and VMPS, the pH sensors successfully worked except for a few failures of measurements due to a problem on a sensor cable. The pH sensor mounted on the AUV "R2D4" recoded a weak low-pH anomaly during a dive at the Yokoniwa site. Representative of the pH data obtained at southern Central Indian Ride will be shown visually on the poster. The spatiotemporally resolved data can be also utilized to develop reliable numerical models to estimate fluxes of energy and matters from geologically active sites. An example of optimization of a numerical model for hydrothermal plume study using 4D pH data obtained at a back-arc hydrothermal system (the Hatoma-knoll, the Okinawa Trough, Japan) will be also presented.

Effect of modified atmospheric packaging on the shelf stability of paneer prepared by adopting hurdle technology.

PubMed

Thippeswamy, L; Venkateshaiah, B V; Patil, Sharanagouda B

2011-04-01

Paneer was prepared by application of hurdle technology (HT) and its shelf stability studied by modified atmospheric packaging (MAP). The hurdles adopted comprised of water activity (aw), pH, preservative and MAP. The aw was reduced by using NaCl (1-3%), citric acid (CA, 0.01-0.1%) and potassium sorbate (0.1%). NaCl and CA at 3 and 0.1% reduced aw from 0.994 to 0.970 and pH from 5.6 to 5.1, respectively. Sensory scores of all samples decreased (p ≤ 0.05) from control during storage at different temperatures, but these scores at the end of 20 days were still under acceptable limit of 6 and above (liked moderately). MAP was carried out by using a mixture of CO2 to N2 in the ratio of 50:50. The HT adopted paneer with MAP had extended the shelf-life from 1 to 12 days at room temperature (30 ± 1°C) and 6 to 20 days at refrigeration (7 ± 1°C) temperatures.

Development of quantitative methods for the detection of enteroviruses in sewage sludges during activation and following land disposal.

PubMed Central

Hurst, C J; Farrah, S R; Gerba, C P; Melnick, J L

1978-01-01

The development and evaluation of methods for the quantitative recovery of enteroviruses from sewage sludge are reported. Activated sewage sludge solids were collected by centrifugation, and elution of the solid-associated virus was accomplished by mechanical agitation in glycine buffer at pH 11.0. Eluted viruses were concentrated either onto an aluminum hydroxide floc or by association with a floc which formed de novo upon adjustment of the glycine eluate to pH 3.5. Viruses which remained in the liquid phase after lowering the pH of glycine eluate were concentrated by adsorption to and elution from membrane filters. The method of choice included high pH glycine elution and subsequent low pH concentration; it yielded an efficiency of recovery from activated sludge of 80% for poliovirus type 1, 68% for echovirus type 7, and 75% for coxsackievirus B3. This method was used to study the survival of naturally occurring virus in sludge at a sewage treatment plant and after subsequent land disposal of the solids after aerobic digestion. Reduction of enterovirus titers per gram (dry weight) of solids were modest during sludge activation but increased to a rate of 2 log 10/week after land disposal. PMID:29559

Development of quantitative methods for the detection of enteroviruses in sewage sludges during activation and following land disposal.

PubMed

Hurst, C J; Farrah, S R; Gerba, C P; Melnick, J L

1978-07-01

The development and evaluation of methods for the quantitative recovery of enteroviruses from sewage sludge are reported. Activated sewage sludge solids were collected by centrifugation, and elution of the solid-associated virus was accomplished by mechanical agitation in glycine buffer at pH 11.0. Eluted viruses were concentrated either onto an aluminum hydroxide floc or by association with a floc which formed de novo upon adjustment of the glycine eluate to pH 3.5. Viruses which remained in the liquid phase after lowering the pH of glycine eluate were concentrated by adsorption to and elution from membrane filters. The method of choice included high pH glycine elution and subsequent low pH concentration; it yielded an efficiency of recovery from activated sludge of 80% for poliovirus type 1, 68% for echovirus type 7, and 75% for coxsackievirus B3. This method was used to study the survival of naturally occurring virus in sludge at a sewage treatment plant and after subsequent land disposal of the solids after aerobic digestion. Reduction of enterovirus titers per gram (dry weight) of solids were modest during sludge activation but increased to a rate of 2 log 10/week after land disposal.

Relation between thallium-201/iodine 123-BMIPP subtraction and fluorine 18 deoxyglucose polar maps in patients with hypertrophic cardiomyopathy.

PubMed

Ito, Y; Hasegawa, S; Yamaguchi, H; Yoshioka, J; Uehara, T; Nishimura, T

2000-01-01

Clinical studies have shown discrepancies in the distribution of thallium-201 and iodine 123-beta-methyl-iodophenylpentadecanoic acid (BMIPP) in patients with hypertrophic cardiomyopathy (HCM). Myocardial uptake of fluorine 18 deoxyglucose (FDG) is increased in the hypertrophic area in HCM. We examined whether the distribution of a Tl-201/BMIPP subtraction polar map correlates with that of an FDG polar map. We normalized to maximum count each Tl-201 and BMIPP bull's-eye polar map of 6 volunteers and obtained a standard Tl-201/BMIPP subtraction polar map by subtracting a normalized BMIPP bull's-eye polar map from a normalized Tl-201 bull's-eye polar map. The Tl-201/BMIPP subtraction polar map was then applied to 8 patients with HCM (mean age 65+/-12 years) to evaluate the discrepancy between Tl-201 and BMIPP distribution. We compared the Tl-201/BMIPP subtraction polar map with an FDG polar map. In patients with HCM, the Tl-201/BMIPP subtraction polar map showed a focal uptake pattern in the hypertrophic area similar to that of the FDG polar map. By quantitative analysis, the severity score of the Tl-201/BMIPP subtraction polar map was significantly correlated with the percent dose uptake of the FDG polar map. These results suggest that this new quantitative method may be an alternative to FDG positron emission tomography for the routine evaluation of HCM.

Watershed scale fungal community characterization along a pH gradient in a subsurface environment co-contaminated with uranium and nitrate

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

Jasrotia, Puja; Green, Stefan; Canion, Andy

2014-01-01

The objective of this study was to characterize fungal communities in a subsurface environment co-contaminated with uranium and nitrate at the watershed scale, and to determine the potential contribution of fungi to contaminant transformation (nitrate attenuation). The abundance, distribution and diversity of fungi in subsurface groundwater samples were determined using quantitative and semi-quantitative molecular techniques, including quantitative PCR of eukaryotic SSU rRNA genes and pyrosequencing of fungal internal transcribed spacer (ITS) regions. Potential bacterial and fungal denitrification was assessed in sediment-groundwater slurries amended with antimicrobial compounds and in fungal pure cultures isolated from subsurface. Our results demonstrate that subsurface fungalmore » communities are dominated by members of the phylum Ascomycota, and a pronounced shift in fungal community composition occurs across the groundwater pH gradient at the field site, with lower diversity observed under acidic (pH < 4.5) conditions. Fungal isolates recovered from subsurface sediments were shown to reduce nitrate to nitrous oxide, including cultures of the genus Coniochaeta that were detected in abundance in pyrosequence libraries of site groundwater samples. Denitrifying fungal isolates recovered from the site were classified, and found to be distributed broadly within the phylum Ascomycota, and within a single genus within the Basidiomycota. Potential denitrification rate assays with sediment-groundwater slurries showed the potential for subsurface fungi to reduce nitrate to nitrous oxide under in situ acidic pH conditions.« less

Bevacizumab impairs oxidative energy metabolism and shows antitumoral effects in recurrent glioblastomas: a 31P/1H MRSI and quantitative magnetic resonance imaging study.

PubMed

Hattingen, Elke; Jurcoane, Alina; Bähr, Oliver; Rieger, Johannes; Magerkurth, Jörg; Anti, Sandra; Steinbach, Joachim P; Pilatus, Ulrich

2011-12-01

Bevacizumab shows unprecedented rates of response in recurrent glioblastomas (GBM), but the detailed mechanisms are still unclear. We employed in vivo magnetic resonance spectroscopic imaging (MRSI) and quantitative magnetic resonance imaging to investigate whether bevacizumab alters oxygen and energy metabolism and whether this effect has antitumoral activity in recurrent GBM. (31)P and (1)H MRSI, apparent diffusion coefficient (ADC), and high-resolution T2 and T2' mapping (indirect marker of oxygen extraction) were investigated in 16 patients with recurrent GBM at 3 Tesla before and 1.5-2 months after initiation of therapy with bevacizumab. Changes of metabolite concentrations and of the quantitative values in the tumor and normal appearing brain tissue were calculated. The Wilcoxon signed-ranks test was used to evaluate differences for tumor/edema versus control as well as changes before versus after commencement of therapy. Survival analyses were performed for significant parameters. Tumor T2', pH, ADC, and T2 decreased significantly in patients responding to bevacizumab therapy (n = 10). Patients with at least 25% T2' decrease during treatment showed longer progression-free and overall survival durations. Levels of high-energy metabolites were lower at baseline; these persisted under therapy. Glycerophosphoethanolamine as catabolic phospholipid metabolite increased in responders. The MRSI data support the hypothesis that bevacizumab induces relative tumor hypoxia (T2' decrease) and affects energy homeostasis in recurrent GBM, suggesting that bevacizumab impairs vascular function. The antiangiogenic effect of bevacizumab is predictive of better outcome and seems to induce antitumoral activity in the responding GBMs.

Development of a fluorescence endoscopic system for pH mapping of gastric tissue

NASA Astrophysics Data System (ADS)

Rochon, Philippe; Mordon, Serge; Buys, Bruno; Dhelin, Guy; Lesage, Jean C.; Chopin, Claude

2003-10-01

Measurement of gastro intestinal intramucosal pH (pHim) has been recognized as an important factor in the detection of hypoxia induced dysfonctions. However, current pH measurements techniques are limited in terms of time and spatial resolutions. A major advance in accurate pH measurement was the development of the ratiometric fluorescent indicator dye, 2',7'-bis(carboxyethyl)-5,6-carboxyfluorescein (BCECF). BCECF which pKa is in the physiological pH range is suitable for pH tissue measurements in vivo. This study aimed to develop and evaluate an endoscopic imaging system for real time pH measurements in the stomach in order to provide to ICU a new tool for gastro intestinal intramucosal pH (pHim) measurements. This fluorescence imaging technique should allow the temporal exploration of sequential events, particularly in ICU where the pHim provides a predictive information of the patient' status. The experimental evaluations of this new and innovative endoscopic fluorescence system confirms the accuracy of pH measurement using BCECF.

Bimodal MR-PET agent for quantitative pH imaging

PubMed Central

Frullano, Luca; Catana, Ciprian; Benner, Thomas; Sherry, A. Dean; Caravan, Peter

2010-01-01

Activatable or “smart” magnetic resonance contrast agents have relaxivities that depend on environmental factors such as pH or enzymatic activity, but the MR signal depends on relaxivity and agent concentration – two unknowns. A bimodal approach, incorporating a positron emitter, solves this problem. Simultaneous positron emission tomography (PET) and MR imaging with the biomodal, pH-responsive MR-PET agent GdDOTA-4AMP-F allows direct determination of both concentration (PET) and T1 (MRI), and hence pH. PMID:20191650

Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers.

PubMed

Li, Faji; Wen, Weie; He, Zhonghu; Liu, Jindong; Jin, Hui; Cao, Shuanghe; Geng, Hongwei; Yan, Jun; Zhang, Pingzhi; Wan, Yingxiu; Xia, Xianchun

2018-06-01

We identified 21 new and stable QTL, and 11 QTL clusters for yield-related traits in three bread wheat populations using the wheat 90 K SNP assay. Identification of quantitative trait loci (QTL) for yield-related traits and closely linked molecular markers is important in order to identify gene/QTL for marker-assisted selection (MAS) in wheat breeding. The objectives of the present study were to identify QTL for yield-related traits and dissect the relationships among different traits in three wheat recombinant inbred line (RIL) populations derived from crosses Doumai × Shi 4185 (D × S), Gaocheng 8901 × Zhoumai 16 (G × Z) and Linmai 2 × Zhong 892 (L × Z). Using the available high-density linkage maps previously constructed with the wheat 90 K iSelect single nucleotide polymorphism (SNP) array, 65, 46 and 53 QTL for 12 traits were identified in the three RIL populations, respectively. Among them, 34, 23 and 27 were likely to be new QTL. Eighteen common QTL were detected across two or three populations. Eleven QTL clusters harboring multiple QTL were detected in different populations, and the interval 15.5-32.3 cM around the Rht-B1 locus on chromosome 4BS harboring 20 QTL is an important region determining grain yield (GY). Thousand-kernel weight (TKW) is significantly affected by kernel width and plant height (PH), whereas flag leaf width can be used to select lines with large kernel number per spike. Eleven candidate genes were identified, including eight cloned genes for kernel, heading date (HD) and PH-related traits as well as predicted genes for TKW, spike length and HD. The closest SNP markers of stable QTL or QTL clusters can be used for MAS in wheat breeding using kompetitive allele-specific PCR or semi-thermal asymmetric reverse PCR assays for improvement of GY.

The application of multiple reaction monitoring and multi-analyte profiling to HDL proteins

PubMed Central

2014-01-01

Background HDL carries a rich protein cargo and examining HDL protein composition promises to improve our understanding of its functions. Conventional mass spectrometry methods can be lengthy and difficult to extend to large populations. In addition, without prior enrichment of the sample, the ability of these methods to detect low abundance proteins is limited. Our objective was to develop a high-throughput approach to examine HDL protein composition applicable to diabetes and cardiovascular disease (CVD). Methods We optimized two multiplexed assays to examine HDL proteins using a quantitative immunoassay (Multi-Analyte Profiling- MAP) and mass spectrometric-based quantitative proteomics (Multiple Reaction Monitoring-MRM). We screened HDL proteins using human xMAP (90 protein panel) and MRM (56 protein panel). We extended the application of these two methods to HDL isolated from a group of participants with diabetes and prior cardiovascular events and a group of non-diabetic controls. Results We were able to quantitate 69 HDL proteins using MAP and 32 proteins using MRM. For several common proteins, the use of MRM and MAP was highly correlated (p < 0.01). Using MAP, several low abundance proteins implicated in atherosclerosis and inflammation were found on HDL. On the other hand, MRM allowed the examination of several HDL proteins not available by MAP. Conclusions MAP and MRM offer a sensitive and high-throughput approach to examine changes in HDL proteins in diabetes and CVD. This approach can be used to measure the presented HDL proteins in large clinical studies. PMID:24397693

Rapid detection methods for viable Mycobacterium avium subspecies paratuberculosis in milk and cheese.

PubMed

Botsaris, George; Slana, Iva; Liapi, Maria; Dodd, Christine; Economides, Constantinos; Rees, Catherine; Pavlik, Ivo

2010-07-31

Mycobacterium avium subsp. paratuberculosis (MAP) may have a role in the development of Crohn's disease in humans via the consumption of contaminated milk and milk products. Detection of MAP from milk and dairy products has been reported from countries on the European continent, Argentina, the UK and Australia. In this study three different methods (quantitative real time PCR, combined phage IS900 PCR and conventional cultivation) were used to detect the presence of MAP in bulk tank milk (BTM) and cheese originating from sheep, goat and mixed milks from farms and products in Cyprus. During the first survey the presence of MAP was detected in 63 (28.6%) of cows' BTM samples by quantitative real time PCR. A second survey of BTM used a new combined phage IS900 PCR assay, and in this case MAP was detected in 50 (22.2%) samples showing a good level of agreement by both methods. None of the herds tested were known to be affected by Johne's disease and the presence of viable MAP was confirmed by conventional culture in only two cases of cows BTM. This suggests that either rapid method used is more sensitive than the conventional culture when testing raw milk samples for MAP. The two isolates recovered from BTM were identified by IS1311 PCR REA as cattle and sheep strains, respectively. In contrast when cheese samples were tested, MAP DNA was detected by quantitative real time PCR in seven (25.0%) samples (n=28). However no viable MAP was detected when either the combined phage IS900 PCR or conventional culture methods were used. Copyright 2010 Elsevier B.V. All rights reserved.

A tutorial in displaying mass spectrometry-based proteomic data using heat maps.

PubMed

Key, Melissa

2012-01-01

Data visualization plays a critical role in interpreting experimental results of proteomic experiments. Heat maps are particularly useful for this task, as they allow us to find quantitative patterns across proteins and biological samples simultaneously. The quality of a heat map can be vastly improved by understanding the options available to display and organize the data in the heat map. This tutorial illustrates how to optimize heat maps for proteomics data by incorporating known characteristics of the data into the image. First, the concepts used to guide the creating of heat maps are demonstrated. Then, these concepts are applied to two types of analysis: visualizing spectral features across biological samples, and presenting the results of tests of statistical significance. For all examples we provide details of computer code in the open-source statistical programming language R, which can be used for biologists and clinicians with little statistical background. Heat maps are a useful tool for presenting quantitative proteomic data organized in a matrix format. Understanding and optimizing the parameters used to create the heat map can vastly improve both the appearance and the interoperation of heat map data.

Five new species of the genus Philydrodes Bernhauer, 1929 from China (Coleoptera: Staphylinidae: Omaliinae: Anthophagini).

PubMed

Shavrin, Alexey V

2017-02-09

Five new species of the subgenus Minyphilydrodes of the genus Philydrodes Bernhauer, 1929 (Coleoptera: Staphylinidae: Omaliinae: Anthophagini) from China are described and illustrated: Ph. tridentatus sp.n. (Hubei, Gansu, Shaanxi and Sichuan), Ph. tibetanus sp.n. (Yunnan), Ph. reticulatus sp.n. (Shaanxi), Ph. wrasei sp.n. (Sichuan) and Ph. michaeli sp.n. (Sichuan). The morphological features of Philydrodes, differences between Japanese and Chinese species, the relations of the genus with other taxa of the tribe Anthophagini Thomson, 1859 are briefly discussed. A key to the species of the genus from China and a distribution map are provided. The genus Philydrodes is recorded from continental Asia and China for the first time.

Genetic and Physiological Characterization of Two Clusters of Quantitative Trait Loci Associated With Seed Dormancy and Plant Height in Rice

PubMed Central

Ye, Heng; Beighley, Donn H.; Feng, Jiuhuan; Gu, Xing-You

2013-01-01

Seed dormancy and plant height have been well-studied in plant genetics, but their relatedness and shared regulatory mechanisms in natural variants remain unclear. The introgression of chromosomal segments from weedy into cultivated rice (Oryza sativa) prompted the detection of two clusters (qSD1-2/qPH1 and qSD7-2/qPH7) of quantitative trait loci both associated with seed dormancy and plant height. Together, these two clusters accounted for >96% of the variances for plant height and ~71% of the variances for germination rate in an isogenic background across two environments. On the initial introgression segments, qSD1-2/qPH1 was dissected genetically from OsVp1 for vivipary and qSD7-2/qPH7 separated from Sdr4 for seed dormancy. The narrowed qSD1-2/qPH1 region encompasses the semidwarf1 (sd1) locus for gibberellin (GA) biosynthesis. The qSD1-2/qPH1 allele from the cultivar reduced germination and stem elongation and the mutant effects were recovered by exogenous GA, suggesting that sd1 is a candidate gene of the cluster. In contrast, the effect-reducing allele at qSD7-2/qPH7 was derived from the weedy line; this allele was GA-insensitive and blocked GA responses of qSD1-2/qPH1, including the transcription of a GA-inducible α-amylase gene in imbibed endosperm, suggesting that qSD7-2/qPH7 may work downstream from qSD1-2/qPH1 in GA signaling. Thus, this research established the seed dormancy-plant height association that is likely mediated by GA biosynthesis and signaling pathways in natural populations. The detected association contributed to weed mimicry for the plant stature in the agro-ecosystem dominated by semidwarf cultivars and revealed the potential benefit of semidwarf genes in resistance to preharvest sprouting. PMID:23390608

Genetic and physiological characterization of two clusters of quantitative trait Loci associated with seed dormancy and plant height in rice.

PubMed

Ye, Heng; Beighley, Donn H; Feng, Jiuhuan; Gu, Xing-You

2013-02-01

Seed dormancy and plant height have been well-studied in plant genetics, but their relatedness and shared regulatory mechanisms in natural variants remain unclear. The introgression of chromosomal segments from weedy into cultivated rice (Oryza sativa) prompted the detection of two clusters (qSD1-2/qPH1 and qSD7-2/qPH7) of quantitative trait loci both associated with seed dormancy and plant height. Together, these two clusters accounted for >96% of the variances for plant height and ~71% of the variances for germination rate in an isogenic background across two environments. On the initial introgression segments, qSD1-2/qPH1 was dissected genetically from OsVp1 for vivipary and qSD7-2/qPH7 separated from Sdr4 for seed dormancy. The narrowed qSD1-2/qPH1 region encompasses the semidwarf1 (sd1) locus for gibberellin (GA) biosynthesis. The qSD1-2/qPH1 allele from the cultivar reduced germination and stem elongation and the mutant effects were recovered by exogenous GA, suggesting that sd1 is a candidate gene of the cluster. In contrast, the effect-reducing allele at qSD7-2/qPH7 was derived from the weedy line; this allele was GA-insensitive and blocked GA responses of qSD1-2/qPH1, including the transcription of a GA-inducible α-amylase gene in imbibed endosperm, suggesting that qSD7-2/qPH7 may work downstream from qSD1-2/qPH1 in GA signaling. Thus, this research established the seed dormancy-plant height association that is likely mediated by GA biosynthesis and signaling pathways in natural populations. The detected association contributed to weed mimicry for the plant stature in the agro-ecosystem dominated by semidwarf cultivars and revealed the potential benefit of semidwarf genes in resistance to preharvest sprouting.

Quantitative Trait Loci Mapping in Brassica rapa Revealed the Structural and Functional Conservation of Genetic Loci Governing Morphological and Yield Component Traits in the A, B, and C Subgenomes of Brassica Species

PubMed Central

Li, Xiaonan; Ramchiary, Nirala; Dhandapani, Vignesh; Choi, Su Ryun; Hur, Yoonkang; Nou, Ill-Sup; Yoon, Moo Kyoung; Lim, Yong Pyo

2013-01-01

Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species. PMID:23223793

Mapping Mixed Methods Research: Methods, Measures, and Meaning

ERIC Educational Resources Information Center

Wheeldon, J.

2010-01-01

This article explores how concept maps and mind maps can be used as data collection tools in mixed methods research to combine the clarity of quantitative counts with the nuance of qualitative reflections. Based on more traditional mixed methods approaches, this article details how the use of pre/post concept maps can be used to design qualitative…

Comparison and quantitative verification of mapping algorithms for whole genome bisulfite sequencing

USDA-ARS?s Scientific Manuscript database

Coupling bisulfite conversion with next-generation sequencing (Bisulfite-seq) enables genome-wide measurement of DNA methylation, but poses unique challenges for mapping. However, despite a proliferation of Bisulfite-seq mapping tools, no systematic comparison of their genomic coverage and quantitat...

33 CFR 332.3 - General compensatory mitigation requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... wetland maps; soil surveys; U.S. Geological Survey topographic and hydrologic maps; aerial photographs... appropriate quantitative assessment tools, where available; (iii) Preservation is determined by the district...

33 CFR 332.3 - General compensatory mitigation requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... wetland maps; soil surveys; U.S. Geological Survey topographic and hydrologic maps; aerial photographs... appropriate quantitative assessment tools, where available; (iii) Preservation is determined by the district...

33 CFR 332.3 - General compensatory mitigation requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... wetland maps; soil surveys; U.S. Geological Survey topographic and hydrologic maps; aerial photographs... appropriate quantitative assessment tools, where available; (iii) Preservation is determined by the district...

33 CFR 332.3 - General compensatory mitigation requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... wetland maps; soil surveys; U.S. Geological Survey topographic and hydrologic maps; aerial photographs... appropriate quantitative assessment tools, where available; (iii) Preservation is determined by the district...

33 CFR 332.3 - General compensatory mitigation requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... wetland maps; soil surveys; U.S. Geological Survey topographic and hydrologic maps; aerial photographs... appropriate quantitative assessment tools, where available; (iii) Preservation is determined by the district...

Analogous on-axis interference topographic phase microscopy (AOITPM).

PubMed

Xiu, P; Liu, Q; Zhou, X; Xu, Y; Kuang, C; Liu, X

2018-05-01

The refractive index (RI) of a sample as an endogenous contrast agent plays an important role in transparent live cell imaging. In tomographic phase microscopy (TPM), 3D quantitative RI maps can be reconstructed based on the measured projections of the RI in multiple directions. The resolution of the RI maps not only depends on the numerical aperture of the employed objective lens, but also is determined by the accuracy of the quantitative phase of the sample measured at multiple scanning illumination angles. This paper reports an analogous on-axis interference TPM, where the interference angle between the sample and reference beams is kept constant for projections in multiple directions to improve the accuracy of the phase maps and the resolution of RI tomograms. The system has been validated with both silica beads and red blood cells. Compared with conventional TPM, the proposed system acquires quantitative RI maps with higher resolution (420 nm @λ = 633 nm) and signal-to-noise ratio that can be beneficial for live cell imaging in biomedical applications. © 2018 The Authors Journal of Microscopy © 2018 Royal Microscopical Society.

Iopamidol as a responsive MRI-chemical exchange saturation transfer contrast agent for pH mapping of kidneys: In vivo studies in mice at 7 T.

PubMed

Longo, Dario Livio; Dastrù, Walter; Digilio, Giuseppe; Keupp, Jochen; Langereis, Sander; Lanzardo, Stefania; Prestigio, Simone; Steinbach, Oliver; Terreno, Enzo; Uggeri, Fulvio; Aime, Silvio

2011-01-01

Iopamidol (Isovue®-Bracco Diagnostic Inc.) is a clinically approved X-Ray contrast agent used in the last 30 years for a wide variety of diagnostic applications with a very good clinical acceptance. Iopamidol contains two types of amide functionalities that can be exploited for the generation of chemical exchange saturation transfer effect. The exchange rate of the two amide proton pools is markedly pH-dependent. Thus, a ratiometric method for pH assessment has been set-up based on the comparison of the saturation transfer effects induced by selective irradiation of the two resonances. This ratiometric approach allows to rule out the concentration effect of the contrast agent and provides accurate pH measurements in the 5.5-7.4 range. Upon injection of Iopamidol into healthy mice, it has been possible to acquire pH maps of kidney regions. Furthermore, it has been also shown that the proposed method is able to report about pH-changes induced in control mice fed with acidified or basified water for a period of a week before image acquisition. © 2010 Wiley-Liss, Inc.

A Quantitative Chemotherapy Genetic Interaction Map Reveals Factors Associated with PARP Inhibitor Resistance. | Office of Cancer Genomics

Cancer.gov

Chemotherapy is used to treat most cancer patients, yet our understanding of factors that dictate response and resistance to such drugs remains limited. We report the generation of a quantitative chemical-genetic interaction map in human mammary epithelial cells charting the impact of the knockdown of 625 genes related to cancer and DNA repair on sensitivity to 29 drugs, covering all classes of chemotherapy.

A quantitative chemotherapy genetic interaction map reveals new factors associated with PARP inhibitor resistance | Office of Cancer Genomics

Cancer.gov

Nearly every cancer patient is treated with chemotherapy yet our understanding of factors that dictate response and resistance to such agents remains limited. We report the generation of a quantitative chemical-genetic interaction map in human mammary epithelial cells that charts the impact of knockdown of 625 cancer and DNA repair related genes on sensitivity to 29 drugs, covering all classes of cancer chemotherapeutics.

Genetic and Quantitative Trait Locus Analysis for Bio-Oil Compounds after Fast Pyrolysis in Maize Cobs.

PubMed

Jeffrey, Brandon; Kuzhiyil, Najeeb; de Leon, Natalia; Lübberstedt, Thomas

2016-01-01

Fast pyrolysis has been identified as one of the biorenewable conversion platforms that could be a part of an alternative energy future, but it has not yet received the same attention as cellulosic ethanol in the analysis of genetic inheritance within potential feedstocks such as maize. Ten bio-oil compounds were measured via pyrolysis/gas chromatography-mass spectrometry (Py/GC-MS) in maize cobs. 184 recombinant inbred lines (RILs) of the intermated B73 x Mo17 (IBM) Syn4 population were analyzed in two environments, using 1339 markers, for quantitative trait locus (QTL) mapping. QTL mapping was performed using composite interval mapping with significance thresholds established by 1000 permutations at α = 0.05. 50 QTL were found in total across those ten traits with R2 values ranging from 1.7 to 5.8%, indicating a complex quantitative inheritance of these traits.

Application of remote sensing to monitoring and studying dispersion in ocean dumping

NASA Technical Reports Server (NTRS)

Johnson, R. W.; Ohlhorst, C. W.

1981-01-01

Remotely sensed wide area synoptic data provides information on ocean dumping that is not readily available by other means. A qualitative approach has been used to map features, such as river plumes. Results of quantitative analyses have been used to develop maps showing quantitative distributions of one or more water quality parameters, such as suspended solids or chlorophyll a. Joint NASA/NOAA experiments have been conducted at designated dump areas in the U.S. coastal zones to determine the applicability of aircraft remote sensing systems to map plumes resulting from ocean dumping of sewage sludge and industrial wastes. A second objective is related to the evaluation of previously developed quantitative analysis techniques for studying dispersion of materials in these plumes. It was found that plumes resulting from dumping of four waste materials have distinctive spectral characteristics. The development of a technology for use in a routine monitoring system, based on remote sensing techniques, is discussed.

Quantitative water content mapping at clinically relevant field strengths: a comparative study at 1.5 T and 3 T.

PubMed

Abbas, Zaheer; Gras, Vincent; Möllenhoff, Klaus; Oros-Peusquens, Ana-Maria; Shah, Nadim Joni

2015-02-01

Quantitative water content mapping in vivo using MRI is a very valuable technique to detect, monitor and understand diseases of the brain. At 1.5 T, this technology has already been successfully used, but it has only recently been applied at 3T because of significantly increased RF field inhomogeneity at the higher field strength. To validate the technology at 3T, we estimate and compare in vivo quantitative water content maps at 1.5 T and 3T obtained with a protocol proposed recently for 3T MRI. The proposed MRI protocol was applied on twenty healthy subjects at 1.5 T and 3T; the same post-processing algorithms were used to estimate the water content maps. The 1.5 T and 3T maps were subsequently aligned and compared on a voxel-by-voxel basis. Statistical analysis was performed to detect possible differences between the estimated 1.5 T and 3T water maps. Our analysis indicates that the water content values obtained at 1.5 T and 3T did not show significant systematic differences. On average the difference did not exceed the standard deviation of the water content at 1.5 T. Furthermore, the contrast-to-noise ratio (CNR) of the estimated water content map was increased at 3T by a factor of at least 1.5. Vulnerability to RF inhomogeneity increases dramatically with the increasing static magnetic field strength. However, using advanced corrections for the sensitivity profile of the MR coils, it is possible to preserve quantitative accuracy while benefiting from the increased CNR at the higher field strength. Indeed, there was no significant difference in the water content values obtained in the brain at 1.5 T and 3T. Copyright © 2014 Elsevier Inc. All rights reserved.

The enhanced cyan fluorescent protein: a sensitive pH sensor for fluorescence lifetime imaging.

PubMed

Poëa-Guyon, Sandrine; Pasquier, Hélène; Mérola, Fabienne; Morel, Nicolas; Erard, Marie

2013-05-01

pH is an important parameter that affects many functions of live cells, from protein structure or function to several crucial steps of their metabolism. Genetically encoded pH sensors based on pH-sensitive fluorescent proteins have been developed and used to monitor the pH of intracellular compartments. The quantitative analysis of pH variations can be performed either by ratiometric or fluorescence lifetime detection. However, most available genetically encoded pH sensors are based on green and yellow fluorescent proteins and are not compatible with multicolor approaches. Taking advantage of the strong pH sensitivity of enhanced cyan fluorescent protein (ECFP), we demonstrate here its suitability as a sensitive pH sensor using fluorescence lifetime imaging. The intracellular ECFP lifetime undergoes large changes (32 %) in the pH 5 to pH 7 range, which allows accurate pH measurements to better than 0.2 pH units. By fusion of ECFP with the granular chromogranin A, we successfully measured the pH in secretory granules of PC12 cells, and we performed a kinetic analysis of intragranular pH variations in living cells exposed to ammonium chloride.

Usability Evaluation of Public Web Mapping Sites

NASA Astrophysics Data System (ADS)

Wang, C.

2014-04-01

Web mapping sites are interactive maps that are accessed via Webpages. With the rapid development of Internet and Geographic Information System (GIS) field, public web mapping sites are not foreign to people. Nowadays, people use these web mapping sites for various reasons, in that increasing maps and related map services of web mapping sites are freely available for end users. Thus, increased users of web mapping sites led to more usability studies. Usability Engineering (UE), for instance, is an approach for analyzing and improving the usability of websites through examining and evaluating an interface. In this research, UE method was employed to explore usability problems of four public web mapping sites, analyze the problems quantitatively and provide guidelines for future design based on the test results. Firstly, the development progress for usability studies were described, and simultaneously several usability evaluation methods such as Usability Engineering (UE), User-Centered Design (UCD) and Human-Computer Interaction (HCI) were generally introduced. Then the method and procedure of experiments for the usability test were presented in detail. In this usability evaluation experiment, four public web mapping sites (Google Maps, Bing maps, Mapquest, Yahoo Maps) were chosen as the testing websites. And 42 people, who having different GIS skills (test users or experts), gender (male or female), age and nationality, participated in this test to complete the several test tasks in different teams. The test comprised three parts: a pretest background information questionnaire, several test tasks for quantitative statistics and progress analysis, and a posttest questionnaire. The pretest and posttest questionnaires focused on gaining the verbal explanation of their actions qualitatively. And the design for test tasks targeted at gathering quantitative data for the errors and problems of the websites. Then, the results mainly from the test part were analyzed. The success rate from different public web mapping sites was calculated and compared, and displayed by the means of diagram. And the answers from questionnaires were also classified and organized in this part. Moreover, based on the analysis, this paper expands the discussion about the layout, map visualization, map tools, search logic and etc. Finally, this paper closed with some valuable guidelines and suggestions for the design of public web mapping sites. Also, limitations for this research stated in the end.

A new global interior ocean mapped climatology: the 1° × 1° GLODAP version 2

NASA Astrophysics Data System (ADS)

Lauvset, Siv K.; Key, Robert M.; Olsen, Are; van Heuven, Steven; Velo, Anton; Lin, Xiaohua; Schirnick, Carsten; Kozyr, Alex; Tanhua, Toste; Hoppema, Mario; Jutterström, Sara; Steinfeldt, Reiner; Jeansson, Emil; Ishii, Masao; Perez, Fiz F.; Suzuki, Toru; Watelet, Sylvain

2016-08-01

We present a mapped climatology (GLODAPv2.2016b) of ocean biogeochemical variables based on the new GLODAP version 2 data product (Olsen et al., 2016; Key et al., 2015), which covers all ocean basins over the years 1972 to 2013. The quality-controlled and internally consistent GLODAPv2 was used to create global 1° × 1° mapped climatologies of salinity, temperature, oxygen, nitrate, phosphate, silicate, total dissolved inorganic carbon (TCO2), total alkalinity (TAlk), pH, and CaCO3 saturation states using the Data-Interpolating Variational Analysis (DIVA) mapping method. Improving on maps based on an earlier but similar dataset, GLODAPv1.1, this climatology also covers the Arctic Ocean. Climatologies were created for 33 standard depth surfaces. The conceivably confounding temporal trends in TCO2 and pH due to anthropogenic influence were removed prior to mapping by normalizing these data to the year 2002 using first-order calculations of anthropogenic carbon accumulation rates. We additionally provide maps of accumulated anthropogenic carbon in the year 2002 and of preindustrial TCO2. For all parameters, all data from the full 1972-2013 period were used, including data that did not receive full secondary quality control. The GLODAPv2.2016b global 1° × 1° mapped climatologies, including error fields and ancillary information, are available at the GLODAPv2 web page at the Carbon Dioxide Information Analysis Center (CDIAC; doi:10.3334/CDIAC/OTG.NDP093_GLODAPv2).

A Semiparametric Approach for Composite Functional Mapping of Dynamic Quantitative Traits

PubMed Central

Yang, Runqing; Gao, Huijiang; Wang, Xin; Zhang, Ji; Zeng, Zhao-Bang; Wu, Rongling

2007-01-01

Functional mapping has emerged as a powerful tool for mapping quantitative trait loci (QTL) that control developmental patterns of complex dynamic traits. Original functional mapping has been constructed within the context of simple interval mapping, without consideration of separate multiple linked QTL for a dynamic trait. In this article, we present a statistical framework for mapping QTL that affect dynamic traits by capitalizing on the strengths of functional mapping and composite interval mapping. Within this so-called composite functional-mapping framework, functional mapping models the time-dependent genetic effects of a QTL tested within a marker interval using a biologically meaningful parametric function, whereas composite interval mapping models the time-dependent genetic effects of the markers outside the test interval to control the genome background using a flexible nonparametric approach based on Legendre polynomials. Such a semiparametric framework was formulated by a maximum-likelihood model and implemented with the EM algorithm, allowing for the estimation and the test of the mathematical parameters that define the QTL effects and the regression coefficients of the Legendre polynomials that describe the marker effects. Simulation studies were performed to investigate the statistical behavior of composite functional mapping and compare its advantage in separating multiple linked QTL as compared to functional mapping. We used the new mapping approach to analyze a genetic mapping example in rice, leading to the identification of multiple QTL, some of which are linked on the same chromosome, that control the developmental trajectory of leaf age. PMID:17947431

Fine Substituent Effects in Sandwich Complexes: A Threshold Ionization Study of Monosubstituted Chromium Bisarene Compounds.

PubMed

Ketkov, Sergey Yu; Markin, Gennady V; Tzeng, Sheng Y; Tzeng, Wen B

2016-03-24

Mass-analyzed threshold ionization spectra of jet-cooled [(η(6) -PhMe)(η(6) -PhH)Cr] and [(η(6) -Ph2 )(η(6) -PhH)Cr] reveal with unprecedented accuracy the effects of methyl and phenyl groups on the electronic structure of bis(η(6) -benzene)chromium. These "pure" substituent effects allow quantitative experimental determination of the ionization energy changes caused by the mutual substituent influence in bisarene systems. Two types of such influence have been revealed for the first time in bis(η(6) -toluene)chromium. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Novel regulatory loci controlling oxygen- and pH-regulated gene expression in Salmonella typhimurium.

PubMed Central

Aliabadi, Z; Park, Y K; Slonczewski, J L; Foster, J W

1988-01-01

Three new loci were discovered, each of which participates in the regulation of anaerobic gene expression. The regulatory gene earA negatively regulates the expression of the anaerobiosis-inducible gene aniG as well as that of at least three other genes, as determined by two-dimensional polyacrylamide gel electrophoresis. The earA locus maps at 86 min. The expression of aniG was also shown to be controlled by changes in external pH under aerobic and anaerobic conditions. Maximal expression was observed under anaerobic conditions at an external pH of 6.0. Significant transcriptional activity was also observed under aerobic conditions at pH 6.0. This was in contrast to hyd, whose expression was dependent upon anaerobiosis and varied with external pH. The pH dependence disappeared under fully aerobic conditions. Mutations in earA had no effect upon hyd expression. The two other regulators identified were oxrF, which controls aniH, and oxrG, which, in concert with oxrA and oxrB, controls aniC and aniI. The oxrG locus was mapped to 88 min and appears to code for a positive regulator. Various oxr mutants were subjected to two-dimensional polyacrylamide electrophoretic analysis of anaerobiosis-inducible proteins. Several pathways of anaerobic control were observed by means of these techniques. Images PMID:3276666

Intracellular pH of Mycobacterium avium subsp. paratuberculosis following exposure to antimicrobial compounds monitored at the single cell level.

PubMed

Gaggìa, Francesca; Nielsen, Dennis Sandris; Biavati, Bruno; Siegumfeldt, Henrik

2010-07-31

Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne's disease; moreover, it seems to be implicated in the development of Crohn's disease in humans. In the present study, fluorescence ratio imaging microscopy (FRIM) was used to assess changes in intracellular pH (pH(i)) of one strain of MAP after exposure to nisin and neutralized cell-free supernatants (NCSs) from five bacteriocin-producing lactic acid bacteria (LAB) with known probiotic properties. The evaluation of pH(i) by FRIM provides information about the physiological state of bacterial cells, bypassing the long and problematic incubations needed for methods relying upon growth of MAP such as determination of colony forming units. The FRIM results showed that both nisin and the cell-free supernatant from Lactobacillus plantarum PCA 236 affected the pH(i) of MAP within a few hours. However, monitoring the population for 24h revealed the presence of a subpopulation of cells probably resistant to the antimicrobial compounds tested. Use of nisin and bacteriocin-producing LAB strains could lead to new intervention strategies for the control of MAP based on in vivo application of probiotic cultures as feed additives at farm level. Copyright 2010 Elsevier B.V. All rights reserved.

Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population

PubMed Central

Serin, Elise A. R.; Snoek, L. B.; Nijveen, Harm; Willems, Leo A. J.; Jiménez-Gómez, Jose M.; Hilhorst, Henk W. M.; Ligterink, Wilco

2017-01-01

High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 single-nucleotide polymorphisms (SNPs) covering the whole genome. Based on a 100-kbp window SNP binning method, 1059 bin-markers were identified, physically anchored on the genome. The total length of the RNA-seq genetic map spans 471.70 centimorgans (cM) with an average marker distance of 0.45 cM and a maximum marker distance of 4.81 cM. This high resolution genotyping revealed new recombination breakpoints in the population. To highlight the advantages of such high-density map, we compared it to two publicly available genetic maps for the same population, comprising 69 PCR-based markers and 497 gene expression markers derived from microarray data, respectively. In this study, we show that SNP markers can effectively be derived from RNA-seq data. The new RNA-seq map closes many existing gaps in marker coverage, saturating the previously available genetic maps. Quantitative trait locus (QTL) analysis for published phenotypes using the available genetic maps showed increased QTL mapping resolution and reduced QTL confidence interval using the RNA-seq map. The new high-density map is a valuable resource that facilitates the identification of candidate genes and map-based cloning approaches. PMID:29259624

Can You Earn a Ph.D. in Economics in Five Years?

ERIC Educational Resources Information Center

Stock, Wendy A.; Finegan, T. Aldrich; Siegfried, John J.

2009-01-01

We investigate graduate school outcomes for students who entered economics Ph.D. programs in Fall 2002. Students in Top-15 ranked programs and those with higher verbal and quantitative GRE scores are less likely to have dropped out, but no more likely to have graduated. Those with undergraduate degrees from Top-60 U.S. liberal arts colleges and…

Quantitative Chemical-Genetic Interaction Map Connects Gene Alterations to Drug Responses | Office of Cancer Genomics

Cancer.gov

In a recent Cancer Discovery report, CTD2 researchers at the University of California in San Francisco developed a new quantitative chemical-genetic interaction mapping approach to evaluate drug sensitivity or resistance in isogenic cell lines. Performing a high-throughput screen with isogenic cell lines allowed the researchers to explore the impact of a panel of emerging and established drugs on cells overexpressing a single cancer-associated gene in isolation.

An in vivo quantitative Raman-pH sensor of arterial blood based on laser trapping of erythrocytes.

PubMed

Lin, Manman; Xu, Bin; Yao, Huilu; Shen, Aiguo; Hu, Jiming

2016-05-10

We report on a continuous and non-invasive approach in vivo to monitor arterial blood pH based on the laser trapping and Raman detection of single live erythrocytes. A home-built confocal laser tweezers Raman system (LTRS) is applied to trace the live erythrocytes at different pH values of the extracellular environment to record their corresponding Raman changes in vitro and in vivo. The analysis results in vitro show that when the extracellular environment pH changes from 6.5 to 9.0, the Raman intensity ratio (R1603, 1616 = I1603/I1616) of single erythrocytes decrease regularly; what is more, there is a good linear relationship between these two variables, and the linearity is 0.985, which is also verified successfully via in vivo Raman measurements. These results demonstrate that the Raman signal of single live erythrocytes is possible as a marker of the extracellular pH value. This in vivo and quantitative Raman-pH sensor of arterial blood will be an important candidate for monitoring the acid-base status during the treatment of ill patients and in some major surgeries because of its continuous and non-invasive characters.

Quantitative color measurement of pH indicator paper using trichromatic LEDs and TCS230 color sensor

NASA Astrophysics Data System (ADS)

Ghorude, T. N.; Chaudhari, A. L.; Shaligram, A. D.

2008-11-01

Quantitative analysis of pH indicator paper color is needed in the various fields. An indigenously developed Tristimulus colorimeter is used in this work for pH Indicator paper color measurement. The colorimeter uses Trichromatic RGB LEDs and a programmable color light to frequency converter (TCS230), combining configurable silicon photodiodes and a current to frequency converter on a single monolithic CMOS integrated circuit. The output is a square wave (50% duty cycle) with frequency directly proportional to light intensity. Digital input and digital output allow directly to a microcontroller. The light to frequency converter reads an 8*8 array of photodiodes. Sixteen photodiodes have red filters, 16 photodiodes have green filters, 16 photodiodes have blue filters, and 16 photodiodes are clear with no filters. All 16 photodiodes of the same colors are connected in parallel and type of photodiode the device uses during operation is pin selectable. Solutions having different standard pH were prepared and indicator paper was dipped in solution, it shows change in color. Using the developed RGB colorimeter chromaticity coordinates were measured and compared with the chromaticity coordinates measured using Ocean Optics HR-4000 high resolution spectrophotometer.

A FRET-Based Ratiometric Chemosensor for in Vitro Cellular Fluorescence Analyses of pH

PubMed Central

Zhou, Xianfeng; Su, Fengyu; Lu, Hongguang; Senechal-Willis, Patti; Tian, Yanqing; Johnson, Roger H.; Meldrum, Deirdre R.

2011-01-01

Ratiometric fluorescence sensing is an important technique for precise and quantitative analysis of biological events occurring under complex conditions by simultaneously recording fluorescence intensities at two wavelengths and calculating their ratios. Herein, we design a ratiometric chemosensor for pH that is based on photo-induced electron transfer (PET) and binding-induced modulation of fluorescence resonance energy transfer (FRET) mechanisms. This ratiometric chemosensor was constructed by introduction of a pH-insensitive coumarin fluorophore as a FRET donor into a pH-sensitive amino-naphthalimide derivative as the FRET acceptor. The sensor exhibited clear dual-mission signal changes in blue and green spectral windows upon pH changes. The pH sensor was applied for not only measuring cellular pH, but also for visualizing stimulus-responsive changes of intracellular pH values. PMID:21982292

Assessment of water resources potential of Ceará state (Brazil)

NASA Astrophysics Data System (ADS)

Araujo, Angelo; Pereira, Diamantino; Pereira, Paulo

2016-04-01

A methodological approach and results on water resources assessment in large areas are described with the case study of Ceará State (148,016 km2, northeast Brazil), where the scarceness of water resources is one of the main challenges in territorial planning and development. This work deals with the quantification and the mapping of water resources potential, being part of methodological approaches applied to the quantification of hydric diversity and geodiversity. Water resources potential is here considered as the sum of the hydric elements rainfall, groundwater specific discharge, water reservoirs, and river hierarchy. The assessment was based in a territorial organization by drainage sub-basins and in vector maps generated and treated with GIS software. Rainfall, groundwater specific discharge and hydrographical data were obtained in official institutions and allowed the construction of the annual mean rainfall map for a forty year period (1974-2014), the annual mean groundwater specific discharge map for a thirty-four year period, and the river and drainage basin hierarchy maps. These delivered rainfall, groundwater specific discharge, water reservoirs and river hierarchy partial indices expressed on quantitative maps with normalized values distributed by level 3 drainage basins. The sum of the partial indices originated the quantitative map of water resources potential index and by the Gaussian interpolation of this quantitative data a map of hydric diversity in Ceará state was created. Therefore, the water resources potential index is higher in 4 regions of the state (Noroeste Cearense, Zona Metropolitana de Fortaleza e da Zona Norte, Vale do Jaguaribe and Zonas Centro-sul e Sul Cearense). The index is low or very low in the whole region of Sertões Cearenses, confirming the important role of climatic features in hydrological diversity. Water resources management must consider technical tools for water resources assessment, in the line of other methods for quantitative assessment of natural features either biotic or abiotic. These results quantify water resources and their distribution in a large region with important climatic differences. They constitute a basis for the knowledge of regional issues concerning water needs, flood and droughts events and even engineering solutions for water resources management.

Chiral separation and quantitation of cetirizine and hydroxyzine by maltodextrin-mediated CE in human plasma: effect of zwitterionic property of cetirizine on enantioseparation.

PubMed

Nojavan, Saeed; Fakhari, Ali Reza

2011-03-01

In the present study, a very simple CE method for chiral separation and quantitation of zwitterionic cetirizine (CTZ), as the main metabolite of hydroxyzine (HZ), and HZ has been developed. In addition, the effect of zwitterionic property of CTZ on enantioseparation was investigated. Maltodextrin, a linear polysaccharide, as a chiral selector was used and several parameters affecting the separation such as pH of BGE, concentration of chiral selector and applied voltage were studied. The best BGE conditions for CTZ and HZ enantiomers were optimized as 75 mM sodium phosphate solution at pH of 2.0, containing 5% w/v maltodextrin. Results showed that, compared to HZ, pH of BGE was an effective parameter in enantioseparation of CTZ due to the zwitterionic property of CTZ. The linear range of the method was over 30-1200 ng/mL for all enantiomers of CTZ and HZ. The quantification and detection limits (S/N=3) of all enantiomers were 30 and 10 ng/mL, respectively. The method was used to quantitative enantioseparation of CTZ and HZ in spiked human plasma. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cerebral metabolic rate of oxygen (CMRO2 ) mapping with hyperventilation challenge using quantitative susceptibility mapping (QSM).

PubMed

Zhang, Jingwei; Zhou, Dong; Nguyen, Thanh D; Spincemaille, Pascal; Gupta, Ajay; Wang, Yi

2017-05-01

Our objective was to demonstrate the feasibility of using hyperventilation as an efficient vasoconstrictive challenge and prior knowledge as denoising constraints for cerebral metabolic rate of oxygen (CMRO 2 ) mapping based upon quantitative susceptibility mapping (QSM). Three-dimensional (3D) multi-echo gradient echo and arterial spin labeling imaging were performed to calculate QSM and perfusion maps before and after a hyperventilation challenge in 11 healthy subjects. For comparison, this was repeated using a caffeine challenge. Whole-brain CMRO 2 and oxygen extraction fraction (OEF) maps were computed using constrained optimization. Hyperventilation scans were repeated to measure reproducibility. Regional agreement of CMRO 2 and OEF maps was analyzed within the cortical gray matter (CGM) using t-test and Bland-Altman plots. Hyperventilation challenge eliminates the 30-min waiting time needed for caffeine to exert its vasoconstrictive effects. Mean CMRO 2 (in µmol/100g/min) obtained in CGM using the caffeine and repeated hyperventilation scans were 149 ± 16, 153 ± 19, and 150 ± 20, respectively. This corresponded to an OEF of 33.6 ± 3.4%, 32.3 ± 3.2%, and 34.1 ± 3.8% at baseline state and 39.8 ± 4.8%, 43.6 ± 6.2%, and 42.8 ± 6.8% at challenged state, respectively. Hyperventilation scans produced a good agreement of CMRO 2 and OEF values. Hyperventilation is a feasible, reproducible, and efficient vasoconstrictive challenge for QSM-based quantitative CMRO 2 mapping. Magn Reson Med 77:1762-1773, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Influence of neighbourhood information on 'Local Climate Zone' mapping in heterogeneous cities

NASA Astrophysics Data System (ADS)

Verdonck, Marie-Leen; Okujeni, Akpona; van der Linden, Sebastian; Demuzere, Matthias; De Wulf, Robert; Van Coillie, Frieke

2017-10-01

Local climate zone (LCZ) mapping is an emerging field in urban climate research. LCZs potentially provide an objective framework to assess urban form and function worldwide. The scheme is currently being used to globally map LCZs as a part of the World Urban Database and Access Portal Tools (WUDAPT) initiative. So far, most of the LCZ maps lack proper quantitative assessment, challenging the generic character of the WUDAPT workflow. Using the standard method introduced by the WUDAPT community difficulties arose concerning the built zones due to high levels of heterogeneity. To overcome this problem a contextual classifier is adopted in the mapping process. This paper quantitatively assesses the influence of neighbourhood information on the LCZ mapping result of three cities in Belgium: Antwerp, Brussels and Ghent. Overall accuracies for the maps were respectively 85.7 ± 0.5, 79.6 ± 0.9, 90.2 ± 0.4%. The approach presented here results in overall accuracies of 93.6 ± 0.2, 92.6 ± 0.3 and 95.6 ± 0.3% for Antwerp, Brussels and Ghent. The results thus indicate a positive influence of neighbourhood information for all study areas with an increase in overall accuracies of 7.9, 13.0 and 5.4%. This paper reaches two main conclusions. Firstly, evidence was introduced on the relevance of a quantitative accuracy assessment in LCZ mapping, showing that the accuracies reported in previous papers are not easily achieved. Secondly, the method presented in this paper proves to be highly effective in Belgian cities, and given its open character shows promise for application in other heterogeneous cities worldwide.

Quantitative autoradiographic mapping of focal herpes simplex virus encephalitis using a radiolabeled antiviral drug

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

Price, R.

1984-12-18

A method of mapping herpes simplex viral infection comprising administering a radiolabeled antiviral active 5-substituted 1-(2'-deoxy-2'-substituted-D-arabinofuranosyl) pyrimidine nucleoside to the infected subject, and scanning the area in which the infection is to be mapped for the radiolabel.

Quantitative Architectural Analysis: A New Approach to Cortical Mapping

ERIC Educational Resources Information Center

Schleicher, Axel; Morosan, Patricia; Amunts, Katrin; Zilles, Karl

2009-01-01

Results from functional imaging studies are often still interpreted using the classical architectonic brain maps of Brodmann and his successors. One obvious weakness in traditional, architectural mapping is the subjective nature of localizing borders between cortical areas by means of a purely visual, microscopical examination of histological…

Detection of Mycobacterium avium subsp. paratuberculosis in Drinking Water and Biofilms Using Quantitative PCR

EPA Science Inventory

Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne’s disease in domestic animals and has been implicated in Crohn’s disease in humans. Cows infected with Johne’s disease shed large quantities of MAP into soil. Further, MAP has been isolated from surface water, is resi...

Mapping as a tool for predicting the risk of anthrax outbreaks in Northern Region of Ghana.

PubMed

Nsoh, Ayamdooh Evans; Kenu, Ernest; Forson, Eric Kofi; Afari, Edwin; Sackey, Samuel; Nyarko, Kofi Mensah; Yebuah, Nathaniel

2016-01-01

Anthrax is a febrile soil-born infectious disease that can affect all warm-blooded animals including man. Outbreaks of anthrax have been reported in northern region of Ghana but no concerted effort has been made to implement risk-based surveillance systems to document outbreaks so as to implement policies to address the disease. We generated predictive maps using soil pH, temperature and rainfall as predictor variables to identify hotspot areas for the outbreaks. A 10-year secondary data records on soil pH, temperature and rainfall were used to create climate-based risk maps using ArcGIS 10.2. The monthly mean values of rainfall and temperature for ten years were calculated and anthrax related evidence based constant raster values were created as weights for the three factors. All maps were generated using the Kriging interpolation method. There were 43 confirmed outbreaks. The deaths involved were 131 cattle, 44 sheep, 15 goats, 562 pigs with 6 human deaths and 22 developed cutaneous anthrax. We found three strata of well delineated distribution pattern indicating levels of risk due to suitability of area for anthrax spore survival. The likelihood of outbreaks occurrence and reoccurrence was higher in Strata I, Strata II and strata III respectively in descending order, due to the suitability of soil pH, temperature and rainfall for the survival and dispersal of B. anthracis spore. The eastern corridor of Northern region is a Hots spot area. Policy makers can develop risk based surveillance system and focus on this area to mitigate anthrax outbreaks and reoccurrence.

A novel approach for monitoring writing interferences during navigated transcranial magnetic stimulation mappings of writing related cortical areas.

PubMed

Rogić Vidaković, Maja; Gabelica, Dragan; Vujović, Igor; Šoda, Joško; Batarelo, Nikolina; Džimbeg, Andrija; Zmajević Schönwald, Marina; Rotim, Krešimir; Đogaš, Zoran

2015-11-30

It has recently been shown that navigated repetitive transcranial magnetic stimulation (nTMS) is useful in preoperative neurosurgical mapping of motor and language brain areas. In TMS mapping of motor cortices the evoked responses can be quantitatively monitored by electromyographic (EMG) recordings. No such setup exists for monitoring of writing during nTMS mappings of writing related cortical areas. We present a novel approach for monitoring writing during nTMS mappings of motor writing related cortical areas. To our best knowledge, this is the first demonstration of quantitative monitoring of motor evoked responses from hand by EMG, and of pen related activity during writing with our custom made pen, together with the application of chronometric TMS design and patterned protocol of rTMS. The method was applied in four healthy subjects participating in writing during nTMS mapping of the premotor cortical area corresponding to BA 6 and close to the superior frontal sulcus. The results showed that stimulation impaired writing in all subjects. The corresponding spectra of measured signal related to writing movements was observed in the frequency band 0-20 Hz. Magnetic stimulation affected writing by suppressing normal writing frequency band. The proposed setup for monitoring of writing provides additional quantitative data for monitoring and the analysis of rTMS induced writing response modifications. The setup can be useful for investigation of neurophysiologic mechanisms of writing, for therapeutic effects of nTMS, and in preoperative mapping of language cortical areas in patients undergoing brain surgery. Copyright © 2015 Elsevier B.V. All rights reserved.

Construction of a high-density linkage map and mapping quantitative trait loci for somatic embryogenesis using leaf petioles as explants in upland cotton (Gossypium hirsutum L.).

PubMed

Xu, Zhenzhen; Zhang, Chaojun; Ge, Xiaoyang; Wang, Ni; Zhou, Kehai; Yang, Xiaojie; Wu, Zhixia; Zhang, Xueyan; Liu, Chuanliang; Yang, Zuoren; Li, Changfeng; Liu, Kun; Yang, Zhaoen; Qian, Yuyuan; Li, Fuguang

2015-07-01

The first high-density linkage map was constructed to identify quantitative trait loci (QTLs) for somatic embryogenesis (SE) in cotton ( Gossypium hirsutum L.) using leaf petioles as explants. Cotton transformation is highly limited by only a few regenerable genotypes and the lack of understanding of the genetic and molecular basis of somatic embryogenesis (SE) in cotton (Gossypium hirsutum L.). To construct a more saturated linkage map and further identify quantitative trait loci (QTLs) for SE using leaf petioles as explants, a high embryogenesis frequency line (W10) from the commercial Chinese cotton cultivar CRI24 was crossed with TM-1, a genetic standard upland cotton with no embryogenesis frequency. The genetic map spanned 2300.41 cM in genetic distance and contained 411 polymorphic simple sequence repeat (SSR) loci. Of the 411 mapped loci, 25 were developed from unigenes identified for SE in our previous study. Six QTLs for SE were detected by composite interval mapping method, each explaining 6.88-37.07% of the phenotypic variance. Single marker analysis was also performed to verify the reliability of QTLs detection, and the SSR markers NAU3325 and DPL0209 were detected by the two methods. Further studies on the relatively stable and anchoring QTLs/markers for SE in an advanced population of W10 × TM-1 and other cross combinations with different SE abilities may shed light on the genetic and molecular mechanism of SE in cotton.

[Phospholipase and proteinase production by Malassezia pachydermatis isolated in dogs with and without otitis].

PubMed

Ortiz, Gustavo; Martín, M Carmen; Carrillo-Muñoz, Alfonso J; Payá, M Jesús

2013-01-01

Malassezia pachydermatis is part of the skin microbiota of dogs and cats. M. pachydermatis has been associated with external otitis and seborrhoeic dermatitis, reported more often in dogs than in cats. When the physical, chemical or immunological mechanisms of the skin are altered, M. pachydermatis could act as a pathogen. Thus, several virulence factors, such as the ability to produce esterase, lipase, lipoxygenase, protease, chondroitin sulphatase, and hyaluronidase, have been studied. In the present study, we aim to identify the phospholipase activity measured at pH 6.3, and the proteinase activity measured at pH 6.3 and pH 6.8 (pH from ears of dogs with external otitis) of M. pachydermatis strains isolated from dogs with and without external otitis. The phospholipase activity was measured using a semi-quantitative method with egg yolk, and the proteinase activity with a semi-quantitative method using bovine serum albumin agar. The study was performed on 96 isolates of M. pachydermatis, 43 isolated from dogs without clinical symptoms of otitis, and 52 isolated from dogs with otitis. In our study, 75.8% of the isolates showed phospholipase activity at pH 6.3, and 81 and 97.9% of them showed proteinase activity measured at pH 6.3 and 6.8, respectively. A higher phospholipase activity was detected in strains isolated from dogs with otitis. The proteinase activity was increased at a pH of 6.8 (97.9%) in comparison to a pH of 6.3 (81%). Our results suggest that the phospholipase activity may play an important role in the invasion of host tissues in chronic canine otitis cases. The proteinase activity results obtained in this study suggest that a reduction in the pH of the treatment may improve its efficacy in the resolution of M. pachydermatis otitis. Copyright © 2012 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

The Fab1/PIKfyve phosphoinositide phosphate kinase is not necessary to maintain the pH of lysosomes and of the yeast vacuole.

PubMed

Ho, Cheuk Y; Choy, Christopher H; Wattson, Christina A; Johnson, Danielle E; Botelho, Roberto J

2015-04-10

Lysosomes and the yeast vacuole are degradative and acidic organelles. Phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2), a master architect of endolysosome and vacuole identity, is thought to be necessary for vacuolar acidification in yeast. There is also evidence that PtdIns(3,5)P2 may play a role in lysosomal acidification in higher eukaryotes. Nevertheless, these conclusions rely on qualitative assays of lysosome/vacuole pH. For example, quinacrine, an acidotropic fluorescent base, does not accumulate in the vacuoles of fab1Δ yeast. Fab1, along with its mammalian ortholog PIKfyve, is the lipid kinase responsible for synthesizing PtdIns(3,5)P2. In this study, we employed several assays that quantitatively assessed the lysosomal and vacuolar pH in PtdIns(3,5)P2-depleted cells. Using ratiometric imaging, we conclude that lysosomes retain a pH < 5 in PIKfyve-inhibited mammalian cells. In addition, quantitative fluorescence microscopy of vacuole-targeted pHluorin, a pH-sensitive GFP variant, indicates that fab1Δ vacuoles are as acidic as wild-type yeast. Importantly, we also employed fluorimetry of vacuoles loaded with cDCFDA, a pH-sensitive dye, to show that both wild-type and fab1Δ vacuoles have a pH < 5.0. In comparison, the vacuolar pH of the V-ATPase mutant vph1Δ or vph1Δ fab1Δ double mutant was 6.1. Although the steady-state vacuolar pH is not affected by PtdIns(3,5)P2 depletion, it may have a role in stabilizing the vacuolar pH during salt shock. Overall, we propose a model in which PtdIns(3,5)P2 does not govern the steady-state pH of vacuoles or lysosomes. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

The Fab1/PIKfyve Phosphoinositide Phosphate Kinase Is Not Necessary to Maintain the pH of Lysosomes and of the Yeast Vacuole*

PubMed Central

Ho, Cheuk Y.; Choy, Christopher H.; Wattson, Christina A.; Johnson, Danielle E.; Botelho, Roberto J.

2015-01-01

Lysosomes and the yeast vacuole are degradative and acidic organelles. Phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2), a master architect of endolysosome and vacuole identity, is thought to be necessary for vacuolar acidification in yeast. There is also evidence that PtdIns(3,5)P2 may play a role in lysosomal acidification in higher eukaryotes. Nevertheless, these conclusions rely on qualitative assays of lysosome/vacuole pH. For example, quinacrine, an acidotropic fluorescent base, does not accumulate in the vacuoles of fab1Δ yeast. Fab1, along with its mammalian ortholog PIKfyve, is the lipid kinase responsible for synthesizing PtdIns(3,5)P2. In this study, we employed several assays that quantitatively assessed the lysosomal and vacuolar pH in PtdIns(3,5)P2-depleted cells. Using ratiometric imaging, we conclude that lysosomes retain a pH < 5 in PIKfyve-inhibited mammalian cells. In addition, quantitative fluorescence microscopy of vacuole-targeted pHluorin, a pH-sensitive GFP variant, indicates that fab1Δ vacuoles are as acidic as wild-type yeast. Importantly, we also employed fluorimetry of vacuoles loaded with cDCFDA, a pH-sensitive dye, to show that both wild-type and fab1Δ vacuoles have a pH < 5.0. In comparison, the vacuolar pH of the V-ATPase mutant vph1Δ or vph1Δ fab1Δ double mutant was 6.1. Although the steady-state vacuolar pH is not affected by PtdIns(3,5)P2 depletion, it may have a role in stabilizing the vacuolar pH during salt shock. Overall, we propose a model in which PtdIns(3,5)P2 does not govern the steady-state pH of vacuoles or lysosomes. PMID:25713145

Mapping the surface charge distribution of amyloid fibril

NASA Astrophysics Data System (ADS)

Lee, Gyudo; Lee, Wonseok; Lee, Hyungbeen; Woo Lee, Sang; Sung Yoon, Dae; Eom, Kilho; Kwon, Taeyun

2012-07-01

It is of high importance to measure and map the surface charge distribution of amyloids, since electrostatic interaction between amyloidogenic proteins and biomolecules plays a vital role in amyloidogenesis. In this work, we have measured and mapped the surface charge distributions of amyloids (i.e., β-lactoglobulin fibril) using Kelvin probe force microscopy. It is shown that the surface charge distribution is highly dependent on the conformation of amyloids (e.g., the helical pitch of amyloid fibrils) as well as the pH of a solvent.

Evaluation of prognostic and predictive value of microtubule associated protein tau in two independent cohorts

PubMed Central

2011-01-01

Introduction Microtubule associated proteins (MAPs) endogenously regulate microtubule stabilization and have been reported as prognostic and predictive markers for taxane response. The microtubule stabilizer, MAP-tau, has shown conflicting results. We quantitatively assessed MAP-tau expression in two independent breast cancer cohorts to determine prognostic and predictive value of this biomarker. Methods MAP-tau expression was evaluated in the retrospective Yale University breast cancer cohort (n = 651) using tissue microarrays and also in the TAX 307 cohort, a clinical trial randomized for TAC versus FAC chemotherapy (n = 140), using conventional whole tissue sections. Expression was measured using the AQUA method for quantitative immunofluorescence. Scores were correlated with clinicopathologic variables, survival, and response to therapy. Results Assessment of the Yale cohort using Cox univariate analysis indicated an improved overall survival (OS) in tumors with a positive correlation between high MAP-tau expression and overall survival (OS) (HR = 0.691, 95% CI = 0.489-0.974; P = 0.004). Kaplan Meier analysis showed 10-year survival for 65% of patients with high MAP-tau expression compared to 52% with low expression (P = .006). In TAX 307, high expression was associated with significantly longer median time to tumor progression (TTP) regardless of treatment arm (33.0 versus 23.4 months, P = 0.010) with mean TTP of 31.2 months. Response rates did not differ by MAP-tau expression (P = 0.518) or by treatment arm (P = 0.584). Conclusions Quantitative measurement of MAP-tau expression has prognostic value in both cohorts, with high expression associated with longer TTP and OS. Differences by treatment arm or response rate in low versus high MAP-tau groups were not observed, indicating that MAP-tau is not associated with response to taxanes and is not a useful predictive marker for taxane-based chemotherapy. PMID:21888627

High-Density Genetic Linkage Map Construction and Quantitative Trait Locus Mapping for Hawthorn (Crataegus pinnatifida Bunge).

PubMed

Zhao, Yuhui; Su, Kai; Wang, Gang; Zhang, Liping; Zhang, Jijun; Li, Junpeng; Guo, Yinshan

2017-07-14

Genetic linkage maps are an important tool in genetic and genomic research. In this study, two hawthorn cultivars, Qiujinxing and Damianqiu, and 107 progenies from a cross between them were used for constructing a high-density genetic linkage map using the 2b-restriction site-associated DNA (2b-RAD) sequencing method, as well as for mapping quantitative trait loci (QTL) for flavonoid content. In total, 206,411,693 single-end reads were obtained, with an average sequencing depth of 57× in the parents and 23× in the progeny. After quality trimming, 117,896 high-quality 2b-RAD tags were retained, of which 42,279 were polymorphic; of these, 12,951 markers were used for constructing the genetic linkage map. The map contained 17 linkage groups and 3,894 markers, with a total map length of 1,551.97 cM and an average marker interval of 0.40 cM. QTL mapping identified 21 QTLs associated with flavonoid content in 10 linkage groups, which explained 16.30-59.00% of the variance. This is the first high-density linkage map for hawthorn, which will serve as a basis for fine-scale QTL mapping and marker-assisted selection of important traits in hawthorn germplasm and will facilitate chromosome assignment for hawthorn whole-genome assemblies in the future.

A general quantitative pH sensor developed with dicyandiamide N-doped high quantum yield graphene quantum dots.

PubMed

Wu, Zhu Lian; Gao, Ming Xuan; Wang, Ting Ting; Wan, Xiao Yan; Zheng, Lin Ling; Huang, Cheng Zhi

2014-04-07

A general quantitative pH sensor for environmental and intracellular applications was developed by the facile hydrothermal preparation of dicyandiamide (DCD) N-doped high quantum yield (QY) graphene quantum dots (GQDs) using citric acid (CA) as the carbon source. The obtained N-doped GQDs have excellent photoluminesence (PL) properties with a relatively high QY of 36.5%, suggesting that N-doped chemistry could promote the QY of carbon nanomaterials. The possible mechanism for the formation of the GQDs involves the CA self-assembling into a nanosheet structure through intermolecular H-bonding at the initial stage of the reaction, and then the pure graphene core with many function groups formed through the dehydration between the carboxyl and hydroxyl of the intermolecules under hydrothermal conditions. These N-doped GQDs have low toxicity, and are photostable and pH-sensitive between 1.81 to 8.96, giving a general pH sensor with a wide range of applications from real water to intracellular contents.

Minimizing target interference in PK immunoassays: new approaches for low-pH-sample treatment.

PubMed

Partridge, Michael A; Pham, John; Dziadiv, Olena; Luong, Onson; Rafique, Ashique; Sumner, Giane; Torri, Albert

2013-08-01

Quantitating total levels of monoclonal antibody (mAb) biotherapeutics in serum using ELISA may be hindered by soluble targets. We developed two low-pH-sample-pretreatment techniques to minimize target interference. The first procedure involves sample pretreatment at pH <3.0 before neutralization and analysis in a target capture ELISA. Careful monitoring of acidification time is required to minimize potential impact on mAb detection. The second approach involves sample dilution into mild acid (pH ∼4.5) before transferring to an anti-human capture-antibody-coated plate without neutralization. Analysis of target-drug and drug-capture antibody interactions at pH 4.5 indicated that the capture antibody binds to the drug, while the drug and the target were dissociated. Using these procedures, total biotherapeutic levels were accurately measured when soluble target was >30-fold molar excess. These techniques provide alternatives for quantitating mAb biotherapeutics in the presence of a target when standard acid-dissociation procedures are ineffective.

Mapping of intracellular pH in the in vivo rodent heart using hyperpolarized [1-13C]pyruvate.

PubMed

Lau, Angus Z; Miller, Jack J; Tyler, Damian J

2017-05-01

To demonstrate the feasibility of mapping intracellular pH within the in vivo rodent heart. Alterations in cardiac acid-base balance can lead to acute contractile depression and alterations in Ca 2+ signaling. The transient reduction in adenosine triphosphate (ATP) consumption and cardiac contractility may be initially beneficial; however, sustained pH changes can be maladaptive, leading to myocardial damage and electrical arrhythmias. Spectrally selective radiofrequency (RF) pulses were used to excite the HCO3- and CO 2 resonances individually while preserving signal from the injected hyperpolarized [1- 13 C]pyruvate. The large flip angle pulses were placed within a three-dimensional (3D) imaging acquisition, which exploited CA-mediated label exchange between HCO3- and CO 2 . Images at 4.5 × 4.5 × 5 mm 3 resolution were obtained in the in vivo rodent heart. The technique was evaluated in healthy rodents scanned at baseline and during high cardiac workload induced by dobutamine infusion. The intracellular pH was measured to be 7.15 ± 0.04 at baseline, and decreased to 6.90 ± 0.06 following 15 min of continuous β-adrenergic stimulation. Volumetric maps of intracellular pH can be obtained following an injection of hyperpolarized [1- 13 C]pyruvate. The new method is anticipated to enable assessment of stress-inducible ischemia and potential ventricular arrythmogenic substrates within the ischemic heart. Magn Reson Med 77:1810-1817, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

In Vivo Monitoring of pH, Redox Status, and Glutathione Using L-Band EPR for Assessment of Therapeutic Effectiveness in Solid Tumors

PubMed Central

Bobko, Andrey A.; Eubank, Timothy D.; Voorhees, Jeffrey L.; Efimova, Olga V.; Kirilyuk, Igor A.; Petryakov, Sergey; Trofimiov, Dmitrii G.; Marsh, Clay B.; Zweier, Jay L.; Grigor’ev, Igor A.; Samouilov, Alexandre; Khramtsov, Valery V.

2011-01-01

Approach for in vivo real-time assessment of tumor tissue extracellular pH (pHe), redox, and intracellular glutathione based on L-band EPR spectroscopy using dual function pH and redox nitroxide probe and disulfide nitroxide biradical, is described. These parameters were monitored in PyMT mice bearing breast cancer tumors during treatment with granulocyte macrophage colony-stimulating factor. It was observed that tumor pHe is about 0.4 pH units lower than that in normal mammary gland tissue. Treatment with granulocyte macrophage colony-stimulating factor decreased the value of pHe by 0.3 units compared with PBS control treatment. Tumor tissue reducing capacity and intracellular glutathione were elevated compared with normal mammary gland tissue. Granulocyte macrophage colony-stimulating factor treatment resulted in a decrease of the tumor tissue reducing capacity and intracellular glutathione content. In addition to spectroscopic studies, pHe mapping was performed using recently proposed variable frequency proton–electron double-resonance imaging. The pH mapping superimposed with MRI image supports probe localization in mammary gland/tumor tissue, shows high heterogeneity of tumor tissue pHe and a difference of about 0.4 pH units between average pHe values in tumor and normal mammary gland. In summary, the developed multifunctional approach allows for in vivo, noninvasive pHe, extracellular redox, and intracellular glutathione content monitoring during investigation of various therapeutic strategies for solid tumors. Magn Reson Med 000:000–000, 2011. PMID:22113626

Imaging of pH in vivo using hyperpolarized 13C-labelled zymonic acid

PubMed Central

Düwel, Stephan; Hundshammer, Christian; Gersch, Malte; Feuerecker, Benedikt; Steiger, Katja; Buck, Achim; Walch, Axel; Haase, Axel; Glaser, Steffen J.; Schwaiger, Markus; Schilling, Franz

2017-01-01

Natural pH regulatory mechanisms can be overruled during several pathologies such as cancer, inflammation and ischaemia, leading to local pH changes in the human body. Here we demonstrate that 13C-labelled zymonic acid (ZA) can be used as hyperpolarized magnetic resonance pH imaging sensor. ZA is synthesized from [1-13C]pyruvic acid and its 13C resonance frequencies shift up to 3.0 p.p.m. per pH unit in the physiological pH range. The long lifetime of the hyperpolarized signal enhancement enables monitoring of pH, independent of concentration, temperature, ionic strength and protein concentration. We show in vivo pH maps within rat kidneys and subcutaneously inoculated tumours derived from a mammary adenocarcinoma cell line and characterize ZA as non-toxic compound predominantly present in the extracellular space. We suggest that ZA represents a reliable and non-invasive extracellular imaging sensor to localize and quantify pH, with the potential to improve understanding, diagnosis and therapy of diseases characterized by aberrant acid-base balance. PMID:28492229

Phased Array Ultrasonic Sound Field Mapping in Cast Austenitic Stainless Steel

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

Crawford, Susan L.; Prowant, Matthew S.; Cinson, Anthony D.

2014-05-31

This study maps the phased array-generated acoustic sound fields through three types of CASS microstructure in four specimens to quantitatively assess the beam formation effectiveness in these materials.

Survivability of Mycobacterium avium subsp paratuberculosis in grass silage after fermentation and exposure to low pH and high organic acids

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp paratuberculosis (Map) is a pathogen of concern in dairy production due to its ability to withstand harsh conditions and cause new infections. Infection is a result of ingesting Map cells from contaminated feed, water, or manure. The goal of this research was to evaluate th...

Monitoring and mapping selected riparian habitat along the lower Snake River

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

Downs, J. L; Tiller, B. L; Witter, M.

Studies in this document were initiated to establish baseline information on riparian and wetland habitat conditions at the areas studied under the current reservoir operations on the lower Snake River. Two approaches were used to assess habitat at 28 study sites selected on the four pools on the lower Snake River. These areas all contribute significant riparian habitat along the river, and several of these areas are designated habitat management units. At 14 of the 28 sites, we monitored riparian habitat on three dates during the growing season to quantify vegetation abundance and composition along three transects: soil nutrients, moisture,more » and pH and water level and pH. A second approach involved identifying any differences in the extent and amount of riparian/wetland habitat currently found at the study areas from that previously documented. We used both ground and boat surveys to map and classify the changes in vegetative cover along the shoreline at the 14 monitoring sites and at 14 additional sites along the lower Snake selected to represent various riparian/wetland habitat conditions. Results of these mapping efforts are compared with maps of cover types previously generated using aerial photography taken in 1987.« less

Effects of packaging systems and fat concentrations on microbiology, sensory and physical properties of ground beef stored at 4±1°C for 25 days.

PubMed

Lavieri, N; Williams, S K

2014-08-01

This study evaluated effects of modified atmosphere (MAP, 0.4% carbon monoxide [CO], 30% carbon dioxide, and 69.6% nitrogen), vacuum (VP) and polyvinyl chloride (PVC) packaging systems and fat levels (10, 20 and 30% fat) on ground beef stored at 4 ± 1°C for 25 days for microbiology, sensory, pH, thiobarbituric acid reactive substances (TBARS), objective color, headspace and residual CO. As storage time increased, pH decreased (P< 0.05) for MAP and VP and increased (P < 0.05) for PVC. TBARS varied (P < 0.05) among MAP and VP treatments. Except for day 1, CO headspace concentrations were similar among fat concentrations, and residual CO absorption in meat increased (P < 0.05) for all MAP treatments. In all treatments, degree of lightness was similar, redness decreased and brown discoloration increased during storage. As psychrotrophic bacteria counts increased, panelists detected color and off-odor deterioration in all systems. The CO treatment had no effect on maintaining the carboxymyoglobin "cherry red" fresh meat color during meat spoilage. Published by Elsevier Ltd.

Fine Mapping and Evolution of a QTL Region on Cattle Chromosome 3

ERIC Educational Resources Information Center

Donthu, Ravikiran

2009-01-01

The goal of my dissertation was to fine map the milk yield and composition quantitative trait loci (QTL) mapped to cattle chromosome 3 (BTA3) by Heyen et al. (1999) and to identify candidate genes affecting these traits. To accomplish this, the region between "BL41" and "TGLA263" was mapped to the cattle genome sequence assembly Btau 3.1 and a…

Quantitative angle-insensitive flow measurement using relative standard deviation OCT.

PubMed

Zhu, Jiang; Zhang, Buyun; Qi, Li; Wang, Ling; Yang, Qiang; Zhu, Zhuqing; Huo, Tiancheng; Chen, Zhongping

2017-10-30

Incorporating different data processing methods, optical coherence tomography (OCT) has the ability for high-resolution angiography and quantitative flow velocity measurements. However, OCT angiography cannot provide quantitative information of flow velocities, and the velocity measurement based on Doppler OCT requires the determination of Doppler angles, which is a challenge in a complex vascular network. In this study, we report on a relative standard deviation OCT (RSD-OCT) method which provides both vascular network mapping and quantitative information for flow velocities within a wide range of Doppler angles. The RSD values are angle-insensitive within a wide range of angles, and a nearly linear relationship was found between the RSD values and the flow velocities. The RSD-OCT measurement in a rat cortex shows that it can quantify the blood flow velocities as well as map the vascular network in vivo .

Quantitative angle-insensitive flow measurement using relative standard deviation OCT

NASA Astrophysics Data System (ADS)

Zhu, Jiang; Zhang, Buyun; Qi, Li; Wang, Ling; Yang, Qiang; Zhu, Zhuqing; Huo, Tiancheng; Chen, Zhongping

2017-10-01

Incorporating different data processing methods, optical coherence tomography (OCT) has the ability for high-resolution angiography and quantitative flow velocity measurements. However, OCT angiography cannot provide quantitative information of flow velocities, and the velocity measurement based on Doppler OCT requires the determination of Doppler angles, which is a challenge in a complex vascular network. In this study, we report on a relative standard deviation OCT (RSD-OCT) method which provides both vascular network mapping and quantitative information for flow velocities within a wide range of Doppler angles. The RSD values are angle-insensitive within a wide range of angles, and a nearly linear relationship was found between the RSD values and the flow velocities. The RSD-OCT measurement in a rat cortex shows that it can quantify the blood flow velocities as well as map the vascular network in vivo.

Taking stock of four decades of quantitative research on stakeholder participation and evaluation use: a systematic map.

PubMed

Daigneault, Pierre-Marc

2014-08-01

Stakeholder participation and evaluation use have attracted a lot of attention from practitioners, theorists and researchers. A common hypothesis is that participation is positively associated with evaluation use. Whereas the number of empirical studies conducted on this topic is impressive, quantitative research has held a minority position within this scientific production. This study mobilizes systematic review methods to 'map' the empirical literature that has quantitatively studied participation and use. The goal is to take stock and assess the strength of evidence of this literature (but not to synthesize the findings) and, based on this assessment, to provide directions for future research. Copyright © 2014 Elsevier Ltd. All rights reserved.

Scanning evanescent electro-magnetic microscope

DOEpatents

Xiang, Xiao-Dong; Gao, Chen; Schultz, Peter G.; Wei, Tao

2003-01-01

A novel scanning microscope is described that uses near-field evanescent electromagnetic waves to probe sample properties. The novel microscope is capable of high resolution imaging and quantitative measurements of the electrical properties of the sample. The inventive scanning evanescent wave electromagnetic microscope (SEMM) can map dielectric constant, tangent loss, conductivity, complex electrical impedance, and other electrical parameters of materials. The quantitative map corresponds to the imaged detail. The novel microscope can be used to measure electrical properties of both dielectric and electrically conducting materials.

Scanning evanescent electro-magnetic microscope

DOEpatents

Xiang, Xiao-Dong; Gao, Chen

2001-01-01

A novel scanning microscope is described that uses near-field evanescent electromagnetic waves to probe sample properties. The novel microscope is capable of high resolution imaging and quantitative measurements of the electrical properties of the sample. The inventive scanning evanescent wave electromagnetic microscope (SEMM) can map dielectric constant, tangent loss, conductivity, complex electrical impedance, and other electrical parameters of materials. The quantitative map corresponds to the imaged detail. The novel microscope can be used to measure electrical properties of both dielectric and electrically conducting materials.

Quantitative EPMA Compositional Mapping of NWA 2995: Characterization, and Petrologic Interpretation of Mafic Clasts

NASA Technical Reports Server (NTRS)

Carpenter, P. K.; Hahn, T. M.; Korotev, R. L.; Ziegler, R. A.; Jolliff, B. L.

2017-01-01

We present the first fully quantitative compositional maps of lunar meteorite NWA 2995 using electron microprobe stage mapping, and compare selected clast mineralogy and chemistry. NWA 2995 is a feldspathic fragmental breccia containing numerous highland fine grained lithologies, including anorthosite, norite, olivine basalt, subophitic basalt, gabbro, KREEP-like basalt, granulitic and glassy impact melts, coarse-grained mineral fragments, Fe-Ni metal, and glassy matrix [1]. Chips of NWA 2995, representing these diverse materials, were analyzed by INAA and fused-bead electron-probe microanalysis (EPMA); comparison of analytical data suggests grouping of lunar meteorites NWA 2995, 2996, 3190, 4503, 5151, and 5152. The mean composition of NWA 2995 corresponds to a 2:1 mixture of feldspathic and mare material, with approximately 5% KREEP component [2]. Clast mineral chemistry and petrologic interpretation of paired stone NWA 2996 has been reported by Mercer et al. [3], and Gross et al. [4]. This study combines advances in quantitative EPMA compositional mapping and data analysis, as applied to selected mafic clasts in a polished section of NWA 2995, to investigate the origin of mafic lithic components and to demonstrate a procedural framework for petrologic analysis.

Background controlled QTL mapping in pure-line genetic populations derived from four-way crosses

PubMed Central

Zhang, S; Meng, L; Wang, J; Zhang, L

2017-01-01

Pure lines derived from multiple parents are becoming more important because of the increased genetic diversity, the possibility to conduct replicated phenotyping trials in multiple environments and potentially high mapping resolution of quantitative trait loci (QTL). In this study, we proposed a new mapping method for QTL detection in pure-line populations derived from four-way crosses, which is able to control the background genetic variation through a two-stage mapping strategy. First, orthogonal variables were created for each marker and used in an inclusive linear model, so as to completely absorb the genetic variation in the mapping population. Second, inclusive composite interval mapping approach was implemented for one-dimensional scanning, during which the inclusive linear model was employed to control the background variation. Simulation studies using different genetic models demonstrated that the new method is efficient when considering high detection power, low false discovery rate and high accuracy in estimating quantitative trait loci locations and effects. For illustration, the proposed method was applied in a reported wheat four-way recombinant inbred line population. PMID:28722705

Background controlled QTL mapping in pure-line genetic populations derived from four-way crosses.

PubMed

Zhang, S; Meng, L; Wang, J; Zhang, L

2017-10-01

Pure lines derived from multiple parents are becoming more important because of the increased genetic diversity, the possibility to conduct replicated phenotyping trials in multiple environments and potentially high mapping resolution of quantitative trait loci (QTL). In this study, we proposed a new mapping method for QTL detection in pure-line populations derived from four-way crosses, which is able to control the background genetic variation through a two-stage mapping strategy. First, orthogonal variables were created for each marker and used in an inclusive linear model, so as to completely absorb the genetic variation in the mapping population. Second, inclusive composite interval mapping approach was implemented for one-dimensional scanning, during which the inclusive linear model was employed to control the background variation. Simulation studies using different genetic models demonstrated that the new method is efficient when considering high detection power, low false discovery rate and high accuracy in estimating quantitative trait loci locations and effects. For illustration, the proposed method was applied in a reported wheat four-way recombinant inbred line population.

Development of gene-based markers for use in construction of the chickpea (Cicer arietinum L.) genetic linkage map and identification of QTLs associated with seed weight and plant height.

PubMed

Gupta, Shefali; Kumar, Tapan; Verma, Subodh; Bharadwaj, Chellapilla; Bhatia, Sabhyata

2015-11-01

Seed weight and plant height are important agronomic traits and contribute to seed yield. The objective of this study was to identify QTLs underlying these traits using an intra-specific mapping population of chickpea. A F11 population of 177 recombinant inbred lines derived from a cross between SBD377 (100-seed weight--48 g and plant height--53 cm) and BGD112 (100-seed weight--15 g and plant height--65 cm) was used. A total of 367 novel EST-derived functional markers were developed which included 187 EST-SSRs, 130 potential intron polymorphisms (PIPs) and 50 expressed sequence tag polymorphisms (ESTPs). Along with these, 590 previously published markers including 385 EST-based markers and 205 genomic SSRs were utilized. Of the 957 markers tested for analysis of parental polymorphism between the two parents of the mapping population, 135 (14.64%) were found to be polymorphic. Of these, 131 polymorphic markers could be mapped to the 8 linkage groups. The linkage map had a total length of 1140.54 cM with an average marker density of 8.7 cM. The map was further used for QTL identification using composite interval mapping method (CIM). Two QTLs each for seed weight, qSW-1 and qSW-2 (explaining 11.54 and 19.24% of phenotypic variance, respectively) and plant height, qPH-1 and qPH-2 (explaining 13.98 and 12.17% of phenotypic variance, respectively) were detected. The novel set of genic markers, the intra-specific linkage map and the QTLs identified in the present study will serve as valuable genomic resources in improving the chickpea seed yield using marker-assisted selection (MAS) strategies.

Synergistic effect of spice extracts and modified atmospheric packaging towards non-thermal preservation of chicken meat under refrigerated storage.

PubMed

Sivarajan, M; Lalithapriya, U; Mariajenita, Peter; Vajiha, B Aafrin; Harini, K; Madhushalini, D; Sukumar, M

2017-08-01

This study investigates the integrated approach of spice extracts and modified atmospheric packaging (MAP) chicken meat preservation. Specifically, extracts from clove (CL), cinnamon (CI) individually and in combination (3% w/w) along with MAP (30% CO2/70% N2 and 10% O2/30% CO2/60% N2) were used to increase the shelf life of fresh chicken meat stored at 4°C. The parameters evaluated as shelf life indications are microbiological (total viable count, Pseudomonas spp., lactic acid bacteria (LAB), and Enterobacteriaceae), physicochemical (pH, Lipid oxidation, color changes) and Sensory attributes. Microbial population were reduced by 2.5 to 5 log cfu/g, with the greater impact being accomplished by the blend of clove and cinnamon extract with 30% CO2/70% N2 MAP. Thiobarbituric values for all treated and MAP packed samples remained lower than 1 mg malondialdehyde (MDA)/kg all through the 24 day storage period. pH values varied from 5.5 for fresh sample on day 0 to 7.11 (day 25) on combined extract treated and MAP packaged samples. The estimations of the color parameters L*, a*, and b* were well maintained in oxygen deficient MAP. Finally, sensory investigation demonstrated that combined clove and cinnamon extract of 3% conferred acceptable sensory attributes to the samples on day 24 of storage. These results indicate the extended shelf life of chicken meat from 4 days to 24 days for samples when coated with 3% of combined clove and cinnamon extract and packaged under MAP without oxygen. These pooled extracts along with MAP displayed expanded the usability and the organoleptic qualities of chicken meat. © 2017 Poultry Science Association Inc.

Mapping Quantitative Traits in Unselected Families: Algorithms and Examples

PubMed Central

Dupuis, Josée; Shi, Jianxin; Manning, Alisa K.; Benjamin, Emelia J.; Meigs, James B.; Cupples, L. Adrienne; Siegmund, David

2009-01-01

Linkage analysis has been widely used to identify from family data genetic variants influencing quantitative traits. Common approaches have both strengths and limitations. Likelihood ratio tests typically computed in variance component analysis can accommodate large families but are highly sensitive to departure from normality assumptions. Regression-based approaches are more robust but their use has primarily been restricted to nuclear families. In this paper, we develop methods for mapping quantitative traits in moderately large pedigrees. Our methods are based on the score statistic which in contrast to the likelihood ratio statistic, can use nonparametric estimators of variability to achieve robustness of the false positive rate against departures from the hypothesized phenotypic model. Because the score statistic is easier to calculate than the likelihood ratio statistic, our basic mapping methods utilize relatively simple computer code that performs statistical analysis on output from any program that computes estimates of identity-by-descent. This simplicity also permits development and evaluation of methods to deal with multivariate and ordinal phenotypes, and with gene-gene and gene-environment interaction. We demonstrate our methods on simulated data and on fasting insulin, a quantitative trait measured in the Framingham Heart Study. PMID:19278016

Nonparametric modeling of longitudinal covariance structure in functional mapping of quantitative trait loci.

PubMed

Yap, John Stephen; Fan, Jianqing; Wu, Rongling

2009-12-01

Estimation of the covariance structure of longitudinal processes is a fundamental prerequisite for the practical deployment of functional mapping designed to study the genetic regulation and network of quantitative variation in dynamic complex traits. We present a nonparametric approach for estimating the covariance structure of a quantitative trait measured repeatedly at a series of time points. Specifically, we adopt Huang et al.'s (2006, Biometrika 93, 85-98) approach of invoking the modified Cholesky decomposition and converting the problem into modeling a sequence of regressions of responses. A regularized covariance estimator is obtained using a normal penalized likelihood with an L(2) penalty. This approach, embedded within a mixture likelihood framework, leads to enhanced accuracy, precision, and flexibility of functional mapping while preserving its biological relevance. Simulation studies are performed to reveal the statistical properties and advantages of the proposed method. A real example from a mouse genome project is analyzed to illustrate the utilization of the methodology. The new method will provide a useful tool for genome-wide scanning for the existence and distribution of quantitative trait loci underlying a dynamic trait important to agriculture, biology, and health sciences.

A high-resolution genetic map of yellow monkeyflower identifies chemical defense QTLs and recombination rate variation.

PubMed

Holeski, Liza M; Monnahan, Patrick; Koseva, Boryana; McCool, Nick; Lindroth, Richard L; Kelly, John K

2014-03-13

Genotyping-by-sequencing methods have vastly improved the resolution and accuracy of genetic linkage maps by increasing both the number of marker loci as well as the number of individuals genotyped at these loci. Using restriction-associated DNA sequencing, we construct a dense linkage map for a panel of recombinant inbred lines derived from a cross between divergent ecotypes of Mimulus guttatus. We used this map to estimate recombination rate across the genome and to identify quantitative trait loci for the production of several secondary compounds (PPGs) of the phenylpropanoid pathway implicated in defense against herbivores. Levels of different PPGs are correlated across recombinant inbred lines suggesting joint regulation of the phenylpropanoid pathway. However, the three quantitative trait loci identified in this study each act on a distinct PPG. Finally, we map three putative genomic inversions differentiating the two parental populations, including a previously characterized inversion that contributes to life-history differences between the annual/perennial ecotypes. Copyright © 2014 Holeski et al.

Intraoperative and postoperative risk factors for anastomotic leakage and pneumonia after esophagectomy for cancer.

PubMed

Goense, L; van Rossum, P S N; Tromp, M; Joore, H C; van Dijk, D; Kroese, A C; Ruurda, J P; van Hillegersberg, R

2017-01-01

Morbidity and mortality after esophagectomy are often related to anastomotic leakage or pneumonia. This study aimed to assess the relationship of intraoperative and postoperative vital parameters with anastomotic leakage and pneumonia after esophagectomy. Consecutive patients who underwent transthoracic esophagectomy with cervical anastomosis for esophageal cancer from January 2012 to December 2013 were analyzed. Univariable and multivariable logistic regression analyses were used to determine potential associations of hemodynamic and respiratory parameters with anastomotic leakage or pneumonia. From a total of 82 included patients, 19 (23%) developed anastomotic leakage and 31 (38%) experienced pneumonia. The single independent factor associated with an increased risk of anastomotic leakage in multivariable analysis included a lower minimum intraoperative pH (OR 0.85, 95% CI 0.77-0.94). An increased risk of pneumonia was associated with a lower mean arterial pressure (MAP) in the first 12 hours after surgery (OR 0.93, 95% CI 0.86-0.99) and a higher maximum intraoperative pH (OR 1.14, 95% CI 1.02-1.27). Interestingly, no differences were noted for the MAP and inotrope requirement between patients with and without anastomotic leakage. A lower minimum intraoperative pH (below 7.25) is associated with an increased risk of anastomotic leakage after esophagectomy, whereas a lower postoperative average MAP (below 83 mmHg) and a higher intraoperative pH (above 7.34) increase the risk of postoperative pneumonia. These parameters indicate the importance of setting strict perioperative goals to be protected intensively. © International Society for Diseases of the Esophagus 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Quality and rigor of the concept mapping methodology: a pooled study analysis.

PubMed

Rosas, Scott R; Kane, Mary

2012-05-01

The use of concept mapping in research and evaluation has expanded dramatically over the past 20 years. Researchers in academic, organizational, and community-based settings have applied concept mapping successfully without the benefit of systematic analyses across studies to identify the features of a methodologically sound study. Quantitative characteristics and estimates of quality and rigor that may guide for future studies are lacking. To address this gap, we conducted a pooled analysis of 69 concept mapping studies to describe characteristics across study phases, generate specific indicators of validity and reliability, and examine the relationship between select study characteristics and quality indicators. Individual study characteristics and estimates were pooled and quantitatively summarized, describing the distribution, variation and parameters for each. In addition, variation in the concept mapping data collection in relation to characteristics and estimates was examined. Overall, results suggest concept mapping yields strong internal representational validity and very strong sorting and rating reliability estimates. Validity and reliability were consistently high despite variation in participation and task completion percentages across data collection modes. The implications of these findings as a practical reference to assess the quality and rigor for future concept mapping studies are discussed. Copyright © 2011 Elsevier Ltd. All rights reserved.

Coordinating, Planning and Control

DTIC Science & Technology

1991-08-31

18] Joseph Jeffrey Finger. Eplosting constrandn in design synthesis. Ph.D. Thesis , Stanford University, 1987. [19] Michael Fischer and Richard...configuration. q, to the goal configuration, q*, is a continuous map / :[0, 1] - Cft ,., subject to the constraints that it(O) = q and r( I) - q°. The...Mathematics and C’omputer Science. University of Aalborg, 1989. (221 Kanazawa. Keij i. Pmbability. Time. arid Action. PhD thesis . Drown UnIiversit y

Genetic linkage map construction and QTL mapping of salt tolerance traits in Zoysiagrass (Zoysia japonica).

PubMed

Guo, Hailin; Ding, Wanwen; Chen, Jingbo; Chen, Xuan; Zheng, Yiqi; Wang, Zhiyong; Liu, Jianxiu

2014-01-01

Zoysiagrass (Zoysia Willd.) is an important warm season turfgrass that is grown in many parts of the world. Salt tolerance is an important trait in zoysiagrass breeding programs. In this study, a genetic linkage map was constructed using sequence-related amplified polymorphism markers and random amplified polymorphic DNA markers based on an F1 population comprising 120 progeny derived from a cross between Zoysia japonica Z105 (salt-tolerant accession) and Z061 (salt-sensitive accession). The linkage map covered 1211 cM with an average marker distance of 5.0 cM and contained 24 linkage groups with 242 marker loci (217 sequence-related amplified polymorphism markers and 25 random amplified polymorphic DNA markers). Quantitative trait loci affecting the salt tolerance of zoysiagrass were identified using the constructed genetic linkage map. Two significant quantitative trait loci (qLF-1 and qLF-2) for leaf firing percentage were detected; qLF-1 at 36.3 cM on linkage group LG4 with a logarithm of odds value of 3.27, which explained 13.1% of the total variation of leaf firing and qLF-2 at 42.3 cM on LG5 with a logarithm of odds value of 2.88, which explained 29.7% of the total variation of leaf firing. A significant quantitative trait locus (qSCW-1) for reduced percentage of dry shoot clipping weight was detected at 44.1 cM on LG5 with a logarithm of odds value of 4.0, which explained 65.6% of the total variation. This study provides important information for further functional analysis of salt-tolerance genes in zoysiagrass. Molecular markers linked with quantitative trait loci for salt tolerance will be useful in zoysiagrass breeding programs using marker-assisted selection.

Effects of Gas Composition in the Modified Atmosphere Packaging on the Shelf-life of Longissimus dorsi of Korean Native Black Pigs-Duroc Crossbred during Refrigerated Storage

PubMed Central

Muhlisin; Panjono; Kim, Dong Soo; Song, Yeong Rae; Lee, Sung-Jin; Lee, Jeong Koo; Lee, Sung Ki

2014-01-01

This study was conducted to observe the effects of gas composition in modified atmosphere packaging (MAP) on the shelf-life of Longissimus dorsi of Korean Native Black Pigs-Duroc Crossbred (KNP×D) during refrigerated storage. Muscle sample was obtained from the left side of carcass of seven months old of KNP×D barrow. The sample was sliced into 1 cm in thickness, placed on trays (two slices/tray) and filled with different gas composition, i.e. 0:20:80/O2:CO2:N2 (MAP1), 30:20:50/O2:CO2:N2 (MAP2) and 70:20:10/O2:CO2:N2 (MAP3). Other slices of sample were vacuum packed (VP) as a control. All packs were stored at 5±1°C. At 12 d of storage, pH value of MAP2 and MAP3 were higher (p<0.05) than that of MAP1 and pH value of MAP1 was higher (p<0.05) than that of VP. At 6 d of storage, redness (a*) value of MAP2 and MAP3 were higher (p<0.05) than that of VP and MAP1 and, at 9 and 12 d of storage, redness value of MAP3 was higher (p<0.05) than that of VP, MAP1, and MAP2. At 3, 6, 9, and 12 d of storage, the 2-thiobarbituric acid reactive substances (TBARS) value of MAP3 was higher than that of MAP2 and TBARS value of MAP2 was higher than that of VP and MAP1. At 3, 6, 9, and 12 d of storage, volatile basic nitrogen values of MAP2 and MAP3 were higher (p<0.05) than those of VP and MAP1. At 3 d of storage, total aerobic plate counts of MAP2 and MAP3 were higher (p<0.05) than those of VP and MAP1 and, at 6 d of storage, total aerobic plate counts of MAP3 was higher (p<0.05) than that of MAP1 and MAP2. However, there was no significant different total aerobic plate count among MAP1, MAP2, and MAP3 at 9 and 12 d of storage. There was no significant different total anaerobic plate count among MAP1, MAP2, and MAP3 during storage. It is concluded that the MAP containing 30:20:50/O2:CO2:N2 gas composition (MAP2) might be ideal for better meat quality for KNP×D meat. PMID:25083110

Quantitative analysis of rib movement based on dynamic chest bone images: preliminary results

NASA Astrophysics Data System (ADS)

Tanaka, R.; Sanada, S.; Oda, M.; Mitsutaka, M.; Suzuki, K.; Sakuta, K.; Kawashima, H.

2014-03-01

Rib movement during respiration is one of the diagnostic criteria in pulmonary impairments. In general, the rib movement is assessed in fluoroscopy. However, the shadows of lung vessels and bronchi overlapping ribs prevent accurate quantitative analysis of rib movement. Recently, an image-processing technique for separating bones from soft tissue in static chest radiographs, called "bone suppression technique", has been developed. Our purpose in this study was to evaluate the usefulness of dynamic bone images created by the bone suppression technique in quantitative analysis of rib movement. Dynamic chest radiographs of 10 patients were obtained using a dynamic flat-panel detector (FPD). Bone suppression technique based on a massive-training artificial neural network (MTANN) was applied to the dynamic chest images to create bone images. Velocity vectors were measured in local areas on the dynamic bone images, which formed a map. The velocity maps obtained with bone and original images for scoliosis and normal cases were compared to assess the advantages of bone images. With dynamic bone images, we were able to quantify and distinguish movements of ribs from those of other lung structures accurately. Limited rib movements of scoliosis patients appeared as reduced rib velocity vectors. Vector maps in all normal cases exhibited left-right symmetric distributions, whereas those in abnormal cases showed nonuniform distributions. In conclusion, dynamic bone images were useful for accurate quantitative analysis of rib movements: Limited rib movements were indicated as a reduction of rib movement and left-right asymmetric distribution on vector maps. Thus, dynamic bone images can be a new diagnostic tool for quantitative analysis of rib movements without additional radiation dose.

Epitope mapping and targeted quantitation of the cardiac biomarker troponin by SID-MRM mass spectrometry.

PubMed

Zhao, Cheng; Trudeau, Beth; Xie, Helen; Prostko, John; Fishpaugh, Jeffrey; Ramsay, Carol

2014-06-01

The absolute quantitation of the targeted protein using MS provides a promising method to evaluate/verify biomarkers used in clinical diagnostics. In this study, a cardiac biomarker, troponin I (TnI), was used as a model protein for method development. The epitope peptide of TnI was characterized by epitope excision followed with LC/MS/MS method and acted as the surrogate peptide for the targeted protein quantitation. The MRM-based MS assay using a stable internal standard that improved the selectivity, specificity, and sensitivity of the protein quantitation. Also, plasma albumin depletion and affinity enrichment of TnI by anti-TnI mAb-coated microparticles reduced the sample complexity, enhanced the dynamic range, and further improved the detecting sensitivity of the targeted protein in the biological matrix. Therefore, quantitation of TnI, a low abundant protein in human plasma, has demonstrated the applicability of the targeted protein quantitation strategy through its epitope peptide determined by epitope mapping method. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Maximum entropy estimation of a Benzene contaminated plume using ecotoxicological assays.

PubMed

Wahyudi, Agung; Bartzke, Mariana; Küster, Eberhard; Bogaert, Patrick

2013-01-01

Ecotoxicological bioassays, e.g. based on Danio rerio teratogenicity (DarT) or the acute luminescence inhibition with Vibrio fischeri, could potentially lead to significant benefits for detecting on site contaminations on qualitative or semi-quantitative bases. The aim was to use the observed effects of two ecotoxicological assays for estimating the extent of a Benzene groundwater contamination plume. We used a Maximum Entropy (MaxEnt) method to rebuild a bivariate probability table that links the observed toxicity from the bioassays with Benzene concentrations. Compared with direct mapping of the contamination plume as obtained from groundwater samples, the MaxEnt concentration map exhibits on average slightly higher concentrations though the global pattern is close to it. This suggest MaxEnt is a valuable method to build a relationship between quantitative data, e.g. contaminant concentrations, and more qualitative or indirect measurements, in a spatial mapping framework, which is especially useful when clear quantitative relation is not at hand. Copyright © 2012 Elsevier Ltd. All rights reserved.

New Tool Quantitatively Maps Minority-Carrier Lifetime of Multicrystalline Silicon Bricks (Fact Sheet)

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

Not Available

2011-11-01

NREL's new imaging tool could provide manufacturers with insight on their processes. Scientists at the National Renewable Energy Laboratory (NREL) have used capabilities within the Process Development and Integration Laboratory (PDIL) to generate quantitative minority-carrier lifetime maps of multicrystalline silicon (mc-Si) bricks. This feat has been accomplished by using the PDIL's photoluminescence (PL) imaging system in conjunction with transient lifetime measurements obtained using a custom NREL-designed resonance-coupled photoconductive decay (RCPCD) system. PL imaging can obtain rapid high-resolution images that provide a qualitative assessment of the material lifetime-with the lifetime proportional to the pixel intensity. In contrast, the RCPCD technique providesmore » a fast quantitative measure of the lifetime with a lower resolution and penetrates millimeters into the mc-Si brick, providing information on bulk lifetimes and material quality. This technique contrasts with commercially available minority-carrier lifetime mapping systems that use microwave conductivity measurements. Such measurements are dominated by surface recombination and lack information on the material quality within the bulk of the brick. By combining these two complementary techniques, we obtain high-resolution lifetime maps at very fast data acquisition times-attributes necessary for a production-based diagnostic tool. These bulk lifetime measurements provide manufacturers with invaluable feedback on their silicon ingot casting processes. NREL has been applying the PL images of lifetime in mc-Si bricks in collaboration with a U.S. photovoltaic industry partner through Recovery Act Funded Project ARRA T24. NREL developed a new tool to quantitatively map minority-carrier lifetime of multicrystalline silicon bricks by using photoluminescence imaging in conjunction with resonance-coupled photoconductive decay measurements. Researchers are not hindered by surface recombination and can look deeper into the material to map bulk lifetimes. The tool is being applied to silicon bricks in a project collaborating with a U.S. photovoltaic industry partner. Photovoltaic manufacturers can use the NREL tool to obtain valuable feedback on their silicon ingot casting processes.« less

Optical Ptychographic Microscope for Quantitative Bio-Mechanical Imaging

NASA Astrophysics Data System (ADS)

Anthony, Nicholas; Cadenazzi, Guido; Nugent, Keith; Abbey, Brian

The role that mechanical forces play in biological processes such as cell movement and death is becoming of significant interest to further develop our understanding of the inner workings of cells. The most common method used to obtain stress information is photoelasticity which maps a samples birefringence, or its direction dependent refractive indices, using polarized light. However this method only provides qualitative data and for stress information to be useful quantitative data is required. Ptychography is a method for quantitatively determining the phase of a samples complex transmission function. The technique relies upon the collection of multiple overlapping coherent diffraction patterns from laterally displaced points on the sample. The overlap of measurement points provides complementary information that significantly aids in the reconstruction of the complex wavefield exiting the sample and allows for quantitative imaging of weakly interacting specimens. Here we describe recent advances at La Trobe University Melbourne on achieving quantitative birefringence mapping using polarized light ptychography with applications in cell mechanics. Australian Synchrotron, ARC Centre of Excellence for Advanced Molecular Imaging.

Bacterial pathogen gene abundance and relation to recreational water quality at seven Great Lakes beaches.

PubMed

Oster, Ryan J; Wijesinghe, Rasanthi U; Haack, Sheridan K; Fogarty, Lisa R; Tucker, Taaja R; Riley, Stephen C

2014-12-16

Quantitative assessment of bacterial pathogens, their geographic variability, and distribution in various matrices at Great Lakes beaches are limited. Quantitative PCR (qPCR) was used to test for genes from E. coli O157:H7 (eaeO157), shiga-toxin producing E. coli (stx2), Campylobacter jejuni (mapA), Shigella spp. (ipaH), and a Salmonella enterica-specific (SE) DNA sequence at seven Great Lakes beaches, in algae, water, and sediment. Overall, detection frequencies were mapA>stx2>ipaH>SE>eaeO157. Results were highly variable among beaches and matrices; some correlations with environmental conditions were observed for mapA, stx2, and ipaH detections. Beach seasonal mean mapA abundance in water was correlated with beach seasonal mean log10 E. coli concentration. At one beach, stx2 gene abundance was positively correlated with concurrent daily E. coli concentrations. Concentration distributions for stx2, ipaH, and mapA within algae, sediment, and water were statistically different (Non-Detect and Data Analysis in R). Assuming 10, 50, or 100% of gene copies represented viable and presumably infective cells, a quantitative microbial risk assessment tool developed by Michigan State University indicated a moderate probability of illness for Campylobacter jejuni at the study beaches, especially where recreational water quality criteria were exceeded. Pathogen gene quantification may be useful for beach water quality management.

Metabolic Mapping: Quantitative Enzyme Cytochemistry and Histochemistry to Determine the Activity of Dehydrogenases in Cells and Tissues.

PubMed

Molenaar, Remco J; Khurshed, Mohammed; Hira, Vashendriya V V; Van Noorden, Cornelis J F

2018-05-26

Altered cellular metabolism is a hallmark of many diseases, including cancer, cardiovascular diseases and infection. The metabolic motor units of cells are enzymes and their activity is heavily regulated at many levels, including the transcriptional, mRNA stability, translational, post-translational and functional level. This complex regulation means that conventional quantitative or imaging assays, such as quantitative mRNA experiments, Western Blots and immunohistochemistry, yield incomplete information regarding the ultimate activity of enzymes, their function and/or their subcellular localization. Quantitative enzyme cytochemistry and histochemistry (i.e., metabolic mapping) show in-depth information on in situ enzymatic activity and its kinetics, function and subcellular localization in an almost true-to-nature situation. We describe a protocol to detect the activity of dehydrogenases, which are enzymes that perform redox reactions to reduce cofactors such as NAD(P) + and FAD. Cells and tissue sections are incubated in a medium that is specific for the enzymatic activity of one dehydrogenase. Subsequently, the dehydrogenase that is the subject of investigation performs its enzymatic activity in its subcellular site. In a chemical reaction with the reaction medium, this ultimately generates blue-colored formazan at the site of the dehydrogenase's activity. The formazan's absorbance is therefore a direct measure of the dehydrogenase's activity and can be quantified using monochromatic light microscopy and image analysis. The quantitative aspect of this protocol enables researchers to draw statistical conclusions from these assays. Besides observational studies, this technique can be used for inhibition studies of specific enzymes. In this context, studies benefit from the true-to-nature advantages of metabolic mapping, giving in situ results that may be physiologically more relevant than in vitro enzyme inhibition studies. In all, metabolic mapping is an indispensable technique to study metabolism at the cellular or tissue level. The technique is easy to adopt, provides in-depth, comprehensive and integrated metabolic information and enables rapid quantitative analysis.

T2* Mapping Provides Information That Is Statistically Comparable to an Arthroscopic Evaluation of Acetabular Cartilage.

PubMed

Morgan, Patrick; Nissi, Mikko J; Hughes, John; Mortazavi, Shabnam; Ellerman, Jutta

2017-07-01

Objectives The purpose of this study was to validate T2* mapping as an objective, noninvasive method for the prediction of acetabular cartilage damage. Methods This is the second step in the validation of T2*. In a previous study, we established a quantitative predictive model for identifying and grading acetabular cartilage damage. In this study, the model was applied to a second cohort of 27 consecutive hips to validate the model. A clinical 3.0-T imaging protocol with T2* mapping was used. Acetabular regions of interest (ROI) were identified on magnetic resonance and graded using the previously established model. Each ROI was then graded in a blinded fashion by arthroscopy. Accurate surgical location of ROIs was facilitated with a 2-dimensional map projection of the acetabulum. A total of 459 ROIs were studied. Results When T2* mapping and arthroscopic assessment were compared, 82% of ROIs were within 1 Beck group (of a total 6 possible) and 32% of ROIs were classified identically. Disease prediction based on receiver operating characteristic curve analysis demonstrated a sensitivity of 0.713 and a specificity of 0.804. Model stability evaluation required no significant changes to the predictive model produced in the initial study. Conclusions These results validate that T2* mapping provides statistically comparable information regarding acetabular cartilage when compared to arthroscopy. In contrast to arthroscopy, T2* mapping is quantitative, noninvasive, and can be used in follow-up. Unlike research quantitative magnetic resonance protocols, T2* takes little time and does not require a contrast agent. This may facilitate its use in the clinical sphere.

Optimalisation of magnesium ammonium phosphate precipitation and its applicability to the removal of ammonium.

PubMed

Demeestere, K; Smet, E; Van Langenhove, H; Galbacs, Z

2001-12-01

Among the physico-chemical abatement technologies, mainly acid scrubbers have been used to control NH3-emission. The disadvantage of this technique is that it yields waste water, highly concentrated in ammonia. In this report, the applicability of the magnesium ammonium phosphate (MAP) process to regenerate the liquid phase, produced by scrubbing NH3-loaded waste gases, was investigated. In the MAP process, ammonium is precipitated as magnesium ammonium phosphate, which can be used as a slow release fertilizer. The influence of a number of parameters, e.g. pH, kinetics, molar ratio NH(+)4/Mg2+/PO(3-)4 on the efficiency of the formation of MAP and on the ammonium removal efficiency was investigated. In this way, optimal conditions were determined for the precipitation reaction. Next to this, interference caused by other precipitation reactions was studied. At aqueous NH(+)4-concentrations of about 600 mg l(-1), ammonium removal efficiencies of 97% could be obtained at a molar ratio NH(+)4/Mg2+/PO(3-)4 of 1/1.5/1.5. To obtain this result, the pH was continuously adjusted to a value of 9 during the reaction. According to this study, it is obvious that the MAP-precipitation technology offers opportunities for ammonium removal from scrubbing liquids. The practical applicability of the MAP-process in waste gas treatment systems, however, should be the subject for further investigations.

Ratiometric photoluminescence sensing based on Ti3C2 MXene quantum dots as an intracellular pH sensor.

PubMed

Chen, Xu; Sun, Xueke; Xu, Wen; Pan, Gencai; Zhou, Donglei; Zhu, Jinyang; Wang, He; Bai, Xue; Dong, Biao; Song, Hongwei

2018-01-18

Intracellular pH sensing is of importance and can be used as an indicator for monitoring the evolution of various diseases and the health of cells. Here, we developed a new class of surface-functionalized MXene quantum dots (QDs), Ti 3 C 2 , by the sonication cutting and hydrothermal approach and further explored their intracellular pH sensing. The functionalized Ti 3 C 2 QDs exhibit bright excitation-dependent blue photoluminescence (PL) originating from the size effect and surface defects. Meanwhile, Ti 3 C 2 QDs demonstrate a high PL response induced by the deprotonation of the surface defects. Furthermore, combining the highly pH sensitive Ti 3 C 2 QDs with the pH insensitive [Ru(dpp) 3 ]Cl 2 , we developed a ratiometric pH sensor to quantitatively monitor the intracellular pH values. These novel MXene quantum dots can serve as a promising platform for developing practical fluorescent nanosensors.

Quantitative workflow based on NN for weighting criteria in landfill suitability mapping

NASA Astrophysics Data System (ADS)

Abujayyab, Sohaib K. M.; Ahamad, Mohd Sanusi S.; Yahya, Ahmad Shukri; Ahmad, Siti Zubaidah; Alkhasawneh, Mutasem Sh.; Aziz, Hamidi Abdul

2017-10-01

Our study aims to introduce a new quantitative workflow that integrates neural networks (NNs) and multi criteria decision analysis (MCDA). Existing MCDA workflows reveal a number of drawbacks, because of the reliance on human knowledge in the weighting stage. Thus, new workflow presented to form suitability maps at the regional scale for solid waste planning based on NNs. A feed-forward neural network employed in the workflow. A total of 34 criteria were pre-processed to establish the input dataset for NN modelling. The final learned network used to acquire the weights of the criteria. Accuracies of 95.2% and 93.2% achieved for the training dataset and testing dataset, respectively. The workflow was found to be capable of reducing human interference to generate highly reliable maps. The proposed workflow reveals the applicability of NN in generating landfill suitability maps and the feasibility of integrating them with existing MCDA workflows.

The Dokuchaev hypothesis as a basis for predictive digital soil mapping (on the 125th anniversary of its publication)

NASA Astrophysics Data System (ADS)

Florinsky, I. V.

2012-04-01

Predictive digital soil mapping is widely used in soil science. Its objective is the prediction of the spatial distribution of soil taxonomic units and quantitative soil properties via the analysis of spatially distributed quantitative characteristics of soil-forming factors. Western pedometrists stress the scientific priority and principal importance of Hans Jenny's book (1941) for the emergence and development of predictive soil mapping. In this paper, we demonstrate that Vasily Dokuchaev explicitly defined the central idea and statement of the problem of contemporary predictive soil mapping in the year 1886. Then, we reconstruct the history of the soil formation equation from 1899 to 1941. We argue that Jenny adopted the soil formation equation from Sergey Zakharov, who published it in a well-known fundamental textbook in 1927. It is encouraging that this issue was clarified in 2011, the anniversary year for publications of Dokuchaev and Jenny.

Construction of a high-density genetic map using specific length amplified fragment markers and identification of a quantitative trait locus for anthracnose resistance in walnut (Juglans regia L.).

PubMed

Zhu, Yufeng; Yin, Yanfei; Yang, Keqiang; Li, Jihong; Sang, Yalin; Huang, Long; Fan, Shu

2015-08-18

Walnut (Juglans regia, 2n = 32, approximately 606 Mb per 1C genome) is an economically important tree crop. Resistance to anthracnose, caused by Colletotrichum gloeosporioides, is a major objective of walnut genetic improvement in China. The recently developed specific length amplified fragment sequencing (SLAF-seq) is an efficient strategy that can obtain large numbers of markers with sufficient sequence information to construct high-density genetic maps and permits detection of quantitative trait loci (QTLs) for molecular breeding. SLAF-seq generated 161.64 M paired-end reads. 153,820 SLAF markers were obtained, of which 49,174 were polymorphic. 13,635 polymorphic markers were sorted into five segregation types and 2,577 markers of them were used to construct genetic linkage maps: 2,395 of these fell into 16 linkage groups (LGs) for the female map, 448 markers for the male map, and 2,577 markers for the integrated map. Taking into account the size of all LGs, the marker coverage was 2,664.36 cM for the female map, 1,305.58 cM for the male map, and 2,457.82 cM for the integrated map. The average intervals between two adjacent mapped markers were 1.11 cM, 2.91 cM and 0.95 cM for three maps, respectively. 'SNP_only' markers accounted for 89.25% of the markers on the integrated map. Mapping markers contained 5,043 single nucleotide polymorphisms (SNPs) loci, which corresponded to two SNP loci per SLAF marker. According to the integrated map, we used interval mapping (Logarithm of odds, LOD > 3.0) to detect our quantitative trait. One QTL was detected for anthracnose resistance. The interval of this QTL ranged from 165.51 cM to 176.33 cM on LG14, and ten markers in this interval that were above the threshold value were considered to be linked markers to the anthracnose resistance trait. The phenotypic variance explained by each marker ranged from 16.2 to 19.9%, and their LOD scores varied from 3.22 to 4.04. High-density genetic maps for walnut containing 16 LGs were constructed using the SLAF-seq method with an F1 population. One QTL for walnut anthracnose resistance was identified based on the map. The results will aid molecular marker-assisted breeding and walnut resistance genes identification.

A Colorimetric Analysis Experiment Not Requiring a Spectrophotometer: Quantitative Determination of Albumin in Powdered Egg White

ERIC Educational Resources Information Center

Charlton, Amanda K.; Sevcik, Richard S.; Tucker, Dorie A.; Schultz, Linda D.

2007-01-01

A general science experiment for high school chemistry students might serve as an excellent review of the concepts of solution preparation, solubility, pH, and qualitative and quantitative analysis of a common food product. The students could learn to use safe laboratory techniques, collect and analyze data using proper scientific methodology and…

Urban College Graduates: Their Investments in and Returns for Strong Quantitative Skills, Social Capital Skills, and Soft Skills

ERIC Educational Resources Information Center

Haynes, Marie Ellen

2010-01-01

This case study examined strong quantitative skills, social capital skills, and soft skills of urban college graduates using data from the Multi-City Study of Urban Inequality Household Survey. The urban college graduates lived in Atlanta, Boston, or Los Angeles and had bachelor's, master's, PhD, and professional degrees. Among the three skills…

Quantitative cervical vertebral maturation assessment in adolescents with normal occlusion: a mixed longitudinal study.

PubMed

Chen, Li-Li; Xu, Tian-Min; Jiang, Jiu-Hui; Zhang, Xing-Zhong; Lin, Jiu-Xiang

2008-12-01

The purpose of this study was to establish a quantitative cervical vertebral maturation (CVM) system for adolescents with normal occlusion. Mixed longitudinal data were used. The subjects included 87 children and adolescents from 8 to 18 years old with normal occlusion (32 boys, 55 girls) selected from 901 candidates. Sequential lateral cephalograms and hand-wrist films were taken once a year for 6 years. The lateral cephalograms of all subjects were divided into 11 maturation groups according to the Fishman skeletal maturity indicators. The morphologic characteristics of the second, third, and fourth cervical vertebrae at 11 developmental stages were measured and analyzed. Three characteristic parameters (H4/W4, AH3/PH3, @2) were selected to determine the classification of CVM. With 3 morphologic variables, the quantitative CVM system including 4 maturational stages was established. An equation that can accurately estimate the maturation of the cervical vertebrae was established: CVM stage=-4.13+3.57xH4/W4+4.07xAH3/PH3+0.03x@2. The quantitative CVM method is an efficient, objective, and relatively simple approach to assess the level of skeletal maturation during adolescence.

Full skin quantitative optical coherence elastography achieved by combining vibration and surface acoustic wave methods

NASA Astrophysics Data System (ADS)

Li, Chunhui; Guan, Guangying; Huang, Zhihong; Wang, Ruikang K.; Nabi, Ghulam

2015-03-01

By combining with the phase sensitive optical coherence tomography (PhS-OCT), vibration and surface acoustic wave (SAW) methods have been reported to provide elastography of skin tissue respectively. However, neither of these two methods can provide the elastography in full skin depth in current systems. This paper presents a feasibility study on an optical coherence elastography method which combines both vibration and SAW in order to give the quantitative mechanical properties of skin tissue with full depth range, including epidermis, dermis and subcutaneous fat. Experiments are carried out on layered tissue mimicking phantoms and in vivo human forearm and palm skin. A ring actuator generates vibration while a line actuator were used to excited SAWs. A PhS-OCT system is employed to provide the ultrahigh sensitive measurement of the generated waves. The experimental results demonstrate that by the combination of vibration and SAW method the full skin bulk mechanical properties can be quantitatively measured and further the elastography can be obtained with a sensing depth from ~0mm to ~4mm. This method is promising to apply in clinics where the quantitative elasticity of localized skin diseases is needed to aid the diagnosis and treatment.

Jupiter Climatological Database from Frequent 5-25 µm Mid-IR Spectral Mapping using IRTF/TEXES

NASA Astrophysics Data System (ADS)

Fletcher, Leigh N.; Orton, Glenn S.; Greathouse, Thomas K.; Sinclair, James; Irwin, Patrick G. J.; Giles, Rohini S.; Encrenaz, Therese; Drossart, Pierre

2015-11-01

We report on the development of a long-term Jovian Climatological Database (JCliD) to explore variability in Jupiter’s atmospheric temperatures, winds, clouds and composition- from long-term seasonal changes to short-term major upheavals. Radiometrically calibrated spectral scan maps of Jupiter have been regularly obtained using the TEXES instrument (Texas Echelon cross Echelle Spectrograph, Lacy et al. 2002, PASP 114, p153-168) between 2012 and 2015. Ten settings between 5 and 25 µm (10-20 cm-1 wide settings at spectral resolutions of 2000-10000) were selected to be sensitive to jovian temperatures (via H2, CH4 and CH3D), tropospheric phosphine and ammonia, tropospheric haze opacity and stratospheric hydrocarbons ethane and acetylene. Diffraction-limited spatial resolutions of 0.6-1.6” were achieved. Observations over consecutive nights allow the creation of full spatial maps for comparison with the visible light record, revealing ephemeral stratospheric wave activity, NEB hotspots, heating at the northern auroral oval, and complex thermal signatures associated with tropospheric vortices, waves and barges. Full spectra are inverted via the NEMESIS retrieval algorithm (Irwin et al., 2008, JSQRT 109, p1136-1150) to map temperatures at multiple altitudes (1-600 mbar), winds, aerosol opacity and gaseous composition. The spatial and spectral resolutions of the resulting maps surpass those obtained during the Cassini flyby of Jupiter in 2000, and permit temporal interpolation to understand the environmental conditions related to the emergence and evolution of discrete features. In December 2014 we find warmer temperatures in the northern stratosphere (a seasonal effect in late northern summer despite Jupiter’s small axial tilt); a hemispheric asymmetry in the tropospheric PH3 distribution due to variations in the vigour of vertical mixing and photolytic shielding; elevated PH3, aerosols and NH3 in the equatorial zone (EZ) related to equatorial uplift; elevated aerosol opacity in the northern and southern tropical zones (NTrZ and STrZ); and enhanced PH3 and aerosols over the Great Red Spot. Maps of retrieved properties will be assembled as a database (JCliD) to aid in the interpretation of Juno data during 2016-2017.

Mapping of a Novel Race Specific Resistance Gene to Phytophthora Root Rot of Pepper (Capsicum annuum) Using Bulked Segregant Analysis Combined with Specific Length Amplified Fragment Sequencing Strategy.

PubMed

Xu, Xiaomei; Chao, Juan; Cheng, Xueli; Wang, Rui; Sun, Baojuan; Wang, Hengming; Luo, Shaobo; Xu, Xiaowan; Wu, Tingquan; Li, Ying

2016-01-01

Phytophthora root rot caused by Phytophthora capsici (P. capsici) is a serious limitation to pepper production in Southern China, with high temperature and humidity. Mapping PRR resistance genes can provide linked DNA markers for breeding PRR resistant varieties by molecular marker-assisted selection (MAS). Two BC1 populations and an F2 population derived from a cross between P. capsici-resistant accession, Criollo de Morelos 334 (CM334) and P. capsici-susceptible accession, New Mexico Capsicum Accession 10399 (NMCA10399) were used to investigate the genetic characteristics of PRR resistance. PRR resistance to isolate Byl4 (race 3) was controlled by a single dominant gene, PhR10, that was mapped to an interval of 16.39Mb at the end of the long arm of chromosome 10. Integration of bulked segregant analysis (BSA) and Specific Length Amplified Fragment sequencing (SLAF-seq) provided an efficient genetic mapping strategy. Ten polymorphic Simple Sequence Repeat (SSR) markers were found within this region and used to screen the genotypes of 636 BC1 plants, delimiting PhR10 to a 2.57 Mb interval between markers P52-11-21 (1.5 cM away) and P52-11-41 (1.1 cM). A total of 163 genes were annotated within this region and 31 were predicted to be associated with disease resistance. PhR10 is a novel race specific gene for PRR, and this paper describes linked SSR markers suitable for marker-assisted selection of PRR resistant varieties, also laying a foundation for cloning the resistance gene.

Integrated Environmental Modeling: Quantitative Microbial Risk Assessment

EPA Science Inventory

The presentation discusses the need for microbial assessments and presents a road map associated with quantitative microbial risk assessments, through an integrated environmental modeling approach. A brief introduction and the strengths of the current knowledge are illustrated. W...

A multiplexed system for quantitative comparisons of chromatin landscapes

PubMed Central

van Galen, Peter; Viny, Aaron D.; Ram, Oren; Ryan, Russell J.H.; Cotton, Matthew J.; Donohue, Laura; Sievers, Cem; Drier, Yotam; Liau, Brian B.; Gillespie, Shawn M.; Carroll, Kaitlin M.; Cross, Michael B.; Levine, Ross L.; Bernstein, Bradley E.

2015-01-01

Genome-wide profiling of histone modifications can provide systematic insight into the regulatory elements and programs engaged in a given cell type. However, conventional chromatin immunoprecipitation and sequencing (ChIP-seq) does not capture quantitative information on histone modification levels, requires large amounts of starting material, and involves tedious processing of each individual sample. Here we address these limitations with a technology that leverages DNA barcoding to profile chromatin quantitatively and in multiplexed format. We concurrently map relative levels of multiple histone modifications across multiple samples, each comprising as few as a thousand cells. We demonstrate the technology by monitoring dynamic changes following inhibition of P300, EZH2 or KDM5, by linking altered epigenetic landscapes to chromatin regulator mutations, and by mapping active and repressive marks in purified human hematopoietic stem cells. Hence, this technology enables quantitative studies of chromatin state dynamics across rare cell types, genotypes, environmental conditions and drug treatments. PMID:26687680

Genetic interactions contribute less than additive effects to quantitative trait variation in yeast

PubMed Central

Bloom, Joshua S.; Kotenko, Iulia; Sadhu, Meru J.; Treusch, Sebastian; Albert, Frank W.; Kruglyak, Leonid

2015-01-01

Genetic mapping studies of quantitative traits typically focus on detecting loci that contribute additively to trait variation. Genetic interactions are often proposed as a contributing factor to trait variation, but the relative contribution of interactions to trait variation is a subject of debate. Here we use a very large cross between two yeast strains to accurately estimate the fraction of phenotypic variance due to pairwise QTL–QTL interactions for 20 quantitative traits. We find that this fraction is 9% on average, substantially less than the contribution of additive QTL (43%). Statistically significant QTL–QTL pairs typically have small individual effect sizes, but collectively explain 40% of the pairwise interaction variance. We show that pairwise interaction variance is largely explained by pairs of loci at least one of which has a significant additive effect. These results refine our understanding of the genetic architecture of quantitative traits and help guide future mapping studies. PMID:26537231

Genome-wide association mapping of crown rust resistance in oat elite germplasm

USDA-ARS?s Scientific Manuscript database

Oat crown rust, caused by Puccinia coronata f. sp. avenae, is a major constraint to oat production in many parts of the world. In this first comprehensive multi-environment genome-wide association map of oat crown rust, we used 2,972 SNPs genotyped on 631 oat lines for association mapping of quantit...

Experiential and Outdoor Education: The Participant Experience Shared through Mind Maps

ERIC Educational Resources Information Center

Jirásek, Ivo; Plevová, Irena; Jirásková, Miroslava; Dvorácková, Adéla

2016-01-01

This paper describes an analysis of mind maps capturing the experiences of the participants in an experiential and outdoor education course. The method of mind mapping is usually limited to a quantitative scoring analysis and comparative content analysis of concepts. As a consequence, the visual elements of the information are usually ignored, but…

The intercrater plains of Mercury and the Moon: Their nature, origin and role in terrestrial planet evolution. Geologic map analyses: Correlation of geologic and cratering histories. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Leake, M. A.

1982-01-01

Geologic map analyses are expanded, beginning with a discussion of particular regions which may illustrate volcanic and ballistic plains emplacement on Mercury. Major attention is focused on the surface history of Mercury through discussion of the areal distribution of plains and craters and the paleogeologic maps of the first quadrant. A summary of the lunar intercrater plains formation similarly interrelates the information from the Moon's geologic and cratering histories.

Determining Optimal Microwave Antigen Retrieval Conditions for Microtubule-Associated Protein 2 Immunohistochemistry in the Guinea Pig Brain

DTIC Science & Technology

2002-12-01

sections of formalin-fixed guinea pig brains using different MAP-2 monoclonal antibodies. Brain sections were boiled in sodium citrate, citric acid...citric acid solution at pH 6.0 is the optimal microwave-assisted AR method for immunolabeling MAP-2 in formalin-fixed, paraffin-processed guinea pig brain...studies on archival guinea pig brain paraffin blocks, ultimately relaxing the use of additional animals to evaluate changes in MAP-2 expression between chemical warfare nerve agent-treated and control samples.

Low Medium pH Value Enhances Anthocyanin Accumulation in Malus Crabapple Leaves

PubMed Central

Tian, Ji; Jin, Kaina; Yao, Yuncong

2014-01-01

Anthocyanin is a critical factor involved in coloration of plant tissues, but the mechanism how medium pH values affect anthocyanin accumulation in woody plants is unknown. We analyzed anthocyanin composition and the expression of elements encoding anthocyanin and flavonols biosynthesis underlying different medium pH values by using three different leave color type cultivars. HPLC analysis demonstrated that high medium pH values treatment induced a dramatic decrease in the concentration of cyaniding in crabapple leaves. Conversely, the high medium pH values induced up-regulation of the content of flavones and flavonols, suggesting that low pH treatment-induced anthocyanin accumulation. Quantitative real time PCR experiment showed the expression level of anthocyanidin synthase (McANS) and uridine diphosphate glucose flavonoid 3-O-glucosyltransferase (McUFGT) was up-regulated by low pH values treatment, and high medium pH value treatment up-regulate the transcription level of flavonol synthase (McFLS). Meanwhile, several MYB TFs have been suggested in the regulation of pH responses. These results strongly indicate that the low pH treatment-induced anthocyanin accumulation is mediated by the variation of mRNA transcription of the anthocyanin biosynthetic genes. PMID:24914811

Dynamic Quantitative Trait Locus Analysis of Plant Phenomic Data.

PubMed

Li, Zitong; Sillanpää, Mikko J

2015-12-01

Advanced platforms have recently become available for automatic and systematic quantification of plant growth and development. These new techniques can efficiently produce multiple measurements of phenotypes over time, and introduce time as an extra dimension to quantitative trait locus (QTL) studies. Functional mapping utilizes a class of statistical models for identifying QTLs associated with the growth characteristics of interest. A major benefit of functional mapping is that it integrates information over multiple timepoints, and therefore could increase the statistical power for QTL detection. We review the current development of computationally efficient functional mapping methods which provide invaluable tools for analyzing large-scale timecourse data that are readily available in our post-genome era. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Role of the medium acidity in the complexes formation of pyropheophorbide a with albumin and lipoproteins].

PubMed

Golovina, G V; Ol'shevskaia, V A; Kalinina, V N; Shtil', A A; Kuz'min, V A

2011-01-01

The spectral characteristics of the photosensitizer pyropheophorbide a (PPP) complexes with its carriers, that is, serum albumin and low density lipoproteins, were investigated in aqueous solutions at pH 7.4 and 5.0. The acidic pH had no effect on the quantitative parameters of PPP binding to lipoproteins but reduces its affinity for albumin. Differential role of acidification in the binding of PPP to biomacromolecules should be considered in the design of PPP-based drugs given that pH is frequently lowered in the sites of the disease.

Electrophoretic separation of proteins in space

NASA Technical Reports Server (NTRS)

Brown, R. K.

1976-01-01

Commercially available and synthetic wide range and short range ampholytes used in the isoelectric focusing of proteins was analyzed by ion exchange chromatography. A pH gradient over the pH range 3.8 to 11.0 was used to elute the ampholytes from a column of a sulfonated polystyrene resin. The wide range ampholytes were resolved into some 60 to 70 ninhydrin positive components. The recovery obtained with the method was quantitative. Acid short range ampholytes have approximately 35 components which elute readily from the ion exchange resin. Basic short range ampholytes gave about 50 components, most of which eluted at alkaline pH.

Sparsity-constrained PET image reconstruction with learned dictionaries

NASA Astrophysics Data System (ADS)

Tang, Jing; Yang, Bao; Wang, Yanhua; Ying, Leslie

2016-09-01

PET imaging plays an important role in scientific and clinical measurement of biochemical and physiological processes. Model-based PET image reconstruction such as the iterative expectation maximization algorithm seeking the maximum likelihood solution leads to increased noise. The maximum a posteriori (MAP) estimate removes divergence at higher iterations. However, a conventional smoothing prior or a total-variation (TV) prior in a MAP reconstruction algorithm causes over smoothing or blocky artifacts in the reconstructed images. We propose to use dictionary learning (DL) based sparse signal representation in the formation of the prior for MAP PET image reconstruction. The dictionary to sparsify the PET images in the reconstruction process is learned from various training images including the corresponding MR structural image and a self-created hollow sphere. Using simulated and patient brain PET data with corresponding MR images, we study the performance of the DL-MAP algorithm and compare it quantitatively with a conventional MAP algorithm, a TV-MAP algorithm, and a patch-based algorithm. The DL-MAP algorithm achieves improved bias and contrast (or regional mean values) at comparable noise to what the other MAP algorithms acquire. The dictionary learned from the hollow sphere leads to similar results as the dictionary learned from the corresponding MR image. Achieving robust performance in various noise-level simulation and patient studies, the DL-MAP algorithm with a general dictionary demonstrates its potential in quantitative PET imaging.

Quantitative iTRAQ secretome analysis of Aspergillus niger reveals novel hydrolytic enzymes.

PubMed

Adav, Sunil S; Li, An A; Manavalan, Arulmani; Punt, Peter; Sze, Siu Kwan

2010-08-06

The natural lifestyle of Aspergillus niger made them more effective secretors of hydrolytic proteins and becomes critical when this species were exploited as hosts for the commercial secretion of heterologous proteins. The protein secretion profile of A. niger and its mutant at different pH was explored using iTRAQ-based quantitative proteomics approach coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). This study characterized 102 highly confident unique proteins in the secretome with zero false discovery rate based on decoy strategy. The iTRAQ technique identified and relatively quantified many hydrolyzing enzymes such as cellulases, hemicellulases, glycoside hydrolases, proteases, peroxidases, and protein translocating transporter proteins during fermentation. The enzymes have potential application in lignocellulosic biomass hydrolysis for biofuel production, for example, the cellulolytic and hemicellulolytic enzymes glucan 1,4-alpha-glucosidase, alpha-glucosidase C, endoglucanase, alpha l-arabinofuranosidase, beta-mannosidase, glycosyl hydrolase; proteases such as tripeptidyl-peptidase, aspergillopepsin, and other enzymes including cytochrome c oxidase, cytochrome c oxidase, glucose oxidase were highly expressed in A. niger and its mutant secretion. In addition, specific enzyme production can be stimulated by controlling pH of the culture medium. Our results showed comprehensive unique secretory protein profile of A. niger, its regulation at different pH, and the potential application of iTRAQ-based quantitative proteomics for the microbial secretome analysis.

Quantitative models for predicting adsorption of oxytetracycline, ciprofloxacin and sulfamerazine to swine manures with contrasting properties.

PubMed

Cheng, Dengmiao; Feng, Yao; Liu, Yuanwang; Li, Jinpeng; Xue, Jianming; Li, Zhaojun

2018-09-01

Understanding antibiotic adsorption in livestock manures is crucial to assess the fate and risk of antibiotics in the environment. In this study, three quantitative models developed with swine manure-water distribution coefficients (LgK d ) for oxytetracycline (OTC), ciprofloxacin (CIP) and sulfamerazine (SM1) in swine manures. Physicochemical parameters (n=12) of the swine manure were used as independent variables using partial least-squares (PLSs) analysis. The cumulative cross-validated regression coefficients (Q 2 cum ) values, standard deviations (SDs) and external validation coefficient (Q 2 ext ) ranged from 0.761 to 0.868, 0.027 to 0.064, and 0.743 to 0.827 for the three models; as such, internal and external predictability of the models were strong. The pH, soluble organic carbon (SOC) and nitrogen (SON), and Ca were important explanatory variables for the OTC-Model, pH, SOC, and SON for the CIP-model, and pH, total organic nitrogen (TON), and SOC for the SM1-model. The high VIPs (variable importance in the projections) of pH (1.178-1.396), SOC (0.968-1.034), and SON (0.822 and 0.865) established these physicochemical parameters as likely being dominant (associatively) in affecting transport of antibiotics in swine manures. Copyright © 2018 Elsevier B.V. All rights reserved.

High-Sensitivity Surface-Enhanced Raman Scattering (SERS) Substrate Based on a Gold Colloid Solution with a pH Change for Detection of Trace-Level Polycyclic Aromatic Hydrocarbons in Aqueous Solution.

PubMed

Shi, Xiaofeng; Liu, Shu; Han, Xiaohong; Ma, Jun; Jiang, Yongchao; Yu, Guifeng

2015-05-01

In this study, a gold colloid solution whose parameters were optimized, and without any surfactants, was developed as a surface-enhanced Raman scattering (SERS) substrate for the detection of trace-level polycyclic aromatic hydrocarbons (PAHs). A gold colloid solution with 57 nm gold particles and pH 13 was prepared to be the SERS substrate. It had impressive enhancement that was two orders of magnitude higher than that of a gold colloid solution with 57 nm gold particles and without pH change (pH 6). Even with a compact field-based Raman spectrometer, naphthalene, phenanthrene, anthracene, fluoranthene, and pyrene were detected, with limits of detection at 6.8 nM, 3.4 nM, 1.8 nM, 0.68 nM (680 pM), and 0.44 nM (440 pM), respectively. The significant enhancement was ascribed to an electromagnetic mechanism and a charge-transfer mechanism. Quantitative analyses for these five PAHs in water were also performed. The SERS intensities of PAHs were found to have good linear dependence relations with the concentrations in low concentration. This high-sensitivity, easily prepared substrate offers a promising technology for the quantitative detection of trace-level PAHs.

Accurate single-shot quantitative phase imaging of biological specimens with telecentric digital holographic microscopy.

PubMed

Doblas, Ana; Sánchez-Ortiga, Emilio; Martínez-Corral, Manuel; Saavedra, Genaro; Garcia-Sucerquia, Jorge

2014-04-01

The advantages of using a telecentric imaging system in digital holographic microscopy (DHM) to study biological specimens are highlighted. To this end, the performances of nontelecentric DHM and telecentric DHM are evaluated from the quantitative phase imaging (QPI) point of view. The evaluated stability of the microscope allows single-shot QPI in DHM by using telecentric imaging systems. Quantitative phase maps of a section of the head of the drosophila melanogaster fly and of red blood cells are obtained via single-shot DHM with no numerical postprocessing. With these maps we show that the use of telecentric DHM provides larger field of view for a given magnification and permits more accurate QPI measurements with less number of computational operations.

Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir

Treesearch

Nicholas C. Wheeler; Kathleen D. Jermstad; Konstantin V. Krutovsky; Sally N. Aitken; Glenn T. Howe; Jodie Krakowski; David B. Neale

2005-01-01

Quantitative trait locus (QTL) analyses are used by geneticists to characterize the genetic architecture of quantitative traits, provide a foundation for marker-aided-selection (MAS), and provide a framework for positional selection of candidate genes. The most useful QTL for breeding applications are those that have been verified in time, space, and/or genetic...

Roughness and pH changes of enamel surface induced by soft drinks in vitro-applications of stylus profilometry, focus variation 3D scanning microscopy and micro pH sensor.

PubMed

Fujii, Mie; Kitasako, Yuichi; Sadr, Alireza; Tagami, Junji

2011-01-01

This study aimed to evaluate enamel surface roughness (Ra) and pH before and after erosion by soft drinks. Enamel was exposed to a soft drink (cola, orange juice or green tea) for 1, 5 or 60 min; Ra was measured using contact-stylus surface profilometry (SSP) and non-contact focus variation 3D microscope (FVM). Surface pH was measured using a micro pH sensor. Data were analyzed at significance level of alpha=0.05. There was a significant correlation in Ra between SSP and FVM. FVM images showed no changes in the surface morphology after various periods of exposure to green tea. Unlike cola and orange juice, exposure to green tea did not significantly affect Ra or pH. A significant correlation was observed between surface pH and Ra change after exposure to the drinks. Optical surface analysis and micro pH sensor may be useful tools for non-damaging, quantitative assessment of soft drinks erosion on enamel.

A comparative study of qualitative and quantitative methods for the assessment of adhesive remnant after bracket debonding.

PubMed

Cehreli, S Burcak; Polat-Ozsoy, Omur; Sar, Cagla; Cubukcu, H Evren; Cehreli, Zafer C

2012-04-01

The amount of the residual adhesive after bracket debonding is frequently assessed in a qualitative manner, utilizing the adhesive remnant index (ARI). This study aimed to investigate whether quantitative assessment of the adhesive remnant yields more precise results compared to qualitative methods utilizing the 4- and 5-point ARI scales. Twenty debonded brackets were selected. Evaluation and scoring of the adhesive remnant on bracket bases were made consecutively using: 1. qualitative assessment (visual scoring) and 2. quantitative measurement (image analysis) on digital photographs. Image analysis was made on scanning electron micrographs (SEM) and high-precision elemental maps of the adhesive remnant as determined by energy dispersed X-ray spectrometry. Evaluations were made in accordance with the original 4-point and the modified 5-point ARI scales. Intra-class correlation coefficients (ICCs) were calculated, and the data were evaluated using Friedman test followed by Wilcoxon signed ranks test with Bonferroni correction. ICC statistics indicated high levels of agreement for qualitative visual scoring among examiners. The 4-point ARI scale was compliant with the SEM assessments but indicated significantly less adhesive remnant compared to the results of quantitative elemental mapping. When the 5-point scale was used, both quantitative techniques yielded similar results with those obtained qualitatively. These results indicate that qualitative visual scoring using the ARI is capable of generating similar results with those assessed by quantitative image analysis techniques. In particular, visual scoring with the 5-point ARI scale can yield similar results with both the SEM analysis and elemental mapping.

Proteomic analysis of cellular soluble proteins from human bronchial smooth muscle cells by combining nondenaturing micro 2DE and quantitative LC-MS/MS. 2. Similarity search between protein maps for the analysis of protein complexes.

PubMed

Jin, Ya; Yuan, Qi; Zhang, Jun; Manabe, Takashi; Tan, Wen

2015-09-01

Human bronchial smooth muscle cell soluble proteins were analyzed by a combined method of nondenaturing micro 2DE, grid gel-cutting, and quantitative LC-MS/MS and a native protein map was prepared for each of the identified 4323 proteins [1]. A method to evaluate the degree of similarity between the protein maps was developed since we expected the proteins comprising a protein complex would be separated together under nondenaturing conditions. The following procedure was employed using Excel macros; (i) maps that have three or more squares with protein quantity data were selected (2328 maps), (ii) within each map, the quantity values of the squares were normalized setting the highest value to be 1.0, (iii) in comparing a map with another map, the smaller normalized quantity in two corresponding squares was taken and summed throughout the map to give an "overlap score," (iv) each map was compared against all the 2328 maps and the largest overlap score, obtained when a map was compared with itself, was set to be 1.0 thus providing 2328 "overlap factors," (v) step (iv) was repeated for all maps providing 2328 × 2328 matrix of overlap factors. From the matrix, protein pairs that showed overlap factors above 0.65 from both protein sides were selected (431 protein pairs). Each protein pair was searched in a database (UniProtKB) on complex formation and 301 protein pairs, which comprise 35 protein complexes, were found to be documented. These results demonstrated that native protein maps and their similarity search would enable simultaneous analysis of multiple protein complexes in cells. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci.

PubMed

Georgi, Laura; Johnson-Cicalese, Jennifer; Honig, Josh; Das, Sushma Parankush; Rajah, Veeran D; Bhattacharya, Debashish; Bassil, Nahla; Rowland, Lisa J; Polashock, James; Vorsa, Nicholi

2013-03-01

The first genetic map of cranberry (Vaccinium macrocarpon) has been constructed, comprising 14 linkage groups totaling 879.9 cM with an estimated coverage of 82.2 %. This map, based on four mapping populations segregating for field fruit-rot resistance, contains 136 distinct loci. Mapped markers include blueberry-derived simple sequence repeat (SSR) and cranberry-derived sequence-characterized amplified region markers previously used for fingerprinting cranberry cultivars. In addition, SSR markers were developed near cranberry sequences resembling genes involved in flavonoid biosynthesis or defense against necrotrophic pathogens, or conserved orthologous set (COS) sequences. The cranberry SSRs were developed from next-generation cranberry genomic sequence assemblies; thus, the positions of these SSRs on the genomic map provide information about the genomic location of the sequence scaffold from which they were derived. The use of SSR markers near COS and other functional sequences, plus 33 SSR markers from blueberry, facilitates comparisons of this map with maps of other plant species. Regions of the cranberry map were identified that showed conservation of synteny with Vitis vinifera and Arabidopsis thaliana. Positioned on this map are quantitative trait loci (QTL) for field fruit-rot resistance (FFRR), fruit weight, titratable acidity, and sound fruit yield (SFY). The SFY QTL is adjacent to one of the fruit weight QTL and may reflect pleiotropy. Two of the FFRR QTL are in regions of conserved synteny with grape and span defense gene markers, and the third FFRR QTL spans a flavonoid biosynthetic gene.

Concept mapping to promote meaningful learning, help relate theory to practice and improve learning self-efficacy in Asian mental health nursing students: A mixed-methods pilot study.

PubMed

Bressington, Daniel T; Wong, Wai-Kit; Lam, Kar Kei Claire; Chien, Wai Tong

2018-01-01

Student nurses are provided with a great deal of knowledge within university, but they can find it difficult to relate theory to nursing practice. This study aimed to test the appropriateness and feasibility of assessing Novak's concept mapping as an educational strategy to strengthen the theory-practice link, encourage meaningful learning and enhance learning self-efficacy in nursing students. This pilot study utilised a mixed-methods quasi-experimental design. The study was conducted in a University school of Nursing in Hong Kong. A total of 40 third-year pre-registration Asian mental health nursing students completed the study; 12 in the concept mapping (CM) group and 28 in the usual teaching methods (UTM) group. The impact of concept mapping was evaluated thorough analysis of quantitative changes in students' learning self-efficacy, analysis of the structure and contents of the concept maps (CM group), a quantitative measure of students' opinions about their reflective learning activities and content analysis of qualitative data from reflective written accounts (CM group). There were no significant differences in self-reported learning self-efficacy between the two groups (p=0.38). The concept mapping helped students identify their current level of understanding, but the increased awareness may cause an initial drop in learning self-efficacy. The results highlight that most CM students were able to demonstrate meaningful learning and perceived that concept mapping was a useful reflective learning strategy to help them to link theory and practice. The results provide preliminary evidence that the concept mapping approach can be useful to help mental health nursing students visualise their learning progress and encourage the integration of theoretical knowledge with clinical knowledge. Combining concept mapping data with quantitative measures and qualitative reflective journal data appears to be a useful way of assessing and understanding the effectiveness of concept mapping. Future studies should utilise a larger sample size and consider using the approach as a targeted intervention immediately before and during clinical learning placements. Copyright © 2017 Elsevier Ltd. All rights reserved.

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A novel approach for rapidly and cost-effectively assessing toxicity of toxic metals in acidic water using an acidophilic iron-oxidizing biosensor.

PubMed

Yang, Shih-Hung; Cheng, Kuo-Chih; Liao, Vivian Hsiu-Chuan

2017-11-01

Contamination by heavy metals and metalloids is a serious environmental and health concern. Acidic wastewaters are often associated with toxic metals which may enter and spread into agricultural soils. Several biological assays have been developed to detect toxic metals; however, most of them can only detect toxic metals in a neutral pH, not in an acidic environment. In this study, an acidophilic iron-oxidizing bacterium (IOB) Strain Y10 was isolated, characterized, and used to detect toxic metals toxicity in acidic water at pH 2.5. The colorimetric acidophilic IOB biosensor was based on the inhibition of the iron oxidizing ability of Strain Y10, an acidophilic iron-oxidizing bacterium, by metals toxicity. Our results showed that Strain Y10 is acidophilic iron-oxidizing bacterium. Thiobacillus caldus medium (TCM) (pH 2.5) supplied with both S 4 O 6 2- and glucose was the optimum growth medium for Strain Y10. The optimum temperature and pH for the growth of Strain Y10 was 45 °C and pH 2.5, respectively. Our study demonstrates that the color-based acidophilic IOB biosensor can be semi-quantitatively observed by eye or quantitatively measured by spectrometer to detect toxicity from multiple toxic metals at pH 2.5 within 45 min. Our study shows that monitoring toxic metals in acidic water is possible by using the acidophilic IOB biosensor. Our study thus provides a novel approach for rapid and cost-effective detection of toxic metals in acidic conditions that can otherwise compromise current methods of chemical analysis. This method also allows for increased efficiency when screening large numbers of environmental samples. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rapid Semi-Quantitative Mapping of Dispersed Caffeine Using an Autosampler/DART/TOFMS

EPA Science Inventory

Introduction: Rapid mapping of contaminant distributions is necessary to assess exposure risksand to plan remediation, when chemicals are dispersed accidentally, deliberately, or by weather-related events. Described previously (Grange, Environ. Forensics, 9, 125-141) were anaut...

The intercrater plains of Mercury and the Moon: Their nature, origin and role in terrestrial planet evolution. Geologic mapping of Mercury and the Moon. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Leake, M. A.

1982-01-01

The geologic framework of the intercrater plains on Mercury and the Moon as determined through geologic mapping is presented. The strategies used in such mapping are discussed first. Then, because the degree of crater degradation is applied to both mapping and crater statistics, the correlation of degradation classification of lunar and Mercurian craters is thoroughly addressed. Different imaging systems can potentially affect this classification, and are therefore also discussed. The techniques used in mapping Mercury are discussed in Section 2, followed by presentation of the Geologic Map of Mercury in Section 3. Material units, structures, and relevant albedo and color data are discussed therein. Preliminary conclusions regarding plains' origins are given there. The last section presents the mapping analyses of the lunar intercrater plains, including tentative conclusions of their origin.

Distributions of glycerol dialkyl glycerol tetraethers in surface soils of Qinghai-Tibetan Plateau: implications of GDGT-based proxies in cold and dry regions

NASA Astrophysics Data System (ADS)

Ding, S.; Xu, Y.; Wang, Y.; He, Y.; Hou, J.; Chen, L.; He, J.-S.

2015-01-01

The methylation index of branched tetraethers (MBT) and cyclization ratio of branched tetraethers (CBT) based on the distribution of bacteria-derived branched glycerol dialkyl glycerol tetraethers (bGDGTs) are useful proxies for the reconstruction of continental paleotemperature and soil pH. Several calibrations of the MBT-CBT index have been proposed based on global and regional soils and lake sediments. However, little is known about the distribution and applicability of GDGTs proxies in the Qinghai-Tibet Plateau (QTP), a critical region of the global climate system. Here, we investigated 33 surface soils covering a large area of the QTP. Redundancy analysis showed that soil pH was the most important factor affecting GDGT distributions, followed by mean annual precipitation (MAP) and mean annual air temperature (MAT). The branched-isoprenoid tetraether (BIT) index, an indicator for estimation of soil organic matter in aquatic environments, varied from 0.48 to 1 and negatively correlated with soil pH (r2 = 0.38), suggesting that the BIT index should be used with caution in the QTP. A transfer function of the CBT index-soil pH was established to estimate paleo-soil pH in the QTP: pH = 8.33-1.43 × CBT (r2 = 0.80, RMSE = 0.27 pH unit). The local calibration of MBT-CBT index presented a weak, still significant correlation with MAT (r2 = 0.36) mainly owing to the additional influence of MAP (r2 = 0.50). Combining our data with previously reported GDGTs for Chinese soils resulted in a new calibration of MBT/CBT-MAT: MAT = 2.68+26.14 × MBT-3.37 × CBT (r2 = 0.73; RMSE = 4.2 °C, n = 164). The correlation coefficient and residual error of this new transfer function is comparable with global calibrations, suggesting that MBT-CBT paleotemperature proxy is still valid in the QTP.

Combined effect of oregano essential oil and modified atmosphere packaging on shelf-life extension of fresh chicken breast meat, stored at 4 degrees C.

PubMed

Chouliara, E; Karatapanis, A; Savvaidis, I N; Kontominas, M G

2007-09-01

The combined effect of oregano essential oil (0.1% and 1% w/w) and modified atmosphere packaging (MAP) (30% CO2/70% N2 and 70% CO2/30% N2) on shelf-life extension of fresh chicken meat stored at 4 degrees C was investigated. The parameters that were monitored were: microbiological (TVC, Pseudomonas spp., lactic acid bacteria (LAB), yeasts, Brochothrix thermosphacta and Enterobacteriaceae), physico-chemical (pH, TBA, color) and sensory (odor and taste) attributes. Microbial populations were reduced by 1-5 log cfu/g for a given sampling day, with the more pronounced effect being achieved by the combination of MAP and oregano essential oil. TBA values for all treatments remained lower than 1 mg malondialdehyde (MDA) kg(-1) throughout the 25-day storage period. pH values varied between 6.4 (day 0) and 5.9 (day 25). The values of the color parameters L*, a* and b* were not considerably affected by oregano oil or by MAP. Finally, sensory analysis showed that oregano oil at a concentration of 1% imparted a very strong taste to the product for which reason these lots of samples were not scored. On the basis of sensory evaluation a shelf-life extension of breast chicken meat by ca. 3-4 days for samples containing 0.1% oregano oil, 2-3 days for samples under MAP and 5-6 days for samples under MAP containing 0.1% of oregano oil was attained. Thus oregano oil and MAP exhibited an additive preservation effect.

Ultrahigh resolution optical coherence tomography for quantitative topographic mapping of retinal and intraretinal architectural morphology

NASA Astrophysics Data System (ADS)

Ko, Tony H.; Hartl, Ingmar; Drexler, Wolfgang; Ghanta, Ravi K.; Fujimoto, James G.

2002-06-01

Quantitative, three-dimensional mapping of retinal architectural morphology was achieved using an ultrahigh resolution ophthalmic OCT system. This OCT system utilizes a broad bandwidth titanium-sapphire laser light source generating bandwidths of up to 300 nm near 800 nm center wavelength. The system enables real-time cross-sectional imaging of the retina with ~3 micrometers axial resolution. The macula and the papillomacular axis of a normal human subject were systematically mapped using a series of linear scans. Edge detection and segmentation algorithms were developed to quantify retinal and intraretinal thicknesses. Topographic mapping of the total retinal thickness and the total ganglion cell/inner plexiform layer thickness was achieved around the macula. A topographic mapping quantifying the progressive thickening of the nerve fiber layer (NFL) nasally approaching the optic disk was also demonstrated. The ability to create three-dimensional topographic mapping of retinal architectural morphology at ~3 micrometers axial resolution will be relevant for the diagnosis of many retinal diseases. The topographic quantification of these structures can serve as a powerful tool for developing algorithms and clinical scanning protocols for the screening and staging of ophthalmic diseases such as glaucoma.

Linkage and mapping of quantitative trait loci associated with angular leaf spot and powdery mildew resistance in common beans.

PubMed

Bassi, Denis; Briñez, Boris; Rosa, Juliana Santa; Oblessuc, Paula Rodrigues; Almeida, Caléo Panhoca de; Nucci, Stella Maris; Silva, Larissa Chariel Domingos da; Chiorato, Alisson Fernando; Vianello, Rosana Pereira; Camargo, Luis Eduardo Aranha; Blair, Matthew Wohlgemuth; Benchimol-Reis, Luciana Lasry

2017-01-01

Angular leaf spot (ALS) and powdery mildew (PWM) are two important fungi diseases causing significant yield losses in common beans. In this study, a new genetic linkage map was constructed using single sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), in a segregating population derived from the AND 277 x SEA 5 cross, with 105 recombinant inbred lines. Phenotypic evaluations were performed in the greenhouse to identify quantitative trait loci (QTLs) associated with resistance by means of the composite interval mapping analysis. Four QTLs were identified for ALS resistance. The QTL ALS11AS, linked on the SNP BAR 5054, mapped on chromosome Pv11, showed the greatest effect (R2 = 26.5%) on ALS phenotypic variance. For PWM resistance, two QTLs were detected, PWM2AS and PWM11AS, on Pv2 and Pv11, explaining 7% and 66% of the phenotypic variation, respectively. Both QTLs on Pv11 were mapped on the same genomic region, suggesting that it is a pleiotropic region. The present study resulted in the identification of new markers closely linked to ALS and PWM QTLs, which can be used for marker-assisted selection, fine mapping and positional cloning.

Mapping carcass and meat quality QTL on Sus Scrofa chromosome 2 in commercial finishing pigs

PubMed Central

Heuven, Henri CM; van Wijk, Rik HJ; Dibbits, Bert; van Kampen, Tony A; Knol, Egbert F; Bovenhuis, Henk

2009-01-01

Quantitative trait loci (QTL) affecting carcass and meat quality located on SSC2 were identified using variance component methods. A large number of traits involved in meat and carcass quality was detected in a commercial crossbred population: 1855 pigs sired by 17 boars from a synthetic line, which where homozygous (A/A) for IGF2. Using combined linkage and linkage disequilibrium mapping (LDLA), several QTL significantly affecting loin muscle mass, ham weight and ham muscles (outer ham and knuckle ham) and meat quality traits, such as Minolta-L* and -b*, ultimate pH and Japanese colour score were detected. These results agreed well with previous QTL-studies involving SSC2. Since our study is carried out on crossbreds, different QTL may be segregating in the parental lines. To address this question, we compared models with a single QTL-variance component with models allowing for separate sire and dam QTL-variance components. The same QTL were identified using a single QTL variance component model compared to a model allowing for separate variances with minor differences with respect to QTL location. However, the variance component method made it possible to detect QTL segregating in the paternal line (e.g. HAMB), the maternal lines (e.g. Ham) or in both (e.g. pHu). Combining association and linkage information among haplotypes improved slightly the significance of the QTL compared to an analysis using linkage information only. PMID:19284675

Comparison of gene-based rare variant association mapping methods for quantitative traits in a bovine population with complex familial relationships.

PubMed

Zhang, Qianqian; Guldbrandtsen, Bernt; Calus, Mario P L; Lund, Mogens Sandø; Sahana, Goutam

2016-08-17

There is growing interest in the role of rare variants in the variation of complex traits due to increasing evidence that rare variants are associated with quantitative traits. However, association methods that are commonly used for mapping common variants are not effective to map rare variants. Besides, livestock populations have large half-sib families and the occurrence of rare variants may be confounded with family structure, which makes it difficult to disentangle their effects from family mean effects. We compared the power of methods that are commonly applied in human genetics to map rare variants in cattle using whole-genome sequence data and simulated phenotypes. We also studied the power of mapping rare variants using linear mixed models (LMM), which are the method of choice to account for both family relationships and population structure in cattle. We observed that the power of the LMM approach was low for mapping a rare variant (defined as those that have frequencies lower than 0.01) with a moderate effect (5 to 8 % of phenotypic variance explained by multiple rare variants that vary from 5 to 21 in number) contributing to a QTL with a sample size of 1000. In contrast, across the scenarios studied, statistical methods that are specialized for mapping rare variants increased power regardless of whether multiple rare variants or a single rare variant underlie a QTL. Different methods for combining rare variants in the test single nucleotide polymorphism set resulted in similar power irrespective of the proportion of total genetic variance explained by the QTL. However, when the QTL variance is very small (only 0.1 % of the total genetic variance), these specialized methods for mapping rare variants and LMM generally had no power to map the variants within a gene with sample sizes of 1000 or 5000. We observed that the methods that combine multiple rare variants within a gene into a meta-variant generally had greater power to map rare variants compared to LMM. Therefore, it is recommended to use rare variant association mapping methods to map rare genetic variants that affect quantitative traits in livestock, such as bovine populations.

Combined use of X-ray fluorescence microscopy, phase contrast imaging for high resolution quantitative iron mapping in inflamed cells

NASA Astrophysics Data System (ADS)

Gramaccioni, C.; Procopio, A.; Farruggia, G.; Malucelli, E.; Iotti, S.; Notargiacomo, A.; Fratini, M.; Yang, Y.; Pacureanu, A.; Cloetens, P.; Bohic, S.; Massimi, L.; Cutone, A.; Valenti, P.; Rosa, L.; Berlutti, F.; Lagomarsino, S.

2017-06-01

X-ray fluorescence microscopy (XRFM) is a powerful technique to detect and localize elements in cells. To derive information useful for biology and medicine, it is essential not only to localize, but also to map quantitatively the element concentration. Here we applied quantitative XRFM to iron in phagocytic cells. Iron, a primary component of living cells, can become toxic when present in excess. In human fluids, free iron is maintained at 10-18 M concentration thanks to iron binding proteins as lactoferrin (Lf). The iron homeostasis, involving the physiological ratio of iron between tissues/secretions and blood, is strictly regulated by ferroportin, the sole protein able to export iron from cells to blood. Inflammatory processes induced by lipopolysaccharide (LPS) or bacterial pathoge inhibit ferroportin synthesis in epithelial and phagocytic cells thus hindering iron export, increasing intracellular iron and bacterial multiplication. In this respect, Lf is emerging as an important regulator of both iron and inflammatory homeostasis. Here we studied phagocytic cells inflamed by bacterial LPS and untreated or treated with milk derived bovine Lf. Quantitative mapping of iron concentration and mass fraction at high spatial resolution is obtained combining X-ray fluorescence microscopy, atomic force microscopy and synchrotron phase contrast imaging.

Prioritising coastal zone management issues through fuzzy cognitive mapping approach.

PubMed

Meliadou, Aleka; Santoro, Francesca; Nader, Manal R; Dagher, Manale Abou; Al Indary, Shadi; Salloum, Bachir Abi

2012-04-30

Effective public participation is an essential component of Integrated Coastal Zone Management implementation. To promote such participation, a shared understanding of stakeholders' objectives has to be built to ultimately result in common coastal management strategies. The application of quantitative and semi-quantitative methods involving tools such as Fuzzy Cognitive Mapping is presently proposed for reaching such understanding. In this paper we apply the Fuzzy Cognitive Mapping tool to elucidate the objectives and priorities of North Lebanon's coastal productive sectors, and to formalize their coastal zone perceptions and knowledge. Then, we investigate the potential of Fuzzy Cognitive Mapping as tool for support coastal zone management. Five round table discussions were organized; one for the municipalities of the area and one for each of the main coastal productive sectors (tourism, industry, fisheries, agriculture), where the participants drew cognitive maps depicting their views. The analysis of the cognitive maps showed a large number of factors perceived as affecting the current situation of the North Lebanon coastal zone that were classified into five major categories: governance, infrastructure, environment, intersectoral interactions and sectoral initiatives. Furthermore, common problems, expectations and management objectives for all sectors were exposed. Within this context, Fuzzy Cognitive Mapping proved to be an essential tool for revealing stakeholder knowledge and perception and understanding complex relationships. Copyright © 2011 Elsevier Ltd. All rights reserved.

Enhancing the Characterization of Epistemic Uncertainties in PM2.5 Risk Analyses.

PubMed

Smith, Anne E; Gans, Will

2015-03-01

The Environmental Benefits Mapping and Analysis Program (BenMAP) is a software tool developed by the U.S. Environmental Protection Agency (EPA) that is widely used inside and outside of EPA to produce quantitative estimates of public health risks from fine particulate matter (PM2.5 ). This article discusses the purpose and appropriate role of a risk analysis tool to support risk management deliberations, and evaluates the functions of BenMAP in this context. It highlights the importance in quantitative risk analyses of characterization of epistemic uncertainty, or outright lack of knowledge, about the true risk relationships being quantified. This article describes and quantitatively illustrates sensitivities of PM2.5 risk estimates to several key forms of epistemic uncertainty that pervade those calculations: the risk coefficient, shape of the risk function, and the relative toxicity of individual PM2.5 constituents. It also summarizes findings from a review of U.S.-based epidemiological evidence regarding the PM2.5 risk coefficient for mortality from long-term exposure. That review shows that the set of risk coefficients embedded in BenMAP substantially understates the range in the literature. We conclude that BenMAP would more usefully fulfill its role as a risk analysis support tool if its functions were extended to better enable and prompt its users to characterize the epistemic uncertainties in their risk calculations. This requires expanded automatic sensitivity analysis functions and more recognition of the full range of uncertainty in risk coefficients. © 2014 Society for Risk Analysis.

2011, 2010 petroleum resource assessment of the National Petroleum Reserve in Alaska: GIS play maps

USGS Publications Warehouse

Garrity, Christopher P.; Houseknecht, David W.; Bird, Kenneth J.

2011-01-01

This report provides digital geographic information systems (GIS) files of maps for each of the 24 plays considered in the U.S. Geological Survey (USGS) 2010 updated petroleum resource assessment of the National Petroleum Reserve in Alaska (NPRA) (Houseknecht and others, 2010). These are the sample plays evaluated in a previous USGS assessment of the NPRA (Bird and Houseknecht, 2002a), maps of which were released in pdf format (Bird and Houseknecht, 2002b). The 2010 updated assessment of the NPRA evaluated each of the previously used 24 plays based on new geologic data available from exploration activities and scientific research. Quantitative assessments were revised for 11 plays, and no revisions were made for 9 plays. Estimates of the volume of technically recoverable, undiscovered oil, and nonassociated gas resources in these 20 plays are reported elsewhere (Houseknecht and others, 2010). Four plays quantitatively assessed in 2002 were eliminated from quantitative assessment for reasons explained by Houseknecht and others (2010). The NPRA assessment study area includes Federal and native onshore land and adjacent State offshore areas. A map showing the areal extent of each play was prepared by USGS geologists as a preliminary step in the assessment process. Boundaries were drawn on the basis of a variety of information, including seismic reflection data, results of exploration drilling, and regional patterns of rock properties. Play boundary polygons were captured by digitizing the play maps prepared by USGS geologists.

Effect of pH on molecular constitution and distribution of hemoglobin in living erythrocyte.

PubMed

Wu, Yue; Huang, Yao-Xiong; Kang, Li-Li; Wu, Zheng-Jie; Luo, Man

2010-04-01

The molecular constitution of in situ hemoglobin (Hb) and their distribution in living erythrocyte were investigated versus pH using the technique of confocal Raman microscopy. Both Raman point spectra and line mapping measurements were performed on living erythrocytes in suspensions with pH values from 4.82 to 9.70. It was found that the Hb inside a living erythrocyte would dissociate into monomer/dimer when the cells are in low and high pH environments. In contrast to the homogeneous distribution of the Hbs in the cells in neutral suspension, there are more Hbs distributing around the cell membrane or binding to the membrane as pH increases. While in low pH, as the cell become spherical, most of the Hbs distribute to the central part of the cell. In summary, our investigation suggests that the variation of the external pH not only brings changes in the morphology and membrane structure of an erythrocyte, but also affects the constitution and distribution of its intracellular Hbs, thereby the flexibility of the cell membrane and the oxygenation ability of the Hb.

Magnetic Resonance and Computed Tomography Imaging for the Evaluation of Pulmonary Hypertension

PubMed Central

Freed, Benjamin H.; Collins, Jeremy D.; François, Christopher J.; Barker, Alex J.; Cuttica, Michael J.; Chesler, Naomi C.; Markl, Michael; Shah, Sanjiv J.

2016-01-01

Imaging plays a central role in the diagnosis and management of all forms of pulmonary hypertension (PH). While Doppler echocardiography is essential for the evaluation of PH, its ability to optimally evaluate the right ventricle (RV) and pulmonary vasculature is limited by its 2D planar capabilities. Magnetic resonance imaging (MRI) and computed tomography (CT) are capable of determining the etiology and pathophysiology of PH, and can be very useful in the management of these patients. Exciting new techniques such as RV tissue characterization with T1 mapping, 4D flow of the RV and pulmonary arteries, and CT lung perfusion imaging are paving the way for a new era of imaging in PH. These imaging modalities complement echocardiography and invasive hemodynamic testing, and may be useful as surrogate endpoints for early-phase PH clinical trials. Here we discuss the role of MRI and CT in the diagnosis and management of PH, including current uses and novel research applications, and we discuss the role of value-based imaging in PH. PMID:27282439

Identification of new mutations in primary hyperoxaluria type 1 (PH1).

PubMed

von Schnakenburg, C; Rumsby, G

1998-01-01

Primary hyperoxaluria type 1 (PH1) is caused by deficiency of the hepatic peroxisomal enzyme alanine:glyoxylate aminotransferase (AGT). The AGXT gene, which codes for the 392 amino acid protein, has been mapped to chromosome 2q37.3. In order to identify new mutations in the AGXT gene we studied 79 PH1 patients using single strand conformation polymorphism analysis. In addition to a cluster of new mutations in exon 7 we report five novel mutations in exons 2, 4, 5, 9 and 10. These are T444C, G640A, G690A, 1008-1010delGCG and G1171A. These five new mutations contribute to our knowledge of the AGXT gene. Their possible consequences for PH1 phenotype and enzyme activity are discussed.

Assessing groundwater quality for irrigation using indicator kriging method

NASA Astrophysics Data System (ADS)

Delbari, Masoomeh; Amiri, Meysam; Motlagh, Masoud Bahraini

2016-11-01

One of the key parameters influencing sprinkler irrigation performance is water quality. In this study, the spatial variability of groundwater quality parameters (EC, SAR, Na+, Cl-, HCO3 - and pH) was investigated by geostatistical methods and the most suitable areas for implementation of sprinkler irrigation systems in terms of water quality are determined. The study was performed in Fasa county of Fars province using 91 water samples. Results indicated that all parameters are moderately to strongly spatially correlated over the study area. The spatial distribution of pH and HCO3 - was mapped using ordinary kriging. The probability of concentrations of EC, SAR, Na+ and Cl- exceeding a threshold limit in groundwater was obtained using indicator kriging (IK). The experimental indicator semivariograms were often fitted well by a spherical model for SAR, EC, Na+ and Cl-. For HCO3 - and pH, an exponential model was fitted to the experimental semivariograms. Probability maps showed that the risk of EC, SAR, Na+ and Cl- exceeding the given critical threshold is higher in lower half of the study area. The most proper agricultural lands for sprinkler irrigation implementation were identified by evaluating all probability maps. The suitable areas for sprinkler irrigation design were determined to be 25,240 hectares, which is about 34 percent of total agricultural lands and are located in northern and eastern parts. Overall the results of this study showed that IK is an appropriate approach for risk assessment of groundwater pollution, which is useful for a proper groundwater resources management.

A Method for Comprehensive Glycosite-Mapping and Direct Quantitation of Serum Glycoproteins.

PubMed

Hong, Qiuting; Ruhaak, L Renee; Stroble, Carol; Parker, Evan; Huang, Jincui; Maverakis, Emanual; Lebrilla, Carlito B

2015-12-04

A comprehensive glycan map was constructed for the top eight abundant glycoproteins in plasma using both specific and nonspecific enzyme digestions followed by nano liquid chromatography (LC)-chip/quadrupole time-of-flight mass spectrometry (MS) analysis. Glycopeptides were identified using an in-house software tool, GPFinder. A sensitive and reproducible multiple reaction monitoring (MRM) technique on a triple quadrupole MS was developed and applied to quantify immunoglobulins G, A, M, and their site-specific glycans simultaneously and directly from human serum/plasma without protein enrichments. A total of 64 glycopeptides and 15 peptides were monitored for IgG, IgA, and IgM in a 20 min ultra high performance (UP)LC gradient. The absolute protein contents were quantified using peptide calibration curves. The glycopeptide ion abundances were normalized to the respective protein abundances to separate protein glycosylation from protein expression. This technique yields higher method reproducibility and less sample loss when compared with the quantitation method that involves protein enrichments. The absolute protein quantitation has a wide linear range (3-4 orders of magnitude) and low limit of quantitation (femtomole level). This rapid and robust quantitation technique, which provides quantitative information for both proteins and glycosylation, will further facilitate disease biomarker discoveries.

Mapping quantitative trait loci for binary trait in the F2:3 design.

PubMed

Zhu, Chengsong; Zhang, Yuan-Ming; Guo, Zhigang

2008-12-01

In the analysis of inheritance of quantitative traits with low heritability, an F(2:3) design that genotypes plants in F(2) and phenotypes plants in F(2:3) progeny is often used in plant genetics. Although statistical approaches for mapping quantitative trait loci (QTL) in the F(2:3) design have been well developed, those for binary traits of biological interest and economic importance are seldom addressed. In this study, an attempt was made to map binary trait loci (BTL) in the F(2:3) design. The fundamental idea was: the F(2) plants were genotyped, all phenotypic values of each F(2:3) progeny were measured for binary trait, and these binary trait values and the marker genotype informations were used to detect BTL under the penetrance and liability models. The proposed method was verified by a series of Monte-Carlo simulation experiments. These results showed that maximum likelihood approaches under the penetrance and liability models provide accurate estimates for the effects and the locations of BTL with high statistical power, even under of low heritability. Moreover, the penetrance model is as efficient as the liability model, and the F(2:3) design is more efficient than classical F(2) design, even though only a single progeny is collected from each F(2:3) family. With the maximum likelihood approaches under the penetrance and the liability models developed in this study, we can map binary traits as we can do for quantitative trait in the F(2:3) design.

Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli

PubMed Central

Morris, Melody K.; Saez-Rodriguez, Julio; Clarke, David C.; Sorger, Peter K.; Lauffenburger, Douglas A.

2011-01-01

Predictive understanding of cell signaling network operation based on general prior knowledge but consistent with empirical data in a specific environmental context is a current challenge in computational biology. Recent work has demonstrated that Boolean logic can be used to create context-specific network models by training proteomic pathway maps to dedicated biochemical data; however, the Boolean formalism is restricted to characterizing protein species as either fully active or inactive. To advance beyond this limitation, we propose a novel form of fuzzy logic sufficiently flexible to model quantitative data but also sufficiently simple to efficiently construct models by training pathway maps on dedicated experimental measurements. Our new approach, termed constrained fuzzy logic (cFL), converts a prior knowledge network (obtained from literature or interactome databases) into a computable model that describes graded values of protein activation across multiple pathways. We train a cFL-converted network to experimental data describing hepatocytic protein activation by inflammatory cytokines and demonstrate the application of the resultant trained models for three important purposes: (a) generating experimentally testable biological hypotheses concerning pathway crosstalk, (b) establishing capability for quantitative prediction of protein activity, and (c) prediction and understanding of the cytokine release phenotypic response. Our methodology systematically and quantitatively trains a protein pathway map summarizing curated literature to context-specific biochemical data. This process generates a computable model yielding successful prediction of new test data and offering biological insight into complex datasets that are difficult to fully analyze by intuition alone. PMID:21408212

Quantitative molecular characterization of bovine vitreous and lens with non-invasive dynamic light scattering

NASA Technical Reports Server (NTRS)

Ansari, R. R.; Suh, K. I.; Dunker, S.; Kitaya, N.; Sebag, J.

2001-01-01

The non-invasive technique of dynamic light scattering (DLS) was used to quantitatively characterize vitreous and lens structure on a molecular level by measuring the sizes of the predominant particles and mapping the three-dimensional topographic distribution of these structural macromolecules in three spatial dimensions. The results of DLS measurements in five fresh adult bovine eyes were compared to DLS measurements in model solutions of hyaluronan (HA) and collagen (Coll). In the bovine eyes DLS measurements were obtained from excised samples of gel and liquid vitreous and compared to the model solutions. Measurements in whole vitreous were obtained at multiple points posterior to the lens to generate a three-dimensional 'map' of molecular structure. The macromolecule distribution in bovine lens was similarly characterized.In each bovine vitreous (Bo Vit) specimen, DLS predominantly detected two distinct particles, which differed in diffusion properties and hence size. Comparisons with model vitreous solutions demonstrated that these most likely corresponded to the Coll and HA components of vitreous. Three-dimensional mapping of Bo Vit found heterogeneity throughout the vitreous body, with different particle size distributions for Coll and HA at different loci. In contrast, the three-dimensional distribution of lens macromolecules was more homogeneous. Thus, the non-invasive DLS technique can quantitate the average sizes of vitreous and lens macromolecules and map their three-dimensional distribution. This method to assess quantitatively the macromolecular structure of vitreous and lens should be useful for clinical as well as experimental applications in health and disease. Copyright 2001 Academic Press.

Hypothalamic GABAergic influences on treadmill exercise responses in rats.

PubMed

Overton, J M; Redding, M W; Yancey, S L; Stremel, R W

1994-01-01

Microinjection of GABAergic antagonists in the posterior hypothalamus (PH) produces exercise-like adjustments in cardiovascular function. To test the hypothesis that a hypothalamic GABAergic mechanism within the PH modulates the cardiovascular adjustments to dynamic exercise in conscious animals, Sprague-Dawley rats (n = 10) were instrumented with bilateral guide cannula directed at the pH, an arterial cannula, and Doppler flow probes on the iliac and mesenteric arteries. Saline (100 nl) or the GABAA receptor agonist muscimol (125 ng.100 nl-1) was bilaterally injected into the PH during treadmill exercise (20 m.min-1). Microinjection of saline had no effect on mean arterial pressure (MAP), heart rate (HR), mesenteric vascular resistance (MR), or iliac vascular resistance (IR) during exercise. Microinjection of muscimol during exercise produced no significant changes in MAP (mean change +/- SE; +0 +/- 1 mmHg), HR (+17 +/- 12 b.min-1), or MR (+7 +/- 13%). However, microinjection of muscimol produced a significant increase in IR during exercise (16 +/- 6%). In addition, muscimol significantly decreased treadmill run time (saline = 19.6 +/- 0.4 min; muscimol = 17.8 +/- 0.6 min) and produced behavioral effects (including mild sedation) that were most evident after exercise. The results of these experiments suggest that while the posterior hypothalamic GABAergic system may modulate iliac blood flow during exercise in rats, this system does not modulate HR and MR responses to dynamic exercise.

Elasticity imaging of speckle-free tissue regions with moving acoustic radiation force and phase-sensitive optical coherence tomography

NASA Astrophysics Data System (ADS)

Hsieh, Bao-Yu; Song, Shaozhen; Nguyen, Thu-Mai; Yoon, Soon Joon; Shen, Tueng; Wang, Ruikang; O'Donnell, Matthew

2016-03-01

Phase-sensitive optical coherence tomography (PhS-OCT) can be utilized for quantitative shear-wave elastography using speckle tracking. However, current approaches cannot directly reconstruct elastic properties in speckle-less or speckle-free regions, for example within the crystalline lens in ophthalmology. Investigating the elasticity of the crystalline lens could improve understanding and help manage presbyopia-related pathologies that change biomechanical properties. We propose to reconstruct the elastic properties in speckle-less regions by sequentially launching shear waves with moving acoustic radiation force (mARF), and then detecting the displacement at a specific speckle-generating position, or limited set of positions, with PhS-OCT. A linear ultrasound array (with a center frequency of 5 MHz) interfaced with a programmable imaging system was designed to launch shear waves by mARF. Acoustic sources were electronically translated to launch shear waves at laterally shifted positions, where displacements were detected by speckle tracking images produced by PhS-OCT operating in M-B mode with a 125-kHz A-line rate. Local displacements were calculated and stitched together sequentially based on the distance between the acoustic source and the detection beam. Shear wave speed, and the associated elasticity map, were then reconstructed based on a time-of-flight algorithm. In this study, moving-source shear wave elasticity imaging (SWEI) can highlight a stiff inclusion within an otherwise homogeneous phantom but with a CNR increased by 3.15 dB compared to a similar image reconstructed with moving-detector SWEI. Partial speckle-free phantoms were also investigated to demonstrate that the moving-source sequence could reconstruct the elastic properties of speckle-free regions. Results show that harder inclusions within the speckle-free region can be detected, suggesting that this imaging method may be able to detect the elastic properties of the crystalline lens.

How do directors of public health perceive leadership?

PubMed

McAreav, M J; Alimo-Metcalfe, B; Connelly, J

2001-01-01

This study examines how directors of public health (DsPH) perceive effective leadership. Kelly's repertory grid technique is used. A total of 13 out of a possible 14 DsPH in one NHS region of England were interviewed. Qualitative and quantitative analysis were carried out. The findings show that male DsPH (n = 8) rate their leadership ability more highly than do female DsPH (n = 5). Qualitative analysis produced a number of categories of constructs, some of which are perceived to be indicative of effective leadership, these being "working for others", "personal attributes", "vision and innovation" and "courage and integrity" Some categories appear to be applicable only to the UK (or to public health) and not to the existing dominant US models of leadership. In general, DsPH perceptions of effective leadership converge with current theories; most specifically the UK-based theories. This study therefore refutes any simple extrapolation of US theories of leadership to UK health organisations.

Comparative analysis of time-scaling properties about water pH in Poyang Lake Inlet and Outlet on the basis of fractal methods.

PubMed

Shi, K; Liu, C Q; Huang, Z W; Zhang, B; Su, Y

2010-01-01

Detrended fluctuation analysis (DFA) and multifractal methods are applied to the time-scaling properties analysis of water pH series in Poyang Lake Inlet and Outlet in China. The results show that these pH series are characterised by long-term memory and multifractal scaling, and these characteristics have obvious differences between the Lake Inlet and Outlet. The comparison results suggest that monofractal and multifractal parameters can be quantitative dynamical indexes reflecting the capability of anti-acidification of Poyang Lake. Furthermore, we investigated the frequency-size distribution of pH series in Poyang Lake Inlet and Outlet. Our findings suggest that water pH is an example of a self-organised criticality (SOC) process. The results show that it is different SOC behaviours that result in the differences of power-law relations between pH series in Poyang Lake Inlet and Outlet. This work can be helpful to improvement of modelling of lake water quality.

Application of quartz crystal microbalance to study the impact of pH and ionic strength on protein-silicone oil interactions.

PubMed

Dixit, Nitin; Maloney, Kevin M; Kalonia, Devendra S

2011-06-30

In this study, we have used quartz crystal microbalance (QCM) to quantitate the adsorption of a protein on silicone oil coated surfaces as a function of protein concentration, pH and ionic strength using a 5 MHz quartz crystal. Protein adsorption isotherms were generated at different solution pH and ionic strengths. Surface saturation concentrations were selected from adsorption isotherms and used to generate adsorption profiles from pH 3.0 to 9.0, and at ionic strengths of 10 mM and 150 mM. At low ionic strength (10mM) and pH 5.0 (close to the isoelectric point of the protein), maximum adsorption of protein to the silicone oil surface was observed. At higher ionic strength (150 mM), no significant pH influence on adsorption was observed. QCM could be used as a reliable technique to study the binding of proteins to silicone oil coated surfaces. Copyright © 2011 Elsevier B.V. All rights reserved.

Polyamine/salt-assembled microspheres coated with hyaluronic acid for targeting and pH sensing.

PubMed

Zhang, Pan; Yang, Hui; Wang, Guojun; Tong, Weijun; Gao, Changyou

2016-06-01

The poly(allylamine hydrochloride)/trisodium citrate aggregates were fabricated and further covalently crosslinked via the coupling reaction of carboxylic sites on trisodium citrate with the amine groups on polyamine, onto which poly-L-lysine and hyaluronic acid were sequentially assembled, forming stable microspheres. The pH sensitive dye and pH insensitive dye were further labeled to enable the microspheres with pH sensing property. Moreover, these microspheres could be specifically targeted to HeLa tumor cells, since hyaluronic acid can specifically recognize and bind to CD44, a receptor overexpressed on many tumor cells. Quantitative pH measurement by confocal laser scanning microscopy demonstrated that the microspheres were internalized into HeLa cells, and accumulated in acidic compartments. By contrast, only a few microspheres were adhered on the NIH 3T3 cells surface. The microspheres with combined pH sensing property and targeting ability can enhance the insight understanding of the targeted drug vehicles trafficking after cellular internalization. Copyright © 2016 Elsevier B.V. All rights reserved.

Molecular Dissection of a Major Gene Effect on a Quantitative Trait: The Level of Alcohol Dehydrogenase Expression in Drosophila Melanogaster

PubMed Central

Stam, L. F.; Laurie, C. C.

1996-01-01

A molecular mapping experiment shows that a major gene effect on a quantitative trait, the level of alcohol dehydrogenase expression in Drosophila melanogaster, is due to multiple polymorphisms within the Adh gene. These polymorphisms are located in an intron, the coding sequence, and the 3' untranslated region. Because of nonrandom associations among polymorphisms at different sites, the individual effects combine (in some cases epistatically) to produce ``superalleles'' with large effect. These results have implications for the interpretation of major gene effects detected by quantitative trait locus mapping methods. They show that large effects due to a single locus may be due to multiple associated polymorphisms (or sequential fixations in isolated populations) rather than individual mutations of large effect. PMID:8978044

Trabecular bone class mapping across resolutions: translating methods from HR-pQCT to clinical CT

NASA Astrophysics Data System (ADS)

Valentinitsch, Alexander; Fischer, Lukas; Patsch, Janina M.; Bauer, Jan; Kainberger, Franz; Langs, Georg; DiFranco, Matthew

2015-03-01

Quantitative assessment of 3D bone microarchitecture in high-resolution peripheral quantitative computed tomography (HR-pQCT) has shown promise in fracture risk assessment and biomechanics, but is limited to the distal radius and tibia. Trabecular microarchitecture classes (TMACs), based on voxel-wise clustering texture and structure tensor features in HRpQCT, is extended in this paper to quantify trabecular bone classes in clinical multi-detector CT (MDCT) images. Our comparison of TMACs in 12 cadaver radii imaged using both HRpQCT and MDCT yields a mean Dice score of up to 0.717+/-0.40 and visually concordant bone quality maps. Further work to develop clinically viable bone quantitative imaging using HR-pQCT validation could have a significant impact on overall bone health assessment.

Spatial and Global Sensory Suppression Mapping Encompassing the Central 10° Field in Anisometropic Amblyopia.

PubMed

Li, Jingjing; Li, Jinrong; Chen, Zidong; Liu, Jing; Yuan, Junpeng; Cai, Xiaoxiao; Deng, Daming; Yu, Minbin

2017-01-01

We investigate the efficacy of a novel dichoptic mapping paradigm in evaluating visual function of anisometropic amblyopes. Using standard clinical measures of visual function (visual acuity, stereo acuity, Bagolini lenses, and neutral density filters) and a novel quantitative mapping technique, 26 patients with anisometropic amblyopia (mean age = 19.15 ± 4.42 years) were assessed. Two additional psychophysical interocular suppression measurements were tested with dichoptic global motion coherence and binocular phase combination tasks. Luminance reduction was achieved by placing neutral density filters in front of the normal eye. Our study revealed that suppression changes across the central 10° visual field by mean luminance modulation in amblyopes as well as normal controls. Using simulation and an elimination of interocular suppression, we identified a novel method to effectively reflect the distribution of suppression in anisometropic amblyopia. Additionally, the new quantitative mapping technique was in good agreement with conventional clinical measures, such as interocular acuity difference (P < 0.001) and stereo acuity (P = 0.005). There was a good consistency between the results of interocular suppression with dichoptic mapping paradigm and the results of the other two psychophysical methods (suppression mapping versus binocular phase combination, P < 0.001; suppression mapping versus global motion coherence, P = 0.005). The dichoptic suppression mapping technique is an effective method to represent impaired visual function in patients with anisometropic amblyopia. It offers a potential in "micro-"antisuppression mapping tests and therapies for amblyopia.

DFT Study of PH3 Physisorption and Chemisorptions on Boron Nitride Nanotubes

NASA Astrophysics Data System (ADS)

Rakhshi, Mahdi; Mohsennia, Mohsen; Rasa, Hossein

2018-03-01

The adsorption of PH3 molecules on the NiB,N-doped(4,4) and (5,5) BNNTS surfaces has been investigated using density functional theory (DFT). The adsorption energies, geometric and electronic structures of the adsorbed systems were studied to judge the possible application of NiB,N-doped BNNTS in PH3 monitoring systems. Our calculated results showed that NiB,N-doped BNNTS had much higher adsorption energy and shorter binding distances than pure BNNTS owning to chemisorptions of the PH3 molecule. The obtained density of states (DOS) and frontier orbitals demonstrated that the orbital hybridization was obvious between the PH3 molecule and NiB,N-doped BNNTS. However, due to weak physisorption according to the total electron density maps, there was no evidence for hybridization between PH3 molecule and pure BNNTS. It was shown that after doping of Ni atom, the primary symmetry of BNNTS decreased which enhanced the chemical activity of BNNTS towards PH3 molecules. According to the obtained results, we highlight the high potential application of NiB,N-doped BNNTS in the design and fabrication of PH3 sensing devices.

Crop biometric maps: the key to prediction.

PubMed

Rovira-Más, Francisco; Sáiz-Rubio, Verónica

2013-09-23

The sustainability of agricultural production in the twenty-first century, both in industrialized and developing countries, benefits from the integration of farm management with information technology such that individual plants, rows, or subfields may be endowed with a singular "identity." This approach approximates the nature of agricultural processes to the engineering of industrial processes. In order to cope with the vast variability of nature and the uncertainties of agricultural production, the concept of crop biometrics is defined as the scientific analysis of agricultural observations confined to spaces of reduced dimensions and known position with the purpose of building prediction models. This article develops the idea of crop biometrics by setting its principles, discussing the selection and quantization of biometric traits, and analyzing the mathematical relationships among measured and predicted traits. Crop biometric maps were applied to the case of a wine-production vineyard, in which vegetation amount, relative altitude in the field, soil compaction, berry size, grape yield, juice pH, and grape sugar content were selected as biometric traits. The enological potential of grapes was assessed with a quality-index map defined as a combination of titratable acidity, sugar content, and must pH. Prediction models for yield and quality were developed for high and low resolution maps, showing the great potential of crop biometric maps as a strategic tool for vineyard growers as well as for crop managers in general, due to the wide versatility of the methodology proposed.

Crop Biometric Maps: The Key to Prediction

PubMed Central

Rovira-Más, Francisco; Sáiz-Rubio, Verónica

2013-01-01

The sustainability of agricultural production in the twenty-first century, both in industrialized and developing countries, benefits from the integration of farm management with information technology such that individual plants, rows, or subfields may be endowed with a singular “identity.” This approach approximates the nature of agricultural processes to the engineering of industrial processes. In order to cope with the vast variability of nature and the uncertainties of agricultural production, the concept of crop biometrics is defined as the scientific analysis of agricultural observations confined to spaces of reduced dimensions and known position with the purpose of building prediction models. This article develops the idea of crop biometrics by setting its principles, discussing the selection and quantization of biometric traits, and analyzing the mathematical relationships among measured and predicted traits. Crop biometric maps were applied to the case of a wine-production vineyard, in which vegetation amount, relative altitude in the field, soil compaction, berry size, grape yield, juice pH, and grape sugar content were selected as biometric traits. The enological potential of grapes was assessed with a quality-index map defined as a combination of titratable acidity, sugar content, and must pH. Prediction models for yield and quality were developed for high and low resolution maps, showing the great potential of crop biometric maps as a strategic tool for vineyard growers as well as for crop managers in general, due to the wide versatility of the methodology proposed. PMID:24064605

Molecularly tagged genes and quantitative trait loci in cucumber

USDA-ARS?s Scientific Manuscript database

Since the release of the cucumber draft genome, significant progress has been made in molecular mapping, tagging or cloning of horticulturally important genes and quantitative trait loci (QTLs) in cucumber, which provides the foundation for practicing marker-assisted selection in cucumber breeding. ...

Forest Connectivity Regions of Canada Using Circuit Theory and Image Analysis

PubMed Central

Pelletier, David; Lapointe, Marc-Élie; Wulder, Michael A.; White, Joanne C.; Cardille, Jeffrey A.

2017-01-01

Ecological processes are increasingly well understood over smaller areas, yet information regarding interconnections and the hierarchical nature of ecosystems remains less studied and understood. Information on connectivity over large areas with high resolution source information provides for both local detail and regional context. The emerging capacity to apply circuit theory to create maps of omnidirectional connectivity provides an opportunity for improved and quantitative depictions of forest connectivity, supporting the formation and testing of hypotheses about the density of animal movement, ecosystem structure, and related links to natural and anthropogenic forces. In this research, our goal was to delineate regions where connectivity regimes are similar across the boreal region of Canada using new quantitative analyses for characterizing connectivity over large areas (e.g., millions of hectares). Utilizing the Earth Observation for Sustainable Development of forests (EOSD) circa 2000 Landsat-derived land-cover map, we created and analyzed a national-scale map of omnidirectional forest connectivity at 25m resolution over 10000 tiles of 625 km2 each, spanning the forested regions of Canada. Using image recognition software to detect corridors, pinch points, and barriers to movements at multiple spatial scales in each tile, we developed a simple measure of the structural complexity of connectivity patterns in omnidirectional connectivity maps. We then mapped the Circuitscape resistance distance measure and used it in conjunction with the complexity data to study connectivity characteristics in each forested ecozone. Ecozone boundaries masked substantial systematic patterns in connectivity characteristics that are uncovered using a new classification of connectivity patterns that revealed six clear groups of forest connectivity patterns found in Canada. The resulting maps allow exploration of omnidirectional forest connectivity patterns at full resolution while permitting quantitative analyses of connectivity over broad areas, informing modeling, planning and monitoring efforts. PMID:28146573

Quantitative trait loci that control the oil content variation of rapeseed (Brassica napus L.).

PubMed

Jiang, Congcong; Shi, Jiaqin; Li, Ruiyuan; Long, Yan; Wang, Hao; Li, Dianrong; Zhao, Jianyi; Meng, Jinling

2014-04-01

This report describes an integrative analysis of seed-oil-content quantitative trait loci (QTL) in Brassica napus , using a high-density genetic map to align QTL among different populations. Rapeseed (Brassica napus) is an important source of edible oil and sustainable energy. Given the challenge involved in using only a few genes to substantially increase the oil content of rapeseed without affecting the fatty acid composition, exploitation of a greater number of genetic loci that regulate the oil content variation among rapeseed germplasm is of fundamental importance. In this study, we investigated variation in the seed-oil content among two related genetic populations of Brassica napus, the TN double-haploid population and its derivative reconstructed-F2 population. Each population was grown in multiple experiments under different environmental conditions. Mapping of quantitative trait loci (QTL) identified 41 QTL in the TN populations. Furthermore, of the 20 pairs of epistatic interaction loci detected, approximately one-third were located within the QTL intervals. The use of common markers on different genetic maps and the TN genetic map as a reference enabled us to project QTL from an additional three genetic populations onto the TN genetic map. In summary, we used the TN genetic map of the B. napus genome to identify 46 distinct QTL regions that control seed-oil content on 16 of the 19 linkage groups of B. napus. Of these, 18 were each detected in multiple populations. The present results are of value for ongoing efforts to breed rapeseed with high oil content, and alignment of the QTL makes an important contribution to the development of an integrative system for genetic studies of rapeseed.

[Ph-Sensor Properties of a Fluorescent Protein from Dendronephthya sp].

PubMed

Pakhomov, A A; Chertkova, R V; Martynov, V I

2015-01-01

Genetically encoded biosensors based on fluorescent proteins are now widely applicable for monitoring pH changes in live cells. Here, we have shown that a fluorescent protein from Dendronephthya sp. (DendFP) exhibits a pronounced pH-sensitivity. Unlike most of known genetically encoded pH-sensors, fluorescence of the protein is not quenched upon medium acidification, but is shifting from the red to green spectral range. Therefore, quantitative measurements of intracellular pH are feasible by ratiometric comparison of emission intensities in the red and green spectral ranges, which makes DendFP advantageous compared with other genetically encoded pH-sensors.

A single pH fluorescent probe for biosensing and imaging of extreme acidity and extreme alkalinity.

PubMed

Chao, Jian-Bin; Wang, Hui-Juan; Zhang, Yong-Bin; Li, Zhi-Qing; Liu, Yu-Hong; Huo, Fang-Jun; Yin, Cai-Xia; Shi, Ya-Wei; Wang, Juan-Juan

2017-07-04

A simple tailor-made pH fluorescent probe 2-benzothiazole (N-ethylcarbazole-3-yl) hydrazone (Probe) is facilely synthesized by the condensation reaction of 2-hydrazinobenzothiazole with N-ethylcarbazole-3-formaldehyde, which is a useful fluorescent probe for monitoring extremely acidic and alkaline pH, quantitatively. The pH titrations indicate that Probe displays a remarkable emission enhancement with a pK a of 2.73 and responds linearly to minor pH fluctuations within the extremely acidic range of 2.21-3.30. Interestingly, Probe also exhibits strong pH-dependent characteristics with pK a 11.28 and linear response to extreme-alkalinity range of 10.41-12.43. In addition, Probe shows a large Stokes shift of 84 nm under extremely acidic and alkaline conditions, high selectivity, excellent sensitivity, good water-solubility and fine stability, all of which are favorable for intracellular pH imaging. The probe is further successfully applied to image extremely acidic and alkaline pH values fluctuations in E. coli cells. Copyright © 2017 Elsevier B.V. All rights reserved.

An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize

USDA-ARS?s Scientific Manuscript database

In this study, we generated a linkage map containing 1,151,856 high quality SNPs between Mo17 and B73, which were verified in the maize intermated B73'×'Mo17 (IBM) Syn10 population. This resource is an excellent complement to existing maize genetic maps available in an online database (iPlant, http:...

IBMISPS (International Brain Mapping & Intraoperative Surgical Planning Symposium)

DTIC Science & Technology

2005-12-01

they received the 2005 Excellence in R, D & E award for their contribution in the feild of prosthetics and brain imaging. Excellence in Educational...specific bipolar magnetic gradient pulses which measure the velocity vector components of motion. Presented here are the development of dynamic MR...movies of quantitative velocity vector components, 30 frames per second. The 3 velocity vector maps with tensor analysis produced maps of the

Laura Jackson, Ph.D.

EPA Pesticide Factsheets

Research Biologist with the EPA. Her current work involves linking natural and built infrastructure to human health and well-being at multiple spatial scales, in order to develop interpretive maps and analytical tools for an interactive, web-based Atlas.

[Quantitative mineralogical analyzes of kidney stones and diagnosing metabolic disorders in female patients with calcium oxalate urolithiasis].

PubMed

Kustov, A V; Moryganov, M A; Strel'nikov, A I; Zhuravleva, N I; Airapetyan, A O

2016-02-01

To conduct a complex examination of female patients with calcium oxalate urolithiasis to detect metabolic disorders, leading to stone formation. The study was carried out using complex physical and chemical methods, including quantitative X-ray phase analysis of urinary stones, pH measurement, volumetry, urine and blood spectrophotometry. Quantitative mineralogical composition of stones, daily urine pH profile, daily urinary excretion of ions of calcium, magnesium, oxalate, phosphate, citrate and uric acid were determined in 20 female patients with calcium oxalate stones. We have shown that most of the stones comprised calcium oxalate monohydrate or mixtures of calcium oxalate dihydrate and hydroxyapatite. Among the identified abnormalities, the most frequent were hypocitraturia and hypercalciuria - 90 and 45%, respectively. Our findings revealed that the daily secretion of citrate and oxalate in patients older than 50 years was significantly lower than in younger patients. In conclusion, daily urinary citrate excretion should be measured in female patients with calcium oxalate stones. This is necessary both to determine the causes of stone formation, and to monitor the effectiveness of citrate therapy.

Global combined precursor isotopic labeling and isobaric tagging (cPILOT) approach with selective MS(3) acquisition.

PubMed

Evans, Adam R; Robinson, Renã A S

2013-11-01

Recently, we reported a novel proteomics quantitation scheme termed "combined precursor isotopic labeling and isobaric tagging (cPILOT)" that allows for the identification and quantitation of nitrated peptides in as many as 12-16 samples in a single experiment. cPILOT offers enhanced multiplexing and posttranslational modification specificity, however excludes global quantitation for all peptides present in a mixture and underestimates reporter ion ratios similar to other isobaric tagging methods due to precursor co-isolation. Here, we present a novel chemical workflow for cPILOT that can be used for global tagging of all peptides in a mixture. Specifically, through low pH precursor dimethylation of tryptic or LysC peptides followed by high pH tandem mass tags, the same reporter ion can be used twice in a single experiment. Also, to improve triple-stage mass spectrometry (MS(3) ) data acquisition, a selective MS(3) method that focuses on product selection of the y1 fragment of lysine-terminated peptides is incorporated into the workflow. This novel cPILOT workflow has potential for global peptide quantitation that could lead to enhanced sample multiplexing and increase the number of quantifiable spectra obtained from MS(3) acquisition methods. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid Semi-Quantitative Surface Mapping of Airborne-Dispersed Chemicals Using Mass Spectrometry

EPA Science Inventory

Chemicals can be dispersed accidentally, deliberately, or by weather-related events. Rapid mapping of contaminant distributions is necessary to assess exposure risks and to plan remediation, when needed. Ten pulverized aspirin or NoDoz^TM tablets containing caffeine wer...

Identification of positional candidates for bovine placental genes responsible for early embryonic death during cloning-attempted pregnancy.

PubMed

Yamada, Takahisa; Muramatsu, Youji; Taniguchi, Yukio; Sasaki, Yoshiyuki

Our previous study detected 291 and 77 genes showing early embryonic death-associated elevation and reduction of expression, respectively, in the fetal placenta of the cow carrying somatic nuclear transfer-derived cloned embryo. In this study, we mapped the 10 genes showing the elevation and the 10 genes doing the reduction most significantly, using somatic cell hybrid and bovine draft genome sequence. We then compared the mapped positions for these genes with the genomic locations of bovine quantitative trait loci for still-birth and/or abortion. Among the mapped genes, peptidylglycine alpha-amidating monooxygenase (PAM), spectrin, beta, nonerythrocytic 1 (SPTBNI), and an unknown novel gene containing AU277832 expressed sequence tag were intriguing, in that the mapped positions were consistent with the genomic locations of bovine still-birth and/or abortion quantitative trait loci, and thus identified as positional candidates for bovine placental genes responsible for the early embryonic death during the pregnancy attempted by somatic nuclear transfer-derived cloning.

Quantitative Analysis of Venus Radar Backscatter Data in ArcGIS

NASA Technical Reports Server (NTRS)

Long, S. M.; Grosfils, E. B.

2005-01-01

Ongoing mapping of the Ganiki Planitia (V14) quadrangle of Venus and definition of material units has involved an integrated but qualitative analysis of Magellan radar backscatter images and topography using standard geomorphological mapping techniques. However, such analyses do not take full advantage of the quantitative information contained within the images. Analysis of the backscatter coefficient allows a much more rigorous statistical comparison between mapped units, permitting first order selfsimilarity tests of geographically separated materials assigned identical geomorphological labels. Such analyses cannot be performed directly on pixel (DN) values from Magellan backscatter images, because the pixels are scaled to the Muhleman law for radar echoes on Venus and are not corrected for latitudinal variations in incidence angle. Therefore, DN values must be converted based on pixel latitude back to their backscatter coefficient values before accurate statistical analysis can occur. Here we present a method for performing the conversions and analysis of Magellan backscatter data using commonly available ArcGIS software and illustrate the advantages of the process for geological mapping.

Quantitatively Mapping Cellular Viscosity with Detailed Organelle Information via a Designed PET Fluorescent Probe

PubMed Central

Liu, Tianyu; Liu, Xiaogang; Spring, David R.; Qian, Xuhong; Cui, Jingnan; Xu, Zhaochao

2014-01-01

Viscosity is a fundamental physical parameter that influences diffusion in biological processes. The distribution of intracellular viscosity is highly heterogeneous, and it is challenging to obtain a full map of cellular viscosity with detailed organelle information. In this work, we report 1 as the first fluorescent viscosity probe which is able to quantitatively map cellular viscosity with detailed organelle information based on the PET mechanism. This probe exhibited a significant ratiometric fluorescence intensity enhancement as solvent viscosity increases. The emission intensity increase was attributed to combined effects of the inhibition of PET due to restricted conformational access (favorable for FRET, but not for PET), and the decreased PET efficiency caused by viscosity-dependent twisted intramolecular charge transfer (TICT). A full map of subcellular viscosity was successfully constructed via fluorescent ratiometric detection and fluorescence lifetime imaging; it was found that lysosomal regions in a cell possess the highest viscosity, followed by mitochondrial regions. PMID:24957323

Averaged ratio between complementary profiles for evaluating shape distortions of map projections and spherical hierarchical tessellations

NASA Astrophysics Data System (ADS)

Yan, Jin; Song, Xiao; Gong, Guanghong

2016-02-01

We describe a metric named averaged ratio between complementary profiles to represent the distortion of map projections, and the shape regularity of spherical cells derived from map projections or non-map-projection methods. The properties and statistical characteristics of our metric are investigated. Our metric (1) is a variable of numerical equivalence to both scale component and angular deformation component of Tissot indicatrix, and avoids the invalidation when using Tissot indicatrix and derived differential calculus for evaluating non-map-projection based tessellations where mathematical formulae do not exist (e.g., direct spherical subdivisions), (2) exhibits simplicity (neither differential nor integral calculus) and uniformity in the form of calculations, (3) requires low computational cost, while maintaining high correlation with the results of differential calculus, (4) is a quasi-invariant under rotations, and (5) reflects the distortions of map projections, distortion of spherical cells, and the associated distortions of texels. As an indicator of quantitative evaluation, we investigated typical spherical tessellation methods, some variants of tessellation methods, and map projections. The tessellation methods we evaluated are based on map projections or direct spherical subdivisions. The evaluation involves commonly used Platonic polyhedrons, Catalan polyhedrons, etc. Quantitative analyses based on our metric of shape regularity and an essential metric of area uniformity implied that (1) Uniform Spherical Grids and its variant show good qualities in both area uniformity and shape regularity, and (2) Crusta, Unicube map, and a variant of Unicube map exhibit fairly acceptable degrees of area uniformity and shape regularity.

Determining fluoride ions in ammonium desulfurization slurry using an ion selective electrode method

NASA Astrophysics Data System (ADS)

Luo, Zhengwei; Guo, Mulin; Chen, Huihui; Lian, Zhouyang; Wei, Wuji

2018-02-01

Determining fluoride ions in ammonia desulphurization slurry using a fluoride ion selective electrode (ISE) is investigated. The influence of pH was studied and the appropriate total ionic strength adjustment buffer and its dosage were optimized. The impact of Fe3+ concentration on the detection results was analyzed under preferable conditions, and the error analysis of the ISE method’s accuracy and precision for measuring fluoride ion concentration in the range of 0.5-2000 mg/L was conducted. The quantitative recovery of F- in ammonium sulfate slurry was assessed. The results showed that when pH ranged from 5.5˜6 and the Fe3+ concentration was less than 750 mg/L, the accuracy and precision test results with quantitative recovery rates of 92.0%-104.2% were obtained.

Rapid quantitative analysis of individual anthocyanin content based on high-performance liquid chromatography with diode array detection with the pH differential method.

PubMed

Wang, Huayin

2014-09-01

A new quantitative technique for the simultaneous quantification of the individual anthocyanins based on the pH differential method and high-performance liquid chromatography with diode array detection is proposed in this paper. The six individual anthocyanins (cyanidin 3-glucoside, cyanidin 3-rutinoside, petunidin 3-glucoside, petunidin 3-rutinoside, and malvidin 3-rutinoside) from mulberry (Morus rubra) and Liriope platyphylla were used for demonstration and validation. The elution of anthocyanins was performed using a C18 column with stepwise gradient elution and individual anthocyanins were identified by high-performance liquid chromatography with tandem mass spectrometry. Based on the pH differential method, the high-performance liquid chromatography peak areas of maximum and reference absorption wavelengths of anthocyanin extracts were conducted to quantify individual anthocyanins. The calibration curves for these anthocyanins were linear within the range of 10-5500 mg/L. The correlation coefficients (r(2)) all exceeded 0.9972, and the limits of detection were in the range of 1-4 mg/L at a signal-to-noise ratio ≥5 for these anthocyanins. The proposed quantitative analysis was reproducible with good accuracy of all individual anthocyanins ranging from 96.3 to 104.2% and relative recoveries were in the range 98.4-103.2%. The proposed technique is performed without anthocyanin standards and is a simple, rapid, accurate, and economical method to determine individual anthocyanin contents. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development and validation of a generic high-performance liquid chromatography for the simultaneous separation and determination of six cough ingredients: Robustness study on core-shell particles.

PubMed

Yehia, Ali Mohamed; Essam, Hebatallah Mohamed

2016-09-01

A generally applicable high-performance liquid chromatographic method for the qualitative and quantitative determination of pharmaceutical preparations containing phenylephrine hydrochloride, paracetamol, ephedrine hydrochloride, guaifenesin, doxylamine succinate, and dextromethorphan hydrobromide is developed. Optimization of chromatographic conditions was performed for the gradient elution using different buffer pH values, flow rates and two C18 stationary phases. The method was developed using a Kinetex® C18 column as a core-shell stationary phase with a gradient profile using buffer pH 5.0 and acetonitrile at 2.0 mL/min flow rate. Detection was carried out at 220 nm and linear calibrations were obtained for all components within the studied ranges. The method was fully validated in agreement with ICH guidelines. The proposed method is specific, accurate and precise (RSD% < 3%). Limits of detection are lower than 2.0 μg/mL. Qualitative and quantitative responses were evaluated using experimental design to assist the method robustness. The method was proved to be highly robust against 10% change in buffer pH and flow rate (RSD% < 10%), however, the flow rate may significantly influence the quantitative responses of phenylephrine, paracetamol, and doxylamine (RSD% > 10%). Satisfactory results were obtained for commercial combinations analyses. Statistical comparison between the proposed chromatographic and official methods revealed no significant difference. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative analysis of zopiclone, N-desmethylzopiclone, zopiclone N-oxide and 2-amino-5-chloropyridine in urine using LC-MS-MS.

PubMed

Nilsson, Gunnel H; Kugelberg, Fredrik C; Ahlner, Johan; Kronstrand, Robert

2014-01-01

A simple liquid chromatography-tandem mass spectrometry method was validated to allow determination of zopiclone (ZOP), N-desmethylzopiclone (NDZOP), zopiclone N-oxide (ZOPNO) and 2-amino-5-chloropyridine (ACP) in urine at concentrations up to 3,000 ng/mL within 3.5 min. This method was used for quantitative analysis of the analytes in authentic urine samples obtained 10 h after oral administration of zopiclone (Imovane(®)) and in aliquots of the same urine samples after different storage conditions. In addition, pH of each studied urine sample was measured over time. The results showed that formation of ACP occurred at elevated pH and/or temperature by degradation of ZOP, NDZOP and ZOPNO. This method was also applied to samples obtained from two female victims of drug-facilitated assault. One sample had been exposed to long-term storage conditions at different temperatures and at pH >8.2, which resulted in high concentrations of ACP. The other sample, which was exposed to pH <6.5, showed no formation of ACP. ACP is formed both from ZOP and from its metabolites NDZOP and ZOPNO depending on the pH of the urine, time of storage and/or the temperature conditions. For correct interpretation in forensic cases, ZOP, its major metabolites and ACP should be analyzed. When ACP is identified in urine, the concentrations of ZOP, NDZOP and ZOPNO should be interpreted with great caution. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Hyperspectral Imaging Using Intracellular Spies: Quantitative Real-Time Measurement of Intracellular Parameters In Vivo during Interaction of the Pathogenic Fungus Aspergillus fumigatus with Human Monocytes

PubMed Central

Mohebbi, Sara; Erfurth, Florian; Hennersdorf, Philipp; Brakhage, Axel A.; Saluz, Hans Peter

2016-01-01

Hyperspectral imaging (HSI) is a technique based on the combination of classical spectroscopy and conventional digital image processing. It is also well suited for the biological assays and quantitative real-time analysis since it provides spectral and spatial data of samples. The method grants detailed information about a sample by recording the entire spectrum in each pixel of the whole image. We applied HSI to quantify the constituent pH variation in a single infected apoptotic monocyte as a model system. Previously, we showed that the human-pathogenic fungus Aspergillus fumigatus conidia interfere with the acidification of phagolysosomes. Here, we extended this finding to monocytes and gained a more detailed analysis of this process. Our data indicate that melanised A. fumigatus conidia have the ability to interfere with apoptosis in human monocytes as they enable the apoptotic cell to recover from mitochondrial acidification and to continue with the cell cycle. We also showed that this ability of A. fumigatus is dependent on the presence of melanin, since a non-pigmented mutant did not stop the progression of apoptosis and consequently, the cell did not recover from the acidic pH. By conducting the current research based on the HSI, we could measure the intracellular pH in an apoptotic infected human monocyte and show the pattern of pH variation during 35 h of measurements. As a conclusion, we showed the importance of melanin for determining the fate of intracellular pH in a single apoptotic cell. PMID:27727286

Improvement of medical content in the curriculum of biomedical engineering based on assessment of students outcomes.

PubMed

Abdulhay, Enas; Khnouf, Ruba; Haddad, Shireen; Al-Bashir, Areen

2017-08-04

Improvement of medical content in Biomedical Engineering curricula based on a qualitative assessment process or on a comparison with another high-standard program has been approached by a number of studies. However, the quantitative assessment tools have not been emphasized. The quantitative assessment tools can be more accurate and robust in cases of challenging multidisciplinary fields like that of Biomedical Engineering which includes biomedicine elements mixed with technology aspects. The major limitations of the previous research are the high dependence on surveys or pure qualitative approaches as well as the absence of strong focus on medical outcomes without implicit confusion with the technical ones. The proposed work presents the development and evaluation of an accurate/robust quantitative approach to the improvement of the medical content in the challenging multidisciplinary BME curriculum. The work presents quantitative assessment tools and subsequent improvement of curriculum medical content applied, as example for explanation, to the ABET (Accreditation Board for Engineering and Technology, USA) accredited biomedical engineering BME department at Jordan University of Science and Technology. The quantitative results of assessment of curriculum/course, capstone, exit exam, course assessment by student (CAS) as well as of surveys filled by alumni, seniors, employers and training supervisors were, first, mapped to the expected students' outcomes related to the medical field (SOsM). The collected data were then analyzed and discussed to find curriculum weakness points by tracking shortcomings in every outcome degree of achievement. Finally, actions were taken to fill in the gaps of the curriculum. Actions were also mapped to the students' medical outcomes (SOsM). Weighted averages of obtained quantitative values, mapped to SOsM, indicated accurately the achievement levels of all outcomes as well as the necessary improvements to be performed in curriculum. Mapping the improvements to SOsM also helps in the assessment of the following cycle. The suggested assessment tools can be generalized and extended to any other BME department. Robust improvement of medical content in BME curriculum can subsequently be achieved.

Iridium Oxide pH Sensor Based on Stainless Steel Wire for pH Mapping on Metal Surface

NASA Astrophysics Data System (ADS)

Shahrestani, S.; Ismail, M. C.; Kakooei, S.; Beheshti, M.; Zabihiazadboni, M.; Zavareh, M. A.

2018-03-01

A simple technique to fabricate the iridium oxide pH sensor is useful in several applications such as medical, food processing and engineering material where it is able to detect the changes of pH. Generally, the fabrication technique can be classified into three types: electro-deposition iridium oxide film (EIrOF), activated iridium oxide film (AIROF) and sputtering iridium oxide film (SIROF). This study focuses on fabricating electrode, calibration and test. Electro-deposition iridium oxide film is a simple and effective method of fabricating this kind of sensor via cyclic voltammetry process. The iridium oxide thick film was successfully electrodeposited on the surface of stainless steel wire with 500 cycles of sweep potential. A further analysis under FESEM shows detailed image of iridium oxide film which has cauliflower-liked microstructure. EDX analysis shows the highest element present are iridium and oxygen which concluded that the process is successful. The iridium oxide based pH sensor has shown a good performance in comparison to conventional glass pH sensor when it is being calibrated in buffer solutions with 2, 4, 7 and 9 pH values. The iridium oxide pH sensor is specifically designed to measure the pH on the surface of metal plate.

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.

Accurate and quantitative polarization-sensitive OCT by unbiased birefringence estimator with noise-stochastic correction

NASA Astrophysics Data System (ADS)

Kasaragod, Deepa; Sugiyama, Satoshi; Ikuno, Yasushi; Alonso-Caneiro, David; Yamanari, Masahiro; Fukuda, Shinichi; Oshika, Tetsuro; Hong, Young-Joo; Li, En; Makita, Shuichi; Miura, Masahiro; Yasuno, Yoshiaki

2016-03-01

Polarization sensitive optical coherence tomography (PS-OCT) is a functional extension of OCT that contrasts the polarization properties of tissues. It has been applied to ophthalmology, cardiology, etc. Proper quantitative imaging is required for a widespread clinical utility. However, the conventional method of averaging to improve the signal to noise ratio (SNR) and the contrast of the phase retardation (or birefringence) images introduce a noise bias offset from the true value. This bias reduces the effectiveness of birefringence contrast for a quantitative study. Although coherent averaging of Jones matrix tomography has been widely utilized and has improved the image quality, the fundamental limitation of nonlinear dependency of phase retardation and birefringence to the SNR was not overcome. So the birefringence obtained by PS-OCT was still not accurate for a quantitative imaging. The nonlinear effect of SNR to phase retardation and birefringence measurement was previously formulated in detail for a Jones matrix OCT (JM-OCT) [1]. Based on this, we had developed a maximum a-posteriori (MAP) estimator and quantitative birefringence imaging was demonstrated [2]. However, this first version of estimator had a theoretical shortcoming. It did not take into account the stochastic nature of SNR of OCT signal. In this paper, we present an improved version of the MAP estimator which takes into account the stochastic property of SNR. This estimator uses a probability distribution function (PDF) of true local retardation, which is proportional to birefringence, under a specific set of measurements of the birefringence and SNR. The PDF was pre-computed by a Monte-Carlo (MC) simulation based on the mathematical model of JM-OCT before the measurement. A comparison between this new MAP estimator, our previous MAP estimator [2], and the standard mean estimator is presented. The comparisons are performed both by numerical simulation and in vivo measurements of anterior and posterior eye segment as well as in skin imaging. The new estimator shows superior performance and also shows clearer image contrast.

Bound Pool Fractions Complement Diffusion Measures to Describe White Matter Micro and Macrostructure

PubMed Central

Stikov, Nikola; Perry, Lee M.; Mezer, Aviv; Rykhlevskaia, Elena; Wandell, Brian A.; Pauly, John M.; Dougherty, Robert F.

2010-01-01

Diffusion imaging and bound pool fraction (BPF) mapping are two quantitative magnetic resonance imaging techniques that measure microstructural features of the white matter of the brain. Diffusion imaging provides a quantitative measure of the diffusivity of water in tissue. BPF mapping is a quantitative magnetization transfer (qMT) technique that estimates the proportion of exchanging protons bound to macromolecules, such as those found in myelin, and is thus a more direct measure of myelin content than diffusion. In this work, we combine BPF estimates of macromolecular content with measurements of diffusivity within human white matter tracts. Within the white matter, the correlation between BPFs and diffusivity measures such as fractional anisotropy and radial diffusivity was modest, suggesting that diffusion tensor imaging and bound pool fractions are complementary techniques. We found that several major tracts have high BPF, suggesting a higher density of myelin in these tracts. We interpret these results in the context of a quantitative tissue model. PMID:20828622

Assessment of Renal Hemodynamics and Oxygenation by Simultaneous Magnetic Resonance Imaging (MRI) and Quantitative Invasive Physiological Measurements.

PubMed

Cantow, Kathleen; Arakelyan, Karen; Seeliger, Erdmann; Niendorf, Thoralf; Pohlmann, Andreas

2016-01-01

In vivo assessment of renal perfusion and oxygenation under (patho)physiological conditions by means of noninvasive diagnostic imaging is conceptually appealing. Blood oxygen level-dependent (BOLD) magnetic resonance imaging (MRI) and quantitative parametric mapping of the magnetic resonance (MR) relaxation times T 2* and T 2 are thought to provide surrogates of renal tissue oxygenation. The validity and efficacy of this technique for quantitative characterization of local tissue oxygenation and its changes under different functional conditions have not been systematically examined yet and remain to be established. For this purpose, the development of an integrative multimodality approaches is essential. Here we describe an integrated hybrid approach (MR-PHYSIOL) that combines established quantitative physiological measurements with T 2* (T 2) mapping and MR-based kidney size measurements. Standardized reversible (patho)physiologically relevant interventions, such as brief periods of aortic occlusion, hypoxia, and hyperoxia, are used for detailing the relation between the MR-PHYSIOL parameters, in particular between renal T 2* and tissue oxygenation.

Energy Dispersive Spectrometry and Quantitative Analysis Short Course. Introduction to X-ray Energy Dispersive Spectrometry and Quantitative Analysis

NASA Technical Reports Server (NTRS)

Carpenter, Paul; Curreri, Peter A. (Technical Monitor)

2002-01-01

This course will cover practical applications of the energy-dispersive spectrometer (EDS) to x-ray microanalysis. Topics covered will include detector technology, advances in pulse processing, resolution and performance monitoring, detector modeling, peak deconvolution and fitting, qualitative and quantitative analysis, compositional mapping, and standards. An emphasis will be placed on use of the EDS for quantitative analysis, with discussion of typical problems encountered in the analysis of a wide range of materials and sample geometries.

Composite Interval Mapping Based on Lattice Design for Error Control May Increase Power of Quantitative Trait Locus Detection.

PubMed

He, Jianbo; Li, Jijie; Huang, Zhongwen; Zhao, Tuanjie; Xing, Guangnan; Gai, Junyi; Guan, Rongzhan

2015-01-01

Experimental error control is very important in quantitative trait locus (QTL) mapping. Although numerous statistical methods have been developed for QTL mapping, a QTL detection model based on an appropriate experimental design that emphasizes error control has not been developed. Lattice design is very suitable for experiments with large sample sizes, which is usually required for accurate mapping of quantitative traits. However, the lack of a QTL mapping method based on lattice design dictates that the arithmetic mean or adjusted mean of each line of observations in the lattice design had to be used as a response variable, resulting in low QTL detection power. As an improvement, we developed a QTL mapping method termed composite interval mapping based on lattice design (CIMLD). In the lattice design, experimental errors are decomposed into random errors and block-within-replication errors. Four levels of block-within-replication errors were simulated to show the power of QTL detection under different error controls. The simulation results showed that the arithmetic mean method, which is equivalent to a method under random complete block design (RCBD), was very sensitive to the size of the block variance and with the increase of block variance, the power of QTL detection decreased from 51.3% to 9.4%. In contrast to the RCBD method, the power of CIMLD and the adjusted mean method did not change for different block variances. The CIMLD method showed 1.2- to 7.6-fold higher power of QTL detection than the arithmetic or adjusted mean methods. Our proposed method was applied to real soybean (Glycine max) data as an example and 10 QTLs for biomass were identified that explained 65.87% of the phenotypic variation, while only three and two QTLs were identified by arithmetic and adjusted mean methods, respectively.

Columbia's Bridge to the Ph.D. Program: A research-focused initiative facilitating the transition to graduate school

NASA Astrophysics Data System (ADS)

Agüeros, Marcel A.

2015-01-01

Columbia University's Bridge to the Ph.D. in the Natural Sciences Program aims to enhance the participation of students from underrepresented groups in Ph.D. programs. To achieve this, the Bridge Program provides an intensive research, coursework, and mentoring experience to post-baccalaureates seeking to strengthen their graduate school applications and to prepare for the transition into graduate school. To date, 20 Bridge Program alumni --- including four in astronomy --- have gone on to Ph.D. programs at Columbia, the University of Michigan, Johns Hopkins, the University of Washington, Albert Einstein, Yale, and SUNY-Albany, among others. In this talk, I will touch on some of the connections between Pre-MAP and the Bridge Program, and particularly how my involvement in the former prepared me to lead the latter.

Genetic architecture of cyst nematode resistance revealed by genome-wide association study in soybean

USDA-ARS?s Scientific Manuscript database

Bi-parental mapping populations have been commonly utilized to identify and characterize quantitative trait loci (QTL) controlling resistance to soybean cyst nematode (SCN, Heterodera glycines Ichinohe). Although this approach successfully mapped a large number of SCN resistance QTL, it captures onl...

Double-Labeled Metabolic Maps of Memory.

ERIC Educational Resources Information Center

John, E. R.; And Others

1986-01-01

Reviews a study which sought to obtain a quantitative metabolic map of the neurons mediating a specific memory. Research results support notions of cooperative processes in which nonrandom behavior of high ensembles of neural elements mediates the integration and processing of information and the retrieval of memory. (ML)

Epicuticular waxes and thrips resistance in onion

USDA-ARS?s Scientific Manuscript database

Next-generation sequencing of normalized cDNAs from two inbred lines of onion revealed over 3000 well supported single nucleotide polymorphisms (SNPs), of which over 800 have been mapped. This SNP-based map was used to identify quantitative trait loci (QTL) controlling the amounts and types of epicu...

Artificial-epitope mapping for CK-MB assay.

PubMed

Tai, Dar-Fu; Ho, Yi-Fang; Wu, Cheng-Hsin; Lin, Tzu-Chieh; Lu, Kuo-Hao; Lin, Kun-Shian

2011-06-07

A quantitative method using artificial antibody to detect creatine kinases was developed. Linear epitope sequences were selected based on an artificial-epitope mapping strategy. Nine different MIPs corresponding to the selected peptides were then fabricated on QCM chips. The subtle conformational changes were also recognized by these chips.

Coordinated Optimization of Visual Cortical Maps (I) Symmetry-based Analysis

PubMed Central

Reichl, Lars; Heide, Dominik; Löwel, Siegrid; Crowley, Justin C.; Kaschube, Matthias; Wolf, Fred

2012-01-01

In the primary visual cortex of primates and carnivores, functional architecture can be characterized by maps of various stimulus features such as orientation preference (OP), ocular dominance (OD), and spatial frequency. It is a long-standing question in theoretical neuroscience whether the observed maps should be interpreted as optima of a specific energy functional that summarizes the design principles of cortical functional architecture. A rigorous evaluation of this optimization hypothesis is particularly demanded by recent evidence that the functional architecture of orientation columns precisely follows species invariant quantitative laws. Because it would be desirable to infer the form of such an optimization principle from the biological data, the optimization approach to explain cortical functional architecture raises the following questions: i) What are the genuine ground states of candidate energy functionals and how can they be calculated with precision and rigor? ii) How do differences in candidate optimization principles impact on the predicted map structure and conversely what can be learned about a hypothetical underlying optimization principle from observations on map structure? iii) Is there a way to analyze the coordinated organization of cortical maps predicted by optimization principles in general? To answer these questions we developed a general dynamical systems approach to the combined optimization of visual cortical maps of OP and another scalar feature such as OD or spatial frequency preference. From basic symmetry assumptions we obtain a comprehensive phenomenological classification of possible inter-map coupling energies and examine representative examples. We show that each individual coupling energy leads to a different class of OP solutions with different correlations among the maps such that inferences about the optimization principle from map layout appear viable. We systematically assess whether quantitative laws resembling experimental observations can result from the coordinated optimization of orientation columns with other feature maps. PMID:23144599

Archaeal Abundance across a pH Gradient in an Arable Soil and Its Relationship to Bacterial and Fungal Growth Rates

PubMed Central

Sterngren, Anna E.; Rousk, Johannes

2012-01-01

Soil pH is one of the most influential factors for the composition of bacterial and fungal communities, but the influence of soil pH on the distribution and composition of soil archaeal communities has yet to be systematically addressed. The primary aim of this study was to determine how total archaeal abundance (quantitative PCR [qPCR]-based estimates of 16S rRNA gene copy numbers) is related to soil pH across a pH gradient (pH 4.0 to 8.3). Secondarily, we wanted to assess how archaeal abundance related to bacterial and fungal growth rates across the same pH gradient. We identified two distinct and opposite effects of pH on the archaeal abundance. In the lowest pH range (pH 4.0 to 4.7), the abundance of archaea did not seem to correspond to pH. Above this pH range, there was a sharp, almost 4-fold decrease in archaeal abundance, reaching a minimum at pH 5.1 to 5.2. The low abundance of archaeal 16S rRNA gene copy numbers at this pH range then sharply increased almost 150-fold with pH, resulting in an increase in the ratio between archaeal and bacterial copy numbers from a minimum of 0.002 to more than 0.07 at pH 8. The nonuniform archaeal response to pH could reflect variation in the archaeal community composition along the gradient, with some archaea adapted to acidic conditions and others to neutral to slightly alkaline conditions. This suggestion is reinforced by observations of contrasting outcomes of the (competitive) interactions between archaea, bacteria, and fungi toward the lower and higher ends of the examined pH gradient. PMID:22706045

Archaeal abundance across a pH gradient in an arable soil and its relationship to bacterial and fungal growth rates.

PubMed

Bengtson, Per; Sterngren, Anna E; Rousk, Johannes

2012-08-01

Soil pH is one of the most influential factors for the composition of bacterial and fungal communities, but the influence of soil pH on the distribution and composition of soil archaeal communities has yet to be systematically addressed. The primary aim of this study was to determine how total archaeal abundance (quantitative PCR [qPCR]-based estimates of 16S rRNA gene copy numbers) is related to soil pH across a pH gradient (pH 4.0 to 8.3). Secondarily, we wanted to assess how archaeal abundance related to bacterial and fungal growth rates across the same pH gradient. We identified two distinct and opposite effects of pH on the archaeal abundance. In the lowest pH range (pH 4.0 to 4.7), the abundance of archaea did not seem to correspond to pH. Above this pH range, there was a sharp, almost 4-fold decrease in archaeal abundance, reaching a minimum at pH 5.1 to 5.2. The low abundance of archaeal 16S rRNA gene copy numbers at this pH range then sharply increased almost 150-fold with pH, resulting in an increase in the ratio between archaeal and bacterial copy numbers from a minimum of 0.002 to more than 0.07 at pH 8. The nonuniform archaeal response to pH could reflect variation in the archaeal community composition along the gradient, with some archaea adapted to acidic conditions and others to neutral to slightly alkaline conditions. This suggestion is reinforced by observations of contrasting outcomes of the (competitive) interactions between archaea, bacteria, and fungi toward the lower and higher ends of the examined pH gradient.

New designs of a complete set of Photonic Crystals logic gates

NASA Astrophysics Data System (ADS)

Hussein, Hussein M. E.; Ali, Tamer A.; Rafat, Nadia H.

2018-03-01

In this paper, we introduce new designs of all-optical OR, AND, XOR, NOT, NOR, NAND and XNOR logic gates based on the interference effect. The designs are built using 2D square lattice Photonic Crystal (PhC) structure of dielectric rods embedded in air background. The lattice constant, a, and the rod radius, r, are designed to achieve maximum operating range of frequencies using the gap map. We use the Plane Wave Expansion (PWE) method to obtain the band structure and the gap map of the proposed designs. The operating wavelengths achieve a wide band range that varies between 1266.9 nm and 1996 nm with center wavelength at 1550 nm. The Finite-Difference Time-Domain (FDTD) method is used to study the field behavior inside the PhC gates. The gates satisfy their truth tables with reasonable power contrast ratio between logic '1' and logic '0'.

Bioanalysis: its past, present, and some future.

PubMed

Righetti, Pier Giorgio

2004-07-01

An overview of about 100 years of bioanalysis is here disastrously attempted. The beginning of rigorous analytical systems can perhaps be traced back to the building and testing of the analytical ultracentrifuge by Svedberg and the apparatus for moving-boundary electrophoresis of Tiselius, both systems relying on expensive and hard to operate machines. In the sixties, Porath discovered porous beads for the determination of relative molecular mass (Mr) of proteins, based on the principle of molecular sieving. Concomitantly, Svensson and his pupil Vesterberg described a revolutionary principle for fractionating proteins in a nonisocratic environment, based on generation of stable pH gradients in an electric field, a technique that went down to history as isoelectric focusing (IEF). Polyacrylamide gel electrophoresis (PAGE), with the brilliant idea of discontinuous buffers, was brought to the limelight and in 1967, sodium dodecyl sulfate (SDS)-PAGE was described, permitting easy assessment of protein purity and reasonable measurements of Mr values of denatured polypeptide chains. By the mid seventies, another explosive concept was realized: orthogonal combination of two unrelated techniques, based on surface charge and mass fractionation, namely, two-dimensional (2-D) PAGE already in the very first papers by O'Farrell elaborated to its utmost sophistication. The eighties saw the systematic growth of 2-D PAGE, accompanied by systematic efforts to develop instrumentation for large-scale production of 2-D maps and computer evaluation for 2-D map analysis, based on the sophisticated algorithms adopted by astronomers for mapping stars in the sky. Another fundamental innovation in the field of IEF was the discovery of immobilized pH gradients (IPGs) that brought the much needed reproducibility in 2-D maps while allowing exquisite resolution in very narrow pH ranges. The nineties were definitely the decade of capillary zone electrophoresis, with the concomitant concept of automation and miniaturization in electrokinetic methodologies. Also 2-D map analysis witnessed a big revival, thanks to the adoption of IPGs for the first dimension. The enormous progress of mass spectrometry resulted in first reports on the analysis of macromolecules and the building of data bases on gene and protein banks. The third millennium is, perhaps, exasperating the concept of miniaturization at all costs, while not disdaining increasingly larger maps for 2-D analysis of complex protein mixtures.

Bayesian B-spline mapping for dynamic quantitative traits.

PubMed

Xing, Jun; Li, Jiahan; Yang, Runqing; Zhou, Xiaojing; Xu, Shizhong

2012-04-01

Owing to their ability and flexibility to describe individual gene expression at different time points, random regression (RR) analyses have become a popular procedure for the genetic analysis of dynamic traits whose phenotypes are collected over time. Specifically, when modelling the dynamic patterns of gene expressions in the RR framework, B-splines have been proved successful as an alternative to orthogonal polynomials. In the so-called Bayesian B-spline quantitative trait locus (QTL) mapping, B-splines are used to characterize the patterns of QTL effects and individual-specific time-dependent environmental errors over time, and the Bayesian shrinkage estimation method is employed to estimate model parameters. Extensive simulations demonstrate that (1) in terms of statistical power, Bayesian B-spline mapping outperforms the interval mapping based on the maximum likelihood; (2) for the simulated dataset with complicated growth curve simulated by B-splines, Legendre polynomial-based Bayesian mapping is not capable of identifying the designed QTLs accurately, even when higher-order Legendre polynomials are considered and (3) for the simulated dataset using Legendre polynomials, the Bayesian B-spline mapping can find the same QTLs as those identified by Legendre polynomial analysis. All simulation results support the necessity and flexibility of B-spline in Bayesian mapping of dynamic traits. The proposed method is also applied to a real dataset, where QTLs controlling the growth trajectory of stem diameters in Populus are located.

Thinking Maps: An innovative way to increase sixth-grade student achievement in social studies

NASA Astrophysics Data System (ADS)

Reed, Tamita

The purpose of this quantitative study was to determine the effect of Thinking Maps on the achievement of 6th-grade social studies students in order to determine its effectiveness. The population of this study came from a suburban middle school in the state of Georgia. The quantitative data included a pretest and posttest. The study was designed to find (a) whether there is a significant difference between the mean posttest scores on the benchmark test of 6th-grade students who are taught with either Thinking Maps or traditional social studies methods, (b) whether there is a significant difference between the mean posttest scores on the benchmark test of 6th-grade male versus female social studies students, and (c) whether there is a significant interaction between 6th-grade students' type of social studies class and gender as to differentially affect their mean posttest scores on the benchmark test. To answer these questions, students' pretest and posttest were compared to determine if there was a statistically significant difference after Thinking Maps were implemented with the treatment group for 9 weeks. The results indicate that there was no significant difference in the test scores between the students who were taught with Thinking Maps and the students who were taught without Thinking Maps. However, the students taught with Thinking Maps had the higher adjusted posttest scores.

Quantitative Susceptibility Mapping of Human Brain Reflects Spatial Variation in Tissue Composition

PubMed Central

Li, Wei; Wu, Bing; Liu, Chunlei

2011-01-01

Image phase from gradient echo MRI provides a unique contrast that reflects brain tissue composition variations, such as iron and myelin distribution. Phase imaging is emerging as a powerful tool for the investigation of functional brain anatomy and disease diagnosis. However, the quantitative value of phase is compromised by its nonlocal and orientation dependent properties. There is an increasing need for reliable quantification of magnetic susceptibility, the intrinsic property of tissue. In this study, we developed a novel and accurate susceptibility mapping method that is also phase-wrap insensitive. The proposed susceptibility mapping method utilized two complementary equations: (1) the Fourier relationship of phase and magnetic susceptibility; and (2) the first-order partial derivative of the first equation in the spatial frequency domain. In numerical simulation, this method reconstructed the susceptibility map almost free of streaking artifact. Further, the iterative implementation of this method allowed for high quality reconstruction of susceptibility maps of human brain in vivo. The reconstructed susceptibility map provided excellent contrast of iron-rich deep nuclei and white matter bundles from surrounding tissues. Further, it also revealed anisotropic magnetic susceptibility in brain white matter. Hence, the proposed susceptibility mapping method may provide a powerful tool for the study of brain physiology and pathophysiology. Further elucidation of anisotropic magnetic susceptibility in vivo may allow us to gain more insight into the white matter microarchitectures. PMID:21224002

Quantitative susceptibility mapping: Report from the 2016 reconstruction challenge.

PubMed

Langkammer, Christian; Schweser, Ferdinand; Shmueli, Karin; Kames, Christian; Li, Xu; Guo, Li; Milovic, Carlos; Kim, Jinsuh; Wei, Hongjiang; Bredies, Kristian; Buch, Sagar; Guo, Yihao; Liu, Zhe; Meineke, Jakob; Rauscher, Alexander; Marques, José P; Bilgic, Berkin

2018-03-01

The aim of the 2016 quantitative susceptibility mapping (QSM) reconstruction challenge was to test the ability of various QSM algorithms to recover the underlying susceptibility from phase data faithfully. Gradient-echo images of a healthy volunteer acquired at 3T in a single orientation with 1.06 mm isotropic resolution. A reference susceptibility map was provided, which was computed using the susceptibility tensor imaging algorithm on data acquired at 12 head orientations. Susceptibility maps calculated from the single orientation data were compared against the reference susceptibility map. Deviations were quantified using the following metrics: root mean squared error (RMSE), structure similarity index (SSIM), high-frequency error norm (HFEN), and the error in selected white and gray matter regions. Twenty-seven submissions were evaluated. Most of the best scoring approaches estimated the spatial frequency content in the ill-conditioned domain of the dipole kernel using compressed sensing strategies. The top 10 maps in each category had similar error metrics but substantially different visual appearance. Because QSM algorithms were optimized to minimize error metrics, the resulting susceptibility maps suffered from over-smoothing and conspicuity loss in fine features such as vessels. As such, the challenge highlighted the need for better numerical image quality criteria. Magn Reson Med 79:1661-1673, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Quantitative T2-Mapping and T2⁎-Mapping Evaluation of Changes in Cartilage Matrix after Acute Anterior Cruciate Ligament Rupture and the Correlation between the Results of Both Methods.

PubMed

Tao, Hongyue; Qiao, Yang; Hu, Yiwen; Xie, Yuxue; Lu, Rong; Yan, Xu; Chen, Shuang

2018-01-01

To quantitatively assess changes in cartilage matrix after acute anterior cruciate ligament (ACL) rupture using T2- and T2 ⁎ -mapping and analyze the correlation between the results of both methods. Twenty-three patients and 23 healthy controls were enrolled and underwent quantitative MRI examination. The knee cartilage was segmented into six compartments, including lateral femur (LF), lateral tibia (LT), medial femur (MF), medial tibia (MT), trochlea (Tr), and patella (Pa). T2 and T2 ⁎ values were measured in full-thickness as well as superficial and deep layers of each cartilage compartment. Differences of T2 and T2 ⁎ values between patients and controls were compared using unpaired Student's t -test, and the correlation between their reciprocals was analyzed using Pearson's correlation coefficient. ACL-ruptured patients showed higher T2 and T2 ⁎ values in full-thickness and superficial layers of medial and lateral tibiofemoral joint. Meanwhile, patients exhibited higher T2 ⁎ values in deep layers of lateral tibiofemoral joint. The elevated percentages of T2 and T2 ⁎ value in superficial LT were most significant (20.738%, 17.525%). The reciprocal of T2 ⁎ value was correlated with that of T2 value ( r = 0.886, P < 0.001). The early degeneration could occur in various knee cartilage compartments after acute ACL rupture, especially in the superficial layer of LT. T2 ⁎ -mapping might be more sensitive in detecting deep layer of cartilage than T2-mapping.

Constrained energy minimization applied to apparent reflectance and single-scattering albedo spectra: a comparison

NASA Astrophysics Data System (ADS)

Resmini, Ronald G.; Graver, William R.; Kappus, Mary E.; Anderson, Mark E.

1996-11-01

Constrained energy minimization (CEM) has been applied to the mapping of the quantitative areal distribution of the mineral alunite in an approximately 1.8 km2 area of the Cuprite mining district, Nevada. CEM is a powerful technique for rapid quantitative mineral mapping which requires only the spectrum of the mineral to be mapped. A priori knowledge of background spectral signatures is not required. Our investigation applies CEM to calibrated radiance data converted to apparent reflectance (AR) and to single scattering albedo (SSA) spectra. The radiance data were acquired by the 210 channel, 0.4 micrometers to 2.5 micrometers airborne Hyperspectral Digital Imagery Collection Experiment sensor. CEM applied to AR spectra assumes linear mixing of the spectra of the materials exposed at the surface. This assumption is likely invalid as surface materials, which are often mixtures of particulates of different substances, are more properly modeled as intimate mixtures and thus spectral mixing analyses must take account of nonlinear effects. One technique for approximating nonlinear mixing requires the conversion of AR spectra to SSA spectra. The results of CEM applied to SSA spectra are compared to those of CEM applied to AR spectra. The occurrence of alunite is similar though not identical to mineral maps produced with both the SSA and AR spectra. Alunite is slightly more widespread based on processing with the SSA spectra. Further, fractional abundances derived from the SSA spectra are, in general, higher than those derived from AR spectra. Implications for the interpretation of quantitative mineral mapping with hyperspectral remote sensing data are discussed.

A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations

PubMed Central

Wang, Chaolong; Zöllner, Sebastian; Rosenberg, Noah A.

2012-01-01

Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure. PMID:22927824

Propagation of error from parameter constraints in quantitative MRI: Example application of multiple spin echo T2 mapping.

PubMed

Lankford, Christopher L; Does, Mark D

2018-02-01

Quantitative MRI may require correcting for nuisance parameters which can or must be constrained to independently measured or assumed values. The noise and/or bias in these constraints propagate to fitted parameters. For example, the case of refocusing pulse flip angle constraint in multiple spin echo T 2 mapping is explored. An analytical expression for the mean-squared error of a parameter of interest was derived as a function of the accuracy and precision of an independent estimate of a nuisance parameter. The expression was validated by simulations and then used to evaluate the effects of flip angle (θ) constraint on the accuracy and precision of T⁁2 for a variety of multi-echo T 2 mapping protocols. Constraining θ improved T⁁2 precision when the θ-map signal-to-noise ratio was greater than approximately one-half that of the first spin echo image. For many practical scenarios, constrained fitting was calculated to reduce not just the variance but the full mean-squared error of T⁁2, for bias in θ⁁≲6%. The analytical expression derived in this work can be applied to inform experimental design in quantitative MRI. The example application to T 2 mapping provided specific cases, depending on θ⁁ accuracy and precision, in which θ⁁ measurement and constraint would be beneficial to T⁁2 variance or mean-squared error. Magn Reson Med 79:673-682, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Bacterial pathogen gene abundance and relation to recreational water quality at seven Great Lakes beaches

USGS Publications Warehouse

Oster, Ryan J.; Wijesinghe, Rasanthi U.; Fogarty, Lisa Reynolds; Haack, Sheridan K.; Fogarty, Lisa R.; Tucker, Taaja R.; Riley, Stephen

2014-01-01

Quantitative assessment of bacterial pathogens, their geographic variability, and distribution in various matrices at Great Lakes beaches are limited. Quantitative PCR (qPCR) was used to test for genes from E. coli O157:H7 (eaeO157), shiga-toxin producing E. coli (stx2), Campylobacter jejuni (mapA), Shigella spp. (ipaH), and a Salmonella enterica-specific (SE) DNA sequence at seven Great Lakes beaches, in algae, water, and sediment. Overall, detection frequencies were mapA>stx2>ipaH>SE>eaeO157. Results were highly variable among beaches and matrices; some correlations with environmental conditions were observed for mapA, stx2, and ipaH detections. Beach seasonal mean mapA abundance in water was correlated with beach seasonal mean log10E. coli concentration. At one beach, stx2 gene abundance was positively correlated with concurrent daily E. coli concentrations. Concentration distributions for stx2, ipaH, and mapA within algae, sediment, and water were statistically different (Non-Detect and Data Analysis in R). Assuming 10, 50, or 100% of gene copies represented viable and presumably infective cells, a quantitative microbial risk assessment tool developed by Michigan State University indicated a moderate probability of illness for Campylobacter jejuni at the study beaches, especially where recreational water quality criteria were exceeded. Pathogen gene quantification may be useful for beach water quality management.

Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.

PubMed

Imprialou, Martha; Kahles, André; Steffen, Joshua G; Osborne, Edward J; Gan, Xiangchao; Lempe, Janne; Bhomra, Amarjit; Belfield, Eric; Visscher, Anne; Greenhalgh, Robert; Harberd, Nicholas P; Goram, Richard; Hein, Jotun; Robert-Seilaniantz, Alexandre; Jones, Jonathan; Stegle, Oliver; Kover, Paula; Tsiantis, Miltos; Nordborg, Magnus; Rätsch, Gunnar; Clark, Richard M; Mott, Richard

2017-04-01

To understand the population genetics of structural variants and their effects on phenotypes, we developed an approach to mapping structural variants that segregate in a population sequenced at low coverage. We avoid calling structural variants directly. Instead, the evidence for a potential structural variant at a locus is indicated by variation in the counts of short-reads that map anomalously to that locus. These structural variant traits are treated as quantitative traits and mapped genetically, analogously to a gene expression study. Association between a structural variant trait at one locus, and genotypes at a distant locus indicate the origin and target of a transposition. Using ultra-low-coverage (0.3×) population sequence data from 488 recombinant inbred Arabidopsis thaliana genomes, we identified 6502 segregating structural variants. Remarkably, 25% of these were transpositions. While many structural variants cannot be delineated precisely, we validated 83% of 44 predicted transposition breakpoints by polymerase chain reaction. We show that specific structural variants may be causative for quantitative trait loci for germination and resistance to infection by the fungus Albugo laibachii , isolate Nc14. Further we show that the phenotypic heritability attributable to read-mapping anomalies differs from, and, in the case of time to germination and bolting, exceeds that due to standard genetic variation. Genes within structural variants are also more likely to be silenced or dysregulated. This approach complements the prevalent strategy of structural variant discovery in fewer individuals sequenced at high coverage. It is generally applicable to large populations sequenced at low-coverage, and is particularly suited to mapping transpositions. Copyright © 2017 by the Genetics Society of America.

A quantitative comparison of transesophageal and epicardial color Doppler echocardiography in the intraoperative assessment of mitral regurgitation.

PubMed

Kleinman, J P; Czer, L S; DeRobertis, M; Chaux, A; Maurer, G

1989-11-15

Epicardial and transesophageal color Doppler echocardiography are both widely used for the intraoperative assessment of mitral regurgitation (MR); however, it has not been established whether grading of regurgitation is comparable when evaluated by these 2 techniques. MR jet size was quantitatively compared in 29 hemodynamically and temporally matched open-chest epicardial and transesophageal color Doppler echocardiography studies from 22 patients (18 with native and 4 with porcine mitral valves) scheduled to undergo mitral valve repair or replacement. Jet area, jet length and left atrial area were analyzed. Comparison of jet area measurements as assessed by epicardial and transesophageal color flow mapping revealed an excellent correlation between the techniques (r = 0.95, p less than 0.001). Epicardial and transesophageal jet length measurements were also similar (r = 0.77, p less than 0.001). Left atrial area could not be measured in 18 transesophageal studies (62%) due to foreshortening, and in 5 epicardial studies (17%) due to poor image resolution. Acoustic interference with left atrial and color flow mapping signals was noted in all patients with mitral valve prostheses when imaged by epicardial echocardiography, but this did not occur with transesophageal imaging. Thus, in patients undergoing valve repair or replacement, transesophageal and epicardial color flow mapping provide similar quantitative assessment of MR jet size. Jet area to left atrial area ratios have limited applicability in transesophageal color flow mapping, due to foreshortening of the left atrial borders in transesophageal views. Transesophageal color flow mapping may be especially useful in assessing dysfunctional mitral prostheses due to the lack of left atrial acoustic interference.

A quantitative comparison of the similarity between genes and geography in worldwide human populations.

PubMed

Wang, Chaolong; Zöllner, Sebastian; Rosenberg, Noah A

2012-08-01

Multivariate statistical techniques such as principal components analysis (PCA) and multidimensional scaling (MDS) have been widely used to summarize the structure of human genetic variation, often in easily visualized two-dimensional maps. Many recent studies have reported similarity between geographic maps of population locations and MDS or PCA maps of genetic variation inferred from single-nucleotide polymorphisms (SNPs). However, this similarity has been evident primarily in a qualitative sense; and, because different multivariate techniques and marker sets have been used in different studies, it has not been possible to formally compare genetic variation datasets in terms of their levels of similarity with geography. In this study, using genome-wide SNP data from 128 populations worldwide, we perform a systematic analysis to quantitatively evaluate the similarity of genes and geography in different geographic regions. For each of a series of regions, we apply a Procrustes analysis approach to find an optimal transformation that maximizes the similarity between PCA maps of genetic variation and geographic maps of population locations. We consider examples in Europe, Sub-Saharan Africa, Asia, East Asia, and Central/South Asia, as well as in a worldwide sample, finding that significant similarity between genes and geography exists in general at different geographic levels. The similarity is highest in our examples for Asia and, once highly distinctive populations have been removed, Sub-Saharan Africa. Our results provide a quantitative assessment of the geographic structure of human genetic variation worldwide, supporting the view that geography plays a strong role in giving rise to human population structure.

Statistical parametric mapping of stimuli-evoked changes in quantitative blood flow using extended-focus optical coherence microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Marchand, Paul J.; Bouwens, Arno; Shamaei, Vincent; Nguyen, David; Extermann, Jerome; Bolmont, Tristan; Lasser, Theo

2016-03-01

Magnetic Resonance Imaging has revolutionised our understanding of brain function through its ability to image human cerebral structures non-invasively over the entire brain. By exploiting the different magnetic properties of oxygenated and deoxygenated blood, functional MRI can indirectly map areas undergoing neural activation. Alongside the development of fMRI, powerful statistical tools have been developed in an effort to shed light on the neural pathways involved in processing of sensory and cognitive information. In spite of the major improvements made in fMRI technology, the obtained spatial resolution of hundreds of microns prevents MRI in resolving and monitoring processes occurring at the cellular level. In this regard, Optical Coherence Microscopy is an ideal instrumentation as it can image at high spatio-temporal resolution. Moreover, by measuring the mean and the width of the Doppler spectra of light scattered by moving particles, OCM allows extracting the axial and lateral velocity components of red blood cells. The ability to assess quantitatively total blood velocity, as opposed to classical axial velocity Doppler OCM, is of paramount importance in brain imaging as a large proportion of cortical vascular is oriented perpendicularly to the optical axis. We combine here quantitative blood flow imaging with extended-focus Optical Coherence Microscopy and Statistical Parametric Mapping tools to generate maps of stimuli-evoked cortical hemodynamics at the capillary level.

Temporal maps and informativeness in associative learning.

PubMed

Balsam, Peter D; Gallistel, C Randy

2009-02-01

Neurobiological research on learning assumes that temporal contiguity is essential for association formation, but what constitutes temporal contiguity has never been specified. We review evidence that learning depends, instead, on learning a temporal map. Temporal relations between events are encoded even from single experiences. The speed with which an anticipatory response emerges is proportional to the informativeness of the encoded relation between a predictive stimulus or event and the event it predicts. This principle yields a quantitative account of the heretofore undefined, but theoretically crucial, concept of temporal pairing, an account in quantitative accord with surprising experimental findings. The same principle explains the basic results in the cue competition literature, which motivated the Rescorla-Wagner model and most other contemporary models of associative learning. The essential feature of a memory mechanism in this account is its ability to encode quantitative information.

Temporal maps and informativeness in associative learning

PubMed Central

Balsam, Peter D; Gallistel, C. Randy

2009-01-01

Neurobiological research on learning assumes that temporal contiguity is essential for association formation, but what constitutes temporal contiguity has never been specified. We review evidence that learning depends, instead, on learning a temporal map. Temporal relations between events are encoded even from single experiences. The speed with which an anticipatory response emerges is proportional to the informativeness of the encoded relation between a predictive stimulus or event and the event it predicts. This principle yields a quantitative account of the heretofore undefined, but theoretically crucial, concept of temporal pairing, an account in quantitative accord with surprising experimental findings. The same principle explains the basic results in the cue competition literature, which motivated the Rescorla–Wagner model and most other contemporary models of associative learning. The essential feature of a memory mechanism in this account is its ability to encode quantitative information. PMID:19136158

Quantitative trait loci associated with anthracnose resistance in sorghum

USDA-ARS?s Scientific Manuscript database

With an aim to develop a durable resistance to the fungal disease anthracnose, two unique genetic sources of resistance were selected to create genetic mapping populations to identify regions of the sorghum genome that encode anthracnose resistance. A series of quantitative trait loci were identifi...

Molecularly Characterized Solvent Extracts and Saponins from Polygonum hydropiper L. Show High Anti-Angiogenic, Anti-Tumor, Brine Shrimp, and Fibroblast NIH/3T3 Cell Line Cytotoxicity

PubMed Central

Ayaz, Muhammad; Junaid, Muhammad; Ullah, Farhat; Sadiq, Abdul; Subhan, Fazal; Khan, Mir Azam; Ahmad, Waqar; Ali, Gowhar; Imran, Muhammad; Ahmad, Sajjad

2016-01-01

Polygonum hydropiper is used as anti-cancer and anti-rheumatic agent in folk medicine. This study was designed to investigate the anti-angiogenic, anti-tumor, and cytotoxic potentials of different solvent extracts and isolated saponins. Samples were analyzed using GC, Gas Chromatography–Mass Spectrometry (GC–MS) to identify major and bioactive compounds. Quantitation of antiangiogenesis for the plant's samples including methanolic extract (Ph.Cr), its subsequent fractions; n-hexane (Ph.Hex), chloroform (Ph.Chf), ethyl acetate (Ph.EtAc), n-Butanol (Ph.Bt), aqueous (Ph.Aq), saponins (Ph.Sp) were performed using the chick embryo chorioallantoic membrane (CAM) assay. Potato disc anti-tumor assay was performed on Agrobacterium tumefaciens containing tumor inducing plasmid. Cytotoxicity was performed against Artemia salina and mouse embryonic fibroblast NIH/3T3 cell line following contact toxicity and MTT cells viability assays, respectively. The GC–MS analysis of Ph.Cr, Ph.Hex, Ph.Chf, Ph.Bt, and Ph.EtAc identified 126, 124, 153, 131, and 164 compounds, respectively. In anti-angiogenic assay, Ph.Chf, Ph.Sp, Ph.EtAc, and Ph.Cr exhibited highest activity with IC50 of 28.65, 19.21, 88.75, and 461.53 μg/ml, respectively. In anti-tumor assay, Ph.Sp, Ph.Chf, Ph.EtAc, and Ph.Cr were most potent with IC50 of 18.39, 73.81, 217.19, and 342.53 μg/ml, respectively. In MTT cells viability assay, Ph.Chf, Ph.EtAc, Ph.Sp were most active causing 79.00, 72.50, and 71.50% cytotoxicity, respectively, at 1000 μg/ml with the LD50 of 140, 160, and 175 μg/ml, respectively. In overall study, Ph.Chf and Ph.Sp have shown overwhelming results which signifies their potentials as sources of therapeutic agents against cancer. PMID:27065865

Linkage and mapping of quantitative trait loci associated with angular leaf spot and powdery mildew resistance in common beans

PubMed Central

Bassi, Denis; Briñez, Boris; Rosa, Juliana Santa; Oblessuc, Paula Rodrigues; de Almeida, Caléo Panhoca; Nucci, Stella Maris; da Silva, Larissa Chariel Domingos; Chiorato, Alisson Fernando; Vianello, Rosana Pereira; Camargo, Luis Eduardo Aranha; Blair, Matthew Wohlgemuth; Benchimol-Reis, Luciana Lasry

2017-01-01

Abstract Angular leaf spot (ALS) and powdery mildew (PWM) are two important fungi diseases causing significant yield losses in common beans. In this study, a new genetic linkage map was constructed using single sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), in a segregating population derived from the AND 277 x SEA 5 cross, with 105 recombinant inbred lines. Phenotypic evaluations were performed in the greenhouse to identify quantitative trait loci (QTLs) associated with resistance by means of the composite interval mapping analysis. Four QTLs were identified for ALS resistance. The QTL ALS11AS, linked on the SNP BAR 5054, mapped on chromosome Pv11, showed the greatest effect (R2 = 26.5%) on ALS phenotypic variance. For PWM resistance, two QTLs were detected, PWM2AS and PWM11AS, on Pv2 and Pv11, explaining 7% and 66% of the phenotypic variation, respectively. Both QTLs on Pv11 were mapped on the same genomic region, suggesting that it is a pleiotropic region. The present study resulted in the identification of new markers closely linked to ALS and PWM QTLs, which can be used for marker-assisted selection, fine mapping and positional cloning. PMID:28222201

Mapping 180° polar domains using electron backscatter diffraction and dynamical scattering simulations

DOE PAGES

Burch, Matthew J.; Fancher, Chris M.; Patala, Srikanth; ...

2016-11-18

A novel technique, which directly and nondestructively maps polar domains using electron backscatter diffraction (EBSD) is described and demonstrated. Through dynamical diffraction simulations and quantitative comparison to experimental EBSD patterns, the absolute orientation of a non-centrosymmetric crystal can be determined. With this information, the polar domains of a material can be mapped. The technique is demonstrated by mapping the non-ferroelastic, or 180°, ferroelectric domains in periodically poled LiNbO 3 single crystals. Furthermore, the authors demonstrate the possibility of mapping polarity using this technique in other polar materials system.

Quantitative genetic bases of anthocyanin variation in grape (Vitis vinifera L. ssp. sativa) berry: a quantitative trait locus to quantitative trait nucleotide integrated study.

PubMed

Fournier-Level, Alexandre; Le Cunff, Loïc; Gomez, Camila; Doligez, Agnès; Ageorges, Agnès; Roux, Catherine; Bertrand, Yves; Souquet, Jean-Marc; Cheynier, Véronique; This, Patrice

2009-11-01

The combination of QTL mapping studies of synthetic lines and association mapping studies of natural diversity represents an opportunity to throw light on the genetically based variation of quantitative traits. With the positional information provided through quantitative trait locus (QTL) mapping, which often leads to wide intervals encompassing numerous genes, it is now feasible to directly target candidate genes that are likely to be responsible for the observed variation in completely sequenced genomes and to test their effects through association genetics. This approach was performed in grape, a newly sequenced genome, to decipher the genetic architecture of anthocyanin content. Grapes may be either white or colored, ranging from the lightest pink to the darkest purple tones according to the amount of anthocyanin accumulated in the berry skin, which is a crucial trait for both wine quality and human nutrition. Although the determinism of the white phenotype has been fully identified, the genetic bases of the quantitative variation of anthocyanin content in berry skin remain unclear. A single QTL responsible for up to 62% of the variation in the anthocyanin content was mapped on a Syrah x Grenache F(1) pseudo-testcross. Among the 68 unigenes identified in the grape genome within the QTL interval, a cluster of four Myb-type genes was selected on the basis of physiological evidence (VvMybA1, VvMybA2, VvMybA3, and VvMybA4). From a core collection of natural resources (141 individuals), 32 polymorphisms revealed significant association, and extended linkage disequilibrium was observed. Using a multivariate regression method, we demonstrated that five polymorphisms in VvMybA genes except VvMybA4 (one retrotransposon, three single nucleotide polymorphisms and one 2-bp insertion/deletion) accounted for 84% of the observed variation. All these polymorphisms led to either structural changes in the MYB proteins or differences in the VvMybAs promoters. We concluded that the continuous variation in anthocyanin content in grape was explained mainly by a single gene cluster of three VvMybA genes. The use of natural diversity helped to reduce one QTL to a set of five quantitative trait nucleotides and gave a clear picture of how isogenes combined their effects to shape grape color. Such analysis also illustrates how isogenes combine their effect to shape a complex quantitative trait and enables the definition of markers directly targeted for upcoming breeding programs.

An ultrasensitive method of real time pH monitoring with complementary metal oxide semiconductor image sensor.

PubMed

Devadhasan, Jasmine Pramila; Kim, Sanghyo

2015-02-09

CMOS sensors are becoming a powerful tool in the biological and chemical field. In this work, we introduce a new approach on quantifying various pH solutions with a CMOS image sensor. The CMOS image sensor based pH measurement produces high-accuracy analysis, making it a truly portable and user friendly system. pH indicator blended hydrogel matrix was fabricated as a thin film to the accurate color development. A distinct color change of red, green and blue (RGB) develops in the hydrogel film by applying various pH solutions (pH 1-14). The semi-quantitative pH evolution was acquired by visual read out. Further, CMOS image sensor absorbs the RGB color intensity of the film and hue value converted into digital numbers with the aid of an analog-to-digital converter (ADC) to determine the pH ranges of solutions. Chromaticity diagram and Euclidean distance represent the RGB color space and differentiation of pH ranges, respectively. This technique is applicable to sense the various toxic chemicals and chemical vapors by situ sensing. Ultimately, the entire approach can be integrated into smartphone and operable with the user friendly manner. Copyright © 2014 Elsevier B.V. All rights reserved.

Quantitative Susceptibility Mapping using Structural Feature based Collaborative Reconstruction (SFCR) in the Human Brain

PubMed Central

Cai, Congbo; Chen, Zhong; van Zijl, Peter C.M.

2017-01-01

The reconstruction of MR quantitative susceptibility mapping (QSM) from local phase measurements is an ill posed inverse problem and different regularization strategies incorporating a priori information extracted from magnitude and phase images have been proposed. However, the anatomy observed in magnitude and phase images does not always coincide spatially with that in susceptibility maps, which could give erroneous estimation in the reconstructed susceptibility map. In this paper, we develop a structural feature based collaborative reconstruction (SFCR) method for QSM including both magnitude and susceptibility based information. The SFCR algorithm is composed of two consecutive steps corresponding to complementary reconstruction models, each with a structural feature based l1 norm constraint and a voxel fidelity based l2 norm constraint, which allows both the structure edges and tiny features to be recovered, whereas the noise and artifacts could be reduced. In the M-step, the initial susceptibility map is reconstructed by employing a k-space based compressed sensing model incorporating magnitude prior. In the S-step, the susceptibility map is fitted in spatial domain using weighted constraints derived from the initial susceptibility map from the M-step. Simulations and in vivo human experiments at 7T MRI show that the SFCR method provides high quality susceptibility maps with improved RMSE and MSSIM. Finally, the susceptibility values of deep gray matter are analyzed in multiple head positions, with the supine position most approximate to the gold standard COSMOS result. PMID:27019480

Quantitative Analysis of Localized Sources Identified by Focal Impulse and Rotor Modulation Mapping in Atrial Fibrillation

PubMed Central

Benharash, Peyman; Buch, Eric; Frank, Paul; Share, Michael; Tung, Roderick; Shivkumar, Kalyanam; Mandapati, Ravi

2015-01-01

Background New approaches to ablation of atrial fibrillation (AF) include focal impulse and rotor modulation (FIRM) mapping, and initial results reported with this technique have been favorable. We sought to independently evaluate the approach by analyzing quantitative characteristics of atrial electrograms used to identify rotors and describe acute procedural outcomes of FIRM-guided ablation. Methods and Results All FIRM-guided ablation procedures (n=24; 50% paroxysmal) at University of California, Los Angeles Medical Center were included for analysis. During AF, unipolar atrial electrograms collected from a 64-pole basket catheter were used to construct phase maps and identify putative AF sources. These sites were targeted for ablation, in conjunction with pulmonary vein isolation in most patients (n=19; 79%). All patients had rotors identified (mean, 2.3±0.9 per patient; 72% in left atrium). Prespecified acute procedural end point was achieved in 12 of 24 (50%) patients: AF termination (n=1), organization (n=3), or >10% slowing of AF cycle length (n=8). Basket electrodes were within 1 cm of 54% of left atrial surface area, and a mean of 31 electrodes per patient showed interpretable atrial electrograms. Offline analysis revealed no differences between rotor and distant sites in dominant frequency or Shannon entropy. Electroanatomic mapping showed no rotational activation at FIRM-identified rotor sites in 23 of 24 patients (96%). Conclusions FIRM-identified rotor sites did not exhibit quantitative atrial electrogram characteristics expected from rotors and did not differ quantitatively from surrounding tissue. Catheter ablation at these sites, in conjunction with pulmonary vein isolation, resulted in AF termination or organization in a minority of patients (4/24; 17%). Further validation of this approach is necessary. PMID:25873718

Quantitative 3D analysis of bone in hip osteoarthritis using clinical computed tomography.

PubMed

Turmezei, Tom D; Treece, Graham M; Gee, Andrew H; Fotiadou, Anastasia F; Poole, Kenneth E S

2016-07-01

To assess the relationship between proximal femoral cortical bone thickness and radiological hip osteoarthritis using quantitative 3D analysis of clinical computed tomography (CT) data. Image analysis was performed on clinical CT imaging data from 203 female volunteers with a technique called cortical bone mapping (CBM). Colour thickness maps were created for each proximal femur. Statistical parametric mapping was performed to identify statistically significant differences in cortical bone thickness that corresponded with the severity of radiological hip osteoarthritis. Kellgren and Lawrence (K&L) grade, minimum joint space width (JSW) and a novel CT-based osteophyte score were also blindly assessed from the CT data. For each increase in K&L grade, cortical thickness increased by up to 25 % in distinct areas of the superolateral femoral head-neck junction and superior subchondral bone plate. For increasing severity of CT osteophytes, the increase in cortical thickness was more circumferential, involving a wider portion of the head-neck junction, with up to a 7 % increase in cortical thickness per increment in score. Results were not significant for minimum JSW. These findings indicate that quantitative 3D analysis of the proximal femur can identify changes in cortical bone thickness relevant to structural hip osteoarthritis. • CT is being increasingly used to assess bony involvement in osteoarthritis • CBM provides accurate and reliable quantitative analysis of cortical bone thickness • Cortical bone is thicker at the superior femoral head-neck with worse osteoarthritis • Regions of increased thickness co-locate with impingement and osteophyte formation • Quantitative 3D bone analysis could enable clinical disease prediction and therapy development.

Au36(SePh)24 nanomolecules: synthesis, optical spectroscopy and theoretical analysis.

PubMed

Rambukwella, Milan; Chang, Le; Ravishanker, Anish; Fortunelli, Alessandro; Stener, Mauro; Dass, Amala

2018-05-16

Here, we report the synthesis of selenophenol (HSePh) protected Au36(SePh)24 nanomolecules via a ligand-exchange reaction of 4-tert-butylbenzenethiol (HSPh-tBu) protected Au36(SPh-tBu)24 with selenophenol, and its spectroscopic and theoretical analysis. Matrix assisted laser desorption ionization (MALDI) mass spectrometry, electrospray ionization (ESI) mass spectrometry and optical characterization confirm that the composition of the as synthesized product is predominantly Au36(SePh)24 nanomolecules. Size exclusion chromatography (SEC) was employed to isolate the Au36(SePh)24 and temperature dependent optical absorption studies and theoretical analysis were performed. Theoretically, an Independent Component Maps of Oscillator Strength (ICM-OS) analysis of simulated spectra shows that the enhancement in absorption intensity in Au36(SePh)24 with respect to Au36(SPh)24 can be ascribed to the absence of interference and/or increased long-range coupling between interband metal core and ligand excitations. This work demonstrates and helps to understand the effect of Au-Se bridging on the properties of gold nanomolecules.

A sprayable luminescent pH sensor and its use for wound imaging in vivo.

PubMed

Schreml, Stephan; Meier, Robert J; Weiß, Katharina T; Cattani, Julia; Flittner, Dagmar; Gehmert, Sebastian; Wolfbeis, Otto S; Landthaler, Michael; Babilas, Philipp

2012-12-01

Non-invasive luminescence imaging is of great interest for studying biological parameters in wound healing, tumors and other biomedical fields. Recently, we developed the first method for 2D luminescence imaging of pH in vivo on humans, and a novel method for one-stop-shop visualization of oxygen and pH using the RGB read-out of digital cameras. Both methods make use of semitransparent sensor foils. Here, we describe a sprayable ratiometric luminescent pH sensor, which combines properties of both these methods. Additionally, a major advantage is that the sensor spray is applicable to very uneven tissue surfaces due to its consistency. A digital RGB image of the spray on tissue is taken. The signal of the pH indicator (fluorescein isothiocyanate) is stored in the green channel (G), while that of the reference dye [ruthenium(II)-tris-(4,7-diphenyl-1,10-phenanthroline)] is stored in the red channel (R). Images are processed by rationing luminescence intensities (G/R) to result in pseudocolor pH maps of tissues, e.g. wounds. © 2012 John Wiley & Sons A/S.

New Therapeutic Approaches and Prognostic Assays for Breast Cancer: Radiolabeled Ligands and Antibodies and Quantitative PCR..

DTIC Science & Technology

1997-11-01

and Quantitative PCR PRINCIPAL INVESTIGATOR: Indra Poola, Ph.D. CONTRACTING ORGANIZATION: Howard university Washington, DC 20059 REPORT DATE... Howard University Washington, DC 20059 8. PERFORMING ORGANIZATION REPORT NUMBER 8. SPONSORING f MONITORING AGENCY NAME(S) AND ADDRESS(ES) U.S...Stollar J.A. Hanover B.L. Vallee C.B. Hirschberg November 21, 1997 Indra Poola Dept. of Pharmacology Howard University School of Medicine 520 W

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.

Cartilage Repair Surgery: Outcome Evaluation by Using Noninvasive Cartilage Biomarkers Based on Quantitative MRI Techniques?

PubMed Central

Jungmann, Pia M.; Baum, Thomas; Bauer, Jan S.; Karampinos, Dimitrios C.; Link, Thomas M.; Li, Xiaojuan; Trattnig, Siegfried; Rummeny, Ernst J.; Woertler, Klaus; Welsch, Goetz H.

2014-01-01

Background. New quantitative magnetic resonance imaging (MRI) techniques are increasingly applied as outcome measures after cartilage repair. Objective. To review the current literature on the use of quantitative MRI biomarkers for evaluation of cartilage repair at the knee and ankle. Methods. Using PubMed literature research, studies on biochemical, quantitative MR imaging of cartilage repair were identified and reviewed. Results. Quantitative MR biomarkers detect early degeneration of articular cartilage, mainly represented by an increasing water content, collagen disruption, and proteoglycan loss. Recently, feasibility of biochemical MR imaging of cartilage repair tissue and surrounding cartilage was demonstrated. Ultrastructural properties of the tissue after different repair procedures resulted in differences in imaging characteristics. T2 mapping, T1rho mapping, delayed gadolinium-enhanced MRI of cartilage (dGEMRIC), and diffusion weighted imaging (DWI) are applicable on most clinical 1.5 T and 3 T MR scanners. Currently, a standard of reference is difficult to define and knowledge is limited concerning correlation of clinical and MR findings. The lack of histological correlations complicates the identification of the exact tissue composition. Conclusions. A multimodal approach combining several quantitative MRI techniques in addition to morphological and clinical evaluation might be promising. Further investigations are required to demonstrate the potential for outcome evaluation after cartilage repair. PMID:24877139

Zeta potential orientation dependence of sapphire substrates.

PubMed

Kershner, Ryan J; Bullard, Joseph W; Cima, Michael J

2004-05-11

The zeta potential of planar sapphire substrates for three different crystallographic orientations was measured by a streaming potential technique in the presence of KCl and (CH3)4NCl electrolytes. The streaming potential was measured for large single crystalline C-plane (0001), A-plane (1120), and R-plane (1102) wafers over a full pH range at three or more ionic strengths ranging from 1 to 100 mM. The roughness of the epi-polished wafers was verified using atomic force microscopy to be on the order of atomic scale, and X-ray photoelectron spectroscopy (XPS) was used to ensure that the samples were free of silica and other contaminants. The results reveal a shift in the isoelectric point (iep) of the three samples by as much as two pH units, with the R-plane surface exhibiting the most acidic behavior and the C-plane samples having the highest iep. The iep at all ionic strengths was tightly centered around a single pH for each wafer. These values of iep are substantially different from the range of pH 8-10 consistently reported in the literature for alpha-Al2O3 particles. Particle zeta potential measurements were performed on a model powder using phase analysis light scattering, and the iep was confirmed to occur at pH 8. Modified Auger parameters (MAP) were calculated from XPS spectra of a monolayer of iridium metal deposited on the sapphire by electron beam deposition. A shift in MAP consistent with the observed differences in iep of the surfaces confirms the effect of surface structure on the transfer of charge between the Ir and sapphire, hence accounting for the changes in acidity as a function of crystallographic orientation.

A High-Density Genetic Map with Array-Based Markers Facilitates Structural and Quantitative Trait Locus Analyses of the Common Wheat Genome

PubMed Central

Iehisa, Julio Cesar Masaru; Ohno, Ryoko; Kimura, Tatsuro; Enoki, Hiroyuki; Nishimura, Satoru; Okamoto, Yuki; Nasuda, Shuhei; Takumi, Shigeo

2014-01-01

The large genome and allohexaploidy of common wheat have complicated construction of a high-density genetic map. Although improvements in the throughput of next-generation sequencing (NGS) technologies have made it possible to obtain a large amount of genotyping data for an entire mapping population by direct sequencing, including hexaploid wheat, a significant number of missing data points are often apparent due to the low coverage of sequencing. In the present study, a microarray-based polymorphism detection system was developed using NGS data obtained from complexity-reduced genomic DNA of two common wheat cultivars, Chinese Spring (CS) and Mironovskaya 808. After design and selection of polymorphic probes, 13,056 new markers were added to the linkage map of a recombinant inbred mapping population between CS and Mironovskaya 808. On average, 2.49 missing data points per marker were observed in the 201 recombinant inbred lines, with a maximum of 42. Around 40% of the new markers were derived from genic regions and 11% from repetitive regions. The low number of retroelements indicated that the new polymorphic markers were mainly derived from the less repetitive region of the wheat genome. Around 25% of the mapped sequences were useful for alignment with the physical map of barley. Quantitative trait locus (QTL) analyses of 14 agronomically important traits related to flowering, spikes, and seeds demonstrated that the new high-density map showed improved QTL detection, resolution, and accuracy over the original simple sequence repeat map. PMID:24972598

A high-density genetic map with array-based markers facilitates structural and quantitative trait locus analyses of the common wheat genome.

PubMed

Iehisa, Julio Cesar Masaru; Ohno, Ryoko; Kimura, Tatsuro; Enoki, Hiroyuki; Nishimura, Satoru; Okamoto, Yuki; Nasuda, Shuhei; Takumi, Shigeo

2014-10-01

The large genome and allohexaploidy of common wheat have complicated construction of a high-density genetic map. Although improvements in the throughput of next-generation sequencing (NGS) technologies have made it possible to obtain a large amount of genotyping data for an entire mapping population by direct sequencing, including hexaploid wheat, a significant number of missing data points are often apparent due to the low coverage of sequencing. In the present study, a microarray-based polymorphism detection system was developed using NGS data obtained from complexity-reduced genomic DNA of two common wheat cultivars, Chinese Spring (CS) and Mironovskaya 808. After design and selection of polymorphic probes, 13,056 new markers were added to the linkage map of a recombinant inbred mapping population between CS and Mironovskaya 808. On average, 2.49 missing data points per marker were observed in the 201 recombinant inbred lines, with a maximum of 42. Around 40% of the new markers were derived from genic regions and 11% from repetitive regions. The low number of retroelements indicated that the new polymorphic markers were mainly derived from the less repetitive region of the wheat genome. Around 25% of the mapped sequences were useful for alignment with the physical map of barley. Quantitative trait locus (QTL) analyses of 14 agronomically important traits related to flowering, spikes, and seeds demonstrated that the new high-density map showed improved QTL detection, resolution, and accuracy over the original simple sequence repeat map. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus.

PubMed

Li, Fagen; Zhou, Changpin; Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

2015-01-01

Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10-56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa.

Comparative Genomics Analyses Reveal Extensive Chromosome Colinearity and Novel Quantitative Trait Loci in Eucalyptus

PubMed Central

Weng, Qijie; Li, Mei; Yu, Xiaoli; Guo, Yong; Wang, Yu; Zhang, Xiaohong; Gan, Siming

2015-01-01

Dense genetic maps, along with quantitative trait loci (QTLs) detected on such maps, are powerful tools for genomics and molecular breeding studies. In the important woody genus Eucalyptus, the recent release of E. grandis genome sequence allows for sequence-based genomic comparison and searching for positional candidate genes within QTL regions. Here, dense genetic maps were constructed for E. urophylla and E. tereticornis using genomic simple sequence repeats (SSR), expressed sequence tag (EST) derived SSR, EST-derived cleaved amplified polymorphic sequence (EST-CAPS), and diversity arrays technology (DArT) markers. The E. urophylla and E. tereticornis maps comprised 700 and 585 markers across 11 linkage groups, totaling at 1,208.2 and 1,241.4 cM in length, respectively. Extensive synteny and colinearity were observed as compared to three earlier DArT-based eucalypt maps (two maps with E. grandis × E. urophylla and one map of E. globulus) and with the E. grandis genome sequence. Fifty-three QTLs for growth (10–56 months of age) and wood density (56 months) were identified in 22 discrete regions on both maps, in which only one colocalizaiton was found between growth and wood density. Novel QTLs were revealed as compared with those previously detected on DArT-based maps for similar ages in Eucalyptus. Eleven to 585 positional candidate genes were obained for a 56-month-old QTL through aligning QTL confidence interval with the E. grandis genome. These results will assist in comparative genomics studies, targeted gene characterization, and marker-assisted selection in Eucalyptus and the related taxa. PMID:26695430

Quantitative trait loci mapping for flowering time in a switchgrass pseudo-F2 population

USDA-ARS?s Scientific Manuscript database

Flowering is an important developmental event in switchgrass (Panicum virgatum) because the onset of flowering causes the cessation of vegetative growth and biomass accumulation. The objective of this study was to generate a linkage map using single nucleotide polymorphism (SNP) markers to identify ...

Allelic analysis of sheath blight resistance with association mapping in rice

USDA-ARS?s Scientific Manuscript database

Sheath blight is one of the most devastating diseases world-wide in rice. For the first time, we adopted association mapping to identify quantitative trait loci for sheath blight resistance from the USDA rice mini-core collection. The phenotyping was conducted with a newly developed micro-chamber me...

Metrics and Mappings: A Framework for Understanding Real-World Quantitative Estimation.

ERIC Educational Resources Information Center

Brown, Norman R.; Siegler, Robert S.

1993-01-01

A metrics and mapping framework is proposed to account for how heuristics, domain-specific reasoning, and intuitive statistical induction processes are integrated to generate estimates. Results of 4 experiments involving 188 undergraduates illustrate framework usefulness and suggest when people use heuristics and when they emphasize…

RAMP: a computer system for mapping regional areas

Treesearch

Bradley B. Nickey

1975-01-01

Until 1972, the U.S. Forest Service's Individual Fire Reports recorded locations by the section-township-range system..These earlier fire reports, therefore, lacked congruent locations. RAMP (Regional Area Mapping Procedure) was designed to make the reports more useful for quantitative analysis. This computer-based technique converts locations expressed in...

Correlation characteristics of phase and amplitude chimeras in an ensemble of nonlocally coupled maps

NASA Astrophysics Data System (ADS)

Vadivasova, T. E.; Strelkova, G. I.; Bogomolov, S. A.; Anishchenko, V. S.

2017-01-01

Correlation characteristics of chimera states have been calculated using the coefficient of mutual correlation of elements in a closed-ring ensemble of nonlocally coupled chaotic maps. Quantitative differences between the coefficients of mutual correlation for phase and amplitude chimeras are established for the first time.

Shelf-Life Extension of Chill-Stored Beef Longissimus Steaks Packaged under Modified Atmospheres with 50% O2 and 40% CO2.

PubMed

Yang, Xiaoyin; Niu, Lebao; Zhu, Lixian; Liang, Rongrong; Zhang, Yimin; Luo, Xin

2016-07-01

This study was conducted to compare the shelf-life of beef steaks stored in different packaging conditions: overwrapped (OW) packaging and 2 modified atmosphere packaging systems (MAP): 80% O2 MAP (80% O2 /20% CO2 ) and 50% O2 MAP (50% O2 /40% CO2 /10% N2 ). Steaks were stored at 2 °C for 20 d. Headspace gas composition, microbial counts, color stability, pH, purge loss, and lipid oxidation were monitored. Among the packaging types, 50% O2 MAP was superior to OW packaging and 80% O2 MAP in delaying bacterial growth and extending shelf-life to 20 d. 50% O2 MAP also gave steaks an acceptable color during storage. No significant differences were observed in color stability of steaks packaged in both 50% O2 MAP and 80% O2 MAP. This study reveals 50% O2 MAP is a realistic alternative to preserve beef steaks efficiently. © 2016 Institute of Food Technologists®

XRF map identification problems based on a PDE electrodeposition model

NASA Astrophysics Data System (ADS)

Sgura, Ivonne; Bozzini, Benedetto

2017-04-01

In this paper we focus on the following map identification problem (MIP): given a morphochemical reaction-diffusion (RD) PDE system modeling an electrodepostion process, we look for a time t *, belonging to the transient dynamics and a set of parameters \\mathbf{p} , such that the PDE solution, for the morphology h≤ft(x,y,{{t}\\ast};\\mathbf{p}\\right) and for the chemistry θ ≤ft(x,y,{{t}\\ast};\\mathbf{p}\\right) approximates a given experimental map M *. Towards this aim, we introduce a numerical algorithm using singular value decomposition (SVD) and Frobenius norm to give a measure of error distance between experimental maps for h and θ and simulated solutions of the RD-PDE system on a fixed time integration interval. The technique proposed allows quantitative use of microspectroscopy images, such as XRF maps. Specifically, in this work we have modelled the morphology and manganese distributions of nanostructured components of innovative batteries and we have followed their changes resulting from ageing under operating conditions. The availability of quantitative information on space-time evolution of active materials in terms of model parameters will allow dramatic improvements in knowledge-based optimization of battery fabrication and operation.

Horizontal and vertical variability of soil properties in a trace element contaminated area

NASA Astrophysics Data System (ADS)

Burgos, Pilar; Madejón, Engracia; Pérez-de-Mora, Alfredo; Cabrera, Francisco

2008-02-01

The spatial distribution of some soil chemical properties and trace element contents of a plot affected by the Aznalcóllar mine spill were investigated using statistical and geostatistical methods to assess the extent of soil contamination. Total and EDTA-extractable soil trace element concentrations and total S content showed great variability and high coefficients of variation in the three examined depths. Soil in the plot was found to be significantly contaminated by As, Cd, Cu, Pb and Zn within a wide range of pH. Total trace element concentrations at all depths (0-60 cm) were much higher than background values of non-affected soil, indicating that despite the clean-up operations, the concentration of trace elements in the experimental plot was still high. The spatial distribution of the different variables was estimated by kriging to design contour maps. These maps allowed the identification of specific zones with high metal concentrations and low pH values corresponding to spots of residual sludge. Moreover, kriged maps showed distinct spatial distribution and hence different behaviour for the elements considered. This information may be applied to optimise remediation strategies in highly and moderately contaminated areas.

The Mapping Model: A Cognitive Theory of Quantitative Estimation

ERIC Educational Resources Information Center

von Helversen, Bettina; Rieskamp, Jorg

2008-01-01

How do people make quantitative estimations, such as estimating a car's selling price? Traditionally, linear-regression-type models have been used to answer this question. These models assume that people weight and integrate all information available to estimate a criterion. The authors propose an alternative cognitive theory for quantitative…

Solving Quantitative Problems: Guidelines for Teaching Derived from Research.

ERIC Educational Resources Information Center

Kramers-Pals, H.; Pilot, A.

1988-01-01

Presents four guidelines for teaching quantitative problem-solving based on research results: analyze difficulties of students, develop a system of heuristics, select and map key relations, and design instruction with proper orientation, exercise, and feedback. Discusses the four guidelines and uses flow charts and diagrams to show how the…

Models of Quantitative Estimations: Rule-Based and Exemplar-Based Processes Compared

ERIC Educational Resources Information Center

von Helversen, Bettina; Rieskamp, Jorg

2009-01-01

The cognitive processes underlying quantitative estimations vary. Past research has identified task-contingent changes between rule-based and exemplar-based processes (P. Juslin, L. Karlsson, & H. Olsson, 2008). B. von Helversen and J. Rieskamp (2008), however, proposed a simple rule-based model--the mapping model--that outperformed the…

University Students' Understanding of the Concepts Empirical, Theoretical, Qualitative and Quantitative Research

ERIC Educational Resources Information Center

Murtonen, Mari

2015-01-01

University research education in many disciplines is frequently confronted by problems with students' weak level of understanding of research concepts. A mind map technique was used to investigate how students understand central methodological concepts of empirical, theoretical, qualitative and quantitative. The main hypothesis was that some…

Scaling up nurse education: An evaluation of a national PhD capacity development programme in South Africa, in the context of the global shortage of nursing graduates.

PubMed

Comiskey, Catherine M; Matthews, Anne; Williamson, Charmaine; Bruce, Judith; Mulaudzi, Mavis; Klopper, Hester

2015-05-01

The global shortage of nursing professionals educated at baccalaureate level and beyond has been highlighted. Within America, services are preparing to treat an additional 32 million individuals under the Health Reform Bill. Within South Africa nursing education outputs do not meet demands. Countries are addressing these shortages by developing advanced nurse roles which require research degrees. To evaluate a national PhD programme within the context of a nurse education strategy and a national health insurance plan. A comparative effectiveness research design was employed. The setting was in South Africa between 2011 and 2013, a county with 51.7 million inhabitants. Participants included PhD candidates, programme facilitators, supervisors and key stakeholders. Data from a one day workshop was analysed using an inductive thematic analysis. Three years of evaluation reports were analysed. A mapping of the alignment of the PhD topics with healthcare priorities, and a comparison of the development of nurse education, of the national and international funder were conducted. The evaluation reports rated the programme highly. Three themes were identified from the workshop. These were, "support" with the sub-themes of burden, leveraging and a physical supportive place; "planning" with the sub-themes of the national context and practice, and "quality" with the sub-themes of processes and monitoring and evaluation. The mapping of PhD topics revealed that research was in line with development priorities. However, further investment and infrastructural changes were necessary to sustain the programme and its impact. To address sustainability and capacity in nations scaling up nurse education and healthcare insurance, it was recommended that top-up degrees for diploma educated nurses be developed along with, the implementation of a national nursing strategy for PhD and post-doctoral training encompassing clinical practice implementation and collaboration. Copyright © 2015 Elsevier Ltd. All rights reserved.

Periplasmic Acid Stress Increases Cell Division Asymmetry (Polar Aging) of Escherichia coli

PubMed Central

Clark, Michelle W.; Yie, Anna M.; Eder, Elizabeth K.; Dennis, Richard G.; Basting, Preston J.; Martinez, Keith A.; Jones, Brian D.; Slonczewski, Joan L.

2015-01-01

Under certain kinds of cytoplasmic stress, Escherichia coli selectively reproduce by distributing the newer cytoplasmic components to new-pole cells while sequestering older, damaged components in cells inheriting the old pole. This phenomenon is termed polar aging or cell division asymmetry. It is unknown whether cell division asymmetry can arise from a periplasmic stress, such as the stress of extracellular acid, which is mediated by the periplasm. We tested the effect of periplasmic acid stress on growth and division of adherent single cells. We tracked individual cell lineages over five or more generations, using fluorescence microscopy with ratiometric pHluorin to measure cytoplasmic pH. Adherent colonies were perfused continually with LBK medium buffered at pH 6.00 or at pH 7.50; the external pH determines periplasmic pH. In each experiment, cell lineages were mapped to correlate division time, pole age and cell generation number. In colonies perfused at pH 6.0, the cells inheriting the oldest pole divided significantly more slowly than the cells inheriting the newest pole. In colonies perfused at pH 7.50 (near or above cytoplasmic pH), no significant cell division asymmetry was observed. Under both conditions (periplasmic pH 6.0 or pH 7.5) the cells maintained cytoplasmic pH values at 7.2–7.3. No evidence of cytoplasmic protein aggregation was seen. Thus, periplasmic acid stress leads to cell division asymmetry with minimal cytoplasmic stress. PMID:26713733

Assessment of source-based nitrogen removal alternatives in leather tanning industry wastewater.

PubMed

Zengin, G; Olmez, T; Doğruel, S; Kabdaşli, I; Tünay, O

2002-01-01

Nitrogen is an important parameter of leather tanning wastewaters. Magnesium ammonium phosphate (MAP) precipitation is a chemical treatment alternative for ammonia removal. In this study, a detailed source-based wastewater characterisation of a bovine leather tannery was made and nitrogen speciation as well as other basic pollutant parameter values was evaluated. This evaluation has led to definition of alternatives for source-based MAP treatment. MAP precipitation experiments conducted on these alternatives have yielded over 90% ammonia removal at pH 9.5 and using stoichiometric doses. Among the alternatives tested liming-deliming and bating-washing was found to be the most advantageous providing 71% ammonia removal.

Mapping of fluoride endemic areas and correlation studies of fluoride with other quality parameters of drinking water of Veppanapalli block of Dharmapuri district in Tamil Nadu.

PubMed

Karthikeyan, G; Sundarraj, A Shunmuga; Elango, K P

2003-10-01

193 drinking water samples from water sources of 27 panchayats of Veppanapalli block of Dharmapuri district of Tamil Nadu were analysed for chemical quality parameters. Based on the fluoride content of the water sources, fluoride maps differentiating regions with high / low fluoride levels were prepared using Isopleth mapping technique. The interdependence among the important chemical quality parameters were assessed using correlation studies. The experimental results of the application of linear and multiple regression equations on the influence of hardness, alkalinity, total dissolved solids and pH on fluoride are discussed.

An open-source computational and data resource to analyze digital maps of immunopeptidomes

DOE PAGES

Caron, Etienne; Espona, Lucia; Kowalewski, Daniel J.; ...

2015-07-08

We present a novel mass spectrometry-based high-throughput workflow and an open-source computational and data resource to reproducibly identify and quantify HLA-associated peptides. Collectively, the resources support the generation of HLA allele-specific peptide assay libraries consisting of consensus fragment ion spectra, and the analysis of quantitative digital maps of HLA peptidomes generated from a range of biological sources by SWATH mass spectrometry (MS). This study represents the first community-based effort to develop a robust platform for the reproducible and quantitative measurement of the entire repertoire of peptides presented by HLA molecules, an essential step towards the design of efficient immunotherapies.

Analyzing the texture changes in the quantitative phase maps of adipocytes

NASA Astrophysics Data System (ADS)

Roitshtain, Darina; Sharabani-Yosef, Orna; Gefen, Amit; Shaked, Natan T.

2016-03-01

We present a new analysis tool for studying texture changes in the quantitative phase maps of live cells acquired by wide-field interferometry. The sensitivity of wide-field interferometry systems to small changes in refractive index enables visualizing cells and inner cell organelles without the using fluorescent dyes or other cell-invasive approaches, which may affect the measurement and require external labeling. Our label-free texture-analysis tool is based directly on the optical path delay profile of the sample and does not necessitate decoupling refractive index and thickness in the cell quantitative phase profile; thus, relevant parameters can be calculated using a single-frame acquisition. Our experimental system includes low-coherence wide-field interferometer, combined with simultaneous florescence microscopy system for validation. We used this system and analysis tool for studying lipid droplets formation in adipocytes. The latter demonstration is relevant for various cellular functions such as lipid metabolism, protein storage and degradation to viral replication. These processes are functionally linked to several physiological and pathological conditions, including obesity and metabolic diseases. Quantification of these biological phenomena based on the texture changes in the cell phase map has a potential as a new cellular diagnosis tool.

Comparative mapping reveals quantitative trait loci that affect spawning time in coho salmon (Oncorhynchus kisutch)

PubMed Central

Araneda, Cristian; Díaz, Nelson F.; Gomez, Gilda; López, María Eugenia; Iturra, Patricia

2012-01-01

Spawning time in salmonids is a sex-limited quantitative trait that can be modified by selection. In rainbow trout (Oncorhynchus mykiss), various quantitative trait loci (QTL) that affect the expression of this trait have been discovered. In this study, we describe four microsatellite loci associated with two possible spawning time QTL regions in coho salmon (Oncorhynchus kisutch). The four loci were identified in females from two populations (early and late spawners) produced by divergent selection from the same base population. Three of the loci (OmyFGT34TUF, One2ASC and One19ASC) that were strongly associated with spawning time in coho salmon (p < 0.0002) were previously associated with QTL for the same trait in rainbow trout; a fourth loci (Oki10) with a suggestive association (p = 0.00035) mapped 10 cM from locus OmyFGT34TUF in rainbow trout. The changes in allelic frequency observed after three generations of selection were greater than expected because of genetic drift. This work shows that comparing information from closely-related species is a valid strategy for identifying QTLs for marker-assisted selection in species whose genomes are poorly characterized or lack a saturated genetic map. PMID:22888302

Quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.

PubMed

Schmid, Volker J; Cremer, Marion; Cremer, Thomas

2017-07-01

Recent advancements of super-resolved fluorescence microscopy have revolutionized microscopic studies of cells, including the exceedingly complex structural organization of cell nuclei in space and time. In this paper we describe and discuss tools for (semi-) automated, quantitative 3D analyses of the spatial nuclear organization. These tools allow the quantitative assessment of highly resolved different chromatin compaction levels in individual cell nuclei, which reflect functionally different regions or sub-compartments of the 3D nuclear landscape, and measurements of absolute distances between sites of different chromatin compaction. In addition, these tools allow 3D mapping of specific DNA/RNA sequences and nuclear proteins relative to the 3D chromatin compaction maps and comparisons of multiple cell nuclei. The tools are available in the free and open source R packages nucim and bioimagetools. We discuss the use of masks for the segmentation of nuclei and the use of DNA stains, such as DAPI, as a proxy for local differences in chromatin compaction. We further discuss the limitations of 3D maps of the nuclear landscape as well as problems of the biological interpretation of such data. Copyright © 2017 Elsevier Inc. All rights reserved.

Recent advances in merging photonic crystals and plasmonics for bioanalytical applications.

PubMed

Liu, Bing; Monshat, Hosein; Gu, Zhongze; Lu, Meng; Zhao, Xiangwei

2018-05-29

Photonic crystals (PhCs) and plasmonic nanostructures offer the unprecedented capability to control the interaction of light and biomolecules at the nanoscale. Based on PhC and plasmonic phenomena, a variety of analytical techniques have been demonstrated and successfully implemented in many fields, such as biological sciences, clinical diagnosis, drug discovery, and environmental monitoring. During the past decades, PhC and plasmonic technologies have progressed in parallel with their pros and cons. The merging of photonic crystals with plasmonics will significantly improve biosensor performances and enlarge the linear detection range of analytical targets. Here, we review the state-of-the-art biosensors that combine PhC and plasmonic nanomaterials for quantitative analysis. The optical mechanisms of PhCs, plasmonic crystals, and metal nanoparticles (NPs) are presented, along with their integration and potential applications. By explaining the optical coupling of photonic crystals and plasmonics, the review manifests how PhC-plasmonic hybrid biosensors can achieve the advantages, including high sensitivity, low cost, and short assay time as well. The review also discusses the challenges and future opportunities in this fascinating field.

Improved fiber-optic chemical sensor for penicillin

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

Healy, B.G.; Walt, D.R.

An optical penicillin biosensor is described, based on the enzyme penicillinase. The sensor is fabricated by selective photodeposition of analyte-sensitive polymer matrices on optical imaging fibers. The penicillin-sensitive matrices are fabricated by immobilizing the enzyme as micrometer-sized particles in a polymer hydrogel with a covalently bound pH indicator. An array of penicillin-sensitive and pH-sensitive matrices are fabricated on the same fiber. This array allows for the simultaneous, independent measurement of pH and penicillin. Independent measurement of the two analytes allows penicillin to be quantitated in the presence of a concurrent pH change. An analysis was conducted of enzyme kinetic parametersmore » in order to model the penicillin response of the sensor at all pH values. This analysis accounts for the varying activity of the immobilized penicillinase at different pH values. The sensor detects penicillin in the range 0.25-10.0 mM in the pH range 6.2-7.5. The sensor was used to quantify penicillin concentration produced during a Penicillium chrysogenum fermentation. 27 refs., 7 figs., 1 tab.« less

Ratiometric fluorescent sensing of pH values in living cells by dual-fluorophore-labeled i-motif nanoprobes.

PubMed

Huang, Jin; Ying, Le; Yang, Xiaohai; Yang, Yanjing; Quan, Ke; Wang, He; Xie, Nuli; Ou, Min; Zhou, Qifeng; Wang, Kemin

2015-09-01

We designed a new ratiometric fluorescent nanoprobe for sensing pH values in living cells. Briefly, the nanoprobe consists of a gold nanoparticle (AuNP), short single-stranded oligonucleotides, and dual-fluorophore-labeled i-motif sequences. The short oligonucleotides are designed to bind with the i-motif sequences and immobilized on the AuNP surface via Au-S bond. At neutral pH, the dual fluorophores are separated, resulting in very low fluorescence resonance energy transfer (FRET) efficiency. At acidic pH, the i-motif strands fold into a quadruplex structure and leave the AuNP, bringing the dual fluorophores into close proximity, resulting in high FRET efficiency, which could be used as a signal for pH sensing. The nanoprobe possesses abilities of cellular transfection, enzymatic protection, fast response and quantitative pH detection. The in vitro and intracellular applications of the nanoprobe were demonstrated, which showed excellent response in the physiological pH range. Furthermore, our experimental results suggested that the nanoprobe showed excellent spatial and temporal resolution in living cells. We think that the ratiometric sensing strategy could potentially be applied to create a variety of new multicolor sensors for intracellular detection.

Genetically Targeted Ratiometric and Activated pH Indicator Complexes (TRApHIC) for Receptor Trafficking.

PubMed

Perkins, Lydia A; Yan, Qi; Schmidt, Brigitte F; Kolodieznyi, Dmytro; Saurabh, Saumya; Larsen, Mads Breum; Watkins, Simon C; Kremer, Laura; Bruchez, Marcel P

2018-02-06

Fluorescent protein-based pH sensors are useful tools for measuring protein trafficking through pH changes associated with endo- and exocytosis. However, commonly used pH-sensing probes are ubiquitously expressed with their protein of interest throughout the cell, hindering our ability to focus on specific trafficking pools of proteins. We developed a family of excitation ratiometric, activatable pH responsive tandem dyes, consisting of a pH sensitive Cy3 donor linked to a fluorogenic malachite green acceptor. These cell-excluded dyes are targeted and activated upon binding to a genetically expressed fluorogen-activating protein and are suitable for selective labeling of surface proteins for analysis of endocytosis and recycling in live cells using both confocal and superresolution microscopy. Quantitative profiling of the endocytosis and recycling of tagged β2-adrenergic receptor (B2AR) at a single-vesicle level revealed differences among B2AR agonists, consistent with more detailed pharmacological profiling.

Dependence of the cyclization of branched tetraethers (CBT) on soil moisture in the Chinese Loess Plateau and the adjacent areas: implications for palaeorainfall reconstructions

NASA Astrophysics Data System (ADS)

Wang, H.; Liu, W.; Zhang, C. L.

2014-06-01

Branched glycerol dialkyl glycerol tetraethers (bGDGTs) have been show promising for continental paleotemperature studies in loess-paleosol sequences (LPSs). Thus far, however, little is known about the effect of soil moisture on their distributions on the Chinese Loess Plateau (CLP). In this study, the relationships between environmental variables and the cyclization of bGDGTs (the so called CBT index) were investigated in a comprehensive set of surface soils in the CLP and its adjacent arid/semi-arid areas. We find that CBT correlates best with soil water content (SWC) or mean annual precipitation (MAP) for the total sample set. Particularly for the CLP soils, there is a significant positive relationship between CBT and MAP (CBT = -0.0021 · MAP + 1.7, n = 37, R2 = 0.87; MAP range: 210-680 mm). This indicates that CBT is mainly controlled by soil moisture in the alkalescent soils (pH > 7) in arid/semi-arid regions, where it is not sensitive to soil pH. Therefore, we suggest that CBT can potentially be used as a palaeorainfall proxy on the CLP. According to the preliminary CBT-MAP relationship for modern CLP soils, palaeorainfall history was reconstructed from three LPSs (Yuanbao, Lantian, and Mangshan) with published bGDGT data spanning the past 70 ka. The CBT-derived MAP records of the three sites consistently show precession-driven variations resembling the speleothem δ18O monsoon record, and are also in general accord with the fluctuations of the respective magnetic susceptibility (MS) record, supporting CBT as a reasonable proxy for palaeorainfall reconstruction in LPS studies. Moreover, the comparison of CBT-derived MAP and bGDGT-derived temperature may enable us to further assess the relative timing and magnitude of hydrological and thermal changes on the CLP, independent of chronology.

Spatial variability of isoproturon mineralizing activity within an agricultural field: geostatistical analysis of simple physicochemical and microbiological soil parameters.

PubMed

El Sebai, T; Lagacherie, B; Soulas, G; Martin-Laurent, F

2007-02-01

We assessed the spatial variability of isoproturon mineralization in relation to that of physicochemical and biological parameters in fifty soil samples regularly collected along a sampling grid delimited across a 0.36 ha field plot (40 x 90 m). Only faint relationships were observed between isoproturon mineralization and the soil pH, microbial C biomass, and organic nitrogen. Considerable spatial variability was observed for six of the nine parameters tested (isoproturon mineralization rates, organic nitrogen, genetic structure of the microbial communities, soil pH, microbial biomass and equivalent humidity). The map of isoproturon mineralization rates distribution was similar to that of soil pH, microbial biomass, and organic nitrogen but different from those of structure of the microbial communities and equivalent humidity. Geostatistics revealed that the spatial heterogeneity in the rate of degradation of isoproturon corresponded to that of soil pH and microbial biomass.

Quantitative accuracy of the simplified strong ion equation to predict serum pH in dogs.

PubMed

Cave, N J; Koo, S T

2015-01-01

Electrochemical approach to the assessment of acid-base states should provide a better mechanistic explanation of the metabolic component than methods that consider only pH and carbon dioxide. Simplified strong ion equation (SSIE), using published dog-specific values, would predict the measured serum pH of diseased dogs. Ten dogs, hospitalized for various reasons. Prospective study of a convenience sample of a consecutive series of dogs admitted to the Massey University Veterinary Teaching Hospital (MUVTH), from which serum biochemistry and blood gas analyses were performed at the same time. Serum pH was calculated (Hcal+) using the SSIE, and published values for the concentration and dissociation constant for the nonvolatile weak acids (Atot and Ka ), and subsequently Hcal+ was compared with the dog's actual pH (Hmeasured+). To determine the source of discordance between Hcal+ and Hmeasured+, the calculations were repeated using a series of substituted values for Atot and Ka . The Hcal+ did not approximate the Hmeasured+ for any dog (P = 0.499, r(2) = 0.068), and was consistently more basic. Substituted values Atot and Ka did not significantly improve the accuracy (r(2) = 0.169 to <0.001). Substituting the effective SID (Atot-[HCO3-]) produced a strong association between Hcal+ and Hmeasured+ (r(2) = 0.977). Using the simplified strong ion equation and the published values for Atot and Ka does not appear to provide a quantitative explanation for the acid-base status of dogs. Efficacy of substituting the effective SID in the simplified strong ion equation suggests the error lies in calculating the SID. Copyright © 2015 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals, Inc. on behalf of the American College of Veterinary Internal Medicine.

Epithelial organic cation transporters ensure pH-dependent drug absorption in the airway.

PubMed

Horvath, Gabor; Schmid, Nathalie; Fragoso, Miryam A; Schmid, Andreas; Conner, Gregory E; Salathe, Matthias; Wanner, Adam

2007-01-01

Most inhaled beta(2)-adrenergic agonist and anticholinergic bronchodilators have low lipid solubility because of their transient or permanent positive net charge at physiologic pH. Airway absorption of these cationic drugs is incompletely understood. We examined carrier-mediated mechanisms of cationic drug uptake by human airway epithelia. Airway tissues and epithelial cells, obtained from lung donors without preexisting lung disease, were evaluated for organic cation transporter expression by quantitative RT-PCR and immunofluorescence. For in vitro functional studies on primary airway epithelial cells, uptake of the cationic fluorophore 4-[4-(dimethylamino)-styryl]-N-methylpyridinium (ASP+) was characterized. Quantitative RT-PCR analysis demonstrated high mRNA levels for two polyspecific organic cation/carnitine transporters, OCTN1 and OCTN2, in human airway epithelia. Immunofluorescence of human airway sections confirmed OCTN1/2 protein expression, with a predominant localization to the apical portion of epithelial cells. Primary airway epithelial cells showed a carrier-mediated, temperature-sensitive and saturable uptake of ASP(+). Seventy-five to eighty percent of ASP(+) uptake was inhibited by L-carnitine, an OCTN2-carried zwitterion. The uptake was pH dependent, with approximately 3-fold lower rates at acidic (pH 5.7) than at alkaline (pH 8.2) extracellular pH. Albuterol and formoterol inhibited ASP(+) uptake, suggesting that all these molecules are carried by the same transport mechanism. These findings demonstrate the existence and functional role of a pH-dependent organic cation uptake machinery, namely OCTN1 and OCTN2, in human airway epithelia. We suggest that epithelial OCTN1/2 are involved in the delivery of inhaled cationic bronchodilators to the airway tissue.

Quantitative description and local structures of trivalent metal ions Eu(III) and Cm(III) complexed with polyacrylic acid.

PubMed

Montavon, G; Bouby, M; Huclier-Markai, S; Grambow, B; Geckeis, H; Rabung, T; Pashalidis, I; Amekraz, B; Moulin, C

2008-11-15

The trivalent metal ion (M(III)=Cm, Eu)/polyacrylic acid (PAA) system was studied in the pH range between 3 and 5.5 for a molar PAA-to-metal ratio above 1. The interaction was studied for a wide range of PAA (0.05 mg L(-1)-50 g L(-1)) and metal ion concentrations (2x10(-9)-10(-3) M). This work aimed at 3 goals (i) to determine the stoichiometry of M(III)-PAA complexes, (ii) to determine the number of complexed species and the local environment of the metal ion, and (iii) to quantify the reaction processes. Asymmetric flow-field-flow fractionation (AsFlFFF) coupled to ICP-MS evidenced that size distributions of Eu-PAA complexes and PAA were identical, suggesting that Eu bound to only one PAA chain. Time-resolved laser fluorescence spectroscopy (TRLFS) measurements performed with Eu and Cm showed a continuous shift of the spectra with increasing pH. The environment of complexed metal ions obviously changes with pH. Most probably, spectral variations arose from conformational changes within the M(III)-PAA complex due to pH variation. Complexation data describing the distribution of complexed and free metal ion were measured with Cm by TRLFS. They could be quantitatively described in the whole pH-range studied by considering the existence of only a single complexed species. This indicates that the slight changes in M(III) speciation with pH observed at the molecular level do not significantly affect the intrinsic binding constant. The interaction constant obtained from the modelling must be considered as a mean interaction constant.

Role of Secondary Transporters and Phosphotransferase Systems in Glucose Transport by Oenococcus oeni ▿

PubMed Central

Kim, Ok Bin; Richter, Hanno; Zaunmüller, Tanja; Graf, Sabrina; Unden, Gottfried

2011-01-01

Glucose uptake by the heterofermentative lactic acid bacterium Oenococcus oeni B1 was studied at the physiological and gene expression levels. Glucose- or fructose-grown bacteria catalyzed uptake of [14C]glucose over a pH range from pH 4 to 9, with maxima at pHs 5.5 and 7. Uptake occurred in two-step kinetics in a high- and low-affinity reaction. The high-affinity uptake followed Michaelis-Menten kinetics and required energization. It accumulated the radioactivity of glucose by a factor of 55 within the bacteria. A large portion (about 80%) of the uptake of glucose was inhibited by protonophores and ionophores. Uptake of the glucose at neutral pH was not sensitive to degradation of the proton potential, Δp. Expression of the genes OEOE_0819 and OEOE_1574 (here referred to as 0819 and 1574), coding for secondary transporters, was induced by glucose as identified by quantitative real-time (RT)-PCR. The genes 1574 and 0819 were able to complement growth of a Bacillus subtilis hexose transport-deficient mutant on glucose but not on fructose. The genes 1574 and 0819 therefore encode secondary transporters for glucose, and the transports are presumably Δp dependent. O. oeni codes, in addition, for a phosphotransferase transport system (PTS) (gene OEOE_0464 [0464] for the permease) with similarity to the fructose- and mannose-specific PTS of lactic acid bacteria. Quantitative RT-PCR showed induction of the gene 0464 by glucose and by fructose. The data suggest that the PTS is responsible for Δp-independent hexose transport at neutral pH and for the residual Δp-independent transport of hexoses at acidic pH. PMID:22020640

An Autoinhibitory Role for the Pleckstrin Homology Domain of Interleukin-2-Inducible Tyrosine Kinase and Its Interplay with Canonical Phospholipid Recognition.

PubMed

Devkota, Sujan; Joseph, Raji E; Boyken, Scott E; Fulton, D Bruce; Andreotti, Amy H

2017-06-13

Pleckstrin homology (PH) domains are well-known as phospholipid binding modules, yet evidence that PH domain function extends beyond lipid recognition is mounting. In this work, we characterize a protein binding function for the PH domain of interleukin-2-inducible tyrosine kinase (ITK), an immune cell specific signaling protein that belongs to the TEC family of nonreceptor tyrosine kinases. Its N-terminal PH domain is a well-characterized lipid binding module that localizes ITK to the membrane via phosphatidylinositol 3,4,5-trisphosphate (PIP 3 ) binding. Using a combination of nuclear magnetic resonance spectroscopy and mutagenesis, we have mapped an autoregulatory protein interaction site on the ITK PH domain that makes direct contact with the catalytic kinase domain of ITK, inhibiting the phospho-transfer reaction. Moreover, we have elucidated an important interplay between lipid binding by the ITK PH domain and the stability of the autoinhibitory complex formed by full length ITK. The ITK activation loop in the kinase domain becomes accessible to phosphorylation to the exogenous kinase LCK upon binding of the ITK PH domain to PIP 3 . By clarifying the allosteric role of the ITK PH domain in controlling ITK function, we have expanded the functional repertoire of the PH domain generally and opened the door to alternative strategies to target this specific kinase in the context of immune cell signaling.

X-Ray Excited Luminescence Chemical Imaging of Bacterial Growth on Surfaces Implanted in Tissue.

PubMed

Wang, Fenglin; Raval, Yash; Tzeng, Tzuen-Rong J; Anker, Jeffrey N

2015-04-22

A pH sensor film is developed that can be coated on an implant surface and imaged using a combination of X-ray excitation and visible spectroscopy to monitor bacterial infection and treatment of implanted medical devices (IMDs) through tissue. X-ray scintillators in the pH sensor film generate light when an X-ray beam irradiates them. This light first passes through a layer containing pH indicator that alters the spectrum according to pH, then passes through and out of the tissue where it is detected by a spectrometer. A reference region on the film is used to account for spectral distortion from wavelength-dependent absorption and scattering in the tissue. pH images are acquired by moving the sample relative to the X-ray beam and collecting a spectrum at each location, with a spatial resolution limited by the X-ray beam width. Using this X-ray excited luminescence chemical imaging (XELCI) to map pH through ex vivo porcine tissue, a pH drop is detected during normal bacterial growth on the sensor surface, and a restoration of the pH to the bulk value during antibiotic treatment over the course of hours with milli-meter resolution. Overall, XELCI provides a novel approach to noninvasively image surface pH for studying implant infections and treatments. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative trait locus gene mapping: a new method for locating alcohol response genes.

PubMed

Crabbe, J C

1996-01-01

Alcoholism is a multigenic trait with important non-genetic determinants. Studies with genetic animal models of susceptibility to several of alcohol's effects suggest that several genes contributing modest effects on susceptibility (Quantitative Trait Loci, or QTLs) are important. A new technique of QTL gene mapping has allowed the identification of the location in mouse genome of several such QTLs. The method is described, and the locations of QTLs affecting the acute alcohol withdrawal reaction are described as an example of the method. Verification of these QTLs in ancillary studies is described and the strengths, limitations, and future directions to be pursued are discussed. QTL mapping is a promising method for identifying genes in rodents with the hope of directly extrapolating the results to the human genome. This review is based on a paper presented at the First International Congress of the Latin American Society for Biomedical Research on Alcoholism, Santiago, Chile, November 1994.

Quantitation of Localized 31P Magnetic Resonance Spectra Based on the Reciprocity Principle

NASA Astrophysics Data System (ADS)

Kreis, R.; Slotboom, J.; Pietz, J.; Jung, B.; Boesch, C.

2001-04-01

There is a need for absolute quantitation methods in 31P magnetic resonance spectroscopy, because none of the phosphorous-containing metabolites is necessarily constant in pathology. Here, a method for absolute quantitation of in vivo31P MR spectra that provides reproducible metabolite contents in institutional or standard units is described. It relies on the reciprocity principle, i.e., the proportionality between the B1 field map and the map of reception strength for a coil with identical relative current distributions in receive and transmit mode. Cerebral tissue contents of 31P metabolites were determined in a predominantly white matter-containing location in healthy subjects. The results are in good agreement with the literature and the interexamination coefficient of variance is better than that in most previous studies. A gender difference found for some of the 31P metabolites may be explained by different voxel composition.

Quantitative analysis of aircraft multispectral-scanner data and mapping of water-quality parameters in the James River in Virginia

NASA Technical Reports Server (NTRS)

Johnson, R. W.; Bahn, G. S.

1977-01-01

Statistical analysis techniques were applied to develop quantitative relationships between in situ river measurements and the remotely sensed data that were obtained over the James River in Virginia on 28 May 1974. The remotely sensed data were collected with a multispectral scanner and with photographs taken from an aircraft platform. Concentration differences among water quality parameters such as suspended sediment, chlorophyll a, and nutrients indicated significant spectral variations. Calibrated equations from the multiple regression analysis were used to develop maps that indicated the quantitative distributions of water quality parameters and the dispersion characteristics of a pollutant plume entering the turbid river system. Results from further analyses that use only three preselected multispectral scanner bands of data indicated that regression coefficients and standard errors of estimate were not appreciably degraded compared with results from the 10-band analysis.

Measuring iron in the brain using quantitative susceptibility mapping and X-ray fluorescence imaging

PubMed Central

Zheng, Weili; Nichol, Helen; Liu, Saifeng; Cheng, Yu-Chung N.; Haacke, E. Mark

2013-01-01

Measuring iron content in the brain has important implications for a number of neurodegenerative diseases. Quantitative susceptibility mapping (QSM), derived from magnetic resonance images, has been used to measure total iron content in vivo and in post mortem brain. In this paper, we show how magnetic susceptibility from QSM correlates with total iron content measured by X-ray fluorescence (XRF) imaging and by inductively coupled plasma mass spectrometry (ICPMS). The relationship between susceptibility and ferritin iron was estimated at 1.10 ± 0.08 ppb susceptibility per μg iron/g wet tissue, similar to that of iron in fixed (frozen/thawed) cadaveric brain and previously published data from unfixed brains. We conclude that magnetic susceptibility can provide a direct and reliable quantitative measurement of iron content and that it can be used clinically at least in regions with high iron content. PMID:23591072

Quantitative Schlieren analysis applied to holograms of crystals grown on Spacelab 3

NASA Technical Reports Server (NTRS)

Brooks, Howard L.

1986-01-01

In order to extract additional information about crystals grown in the microgravity environment of Spacelab, a quantitative schlieren analysis technique was developed for use in a Holography Ground System of the Fluid Experiment System. Utilizing the Unidex position controller, it was possible to measure deviation angles produced by refractive index gradients of 0.5 milliradians. Additionally, refractive index gradient maps for any recorded time during the crystal growth were drawn and used to create solute concentration maps for the environment around the crystal. The technique was applied to flight holograms of Cell 204 of the Fluid Experiment System that were recorded during the Spacelab 3 mission on STS 51B. A triglycine sulfate crystal was grown under isothermal conditions in the cell and the data gathered with the quantitative schlieren analysis technique is consistent with a diffusion limited growth process.

Robust red-emission spectra and yields in firefly bioluminescence against temperature changes

NASA Astrophysics Data System (ADS)

Mochizuki, Toshimitsu; Wang, Yu; Hiyama, Miyabi; Akiyama, Hidefumi

2014-05-01

We measured the quantitative spectra of firefly (Photinus pyralis) bioluminescence at various temperatures to investigate the temperature dependence of the luciferin-luciferase reaction at 15-34 °C. The quantitative spectra were decomposed very well into red (1.9 eV), orange (2.0 eV), and green (2.2 eV) Gaussian components. The intensity of the green component was the only temperature sensitive quantity that linearly decreased as the temperature increased at pH 7 and 8. We found the quantitative bioluminescence spectra to be robust below 2.0 eV against temperature and other experimental conditions. The revealed robustness of the red emissions should be useful for quantitative applications such as adenosine-5'-triphosphate detection.

The Genetic Basis of Plant Architecture in 10 Maize Recombinant Inbred Line Populations1[OPEN

PubMed Central

Pan, Qingchun; Xu, Yuancheng; Peng, Yong; Zhan, Wei; Li, Wenqiang; Li, Lin

2017-01-01

Plant architecture is a key factor affecting planting density and grain yield in maize (Zea mays). However, the genetic mechanisms underlying plant architecture in diverse genetic backgrounds have not been fully addressed. Here, we performed a large-scale phenotyping of 10 plant architecture-related traits and dissected the genetic loci controlling these traits in 10 recombinant inbred line populations derived from 14 diverse genetic backgrounds. Nearly 800 quantitative trait loci (QTLs) with major and minor effects were identified as contributing to the phenotypic variation of plant architecture-related traits. Ninety-two percent of these QTLs were detected in only one population, confirming the diverse genetic backgrounds of the mapping populations and the prevalence of rare alleles in maize. The numbers and effects of QTLs are positively associated with the phenotypic variation in the population, which, in turn, correlates positively with parental phenotypic and genetic variations. A large proportion (38.5%) of QTLs was associated with at least two traits, suggestive of the frequent occurrence of pleiotropic loci or closely linked loci. Key developmental genes, which previously were shown to affect plant architecture in mutant studies, were found to colocalize with many QTLs. Five QTLs were further validated using the segregating populations developed from residual heterozygous lines present in the recombinant inbred line populations. Additionally, one new plant height QTL, qPH3, has been fine-mapped to a 600-kb genomic region where three candidate genes are located. These results provide insights into the genetic mechanisms controlling plant architecture and will benefit the selection of ideal plant architecture in maize breeding. PMID:28838954

Quantitative elasticity measurement of urinary bladder wall using laser-induced surface acoustic waves.

PubMed

Li, Chunhui; Guan, Guangying; Zhang, Fan; Song, Shaozhen; Wang, Ruikang K; Huang, Zhihong; Nabi, Ghulam

2014-12-01

The maintenance of urinary bladder elasticity is essential to its functions, including the storage and voiding phases of the micturition cycle. The bladder stiffness can be changed by various pathophysiological conditions. Quantitative measurement of bladder elasticity is an essential step toward understanding various urinary bladder disease processes and improving patient care. As a nondestructive, and noncontact method, laser-induced surface acoustic waves (SAWs) can accurately characterize the elastic properties of different layers of organs such as the urinary bladder. This initial investigation evaluates the feasibility of a noncontact, all-optical method of generating and measuring the elasticity of the urinary bladder. Quantitative elasticity measurements of ex vivo porcine urinary bladder were made using the laser-induced SAW technique. A pulsed laser was used to excite SAWs that propagated on the bladder wall surface. A dedicated phase-sensitive optical coherence tomography (PhS-OCT) system remotely recorded the SAWs, from which the elasticity properties of different layers of the bladder were estimated. During the experiments, series of measurements were performed under five precisely controlled bladder volumes using water to estimate changes in the elasticity in relation to various urinary bladder contents. The results, validated by optical coherence elastography, show that the laser-induced SAW technique combined with PhS-OCT can be a feasible method of quantitative estimation of biomechanical properties.

Optimising hydrogen peroxide measurement in exhaled breath condensate.

PubMed

Brooks, Wendy M; Lash, Heath; Kettle, Anthony J; Epton, Michael J

2006-01-01

Exhaled breath condensate (EBC) analysis has been proposed as a non-invasive method of assessing airway pathology. A number of substances, including hydrogen peroxide (H2O2), have been measured in EBC, without adequate published details of validation and optimisation. To explore factors that affect accurate quantitation of H2O2 in EBC. H2O2 was measured in EBC samples using fluorometry with 4-hydroxyphenylacetic acid. A number of factors that might alter quantitation were studied including pH and buffering conditions, reagent storage, and assay temperature. Standard curve slope was significantly altered by pH, leading to a potential difference in H2O2 quantification of up to 42%. These differences were resolved by increasing the buffering capacity of the reaction mix. H2O2 added to EBC remained stable for 1 h when stored on ice. The assay was unaffected by freezing assay reagents. The limit of detection for H2O2 ranged from 3.4 nM to 8.8 nM depending on the buffer used. The reagents required for this assay can be stored for several months allowing valuable consistency in longitudinal studies. The quantitation of H2O2 in EBC is pH-dependent but increasing assay buffering reduces this effect. Sensitive reproducible quantitation of H2O2 in EBC requires rigorous optimisation.

Evaluating nanoparticle sensor design for intracellular pH measurements.

PubMed

Benjaminsen, Rikke V; Sun, Honghao; Henriksen, Jonas R; Christensen, Nynne M; Almdal, Kristoffer; Andresen, Thomas L

2011-07-26

Particle-based nanosensors have over the past decade been designed for optical fluorescent-based ratiometric measurements of pH in living cells. However, quantitative and time-resolved intracellular measurements of pH in endosomes and lysosomes using particle nanosensors are challenging, and there is a need to improve measurement methodology. In the present paper, we have successfully carried out time-resolved pH measurements in endosomes and lyosomes in living cells using nanoparticle sensors and show the importance of sensor choice for successful quantification. We have studied two nanoparticle-based sensor systems that are internalized by endocytosis and elucidated important factors in nanosensor design that should be considered in future development of new sensors. From our experiments it is clear that it is highly important to use sensors that have a broad measurement range, as erroneous quantification of pH is an unfortunate result when measuring pH too close to the limit of the sensitive range of the sensors. Triple-labeled nanosensors with a pH measurement range of 3.2-7.0, which was synthesized by adding two pH-sensitive fluorophores with different pK(a) to each sensor, seem to be a solution to some of the earlier problems found when measuring pH in the endosome-lysosome pathway.

Preformulation considerations for controlled release dosage forms. Part II. Selected candidate support.

PubMed

Chrzanowski, Frank

2008-01-01

Practical examples of preformulation support of the form selected for formulation development are provided using several drug substances (DSs). The examples include determination of the solubilities vs. pH particularly for the range pH 1 to 8 because of its relationship to gastrointestinal (GI) conditions and dissolution method development. The advantages of equilibrium solubility and trial solubility methods are described. The equilibrium method is related to detecting polymorphism and the trial solubility method, to simplifying difficult solubility problems. An example of two polymorphs existing in mixtures of DS is presented in which one of the forms is very unstable. Accelerating stability studies are used in conjunction with HPLC and quantitative X-ray powder diffraction (QXRD) to demonstrate the differences in chemical and polymorphic stabilities. The results from two model excipient compatibility methods are compared to determine which has better predictive accuracy for room temperature stability. A DSC (calorimetric) method and an isothermal stress with quantitative analysis (ISQA) method that simulates wet granulation conditions were compared using a 2 year room temperature sample set as reference. An example of a pH stability profile for understanding stability and extrapolating stability to other environments is provided. The pH-stability of omeprazole and lansoprazole, which are extremely unstable in acidic and even mildly acidic conditions, are related to the formulation of delayed release dosage forms and the resolution of the problem associated with free carboxyl groups from the enteric coating polymers reacting with the DSs. Dissolution method requirements for CR dosage forms are discussed. The applicability of a modified disintegration time (DT) apparatus for supporting CR dosage form development of a pH sensitive DS at a specific pH such as duodenal pH 5.6 is related. This method is applicable for DSs such as peptides, proteins, enzymes and natural products where physical observation can be used in place of a difficult to perform analytical method, saving resources and providing rapid preformulation support.

Quantitative analysis of oyster larval proteome provides new insights into the effects of multiple climate change stressors.

PubMed

Dineshram, Ramadoss; Chandramouli, Kondethimmanahalli; Ko, Ginger Wai Kuen; Zhang, Huoming; Qian, Pei-Yuan; Ravasi, Timothy; Thiyagarajan, Vengatesen

2016-06-01

The metamorphosis of planktonic larvae of the Pacific oyster (Crassostrea gigas) underpins their complex life-history strategy by switching on the molecular machinery required for sessile life and building calcite shells. Metamorphosis becomes a survival bottleneck, which will be pressured by different anthropogenically induced climate change-related variables. Therefore, it is important to understand how metamorphosing larvae interact with emerging climate change stressors. To predict how larvae might be affected in a future ocean, we examined changes in the proteome of metamorphosing larvae under multiple stressors: decreased pH (pH 7.4), increased temperature (30 °C), and reduced salinity (15 psu). Quantitative protein expression profiling using iTRAQ-LC-MS/MS identified more than 1300 proteins. Decreased pH had a negative effect on metamorphosis by down-regulating several proteins involved in energy production, metabolism, and protein synthesis. However, warming switched on these down-regulated pathways at pH 7.4. Under multiple stressors, cell signaling, energy production, growth, and developmental pathways were up-regulated, although metamorphosis was still reduced. Despite the lack of lethal effects, significant physiological responses to both individual and interacting climate change related stressors were observed at proteome level. The metamorphosing larvae of the C. gigas population in the Yellow Sea appear to have adequate phenotypic plasticity at the proteome level to survive in future coastal oceans, but with developmental and physiological costs. © 2016 John Wiley & Sons Ltd.

Watershed-Scale Fungal Community Characterization along a pH Gradient in a Subsurface Environment Cocontaminated with Uranium and Nitrate

PubMed Central

Jasrotia, Puja; Green, Stefan J.; Canion, Andy; Overholt, Will A.; Prakash, Om; Wafula, Denis; Hubbard, Daniela; Watson, David B.; Schadt, Christopher W.; Brooks, Scott C.

2014-01-01

The objective of this study was to characterize fungal communities in a subsurface environment cocontaminated with uranium and nitrate at the watershed scale and to determine the potential contribution of fungi to contaminant transformation (nitrate attenuation). The abundance, distribution, and diversity of fungi in subsurface groundwater samples were determined using quantitative and semiquantitative molecular techniques, including quantitative PCR of eukaryotic small-subunit rRNA genes and pyrosequencing of fungal internal transcribed spacer (ITS) regions. Potential bacterial and fungal denitrification was assessed in sediment-groundwater slurries amended with antimicrobial compounds and in fungal pure cultures isolated from the subsurface. Our results demonstrate that subsurface fungal communities are dominated by members of the phylum Ascomycota, and a pronounced shift in fungal community composition occurs across the groundwater pH gradient at the field site, with lower diversity observed under acidic (pH <4.5) conditions. Fungal isolates recovered from subsurface sediments, including cultures of the genus Coniochaeta, which were detected in abundance in pyrosequence libraries of site groundwater samples, were shown to reduce nitrate to nitrous oxide. Denitrifying fungal isolates recovered from the site were classified and found to be distributed broadly within the phylum Ascomycota and within a single genus of the Basidiomycota. Potential denitrification rate assays with sediment-groundwater slurries showed the potential for subsurface fungi to reduce nitrate to nitrous oxide under in situ acidic pH conditions. PMID:24389927