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Sample records for based enrichment method

  1. Co-enriching microflora associated with culture based methods to detect Salmonella from tomato phyllosphere.

    PubMed

    Ottesen, Andrea R; Gonzalez, Antonio; Bell, Rebecca; Arce, Caroline; Rideout, Steven; Allard, Marc; Evans, Peter; Strain, Errol; Musser, Steven; Knight, Rob; Brown, Eric; Pettengill, James B

    2013-01-01

    The ability to detect a specific organism from a complex environment is vitally important to many fields of public health, including food safety. For example, tomatoes have been implicated numerous times as vehicles of foodborne outbreaks due to strains of Salmonella but few studies have ever recovered Salmonella from a tomato phyllosphere environment. Precision of culturing techniques that target agents associated with outbreaks depend on numerous factors. One important factor to better understand is which species co-enrich during enrichment procedures and how microbial dynamics may impede or enhance detection of target pathogens. We used a shotgun sequence approach to describe taxa associated with samples pre-enrichment and throughout the enrichment steps of the Bacteriological Analytical Manual's (BAM) protocol for detection of Salmonella from environmental tomato samples. Recent work has shown that during efforts to enrich Salmonella (Proteobacteria) from tomato field samples, Firmicute genera are also co-enriched and at least one co-enriching Firmicute genus (Paenibacillus sp.) can inhibit and even kills strains of Salmonella. Here we provide a baseline description of microflora that co-culture during detection efforts and the utility of a bioinformatic approach to detect specific taxa from metagenomic sequence data. We observed that uncultured samples clustered together with distinct taxonomic profiles relative to the three cultured treatments (Universal Pre-enrichment broth (UPB), Tetrathionate (TT), and Rappaport-Vassiliadis (RV)). There was little consistency among samples exposed to the same culturing medias, suggesting significant microbial differences in starting matrices or stochasticity associated with enrichment processes. Interestingly, Paenibacillus sp. (Salmonella inhibitor) was significantly enriched from uncultured to cultured (UPB) samples. Also of interest was the sequence based identification of a number of sequences as Salmonella despite

  2. Co-enriching microflora associated with culture based methods to detect Salmonella from tomato phyllosphere.

    PubMed

    Ottesen, Andrea R; Gonzalez, Antonio; Bell, Rebecca; Arce, Caroline; Rideout, Steven; Allard, Marc; Evans, Peter; Strain, Errol; Musser, Steven; Knight, Rob; Brown, Eric; Pettengill, James B

    2013-01-01

    The ability to detect a specific organism from a complex environment is vitally important to many fields of public health, including food safety. For example, tomatoes have been implicated numerous times as vehicles of foodborne outbreaks due to strains of Salmonella but few studies have ever recovered Salmonella from a tomato phyllosphere environment. Precision of culturing techniques that target agents associated with outbreaks depend on numerous factors. One important factor to better understand is which species co-enrich during enrichment procedures and how microbial dynamics may impede or enhance detection of target pathogens. We used a shotgun sequence approach to describe taxa associated with samples pre-enrichment and throughout the enrichment steps of the Bacteriological Analytical Manual's (BAM) protocol for detection of Salmonella from environmental tomato samples. Recent work has shown that during efforts to enrich Salmonella (Proteobacteria) from tomato field samples, Firmicute genera are also co-enriched and at least one co-enriching Firmicute genus (Paenibacillus sp.) can inhibit and even kills strains of Salmonella. Here we provide a baseline description of microflora that co-culture during detection efforts and the utility of a bioinformatic approach to detect specific taxa from metagenomic sequence data. We observed that uncultured samples clustered together with distinct taxonomic profiles relative to the three cultured treatments (Universal Pre-enrichment broth (UPB), Tetrathionate (TT), and Rappaport-Vassiliadis (RV)). There was little consistency among samples exposed to the same culturing medias, suggesting significant microbial differences in starting matrices or stochasticity associated with enrichment processes. Interestingly, Paenibacillus sp. (Salmonella inhibitor) was significantly enriched from uncultured to cultured (UPB) samples. Also of interest was the sequence based identification of a number of sequences as Salmonella despite

  3. Co-Enriching Microflora Associated with Culture Based Methods to Detect Salmonella from Tomato Phyllosphere

    PubMed Central

    Ottesen, Andrea R.; Gonzalez, Antonio; Bell, Rebecca; Arce, Caroline; Rideout, Steven; Allard, Marc; Evans, Peter; Strain, Errol; Musser, Steven; Knight, Rob; Brown, Eric; Pettengill, James B.

    2013-01-01

    The ability to detect a specific organism from a complex environment is vitally important to many fields of public health, including food safety. For example, tomatoes have been implicated numerous times as vehicles of foodborne outbreaks due to strains of Salmonella but few studies have ever recovered Salmonella from a tomato phyllosphere environment. Precision of culturing techniques that target agents associated with outbreaks depend on numerous factors. One important factor to better understand is which species co-enrich during enrichment procedures and how microbial dynamics may impede or enhance detection of target pathogens. We used a shotgun sequence approach to describe taxa associated with samples pre-enrichment and throughout the enrichment steps of the Bacteriological Analytical Manual's (BAM) protocol for detection of Salmonella from environmental tomato samples. Recent work has shown that during efforts to enrich Salmonella (Proteobacteria) from tomato field samples, Firmicute genera are also co-enriched and at least one co-enriching Firmicute genus (Paenibacillus sp.) can inhibit and even kills strains of Salmonella. Here we provide a baseline description of microflora that co-culture during detection efforts and the utility of a bioinformatic approach to detect specific taxa from metagenomic sequence data. We observed that uncultured samples clustered together with distinct taxonomic profiles relative to the three cultured treatments (Universal Pre-enrichment broth (UPB), Tetrathionate (TT), and Rappaport-Vassiliadis (RV)). There was little consistency among samples exposed to the same culturing medias, suggesting significant microbial differences in starting matrices or stochasticity associated with enrichment processes. Interestingly, Paenibacillus sp. (Salmonella inhibitor) was significantly enriched from uncultured to cultured (UPB) samples. Also of interest was the sequence based identification of a number of sequences as Salmonella despite

  4. Pros and cons of methylation-based enrichment methods for ancient DNA.

    PubMed

    Seguin-Orlando, Andaine; Gamba, Cristina; Der Sarkissian, Clio; Ermini, Luca; Louvel, Guillaume; Boulygina, Eugenia; Sokolov, Alexey; Nedoluzhko, Artem; Lorenzen, Eline D; Lopez, Patricio; McDonald, H Gregory; Scott, Eric; Tikhonov, Alexei; Stafford, Thomas W; Alfarhan, Ahmed H; Alquraishi, Saleh A; Al-Rasheid, Khaled A S; Shapiro, Beth; Willerslev, Eske; Prokhortchouk, Egor; Orlando, Ludovic

    2015-07-02

    The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions.

  5. Pros and cons of methylation-based enrichment methods for ancient DNA.

    PubMed

    Seguin-Orlando, Andaine; Gamba, Cristina; Der Sarkissian, Clio; Ermini, Luca; Louvel, Guillaume; Boulygina, Eugenia; Sokolov, Alexey; Nedoluzhko, Artem; Lorenzen, Eline D; Lopez, Patricio; McDonald, H Gregory; Scott, Eric; Tikhonov, Alexei; Stafford, Thomas W; Alfarhan, Ahmed H; Alquraishi, Saleh A; Al-Rasheid, Khaled A S; Shapiro, Beth; Willerslev, Eske; Prokhortchouk, Egor; Orlando, Ludovic

    2015-01-01

    The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions. PMID:26134828

  6. Pros and cons of methylation-based enrichment methods for ancient DNA

    PubMed Central

    Seguin-Orlando, Andaine; Gamba, Cristina; Sarkissian, Clio Der; Ermini, Luca; Louvel, Guillaume; Boulygina, Eugenia; Sokolov, Alexey; Nedoluzhko, Artem; Lorenzen, Eline D.; Lopez, Patricio; McDonald, H. Gregory; Scott, Eric; Tikhonov, Alexei; Stafford,, Thomas W.; Alfarhan, Ahmed H.; Alquraishi, Saleh A.; Al-Rasheid, Khaled A. S.; Shapiro, Beth; Willerslev, Eske; Prokhortchouk, Egor; Orlando, Ludovic

    2015-01-01

    The recent discovery that DNA methylation survives in fossil material provides an opportunity for novel molecular approaches in palaeogenomics. Here, we apply to ancient DNA extracts the probe-independent Methylated Binding Domains (MBD)-based enrichment method, which targets DNA molecules containing methylated CpGs. Using remains of a Palaeo-Eskimo Saqqaq individual, woolly mammoths, polar bears and two equine species, we confirm that DNA methylation survives in a variety of tissues, environmental contexts and over a large temporal range (4,000 to over 45,000 years before present). MBD enrichment, however, appears principally biased towards the recovery of CpG-rich and long DNA templates and is limited by the fast post-mortem cytosine deamination rates of methylated epialleles. This method, thus, appears only appropriate for the analysis of ancient methylomes from very well preserved samples, where both DNA fragmentation and deamination have been limited. This work represents an essential step toward the characterization of ancient methylation signatures, which will help understanding the role of epigenetic changes in past environmental and cultural transitions. PMID:26134828

  7. Validation of Flow Cytometry and Magnetic Bead-Based Methods to Enrich CNS Single Cell Suspensions for Quiescent Microglia.

    PubMed

    Volden, T A; Reyelts, C D; Hoke, T A; Arikkath, J; Bonasera, S J

    2015-12-01

    Microglia are resident mononuclear phagocytes within the CNS parenchyma that intimately interact with neurons and astrocytes to remodel synapses and extracellular matrix. We briefly review studies elucidating the molecular pathways that underlie microglial surveillance, activation, chemotaxis, and phagocytosis; we additionally place these studies in a clinical context. We describe and validate an inexpensive and simple approach to obtain enriched single cell suspensions of quiescent parenchymal and perivascular microglia from the mouse cerebellum and hypothalamus. Following preparation of regional CNS single cell suspensions, we remove myelin debris, and then perform two serial enrichment steps for cells expressing surface CD11b. Myelin depletion and CD11b enrichment are both accomplished using antigen-specific magnetic beads in an automated cell separation system. Flow cytometry of the resultant suspensions shows a significant enrichment for CD11b(+)/CD45(+) cells (perivascular microglia) and CD11b(+)/CD45(-) cells (parenchymal microglia) compared to starting suspensions. Of note, cells from these enriched suspensions minimally express Aif1 (aka Iba1), suggesting that the enrichment process does not evoke significant microglial activation. However, these cells readily respond to a functional challenge (LPS) with significant changes in the expression of molecules specifically associated with microglia. We conclude that methods employing a combination of magnetic-bead based sorting and flow cytometry produce suspensions highly enriched for microglia that are appropriate for a variety of molecular and cellular assays.

  8. A Laser-Based Method for On-Site Analysis of UF6 at Enrichment Plants

    SciTech Connect

    Anheier, Norman C.; Cannon, Bret D.; Martinez, Alonzo; Barrett, Christopher A.; Taubman, Matthew S.; Anderson, Kevin K.; Smith, Leon E.

    2014-11-23

    The International Atomic Energy Agency’s (IAEA’s) long-term research and development plan calls for more cost-effective and efficient safeguard methods to detect and deter misuse of gaseous centrifuge enrichment plants (GCEPs). The IAEA’s current safeguards approaches at GCEPs are based on a combination of routine and random inspections that include environmental sampling and destructive assay (DA) sample collection from UF6 in-process material and selected cylinders. Samples are then shipped offsite for subsequent laboratory analysis. In this paper, a new DA sample collection and onsite analysis approach that could help to meet challenges in transportation and chain of custody for UF6 DA samples is introduced. This approach uses a handheld sampler concept and a Laser Ablation, Laser Absorbance Spectrometry (LAARS) analysis instrument, both currently under development at the Pacific Northwest National Laboratory. A LAARS analysis instrument could be temporarily or permanently deployed in the IAEA control room of the facility, in the IAEA data acquisition cabinet, for example. The handheld PNNL DA sampler design collects and stabilizes a much smaller DA sample mass compared to current sampling methods. The significantly lower uranium mass reduces the sample radioactivity and the stabilization approach diminishes the risk of uranium and hydrogen fluoride release. These attributes enable safe sample handling needed during onsite LAARS assay and may help ease shipping challenges for samples to be processed at the IAEA’s offsite laboratory. The LAARS and DA sampler implementation concepts will be described and preliminary technical viability results presented.

  9. ExtraPEG: A Polyethylene Glycol-Based Method for Enrichment of Extracellular Vesicles

    PubMed Central

    Rider, Mark A.; Hurwitz, Stephanie N.; Meckes, David G.

    2016-01-01

    Initially thought to be a means for cells to eliminate waste, secreted extracellular vesicles, known as exosomes, are now understood to mediate numerous healthy and pathological processes. Though abundant in biological fluids, purifying exosomes has been challenging because their biophysical properties overlap with other secreted cell products. Easy-to-use commercial kits for harvesting exosomes are now widely used, but the relative low-purity and high-cost of the preparations restricts their utility. Here we describe a method for purifying exosomes and other extracellular vesicles by adapting methods for isolating viruses using polyethylene glycol. This technique, called ExtraPEG, enriches exosomes from large volumes of media rapidly and inexpensively using low-speed centrifugation, followed by a single small-volume ultracentrifugation purification step. Total protein and RNA harvested from vesicles is sufficient in quantity and quality for proteomics and sequencing analyses, demonstrating the utility of this method for biomarker discovery and diagnostics. Additionally, confocal microscopy studies suggest that the biological activity of vesicles is not impaired. The ExtraPEG method can be easily adapted to enrich for different vesicle populations, or as an efficient precursor to subsequent purification techniques, providing a means to harvest exosomes from many different biological fluids and for a wide variety of purposes. PMID:27068479

  10. Inhibition of recombinase polymerase amplification by background DNA: a lateral flow-based method for enriching target DNA.

    PubMed

    Rohrman, Brittany; Richards-Kortum, Rebecca

    2015-02-01

    Recombinase polymerase amplification (RPA) may be used to detect a variety of pathogens, often after minimal sample preparation. However, previous work has shown that whole blood inhibits RPA. In this paper, we show that the concentrations of background DNA found in whole blood prevent the amplification of target DNA by RPA. First, using an HIV-1 RPA assay with known concentrations of nonspecific background DNA, we show that RPA tolerates more background DNA when higher HIV-1 target concentrations are present. Then, using three additional assays, we demonstrate that the maximum amount of background DNA that may be tolerated in RPA reactions depends on the DNA sequences used in the assay. We also show that changing the RPA reaction conditions, such as incubation time and primer concentration, has little effect on the ability of RPA to function when high concentrations of background DNA are present. Finally, we develop and characterize a lateral flow-based method for enriching the target DNA concentration relative to the background DNA concentration. This sample processing method enables RPA of 10(4) copies of HIV-1 DNA in a background of 0-14 μg of background DNA. Without lateral flow sample enrichment, the maximum amount of background DNA tolerated is 2 μg when 10(6) copies of HIV-1 DNA are present. This method requires no heating or other external equipment, may be integrated with upstream DNA extraction and purification processes, is compatible with the components of lysed blood, and has the potential to detect HIV-1 DNA in infant whole blood with high proviral loads.

  11. Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

    PubMed Central

    Ávila-Arcos, María C.; Cappellini, Enrico; Romero-Navarro, J. Alberto; Wales, Nathan; Moreno-Mayar, J. Víctor; Rasmussen, Morten; Fordyce, Sarah L.; Montiel, Rafael; Vielle-Calzada, Jean-Philippe; Willerslev, Eske; Gilbert, M. Thomas P.

    2011-01-01

    The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA. PMID:22355593

  12. Method for laser induced isotope enrichment

    SciTech Connect

    Pronko, Peter P.; Vanrompay, Paul A.; Zhang, Zhiyu

    2004-09-07

    Methods for separating isotopes or chemical species of an element and causing enrichment of a desired isotope or chemical species of an element utilizing laser ablation plasmas to modify or fabricate a material containing such isotopes or chemical species are provided. This invention may be used for a wide variety of materials which contain elements having different isotopes or chemical species.

  13. Enrichment of phosphorylated peptides and proteins by selective precipitation methods.

    PubMed

    Rainer, Matthias; Bonn, Günther K

    2015-01-01

    Protein phosphorylation is one of the most prominent post-translational modifications involved in the regulation of cellular processes. Fundamental understanding of biological processes requires appropriate bioanalytical methods for selectively enriching phosphorylated peptides and proteins. Most of the commonly applied enrichment approaches include chromatographic materials including Fe(3+)-immobilized metal-ion affinity chromatography or metal oxides. In the last years, the introduction of several non-chromatographic isolation technologies has increasingly attracted the interest of many scientists. Such approaches are based on the selective precipitation of phosphorylated peptides and proteins by applying various metal cations. The excellent performance of precipitation-based enrichment methods can be explained by the absence of any stationary phase, resin or sorbent, which usually leads to unspecific binding. This review provides an overview of recently published methods for the selective precipitation of phosphorylated peptides and proteins. PMID:25587840

  14. Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods.

    PubMed

    Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

    2015-01-01

    Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. PMID:24889823

  15. Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods.

    PubMed

    Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

    2015-01-01

    Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies.

  16. Effect of cooking method on the fatty acid content of reduced-fat and PUFA-enriched pork patties formulated with a konjac-based oil bulking system.

    PubMed

    Salcedo-Sandoval, Lorena; Cofrades, Susana; Ruiz-Capillas, Claudia; Jiménez-Colmenero, Francisco

    2014-12-01

    The effect of cooking methods (electric grilling and pan-frying in olive oil) on the composition of reduced-fat and reduced-fat/PUFA enriched pork patties was studied. Fat reduction was performed by replacing pork backfat (38% and 100%) with konjac gel and PUFA-enrichment by replacing pork backfat (49%) with a konjac-based oil bulking system stabilizing a healthier oil combination (olive, linseed and fish oils). Cooking losses (13%-27%) were affected (p<0.05) by formulation and cooking procedure. Compared with raw products, cooked samples had higher (p<0.05) concentrations of MUFAs and PUFAs (both n-3 and n-6); the difference was greater (p<0.05) in the pan-fried patties. Fatty acid retention was generally better in pan-fried than in grilled samples. When cooked, the PUFA levels in the medium-fat/improved sample containing the oil bulking system ranged between 1.4 and 1.6g/100g (0.47-0.51 from n-3 PUFAs), with EPA+DHA concentrations of around 75mg/100g. Konjac materials were successfully used to produce pork patties with a better lipid composition.

  17. Comparing multistep immobilized metal affinity chromatography and multistep TiO2 methods for phosphopeptide enrichment.

    PubMed

    Yue, Xiaoshan; Schunter, Alissa; Hummon, Amanda B

    2015-09-01

    Phosphopeptide enrichment from complicated peptide mixtures is an essential step for mass spectrometry-based phosphoproteomic studies to reduce sample complexity and ionization suppression effects. Typical methods for enriching phosphopeptides include immobilized metal affinity chromatography (IMAC) or titanium dioxide (TiO2) beads, which have selective affinity and can interact with phosphopeptides. In this study, the IMAC enrichment method was compared with the TiO2 enrichment method, using a multistep enrichment strategy from whole cell lysate, to evaluate their abilities to enrich for different types of phosphopeptides. The peptide-to-beads ratios were optimized for both IMAC and TiO2 beads. Both IMAC and TiO2 enrichments were performed for three rounds to enable the maximum extraction of phosphopeptides from the whole cell lysates. The phosphopeptides that are unique to IMAC enrichment, unique to TiO2 enrichment, and identified with both IMAC and TiO2 enrichment were analyzed for their characteristics. Both IMAC and TiO2 enriched similar amounts of phosphopeptides with comparable enrichment efficiency. However, phosphopeptides that are unique to IMAC enrichment showed a higher percentage of multiphosphopeptides as well as a higher percentage of longer, basic, and hydrophilic phosphopeptides. Also, the IMAC and TiO2 procedures clearly enriched phosphopeptides with different motifs. Finally, further enriching with two rounds of TiO2 from the supernatant after IMAC enrichment or further enriching with two rounds of IMAC from the supernatant TiO2 enrichment does not fully recover the phosphopeptides that are not identified with the corresponding multistep enrichment. PMID:26237447

  18. Method for isotope enrichment by photoinduced chemiionization

    DOEpatents

    Dubrin, James W.

    1985-01-01

    Isotope enrichment, particularly .sup.235 U enrichment, is achieved by irradiating an isotopically mixed vapor feed with radiant energy at a wavelength or wavelengths chosen to selectively excite the species containing a desired isotope to a predetermined energy level. The vapor feed if simultaneously reacted with an atomic or molecular reactant species capable of preferentially transforming the excited species into an ionic product by a chemiionization reaction. The ionic product, enriched in the desired isotope, is electrostatically or electromagnetically extracted from the reaction system.

  19. The Combination of Functional Metagenomics and an Oil-Fed Enrichment Strategy Revealed the Phylogenetic Diversity of Lipolytic Bacteria Overlooked by the Cultivation-Based Method

    PubMed Central

    Narihiro, Takashi; Suzuki, Aya; Yoshimune, Kazuaki; Hori, Tomoyuki; Hoshino, Tamotsu; Yumoto, Isao; Yokota, Atsushi; Kimura, Nobutada; Kamagata, Yoichi

    2014-01-01

    Metagenomic screening and conventional cultivation have been used to exploit microbial lipolytic enzymes in nature. We used an indigenous forest soil (NS) and oil-fed enriched soil (OS) as microbial and genetic resources. Thirty-four strains (17 each) of lipolytic bacteria were isolated from the NS and OS microcosms. These isolates were classified into the (sub)phyla Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria, all of which are known to be the main microbial resources of commercially available lipolytic enzymes. Seven and 39 lipolytic enzymes were successfully retrieved from the metagenomic libraries of the NS and OS microcosms, respectively. The screening efficiency (a ratio of positive lipolytic clones to the total number of environmental clones) was markedly higher in the OS microcosm than in the NS microcosm. Moreover, metagenomic clones encoding the lipolytic enzymes associated with Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Armatimonadetes, and Planctomycetes and hitherto-uncultivated microbes were recovered from these libraries. The results of the present study indicate that functional metagenomics can be effectively used to capture as yet undiscovered lipolytic enzymes that have eluded the cultivation-based method, and these combined approaches may be able to provide an overview of lipolytic organisms potentially present in nature. PMID:24859309

  20. QUANTITATIVE MASS SPECTROMETRIC ANALYSIS OF GLYCOPROTEINS COMBINED WITH ENRICHMENT METHODS

    PubMed Central

    Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

    2015-01-01

    Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Rapid Commun. Mass Spec Rev 34:148–165, 2015. PMID:24889823

  1. Using Enrichment Clusters for Performance Based Identification.

    ERIC Educational Resources Information Center

    Renzulli, Joseph S.

    2000-01-01

    This article describes an enrichment cluster approach designed to create highly challenging learning opportunities that allow high potential students to identify themselves. The enrichment clusters focus students' attention on authentic learning applied to real-life problems. Guidelines for enrichment clusters are discussed, along with the teacher…

  2. An effective and in-situ method based tresyl-functionalized porous polymer material for enrichment and digestion of membrane proteins and its application in extraction tips.

    PubMed

    Wang, Jiaxi; Gao, Mingxia; Yan, Guoquan; Zhang, Xiangmin

    2015-06-23

    Membrane proteins are one of promising targets for drug discovery because of the unique properties in physiological processes. Due to their low abundance and extremely hydrophobic nature, the analysis of membrane proteins is still a great challenge. In this work, an effective and in-situ method were developed to enrich and digest membrane proteins by adopting tresyl-functionalized porous polymer material. With tresyl groups, the material can effectively immobilize membrane proteins via covalent bonding on the surface. The material became a facile carrier to enrich membrane proteins from the rat liver in detergents and organic solvents owing to its outstanding binding capacity and excellent biocompatibility. Moreover, it was further applied in extraction tips to capture and in-situ digest the pretreatment membrane proteins in two different solutions. A total of 600 membrane proteins (51% of total protein groups) and 359 transmembrane proteins were identified by nano-LC-ESI-MS/MS in 4% sodium dodecyl sulfate (SDS), and similar results were achieved in the 60% methanol solution. All these results demonstrated that the new approach is of great promise for large-scale characterization of membrane proteins.

  3. Feeding enrichment methods for Pacific walrus calves.

    PubMed

    Kastelein, Ronald A; Jennings, Nancy; Postma, Jacobus

    2007-05-01

    In the wild, walrus calves are occupied with many behaviors necessary for survival. In captivity there is usually less to occupy them. Therefore it is necessary to develop other ways to occupy the animals to prevent negative behavior. In the present study, food in four different types of dispensers were tested on two walrus calves: fish in ice, fish in a nine-hole container, fish in a two-hole container, and fish in ice in a one-hole container. All four methods of offering fish had an effect on the animals' behavior. There were differences in the way the two animals responded to each of the four dispensers. The dispensers occupied one animal on average between 32-95% of the 90-min test periods, and the other animal for between 14-57% of the test periods. Due to the effect of learning and rapid development of the calves, which were shifting from a 100% formula diet to a 100% fish diet during the study period, the four methods cannot be compared. Besides the time feeding methods occupy animals, the practicality of a dispenser determines how often it will be used by the keepers. Of the four dispenser types tested in the present study, the nine-hole container was the most practical and was still used frequently by the keepers years after the study. Zoo Biol 0:1-12, 2007. (c) 2007 Wiley-Liss, Inc.

  4. 77 FR 13367 - General Electric-Hitachi Global Laser Enrichment, LLC, Proposed Laser-Based Uranium Enrichment...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-06

    ... Preparation, 75 FR 1819 (January 13, 2010). Documents related to this notice are available on the NRC's GE... COMMISSION General Electric-Hitachi Global Laser Enrichment, LLC, Proposed Laser-Based Uranium Enrichment...- Hitachi Global Laser Enrichment, LLC (GLE) Uranium Enrichment Facility. On June 26, 2009, GLE submitted...

  5. Microchip method for the enrichment of specific DNA sequences

    DOEpatents

    Mirzabekov, A.D.; Lysov, Y.P.; Shick, V.V.; Dubiley, S.A.

    1998-12-22

    A method for enriching specific genetic material sequences is provided, whereby oligonucleotide molecules complementary to the desired genetic material is first used to isolate the genetic material from a first source of genomic material. Then the genetic material is used as a label to isolate similar genetic sequences from other sources. 4 figs.

  6. Microchip method for the enrichment of specific DNA sequences

    DOEpatents

    Mirzabekov, Andrei Darievich; Lysov, Yuri Petrovich; Shick, Valentine Vladimirovich; Dubiley, Svetlana Alekseevna

    1998-01-01

    A method for enriching specific genetic material sequences is provided, whereby oligonucleotide molecules complementary to the desired genetic material is first used to isolate the genetic material from a first source of genomic material. Then the genetic material is used as a label to isolate similar genetic sequences from other sources.

  7. Fuel enrichment apparatus and method for gaseous fuel mixers

    SciTech Connect

    Fox, C.D.

    1981-08-25

    A fuel enrichment apparatus and method is shown for a gaseous fuel carburetor of either a fixed venturi or air valve type. The apparatus provides fuel enriching at the starting and wide open throttle conditions of the carburetor when the pressure drop in the induction passage is at a minimum. The apparatus also economizes on fuel usage by being closed to fuel transfer at idle speed and normal engine speed. The apparatus operates from the fuel supply line to the carburetor with only the fuel pressure available in that line, thereby obviating the need for either a second fuel line or a high pressure fuel line.

  8. Glycoprotein enrichment method using a selective magnetic nano-probe platform (MNP) functionalized with lectins.

    PubMed

    Cova, Marta; Oliveira-Silva, Rui; Ferreira, José Alexandre; Ferreira, Rita; Amado, Francisco; Daniel-da-Silva, Ana Luísa; Vitorino, Rui

    2015-01-01

    Protein post-translational modifications (PTMs) have increasingly become a research field of incredible importance to fully understand the regulation of biological processes in health and disease. Among PTMs, glycosylation is one of the most studied for which contributed the development and improvement of enrichment techniques. Nowadays, glycoprotein enrichment methods are based on lectin affinity, covalent interactions, and hydrophilic interaction liquid chromatography (HILIC). Nonetheless, the nanotechnology era has fetched new methods to enrich glycoproteins from complex samples as human biological fluids. For instance, magnetic nanoparticles (MNPs) are being used as an interesting enrichment approach allowing a better characterization of glycoproteins and glycopeptides.In this chapter, we describe an enrichment method based on MNPs functionalized with lectins (Concavalin A, wheat germ agglutinin, and Maackia amurensis lectin) to enrich specific sets of glycoproteins from biological fluids. Moreover, it is proposed a bioinformatic strategy to deal with data retrieved from mass spectrometry analysis of enriched samples aiming the identification of relevant biological processes modulated by a given stimuli and, ultimately, of new biomarkers for disease screening/management.

  9. Method for production of an isotopically enriched compound

    SciTech Connect

    Watrous, Matthew G.

    2012-12-11

    A method is presented for producing and isolating an isotopically enriched compound of a desired isotope from a parent radionuclide. The method includes forming, or placing, a precipitate containing a parent radionuclide of the desired daughter isotope in a first reaction zone and allowing sufficient time for the parent to decay into the desired gaseous daughter radioisotope. The method further contemplates collecting the desired daughter isotope as a solid in a second reaction zone through the application of temperatures below the freezing point of the desired isotope to a second reaction zone that is connected to the first reaction zone. Specifically, a method is presented for producing isotopically enriched compounds of xenon, including the radioactive isotope Xe-131m and the stable isotope Xe-131.

  10. Coupling enrichment methods with proteomics for understanding and treating disease.

    PubMed

    Kumar, Amit; Baycin-Hizal, Deniz; Shiloach, Joseph; Bowen, Michael A; Betenbaugh, Michael J

    2015-02-01

    Owing to recent advances in proteomics analytical methods and bioinformatics capabilities there is a growing trend toward using these capabilities for the development of drugs to treat human disease, including target and drug evaluation, understanding mechanisms of drug action, and biomarker discovery. Currently, the genetic sequences of many major organisms are available, which have helped greatly in characterizing proteomes in model animal systems and humans. Through proteomics, global profiles of different disease states can be characterized (e.g. changes in types and relative levels as well as changes in PTMs such as glycosylation or phosphorylation). Although intracellular proteomics can provide a broad overview of physiology of cells and tissues, it has been difficult to quantify the low abundance proteins which can be important for understanding the diseased states and treatment progression. For this reason, there is increasing interest in coupling comparative proteomics methods with subcellular fractionation and enrichment techniques for membranes, nucleus, phosphoproteome, glycoproteome as well as low abundance serum proteins. In this review, we will provide examples of where the utilization of different proteomics-coupled enrichment techniques has aided target and biomarker discovery, understanding the drug targeting mechanism, and mAb discovery. Taken together, these improvements will help to provide a better understanding of the pathophysiology of various diseases including cancer, autoimmunity, inflammation, cardiovascular disease, and neurological conditions, and in the design and development of better medicines for treating these afflictions. PMID:25523641

  11. A Method for Selective Enrichment and Analysis of Nitrotyrosine-Containing Peptides in Complex Proteome Samples

    SciTech Connect

    Zhang, Qibin; Qian, Weijun; Knyushko, Tanya V.; Clauss, Therese RW; Purvine, Samuel O.; Moore, Ronald J.; Sacksteder, Colette A.; Chin, Mark H.; Smith, Desmond J.; Camp, David G.; Bigelow, Diana J.; Smith, Richard D.

    2007-06-01

    Elevated levels of protein tyrosine nitration have been found in various neurodegenerative diseases and aging related pathologies; however, the lack of an efficient enrichment method has prevented the analysis of this important low level protein modification. We have developed an efficient method for specific enrichment of nitrotyrosine containing peptides that permits nitrotyrosine peptides and specific nitration sites to be unambiguously identified with LC-MS/MS. The method is based on the derivatization of nitrotyrosine into free sulfhydryl groups followed by high efficiency enrichment of sulfhydryl-containing peptides with thiopropyl sepharose beads. The derivatization process starts with acetylation with acetic anhydride to block all primary amines, followed by reduction of nitrotyrosine to aminotyrosine, then derivatization of aminotyrosine with N-Succinimidyl S-Acetylthioacetate (SATA), and finally deprotecting of S-acetyl on SATA to form free sulfhydryl groups. This method was evaluated using nitrotyrosine containing peptides, in-vitro nitrated human histone 1.2, and bovine serum albumin (BSA). 91% and 62% of the identified peptides from enriched histone and BSA samples were nitrotyrosine derivatized peptides, respectively, suggesting relative high specificity of the enrichment method. The application of this method to in-vitro nitrated mouse brain homogenate resulted in 35% of identified peptides containing nitrotyrosine (compared to only 5.9% observed from the global analysis of unenriched sample), and a total of 150 unique nitrated peptides covering 102 proteins were identified with a false discovery rate estimated at 3.3% from duplicate LC-MS/MS analyses of a single enriched sample.

  12. Improved Methods for the Enrichment and Analysis of Glycated Peptides

    SciTech Connect

    Zhang, Qibin; Schepmoes, Athena A; Brock, Jonathan W; Wu, Si; Moore, Ronald J; Purvine, Samuel O; Baynes, John; Smith, Richard D; Metz, Thomas O

    2008-12-15

    Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. Herein we report improved methods for the enrichment and analysis of glycated peptides using boronate affinity chromatography and electron transfer dissociation mass spectrometry, respectively. The enrichment of glycated peptides was improved by replacing an off-line desalting step with an on-line wash of column-bound glycated peptides using 50 mM ammonium acetate. The analysis of glycated peptides by MS/MS was improved by considering only higher charged (≥3) precursor-ions during data-dependent acquisition, which increased the number of glycated peptide identifications. Similarly, the use of supplemental collisional activation after electron transfer (ETcaD) resulted in more glycated peptide identifications when the MS survey scan was acquired with enhanced resolution. In general, acquiring ETD-MS/MS data at a normal MS survey scan rate, in conjunction with the rejection of both 1+ and 2+ precursor-ions, increased the number of identified glycated peptides relative to ETcaD or the enhanced MS survey scan rate. Finally, an evaluation of trypsin, Arg-C, and Lys-C showed that tryptic digestion of glycated proteins was comparable to digestion with Lys-C and that both were better than Arg-C in terms of the number glycated peptides identified by LC-MS/MS.

  13. eSNPO: An eQTL-based SNP Ontology and SNP functional enrichment analysis platform

    PubMed Central

    Li, Jin; Wang, Limei; Jiang, Tao; Wang, Jizhe; Li, Xue; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Zhang, Ruijie; Lv, Hongchao; Guo, Maozu

    2016-01-01

    Genome-wide association studies (GWASs) have mined many common genetic variants associated with human complex traits like diseases. After that, the functional annotation and enrichment analysis of significant SNPs are important tasks. Classic methods are always based on physical positions of SNPs and genes. Expression quantitative trait loci (eQTLs) are genomic loci that contribute to variation in gene expression levels and have been proven efficient to connect SNPs and genes. In this work, we integrated the eQTL data and Gene Ontology (GO), constructed associations between SNPs and GO terms, then performed functional enrichment analysis. Finally, we constructed an eQTL-based SNP Ontology and SNP functional enrichment analysis platform. Taking Parkinson Disease (PD) as an example, the proposed platform and method are efficient. We believe eSNPO will be a useful resource for SNP functional annotation and enrichment analysis after we have got significant disease related SNPs. PMID:27470167

  14. eSNPO: An eQTL-based SNP Ontology and SNP functional enrichment analysis platform.

    PubMed

    Li, Jin; Wang, Limei; Jiang, Tao; Wang, Jizhe; Li, Xue; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Zhang, Ruijie; Lv, Hongchao; Guo, Maozu

    2016-01-01

    Genome-wide association studies (GWASs) have mined many common genetic variants associated with human complex traits like diseases. After that, the functional annotation and enrichment analysis of significant SNPs are important tasks. Classic methods are always based on physical positions of SNPs and genes. Expression quantitative trait loci (eQTLs) are genomic loci that contribute to variation in gene expression levels and have been proven efficient to connect SNPs and genes. In this work, we integrated the eQTL data and Gene Ontology (GO), constructed associations between SNPs and GO terms, then performed functional enrichment analysis. Finally, we constructed an eQTL-based SNP Ontology and SNP functional enrichment analysis platform. Taking Parkinson Disease (PD) as an example, the proposed platform and method are efficient. We believe eSNPO will be a useful resource for SNP functional annotation and enrichment analysis after we have got significant disease related SNPs. PMID:27470167

  15. An Enriched Radial Point Interpolation Method (e-RPIM) for the Analysis of Crack Tip

    NASA Astrophysics Data System (ADS)

    Gu, Y. T.; Wang, W. L.; Fu, Q.

    2010-05-01

    In this paper, an enriched radial point interpolation method (e-RPIM) is developed for the determination of crack tip fields. The conventional RBF interpolation is novelly augmented by the suitable trigonometric basis functions to reflect the properties of stresses for the crack tip fields. The performance of the enriched meshfree RBF shape functions is firstly investigated using the surface fitting. The surface fitting results have proven that, comparing with the conventional RBF, the enriched RBF interpolation has: 1) a similar accuracy to fit a polynomial surface; and 2) a much better accuracy to fit a trigonometric surface then the conventional RBF interpolation. It has proven that the enriched RBF shape function will not only possess all advantages of conventional RBF interpolation, but also can accurately reflect the properties of stresses for the crack tip fields. The system of equations for the crack analysis is then derived based on the enriched RBF shape function and the meshfree weak-form. Crack problems are simulated using this newly developed e-RPIM method. It has been demonstrated that the present e-RPIM is very accurate and stable, and it has very good potential to develop a practical simulation tool for fracture mechanics problems.

  16. Method and apparatus for measuring enrichment of UF6

    DOEpatents

    Hill, Thomas Roy; Ianakiev, Kiril Dimitrov

    2011-06-07

    A system and method are disclosed for determining the enrichment of .sup.235U in Uranium Hexafluoride (UF6) utilizing synthesized X-rays which are directed at a container test zone containing a sample of UF6. A detector placed behind the container test zone then detects and counts the X-rays which pass through the container and the UF6. In order to determine the portion of the attenuation due to the UF6 gas alone, this count rate may then be compared to a calibration count rate of X-rays passing through a calibration test zone which contains a vacuum, the test zone having experienced substantially similar environmental conditions as the actual test zone. Alternatively, X-rays of two differing energy levels may be alternately directed at the container, where either the container or the UF6 has a high sensitivity to the difference in the energy levels, and the other having a low sensitivity.

  17. Heat-transfer resistance measurement method (HTM)-based cell detection at trace levels using a progressive enrichment approach with highly selective cell-binding surface imprints.

    PubMed

    Bers, Karolien; Eersels, Kasper; van Grinsven, Bart; Daemen, Mat; Bogie, Jeroen F J; Hendriks, Jerome J A; Bouwmans, Evelien E; Püttmann, Christiane; Stein, Christoph; Barth, Stefan; Bos, Gerard M J; Germeraad, Wilfred T V; De Ceuninck, Ward; Wagner, Patrick

    2014-04-01

    Surface-imprinted polymers allow for specific cell detection based on simultaneous recognition of the cell shape, cell size, and cell membrane functionalities by macromolecular cell imprints. In this study, the specificity of detection and the detection sensitivity for target cells within a pool of non-target cells were analyzed for a cell-specific surface-imprinted polymer combined with a heat-transfer-based read-out technique (HTM). A modified Chinese hamster ovarian cell line (CHO-ldlD) was used as a model system on which the transmembrane protein mucin-1 (MUC1) could be excessively expressed and for which the occurrence of MUC1 glycosylation could be controlled. In specific cancer cells, the overexpressed MUC1 protein typically shows an aberrant apical distribution and glycosylation. We show that surface-imprinted polymers discriminate between cell types that (1) only differ in the expression of a specific membrane protein (MUC1) or (2) only differ in the membrane protein being glycosylated or not. Moreover, surface-imprinted polymers of cells carrying different glycoforms of the same membrane protein do target both types of cells. These findings illustrate the high specificity of cell detection that can be reached by the structural imprinting of cells in polymer layers. Competitiveness between target and non-target cells was proven to negatively affect the detection sensitivity of target cells. Furthermore, we show that the detection sensitivity can be increased significantly by repetitively exposing the surface to the sample and eliminating non-specifically bound cells by flushing between consecutive cell exposures.

  18. Hybrid Enrichment Assay Methods for a UF6 Cylinder Verification Station: FY10 Progress Report

    SciTech Connect

    Smith, Leon E.; Jordan, David V.; Orton, Christopher R.; Misner, Alex C.; Mace, Emily K.

    2010-08-01

    Pacific Northwest National Laboratory (PNNL) is developing the concept of an automated UF6 cylinder verification station that would be located at key measurement points to positively identify each cylinder, measure its mass and enrichment, store the collected data in a secure database, and maintain continuity of knowledge on measured cylinders until the arrival of International Atomic Energy Agency (IAEA) inspectors. At the center of this unattended system is a hybrid enrichment assay technique that combines the traditional enrichment-meter method (based on the 186 keV peak from 235U) with non-traditional neutron-induced high-energy gamma-ray signatures (spawned primarily by 234U alpha emissions and 19F(alpha, neutron) reactions). Previous work by PNNL provided proof-of-principle for the non-traditional signatures to support accurate, full-volume interrogation of the cylinder enrichment, thereby reducing the systematic uncertainties in enrichment assay due to UF6 heterogeneity and providing greater sensitivity to material substitution scenarios. The work described here builds on that preliminary evaluation of the non-traditional signatures, but focuses on a prototype field system utilizing NaI(Tl) and LaBr3(Ce) spectrometers, and enrichment analysis algorithms that integrate the traditional and non-traditional signatures. Results for the assay of Type-30B cylinders ranging from 0.2 to 4.95 wt% 235U, at an AREVA fuel fabrication plant in Richland, WA, are described for the following enrichment analysis methods: 1) traditional enrichment meter signature (186 keV peak) as calculated using a square-wave convolute (SWC) algorithm; 2) non-traditional high-energy gamma-ray signature that provides neutron detection without neutron detectors and 3) hybrid algorithm that merges the traditional and non-traditional signatures. Uncertainties for each method, relative to the declared enrichment for each cylinder, are calculated and compared to the uncertainties from an attended

  19. Highly Selective Enrichment of Glycopeptides Based on Zwitterionically Functionalized Soluble Nanopolymers

    PubMed Central

    Cao, Weiqian; Huang, Jiangming; Jiang, Biyun; Gao, Xing; Yang, Pengyuan

    2016-01-01

    Efficient glycopeptides enrichment prior to mass spectrometry analysis is essential for glycoproteome study. ZIC-HILIC (zwitterionic hydrophilic interaction liquid chromatography) based glycopeptides enrichment approaches have been attracting more attention for several benefits like easy operating, high enrichment specificity and intact glycopeptide retained. In this study, Poly (amidoamine) dendrimer (PAMAM) was adopted for the synthesis of zwitterionically functionalized (ZICF) materials for glycopeptide enrichment. The multiple branched structure and good solubility of ZICF-PAMAM enables a sufficient interaction with glycopeptides. The ZICF-PAMAM combined with the FASP-mode enrichment strategy exhibits more superior performance compared with the existing methods. It has the minimum detectable concentration of femtomolar level and high recovery rate of over 90.01%, and can efficiently enrich glycopeptides from complex biological samples even for merely 0.1 μL human serum. The remarkable glycopeptides enrichment capacity of ZICF-PAMAM highlights the potential application in in-depth glycoproteome research, which may open up new opportunities for the development of glycoproteomics. PMID:27412817

  20. Highly Selective Enrichment of Glycopeptides Based on Zwitterionically Functionalized Soluble Nanopolymers

    NASA Astrophysics Data System (ADS)

    Cao, Weiqian; Huang, Jiangming; Jiang, Biyun; Gao, Xing; Yang, Pengyuan

    2016-07-01

    Efficient glycopeptides enrichment prior to mass spectrometry analysis is essential for glycoproteome study. ZIC-HILIC (zwitterionic hydrophilic interaction liquid chromatography) based glycopeptides enrichment approaches have been attracting more attention for several benefits like easy operating, high enrichment specificity and intact glycopeptide retained. In this study, Poly (amidoamine) dendrimer (PAMAM) was adopted for the synthesis of zwitterionically functionalized (ZICF) materials for glycopeptide enrichment. The multiple branched structure and good solubility of ZICF-PAMAM enables a sufficient interaction with glycopeptides. The ZICF-PAMAM combined with the FASP-mode enrichment strategy exhibits more superior performance compared with the existing methods. It has the minimum detectable concentration of femtomolar level and high recovery rate of over 90.01%, and can efficiently enrich glycopeptides from complex biological samples even for merely 0.1 μL human serum. The remarkable glycopeptides enrichment capacity of ZICF-PAMAM highlights the potential application in in-depth glycoproteome research, which may open up new opportunities for the development of glycoproteomics.

  1. Hope-Focused and Forgiveness-Based Group Interventions To Promote Marital Enrichment.

    ERIC Educational Resources Information Center

    Ripley, Jennifer S.; Worthington, Everett L., Jr.

    2002-01-01

    Reports on a clinical trial (N = 43 couples) that compares a hope-focused marital enrichment with empathy-centered forgiveness-based marital enrichment Hope-focused marital enrichment produced clinically relevant changes in marital communication. The forgiveness-based marital enrichment psychoeducational group is one of the first studies of…

  2. Benchmarking methods and data sets for ligand enrichment assessment in virtual screening.

    PubMed

    Xia, Jie; Tilahun, Ermias Lemma; Reid, Terry-Elinor; Zhang, Liangren; Wang, Xiang Simon

    2015-01-01

    Retrospective small-scale virtual screening (VS) based on benchmarking data sets has been widely used to estimate ligand enrichments of VS approaches in the prospective (i.e. real-world) efforts. However, the intrinsic differences of benchmarking sets to the real screening chemical libraries can cause biased assessment. Herein, we summarize the history of benchmarking methods as well as data sets and highlight three main types of biases found in benchmarking sets, i.e. "analogue bias", "artificial enrichment" and "false negative". In addition, we introduce our recent algorithm to build maximum-unbiased benchmarking sets applicable to both ligand-based and structure-based VS approaches, and its implementations to three important human histone deacetylases (HDACs) isoforms, i.e. HDAC1, HDAC6 and HDAC8. The leave-one-out cross-validation (LOO CV) demonstrates that the benchmarking sets built by our algorithm are maximum-unbiased as measured by property matching, ROC curves and AUCs.

  3. Tweezing-adsorptive bubble separation. Analytical method for the selective and high enrichment of metalloenzymes.

    PubMed

    Gerken, Birte M; Wattenbach, Carsten; Linke, Diana; Zorn, Holger; Berger, Ralf G; Parlar, Harun

    2005-10-01

    A novelly developed tweezing-adsorptive bubble separation (ABS) method for the enrichment of metalloenzymes (laccase C and horseradish peroxidase) is introduced. The method is based on the chelation of the enzymes' active center and can also be applied for analysis. N-(2-acetamido)iminodiacetic acid served as a chelator and was synthesized with an octyl unit to become ADA-C8. Laccase was enriched 13.3-fold (66.31% recovery) and HPOX 17.8-fold (85.34%) without a significant loss of enzymatic activity. To prove that the entire enzyme is tweezed at the active center, ABS trials were done using ADA-C8 already complexed with Cu2+ and Fe3+. As only marginal enrichment occurred (ER laccase, 0.17; ER HPOX, 0.44), no chelating effect was concluded. It was determined how the chelation toward the active center was directed by applying other chelators such as EDTA, NTA, N,N-dimethylaminoglycine, oxalic acid, malonic acid, adipinic acid, and tripropylamine, which are similar in structure to ADA-C8. The results concluded that the chelation is 3-fold coordinated on the type 1 copper center of laccase, whereas that of HPOX only 1-fold at Fe3+ and additionally at the cationic amino acid arginine, which is also located at the active center. Tweezing-ABS has been proven to selectively and effectively enrich metalloenzymes.

  4. Taguchi methods applied to oxygen-enriched diesel engine experiments

    SciTech Connect

    Marr, W.W.; Sekar, R.R.; Cole, R.L.; Marciniak, T.J. ); Longman, D.E. )

    1992-01-01

    This paper describes a test series conducted on a six-cylinder diesel engine to study the impacts of controlled factors (i.e., oxygen content of the combustion air, water content of the fuel, fuel rate, and fuel-injection timing) on engine emissions using Taguchi methods. Three levels of each factor were used in the tests. Only the main effects of the factors were examined; no attempt was made to analyze the interactions among the factors. It was found that, as in the case of the single-cylinder engine tests, oxygen in the combustion air was very effective in reducing particulate and smoke emissions. Increases in NO[sub x] due to the oxygen enrichment observed in the single-cylinder tests also occurred in the present six-cylinder tests. Water in the emulsified fuel was found to be much less effective in decreasing NO[sub x] emissions for the six-cylinder engine than it was for the single-cylinder engine.

  5. Taguchi methods applied to oxygen-enriched diesel engine experiments

    SciTech Connect

    Marr, W.W.; Sekar, R.R.; Cole, R.L.; Marciniak, T.J.; Longman, D.E.

    1992-12-01

    This paper describes a test series conducted on a six-cylinder diesel engine to study the impacts of controlled factors (i.e., oxygen content of the combustion air, water content of the fuel, fuel rate, and fuel-injection timing) on engine emissions using Taguchi methods. Three levels of each factor were used in the tests. Only the main effects of the factors were examined; no attempt was made to analyze the interactions among the factors. It was found that, as in the case of the single-cylinder engine tests, oxygen in the combustion air was very effective in reducing particulate and smoke emissions. Increases in NO{sub x} due to the oxygen enrichment observed in the single-cylinder tests also occurred in the present six-cylinder tests. Water in the emulsified fuel was found to be much less effective in decreasing NO{sub x} emissions for the six-cylinder engine than it was for the single-cylinder engine.

  6. Mercury release from deforested soils triggered by base cation enrichment.

    PubMed

    Farella, N; Lucotte, M; Davidson, R; Daigle, S

    2006-09-01

    The Brazilian Amazon has experienced considerable colonization in the last few decades. Family agriculture based on slash-and-burn enables millions of people to live in that region. However, the poor nutrient content of most Amazonian soils requires cation-rich ashes from the burning of the vegetation biomass for cultivation to be successful, which leads to forest ecosystem degradation, soil erosion and mercury contamination. While recent studies have suggested that mercury present in soils was transferred towards rivers upon deforestation, little is known about the dynamics between agricultural land-use and mercury leaching. In this context, the present study proposes an explanation that illustrates how agricultural land-use triggers mercury loss from soils. This explanation lies in the competition between base cations and mercury in soils which are characterized by a low adsorption capacity. Since these soils are naturally very poor in base cations, the burning of the forest biomass suddenly brings high quantities of base cations to soils, destabilizing the previous equilibrium amongst cations. Base cation enrichment triggers mobility in soil cations, rapidly dislocating mercury atoms. This conclusion comes from principal component analyses illustrating that agricultural land-use was associated with base cation enrichment and mercury depletion. The overall conclusions highlight a pernicious cycle: while soil nutrient enrichment actually occurs through biomass burning, although on a temporary basis, there is a loss in Hg content, which is leached to rivers, entering the aquatic chain, and posing a potential health threat to local populations. Data presented here reflects three decades of deforestation activities, but little is known about the long-term impact of such a disequilibrium. These findings may have repercussions on our understanding of the complex dynamics of deforestation and agriculture worldwide. PMID:16781764

  7. Method for enriching a middle isotope using vibration-vibration pumping

    DOEpatents

    Rich, Joseph W.; Homicz, Gregory F.; Bergman, Richard C.

    1989-01-01

    Method for producing isotopically enriched material by vibration-vibration excitation of gaseous molecules wherein a middle mass isotope of an isotopic mixture including lighter and heavier mass isotopes preferentially populates a higher vibrational mode and chemically reacts to provide a product in which it is enriched. The method can be used for vibration-vibration enrichment of .sup.17 O in a CO reactant mixture.

  8. Large-scale All-electron Density Functional Theory Calculations using Enriched Finite Element Method

    NASA Astrophysics Data System (ADS)

    Kanungo, Bikash; Gavini, Vikram

    We present a computationally efficient method to perform large-scale all-electron density functional theory calculations by enriching the Lagrange polynomial basis in classical finite element (FE) discretization with atom-centered numerical basis functions, which are obtained from the solutions of the Kohn-Sham (KS) problem for single atoms. We term these atom-centered numerical basis functions as enrichment functions. The integrals involved in the construction of the discrete KS Hamiltonian and overlap matrix are computed using an adaptive quadrature grid based on gradients in the enrichment functions. Further, we propose an efficient scheme to invert the overlap matrix by exploiting its LDL factorization and employing spectral finite elements along with Gauss-Lobatto quadrature rules. Finally, we use a Chebyshev polynomial based acceleration technique to compute the occupied eigenspace in each self-consistent iteration. We demonstrate the accuracy, efficiency and scalability of the proposed method on various metallic and insulating benchmark systems, with systems ranging in the order of 10,000 electrons. We observe a 50-100 fold reduction in the overall computational time when compared to classical FE calculations while being commensurate with the desired chemical accuracy. We acknowledge the support of NSF (Grant No. 1053145) and ARO (Grant No. W911NF-15-1-0158) in conducting this work.

  9. Enrichment Assay Methods Development for the Integrated Cylinder Verification System

    SciTech Connect

    Smith, Leon E.; Misner, Alex C.; Hatchell, Brian K.; Curtis, Michael M.

    2009-10-22

    International Atomic Energy Agency (IAEA) inspectors currently perform periodic inspections at uranium enrichment plants to verify UF6 cylinder enrichment declarations. Measurements are typically performed with handheld high-resolution sensors on a sampling of cylinders taken to be representative of the facility's entire product-cylinder inventory. Pacific Northwest National Laboratory (PNNL) is developing a concept to automate the verification of enrichment plant cylinders to enable 100 percent product-cylinder verification and potentially, mass-balance calculations on the facility as a whole (by also measuring feed and tails cylinders). The Integrated Cylinder Verification System (ICVS) could be located at key measurement points to positively identify each cylinder, measure its mass and enrichment, store the collected data in a secure database, and maintain continuity of knowledge on measured cylinders until IAEA inspector arrival. The three main objectives of this FY09 project are summarized here and described in more detail in the report: (1) Develop a preliminary design for a prototype NDA system, (2) Refine PNNL's MCNP models of the NDA system, and (3) Procure and test key pulse-processing components. Progress against these tasks to date, and next steps, are discussed.

  10. Enriching semantic knowledge bases for opinion mining in big data applications.

    PubMed

    Weichselbraun, A; Gindl, S; Scharl, A

    2014-10-01

    This paper presents a novel method for contextualizing and enriching large semantic knowledge bases for opinion mining with a focus on Web intelligence platforms and other high-throughput big data applications. The method is not only applicable to traditional sentiment lexicons, but also to more comprehensive, multi-dimensional affective resources such as SenticNet. It comprises the following steps: (i) identify ambiguous sentiment terms, (ii) provide context information extracted from a domain-specific training corpus, and (iii) ground this contextual information to structured background knowledge sources such as ConceptNet and WordNet. A quantitative evaluation shows a significant improvement when using an enriched version of SenticNet for polarity classification. Crowdsourced gold standard data in conjunction with a qualitative evaluation sheds light on the strengths and weaknesses of the concept grounding, and on the quality of the enrichment process.

  11. Enriching semantic knowledge bases for opinion mining in big data applications

    PubMed Central

    Weichselbraun, A.; Gindl, S.; Scharl, A.

    2014-01-01

    This paper presents a novel method for contextualizing and enriching large semantic knowledge bases for opinion mining with a focus on Web intelligence platforms and other high-throughput big data applications. The method is not only applicable to traditional sentiment lexicons, but also to more comprehensive, multi-dimensional affective resources such as SenticNet. It comprises the following steps: (i) identify ambiguous sentiment terms, (ii) provide context information extracted from a domain-specific training corpus, and (iii) ground this contextual information to structured background knowledge sources such as ConceptNet and WordNet. A quantitative evaluation shows a significant improvement when using an enriched version of SenticNet for polarity classification. Crowdsourced gold standard data in conjunction with a qualitative evaluation sheds light on the strengths and weaknesses of the concept grounding, and on the quality of the enrichment process. PMID:25431524

  12. What Is the Best NGS Enrichment Method for the Molecular Diagnosis of Monogenic Diabetes and Obesity?

    PubMed

    Philippe, Julien; Derhourhi, Mehdi; Durand, Emmanuelle; Vaillant, Emmanuel; Dechaume, Aurélie; Rabearivelo, Iandry; Dhennin, Véronique; Vaxillaire, Martine; De Graeve, Franck; Sand, Olivier; Froguel, Philippe; Bonnefond, Amélie

    2015-01-01

    Molecular diagnosis of monogenic diabetes and obesity is of paramount importance for both the patient and society, as it can result in personalized medicine associated with a better life and it eventually saves health care spending. Genetic clinical laboratories are currently switching from Sanger sequencing to next-generation sequencing (NGS) approaches but choosing the optimal protocols is not easy. Here, we compared the sequencing coverage of 43 genes involved in monogenic forms of diabetes and obesity, and variant detection rates, resulting from four enrichment methods based on the sonication of DNA (Agilent SureSelect, RainDance technologies), or using enzymes for DNA fragmentation (Illumina Nextera, Agilent HaloPlex). We analyzed coding exons and untranslated regions of the 43 genes involved in monogenic diabetes and obesity. We found that none of the methods achieves yet full sequencing of the gene targets. Nonetheless, the RainDance, SureSelect and HaloPlex enrichment methods led to the best sequencing coverage of the targets; while the Nextera method resulted in the poorest sequencing coverage. Although the sequencing coverage was high, we unexpectedly found that the HaloPlex method missed 20% of variants detected by the three other methods and Nextera missed 10%. The question of which NGS technique for genetic diagnosis yields the highest diagnosis rate is frequently discussed in the literature and the response is still unclear. Here, we showed that the RainDance enrichment method as well as SureSelect, which are both based on the sonication of DNA, resulted in a good sequencing quality and variant detection, while the use of enzymes to fragment DNA (HaloPlex or Nextera) might not be the best strategy to get an accurate sequencing. PMID:26599467

  13. Prospects of lithium enrichment on 7Li isotope by method of controlled ions electro-migration

    NASA Astrophysics Data System (ADS)

    Martoyan, G. A.; Kalugin, M. M.; Gabrielyan, A. V.; Martoyan, A. G.

    2016-01-01

    This paper deals with a new electro-membrane method of enrichment of 7Li isotope. The data are presented on the importance and application fields regarding the use of 7Li isotopes. Existing methods and criteria of separation of lithium isotopes are discussed. The principle of new technology, regimes of enrichment experiments, and analysis details of obtained products are briefly described.

  14. Foraging-Based Enrichment Promotes More Varied Behaviour in Captive Australian Fur Seals (Arctocephalus pusillus doriferus)

    PubMed Central

    Hocking, David P.; Salverson, Marcia; Evans, Alistair R.

    2015-01-01

    During wild foraging, Australian fur seals (Arctocephalus pusillus doriferus) encounter many different types of prey in a wide range of scenarios, yet in captive environments they are typically provided with a narrower range of opportunities to display their full repertoire of behaviours. This study aimed to quantitatively explore the effect of foraging-based enrichment on the behaviour and activity patterns displayed by two captive Australian fur seals at Melbourne Zoo, Australia. Food was presented as a scatter in open water, in a free-floating ball device, or in a static box device, with each treatment separated by control trials with no enrichment. Both subjects spent more time interacting with the ball and static box devices than the scatter feed. The total time spent pattern swimming was reduced in the enrichment treatments compared to the controls, while the time spent performing random swimming behaviours increased. There was also a significant increase in the total number of bouts of behaviour performed in all three enrichment treatments compared to controls. Each enrichment method also promoted a different suit of foraging behaviours. Hence, rather than choosing one method, the most effective way to increase the diversity of foraging behaviours, while also increasing variation in general activity patterns, is to provide seals with a wide range of foraging scenarios where food is encountered in different ways. PMID:25946412

  15. Foraging-Based Enrichment Promotes More Varied Behaviour in Captive Australian Fur Seals (Arctocephalus pusillus doriferus).

    PubMed

    Hocking, David P; Salverson, Marcia; Evans, Alistair R

    2015-01-01

    During wild foraging, Australian fur seals (Arctocephalus pusillus doriferus) encounter many different types of prey in a wide range of scenarios, yet in captive environments they are typically provided with a narrower range of opportunities to display their full repertoire of behaviours. This study aimed to quantitatively explore the effect of foraging-based enrichment on the behaviour and activity patterns displayed by two captive Australian fur seals at Melbourne Zoo, Australia. Food was presented as a scatter in open water, in a free-floating ball device, or in a static box device, with each treatment separated by control trials with no enrichment. Both subjects spent more time interacting with the ball and static box devices than the scatter feed. The total time spent pattern swimming was reduced in the enrichment treatments compared to the controls, while the time spent performing random swimming behaviours increased. There was also a significant increase in the total number of bouts of behaviour performed in all three enrichment treatments compared to controls. Each enrichment method also promoted a different suit of foraging behaviours. Hence, rather than choosing one method, the most effective way to increase the diversity of foraging behaviours, while also increasing variation in general activity patterns, is to provide seals with a wide range of foraging scenarios where food is encountered in different ways.

  16. A Clustering-Based Approach to Enriching Code Foraging Environment.

    PubMed

    Niu, Nan; Jin, Xiaoyu; Niu, Zhendong; Cheng, Jing-Ru C; Li, Ling; Kataev, Mikhail Yu

    2016-09-01

    Developers often spend valuable time navigating and seeking relevant code in software maintenance. Currently, there is a lack of theoretical foundations to guide tool design and evaluation to best shape the code base to developers. This paper contributes a unified code navigation theory in light of the optimal food-foraging principles. We further develop a novel framework for automatically assessing the foraging mechanisms in the context of program investigation. We use the framework to examine to what extent the clustering of software entities affects code foraging. Our quantitative analysis of long-lived open-source projects suggests that clustering enriches the software environment and improves foraging efficiency. Our qualitative inquiry reveals concrete insights into real developer's behavior. Our research opens the avenue toward building a new set of ecologically valid code navigation tools. PMID:25910273

  17. Development of a new 48Ca enrichment method and the CANDLES experiment

    NASA Astrophysics Data System (ADS)

    Kishimoto, Tadafumi

    2015-10-01

    CANDLES is a project to study double beta decay of 48Ca. CANDLES could become the most competitive experiment if we could have an efficient method to enrich 48Ca. We developed a new method for enrichment of large amount of calcium isotopes. The method is called Multi-Channel Counter-Current Electrophoresis (MCCCE) which can be found elsewhre. Essential point is the increase of the power density in the migration path. In MCCCE, ions migrate in multi-channels on a boron nitride (BN) plate by which substantial increase of the power density was achieved. We made a tiny prototype instrument with a 10 mm thick BN plate and obtained 3 for an enrichment factor for the ratio of abundance of 48Ca to 43Ca over that of natural abundance. It corresponds to 6 for the enrichment factor of 48Ca to 40Ca. Recently we obtained 10 for the enrichment factor by using 20 mm BN plate. This remarkably large enrichment factor demonstrates that the MCCCE is a realistic and promising method for the enrichment of large amount of ions. This method can be applied to many other elements and compounds. I will describe MCCCE and its effect on the study of double beta decay and other fields.

  18. Unattended Environmental Sampling and Laser-based Enrichment Assay for Detection of Undeclared HEU Production in Enrichment Plants

    SciTech Connect

    Anheier, Norman C.; Bushaw, Bruce A.

    2010-04-15

    Nuclear power is enjoying rapid growth as government energy policies and public demand shift toward carbon neutral energy production. Accompanying the growth in nuclear power is the requirement for increased nuclear fuel production, including a significant expansion in uranium enrichment capacity. Essential to the success of the nuclear energy renaissance is the development and implementation of sustainable, proliferation-resistant nuclear power generation. Unauthorized production of highly enriched uranium (HEU) remains the primary proliferation concern for modern gaseous centrifuge enrichment plants (GCEPs). While to date there has been no indication of declared, safeguarded GCEPs producing HEU, the massive separative work unit (SWU) processing power of modern GCEPs presents a significant latent risk of nuclear breakout and suggests the need for more timely detection of potential facility misuse. The Pacific Northwest National Laboratory is developing an unattended safeguards instrument, combining continuous aerosol particulate collection with uranium isotope assay, to provide timely HEU detection within a GCEP. This approach is based on laser vaporization of aerosol particulates, followed by laser spectroscopy to characterize the uranium enrichment level. We demonstrate enrichment assay, with relative isotope abundance uncertainty <5%, on individual micron-sized particles that are trace components within a mixture ‘background’ particles

  19. Adaptation of the doubly labeled water method for subjects consuming isotopically enriched water.

    PubMed

    Gretebeck, R J; Schoeller, D A; Socki, R A; Davis-Street, J; Gibson, E K; Schulz, L O; Lane, H W

    1997-02-01

    The use of doubly labeled water (DLW) to measure energy expenditure is subject to error if the background abundance of the oxygen and hydrogen isotope tracers changes during the test period. This study evaluated the accuracy and precision of different methods by which such background isotope changes can be corrected, including a modified method that allows prediction of the baseline that would be achieved if subjects were to consume water from a given source indefinitely. Subjects in this study were eight women (4 test subjects and 4 control subjects) who consumed for 28 days water enriched to resemble drinking water aboard the United States space shuttle. Test subjects and control subjects were given a DLW dose on days 1 and 15, respectively. The change to an enriched water source produced a bias in expenditure calculations that exceeded 2.9 MJ/day (35%), relative to calculations from intake-balance. The proposed correction based on the predicted final abundance of 18O and deuterium after equilibration to the new water source eliminated this bias, as did the traditional use of a control group. This new modified correction method is advantageous under field conditions when subject numbers are limited.

  20. Isolation Method (direct plating or enrichment) does not affect Antimicrobial Susceptibility of Campylobacter from Chicken Carcasses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To determine if Campylobacter isolation method influenced antimicrobial susceptibility results, the minimum inhibitory concentrations (MIC) of nine antimicrobials were compared for 291 pairs of Campylobacter isolates recovered from chicken carcass rinse samples using direct plating and an enrichment...

  1. Enriched Title-Based Keyword Index Generation Using dBase II.

    ERIC Educational Resources Information Center

    Rajendran, P. P.

    1986-01-01

    Describes the use of a database management system (DBMS)--dBaseII--to create an enriched title-based keyword index for a collection of news items at the Renewable Energy Resources Information Center of the Asian Institute of Technology. The use of DBMSs in libraries in developing countries is emphasized. (Author/LRW)

  2. Unattended Monitoring of HEU Production in Gaseous Centrifuge Enrichment Plants using Automated Aerosol Collection and Laser-based Enrichment Assay

    SciTech Connect

    Anheier, Norman C.; Bushaw, Bruce A.

    2010-08-11

    Nuclear power is enjoying rapid growth as government energy policies and public demand shift toward low carbon energy production. Pivotal to the global nuclear power renaissance is the development and deployment of robust safeguards instrumentation that allows the limited resources of the IAEA to keep pace with the expansion of the nuclear fuel cycle. Undeclared production of highly enriched uranium (HEU) remains a primary proliferation concern for modern gaseous centrifuge enrichment plants (GCEPs), due to their massive separative work unit (SWU) processing power and comparably short cascade equilibrium timescale. The Pacific Northwest National Laboratory is developing an unattended safeguards instrument, combining continuous aerosol particulate collection with uranium isotope assay, to provide timely detection of HEU production within a GCEP. This approach is based on laser vaporization of aerosol particulates, followed by laser spectroscopy to characterize the uranium enrichment level. Our prior investigation demonstrated single-shot detection sensitivity approaching the femtogram range and relative isotope ratio uncertainty better than 10% using gadolinium as a surrogate for uranium. In this paper we present measurement results on standard samples containing traces of depleted, natural, and low enriched uranium, as well as measurements on aerodynamic size uranium particles mixed in background materials (e.g., dust, minerals, soils). Improvements and optimizations in the detection electronics, signal timing, calibration, and laser alignment have lead to significant improvements in detection sensitivity and enrichment accuracy, contributing to an overall reduction in the false alarm probability. The sample substrate media was also found to play a significant role in facilitating laser-induced vaporization and the production of energetic plasma conditions, resulting in ablation optimization and further improvements in the isotope abundance sensitivity.

  3. Batch methods for enriching trace impurities in hydrogen gas for their further analysis

    DOEpatents

    Ahmed, Shabbir; Lee, Sheldon H.D.; Kumar, Romesh; Papdias, Dionissios D.

    2014-07-15

    Provided herein are batch methods and devices for enriching trace quantities of impurities in gaseous mixtures, such as hydrogen fuel. The methods and devices rely on concentrating impurities using hydrogen transport membranes wherein the time period for concentrating the sample is calculated on the basis of optimized membrane characteristics, comprising its thickness and permeance, with optimization of temperature, and wherein the enrichment of trace impurities is proportional to the pressure ratio P.sub.hi/P.sub.lo and the volume ratio V.sub.1/V.sub.2, with following detection of the impurities using commonly-available detection methods.

  4. Methods for Baiting and Enriching Fungus-Feeding (Mycophagous) Rhizosphere Bacteria

    PubMed Central

    Ballhausen, Max-Bernhard; van Veen, Johannes A.; Hundscheid, Maria P. J.; de Boer, Wietse

    2015-01-01

    Mycophagous soil bacteria are able to obtain nutrients from living fungal hyphae. However, with exception of the soil bacterial genus Collimonas, occurrence of this feeding strategy has not been well examined. Evaluation of the importance of mycophagy in soil bacterial communities requires targeted isolation methods. In this study, we compared two different approaches to obtain mycophagous bacteria from rhizospheric soil. A short-term method based on baiting for bacteria that can rapidly adhere to fungal hyphae and a long-term method based on the enrichment of bacteria on fungal hyphae via repeated transfer. Hyphae-adhering bacteria were isolated, identified by 16S rDNA sequencing and tested for antifungal activity and the ability to feed on fungi as the sole source of carbon. Both methods yielded a range of potentially mycophagous bacterial isolates with little phylogenetic overlap. We also found indications for feeding preferences among the potentially mycophagous bacteria. Our results indicate that mycophagy could be an important growth strategy for rhizosphere bacteria. To our surprise, we found several potential plant pathogenic bacteria among the mycophagous isolates. We discuss the possible benefits that these bacteria might gain from colonizing fungal hyphae. PMID:26733962

  5. A Pharmacology-Based Enrichment Program for Undergraduates Promotes Interest in Science.

    PubMed

    Godin, Elizabeth A; Wormington, Stephanie V; Perez, Tony; Barger, Michael M; Snyder, Kate E; Richman, Laura Smart; Schwartz-Bloom, Rochelle; Linnenbrink-Garcia, Lisa

    2015-01-01

    There is a strong need to increase the number of undergraduate students who pursue careers in science to provide the "fuel" that will power a science and technology-driven U.S. economy. Prior research suggests that both evidence-based teaching methods and early undergraduate research experiences may help to increase retention rates in the sciences. In this study, we examined the effect of a program that included 1) a Summer enrichment 2-wk minicourse and 2) an authentic Fall research course, both of which were designed specifically to support students' science motivation. Undergraduates who participated in the pharmacology-based enrichment program significantly improved their knowledge of basic biology and chemistry concepts; reported high levels of science motivation; and were likely to major in a biological, chemical, or biomedical field. Additionally, program participants who decided to major in biology or chemistry were significantly more likely to choose a pharmacology concentration than those majoring in biology or chemistry who did not participate in the enrichment program. Thus, by supporting students' science motivation, we can increase the number of students who are interested in science and science careers.

  6. A Pharmacology-Based Enrichment Program for Undergraduates Promotes Interest in Science

    PubMed Central

    Godin, Elizabeth A.; Wormington, Stephanie V.; Perez, Tony; Barger, Michael M.; Snyder, Kate E.; Richman, Laura Smart; Schwartz-Bloom, Rochelle; Linnenbrink-Garcia, Lisa

    2015-01-01

    There is a strong need to increase the number of undergraduate students who pursue careers in science to provide the “fuel” that will power a science and technology–driven U.S. economy. Prior research suggests that both evidence-based teaching methods and early undergraduate research experiences may help to increase retention rates in the sciences. In this study, we examined the effect of a program that included 1) a Summer enrichment 2-wk minicourse and 2) an authentic Fall research course, both of which were designed specifically to support students' science motivation. Undergraduates who participated in the pharmacology-based enrichment program significantly improved their knowledge of basic biology and chemistry concepts; reported high levels of science motivation; and were likely to major in a biological, chemical, or biomedical field. Additionally, program participants who decided to major in biology or chemistry were significantly more likely to choose a pharmacology concentration than those majoring in biology or chemistry who did not participate in the enrichment program. Thus, by supporting students' science motivation, we can increase the number of students who are interested in science and science careers. PMID:26538389

  7. Key genes and pathways in thyroid cancer based on gene set enrichment analysis.

    PubMed

    He, Wenwu; Qi, Bin; Zhou, Qiuxi; Lu, Chuansen; Huang, Qi; Xian, Lei; Chen, Mingwu

    2013-09-01

    The incidence of thyroid cancer and its associated morbidity has shown the most rapid increase among all cancers since 1982, but the mechanisms involved in thyroid cancer, particularly significant key genes induced in thyroid cancer, remain undefined. In many studies, gene probes have been used to search for key genes involved in causing and facilitating thyroid cancer. As a result, many possible virulence genes and pathways have been identified. However, these studies lack a case contrast for selecting the most possible virulence genes and pathways, as well as conclusive results with which to clarify the mechanisms of cancer development. In the present study, we used gene set enrichment and meta-analysis to select key genes and pathways. Based on gene set enrichment, we identified 5 downregulated and 4 upregulated mixed pathways in 6 tissue datasets. Based on the meta-analysis, there were 17 common pathways in the tissue datasets. One pathway, the p53 signaling pathway, which includes 13 genes, was identified by both the gene set enrichment analysis and meta-analysis. Genes are important elements that form key pathways. These pathways can induce the development of thyroid cancer later in life. The key pathways and genes identified in the present study can be used in the next stage of research, which will involve gene elimination and other methods of experimentation.

  8. Gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia

    PubMed Central

    SUI, SHUXIANG; WANG, XIN; ZHENG, HUA; GUO, HUA; CHEN, TONG; JI, DONG-MEI

    2015-01-01

    Pediatric acute lymphoblastic leukemia (ALL) accounts for over one-quarter of all pediatric cancers. Interacting genes and proteins within the larger human gene interaction network of the human genome are rarely investigated by studies investigating pediatric ALL. In the present study, interaction networks were constructed using the empirical Bayesian approach and the Search Tool for the Retrieval of Interacting Genes/proteins database, based on the differentially-expressed (DE) genes in pediatric ALL, which were identified using the RankProd package. Enrichment analysis of the interaction network was performed using the network-based methods EnrichNet and PathExpand, which were compared with the traditional expression analysis systematic explored (EASE) method. In total, 398 DE genes were identified in pediatric ALL, and LIF was the most significantly DE gene. The co-expression network consisted of 272 nodes, which indicated genes and proteins, and 602 edges, which indicated the number of interactions adjacent to the node. Comparison between EASE and PathExpand revealed that PathExpand detected more pathways or processes that were closely associated with pediatric ALL compared with the EASE method. There were 294 nodes and 1,588 edges in the protein-protein interaction network, with the processes of hematopoietic cell lineage and porphyrin metabolism demonstrating a close association with pediatric ALL. Network enrichment analysis based on the PathExpand algorithm was revealed to be more powerful for the analysis of interaction networks in pediatric ALL compared with the EASE method. LIF and MLLT11 were identified as the most significantly DE genes in pediatric ALL. The process of hematopoietic cell lineage was the pathway most significantly associated with pediatric ALL. PMID:26788135

  9. Assessment of the latest NGS enrichment capture methods in clinical context.

    PubMed

    García-García, Gema; Baux, David; Faugère, Valérie; Moclyn, Mélody; Koenig, Michel; Claustres, Mireille; Roux, Anne-Françoise

    2016-02-11

    Enrichment capture methods for NGS are widely used, however, they evolve rapidly and it is necessary to periodically measure their strengths and weaknesses before transfer to diagnostic services. We assessed two recently released custom DNA solution-capture enrichment methods for NGS, namely Illumina NRCCE and Agilent SureSelect(QXT), against a reference method NimbleGen SeqCap EZ Choice on a similar gene panel, sharing 678 kb and 110 genes. Two Illumina MiSeq runs of 12 samples each have been performed, for each of the three methods, using the same 24 patients (affected with sensorineural disorders). Technical outcomes have been computed and compared, including depth and evenness of coverage, enrichment in targeted regions, performance in GC-rich regions and ability to generate consistent variant datasets. While we show that the three methods resulted in suitable datasets for standard DNA variant discovery, we describe significant differences between the results for the above parameters. NimbleGen offered the best depth of coverage and evenness, while NRCCE showed the highest on target levels but high duplicate rates. SureSelect(QXT) showed an overall quality close to that of NimbleGen. The new methods exhibit reduced preparation time but behave differently. These findings will guide laboratories in their choice of library enrichment approach.

  10. Assessment of the latest NGS enrichment capture methods in clinical context

    PubMed Central

    García-García, Gema; Baux, David; Faugère, Valérie; Moclyn, Mélody; Koenig, Michel; Claustres, Mireille; Roux, Anne-Françoise

    2016-01-01

    Enrichment capture methods for NGS are widely used, however, they evolve rapidly and it is necessary to periodically measure their strengths and weaknesses before transfer to diagnostic services. We assessed two recently released custom DNA solution-capture enrichment methods for NGS, namely Illumina NRCCE and Agilent SureSelectQXT, against a reference method NimbleGen SeqCap EZ Choice on a similar gene panel, sharing 678 kb and 110 genes. Two Illumina MiSeq runs of 12 samples each have been performed, for each of the three methods, using the same 24 patients (affected with sensorineural disorders). Technical outcomes have been computed and compared, including depth and evenness of coverage, enrichment in targeted regions, performance in GC-rich regions and ability to generate consistent variant datasets. While we show that the three methods resulted in suitable datasets for standard DNA variant discovery, we describe significant differences between the results for the above parameters. NimbleGen offered the best depth of coverage and evenness, while NRCCE showed the highest on target levels but high duplicate rates. SureSelectQXT showed an overall quality close to that of NimbleGen. The new methods exhibit reduced preparation time but behave differently. These findings will guide laboratories in their choice of library enrichment approach. PMID:26864517

  11. A Novel Scoring Based Distributed Protein Docking Application to Improve Enrichment

    PubMed Central

    Pradeep, Prachi; Struble, Craig; Neumann, Terrence; Sem, Daniel S.; Merrill, Stephen J.

    2016-01-01

    Molecular docking is a computational technique which predicts the binding energy and the preferred binding mode of a ligand to a protein target. Virtual screening is a tool which uses docking to investigate large chemical libraries to identify ligands that bind favorably to a protein target. We have developed a novel scoring based distributed protein docking application to improve enrichment in virtual screening. The application addresses the issue of time and cost of screening in contrast to conventional systematic parallel virtual screening methods in two ways. Firstly, it automates the process of creating and launching multiple independent dockings on a high performance computing cluster. Secondly, it uses a Nȧive Bayes scoring function to calculate binding energy of un-docked ligands to identify and preferentially dock (Autodock predicted) better binders. The application was tested on four proteins using a library of 10,573 ligands. In all the experiments, (i). 200 of the 1000 best binders are identified after docking only ∼ 14% of the chemical library, (ii). 9 or 10 best-binders are identified after docking only ∼ 19% of the chemical library, and (iii). no significant enrichment is observed after docking ∼ 70% of the chemical library. The results show significant increase in enrichment of potential drug leads in early rounds of virtual screening. PMID:26671816

  12. Circulating tumor cell enrichment based on physical properties

    PubMed Central

    Harouaka, Ramdane A.; Nisic, Merisa; Zheng, Si-Yang

    2013-01-01

    The metastatic dissemination and spread of malignant circulating tumor cells (CTCs) accounts for over 90% of cancer related deaths. CTCs detach from a primary tumor, travel through the circulatory system, then invade and proliferate in distant organs. The detection of CTCs from blood has been established for prognostic monitoring and is predictive of patient outcome. Analysis of CTCs could enable the means for early detection and screening in cancer, as well as provide diagnostic access to tumor tissues in a minimally invasive way. The fundamental challenge with analyzing CTCs is the fact that they occur at extremely low concentrations in blood, on the order of one out of a billion cells. Various technologies have been proposed to isolate CTCs for enrichment. Here we focus on antigen-independent approaches that are not limited by specific capture antibodies. Intrinsic physical properties of CTCs including cell size, deformability, and electrical properties are reviewed, and technologies developed to exploit them for enrichment from blood are summarized. Physical enrichment technologies are of particular interest as they have the potential to increase yield, and enable the analysis of rare CTC phenotypes that may not be otherwise obtained. PMID:23832928

  13. Numerical simulation of premixed combustion using an enriched finite element method

    NASA Astrophysics Data System (ADS)

    van der Bos, Fedderik; Gravemeier, Volker

    2009-06-01

    In this paper we present a novel discretization technique for the simulation of premixed combustion based on a locally enriched finite element method (FEM). Use is made of the G-function approach to premixed combustion in which the domain is divided into two parts, one part containing the burned and another containing the unburned gases. A level-set or G-function is used to define the flame interface separating burned from unburned gases. The eXtended finite element method (X-FEM) is employed, which allows for velocity and pressure fields that are discontinuous across the flame interface. Lagrange multipliers are used to enforce the correct essential interface conditions in the form of jump conditions across the embedded flame interface. A persisting problem with the use of Lagrange multipliers in X-FEM has been the discretization of the Lagrange multipliers. In this paper the distributed Lagrange multiplier technique is adopted. We will provide results from a spatial convergence analysis showing good convergence. However, a small modification of the interface is required to ensure a unique solution. Finally, results are presented from the application of the method to the problems of moving flame fronts, the Darrieus-Landau instability and a piloted Bunsen burner flame.

  14. Benchmarking Methods and Data Sets for Ligand Enrichment Assessment in Virtual Screening

    PubMed Central

    Xia, Jie; Tilahun, Ermias Lemma; Reid, Terry-Elinor; Zhang, Liangren; Wang, Xiang Simon

    2014-01-01

    Retrospective small-scale virtual screening (VS) based on benchmarking data sets has been widely used to estimate ligand enrichments of VS approaches in the prospective (i.e. real-world) efforts. However, the intrinsic differences of benchmarking sets to the real screening chemical libraries can cause biased assessment. Herein, we summarize the history of benchmarking methods as well as data sets and highlight three main types of biases found in benchmarking sets, i.e. “analogue bias”, “artificial enrichment” and “false negative”. In addition, we introduced our recent algorithm to build maximum-unbiased benchmarking sets applicable to both ligand-based and structure-based VS approaches, and its implementations to three important human histone deacetylase (HDAC) isoforms, i.e. HDAC1, HDAC6 and HDAC8. The Leave-One-Out Cross-Validation (LOO CV) demonstrates that the benchmarking sets built by our algorithm are maximum-unbiased in terms of property matching, ROC curves and AUCs. PMID:25481478

  15. Nucleotide analogs and new buffers improve a generalized method to enrich for low abundance mutations.

    PubMed

    Day, J P; Hammer, R P; Bergstrom, D; Barany, F

    1999-04-15

    A high sensitivity method for detecting low level mutations is under development. A PCR reaction is performed in which a restriction site is introduced in wild-type DNA by alteration of specific bases. Digestion of wild-type DNA by the cognate restriction endonuclease (RE) enriches for products with mutations within the recognition site. After reamplification, mutations are identified by a ligation detection reaction (LDR). This PCR/RE/LDR assay was initially used to detect PCR error in known wild-type samples. PCR error was measured in low |Deltap K a| buffers containing tricine, EPPS and citrate, as well as otherwise identical buffers containing Tris. PCR conditions were optimized to minimize PCR error using perfect match primers at the Msp I site in the p53 tumor suppressor gene at codon 248. However, since mutations do not always occur within pre-existing restriction sites, a generalized PCR/RE/LDR method requires the introduction of a new restriction site. In principle, PCR with mismatch primers can alter specific bases in a sequence and generate a new restriction site. However, extension from 3' mismatch primers may generate misextension products. We tested conversion of the Msp I (CCGG) site to a Taq I site (TCGA). Conversion was unsuccessful using a natural base T mismatch primer set. Conversion was successful when modified primers containing the 6 H,8 H -3, 4-dihydropyrimido[4,5- c ][1,2]oxazine-7-one (Q6) base at 3'-ends were used in three cycles of preconversion PCR prior to conversion PCR using the 3' natural base T primers. The ability of the pyrimidine analog Q6 to access both a T-like and C-like tautomer appears to greatly facilitate the conversion. PMID:10101189

  16. A simple method for the enrichment of bisphenols using boron nitride.

    PubMed

    Fischnaller, Martin; Bakry, Rania; Bonn, Günther K

    2016-03-01

    A simple solid-phase extraction method for the enrichment of 5 bisphenol derivatives using hexagonal boron nitride (BN) was developed. BN was applied to concentrate bisphenol derivatives in spiked water samples and the compounds were analyzed using HPLC coupled to fluorescence detection. The effect of pH and organic solvents on the extraction efficiency was investigated. An enrichment factor up to 100 was achieved without evaporation and reconstitution. The developed method was applied for the determination of bisphenol A migrated from some polycarbonate plastic products. Furthermore, bisphenol derivatives were analyzed in spiked and non-spiked canned food and beverages. None of the analyzed samples exceeded the migration limit set by the European Union of 0.6mg/kg food. The method showed good recovery rates ranging from 80% to 110%. Validation of the method was performed in terms of accuracy and precision. The applied method is robust, fast, efficient and easily adaptable to different analytical problems. PMID:26471538

  17. ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis

    PubMed Central

    Han, Junwei; Shi, Xinrui; Zhang, Yunpeng; Xu, Yanjun; Jiang, Ying; Zhang, Chunlong; Feng, Li; Yang, Haixiu; Shang, Desi; Sun, Zeguo; Su, Fei; Li, Chunquan; Li, Xia

    2015-01-01

    Pathway analyses are playing an increasingly important role in understanding biological mechanism, cellular function and disease states. Current pathway-identification methods generally focus on only the changes of gene expression levels; however, the biological relationships among genes are also the fundamental components of pathways, and the dysregulated relationships may also alter the pathway activities. We propose a powerful computational method, Edge Set Enrichment Analysis (ESEA), for the identification of dysregulated pathways. This provides a novel way of pathway analysis by investigating the changes of biological relationships of pathways in the context of gene expression data. Simulation studies illustrate the power and performance of ESEA under various simulated conditions. Using real datasets from p53 mutation, Type 2 diabetes and lung cancer, we validate effectiveness of ESEA in identifying dysregulated pathways. We further compare our results with five other pathway enrichment analysis methods. With these analyses, we show that ESEA is able to help uncover dysregulated biological pathways underlying complex traits and human diseases via specific use of the dysregulated biological relationships. We develop a freely available R-based tool of ESEA. Currently, ESEA can support pathway analysis of the seven public databases (KEGG; Reactome; Biocarta; NCI; SPIKE; HumanCyc; Panther). PMID:26267116

  18. Isolation and enumeration of Campylobacter jejuni from poultry products by a selective enrichment method.

    PubMed

    Wesley, R D; Swaminathan, B; Stadelman, W J

    1983-11-01

    A direct selective enrichment procedure was developed for the isolation of Campylobacter jejuni from poultry products. The selective enrichment medium (ATB) consisted of (per liter) tryptose (20 g), yeast extract (2.5 g), sodium chloride (5 g), FBP supplement (ferrous sulfate [0.25 g], sodium metabisulfite [0.25 g], sodium pyruvate [0.25 g]), bicine (10 g), and agar (1 g). Hematin solution (6.25 ml; prepared by dissolving 0.032 g of bovine hemin in 10 ml of 0.15 N sodium hydroxide solution and autoclaving at 0.35 kg/cm2 for 30 min), rifampin (25 mg), cefsulodin (6.25 mg), and polymyxin B sulfate (20,000 IU) were added after the medium was sterilized. The pH was adjusted to 8.0. Samples were enriched in the above medium at 42 degrees C for 48 h under an atmosphere of 5% O2, 10% CO2, and 85% N2. Enrichment cultures were streaked on a plating medium composed of Brucella agar, hematin solution, FBP supplement, and the above antibiotics. Plates were incubated under the same conditions as above. Suspect colonies from the plates were confirmed to be C. jejuni by morphological examination, growth characteristics, and biochemical tests. The above method yielded 25 isolates of C. jejuni from 50 samples of retail cut-up chicken and chicken parts, whereas a more complex method involving filtration, centrifugation, selective enrichment under a flowing atmosphere, and membrane filtration yielded only 6 positives from the same samples. The new isolation procedure was particularly effective in isolating C. jejuni in the presence of large numbers of Pseudomonas aeruginosa.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:6651294

  19. An assessment of gum-based environmental enrichment for captive gummivorous primates.

    PubMed

    Huber, Hillary F; Lewis, Kerrie P

    2011-01-01

    In the wild, many primates consume gums exuded from trees, and many species are gum specialists. In spite of this, few data exist concerning gum feeding in captivity. Using a web-based survey of 46 zoos in 12 countries, we evaluated the extent to which zoos feed gum to primates. We found that although callitrichids and galagos receive gum-based enrichment, cercopithecines generally do not. Environmental enrichment is important for stimulating naturalistic behavior to promote the psychological wellbeing of animals. Thus, gum-based enrichment is important for captive gummivores. Our study highlights the need to improve environmental enrichment for captive gummivores, in particular that of cercopithecines. This is most striking for the patas monkey (Erythrocebus patas), an obligate gummivore. The exchange of ecological data between field research and captive settings is crucial, and is just one way primate caretakers can contribute to the conservation and welfare of some of our closest living relatives.

  20. Improved 2-nitrobenzenesulfenyl method: optimization of the protocol and improved enrichment for labeled peptides.

    PubMed

    Matsuo, Ei-Ichi; Toda, Chikako; Watanabe, Makoto; Iida, Tetsuo; Masuda, Taro; Minohata, Toshikazu; Ando, Eiji; Tsunasawa, Susumu; Nishimura, Osamu

    2006-01-01

    We have developed the NBS (2-nitrobenzenesulfenyl) method, a quantitative proteome analysis method utilizing stable isotope labeling followed by mass spectrometry. The potential of this method was reported previously, and the procedure has now been further optimized. Here, we describe a procedure utilizing urea or guanidine hydrochloride as a protein denaturant, in conjunction with an improved chromatographic enrichment method for the NBS-labeled peptides using a phenyl resin column. By using this new protocol, both sample loss throughout the protocol and the elution of unwanted unlabeled peptides can be minimized, improving the efficiency of the analysis significantly.

  1. Filter-based pathogen enrichment technology for detection of multiple viable foodborne pathogens in 1 day.

    PubMed

    Murakami, Taku

    2012-09-01

    Conventional foodborne pathogen assays currently used in the food industry often require long culture enrichments to increase pathogen levels so they can be detected. Even using sensitive real-time PCR assays, culture enrichment at least overnight is necessary especially for detection of pathogens with slow growth rates such as Listeria monocytogenes. To eliminate this cumbersome enrichment step and detect minute amounts of pathogens within 1 day, filter-based pathogen enrichment technology was developed utilizing a unique combination of glass fiber depth filter and porous filter aid materials to efficiently separate pathogens from food homogenates and avoid filter clogging by food particles. After pathogen immobilization in depth filters, only viable pathogens were selectively collected in a small volume of growth medium via microbial multiplication and migration; nonviable pathogens remained inside the filters. By assaying viable pathogens using real-time PCRs, multiple species of foodborne pathogens were detected, including L. monocytogenes, Salmonella enterica, and Escherichia coli O157:H7, at around 1 CFU/ml or 1 CFU/g in various food samples. This filter-based pathogen enrichment technology is a unique bacterial enrichment alternative to the conventional culture enrichment step and can significantly shorten the time necessary to obtain assay results.

  2. Assay of Protein and Peptide Adducts of Cholesterol Ozonolysis Products by Hydrophobic and Click Enrichment Methods

    PubMed Central

    2015-01-01

    Cholesterol undergoes ozonolysis to afford a variety of oxysterol products, including cholesterol-5,6-epoxide (CholEp) and the isomeric aldehydes secosterol A (seco A) and secosterol B (seco B). These oxysterols display numerous important biological activities, including protein adduction; however, much remains to be learned about the identity of the reactive species and the range of proteins modified by these oxysterols. Here, we synthesized alkynyl derivatives of cholesterol-derived oxysterols and employed a straightforward detection method to establish secosterols A and B as the most protein-reactive of the oxysterols tested. Model adduction studies with an amino acid, peptides, and proteins provide evidence for the potential role of secosterol dehydration products in protein adduction. Hydrophobic separation methods—Folch extraction and solid phase extraction (SPE)—were successfully applied to enrich oxysterol-adducted peptide species, and LC-MS/MS analysis of a model peptide–seco adduct revealed a unique fragmentation pattern (neutral loss of 390 Da) for that species. Coupling a hydrophobic enrichment method with proteomic analysis utilizing characteristic fragmentation patterns facilitates the identification of secosterol-modified peptides and proteins in an adducted protein. More broadly, these improved enrichment methods may give insight into the role of oxysterols and ozone exposure in the pathogenesis of a variety of diseases, including atherosclerosis, Alzheimer’s disease, Parkinson’s disease, and asthma. PMID:25185119

  3. Different EV enrichment methods suitable for clinical settings yield different subpopulations of urinary extracellular vesicles from human samples

    PubMed Central

    Royo, Felix; Zuñiga-Garcia, Patricia; Sanchez-Mosquera, Pilar; Egia, Ainara; Perez, Amparo; Loizaga, Ana; Arceo, Raquel; Lacasa, Isabel; Rabade, Ainara; Arrieta, Edurne; Bilbao, Roberto; Unda, Miguel; Carracedo, Arkaitz; Falcon-Perez, Juan M.

    2016-01-01

    Urine sample analysis is irreplaceable as a non-invasive method for disease diagnosis and follow-up. However, in urine samples, non-degraded protein and RNA may be only found in urinary extracellular vesicles (uEVs). In recent years, various methods of uEV enrichment using low volumes of urine and unsophisticated equipment have been developed, with variable success. We compared the results of the differential ultracentrifugation procedure with 4 of these methods. The methods tested were a lectin-based purification, Exoquick (System Biosciences), Total Exosome Isolation from Invitrogen and an in-house modified procedure employing the Exosomal RNA Kit from Norgen Biotek Corp. The analysis of selected gene transcripts and protein markers of extracellular vesicles (EVs) revealed that each method isolates a different mixture of uEV protein markers. In our conditions, the extraction with Norgen's reagent achieved the best performance in terms of gene transcript and protein detection and reproducibility. By using this method, we were able to detect alterations of EVs protein markers in urine samples from prostate cancer adenoma patients. Taken together, our results show that the isolation of uEVs is feasible from small volumes of urine and avoiding ultracentrifugation, making easier the analysis in a clinical facility. However, caution should be taken in the selection of the enrichment method since they have a differential affinity for protein uEVs markers and by extension for different subpopulation of EVs. PMID:26895490

  4. A Microbiome DNA Enrichment Method for Next-Generation Sequencing Sample Preparation.

    PubMed

    Yigit, Erbay; Feehery, George R; Langhorst, Bradley W; Stewart, Fiona J; Dimalanta, Eileen T; Pradhan, Sriharsa; Slatko, Barton; Gardner, Andrew F; McFarland, James; Sumner, Christine; Davis, Theodore B

    2016-01-01

    "Microbiome" is used to describe the communities of microorganisms and their genes in a particular environment, including communities in association with a eukaryotic host or part of a host. One challenge in microbiome analysis concerns the presence of host DNA in samples. Removal of host DNA before sequencing results in greater sequence depth of the intended microbiome target population. This unit describes a novel method of microbial DNA enrichment in which methylated host DNA such as human genomic DNA is selectively bound and separated from microbial DNA before next-generation sequencing (NGS) library construction. This microbiome enrichment technique yields a higher fraction of microbial sequencing reads and improved read quality resulting in a reduced cost of downstream data generation and analysis. © 2016 by John Wiley & Sons, Inc. PMID:27366894

  5. Pedagogical Quality Enrichment in OER-Based Courseware: Guiding Principles

    ERIC Educational Resources Information Center

    Misra, Pradeep Kumar

    2013-01-01

    This is a critical phase for Open Educational Resources (OER) movement: on one side the number of OER is increasing rapidly, and on other side debates about quality of OER-based courseware are heating up. These debates emanate from the fact that OER-based courseware are supposed to help users to follow a logical learning path and get an engaging,…

  6. Protein expression and isotopic enrichment based on induction of the Entner-Doudoroff pathway in Escherichia coli

    SciTech Connect

    Refaeli, Bosmat; Goldbourt, Amir

    2012-10-12

    Highlights: Black-Right-Pointing-Pointer The Entner-Doudoroff pathway is induced during protein expression in E. coli. Black-Right-Pointing-Pointer 1-{sup 13}C-gluconate and {sup 15}NH{sub 4}Cl provide a carbonyl-amide protein backbone labeling scheme. Black-Right-Pointing-Pointer The enrichment pattern is determined by nuclear magnetic resonance. -- Abstract: The Entner-Doudoroff pathway is known to exist in many organisms including bacteria, archea and eukarya. Although the common route for carbon catabolism in Escherichia coli is the Embden-Meyerhof-Parnas pathway, it was shown that gluconate catabolism in E. coli occurs via the Entner-Doudoroff pathway. We demonstrate here that by supplying BL21(DE3) competent E.coli cells with gluconate in a minimal growth medium, protein expression can be induced. Nuclear magnetic resonance data of over-expressed ubiquitin show that by using [1-{sup 13}C]-gluconate as the only carbon source, and {sup 15}N-enriched ammonium chloride, sparse isotopic enrichment in the form of a spin-pair carbonyl-amide backbone enrichment is obtained. The specific amino acid labeling pattern is analyzed and is shown to be compatible with Entner-Doudoroff metabolism. Isotopic enrichment serves as a key factor in the biophysical characterization of proteins by various methods including nuclear magnetic resonance, mass spectrometry, infrared spectroscopy and more. Therefore, the method presented here can be applied to study proteins by obtaining sparse enrichment schemes that are not based on the regular glycolytic pathway, or to study the Entner-Doudoroff metabolism during protein expression.

  7. Vita-Assay™ Method of Enrichment and Identification of Circulating Cancer Cells/Circulating Tumor Cells (CTCs).

    PubMed

    Tulley, Shaun; Zhao, Qiang; Dong, Huan; Pearl, Michael L; Chen, Wen-Tien

    2016-01-01

    The ability to capture, enrich, and propagate circulating cancer cells/circulating tumor cells (CTCs) for downstream analyses such as ex vivo drug-sensitivity testing of short-term cultures of CTCs, single cell sorting of CTCs by fluorescence activated cell sorting (FACS), animal injection tumor and/or metastasis formation studies, next generation sequencing (NGS), gene expression profiling, gene copy number determination, and epigenomic analyses is of high priority and of immense importance to both the basic research and translational/clinical research communities. Vitatex Inc.'s functional cell separation technology, constructed as Vita-Assay™ (AG6W, AN6W, AR6W) culture plates, is based on the preferential adhesion of invasive rare blood cells of tissue origin to a tissue or tumor microenvironment mimic-the so-called cell adhesion matrix (CAM), which has a demonstrated ability to enrich viable CTCs from blood up to one-million fold.The CAM-scaffold allows for the functional capture and identification of invasive CTCs (iCTCs) including invasive tumor progenitor (TP) cells from cancer-patients' blood. CAM-captured CTCs are capable of ingesting the CAM (CAM+) itself. Green and red fluorescent versions of Vita-Assay™ (AG6W and AR6W) allow for direct visualization of CAM-uptake by cancer cells. Vita-Assay™ CAM-enrichment has allowed for sensitive multiplex flow cytometric and microscopic detection of iCTCs from patients with cancers of the breast, ovary, prostate, pancreas, colorectum, and lung; it has also been successfully utilized for ex vivo drug-sensitivity testing of ovarian-cancer patient CTCs. The CAM enrichment method is equally suitable for the separation of iCTCs and TP cells in ascites and pleural fluid.

  8. Mung Bean Nuclease Treatment Increases Capture Specificity of Microdroplet-PCR Based Targeted DNA Enrichment

    PubMed Central

    Yu, Zhenming; Cao, Kajia; Tischler, Tanya; Stolle, Catherine A.; Santani, Avni B.

    2014-01-01

    Targeted DNA enrichment coupled with next generation sequencing has been increasingly used for interrogation of select sub-genomic regions at high depth of coverage in a cost effective manner. Specificity measured by on-target efficiency is a key performance metric for target enrichment. Non-specific capture leads to off-target reads, resulting in waste of sequencing throughput on irrelevant regions. Microdroplet-PCR allows simultaneous amplification of up to thousands of regions in the genome and is among the most commonly used strategies for target enrichment. Here we show that carryover of single-stranded template genomic DNA from microdroplet-PCR constitutes a major contributing factor for off-target reads in the resultant libraries. Moreover, treatment of microdroplet-PCR enrichment products with a nuclease specific to single-stranded DNA alleviates off-target load and improves enrichment specificity. We propose that nuclease treatment of enrichment products should be incorporated in the workflow of targeted sequencing using microdroplet-PCR for target capture. These findings may have a broad impact on other PCR based applications for which removal of template DNA is beneficial. PMID:25058678

  9. Ultratrace DNA Detection Based on the Condensing-Enrichment Effect of Superwettable Microchips.

    PubMed

    Xu, Li-Ping; Chen, Yanxia; Yang, Gao; Shi, Wanxin; Dai, Bing; Li, Guannan; Cao, Yanhua; Wen, Yongqiang; Zhang, Xueji; Wang, Shutao

    2015-11-18

    A sensitive nucleic acid detection platform based on superhydrophilic microwells spotted on a superhydrophobic substrate is fabricated. Due to the wettability differences, ultratrace DNA molecules are enriched and the fluorescent signals are amplified to allow more sensitive detection. The biosensing interface based on superwettable materials provides a simple and cost-effective way for ultratrace DNA sensing. PMID:26426114

  10. Ultratrace DNA Detection Based on the Condensing-Enrichment Effect of Superwettable Microchips.

    PubMed

    Xu, Li-Ping; Chen, Yanxia; Yang, Gao; Shi, Wanxin; Dai, Bing; Li, Guannan; Cao, Yanhua; Wen, Yongqiang; Zhang, Xueji; Wang, Shutao

    2015-11-18

    A sensitive nucleic acid detection platform based on superhydrophilic microwells spotted on a superhydrophobic substrate is fabricated. Due to the wettability differences, ultratrace DNA molecules are enriched and the fluorescent signals are amplified to allow more sensitive detection. The biosensing interface based on superwettable materials provides a simple and cost-effective way for ultratrace DNA sensing.

  11. SHAPE Selection (SHAPES) enrich for RNA structure signal in SHAPE sequencing-based probing data.

    PubMed

    Poulsen, Line Dahl; Kielpinski, Lukasz Jan; Salama, Sofie R; Krogh, Anders; Vinther, Jeppe

    2015-05-01

    Selective 2' Hydroxyl Acylation analyzed by Primer Extension (SHAPE) is an accurate method for probing of RNA secondary structure. In existing SHAPE methods, the SHAPE probing signal is normalized to a no-reagent control to correct for the background caused by premature termination of the reverse transcriptase. Here, we introduce a SHAPE Selection (SHAPES) reagent, N-propanone isatoic anhydride (NPIA), which retains the ability of SHAPE reagents to accurately probe RNA structure, but also allows covalent coupling between the SHAPES reagent and a biotin molecule. We demonstrate that SHAPES-based selection of cDNA-RNA hybrids on streptavidin beads effectively removes the large majority of background signal present in SHAPE probing data and that sequencing-based SHAPES data contain the same amount of RNA structure data as regular sequencing-based SHAPE data obtained through normalization to a no-reagent control. Moreover, the selection efficiently enriches for probed RNAs, suggesting that the SHAPES strategy will be useful for applications with high-background and low-probing signal such as in vivo RNA structure probing.

  12. Selective enrichment of phenols from coal liquefaction oil by solid phase extraction method

    SciTech Connect

    Tian, M.; Feng, J.

    2009-07-01

    This study focuses on the solid phase extraction method for the enrichment and separation of phenol from coal liquefaction oil. The phenols' separation efficiency was compared on different solid phase extraction (SPE) cartridges, and the effect of solvents with different polarity and solubility parameter on amino-bonded silica was compared for selection of optimal elution solution. The result showed that amino-bonded silica has the highest selectivity and best extraction capability due to two factors, weak anion exchange adsorption and polar attraction adsorption.

  13. Chasing Phosphoarginine Proteins: Development of a Selective Enrichment Method Using a Phosphatase Trap*

    PubMed Central

    Trentini, Débora Broch; Fuhrmann, Jakob; Mechtler, Karl; Clausen, Tim

    2014-01-01

    Arginine phosphorylation is an emerging post-translational protein modification implicated in the bacterial stress response. Although early reports suggested that arginine phosphorylation also occurs in higher eukaryotes, its overall prevalence was never studied using modern mass spectrometry methods, owing to technical difficulties arising from the acid lability of phosphoarginine. As shown recently, the McsB and YwlE proteins from Bacillus subtilis function as a highly specific protein arginine kinase and phosphatase couple, shaping the phosphoarginine proteome. Using a B. subtilis ΔywlE strain as a source for arginine-phosphorylated proteins, we were able to adapt mass spectrometry (MS) protocols to the special chemical properties of the arginine modification. Despite this progress, the analysis of protein arginine phosphorylation in eukaryotes is still challenging, given the great abundance of serine/threonine phosphorylations that would compete with phosphoarginine during the phosphopeptide enrichment procedure, as well as during data-dependent MS acquisition. We thus set out to establish a method for the selective enrichment of arginine-phosphorylated proteins as an initial step in the phosphoproteomic analysis. For this purpose, we developed a substrate-trapping mutant of the YwlE phosphatase that retains binding affinity toward arginine-phosphorylated proteins but cannot hydrolyze the captured substrates. By testing a number of active site substitutions, we identified a YwlE mutant (C9A) that stably binds to arginine-phosphorylated proteins. We further improved the substrate-trapping efficiency by impeding the oligomerization of the phosphatase mutant. The engineered YwlE trap efficiently captured arginine-phosphorylated proteins from complex B. subtilis ΔywlE cell extracts, thus facilitating identification of phosphoarginine sites in the large pool of cellular protein modifications. In conclusion, we present a novel tool for the selective enrichment and

  14. A mathematical analysis of the selective enrichment of NECEEM-based non-SELEX.

    PubMed

    Yu, Xinliang; Yu, Yixiong

    2014-08-01

    Non-Systematic Evolution of Ligands by EXponential enrichment (SELEX)selection of aptamers, a novel technology for aptamer selection from libraries of random DNA (or RNA) sequences, involves repetitive steps of partitioning without polymerase chain reaction (PCR) amplification between them. This selection is based on non-equilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) and has exceptionally high efficiency. In this paper, a mathematical analysis was carried out to predict the levels of enrichment of non-SELEX selection under different conditions such as different protein concentrations and different efficiencies of partitioning. Investigated results suggest that the magnitude of the bulk affinity (k d) being 10(4) or 10(5) μM for the initial pool has no obvious effect on selective enrichment and that the first, second, and third rounds of non-SELEX selection have different optimum protein concentration values [T f] that give maximum enrichment levels when [T f] ranges from 0.0005 to 0.5 μM. The significance of analyzing selective enrichment of NECEEM-based non-SELEX with the efficiency of partitioning target-bound ligands from free ligands has been demonstrated.

  15. MARCC (Matrix-Assisted Reader Chromatin Capture): An Antibody-Free Method to Enrich and Analyze Combinatorial Nucleosome Modifications.

    PubMed

    Su, Zhangli; Denu, John M

    2015-07-01

    Combinatorial patterns of histone modifications are key indicators of different chromatin states. Most of the current approaches rely on the usage of antibodies to analyze combinatorial histone modifications. Here we detail an antibody-free method named MARCC (Matrix-Assisted Reader Chromatin Capture) to enrich combinatorial histone modifications. The combinatorial patterns are enriched on native nucleosomes extracted from cultured mammalian cells and prepared by micrococcal nuclease digestion. Such enrichment is achieved by recombinant chromatin-interacting protein modules, or so-called reader domains, which can bind in a combinatorial modification-dependent manner. The enriched chromatin can be quantified by immunoblotting or mass spectrometry for the co-existence of histone modifications, while the associated DNA content can be analyzed by qPCR or next-generation sequencing. Altogether, MARCC provides a reproducible, efficient and customizable solution to enrich and analyze combinatorial histone modifications.

  16. Synteny-based mapping-by-sequencing enabled by targeted enrichment.

    PubMed

    Galvão, Vinicius C; Nordström, Karl J V; Lanz, Christa; Sulz, Patric; Mathieu, Johannes; Posé, David; Schmid, Markus; Weigel, Detlef; Schneeberger, Korbinian

    2012-08-01

    Mapping-by-sequencing, as implemented in SHOREmap ('SHOREmapping'), is greatly accelerating the identification of causal mutations. The original SHOREmap approach based on resequencing of bulked segregants required a highly accurate and complete reference sequence. However, current whole-genome or transcriptome assemblies from next-generation sequencing data of non-model organisms do not produce chromosome-length scaffolds. We have therefore developed a method that exploits synteny with a related genome for genetic mapping. We first demonstrate how mapping-by-sequencing can be performed using a reduced number of markers, and how the associated decrease in the number of markers can be compensated for by enrichment of marker sequences. As proof of concept, we apply this method to Arabidopsis thaliana gene models ordered by synteny with the genome sequence of the distant relative Brassica rapa, whose genome has several large-scale rearrangements relative to A. thaliana. Our approach provides an alternative method for high-resolution genetic mapping in species that lack finished genome reference sequences or for which only RNA-seq assemblies are available. Finally, for improved identification of causal mutations by fine-mapping, we introduce a new likelihood ratio test statistic, transforming local allele frequency estimations into a confidence interval similar to conventional mapping intervals.

  17. Recent advances in enrichment and separation strategies for mass spectrometry-based phosphoproteomics

    PubMed Central

    Yang, Chenxi; Zhong, Xuefei; Li, Lingjun

    2016-01-01

    Due to the significance of protein phosphorylation in various biological processes and signaling events, new analytical techniques for enhanced phosphoproteomics have been rapidly introduced in recent years. The combinatorial use of the phospho-specific enrichment techniques and prefractionation methods prior to MS analysis enables comprehensive profiling of the phosphoproteome and facilitates deciphering the critical roles that phosphorylation plays in signaling pathways in various biological systems. This review places special emphasis on the recent five-year (2009–2013) advances for enrichment and separation techniques that have been utilized for phosphopeptides prior to MS analysis. PMID:24687451

  18. Remediating and Enriching Performance Learning. Implementing Competency Based Education in Community Colleges, 8.

    ERIC Educational Resources Information Center

    Loomis, Katherine A.; And Others

    Part of a series on implementing competency-based education, this monograph discusses some diagnostic and prescriptive techniques which can be used in the day-to-day management of performance learning to determine which students need remediation or enrichment. Using analogies from detective work, the monograph suggests ways of assessing students'…

  19. Inquiry-Based Science and Technology Enrichment Program for Middle School-Aged Female Students

    ERIC Educational Resources Information Center

    Kim, Hanna

    2016-01-01

    This study investigates the effects of an intensive 1-week Inquiry-Based Science and Technology Enrichment Program (InSTEP) designed for middle school-aged female students. InSTEP uses a guided/open inquiry approach that is deepened and redefined as eight sciences and engineering practices in the Next Generation Science Standards, which aimed at…

  20. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome.

    PubMed

    Cui, Pin; Löber, Ulrike; Alquezar-Planas, David E; Ishida, Yasuko; Courtiol, Alexandre; Timms, Peter; Johnson, Rebecca N; Lenz, Dorina; Helgen, Kristofer M; Roca, Alfred L; Hartman, Stefanie; Greenwood, Alex D

    2016-01-01

    Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.

  1. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome

    PubMed Central

    Alquezar-Planas, David E.; Ishida, Yasuko; Courtiol, Alexandre; Timms, Peter; Johnson, Rebecca N.; Lenz, Dorina; Helgen, Kristofer M.; Roca, Alfred L.; Hartman, Stefanie

    2016-01-01

    Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small. PMID:27069793

  2. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome.

    PubMed

    Cui, Pin; Löber, Ulrike; Alquezar-Planas, David E; Ishida, Yasuko; Courtiol, Alexandre; Timms, Peter; Johnson, Rebecca N; Lenz, Dorina; Helgen, Kristofer M; Roca, Alfred L; Hartman, Stefanie; Greenwood, Alex D

    2016-01-01

    Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small. PMID:27069793

  3. Behavioral analysis of Wistar rats fed with a flaxseed based diet added to an environmental enrichment.

    PubMed

    Azevedo de Meneses, J; Junqueira Lopes, C A; Coca Velarde, L G; Teles Boaventura, G

    2011-01-01

    Flaxseed has a high content of n-3 fatty acids and its intake associated with an environmental enrichment may promote distinct behavioral results upon habituation and animal behavior. This work aimed to evaluating animal behavior under the use of these two tools in the Open Field Test. Thirty-six male Wistar rats were divided into 6 groups (n = 6): FEEG, receiving chow made up of flaxseed and kept in enriched environment; FSEG, receiving flaxseed based diet and kept in a standard environment; CEEG, receiving casein based diet and kept in enriched environment; CSEG, receiving casein based chow and kept in standard environment; MCEEG, receiving chow made up of casein but modified so as to provide the same content of fibers and lipids found in flaxseed diet and kept in enriched environment; MCSEG, receiving modified casein based diet and kept in standard environment. All animals were kept under controlled temperature, collective cages and dark/light cycle, receiving chow and water ad libitum, except for MCEEG and MCSEG, which were pair fed with FEEG and FSEG, respectively. Chow intake and animal body weight were evaluated twice in a week. Animals were maintained in these groups from the first until the second month of life, by the time when 3 day tests in Open Field Test began. Finishing the tests, animals were sacrificed and their brains were obtained in order to calculate the relative brain weight. Our results show an interplay between flaxseed and environmental enrichment in habituation to a new environment, making the animals more manageable and less stressed.

  4. A study on the vibration-based self-monitoring capabilities of nano-enriched composite laminated beams

    NASA Astrophysics Data System (ADS)

    García, David; Trendafilova, Irina; Inman, Daniel J.

    2016-04-01

    This is an exploratory investigation on the self-sensing capabilities of nano-enriched glass/fibre laminates for damage detection purposes through changes in the dynamic responses, which are estimated by measuring the changes in voltage due to a dynamic strain. The deformation of the nano-enriched structure introduces changes in the resistance/voltage of the nanocomposites. The measured voltage signals contain information of the vibratory response of the laminated beam. This research uses a vibration-based data driven methodology for damage detection applied for the estimated vibratory signals using the conductivity properties of the embedded nano-particles. The structure considered in this study is a glass/fibre laminated beam enriched with carbon black nanoparticles (CB). The structure is subjected to a direct electric current and the voltage signal is measured. The vibration based monitoring method used is generally based on singular spectrum analysis applied on the estimated vibratory response. The voltage response signal is divided into a certain number of principal components which contain the oscillatory components distributed by their content of variance in the voltage signal. The components with more variance are used to define a reference state based on the status of the healthy structure. Consequently, the estimated vibratory signals from beams with a simulated damage are compared to the healthy state which eventually results in the damage detection procedure. The damage was simulated firstly by adding an additional mass on the beam tip and secondly by drilling a hole on the beam tip. The results demonstrate the potential for using the voltage estimated vibratory signals for self-sensing damage detection purposes in carbon nano-enriched glass/fibre structures.

  5. Rapid, sensitive, and validated method for detection of Salmonella in food by an enrichment broth culture - nested PCR combination assay.

    PubMed

    Saroj, Sunil D; Shashidhar, R; Karani, Manisha; Bandekar, Jayant R

    2008-06-01

    A rapid nested PCR assay for detection of Salmonella from food was developed. The sensitivity of the assay developed was comparable to the traditional culture based methods with an advantage in reduction of assay time. The assay procedure with artificially contaminated samples was able to detect as low as 4CFU Salmonella/25g of food samples (sprout, carrot, cucumber and poultry meat). With two synthetic primers of 26 mer TS11 and 25 mer TS4, a 1.2kb fragment was amplified which served as a template for amplification of final 375bp product using TS11 and TS5 primers. No non-specific amplification from the native microbial flora of food samples was observed. The reaction generates a single band specific to Salmonella which allows the analyst to interpret data at ease and without any confusion. Enriched broth serves as template for the reaction which removes labour intensive DNA isolation procedures. In case of artificially contaminated samples, 6h enriched lactose broth can serve as template. However, for market samples where the organisms are under environmental stress, it is desirable to use template from Rappaport Vasiliadis medium. The assay also employes internal amplification control, which is amplified into a 300bp fragment and thus serves as positive control for the reaction and any possibility of false negative due to inhibitory action of food components on PCR reaction can be ruled out. PMID:18406104

  6. Enrichment of steroid hormones in water with porous and hydrophobic polymer-based SPE followed by HPLC-UV determination.

    PubMed

    Hu, Yinfen; Zhang, Man; Tong, Changlun; Wu, Jianmin; Liu, Weiping

    2013-10-01

    There have been great concerns about the persistence of steroid hormones in surface water. Since the concentrations of these compounds in water samples are usually at a trace level, the efficient enrichment of steroid hormones is vital for further analysis. In this work, a porous and hydrophobic polymer was synthesized and characterized. The composition of solvent used as porogen in the synthetic process was shown to have an effect on the morphology of the polymer, which was successfully used as an SPE sorbent for simultaneously enriching steroid hormones in surface water samples. The recoveries of the steroid hormones on the custom-made polymer ranged from 93.4 to 106.2%, whereas those on commercialized ENVI-18, LC-18, and Oasis HLB ranged from 54.8 to 104.9, 66 to 93.6, and 77.2 to 106%, respectively. Five types of steroid hormones were simultaneously measured using HPLC-UV after they were enriched by the custom-made sorbent. Based on these findings, the SPE-HPLC method was developed. The LODs of this method for estriol, estradiol, estrone, androstenedione, progesterone were 0.07, 0.43, 0.61, 0.27, and 0.42 μg/L, respectively, while precision and reproducibility RSDs were <6.40 and 7.49%, respectively.

  7. Virus Enrichment for Single Virus Infection by Using 3D Insulator Based Dielectrophoresis

    PubMed Central

    Masuda, Taisuke; Maruyama, Hisataka; Honda, Ayae; Arai, Fumihito

    2014-01-01

    We developed an active virus filter (AVF) that enables virus enrichment for single virus infection, by using insulator-based dielectrophoresis (iDEP). A 3D-constricted flow channel design enabled the production of an iDEP force in the microfluidic chip. iDEP using a chip with multiple active virus filters (AVFs) was more accurate and faster than using a chip with a single AVF, and improved the efficiency of virus trapping. We utilized maskless photolithography to achieve the precise 3D gray-scale exposure required for fabrication of constricted flow channel. Influenza virus (A PR/8) was enriched by a negative DEP force when sinusoidal wave was applied to the electrodes within an amplitude range of 20 Vp-p and a frequency of 10 MHz. AVF-mediated virus enrichment can be repeated simply by turning the current ON or OFF. Furthermore, the negative AVF can inhibit virus adhesion onto the glass substrate. We then trapped and transported one of the enriched viruses by using optical tweezers. This microfluidic chip facilitated the effective transport of a single virus from AVFs towards the cell-containing chamber without crossing an electrode. We successfully transported the virus to the cell chamber (v = 10 µm/s) and brought it infected with a selected single H292 cell. PMID:24918921

  8. Rheology, fatty acid profile and quality characteristics of nutrient enriched pizza base.

    PubMed

    Gupta, Chaitali Sen; Milind; Jeyarani, T; Rajiv, Jyotsna

    2015-05-01

    Enrichment of thick bread type pizza base (PZB) was done by substituting wheat flour (WF) with 5, 10 and 15 % soya protein isolate (SPI). The rheological characteristics of WF showed that water absorption increased, extensibility and peak viscosity decreased when level of SPI increased from 5 to 15 %. Baking studies showed that spread ratio decreased and hardness values of PZB increased with the increase in amount of SPI from 5 to15 %. Beyond 10 % SPI, the overall quality of PZB was adversely affected. To the optimal blend of 10 % SPI, 5 % psyllium husk (PH) was added and the hydrogenated fat was replaced by canola oil (CAN) in enriched PZB. The enriched PZB treated with combination of additives had 1.7 and 1.6 times more protein and dietary fiber than the control PZB. Fatty acid analysis showed that the enriched PZB had 58.65 % oleic, 6.58 % linolenic acid and 31.28 % polyunsaturated fatty acid and no Trans fat was present.

  9. Comparison of Commercially Available Target Enrichment Methods for Next-Generation Sequencing

    PubMed Central

    Bodi, K.; Perera, A. G.; Adams, P. S.; Bintzler, D.; Dewar, K.; Grove, D. S.; Kieleczawa, J.; Lyons, R. H.; Neubert, T. A.; Noll, A. C.; Singh, S.; Steen, R.; Zianni, M.

    2013-01-01

    Isolating high-priority segments of genomes greatly enhances the efficiency of next-generation sequencing (NGS) by allowing researchers to focus on their regions of interest. For the 2010–11 DNA Sequencing Research Group (DSRG) study, we compared outcomes from two leading companies, Agilent Technologies (Santa Clara, CA, USA) and Roche NimbleGen (Madison, WI, USA), which offer custom-targeted genomic enrichment methods. Both companies were provided with the same genomic sample and challenged to capture identical genomic locations for DNA NGS. The target region totaled 3.5 Mb and included 31 individual genes and a 2-Mb contiguous interval. Each company was asked to design its best assay, perform the capture in replicates, and return the captured material to the DSRG-participating laboratories. Sequencing was performed in two different laboratories on Genome Analyzer IIx systems (Illumina, San Diego, CA, USA). Sequencing data were analyzed for sensitivity, specificity, and coverage of the desired regions. The success of the enrichment was highly dependent on the design of the capture probes. Overall, coverage variability was higher for the Agilent samples. As variant discovery is the ultimate goal for a typical targeted sequencing project, we compared samples for their ability to sequence single-nucleotide polymorphisms (SNPs) as a test of the ability to capture both chromosomes from the sample. In the targeted regions, we detected 2546 SNPs with the NimbleGen samples and 2071 with Agilent's. When limited to the regions that both companies included as baits, the number of SNPs was ∼1000 for each, with Agilent and NimbleGen finding a small number of unique SNPs not found by the other. PMID:23814499

  10. Development of gel-filter method for high enrichment of low-molecular weight proteins from serum.

    PubMed

    Chen, Lingsheng; Zhai, Linhui; Li, Yanchang; Li, Ning; Zhang, Chengpu; Ping, Lingyan; Chang, Lei; Wu, Junzhu; Li, Xiangping; Shi, Deshun; Xu, Ping

    2015-01-01

    The human serum proteome has been extensively screened for biomarkers. However, the large dynamic range of protein concentrations in serum and the presence of highly abundant and large molecular weight proteins, make identification and detection changes in the amount of low-molecular weight proteins (LMW, molecular weight ≤ 30kDa) difficult. Here, we developed a gel-filter method including four layers of different concentration of tricine SDS-PAGE-based gels to block high-molecular weight proteins and enrich LMW proteins. By utilizing this method, we identified 1,576 proteins (n = 2) from 10 μL serum. Among them, 559 (n = 2) proteins belonged to LMW proteins. Furthermore, this gel-filter method could identify 67.4% and 39.8% more LMW proteins than that in representative methods of glycine SDS-PAGE and optimized-DS, respectively. By utilizing SILAC-AQUA approach with labeled recombinant protein as internal standard, the recovery rate for GST spiked in serum during the treatment of gel-filter, optimized-DS, and ProteoMiner was 33.1 ± 0.01%, 18.7 ± 0.01% and 9.6 ± 0.03%, respectively. These results demonstrate that the gel-filter method offers a rapid, highly reproducible and efficient approach for screening biomarkers from serum through proteomic analyses.

  11. Method for Recovery and Immunoaffinity Enrichment of Membrane Proteins Illustrated with Metastatic Ovarian Cancer Tissues

    PubMed Central

    Schneider, Luke V.; Likhte, Varsha; Wright, William H.; Chu, Frances; Cambron, Emma; Baldwin-Burnett, Anne; Krakow, Jessica; Smejkal, Gary B.

    2012-01-01

    Integral membrane proteins play key biological roles in cell signaling, transport, and pathogen invasion. However, quantitative clinical assays for this critical class of proteins remain elusive and are generally limited to serum-soluble extracellular fragments. Furthermore, classic proteomic approaches to membrane protein analysis typically involve proteolytic digestion of the soluble pieces, resulting in separation of intra- and extracellular segments and significant informational loss. In this paper, we describe the development of a new method for the quantitative extraction of intact integral membrane proteins (including GPCRs) from solid metastatic ovarian tumors using pressure cycling technology in combination with a new (ProteoSolve-TD) buffer system. This new extraction buffer is compatible with immunoaffinity methods (e.g., ELISA and immunoaffinity chromatography), as well as conventional proteomic techniques (e.g., 2D gels, western blots). We demonstrate near quantitative recovery of membrane proteins EDG2, EDG4, FASLG, KDR, and LAMP-3 by western blots. We have also adapted commercial ELISAs for serum-soluble membrane protein fragments (e.g., sVEGFR2) to measure the tissue titers of their transmembrane progenitors. Finally, we demonstrate the compatibility of the new buffers with immunoaffinity enrichment/mass spectrometric characterization of tissue proteins. PMID:22919487

  12. Surrogate reporter-based enrichment of cells containing RNA-guided Cas9 nuclease-induced mutations.

    PubMed

    Ramakrishna, Suresh; Cho, Seung Woo; Kim, Sojung; Song, Myungjae; Gopalappa, Ramu; Kim, Jin-Soo; Kim, Hyongbum

    2014-01-01

    RNA-guided endonucleases (RGENs), which are based on the clustered, regularly interspaced, short palindromic repeat (CRISPR)-CRISPR-associated (Cas) system, have recently emerged as a simple and efficient tool for genome editing. However, the activities of prepared RGENs are sometimes low, hampering the generation of cells containing RGEN-induced mutations. Here we report efficient methods to enrich cells containing RGEN-induced mutations by using surrogate reporters. HEK293T cells are cotransfected with the reporter plasmid, a plasmid encoding Cas9 and a plasmid encoding crRNA and tracrRNA, and subjected to flow cytometric sorting, magnetic separation or hygromycin selection. The selected cell populations are highly enriched with cells containing RGEN-induced mutations, by a factor of up to 11-fold as compared with the unselected population. The fold enrichment tends to be high when RGEN activity is low. We envision that these reporters will facilitate the use of RGEN in a wide range of biomedical research. PMID:24569644

  13. Production of Mutated Porcine Embryos Using Zinc Finger Nucleases and a Reporter-based Cell Enrichment System

    PubMed Central

    Koo, Ok Jae; Park, Sol Ji; Lee, Choongil; Kang, Jung Taek; Kim, Sujin; Moon, Joon Ho; Choi, Ji Yei; Kim, Hyojin; Jang, Goo; Kim, Jin-Soo; Kim, Seokjoong; Lee, Byeong-Chun

    2014-01-01

    To facilitate the construction of genetically-modified pigs, we produced cloned embryos derived from porcine fibroblasts transfected with a pair of engineered zinc finger nuclease (ZFN) plasmids to create targeted mutations and enriched using a reporter plasmid system. The reporter expresses RFP and eGFP simultaneously when ZFN-mediated site-specific mutations occur. Thus, double positive cells (RFP+/eGFP+) were selected and used for somatic cell nuclear transfer. Two types of reporter based enrichment systems were used in this study; the cloned embryos derived from cells enriched using a magnetic sorting-based system showed better developmental competence than did those derived from cells enriched by flow cytometry. Mutated sequences, such as insertions, deletions, or substitutions, together with the wild-type sequence, were found in the cloned porcine blastocysts. Therefore, genetic mutations can be achieved in cloned porcine embryos reconstructed with ZFN-treated cells that were enriched by a reporter-based system. PMID:25049958

  14. [Enrichment of nicotine in plasma with three-phase hollow fiber based liquid phase microextraction].

    PubMed

    Yang, Xinlei; Luo, Mingbiao; Tang, Yuping

    2006-11-01

    A novel method for fast determination of nicotine in plasma was established by using high performance liquid chromatography (HPLC) coupled with a three-phase hollow fiber based liquid phase microextraction (TP-HF-LPME) technique for sample preparation. The microextraction was mediated by the pH difference between the environment inside and outside of an organic phase immobilized in the pores formed in the wall of a polypropylene hollow fiber. The pH value of the medium outside the organic phase was adjusted by adding a dilute KOH solution to form a basic donor phase while the pH value of the inner media was set to pH 3 to form an acceptor phase using a 10 mmol/L KH2PO4 solution. On working conditions, neutral nicotine molecules were firstly extracted from the original sample solution to the organic phase, and then the analyte was extracted from the organic phase to the acceptor phase. After described extraction time, 4 microL of acceptor phase was withdrawn and directly injected into HPLC system for analysis. Parameters related to TP-HF-LPME (organic solvent, pH of acceptor and donor phase, stirring rate, salt effect, methanol content in acceptor phase and extraction time) were also optimized experimentally. The proposed method integrates extraction, enrichment and clean-up into a single step, dramatically simplifying the traditional procedure to prepare a liquid sample with complex matrices such as plasma. It has been demonstrated to be a very fast, effective and virtually "green" sample preparation technique, which provided a good linear range (0.1 - 50 mg/L) with Nu of 0.999 6, a low detection limit (0.05 mg/L, S/N = 3) and a satisfactory relative standard deviation (< 5%).

  15. Evaluation of a RF-Based Approach for Tracking UF6 Cylinders at a Uranium Enrichment Plant

    SciTech Connect

    Pickett, Chris A; Younkin, James R; Kovacic, Donald N; Laughter, Mark D; Hines, Jairus B; Boyer, Brian; Martinez, B.

    2008-01-01

    Approved industry-standard cylinders are used globally to handle and store uranium hexafluoride (UF{sub 6}) feed, product, tails, and samples at uranium enrichment plants. The International Atomic Energy Agency (IAEA) relies on time-consuming physical inspections to verify operator declarations and detect possible diversion of UF{sub 6}. Development of a reliable, automated, and tamper-resistant system for near real-time tracking and monitoring UF{sub 6} cylinders (as they move within an enrichment facility) would greatly improve the inspector function. This type of system can reduce the risk of false or misreported cylinder tare weights, diversion of nuclear material, concealment of excess production, utilization of undeclared cylinders, and misrepresentation of the cylinders contents. This paper will describe a proof-of-concept approach that was designed to evaluate the feasibility of using radio frequency (RF)-based technologies to track individual UF{sub 6} cylinders throughout a portion of their life cycle, and thus demonstrate the potential for improved domestic accountability of materials, and a more effective and efficient method for application of site-level IAEA safeguards. The evaluation system incorporates RF-based identification devices (RFID) which provide a foundation for establishing a reliable, automated, and near real-time tracking system that can be set up to utilize site-specific, rules-based detection algorithms. This paper will report results from a proof-of-concept demonstration at a real enrichment facility that is specifically designed to evaluate both the feasibility of using RF to track cylinders and the durability of the RF equipment to survive the rigors of operational processing and handling. The paper also discusses methods for securely attaching RF devices and describes how the technology can effectively be layered with other safeguard systems and approaches to build a robust system for detecting cylinder diversion. Additionally

  16. Stirred suspension bioreactors as a novel method to enrich germ cells from pre-pubertal pig testis.

    PubMed

    Dores, C; Rancourt, D; Dobrinski, I

    2015-05-01

    To study spermatogonial stem cells the heterogeneous testicular cell population first needs to be enriched for undifferentiated spermatogonia, which contain the stem cell population. When working with non-rodent models, this step requires working with large numbers of cells. Available cell separation methods rely on differential properties of testicular cell types such as expression of specific cell surface proteins, size, density, or differential adhesion to substrates to separate germ cells from somatic cells. The objective of this study was to develop an approach that allowed germ cell enrichment while providing efficiency of handling large cell numbers. Here, we report the use of stirred suspension bioreactors (SSB) to exploit the adhesion properties of Sertoli cells to enrich cells obtained from pre-pubertal porcine testes for undifferentiated spermatogonia. We also compared the bioreactor approach with an established differential plating method and the combination of both: SSB followed by differential plating. After 66 h of culture, germ cell enrichment in SSBs provided 7.3 ± 1.0-fold (n = 9), differential plating 9.8 ± 2.4-fold (n = 6) and combination of both methods resulted in 9.1 ± 0.3-fold enrichment of germ cells from the initial germ cell population (n = 3). To document functionality of cells recovered from the bioreactor, we demonstrated that cells retained their functional ability to reassemble seminiferous tubules de novo after grafting to mouse hosts and to support spermatogenesis. These results demonstrate that the SSB allows enrichment of germ cells in a controlled and scalable environment providing an efficient method when handling large cell numbers while reducing variability owing to handling.

  17. Variational multiscale enrichment method with mixed boundary conditions for elasto-viscoplastic problems

    NASA Astrophysics Data System (ADS)

    Zhang, Shuhai; Oskay, Caglar

    2015-04-01

    This manuscript presents the formulation and implementation of the variational multiscale enrichment (VME) method for the analysis of elasto-viscoplastic problems. VME is a global-local approach that allows accurate fine scale representation at small subdomains, where important physical phenomena are likely to occur. The response within far-fields is idealized using a coarse scale representation. The fine scale representation not only approximates the coarse grid residual, but also accounts for the material heterogeneity. A one-parameter family of mixed boundary conditions that range from Dirichlet to Neumann is employed to study the effect of the choice of the boundary conditions at the fine scale on accuracy. The inelastic material behavior is modeled using Perzyna type viscoplasticity coupled with flow stress evolution idealized by the Johnson-Cook model. Numerical verifications are performed to assess the performance of the proposed approach against the direct finite element simulations. The results of verification studies demonstrate that VME with proper boundary conditions accurately model the inelastic response accounting for material heterogeneity.

  18. Redox proteomics: Methods for the identification and enrichment of redox-modified proteins and their applications.

    PubMed

    Lennicke, Claudia; Rahn, Jette; Heimer, Nadine; Lichtenfels, Rudolf; Wessjohann, Ludger A; Seliger, Barbara

    2016-01-01

    PTMs are defined as covalent additions to functional groups of amino acid residues in proteins like phosphorylation, glycosylation, S-nitrosylation, acetylation, methylation, lipidation, SUMOylation as well as oxidation. Oxidation of proteins has been characterized as a double-edged sword. While oxidative modifications, in particular of cysteine residues, are widely involved in the regulation of cellular homeostasis, oxidative stress resulting in the oxidation of biomolecules along with the disruption of their biological functions can be associated with the development of diseases, such as cancer, diabetes, and neurodegenerative diseases, respectively. This is also the case for advanced glycation end products, which result from chemical reactions of keto compounds such as oxidized sugars with proteins. The role of oxidative modifications under physiological and pathophysiological conditions remains largely unknown. Recently, novel technologies have been established that allow the enrichment, identification, and characterization of specific oxidative PTMs (oxPTMs). This is essential to develop strategies to prevent and treat diseases that are associated with oxidative stress. Therefore this review will focus on (i) the methods and technologies, which are currently applied for the detection, identification, and quantification of oxPTMs including the design of high throughput approaches and (ii) the analyses of oxPTMs related to physiological and pathological conditions.

  19. Numerical modeling of undersea acoustics using a partition of unity method with plane waves enrichment

    NASA Astrophysics Data System (ADS)

    Hospital-Bravo, Raúl; Sarrate, Josep; Díez, Pedro

    2016-05-01

    A new 2D numerical model to predict the underwater acoustic propagation is obtained by exploring the potential of the Partition of Unity Method (PUM) enriched with plane waves. The aim of the work is to obtain sound pressure level distributions when multiple operational noise sources are present, in order to assess the acoustic impact over the marine fauna. The model takes advantage of the suitability of the PUM for solving the Helmholtz equation, especially for the practical case of large domains and medium frequencies. The seawater acoustic absorption and the acoustic reflectance of the sea surface and sea bottom are explicitly considered, and perfectly matched layers (PML) are placed at the lateral artificial boundaries to avoid spurious reflexions. The model includes semi-analytical integration rules which are adapted to highly oscillatory integrands with the aim of reducing the computational cost of the integration step. In addition, we develop a novel strategy to mitigate the ill-conditioning of the elemental and global system matrices. Specifically, we compute a low-rank approximation of the local space of solutions, which in turn reduces the number of degrees of freedom, the CPU time and the memory footprint. Numerical examples are presented to illustrate the capabilities of the model and to assess its accuracy.

  20. The effect of feeding enrichment methods on the behavior of captive Western lowland gorillas.

    PubMed

    Ryan, Erin B; Proudfoot, Kathryn L; Fraser, David

    2012-01-01

    Three feeding enrichment treatments were tested in an outdoor yard used by six Western lowland gorillas (Gorilla gorilla gorilla). In "Yard-toss," forage was thrown by hand over one third of the yard. In "Set-up," forage and browse were hand-scattered throughout the yard. "Set-up Enriched" was similar with the addition of either a hay- and forage-filled feeder or forage-filled boomer ball(s) suspended from a climbing structure. Each treatment was presented on 5 d. Behavior was recorded for 30 min before (baseline) and 30 min after the start of each treatment. All treatments led to more foraging and less inactivity compared with baseline (P80.05), but Yard-toss was the least effective, likely because resources were clumped and monopolized by dominant animals. In Set-up Enriched, dominant animals had the greatest increase in foraging (P=0.03), partly because they generally monopolized the suspended items, but this allowed others to forage at ground level. This separation of the animals likely explains why Set-Up Enriched led to more foraging than all other treatments (P80.05). Findings show that for these hierarchical animals, enrichment resources are most effective when distributed widely, including vertically, and that enrichment strategies must take social structure into account.

  1. Sonication-based isolation and enrichment of Chlorella protothecoides chloroplasts for illumina genome sequencing

    SciTech Connect

    Angelova, Angelina; Park, Sang-Hycuk; Kyndt, John; Fitzsimmons, Kevin; Brown, Judith K

    2013-09-01

    With the increasing world demand for biofuel, a number of oleaginous algal species are being considered as renewable sources of oil. Chlorella protothecoides Krüger synthesizes triacylglycerols (TAGs) as storage compounds that can be converted into renewable fuel utilizing an anabolic pathway that is poorly understood. The paucity of algal chloroplast genome sequences has been an important constraint to chloroplast transformation and for studying gene expression in TAGs pathways. In this study, the intact chloroplasts were released from algal cells using sonication followed by sucrose gradient centrifugation, resulting in a 2.36-fold enrichment of chloroplasts from C. protothecoides, based on qPCR analysis. The C. protothecoides chloroplast genome (cpDNA) was determined using the Illumina HiSeq 2000 sequencing platform and found to be 84,576 Kb in size (8.57 Kb) in size, with a GC content of 30.8 %. This is the first report of an optimized protocol that uses a sonication step, followed by sucrose gradient centrifugation, to release and enrich intact chloroplasts from a microalga (C. prototheocoides) of sufficient quality to permit chloroplast genome sequencing with high coverage, while minimizing nuclear genome contamination. The approach is expected to guide chloroplast isolation from other oleaginous algal species for a variety of uses that benefit from enrichment of chloroplasts, ranging from biochemical analysis to genomics studies.

  2. Erythrocyte enrichment in hematopoietic progenitor cell cultures based on magnetic susceptibility of the hemoglobin.

    PubMed

    Jin, Xiaoxia; Abbot, Stewart; Zhang, Xiaokui; Kang, Lin; Voskinarian-Berse, Vanessa; Zhao, Rui; Kameneva, Marina V; Moore, Lee R; Chalmers, Jeffrey J; Zborowski, Maciej

    2012-01-01

    Using novel media formulations, it has been demonstrated that human placenta and umbilical cord blood-derived CD34+ cells can be expanded and differentiated into erythroid cells with high efficiency. However, obtaining mature and functional erythrocytes from the immature cell cultures with high purity and in an efficient manner remains a significant challenge. A distinguishing feature of a reticulocyte and maturing erythrocyte is the increasing concentration of hemoglobin and decreasing cell volume that results in increased cell magnetophoretic mobility (MM) when exposed to high magnetic fields and gradients, under anoxic conditions. Taking advantage of these initial observations, we studied a noninvasive (label-free) magnetic separation and analysis process to enrich and identify cultured functional erythrocytes. In addition to the magnetic cell separation and cell motion analysis in the magnetic field, the cell cultures were characterized for cell sedimentation rate, cell volume distributions using differential interference microscopy, immunophenotyping (glycophorin A), hemoglobin concentration and shear-induced deformability (elongation index, EI, by ektacytometry) to test for mature erythrocyte attributes. A commercial, packed column high-gradient magnetic separator (HGMS) was used for magnetic separation. The magnetically enriched fraction comprised 80% of the maturing cells (predominantly reticulocytes) that showed near 70% overlap of EI with the reference cord blood-derived RBC and over 50% overlap with the adult donor RBCs. The results demonstrate feasibility of label-free magnetic enrichment of erythrocyte fraction of CD34+ progenitor-derived cultures based on the presence of paramagnetic hemoglobin in the maturing erythrocytes.

  3. LENS: web-based lens for enrichment and network studies of human proteins

    PubMed Central

    2015-01-01

    Background Network analysis is a common approach for the study of genetic view of diseases and biological pathways. Typically, when a set of genes are identified to be of interest in relation to a disease, say through a genome wide association study (GWAS) or a different gene expression study, these genes are typically analyzed in the context of their protein-protein interaction (PPI) networks. Further analysis is carried out to compute the enrichment of known pathways and disease-associations in the network. Having tools for such analysis at the fingertips of biologists without the requirement for computer programming or curation of data would accelerate the characterization of genes of interest. Currently available tools do not integrate network and enrichment analysis and their visualizations, and most of them present results in formats not most conducive to human cognition. Results We developed the tool Lens for Enrichment and Network Studies of human proteins (LENS) that performs network and pathway and diseases enrichment analyses on genes of interest to users. The tool creates a visualization of the network, provides easy to read statistics on network connectivity, and displays Venn diagrams with statistical significance values of the network's association with drugs, diseases, pathways, and GWASs. We used the tool to analyze gene sets related to craniofacial development, autism, and schizophrenia. Conclusion LENS is a web-based tool that does not require and download or plugins to use. The tool is free and does not require login for use, and is available at http://severus.dbmi.pitt.edu/LENS. PMID:26680011

  4. Top-down Feedback Exacerbates Effects of Nutrient Enrichment in Detritus-based Ecosystems via Increased Loss of Basal Carbon

    NASA Astrophysics Data System (ADS)

    Rosemond, A. D.; Suberkropp, K.; Cross, W. F.; Greenwood, J. L.; Eggert, S. L.; Taylor, N.; Wallace, J.

    2005-05-01

    In primary producer-based food webs faced with chronic nutrient enrichment, increased plant biomass may ultimately be suppressed by consumers. Effects of chronic enrichment of detritus-based ecosystems may be fundamentally different, with consumers exacerbating, rather than suppressing, the effects of enrichment on basal resources. We have continuously enriched a headwater stream at the Coweeta LongTerm Ecological Research site (North Carolina, USA) with N & P (to ca. 400 ug/L dissolved inorganic nitrogen and 50 ug/L soluble reactive phosphorus) for 4.5 yrs and quantified leaf breakdown rates, microbial production, invertebrate production, and leaf litter standing crop in the enriched stream and in an adjacent reference stream. Whereas nutrient enrichment largely increases basal carbon in primary producer-based systems, detrital carbon in the treatment stream was drastically diminished relative to the reference stream. During each successive year of enrichment, rates of leaf breakdown were progressively faster and standing crops of detrital carbon were progressively lower. This `ramping up' of loss rates of carbon appear to be driven by increased consumption by invertebrates, rather than increased microbial activity. Our results illustrate that fundamentally different trophic feedback effects can potentially occur in detrital vs primary producer components of food webs in response to increased nutrient concentrations.

  5. Self-generating density gradients of Percoll provide a simple and rapid method that consistently enriches natural killer cells.

    PubMed

    Ravnik, S E; Gage, S; Pollack, S B

    1988-06-13

    The separation or enrichment of natural killer (NK) cells from the heterogeneous cell populations in murine spleen or bone marrow is a vital step for the study of NK cells. We report in this study a simple and rapid method for the enrichment of NK cells from B cell-depleted spleen cells, using a self-generating density gradient of polyvinyl pyrrolidone-coated silica (Percoll). Nylon wool-passed spleen cells are suspended in Percoll that is isotonic and isosmotic with mouse blood at a density of 1.087 g/ml and ultracentrifuged at 30,000 x g for 10 min. This method consistently enriches for NK cell cytotoxic activity, in spleen cells of both unstimulated and interferon-stimulated mice, as measured in the chromium release assay. There is a concomitant enrichment for cells bearing the NK marker asialo GM-1 and depletion of L3T4 or Lyt-2-bearing T cells. In contrast to discontinuous, step-wise gradients, the self-generating Percoll gradient, which relies on the intrinsic property of Percoll to form a continuous density gradient, appears to provide the cells with a physiological environment both before and during the centrifugation step.

  6. Weighted Feature Significance: A Simple, Interpretable Model of Compound Toxicity Based on the Statistical Enrichment of Structural Features

    PubMed Central

    Huang, Ruili; Southall, Noel; Xia, Menghang; Cho, Ming-Hsuang; Jadhav, Ajit; Nguyen, Dac-Trung; Inglese, James; Tice, Raymond R.; Austin, Christopher P.

    2009-01-01

    In support of the U.S. Tox21 program, we have developed a simple and chemically intuitive model we call weighted feature significance (WFS) to predict the toxicological activity of compounds, based on the statistical enrichment of structural features in toxic compounds. We trained and tested the model on the following: (1) data from quantitative high–throughput screening cytotoxicity and caspase activation assays conducted at the National Institutes of Health Chemical Genomics Center, (2) data from Salmonella typhimurium reverse mutagenicity assays conducted by the U.S. National Toxicology Program, and (3) hepatotoxicity data published in the Registry of Toxic Effects of Chemical Substances. Enrichments of structural features in toxic compounds are evaluated for their statistical significance and compiled into a simple additive model of toxicity and then used to score new compounds for potential toxicity. The predictive power of the model for cytotoxicity was validated using an independent set of compounds from the U.S. Environmental Protection Agency tested also at the National Institutes of Health Chemical Genomics Center. We compared the performance of our WFS approach with classical classification methods such as Naive Bayesian clustering and support vector machines. In most test cases, WFS showed similar or slightly better predictive power, especially in the prediction of hepatotoxic compounds, where WFS appeared to have the best performance among the three methods. The new algorithm has the important advantages of simplicity, power, interpretability, and ease of implementation. PMID:19805409

  7. PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data.

    PubMed

    Lavallée-Adam, Mathieu; Rauniyar, Navin; McClatchy, Daniel B; Yates, John R

    2014-12-01

    The majority of large-scale proteomics quantification methods yield long lists of quantified proteins that are often difficult to interpret and poorly reproduced. Computational approaches are required to analyze such intricate quantitative proteomics data sets. We propose a statistical approach to computationally identify protein sets (e.g., Gene Ontology (GO) terms) that are significantly enriched with abundant proteins with reproducible quantification measurements across a set of replicates. To this end, we developed PSEA-Quant, a protein set enrichment analysis algorithm for label-free and label-based protein quantification data sets. It offers an alternative approach to classic GO analyses, models protein annotation biases, and allows the analysis of samples originating from a single condition, unlike analogous approaches such as GSEA and PSEA. We demonstrate that PSEA-Quant produces results complementary to GO analyses. We also show that PSEA-Quant provides valuable information about the biological processes involved in cystic fibrosis using label-free protein quantification of a cell line expressing a CFTR mutant. Finally, PSEA-Quant highlights the differences in the mechanisms taking place in the human, rat, and mouse brain frontal cortices based on tandem mass tag quantification. Our approach, which is available online, will thus improve the analysis of proteomics quantification data sets by providing meaningful biological insights. PMID:25177766

  8. An agarose gel-based neurosphere culture system leads to enrichment of neuronal lineage cells in vitro.

    PubMed

    Park, Kyuhee; Nam, Yeonju; Choi, Yongmun

    2015-05-01

    Stem cell-based therapy holds great potential especially for neurological disorders. However, clinical applications await further understanding of many aspects of stem cell differentiation and development of technology enabling manipulation of stem cells into desired cell types in the central nervous system. Here, we developed a new method that leads to enrichment of neuronal lineage cells in neural stem cell cultures. The protocol involves cultivation of primary cells derived from the forebrains of rat E18 embryos above a layer of nonadhesive hard agarose gel in the form of neurospheres. In contrast to the neurospheres that were cultured above an anti-adhesive hydrogel layer, the primary cells that were cultured above a layer of agarose gel preferentially differentiated into β-III tubulin-positive neurons when allowed to undergo differentiation in vitro.In an effort to investigate the mechanism behind this observation, we found that the gene expression of a vertebrate neuronal determination gene (neurogenin1) was enhanced in the neurospheres that proliferated above a layer of agarose gel as compared with the control, and the gene expression level of neurogenin1 was quite well correlated with the rigidity of agarose gel. These results indicate that agarose gel can contribute, at least in part, to enrich neuronal progenitors and immature postmitotic neurons during neurosphere formation and may provide additional information to establish efficient protocols for the neural stem cell-based study.

  9. Enrichment Wastes' Processing of Manganiferous Ores with the Use of Mechanochemical Methods

    ERIC Educational Resources Information Center

    Kubekova, Sholpan N.; Kapralova, Viktoria I.; Ibraimova, Gulnur T.; Batyrbayeva, Aigul A.

    2016-01-01

    The aim of the research is the study of the chemical and phase composition of enrichment wastes of manganiferous ore in Ushkatyn-III deposit and the synthesis of new materials by mechanochemical activation and subsequent heat treatment of the mechanical activation products. The use of XFA, infrared spectroscopy and electron probe microanalysis…

  10. Centrifuge enrichment plants. (Latest citations from the NTIS data base). Published Search

    SciTech Connect

    Not Available

    1992-09-01

    The bibliography contains citations concerning the design, control, monitoring, and safety of centrifuge enrichment plants. Power supplies, enrichment plant safeguards, facility design, cascade heater test loops to monitor the enrichment process, inspection strategies, and the socioeconomic effects of centrifuge enrichment plants are examined. Radioactive waste disposal problems are briefly considered. (Contains a minimum of 169 citations and includes a subject term index and title list.)

  11. 10 CFR Appendix F to Part 110 - Illustrative List of Laser-Based Enrichment Plant Equipment and Components Under NRC Export...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Illustrative List of Laser-Based Enrichment Plant... Appendix F to Part 110—Illustrative List of Laser-Based Enrichment Plant Equipment and Components Under NRC Export Licensing Authority Note—Present systems for enrichment processes using lasers fall into...

  12. Efficient dielectrophoretic cell enrichment using a dielectrophoresis-well based system.

    PubMed

    Abdul Razak, Mohd Azhar; Hoettges, Kai F; Fatoyinbo, Henry O; Labeed, Fatima H; Hughes, Michael P

    2013-01-01

    Whilst laboratory-on-chip cell separation systems using dielectrophoresis are increasingly reported in the literature, many systems are afflicted by factors which impede "real world" performance, chief among these being cell loss (in dead spaces, attached to glass and tubing surfaces, or sedimentation from flow), and designs with large channel height-to-width ratios (large channel widths, small channel heights) that make the systems difficult to interface with other microfluidic systems. In this paper, we present a scalable structure based on 3D wells with approximately unity height-to-width ratios (based on tubes with electrodes on the sides), which is capable of enriching yeast cell populations whilst ensuring that up to 94.3% of cells processed through the device can be collected in tubes beyond the output.

  13. Efficient dielectrophoretic cell enrichment using a dielectrophoresis-well based system

    PubMed Central

    Abdul Razak, Mohd Azhar; Hoettges, Kai F.; Fatoyinbo, Henry O.; Labeed, Fatima H.; Hughes, Michael P.

    2013-01-01

    Whilst laboratory-on-chip cell separation systems using dielectrophoresis are increasingly reported in the literature, many systems are afflicted by factors which impede “real world” performance, chief among these being cell loss (in dead spaces, attached to glass and tubing surfaces, or sedimentation from flow), and designs with large channel height-to-width ratios (large channel widths, small channel heights) that make the systems difficult to interface with other microfluidic systems. In this paper, we present a scalable structure based on 3D wells with approximately unity height-to-width ratios (based on tubes with electrodes on the sides), which is capable of enriching yeast cell populations whilst ensuring that up to 94.3% of cells processed through the device can be collected in tubes beyond the output. PMID:24396544

  14. Enriched glucose and dextrin mannitol-based media modulates fibroblast behavior on bacterial cellulose membranes.

    PubMed

    Stumpf, Taisa R; Pértile, Renata A N; Rambo, Carlos R; Porto, Luismar M

    2013-12-01

    Bacterial cellulose (BC) produced by Gluconacetobacter hansenii is a suitable biopolymer for biomedical applications. In order to modulate the properties of BC and expand its use as substrate for tissue engineering mainly in the form of biomembranes, glucose or dextrin were added into a BC fermentation mannitol-based medium (BCGl and BCDe, respectively) under static culture conditions. SEM images showed effects on fiber density and porosity on both sides of the BC membranes. Both enriched media decreased the BET surface area, water holding capacity, and rehydration rate. Fourier transform infrared (attenuated total reflectance mode) spectroscopy (FTIR-ATR) analysis revealed no change in the chemical structure of BC. L929 fibroblast cells were seeded on all BC-based membranes and evaluated in aspects of cell adhesion, proliferation and morphology. BCG1 membranes showed the highest biological performance and hold promise for the use in tissue engineering applications.

  15. Comparison of subtypes of Listeria monocytogenes isolates from naturally contaminated watershed samples using a combination of non-selective and selective enrichment methods

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two enrichment methods for Listeria monocytogenes using Immuno Magnetic Separation were tested to determine if they selected the same subtypes of isolates. Both methods included a non-selective enrichment and one included subculture in Fraser Broth. Naturally contaminated watershed samples from the ...

  16. Enriching step-based product information models to support product life-cycle activities

    NASA Astrophysics Data System (ADS)

    Sarigecili, Mehmet Ilteris

    The representation and management of product information in its life-cycle requires standardized data exchange protocols. Standard for Exchange of Product Model Data (STEP) is such a standard that has been used widely by the industries. Even though STEP-based product models are well defined and syntactically correct, populating product data according to these models is not easy because they are too big and disorganized. Data exchange specifications (DEXs) and templates provide re-organized information models required in data exchange of specific activities for various businesses. DEXs show us it would be possible to organize STEP-based product models in order to support different engineering activities at various stages of product life-cycle. In this study, STEP-based models are enriched and organized to support two engineering activities: materials information declaration and tolerance analysis. Due to new environmental regulations, the substance and materials information in products have to be screened closely by manufacturing industries. This requires a fast, unambiguous and complete product information exchange between the members of a supply chain. Tolerance analysis activity, on the other hand, is used to verify the functional requirements of an assembly considering the worst case (i.e., maximum and minimum) conditions for the part/assembly dimensions. Another issue with STEP-based product models is that the semantics of product data are represented implicitly. Hence, it is difficult to interpret the semantics of data for different product life-cycle phases for various application domains. OntoSTEP, developed at NIST, provides semantically enriched product models in OWL. In this thesis, we would like to present how to interpret the GD & T specifications in STEP for tolerance analysis by utilizing OntoSTEP.

  17. Simultaneous enrichment and separation of flavonoids from Herba Epimedii by macroporous resins coupled with preparative chromatographic method.

    PubMed

    Zhou, Zhengzheng; Luo, Jianguang; Wang, Junsong; Li, Liang; Kong, Lingyi

    2015-01-01

    An efficient, feasible enrichment and separation method of epimedins A, B, C and icariin from Herba Epimedii was developed by the combination of microwave-assisted extraction, macroporous resins and preparative HPLC. WDX-5 macroporous resin shows better recoveries at 96.2%, 97.0%, 98.2% and 97.1% for epimedins A, B, C and icariin than other macroporous resins used in the experiments. As a result, epimedins A (5.1 mg), B (15.3 mg), C (7.6 mg) and icariin (14.3 mg) were obtained from 6.0 g crude Herba Epimedii with the recoveries at 70.8%, 68.9%, 66.7% and 95.3%, respectively. The method developed in this study may provide scientific references for the enrichment and separation of flavonoids from Herba Epimedii. PMID:25277166

  18. Imaging-based enrichment criteria using deep learning algorithms for efficient clinical trials in mild cognitive impairment.

    PubMed

    Ithapu, Vamsi K; Singh, Vikas; Okonkwo, Ozioma C; Chappell, Richard J; Dowling, N Maritza; Johnson, Sterling C

    2015-12-01

    The mild cognitive impairment (MCI) stage of Alzheimer's disease (AD) may be optimal for clinical trials to test potential treatments for preventing or delaying decline to dementia. However, MCI is heterogeneous in that not all cases progress to dementia within the time frame of a trial and some may not have underlying AD pathology. Identifying those MCIs who are most likely to decline during a trial and thus most likely to benefit from treatment will improve trial efficiency and power to detect treatment effects. To this end, using multimodal, imaging-derived, inclusion criteria may be especially beneficial. Here, we present a novel multimodal imaging marker that predicts future cognitive and neural decline from [F-18]fluorodeoxyglucose positron emission tomography (PET), amyloid florbetapir PET, and structural magnetic resonance imaging, based on a new deep learning algorithm (randomized denoising autoencoder marker, rDAm). Using ADNI2 MCI data, we show that using rDAm as a trial enrichment criterion reduces the required sample estimates by at least five times compared with the no-enrichment regime and leads to smaller trials with high statistical power, compared with existing methods.

  19. Ground-Based Network and Supersite Observations to Complement and Enrich EOS Research

    NASA Technical Reports Server (NTRS)

    Tsay, Si-Chee; Holben, Brent N.; Welton, Ellsworth J.

    2011-01-01

    Since 1997 NASA has been successfully launching a series of satellites - the Earth Observing System (EOS) - to intensively study, and gain a better understanding of, the Earth as an integrated system. Space-borne remote sensing observations, however, are often plagued by contamination of surface signatures. Thus, ground-based in-situ and remote-sensing measurements, where signals come directly from atmospheric constituents, the sun, and/or the Earth-atmosphere interactions, provide additional information content for comparisons that confirm quantitatively the usefulness of the integrated surface, aircraft, and satellite datasets. Through numerous participations, particularly but not limited to the EOS remote-sensing/retrieval and validation projects over the years, NASA/GSFC has developed and continuously refined ground-based networks and mobile observatories that proved to be vital in providing high temporal measurements, which complement and enrich the satellite observations. These are: the AERO NET (AErosol RObotic NETwork) a federation of ground-based globally distributed network of spectral sun-sky photometers; the MPLNET (Micro-Pulse Lidar NETwork, a similarly organized network of micro-pulse lidar systems measuring aerosol and cloud vertical structure continuously; and the SMART-COMMIT (Surface-sensing Measurements for Atmospheric Radiative Transfer - Chemical, Optical & Microphysical Measurements of In-situ Troposphere, mobile observatories, a suite of spectral radiometers and in-situ probes acquiring supersite measurements. Most MPLNET sites are collocated with those of AERONET, and both networks always support the deployment of SMART-COMMIT worldwide. These data products follow the data structure of EOS conventions: Level-0, instrument archived raw data; Level-1 (or 1.5), real-time data with no (or limited) quality assurance; Level-2, not real high temporal and spectral resolutions. In this talk, we will present NASA/GSFC groundbased facilities, serving

  20. Robust physical methods that enrich genomic regions identical by descent for linkage studies: confirmation of a locus for osteogenesis imperfecta

    PubMed Central

    Brooks, Peter; Marcaillou, Charles; Vanpeene, Maud; Saraiva, Jean-Paul; Stockholm, Daniel; Francke, Stephan; Favis, Reyna; Cohen, Nadine; Rousseau, Francis; Tores, Frédéric; Lindenbaum, Pierre; Hager, Jörg; Philippi, Anne

    2009-01-01

    Background The monogenic disease osteogenesis imperfecta (OI) is due to single mutations in either of the collagen genes ColA1 or ColA2, but within the same family a given mutation is accompanied by a wide range of disease severity. Although this phenotypic variability implies the existence of modifier gene variants, genome wide scanning of DNA from OI patients has not been reported. Promising genome wide marker-independent physical methods for identifying disease-related loci have lacked robustness for widespread applicability. Therefore we sought to improve these methods and demonstrate their performance to identify known and novel loci relevant to OI. Results We have improved methods for enriching regions of identity-by-descent (IBD) shared between related, afflicted individuals. The extent of enrichment exceeds 10- to 50-fold for some loci. The efficiency of the new process is shown by confirmation of the identification of the Col1A2 locus in osteogenesis imperfecta patients from Amish families. Moreover the analysis revealed additional candidate linkage loci that may harbour modifier genes for OI; a locus on chromosome 1q includes COX-2, a gene implicated in osteogenesis. Conclusion Technology for physical enrichment of IBD loci is now robust and applicable for finding genes for monogenic diseases and genes for complex diseases. The data support the further investigation of genetic loci other than collagen gene loci to identify genes affecting the clinical expression of osteogenesis imperfecta. The discrimination of IBD mapping will be enhanced when the IBD enrichment procedure is coupled with deep resequencing. PMID:19331686

  1. Constituting a receptor-ligand information base from quality-enriched data

    SciTech Connect

    Hemm, K.; Aberer, K.; Hendlich, M.

    1995-12-31

    Many different resources are needed for analyzing relevant experimental data in drug design. Currently this data is difficult to access, because it is stored in heterogeneous data-bases, spread over many platforms, poorly interconnected, incomplete, erroneous, or just not electronically available. In order to establish a high quality database for drug design we have developed a new demand-driven methodology for integrating and semantically enriching heterogeneous data from different research areas and for migrating the data into an object-oriented database management system. In this way we have established a database containing well-prepared, relevant data needed for drug design and offering the advantages of modern database technology, like a comprehensive object-oriented data model, a flexible declarative query language and support for persistent storage and sharing of data in a multi-user environment.

  2. Vital pulp therapy using calcium-enriched mixture: An evidence-based review

    PubMed Central

    Asgary, Saeed; Ahmadyar, Maryam

    2013-01-01

    Worldwide, casecontrol studies have revealed that the treatment outcomes of root canal therapy (RCT) are generally favorable; however, the overall epidemiological success rate of RCT in the general population is relatively low. On the other hand, vitality of dental pulp is a key factor in the long-term prognosis of permanent teeth; in recent years, vital pulp therapy (VPT) has received significant consideration as it has been revealed that the inflamed pulp has the potential to heal. In this review article, the current best evidence with regard to VPT using calcium-enriched mixture (CEM) cement in human permanent/primary teeth is discussed. A strategy based on a search using keywords for CEM cement as well as VPT was applied. PMID:23716958

  3. Evaluation of Different N-Glycopeptide Enrichment Methods for N-Glycosylation Sites Mapping in Mouse Brain.

    PubMed

    Zhang, Chengqian; Ye, Zilu; Xue, Peng; Shu, Qingbo; Zhou, Yue; Ji, Yanlong; Fu, Ying; Wang, Jifeng; Yang, Fuquan

    2016-09-01

    N-Glycosylation of proteins plays a critical role in many biological pathways. Because highly heterogeneous N-glycopeptides are present in biological sources, the enrichment procedure is a crucial step for mass spectrometry analysis. Five enrichment methods, including IP-ZIC-HILIC, hydrazide chemistry, lectin affinity, ZIC-HILIC-FA, and TiO2 affinity were evaluated and compared in the study of mapping N-glycosylation sites in mouse brain. On the basis of our results, the identified N-glycosylation sites were 1891, 1241, 891, 869, and 710 and the FDR values were 3.29, 5.62, 9.54, 9.54, and 20.02%, respectively. Therefore, IP-ZIC-HILIC enrichment method displayed the highest sensitivity and specificity. In this work, we identified a total of 3446 unique glycosylation sites conforming to the N-glycosylation consensus motif (N-X-T/S/C; X ≠ P) with (18)O labeling in 1597 N-glycoproteins. N-glycosylation site information was used to confirm or correct the transmembrane topology of the 57 novel transmembrane N-glycoproteins.

  4. Evaluation of Different N-Glycopeptide Enrichment Methods for N-Glycosylation Sites Mapping in Mouse Brain.

    PubMed

    Zhang, Chengqian; Ye, Zilu; Xue, Peng; Shu, Qingbo; Zhou, Yue; Ji, Yanlong; Fu, Ying; Wang, Jifeng; Yang, Fuquan

    2016-09-01

    N-Glycosylation of proteins plays a critical role in many biological pathways. Because highly heterogeneous N-glycopeptides are present in biological sources, the enrichment procedure is a crucial step for mass spectrometry analysis. Five enrichment methods, including IP-ZIC-HILIC, hydrazide chemistry, lectin affinity, ZIC-HILIC-FA, and TiO2 affinity were evaluated and compared in the study of mapping N-glycosylation sites in mouse brain. On the basis of our results, the identified N-glycosylation sites were 1891, 1241, 891, 869, and 710 and the FDR values were 3.29, 5.62, 9.54, 9.54, and 20.02%, respectively. Therefore, IP-ZIC-HILIC enrichment method displayed the highest sensitivity and specificity. In this work, we identified a total of 3446 unique glycosylation sites conforming to the N-glycosylation consensus motif (N-X-T/S/C; X ≠ P) with (18)O labeling in 1597 N-glycoproteins. N-glycosylation site information was used to confirm or correct the transmembrane topology of the 57 novel transmembrane N-glycoproteins. PMID:27480293

  5. Visual detection technique for efficient screening and isolation of Salmonella based on a novel enrichment assay using chromatography membrane.

    PubMed

    Tang, F; Xiong, Y; Zhang, H; Wu, K; Xiang, Y; Shao, J-B; Ai, H-W; Xiang, Y-P; Zheng, X-L; Lv, J-R; Sun, H; Bao, L-S; Zhang, Z; Hu, H-B; Zhang, J-Y; Chen, L; Lu, J; Liu, W-Y; Mei, H; Ma, Y; Xu, C-F; Fang, A-Y; Gu, M; Xu, C-Y; Chen, Y; Chen, Z; Sun, Z-Y

    2016-03-01

    To detect Salmonella more efficiently and isolate strains more easily, a novel and simple detection method that uses an enrichment assay and two chromogenic reactions on a chromatography membrane was developed. Grade 3 chromatography paper is used as functionalized solid phase support (SPS), which contains specially optimized medium. One reaction for screening is based on the sulfate-reducing capacity of Salmonella. Hydrogen sulfide (H2S) generated by Salmonella reacts with ammonium ferric citrate to produce black colored ferrous sulfide. Another reaction is based on Salmonella C8 esterase that is unique for Enterobacteriaceae except Serratia and interacts with 4-methylumbelliferyl caprylate (MUCAP) to produce fluorescent umbelliferone, which is visible under ultraviolet light. A very low detection limit (10(1) CFU ml(-1)) for Salmonella was achieved on the background of 10(5) CFU ml(-1) Escherichia coli. More importantly, testing with more than 1,000 anal samples indicated that our method has a high positive detection rate and is relatively low cost, compared with the traditional culture-based method. It took only 1 day for the preliminary screening and 2 days to efficiently isolate the Salmonella cells, indicating that the new assay is specific, rapid, and simple for Salmonella detection. In contrast to the traditional culture-based method, this method can be easily used to screen and isolate targeted strains with the naked eye. The results of quantitative and comparative experiments showed that the visual detection technique is an efficient alternative method for the screening of Salmonella spp. in many applications of large-sized samples related to public health surveillance. PMID:26796551

  6. Visual detection technique for efficient screening and isolation of Salmonella based on a novel enrichment assay using chromatography membrane.

    PubMed

    Tang, F; Xiong, Y; Zhang, H; Wu, K; Xiang, Y; Shao, J-B; Ai, H-W; Xiang, Y-P; Zheng, X-L; Lv, J-R; Sun, H; Bao, L-S; Zhang, Z; Hu, H-B; Zhang, J-Y; Chen, L; Lu, J; Liu, W-Y; Mei, H; Ma, Y; Xu, C-F; Fang, A-Y; Gu, M; Xu, C-Y; Chen, Y; Chen, Z; Sun, Z-Y

    2016-03-01

    To detect Salmonella more efficiently and isolate strains more easily, a novel and simple detection method that uses an enrichment assay and two chromogenic reactions on a chromatography membrane was developed. Grade 3 chromatography paper is used as functionalized solid phase support (SPS), which contains specially optimized medium. One reaction for screening is based on the sulfate-reducing capacity of Salmonella. Hydrogen sulfide (H2S) generated by Salmonella reacts with ammonium ferric citrate to produce black colored ferrous sulfide. Another reaction is based on Salmonella C8 esterase that is unique for Enterobacteriaceae except Serratia and interacts with 4-methylumbelliferyl caprylate (MUCAP) to produce fluorescent umbelliferone, which is visible under ultraviolet light. A very low detection limit (10(1) CFU ml(-1)) for Salmonella was achieved on the background of 10(5) CFU ml(-1) Escherichia coli. More importantly, testing with more than 1,000 anal samples indicated that our method has a high positive detection rate and is relatively low cost, compared with the traditional culture-based method. It took only 1 day for the preliminary screening and 2 days to efficiently isolate the Salmonella cells, indicating that the new assay is specific, rapid, and simple for Salmonella detection. In contrast to the traditional culture-based method, this method can be easily used to screen and isolate targeted strains with the naked eye. The results of quantitative and comparative experiments showed that the visual detection technique is an efficient alternative method for the screening of Salmonella spp. in many applications of large-sized samples related to public health surveillance.

  7. A non-aqueous solid phase extraction method for alkaloid enrichment and its application in the determination of hyoscyamine and scopolamine.

    PubMed

    Long, Zhen; Wang, Chaoran; Guo, Zhimou; Zhang, Xiuli; Nordahl, Lilly; Zeng, Jing; Zeng, Jianguo; Liang, Xinmiao

    2012-03-21

    A non-aqueous solid phase extraction (SPE) method utilizing silica based strong cation exchange (SCX) was developed and optimized for the enrichment of alkaloids. In this method, silica based SCX SPE columns were used for the elimination of non-alkaloid compounds and the preconcentration of alkaloids from the extracts. Mass spectrometry was employed to analyze the alkaloid-enriched fraction, and results showed that the SPE method developed in this study was effective for the removal of non-alkaloids. Then, this pretreatment method was combined with high performance liquid chromatography for the quantification of scopolamine and hyoscyamine from Scopolia tangutica Maxim. The recoveries of scopolamine and (-)-hyoscyamine were 98.51% and 91.12%, respectively. Relative standard deviation values were 1.4% for scopolamine and 1.6% for (-)-hyoscyamine. The linearity was good in the 0.01-0.8 mg mL(-1) range for hyoscyamine and 0.01-0.4 mg mL(-1) range for scopolamine.

  8. Method and apparatus for reducing cold-phase emissions by utilizing oxygen-enriched intake air

    DOEpatents

    Poola, Ramesh B.; Sekar, Ramanujam R.; Stork, Kevin C.

    1997-01-01

    An oxygen-enriched air intake control system for an internal combustion engine includes air directing apparatus to control the air flow into the intake of the engine. During normal operation of the engine, ambient air flowing from an air filter of the engine flows through the air directing apparatus into the intake of the engine. In order to decrease the amount of carbon monoxide (CO) and hydrocarbon (HC) emissions that tend to be produced by the engine during a short period of time after the engine is started, the air directing apparatus diverts for a short period of time following the start up of the engine at least a portion of the ambient air from the air filter through a secondary path. The secondary path includes a selectively permeable membrane through which the diverted portion of the ambient air flows. The selectively permeable membrane separates nitrogen and oxygen from the diverted air so that oxygen enriched air containing from about 23% to 25% oxygen by volume is supplied to the intake of the engine.

  9. Bulk purification and deposition methods for selective enrichment in high aspect ratio single-walled carbon nanotubes.

    PubMed

    Bhatt, Nidhi P; Vichchulada, Pornnipa; Lay, Marcus D

    2012-06-01

    Aqueous batch processing methods for the concurrent purification of single-walled carbon nanotube (SWNT) soot and enrichment in high aspect ratio nanotubes are essential to their use in a wide variety of electronic, structural, and mechanical applications. This manuscript presents a new route to the bulk purification and enrichment of unbundled SWNTs having average lengths in excess of 2 μm. Iterative centrifugation cycles at low centripetal force not only removed amorphous C and catalyst nanoparticles but also allowed the enhanced buoyancy of surfactant encapsulated, unbundled, high aspect ratio SWNTs to be used to isolate them in the supernatant. UV-vis-NIR and Raman spectroscopy were used to verify the removal of residual impurities from as-produced (AP-grade) arc discharge soot and the simultaneous enrichment in unbundled, undamaged, high aspect ratio SWNTs. The laminar flow deposition process (LFD) used to form two-dimensional networks of SWNTs prevented bundle formation during network growth. Additionally, it further enhanced the quality of deposits by taking advantage of the inverse relationship between the translational diffusion coefficient and length for suspended nanoparticles. This resulted in preferential deposition of pristine, unbundled, high aspect ratio SWNTs over residual impurities, as observed by Raman spectroscopy and atomic force microscopy (AFM). PMID:22571337

  10. A "Proof-of-Concept" Demonstration of RF-Based Technologies for UF6 Cylinder Tracking at Centrifuge Enrichment Plant

    SciTech Connect

    Pickett, Chris A; Younkin, James R; Kovacic, Donald N; Dixon, E. T.; Martinez, B.

    2007-01-01

    This effort describes how radio-frequency (RF) technology can be integrated into a uranium enrichment facility's nuclear materials accounting and control program to enhance uranium hexafluoride (UF6) cylinder tracking and thus provide benefits to both domestic and international safeguards. Approved industry-standard cylinders are used to handle and store UF6 feed, product, tails, and samples at uranium enrichment plants. In the international arena, the International Atomic Energy Agency (IAEA) relies on time-consuming manual cylinder inventory and tracking techniques to verify operator declarations and to detect potential diversion of UF6. Development of a reliable, automated, and tamper-resistant process for tracking and monitoring UF6 cylinders would greatly reduce the risk of false or misreported cylinder tare weights, diversion of nuclear material, concealment of excess production, utilization of undeclared cylinders, and misrepresentation of the cylinders contents. This paper will describe a "proof-of concept" system that was designed show the feasibility of using RF based technologies to track individual UF6 cylinders throughout their entire life cycle, and thus ensure both increased domestic accountability of materials and a more effective and efficient method for application of IAEA international safeguards at the site level. The proposed system incorporates RF-based identification devices, which provide a mechanism for a reliable, automated, and tamper-resistant tracking network. We explore how securely attached RF tags can be integrated with other safeguards technologies to better detect diversion of cylinders. The tracking system could also provide a foundation for integration of other types of safeguards that would further enhance detection of undeclared activities.

  11. Neutron source, linear-accelerator fuel enricher and regenerator and associated methods

    DOEpatents

    Steinberg, Meyer; Powell, James R.; Takahashi, Hiroshi; Grand, Pierre; Kouts, Herbert

    1982-01-01

    A device for producing fissile material inside of fabricated nuclear elements so that they can be used to produce power in nuclear power reactors. Fuel elements, for example, of a LWR are placed in pressure tubes in a vessel surrounding a liquid lead-bismuth flowing columnar target. A linear-accelerator proton beam enters the side of the vessel and impinges on the dispersed liquid lead-bismuth columns and produces neutrons which radiate through the surrounding pressure tube assembly or blanket containing the nuclear fuel elements. These neutrons are absorbed by the natural fertile uranium-238 elements and are transformed to fissile plutonium-239. The fertile fuel is thus enriched in fissile material to a concentration whereby they can be used in power reactors. After use in the power reactors, dispensed depleted fuel elements can be reinserted into the pressure tubes surrounding the target and the nuclear fuel regenerated for further burning in the power reactor.

  12. Development of particle induced gamma-ray emission methods for nondestructive determination of isotopic composition of boron and its total concentration in natural and enriched samples.

    PubMed

    Chhillar, Sumit; Acharya, Raghunath; Sodaye, Suparna; Pujari, Pradeep K

    2014-11-18

    We report simple particle induced gamma-ray emission (PIGE) methods using a 4 MeV proton beam for simultaneous and nondestructive determination of the isotopic composition of boron ((10)B/(11)B atom ratio) and total boron concentrations in various solid samples with natural isotopic composition and enriched with (10)B. It involves measurement of prompt gamma-rays at 429, 718, and 2125 keV from (10)B(p,αγ)(7)Be, (10)B(p, p'γ)(10)B, and (11)B(p, p'γ)(11)B reactions, respectively. The isotopic composition of boron in natural and enriched samples was determined by comparing peak area ratios corresponding to (10)B and (11)B of samples to natural boric acid standard. An in situ current normalized PIGE method, using F or Al, was standardized for total B concentration determination. The methods were validated by analyzing stoichiometric boron compounds and applied to samples such as boron carbide, boric acid, carborane, and borosilicate glass. Isotopic compositions of boron in the range of 0.247-2.0 corresponding to (10)B in the range of 19.8-67.0 atom % and total B concentrations in the range of 5-78 wt % were determined. It has been demonstrated that PIGE offers a simple and alternate method for total boron as well as isotopic composition determination in boron based solid samples, including neutron absorbers that are important in nuclear technology.

  13. Effects of four different cooking methods on some quality characteristics of low fat Inegol meatball enriched with flaxseed flour.

    PubMed

    Turp, Gulen Yildiz

    2016-11-01

    The present study is concerned with the effects of four different cooking methods (grill, oven, pan and ohmic cooking) on physicochemical parameters (cooking yield moisture retention, fat retention, color, texture), fatty acid composition and sensory characteristics of low fat Turkish traditional Inegol meatball. Flaxseed flour was used as a fat substitute in the production of meatballs. Meatball proximate composition was affected by the cooking methods mainly as a consequence of the weight losses. The highest cooking yield was found in samples cooked in the oven. Flaxseed flour contains high amount of α-linolenic acid and ohmic cooking seems to be the best cooking method in terms of retaining this fatty acid in meatballs enriched with flaxseed flour. However ohmic cooked meatball samples had a brighter surface color and harder texture in comparison with meatball samples cooked via traditional methods. There was no significant difference between the sensory evaluation scores of meatballs. PMID:27258146

  14. Effects of four different cooking methods on some quality characteristics of low fat Inegol meatball enriched with flaxseed flour.

    PubMed

    Turp, Gulen Yildiz

    2016-11-01

    The present study is concerned with the effects of four different cooking methods (grill, oven, pan and ohmic cooking) on physicochemical parameters (cooking yield moisture retention, fat retention, color, texture), fatty acid composition and sensory characteristics of low fat Turkish traditional Inegol meatball. Flaxseed flour was used as a fat substitute in the production of meatballs. Meatball proximate composition was affected by the cooking methods mainly as a consequence of the weight losses. The highest cooking yield was found in samples cooked in the oven. Flaxseed flour contains high amount of α-linolenic acid and ohmic cooking seems to be the best cooking method in terms of retaining this fatty acid in meatballs enriched with flaxseed flour. However ohmic cooked meatball samples had a brighter surface color and harder texture in comparison with meatball samples cooked via traditional methods. There was no significant difference between the sensory evaluation scores of meatballs.

  15. A sensory- and consumer-based approach to optimize cheese enrichment with grape skin powders.

    PubMed

    Torri, L; Piochi, M; Marchiani, R; Zeppa, G; Dinnella, C; Monteleone, E

    2016-01-01

    The present study aimed to present a sensory- and consumer-based approach to optimize cheese enrichment with grape skin powders (GSP). The combined sensory evaluation approach, involving a descriptive and an affective test, respectively, was applied to evaluate the effect of the addition of grape skin powders from 2 grape varieties (Barbera and Chardonnay) at different levels [0.8, 1.6, and 2.4%; weight (wt) powder/wt curd] on the sensory properties and consumer acceptability of innovative soft cow milk cheeses. The experimental plan envisaged 7 products, 6 fortified prototypes (at rates of Barbera and Chardonnay of 0.8, 1.6, and 2.4%) and a control sample, with 1 wk of ripening. By means of a free choice profile, 21 cheese experts described the sensory properties of prototypes. A central location test with 90 consumers was subsequently conducted to assess the acceptability of samples. The GSP enrichment strongly affected the sensory properties of innovative products, mainly in terms of appearance and texture. Fortified samples were typically described with a marbling aspect (violet or brown as function of the grape variety) and with an increased granularity, sourness, saltiness, and astringency. The fortification also contributed certain vegetable sensations perceived at low intensity (grassy, cereal, nuts), and some potential negative sensations (earthy, animal, winy, varnish). The white color, the homogeneous dough, the compact and elastic texture, and the presence of lactic flavors resulted the positive drivers of preference. On the contrary, the marbling aspect, granularity, sandiness, sourness, saltiness, and astringency negatively affected the cheese acceptability for amounts of powder, exceeding 0.8 and 1.6% for the Barbera and Chardonnay prototypes, respectively. Therefore, the amount of powder resulted a critical parameter for liking of fortified cheeses and a discriminant between the 2 varieties. Reducing the GSP particle size and improving the GSP

  16. Development of microsatellite markers for common bean (Phaseolus vulgaris L.) based on screening of non-enriched, small-insert genomic libraries.

    PubMed

    Blair, Matthew W; Torres, Monica Muñoz; Pedraza, Fabio; Giraldo, Martha C; Buendía, Hector F; Hurtado, Natalia

    2009-09-01

    Microsatellite markers are useful genetic tools for a wide array of genomic analyses although their development is time-consuming and requires the identification of simple sequence repeats (SSRs) from genomic sequences. Screening of non-enriched, small-insert libraries is an effective method of SSR isolation that can give an unbiased picture of motif frequency. Here we adapt high-throughput protocols for the screening of plasmid-based libraries using robotic colony picking and filter preparation. Seven non-enriched genomic libraries from common bean genomic DNA were made by digestion with four frequently cutting restriction enzymes, double digestion with a frequently cutting restriction enzyme and a less frequently cutting restriction enzyme, or sonication. Library quality was compared and three of the small-insert libraries were selected for further analysis. Each library was plated and picked into 384-well plates that were used to create high-density filter arrays of over 18 000 clones each, which were screened with oligonucleotide probes for various SSR motifs. Positive clones were found to have low redundancy. One hundred SSR markers were developed and 80 were tested for polymorphism in a standard parental survey. These microsatellite markers derived from non-SSR-enriched libraries should be useful additions to previous markers developed from enriched libraries.

  17. Development of microsatellite markers for common bean (Phaseolus vulgaris L.) based on screening of non-enriched, small-insert genomic libraries.

    PubMed

    Blair, Matthew W; Torres, Monica Muñoz; Pedraza, Fabio; Giraldo, Martha C; Buendía, Hector F; Hurtado, Natalia

    2009-09-01

    Microsatellite markers are useful genetic tools for a wide array of genomic analyses although their development is time-consuming and requires the identification of simple sequence repeats (SSRs) from genomic sequences. Screening of non-enriched, small-insert libraries is an effective method of SSR isolation that can give an unbiased picture of motif frequency. Here we adapt high-throughput protocols for the screening of plasmid-based libraries using robotic colony picking and filter preparation. Seven non-enriched genomic libraries from common bean genomic DNA were made by digestion with four frequently cutting restriction enzymes, double digestion with a frequently cutting restriction enzyme and a less frequently cutting restriction enzyme, or sonication. Library quality was compared and three of the small-insert libraries were selected for further analysis. Each library was plated and picked into 384-well plates that were used to create high-density filter arrays of over 18 000 clones each, which were screened with oligonucleotide probes for various SSR motifs. Positive clones were found to have low redundancy. One hundred SSR markers were developed and 80 were tested for polymorphism in a standard parental survey. These microsatellite markers derived from non-SSR-enriched libraries should be useful additions to previous markers developed from enriched libraries. PMID:19935925

  18. Simple and rapid detection of Campylobacter spp. in naturally contaminated chicken-meat samples by combination of a two-step enrichment method with an immunochromatographic assay.

    PubMed

    Kawatsu, K; Taguchi, M; Yonekita, T; Matsumoto, T; Morimatsu, F; Kumeda, Y

    2010-08-15

    A simple and rapid method to detect Campylobacter spp. in chicken-meat samples was established. This method consisted of a combination of a two-step enrichment method with a commercially available immunochromatographic assay, named NH Immunochromato Campylobacter (NH IC Campy, Nippon Meat Packers, Ibaraki, Japan), which is able to detect Campylobacter antigen in an enrichment culture within 15 min. The enrichment method did not require much blood or a particular system of generating a microaerobic atmosphere, in contrast to the standard method of enriching Campylobacter spp. in chicken-meat samples. The sensitivity of a combination of the two-step enrichment method with NH IC Campy for detection of non- and freeze-stressed Campylobacter spp. in spiked chicken meat was determined using bacterial cells of Campylobacter jejuni and Campylobacter coli. The detection sensitivities for non-stressed C. jejuni and C. coli were found to range from 5.5 to 1.3x10(1) CFU per 25 g of chicken meat, and those for freeze-stressed C. jejuni and C. coli were found to range from 9.2x10(1) to 1.5x10(2) CFU per 25 g of chicken meat. When a total of 68 chicken-meat samples were tested, the combination method determined that 61 samples were positive for Campylobacter spp. This method was more sensitive than a bacterial culture test, which consists of standard enrichment culturing and plating onto selective agars. Because the combination could be conducted in approximately 48 h, from the beginning of the enrichment culture to final determination, it was more rapid than the bacterial culture test, which requires four to five days. Moreover, the combination was simple to perform. These results suggest that combining the two-step enrichment method with NH IC Campy is useful as a simple and rapid alternative to the conventional bacterial culture test for detecting Campylobacter spp. in naturally contaminated chicken meat samples.

  19. The Effects of the Marriage Enrichment Program Based on the Cognitive-Behavioral Approach on the Marital Adjustment of Couples

    ERIC Educational Resources Information Center

    Kalkan, Melek; Ersanli, Ercumend

    2008-01-01

    The aim of this study is to investigate the effects of the marriage enrichment program based on the cognitive-behavioral approach on levels of marital adjustment of individuals. The experimental and control group of this research was totally composed of 30 individuals. A pre-test post-test research model with control group was used in this…

  20. Determination of plant stanols and plant sterols in phytosterol enriched foods with a gas chromatographic-flame ionization detection method: NMKL collaborative study.

    PubMed

    Laakso, Päivi H

    2014-01-01

    This collaborative study with nine participating laboratories was conducted to determine the total plant sterol and/or plant stanol contents in phytosterol fortified foods with a gas chromatographic method. Four practice and 12 test samples representing mainly commercially available foodstuffs were analyzed as known replicates. Twelve samples were enriched with phytosterols, whereas four samples contained only natural contents of phytosterols. The analytical procedure consisted of two alternative approaches: hot saponification method, and acid hydrolysis treatment prior to hot saponification. As a result, sterol/stanol compositions and contents in the samples were measured. The amounts of total plant sterols and total plant stanols varying from 0.005 to 8.04 g/100 g product were statistically evaluated after outliers were eliminated. The repeatability RSD (RSDr) varied from 1.34 to 17.13%. The reproducibility RSD (RSDR) ranged from 3.03 to 17.70%, with HorRat values ranging from 0.8 to 2.1. When only phytosterol enriched food test samples are considered, the RSDr ranged from 1.48 to 6.13%, the RSD, ranged from 3.03 to 7.74%, and HorRat values ranged from 0.8 to 2.1. Based on the results of this collaborative study, the study coordinator concludes the method is fit for its purpose.

  1. Enrichment, amplification, and sequence-based typing of Salmonella enterica and other foodborne pathogens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Detection and characterization of foodborne pathogens typically involves microbiological enrichment with subsequent isolation and identification of a pure culture; this is ideally followed by strain typing which provides information critical to outbreak and source investigations. Pulsed-field gel e...

  2. An Independent Filter for Gene Set Testing Based on Spectral Enrichment.

    PubMed

    Frost, H Robert; Li, Zhigang; Asselbergs, Folkert W; Moore, Jason H

    2015-01-01

    Gene set testing has become an indispensable tool for the analysis of high-dimensional genomic data. An important motivation for testing gene sets, rather than individual genomic variables, is to improve statistical power by reducing the number of tested hypotheses. Given the dramatic growth in common gene set collections, however, testing is often performed with nearly as many gene sets as underlying genomic variables. To address the challenge to statistical power posed by large gene set collections, we have developed spectral gene set filtering (SGSF), a novel technique for independent filtering of gene set collections prior to gene set testing. The SGSF method uses as a filter statistic the p-value measuring the statistical significance of the association between each gene set and the sample principal components (PCs), taking into account the significance of the associated eigenvalues. Because this filter statistic is independent of standard gene set test statistics under the null hypothesis but dependent under the alternative, the proportion of enriched gene sets is increased without impacting the type I error rate. As shown using simulated and real gene expression data, the SGSF algorithm accurately filters gene sets unrelated to the experimental outcome resulting in significantly increased gene set testing power.

  3. Evaluation and comparison of rapid methods for the detection of Salmonella in naturally contaminated pine nuts using different pre enrichment media.

    PubMed

    Wang, Hua; Gill, Vikas S; Cheng, Chorng-Ming; Gonzalez-Escalona, Narjol; Irvin, Kari A; Zheng, Jie; Bell, Rebecca L; Jacobson, Andrew P; Hammack, Thomas S

    2015-04-01

    Foodborne outbreaks, involving pine nuts and peanut butter, illustrate the need to rapidly detect Salmonella in low moisture foods. However, the current Bacteriological Analytical Manual (BAM) culture method for Salmonella, using lactose broth (LB) as a pre enrichment medium, has not reliably supported real-time quantitative PCR (qPCR) assays for certain foods. We evaluated two qPCR assays in LB and four other pre enrichment media: buffered peptone water (BPW), modified BPW (mBPW), Universal Pre enrichment broth (UPB), and BAX(®) MP media to detect Salmonella in naturally-contaminated pine nuts (2011 outbreak). A four-way comparison among culture method, Pathatrix(®) Auto, VIDAS(®) Easy SLM, and qPCR was conducted. Automated DNA extraction techniques were compared with manual extraction methods (boiling or InstaGene™). There were no significant differences (P > 0.05) among the five pre enrichment media for pine nuts using the culture method. While both qPCR assays produced significantly (P ≤ 0.05) higher false negatives in 24 h pre enriched LB than in the other four media, they were as sensitive as the culture method in BPW, mBPW, UPB, and BAX media. The VIDAS Easy and qPCR were equivalent; Pathatrix was the least effective method. The Automatic PrepSEQ™ DNA extraction, using 1000 μL of pre enrichment, was as effective as manual extraction methods. PMID:25475267

  4. Evaluation and comparison of rapid methods for the detection of Salmonella in naturally contaminated pine nuts using different pre enrichment media.

    PubMed

    Wang, Hua; Gill, Vikas S; Cheng, Chorng-Ming; Gonzalez-Escalona, Narjol; Irvin, Kari A; Zheng, Jie; Bell, Rebecca L; Jacobson, Andrew P; Hammack, Thomas S

    2015-04-01

    Foodborne outbreaks, involving pine nuts and peanut butter, illustrate the need to rapidly detect Salmonella in low moisture foods. However, the current Bacteriological Analytical Manual (BAM) culture method for Salmonella, using lactose broth (LB) as a pre enrichment medium, has not reliably supported real-time quantitative PCR (qPCR) assays for certain foods. We evaluated two qPCR assays in LB and four other pre enrichment media: buffered peptone water (BPW), modified BPW (mBPW), Universal Pre enrichment broth (UPB), and BAX(®) MP media to detect Salmonella in naturally-contaminated pine nuts (2011 outbreak). A four-way comparison among culture method, Pathatrix(®) Auto, VIDAS(®) Easy SLM, and qPCR was conducted. Automated DNA extraction techniques were compared with manual extraction methods (boiling or InstaGene™). There were no significant differences (P > 0.05) among the five pre enrichment media for pine nuts using the culture method. While both qPCR assays produced significantly (P ≤ 0.05) higher false negatives in 24 h pre enriched LB than in the other four media, they were as sensitive as the culture method in BPW, mBPW, UPB, and BAX media. The VIDAS Easy and qPCR were equivalent; Pathatrix was the least effective method. The Automatic PrepSEQ™ DNA extraction, using 1000 μL of pre enrichment, was as effective as manual extraction methods.

  5. Combining auctions and performance-based payments in a forest enrichment field trial in Western Kenya.

    PubMed

    Khalumba, Mercelyne; Wünscher, Tobias; Wunder, Sven; Büdenbender, Mirjam; Holm-Müller, Karin

    2014-06-01

    Cost-effectiveness is an important aspect in the assessment of payments for environmental services (PES) initiatives. In participatory field trials with communities in Western Kenya, we combined procurement auctions for forest enrichment contracts with performance-based payments and compared the outcomes with a baseline scenario currently used by the Kenyan Forest Service. Procurement auctions were the most cost-effective. The competitive nature of the auction reduced contracting expenses (provision costs), and the result-oriented payments provided additional incentives to care for the planted seedlings, resulting in their improved survival rates (service quantity). These gains clearly exceeded increases in transaction costs associated with conducting an auction. The number of income-poor auction participants and winners was disproportionately high and local institutional buy-in was remarkably strong. Our participatory approach may, however, require adaptations when conducted at a larger scale. Although the number of contracts we monitored was limited and prohibited the use of statistical tests, our study is one of the first to reveal the benefits of using auctions for PES in developing countries.

  6. Zein based oil-in-glycerol emulgels enriched with β-carotene as margarine alternatives.

    PubMed

    Chen, Xiao-Wei; Fu, Shi-Yao; Hou, Jun-Jie; Guo, Jian; Wang, Jin-Mei; Yang, Xiao-Quan

    2016-11-15

    Structuring edible oils into solid lipids without saturated and trans fats has attracted increasing interest due to the benefits for human health and promises potential as novel delivery systems for lipophilic bioactive ingredients. The study shows that a zein stabilized high (ϕ=0.6) oil-in-glycerol (O/G) emulgels enriched with β-carotene was performed, by a facile one-step homogenization. Rheological measurements and morphologies observations indicated that increasing β-carotene resulted in a progressive strengthening of gel-like network and improving their spreadability in the O/G emulgels stabilized by zein, which was closely related to the hydrophobic interaction of zein and β-carotene. The formation of emulgels significantly enhanced the UV photo-stability of β-carotene, and more than 88% of β-carotene was retained in 64h storage under UV exposure, and consequently retarded oil oxidation while storage. Further, cakes prepared using zein-based O/G emulgels as a margarine alternative showed comparable functionalities (texture and sensory attributes) to the standard cake. PMID:27283703

  7. Inquiry-Based Science and Technology Enrichment Program for Middle School-Aged Female Students

    NASA Astrophysics Data System (ADS)

    Kim, Hanna

    2016-04-01

    This study investigates the effects of an intensive 1-week Inquiry-Based Science and Technology Enrichment Program (InSTEP) designed for middle school-aged female students. InSTEP uses a guided/open inquiry approach that is deepened and redefined as eight sciences and engineering practices in the Next Generation Science Standards, which aimed at increasing female students' interest in science and science-related careers. This study examined the effectiveness of InSTEP on 123 female students' pre-assessment and post-assessment changes in attitudes toward science and content knowledge of selected science concepts. An attitude survey, a science content test with multiple-choice questions, written assignments, and interviews to collect data were all used to measure students' attitudes and content knowledge. A within-group, repeated measure design was conducted, and the results indicated that at the post-intervention level, InSTEP increased the participants' positive attitudes toward science, science-related careers, and content knowledge of selected science concepts.

  8. Combining auctions and performance-based payments in a forest enrichment field trial in Western Kenya.

    PubMed

    Khalumba, Mercelyne; Wünscher, Tobias; Wunder, Sven; Büdenbender, Mirjam; Holm-Müller, Karin

    2014-06-01

    Cost-effectiveness is an important aspect in the assessment of payments for environmental services (PES) initiatives. In participatory field trials with communities in Western Kenya, we combined procurement auctions for forest enrichment contracts with performance-based payments and compared the outcomes with a baseline scenario currently used by the Kenyan Forest Service. Procurement auctions were the most cost-effective. The competitive nature of the auction reduced contracting expenses (provision costs), and the result-oriented payments provided additional incentives to care for the planted seedlings, resulting in their improved survival rates (service quantity). These gains clearly exceeded increases in transaction costs associated with conducting an auction. The number of income-poor auction participants and winners was disproportionately high and local institutional buy-in was remarkably strong. Our participatory approach may, however, require adaptations when conducted at a larger scale. Although the number of contracts we monitored was limited and prohibited the use of statistical tests, our study is one of the first to reveal the benefits of using auctions for PES in developing countries. PMID:24665907

  9. Assessment of adrenocortical activity and behavior of the collared anteater (Tamandua tetradactyla) in response to food-based environmental enrichment.

    PubMed

    Eguizábal, Gabina V; Palme, Rupert; Villarreal, Daniel; Dal Borgo, Carla; Di Rienzo, Julio A; Busso, Juan M

    2013-01-01

    One of the current standard approaches to the study of animal welfare is measuring hypothalamic-pituitary-adrenal activity, frequently in association with behavioral assessment. We studied the effects of food-based environmental enrichment on adrenocortical activity and behavior in zoo-housed collared anteaters (Tamandua tetradactyla; n = 5). We successfully validated measurements of fecal cortisol metabolites (FCMs) using an 11-oxoetiocholanolone enzyme immunoassay by stimulating (ACTH injection) and suppressing (dexamethasone administration) adrenocortical activity. Three months later, we subjected animals to an ABA-type experiment (three 6-week periods): pre-enrichment (routine diet: A), enrichment (modified diet: B), and post-enrichment (routine diet: A) periods. We assessed adrenocortical activity by collecting individual feces three times a week (total number of samples: 228), and evaluated behavior by performing 3 days of behavioral observations per period (with a total of 3,600 behavioral data points for the individuals studied). Statistical analysis revealed changes in FCM concentrations (µg/g) over the periods (3.04 ± 0.68, 2.98 ± 0.66, and 4.04 ± 0.90, respectively). Additionally, it showed that the number of FCM peaks was highly reduced during enrichment; meanwhile active natural behaviors were significantly increased. We consider that these changes in response to food-based environmental enrichment improved the welfare of individual zoo-housed collared anteaters. This research might contribute to in situ and ex situ studies on the physiology and behavior of this endemic South American species. PMID:24307059

  10. Assessment of adrenocortical activity and behavior of the collared anteater (Tamandua tetradactyla) in response to food-based environmental enrichment.

    PubMed

    Eguizábal, Gabina V; Palme, Rupert; Villarreal, Daniel; Dal Borgo, Carla; Di Rienzo, Julio A; Busso, Juan M

    2013-01-01

    One of the current standard approaches to the study of animal welfare is measuring hypothalamic-pituitary-adrenal activity, frequently in association with behavioral assessment. We studied the effects of food-based environmental enrichment on adrenocortical activity and behavior in zoo-housed collared anteaters (Tamandua tetradactyla; n = 5). We successfully validated measurements of fecal cortisol metabolites (FCMs) using an 11-oxoetiocholanolone enzyme immunoassay by stimulating (ACTH injection) and suppressing (dexamethasone administration) adrenocortical activity. Three months later, we subjected animals to an ABA-type experiment (three 6-week periods): pre-enrichment (routine diet: A), enrichment (modified diet: B), and post-enrichment (routine diet: A) periods. We assessed adrenocortical activity by collecting individual feces three times a week (total number of samples: 228), and evaluated behavior by performing 3 days of behavioral observations per period (with a total of 3,600 behavioral data points for the individuals studied). Statistical analysis revealed changes in FCM concentrations (µg/g) over the periods (3.04 ± 0.68, 2.98 ± 0.66, and 4.04 ± 0.90, respectively). Additionally, it showed that the number of FCM peaks was highly reduced during enrichment; meanwhile active natural behaviors were significantly increased. We consider that these changes in response to food-based environmental enrichment improved the welfare of individual zoo-housed collared anteaters. This research might contribute to in situ and ex situ studies on the physiology and behavior of this endemic South American species.

  11. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylat...

  12. Laser and gas centrifuge enrichment

    NASA Astrophysics Data System (ADS)

    Heinonen, Olli

    2014-05-01

    Principles of uranium isotope enrichment using various laser and gas centrifuge techniques are briefly discussed. Examples on production of high enriched uranium are given. Concerns regarding the possibility of using low end technologies to produce weapons grade uranium are explained. Based on current assessments commercial enrichment services are able to cover the global needs of enriched uranium in the foreseeable future.

  13. Laser and gas centrifuge enrichment

    SciTech Connect

    Heinonen, Olli

    2014-05-09

    Principles of uranium isotope enrichment using various laser and gas centrifuge techniques are briefly discussed. Examples on production of high enriched uranium are given. Concerns regarding the possibility of using low end technologies to produce weapons grade uranium are explained. Based on current assessments commercial enrichment services are able to cover the global needs of enriched uranium in the foreseeable future.

  14. A new virus discovered by immunocapture of double-stranded RNA, a rapid method for virus enrichment in metagenomic studies.

    PubMed

    Blouin, Arnaud G; Ross, Howard A; Hobson-Peters, Jody; O'Brien, Caitlin A; Warren, Ben; MacDiarmid, Robin

    2016-09-01

    Next-generation sequencing technologies enable the rapid identification of viral infection of diseased organisms. However, despite a consistent decrease in sequencing costs, it is difficult to justify their use in large-scale surveys without a virus sequence enrichment technique. As the majority of plant viruses have an RNA genome, a common approach is to extract the double-stranded RNA (dsRNA) replicative form, to enrich the replicating virus genetic material over the host background. The traditional dsRNA extraction is time-consuming and labour-intensive. We present an alternative method to enrich dsRNA from plant extracts using anti-dsRNA monoclonal antibodies in a pull-down assay. The extracted dsRNA can be amplified by reverse transcriptase-polymerase chain reaction and sequenced by next-generation sequencing. In our study, we have selected three distinct plant hosts: Māori potato (Solanum tuberosum), rengarenga (Arthropodium cirratum) and broadleaved dock (Rumex obtusifolius) representing a cultivated crop, a New Zealand-native ornamental plant and a weed, respectively. Of the sequence data obtained, 31-74% of the reads were of viral origin, and we identified five viruses including Potato virus Y and Potato virus S in potato; Turnip mosaic virus in rengarenga (a new host record); and in the dock sample Cherry leaf roll virus and a novel virus belonging to the genus Macluravirus. We believe that this new assay represents a significant opportunity to upscale virus ecology studies from environmental, primary industry and/or medical samples. PMID:26990372

  15. A new virus discovered by immunocapture of double-stranded RNA, a rapid method for virus enrichment in metagenomic studies.

    PubMed

    Blouin, Arnaud G; Ross, Howard A; Hobson-Peters, Jody; O'Brien, Caitlin A; Warren, Ben; MacDiarmid, Robin

    2016-09-01

    Next-generation sequencing technologies enable the rapid identification of viral infection of diseased organisms. However, despite a consistent decrease in sequencing costs, it is difficult to justify their use in large-scale surveys without a virus sequence enrichment technique. As the majority of plant viruses have an RNA genome, a common approach is to extract the double-stranded RNA (dsRNA) replicative form, to enrich the replicating virus genetic material over the host background. The traditional dsRNA extraction is time-consuming and labour-intensive. We present an alternative method to enrich dsRNA from plant extracts using anti-dsRNA monoclonal antibodies in a pull-down assay. The extracted dsRNA can be amplified by reverse transcriptase-polymerase chain reaction and sequenced by next-generation sequencing. In our study, we have selected three distinct plant hosts: Māori potato (Solanum tuberosum), rengarenga (Arthropodium cirratum) and broadleaved dock (Rumex obtusifolius) representing a cultivated crop, a New Zealand-native ornamental plant and a weed, respectively. Of the sequence data obtained, 31-74% of the reads were of viral origin, and we identified five viruses including Potato virus Y and Potato virus S in potato; Turnip mosaic virus in rengarenga (a new host record); and in the dock sample Cherry leaf roll virus and a novel virus belonging to the genus Macluravirus. We believe that this new assay represents a significant opportunity to upscale virus ecology studies from environmental, primary industry and/or medical samples.

  16. RNA Enrichment Method for Quantitative Transcriptional Analysis of Pathogens In Vivo Applied to the Fungus Candida albicans

    PubMed Central

    Amorim-Vaz, Sara; Tran, Van Du T.; Pradervand, Sylvain; Pagni, Marco; Coste, Alix T.

    2015-01-01

    ABSTRACT In vivo transcriptional analyses of microbial pathogens are often hampered by low proportions of pathogen biomass in host organs, hindering the coverage of full pathogen transcriptome. We aimed to address the transcriptome profiles of Candida albicans, the most prevalent fungal pathogen in systemically infected immunocompromised patients, during systemic infection in different hosts. We developed a strategy for high-resolution quantitative analysis of the C. albicans transcriptome directly from early and late stages of systemic infection in two different host models, mouse and the insect Galleria mellonella. Our results show that transcriptome sequencing (RNA-seq) libraries were enriched for fungal transcripts up to 1,600-fold using biotinylated bait probes to capture C. albicans sequences. This enrichment biased the read counts of only ~3% of the genes, which can be identified and removed based on a priori criteria. This allowed an unprecedented resolution of C. albicans transcriptome in vivo, with detection of over 86% of its genes. The transcriptional response of the fungus was surprisingly similar during infection of the two hosts and at the two time points, although some host- and time point-specific genes could be identified. Genes that were highly induced during infection were involved, for instance, in stress response, adhesion, iron acquisition, and biofilm formation. Of the in vivo-regulated genes, 10% are still of unknown function, and their future study will be of great interest. The fungal RNA enrichment procedure used here will help a better characterization of the C. albicans response in infected hosts and may be applied to other microbial pathogens. PMID:26396240

  17. Improved accountability method for measuring enriched uranium in H-Canyon dissolver solution at the Savannah River Site

    SciTech Connect

    Maxwell, S.L. III; Satkowski, J.; Mahannah, R.N.

    1992-01-01

    At the Savannah River Site (SRS), accountability measurement of enriched uranium dissolved in H-Canyon is performed using isotope dilution mass spectrometry (IDMS). In the IDMS analytical method, a known quantity of uranium{sup 233} is added to the sample solution containing enriched uranium and fission products. The resulting uranium mixture must first be purified using a separation technique in the shielded analytical( hot'') cells to lower radioactivity levels by removing fission products. Following this purification, the sample is analyzed by mass spectrometry to determine the total uranium content and isotopic abundance. The magnitude of the response of each uranium isotope in the sample solution and the response of the U{sup 233} spike is measured. By ratioing these responses, relative to the known quantity of the U{sup 233} spike, the uranium content can be determined. A hexane solvent extraction technique, used for years at SRS to remove fission products prior to the mass spectrometry analysis of uranium, has several problems. The hexone method is tedious, requires additional sample clean-up after the purified sample is removed from the shielded cells and requires the use of Resource Conservation and Recovery Act (RCRA)-listed hazardous materials (hexone and chromium compounds). A new high speed separation method that enables a rapid removal of fission products in a shielded cells environment has been developed by the SRS Central Laboratory to replace the hexone method. The new high speed column extraction chromatography technique employs applied vacuum and columns containing tri (2-ethyl-hexyl) phosphate (TEHP) solvent coated on a small particle inert support (SM-7 Bio Beads). The new separation is rapid, user friendly, eliminates the use of the RCA-listed hazardous chemicals and reduces the amount of solid waste generated by the separation method. 2 tabs. 4 figs.

  18. Improved accountability method for measuring enriched uranium in H-Canyon dissolver solution at the Savannah River Site

    SciTech Connect

    Maxwell, S.L. III; Satkowski, J.; Mahannah, R.N.

    1992-08-01

    At the Savannah River Site (SRS), accountability measurement of enriched uranium dissolved in H-Canyon is performed using isotope dilution mass spectrometry (IDMS). In the IDMS analytical method, a known quantity of uranium{sup 233} is added to the sample solution containing enriched uranium and fission products. The resulting uranium mixture must first be purified using a separation technique in the shielded analytical(``hot``) cells to lower radioactivity levels by removing fission products. Following this purification, the sample is analyzed by mass spectrometry to determine the total uranium content and isotopic abundance. The magnitude of the response of each uranium isotope in the sample solution and the response of the U{sup 233} spike is measured. By ratioing these responses, relative to the known quantity of the U{sup 233} spike, the uranium content can be determined. A hexane solvent extraction technique, used for years at SRS to remove fission products prior to the mass spectrometry analysis of uranium, has several problems. The hexone method is tedious, requires additional sample clean-up after the purified sample is removed from the shielded cells and requires the use of Resource Conservation and Recovery Act (RCRA)-listed hazardous materials (hexone and chromium compounds). A new high speed separation method that enables a rapid removal of fission products in a shielded cells environment has been developed by the SRS Central Laboratory to replace the hexone method. The new high speed column extraction chromatography technique employs applied vacuum and columns containing tri (2-ethyl-hexyl) phosphate (TEHP) solvent coated on a small particle inert support (SM-7 Bio Beads). The new separation is rapid, user friendly, eliminates the use of the RCA-listed hazardous chemicals and reduces the amount of solid waste generated by the separation method. 2 tabs. 4 figs.

  19. Enchytraeus albidus Microarray: Enrichment, Design, Annotation and Database (EnchyBASE)

    PubMed Central

    Novais, Sara C.; Arrais, Joel; Lopes, Pedro; Vandenbrouck, Tine; De Coen, Wim; Roelofs, Dick; Soares, Amadeu M. V. M.; Amorim, Mónica J. B.

    2012-01-01

    Enchytraeus albidus (Oligochaeta) is an ecologically relevant species used as standard test organisms for risk assessment. Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints. The assessment of transcriptomic responses can be very useful e.g. to understand underlying mechanisms of toxicity with gene expression fingerprinting. In the present paper the following is being addressed: 1) development of suppressive subtractive hybridization (SSH) libraries enriched for differentially expressed genes after metal and pesticide exposures; 2) sequencing and characterization of all generated cDNA inserts; 3) development of a publicly available genomic database on E. albidus. A total of 2100 Expressed Sequence Tags (ESTs) were isolated, sequenced and assembled into 1124 clusters (947 singletons and 177 contigs). From these sequences, 41% matched known proteins in GenBank (BLASTX, e-value≤10-5) and 37% had at least one Gene Ontology (GO) term assigned. In total, 5.5% of the sequences were assigned to a metabolic pathway, based on KEGG. With this new sequencing information, an Agilent custom oligonucleotide microarray was designed, representing a potential tool for transcriptomic studies. EnchyBASE (http://bioinformatics.ua.pt/enchybase/) was developed as a web freely available database containing genomic information on E. albidus and will be further extended in the near future for other enchytraeid species. The database so far includes all ESTs generated for E. albidus from three cDNA libraries. This information can be downloaded and applied in functional genomics and transcription studies. PMID:22558086

  20. Frequency of Salmonella and Listeria monocytogenes in five commercial brands of chicken eggs using a combined method of enrichment and nested-PCR.

    PubMed

    Guzmán-Gómez, Gerardo; Ayala Valdovinos, Miguel A; Cabrera-Díaz, Elisa; Pérez-Montaño, Julia A; Muñoz-Valle, José Francisco; Torres-Vitela, M R; Ruiz-Quezada, Sandra L

    2013-03-01

    Eggs or egg-based foods, either raw or undercooked, have been identified as vehicles of Salmonella outbreaks. The low numbers of Salmonella organisms in eggs makes it difficult to detect them in frequency studies. The nested-PCR (n-PCR) technique shows more sensitivity and specificity than bacteriological culture methods (BCMs). A preenrichment method followed by enrichment and n-PCR is a good alternative for the investigation of Salmonella and Listeria monocytogenes in eggs. A total of 2,650 chicken eggs representing five commercial brands were purchased from 10 grocery stores. Ten eggs of each brand were combined in order to obtain 265 pooled samples (53 per brand). The shells and yolks of 100 pooled samples were analyzed for Salmonella, while the shells of 65 pooled samples were analyzed for L. monocytogenes, using BCM and a combined method of enrichment and n-PCR (CM-n-PCR). Sixteen eggshell pooled samples tested positive for Salmonella by CM-n-PCR, compared with only two by BCM. Three egg yolk pooled samples tested positive for this pathogen by CM-n-PCR; none tested positive by BCM. Three eggshell pooled samples tested positive for L. monocytogenes by CM-n-PCR and none by BCM. In Mexico, as in other countries, official methods for detection of Salmonella and L. monocytogenes in foods are based on standard bacteriological culture techniques. The inclusion of more sensitive methods such as the one used in the present investigation would increase the probability of detecting positive samples, particularly in those foods in which a very low number of cells is expected. PMID:23462079

  1. Circulating tumour cells: the evolving concept and the inadequacy of their enrichment by EpCAM-based methodology for basic and clinical cancer research.

    PubMed

    Grover, P K; Cummins, A G; Price, T J; Roberts-Thomson, I C; Hardingham, J E

    2014-08-01

    Increasing evidence suggests that circulating tumour cells (CTCs) are responsible for metastatic relapse and this has fuelled interest in their detection and quantification. Although numerous methods have been developed for the enrichment and detection of CTCs, none has yet reached the 'gold' standard. Since epithelial cell adhesion molecule (EpCAM)-based enrichment of CTCs offers several advantages, it is one of the most commonly used and has been adapted for high-throughput technology. However, emerging evidence suggests that CTCs are highly heterogeneous: they consist of epithelial tumour cells, epithelial-to-mesenchymal transition (EMT) cells, hybrid (epithelial/EMT(+)) tumour cells, irreversible EMT(+) tumour cells, and circulating tumour stem cells (CTSCs). The EpCAM-based approach does not detect CTCs expressing low levels of EpCAM and non-epithelial phenotypes such as CTSCs and those that have undergone EMT and no longer express EpCAM. Thus, the approach may lead to underestimation of the significance of CTCs, in general, and CTSCs and EMT(+) tumour cells, in particular, in cancer dissemination. Here, we provide a critical review of research literature on the evolving concept of CTCs and the inadequacy of their enrichment by EpCAM-based technology for basic and clinical cancer research. The review also outlines future perspectives in the field.

  2. Click Synthesis of Hydrophilic Maltose-Functionalized Iron Oxide Magnetic Nanoparticles Based on Dopamine Anchors for Highly Selective Enrichment of Glycopeptides.

    PubMed

    Bi, Changfen; Zhao, Yingran; Shen, Lijin; Zhang, Kai; He, Xiwen; Chen, Langxing; Zhang, Yukui

    2015-11-11

    The development of methods to isolate and enrich low-abundance glycopeptides from biological samples is crucial to glycoproteomics. Herein, we present an easy and one-step surface modification strategy to prepare hydrophilic maltose functionalized Fe3O4 nanoparticles (NPs). First, based on the chelation of the catechol ligand with iron atoms, azido-terminated dopamine (DA) derivative was assembled on the surface of magnetic Fe3O4 nanoparticles by sonication. Second, the hydrophilic maltose-functionalized Fe3O4 (Fe3O4-DA-Maltose) NPs were obtained via copper(I)-catalyzed azide-alkyne cycloaddition (click chemistry). The morphology, structure, and composition of Fe3O4-DA-Maltose NPs were investigated by Fourier transform infrared spectroscopy (FT-IR), transmission electron microscopy (TEM), X-ray powder diffraction (XRD), X-ray photoelectron spectrometer (XPS), and vibrating sample magnetometer (VSM). Meanwhile, hydrophilicity of the obtained NPs was evaluated by water contact angle measurement. The hydrophilic Fe3O4-DA-Maltose NPs were applied in isolation and enrichment of glycopeptides from horseradish peroxidase (HRP), immunoglobulin (IgG) digests. The MALDI-TOF mass spectrometric analysis indicated that the novel NPs exhibited high detection sensitivity in enrichment from HRP digests at concentration as low as 0.05 ng μL(-1), a large binding capacity up to 43 mg g(-1), and good recovery for glycopeptides enrichment (85-110%). Moreover, the Fe3O4-DA-Maltose NPs were applied to enrich glycopeptides from human renal mesangial cells (HRMC) for identification of N-glycosylation sites. Finally, we identified 115 different N-linked glycopeptides, representing 93 gene products and 124 glycosylation sites in HRMC.

  3. A modified method by differential adhesion for enrichment of bladder cancer stem cells

    PubMed Central

    Zhu, Yong-tong; Pang, Shi-yu; Luo, Yang; Chen, Wei; Bao, Ji-ming; Tan, Wan-long

    2016-01-01

    ABSTRACT Purpose: In a previous study the vaccine was effective against bladder cancer in a mouse model. However, a small portion of tumors regrew because the vaccine could not eliminate bladder cancer stem cells (CSCs). In this study, we showed a modified method for the isolation of bladder CSCs using a combination of differential adhesion method and serum-free culture medium (SFM) method. Materials and Methods: Trypsin-resistant cells and trypsin-sensitive cells were isolated from MB49, EJ and 5637 cells by a combination of differential adhesion method and SFM method. The CSCs characterizations of trypsin-resistant cells were verified by the flow cytometry, the western blotting, the quantitative polymerase chain reaction, the resistance to chemotherapy assay, the transwell assay, and the tumor xenograft formation assay. Results: Trypsin-resistant cells were isolated and identified in CSCs characters, with high expression of CSCs markers, higher resistance to chemotherapy, greater migration in vitro, and stronger tumorigenicity in vivo. Conclusion: Trypsin-resistant cells displayed specific CSCs properties. Our study showed trypsin-resistant cells were isolated successfully with a modified method using a combination of differential adhesion method and SFM method. PMID:27564296

  4. Comparison of CF4 and SF6 based plasmas for ECR etching of isotopically enriched 10Boron films

    SciTech Connect

    Voss, L F; Reinhardt, C E; Graff, R T; Conway, A M; Nikolic, R J; Deo, N; Cheung, C L

    2009-02-23

    Isotopically enriched {sup 10}boron films have been successfully etched in an ECR etching tool using CF{sub 4} and SF{sub 6} based plasmas. Comparisons between the two are made with regards to etch rate, selectivity to the underlying Si device structure, and morphology of the {sup 10}boron post-etching. The present film etching development is expected to be critical for the fabrication of next generation thermal neutron solid state detectors based on {sup 10}boron.

  5. Qualitative Methods Can Enrich Quantitative Research on Occupational Stress: An Example from One Occupational Group

    ERIC Educational Resources Information Center

    Schonfeld, Irvin Sam; Farrell, Edwin

    2010-01-01

    The chapter examines the ways in which qualitative and quantitative methods support each other in research on occupational stress. Qualitative methods include eliciting from workers unconstrained descriptions of work experiences, careful first-hand observations of the workplace, and participant-observers describing "from the inside" a particular…

  6. Method of controlling the mercury vapor pressure in a photo-chemical lamp or vapor filter used for Hg[sup 196] enrichment

    DOEpatents

    Grossman, M.W.

    1993-02-16

    The present invention is directed to a method of eliminating the cold spot zones presently used on Hg[sup 196] isotope separation lamps and filters by the use of a mercury amalgams, preferably mercury - indium amalgams. The use of an amalgam affords optimization of the mercury density in the lamp and filter of a mercury enrichment reactor, particularly multilamp enrichment reactors. Moreover, the use of an amalgam in such lamps and/or filters affords the ability to control the spectral line width of radiation emitted from lamps, a requirement for mercury enrichment.

  7. Method of controlling the mercury vapor pressure in a photo-chemical lamp or vapor filter used for Hg.sup.196 enrichment

    DOEpatents

    Grossman, Mark W.

    1993-01-01

    The present invention is directed to a method of eliminating the cold spot zones presently used on Hg.sup.196 isotope separation lamps and filters by the use of a mercury amalgams, preferably mercury - indium amalgams. The use of an amalgam affords optimization of the mercury density in the lamp and filter of a mercury enrichment reactor, particularly multilamp enrichment reactors. Moreover, the use of an amalgam in such lamps and/or filters affords the ability to control the spectral line width of radiation emitted from lamps, a requirement for mercury enrichment.

  8. A novel method for the multiplexed target enrichment of MinION next generation sequencing libraries using PCR-generated baits.

    PubMed

    Karamitros, Timokratis; Magiorkinis, Gkikas

    2015-12-15

    The enrichment of targeted regions within complex next generation sequencing libraries commonly uses biotinylated baits to capture the desired sequences. This method results in high read coverage over the targets and their flanking regions. Oxford Nanopore Technologies recently released an USB3.0-interfaced sequencer, the MinION. To date no particular method for enriching MinION libraries has been standardized. Here, using biotinylated PCR-generated baits in a novel approach, we describe a simple and efficient way for multiplexed enrichment of MinION libraries, overcoming technical limitations related with the chemistry of the sequencing-adapters and the length of the DNA fragments. Using Phage Lambda and Escherichia coli as models we selectively enrich for specific targets, significantly increasing the corresponding read-coverage, eliminating unwanted regions. We show that by capturing genomic fragments, which contain the target sequences, we recover reads extending targeted regions and thus can be used for the determination of potentially unknown flanking sequences. By pooling enriched libraries derived from two distinct E. coli strains and analyzing them in parallel, we demonstrate the efficiency of this method in multiplexed format. Crucially we evaluated the optimal bait size for large fragment libraries and we describe for the first time a standardized method for target enrichment in MinION platform.

  9. Test methods for determining the suitability of metal alloys for use in oxygen-enriched environments

    NASA Technical Reports Server (NTRS)

    Stoltzfus, Joel M.; Gunaji, Mohan V.

    1991-01-01

    Materials are more flammable in oxygen rich environments than in air. When the structural elements of a system containing oxygen ignite and burn, the results are often catastrophic, causing loss of equipment and perhaps even human lives. Therefore, selection of the proper metallic and non-metallic materials for use in oxygen systems is extremely important. While test methods for the selection of non-metallic materials have been available for years, test methods for the selection of alloys have not been available until recently. Presented here are several test methods that were developed recently at NASA's White Sands Test Facility (WSTF) to study the ignition and combustion of alloys, including the supersonic and subsonic speed particle impact tests, the frictional heating and coefficient of friction tests, and the promoted combustion test. These test methods are available for commercial use.

  10. The Impact of a Cryogenics-Based Enrichment Programme on Attitude Towards Science and the Learning of Science Concepts. Research Report

    ERIC Educational Resources Information Center

    Caleon, Imelda; Subramaniam, R.

    2005-01-01

    This study explores the impact of a cryogenics-based enrichment programme, which involves demonstrations that use liquid nitrogen, on attitudes towards science and the learning of science concepts. The findings presented in this paper are based on a sample of 214 fifth-grade students from two schools in Singapore who had their enrichment lesson in…

  11. Amine Chemistry Method for Selective Enrichment of N-Linked Glycopeptides for Glycoproteomics Analysis.

    PubMed

    Zhang, Zhang; Sun, Deguang; Cong, Yuting; Mao, Jiawei; Huang, Junfeng; Qin, Hongqiang; Liu, Jing; Huang, Guang; Wang, Liming; Ye, Mingliang; Zou, Hanfa

    2015-09-01

    An amine chemistry method was developed for the extraction of N-glycopeptides using amine-functionalized beads for glycoproteomics analysis. Two reductive amination reactions between primary amine and aldehyde were employed in this approach. The first one was to block the primary amines in the peptides by addition of formaldehyde and sodium cyanoborohydride into the peptide sample, and the second one was to couple the glycopeptides onto solid phase beads by incubating the glycopeptides containing aldehyde groups (oxidized by periodate) with the amine-functionalized beads in the presence of sodium cyanoborohydride. It was demonstrated that the blocking of primary amines in the peptides by the first reductive amination reaction prior to the periodate oxidation made the amine chemistry method very efficient and sensitive. This new method was validated by analysis of glycoprotein standards as well as proteome samples. It was found that this new method led to significant increase in the identification of N-glycosites compared with the conventional hydrazide chemistry method.

  12. Oxidized dextran facilitated synthesis of a silica-based concanavalin a material for lectin affinity enrichment of glycoproteins/glycopeptides.

    PubMed

    Liu, Yujie; Fu, Dongmei; Yu, Long; Xiao, Yuansheng; Peng, Xiaojun; Liang, Xinmiao

    2016-07-15

    Lectin affinity chromatography (LAC) is an important enrichment technique in glycoproteomics analysis. In order to improve the effectiveness of enrichment, it is necessary to develop LAC materials with high specificity and efficiency. Herein, using oxidized dextran as the spacer, a silica-based concanavalin A material (SiO2-ODex Con A) was synthesized to enrich glycoproteins/glycopeptides. For comparison, the SiO2-Ald Con A material was synthesized using conventional (3-glycidoxypropyl) triethoxysilane (GPMS) as the initial spacer arm. The analytical merits of both Con A materials, such as non-specific adsorption, binding capacity and trapping efficiency, have been evaluated using ovalbumin. Under high performance liquid affinity chromatography (HPLAC) mode, the SiO2-ODex Con A material was highly effective in the enrichment of glycoproteins/glycopeptides attached to high-mannose-type and bi-antennary complex-type glycans. The promising potential of the SiO2-ODex Con A material was demonstrated by selective fractionation of glycoproteins from complex biological samples for glycosylation analysis.

  13. Replacements of rare herbs and simplifications of traditional chinese medicine formulae based on attribute similarities and pathway enrichment analysis.

    PubMed

    Fang, Zhao; Zhang, Meixia; Yi, Zhenghui; Wen, Chengping; Qian, Min; Shi, Tieliu

    2013-01-01

    A Traditional Chinese Medicine (TCM) formula is a collection of several herbs. TCM formulae have been used to treat various diseases for several thousand years. However, wide usage of TCM formulae has results in rapid decline of some rare herbs. So it is urgent to find common available replacements for those rare herbs with the similar effects. In addition, a formula can be simplified by reducing herbs with unchanged effects. Based on this consideration, we propose a method, called "formula pair," to replace the rare herbs and simplify TCM formulae. We show its reasonableness from a perspective of pathway enrichment analysis. Both the replacements of rare herbs and simplifications of formulae provide new approaches for a new formula discovery. We demonstrate our approach by replacing a rare herb "Forsythia suspensa" in the formula "the seventh of Sang Ju Yin plus/minus herbs (SSJY)" with a common herb "Thunberg Fritillary Bulb" and simplifying two formulae, "the fifth of Du Huo Ji Sheng Tang plus/minus herbs (FDHJST)" and "Fang Feng Tang" (FFT) to a new formula "Fang Feng Du Huo Tang" (FFDHT).

  14. An Effectiveness Study of a Culturally Enriched School-Based CBT Anxiety Prevention Program

    ERIC Educational Resources Information Center

    Miller, Lynn D.; Laye-Gindhu, Aviva; Bennett, Joanna L.; Liu, Yan; Gold, Stephenie; March, John S.; Olson, Brent F.; Waechtler, Vanessa E.

    2011-01-01

    Anxiety disorders are prevalent in the school-aged population and are present across cultural groups. Scant research exists on culturally relevant prevention and intervention programs for mental health problems in the Aboriginal populations. An established cognitive behavioral program, FRIENDS for Life, was enriched to include content that was…

  15. twzPEA: A Topology and Working Zone Based Pathway Enrichment Analysis Framework

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sensitive detection of involvement and adaptation of key signaling, regulatory, and metabolic pathways holds the key to deciphering molecular mechanisms such as those in the biomass-to-biofuel conversion process in yeast. Typical gene set enrichment analyses often do not use topology information in...

  16. Literature-Based Social Studies: Children's Books & Activities To Enrich the K-5 Curriculum.

    ERIC Educational Resources Information Center

    Laughlin, Mildred Knight; Kardaleff, Patricia Payne

    Ideas for using children's literature suggest ways to extend and enrich the elementary school social studies curriculum beyond the adopted textbook or scope and sequence developed in a local school district or at the state level. The focus of kindergarten through grade three is the study of family and communities and the acquisition of individual…

  17. Method of synthesizing enriched decaborane for use in generating boron neutron capture therapy pharmaceuticals

    DOEpatents

    Cowan, Robert L.; Ginosar, Daniel M.; Dunks, Gary B.

    2000-01-01

    A method is described for synthesizing decaborane wherein at least about 90% of the boron atoms in the decaborane are the .sup.10 B isotope, comprising the steps of: (a) reacting boric acid with a C.sub.1 to C.sub.10 alkanol to form a .sup.10 B-alkyl borate wherein at least about 90% of the boron atoms in the boric acid are the .sup.10 B isotope; (b) reducing the .sup.10 B-alkyl borate to form an alkali metal .sup.10 B-borohydride; (c) converting the alkali metal .sup.10 B-borohydride to a .sup.10 B-tetradecahydroundecaborate ion; and (d) converting the .sup.10 B-tetradecahydroundecaborate ion to .sup.10 B-decaborane. Methods of preparing tetradecahydroundecaborate ions and decaborane from alkali metal borohydrides are also described.

  18. Use of a Microcomputer-Based Simulation to Enrich Teacher Training.

    ERIC Educational Resources Information Center

    Loper, Ann Booker; And Others

    Designed to provide teacher-trainees with practice before entering a real classroom, a microcomputer-based simulation of classroom interaction became a key component in the curriculum of two introductory methods courses offered at the University of Virginia. Twenty-two participants used IBM-PC equipment to complete two skill modules. Each module…

  19. Selection Based on Indirect Genetic Effects for Growth, Environmental Enrichment and Coping Style Affect the Immune Status of Pigs

    PubMed Central

    Reimert, Inonge; Rodenburg, T. Bas; Ursinus, Winanda W.; Kemp, Bas; Bolhuis, J. Elizabeth

    2014-01-01

    Pigs living in intensive husbandry systems may experience both acute and chronic stress through standard management procedures and limitations in their physical and social environment, which may have implications for their immune status. Here, the effect of a new breeding method where pigs were selected on their heritable influence on their pen mates' growth, and environmental enrichment on the immune status of pigs was investigated. Hereto, 240 pigs with a relatively positive genetic effect on the growth of their pen mates (+SBV) and 240 pigs with a relatively negative genetic effect on the growth of their pen mates (−SBV) were housed in barren or straw-enriched pens from 4 to 23 weeks of age (n  =  80 pens in total). A blood sample was taken from the pigs before, three days after a 24 h regrouping test, and at week 22. In addition, effects of coping style, as assessed in a backtest, and gender were also investigated. Mainly, +SBV were found to have lower leukocyte, lymphocyte and haptoglobin concentrations than -SBV pigs. Enriched housed pigs had a lower neutrophil to lymphocyte (N:L) ratio and lower haptoglobin concentrations, but had higher antibody titers specific for Keyhole Limpet Hemocyanin (KLH) than barren housed pigs. No interactions were found between SBV class and housing. Furthermore, pigs with a proactive coping style had higher alternative complement activity and, in the enriched pens, higher antibody titers specific for KLH than pigs with a reactive coping style. Lastly, females tended to have lower leukocyte, but higher haptoglobin concentrations than castrated males. Overall, these results suggest that +SBV pigs and enriched housed pigs were less affected by stress than -SBV and barren housed pigs, respectively. Moreover, immune activation might be differently organized in individuals with different coping styles and to a lesser extent in individuals of opposite genders. PMID:25275507

  20. Compton DIV: Using a Compton-Based Gamma-Ray Imager for Design Information Verification of Uranium Enrichment Plants

    SciTech Connect

    Burks, M; Verbeke, J; Dougan, A; Wang, T; Decman, D

    2009-07-04

    A feasibility study has been performed to determine the potential usefulness of Compton imaging as a tool for design information verification (DIV) of uranium enrichment plants. Compton imaging is a method of gamma-ray imaging capable of imaging with a 360-degree field of view over a broad range of energies. These systems can image a room (with a time span on the order of one hour) and return a picture of the distribution and composition of radioactive material in that room. The effectiveness of Compton imaging depends on the sensitivity and resolution of the instrument as well the strength and energy of the radioactive material to be imaged. This study combined measurements and simulations to examine the specific issue of UF{sub 6} gas flow in pipes, at various enrichment levels, as well as hold-up resulting from the accumulation of enriched material in those pipes. It was found that current generation imagers could image pipes carrying UF{sub 6} in less than one hour at moderate to high enrichment. Pipes with low enriched gas would require more time. It was also found that hold-up was more amenable to this technique and could be imaged in gram quantities in a fraction of an hour. another questions arises regarding the ability to separately image two pipes spaced closely together. This depends on the capabilities of the instrument in question. These results are described in detail. In addition, suggestions are given as to how to develop Compton imaging as a tool for DIV.

  1. Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data

    PubMed Central

    Kawakami, Eiryo; Nakaoka, Shinji; Ohta, Tazro; Kitano, Hiroaki

    2016-01-01

    Predicting responsible transcription regulators on the basis of transcriptome data is one of the most promising computational approaches to understanding cellular processes and characteristics. Here, we present a novel method employing vast amounts of chromatin immunoprecipitation (ChIP) experimental data to address this issue. Global high-throughput ChIP data was collected to construct a comprehensive database, containing 8 578 738 binding interactions of 454 transcription regulators. To incorporate information about heterogeneous frequencies of transcription factor (TF)-binding events, we developed a flexible framework for gene set analysis employing the weighted t-test procedure, namely weighted parametric gene set analysis (wPGSA). Using transcriptome data as an input, wPGSA predicts the activities of transcription regulators responsible for observed gene expression. Validation of wPGSA with published transcriptome data, including that from over-expressed TFs, showed that the method can predict activities of various TFs, regardless of cell type and conditions, with results totally consistent with biological observations. We also applied wPGSA to other published transcriptome data and identified potential key regulators of cell reprogramming and influenza virus pathogenesis, generating compelling hypotheses regarding underlying regulatory mechanisms. This flexible framework will contribute to uncovering the dynamic and robust architectures of biological regulation, by incorporating high-throughput experimental data in the form of weights. PMID:27131787

  2. Metal Oxide-Based Selective Enrichment Combined with Stable Isotope Labeling-Mass Spectrometry Analysis for Profiling of Ribose Conjugates.

    PubMed

    Chu, Jie-Mei; Qi, Chu-Bo; Huang, Yun-Qing; Jiang, Han-Peng; Hao, Yan-Hong; Yuan, Bi-Feng; Feng, Yu-Qi

    2015-07-21

    Some modified ribonucleosides in biological fluids have been evaluated as cancer-related metabolites. Detection of endogenous modified ribonucleosides in biological fluids may serve as a noninvasive cancers diagnostic method. However, determination of modified ribonucleosides is still challenging because of their low abundance and serious matrix interferences in biological fluids. Here, we developed a novel strategy for comprehensive profiling of ribose conjugates from biological fluids using metal oxide-based dispersive solid-phase extraction (DSPE) followed with in vitro stable isotope labeling and double neutral loss scan-mass spectrometry analysis (DSPE-SIL-LC-DNLS-MS). Cerium dioxide (CeO2) was used to selectively recognize and capture ribose conjugates from complex biological samples under basic environment. The enriched ribose conjugates were subsequently labeled with a pair of isotope labeling reagents (acetone and acetone-d6). The glucosidic bond of acetone labeled ribose conjugates is readily ruptured, and the generated ribose that carries an isotope tag can be lost as a neutral fragment under collision induced dissociation (CID). Since the light (acetone) and heavy (acetone-d6) labeled compounds have the same chemical structures and can generate different neutral loss fragments (NL 172 and 178 Da), it is therefore highly convenient to profile ribose conjugates by double neutral loss scan mode in mass spectrometry analysis. In this respect, the light and heavy labeled compounds were ionized at the same condition but recorded separately on MS spectra, which can significantly improve the detection specificity and facilitate the identification of ribose conjugates. Using the developed DSPE-SIL-LC-DNLS-MS strategy, we profiled the ribose conjugates in human urine, and 49 ribose conjugates were readily identified, among which 7 ribose conjugates exhibited significant contents change between healthy controls and lymphoma patients. The DSPE

  3. A lectin HPLC method to enrich selectively-glycosylated peptides from complex biological samples.

    PubMed

    Johansen, Eric; Schilling, Birgit; Lerch, Michael; Niles, Richard K; Liu, Haichuan; Li, Bensheng; Allen, Simon; Hall, Steven C; Witkowska, H Ewa; Regnier, Fred E; Gibson, Bradford W; Fisher, Susan J; Drake, Penelope M

    2009-01-01

    Glycans are an important class of post-translational modifications. Typically found on secreted and extracellular molecules, glycan structures signal the internal status of the cell. Glycans on tumor cells tend to have abundant sialic acid and fucose moieties. We propose that these cancer-associated glycan variants be exploited for biomarker development aimed at diagnosing early-stage disease. Accordingly, we developed a mass spectrometry-based workflow that incorporates chromatography on affinity matrices formed from lectins, proteins that bind specific glycan structures. The lectins Sambucus nigra (SNA) and Aleuria aurantia (AAL), which bind sialic acid and fucose, respectively, were covalently coupled to POROS beads (Applied Biosystems) and packed into PEEK columns for high pressure liquid chromatography (HPLC). Briefly, plasma was depleted of the fourteen most abundant proteins using a multiple affinity removal system (MARS-14; Agilent). Depleted plasma was trypsin-digested and separated into flow-through and bound fractions by SNA or AAL HPLC. The fractions were treated with PNGaseF to remove N-linked glycans, and analyzed by LC-MS/MS on a QStar Elite. Data were analyzed using Mascot software. The experimental design included positive controls-fucosylated and sialylated human lactoferrin glycopeptides-and negative controls-high mannose glycopeptides from Saccharomyces cerevisiae-that were used to monitor the specificity of lectin capture. Key features of this workflow include the reproducibility derived from the HPLC format, the positive identification of the captured and PNGaseF-treated glycopeptides from their deamidated Asn-Xxx-Ser/Thr motifs, and quality assessment using glycoprotein standards. Protocol optimization also included determining the appropriate ratio of starting material to column capacity, identifying the most efficient capture and elution buffers, and monitoring the PNGaseF-treatment to ensure full deglycosylation. Future directions include

  4. ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems.

    PubMed

    Kaimal, Vivek; Bardes, Eric E; Tabar, Scott C; Jegga, Anil G; Aronow, Bruce J

    2010-07-01

    ToppCluster is a web server application that leverages a powerful enrichment analysis and underlying data environment for comparative analyses of multiple gene lists. It generates heatmaps or connectivity networks that reveal functional features shared or specific to multiple gene lists. ToppCluster uses hypergeometric tests to obtain list-specific feature enrichment P-values for currently 17 categories of annotations of human-ortholog genes, and provides user-selectable cutoffs and multiple testing correction methods to control false discovery. Each nameable gene list represents a column input to a resulting matrix whose rows are overrepresented features, and individual cells per-list P-values and corresponding genes per feature. ToppCluster provides users with choices of tabular outputs, hierarchical clustering and heatmap generation, or the ability to interactively select features from the functional enrichment matrix to be transformed into XGMML or GEXF network format documents for use in Cytoscape or Gephi applications, respectively. Here, as example, we demonstrate the ability of ToppCluster to enable identification of list-specific phenotypic and regulatory element features (both cis-elements and 3'UTR microRNA binding sites) among tissue-specific gene lists. ToppCluster's functionalities enable the identification of specialized biological functions and regulatory networks and systems biology-based dissection of biological states. ToppCluster can be accessed freely at http://toppcluster.cchmc.org.

  5. Multilevel correlations in the biological phosphorus removal process: From bacterial enrichment to conductivity-based metabolic batch tests and polyphosphatase assays.

    PubMed

    Weissbrodt, David G; Maillard, Julien; Brovelli, Alessandro; Chabrelie, Alexandre; May, Jonathan; Holliger, Christof

    2014-12-01

    Enhanced biological phosphorus removal (EBPR) from wastewater relies on the preferential selection of active polyphosphate-accumulating organisms (PAO) in the underlying bacterial community continuum. Efficient management of the bacterial resource requires understanding of population dynamics as well as availability of bioanalytical methods for rapid and regular assessment of relative abundances of active PAOs and their glycogen-accumulating competitors (GAO). A systems approach was adopted here toward the investigation of multilevel correlations from the EBPR bioprocess to the bacterial community, metabolic, and enzymatic levels. Two anaerobic-aerobic sequencing-batch reactors were operated to enrich activated sludge in PAOs and GAOs affiliating with "Candidati Accumulibacter and Competibacter phosphates", respectively. Bacterial selection was optimized by dynamic control of the organic loading rate and the anaerobic contact time. The distinct core bacteriomes mainly comprised populations related to the classes Betaproteobacteria, Cytophagia, and Chloroflexi in the PAO enrichment and of Gammaproteobacteria, Alphaproteobacteria, Acidobacteria, and Sphingobacteria in the GAO enrichment. An anaerobic metabolic batch test based on electrical conductivity evolution and a polyphosphatase enzymatic assay were developed for rapid and low-cost assessment of the active PAO fraction and dephosphatation potential of activated sludge. Linear correlations were obtained between the PAO fraction, biomass specific rate of conductivity increase under anaerobic conditions, and polyphosphate-hydrolyzing activity of PAO/GAO mixtures. The correlations between PAO/GAO ratios, metabolic activities, and conductivity profiles were confirmed by simulations with a mathematical model developed in the aqueous geochemistry software PHREEQC.

  6. Multilevel correlations in the biological phosphorus removal process: From bacterial enrichment to conductivity-based metabolic batch tests and polyphosphatase assays.

    PubMed

    Weissbrodt, David G; Maillard, Julien; Brovelli, Alessandro; Chabrelie, Alexandre; May, Jonathan; Holliger, Christof

    2014-12-01

    Enhanced biological phosphorus removal (EBPR) from wastewater relies on the preferential selection of active polyphosphate-accumulating organisms (PAO) in the underlying bacterial community continuum. Efficient management of the bacterial resource requires understanding of population dynamics as well as availability of bioanalytical methods for rapid and regular assessment of relative abundances of active PAOs and their glycogen-accumulating competitors (GAO). A systems approach was adopted here toward the investigation of multilevel correlations from the EBPR bioprocess to the bacterial community, metabolic, and enzymatic levels. Two anaerobic-aerobic sequencing-batch reactors were operated to enrich activated sludge in PAOs and GAOs affiliating with "Candidati Accumulibacter and Competibacter phosphates", respectively. Bacterial selection was optimized by dynamic control of the organic loading rate and the anaerobic contact time. The distinct core bacteriomes mainly comprised populations related to the classes Betaproteobacteria, Cytophagia, and Chloroflexi in the PAO enrichment and of Gammaproteobacteria, Alphaproteobacteria, Acidobacteria, and Sphingobacteria in the GAO enrichment. An anaerobic metabolic batch test based on electrical conductivity evolution and a polyphosphatase enzymatic assay were developed for rapid and low-cost assessment of the active PAO fraction and dephosphatation potential of activated sludge. Linear correlations were obtained between the PAO fraction, biomass specific rate of conductivity increase under anaerobic conditions, and polyphosphate-hydrolyzing activity of PAO/GAO mixtures. The correlations between PAO/GAO ratios, metabolic activities, and conductivity profiles were confirmed by simulations with a mathematical model developed in the aqueous geochemistry software PHREEQC. PMID:24975745

  7. Isotope Enrichment Detection by Laser Ablation - Laser Absorption Spectrometry: Automated Environmental Sampling and Laser-Based Analysis for HEU Detection

    SciTech Connect

    Anheier, Norman C.; Bushaw, Bruce A.

    2010-01-01

    The global expansion of nuclear power, and consequently the uranium enrichment industry, requires the development of new safeguards technology to mitigate proliferation risks. Current enrichment monitoring instruments exist that provide only yes/no detection of highly enriched uranium (HEU) production. More accurate accountancy measurements are typically restricted to gamma-ray and weight measurements taken in cylinder storage yards. Analysis of environmental and cylinder content samples have much higher effectiveness, but this approach requires onsite sampling, shipping, and time-consuming laboratory analysis and reporting. Given that large modern gaseous centrifuge enrichment plants (GCEPs) can quickly produce a significant quantity (SQ ) of HEU, these limitations in verification suggest the need for more timely detection of potential facility misuse. The Pacific Northwest National Laboratory (PNNL) is developing an unattended safeguards instrument concept, combining continuous aerosol particulate collection with uranium isotope assay, to provide timely analysis of enrichment levels within low enriched uranium facilities. This approach is based on laser vaporization of aerosol particulate samples, followed by wavelength tuned laser diode spectroscopy to characterize the uranium isotopic ratio through subtle differences in atomic absorption wavelengths. Environmental sampling (ES) media from an integrated aerosol collector is introduced into a small, reduced pressure chamber, where a focused pulsed laser vaporizes material from a 10 to 20-µm diameter spot of the surface of the sampling media. The plume of ejected material begins as high-temperature plasma that yields ions and atoms, as well as molecules and molecular ions. We concentrate on the plume of atomic vapor that remains after the plasma has expanded and then cooled by the surrounding cover gas. Tunable diode lasers are directed through this plume and each isotope is detected by monitoring absorbance

  8. Enrichment of calcifying extracellular vesicles using density-based ultracentrifugation protocol

    PubMed Central

    Hutcheson, Joshua D.; Goettsch, Claudia; Pham, Tan; Iwashita, Masaya; Aikawa, Masanori; Singh, Sasha A.; Aikawa, Elena

    2014-01-01

    Calcifying extracellular vesicles (EVs) released from cells within atherosclerotic plaques have received increased attention for their role in mediating vascular calcification, a major predictor of cardiovascular morbidity and mortality. However, little is known about the difference between this pathologic vesicle population and other EVs that contribute to physiological cellular processes. One major challenge that hinders research into these differences is the inability to selectively isolate calcifying EVs from other vesicle populations. In this study, we hypothesized that the formation of mineral within calcifying EVs would increase the density of the vesicles such that they would pellet at a faster rate during ultracentrifugation. We show that after 10 min of ultracentrifugation at 100,000×g, calcifying EVs are depleted from the conditioned media of calcifying coronary artery smooth muscle cells and are enriched in the pelleted portion. We utilized mass spectrometry to establish functional proteomic differences between the calcifying EVs enriched in the 10 min ultracentrifugation compared to other vesicle populations preferentially pelleted by longer ultracentrifugation times. The procedures established in this study will allow us to enrich the vesicle population of interest and perform advanced proteomic analyses to find subtle differences between calcifying EVs and other vesicle populations that may be translated into therapeutic targets for vascular calcification. Finally, we will show that the differences in ultracentrifugation times required to pellet the vesicle populations can also be used to estimate physical differences between the vesicles. PMID:25491249

  9. Direct analysis of δ2H and δ18O in natural and enriched human urine using laser-based, off-axis integrated cavity output spectroscopy.

    PubMed

    Berman, Elena S F; Fortson, Susan L; Snaith, Steven P; Gupta, Manish; Baer, Douglas S; Chery, Isabelle; Blanc, Stephane; Melanson, Edward L; Thomson, Peter J; Speakman, John R

    2012-11-20

    The stable isotopes of hydrogen (δ(2)H) and oxygen (δ(18)O) in human urine are measured during studies of total energy expenditure by the doubly labeled water method, measurement of total body water, and measurement of insulin resistance by glucose disposal among other applications. An ultrasensitive laser absorption spectrometer based on off-axis integrated cavity output spectroscopy was demonstrated for simple and inexpensive measurement of stable isotopes in natural isotopic abundance and isotopically enriched human urine. Preparation of urine for analysis was simple and rapid (approximately 25 samples per hour), requiring no decolorizing or distillation steps. Analysis schemes were demonstrated to address sample-to-sample memory while still allowing analysis of 45 natural or 30 enriched urine samples per day. The instrument was linear over a wide range of water isotopes (δ(2)H = -454 to +1702 ‰ and δ(18)O = -58.3 to +265 ‰). Measurements of human urine were precise to better than 0.65 ‰ 1σ for δ(2)H and 0.09 ‰ 1σ for δ(18)O for natural urines, 1.1 ‰ 1σ for δ(2)H and 0.13 ‰ 1σ for δ(18)O for low enriched urines, and 1.0 ‰ 1σ for δ(2)H and 0.08 ‰ 1σ for δ(18)O for high enriched urines. Furthermore, the accuracy of the isotope measurements of human urines was verified to better than ±0.81 ‰ in δ(2)H and ±0.13 ‰ in δ(18)O (average deviation) against three independent isotope-ratio mass spectrometry laboratories. The ability to immediately and inexpensively measure the stable isotopes of water in human urine is expected to increase the number and variety of experiments which can be undertaken.

  10. Direct analysis of δ2H and δ18O in natural and enriched human urine using laser-based, off-axis integrated cavity output spectroscopy.

    PubMed

    Berman, Elena S F; Fortson, Susan L; Snaith, Steven P; Gupta, Manish; Baer, Douglas S; Chery, Isabelle; Blanc, Stephane; Melanson, Edward L; Thomson, Peter J; Speakman, John R

    2012-11-20

    The stable isotopes of hydrogen (δ(2)H) and oxygen (δ(18)O) in human urine are measured during studies of total energy expenditure by the doubly labeled water method, measurement of total body water, and measurement of insulin resistance by glucose disposal among other applications. An ultrasensitive laser absorption spectrometer based on off-axis integrated cavity output spectroscopy was demonstrated for simple and inexpensive measurement of stable isotopes in natural isotopic abundance and isotopically enriched human urine. Preparation of urine for analysis was simple and rapid (approximately 25 samples per hour), requiring no decolorizing or distillation steps. Analysis schemes were demonstrated to address sample-to-sample memory while still allowing analysis of 45 natural or 30 enriched urine samples per day. The instrument was linear over a wide range of water isotopes (δ(2)H = -454 to +1702 ‰ and δ(18)O = -58.3 to +265 ‰). Measurements of human urine were precise to better than 0.65 ‰ 1σ for δ(2)H and 0.09 ‰ 1σ for δ(18)O for natural urines, 1.1 ‰ 1σ for δ(2)H and 0.13 ‰ 1σ for δ(18)O for low enriched urines, and 1.0 ‰ 1σ for δ(2)H and 0.08 ‰ 1σ for δ(18)O for high enriched urines. Furthermore, the accuracy of the isotope measurements of human urines was verified to better than ±0.81 ‰ in δ(2)H and ±0.13 ‰ in δ(18)O (average deviation) against three independent isotope-ratio mass spectrometry laboratories. The ability to immediately and inexpensively measure the stable isotopes of water in human urine is expected to increase the number and variety of experiments which can be undertaken. PMID:23075099

  11. L-Lactate-selective microbial sensor based on flavocytochrome b2-enriched yeast cells using recombinant and nanotechnology approaches.

    PubMed

    Karkovska, Maria; Smutok, Oleh; Stasyuk, Nataliya; Gonchar, Mykhailo

    2015-11-01

    In the recent years, nanotechnology is the most developing branch due to a wide variety of potential applications in biomedical, biotechnological and agriculture fields. The binding nanoparticles with various biological molecules makes them attractive candidates for using in sensor technologies. The particularly actual is obtaining the bionanomembranes based on biocatalytic elements with improved sensing characteristics. The aim of this investigation is to study the properties of microbial L-lactate-selective sensor based on using the recombinant Hansenula polymorpha yeast cells overproducing flavocytochrome b2 (FC b2), as well as additionally enriched by the enzyme bound with gold nanoparticles (FC b2-nAu). Although, the high permeability of the living cells to nanoparticles is being intensively studied (mostly for delivery of drugs), the idea of using both recombinant technology and nanotechnology to increase the amount of the target enzyme in the biosensing layer is really novel. The FC b2-nAu-enriched living and permeabilized yeast cells were used for construction of a bioselective membrane of microbial L-lactate-selective amperometric biosensor. Phenazine methosulphate was served as a free defusing electron transfer mediator which provides effective electron transfer from the reduced enzyme to the electrode surface. It was shown that the output to L-lactate of FC b2-nAu-enriched permeabilized yeast cells is 2.5-fold higher when compared to the control cells. The obtained results confirm that additional enrichment of the recombinant yeast cell by the enzyme bound with nanoparticles improves the analytical parameters of microbial sensor.

  12. Validation of a novel cognitive bias task based on difference in quantity of reinforcement for assessing environmental enrichment.

    PubMed

    Keen, Heidi A; Nelson, O Lynne; Robbins, Charles T; Evans, Marc; Shepherdson, David J; Newberry, Ruth C

    2014-05-01

    Cognitive bias tasks purport to assess affective states via responses to ambiguous stimuli. We hypothesized that a novel cognitive bias task based on positive reinforcement using quantity differences would detect changes in affect in captive grizzly bears (Ursus arctos horribilis). We trained bears (n = 8) to respond differently (nose or paw touch) to two stimuli (light or dark gray cue cards), with responses counterbalanced across bears. The two cues signaled a small or large food reward, respectively. Responses to ambiguous probe stimuli (i.e., shades of gray) intermediate to the trained stimuli were classified as either 'optimistic,' appropriate for the larger reward, or 'pessimistic,' appropriate for the smaller reward. In Experiment 1, we explored the contrast in reward size necessary to detect a change in response across probe stimuli (large reward, 3 or 6 apple slices: small reward, 1 slice). We observed a change in response across probe stimuli, with no difference in response between reward-value groups, indicating that a contrast of 3:1 apple slices was sufficient to affect responses. In Experiment 2, we investigated cognitive bias after 2.1 h of exposure to enrichment items varying in attractiveness. Results were unaffected by enrichment type or time spent interacting with enrichments, indicating that the task failed to demonstrate criterion validity for comparing mood following exposure to different enrichment items. However, greater time spent pacing prior to testing was associated with 'optimistic' judgments. The data provide some support for use of cognitive bias tasks based on quantity differences in animal welfare assessments involving captive wildlife.

  13. Validation of a novel cognitive bias task based on difference in quantity of reinforcement for assessing environmental enrichment.

    PubMed

    Keen, Heidi A; Nelson, O Lynne; Robbins, Charles T; Evans, Marc; Shepherdson, David J; Newberry, Ruth C

    2014-05-01

    Cognitive bias tasks purport to assess affective states via responses to ambiguous stimuli. We hypothesized that a novel cognitive bias task based on positive reinforcement using quantity differences would detect changes in affect in captive grizzly bears (Ursus arctos horribilis). We trained bears (n = 8) to respond differently (nose or paw touch) to two stimuli (light or dark gray cue cards), with responses counterbalanced across bears. The two cues signaled a small or large food reward, respectively. Responses to ambiguous probe stimuli (i.e., shades of gray) intermediate to the trained stimuli were classified as either 'optimistic,' appropriate for the larger reward, or 'pessimistic,' appropriate for the smaller reward. In Experiment 1, we explored the contrast in reward size necessary to detect a change in response across probe stimuli (large reward, 3 or 6 apple slices: small reward, 1 slice). We observed a change in response across probe stimuli, with no difference in response between reward-value groups, indicating that a contrast of 3:1 apple slices was sufficient to affect responses. In Experiment 2, we investigated cognitive bias after 2.1 h of exposure to enrichment items varying in attractiveness. Results were unaffected by enrichment type or time spent interacting with enrichments, indicating that the task failed to demonstrate criterion validity for comparing mood following exposure to different enrichment items. However, greater time spent pacing prior to testing was associated with 'optimistic' judgments. The data provide some support for use of cognitive bias tasks based on quantity differences in animal welfare assessments involving captive wildlife. PMID:24045850

  14. A more accurate and penetrating method to measure the enrichment and mass of UF6 storage containers using passive neutron self-interrogation

    SciTech Connect

    Menlove, Howard O; Swinhoe, Martyn T; Miller, Karen A

    2010-01-01

    This paper describes an unattended mode neutron measurement that can provide the enrichment of the uranium in UF{sub 6} cylinders. The new passive neutron measurement provides better penetration into the uranium mass than prior gamma-ray enrichment measurement methods. The Passive Neutron Enrichment Monitor (PNEM) provides a new measurement technique that uses passive neutron totals and coincidence counting together with neutron self-interrogation to measure the enrichment in the cylinders. The measurement uses the neutron rates from two detector pods. One of the pods has a bare polyethylene surface next to the cylinder and the other polyethylene surface is covered with Cd to prevent thermal neutrons from returning to the cylinder. The primary neutron source from the enriched UF{sub 6} is the alpha-particle decay from the {sub 234}U that interacts with the fluorine to produce random neutrons. The singles neutron counting rate is dominated by the {sub 234}U neutrons with a minor contribution from the induced fissions in the {sub 235}U. However, the doubles counting rate comes primarily from the induced fissions (i.e., multiplication) in the {sub 235}U in enriched uranium. The PNEM concept makes use of the passive neutrons that are initially produced from the {sub 234}U reactions that track the {sub 235}U enrichment during the enrichment process. The induced fission reactions from the thermal-neutron albedo are all from the {sub 235}U and provide a measurement of the {sub 235}U. The Cd ratio has the desirable feature that all of the thermal-neutron-induced fissions in {sub 235}U are independent of the original neutron source. Thus, the ratio is independent of the uranium age, purity, and prior reactor history.

  15. Pruned-enriched Rosenbluth method: Simulations of θ polymers of chain length up to 1 000 000

    NASA Astrophysics Data System (ADS)

    Grassberger, Peter

    1997-09-01

    We present an algorithm for simulating flexible chain polymers. It combines the Rosenbluth-Rosenbluth method with recursive enrichment. Although it can be applied also in more general situations, it is most efficient for three-dimensional θ polymers on the simple-cubic lattice. There it allows high statistics simulations of chains of length up to N=106. For storage reasons, this is feasable only for polymers in a finite volume. For free θ polymers in infinite volume, we present very high statistics runs with N=10 000. These simulations fully agree with previous simulations made by Hegger and Grassberger [J. Chem. Phys. 102, 6681 (1995)] with a similar but less efficient algorithm, showing that logarithmic corrections to mean field behavior are much stronger than predicted by field theory. But the finite volume simulations show that the density inside a collapsed globule scales with the distance from the θ point as predicted by mean field theory, in contrast to claims in the work mentioned above. In addition to the simple-cubic lattice, we also studied two versions of the bond fluctuation model, but with much shorter chains. Finally, we show that our method can be applied also to off-lattice models, and illustrate this with simulations of a model studied in detail by Freire et al. [Macromolecules 19, 452 (1986) and later work].

  16. Centrifuge enrichment plants. January 1970-October 1988 (Citations from the NTIS data base). Report for January 1970-October 1988

    SciTech Connect

    Not Available

    1988-11-01

    This bibliography contains citations concerning the design, control, monitoring, and safety of centrifuge enrichment plants. Power supplies, enrichment plant safeguards, facility design, cascade heater test loops to monitor the enrichment process, inspection strategies, and the socio-economic effects of centrifuge enrichment plants are examined. Radioactive waste disposal problems are briefly considered. (Contains 151 citations fully indexed and including a title list.)

  17. Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications

    SciTech Connect

    Guo, Jia; Gaffrey, Matthew J.; Su, Dian; Liu, Tao; Camp, David G.; Smith, Richard D.; Qian, Weijun

    2013-12-12

    Reversible modifications on cysteine thiols play a significant role in redox signaling and regulation. A number of reversible redox modifications, including disulfide formation, S-nitrosylation, and S-glutathionylation, have been recognized for their significance in various physiological and pathological processes. Here we describe in detail a resin-assisted thiol-affinity enrichment protocol for both biochemical and proteomics applications. This protocol serves as a general approach for specific isolation of thiol-containing proteins or peptides derived from reversible redox-modified proteins. This approach utilizes thiol-affinity resins to directly capture thiol-containing proteins or peptides through a disulfide exchange reaction followed by on-resin protein digestion and on-resin multiplexed isobaric labeling to facilitate LC-MS/MS based quantitative site-specific analysis of redox modifications. The overall approach requires a much simpler workflow with increased specificity compared to the commonly used biotin switch technique. By coupling different selective reduction strategies, the resin-assisted approach provides the researcher with a useful tool capable of enriching different types of reversible modifications on protein thiols. Procedures for selective enrichment and analyses of S-nitrosylation and total reversible cysteine oxidation are presented to demonstrate the utility of this general strategy.

  18. Rapid enrichment of leucocytes and genomic DNA from blood based on bifunctional core shell magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Xie, Xin; Nie, Xiaorong; Yu, Bingbin; Zhang, Xu

    2007-04-01

    A series of protocols are proposed to extract genomic DNA from whole blood at different scales using carboxyl-functionalized magnetic nanoparticles as solid-phase absorbents. The enrichment of leucocytes and the adsorption of genomic DNA can be achieved with the same carboxyl-functionalized magnetic nanoparticles. The DNA bound to the bead surfaces can be used directly as PCR templates. By coupling cell separation and DNA purification, the whole operation can be accomplished in a few minutes. Our simplified protocols proved to be rapid, low cost, and biologically and chemically non-hazardous, and are therefore promising for microfabrication of a DNA-preparation chip and routine laboratory use.

  19. Highly specific purification of N-glycans using phosphate-based derivatization as an affinity tag in combination with Ti(4+)-SPE enrichment for mass spectrometric analysis.

    PubMed

    Zhang, Ying; Peng, Ye; Bin, Zhichao; Wang, Huijie; Lu, Haojie

    2016-08-31

    N-linked protein glycosylation is involved in regulation of a wide variety of cellular processes and associated with numerous diseases. Highly specific identification of N-glycome remains a challenge while its biological significance is acknowledged. The relatively low abundance of glycan in complex biological mixtures, lack of basic sites for protonation, and suppression by other highly abundant proteins/peptides lead to the particularly poor detection sensitivity of N-glycans in the MS analysis. Therefore, the highly specific purification procedure becomes a crucial step prior to MS analysis of the N-glycome. Herein, a novel N-glycans enrichment approach based on phosphate derivatization combined with Ti(4+)-SPE (solid phase extraction) was developed. Briefly, in this strategy, N-glycans were chemically labeled with a phospho-group at their reducing ends, such that the Ti(4+)-SPE microspheres were able to capture the phospho-containing glycans. The enrichment method was developed and optimized using model oligosaccharides (maltoheptaose DP7 and sialylated glycan A1) and also glycans from a standard glycoprotein (asialofetuin, ASF). This method experimentally showed high derivatization efficiency (almost 100%), excellent selectivity (analyzing DP7 in the digests of bovine serum albumin at a mass ratio of 1:100), high enriching recovery (90%), good reproducibility (CV<15%) as well as high sensitivity (LOD at fmol level). At last, the proposed method was successfully applied in the profiling of N-glycome in human serum, in which a total of 31 N-glycan masses were identified. PMID:27506354

  20. Highly specific purification of N-glycans using phosphate-based derivatization as an affinity tag in combination with Ti(4+)-SPE enrichment for mass spectrometric analysis.

    PubMed

    Zhang, Ying; Peng, Ye; Bin, Zhichao; Wang, Huijie; Lu, Haojie

    2016-08-31

    N-linked protein glycosylation is involved in regulation of a wide variety of cellular processes and associated with numerous diseases. Highly specific identification of N-glycome remains a challenge while its biological significance is acknowledged. The relatively low abundance of glycan in complex biological mixtures, lack of basic sites for protonation, and suppression by other highly abundant proteins/peptides lead to the particularly poor detection sensitivity of N-glycans in the MS analysis. Therefore, the highly specific purification procedure becomes a crucial step prior to MS analysis of the N-glycome. Herein, a novel N-glycans enrichment approach based on phosphate derivatization combined with Ti(4+)-SPE (solid phase extraction) was developed. Briefly, in this strategy, N-glycans were chemically labeled with a phospho-group at their reducing ends, such that the Ti(4+)-SPE microspheres were able to capture the phospho-containing glycans. The enrichment method was developed and optimized using model oligosaccharides (maltoheptaose DP7 and sialylated glycan A1) and also glycans from a standard glycoprotein (asialofetuin, ASF). This method experimentally showed high derivatization efficiency (almost 100%), excellent selectivity (analyzing DP7 in the digests of bovine serum albumin at a mass ratio of 1:100), high enriching recovery (90%), good reproducibility (CV<15%) as well as high sensitivity (LOD at fmol level). At last, the proposed method was successfully applied in the profiling of N-glycome in human serum, in which a total of 31 N-glycan masses were identified.

  1. Community Cosmos -- A Park-based Educator Enrichment Program in the Earth and Space Sciences

    NASA Astrophysics Data System (ADS)

    Waller, W. H.

    2005-05-01

    I will describe a community-wide educator enrichment program in the Earth and Space Sciences that is being developed at Halibut Point State Park in Rockport, MA. Through wide-ranging partnerships, we will provide two on-site hands-on workshops in Earth and Space Science that will serve the interests of school teachers, scout leaders, park interpreters, amateur astronomers, and other community educators. Each 3-day workshop will address the 3 broad topics of (1) living on Earth, (2) the Earth in space, and (3) the origins of the Earth, Solar System, Milky Way, and Universe. Natural resources at Halibut Point State Park will be used to enrich each of these topics. Astrobiology will be the topical "glue" that binds all 3 topics. Research of the PI will be featured through personal presentations on starbirth and starburst activity in galaxies. A wide selection of NASA education materials will be showcased -- including those developed for Project ASTRO, Family ASTRO, Great Explorations in Math and Science (GEMS), EarthKam, the Night Sky Network, and the Spitzer E/PO Program. These workshops will serve as models for similar programs in Earth and Space Science Education at state and national parks throughout the United States.

  2. Application of an efficient strategy based on liquid-liquid extraction, high-speed counter-current chromatography, and preparative HPLC for the rapid enrichment, separation, and purification of four anthraquinones from Rheum tanguticum.

    PubMed

    Chen, Tao; Liu, Yongling; Zou, Denglang; Chen, Chen; You, Jinmao; Zhou, Guoying; Sun, Jing; Li, Yulin

    2014-01-01

    This study presents an efficient strategy based on liquid-liquid extraction, high-speed counter-current chromatography, and preparative HPLC for the rapid enrichment, separation, and purification of four anthraquinones from Rheum tanguticum. A new solvent system composed of petroleum ether/ethyl acetate/water (4:2:1, v/v/v) was developed for the liquid-liquid extraction of the crude extract from R. tanguticum. As a result, emodin, aloe-emodin, physcion, and chrysophanol were greatly enriched in the organic layer. In addition, an efficient method was successfully established to separate and purify the above anthraquinones by high-speed counter-current chromatography and preparative HPLC. This study supplies a new alternative method for the rapid enrichment, separation, and purification of emodin, aloe-emodin, physcione, and chrysophanol.

  3. Classification method based on KCCA

    NASA Astrophysics Data System (ADS)

    Wang, Zhanqing; Zhang, Guilin; Zhao, Guangzhou

    2007-11-01

    Nonlinear CCA extends the linear CCA in that it operates in the kernel space and thus implies the nonlinear combinations in the original space. This paper presents a classification method based on the kernel canonical correlation analysis (KCCA). We introduce the probabilistic label vectors (PLV) for a give pattern which extend the conventional concept of class label, and investigate the correlation between feature variables and PLV variables. A PLV predictor is presented based on KCCA, and then classification is performed on the predicted PLV. We formulate a frame for classification by integrating class information through PLV. Experimental results on Iris data set classification and facial expression recognition show the efficiencies of the proposed method.

  4. Network-Based Enriched Gene Subnetwork Identification: A Game-Theoretic Approach.

    PubMed

    Razi, Abolfazl; Afghah, Fatemeh; Singh, Salendra; Varadan, Vinay

    2016-01-01

    Identifying subsets of genes that jointly mediate cancer etiology, progression, or therapy response remains a challenging problem due to the complexity and heterogeneity in cancer biology, a problem further exacerbated by the relatively small number of cancer samples profiled as compared with the sheer number of potential molecular factors involved. Pure data-driven methods that merely rely on multiomics data have been successful in discovering potentially functional genes but suffer from high false-positive rates and tend to report subsets of genes whose biological interrelationships are unclear. Recently, integrative data-driven models have been developed to integrate multiomics data with signaling pathway networks in order to identify pathways associated with clinical or biological phenotypes. However, these approaches suffer from an important drawback of being restricted to previously discovered pathway structures and miss novel genomic interactions as well as potential crosstalk among the pathways. In this article, we propose a novel coalition-based game-theoretic approach to overcome the challenge of identifying biologically relevant gene subnetworks associated with disease phenotypes. The algorithm starts from a set of seed genes and traverses a protein-protein interaction network to identify modulated subnetworks. The optimal set of modulated subnetworks is identified using Shapley value that accounts for both individual and collective utility of the subnetwork of genes. The algorithm is applied to two illustrative applications, including the identification of subnetworks associated with (i) disease progression risk in response to platinum-based therapy in ovarian cancer and (ii) immune infiltration in triple-negative breast cancer. The results demonstrate an improved predictive power of the proposed method when compared with state-of-the-art feature selection methods, with the added advantage of identifying novel potentially functional gene subnetworks

  5. Network-Based Enriched Gene Subnetwork Identification: A Game-Theoretic Approach.

    PubMed

    Razi, Abolfazl; Afghah, Fatemeh; Singh, Salendra; Varadan, Vinay

    2016-01-01

    Identifying subsets of genes that jointly mediate cancer etiology, progression, or therapy response remains a challenging problem due to the complexity and heterogeneity in cancer biology, a problem further exacerbated by the relatively small number of cancer samples profiled as compared with the sheer number of potential molecular factors involved. Pure data-driven methods that merely rely on multiomics data have been successful in discovering potentially functional genes but suffer from high false-positive rates and tend to report subsets of genes whose biological interrelationships are unclear. Recently, integrative data-driven models have been developed to integrate multiomics data with signaling pathway networks in order to identify pathways associated with clinical or biological phenotypes. However, these approaches suffer from an important drawback of being restricted to previously discovered pathway structures and miss novel genomic interactions as well as potential crosstalk among the pathways. In this article, we propose a novel coalition-based game-theoretic approach to overcome the challenge of identifying biologically relevant gene subnetworks associated with disease phenotypes. The algorithm starts from a set of seed genes and traverses a protein-protein interaction network to identify modulated subnetworks. The optimal set of modulated subnetworks is identified using Shapley value that accounts for both individual and collective utility of the subnetwork of genes. The algorithm is applied to two illustrative applications, including the identification of subnetworks associated with (i) disease progression risk in response to platinum-based therapy in ovarian cancer and (ii) immune infiltration in triple-negative breast cancer. The results demonstrate an improved predictive power of the proposed method when compared with state-of-the-art feature selection methods, with the added advantage of identifying novel potentially functional gene subnetworks

  6. A Comparison of Platelet Count and Enrichment Percentages in the Platelet Rich Plasma (PRP) Obtained Following Preparation by Three Different Methods

    PubMed Central

    Sabarish, Ram; Lavu, Vamsi

    2015-01-01

    Introduction: Platelet rich plasma (PRP) represents an easily accessible and rich source of autologous growth factors. Different manual methods for the preparation of PRP have been suggested. Lacuna in knowledge exists about the efficacy of PRP preparation by these different manual methods. Aims: This study was performed to determine the effects of centrifugation rate revolutions per minute (RPM) and time on the platelet count and enrichment percentages in the concentrates obtained following the three different manual methods of PRP preparation. Setting and Design: In vitro experimental study. Materials and Methods: This was an experimental study in which platelet concentration was assessed in the PRP prepared by three different protocols as suggested by Marx R (method 1), Okuda K (method 2) and Landesberg R (method 3). A total of 60 peripheral blood samples, (n=20 per method) were obtained from healthy volunteers. Baseline platelet count was assessed for all the subjects following which PRP was prepared. The platelet count in the PRP was determined using coulter counter (Sysmex XT 2000i). Statistical Method: The mean of the platelet count obtained and their enrichment percentage were calculated and intergroup comparison was done (Tukey’s HSD test). Results: The number of platelets and enrichment percentage in PRP prepared by method 1 was higher compared to method 2 and method 3; this difference in platelet concentrates was found to be statistically significant (p < 0.05). Conclusion: The centrifugation rate and time appear to be important parameters, which influence the platelet yield. Method 1 which had lower centrifugation rate and time yielded a greater platelet count and enrichment percentage. PMID:25859516

  7. Application of Condition-Based Monitoring Techniques for Remote Monitoring of a Simulated Gas Centrifuge Enrichment Plant

    SciTech Connect

    Hooper, David A; Henkel, James J; Whitaker, Michael

    2012-01-01

    This paper presents research into the adaptation of monitoring techniques from maintainability and reliability (M&R) engineering for remote unattended monitoring of gas centrifuge enrichment plants (GCEPs) for international safeguards. Two categories of techniques are discussed: the sequential probability ratio test (SPRT) for diagnostic monitoring, and sequential Monte Carlo (SMC or, more commonly, particle filtering ) for prognostic monitoring. Development and testing of the application of condition-based monitoring (CBM) techniques was performed on the Oak Ridge Mock Feed and Withdrawal (F&W) facility as a proof of principle. CBM techniques have been extensively developed for M&R assessment of physical processes, such as manufacturing and power plants. These techniques are normally used to locate and diagnose the effects of mechanical degradation of equipment to aid in planning of maintenance and repair cycles. In a safeguards environment, however, the goal is not to identify mechanical deterioration, but to detect and diagnose (and potentially predict) attempts to circumvent normal, declared facility operations, such as through protracted diversion of enriched material. The CBM techniques are first explained from the traditional perspective of maintenance and reliability engineering. The adaptation of CBM techniques to inspector monitoring is then discussed, focusing on the unique challenges of decision-based effects rather than equipment degradation effects. These techniques are then applied to the Oak Ridge Mock F&W facility a water-based physical simulation of a material feed and withdrawal process used at enrichment plants that is used to develop and test online monitoring techniques for fully information-driven safeguards of GCEPs. Advantages and limitations of the CBM approach to online monitoring are discussed, as well as the potential challenges of adapting CBM concepts to safeguards applications.

  8. Resin-assisted enrichment of thiols as a general strategy for proteomic profiling of cysteine-based reversible modifications.

    PubMed

    Guo, Jia; Gaffrey, Matthew J; Su, Dian; Liu, Tao; Camp, David G; Smith, Richard D; Qian, Wei-Jun

    2014-01-01

    Reversible modifications of cysteine thiols have a key role in redox signaling and regulation. A number of reversible redox modifications, including disulfide formation, S-nitrosylation (SNO) and S-glutathionylation (SSG), have been recognized for their significance in various physiological and pathological processes. Here we describe a procedure for the enrichment of peptides containing reversible cysteine modifications. Starting with tissue or cell lysate samples, all of the unmodified free thiols are blocked using N-ethylmaleimide (NEM). This is followed by the selective reduction of those cysteines bearing the reversible modification(s) of interest. The reduction is achieved by using different reducing reagents that react specifically with each type of cysteine modification (e.g., ascorbate for SNO). This protocol serves as a general approach for enrichment of thiol-containing proteins or peptides derived from reversibly modified proteins. The approach uses a commercially available thiol-affinity resin (thiopropyl Sepharose 6B) to directly capture free thiol-containing proteins through a disulfide exchange reaction, followed by on-resin protein digestion and multiplexed isobaric labeling to facilitate liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based quantitative site-specific analysis of cysteine-based reversible modifications. The overall approach requires a simpler workflow with increased specificity compared with the commonly used biotinylation-based assays. The procedure for selective enrichment and analyses of SNO and the level of total reversible cysteine modifications (or total oxidation) is presented to demonstrate the utility of this general strategy. The entire protocol requires ∼3 d for sample processing with an additional day for LC-MS/MS and data analysis.

  9. A simple method to quickly and simultaneously purify and enrich intact rat brain microcapillaries and endothelial and glial cells for ex vivo studies and cell culture.

    PubMed

    Lenhard, Thorsten; Hülsermann, Uta; Martinez-Torres, Francisco; Fricker, Gert; Meyding-Lamadé, Uta

    2013-06-26

    The blood-brain barrier is morphologically composed of cerebral microcapillary endothelium through its tight junctions. It serves as a mechanical, metabolic and cellular barrier and can also protect the brain from pathogen invasion. Many brain diseases involve a disturbance of blood-brain barrier function either as a consequence of a noxa or as primary failure. In vitro models of the blood-brain barrier are suitable tools to study drug transport, pathogen transmigration and leukocyte diapedesis across the cerebral endothelium. Such models have previously been derived mainly from porcine or bovine brain tissues. We describe here a simple method by which rat cerebral microcapillaries and cells of glial origin can be quickly and simultaneously purified. By using a capillary fragment size restriction method based on glass bead columns different fractions can be separated: vital, long capillary fragments for ex vivo uptake studies and smaller capillary fragments for endothelial culture. Furthermore, fractions can be obtained for astroglial and oligodendroglial cell cultures. With this method both microcapillary enrichment and glial cell purification are quickly achieved, which reduces expenditure, number of required animals and laboratory working time. PMID:23665392

  10. A simple method to quickly and simultaneously purify and enrich intact rat brain microcapillaries and endothelial and glial cells for ex vivo studies and cell culture.

    PubMed

    Lenhard, Thorsten; Hülsermann, Uta; Martinez-Torres, Francisco; Fricker, Gert; Meyding-Lamadé, Uta

    2013-06-26

    The blood-brain barrier is morphologically composed of cerebral microcapillary endothelium through its tight junctions. It serves as a mechanical, metabolic and cellular barrier and can also protect the brain from pathogen invasion. Many brain diseases involve a disturbance of blood-brain barrier function either as a consequence of a noxa or as primary failure. In vitro models of the blood-brain barrier are suitable tools to study drug transport, pathogen transmigration and leukocyte diapedesis across the cerebral endothelium. Such models have previously been derived mainly from porcine or bovine brain tissues. We describe here a simple method by which rat cerebral microcapillaries and cells of glial origin can be quickly and simultaneously purified. By using a capillary fragment size restriction method based on glass bead columns different fractions can be separated: vital, long capillary fragments for ex vivo uptake studies and smaller capillary fragments for endothelial culture. Furthermore, fractions can be obtained for astroglial and oligodendroglial cell cultures. With this method both microcapillary enrichment and glial cell purification are quickly achieved, which reduces expenditure, number of required animals and laboratory working time.

  11. Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation.

    PubMed

    Junker, Astrid; Rohn, Hendrik; Czauderna, Tobias; Klukas, Christian; Hartmann, Anja; Schreiber, Falk

    2012-03-01

    The Systems Biology Graphical Notation (SBGN) is an emerging standard for the uniform representation of biological processes and networks. By using examples from gene regulation and metabolism, this protocol shows the construction of SBGN maps by either manual drawing or automatic translation using the tool SBGN-ED. In addition, it discusses the enrichment of SBGN maps with different kinds of -omics data to bring numerical data into the context of these networks in order to facilitate the interpretation of experimental data. Finally, the export of such maps to public websites, including clickable images, supports the communication of results within the scientific community. With regard to the described functionalities, other tools partially overlap with SBGN-ED. However, currently, SBGN-ED is the only tool that combines all of these functions, including the representation in SBGN, data mapping and website export. This protocol aims to assist scientists with the step-by-step procedure, which altogether takes ∼90 min.

  12. Simple procedures for enrichment of chlorinated aromatic pollutants from fat, water and milk for subsequent analysis by high-resolution methods

    SciTech Connect

    Egestad, B.; Curstedt, T.; Sjoevall, J.

    1982-01-01

    Procedures for enrichment of non-volatile chlorinated aromatic pollutants from fat, water and milk are described. /sup 14/C-DDT was used as a model compound in recovery experiments. A several thousand-fold enrichment of DDT added to butter was achieved by two consecutive straight-phase chromatographies on Lipidex 5000. Trace amounts of DDT in liter volumes of water could be quantitatively extracted by rapid filtration through 2 ml beds of Lipidex 1000. A batch extraction procedure permitted enrichment of DDT from milk after addition of n-pentylamine, methanol and water. DDT could then be eluted from the gel with retention of more than 90% of the lipids. A reversed-phase system with Lipidex 5000 could be used for separation of TCDD from DDT and PCBs. The liquid-gel chromatographic procedures are simple and suitable for clean-up of samples prior to application of high-resolution methods. 5 tables.

  13. Method for fabricating {sup 99}Mo production targets using low enriched uranium, {sup 99}Mo production targets comprising low enriched uranium

    DOEpatents

    Wiencek, T.C.; Matos, J.E.; Hofman, G.L.

    1997-03-25

    A radioisotope production target and a method for fabricating a radioisotope production target is provided, wherein the target comprises an inner cylinder, a foil of fissionable material circumferentially contacting the outer surface of the inner cylinder, and an outer hollow cylinder adapted to receive the substantially foil-covered inner cylinder and compress tightly against the foil to provide good mechanical contact therewith. The method for fabricating a primary target for the production of fission products comprises preparing a first substrate to receive a foil of fissionable material so as to allow for later removal of the foil from the first substrate, preparing a second substrate to receive the foil so as to allow for later removal of the foil from the second substrate; attaching the first substrate to the second substrate such that the foil is sandwiched between the first substrate and second substrate to prevent foil exposure to ambient atmosphere, and compressing the exposed surfaces of the first and second substrate to assure snug mechanical contact between the foil, the first substrate and the second substrate. 3 figs.

  14. Method for fabricating .sup.99 Mo production targets using low enriched uranium, .sup.99 Mo production targets comprising low enriched uranium

    DOEpatents

    Wiencek, Thomas C.; Matos, James E.; Hofman, Gerard L.

    1997-01-01

    A radioisotope production target and a method for fabricating a radioisotope production target is provided, wherein the target comprises an inner cylinder, a foil of fissionable material circumferentially contacting the outer surface of the inner cylinder, and an outer hollow cylinder adapted to receive the substantially foil-covered inner cylinder and compress tightly against the foil to provide good mechanical contact therewith. The method for fabricating a primary target for the production of fission products comprises preparing a first substrate to receive a foil of fissionable material so as to allow for later removal of the foil from the first substrate, preparing a second substrate to receive the foil so as to allow for later removal of the foil from the second substrate; attaching the first substrate to the second substrate such that the foil is sandwiched between the first substrate and second substrate to prevent foil exposure to ambient atmosphere, and compressing the exposed surfaces of the first and second substrate to assure snug mechanical contact between the foil, the first substrate and the second substrate.

  15. Method for fabricating .sup.99 Mo production targets using low enriched uranium, .sup.99 Mo production targets comprising low enriched uranium

    DOEpatents

    Wiencek, Thomas C.; Matos, James E.; Hofman, Gerard L.

    2000-12-12

    A radioisotope production target and a method for fabricating a radioisotope production target is provided, wherein the target comprises an inner cylinder, a foil of fissionable material circumferentially contacting the outer surface of the inner cylinder, and an outer hollow cylinder adapted to receive the substantially foil-covered inner cylinder and compress tightly against the foil to provide good mechanical contact therewith. The method for fabricating a primary target for the production of fission products comprises preparing a first substrate to receive a foil of fissionable material so as to allow for later removal of the foil from the first substrate, preparing a second substrate to receive the foil so as to allow for later removal of the foil from the second substrate; attaching the first substrate to the second substrate such that the foil is sandwiched between the first substrate and second substrate to prevent foil exposure to ambient atmosphere, and compressing the exposed surfaces of the first and second substrate to assure snug mechanical contact between the foil, the first substrate and the second substrate.

  16. A novel multi-commutated method for the determination of hydroxytyrosol in enriched foods using mercaptopropionic acid-capped CdTe quantum dots.

    PubMed

    Llorent-Martínez, E J; Molina-García, L; Fernández-de Córdova, M L; Santos, J L M; Rodrigues, S S M; Ruiz-Medina, A

    2013-01-01

    Hydroxytyrosol (HXT) has been reported to have beneficial effects for human health, such as antioxidant and antimicrobial properties and an important contribution to the prevention of cardiovascular disease. Hence, exhaustive research is currently being performed to prepare functional foods, such as tomato juice or milk, with HXT. This paper presents a multi-commutated flow method based on the quenching effect that HXT has on the fluorescence of water-soluble mercaptopropionic acid-capped CdTe quantum dots. Under optimal conditions a linear working range was obtained for concentrations between 10 and 250 ng µl⁻¹. In order to demonstrate the suitability of the proposed method for the determination of HXT, HXT-enriched samples were prepared. Using a QuEChERS (quick, easy, cheap, effective, rugged and safe) procedure for extraction, HXT was determined in the prepared functional foods (milk, infant formula, tomato juice and tomato soup). Recoveries of 100% ± 8%, relative standard deviations (RSDs) lower than 5% and high sample throughput of 70 samples per h show the potential of the system for the analysis of HXT in food samples.

  17. New Procedure to Obtain Polyphenol-Enriched Grapes Based on the Use of Chemical Elicitors.

    PubMed

    Flores, Gema; Del Castillo, Maria Luisa Ruiz

    2016-09-01

    The effect of the postharvest treatment of methyl jasmonate enantiomers in conjunction with ethanol on bioformation of resveratrol and quercetin glycosides in grapes was evaluated. The antioxidant activity of treated grape extracts as compared with untreated extracts was also assayed. Exogenous (-)-methyl jasmonate in combination with ethanol induced a significant increase in the levels of resveratrol (from 27 to 39 μg g(-1)), quercetin-3-O-glucoside (from 59 to 136 μg g(-1)), quercetin-3-O-galactoside (from 398 to 807 μg g(-1)) and quercetin-3-O-rutinoside (from 23 to 43 μg g(-1)). (+)-Methyl jasmonate with ethanol also resulted in increase of quercetin-3-O-glucoside and quercetin-3-O-rutinoside. However, no (+)-methyl jasmonate effect was observed for resveratrol and quercetin-3-O-galactoside. Both (-)- and (+)-methyl jasmonate treatments provided with extracts with higher antioxidant activity. From the results found in the present work postharvest treatment with (-)-methyl jasmonate in conjunction with ethanol is proposed as a mean to obtain polyphenol-enriched grape extracts with improved antioxidant properties. The procedure here developed is proposed as a mean to obtain functional grapes. Extracts obtained from grapes treated with (-)-methyl jasmonate with ethanol can be particularly useful for industry due to their high antioxidant capacity.

  18. New Procedure to Obtain Polyphenol-Enriched Grapes Based on the Use of Chemical Elicitors.

    PubMed

    Flores, Gema; Del Castillo, Maria Luisa Ruiz

    2016-09-01

    The effect of the postharvest treatment of methyl jasmonate enantiomers in conjunction with ethanol on bioformation of resveratrol and quercetin glycosides in grapes was evaluated. The antioxidant activity of treated grape extracts as compared with untreated extracts was also assayed. Exogenous (-)-methyl jasmonate in combination with ethanol induced a significant increase in the levels of resveratrol (from 27 to 39 μg g(-1)), quercetin-3-O-glucoside (from 59 to 136 μg g(-1)), quercetin-3-O-galactoside (from 398 to 807 μg g(-1)) and quercetin-3-O-rutinoside (from 23 to 43 μg g(-1)). (+)-Methyl jasmonate with ethanol also resulted in increase of quercetin-3-O-glucoside and quercetin-3-O-rutinoside. However, no (+)-methyl jasmonate effect was observed for resveratrol and quercetin-3-O-galactoside. Both (-)- and (+)-methyl jasmonate treatments provided with extracts with higher antioxidant activity. From the results found in the present work postharvest treatment with (-)-methyl jasmonate in conjunction with ethanol is proposed as a mean to obtain polyphenol-enriched grape extracts with improved antioxidant properties. The procedure here developed is proposed as a mean to obtain functional grapes. Extracts obtained from grapes treated with (-)-methyl jasmonate with ethanol can be particularly useful for industry due to their high antioxidant capacity. PMID:27193018

  19. Edge-enriched, porous carbon-based, high energy density supercapacitors for hybrid electric vehicles.

    PubMed

    Kim, Yong Jung; Yang, Cheol-Min; Park, Ki Chul; Kaneko, Katsumi; Kim, Yoong Ahm; Noguchi, Minoru; Fujino, Takeshi; Oyama, Shigeki; Endo, Morinobu

    2012-03-12

    Supercapacitors can store and deliver energy by a simple charge separation, and thus they could be an attractive option to meet transient high energy density in operating fuel cells and in electric and hybrid electric vehicles. To achieve such requirements, intensive studies have been carried out to improve the volumetric capacitance in supercapacitors using various types and forms of carbons including carbon nanotubes and graphenes. However, conventional porous carbons are not suitable for use as electrode material in supercapacitors for such high energy density applications. Here, we show that edge-enriched porous carbons are the best electrode material for high energy density supercapacitors to be used in vehicles as an auxiliary powertrain. Molten potassium hydroxide penetrates well-aligned graphene layers vertically and consequently generates both suitable pores that are easily accessible to the electrolyte and a large fraction of electrochemically active edge sites. We expect that our findings will motivate further research related to energy storage devices and also environmentally friendly electric vehicles. PMID:22378623

  20. Edge-enriched, porous carbon-based, high energy density supercapacitors for hybrid electric vehicles.

    PubMed

    Kim, Yong Jung; Yang, Cheol-Min; Park, Ki Chul; Kaneko, Katsumi; Kim, Yoong Ahm; Noguchi, Minoru; Fujino, Takeshi; Oyama, Shigeki; Endo, Morinobu

    2012-03-12

    Supercapacitors can store and deliver energy by a simple charge separation, and thus they could be an attractive option to meet transient high energy density in operating fuel cells and in electric and hybrid electric vehicles. To achieve such requirements, intensive studies have been carried out to improve the volumetric capacitance in supercapacitors using various types and forms of carbons including carbon nanotubes and graphenes. However, conventional porous carbons are not suitable for use as electrode material in supercapacitors for such high energy density applications. Here, we show that edge-enriched porous carbons are the best electrode material for high energy density supercapacitors to be used in vehicles as an auxiliary powertrain. Molten potassium hydroxide penetrates well-aligned graphene layers vertically and consequently generates both suitable pores that are easily accessible to the electrolyte and a large fraction of electrochemically active edge sites. We expect that our findings will motivate further research related to energy storage devices and also environmentally friendly electric vehicles.

  1. In Vitro Amphotericin B Susceptibility of Malassezia pachydermatis Determined by the CLSI Broth Microdilution Method and Etest Using Lipid-Enriched Media

    PubMed Central

    Álvarez-Pérez, Sergio; Peláez, Teresa; Cutuli, Maite; García, Marta E.

    2014-01-01

    We determined the in vitro amphotericin B susceptibility of 60 Malassezia pachydermatis isolates by the CLSI broth microdilution method and the Etest using lipid-enriched media. All isolates were susceptible at MICs of ≤1 μg/ml, confirming the high activity of amphotericin B against this yeast species. Overall, the essential agreement between the tested methods was high (80% and 96.7% after 48 h and 72 h, respectively), and all discrepancies were regarded as nonsubstantial. PMID:24752258

  2. Separation and Enrichment of the Active Component of Carbon Based Paramagnetic Materials for Use in EPR Oximetry

    NASA Astrophysics Data System (ADS)

    Liu, K. J.; Miyake, M.; James, P. E.; Swartz, H. M.

    1998-08-01

    Carbon based paramagnetic materials are frequently used for EPR oximetry, especiallyin vivo,but the EPR spectra of these materials often have more than one paramagnetic center and/or relatively low signal intensity. To determine whether the multi-components of carbon based materials could be separated and enriched in the active component, we used density gradient centrifugation to separate the materials into several fractions. We studied two types of coals, gloxy and Pocahontas, and found these materials to have large density distribution. The separated density fractions had very different EPR spectra and intensities. The active component from the coal material had a more homogeneous EPR signal and significantly increased EPR signal intensity, whereas for India ink, only slight changes were observed. This result can be very useful in the development of better probes for EPR oximetry.

  3. Separation and enrichment of the active component of carbon based paramagnetic materials for use in EPR oximetry.

    PubMed

    Liu, K J; Miyake, M; James, P E; Swartz, H M

    1998-08-01

    Carbon based paramagnetic materials are frequently used for EPR oximetry, especially in vivo, but the EPR spectra of these materials often have more than one paramagnetic center and/or relatively low signal intensity. To determine whether the multi-components of carbon based materials could be separated and enriched in the active component, we used density gradient centrifugation to separate the materials into several fractions. We studied two types of coals, gloxy and Pocahontas, and found these materials to have large density distribution. The separated density fractions had very different EPR spectra and intensities. The active component from the coal material had a more homogeneous EPR signal and significantly increased EPR signal intensity, whereas for India ink, only slight changes were observed. This result can be very useful in the development of better probes for EPR oximetry.

  4. Substrate-Based Fragment Identification for the Development of Selective, Nonpeptidic Inhibitors of Striatal-Enriched Protein Tyrosine Phosphatase

    PubMed Central

    Baguley, Tyler D.; Xu, Hai-Chao; Chatterjee, Manavi; Nairn, Angus C.; Lombroso, Paul J.; Ellman, Jonathan A.

    2013-01-01

    High levels of striatal-enriched protein tyrosine phosphatase (STEP) activity are observed in a number of neuropsychiatric disorders such as Alzheimer’s disease. Over-expression of STEP results in the dephosphorylation and inactivation of many key neuronal signaling molecules, including ionotropic glutamate receptors. Moreover, genetically reducing STEP levels in AD mouse models significantly reversed cognitive deficits and decreased glutamate receptor internalization. These results support STEP as a potential target for drug discovery for the treatment of Alzheimer’s disease. Herein, a substrate-based approach for the discovery and optimization of fragments called substrate activity screening (SAS) has been applied to the development of low molecular weight (<450 Da) and non-peptidic, single-digit micromolar mechanism-based STEP inhibitors with greater than 20-fold selectivity across multiple tyrosine and dual specificity phosphatases. Significant levels of STEP inhibition in rat cortical neurons are also observed. PMID:24083656

  5. Selective extraction and enrichment of glycoproteins based on boronate affinity SPME and determination by CIEF-WCID.

    PubMed

    Li, Lixian; Xia, Zhining; Pawliszyn, Janusz

    2015-07-30

    In this study, a new thin-film boronic acid coating was developed for solid-phase microextraction (SPME) followed by capillary isoelectric focusing with whole-column imaging detection (CIEF-WCID). Boronate functionalized particles of phenylboronic acid (PBA) and 3-aminophenylboronic acid (3-aPBA) were utilized as boronate affinity solid phase coating on thin-film stainless steel blades for selective extraction and enrichment of glycoproteins. The process of extraction and elution could be easily controlled by adjusting pH. To test specificity, asialofetuin and lactoferrin were selected as glycoproteins test molecules, while BSA and myoglobin were used as control non-glycoproteins in this study. The boronate affinity coating was characterized. The effect of buffer, pH, extraction profiles and elution profiles were investigated. The developed method was successfully applied to extract glycoproteins from standard buffer, PBS, human plasma and 10-fold diluted human blood using two kinds of boronate affinity blades. Boronate affinity SPME could be a promising tool for selective extraction and enrichment of low-abundance glycoproteins in real biological samples.

  6. Network motif-based method for identifying coronary artery disease

    PubMed Central

    LI, YIN; CONG, YAN; ZHAO, YUN

    2016-01-01

    The present study aimed to develop a more efficient method for identifying coronary artery disease (CAD) than the conventional method using individual differentially expressed genes (DEGs). GSE42148 gene microarray data were downloaded, preprocessed and screened for DEGs. Additionally, based on transcriptional regulation data obtained from ENCODE database and protein-protein interaction data from the HPRD, the common genes were downloaded and compared with genes annotated from gene microarrays to screen additional common genes in order to construct an integrated regulation network. FANMOD was then used to detect significant three-gene network motifs. Subsequently, GlobalAncova was used to screen differential three-gene network motifs between the CAD group and the normal control data from GSE42148. Genes involved in the differential network motifs were then subjected to functional annotation and pathway enrichment analysis. Finally, clustering analysis of the CAD and control samples was performed based on individual DEGs and the top 20 network motifs identified. In total, 9,008 significant three-node network motifs were detected from the integrated regulation network; these were categorized into 22 interaction modes, each containing a minimum of one transcription factor. Subsequently, 1,132 differential network motifs involving 697 genes were screened between the CAD and control group. The 697 genes were enriched in 154 gene ontology terms, including 119 biological processes, and 14 KEGG pathways. Identifying patients with CAD based on the top 20 network motifs provided increased accuracy compared with the conventional method based on individual DEGs. The results of the present study indicate that the network motif-based method is more efficient and accurate for identifying CAD patients than the conventional method based on individual DEGs. PMID:27347046

  7. Rapid enrichment of rare-earth metals by carboxymethyl cellulose-based open-cellular hydrogel adsorbent from HIPEs template.

    PubMed

    Zhu, Yongfeng; Wang, Wenbo; Zheng, Yian; Wang, Feng; Wang, Aiqin

    2016-04-20

    A series of monolithic open-cellular hydrogel adsorbents based on carboxymethylcellulose (CMC) were prepared through high internal phase emulsions (HIPEs) and used to enrich the rare-earth metals La(3+) and Ce(3+). The changes of pore structure, and the effects of pH, contact time, initial concentration on the adsorption performance were systematically studied. The results show that the as-prepared monolithic hydrogel adsorbents possess good open-cellular framework structure and have fast adsorption kinetics and high adsorption capacity for La(3+) and Ce(3+). The involved adsorption system can reach equilibrium within 30min and the maximal adsorption capacity is determined to be 384.62mg/g for La(3+) and 333.33mg/g for Ce(3+). Moreover, these porous hydrogel adsorbents show an excellent adsorptive reusability for La(3+) and Ce(3+) through five adsorption-desorption cycles. Such a pore hierarchy structure makes this monolithic open-cellular hydrogel adsorbent be an effective adsorbent for effective enrichment of La(3+) and Ce(3+) from aqueous solution. PMID:26876827

  8. Rapid enrichment of rare-earth metals by carboxymethyl cellulose-based open-cellular hydrogel adsorbent from HIPEs template.

    PubMed

    Zhu, Yongfeng; Wang, Wenbo; Zheng, Yian; Wang, Feng; Wang, Aiqin

    2016-04-20

    A series of monolithic open-cellular hydrogel adsorbents based on carboxymethylcellulose (CMC) were prepared through high internal phase emulsions (HIPEs) and used to enrich the rare-earth metals La(3+) and Ce(3+). The changes of pore structure, and the effects of pH, contact time, initial concentration on the adsorption performance were systematically studied. The results show that the as-prepared monolithic hydrogel adsorbents possess good open-cellular framework structure and have fast adsorption kinetics and high adsorption capacity for La(3+) and Ce(3+). The involved adsorption system can reach equilibrium within 30min and the maximal adsorption capacity is determined to be 384.62mg/g for La(3+) and 333.33mg/g for Ce(3+). Moreover, these porous hydrogel adsorbents show an excellent adsorptive reusability for La(3+) and Ce(3+) through five adsorption-desorption cycles. Such a pore hierarchy structure makes this monolithic open-cellular hydrogel adsorbent be an effective adsorbent for effective enrichment of La(3+) and Ce(3+) from aqueous solution.

  9. Preparation and loading buffer study of polyvinyl alcohol-based immobilized Ti4+ affinity chromatography for phosphopeptide enrichment.

    PubMed

    Hu, Yufeng; Guo, Shuangxi; Ma, Hongbo; Ye, Ning; Ren, Xueqin

    2013-11-01

    Despite recent advances in phosphoproteomics, an efficient and simple enrichment protocol is still a challenge and of high demand aiming at large-scale plant phosphoproteomics studies. Here, we developed a novel loading buffer system for synthesized immobilized metal affinity chromatography material targeting plant samples, which was prepared by a simple one-step esterification between polyvinyl alcohol and phosphoric acid and then was subjected to immobilize Ti(4+). SEM and Fourier transform IR spectroscopy were used to assure the synthesis protocol of the polyvinyl alcohol-based Ti(4+) immobilized material, and the specific surface areas and pore volumes of the polymers were measured. The selectivity for phosphopeptide enrichment from α-casein was improved by optimizing the pH and components of the loading buffer. By using potassium hydrogen phthalate/hydrochloric acid with pH at 2.50 as the loading buffer, 19 phosphopeptides with high intensity were identified. The final optimized protocol was adapted to salt-stressed maize leaves for phosphoproteome analysis. A total of 57 phosphopeptides containing 59 phosphorylated sites from 50 phosphoproteins were identified in salt-stressed maize leaf. The research was meaningful to obtain much more information about phosphoproteins leading to the comprehension of salt resistance and salt-inducible phosphorylated processes of maize leaves.

  10. Synthesis and Oxidation Behavior of Platinum-Enriched γ+γ' Bond Coatings on Ni-Based Superalloys

    SciTech Connect

    Zhang, Ying; Ballard, D A; Stacy, J P; Pint, Bruce A; Haynes, James A

    2006-01-01

    Simple Pt-enriched {gamma}+{gamma}{prime} coatings were synthesized on Rene 142 and Rene N5 Ni-based superalloys by electroplating a thin layer of Pt followed by a diffusion treatment at 1150-1175 C. The Al content in the resulting {gamma}+{gamma}{prime} coating was in the range of 16-19 at.% on superalloys with 13-14 at.% Al. After oxidation testing, alumina scale adherence to these {gamma}+{gamma}{prime} coatings was not as uniform as to the {beta}-(Ni,Pt)Al coatings on the same superalloy substrates. To better understand the effect of Al, Pt and Hf concentrations on coating oxidation resistance, a number of Ni-Pt-Al cast alloys with {gamma}+{gamma}{prime} or {beta} phase were cyclically oxidized at 1100 C. The Hf-containing {gamma}+{gamma}{prime} alloys with 22 at.% Al and 10-30 at.% Pt exhibited similar oxidation resistance to the {beta} alloys with 50 at.% Al. An initial effort was made to increase the Al content in the Pt-enriched {gamma}+{gamma}{prime} coatings by introducing a short-term aluminizing process via chemical vapor deposition or pack cementation. However, too much Al was deposited, leading to the formation of {beta} or martensitic phase on the coating surface.

  11. Ion Enrichment on the Hydrophobic Carbon-based Surface in Aqueous Salt Solutions due to Cation-π Interactions

    PubMed Central

    Shi, Guosheng; Liu, Jian; Wang, Chunlei; Song, Bo; Tu, Yusong; Hu, Jun; Fang, Haiping

    2013-01-01

    By incorporating cation-π interactions to classic all-atoms force fields, we show that there is a clear enrichment of Na+ on a carbon-based π electron-rich surface in NaCl solutions using molecular dynamics simulations. Interestingly, Cl− is also enriched to some extend on the surface due to the electrostatic interaction between Na+ and Cl−, although the hydrated Cl−-π interaction is weak. The difference of the numbers of Na+ and Cl− accumulated at the interface leads to a significant negatively charged behavior in the solution, especially in nanoscale systems. Moreover, we find that the accumulation of the cations at the interfaces is universal since other cations (Li+, K+, Mg2+, Ca2+, Fe2+, Co2+, Cu2+, Cd2+, Cr2+, and Pb2+) have similar adsorption behaviors. For comparison, as in usual force field without the proper consideration of cation-π interactions, the ions near the surfaces have a similar density of ions in the solution. PMID:24310448

  12. A Platinum-Enriched gamma+gamma' Two-Phase Bond Coat on Ni-Base Superalloys

    SciTech Connect

    Zhang, Ying; Pint, Bruce A; Haynes, James A; Wright, Ian G

    2005-01-01

    Pt-enriched {gamma} + {gamma}{prime} two-phase coating was applied to directionally-solidified Ni-based superalloy Ren{acute e} 142 substrates with three different Hf levels (0.02, 0.76, and 1.37 wt.%). The coating was prepared by electroplating a thin layer of Pt on the superalloy followed by a diffusion treatment. The as-deposited coating exhibited a {gamma} + {gamma}{prime} two-phase microstructure with a major composition of Ni-16Al-18Pt-7Cr-9Co (in at.%) along with some incorporation of refractory elements from the substrates. Cyclic oxidation testing at 1100 C in air indicated improved oxidation resistance of the Ren{acute e} 142 alloys with the Pt-enriched {gamma} + {gamma}{prime} coatings. In addition, the oxidation resistance of both uncoated and coated alloys was proportional to the Hf content in the substrate. Compared with the single-phase {beta}-(Ni,Pt)Al coating, slightly higher mass gains and localized spallation were observed on the {gamma} + {gamma}{prime} two-phase coating, which might be due to the segregation of refractory elements and high sulfur levels in these superalloy substrates.

  13. Enrichment of polyphenol contents and antioxidant activities of Irish brown macroalgae using food-friendly techniques based on polarity and molecular size.

    PubMed

    Tierney, Michelle S; Smyth, Thomas J; Rai, Dilip K; Soler-Vila, Anna; Croft, Anna K; Brunton, Nigel

    2013-08-15

    An efficient, food-friendly process for the enrichment of macroalgal phlorotannins from solid-liquid extracts (SLE) of three brown macroalgae, namely Fucus spiralis Linnaeus, Pelvetia canaliculata (Linnaeus) Decaisne & Thuret and Ascophyllum nodosum (Linnaeus) Le Jolis, has been demonstrated. The initial utilisation of molecular weight cut-off (MWCO) dialysis generated fractions of low molecular weight (LMW) (<3.5 kDa) and of high molecular weight (HMW) (3.5-100 kDa and >100 kDa) from cold water, hot water and aqueous ethanolic SLE extracts. An enhancement of the total phenolic content (TPC), radical scavenging abilities (RSA) and ferric reducing antioxidant power (FRAP) in the HMW fractions of 3.5-100 kDa and/or >100 kDa from the cold water and aqueous ethanolic extracts was observed. The initial weak TPC, RSA and FRAP observed in the LMW fractions relative to the HMW fractions were substantially enhanced following a reverse-phase flash chromatography fractionation method. Quadrupole time-of-flight mass spectrometry (Q-Tof-MS) suggests that phlorotannins of varying degrees of phloroglucinol polymerisation are present in LMW fractions of the three brown macroalgal species. The development of a food-friendly process for the extraction and enrichment of phlorotannins from Irish macroalgae is vital to facilitate the use of this valuable resource in future developments of macroalgal-based functional foods. PMID:23561170

  14. Automated Microchromatography Enables Multiplexing of Immunoaffinity Enrichment of Peptides to Greater than 150 for Targeted MS-Based Assays.

    PubMed

    Ippoliti, Paul J; Kuhn, Eric; Mani, D R; Fagbami, Lola; Keshishian, Hasmik; Burgess, Michael W; Jaffe, Jacob D; Carr, Steven A

    2016-08-01

    Immunoaffinity enrichment of peptides coupled with analysis by stable isotope dilution multiple reaction mass spectrometry has been shown to have analytical performance and detection limits suitable for many biomarker verification studies and biological applications. Prior studies have shown that antipeptide antibodies can be multiplexed up to 50 in a single assay without significant loss of performance. Achieving higher multiplex levels is relevant to all studies involving precious biological material as this minimizes the amount of sample that must be consumed to measure a given set of analytes and reduces the assay cost per analyte. Here we developed automated methods employing the Agilent AssayMAP Bravo microchromatography platform and used these methods to characterize the performance of immunoaffinity enrichment of peptides up to multiplex levels of 172. Median capture efficiency for the target peptides remained high (88%) even at levels of 150-plex and declined to 70% at 172-plex compared to antibody performance observed at standard lower multiplex levels (n = 25). Subsequently, we developed and analytically characterized a multiplexed immuno-multiple reaction monitoring-mass spectrometry (immuno-MRM-MS) assay (n = 110) and applied it to measure candidate protein biomarkers of cardiovascular disease in plasma of patients undergoing planned myocardial infarction. The median lower limit of detection of all peptides was 71.5 amol/μL (nM), and the coefficient of variation (CV) was less than 15% at the lower limit of quantification. The results demonstrate that high multiplexed immuno-MRM-MS assays are readily achievable using the optimized sample processing and peptide capture methods described here. PMID:27321643

  15. A history-based method to estimate animal preference.

    PubMed

    Maia, Caroline Marques; Volpato, Gilson Luiz

    2016-01-01

    Giving animals their preferred items (e.g., environmental enrichment) has been suggested as a method to improve animal welfare, thus raising the question of how to determine what animals want. Most studies have employed choice tests for detecting animal preferences. However, whether choice tests represent animal preferences remains a matter of controversy. Here, we present a history-based method to analyse data from individual choice tests to discriminate between preferred and non-preferred items. This method differentially weighs choices from older and recent tests performed over time. Accordingly, we provide both a preference index that identifies preferred items contrasted with non-preferred items in successive multiple-choice tests and methods to detect the strength of animal preferences for each item. We achieved this goal by investigating colour choices in the Nile tilapia fish species. PMID:27350213

  16. A history-based method to estimate animal preference

    PubMed Central

    Maia, Caroline Marques; Volpato, Gilson Luiz

    2016-01-01

    Giving animals their preferred items (e.g., environmental enrichment) has been suggested as a method to improve animal welfare, thus raising the question of how to determine what animals want. Most studies have employed choice tests for detecting animal preferences. However, whether choice tests represent animal preferences remains a matter of controversy. Here, we present a history-based method to analyse data from individual choice tests to discriminate between preferred and non-preferred items. This method differentially weighs choices from older and recent tests performed over time. Accordingly, we provide both a preference index that identifies preferred items contrasted with non-preferred items in successive multiple-choice tests and methods to detect the strength of animal preferences for each item. We achieved this goal by investigating colour choices in the Nile tilapia fish species. PMID:27350213

  17. Enriching Project-Based Learning Environments with Virtual Manipulatives: A Comparative Study

    ERIC Educational Resources Information Center

    Çakiroglu, Ünal

    2014-01-01

    Problem statement: Although there is agreement on the potential of project based learning (PBL) and virtual manipulatives (VMs), their positive impact depends on how they are used. This study was based on supporting the use of online PBL environments and improving the efficacy of the instructional practices in PBL by combining the potentials of…

  18. Universal screening test based on analysis of circulating organ-enriched microRNAs: a novel approach to diagnostic screening.

    PubMed

    Sheinerman, Kira S; Umansky, Samuil

    2015-03-01

    Early disease detection leads to more effective and cost-efficient treatment. It is especially important for cancer and neurodegenerative diseases, because progression of these pathologies leads to significant and frequently irreversible changes in underlying pathophysiological processes. At the same time, the development of specific screening tests for detection of each of the hundreds of human pathologies in asymptomatic stage may be impractical. Here, we discuss a recently proposed concept: the development of minimally invasive Universal Screening Test (UST) based on analysis of organ-enriched microRNAs in plasma and other bodily fluids. The UST is designed to detect the presence of a pathology in particular organ systems, organs, tissues or cell types without diagnosing a specific disease. Once the pathology is detected, more specific, and if necessary invasive and expensive, tests can be administered to precisely define the nature of the disease. Here, we discuss recent studies and analyze the data supporting the UST approach.

  19. Synchrotron based infrared imaging and spectroscopy via focal plane array on live fibroblasts in D2O enriched medium

    SciTech Connect

    Quaroni, Luca; Zlateva, Theodora; Sarafimov, Blagoj; Kreuzer, Helen W.; Wehbe, Katia; Hegg, Eric L.; Cinque, Gianfelice

    2014-03-26

    We tested the viability of using synchrotron based infrared imaging to study biochemical processes inside living cells. As a model system, we studied fibroblast cells exposed to a medium highly enriched with D2O. We could show that the experimental technique allows us to reproduce at the cellular level measurements that are normally performed on purified biological molecules. We can obtain information about lipid conformation and distribution, kinetics of hydrogen/deuterium exchange, and the formation of concentration gradients of H and O isotopes in water that are associated with cell metabolism. The implementation of the full field technique in a sequential imaging format gives a description of cellular biochemistry and biophysics that contains both spatial and temporal information.

  20. Enriched branched-chain amino acid formula versus a casein-based supplement in the treatment of cirrhosis.

    PubMed

    Christie, M L; Sack, D M; Pomposelli, J; Horst, D

    1985-01-01

    An orally administered branched-chain amino acid (BCAA) rich supplement (T), Travasorb-Hepatic was compared to a casein based supplement (E), Ensure, in a randomized double-blind cross-over study in eight malnourished, stable cirrhotics unable to achieve a daily dietary protein intake of 1.0 g/kg. Doses of antiportal systemic encephalopathy drugs remained constant and a baseline 1000 kcal, 40 g dietary protein intake was encouraged. To this diet, supplemental protein was added in daily 20-g increments to a maximum of 60 g supplemental protein. Mental status, asterixis, and number connection tests were assessed daily and an antiportal systemic encephalopathy index calculated. There was no significant difference in the mean intake of dietary protein (T, 33.7 +/- 4.0 g; E, 26.7 +/- 10.8 g), supplemental protein (T, 43.1 +/- 8.3 g; E, 47.9 +/- 7.1 g), or N2 balance (T, 4.2 +/- 3.7 g; E, 3.4 +/- 4.4) between treatment trials. The antiportal systemic encephalopathy index improved on E, with no significant change in the BCAA:aromatic acid molar ratio. This ratio improved on T (1.02 +/- 2.0 to 2.7 +/- 1.1), but was not accompanied by improvement in the antiportal systemic encephalopathy index. The improved protein tolerance in both groups was not further increased by a highly enriched BCAA formula compared to one with a moderate BCAA content from a natural dietary protein source. Thus, both conventional casein-based supplements and enriched BCAA formulas are well tolerated and can be safely and effectively used as an integral part of diet therapy.

  1. A method to assess relative preference for training and environmental enrichment in captive wolves (Canis lupus and Canis lupus arctos).

    PubMed

    Dorey, Nicole R; Mehrkam, Lindsay R; Tacey, Jay

    2015-11-01

    It is currently debated as to whether or not positive reinforcement training is enriching to captive animals. Although both husbandry training and environmental enrichment (EE) have been found to benefit animal welfare in captivity, to date, no systematic investigation has compared an animal's preference for performing a trained behavior to engaging freely with a stimuli provided as EE. In the current paper, we used four captive wolves to (1) test the efficacy of a paired-stimulus preference assessment to determine preference for engaging in a trained behavior as a choice; and to (2) use a paired-stimulus preference assessment to determine whether or not individuals prefer to engage in a previously trained behavior versus a previously encountered EE stimuli. Of the four subjects tested, visual inspection of the graphs revealed that two of the subjects preferred trained behavior stimuli and two of the subjects preferred EE stimuli; only one of the wolves had a statically higher preference for an EE stimulus over a trained behavior. We believe that letting the animals choose between these two events is the first step in answering the question of whether or not is training enriching, however more research needs to be done and suggestions for future research is discussed.

  2. A method to assess relative preference for training and environmental enrichment in captive wolves (Canis lupus and Canis lupus arctos).

    PubMed

    Dorey, Nicole R; Mehrkam, Lindsay R; Tacey, Jay

    2015-11-01

    It is currently debated as to whether or not positive reinforcement training is enriching to captive animals. Although both husbandry training and environmental enrichment (EE) have been found to benefit animal welfare in captivity, to date, no systematic investigation has compared an animal's preference for performing a trained behavior to engaging freely with a stimuli provided as EE. In the current paper, we used four captive wolves to (1) test the efficacy of a paired-stimulus preference assessment to determine preference for engaging in a trained behavior as a choice; and to (2) use a paired-stimulus preference assessment to determine whether or not individuals prefer to engage in a previously trained behavior versus a previously encountered EE stimuli. Of the four subjects tested, visual inspection of the graphs revealed that two of the subjects preferred trained behavior stimuli and two of the subjects preferred EE stimuli; only one of the wolves had a statically higher preference for an EE stimulus over a trained behavior. We believe that letting the animals choose between these two events is the first step in answering the question of whether or not is training enriching, however more research needs to be done and suggestions for future research is discussed. PMID:26274933

  3. The Perspectives of Major Stakeholders on Video Enriched Problem-Based Learning for Chinese Teacher Education

    ERIC Educational Resources Information Center

    Ma, Angela Kit Fong; O'Toole, John Mitchell

    2013-01-01

    The study described in this paper investigated how the major stakeholders of a teacher education institution responded to a particular suite of educational products that involved video-based educational learning objects. It aims to look into stakeholder attitudes to potential technological development in fostering student-centred learning in…

  4. Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

    SciTech Connect

    Babauta, Jerome T.; Atci, Erhan; Ha, Phuc T.; Lindemann, Stephen R.; Ewing, Timothy; Call, Douglas R.; Fredrickson, James K.; Beyenal, Haluk

    2014-01-01

    Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode- associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1-V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.

  5. Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

    PubMed Central

    Babauta, Jerome T.; Atci, Erhan; Ha, Phuc T.; Lindemann, Stephen R.; Ewing, Timothy; Call, Douglas R.; Fredrickson, James K.; Beyenal, Haluk

    2014-01-01

    Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode-associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1–V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community. PMID:24478768

  6. Effect of Model Sorptive Phases on Phenanthrene Biodegradation: Molecular Analysis of Enrichments and Isolates Suggests Selection Based on Bioavailability

    PubMed Central

    Friedrich, M.; Grosser, R. J.; Kern, E. A.; Inskeep, W. P.; Ward, D. M.

    2000-01-01

    Reduced bioavailability of nonpolar contaminants due to sorption to natural organic matter is an important factor controlling biodegradation of pollutants in the environment. We established enrichment cultures in which solid organic phases were used to reduce phenanthrene bioavailability to different degrees (R. J. Grosser, M. Friedrich, D. M. Ward, and W. P. Inskeep, Appl. Environ. Microbiol. 66:2695–2702, 2000). Bacteria enriched and isolated from contaminated soils under these conditions were analyzed by denaturing gradient gel electrophoresis (DGGE) and sequencing of PCR-amplified 16S ribosomal DNA segments. Compared to DGGE patterns obtained with enrichment cultures containing sand or no sorptive solid phase, different DGGE patterns were obtained with enrichment cultures containing phenanthrene sorbed to beads of Amberlite IRC-50 (AMB), a weak cation-exchange resin, and especially Biobead SM7 (SM7), a polyacrylic resin that sorbed phenanthrene more strongly. SM7 enrichments selected for mycobacterial phenanthrene mineralizers, whereas AMB enrichments selected for a Burkholderia sp. that degrades phenanthrene. Identical mycobacterial and Burkholderia 16S rRNA sequence segments were found in SM7 and AMB enrichment cultures inoculated with contaminated soil from two geographically distant sites. Other closely related Burkholderia sp. populations, some of which utilized phenanthrene, were detected in sand and control enrichment cultures. Our results are consistent with the hypothesis that different phenanthrene-utilizing bacteria inhabiting the same soils may be adapted to different phenanthrene bioavailabilities. PMID:10877758

  7. Addressing Loss of Efficiency Due to Misclassification Error in Enriched Clinical Trials for the Evaluation of Targeted Therapies Based on the Cox Proportional Hazards Model

    PubMed Central

    Tsai, Chen-An; Lee, Kuan-Ting; Liu, Jen-pei

    2016-01-01

    A key feature of precision medicine is that it takes individual variability at the genetic or molecular level into account in determining the best treatment for patients diagnosed with diseases detected by recently developed novel biotechnologies. The enrichment design is an efficient design that enrolls only the patients testing positive for specific molecular targets and randomly assigns them for the targeted treatment or the concurrent control. However there is no diagnostic device with perfect accuracy and precision for detecting molecular targets. In particular, the positive predictive value (PPV) can be quite low for rare diseases with low prevalence. Under the enrichment design, some patients testing positive for specific molecular targets may not have the molecular targets. The efficacy of the targeted therapy may be underestimated in the patients that actually do have the molecular targets. To address the loss of efficiency due to misclassification error, we apply the discrete mixture modeling for time-to-event data proposed by Eng and Hanlon [8] to develop an inferential procedure, based on the Cox proportional hazard model, for treatment effects of the targeted treatment effect for the true-positive patients with the molecular targets. Our proposed procedure incorporates both inaccuracy of diagnostic devices and uncertainty of estimated accuracy measures. We employed the expectation-maximization algorithm in conjunction with the bootstrap technique for estimation of the hazard ratio and its estimated variance. We report the results of simulation studies which empirically investigated the performance of the proposed method. Our proposed method is illustrated by a numerical example. PMID:27120450

  8. About Prospects of Enrichment of Mineral Raw Materials and Chemical Activation of Water Suspensions by Electroexplosive Method

    NASA Astrophysics Data System (ADS)

    Bordunov, S. V.; Galtseva, O. V.

    2016-01-01

    A series of experiments is conducted on laboratory and pilot-production installation for the application of high-voltage pulsed discharge in the processes of enrichment of goldbearing mineral raw materials with a relatively low energy electrical discharge in the pulse of 120 J. At the same time the conglomerates of clay components are breaking down to micron and submicron sizes completely. Solid minerals such as quartz are simultaneously destroyed by defects and grains and withdrawn from the installation with water, thus increasing degree of enrichment of concentrate. The results of the processing by high-voltage pulsed discharges of building sand from the Ob riverbed are given. Discharge energy is 45 J. Relations of fractions in the original sand and in the sand after electroexplosive process show the uniform crushing of sand particles with splitting off particles with size of less than 0.045 mm. A content of chipped particles is 18%. The results of particle-size and X-ray structural analyses are shown.

  9. Enrichment of DNRA bacteria in a continuous culture

    PubMed Central

    van den Berg, Eveline M; van Dongen, Udo; Abbas, Ben; van Loosdrecht, Mark CM

    2015-01-01

    Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are competing microbial nitrate-reduction processes. The occurrence of DNRA has been shown to be effected qualitatively by various parameters in the environment. A more quantitative understanding can be obtained using enrichment cultures in a laboratory reactor, yet no successful DNRA enrichment culture has been described. We showed that a stable DNRA-dominated enrichment culture can be obtained in a chemostat system. The enrichment was based on the hypothesis that nitrate limitation is the dominant factor in selecting for DNRA. First, a conventional denitrifying culture was enriched from activated sludge, with acetate and nitrate as substrates. Next, the acetate concentration in the medium was increased to obtain nitrate-limiting conditions. As a result, conversions shifted from denitrification to DNRA. In this selection of a DNRA culture, two important factors were the nitrate limitation and a relatively low dilution rate (0.026 h−1). The culture was a highly enriched population of Deltaproteobacteria most closely related to Geobacter lovleyi, based on 16S rRNA gene sequencing (97% similarity). We established a stable and reproducible cultivation method for the enrichment of DNRA bacteria in a continuously operated reactor system. This enrichment method allows to further investigate the DNRA process and address the factors for competition between DNRA and denitrification, or other N-conversion pathways. PMID:25909972

  10. Comparison of cold enrichment and U.S. Department of Agriculture methods for isolating Listeria monocytogenes from naturally contaminated foods. The Listeria Study Group.

    PubMed Central

    Hayes, P S; Graves, L M; Ajello, G W; Swaminathan, B; Weaver, R E; Wenger, J D; Schuchat, A; Broome, C V

    1991-01-01

    We compared the cold enrichment (CE) and U.S. Department of Agriculture (USDA) methods for isolating Listeria monocytogenes by examining 402 food samples. The food samples were collected from refrigerators of listeriosis patients as part of a multistate active surveillance project to determine the role of foods in sporadic listeriosis in the United States. L. monocytogenes was isolated from 51 food samples (13%). The USDA method was significantly better (P less than 0.001) than the CE method. The isolation efficiencies of the USDA and CE methods were 96 and 59%, respectively. Quantitation of L. monocytogenes in the food samples revealed that many food samples containing less than 0.3 CFU/g were negative as determined by the CE method but positive as determined by the USDA method. PMID:1768082

  11. CULTURAL ENRICHMENT PROGRAMS.

    ERIC Educational Resources Information Center

    WASHINGTON, BENNETTA B.

    METHODS BY WHICH CULTURAL ENRICHMENT PROGRAMS CAN HELP TO ELIMINATE JUVENILE DELINQUENCY ARE DISCUSSED. IT IS STRESSED THAT CULTURE IS A SET OF VALUES, RATHER THAN A SERIES OF CONCEPTS. IF CULTURE IS TO BE TRANSMITTED TO STUDENTS, TEACHERS MUST LIVE ITS VALUES. ATTENDING CONCERTS AND PLAYS IS NOT SUFFICIENT. ONLY IN THE BROAD SETTING OF A TOTAL…

  12. Targeted toxin-based selectable drug-free enrichment of Mammalian cells with high transgene expression.

    PubMed

    Sato, Masahiro; Akasaka, Eri; Saitoh, Issei; Ohtsuka, Masato; Nakamura, Shingo; Sakurai, Takayuki; Watanabe, Satoshi

    2013-01-01

    Almost all transfection protocols for mammalian cells use a drug resistance gene for the selection of transfected cells. However, it always requires the characterization of each isolated clone regarding transgene expression, which is time-consuming and labor-intensive. In the current study, we developed a novel method to selectively isolate clones with high transgene expression without drug selection. Porcine embryonic fibroblasts were transfected with pCEIEnd, an expression vector that simultaneously expresses enhanced green fluorescent protein (EGFP) and endo-b-galactosidase C(EndoGalC; an enzyme capable of digesting cell surface a-Gal epitope) upon transfection. After transfection, the surviving cells were briefly treated with IB4SAP (a-Gal epitope-specific BS-I-B4 lectin conjugated with a toxin saporin). The treated cells were then allowed to grow in normal medium, during which only cells strongly expressing EndoGalC and EGFP would survive because of the absence of a-Gal epitopes on their cell surface. Almost all the surviving colonies after IB4SAP treatment were in fact negative for BS-I-B4 staining, and also strongly expressed EGFP. This system would be particularly valuable for researchers who wish to perform large-scale production of therapeutically important recombinant proteins. PMID:24832665

  13. Network diffusion-based analysis of high-throughput data for the detection of differentially enriched modules

    PubMed Central

    Bersanelli, Matteo; Mosca, Ettore; Remondini, Daniel; Castellani, Gastone; Milanesi, Luciano

    2016-01-01

    A relation exists between network proximity of molecular entities in interaction networks, functional similarity and association with diseases. The identification of network regions associated with biological functions and pathologies is a major goal in systems biology. We describe a network diffusion-based pipeline for the interpretation of different types of omics in the context of molecular interaction networks. We introduce the network smoothing index, a network-based quantity that allows to jointly quantify the amount of omics information in genes and in their network neighbourhood, using network diffusion to define network proximity. The approach is applicable to both descriptive and inferential statistics calculated on omics data. We also show that network resampling, applied to gene lists ranked by quantities derived from the network smoothing index, indicates the presence of significantly connected genes. As a proof of principle, we identified gene modules enriched in somatic mutations and transcriptional variations observed in samples of prostate adenocarcinoma (PRAD). In line with the local hypothesis, network smoothing index and network resampling underlined the existence of a connected component of genes harbouring molecular alterations in PRAD. PMID:27731320

  14. Thermal breeder fuel enrichment zoning

    DOEpatents

    Capossela, Harry J.; Dwyer, Joseph R.; Luce, Robert G.; McCoy, Daniel F.; Merriman, Floyd C.

    1992-01-01

    A method and apparatus for improving the performance of a thermal breeder reactor having regions of higher than average moderator concentration are disclosed. The fuel modules of the reactor core contain at least two different types of fuel elements, a high enrichment fuel element and a low enrichment fuel element. The two types of fuel elements are arranged in the fuel module with the low enrichment fuel elements located between the high moderator regions and the high enrichment fuel elements. Preferably, shim rods made of a fertile material are provided in selective regions for controlling the reactivity of the reactor by movement of the shim rods into and out of the reactor core. The moderation of neutrons adjacent the high enrichment fuel elements is preferably minimized as by reducing the spacing of the high enrichment fuel elements and/or using a moderator having a reduced moderating effect.

  15. Development of a real-time PCR method coupled with a selective pre-enrichment step for quantification of Morganella morganii and Morganella psychrotolerans in fish products.

    PubMed

    Podeur, Gaëtan; Dalgaard, Paw; Leroi, Francoise; Prévost, Hervé; Emborg, Jette; Martinussen, Jan; Hansen, Lars Hestbjerg; Pilet, Marie-France

    2015-06-16

    Histamine fish poisoning is common and due to toxic concentrations of histamine often produced by Gram-negative bacteria in fin-fish products with a high content of the free amino acid histidine. The genus Morganella includes two species previously reported to cause incidents of histamine fish poisoning. Morganella morganii and Morganella psychrotolerans are both strong producer of histamine. However, little is known about the occurrence and critical stages for fish contamination with these bacteria. To elucidate contamination routes of Morganella, specific real-time quantitative PCR (RTi qPCR) methods for quantification of M. morganii and M. psychrotolerans have been developed. Selective primers amplified a 110 bp region of the vasD gene for M. psychrotolerans and a 171 bp region of the galactokinase gene for M. morganii. These primer-sets showed high specificity as demonstrated by using purified DNA from 23 other histamine producing bacteria and 26 isolates with no or limited histamine production. The efficiency of the qPCR reactions on artificially contaminated fish samples were 100.8% and 96.3% respectively. The limit of quantification (LOQ) without enrichment was 4 log CFU/g. A quantitative enrichment step with a selective medium was included and improved the sensitivity of the methods to a LOQ of below 50 CFU/g in seafood. RTi qPCR methods with or without enrichment were evaluated for enumeration of Morganella species in naturally contaminated fresh fish and lightly preserved seafood from Denmark. These new methods will contribute to a better understanding of the occurrence and histamine production by Morganella species in fish products, information that is essential to reduce the unacceptably high frequency of histamine fish poisoning.

  16. Fire extinguishment in oxygen enriched atmospheres

    NASA Technical Reports Server (NTRS)

    Robertson, A. F.; Rappaport, M. W.

    1973-01-01

    Current state-of-the-art of fire suppression and extinguishment techniques in oxygen enriched atmosphere is reviewed. Four classes of extinguishment action are considered: cooling, separation of reactants, dilution or removal of fuel, and use of chemically reactive agents. Current practice seems to show preference for very fast acting water spray applications to all interior surfaces of earth-based chambers. In space, reliance has been placed on fire prevention methods through the removal of ignition sources and use of nonflammable materials. Recommendations are made for further work related to fire suppression and extinguishment in oxygen enriched atmospheres, and an extensive bibliography is appended.

  17. A Mimic of the Tumor Microenvironment: A Simple Method for Generating Enriched Cell Populations and Investigating Intercellular Communication.

    PubMed

    Domogauer, Jason D; de Toledo, Sonia M; Azzam, Edouard I

    2016-09-20

    Understanding the early heterotypic interactions between cancer cells and the surrounding non-cancerous stroma is important in elucidating the events leading to stromal activation and establishment of the tumor microenvironment (TME). Several in vitro and in vivo models of the TME have been developed; however, in general these models do not readily permit isolation of individual cell populations, under non-perturbing conditions, for further study. To circumvent this difficulty, we have employed an in vitro TME model using a cell growth substrate consisting of a permeable microporous membrane insert that permits simple generation of highly enriched cell populations grown intimately, yet separately, on either side of the insert's membrane for extended co-culture times. Through use of this model, we are capable of generating greatly enriched cancer-associated fibroblast (CAF) populations from normal diploid human fibroblasts following co-culture (120 hr) with highly metastatic human breast carcinoma cells, without the use of fluorescent tagging and/or cell sorting. Additionally, by modulating the pore-size of the insert, we can control for the mode of intercellular communication (e.g., gap-junction communication, secreted factors) between the two heterotypic cell populations, which permits investigation of the mechanisms underlying the development of the TME, including the role of gap-junction permeability. This model serves as a valuable tool in enhancing our understanding of the initial events leading to cancer-stroma initiation, the early evolution of the TME, and the modulating effect of the stroma on the responses of cancer cells to therapeutic agents.

  18. A Mimic of the Tumor Microenvironment: A Simple Method for Generating Enriched Cell Populations and Investigating Intercellular Communication.

    PubMed

    Domogauer, Jason D; de Toledo, Sonia M; Azzam, Edouard I

    2016-01-01

    Understanding the early heterotypic interactions between cancer cells and the surrounding non-cancerous stroma is important in elucidating the events leading to stromal activation and establishment of the tumor microenvironment (TME). Several in vitro and in vivo models of the TME have been developed; however, in general these models do not readily permit isolation of individual cell populations, under non-perturbing conditions, for further study. To circumvent this difficulty, we have employed an in vitro TME model using a cell growth substrate consisting of a permeable microporous membrane insert that permits simple generation of highly enriched cell populations grown intimately, yet separately, on either side of the insert's membrane for extended co-culture times. Through use of this model, we are capable of generating greatly enriched cancer-associated fibroblast (CAF) populations from normal diploid human fibroblasts following co-culture (120 hr) with highly metastatic human breast carcinoma cells, without the use of fluorescent tagging and/or cell sorting. Additionally, by modulating the pore-size of the insert, we can control for the mode of intercellular communication (e.g., gap-junction communication, secreted factors) between the two heterotypic cell populations, which permits investigation of the mechanisms underlying the development of the TME, including the role of gap-junction permeability. This model serves as a valuable tool in enhancing our understanding of the initial events leading to cancer-stroma initiation, the early evolution of the TME, and the modulating effect of the stroma on the responses of cancer cells to therapeutic agents. PMID:27684198

  19. Mixed housing with DBA/2 mice induces stress in C57BL/6 mice: implications for interventions based on social enrichment.

    PubMed

    Kulesskaya, Natalia; Karpova, Nina N; Ma, Li; Tian, Li; Voikar, Vootele

    2014-01-01

    Several behavioral interventions, based on social enrichment and observational learning are applied in treatment of neuropsychiatric disorders. However, the mechanism of such modulatory effect and the safety of applied methods on individuals involved in social support need further investigation. We took advantage of known differences between inbred mouse strains to reveal the effect of social enrichment on behavior and neurobiology of animals with different behavioral phenotypes. C57BL/6 and DBA/2 female mice displaying multiple differences in cognitive, social, and emotional behavior were group-housed either in same-strain or in mixed-strain conditions. Comprehensive behavioral phenotyping and analysis of expression of several plasticity- and stress-related genes were done to measure the reciprocal effects of social interaction between the strains. Contrary to our expectation, mixed housing did not change the behavior of DBA/2 mice. Nevertheless, the level of serum corticosterone and the expression of glucocorticoid receptor Nr3c1 in the brain were increased in mixed housed DBA/2 as compared with those of separately housed DBA/2 mice. In contrast, socially active C57BL/6 animals were more sensitive to the mixed housing, displaying several signs of stress: alterations in learning, social, and anxiety-like behavior and anhedonia. These behavioral impairments were accompanied by the elevated serum corticosterone and the reduced expression of Nr3c1, as well as the elevated Bdnf levels in the cortex and hippocampus. Our results demonstrate the importance of social factors in modulation of both behavior and the underlying neurobiological mechanisms in stress response, and draw attention to the potential negative impact of social interventions for individuals involved in social support.

  20. Augmenting Learning in an Out-of-School Context: The Cognitive and Affective Impact of Two Cryogenics-Based Enrichment Programmes on Upper Primary Students

    ERIC Educational Resources Information Center

    Caleon, Imelda S.; Subramaniam, R.

    2007-01-01

    Concepts learned in the classroom were reinforced and augmented by presenting them in a different context using cryogenics-based enrichment programmes (CBEPs) held in an out-of-school setting. The effectiveness of two CBEPs, which involve the use of liquid nitrogen and liquid oxygen, was explored. Using a sample of 265 upper primary students, it…

  1. Asset-Based Civics for, with, and by Immigrant Students: Three Sites of Enriched Teaching and Learning for Immigrant and Native-Born Students

    ERIC Educational Resources Information Center

    Hilburn, Jeremy

    2015-01-01

    In this qualitative collective case study with 6 high school civics teachers, I found that using an asset-based approach to teaching civics for, with, and by immigrant students enriched teaching and learning for immigrant and native-born students, although participants missed some opportunities for deeper exploration. I used a combined theoretical…

  2. Lutein-enriched emulsion-based delivery systems: Influence of pH and temperature on physical and chemical stability.

    PubMed

    Davidov-Pardo, Gabriel; Gumus, Cansu Ekin; McClements, David Julian

    2016-04-01

    Lutein may be utilized in foods as a natural pigment or nutraceutical ingredient to improve eye health. Nevertheless, its use is limited by its poor water-solubility and chemical instability. We evaluated the effect of storage temperature and pH on the physical and chemical stability of lutein-enriched emulsions prepared using caseinate. The emulsions (initial droplet diameter=232 nm) remained physically stable at all incubation temperatures (5-70 °C); however the chemical degradation of lutein increased with increasing temperature (activation energy=38 kJ/mol). Solution pH had a major impact on the physical stability of the emulsions, causing droplet aggregation at pH 4 and 5. Conversely, the chemical stability of lutein was largely independent of the pH, with only a slight decrease in degradation at pH 8. This work provides important information for the rational design of emulsion-based delivery systems for a lipophilic natural dye and nutraceutical. PMID:26593560

  3. Lutein-enriched emulsion-based delivery systems: Influence of pH and temperature on physical and chemical stability.

    PubMed

    Davidov-Pardo, Gabriel; Gumus, Cansu Ekin; McClements, David Julian

    2016-04-01

    Lutein may be utilized in foods as a natural pigment or nutraceutical ingredient to improve eye health. Nevertheless, its use is limited by its poor water-solubility and chemical instability. We evaluated the effect of storage temperature and pH on the physical and chemical stability of lutein-enriched emulsions prepared using caseinate. The emulsions (initial droplet diameter=232 nm) remained physically stable at all incubation temperatures (5-70 °C); however the chemical degradation of lutein increased with increasing temperature (activation energy=38 kJ/mol). Solution pH had a major impact on the physical stability of the emulsions, causing droplet aggregation at pH 4 and 5. Conversely, the chemical stability of lutein was largely independent of the pH, with only a slight decrease in degradation at pH 8. This work provides important information for the rational design of emulsion-based delivery systems for a lipophilic natural dye and nutraceutical.

  4. Family, employment, and individual resource-based antecedents of maternal work-family enrichment from infancy through middle childhood.

    PubMed

    Zhou, Nan; Buehler, Cheryl

    2016-07-01

    This study used data from the National Institute of Child Health and Human Development (NICHD) Study of Early Child Care and Youth Development (N = 1,019) to examine family, employment, and individual antecedents of maternal work-family enrichment from infancy through middle childhood. Work-family conflict and important confounding factors were controlled. From the family domain, higher income-to-needs ratio and social support were associated with higher work-family enrichment. From the employment domain, greater job rewards, benefits of employment for children, and work commitment were associated with higher work-family enrichment. From the individual domain, higher maternal education and extroversion were associated with higher work-family enrichment. No family, employment, and individual characteristics were associated with work-family conflict across time except for partner intimacy. In general, the results supported antecedents of work-family enrichment that supply needed resources. The present study contributed to the literature by identifying antecedents of maternal work-family enrichment across early child developmental stages, which goes beyond examinations of particular life stages and a work-family conflict perspective. Implications for theory and practice are discussed. (PsycINFO Database Record

  5. GC/MS method for determining carbon isotope enrichment and concentration of underivatized short-chain fatty acids by direct aqueous solution injection of biogas digester samples.

    PubMed

    Mulat, Daniel Girma; Feilberg, Anders

    2015-10-01

    In anaerobic digestion of organic matter, several metabolic pathways are involved during the simultaneous production and consumption of short-chain fatty acids (SCFA) in general and acetate in particular. Understanding the role of each pathway requires both the determination of the concentration and isotope enrichment of intermediates in conjunction with isotope labeled substrates. The objective of this study was to establish a rapid and simple GC/MS method for determining the isotope enrichment of acetate and concentration of underivatized short-chain fatty acids (SCFA) in biogas digester samples by direct liquid injection of acidified aqueous samples. Sample preparation involves only acidification, centrifugation and filtration of the aqueous solution followed by direct injection of the aqueous supernatant solution onto a polar column. With the sample preparation and GC/MS conditions employed, well-resolved and sharp peaks of underivatized SCFA were obtained in a reasonably short time. Good recovery (96.6-102.3%) as well as low detection (4-7 µmol/L) and quantification limits (14-22 µmol/L) were obtained for all the 6 SCFA studied. Good linearity was achieved for both concentration and isotope enrichment measurement with regression coefficients higher than 0.9978 and 0.9996, respectively. The method has a good intra- and inter-day precision with a relative standard deviation (RSD) below 6% for determining the tracer-to-tracee ratio (TTR) of both [2-(13)C]acetate and [U-(13)C]acetate. It has also a good intra- and inter-day precision with a RSD below 6% and 5% for determining the concentration of standard solution and biogas digester samples, respectively. Acidification of biogas digester samples with oxalic acid provided the low pH required for the protonation of SCFA and thus, allows the extraction of SCFA from the complex sample matrix. Moreover, oxalic acid was the source of formic acid which was produced in the injector set at high temperature. The produced

  6. DOM Based XSS Detecting Method Based on Phantomjs

    NASA Astrophysics Data System (ADS)

    Dong, Ri-Zhan; Ling, Jie; Liu, Yi

    Because malicious code does not appear in html source code, DOM based XSS cannot be detected by traditional methods. By analyzing the causes of DOM based XSS, this paper proposes a detection method of DOM based XSS based on phantomjs. This paper uses function hijacking to detect dangerous operation and achieves a prototype system. Comparing with existing tools shows that the system improves the detection rate and the method is effective to detect DOM based XSS.

  7. A novel thiol-affinity micropipette tip method using zinc(II)-cyclen-attached agarose beads for enrichment of cysteine-containing molecules.

    PubMed

    Kusamoto, Hiroshi; Shiba, Akio; Koretake, Norinao; Fujioka, Haruto; Hieda, Yuhzo; Kinoshita-Kikuta, Emiko; Kinoshita, Eiji; Koike, Tohru

    2016-09-15

    Cysteine-containing biomolecules are attractive targets in the study of thiol biology. Here we introduce a novel method for the selective enrichment of thiol-containing molecules using a thiol-capture zinc(II) complex of 1,4,7,10-tetraazacyclododecane (Zn(2+)-cyclen). Recognition of N-acetylcysteine amide by Zn(2+)-cyclen has been studied by potentiometric pH titration, revealing formation of a 1:1 thiolate-bound Zn(2+)-cyclen complex with a large thiolate-affinity constant of 10(6.2)M(-1) at 25°C and I=0.10M (NaCl). The Zn(2+)-bound thiolate anion is unexpectedly stable in aqueous solution at pH 7.8 under atmospheric conditions for a few days. These findings have contributed to the development of a convenient method for separation of thiol compounds by using a micropipette tip. A 200μL micropipette tip containing 10μL of hydrophilic cross-linked agarose beads attached to Zn(2+)-cyclen moieties was prepared. All steps for thiol-affinity separation (binding, washing, and eluting) are conducted using aqueous buffers at room temperature. The entire separation protocol requires less than 15min per sample. We demonstrate practical example separations of cysteine-containing molecules. This micropipette tip method would be used preferentially as an alternative to existing tools for reliable enrichment of thiol-containing molecules. PMID:27498090

  8. A novel thiol-affinity micropipette tip method using zinc(II)-cyclen-attached agarose beads for enrichment of cysteine-containing molecules.

    PubMed

    Kusamoto, Hiroshi; Shiba, Akio; Koretake, Norinao; Fujioka, Haruto; Hieda, Yuhzo; Kinoshita-Kikuta, Emiko; Kinoshita, Eiji; Koike, Tohru

    2016-09-15

    Cysteine-containing biomolecules are attractive targets in the study of thiol biology. Here we introduce a novel method for the selective enrichment of thiol-containing molecules using a thiol-capture zinc(II) complex of 1,4,7,10-tetraazacyclododecane (Zn(2+)-cyclen). Recognition of N-acetylcysteine amide by Zn(2+)-cyclen has been studied by potentiometric pH titration, revealing formation of a 1:1 thiolate-bound Zn(2+)-cyclen complex with a large thiolate-affinity constant of 10(6.2)M(-1) at 25°C and I=0.10M (NaCl). The Zn(2+)-bound thiolate anion is unexpectedly stable in aqueous solution at pH 7.8 under atmospheric conditions for a few days. These findings have contributed to the development of a convenient method for separation of thiol compounds by using a micropipette tip. A 200μL micropipette tip containing 10μL of hydrophilic cross-linked agarose beads attached to Zn(2+)-cyclen moieties was prepared. All steps for thiol-affinity separation (binding, washing, and eluting) are conducted using aqueous buffers at room temperature. The entire separation protocol requires less than 15min per sample. We demonstrate practical example separations of cysteine-containing molecules. This micropipette tip method would be used preferentially as an alternative to existing tools for reliable enrichment of thiol-containing molecules.

  9. Evaluation of different buffered peptone water (BPW) based enrichment broths for detection of Gram-negative foodborne pathogens from various food matrices.

    PubMed

    Margot, H; Zwietering, M H; Joosten, H; O'Mahony, Emer; Stephan, R

    2015-12-01

    This study evaluated the effects of changing the composition of the pre-enrichment medium buffered peptone water (BPW) on the growth of stressed and unstressed Gram-negative foodborne pathogens in a one-broth enrichment strategy. BPW supplemented with an available iron source and sodium pyruvate, along with low levels of 8-hydroxyquinoline and sodium deoxycholate (BPW-S) improved the recovery of desiccated Cronobacter spp. from powdered infant formula. Growth of Salmonella and STEC was comparable in all BPW variants tested for different food matrices. In products with high levels of Gram-negative background flora (e.g. sprouts), the target organisms could not be reliably detected by PCR in any of the BPW variants tested unless the initial level exceeded 10(3) cfu/10 g of sprouts. Based on these results we suggest BPW-S for a one-broth enrichment strategy of stressed Gram-negative foodborne pathogens from dry products. However, a one-broth enrichment strategy based on BPW variants tested in this evaluation is not recommended for produce with a high level of Gram-negative background flora due to very high detection limits. PMID:26267889

  10. Evaluation of different buffered peptone water (BPW) based enrichment broths for detection of Gram-negative foodborne pathogens from various food matrices.

    PubMed

    Margot, H; Zwietering, M H; Joosten, H; O'Mahony, Emer; Stephan, R

    2015-12-01

    This study evaluated the effects of changing the composition of the pre-enrichment medium buffered peptone water (BPW) on the growth of stressed and unstressed Gram-negative foodborne pathogens in a one-broth enrichment strategy. BPW supplemented with an available iron source and sodium pyruvate, along with low levels of 8-hydroxyquinoline and sodium deoxycholate (BPW-S) improved the recovery of desiccated Cronobacter spp. from powdered infant formula. Growth of Salmonella and STEC was comparable in all BPW variants tested for different food matrices. In products with high levels of Gram-negative background flora (e.g. sprouts), the target organisms could not be reliably detected by PCR in any of the BPW variants tested unless the initial level exceeded 10(3) cfu/10 g of sprouts. Based on these results we suggest BPW-S for a one-broth enrichment strategy of stressed Gram-negative foodborne pathogens from dry products. However, a one-broth enrichment strategy based on BPW variants tested in this evaluation is not recommended for produce with a high level of Gram-negative background flora due to very high detection limits.

  11. Pressure-assisted electrokinetic injection for on-line enrichment in capillary electrophoresis-mass spectrometry: a sensitive method for measurement of ten haloacetic acids in drinking water.

    PubMed

    Zhang, Huijuan; Zhu, Jiping; Aranda-Rodriguez, Rocio; Feng, Yong-Lai

    2011-11-01

    Haloacetic acids (HAAs) are by-products of the chlorination of drinking water containing natural organic matter and bromide. A simple and sensitive method has been developed for determination of ten HAAs in drinking water. The pressure-assisted electrokinetic injection (PAEKI), an on-line enrichment technique, was employed to introduce the sample into a capillary electrophoresis (CE)-electrospray ionization-tandem mass spectrometry system (ESI-MS/MS). HAAs were monitored in selected reaction monitoring mode. With 3 min of PAEKI time, the ten major HAAs (HAA10) in drinking water were enriched up to 20,000-fold into the capillary without compromising resolution. A simple solid phase clean-up method has been developed to eliminate the influence of ionic matrices from drinking water on PAEKI. Under conditions optimized for mass spectrometry, PAEKI and capillary electrophoresis, detection limits defined as three times ratio of signal to noise have been achieved in a range of 0.013-0.12 μg L(-1) for ten HAAs in water sample. The overall recoveries for all ten HAAs in drinking water samples were between 76 and 125%. Six HAAs including monochloro- (MCAA), dichloro- (DCAA), trichloro- (TCAA), monobromo- (MBAA), bromochloro- (BCAA), and bromodichloroacetic acids (BDCAA) were found in tap water samples collected.

  12. Quantitative analysis of low-abundance serological proteins with peptide affinity-based enrichment and pseudo-multiple reaction monitoring by hybrid quadrupole time-of-flight mass spectrometry.

    PubMed

    Kim, Kwang Hoe; Ahn, Yeong Hee; Ji, Eun Sun; Lee, Ju Yeon; Kim, Jin Young; An, Hyun Joo; Yoo, Jong Shin

    2015-07-01

    Multiple reaction monitoring (MRM) is commonly used for the quantitative analysis of proteins during mass pectrometry (MS), and has excellent specificity and sensitivity for an analyte in a complex sample. In this study, a pseudo-MRM method for the quantitative analysis of low-abundance serological proteins was developed using hybrid quadrupole time-of-flight (hybrid Q-TOF) MS and peptide affinity-based enrichment. First, a pseudo-MRM-based analysis using hybrid Q-TOF MS was performed for synthetic peptides selected as targets and spiked into tryptic digests of human serum. By integrating multiple transition signals corresponding to fragment ions in the full scan MS/MS spectrum of a precursor ion of the target peptide, a pseudo-MRM MS analysis of the target peptide showed an increased signal-to-noise (S/N) ratio and sensitivity, as well as an improved reproducibility. The pseudo-MRM method was then used for the quantitative analysis of the tryptic peptides of two low-abundance serological proteins, tissue inhibitor of metalloproteinase 1 (TIMP1) and tissue-type protein tyrosine phosphatase kappa (PTPκ), which were prepared with peptide affinity-based enrichment from human serum. Finally, this method was used to detect femtomolar amounts of target peptides derived from TIMP1 and PTPκ, with good coefficients of variation (CV 2.7% and 9.8%, respectively), using a few microliters of human serum from colorectal cancer patients. The results suggest that pseudo-MRM using hybrid Q-TOF MS, combined with peptide affinity-based enrichment, could become a promising alternative for the quantitative analysis of low-abundance target proteins of interest in complex serum samples that avoids protein depletion.

  13. Enriching Careers and Lives: Introducing a Positive, Holistic, and Narrative Career Counseling Method that Bridges Theory and Practice

    ERIC Educational Resources Information Center

    Zikic, Jelena; Franklin, Mark

    2010-01-01

    CareerCycles (CC) career counseling framework and method of practice integrates and builds on aspects of positive psychology. Through its holistic and narrative approach, the CC method seeks to collaboratively identify and understand clients' career and life stories. It focuses on their strengths, desires, preferences, assets, future…

  14. Impulse-based methods for fluid flow

    SciTech Connect

    Cortez, R.

    1995-05-01

    A Lagrangian numerical method based on impulse variables is analyzed. A relation between impulse vectors and vortex dipoles with a prescribed dipole moment is presented. This relation is used to adapt the high-accuracy cutoff functions of vortex methods for use in impulse-based methods. A source of error in the long-time implementation of the impulse method is explained and two techniques for avoiding this error are presented. An application of impulse methods to the motion of a fluid surrounded by an elastic membrane is presented.

  15. Development of a microprocessing-assisted cell-systematic evolution of ligands by exponential enrichment method for human umbilical vein endothelial cells

    NASA Astrophysics Data System (ADS)

    Terazono, Hideyuki; Kim, Hyonchol; Nomura, Fumimasa; Yasuda, Kenji

    2016-06-01

    We developed a microprocessing-assisted technique to select single-strand DNA aptamers that bind to unknown targets on the cell surface by modifying the conventional systematic evolution of ligands by exponential enrichment (cell-SELEX). Our technique involves 1) the specific selection of target-cell-surface-bound aptamers without leakage of intracellular components by trypsinization and 2) cloning of aptamers by microprocessing-assisted picking of single cells using magnetic beads. After cell-SELEX, the enriched aptamers were conjugated with magnetic beads. The aptamer-magnetic beads conjugates attached to target cells were collected individually by microassisted procedures using microneedles under a microscope. After that, the sequences of the collected magnetic-bead-bound aptamers were identified. As a result, a specific aptamer for the surface of target cells, e.g., human umbilical vein endothelial cells (HUVECs), was chosen and its specificity was examined using other cell types, e.g., HeLa cells. The results indicate that this microprocessing-assisted cell-SELEX method for identifying aptamers is applicable in biological research and clinical diagnostics.

  16. A novel reductive graphene oxide-based magnetic molecularly imprinted poly(ethylene-co-vinyl alcohol) polymers for the enrichment and determination of polychlorinated biphenyls in fish samples.

    PubMed

    Lin, Saichai; Gan, Ning; Zhang, Jiabin; Chen, Xidong; Cao, Yuting; Li, Tianhua

    2015-06-01

    The novel reductive graphene oxide-based magnetic molecularly imprinted poly(ethylene-co-vinyl alcohol) polymers (rGO@m-MIPs) were successfully synthesized as adsorbents for six kinds of polychlorinated biphenyls (PCBs) in fish samples. rGO@m-MIPs was prepared by surface molecular imprinting technique. Besides, Fe3 O4 nanoparticles (NPs) were employed as magnetic supporters, and rGO@Fe3 O4 was in situ synthesis. Different from functional monomer and cross-linker in traditional molecularly imprinted polymer, here, 3,4-dichlorobenzidine was employed as dummy molecular and poly(ethylene-co-vinyl alcohol) was adopted as the imprinted polymers. After morphology and inner structure of the magnetic adsorbent were characterized, the adsorbent was employed for disperse solid phase extraction toward PCBs and exhibited great selectivity and high adsorption efficiency. This material was verified by determination of PCBs in fish samples combined with gas chromatography-mass spectrometry (GC-MS) method. According to the detection, the low detection limits (LODs) of PCBs were 0.0035-0.0070 µg l(-1) and spiked recoveries ranged between 79.90 and 94.23%. The prepared adsorbent can be renewable for at least 16 times and expected to be a new material for the enrichment and determination of PCBs from contaminated fish samples. PMID:25736423

  17. No Pain, No Gain? A Resource-Based Model of Work-to-Family Enrichment and Conflict

    ERIC Educational Resources Information Center

    Chen, Zheng; Powell, Gary N.

    2012-01-01

    Work-family scholars tend to work in two largely disconnected research streams, focusing on either work-family enrichment--the positive side of the work-family interface--or work-family conflict--the negative side of this interface. The purpose of this study is to suggest a reconciliation of the two research streams by proposing and testing a…

  18. Real-time pathogen monitoring during enrichment: a novel nanotechnology-based approach to food safety testing.

    PubMed

    Weidemaier, Kristin; Carruthers, Erin; Curry, Adam; Kuroda, Melody; Fallows, Eric; Thomas, Joseph; Sherman, Douglas; Muldoon, Mark

    2015-04-01

    We describe a new approach for the real-time detection and identification of pathogens in food and environmental samples undergoing culture. Surface Enhanced Raman Scattering (SERS) nanoparticles are combined with a novel homogeneous immunoassay to allow sensitive detection of pathogens in complex samples such as stomached food without the need for wash steps or extensive sample preparation. SERS-labeled immunoassay reagents are present in the cultural enrichment vessel, and the signal is monitored real-time through the wall of the vessel while culture is ongoing. This continuous monitoring of pathogen load throughout the enrichment process enables rapid, hands-free detection of food pathogens. Furthermore, the integration of the food pathogen immunoassay directly into the enrichment vessel enables fully biocontained food safety testing, thereby significantly reducing the risk of contaminating the surrounding environment with enriched pathogens. Here, we present experimental results showing the detection of E. coli, Salmonella, or Listeria in several matrices (raw ground beef, raw ground poultry, chocolate milk, tuna salad, spinach, brie cheese, hot dogs, deli turkey, orange juice, cola, and swabs and sponges used to sample a stainless steel surface) using the SERS system and demonstrate the accuracy of the approach compared to plating results.

  19. Juvenile psittacine environmental enrichment.

    PubMed

    Simone-Freilicher, Elisabeth; Rupley, Agnes E

    2015-05-01

    Environmental enrichment is of great import to the emotional, intellectual, and physical development of the juvenile psittacine and their success in the human home environment. Five major types of enrichment include social, occupational, physical, sensory, and nutritional. Occupational enrichment includes exercise and psychological enrichment. Physical enrichment includes the cage and accessories and the external home environment. Sensory enrichment may be visual, auditory, tactile, olfactory, or taste oriented. Nutritional enrichment includes variations in appearance, type, and frequency of diet, and treats, novelty, and foraging. Two phases of the preadult period deserve special enrichment considerations: the development of autonomy and puberty.

  20. A new automatic baseline correction method based on iterative method

    NASA Astrophysics Data System (ADS)

    Bao, Qingjia; Feng, Jiwen; Chen, Fang; Mao, Wenping; Liu, Zao; Liu, Kewen; Liu, Chaoyang

    2012-05-01

    A new automatic baseline correction method for Nuclear Magnetic Resonance (NMR) spectra is presented. It is based on an improved baseline recognition method and a new iterative baseline modeling method. The presented baseline recognition method takes advantages of three baseline recognition algorithms in order to recognize all signals in spectra. While in the iterative baseline modeling method, besides the well-recognized baseline points in signal-free regions, the 'quasi-baseline points' in the signal-crowded regions are also identified and then utilized to improve robustness by preventing the negative regions. The experimental results on both simulated data and real metabolomics spectra with over-crowded peaks show the efficiency of this automatic method.

  1. EVALUATION OF CORE PHYSICS ANALYSIS METHODS FOR CONVERSION OF THE INL ADVANCED TEST REACTOR TO LOW-ENRICHMENT FUEL

    SciTech Connect

    Mark DeHart; Gray S. Chang

    2012-04-01

    Computational neutronics studies to support the possible conversion of the ATR to LEU are underway. Simultaneously, INL is engaged in a physics methods upgrade project to put into place modern computational neutronics tools for future support of ATR fuel cycle and experiment analysis. A number of experimental measurements have been performed in the ATRC in support of the methods upgrade project, and are being used to validate the new core physics methods. The current computational neutronics work is focused on performance of scoping calculations for the ATR core loaded with a candidate LEU fuel design. This will serve as independent confirmation of analyses that have been performed previously, and will evaluate some of the new computational methods for analysis of a candidate LEU fuel for ATR.

  2. Enrichment Strategies in Phosphoproteomics.

    PubMed

    Leitner, Alexander

    2016-01-01

    The comprehensive study of the phosphoproteome is heavily dependent on appropriate enrichment strategies that are most often, but not exclusively, carried out on the peptide level. In this chapter, I give an overview of the most widely used techniques. In addition to dedicated antibodies, phosphopeptides are enriched by their selective interaction with metals in the form of chelated metal ions or metal oxides. The negative charge of the phosphate group is also exploited in a variety of chromatographic fractionation methods that include different types of ion exchange chromatography, hydrophilic interaction chromatography (HILIC), and electrostatic repulsion HILIC (ERLIC) chromatography. Selected examples from the literature will demonstrate how a combination of these techniques with current high-performance mass spectrometry enables the identification of thousands of phosphorylation sites from various sample types. PMID:26584921

  3. A novel tantalum-based sol-gel packed microextraction syringe for highly specific enrichment of phosphopeptides in MALDI-MS applications.

    PubMed

    Çelikbıçak, Ömür; Atakay, Mehmet; Güler, Ülkü; Salih, Bekir

    2013-08-01

    A new tantalum-based sol-gel material was synthesized using a unique sol-gel synthesis pathway by PEG incorporation into the sol-gel structure without performing a calcination step. This improved its chemical and physical properties for the high capacity and selective enrichment of phosphopeptides from protein digests in complex biological media. The specificity of the tantalum-based sol-gel material for phosphopeptides was evaluated and compared with tantalum(V) oxide (Ta2O5) in different phosphopeptide enrichment applications. The tantalum-based sol-gel and tantalum(V) oxide were characterized in detail using FT-IR spectroscopy, X-ray diffraction (XRD) and scanning electron microscopy (SEM), and also using a surface area and pore size analyzer. In the characterization studies, the surface morphology, pore volume, crystallinity of the materials and PEG incorporation into the sol-gel structure to produce a more hydrophilic material were successfully demonstrated. The X-ray diffractograms of the two different materials were compared and it was noted that the broad signals of the tantalum-based sol-gel clearly represented the amorphous structure of the sol-gel material, which was more likely to create enough surface area and to provide more accessible tantalum atoms for phosphopeptides to be easily adsorbed when compared with the neat and more crystalline structure of Ta2O5. Therefore, the phosphopeptide enrichment performance of the tantalum-based sol-gels was found to be remarkably higher than the more crystalline Ta2O5 in our studies. Phosphopeptides at femtomole levels could be selectively enriched using the tantalum-based sol-gel and detected with a higher signal-to-noise ratio by matrix-assisted laser desorption/ionization-mass spectrometer (MALDI-MS). Moreover, phosphopeptides in a tryptic digest of non-fat bovine milk as a complex real-world biological sample were retained with higher yield using a tantalum-based sol-gel. Additionally, the sol-gel material

  4. METHOD OF JOINING CARBIDES TO BASE METALS

    DOEpatents

    Krikorian, N.H.; Farr, J.D.; Witteman, W.G.

    1962-02-13

    A method is described for joining a refractory metal carbide such as UC or ZrC to a refractory metal base such as Ta or Nb. The method comprises carburizing the surface of the metal base and then sintering the base and carbide at temperatures of about 2000 deg C in a non-oxidizing atmosphere, the base and carbide being held in contact during the sintering step. To reduce the sintering temperature and time, a sintering aid such as iron, nickel, or cobait is added to the carbide, not to exceed 5 wt%. (AEC)

  5. A new test method for the assessment of the arc tracking properties of wire insulation in air, oxygen enriched atmospheres and vacuum

    NASA Technical Reports Server (NTRS)

    Koenig, Dieter

    1994-01-01

    Development of a new test method suitable for the assessment of the resistance of aerospace cables to arc tracking for different specific environmental and network conditions of spacecraft is given in view-graph format. The equipment can be easily adapted for tests at different realistic electrical network conditions incorporating circuit protection and the test system works equally well whatever the test atmosphere. Test results confirm that pure Kapton insulated wire has bad arcing characteristics and ETFE insulated wire is considerably better in air. For certain wires, arc tracking effects are increased at higher oxygen concentrations and significantly increased under vacuum. All tests on different cable insulation materials and in different environments, including enriched oxygen atmospheres, resulted in a more or less rapid extinguishing of all high temperature effects at the beginning of the post-test phase. In no case was a self-maintained fire initiated by the arc.

  6. An efficient and target-oriented sample enrichment method for preparative separation of minor alkaloids by pH-zone-refining counter-current chromatography.

    PubMed

    Feng, Rui-Hong; Hou, Jin-Jun; Zhang, Yi-Bei; Pan, Hui-Qin; Yang, Wenzhi; Qi, Peng; Yao, Shuai; Cai, Lu-Ying; Yang, Min; Jiang, Bao-Hong; Liu, Xuan; Wu, Wan-Ying; Guo, De-An

    2015-08-28

    An efficient and target-oriented sample enrichment method was established to increase the content of the minor alkaloids in crude extract by using the corresponding two-phase solvent system applied in pH-zone-refining counter-current chromatography. The enrichment and separation of seven minor indole alkaloids from Uncaria rhynchophylla (Miq.) Miq. ex Havil(UR) were selected as an example to show the advantage of this method. An optimized two-phase solvent system composed of n-hexane-ethyl acetate-methanol-water (3:7:1:9, v/v) was used in this study, where triethylamine (TEA) as the retainer and hydrochloric acid (HCl) as the eluter were added at the equimolar of 10mM. Crude alkaloids of UR dissolved in the corresponding upper phase (containing 10mM TEA) were extracted twice with lower phase (containing 10mM TEA) and lower phase (containing 10mM HCl), respectively, the second lower phase extract was subjected to pH-zone-refining CCC separation after alkalization and desalination. Finally, from 10g of crude alkaloids, 4g of refined alkaloids was obtained and the total content of seven target indole alkaloids was increased from 4.64% to 15.78%. Seven indole alkaloids, including 54mg isocorynoxeine, 21mg corynoxeine, 46mg isorhynchophylline, 35mg rhynchophylline, 65mg hirsutine, 51mg hirsuteine and 27mg geissoschizine methylether were all simultaneously separated from 2.5g of refined alkaloids, with the purity of 86.4%, 97.5%, 90.3%, 92.1%, 98.5%, 92.3%, and 92.8%, respectively. The total content and purities of the seven minor indole alkaloids were tested by HPLC and their chemical structures were elucidated by ESI-HRMS and (1)H NMR.

  7. Environmental enrichment for aquatic animals.

    PubMed

    Corcoran, Mike

    2015-05-01

    Aquatic animals are the most popular pets in the United States based on the number of owned pets. They are popular display animals and are increasingly used in research settings. Enrichment of captive animals is an important element of zoo and laboratory medicine. The importance of enrichment for aquatic animals has been slower in implementation. For a long time, there was debate over whether or not fish were able to experience pain or form long-term memories. As that debate has reduced and the consciousness of more aquatic animals is accepted, the need to discuss enrichment for these animals has increased.

  8. Impact of McKenzie Method Therapy Enriched by Muscular Energy Techniques on Subjective and Objective Parameters Related to Spine Function in Patients with Chronic Low Back Pain

    PubMed Central

    Szulc, Paweł; Wendt, Michał; Waszak, Małgorzata; Tomczak, Maciej; Cieślik, Krystyna; Trzaska, Tadeusz

    2015-01-01

    Background The high incidence and inconsistencies in diagnostic and therapeutic process of low back pain (LBP) stimulate the continuing search for more efficient treatment modalities. Integration of the information obtained with various therapeutic methods and a holistic approach to the patient seem to be associated with positive outcomes. The aim of this study was to analyze the efficacy of combined treatment with McKenzie method and Muscle Energy Technique (MET), and to compare it with the outcomes of treatment with McKenzie method or standard physiotherapy in specific chronic lumbar pain. Material/Methods The study included 60 men and women with LBP (mean age 44 years). The patients were randomly assigned to 1 of 3 therapeutic groups, which were further treated with: 1) McKenzie method and MET, 2) McKenzie method alone, or 3) standard physiotherapy for 10 days. The extent of spinal movements (electrogoniometry), level of experienced pain (Visual Analogue Scale and Revised Oswestry Pain Questionnaire), and structure of the spinal discs (MRI) were examined prior to the intervention, immediately thereafter, and 3 months after the intervention. Results McKenzie method enriched with MET had the best therapeutic outcomes. The mobility of cervical, thoracic, and lumbar spine normalized at levels corresponding to 87.1%, 66.7%, and 95% of respective average normative values. Implementation of McKenzie method, both alone and combined with MET, was associated with a significant decrease in Oswestry Disability Index, significant alleviation of pain (VAS), and significantly reduced size of spinal disc herniation. Conclusions The combined method can be effectively used in the treatment of chronic LBP. PMID:26418868

  9. Augmenting Learning in an Out-of-school Context: The Cognitive and Affective Impact of Two Cryogenics-based Enrichment Programmes on Upper Primary Students

    NASA Astrophysics Data System (ADS)

    Caleon, Imelda S.; Subramaniam, R.

    2007-07-01

    Concepts learned in the classroom were reinforced and augmented by presenting them in a different context using cryogenics-based enrichment programmes (CBEPs) held in an out-of-school setting. The effectiveness of two CBEPs, which involve the use of liquid nitrogen and liquid oxygen, was explored. Using a sample of 265 upper primary students, it was found that both enrichment programmes were effective in promoting the learning of science concepts. Fair improvements, albeit only transient, in two attitude constructs, enjoyment of science and career preference, due to either CBEPs were detected. The CBEPs did not have any significant impact on the attitude construct relating to students’ views on the social implications of science. The impact of CBEPs showed signs of retention, specifically in the cognitive realm, and reasonable indications of influencing subsequent learning and activities of students.

  10. [Identification of special quality eggs with NIR spectroscopy technology based on symbol entropy feature extraction method].

    PubMed

    Zhao, Yong; Hong, Wen-Xue

    2011-11-01

    Fast, nondestructive and accurate identification of special quality eggs is an urgent problem. The present paper proposed a new feature extraction method based on symbol entropy to identify near infrared spectroscopy of special quality eggs. The authors selected normal eggs, free range eggs, selenium-enriched eggs and zinc-enriched eggs as research objects and measured the near-infrared diffuse reflectance spectra in the range of 12 000-4 000 cm(-1). Raw spectra were symbolically represented with aggregation approximation algorithm and symbolic entropy was extracted as feature vector. An error-correcting output codes multiclass support vector machine classifier was designed to identify the spectrum. Symbolic entropy feature is robust when parameter changed and the highest recognition rate reaches up to 100%. The results show that the identification method of special quality eggs using near-infrared is feasible and the symbol entropy can be used as a new feature extraction method of near-infrared spectra.

  11. Model-Based Method for Sensor Validation

    NASA Technical Reports Server (NTRS)

    Vatan, Farrokh

    2012-01-01

    Fault detection, diagnosis, and prognosis are essential tasks in the operation of autonomous spacecraft, instruments, and in situ platforms. One of NASA s key mission requirements is robust state estimation. Sensing, using a wide range of sensors and sensor fusion approaches, plays a central role in robust state estimation, and there is a need to diagnose sensor failure as well as component failure. Sensor validation can be considered to be part of the larger effort of improving reliability and safety. The standard methods for solving the sensor validation problem are based on probabilistic analysis of the system, from which the method based on Bayesian networks is most popular. Therefore, these methods can only predict the most probable faulty sensors, which are subject to the initial probabilities defined for the failures. The method developed in this work is based on a model-based approach and provides the faulty sensors (if any), which can be logically inferred from the model of the system and the sensor readings (observations). The method is also more suitable for the systems when it is hard, or even impossible, to find the probability functions of the system. The method starts by a new mathematical description of the problem and develops a very efficient and systematic algorithm for its solution. The method builds on the concepts of analytical redundant relations (ARRs).

  12. Manifold based methods in facial expression recognition

    NASA Astrophysics Data System (ADS)

    Xie, Kun

    2013-07-01

    This paper describes a novel method for facial expression recognition based on non-linear manifold techniques. The graph-based algorithms are designed to treat structure in data, and regularize accordingly. This same goal is shared by several other algorithms, from linear method principal components analysis (PCA) to modern variants such as Laplacian eigenmaps. In this paper we focus on manifold learning for dimensionality reduction and clustering using Laplacian eigenmaps for facial expression recognition. We evaluate the algorithm by using all the pixels and selected features respectively and compare the performance of the proposed non-linear manifold method with the previous linear manifold approach, and the non linear method produces higher recognition rate than the facial expression representation using linear methods.

  13. Annular subaperture stitching method based on autocollimation

    NASA Astrophysics Data System (ADS)

    Yiwei, Chen; Erlong, Miao; Yongxin, Sui; Huaijiang, Yang

    2014-11-01

    In this paper, we propose an annular subaperture stitching method based on an autocollimation method to relax the requirements on mechanical location accuracy. In this approach, we move a ball instead of the interferometer and the aspheric surface so that testing results for adjacent annular subapertures are registered. Thus, the stitching algorithm can easily stitch the subaperture testing results together when large mechanical location errors exist. To verify this new method, we perform a simulation experiment. The simulation results demonstrate that this method can stitch together the subaperture testing results under large mechanical location errors.

  14. Gene set enrichment analysis.

    PubMed

    Tilford, Charles A; Siemers, Nathan O

    2009-01-01

    Set enrichment analytical methods have become commonplace tools applied to the analysis and interpretation of biological data. The statistical techniques are used to identify categorical biases within lists of genes, proteins, or metabolites. The goal is to discover the shared functions or properties of the biological items represented within the lists. Application of these methods can provide great biological insight, including the discovery of participation in the same biological activity or pathway, shared interacting genes or regulators, common cellular compartmentalization, or association with disease. The methods require ordered or unordered lists of biological items as input, understanding of the reference set from which the lists were selected, categorical classifiers describing the items, and a statistical algorithm to assess bias of each classifier. Due to the complexity of most algorithms and the number of calculations performed, computer software is almost always used for execution of the algorithm, as well as for presentation of the results. This chapter will provide an overview of the statistical methods used to perform an enrichment analysis. Guidelines for assembly of the requisite information will be presented, with a focus on careful definition of the sets used by the statistical algorithms. The need for multiple test correction when working with large libraries of classifiers is emphasized, and we outline several options for performing the corrections. Finally, interpreting the results of such analysis will be discussed along with examples of recent research utilizing the techniques.

  15. Opportunities for Scientist Involvement in Park-Based Educator Enrichment Programs in the Earth and Space Sciences

    NASA Astrophysics Data System (ADS)

    Waller, W. H.; Clemens, C.; Dunne, M.; Edwards, T.

    2005-12-01

    National and state parks provide space scientists with many opportunities for involvement in education and public outreach (E/PO). Towards these ends, NASA's Space Science E/PO Support Network can help initiate and foster the necessary partnerships between scientists and park personnel. For example, the professional development of national park interpreters has been pursued with the "Earth to Sky" program that was led by the Sun-Earth Connection Education Forum. Through partnerships with space scientists and E/PO professionals, park rangers are now developing interpretive products and programs to enrich the experiences of more than 100 million park visitors across the U.S. On a smaller scale, we have developed a community-wide educator enrichment program in the Earth and Space Sciences that is being implemented at Halibut Point State Park in Rockport, MA. Through wide-ranging partnerships, we are providing on-site hands-on workshops in Earth and Space Science that serve the interests of school teachers, scout leaders, park interpreters, amateur astronomers, and other community educators. Each 3-day workshop addresses the 3 broad topics of (1) living on Earth, (2) the Earth in space, and (3) our cosmic origins. Natural resources at Halibut Point State Park are used to enrich each of these topics. Astrobiology is the topical "glue" that binds all 3 topics. Research of the PI is featured through personal presentations on starbirth and starburst activity in galaxies. A wide selection of NASA education materials are showcased -- including those developed for Project ASTRO, Family ASTRO, Great Explorations in Math and Science (GEMS), EarthKam, the Night Sky Network, and the Spitzer E/PO Program. These workshops serve as models for similar programs in Earth and Space Science Education at state and national parks throughout the United States. WHW gratefully acknowledges support from a Spitzer E/PO grant supplement.

  16. Liquid-phase microextraction in a microfluidic-chip--high enrichment and sample clean-up from small sample volumes based on three-phase extraction.

    PubMed

    Ramos Payán, María D; Jensen, Henrik; Petersen, Nickolaj Jacob; Hansen, Steen Honoré; Pedersen-Bjergaard, Stig

    2012-07-20

    In this work, a microfluidic-chip based system for liquid-phase microextraction (LPME-chip) was developed. Sample solutions were pumped into the LPME-chip with a micro-syringe pump at a flow rate of 3-4 μL min(-1). Inside the LPME chip, the sample was in direct contact with a supported liquid membrane (SLM) composed of 0.2 μL dodecyl acetate immobilized in the pores of a flat membrane of polypropylene (25 μm thickness). On the other side of the SLM, the acceptor phase was present. The acceptor phase was either pumped at 1 μL min(-1) during extraction or kept stagnant (stop-flow). Amitriptyline, methadone, haloperidol, loperamide, and pethidine were selected as model analytes, and they were extracted from alkaline sample solution, through the SLM, and into 10 mM HCl or 100mM HCOOH functioning as acceptor phase. Subsequently, the acceptor phase was either analyzed off-line by capillary electrophoresis for exact quantification, or on-line by UV detection or electrospray ionization mass spectrometry for time profiling of concentrations. The LPME-chip was found to be highly effective, and extraction efficiencies were in the range of 52-91%. When the flow of acceptor phase was turned off during extraction (stop-flow), analyte enrichment increased linearly with the extraction time. After 10 min as an example, amitriptyline was enriched by a factor of 42 from only 30 μL sample solution, and after 120 min amitriptyline was enriched by a factor of 500 from 320 μL sample solution. This suggested that the LPME-chip has great potentials for very efficient analyte enrichments from limited sample volumes in the future.

  17. A Property Restriction Based Knowledge Merging Method

    NASA Astrophysics Data System (ADS)

    Che, Haiyan; Chen, Wei; Feng, Tie; Zhang, Jiachen

    Merging new instance knowledge extracted from the Web according to certain domain ontology into the knowledge base (KB for short) is essential for the knowledge management and should be processed carefully, since this may introduce redundant or contradictory knowledge, and the quality of the knowledge in the KB, which is very important for a knowledge-based system to provide users high quality services, will suffer from such "bad" knowledge. Advocates a property restriction based knowledge merging method, it can identify the equivalent instances, redundant or contradictory knowledge according to the property restrictions defined in the domain ontology and can consolidate the knowledge about equivalent instances and discard the redundancy and conflict to keep the KB compact and consistent. This knowledge merging method has been used in a semantic-based search engine project: CRAB and the effect is satisfactory.

  18. Recommendation advertising method based on behavior retargeting

    NASA Astrophysics Data System (ADS)

    Zhao, Yao; YIN, Xin-Chun; CHEN, Zhi-Min

    2011-10-01

    Online advertising has become an important business in e-commerce. Ad recommended algorithms are the most critical part in recommendation systems. We propose a recommendation advertising method based on behavior retargeting which can avoid leakage click of advertising due to objective reasons and can observe the changes of the user's interest in time. Experiments show that our new method can have a significant effect and can be further to apply to online system.

  19. Selection Based on FOXA2 Expression Is Not Sufficient to Enrich for Dopamine Neurons From Human Pluripotent Stem Cells

    PubMed Central

    Aguila, Julio Cesar; Blak, Alexandra; van Arensbergen, Joris; Sousa, Amaia; Vázquez, Nerea; Aduriz, Ariane; Gayosso, Mayela; Lopez Mato, Maria Paz; Lopez de Maturana, Rakel; Hedlund, Eva; Sonntag, Kai-Christian

    2014-01-01

    Human embryonic and induced pluripotent stem cells are potential cell sources for regenerative approaches in Parkinson disease. Inductive differentiation protocols can generate midbrain dopamine neurons but result in heterogeneous cell mixtures. Therefore, selection strategies are necessary to obtain uniform dopamine cell populations. Here, we developed a selection approach using lentivirus vectors to express green fluorescent protein under the promoter region of FOXA2, a transcription factor that is expressed in the floor plate domain that gives rise to dopamine neurons during embryogenesis. We first validated the specificity of the vectors in human cell lines against a promoterless construct. We then selected FOXA2-positive neural progenitors from several human pluripotent stem cell lines, which demonstrated a gene expression profile typical for the ventral domain of the midbrain and floor plate, but failed to enrich for dopamine neurons. To investigate whether this was due to the selection approach, we overexpressed FOXA2 in neural progenitors derived from human pluripotent stem cell lines. FOXA2 forced expression resulted in an increased expression of floor plate but not mature neuronal markers. Furthermore, selection of the FOXA2 overexpressing fraction also failed to enrich for dopamine neurons. Collectively, our results suggest that FOXA2 is not sufficient to induce a dopaminergic fate in this system. On the other hand, our study demonstrates that a combined approach of promoter activation and lentivirus vector technology can be used as a versatile tool for the selection of a defined cell population from a variety of human pluripotent stem cell lines. PMID:25024431

  20. The Effect of Different Mixing Methods on the Flow Rate and Compressive Strength of Mineral Trioxide Aggregate and Calcium-Enriched Mixture

    PubMed Central

    Shahi, Shahriar; Ghasemi, Negin; Rahimi, Saeed; Yavari, Hamid Reza; Samiei, Mohammad; Janani, Maryam; Bahari, Mahmood; Moheb, Sanaz

    2015-01-01

    Introduction: Flow rate (FR) and compressive strength (CS) are important properties of endodontic biomaterials that may be affected by various mixing methods. The aim of this experimental study was to evaluate the effect of different mixing methods on these properties of mineral trioxide aggregate (MTA) and calcium-enriched mixture (CEM) cement. Materials and methods: Hand, amalgamator and ultrasonic techniques were used to mix both biomaterials. Then 0.5 mL of each mixture was placed on a glass slab to measure FR. The second glass slab (100 g) was placed on the samples and 180 sec after the initiation of mixing a 100-g force was applied on it for 10 min. After 10 min, the load was removed, and the minimum and maximum diameters of the sample disks were measured. To measure the CS, 6 sample of each group were placed in steel molds and were then stored in distilled water for 21 h and 21 days. Afterwards, the CS test was performed. Data were analyzed with multi-variant ANOVA and post hoc Tukey tests. The level of significance was set at 0.05. Results: There were significant differences in FR of MTA and CEM cement with different mixing techniques (P<0.05). In the MTA group, none of the mixing techniques exhibited a significant effect on CS (P>0.05); however, in CEM group the CS at 21-h and 21-day intervals was higher with the hand technique (P<0.05). Conclusion: Mixing methods affected the flowability of both biomaterials and compressive strength of CEM cement. PMID:25598811

  1. MRI-based brain atrophy rates in ADNI phase 2: acceleration and enrichment considerations for clinical trials.

    PubMed

    Hua, Xue; Ching, Christopher R K; Mezher, Adam; Gutman, Boris A; Hibar, Derrek P; Bhatt, Priya; Leow, Alex D; Jack, Clifford R; Bernstein, Matt A; Weiner, Michael W; Thompson, Paul M

    2016-01-01

    The goal of this work was to assess statistical power to detect treatment effects in Alzheimer's disease (AD) clinical trials using magnetic resonance imaging (MRI)-derived brain biomarkers. We used unbiased tensor-based morphometry (TBM) to analyze n = 5,738 scans, from Alzheimer's Disease Neuroimaging Initiative 2 participants scanned with both accelerated and nonaccelerated T1-weighted MRI at 3T. The study cohort included 198 healthy controls, 111 participants with significant memory complaint, 182 with early mild cognitive impairment (EMCI) and 177 late mild cognitive impairment (LMCI), and 155 AD patients, scanned at screening and 3, 6, 12, and 24 months. The statistical power to track brain change in TBM-based imaging biomarkers depends on the interscan interval, disease stage, and methods used to extract numerical summaries. To achieve reasonable sample size estimates for potential clinical trials, the minimal scan interval was 6 months for LMCI and AD and 12 months for EMCI. TBM-based imaging biomarkers were not sensitive to MRI scan acceleration, which gave results comparable with nonaccelerated sequences. ApoE status and baseline amyloid-beta positron emission tomography data improved statistical power. Among healthy, EMCI, and LMCI participants, sample size requirements were significantly lower in the amyloid+/ApoE4+ group than for the amyloid-/ApoE4- group. ApoE4 strongly predicted atrophy rates across brain regions most affected by AD, but the remaining 9 of the top 10 AD risk genes offered no added predictive value in this cohort.

  2. Results from a "Proof-of-Concept" Demonstration of RF-Based Tracking of UF6 Cylinders during a Processing Operation at a Uranium Enrichment Plant

    SciTech Connect

    Pickett, Chris A; Kovacic, Donald N; Whitaker, J Michael; Younkin, James R; Hines, Jairus B; Laughter, Mark D; Morgan, Jim; Carrick, Bernie; Boyer, Brian; Whittle, K.

    2008-01-01

    Approved industry-standard cylinders are used globally for processing, storing, and transporting uranium hexafluoride (UF{sub 6}) at uranium enrichment plants. To ensure that cylinder movements at enrichment facilities occur as declared, the International Atomic Energy Agency (IAEA) must conduct time-consuming periodic physical inspections to validate facility records, cylinder identity, and containment. By using a robust system design that includes the capability for real-time unattended monitoring (of cylinder movements), site-specific rules-based event detection algorithms, and the capability to integrate with other types of monitoring technologies, one can build a system that will improve overall inspector effectiveness. This type of monitoring system can provide timely detection of safeguard events that could be used to ensure more timely and appropriate responses by the IAEA. It also could reduce reliance on facility records and have the additional benefit of enhancing domestic safeguards at the installed facilities. This paper will discuss the installation and evaluation of a radio-frequency- (RF-) based cylinder tracking system that was installed at a United States Enrichment Corporation Centrifuge Facility. This system was installed primarily to evaluate the feasibility of using RF technology at a site and the operational durability of the components under harsh processing conditions. The installation included a basic system that is designed to support layering with other safeguard system technologies and that applies fundamental rules-based event processing methodologies. This paper will discuss the fundamental elements of the system design, the results from this site installation, and future efforts needed to make this technology ready for IAEA consideration.

  3. Bayesian individualization via sampling-based methods.

    PubMed

    Wakefield, J

    1996-02-01

    We consider the situation where we wish to adjust the dosage regimen of a patient based on (in general) sparse concentration measurements taken on-line. A Bayesian decision theory approach is taken which requires the specification of an appropriate prior distribution and loss function. A simple method for obtaining samples from the posterior distribution of the pharmacokinetic parameters of the patient is described. In general, these samples are used to obtain a Monte Carlo estimate of the expected loss which is then minimized with respect to the dosage regimen. Some special cases which yield analytic solutions are described. When the prior distribution is based on a population analysis then a method of accounting for the uncertainty in the population parameters is described. Two simulation studies showing how the methods work in practice are presented. PMID:8827585

  4. Graphene based soft nanoreactors for facile "one-step" glycan enrichment and derivatization for MALDI-TOF-MS analysis.

    PubMed

    Bai, Haihong; Pan, Yiting; Tong, Wei; Zhang, Wanjun; Ren, Xiaojun; Tian, Fang; Peng, Bo; Wang, Xin; Zhang, Yangjun; Deng, Yulin; Qin, Weijie; Qian, Xiaohong

    2013-12-15

    Protein glycosylation is involved in the control of many important biological processes and structural alterations of the N-linked glycans are correlated with various kinds of disease. High-throughput N-glycan profiling is a key technique for elucidating the functions of glycans in biological process and disease development as well as discovering new diagnostic biomarkers. However, the low abundance of glycans existing in living organism, the competition/suppression effect of other highly abundant biological molecules and the inherent lack of alkalinity and hydrophobicity of glycans leads to particularly poor detection sensitivity in MS analysis. Here, we demonstrated the first "one-step" approach for highly efficient glycan enrichment and derivatization using reduced graphene oxide as nanoreactors and 1-pyrenebutyric hydrazide for glycan capture and derivatization, which resulted in a 33-fold increase in the glycan detection sensitivity in MALDI-TOF-MS and the identification of 48N-glycoforms from human plasma.

  5. Derived enriched uranium market

    SciTech Connect

    Rutkowski, E.

    1996-12-01

    The potential impact on the uranium market of highly enriched uranium from nuclear weapons dismantling in the Russian Federation and the USA is analyzed. Uranium supply, conversion, and enrichment factors are outlined for each country; inventories are also listed. The enrichment component and conversion components are expected to cause little disruption to uranium markets. The uranium component of Russian derived enriched uranium hexafluoride is unresolved; US legislation places constraints on its introduction into the US market.

  6. The Effect of Different Mixing Methods on Working Time, Setting Time, Dimensional Changes and Film Thickness of Mineral Trioxide Aggregate and Calcium-Enriched Mixture

    PubMed Central

    Shahi, Shahriar; Ghasemi, Negin; Rahimi, Saeed; Yavari, Hamidreza; Janani, Maryam; Mokhtari, Hadi; Bahari, Mahmood; Rabbani, Parastu

    2015-01-01

    Introduction: The aim of the present study was to evaluate the effect of different mixing techniques (conventional, amalgamator and ultrasonic mixing) on the physical properties the working time (WT), setting time (ST), dimensional changes (DC) and film thickness (FT)] of calcium-enriched mixture (CEM) cement and mineral trioxide aggregate (MTA). Methods and Materials: The mentioned physical properties were determined using the ISO 6786:2001 specification. Six samples of each material were prepared for three mixing techniques (totally 36 samples). Data were analyzed using descriptive statistics, two-way ANOVA and Post Hoc Tukey’s tests. The level of significance was defined at 0.05. Results: Irrespective of mixing technique, there was no significant difference between the WT and FT of the tested materials. Except for the DC of MTA and the FT of the all materials, other properties were significantly affected with mixing techniques (P<0.05). The ultrasonic technique decreased the ST of MTA and CEM cement and increased the WT of CEM cement (P<0.05). Conclusion: The mixing technique of the materials had no significant effect on the dimensional changes of MTA and the film thickness of both materials. PMID:26523140

  7. A new method to measure muscle protein synthesis in humans by endogenously introduced d9-leucine and using blood for precursor enrichment determination.

    PubMed

    Tran, Lee; Masters, Haley; Roust, Lori R; Katsanos, Christos S

    2015-08-01

    Enrichment from the easily accessible blood amino acid pool is commonly used as precursor enrichment to calculate rates of muscle protein fractional synthesis in relevant human studies in lieu of the less accessible muscle fluid amino acid pool. However, the accuracy of this approach depends largely on the extent to which there is low discrepancy in free amino acid enrichment between blood and muscle. Steady-state gradient (i.e., ratio) of amino acid enrichment between blood and muscle fluid in the basal state and in response to amino acid infusion were determined in five healthy subjects, and in association with two separate tracers: d9-leucine, introduced endogenously by the metabolism of d10-leucine (i.e., l-[2,3,3,4,5,5,5,6,6,6-(2)H10]leucine) infused in blood, and (13)C6-phenylalanine introduced/infused in blood. The blood-to-muscle fluid amino acid enrichment ratio was lower (P < 0.05) for d9-leucine compared to (13)C6-phenylalanine both before (1.5 ± 0.1 vs. 2.5 ± 0.1) and during (1.1 ± 0.1 vs. 1.2 ± 0.1) amino acid infusion. Importantly, the decrease in this ratio in association with the amino acid infusion was considerably less for the d9-leucine than the (13)C6-phenylalanine (-0.38 ± 0.03 vs. -1.29 ± 0.07; P < 0.05). In conclusion, blood d9-leucine enrichment introduced endogenously by intravenous infusion of d10-leucine provides a closer estimate of the muscle fluid amino acid enrichment, and its associated changes, than blood phenylalanine enrichment to calculate rates of muscle protein synthesis in humans. PMID:26243214

  8. A new method to measure muscle protein synthesis in humans by endogenously introduced d9-leucine and using blood for precursor enrichment determination

    PubMed Central

    Tran, Lee; Masters, Haley; Roust, Lori R; Katsanos, Christos S

    2015-01-01

    Enrichment from the easily accessible blood amino acid pool is commonly used as precursor enrichment to calculate rates of muscle protein fractional synthesis in relevant human studies in lieu of the less accessible muscle fluid amino acid pool. However, the accuracy of this approach depends largely on the extent to which there is low discrepancy in free amino acid enrichment between blood and muscle. Steady-state gradient (i.e., ratio) of amino acid enrichment between blood and muscle fluid in the basal state and in response to amino acid infusion were determined in five healthy subjects, and in association with two separate tracers: d9-leucine, introduced endogenously by the metabolism of d10-leucine (i.e., l-[2,3,3,4,5,5,5,6,6,6-2H10]leucine) infused in blood, and 13C6-phenylalanine introduced/infused in blood. The blood-to-muscle fluid amino acid enrichment ratio was lower (P < 0.05) for d9-leucine compared to 13C6-phenylalanine both before (1.5 ± 0.1 vs. 2.5 ± 0.1) and during (1.1 ± 0.1 vs. 1.2 ± 0.1) amino acid infusion. Importantly, the decrease in this ratio in association with the amino acid infusion was considerably less for the d9-leucine than the 13C6-phenylalanine (−0.38 ± 0.03 vs. −1.29 ± 0.07; P < 0.05). In conclusion, blood d9-leucine enrichment introduced endogenously by intravenous infusion of d10-leucine provides a closer estimate of the muscle fluid amino acid enrichment, and its associated changes, than blood phenylalanine enrichment to calculate rates of muscle protein synthesis in humans. PMID:26243214

  9. MRI-based brain atrophy rates in ADNI phase 2: acceleration and enrichment considerations for clinical trials.

    PubMed

    Hua, Xue; Ching, Christopher R K; Mezher, Adam; Gutman, Boris A; Hibar, Derrek P; Bhatt, Priya; Leow, Alex D; Jack, Clifford R; Bernstein, Matt A; Weiner, Michael W; Thompson, Paul M

    2016-01-01

    The goal of this work was to assess statistical power to detect treatment effects in Alzheimer's disease (AD) clinical trials using magnetic resonance imaging (MRI)-derived brain biomarkers. We used unbiased tensor-based morphometry (TBM) to analyze n = 5,738 scans, from Alzheimer's Disease Neuroimaging Initiative 2 participants scanned with both accelerated and nonaccelerated T1-weighted MRI at 3T. The study cohort included 198 healthy controls, 111 participants with significant memory complaint, 182 with early mild cognitive impairment (EMCI) and 177 late mild cognitive impairment (LMCI), and 155 AD patients, scanned at screening and 3, 6, 12, and 24 months. The statistical power to track brain change in TBM-based imaging biomarkers depends on the interscan interval, disease stage, and methods used to extract numerical summaries. To achieve reasonable sample size estimates for potential clinical trials, the minimal scan interval was 6 months for LMCI and AD and 12 months for EMCI. TBM-based imaging biomarkers were not sensitive to MRI scan acceleration, which gave results comparable with nonaccelerated sequences. ApoE status and baseline amyloid-beta positron emission tomography data improved statistical power. Among healthy, EMCI, and LMCI participants, sample size requirements were significantly lower in the amyloid+/ApoE4+ group than for the amyloid-/ApoE4- group. ApoE4 strongly predicted atrophy rates across brain regions most affected by AD, but the remaining 9 of the top 10 AD risk genes offered no added predictive value in this cohort. PMID:26545631

  10. Topology based methods for vector field comparisons

    NASA Astrophysics Data System (ADS)

    Batra, Rajesh Kumar

    Vector fields are commonly found in almost all branches of the physical sciences. Aerodynamics, dynamical systems, electromagnetism, and global climate modeling are a few examples. These multivariate data fields are often large, and no general, automated method exists for comparing these fields. Existing methods require either subjective visual judgments, or data interface compatibility, or domain specific knowledge. A topology based method intrinsically eliminates all of the above limitations and has the additional advantage of significantly compressing the vector field by representing only key features of the flow. Therefore, large databases are compactly represented and quickly searched. Topology is a natural framework for the study of many vector fields. It provides rules of an organizing principle, a flow grammar, that can describe and connect together the properties common to flows. Helman and Hesselink first introduced automated methods to extract and visualize this grammar. This work extends their method by introducing automated methods for vector topology comparison. Basic two-dimensional flows are first compared. The theory is extended to compare three-dimensional flow fields and the topology on no-slip surfaces. Concepts from graph theory and linear programming are utilized to solve these problems. Finally, the first automated method for higher order singularity comparisons is introduced using mathematical theories from geometric (Clifford) algebra.

  11. The response of amphibian larvae to exposure to a glyphosate-based herbicide (Roundup WeatherMax) and nutrient enrichment in an ecosystem experiment.

    PubMed

    Edge, Christopher; Thompson, Dean; Hao, Chunyan; Houlahan, Jeff

    2014-11-01

    Herbicides and fertilizers are widely used throughout the world and pose a threat to aquatic ecosystems. Using a replicated, whole ecosystem experiment in which 24 small wetlands were split in half with an impermeable barrier we tested whether exposure to a glyphosate-based herbicide, Roundup WeatherMax™, alone or in combination with nutrient enrichment has an effect on the survival, growth or development of amphibians. The herbicide was applied at one of two concentrations (low=210 μg a.e./L, high=2880 μg a.e./L) alone and in combination with nutrient enrichment to one side of wetlands and the other was left as an untreated control. Each treatment was replicated with six wetlands, and the experiment was repeated over two years. In the high glyphosate and nutrient enrichment treatment the survival of wood frog (Lithobates sylvaticus) larvae was lower in enclosures placed in situ on the treated sides than the control sides of wetlands. However, these results were not replicated in the second year of study and they were not observed in free swimming wood frog larvae in the wetlands. In all treatments, wood frog larvae on the treated sides of wetlands were slightly larger (<10%) than those on the control side, but no effect on development was observed. The most dramatic finding was that the abundance of green frog larvae (Lithobates clamitans) was higher on the treated sides than the control sides of wetlands in the herbicide and nutrient treatments during the second year of the study. The results observed in this field study indicate that caution is necessary when extrapolating results from artificial systems to predict effects in natural systems. In this experiment, the lack of toxicity to amphibian larvae was probably due to the fact the pH of the wetlands was relatively low and the presence of sediments and organic surfaces which would have mitigated the exposure duration.

  12. The response of amphibian larvae to exposure to a glyphosate-based herbicide (Roundup WeatherMax) and nutrient enrichment in an ecosystem experiment.

    PubMed

    Edge, Christopher; Thompson, Dean; Hao, Chunyan; Houlahan, Jeff

    2014-11-01

    Herbicides and fertilizers are widely used throughout the world and pose a threat to aquatic ecosystems. Using a replicated, whole ecosystem experiment in which 24 small wetlands were split in half with an impermeable barrier we tested whether exposure to a glyphosate-based herbicide, Roundup WeatherMax™, alone or in combination with nutrient enrichment has an effect on the survival, growth or development of amphibians. The herbicide was applied at one of two concentrations (low=210 μg a.e./L, high=2880 μg a.e./L) alone and in combination with nutrient enrichment to one side of wetlands and the other was left as an untreated control. Each treatment was replicated with six wetlands, and the experiment was repeated over two years. In the high glyphosate and nutrient enrichment treatment the survival of wood frog (Lithobates sylvaticus) larvae was lower in enclosures placed in situ on the treated sides than the control sides of wetlands. However, these results were not replicated in the second year of study and they were not observed in free swimming wood frog larvae in the wetlands. In all treatments, wood frog larvae on the treated sides of wetlands were slightly larger (<10%) than those on the control side, but no effect on development was observed. The most dramatic finding was that the abundance of green frog larvae (Lithobates clamitans) was higher on the treated sides than the control sides of wetlands in the herbicide and nutrient treatments during the second year of the study. The results observed in this field study indicate that caution is necessary when extrapolating results from artificial systems to predict effects in natural systems. In this experiment, the lack of toxicity to amphibian larvae was probably due to the fact the pH of the wetlands was relatively low and the presence of sediments and organic surfaces which would have mitigated the exposure duration. PMID:25173748

  13. A multicore based parallel image registration method.

    PubMed

    Yang, Lin; Gong, Leiguang; Zhang, Hong; Nosher, John L; Foran, David J

    2009-01-01

    Image registration is a crucial step for many image-assisted clinical applications such as surgery planning and treatment evaluation. In this paper we proposed a landmark based nonlinear image registration algorithm for matching 2D image pairs. The algorithm was shown to be effective and robust under conditions of large deformations. In landmark based registration, the most important step is establishing the correspondence among the selected landmark points. This usually requires an extensive search which is often computationally expensive. We introduced a nonregular data partition algorithm using the K-means clustering algorithm to group the landmarks based on the number of available processing cores. The step optimizes the memory usage and data transfer. We have tested our method using IBM Cell Broadband Engine (Cell/B.E.) platform. PMID:19964921

  14. Enriched rearing improves behavioral responses of an animal model for CNV-based autistic-like traits.

    PubMed

    Lacaria, Melanie; Spencer, Corinne; Gu, Wenli; Paylor, Richard; Lupski, James R

    2012-07-15

    Potocki-Lupski syndrome (PTLS; MIM #610883), characterized by neurobehavioral abnormalities, intellectual disability and congenital anomalies, is caused by a 3.7-Mb duplication in 17p11.2. Neurobehavioral studies determined that ∼70-90% of PTLS subjects tested positive for autism or autism spectrum disorder (ASD). We previously chromosomally engineered a mouse model for PTLS (Dp(11)17/+) with a duplication of a 2-Mb genomic interval syntenic to the PTLS region and identified consistent behavioral abnormalities in this mouse model. We now report extensive phenotyping with behavioral assays established to evaluate core and associated autistic-like traits, including tests for social abnormalities, ultrasonic vocalizations, perseverative and stereotypic behaviors, anxiety, learning and memory deficits and motor defects. Alterations were identified in both core and associated ASD-like traits. Rearing this animal model in an enriched environment mitigated some, and even rescued selected, neurobehavioral abnormalities, suggesting a role for gene-environment interactions in the determination of copy number variation-mediated autism severity.

  15. An analytical method for hydrogeochemical surveys: Inductively coupled plasma-atomic emission spectrometry after using enrichment coprecipitation with cobalt and ammonium pyrrolidine dithiocarbamate

    USGS Publications Warehouse

    Hopkins, D.M.

    1991-01-01

    Trace metals that are commonly associated with mineralization were concentrated and separated from natural water by coprecipitation with ammonium pyrollidine dithiocarbamate (APDC) and cobalt and determined by inductively coupled plasma-atomic emission spectroscopy (ICP-AES). The method is useful in hydrogeochemical surveys because it permits preconcentration near the sample sites, and selected metals are preserved shortly after the samples are collected. The procedure is relatively simple: (1) a liter of water is filtered; (2) the pH is adjusted; (3) Co chloride and APDC are added to coprecipitate the trace metals; and (4) later, the precipitate is filtered, dissolved, and diluted to 10 ml for a 100-fold concentration enrichment of the separated metals. Sb(III), As(III), Cd, Cr, Cu, Fe, Pb, Mo, Ni, Ag, V, and Zn can then be determined simultaneously by ICP-AES. In an experiment designed to measure the coprecipitation efficiency, Sb(III), Cd and Ag were recovered at 70 to 75% of their original concentration. The remaining metals were recovered at 85 to 100% of their original concentrations, however. The range for the lower limits of determination for the metals after preconcentration is 0.1 to 3.0 ??g/l. The precision of the method was evaluated by replicate analyses of a Colorado creek water and two simulated water samples. The accuracy of the method was estimated using a water reference standard (SRM 1643a) certified by the U.S. National Bureau of Standards. In addition, the method was evaluated by analyzing groundwater samples collected near a porphyry copper deposit in Arizona and by analyzing meltwater from glacier-covered areas favorable for mineralization in south-central Alaska. The results for the ICP-AES analyses compared favorably with those obtained using the sequential technique of GFAAS on the acidified but unconcentrated water samples. ICP-AES analysis of trace-metal preconcentrates for hydrogeochemical surveys is more efficient than GFAAS because a

  16. Lagrangian based methods for coherent structure detection.

    PubMed

    Allshouse, Michael R; Peacock, Thomas

    2015-09-01

    There has been a proliferation in the development of Lagrangian analytical methods for detecting coherent structures in fluid flow transport, yielding a variety of qualitatively different approaches. We present a review of four approaches and demonstrate the utility of these methods via their application to the same sample analytic model, the canonical double-gyre flow, highlighting the pros and cons of each approach. Two of the methods, the geometric and probabilistic approaches, are well established and require velocity field data over the time interval of interest to identify particularly important material lines and surfaces, and influential regions, respectively. The other two approaches, implementing tools from cluster and braid theory, seek coherent structures based on limited trajectory data, attempting to partition the flow transport into distinct regions. All four of these approaches share the common trait that they are objective methods, meaning that their results do not depend on the frame of reference used. For each method, we also present a number of example applications ranging from blood flow and chemical reactions to ocean and atmospheric flows. PMID:26428570

  17. Lagrangian based methods for coherent structure detection

    SciTech Connect

    Allshouse, Michael R.; Peacock, Thomas

    2015-09-15

    There has been a proliferation in the development of Lagrangian analytical methods for detecting coherent structures in fluid flow transport, yielding a variety of qualitatively different approaches. We present a review of four approaches and demonstrate the utility of these methods via their application to the same sample analytic model, the canonical double-gyre flow, highlighting the pros and cons of each approach. Two of the methods, the geometric and probabilistic approaches, are well established and require velocity field data over the time interval of interest to identify particularly important material lines and surfaces, and influential regions, respectively. The other two approaches, implementing tools from cluster and braid theory, seek coherent structures based on limited trajectory data, attempting to partition the flow transport into distinct regions. All four of these approaches share the common trait that they are objective methods, meaning that their results do not depend on the frame of reference used. For each method, we also present a number of example applications ranging from blood flow and chemical reactions to ocean and atmospheric flows.

  18. In-Solution Hybridization for the Targeted Enrichment of the Whole Mitochondrial Genome.

    PubMed

    Bekaert, B; Ellerington, R; Van den Abbeele, L; Decorte, R

    2016-01-01

    A detailed protocol is presented for the targeted enrichment of whole mitochondrial genomes based on an in-solution hybridization strategy. Bait is produced in-house by sonication of two long-range PCR amplicons and ligation of biotinylated double-stranded adapters. Indexed target DNA is hybridized with the bait in a multiplex enrichment reaction and pulled down using magnetic streptavidin beads followed by subsequent post-enrichment PCR and sequencing on an Illumina MiSeq. This strategy removes the need for expensive commercial bait probes while allowing enrichment of multiple samples in a single hybridization reaction. The method is particularly suitable for degraded DNA as it is able to enrich short DNA fragments and is not susceptible to polymerase artifacts introduced during PCR-based assays. PMID:27259740

  19. Chapter 11. Community analysis-based methods

    SciTech Connect

    Cao, Y.; Wu, C.H.; Andersen, G.L.; Holden, P.A.

    2010-05-01

    Microbial communities are each a composite of populations whose presence and relative abundance in water or other environmental samples are a direct manifestation of environmental conditions, including the introduction of microbe-rich fecal material and factors promoting persistence of the microbes therein. As shown by culture-independent methods, different animal-host fecal microbial communities appear distinctive, suggesting that their community profiles can be used to differentiate fecal samples and to potentially reveal the presence of host fecal material in environmental waters. Cross-comparisons of microbial communities from different hosts also reveal relative abundances of genetic groups that can be used to distinguish sources. In increasing order of their information richness, several community analysis methods hold promise for MST applications: phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), cloning/sequencing, and PhyloChip. Specific case studies involving TRFLP and PhyloChip approaches demonstrate the ability of community-based analyses of contaminated waters to confirm a diagnosis of water quality based on host-specific marker(s). The success of community-based MST for comprehensively confirming fecal sources relies extensively upon using appropriate multivariate statistical approaches. While community-based MST is still under evaluation and development as a primary diagnostic tool, results presented herein demonstrate its promise. Coupled with its inherently comprehensive ability to capture an unprecedented amount of microbiological data that is relevant to water quality, the tools for microbial community analysis are increasingly accessible, and community-based approaches have unparalleled potential for translation into rapid, perhaps real-time, monitoring platforms.

  20. Enrichment, development, and assessment of Indian basil oil based antiseptic cream formulation utilizing hydrophilic-lipophilic balance approach.

    PubMed

    Yadav, Narayan Prasad; Meher, Jaya Gopal; Pandey, Neelam; Luqman, Suaib; Yadav, Kuldeep Singh; Chanda, Debabrata

    2013-01-01

    The present work was aimed to develop an antiseptic cream formulation of Indian basil oil utilizing hydrophilic-lipophilic balance approach. In order to determine the required-hydrophilic lipophilic balance (rHLB) of basil oil, emulsions of basil oil were prepared by phase inversion temperature technique using water, Tween 80, and Span 80. Formulated emulsions were assessed for creaming (BE9; 9.8, BE10; 10.2), droplet size (BE18; 3.22 ± 0.09 μ m), and turbidity (BE18; 86.12 ± 2.1%). To ensure correctness of the applied methodology, rHLB of light liquid paraffin was also determined. After rHLB determination, basil oil creams were prepared with two different combinations of surfactants, namely, GMS : Tween 80 (1 : 3.45) and SLS : GMS (1 : 3.68), and evaluated for in vitro antimicrobial activity, skin irritation test, viscosity and consistency. The rHLB of basil oil and light liquid paraffin were found to be 13.36 ± 0.36 and 11.5 ± 0.35, respectively. Viscosity, and consistency parameters of cream was found to be consistent over 90 days. Cream formulations showed net zone of growth inhibition in the range of 5.0-11.3 mm against bacteria and 4.3-7.6 mm against fungi. Primary irritation index was found to be between 0.38 and1.05. Conclusively stable, consistent, non-irritant, enriched antiseptic basil oil cream formulations were developed utilizing HLB approach.

  1. A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

    PubMed Central

    McCormack, John E.; Harvey, Michael G.; Faircloth, Brant C.; Crawford, Nicholas G.; Glenn, Travis C.; Brumfield, Robb T.

    2013-01-01

    Evolutionary relationships among birds in Neoaves, the clade comprising the vast majority of avian diversity, have vexed systematists due to the ancient, rapid radiation of numerous lineages. We applied a new phylogenomic approach to resolve relationships in Neoaves using target enrichment (sequence capture) and high-throughput sequencing of ultraconserved elements (UCEs) in avian genomes. We collected sequence data from UCE loci for 32 members of Neoaves and one outgroup (chicken) and analyzed data sets that differed in their amount of missing data. An alignment of 1,541 loci that allowed missing data was 87% complete and resulted in a highly resolved phylogeny with broad agreement between the Bayesian and maximum-likelihood (ML) trees. Although results from the 100% complete matrix of 416 UCE loci were similar, the Bayesian and ML trees differed to a greater extent in this analysis, suggesting that increasing from 416 to 1,541 loci led to increased stability and resolution of the tree. Novel results of our study include surprisingly close relationships between phenotypically divergent bird families, such as tropicbirds (Phaethontidae) and the sunbittern (Eurypygidae) as well as between bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters support for monophyletic waterbird and landbird clades and also strongly supports controversial results from previous studies, including the sister relationship between passerines and parrots and the non-monophyly of raptorial birds in the hawk and falcon families. Although significant challenges remain to fully resolving some of the deep relationships in Neoaves, especially among lineages outside the waterbirds and landbirds, this study suggests that increased data will yield an increasingly resolved avian phylogeny. PMID:23382987

  2. Phosphopeptide enrichment with inorganic nanofibers prepared by forcespinning technology.

    PubMed

    Krenkova, Jana; Moravkova, Jaroslava; Buk, Jan; Foret, Frantisek

    2016-01-01

    Efficient selective sample enrichment is often a key procedure in protocols for analyses of complex samples. This applies not only to trace sample components but also to species with weak detection response. For example enrichment of phosphopeptides using selective affinity techniques prior to mass spectrometry analysis is necessary to increase detection sensitivity of phosphopeptides from highly complex peptide mixtures. In this work we have developed inorganic nanofibrous materials based on titanium or zirconium dioxides for selective and efficient enrichment of phosphopeptides for MALDI/MS detection. In comparison to the common bead based materials the presented nanofibrous materials exhibit much higher permeability allowing their use not only for batch mode or packed in the column operation, but also in the pipette tip format without the need for high pressure. Both the methods of preparation and characterization of the resulting materials are presented. PMID:26689825

  3. eEF1A1 binds and enriches protoporphyrin IX in cancer cells in 5-aminolevulinic acid based photodynamic therapy.

    PubMed

    Fan, Zhichao; Cui, Xiaojun; Wei, Dan; Liu, Wei; Li, Buhong; He, Hao; Ye, Huamao; Zhu, Naishuo; Wei, Xunbin

    2016-01-01

    Photodynamic therapy (PDT) with protoporphyrin IX (PpIX), which is endogenously derived from 5-aminolevulinic acid (5-ALA) or its derivatives, is a promising modality for the treatment of both pre-malignant and malignant lesions. However, the mechanisms of how ALA-induced PpIX selectively accumulated in the tumors are not fully elucidated. Here we discovered that eukaryotic translation elongation factor 1 alpha 1 (eEF1A1) interacted with PpIX (with an affinity constant of 2.96 × 10(6) M(-1)). Microscopy imaging showed that ALA-induced PpIX was co-localized with eEF1A1 in cancer cells. eEF1A1 was found to enrich ALA-induced PpIX in cells by competitively blocking the downstream bioavailability of PpIX. Taken together, our study discovered eEF1A1 as a novel photosensitizer binding protein, which may play an essential role in the enrichment of ALA-induced PpIX in cancer cells during PDT. These suggested eEF1A1 as a molecular marker to predict the selectivity and efficiency of 5-ALA based PDT in cancer therapy. PMID:27150264

  4. eEF1A1 binds and enriches protoporphyrin IX in cancer cells in 5-aminolevulinic acid based photodynamic therapy

    NASA Astrophysics Data System (ADS)

    Fan, Zhichao; Cui, Xiaojun; Wei, Dan; Liu, Wei; Li, Buhong; He, Hao; Ye, Huamao; Zhu, Naishuo; Wei, Xunbin

    2016-05-01

    Photodynamic therapy (PDT) with protoporphyrin IX (PpIX), which is endogenously derived from 5-aminolevulinic acid (5-ALA) or its derivatives, is a promising modality for the treatment of both pre-malignant and malignant lesions. However, the mechanisms of how ALA-induced PpIX selectively accumulated in the tumors are not fully elucidated. Here we discovered that eukaryotic translation elongation factor 1 alpha 1 (eEF1A1) interacted with PpIX (with an affinity constant of 2.96 × 106 M‑1). Microscopy imaging showed that ALA-induced PpIX was co-localized with eEF1A1 in cancer cells. eEF1A1 was found to enrich ALA-induced PpIX in cells by competitively blocking the downstream bioavailability of PpIX. Taken together, our study discovered eEF1A1 as a novel photosensitizer binding protein, which may play an essential role in the enrichment of ALA-induced PpIX in cancer cells during PDT. These suggested eEF1A1 as a molecular marker to predict the selectivity and efficiency of 5-ALA based PDT in cancer therapy.

  5. eEF1A1 binds and enriches protoporphyrin IX in cancer cells in 5-aminolevulinic acid based photodynamic therapy

    PubMed Central

    Fan, Zhichao; Cui, Xiaojun; Wei, Dan; Liu, Wei; Li, Buhong; He, Hao; Ye, Huamao; Zhu, Naishuo; Wei, Xunbin

    2016-01-01

    Photodynamic therapy (PDT) with protoporphyrin IX (PpIX), which is endogenously derived from 5-aminolevulinic acid (5-ALA) or its derivatives, is a promising modality for the treatment of both pre-malignant and malignant lesions. However, the mechanisms of how ALA-induced PpIX selectively accumulated in the tumors are not fully elucidated. Here we discovered that eukaryotic translation elongation factor 1 alpha 1 (eEF1A1) interacted with PpIX (with an affinity constant of 2.96 × 106 M−1). Microscopy imaging showed that ALA-induced PpIX was co-localized with eEF1A1 in cancer cells. eEF1A1 was found to enrich ALA-induced PpIX in cells by competitively blocking the downstream bioavailability of PpIX. Taken together, our study discovered eEF1A1 as a novel photosensitizer binding protein, which may play an essential role in the enrichment of ALA-induced PpIX in cancer cells during PDT. These suggested eEF1A1 as a molecular marker to predict the selectivity and efficiency of 5-ALA based PDT in cancer therapy. PMID:27150264

  6. A flocking based method for brain tractography.

    PubMed

    Aranda, Ramon; Rivera, Mariano; Ramirez-Manzanares, Alonso

    2014-04-01

    We propose a new method to estimate axonal fiber pathways from Multiple Intra-Voxel Diffusion Orientations. Our method uses the multiple local orientation information for leading stochastic walks of particles. These stochastic particles are modeled with mass and thus they are subject to gravitational and inertial forces. As result, we obtain smooth, filtered and compact trajectory bundles. This gravitational interaction can be seen as a flocking behavior among particles that promotes better and robust axon fiber estimations because they use collective information to move. However, the stochastic walks may generate paths with low support (outliers), generally associated to incorrect brain connections. In order to eliminate the outlier pathways, we propose a filtering procedure based on principal component analysis and spectral clustering. The performance of the proposal is evaluated on Multiple Intra-Voxel Diffusion Orientations from two realistic numeric diffusion phantoms and a physical diffusion phantom. Additionally, we qualitatively demonstrate the performance on in vivo human brain data. PMID:24583805

  7. Method for extruding pitch based foam

    SciTech Connect

    Klett, James W.

    2002-01-01

    A method and apparatus for extruding pitch based foam is disclosed. The method includes the steps of: forming a viscous pitch foam; passing the precursor through an extrusion tube; and subjecting the precursor in said extrusion tube to a temperature gradient which varies along the length of the extrusion tube to form an extruded carbon foam. The apparatus includes an extrusion tube having a passageway communicatively connected to a chamber in which a viscous pitch foam formed in the chamber paring through the extrusion tube, and a heating mechanism in thermal communication with the tube for heating the viscous pitch foam along the length of the tube in accordance with a predetermined temperature gradient.

  8. Homogenization method based on the inverse problem

    SciTech Connect

    Tota, A.; Makai, M.

    2013-07-01

    We present a method for deriving homogeneous multi-group cross sections to replace a heterogeneous region's multi-group cross sections; providing that the fluxes and the currents on the external boundary, and the region averaged fluxes are preserved. The method is developed using diffusion approximation to the neutron transport equation in a symmetrical slab geometry. Assuming that the boundary fluxes are given, two response matrices (RMs) can be defined. The first derives the boundary current from the boundary flux, the second derives the flux integral over the region from the boundary flux. Assuming that these RMs are known, we present a formula which reconstructs the multi-group cross-section matrix and the diffusion coefficients from the RMs of a homogeneous slab. Applying this formula to the RMs of a slab with multiple homogeneous regions yields a homogenization method; which produce such homogenized multi-group cross sections and homogenized diffusion coefficients, that the fluxes and the currents on the external boundary, and the region averaged fluxes are preserved. The method is based on the determination of the eigenvalues and the eigenvectors of the RMs. We reproduce the four-group cross section matrix and the diffusion constants from the RMs in numerical examples. We give conditions for replacing a heterogeneous region by a homogeneous one so that the boundary current and the region-averaged flux are preserved for a given boundary flux. (authors)

  9. Dreamlet-based interpolation using POCS method

    NASA Astrophysics Data System (ADS)

    Wang, Benfeng; Wu, Ru-Shan; Geng, Yu; Chen, Xiaohong

    2014-10-01

    Due to incomplete and non-uniform coverage of the acquisition system and dead traces, real seismic data always has some missing traces which affect the performance of a multi-channel algorithm, such as Surface-Related Multiple Elimination (SRME), imaging and inversion. Therefore, it is necessary to interpolate seismic data. Dreamlet transform has been successfully used in the modeling of seismic wave propagation and imaging, and this paper explains the application of dreamlet transform to seismic data interpolation. In order to avoid spatial aliasing in transform domain thus getting arbitrary under-sampling rate, improved Jittered under-sampling strategy is proposed to better control the dataset. With L0 constraint and Projection Onto Convex Sets (POCS) method, performances of dreamlet-based and curvelet-based interpolation are compared in terms of recovered signal to noise ratio (SNR) and convergence rate. Tests on synthetic and real cases demonstrate that dreamlet transform has superior performance to curvelet transform.

  10. Evaluation of Hybridization Capture Versus Amplicon‐Based Methods for Whole‐Exome Sequencing

    PubMed Central

    Samorodnitsky, Eric; Jewell, Benjamin M.; Hagopian, Raffi; Miya, Jharna; Wing, Michele R.; Lyon, Ezra; Damodaran, Senthilkumar; Bhatt, Darshna; Reeser, Julie W.; Datta, Jharna

    2015-01-01

    ABSTRACT Next‐generation sequencing has aided characterization of genomic variation. While whole‐genome sequencing may capture all possible mutations, whole‐exome sequencing remains cost‐effective and captures most phenotype‐altering mutations. Initial strategies for exome enrichment utilized a hybridization‐based capture approach. Recently, amplicon‐based methods were designed to simplify preparation and utilize smaller DNA inputs. We evaluated two hybridization capture‐based and two amplicon‐based whole‐exome sequencing approaches, utilizing both Illumina and Ion Torrent sequencers, comparing on‐target alignment, uniformity, and variant calling. While the amplicon methods had higher on‐target rates, the hybridization capture‐based approaches demonstrated better uniformity. All methods identified many of the same single‐nucleotide variants, but each amplicon‐based method missed variants detected by the other three methods and reported additional variants discordant with all three other technologies. Many of these potential false positives or negatives appear to result from limited coverage, low variant frequency, vicinity to read starts/ends, or the need for platform‐specific variant calling algorithms. All methods demonstrated effective copy‐number variant calling when evaluated against a single‐nucleotide polymorphism array. This study illustrates some differences between whole‐exome sequencing approaches, highlights the need for selecting appropriate variant calling based on capture method, and will aid laboratories in selecting their preferred approach. PMID:26110913

  11. An Implicit Characteristic Based Method for Electromagnetics

    NASA Technical Reports Server (NTRS)

    Beggs, John H.; Briley, W. Roger

    2001-01-01

    An implicit characteristic-based approach for numerical solution of Maxwell's time-dependent curl equations in flux conservative form is introduced. This method combines a characteristic based finite difference spatial approximation with an implicit lower-upper approximate factorization (LU/AF) time integration scheme. This approach is advantageous for three-dimensional applications because the characteristic differencing enables a two-factor approximate factorization that retains its unconditional stability in three space dimensions, and it does not require solution of tridiagonal systems. Results are given both for a Fourier analysis of stability, damping and dispersion properties, and for one-dimensional model problems involving propagation and scattering for free space and dielectric materials using both uniform and nonuniform grids. The explicit Finite Difference Time Domain Method (FDTD) algorithm is used as a convenient reference algorithm for comparison. The one-dimensional results indicate that for low frequency problems on a highly resolved uniform or nonuniform grid, this LU/AF algorithm can produce accurate solutions at Courant numbers significantly greater than one, with a corresponding improvement in efficiency for simulating a given period of time. This approach appears promising for development of dispersion optimized LU/AF schemes for three dimensional applications.

  12. The effects of inquiry-based summer enrichment activities on rising eighth graders' knowledge of science processes, attitude toward science, and perceptions of scientists

    NASA Astrophysics Data System (ADS)

    Moore, Juanita Martin

    The purpose of this research was to examine the effects of summer science enrichment on eighth-graders' science process skills knowledge, attitude toward science and perceptions of scientists. A single group pre- and post-test design was used to test participants in a summer science enrichment camp, which took place over a three-week period in the summer of 2000. Participants, all of whom were residents of the Mississippi area known as the Delta, lived on the campus of Mississippi Valley State University for the entire course of the camp. Activities included several guided inquiry-based projects such as water rocket design and solar or battery-powered car design. Participants also took trips to an environmental camp in north Mississippi and to the Stennis Space Center on the Mississippi Gulf Coast. Participants worked on their projects in groups, supervised by an undergraduate student "mentor". Participants were encouraged to keep journals of their experiences throughout the camp, and the researcher developed a rubric to evaluate student journals for process knowledge, evidence of planning, reflective thought, and disposition toward science. Tests were used to evaluate student knowledge of process skills, attitude toward science, and perceptions of scientists. On the Test of Integrated Process Skills (Dillashaw & Okey, 1983), the students showed significant improvement overall, but when evaluated separately, males showed significant improvement while females did not. On the Attitude toward Science in School Assessment (Germane, 1988), data indicated that attitude toward science improved significantly for the group as a whole, but upon closer inspection, indicated a significant improvement for the female students only. On Chamber's Draw-a-Scientist Test (1983), analysis of student drawings indicated no significant change in stereotypical images of scientists for the group overall. However, boys' scores indicated a significant improvement when analyzed separately

  13. Monitoring of an Alkaline 2,4,6-Trichlorophenol-Degrading Enrichment Culture by DNA Fingerprinting Methods and Isolation of the Responsible Organism, Haloalkaliphilic Nocardioides sp. Strain M6

    PubMed Central

    Maltseva, O.; Oriel, P.

    1997-01-01

    A site situated near Alkali Lake (Oregon) and highly contaminated by chloroaromatic compounds was chosen for isolation of alkaliphilic chlorophenol-degrading bacteria. Prolonged cultivation of an enrichment culture followed by successive transfers resulted in a strong increase in the 2,4,6-trichlorophenol (2,4,6-TCP) degradation rate. Repetitive extragenic palindromic PCR and amplified ribosomal DNA restriction analysis were applied to distinguish members of the enrichment culture and monitor them during the enrichment procedure. Comparison of the fingerprints of the isolates obtained from the enrichment culture and its total DNA fingerprint indicated the presence of an unidentified bacterium in the enrichment culture, assisting in its isolation. The 2,4,6-TCP-degrading isolate, M6, was tentatively identified as a Nocardioides sp. strain based on its partial 16S RNA sequence and fatty acid profile. Strain M6 was capable of utilizing up to 1.6 g of 2,4,6-TCP per liter as a sole carbon and energy source and could also grow on 2,4-dichlorophenol and 2,4,5-trichlorophenol. A high-cell-density suspension of this strain degraded a wide range of chlorinated phenols from di- to pentachlorophenol while showing a clear preference for phenols containing chlorine substituents in positions 2 plus 4. Based on its optimal pH (9.0 to 9.4) and sodium ion concentration (0.2 to 0.4 M) for growth, Nocardioides sp. strain M6 is a slightly halophilic alkaliphile. PMID:16535723

  14. Graph-based Methods for Orbit Classification

    SciTech Connect

    Bagherjeiran, A; Kamath, C

    2005-09-29

    An important step in the quest for low-cost fusion power is the ability to perform and analyze experiments in prototype fusion reactors. One of the tasks in the analysis of experimental data is the classification of orbits in Poincare plots. These plots are generated by the particles in a fusion reactor as they move within the toroidal device. In this paper, we describe the use of graph-based methods to extract features from orbits. These features are then used to classify the orbits into several categories. Our results show that existing machine learning algorithms are successful in classifying orbits with few points, a situation which can arise in data from experiments.

  15. Enrichment through Creative Arts.

    ERIC Educational Resources Information Center

    Krause, Claire S.

    The CREST (Creative Resources Enriching Student Talents) Project, an enrichment approach for elementary gifted, talented, and creative students, is described. The project is explained to incorporate an interdisciplinary approach to instruction in art and science using resources within the community. Chapter 1 outlines the project philosophy,…

  16. DNA enrichment approaches to identify unauthorized genetically modified organisms (GMOs).

    PubMed

    Arulandhu, Alfred J; van Dijk, Jeroen P; Dobnik, David; Holst-Jensen, Arne; Shi, Jianxin; Zel, Jana; Kok, Esther J

    2016-07-01

    With the increased global production of different genetically modified (GM) plant varieties, chances increase that unauthorized GM organisms (UGMOs) may enter the food chain. At the same time, the detection of UGMOs is a challenging task because of the limited sequence information that will generally be available. PCR-based methods are available to detect and quantify known UGMOs in specific cases. If this approach is not feasible, DNA enrichment of the unknown adjacent sequences of known GMO elements is one way to detect the presence of UGMOs in a food or feed product. These enrichment approaches are also known as chromosome walking or gene walking (GW). In recent years, enrichment approaches have been coupled with next generation sequencing (NGS) analysis and implemented in, amongst others, the medical and microbiological fields. The present review will provide an overview of these approaches and an evaluation of their applicability in the identification of UGMOs in complex food or feed samples. PMID:27086015

  17. DNA enrichment approaches to identify unauthorized genetically modified organisms (GMOs).

    PubMed

    Arulandhu, Alfred J; van Dijk, Jeroen P; Dobnik, David; Holst-Jensen, Arne; Shi, Jianxin; Zel, Jana; Kok, Esther J

    2016-07-01

    With the increased global production of different genetically modified (GM) plant varieties, chances increase that unauthorized GM organisms (UGMOs) may enter the food chain. At the same time, the detection of UGMOs is a challenging task because of the limited sequence information that will generally be available. PCR-based methods are available to detect and quantify known UGMOs in specific cases. If this approach is not feasible, DNA enrichment of the unknown adjacent sequences of known GMO elements is one way to detect the presence of UGMOs in a food or feed product. These enrichment approaches are also known as chromosome walking or gene walking (GW). In recent years, enrichment approaches have been coupled with next generation sequencing (NGS) analysis and implemented in, amongst others, the medical and microbiological fields. The present review will provide an overview of these approaches and an evaluation of their applicability in the identification of UGMOs in complex food or feed samples.

  18. Optimized culturing and nucleic acid-based methods for the detection of Salmonella enterica in poultry environments.

    PubMed

    Schultz, J; Jarquin, R; Ricke, S C; Hanning, I

    2012-11-01

    The main objective of this trial was to set up a series of assays following quantified inoculation of Salmonella samples in 2 initial enrichment methods to ultimately determine the most effective and fastest detection method for recovery of Salmonella in a poultry environment matrix. Samples were randomly split into 2 different containers containing either buffered peptone water (BPW) + yeast extract, or tetrathionate broth (TT) with added iodine and Brilliant Green solution 0.1%. A frozen stock Salmonella culture was thawed and serially diluted 10-fold to inoculate 100 µL of the dilution into the enriched samples. The samples were incubated at 42 and 37°C, respectively, for 24 h and secondarily enriched in modified semi-solid Rappaport Vassiliadis (MSRV) incubated at 42°C. All samples then were reincubated under the same conditions. After secondary enrichment, the samples were streaked onto Chromogenic agar/ XLT4 bi-plates and incubated under the same conditions. After initial inoculation and each 24-h incubation, a portion of the enriched samples was analyzed using a real-time PCR assay. The results of this trial indicate that recovery of Salmonella in a culture-based assay may be enhanced by up to 3 logs by using the TT as the initial enrichment media compared with BPW. The incorporation of MSRV as a secondary cultural selective media after the TT gave the best recovery of Salmonella. These data indicate that considerable time can be saved by using TT as an initial media for Salmonella recovery. PMID:23091129

  19. Towards Designing Cognitively-Enriched Project-Oriented Courses within a Blended Problem-Based Learning Context

    ERIC Educational Resources Information Center

    Tambouris, Efthimios; Zotou, Maria; Tarabanis, Konstantinos

    2014-01-01

    Traditional education seems to gradually and moderately make way for self-directed and student-centred learning strategies that will efficiently enable students to reach their full potentials and will sufficiently prepare them for their upcoming professional careers. Problem-Based Learning (PBL) is such a strategy, since it enables active…

  20. Numerical manifold method based on the method of weighted residuals

    NASA Astrophysics Data System (ADS)

    Li, S.; Cheng, Y.; Wu, Y.-F.

    2005-05-01

    Usually, the governing equations of the numerical manifold method (NMM) are derived from the minimum potential energy principle. For many applied problems it is difficult to derive in general outset the functional forms of the governing equations. This obviously strongly restricts the implementation of the minimum potential energy principle or other variational principles in NMM. In fact, the governing equations of NMM can be derived from a more general method of weighted residuals. By choosing suitable weight functions, the derivation of the governing equations of the NMM from the weighted residual method leads to the same result as that derived from the minimum potential energy principle. This is demonstrated in the paper by deriving the governing equations of the NMM for linear elasticity problems, and also for Laplace's equation for which the governing equations of the NMM cannot be derived from the minimum potential energy principle. The performance of the method is illustrated by three numerical examples.

  1. Improving data management and dissemination in web based information systems by semantic enrichment of descriptive data aspects

    NASA Astrophysics Data System (ADS)

    Gebhardt, Steffen; Wehrmann, Thilo; Klinger, Verena; Schettler, Ingo; Huth, Juliane; Künzer, Claudia; Dech, Stefan

    2010-10-01

    The German-Vietnamese water-related information system for the Mekong Delta (WISDOM) project supports business processes in Integrated Water Resources Management in Vietnam. Multiple disciplines bring together earth and ground based observation themes, such as environmental monitoring, water management, demographics, economy, information technology, and infrastructural systems. This paper introduces the components of the web-based WISDOM system including data, logic and presentation tier. It focuses on the data models upon which the database management system is built, including techniques for tagging or linking metadata with the stored information. The model also uses ordered groupings of spatial, thematic and temporal reference objects to semantically tag datasets to enable fast data retrieval, such as finding all data in a specific administrative unit belonging to a specific theme. A spatial database extension is employed by the PostgreSQL database. This object-oriented database was chosen over a relational database to tag spatial objects to tabular data, improving the retrieval of census and observational data at regional, provincial, and local areas. While the spatial database hinders processing raster data, a "work-around" was built into WISDOM to permit efficient management of both raster and vector data. The data model also incorporates styling aspects of the spatial datasets through styled layer descriptions (SLD) and web mapping service (WMS) layer specifications, allowing retrieval of rendered maps. Metadata elements of the spatial data are based on the ISO19115 standard. XML structured information of the SLD and metadata are stored in an XML database. The data models and the data management system are robust for managing the large quantity of spatial objects, sensor observations, census and document data. The operational WISDOM information system prototype contains modules for data management, automatic data integration, and web services for data

  2. Effects of polysaccharide-based edible coatings enriched with dietary fiber on quality attributes of fresh-cut apples.

    PubMed

    Moreira, Maria R; Cassani, Lucía; Martín-Belloso, Olga; Soliva-Fortuny, Robert

    2015-12-01

    Little information is available regarding the incorporation of dietary fiber into edible films and coatings. In this work, apple fiber and inulin were incorporated into polysaccharide-based (alginate, pectine and gellan gum) edible coating formulations and their effects on the quality attributes of fresh-cut apples were evaluated. Antioxidant properties, color, firmness, sensory quality and microbial growth of fresh-cut apple were studied during 16 days of storage at 4 °C. Results show that dietary fiber extracts incorporated to gellan gum, pectin and alginate-based coatings together with calcium chloride and ascorbic acid successfully maintained the firmness and color of coated fresh-cut apples in comparison with uncoated control samples, which presented severe texture softening and browning. The firmness of apple pieces coated with polysaccharide-based coating formulations incorporating apple fiber doubled, and sometimes tripled, that of uncoated samples. Any of the assayed coatings exhibited a positive effect on the sensory properties of fresh-cut apples. The incorporation of apple fiber, together with the use of ascorbic acid, contributed to keep the antioxidant potential of the fruit at least during the first week of storage. Furthermore, gellan gum coatings had a marked effect in reducing mesophilic and psychrophilic counts on fresh-cut apples throughout storage regardless the addition of dietary fibers. The results achieved demonstrate the feasibility of the addition of dietary fiber to edible coating formulations for increasing the nutritional value of fresh-cut apples without compromising their fresh-like quality attributes.

  3. Variation in visitor perceptions of a polar bear enclosure based on the presence of natural vs. un-natural enrichment items.

    PubMed

    Kutska, Debra

    2009-07-01

    A debate exists among modern zoo staff as to whether or not the addition of un-naturalistic enrichment takes away from, or even defeats, the educational messages designers are trying to incorporate in naturalistic exhibits. A visitor study was conducted at the Central Park Zoo's polar bear exhibit in order to determine whether or not the type of enrichment in an enclosure actually alters guest perceptions. Visitors were exposed to one of two enrichment treatments in the bear enclosure: Naturalistic or Un-naturalistic. The results of this study suggest that enrichment type did not alter the perceptions of visitors. However, it did identify some of the different ways adults and youths perceive animals and zoos. Additionally, the study highlighted the varying perceptions individuals have of the concept of polar bears vs. their perceptions of the captive individuals at the Central Park Zoo. Implications for enrichment usage and exhibit design are discussed.

  4. Subjective evidence based ethnography: method and applications.

    PubMed

    Lahlou, Saadi; Le Bellu, Sophie; Boesen-Mariani, Sabine

    2015-06-01

    Subjective Evidence Based Ethnography (SEBE) is a method designed to access subjective experience. It uses First Person Perspective (FPP) digital recordings as a basis for analytic Replay Interviews (RIW) with the participants. This triggers their memory and enables a detailed step by step understanding of activity: goals, subgoals, determinants of actions, decision-making processes, etc. This paper describes the technique and two applications. First, the analysis of professional practices for know-how transferring purposes in industry is illustrated with the analysis of nuclear power-plant operators' gestures. This shows how SEBE enables modelling activity, describing good and bad practices, risky situations, and expert tacit knowledge. Second, the analysis of full days lived by Polish mothers taking care of their children is described, with a specific focus on how they manage their eating and drinking. This research has been done on a sub-sample of a large scale intervention designed to increase plain water drinking vs sweet beverages. It illustrates the interest of SEBE as an exploratory technique in complement to other more classic approaches such as questionnaires and behavioural diaries. It provides the detailed "how" of the effects that are measured at aggregate level by other techniques.

  5. Subjective evidence based ethnography: method and applications.

    PubMed

    Lahlou, Saadi; Le Bellu, Sophie; Boesen-Mariani, Sabine

    2015-06-01

    Subjective Evidence Based Ethnography (SEBE) is a method designed to access subjective experience. It uses First Person Perspective (FPP) digital recordings as a basis for analytic Replay Interviews (RIW) with the participants. This triggers their memory and enables a detailed step by step understanding of activity: goals, subgoals, determinants of actions, decision-making processes, etc. This paper describes the technique and two applications. First, the analysis of professional practices for know-how transferring purposes in industry is illustrated with the analysis of nuclear power-plant operators' gestures. This shows how SEBE enables modelling activity, describing good and bad practices, risky situations, and expert tacit knowledge. Second, the analysis of full days lived by Polish mothers taking care of their children is described, with a specific focus on how they manage their eating and drinking. This research has been done on a sub-sample of a large scale intervention designed to increase plain water drinking vs sweet beverages. It illustrates the interest of SEBE as an exploratory technique in complement to other more classic approaches such as questionnaires and behavioural diaries. It provides the detailed "how" of the effects that are measured at aggregate level by other techniques. PMID:25579747

  6. A long PCR–based approach for DNA enrichment prior to next-generation sequencing for systematic studies1

    PubMed Central

    Uribe-Convers, Simon; Duke, Justin R.; Moore, Michael J.; Tank, David C.

    2014-01-01

    • Premise of the study: We present an alternative approach for molecular systematic studies that combines long PCR and next-generation sequencing. Our approach can be used to generate templates from any DNA source for next-generation sequencing. Here we test our approach by amplifying complete chloroplast genomes, and we present a set of 58 potentially universal primers for angiosperms to do so. Additionally, this approach is likely to be particularly useful for nuclear and mitochondrial regions. • Methods and Results: Chloroplast genomes of 30 species across angiosperms were amplified to test our approach. Amplification success varied depending on whether PCR conditions were optimized for a given taxon. To further test our approach, some amplicons were sequenced on an Illumina HiSeq 2000. • Conclusions: Although here we tested this approach by sequencing plastomes, long PCR amplicons could be generated using DNA from any genome, expanding the possibilities of this approach for molecular systematic studies. PMID:25202592

  7. A rapid method for capture and identification of immunogenic proteins in Bordetella pertussis enriched membranes fractions: a fast-track strategy applicable to other microorganisms.

    PubMed

    West, Rolieria; Whitmon, Jennifer; Williamson, Yulanda M; Moura, Hercules; Nelson, Marguerite; Melnick, Nikkol; Tondella, Maria Lucia C; Schieltz, David; Rees, Jon; Woolfitt, Adrian R; Barr, John R; Ades, Edwin W; Carlone, George M; Sampson, Jacquelyn S

    2012-03-16

    Mass spectrometry (MS) coupled with 1-D and 2-D electrophoresis can be utilized to detect and identify immunogenic proteins, but these methods are laborious and time-consuming. We describe an alternative, simple, rapid gel-free strategy to identify multiple immunogenic proteins from Bordetella pertussis (Bp). It couples immunoprecipitation to nano liquid chromatography- tandem mass spectrometry (IP-nLC-MS/MS) and is significantly both time- and labor-saving. We developed a gel-free magnetic bead-based immunoprecipitation (IP) method using different NP-40/PBS concentrations in which solubilized proteins of Bp Tohama I membrane fractions were precipitated with polyclonal rabbit anti-Bp whole cell immune sera. Immune complexes were analyzed by MS and Scaffold analysis (>95% protein identification probability). Total immunoproteins identified were 50, 63 and 49 for 0.90%, 0.45% and 0.22% NP-40/PBS buffer concentrations respectively. Known Bp proteins identified included pertactin, serotype 2 fimbrial subunit and filamentous hemagglutinin. As proof of concept that this gel-free protein immunoprecipitation method enabled the capture of multiple immunogenic proteins, IP samples were also analyzed by SDS-PAGE and immunoblotting. Bypassing gels and subjecting immunoprecipitated proteins directly to MS is a simple and rapid antigen identification method with relatively high throughput. IP-nLC-MS/MS provides a novel alternative approach for current methods used for the identification of immunogenic proteins.

  8. Status of laser enrichment technology updated

    NASA Astrophysics Data System (ADS)

    Sakabe, Y.

    1986-08-01

    The principles of uranium enrichment by a laser method, the technology's current status and future prospects, centered on research and development activity at the Japan Atomic Energy Research Institute and the Institute of Physical and Chemical Research are described.

  9. DNA-based methods of geochemical prospecting

    DOEpatents

    Ashby, Matthew

    2011-12-06

    The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

  10. Development and characterization of a nanodendritic silver-based solid-phase extraction sorbent for selective enrichment of endocrine-disrupting chemicals in water and milk samples.

    PubMed

    Gao, Yuanji; Xia, Bing; Liu, Jie; Ji, Baocheng; Ma, Fengwei; Ding, Lisheng; Li, Bangjing; Zhou, Yan

    2015-11-01

    In this study, 4-[4-phenylazo-phenoxy] butyl-1-thiol (AzSH) functionalized nanodendritic silver (AzS@AgNDs) materials were prepared as a solid-phase extraction (SPE) sorbent for the selective extraction of estrogens. AzS@AgNDs possess an extremely large surface-to-volume ratio and a small average particle size. The performance of the material was evaluated by selective enrichment of hexestrol, diethylstilbestrol, dienestrol and bisphenol A in water and milk samples followed by rapid ultra-performance liquid chromatography-electrospray ionization mass spectrometry (UPLC-ESI-MS) analyses. The results exhibited that AzS@AgNDs had excellent adsorption capability for the targeted estrogens. The limits of detection of the four estrogens ranged from 0.1 to 5.0 pg/mL. The recoveries of the estrogens spiked into tap water were over the range of 83.6-105.3% with relative standard deviations of 2.8-6.0%. The results indicated the capability of this method for the rapid determination of estrogens in milk and other environmental water samples. In addition, this method would be useful for the determination of human exposure and health risk assessments trace level of endocrine-disrupting compounds (EDCs) in drinking water.

  11. Development and characterization of a nanodendritic silver-based solid-phase extraction sorbent for selective enrichment of endocrine-disrupting chemicals in water and milk samples.

    PubMed

    Gao, Yuanji; Xia, Bing; Liu, Jie; Ji, Baocheng; Ma, Fengwei; Ding, Lisheng; Li, Bangjing; Zhou, Yan

    2015-11-01

    In this study, 4-[4-phenylazo-phenoxy] butyl-1-thiol (AzSH) functionalized nanodendritic silver (AzS@AgNDs) materials were prepared as a solid-phase extraction (SPE) sorbent for the selective extraction of estrogens. AzS@AgNDs possess an extremely large surface-to-volume ratio and a small average particle size. The performance of the material was evaluated by selective enrichment of hexestrol, diethylstilbestrol, dienestrol and bisphenol A in water and milk samples followed by rapid ultra-performance liquid chromatography-electrospray ionization mass spectrometry (UPLC-ESI-MS) analyses. The results exhibited that AzS@AgNDs had excellent adsorption capability for the targeted estrogens. The limits of detection of the four estrogens ranged from 0.1 to 5.0 pg/mL. The recoveries of the estrogens spiked into tap water were over the range of 83.6-105.3% with relative standard deviations of 2.8-6.0%. The results indicated the capability of this method for the rapid determination of estrogens in milk and other environmental water samples. In addition, this method would be useful for the determination of human exposure and health risk assessments trace level of endocrine-disrupting compounds (EDCs) in drinking water. PMID:26572841

  12. A gelatin based antioxidant enriched biomaterial by grafting and saturation: towards sustained drug delivery from antioxidant matrix.

    PubMed

    Raja, I Selestin; Fathima, Nishter Nishad

    2015-04-01

    Proteins grafted with antioxidant molecules have drawn much attention due to their increased life time and biocompatibility. When protein macromolecules are cross linked chemically and physically with antioxidant molecules, they can act as antioxidant biomaterials as well as scaffolds to release the antioxidant molecules by diffusion. In our work, we have attempted to release catechin molecules from the matrix of glutathione grafted gelatin. Conjugation of glutathione and cross linkage was done by carbodiimide method to achieve smaller pores in the gelatin matrix and the characterization was performed by means of FTIR-ATR and calorimetric analyses. The glutathione grafted gelatin (GGSH) has been shown to have more thermal stability and pores with lesser radii than blank gelatin (bGEL). Free radical scavenging activity of GGSH was also found to be more than that of bGEL. Catechin was added to GGSH and bGEL by physical blending in order to achieve short term release of antioxidant molecules. CD spectra revealed that significant conformational changes occurred in secondary structure of gelatin upon interaction with catechin. Slower rate of catechin release from GGSH reflected the influence of cross linkage and physical interactive forces on the drug release properties. We conclude that the mixture of catechin with GGSH can be a potent antioxidant biomaterial releasing catechin at slower rate than the mixture of catechin with bGEL.

  13. Interaction modes and approaches to glycopeptide and glycoprotein enrichment.

    PubMed

    Chen, Chen-Chun; Su, Wan-Chih; Huang, Bao-Yu; Chen, Yu-Ju; Tai, Hwan-Ching; Obena, Rofeamor P

    2014-02-21

    Protein glycosylation has received increased attention for its critical role in cell biology and diseases. Developing new methodologies to discern phenotype-dependent glycosylation will not only elucidate the mechanistic aspects of cell signaling cascades but also accelerate biomarker discovery for disease diagnosis or prognosis. In the analytical pipeline, enrichment at either the protein or peptide level is the most critical prerequisite for analyzing heterogeneous glycan composition, linkage, site occupancy and carrier proteins. Because the critical factor for choosing a suitable enrichment method is primarily a particular technique's selectivity and affinity towards target glycoproteins/glycopeptides, it is important to fully understand the working principles for the different approaches. For mechanistic insight into the enrichment protocol, we focused on the fundamental chemical and physical processes for the commonly used approaches based on: (a) glycan/peptide physicochemical properties (hydrophilic interactions, chelation/coordination chemistry) and (b) glycan-specific recognition (lectin-based affinity, covalent bond formation by hydrazide/boronic acid). Various interaction modes, such as hydrogen bonding, van der Waals interaction, multivalency, and metal- or water-mediated stabilization, are discussed in detail. In addition, we will review the design of and modifications to such methods, hyphenated approaches, and glycoproteomic applications. Finally, we will outline challenges to existing strategies and offer novel proposals for glycoproteome enrichment. PMID:24336240

  14. Iterative methods based upon residual averaging

    NASA Technical Reports Server (NTRS)

    Neuberger, J. W.

    1980-01-01

    Iterative methods for solving boundary value problems for systems of nonlinear partial differential equations are discussed. The methods involve subtracting an average of residuals from one approximation in order to arrive at a subsequent approximation. Two abstract methods in Hilbert space are given and application of these methods to quasilinear systems to give numerical schemes for such problems is demonstrated. Potential theoretic matters related to the iteration schemes are discussed.

  15. Try the Enrichment Triad in Reading Class.

    ERIC Educational Resources Information Center

    Noyce, Ruth M.

    1981-01-01

    Offers suggestions for differentiation of reading instruction based on Joseph Renzulli's Enrichment Triad Model, which provides for general exploratory activities, group training activities, and individual investigations of real problems. (MKM)

  16. Heteronuclear NMR studies of cobalamins. 9. Temperature-dependent NMR of organocobalt corrins enriched in /sup 13/C in the organic ligand and the thermodynamics of the base-on/base-off reaction

    SciTech Connect

    Brown, K.L.; Peck-Siler, S.

    1988-10-05

    The synthesis of alkylcobinamides (RCbi) enriched in /sup 13/C in the organic axial ligand by standard reductive alkylation procedures from /sup 13/C-enriched alkyl halides has been shown to lead essentially exclusively to ..beta..-alkylcobamides (i.e., the organic ligand in the upper axial ligand position) by uv-visible and NMR spectroscopy and HPLC coupled with direct synthesis of /sup 13/CH/sub 3/Cbi of known stereochemistry from /sup 13/C-enriched methylcobalamin (/sup 13/CH/sub 3/Cbl). The ionic strength dependence of the on/off pK/sub a/ of CH/sub 3/Cbl, CH/sub 3/CH/sub 2/Cbl, and ..cap alpha..-ribazole has also been investigated. Measurements of the relative /sup 13/C resonance frequency of /sup 13/CH/sub 3/Cbl and /sup 13/CH/sub 3/Cbi as a function of temperature at several ionic strengths have been used to investigate the thermodynamics of the base-on/base-off reaction of cobalamins. Additional evidence has thus been obtained for a previously detected species of base-off, but benzimidazole-deprotonated, cobalamin in which the benzimidazole B3 nitrogen atom is hydrogen-bonded to an e side chain N-H, and the thermodynamics of formation of this species have been evaluated. These results have been confirmed by similar measurements on mixtures of /sup -/OOC/sup 13/CH/sub 2/Cbl and /sup -/OOC/sup 13/CH/sub 2/Cbi. Although the new species is the predominant form (80-90%) of the base-off but benzimidazole-deprotonated cobalamins in solution at all ionic strengths, its presence has only a minor effect on the primary on/off equilibrium constants previously calculated for RCbl's. 45 references, 4 figures, 8 tables.

  17. An Evolution-Based Screen for Genetic Differentiation between Anopheles Sister Taxa Enriches for Detection of Functional Immune Factors

    PubMed Central

    Takashima, Eizo; Williams, Marni; Eiglmeier, Karin; Pain, Adrien; Guelbeogo, Wamdaogo M.; Gneme, Awa; Brito-Fravallo, Emma; Holm, Inge; Lavazec, Catherine; Sagnon, N’Fale; Baxter, Richard H.; Riehle, Michelle M.; Vernick, Kenneth D.

    2015-01-01

    Nucleotide variation patterns across species are shaped by the processes of natural selection, including exposure to environmental pathogens. We examined patterns of genetic variation in two sister species, Anopheles gambiae and Anopheles coluzzii, both efficient natural vectors of human malaria in West Africa. We used the differentiation signature displayed by a known coordinate selective sweep of immune genes APL1 and TEP1 in A. coluzzii to design a population genetic screen trained on the sweep, classified a panel of 26 potential immune genes for concordance with the signature, and functionally tested their immune phenotypes. The screen results were strongly predictive for genes with protective immune phenotypes: genes meeting the screen criteria were significantly more likely to display a functional phenotype against malaria infection than genes not meeting the criteria (p = 0.0005). Thus, an evolution-based screen can efficiently prioritize candidate genes for labor-intensive downstream functional testing, and safely allow the elimination of genes not meeting the screen criteria. The suite of immune genes with characteristics similar to the APL1-TEP1 selective sweep appears to be more widespread in the A. coluzzii genome than previously recognized. The immune gene differentiation may be a consequence of adaptation of A. coluzzii to new pathogens encountered in its niche expansion during the separation from A. gambiae, although the role, if any of natural selection by Plasmodium is unknown. Application of the screen allowed identification of new functional immune factors, and assignment of new functions to known factors. We describe biochemical binding interactions between immune proteins that underlie functional activity for malaria infection, which highlights the interplay between pathogen specificity and the structure of immune complexes. We also find that most malaria-protective immune factors display phenotypes for either human or rodent malaria, with

  18. An Evolution-Based Screen for Genetic Differentiation between Anopheles Sister Taxa Enriches for Detection of Functional Immune Factors.

    PubMed

    Mitri, Christian; Bischoff, Emmanuel; Takashima, Eizo; Williams, Marni; Eiglmeier, Karin; Pain, Adrien; Guelbeogo, Wamdaogo M; Gneme, Awa; Brito-Fravallo, Emma; Holm, Inge; Lavazec, Catherine; Sagnon, N'Fale; Baxter, Richard H; Riehle, Michelle M; Vernick, Kenneth D

    2015-12-01

    Nucleotide variation patterns across species are shaped by the processes of natural selection, including exposure to environmental pathogens. We examined patterns of genetic variation in two sister species, Anopheles gambiae and Anopheles coluzzii, both efficient natural vectors of human malaria in West Africa. We used the differentiation signature displayed by a known coordinate selective sweep of immune genes APL1 and TEP1 in A. coluzzii to design a population genetic screen trained on the sweep, classified a panel of 26 potential immune genes for concordance with the signature, and functionally tested their immune phenotypes. The screen results were strongly predictive for genes with protective immune phenotypes: genes meeting the screen criteria were significantly more likely to display a functional phenotype against malaria infection than genes not meeting the criteria (p = 0.0005). Thus, an evolution-based screen can efficiently prioritize candidate genes for labor-intensive downstream functional testing, and safely allow the elimination of genes not meeting the screen criteria. The suite of immune genes with characteristics similar to the APL1-TEP1 selective sweep appears to be more widespread in the A. coluzzii genome than previously recognized. The immune gene differentiation may be a consequence of adaptation of A. coluzzii to new pathogens encountered in its niche expansion during the separation from A. gambiae, although the role, if any of natural selection by Plasmodium is unknown. Application of the screen allowed identification of new functional immune factors, and assignment of new functions to known factors. We describe biochemical binding interactions between immune proteins that underlie functional activity for malaria infection, which highlights the interplay between pathogen specificity and the structure of immune complexes. We also find that most malaria-protective immune factors display phenotypes for either human or rodent malaria, with

  19. Multifractal Framework Based on Blanket Method

    PubMed Central

    Paskaš, Milorad P.; Reljin, Irini S.; Reljin, Branimir D.

    2014-01-01

    This paper proposes two local multifractal measures motivated by blanket method for calculation of fractal dimension. They cover both fractal approaches familiar in image processing. The first two measures (proposed Methods 1 and 3) support model of image with embedded dimension three, while the other supports model of image embedded in space of dimension three (proposed Method 2). While the classical blanket method provides only one value for an image (fractal dimension) multifractal spectrum obtained by any of the proposed measures gives a whole range of dimensional values. This means that proposed multifractal blanket model generalizes classical (monofractal) blanket method and other versions of this monofractal approach implemented locally. Proposed measures are validated on Brodatz image database through texture classification. All proposed methods give similar classification results, while average computation time of Method 3 is substantially longer. PMID:24578664

  20. Adaptation strategies for high order discontinuous Galerkin methods based on Tau-estimation

    NASA Astrophysics Data System (ADS)

    Kompenhans, Moritz; Rubio, Gonzalo; Ferrer, Esteban; Valero, Eusebio

    2016-02-01

    In this paper three p-adaptation strategies based on the minimization of the truncation error are presented for high order discontinuous Galerkin methods. The truncation error is approximated by means of a τ-estimation procedure and enables the identification of mesh regions that require adaptation. Three adaptation strategies are developed and termed a posteriori, quasi-a priori and quasi-a priori corrected. All strategies require fine solutions, which are obtained by enriching the polynomial order, but while the former needs time converged solutions, the last two rely on non-converged solutions, which lead to faster computations. In addition, the high order method permits the spatial decoupling for the estimated errors and enables anisotropic p-adaptation. These strategies are verified and compared in terms of accuracy and computational cost for the Euler and the compressible Navier-Stokes equations. It is shown that the two quasi-a priori methods achieve a significant reduction in computational cost when compared to a uniform polynomial enrichment. Namely, for a viscous boundary layer flow, we obtain a speedup of 6.6 and 7.6 for the quasi-a priori and quasi-a priori corrected approaches, respectively.

  1. Mixed hemimicelles solid-phase extraction based on sodium dodecyl sulfate-coated nano-magnets for selective adsorption and enrichment of illegal cationic dyes in food matrices prior to high-performance liquid chromatography-diode array detection detection.

    PubMed

    Qi, Ping; Liang, Zhi-an; Wang, Yu; Xiao, Jian; Liu, Jia; Zhou, Qing-qiong; Zheng, Chun-hao; Luo, Li-Ni; Lin, Zi-hao; Zhu, Fang; Zhang, Xue-wu

    2016-03-11

    In this study, mixed hemimicelles solid-phase extraction (MHSPE) based on sodium dodecyl sulfate (SDS) coated nano-magnets Fe3O4 was investigated as a novel method for the extraction and separation of four banned cationic dyes, Auramine O, Rhodamine B, Basic orange 21 and Basic orange 22, in condiments prior to HPLC detection. The main factors affecting the extraction of analysts, such as pH, surfactant and adsorbent concentrations and zeta potential were studied and optimized. Under optimized conditions, the proposed method was successful applied for the analysis of banned cationic dyes in food samples such as chili sauce, soybean paste and tomato sauce. Validation data showed the good recoveries in the range of 70.1-104.5%, with relative standard deviations less than 15%. The method limits of determination/quantification were in the range of 0.2-0.9 and 0.7-3μgkg(-1), respectively. The selective adsorption and enrichment of cationic dyes were achieved by the synergistic effects of hydrophobic interactions and electrostatic attraction between mixed hemimicelles and the cationic dyes, which also resulted in the removal of natural pigments interferences from sample extracts. When applied to real samples, RB was detected in several positive samples (chili powders) within the range from 0.042 to 0.177mgkg(-1). These results indicate that magnetic MHSPE is an efficient and selective sample preparation technique for the extraction of banned cationic dyes in a complex matrix. PMID:26877180

  2. Mixed hemimicelles solid-phase extraction based on sodium dodecyl sulfate-coated nano-magnets for selective adsorption and enrichment of illegal cationic dyes in food matrices prior to high-performance liquid chromatography-diode array detection detection.

    PubMed

    Qi, Ping; Liang, Zhi-an; Wang, Yu; Xiao, Jian; Liu, Jia; Zhou, Qing-qiong; Zheng, Chun-hao; Luo, Li-Ni; Lin, Zi-hao; Zhu, Fang; Zhang, Xue-wu

    2016-03-11

    In this study, mixed hemimicelles solid-phase extraction (MHSPE) based on sodium dodecyl sulfate (SDS) coated nano-magnets Fe3O4 was investigated as a novel method for the extraction and separation of four banned cationic dyes, Auramine O, Rhodamine B, Basic orange 21 and Basic orange 22, in condiments prior to HPLC detection. The main factors affecting the extraction of analysts, such as pH, surfactant and adsorbent concentrations and zeta potential were studied and optimized. Under optimized conditions, the proposed method was successful applied for the analysis of banned cationic dyes in food samples such as chili sauce, soybean paste and tomato sauce. Validation data showed the good recoveries in the range of 70.1-104.5%, with relative standard deviations less than 15%. The method limits of determination/quantification were in the range of 0.2-0.9 and 0.7-3μgkg(-1), respectively. The selective adsorption and enrichment of cationic dyes were achieved by the synergistic effects of hydrophobic interactions and electrostatic attraction between mixed hemimicelles and the cationic dyes, which also resulted in the removal of natural pigments interferences from sample extracts. When applied to real samples, RB was detected in several positive samples (chili powders) within the range from 0.042 to 0.177mgkg(-1). These results indicate that magnetic MHSPE is an efficient and selective sample preparation technique for the extraction of banned cationic dyes in a complex matrix.

  3. Method for sequencing DNA base pairs

    DOEpatents

    Sessler, Andrew M.; Dawson, John

    1993-01-01

    The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source.

  4. Deuterium enrichment of interstellar dusts

    NASA Astrophysics Data System (ADS)

    Das, Ankan; Chakrabarti, Sandip Kumar; Majumdar, Liton; Sahu, Dipen

    2016-07-01

    High abundance of some abundant and simple interstellar species could be explained by considering the chemistry that occurs on interstellar dusts. Because of its simplicity, the rate equation method is widely used to study the surface chemistry. However, because the recombination efficiency for the formation of any surface species is highly dependent on various physical and chemical parameters, the Monte Carlo method is best suited for addressing the randomness of the processes. We carry out Monte-Carlo simulation to study deuterium enrichment of interstellar grain mantle under various physical conditions. Based on the physical properties, various types of clouds are considered. We find that in diffuse cloud regions, very strong radiation fields persists and hardly a few layers of surface species are formed. In translucent cloud regions with a moderate radiation field, significant number of layers would be produced and surface coverage is mainly dominated by photo-dissociation products such as, C, CH_3, CH_2D, OH and OD. In the intermediate dense cloud regions (having number density of total hydrogen nuclei in all forms ˜2 × 10^4 cm^{-3}), water and methanol along with their deuterated derivatives are efficiently formed. For much higher density regions (˜10^6 cm^{-3}), water and methanol productions are suppressed but surface coverage of CO, CO_2, O_2, O_3 are dramatically increased. We find a very high degree of fractionation of water and methanol. Observational results support a high fractionation of methanol but surprisingly water fractionation is found to be low. This is in contradiction with our model results indicating alternative routes for de-fractionation of water.

  5. Effects of glucomannan-enriched, aronia juice-based supplement on cellular antioxidant enzymes and membrane lipid status in subjects with abdominal obesity.

    PubMed

    Kardum, Nevena; Petrović-Oggiano, Gordana; Takic, Marija; Glibetić, Natalija; Zec, Manja; Debeljak-Martacic, Jasmina; Konić-Ristić, Aleksandra

    2014-01-01

    The aim of this study was to analyze the effects of a 4-week-long consumption of glucomannan-enriched, aronia juice-based supplement on anthropometric parameters, membrane fatty acid profile, and status of antioxidant enzymes in erythrocytes obtained from postmenopausal women with abdominal obesity. Twenty women aged 45-65 with a mean body mass index (BMI) of 36.1 ± 4.4 kg/m(2) and waist circumference of 104.8 ± 10.1 cm were enrolled. Participants were instructed to consume 100 mL of supplement per day as part of their regular diet. A significant increase in the content of n-3 (P < 0.05) polyunsaturated fatty acids in membrane phospholipids was observed, with a marked increase in the level of docosahexaenoic fatty acid (P < 0.05). Accordingly, a decrease in the n-6 and n-3 fatty acids ratio was observed (P < 0.05). The observed effects were accompanied with an increase in glutathione peroxidase activity (P < 0.05). Values for BMI (P < 0.001), waist circumference (P < 0.001), and systolic blood pressure (P < 0.05) were significantly lower after the intervention. The obtained results indicate a positive impact of tested supplement on cellular oxidative damage, blood pressure, and anthropometric indices of obesity.

  6. Effects of Glucomannan-Enriched, Aronia Juice-Based Supplement on Cellular Antioxidant Enzymes and Membrane Lipid Status in Subjects with Abdominal Obesity

    PubMed Central

    Petrović-Oggiano, Gordana; Glibetić, Natalija; Zec, Manja; Debeljak-Martacic, Jasmina; Konić-Ristić, Aleksandra

    2014-01-01

    The aim of this study was to analyze the effects of a 4-week-long consumption of glucomannan-enriched, aronia juice-based supplement on anthropometric parameters, membrane fatty acid profile, and status of antioxidant enzymes in erythrocytes obtained from postmenopausal women with abdominal obesity. Twenty women aged 45–65 with a mean body mass index (BMI) of 36.1 ± 4.4 kg/m2 and waist circumference of 104.8 ± 10.1 cm were enrolled. Participants were instructed to consume 100 mL of supplement per day as part of their regular diet. A significant increase in the content of n-3 (P < 0.05) polyunsaturated fatty acids in membrane phospholipids was observed, with a marked increase in the level of docosahexaenoic fatty acid (P < 0.05). Accordingly, a decrease in the n-6 and n-3 fatty acids ratio was observed (P < 0.05). The observed effects were accompanied with an increase in glutathione peroxidase activity (P < 0.05). Values for BMI (P < 0.001), waist circumference (P < 0.001), and systolic blood pressure (P < 0.05) were significantly lower after the intervention. The obtained results indicate a positive impact of tested supplement on cellular oxidative damage, blood pressure, and anthropometric indices of obesity. PMID:25574495

  7. Direct Measurement of Initial Enrichment and Burn-up of Spent Fuel Assembly with a Differential Die-Away Technique Based Instrument

    SciTech Connect

    Henzl, Vladimir; Swinhoe, Martyn T.; Tobin, Stephen J.

    2012-07-16

    A key objective of the Next Generation Safeguards Initiative (NGSI) is to utilize non-destructive assay (NDA) techniques to determine the elemental plutonium (Pu) content in a commercial-grade nuclear spent fuel assembly (SFA). In the third year of the NGSI Spent Fuel NDA project, the research focus is on the integration of a few NDA techniques. One of the reoccurring challenges to the accurate determination of Pu content has been the explicit dependence of the measured signal on the presence of neutron absorbers which build up in the assembly in accordance with its operating and irradiation history. The history of any SFA is often summarized by the parameters of burn-up (BU), initial enrichment (IE) and cooling time (CT). While such parameters can typically be provided by the operator, the ability to directly measure and verify them would significantly enhance the autonomy of the IAEA inspectorate. Within this paper, we demonstrate that an instrument based on a Differential Die-Away technique is in principle capable of direct measurement of IE and, should the CT be known, also the BU.

  8. Continuous enrichment of low-abundance cell samples using standing surface acoustic waves (SSAW)†

    PubMed Central

    Chen, Yuchao; Li, Sixing; Gu, Yeyi; Li, Peng; Ding, Xiaoyun; Wang, Lin; McCoy, J. Philip; Levine, Stewart J.; Huang, Tony Jun

    2015-01-01

    Cell enrichment is a powerful tool in a variety of cellular studies, especially in applications with low-abundance cell types. In this work, we developed a standing surface acoustic wave (SSAW) based microfluidic device for non-contact, continuous cell enrichment. With a pair of parallel interdigital transducers (IDT) deposited on a piezoelectric substrate, a one-dimensional SSAW field was established along disposable micro-tubing channels, generating numerous pressure nodes (and thus numerous cell-enrichment regions). Our method is able to concentrate highly diluted blood cells by more than 100 fold with a recovery efficiency of up to 99%. Such highly effective cell enrichment was achieved without using sheath flow. The SSAW-based technique presented here is simple, bio-compatible, label-free, and sheath-flow-free. With these advantages, it could be valuable for many biomedical applications. PMID:24413889

  9. Highly efficient preparation of sphingoid bases from glucosylceramides by chemoenzymatic method.

    PubMed

    Gowda, Siddabasave Gowda B; Usuki, Seigo; Hammam, Mostafa A S; Murai, Yuta; Igarashi, Yasuyuki; Monde, Kenji

    2016-02-01

    Sphingoid base derivatives have attracted increasing attention as promising chemotherapeutic candidates against lifestyle diseases such as diabetes and cancer. Natural sphingoid bases can be a potential resource instead of those derived by time-consuming total organic synthesis. In particular, glucosylceramides (GlcCers) in food plants are enriched sources of sphingoid bases, differing from those of animals. Several chemical methodologies to transform GlcCers to sphingoid bases have already investigated; however, these conventional methods using acid or alkaline hydrolysis are not efficient due to poor reaction yield, producing complex by-products and resulting in separation problems. In this study, an extremely efficient and practical chemoenzymatic transformation method has been developed using microwave-enhanced butanolysis of GlcCers and a large amount of readily available almond β-glucosidase for its deglycosylation reaction of lysoGlcCers. The method is superior to conventional acid/base hydrolysis methods in its rapidity and its reaction cleanness (no isomerization, no rearrangement) with excellent overall yield.

  10. A cellular automaton method to simulate the microstructure and evolution of low-enriched uranium (LEU) U-Mo/Al dispersion type fuel plates

    NASA Astrophysics Data System (ADS)

    Drera, Saleem S.; Hofman, Gerard L.; Kee, Robert J.; King, Jeffrey C.

    2014-10-01

    Low-enriched uranium (LEU) fuel plates for high power materials test reactors (MTR) are composed of nominally spherical uranium-molybdenum (U-Mo) particles within an aluminum matrix. Fresh U-Mo particles typically range between 10 and 100 μm in diameter, with particle volume fractions up to 50%. As the fuel ages, reaction-diffusion processes cause the formation and growth of interaction layers that surround the fuel particles. The growth rate depends upon the temperature and radiation environment. The cellular automaton algorithm described in this paper can synthesize realistic random fuel-particle structures and simulate the growth of the intermetallic interaction layers. Examples in the present paper pack approximately 1000 particles into three-dimensional rectangular fuel structures that are approximately 1 mm on each side. The computational approach is designed to yield synthetic microstructures consistent with images from actual fuel plates and is validated by comparison with empirical data on actual fuel plates.

  11. Method for sequencing DNA base pairs

    DOEpatents

    Sessler, A.M.; Dawson, J.

    1993-12-14

    The base pairs of a DNA structure are sequenced with the use of a scanning tunneling microscope (STM). The DNA structure is scanned by the STM probe tip, and, as it is being scanned, the DNA structure is separately subjected to a sequence of infrared radiation from four different sources, each source being selected to preferentially excite one of the four different bases in the DNA structure. Each particular base being scanned is subjected to such sequence of infrared radiation from the four different sources as that particular base is being scanned. The DNA structure as a whole is separately imaged for each subjection thereof to radiation from one only of each source. 6 figures.

  12. Use of Stirred Suspension Bioreactors for Male Germ Cell Enrichment.

    PubMed

    Sakib, Sadman; Dores, Camila; Rancourt, Derrick; Dobrinski, Ina

    2016-01-01

    Spermatogenesis is a stem cell based system. Both therapeutic and biomedical research applications of spermatogonial stem cells require a large number of cells. However, there are only few germ line stem cells in the testis, contained in the fraction of undifferentiated spermatogonia. The lack of specific markers makes it difficult to isolate these cells. The long term maintenance and proliferation of nonrodent germ cells in culture has so far been met with limited success, partially due to the lack of highly enriched starting populations. Differential plating, which depends on the differential adhesion properties of testicular somatic and germ cells to tissue culture dishes, has been the method of choice for germ cell enrichment, especially for nonrodent germ cells. However, for large animals, this process becomes labor intensive and increases variability due to the need for extensive handling. Here, we describe the use of stirred suspension bioreactors, as a novel system for enriching undifferentiated germ cells from 1-week-old pigs. This method capitalizes on the adherent properties of somatic cells within a controlled environment, thus promoting the enrichment of progenitor cells with minimal handling and variability.

  13. Preparation of stir cake sorptive extraction based on polymeric ionic liquid for the enrichment of benzimidazole anthelmintics in water, honey and milk samples.

    PubMed

    Wang, Yulei; Zhang, Jie; Huang, Xiaojia; Yuan, Dongxing

    2014-08-20

    In this work, a new stir cake sorptive extraction (SCSE) using polymeric ionic liquid monolith as sorbent was prepared. The sorbent was obtained by in situ copolymerization of an ionic liquid, 1-allyl-3-methylimidazolium bis[(trifluoro methyl)sulfonyl]imide (AMII) and divinylbenzene (DB) in the presence of N,N-dimethylformamide. The influence of the content of ionic liquid and the porogen in the polymerization mixture on extraction performance was studied thoroughly. The physicochemical properties of the polymeric ionic liquid were characterized by infrared spectroscopy, elemental analysis, scanning electron microscopy and mercury intrusion porosimetry. The usefulness of SCSE-AMIIDB was demonstrated by the enrichment of trace benzimidazole anthelmintics. Several parameters affecting the extraction efficiency were investigated, and under the optimized conditions, a simple and effective method for the determination of trace benzimidazoles residues in water, milk and honey samples was established by coupling SCSE-AMIIDB with high performance liquid chromatography/diode array detection (SCSE-AMIIDB-HPLC/DAD). Results indicated that the limits of detection (S/N=3) for target compounds were 0.020-0.072 μg L(-1), 0.035-0.10 μg L(-1) and 0.026-0.076 μg L(-1) in water, milk and honey samples, respectively. In addition, an acceptable reproducibility was achieved by evaluating the repeatability and intermediate precision with relative standard deviations (RSD) of less than 9% and 11%, respectively. Finally, the established AMII-SCSE-HPLC/DAD method was successfully applied for the determination of benzimidazoles residues in milk, honey and environmental water samples. Recoveries obtained for the determination of benzimidazole anthelmintics in spiking samples ranged from 70.2% to 117.6%, with RSD below 12% in all cases.

  14. New ITF measure method based on fringes

    NASA Astrophysics Data System (ADS)

    Fang, Qiaoran; Liu, Shijie; Gao, Wanrong; Zhou, You; Liu, HuanHuan

    2016-01-01

    With the unprecedented developments of the intense laser and aerospace projects', the interferometer is widely used in detecting middle frequency indicators of the optical elements, which put forward very high request towards the interferometer system transfer function (ITF). Conventionally, the ITF is measured by comparing the power spectra of known phase objects such as high-quality phase step. However, the fabrication of phase step is complex and high-cost, especially in the measurement of large-aperture interferometer. In this paper, a new fringe method is proposed to measure the ITF without additional objects. The frequency was changed by adjusting the number of fringes, and the normalized transfer function value was measured at different frequencies. The ITF value measured by fringe method was consistent with the traditional phase step method, which confirms the feasibility of proposed method. Moreover, the measurement error caused by defocus was analyzed. The proposed method does not require the preparation of a step artifact, which greatly reduces the test cost, and is of great significance to the ITF measurement of large aperture interferometer.

  15. Genetic diversity through the looking glass: Effect of enrichment bias

    SciTech Connect

    Dunbar, J.; Forney, L.; White, S.

    1997-04-01

    The effect of enrichment bias on the diversity of 2,4-dichlorophenoxyacetate (2,4-D)-degrading (2,4-D{sup +}) bacteria recovered from soil was evaluated by comparing the diversity of isolates obtained by direct plating to the diversity of isolates obtained from 85 liquid batch cultures. By the two methods, a total of 159 isolates were purified from 1 g of soil and divided into populations based on repeated extragenic palindromic sequence PCR (rep-PCR) genomic fingerprints. Approximately 42% of the direct-plating isolates hybridized with the tfdA and tfdB genes from Alcaligenes eutrophus JMP134(pJP4), 27% hybridized with the tfdA and tfdB genes from Burk holderia sp. strain RASC, and 30% hybridized with none of the probes. In contrast, the enrichment isolates not only represented fewer populations than the isolates obtained by direct plating but also exhibited, almost exclusively, a single hybridization pattern with 2,4-D catabolic gene probes. Approximately 98% of the enrichment isolates possessed pJP4-type tfd4 and tfdB genes, whereas isolates containing RASC-type tfdA and tfdB genes were obtained from only 2 of the 85 enrichment cultures. The skewed occurrence of the pJP4-type genes among the isolates obtained by enrichment suggests that the competitive fitness of 2,4-D{sup +} populations during growth with 2,4-D may be influenced either by specific tfd alleles or by genetic factors linked to these alleles. Moreover, the results indicate that evaluation of the diversity and distribution of catabolic pathways in nature can be highly distorted by the use of enrichment culture techniques. 34 refs., 4 figs., 1 tab.

  16. A novel method for simultaneous measurement of concentration and enrichment of NO synthesis-specific amino acids in human plasma using stable isotopes and LC/MS ion trap analysis.

    PubMed

    Oosterink, J Efraim; Buijs, Nikki; van Goudoever, Johannes B; Schierbeek, Henk

    2014-05-01

    Stable isotope studies offer the opportunity to study the in-depth metabolic pathway of glutamine, citrulline, and arginine amino acids involved in NO synthesis. The use of multiple stable isotopes can be used to elucidate the exact transformation of glutamine to citrulline and arginine de novo synthesis. This novel method provides a purification step using cation exchange resin in combination with a rapid and easy derivatization procedure for a precise and robust measurement of the concentration and isotopic enrichments of NO synthesis-specific amino acids using a liquid chromatography mass spectrometry (LC/MS) ion trap system with high sensitivity and selectivity. The ethyl chloroformate derivatization procedure is beneficial in terms of robustness, velocity, simplicity, and derivative stability. In addition, the ethyl chloroformate derivatization can be performed at room temperature in an aqueous environment without incubation and the isolation of the derivatives from the reaction mixture also serves as a purification step. The concentration and enrichment of NO synthesis-specific amino acids as well as phenylalanine and tyrosine to determine protein turnover, were measured with good inter-day precision for the concentration (<7.4%) and enrichment (<12.7%) in plasma samples at low and high levels. The low limit of quantification was 0.2μmol/L for most of the amino acids and the purification method showed to have good recoveries between 78% and 98%. No ion-suppression was observed by post-column infusion experiments. In order to develop new nutritional strategies, this novel method can be used to support the elucidation of the effect of administration of specific supplements on the glutamine-citrulline-arginine pathway by using stable isotope studies.

  17. LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights.

    PubMed

    Dong, Xinran; Hao, Yun; Wang, Xiao; Tian, Weidong

    2016-01-11

    Pathway or gene set over-representation analysis (ORA) has become a routine task in functional genomics studies. However, currently widely used ORA tools employ statistical methods such as Fisher's exact test that reduce a pathway into a list of genes, ignoring the constitutive functional non-equivalent roles of genes and the complex gene-gene interactions. Here, we develop a novel method named LEGO (functional Link Enrichment of Gene Ontology or gene sets) that takes into consideration these two types of information by incorporating network-based gene weights in ORA analysis. In three benchmarks, LEGO achieves better performance than Fisher and three other network-based methods. To further evaluate LEGO's usefulness, we compare LEGO with five gene expression-based and three pathway topology-based methods using a benchmark of 34 disease gene expression datasets compiled by a recent publication, and show that LEGO is among the top-ranked methods in terms of both sensitivity and prioritization for detecting target KEGG pathways. In addition, we develop a cluster-and-filter approach to reduce the redundancy among the enriched gene sets, making the results more interpretable to biologists. Finally, we apply LEGO to two lists of autism genes, and identify relevant gene sets to autism that could not be found by Fisher.

  18. HMM-Based Gene Annotation Methods

    SciTech Connect

    Haussler, David; Hughey, Richard; Karplus, Keven

    1999-09-20

    Development of new statistical methods and computational tools to identify genes in human genomic DNA, and to provide clues to their functions by identifying features such as transcription factor binding sites, tissue, specific expression and splicing patterns, and remove homologies at the protein level with genes of known function.

  19. Enrichment of Acinetobacter spp. from food samples.

    PubMed

    Carvalheira, Ana; Ferreira, Vânia; Silva, Joana; Teixeira, Paula

    2016-05-01

    Relatively little is known about the role of foods in the chain of transmission of acinetobacters and the occurrence of different Acinetobacter spp. in foods. Currently, there is no standard procedure to recover acinetobacters from food in order to gain insight into the food-related ecology and epidemiology of acinetobacters. This study aimed to assess whether enrichment in Dijkshoorn enrichment medium followed by plating in CHROMagar™ Acinetobacter medium is a useful method for the isolation of Acinetobacter spp. from foods. Recovery of six Acinetobacter species from food spiked with these organisms was compared for two selective enrichment media (Baumann's enrichment and Dijkshoorn's enrichment). Significantly (p < 0.01) higher cell counts were obtained in Dijkshoorn's enrichment. Next, the Dijkshoorn's enrichment followed by direct plating on CHROMagar™ Acinetobacter was applied to detect Acinetobacter spp. in different foods. Fourteen different presumptive acinetobacters were recovered and assumed to represent nine different strains on the basis of REP-PCR typing. Eight of these strains were identified by rpoB gene analysis as belonging to the species Acinetobacter johnsonii, Acinetobacter calcoaceticus, Acinetobacter guillouiae and Acinetobacter gandensis. It was not possible to identify the species level of one strain which may suggests that it represents a distinct species.

  20. Reactor Physics Methods and Preconceptual Core Design Analyses for Conversion of the Advanced Test Reactor to Low-Enriched Uranium Fuel Annual Report for Fiscal Year 2012

    SciTech Connect

    David W. Nigg; Sean R. Morrell

    2012-09-01

    Under the current long-term DOE policy and planning scenario, both the ATR and the ATRC will be reconfigured at an appropriate time within the next several years to operate with low-enriched uranium (LEU) fuel. This will be accomplished under the auspices of the Reduced Enrichment Research and Test Reactor (RERTR) Program, administered by the DOE National Nuclear Security Administration (NNSA). At a minimum, the internal design and composition of the fuel element plates and support structure will change, to accommodate the need for low enrichment in a manner that maintains total core excess reactivity at a suitable level for anticipated operational needs throughout each cycle while respecting all control and shutdown margin requirements and power distribution limits. The complete engineering design and optimization of LEU cores for the ATR and the ATRC will require significant multi-year efforts in the areas of fuel design, development and testing, as well as a complete re-analysis of the relevant reactor physics parameters for a core composed of LEU fuel, with possible control system modifications. Ultimately, revalidation of the computational physics parameters per applicable national and international standards against data from experimental measurements for prototypes of the new ATR and ATRC core designs will also be required for Safety Analysis Report (SAR) changes to support routine operations with LEU. This report is focused on reactor physics analyses conducted during Fiscal Year (FY) 2012 to support the initial development of several potential preconceptual fuel element designs that are suitable candidates for further study and refinement during FY-2013 and beyond. In a separate, but related, effort in the general area of computational support for ATR operations, the Idaho National Laboratory (INL) is conducting a focused multiyear effort to introduce modern high-fidelity computational reactor physics software and associated validation protocols to replace

  1. Method of casting pitch based foam

    DOEpatents

    Klett, James W.

    2002-01-01

    A process for producing molded pitch based foam is disclosed which minimizes cracking. The process includes forming a viscous pitch foam in a container, and then transferring the viscous pitch foam from the container into a mold. The viscous pitch foam in the mold is hardened to provide a carbon foam having a relatively uniform distribution of pore sizes and a highly aligned graphic structure in the struts.

  2. Roadside-based communication system and method

    NASA Technical Reports Server (NTRS)

    Bachelder, Aaron D. (Inventor)

    2007-01-01

    A roadside-based communication system providing backup communication between emergency mobile units and emergency command centers. In the event of failure of a primary communication, the mobile units transmit wireless messages to nearby roadside controllers that may take the form of intersection controllers. The intersection controllers receive the wireless messages, convert the messages into standard digital streams, and transmit the digital streams along a citywide network to a destination intersection or command center.

  3. Selective trace enrichment of acidic pharmaceuticals in real water and sediment samples based on solid-phase extraction using multi-templates molecularly imprinted polymers.

    PubMed

    Duan, Yan-Ping; Dai, Chao-Meng; Zhang, Ya-Lei; Ling-Chen

    2013-01-01

    A novel multi-templates molecularly imprinted polymer (MIP), using acidic pharmaceuticals mixture (ibuprofen (IBP), naproxen (NPX), ketoprofen (KEP), diclofenac (DFC), and clofibric acid (CA)) as the template, was prepared as solid-phase extraction (SPE) material for the quantitative enrichment of acidic pharmaceuticals in environmental samples and off-line coupled with liquid chromatography-mass spectrometry (LC/MS/MS). Washing solvent was optimized in terms of kind and volume for removing the matrix constituents nonspecifically adsorbed on the MIP. When 1L of water sample spiked at 1μg/L was loaded onto the cartridge, the binding capacity of the MIP cartridge were 48.7μg/g for KEP, 60.7μg/g for NPX, 52μg/g for CA, 61.3μg/g for DFC and 60.7μg/g for IBP, respectively, which are higher than those of the commercial single template MIP in organic medium (e.g. toluene) reported in the literature. Recoveries of the five acidic pharmaceuticals extracted from 1L of real water samples such as lake water and wastewater spiked at 1μg/L were more than 95%. The recoveries of acidic pharmaceuticals extracted from 10-g sediment sample spiked at the 10ng/g level were in the range of 77.4-90.6%. To demonstrate the potential of the MIP obtained, a comparison with commercial C18 SPE cartridge was performed. Molecularly imprinted solid-phase extraction (MISPE) cartridge showed higher recoveries than commercial C18 SPE cartridge for acidic pharmaceuticals. These results showed the suitability of the MISPE method for the selective extraction of a group of structurally related compounds such as acidic pharmaceuticals. PMID:23245900

  4. Identification of RIP-II toxins by affinity enrichment, enzymatic digestion and LC-MS.

    PubMed

    Fredriksson, Sten-Åke; Artursson, Elisabet; Bergström, Tomas; Östin, Anders; Nilsson, Calle; Åstot, Crister

    2015-01-20

    Type 2 ribosome-inactivating protein toxins (RIP-II toxins) were enriched and purified prior to enzymatic digestion and LC-MS analysis. The enrichment of the RIP-II family of plant proteins, such as ricin, abrin, viscumin, and volkensin was based on their affinity for galactosyl moieties. A macroporous chromatographic material was modified with a galactose-terminated substituent and packed into miniaturized columns that were used in a chromatographic system to achieve up to 1000-fold toxin enrichment. The galactose affinity of the RIP-II proteins enabled their selective enrichment from water, beverages, and extracts of powder and wipe samples. The enriched fractions were digested with trypsin and RIP-II peptides were identified based on accurate mass LC-MS data. Their identities were unambiguously confirmed by LC-MS/MS product ion scans of peptides unique to each of the toxins. The LC-MS detection limit achieved for ricin target peptides was 10 amol and the corresponding detection limit for the full method was 10 fmol/mL (0.6 ng/mL). The affinity enrichment method was applied to samples from a forensic investigation into a case involving the illegal production of ricin and abrin toxins.

  5. Tailor-Made Stable Zr(IV)-Based Metal-Organic Frameworks for Laser Desorption/Ionization Mass Spectrometry Analysis of Small Molecules and Simultaneous Enrichment of Phosphopeptides.

    PubMed

    Chen, Lianfang; Ou, Junjie; Wang, Hongwei; Liu, Zhongshan; Ye, Mingliang; Zou, Hanfa

    2016-08-10

    Although thousands of metal-organic frameworks (MOFs) have been fabricated and widely applied in gas storage/separations, adsorption, catalysis, and so on, few kinds of MOFs have been used as adsorption materials while simultaneously serving as matrixes to analyze small molecules for laser desorption/ionization mass spectrometry (LDI-MS). Herein, a new concept is introduced to design and synthesize MOFs as both adsorption materials and matrixes according to the structure of ligands and common matrixes. The proof of concept design was demonstrated by selection of 2,5-pyridinedicarboxylic acid (PDC) and 2,5-dihydroxyterephthalic acid (DHT) as ligands for synthesis of MOFs. Two Zr(IV)-based MOFs of UiO-66-PDC and UiO-66-(OH)2 were synthesized and applied for the first time as new matrixes for analysis of small molecules by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Both of them showed low matrix interferences, high ionization efficiency, and good reproducibility when used as matrixes. A variety of small molecules, including saccharides, amino acids, nucleosides, peptides, alkaline drugs, and natural products, were analyzed. In addition, UiO-66-(OH)2 exhibited potential for application in the quantitative determination of glucose and pyridoxal 5'-phosphate. Furthermore, thanks to its intrinsically large surface area and highly ordered pores, UiO-66-(OH)2 also showed sensitive and specific enrichment of phosphopeptides prior to MS analysis. These results demonstrated that this strategy can be used to efficiently screen tailor-made MOFs as matrixes to analyze small molecules by MALDI-TOF-MS. PMID:27427857

  6. Shelf-life study of Indian traditional food based nutraceutical (oryzanol) enriched instant mixes Bhath-OZ and Upma-OZ.

    PubMed

    Baby Latha, R; Debnath, Sukumar; Sarmandal, C V; Hemavathy, J; Khatoon, Sakina; Gopala Krishna, A G; Lokesh, B R

    2014-01-01

    To provide nutraceutical such as oryzanol through food, two instant mixes based on the Indian traditional food cuisine Bisibele bhath and Upma(Bhath-OZ and Upma-OZ) were developed and evaluated for shelf-life. The formulations contained cereals, pulses, and spices along with oryzanol enriched oil and were packed in 200gauge/50 gauge metallized polyester packaging material and stored under ambient (27 °C 65%RH) and accelerated conditions (37 °C/92%RH). Samples were withdrawn periodically and peroxide value (PV), free fatty acid value (FFA), fatty acid composition, oryzanol, and total tocopherols content were estimated. Sensory evaluation of reconstituted products was also carried out. Oryzanol content (610 and 550 mg%) did not change appreciably in Bhath-OZ and Upma-OZ respectively. The peroxide value under ambient condition increased from 1.1 to 9.3 meq.O2/kg and 2.24 to 9.02 meq.O2/kg during the 6 month storage study at 27 °C and 65% RH, while under accelerated conditions at 37 °C and 92%RH, it increased from 1.12 to 8.54 meq. O2/kg and 2.24 to 6.96 meq. O2/kg during 2 month storage period. Bhath-OZ and Upma-OZ packed in metallized polyester pouches stored at 27 °C and 65% RH had a shelf-life of 4 months without affecting the oryzanol content and quality of instant mixes during the storage period. PMID:24426057

  7. Method for producing iron-based catalysts

    DOEpatents

    Farcasiu, Malvina; Kaufman, Phillip B.; Diehl, J. Rodney; Kathrein, Hendrik

    1999-01-01

    A method for preparing an acid catalyst having a long shelf-life is provided comprising doping crystalline iron oxides with lattice-compatible metals and heating the now-doped oxide with halogen compounds at elevated temperatures. The invention also provides for a catalyst comprising an iron oxide particle having a predetermined lattice structure, one or more metal dopants for said iron oxide, said dopants having an ionic radius compatible with said lattice structure; and a halogen bound with the iron and the metal dopants on the surface of the particle.

  8. Science Student Enrichment Opportunities.

    ERIC Educational Resources Information Center

    California State Dept. of Education, Sacramento.

    This document was developed with the intention of increasing California public school students' awareness of and participation in science-related enrichment activities. Some of the activities are intended for participation by individuals, while others are meant for teams of students. These annual events are listed in chronological order for a…

  9. EDUCATIONAL ENRICHMENT PROGRAM - 1964.

    ERIC Educational Resources Information Center

    FUNK, JOHN H.

    THE EDUCATIONAL ENRICHMENT PROGRAM - 1964 WAS A COOPERATIVE UNDERTAKING OF SIX INDEPENDENT SCHOOLS IN OR NEAR BOSTON AND A NUMBER OF INTERESTED ORGANIZATIONS THAT OFFERED THE USE OF THEIR FACILITIES AND PERSONNEL TO AN URBAN COMMUNITY DURING THE NONSCHOOL MONTHS. THE AIM OF THE PROGRAM WAS TO OFFER CHALLENGING AND EXPLORATORY STUDY WHICH COULD…

  10. Reversing Underachievement through Enrichment.

    ERIC Educational Resources Information Center

    Renzulli, Joseph S.; Baum, Susan M.; Hebert, Thomas; McCluskey, Ken W.

    1999-01-01

    Discusses problems of underachievement, especially among potentially high ability students, and the difficulties inherent in reversing this process. Presents new perspective and strategies that promote success. Describes Type III enrichment experiences as a means to unleash students' potential. Speculates as to what causes turnaround within an…

  11. Economic Analysis. Enrichment.

    ERIC Educational Resources Information Center

    Sterling Inst., Washington, DC. Educational Technology Center.

    A multimedia course in economic analysis was prepared for the United States Naval Academy. (ED 043 790 and ED 043 791 are the final reports of the project evaluation and development model.) This report presents enrichment segments for selected core segments in concept areas one and two, covering a spectrum of economic systems, the influence of…

  12. Enriching the Catalog

    ERIC Educational Resources Information Center

    Tennant, Roy

    2004-01-01

    After decades of costly and time-consuming effort, nearly all libraries have completed the retrospective conversion of their card catalogs to electronic form. However, bibliographic systems still are really not much more than card catalogs on wheels. Enriched content that Amazon.com takes for granted--such as digitized tables of contents, cover…

  13. Enriching Number Knowledge

    ERIC Educational Resources Information Center

    Mack, Nancy K.

    2011-01-01

    Exploring number systems of other cultures can be an enjoyable learning experience that enriches students' knowledge of numbers and number systems in important ways. It helps students deepen mental computation fluency, knowledge of place value, and equivalent representations for numbers. This article describes how the author designed her…

  14. [Culture based diagnostic methods for tuberculosis].

    PubMed

    Baylan, Orhan

    2005-01-01

    Culture methods providing isolates for identification and drug susceptibility testing, still represent the gold standard for the definitive diagnosis of tuberculosis, although the delay in obtaining results still remains a problem. Traditional solid media are recommended for use along with liquid media in primary isolation of mycobacteria. At present, a number of elaborate culture systems are available commercially. They range from simple bottles and tubes such as MGIT (BD Diagnostic Systems, USA), Septi-Chek AFB (BD, USA) and MB Redox (Biotest Diagnostics, USA) to semiautomated system (BACTEC 460TB, BD, USA) and fully automated systems (BACTEC 9000 MB [BD, USA], BACTEC MGIT 960 [BD, USA], ESP Culture System II [Trek Diagnostics, USA], MB/BacT ALERT 3D System [BioMérieux, NC], TK Culture System [Salubris Inc, Turkey]). Culture methods available today are sufficient to permit laboratories to develop an algoritm that is optimal for patients and administrative needs. In this review article, the culture systems used for the diagnosis of tuberculosis, their mechanisms, advantages and disadvantages have been discussed under the light of recent literature.

  15. Enriching regulatory networks by bootstrap learning using optimised GO-based gene similarity and gene links mined from PubMed abstracts

    SciTech Connect

    Taylor, Ronald C.; Sanfilippo, Antonio P.; McDermott, Jason E.; Baddeley, Robert L.; Riensche, Roderick M.; Jensen, Russell S.; Verhagen, Marc; Pustejovsky, James

    2011-02-18

    Transcriptional regulatory networks are being determined using “reverse engineering” methods that infer connections based on correlations in gene state. Corroboration of such networks through independent means such as evidence from the biomedical literature is desirable. Here, we explore a novel approach, a bootstrapping version of our previous Cross-Ontological Analytic method (XOA) that can be used for semi-automated annotation and verification of inferred regulatory connections, as well as for discovery of additional functional relationships between the genes. First, we use our annotation and network expansion method on a biological network learned entirely from the literature. We show how new relevant links between genes can be iteratively derived using a gene similarity measure based on the Gene Ontology that is optimized on the input network at each iteration. Second, we apply our method to annotation, verification, and expansion of a set of regulatory connections found by the Context Likelihood of Relatedness algorithm.

  16. Stable Isotope Enrichment Capabilities at ORNL

    SciTech Connect

    Egle, Brian; Aaron, W Scott; Hart, Kevin J

    2013-01-01

    The Oak Ridge National Laboratory (ORNL) and the US Department of Energy Nuclear Physics Program have built a high-resolution Electromagnetic Isotope Separator (EMIS) as a prototype for reestablishing a US based enrichment capability for stable isotopes. ORNL has over 60 years of experience providing enriched stable isotopes and related technical services to the international accelerator target community, as well as medical, research, industrial, national security, and other communities. ORNL is investigating the combined use of electromagnetic and gas centrifuge isotope separation technologies to provide research quantities (milligram to several kilograms) of enriched stable isotopes. In preparation for implementing a larger scale production facility, a 10 mA high-resolution EMIS prototype has been built and tested. Initial testing of the device has simultaneously collected greater than 98% enriched samples of all the molybdenum isotopes from natural abundance feedstock.

  17. Rapid Column-Free Enrichment of Mononuclear Cells from Solid Tissues.

    PubMed

    Scoville, Steven D; Keller, Karen A; Cheng, Stephanie; Zhang, Michael; Zhang, Xiaoli; Caligiuri, Michael A; Freud, Aharon G

    2015-07-30

    We have developed a rapid negative selection method to enrich rare mononuclear cells from human tissues. Unwanted and antibody-tethered cells are selectively depleted during a Ficoll separation step, and there is no need for magnetic-based reagents and equipment. The new method is fast, customizable, inexpensive, remarkably efficient, and easy to perform, and per sample the overall cost is less than one-tenth the cost associated with a magnetic column-based method.

  18. Possibility of nuclear pumped laser experiment using low enriched uranium

    NASA Astrophysics Data System (ADS)

    Obara, Toru; Takezawa, Hiroki

    2012-06-01

    Possibility to perform experiments for nuclear pumped laser oscillation by using low enriched uranium is investigated. Kinetic analyses are performed for two types of reactor design, one is using highly enriched uranium and the other is using low enriched uranium. The reactor design is based on the experiment reactor in IPPE. The results show the oscillation of nuclear pumped laser in the case of low enriched uranium reactor is also possible. The use of low enriched uranium in the experiment will make experiment easier.

  19. PCLC flake-based apparatus and method

    DOEpatents

    Cox, Gerald P; Fromen, Cathy A; Marshall, Kenneth L; Jacobs, Stephen D

    2012-10-23

    A PCLC flake/fluid host suspension that enables dual-frequency, reverse drive reorientation and relaxation of the PCLC flakes is composed of a fluid host that is a mixture of: 94 to 99.5 wt % of a non-aqueous fluid medium having a dielectric constant value .di-elect cons., where 1<.di-elect cons.<7, a conductivity value .sigma., where 10.sup.-9>.sigma.>10.sup.-7 Siemens per meter (S/m), and a resistivity r, where 10.sup.7>r>10.sup.10 ohm-meters (.OMEGA.-m), and which is optically transparent in a selected wavelength range .DELTA..lamda.; 0.0025 to 0.25 wt % of an inorganic chloride salt; 0.0475 to 4.75 wt % water; and 0.25 to 2 wt % of an anionic surfactant; and 1 to 5 wt % of PCLC flakes suspended in the fluid host mixture. Various encapsulation forms and methods are disclosed including a Basic test cell, a Microwell, a Microcube, Direct encapsulation (I), Direct encapsulation (II), and Coacervation encapsulation. Applications to display devices are disclosed.

  20. Whole-Exome Enrichment with the Illumina TruSeq Exome Enrichment Platform.

    PubMed

    Chen, Rui; Im, Hogune; Snyder, Michael

    2015-07-01

    Multiple platforms are available for whole-exome enrichment and sequencing (WES). This protocol is based on the Illumina TruSeq Exome Enrichment platform, which captures ∼62 Mb of the human exonic regions using 95-base DNA probes. In addition to covering the RefSeq and Ensembl coding sequences, the enriched sequences also include ∼28 Mb of RefSeq untranslated regions (UTR). The protocol can be performed at the benchside without the need for automation, and the resulting library can be used for targeted next-generation sequencing on an Illumina HiSeq 2000 sequencer.

  1. Effects of single-use and group-use enrichment on stereotypy and intragroup aggressive and affiliative behaviors of a social group of squirrel monkeys (Saimiri sciureus) at the Singapore Zoo.

    PubMed

    Sha, John; Han, Sharleen; Marlena, Diana; Kee, Julienne

    2012-01-01

    Four food-based enrichment devices were used to test the effects of single-use and group-use enrichment devices on stereotypy, intragroup aggression, and affiliation in a compatible group of 5 squirrel monkeys (Saimiri sciureus). All enrichment devices were found to reduce overall stereotypic behavior from baseline levels (without enrichment). The occurrence of stereotypic behavior differed between individual squirrel monkeys with an adult female showing the highest level of stereotypic behavior. This individual also showed the highest usage of enrichment devices, and stereotypic behavior was significantly reduced when enrichment was applied. The occurrence of stereotypic behavior did not differ significantly between single-use and group-use enrichment treatments. Higher intragroup aggression and lower affiliation were observed during the provision of enrichment compared with baseline levels. However, aggressive behavior was higher and affiliation lower during single-use enrichment compared with group-use enrichment. The results of this study showed that enrichment had positive effects on alleviating stereotypic behavior in a group of zoo-housed squirrel monkeys and such effects were similar when group-use and single-use enrichment devices were used, but with variations between individuals. The application of enrichment, particularly single-use enrichment devices, elicited higher levels of aggression within the group and lower affiliation. Such effects could curtail the benefits of original enrichment goals as higher intragroup aggression could lead to higher stress levels within the group. When food-based enrichment for social nonhuman primates is implemented, the most appropriate methods to alleviate undesirable behavior without additional negative effects such as increased group aggression should be considered.

  2. Brain Based Teaching: Fad or Promising Teaching Method.

    ERIC Educational Resources Information Center

    Winters, Clyde A.

    This paper discusses brain-based teaching and examines its relevance as a teaching method and knowledge base. Brain-based teaching is very popular among early childhood educators. Positive attributes of brain-based education include student engagement and active involvement in their own learning, teachers teaching for meaning and understanding,…

  3. Shrinkage regression-based methods for microarray missing value imputation

    PubMed Central

    2013-01-01

    Background Missing values commonly occur in the microarray data, which usually contain more than 5% missing values with up to 90% of genes affected. Inaccurate missing value estimation results in reducing the power of downstream microarray data analyses. Many types of methods have been developed to estimate missing values. Among them, the regression-based methods are very popular and have been shown to perform better than the other types of methods in many testing microarray datasets. Results To further improve the performances of the regression-based methods, we propose shrinkage regression-based methods. Our methods take the advantage of the correlation structure in the microarray data and select similar genes for the target gene by Pearson correlation coefficients. Besides, our methods incorporate the least squares principle, utilize a shrinkage estimation approach to adjust the coefficients of the regression model, and then use the new coefficients to estimate missing values. Simulation results show that the proposed methods provide more accurate missing value estimation in six testing microarray datasets than the existing regression-based methods do. Conclusions Imputation of missing values is a very important aspect of microarray data analyses because most of the downstream analyses require a complete dataset. Therefore, exploring accurate and efficient methods for estimating missing values has become an essential issue. Since our proposed shrinkage regression-based methods can provide accurate missing value estimation, they are competitive alternatives to the existing regression-based methods. PMID:24565159

  4. Profile of World Uranium Enrichment Programs - 2007

    SciTech Connect

    Laughter, Mark D

    2007-11-01

    of the future, but has yet to be demonstrated commercially. In the early 1980s, six countries developing gas centrifuge technology (United States, United Kingdom, Germany, the Netherlands, Japan, and Australia) along with the International Atomic Energy Agency (IAEA) and the European Atomic Energy Community (EURATOM) began developing effective safeguards techniques for GCEPs. This effort was known as the Hexapartite Safeguards Project (HSP). The HSP had the goal of maximizing safeguards effectiveness while minimizing the cost to the operator and inspectorate, and adopted several recommendations, such as the acceptance of limited-frequency unannounced access (LFUA) inspections in cascade halls, and the use of nondestructive assay (NDA) measurements and tamper-indicating seals. While only the HSP participants initially committed to implementing all the measures of the approach, it has been used as a model for the safeguards applied to GCEPs in additional states. This report provides a snapshot overview of world enrichment capacity in 2007, including profiles of the uranium enrichment programs of individual states. It is based on open-source information, which is dependent on unclassified sources and may therefore not reflect the most recent developments. In addition, it briefly describes some of the safeguards techniques being used at various enrichment plants, including implementation of HSP recommendations.

  5. Effective Enrichment and Mass Spectrometry Analysis of Phosphopeptides Using Mesoporous Metal Oxide Nanomaterials

    PubMed Central

    Nelson, Cory A.; Szczech, Jeannine R.; Dooley, Chad J.; Xu, Qingge; Lawrence, Matthew J.; Zhu, Haoyue; Jin, Song; Ge, Ying

    2010-01-01

    Mass spectrometry (MS)-based phosphoproteomics remains challenging due to the low abundance of phosphoproteins and substoichiometric phosphorylation. This demands better methods to effectively enrich phosphoproteins/peptides prior to MS analysis. We have previously communicated the first use of mesoporous zirconium oxide (ZrO2) nanomaterials for effective phosphopeptide enrichment. Here we present the full report including the synthesis, characterization, and application of mesoporous titanium dioxide (TiO2), ZrO2, and hafnium oxide (HfO2) in phosphopeptide enrichment and MS analysis. Mesoporous ZrO2 and HfO2 are demonstrated to be superior to TiO2 for phosphopeptide enrichment from a complex mixture with high specificity (>99%), which could almost be considered as “a purification”, mainly because of the extremely large active surface area of mesoporous nanomaterials. A single enrichment and Fourier transform MS analysis of phosphopeptides digested from a complex mixture containing 7% of α-casein identified 21 out of 22 phosphorylation sites for α-casein. Moreover, the mesoporous ZrO2 and HfO2 can be reused after a simple solution regeneration procedure with comparable enrichment performance to that of fresh materials. Mesoporous ZrO2 and HfO2 nanomaterials hold great promise for applications in MS-based phosphoproteomics. PMID:20704311

  6. Effective enrichment and mass spectrometry analysis of phosphopeptides using mesoporous metal oxide nanomaterials.

    PubMed

    Nelson, Cory A; Szczech, Jeannine R; Dooley, Chad J; Xu, Qingge; Lawrence, Matthew J; Zhu, Haoyue; Jin, Song; Ge, Ying

    2010-09-01

    Mass spectrometry (MS)-based phosphoproteomics remains challenging due to the low abundance of phosphoproteins and substoichiometric phosphorylation. This demands better methods to effectively enrich phosphoproteins/peptides prior to MS analysis. We have previously communicated the first use of mesoporous zirconium dioxide (ZrO(2)) nanomaterials for effective phosphopeptide enrichment. Here, we present the full report including the synthesis, characterization, and application of mesoporous titanium dioxide (TiO(2)), ZrO(2), and hafnium dioxide (HfO(2)) in phosphopeptide enrichment and MS analysis. Mesoporous ZrO(2) and HfO(2) are demonstrated to be superior to TiO(2) for phosphopeptide enrichment from a complex mixture with high specificity (>99%), which could almost be considered as a "purification", mainly because of the extremely large active surface area of mesoporous nanomaterials. A single enrichment and Fourier transform MS analysis of phosphopeptides digested from a complex mixture containing 7% of alpha-casein identified 21 out of 22 phosphorylation sites for alpha-casein. Moreover, the mesoporous ZrO(2) and HfO(2) can be reused after a simple solution regeneration procedure with comparable enrichment performance to that of fresh materials. Mesoporous ZrO(2) and HfO(2) nanomaterials hold great promise for applications in MS-based phosphoproteomics.

  7. Microfluidic droplet enrichment for targeted sequencing

    PubMed Central

    Eastburn, Dennis J.; Huang, Yong; Pellegrino, Maurizio; Sciambi, Adam; Ptáček, Louis J.; Abate, Adam R.

    2015-01-01

    Targeted sequence enrichment enables better identification of genetic variation by providing increased sequencing coverage for genomic regions of interest. Here, we report the development of a new target enrichment technology that is highly differentiated from other approaches currently in use. Our method, MESA (Microfluidic droplet Enrichment for Sequence Analysis), isolates genomic DNA fragments in microfluidic droplets and performs TaqMan PCR reactions to identify droplets containing a desired target sequence. The TaqMan positive droplets are subsequently recovered via dielectrophoretic sorting, and the TaqMan amplicons are removed enzymatically prior to sequencing. We demonstrated the utility of this approach by generating an average 31.6-fold sequence enrichment across 250 kb of targeted genomic DNA from five unique genomic loci. Significantly, this enrichment enabled a more comprehensive identification of genetic polymorphisms within the targeted loci. MESA requires low amounts of input DNA, minimal prior locus sequence information and enriches the target region without PCR bias or artifacts. These features make it well suited for the study of genetic variation in a number of research and diagnostic applications. PMID:25873629

  8. New search method based on hash table and heuristic search method

    NASA Astrophysics Data System (ADS)

    Wang, He-Chen; Xian, Wu; Luo, Da L.; Song, Xiang

    1991-02-01

    The article ut forword a new method of dynamic search based on hash tabIeand heuristic search method. The method can inQrove the speed of search oijeration when ful control knowledge about the solution space to objects is known. An example about using the search method to decode the Haffman code is discussed in detai I.

  9. ProSim: A Method for Prioritizing Disease Genes Based on Protein Proximity and Disease Similarity

    PubMed Central

    Ganegoda, Gamage Upeksha; Sheng, Yu; Wang, Jianxin

    2015-01-01

    Predicting disease genes for a particular genetic disease is very challenging in bioinformatics. Based on current research studies, this challenge can be tackled via network-based approaches. Furthermore, it has been highlighted that it is necessary to consider disease similarity along with the protein's proximity to disease genes in a protein-protein interaction (PPI) network in order to improve the accuracy of disease gene prioritization. In this study we propose a new algorithm called proximity disease similarity algorithm (ProSim), which takes both of the aforementioned properties into consideration, to prioritize disease genes. To illustrate the proposed algorithm, we have conducted six case studies, namely, prostate cancer, Alzheimer's disease, diabetes mellitus type 2, breast cancer, colorectal cancer, and lung cancer. We employed leave-one-out cross validation, mean enrichment, tenfold cross validation, and ROC curves to evaluate our proposed method and other existing methods. The results show that our proposed method outperforms existing methods such as PRINCE, RWR, and DADA. PMID:26339594

  10. A Cluster-Based Method for Test Construction.

    ERIC Educational Resources Information Center

    Boekkooi-Timminga, Ellen

    1990-01-01

    A new test construction model based on the Rasch model is proposed. This model, the cluster-based method, considers groups of interchangeable items rather than individual items and uses integer programing. Results for six test construction problems indicate that the method produces accurate results in small amounts of time. (SLD)

  11. Pyrolyzed-parylene based sensors and method of manufacture

    NASA Technical Reports Server (NTRS)

    Tai, Yu-Chong (Inventor); Liger, Matthieu (Inventor); Miserendino, Scott (Inventor); Konishi, Satoshi (Inventor)

    2007-01-01

    A method (and resulting structure) for fabricating a sensing device. The method includes providing a substrate comprising a surface region and forming an insulating material overlying the surface region. The method also includes forming a film of carbon based material overlying the insulating material and treating to the film of carbon based material to pyrolyzed the carbon based material to cause formation of a film of substantially carbon based material having a resistivity ranging within a predetermined range. The method also provides at least a portion of the pyrolyzed carbon based material in a sensor application and uses the portion of the pyrolyzed carbon based material in the sensing application. In a specific embodiment, the sensing application is selected from chemical, humidity, piezoelectric, radiation, mechanical strain or temperature.

  12. Correlation theory-based signal processing method for CMF signals

    NASA Astrophysics Data System (ADS)

    Shen, Yan-lin; Tu, Ya-qing

    2016-06-01

    Signal processing precision of Coriolis mass flowmeter (CMF) signals affects measurement accuracy of Coriolis mass flowmeters directly. To improve the measurement accuracy of CMFs, a correlation theory-based signal processing method for CMF signals is proposed, which is comprised of the correlation theory-based frequency estimation method and phase difference estimation method. Theoretical analysis shows that the proposed method eliminates the effect of non-integral period sampling signals on frequency and phase difference estimation. The results of simulations and field experiments demonstrate that the proposed method improves the anti-interference performance of frequency and phase difference estimation and has better estimation performance than the adaptive notch filter, discrete Fourier transform and autocorrelation methods in terms of frequency estimation and the data extension-based correlation, Hilbert transform, quadrature delay estimator and discrete Fourier transform methods in terms of phase difference estimation, which contributes to improving the measurement accuracy of Coriolis mass flowmeters.

  13. Pathogen enrichment device (PED) enables one-step growth, enrichment and separation of pathogen from food matrices for detection using bioanalytical platforms.

    PubMed

    Hahm, Byoung-Kwon; Kim, Hyochin; Singh, Atul K; Bhunia, Arun K

    2015-10-01

    The bottleneck for accurate detection of foodborne pathogens is separation of target analytes from complex food matrices. Currently used sample preparation methods are cumbersome, arduous and lengthy; thus, a user-friendly system is desirable. A hand-held sample preparation system designated pathogen enrichment device (PED) was built that contains a growth chamber, filters, and an ion exchange cartridge to deliver bacteria directly onto the detection platforms. Escherichia coli O157:H7, Salmonella enterica and Listeria monocytogenes were used as model pathogens. Spinach, ground beef, hotdogs, and eggs were used as model foods to evaluate PED performance, and results were compared with traditional bag enrichment method. Bacterial cells were inoculated at 1, 10, and 100 CFU/g of the sample and enriched in PED using appropriate pathogen-specific selective enrichment broths. The bacterial cell counts in both PED and stomacher-bag were comparable and the pH in PED-recovered cell suspension was close to neutral whereas the pH of cell suspension in the stomacher-bag was slightly acidic. The bacterial recovery from the PED was 79-100% and was directly detected by lateral-flow immunoassay (LFIA), quantitative PCR (qPCR) and light scattering sensor with sample-to-result time of 8-24h with a detection limit of 1CFU/g. In qPCR, the amplified PCR products appeared in 4-5 cycles earlier with PED-enriched cultures compared to the cultures enriched in stomacher-bag. The hand-held PED proved to be a one-step procedure for enrichment and recovery of homogenous particle-free bacterial cells for detection using immunological, molecular or biosensor-based platforms.

  14. A Meta-Path-Based Prediction Method for Human miRNA-Target Association

    PubMed Central

    Huang, Cong; Ding, Pingjian

    2016-01-01

    MicroRNAs (miRNAs) are short noncoding RNAs that play important roles in regulating gene expressing, and the perturbed miRNAs are often associated with development and tumorigenesis as they have effects on their target mRNA. Predicting potential miRNA-target associations from multiple types of genomic data is a considerable problem in the bioinformatics research. However, most of the existing methods did not fully use the experimentally validated miRNA-mRNA interactions. Here, we developed RMLM and RMLMSe to predict the relationship between miRNAs and their targets. RMLM and RMLMSe are global approaches as they can reconstruct the missing associations for all the miRNA-target simultaneously and RMLMSe demonstrates that the integration of sequence information can improve the performance of RMLM. In RMLM, we use RM measure to evaluate different relatedness between miRNA and its target based on different meta-paths; logistic regression and MLE method are employed to estimate the weight of different meta-paths. In RMLMSe, sequence information is utilized to improve the performance of RMLM. Here, we carry on fivefold cross validation and pathway enrichment analysis to prove the performance of our methods. The fivefold experiments show that our methods have higher AUC scores compared with other methods and the integration of sequence information can improve the performance of miRNA-target association prediction. PMID:27703979

  15. Motivational Multimedia: Examining Students' Learning and Motivation as They Use a Multimedia Enriched Learning Environment

    ERIC Educational Resources Information Center

    Liu, Min; Olmanson, Justin; Horton, Lucas; Toprac, Paul

    2011-01-01

    This study examines middle school students' learning and motivation as they engaged in a multimedia enriched problem-based learning (PBL) environment for middle school science. Using a mixed-method design with both quantitative and qualitative data, we investigated the effect of a multimedia environment on sixth graders' science learning, their…

  16. A Study of Learning and Motivation in a New Media Enriched Environment for Middle School Science

    ERIC Educational Resources Information Center

    Liu, Min; Horton, Lucas; Olmanson, Justin; Toprac, Paul

    2011-01-01

    This study examines middle school students' learning and motivation as they engaged in a new media enriched problem-based learning (PBL) environment for middle school science. Using a mixed-method design with both quantitative and qualitative data, we investigated the effect of a new media environment on sixth graders' science learning, their…

  17. Evaluation of PCR-based screening for vancomycin-resistant enterococci compared with a chromogenic agar-based culture method.

    PubMed

    Seo, Ja Young; Kim, Pyung-Whan; Lee, Jang-Ho; Song, Jae-Hoon; Peck, Kyong-Ran; Chung, Doo-Ryeon; Kang, Cheol-In; Ki, Chang-Seok; Lee, Nam Yong

    2011-07-01

    Rapid detection of vancomycin-resistant enterococci (VRE) infection is very important for control and prevention of nosocomial spread of these bacteria. A multiplex PCR method for rapid screening of VRE has recently been developed. We performed a prospective study of VRE screening tests to compare the performance of PCR to that of a chromogenic agar-based culture method. From January to December 2009, a total of 8815 rectal swab specimens were tested simultaneously for VRE by VRE selective culture and by PCR. The specimens were inoculated onto ChromID VRE agar containing 8 µg vancomycin ml⁻¹ and examined after 24 and 48 h of incubation. Identification and antibiotic susceptibility tests were performed using the automated VITEK-2 system and a supplementary E-test and disk diffusion test. Detection of the vanA and vanB genes was performed with the Seeplex VRE detection kit. Specimens were inoculated in enterococcosel broth for 16-24 h before PCR for enrichment of VRE. VRE were isolated from 741 of the 8815 specimens by chromogenic agar-based culture (8.4 %). vanA and vanB genotypes were detected in 758 (8.6 %) and 3 (0.03 %) specimens, respectively, by multiplex PCR. Sensitivity, specificity, positive predictive value and negative predictive value of PCR for detection of VRE were 98.2 %, 99.6 %, 95.7 %, and 99.8 %. No VRE were isolated from vanB-positive specimens. The overall performance of PCR is comparable to that of a chromogenic agar-based culture method for screening of VRE, so PCR could be an alternative or supportive method for effective control of nosocomial VRE infection.

  18. Highly sensitive methods for electroanalytical chemistry based on nanotubule membranes.

    PubMed

    Kobayashi, Y; Martin, C R

    1999-09-01

    Two new methods of electroanalysis are described. These methods are based on membranes containing monodisperse Au nanotubules with inside diameters approaching molecular dimensions. In one method, the analyte species is detected by measuring the change in trans-membrane current when the analyte is added to the nanotubule-based cell. The second method entails the use of a concentration cell based on the nanotubule membrane. In this case, the change in membrane potential is used to detect the analyte. Detection limits as low as 10(-11) M have been achieved. Hence, these methods compete with even the most sensitive of modern analytical methodologies. In addition, excellent molecular-sized-based selectivity is observed.

  19. A New Adaptive Image Denoising Method Based on Neighboring Coefficients

    NASA Astrophysics Data System (ADS)

    Biswas, Mantosh; Om, Hari

    2016-03-01

    Many good techniques have been discussed for image denoising that include NeighShrink, improved adaptive wavelet denoising method based on neighboring coefficients (IAWDMBNC), improved wavelet shrinkage technique for image denoising (IWST), local adaptive wiener filter (LAWF), wavelet packet thresholding using median and wiener filters (WPTMWF), adaptive image denoising method based on thresholding (AIDMT). These techniques are based on local statistical description of the neighboring coefficients in a window. These methods however do not give good quality of the images since they cannot modify and remove too many small wavelet coefficients simultaneously due to the threshold. In this paper, a new image denoising method is proposed that shrinks the noisy coefficients using an adaptive threshold. Our method overcomes these drawbacks and it has better performance than the NeighShrink, IAWDMBNC, IWST, LAWF, WPTMWF, and AIDMT denoising methods.

  20. New Robust Face Recognition Methods Based on Linear Regression

    PubMed Central

    Mi, Jian-Xun; Liu, Jin-Xing; Wen, Jiajun

    2012-01-01

    Nearest subspace (NS) classification based on linear regression technique is a very straightforward and efficient method for face recognition. A recently developed NS method, namely the linear regression-based classification (LRC), uses downsampled face images as features to perform face recognition. The basic assumption behind this kind method is that samples from a certain class lie on their own class-specific subspace. Since there are only few training samples for each individual class, which will cause the small sample size (SSS) problem, this problem gives rise to misclassification of previous NS methods. In this paper, we propose two novel LRC methods using the idea that every class-specific subspace has its unique basis vectors. Thus, we consider that each class-specific subspace is spanned by two kinds of basis vectors which are the common basis vectors shared by many classes and the class-specific basis vectors owned by one class only. Based on this concept, two classification methods, namely robust LRC 1 and 2 (RLRC 1 and 2), are given to achieve more robust face recognition. Unlike some previous methods which need to extract class-specific basis vectors, the proposed methods are developed merely based on the existence of the class-specific basis vectors but without actually calculating them. Experiments on three well known face databases demonstrate very good performance of the new methods compared with other state-of-the-art methods. PMID:22879992

  1. Spatial variation of deuterium enrichment in bulk water of snowgum leaves.

    PubMed

    Santrucek, Jirí; Kveton, Jirí; Setlík, Jirí; Bulícková, Lenka

    2007-01-01

    Deuterium enrichment of bulk water was measured and modeled in snowgum (Eucalyptus pauciflora Sieber ex Sprengel) leaves grown under contrasting air and soil humidity in arid and wet conditions in a glasshouse. A map of the enrichment was constructed with a resolution of 4 mm by using a newly designed cryodistillation method. There was progressively increasing enrichment in both longitudinal (along the leaf midrib) and transversal (perpendicular to the midrib) directions, most pronounced in the arid-grown leaf. The whole-leaf average of the enrichment was well below the value estimated by the Craig-Gordon model. The discrepancy between model and measurements persisted when the estimates were carried out separately for the leaf base and tip, which differed in temperature and stomatal conductance. The discrepancy was proportional to the transpiration rate, indicating the significance of diffusion-advection interplay (Péclet effect) of deuterium-containing water molecules in small veins close to the evaporating sites in the leaf. Combined Craig-Gordon and desert-river models, with or without the Péclet number, P, were used for predicting the leaf longitudinal enrichment. The predictions without P overestimated the measured values of deltadeuterium. Fixed P value partially improved the coincidence. We suggest that P should vary along the leaf length l to reconcile the modeled data with observations of longitudinal enrichment. Local values of P, P(l), integrating the upstream fraction of water used or the leaf area, substantially improved the model predictions. PMID:17158587

  2. An image restoration method based on sparse constraint

    NASA Astrophysics Data System (ADS)

    Qiang, Zhenping; Liu, Hui; Chen, Xu; Shang, Zhenhong; Zeng, Lingjun

    2013-07-01

    In this paper, proposed an image restoration method which base on the sparse constraint. Based on the principle of Compressed Sensing, the observed image is transformed into the wavelet domain, and then converted the image restoration problem to a convex set unrestricted optimization problem by limiting the number of non-zero elements of the wavelet domain, using the gradient projection method for solving the optimization problem to achieve the restoration of the input image. Experiments show that the method presented has the fast convergence and good robustness compared to the traditional total variation regularization restoration method.

  3. Recent methods for the determination of peroxide-based explosives.

    PubMed

    Schulte-Ladbeck, Rasmus; Vogel, Martin; Karst, Uwe

    2006-10-01

    In the last few years, the need to determine peroxide-based explosives in solid samples and air samples has resulted in the development of a series of new analytical methods for triacetonetriperoxide (TATP, acetone peroxide) and hexamethylenetriperoxidediamine (HMTD). In this review, after a short introduction describing the state of the art in the field, these new analytical methods are critically discussed. Particular emphasis is placed on spectroscopic and mass spectrometric methods as well as on chromatographic techniques with selective detection schemes. The potential of these methods to analyse unknown solid samples that might contain one or more of the explosives and to analyse peroxide-based explosives in air is evaluated.

  4. Determination of trace anions in liquefied petroleum gas using liquid absorption and electrokinetic migration for enrichment followed by ion chromatography.

    PubMed

    Li, Meilan; Yang, Jianmin; Li, Hai-Fang; Lin, Jin-Ming

    2012-06-01

    A simple sample enrichment technique, electrokinetic migration enrichment in single phase using a designed device, coupled with ion chromatography is presented for the determination of four anions (H(2)PO(4)(-), Cl(-), NO(3)(-), and SO(4)(2-)) in liquefied petroleum gas by liquid adsorption. The electrokinetic migration enrichment is based on the phenomenon of ion electrokinetic migration to the opposite electrode. When the anions migrated to the anode in a smaller volume chamber under the electric field, the concentration was realized. The main parameters affecting enrichment efficiency of applied voltage and enrichment time were investigated. The ion chromatography condition for anions separation was also studied. Under the optimal electrokinetic migration enrichment and ion chromatography conditions, the four anions were detected simultaneously with good linear relationship (r(2) = 0.9908-0.9968) and high precisions (less than 5% of the relative standard deviations of peak areas). The limits of detection of anions (S/N of 3) were in the range of 8-600 μg L(-1). The enrichment factors of the four anions ranged from 3.1 to 5.8. The established method was successfully applied to the analysis of the trace anions in liquefied petroleum gas by liquid adsorption with satisfactory results. The advantages of this method are simple operation and low cost.

  5. DNA-Based Methods in the Immunohematology Reference Laboratory

    PubMed Central

    Denomme, Gregory A

    2010-01-01

    Although hemagglutination serves the immunohematology reference laboratory well, when used alone, it has limited capability to resolve complex problems. This overview discusses how molecular approaches can be used in the immunohematology reference laboratory. In order to apply molecular approaches to immunohematology, knowledge of genes, DNA-based methods, and the molecular bases of blood groups are required. When applied correctly, DNA-based methods can predict blood groups to resolve ABO/Rh discrepancies, identify variant alleles, and screen donors for antigen-negative units. DNA-based testing in immunohematology is a valuable tool used to resolve blood group incompatibilities and to support patients in their transfusion needs. PMID:21257350

  6. DNA-based methods in the immunohematology reference laboratory.

    PubMed

    Reid, Marion E; Denomme, Gregory A

    2011-02-01

    Although hemagglutination serves the immunohematology reference laboratory well, when used alone, it has limited capability to resolve complex problems. This overview discusses how molecular approaches can be used in the immunohematology reference laboratory. In order to apply molecular approaches to immunohematology, knowledge of genes, DNA-based methods, and the molecular bases of blood groups are required. When applied correctly, DNA-based methods can predict blood groups to resolve ABO/Rh discrepancies, identify variant alleles, and screen donors for antigen-negative units. DNA-based testing in immunohematology is a valuable tool used to resolve blood group incompatibilities and to support patients in their transfusion needs.

  7. Iron oxide/niobium oxide core-shell magnetic nanoparticle-based phosphopeptide enrichment from biological samples for MALDI MS analysis.

    PubMed

    Lin, Hong-Yi; Chen, Wei-Yu; Chen, Yu-Chie

    2009-04-01

    The feasibility of using niobium oxide-coated magnetic nanoparticles (NPs) as affinity probes for selectively trapping phosphopeptides from peptide mixtures including tryptic digest of caseins, serum, and cell lysate was demonstrated in this study. Phosphopeptide enrichment was rapid when subjecting these systems to microwave heating for 1 min; the probe-target species, which were readily isolated through magnetic separation, were then analyzed using matrix-assisted laser desorption/ ionization mass spectrometry (MALDI MS). Only signals for phosphopeptides were present in the resulting mass spectra. The detection limit for monophosphopeptide was as low as 5 fmol.

  8. Direct Measurement of Initial Enrichment, Burn-up and Cooling Time of Spent Fuel Assembly with a Differential Die-Away Technique Based Instrument

    SciTech Connect

    Henzl, Vladimir; Swinhoe, Martyn T.; Tobin, Stephen J.

    2012-07-13

    An outline of this presentation of what a Differential Die-Away (DDA) instrument can do are: (1) Principle of operation of DDA instrument; (2) Determination of initial enrichment (IE) ({sigma} < 5%); (3) Determination of burn up (BU) ({sigma} {approx} 6%); (4) Determination of cooling time (CT) ({sigma} {approx} 20-50%); and (5) DDA instrument as a standalone device. DDA response (fresh fuel vs. spent fuel) is: (1) Fresh fuel => DDA response increases (die-away time is longer) with increasing fissile content; and (2) Spent fuel => DDA response decreases (die-away time is shorter) with higher burn-up (i.e. more neutron absorbers present).

  9. EEG feature selection method based on decision tree.

    PubMed

    Duan, Lijuan; Ge, Hui; Ma, Wei; Miao, Jun

    2015-01-01

    This paper aims to solve automated feature selection problem in brain computer interface (BCI). In order to automate feature selection process, we proposed a novel EEG feature selection method based on decision tree (DT). During the electroencephalogram (EEG) signal processing, a feature extraction method based on principle component analysis (PCA) was used, and the selection process based on decision tree was performed by searching the feature space and automatically selecting optimal features. Considering that EEG signals are a series of non-linear signals, a generalized linear classifier named support vector machine (SVM) was chosen. In order to test the validity of the proposed method, we applied the EEG feature selection method based on decision tree to BCI Competition II datasets Ia, and the experiment showed encouraging results.

  10. Propensity Score–Based Methods versus MTE-Based Methods in Causal Inference: Identification, Estimation, and Application*

    PubMed Central

    ZHOU, XIANG; XIE, YU

    2012-01-01

    Since the seminal introduction of the propensity score by Rosenbaum and Rubin, propensity-score-based (PS-based) methods have been widely used for drawing causal inferences in the behavioral and social sciences. However, the propensity score approach depends on the ignorability assumption: there are no unobserved confounders once observed covariates are taken into account. For situations where this assumption may be violated, Heckman and his associates have recently developed a novel approach based on marginal treatment effects (MTE). In this paper, we (1) explicate consequences for PS-based methods when aspects of the ignorability assumption are violated; (2) compare PS-based methods and MTE-based methods by making a close examination of their identification assumptions and estimation performances; (3) apply these two approaches in estimating the economic return to college using data from NLSY 1979 and discuss their discrepancies in results. When there is a sorting gain but no systematic baseline difference between treated and untreated units given observed covariates, PS-based methods can identify the treatment effect of the treated (TT). The MTE approach performs best when there is a valid and strong instrumental variable (IV). In addition, this paper introduces the “smoothing-difference PS-based method,” which enables us to uncover heterogeneity across people of different propensity scores in both counterfactual outcomes and treatment effects. PMID:26877562

  11. Evaluation of PCR-based beef sexing methods.

    PubMed

    Zeleny, Reinhard; Bernreuther, Alexander; Schimmel, Heinz; Pauwels, Jean

    2002-07-17

    Analysis of the sex of beef meat by fast and reliable molecular methods is an important measure to ensure correct allocation of export refunds, which are considerably higher for male beef meat. Two PCR-based beef sexing methods have been optimized and evaluated. The amelogenin-type method revealed excellent accuracy and robustness, whereas the bovine satellite/Y-chromosome duplex PCR procedure showed more ambiguous results. In addition, an interlaboratory comparison was organized to evaluate currently applied PCR-based sexing methods in European customs laboratories. From a total of 375 samples sent out, only 1 false result was reported (female identified as male). However, differences in the performances of the applied methods became apparent. The collected data contribute to specify technical requirements for a common European beef sexing methodology based on PCR. PMID:12105941

  12. Rare-cell enrichment by a rapid, label-free, ultrasonic isopycnic technique for medical diagnostics.

    PubMed

    Bourquin, Yannyk; Syed, Abeer; Reboud, Julien; Ranford-Cartwright, Lisa C; Barrett, Michael P; Cooper, Jonathan M

    2014-05-26

    One significant challenge in medical diagnostics lies in the development of label-free methods to separate different cells within complex biological samples. Here we demonstrate a generic, low-power ultrasonic separation technique, able to enrich different cell types based upon their physical properties. For malaria, we differentiate between infected and non-infected red blood cells in a fingerprick-sized drop of blood. We are able to achieve an enrichment of circulating cells infected by the ring stage of the parasite over nonparasitized red blood cells by between two and three orders of magnitude in less than 3 seconds (enabling detection at parasitemia levels as low as 0.0005%). In a second example, we also show that our methods can be used to enrich different cell types, concentrating Trypanosoma in blood at very low levels of infection, on disposable, low-cost chips. PMID:24677583

  13. Rare-Cell Enrichment by a Rapid, Label-Free, Ultrasonic Isopycnic Technique for Medical Diagnostics**

    PubMed Central

    Bourquin, Yannyk; Syed, Abeer; Reboud, Julien; Ranford-Cartwright, Lisa C; Barrett, Michael P; Cooper, Jonathan M

    2014-01-01

    One significant challenge in medical diagnostics lies in the development of label-free methods to separate different cells within complex biological samples. Here we demonstrate a generic, low-power ultrasonic separation technique, able to enrich different cell types based upon their physical properties. For malaria, we differentiate between infected and non-infected red blood cells in a fingerprick-sized drop of blood. We are able to achieve an enrichment of circulating cells infected by the ring stage of the parasite over nonparasitized red blood cells by between two and three orders of magnitude in less than 3 seconds (enabling detection at parasitemia levels as low as 0.0005 %). In a second example, we also show that our methods can be used to enrich different cell types, concentrating Trypanosoma in blood at very low levels of infection, on disposable, low-cost chips. PMID:24677583

  14. Error reduction in gamma-spectrometric measurements of nuclear materials enrichment

    NASA Astrophysics Data System (ADS)

    Zaplatkina, D.; Semenov, A.; Tarasova, E.; Zakusilov, V.; Kuznetsov, M.

    2016-06-01

    The paper provides the analysis of the uncertainty in determining the uranium samples enrichment using non-destructive methods to ensure the functioning of the nuclear materials accounting and control system. The measurements were performed by a scintillation detector based on a sodium iodide crystal and the semiconductor germanium detector. Samples containing uranium oxide of different masses were used for the measurements. Statistical analysis of the results showed that the maximum enrichment error in a scintillation detector measurement can reach 82%. The bias correction, calculated from the data obtained by the semiconductor detector, reduces the error in the determination of uranium enrichment by 47.2% in average. Thus, the use of bias correction, calculated by the statistical methods, allows the use of scintillation detectors to account and control nuclear materials.

  15. Mitoxantrone loaded superparamagnetic nanoparticles for drug targeting: a versatile and sensitive method for quantification of drug enrichment in rabbit tissues using HPLC-UV.

    PubMed

    Tietze, Rainer; Schreiber, Eveline; Lyer, Stefan; Alexiou, Christoph

    2010-01-01

    In medicine, superparamagnetic nanoparticles bound to chemotherapeutics are currently investigated for their feasibility in local tumor therapy. After intraarterial application, these particles can be accumulated in the targeted area by an external magnetic field to increase the drug concentration in the region of interest (Magnetic-Drug-Targeting). We here present an analytical method (HPLC-UV), to detect pure or ferrofluid-bound mitoxantrone in a complex matrix even in trace amounts in order to perform biodistribution studies. Mitoxantrone could be extracted in high yields from different tissues. Recovery of mitoxantrone in liver tissue (5000 ng/g) was 76 +/- 2%. The limit of quantification of mitoxantrone standard was 10 ng/mL +/-12%. Validation criteria such as linearity, precision, and stability were evaluated in ranges achieving the FDA requirements. As shown for pilot samples, biodistribution studies can easily be performed after application of pure or ferrofluid-bound mitoxantrone. PMID:20490266

  16. A new pollen extraction method for pyrite-enriched organic deposits from dryland environments, and associated results from a wetland in semi-arid Southern Levant (Jordan)

    NASA Astrophysics Data System (ADS)

    Rambeau, Claire; Gobet, Erika; van Leeuwen, Jacqueline; van der Knaap, Pim

    2016-04-01

    Wetlands are invaluable stores of palaeoenvironmental information; this is particularly true in arid or semi-arid environments where archives of past environmental change are usually scarce. However, depending on local conditions, the palaeoenvironmental proxies that wetlands developing in arid environments may contain, in particular pollen, can be challenging to extract. Here we describe a new technique to separate palynomorphs (pollen and spores) from pyrite-rich peat-like deposits, using a controlled nitric acid digestion instead of acetolysis. The results obtained by applying this method to organic deposits from small 'desert' wetlands, located close to the edge of the Dead Sea in Jordan, provided new data about the local evolution of environmental conditions in semi-arid to arid Southern Levant for the last ca. 40,000 years, which adds to the presently restricted information available for the area.

  17. The Effects of Early Language Enrichment

    ERIC Educational Resources Information Center

    Fowler, William; Ogston, Karen; Roberts, Gloria; Swenson, Amy

    2006-01-01

    Over two decades, six studies evaluated the effects of a home-based early language program on the development of 101 infants. Parents engaged in enrichment activities with their infants over a one-year period that began when the infants were between three and 13 months of age. Participants from families with varied levels of education were…

  18. A new ultrasound based method for rapid microorganism detection

    NASA Astrophysics Data System (ADS)

    Shukla, Shiva Kant; Segura, Luis Elvira; Sánchez, Carlos José Sierra; López, Pablo Resa

    2012-05-01

    A new method for rapid detection of catalase positive microorganisms by using an ultrasonic measuring method is proposed in this work. The developed technique is based on the detection of oxygen bubbles produced by the hydrolysis of hydrogen peroxide induced by the enzyme catalase which is present in many microorganisms. The bubbles are trapped in a media based on agar gel which was especially developed for microbiological evaluation. It is found that microorganism concentrations of the order of 105 c.f.u./ml can be detected by using this method. The results obtained show up that the proposed method is competitive with other modern commercial methods like luminescence by ATP system. The method can also be used for characterization of enzyme activity.

  19. Enrichment of spermatogonial stem cells using side population in teleost.

    PubMed

    Hayashi, Makoto; Sato, Masanao; Nagasaka, Yasuhiko; Sadaie, Sakiko; Kobayashi, Satoru; Yoshizaki, Goro

    2014-07-01

    Spermatogenesis originates from a small population of spermatogonial stem cells; this population can maintain continuous sperm production throughout the life of fish via self-renewal and differentiation. Despite their biological importance, spermatogonial stem cells are not thoroughly characterized because they are difficult to distinguish from their progeny cells that become committed to differentiation. We previously established a novel technique for germ cell transplantation to identify spermatogonial stem cells based on their colonizing activity and their ability to initiate donor-derived gametogenesis in the rainbow trout (Oncorhynchus mykiss). Although spermatogonial stem cells can be retrospectively identified after transplantation, there is currently no technique to prospectively enrich for or purify spermatogonial stem cells. Here, we describe a method for spermatogonial stem cell enrichment using a side population. With optimized Hoechst 33342 staining conditions, we successfully identified side-population cells among type A spermatogonia. Side-population cells were transcriptomically and morphologically distinct from non-side-population cells. To functionally determine whether the transplantable spermatogonial stem cells were enriched in the side-population fraction, we compared the colonization activity of side-population cells with that of non-side-population cells. Colonization efficiency was significantly higher with side-population cells than with non-side-population cells or with total type A spermatogonia. In addition, side-population cells could produce billions of sperm in recipients. These results indicated that transplantable spermatogonial stem cells were enriched in the side-population fraction. This method will provide biological information that may advance our understanding of spermatogonial stem cells in teleosts. Additionally, this technique will increase the efficiency of germ cell transplantation used in surrogate broodstock

  20. A Channelization-Based DOA Estimation Method for Wideband Signals.

    PubMed

    Guo, Rui; Zhang, Yue; Lin, Qianqiang; Chen, Zengping

    2016-01-01

    In this paper, we propose a novel direction of arrival (DOA) estimation method for wideband signals with sensor arrays. The proposed method splits the wideband array output into multiple frequency sub-channels and estimates the signal parameters using a digital channelization receiver. Based on the output sub-channels, a channelization-based incoherent signal subspace method (Channelization-ISM) and a channelization-based test of orthogonality of projected subspaces method (Channelization-TOPS) are proposed. Channelization-ISM applies narrowband signal subspace methods on each sub-channel independently. Then the arithmetic mean or geometric mean of the estimated DOAs from each sub-channel gives the final result. Channelization-TOPS measures the orthogonality between the signal and the noise subspaces of the output sub-channels to estimate DOAs. The proposed channelization-based method isolates signals in different bandwidths reasonably and improves the output SNR. It outperforms the conventional ISM and TOPS methods on estimation accuracy and dynamic range, especially in real environments. Besides, the parallel processing architecture makes it easy to implement on hardware. A wideband digital array radar (DAR) using direct wideband radio frequency (RF) digitization is presented. Experiments carried out in a microwave anechoic chamber with the wideband DAR are presented to demonstrate the performance. The results verify the effectiveness of the proposed method. PMID:27384566

  1. A Novel Method for Learner Assessment Based on Learner Annotations

    ERIC Educational Resources Information Center

    Noorbehbahani, Fakhroddin; Samani, Elaheh Biglar Beigi; Jazi, Hossein Hadian

    2013-01-01

    Assessment is one of the most essential parts of any instructive learning process which aims to evaluate a learner's knowledge about learning concepts. In this work, a new method for learner assessment based on learner annotations is presented. The proposed method exploits the M-BLEU algorithm to find the most similar reference annotations…

  2. A Channelization-Based DOA Estimation Method for Wideband Signals

    PubMed Central

    Guo, Rui; Zhang, Yue; Lin, Qianqiang; Chen, Zengping

    2016-01-01

    In this paper, we propose a novel direction of arrival (DOA) estimation method for wideband signals with sensor arrays. The proposed method splits the wideband array output into multiple frequency sub-channels and estimates the signal parameters using a digital channelization receiver. Based on the output sub-channels, a channelization-based incoherent signal subspace method (Channelization-ISM) and a channelization-based test of orthogonality of projected subspaces method (Channelization-TOPS) are proposed. Channelization-ISM applies narrowband signal subspace methods on each sub-channel independently. Then the arithmetic mean or geometric mean of the estimated DOAs from each sub-channel gives the final result. Channelization-TOPS measures the orthogonality between the signal and the noise subspaces of the output sub-channels to estimate DOAs. The proposed channelization-based method isolates signals in different bandwidths reasonably and improves the output SNR. It outperforms the conventional ISM and TOPS methods on estimation accuracy and dynamic range, especially in real environments. Besides, the parallel processing architecture makes it easy to implement on hardware. A wideband digital array radar (DAR) using direct wideband radio frequency (RF) digitization is presented. Experiments carried out in a microwave anechoic chamber with the wideband DAR are presented to demonstrate the performance. The results verify the effectiveness of the proposed method. PMID:27384566

  3. 2H2O incorporation into hepatic acetyl-CoA and de novo lipogenesis as measured by Krebs cycle-mediated 2H-enrichment of glutamate and glutamine.

    PubMed

    Silva, Ana Maria; Martins, Fatima; Jones, John G; Carvalho, Rui

    2011-12-01

    Deuterated water is widely used for measuring de novo lipogenesis on the basis of quantifying lipid (2)H-enrichment relative to that of body water. However, incorporation of (2)H-enrichment from body water into newly synthesized lipid molecules is incomplete therefore the true lipid precursor enrichment differs from that of body water. We describe a novel measurement of de novo lipogenesis that is based on a true precursor-product analysis of hepatic acetyl-CoA and triglyceride methyl enrichments from deuterated water. After deuterated water administration to seven in situ and seven perfused livers, acetyl-CoA methyl enrichment was inferred from (2)H nuclear magnetic resonance analysis of hepatic glutamate/glutamine (Glx) enrichment and triglyceride methyl enrichment was directly determined by (2)H nuclear magnetic resonance of triglycerides. Acetyl-CoA (2) H-enrichment was 71% ± 1% that of body water for in situ livers and 53% ± 2% of perfusate water for perfused livers. From the ratio of triglyceride-methyl/acetyl-CoA enrichments, fractional de novo lipogenesis rates of 0.97% ± 0.09%/2 hr and 7.92% ± 1.47%/48 hr were obtained for perfused and in situ liver triglycerides, respectively. Our method reveals that acetyl-CoA enrichment is significantly less than body water both for in situ and perfused livers. Furthermore, the difference between acetyl-CoA and body water enrichments is sensitive to the experimental setting.

  4. Method of removing and detoxifying a phosphorus-based substance

    DOEpatents

    Vandegrift, G.F.; Steindler, M.J.

    1985-05-21

    A method of removing a phosphorus-based poisonous substance from water contaminated is presented. In addition, the toxicity of the phosphorus-based substance is also subsequently destroyed. A water-immiscible organic solvent is first immobilized on a supported liquid membrane before the contaminated water is contacted with one side of the supported liquid membrane to absorb the phosphorus-based substance in the organic solvent. The other side of the supported liquid membrane is contacted with a hydroxy-affording strong base to react with phosphorus-based solvated species to form a non-toxic product.

  5. A novel real-time polymerase chain reaction-based method for the detection and quantification of lactose-fermenting Enterobacteriaceae in the dairy and other food industries.

    PubMed

    Martín, M C; Martínez, N; del Rio, B; Ladero, V; Fernández, M; Alvarez, M A

    2010-03-01

    The presence of lactose-fermenting Enterobacteriaceae and coliforms is routinely assessed to determine the hygienic quality of water and foods, particularly dairy products. This paper reports the use of lacZ-specific primers in an SYBR green I-based real-time PCR method for the easy and rapid detection of coliforms in dairy products. A large number of bacterial species were assayed to establish the specificity of the method. The sensitivity of the method was assessed using artificially contaminated cheeses. The limit of detection was 1 coliform cell in cheese samples enriched for 8h in a culture medium. The entire procedure, including sample processing, enrichment, DNA extraction, and real-time PCR amplification, can be completed within 10 to 12h, making it a single-day assay. PMID:20172205

  6. Searching chromosomal landmarks in Indian lentils through EMA-based Giemsa staining method.

    PubMed

    Jha, Timir Baran; Halder, Mihir

    2016-09-01

    Lentil is one of the oldest protein-rich food crop with only one cultivated and six wild species. India is one important cultivator, producer and consumer of lentils and possesses a large number of germplasms. All species of lentil show 2n = 14 chromosomes. The primary objective of the present paper is to search chromosomal landmarks through enzymatic maceration and air drying (EMA)-based Giemsa staining method in five Indian lentil species not reported elsewhere at a time. Additionally, gametic chromosome analysis, tendril formation and seed morphology have been studied to ascertain interspecific relationships in lentils. Chromosome analysis in Lens culinaris, Lens orientalis and Lens odemensis revealed that they contain intercalary sat chromosome and similar karyotypic formula, while Lens nigricans and Lens lamottei showed presence of terminal sat chromosomes not reported earlier. This distinct morphological feature in L. nigricans and L. lamottei may be considered as chromosomal landmark. Meiotic analysis showed n = 7 bivalents in L. culinaris, L. nigricans and L. lamottei. No tendril formation was observed in L. culinaris, L. orientalis and L. odemensis while L. nigricans and L. lamottei developed very prominent tendrils. Based on chromosomal analysis, tendril formation and seed morphology, the five lentil species can be separated into two distinct groups. The outcome of this research may enrich conventional and biotechnological breeding programmes in lentil and may facilitate an easy and alternative method for identification of interspecific hybrids.

  7. Searching chromosomal landmarks in Indian lentils through EMA-based Giemsa staining method.

    PubMed

    Jha, Timir Baran; Halder, Mihir

    2016-09-01

    Lentil is one of the oldest protein-rich food crop with only one cultivated and six wild species. India is one important cultivator, producer and consumer of lentils and possesses a large number of germplasms. All species of lentil show 2n = 14 chromosomes. The primary objective of the present paper is to search chromosomal landmarks through enzymatic maceration and air drying (EMA)-based Giemsa staining method in five Indian lentil species not reported elsewhere at a time. Additionally, gametic chromosome analysis, tendril formation and seed morphology have been studied to ascertain interspecific relationships in lentils. Chromosome analysis in Lens culinaris, Lens orientalis and Lens odemensis revealed that they contain intercalary sat chromosome and similar karyotypic formula, while Lens nigricans and Lens lamottei showed presence of terminal sat chromosomes not reported earlier. This distinct morphological feature in L. nigricans and L. lamottei may be considered as chromosomal landmark. Meiotic analysis showed n = 7 bivalents in L. culinaris, L. nigricans and L. lamottei. No tendril formation was observed in L. culinaris, L. orientalis and L. odemensis while L. nigricans and L. lamottei developed very prominent tendrils. Based on chromosomal analysis, tendril formation and seed morphology, the five lentil species can be separated into two distinct groups. The outcome of this research may enrich conventional and biotechnological breeding programmes in lentil and may facilitate an easy and alternative method for identification of interspecific hybrids. PMID:26342302

  8. A method for selecting training samples based on camera response

    NASA Astrophysics Data System (ADS)

    Zhang, Leihong; Li, Bei; Pan, Zilan; Liang, Dong; Kang, Yi; Zhang, Dawei; Ma, Xiuhua

    2016-09-01

    In the process of spectral reflectance reconstruction, sample selection plays an important role in the accuracy of the constructed model and in reconstruction effects. In this paper, a method for training sample selection based on camera response is proposed. It has been proved that the camera response value has a close correlation with the spectral reflectance. Consequently, in this paper we adopt the technique of drawing a sphere in camera response value space to select the training samples which have a higher correlation with the test samples. In addition, the Wiener estimation method is used to reconstruct the spectral reflectance. Finally, we find that the method of sample selection based on camera response value has the smallest color difference and root mean square error after reconstruction compared to the method using the full set of Munsell color charts, the Mohammadi training sample selection method, and the stratified sampling method. Moreover, the goodness of fit coefficient of this method is also the highest among the four sample selection methods. Taking all the factors mentioned above into consideration, the method of training sample selection based on camera response value enhances the reconstruction accuracy from both the colorimetric and spectral perspectives.

  9. Method for rapid base sequencing in DNA and RNA

    DOEpatents

    Jett, J.H.; Keller, R.A.; Martin, J.C.; Moyzis, R.K.; Ratliff, R.L.; Shera, E.B.; Stewart, C.C.

    1990-10-09

    A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed. 2 figs.

  10. Method for rapid base sequencing in DNA and RNA

    DOEpatents

    Jett, J.H.; Keller, R.A.; Martin, J.C.; Moyzis, R.K.; Ratliff, R.L.; Shera, E.B.; Stewart, C.C.

    1987-10-07

    A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed. 2 figs.

  11. Method for rapid base sequencing in DNA and RNA

    DOEpatents

    Jett, James H.; Keller, Richard A.; Martin, John C.; Moyzis, Robert K.; Ratliff, Robert L.; Shera, E. Brooks; Stewart, Carleton C.

    1990-01-01

    A method is provided for the rapid base sequencing of DNA or RNA fragments wherein a single fragment of DNA or RNA is provided with identifiable bases and suspended in a moving flow stream. An exonuclease sequentially cleaves individual bases from the end of the suspended fragment. The moving flow stream maintains the cleaved bases in an orderly train for subsequent detection and identification. In a particular embodiment, individual bases forming the DNA or RNA fragments are individually tagged with a characteristic fluorescent dye. The train of bases is then excited to fluorescence with an output spectrum characteristic of the individual bases. Accordingly, the base sequence of the original DNA or RNA fragment can be reconstructed.

  12. Comparing Methods for UAV-Based Autonomous Surveillance

    NASA Technical Reports Server (NTRS)

    Freed, Michael; Harris, Robert; Shafto, Michael

    2004-01-01

    We describe an approach to evaluating algorithmic and human performance in directing UAV-based surveillance. Its key elements are a decision-theoretic framework for measuring the utility of a surveillance schedule and an evaluation testbed consisting of 243 scenarios covering a well-defined space of possible missions. We apply this approach to two example UAV-based surveillance methods, a TSP-based algorithm and a human-directed approach, then compare them to identify general strengths, and weaknesses of each method.

  13. IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis

    PubMed Central

    2012-01-01

    ) cross-linking of multiple available data sources. IPAD is a comprehensive database covering about 22,498 genes, 25,469 proteins, 1956 pathways, 6704 diseases, 5615 drugs, and 52 organs integrated from databases including the BioCarta, KEGG, NCI-Nature curated, Reactome, CTD, PharmGKB, DrugBank, PharmGKB, and HOMER. The database has a web-based user interface that allows users to perform enrichment analysis from genes/proteins/molecules and inter-association analysis from a pathway, disease, drug, and organ. Moreover, the quality of the database was validated with the context of the existing biological knowledge and a "gold standard" constructed from reputable and reliable sources. Two case studies were also presented to demonstrate: 1) self-validation of enrichment analysis and inter-association analysis on brain-specific markers, and 2) identification of previously undiscovered components by the enrichment analysis from a prostate cancer study. Conclusions IPAD is a new resource for analyzing, identifying, and validating pathway, disease, drug, organ specificity and their inter-associations. The statistical method we developed for enrichment and similarity measurement and the two criteria we described for setting the threshold parameters can be extended to other enrichment applications. Enriched pathways, diseases, drugs, organs and their inter-associations can be searched, displayed, and downloaded from our online user interface. The current IPAD database can help users address a wide range of biological pathway related, disease susceptibility related, drug target related and organ specificity related questions in human disease studies. PMID:23046449

  14. Low-resolution gamma-ray measurements of uranium enrichment

    SciTech Connect

    Sprinkle, J.K. Jr.; Christiansen, A.; Cole, R.; Collins, M.L.

    1996-11-01

    Facilities that process special nuclear material perform periodic inventories. In bulk facilities that process low-enriched uranium, these inventories and their audits are based primarily on weight and enrichment measurements. Enrichment measurements determine the {sup 211}U weight fraction of the uranium compound from the passive gamma-ray emissions of the sample. Both international inspectors and facility operators rely on the capability to make in-field gamma-ray measurements of uranium enrichment. These users require rapid, portable measurement capability. Some in-field measurements have been biased, forcing the inspectors to resort to high-resolution measurements or mass spectrometry to accomplish their goals.

  15. An algorithmic method for reducing conductance-based neuron models.

    PubMed

    Sorensen, Michael E; DeWeerth, Stephen P

    2006-08-01

    Although conductance-based neural models provide a realistic depiction of neuronal activity, their complexity often limits effective implementation and analysis. Neuronal model reduction methods provide a means to reduce model complexity while retaining the original model's realism and relevance. Such methods, however, typically include ad hoc components that require that the modeler already be intimately familiar with the dynamics of the original model. We present an automated, algorithmic method for reducing conductance-based neuron models using the method of equivalent potentials (Kelper et al., Biol Cybern 66(5):381-387, 1992) Our results demonstrate that this algorithm is able to reduce the complexity of the original model with minimal performance loss, and requires minimal prior knowledge of the model's dynamics. Furthermore, by utilizing a cost function based on the contribution of each state variable to the total conductance of the model, the performance of the algorithm can be significantly improved.

  16. Optimizing distance-based methods for large data sets

    NASA Astrophysics Data System (ADS)

    Scholl, Tobias; Brenner, Thomas

    2015-10-01

    Distance-based methods for measuring spatial concentration of industries have received an increasing popularity in the spatial econometrics community. However, a limiting factor for using these methods is their computational complexity since both their memory requirements and running times are in {{O}}(n^2). In this paper, we present an algorithm with constant memory requirements and shorter running time, enabling distance-based methods to deal with large data sets. We discuss three recent distance-based methods in spatial econometrics: the D&O-Index by Duranton and Overman (Rev Econ Stud 72(4):1077-1106, 2005), the M-function by Marcon and Puech (J Econ Geogr 10(5):745-762, 2010) and the Cluster-Index by Scholl and Brenner (Reg Stud (ahead-of-print):1-15, 2014). Finally, we present an alternative calculation for the latter index that allows the use of data sets with millions of firms.

  17. Leaf image segmentation method based on multifractal detrended fluctuation analysis

    NASA Astrophysics Data System (ADS)

    Wang, Fang; Li, Jin-Wei; Shi, Wen; Liao, Gui-Ping

    2013-12-01

    To identify singular regions of crop leaf affected by diseases, based on multifractal detrended fluctuation analysis (MF-DFA), an image segmentation method is proposed. In the proposed method, first, we defend a new texture descriptor: local generalized Hurst exponent, recorded as LHq based on MF-DFA. And then, box-counting dimension f(LHq) is calculated for sub-images constituted by the LHq of some pixels, which come from a specific region. Consequently, series of f(LHq) of the different regions can be obtained. Finally, the singular regions are segmented according to the corresponding f(LHq). Six kinds of corn diseases leaf's images are tested in our experiments. Both the proposed method and other two segmentation methods—multifractal spectrum based and fuzzy C-means clustering have been compared in the experiments. The comparison results demonstrate that the proposed method can recognize the lesion regions more effectively and provide more robust segmentations.

  18. Folding to Curved Surfaces: A Generalized Design Method and Mechanics of Origami-based Cylindrical Structures.

    PubMed

    Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C Q

    2016-01-01

    Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson's ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering.

  19. Folding to Curved Surfaces: A Generalized Design Method and Mechanics of Origami-based Cylindrical Structures

    PubMed Central

    Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C. Q.

    2016-01-01

    Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson’s ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering. PMID:27624892

  20. Folding to Curved Surfaces: A Generalized Design Method and Mechanics of Origami-based Cylindrical Structures

    NASA Astrophysics Data System (ADS)

    Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C. Q.

    2016-09-01

    Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson’s ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering.

  1. Folding to Curved Surfaces: A Generalized Design Method and Mechanics of Origami-based Cylindrical Structures.

    PubMed

    Wang, Fei; Gong, Haoran; Chen, Xi; Chen, C Q

    2016-01-01

    Origami structures enrich the field of mechanical metamaterials with the ability to convert morphologically and systematically between two-dimensional (2D) thin sheets and three-dimensional (3D) spatial structures. In this study, an in-plane design method is proposed to approximate curved surfaces of interest with generalized Miura-ori units. Using this method, two combination types of crease lines are unified in one reprogrammable procedure, generating multiple types of cylindrical structures. Structural completeness conditions of the finite-thickness counterparts to the two types are also proposed. As an example of the design method, the kinematics and elastic properties of an origami-based circular cylindrical shell are analysed. The concept of Poisson's ratio is extended to the cylindrical structures, demonstrating their auxetic property. An analytical model of rigid plates linked by elastic hinges, consistent with numerical simulations, is employed to describe the mechanical response of the structures. Under particular load patterns, the circular shells display novel mechanical behaviour such as snap-through and limiting folding positions. By analysing the geometry and mechanics of the origami structures, we extend the design space of mechanical metamaterials and provide a basis for their practical applications in science and engineering. PMID:27624892

  2. Raster-based outranking method: a new approach for municipal solid waste landfill (MSW) siting.

    PubMed

    Hamzeh, Mohamad; Abbaspour, Rahim Ali; Davalou, Romina

    2015-08-01

    MSW landfill siting is a complicated process because it requires integration of several factors. In this paper, geographic information system (GIS) and multiple criteria decision analysis (MCDA) were combined to handle the municipal solid waste (MSW) landfill siting. For this purpose, first, 16 input data layers were prepared in GIS environment. Then, the exclusionary lands were eliminated and potentially suitable areas for the MSW disposal were identified. These potentially suitable areas, in an innovative approach, were further examined by deploying Preference Ranking Organization Method for Enrichment Evaluations (PROMETHEE) II and analytic network process (ANP), which are two of the most recent MCDA methods, in order to determine land suitability for landfilling. PROMETHEE II was used to determine a complete ranking of the alternatives, while ANP was employed to quantify the subjective judgments of evaluators as criteria weights. The resulting land suitability was reported on a grading scale of 1-5 from 1 to 5, which is the least to the most suitable area, respectively. Finally, three optimal sites were selected by taking into consideration the local conditions of 15 sites, which were candidates for MSW landfilling. Research findings show that the raster-based method yields effective results.

  3. An overview of modal-based damage identification methods

    SciTech Connect

    Farrar, C.R.; Doebling, S.W.

    1997-09-01

    This paper provides an overview of methods that examine changes in measured vibration response to detect, locate, and characterize damage in structural and mechanical systems. The basic idea behind this technology is that modal parameters (notably frequencies, mode shapes, and modal damping) are functions of the physical properties of the structure (mass, damping, and stiffness). Therefore, changes in the physical properties will cause detectable changes in the modal properties. The motivation for the development of this technology is first provided. The methods are then categorized according to various criteria such as the level of damage detection provided, model-based vs. non-model-based methods and linear vs. nonlinear methods. This overview is limited to methods that can be adapted to a wide range of structures (i.e., are not dependent on a particular assumed model form for the system such as beam-bending behavior and methods and that are not based on updating finite element models). Next, the methods are described in general terms including difficulties associated with their implementation and their fidelity. Past, current and future-planned applications of this technology to actual engineering systems are summarized. The paper concludes with a discussion of critical issues for future research in the area of modal-based damage identification.

  4. Photon and neutron active interrogation of highly enriched uranium.

    SciTech Connect

    Myers, W. L.; Goulding, C. A.; Hollas, C. L.; Moss, C. E.

    2004-01-01

    The physics of photon and neutron active interrogation of highly enriched uranium (HEU) using the delayed neutron reinterrogation method is described in this paper. Two sets of active interrogation experiments were performed using a set of subcritical configurations of cocentric HEU metal hemishells. One set of measurements utilized a pulsed 14-MeV neutron generator as the active source. The second set of measurements utilized a linear accelerator-based bremsstrahlung photon source as an active interrogation source. The neutron responses were measured for both sets of experiments. The operational details and results for both measurement sets are described.

  5. Enrichment of Phosphopeptides via Immobilized Metal Affinity Chromatography.

    PubMed

    Swaney, Danielle L; Villén, Judit

    2016-03-01

    Immobilized metal affinity chromatography (IMAC) is a frequently used method for the enrichment of phosphorylated peptides from complex, cellular lysate-derived peptide mixtures. Here we outline an IMAC protocol that uses iron-chelated magnetic beads to selectively isolate phosphorylated peptides for mass spectrometry-based proteomic analysis. Under acidic conditions, negatively charged phosphoryl modifications preferentially bind to positively charged metal ions (e.g., Fe(3+), Ga(3+)) on the beads. After washing away nonphosphorylated peptides, a pH shift to basic conditions causes the elution of bound phosphopeptides from the metal ion. Under optimal conditions, very high specificity for phosphopeptides can be achieved. PMID:26933247

  6. Meta-analysis of pathway enrichment: combining independent and dependent omics data sets.

    PubMed

    Kaever, Alexander; Landesfeind, Manuel; Feussner, Kirstin; Morgenstern, Burkhard; Feussner, Ivo; Meinicke, Peter

    2014-01-01

    A major challenge in current systems biology is the combination and integrative analysis of large data sets obtained from different high-throughput omics platforms, such as mass spectrometry based Metabolomics and Proteomics or DNA microarray or RNA-seq-based Transcriptomics. Especially in the case of non-targeted Metabolomics experiments, where it is often impossible to unambiguously map ion features from mass spectrometry analysis to metabolites, the integration of more reliable omics technologies is highly desirable. A popular method for the knowledge-based interpretation of single data sets is the (Gene) Set Enrichment Analysis. In order to combine the results from different analyses, we introduce a methodical framework for the meta-analysis of p-values obtained from Pathway Enrichment Analysis (Set Enrichment Analysis based on pathways) of multiple dependent or independent data sets from different omics platforms. For dependent data sets, e.g. obtained from the same biological samples, the framework utilizes a covariance estimation procedure based on the nonsignificant pathways in single data set enrichment analysis. The framework is evaluated and applied in the joint analysis of Metabolomics mass spectrometry and Transcriptomics DNA microarray data in the context of plant wounding. In extensive studies of simulated data set dependence, the introduced correlation could be fully reconstructed by means of the covariance estimation based on pathway enrichment. By restricting the range of p-values of pathways considered in the estimation, the overestimation of correlation, which is introduced by the significant pathways, could be reduced. When applying the proposed methods to the real data sets, the meta-analysis was shown not only to be a powerful tool to investigate the correlation between different data sets and summarize the results of multiple analyses but also to distinguish experiment-specific key pathways.

  7. Integrated navigation method based on inertial navigation system and Lidar

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoyue; Shi, Haitao; Pan, Jianye; Zhang, Chunxi

    2016-04-01

    An integrated navigation method based on the inertial navigational system (INS) and Lidar was proposed for land navigation. Compared with the traditional integrated navigational method and dead reckoning (DR) method, the influence of the inertial measurement unit (IMU) scale factor and misalignment was considered in the new method. First, the influence of the IMU scale factor and misalignment on navigation accuracy was analyzed. Based on the analysis, the integrated system error model of INS and Lidar was established, in which the IMU scale factor and misalignment error states were included. Then the observability of IMU error states was analyzed. According to the results of the observability analysis, the integrated system was optimized. Finally, numerical simulation and a vehicle test were carried out to validate the availability and utility of the proposed INS/Lidar integrated navigational method. Compared with the test result of a traditional integrated navigation method and DR method, the proposed integrated navigational method could result in a higher navigation precision. Consequently, the IMU scale factor and misalignment error were effectively compensated by the proposed method and the new integrated navigational method is valid.

  8. Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles

    PubMed Central

    2016-01-01

    Ensemble docking can be a successful virtual screening technique that addresses the innate conformational heterogeneity of macromolecular drug targets. Yet, lacking a method to identify a subset of conformational states that effectively segregates active and inactive small molecules, ensemble docking may result in the recommendation of a large number of false positives. Here, three knowledge-based methods that construct structural ensembles for virtual screening are presented. Each method selects ensembles by optimizing an objective function calculated using the receiver operating characteristic (ROC) curve: either the area under the ROC curve (AUC) or a ROC enrichment factor (EF). As the number of receptor conformations, N, becomes large, the methods differ in their asymptotic scaling. Given a set of small molecules with known activities and a collection of target conformations, the most resource intense method is guaranteed to find the optimal ensemble but scales as O(2N). A recursive approximation to the optimal solution scales as O(N2), and a more severe approximation leads to a faster method that scales linearly, O(N). The techniques are generally applicable to any system, and we demonstrate their effectiveness on the androgen nuclear hormone receptor (AR), cyclin-dependent kinase 2 (CDK2), and the peroxisome proliferator-activated receptor δ (PPAR-δ) drug targets. Conformations that consisted of a crystal structure and molecular dynamics simulation cluster centroids were used to form AR and CDK2 ensembles. Multiple available crystal structures were used to form PPAR-δ ensembles. For each target, we show that the three methods perform similarly to one another on both the training and test sets. PMID:27097522

  9. Differential equation based method for accurate approximations in optimization

    NASA Technical Reports Server (NTRS)

    Pritchard, Jocelyn I.; Adelman, Howard M.

    1990-01-01

    A method to efficiently and accurately approximate the effect of design changes on structural response is described. The key to this method is to interpret sensitivity equations as differential equations that may be solved explicitly for closed form approximations, hence, the method is denoted the Differential Equation Based (DEB) method. Approximations were developed for vibration frequencies, mode shapes and static displacements. The DEB approximation method was applied to a cantilever beam and results compared with the commonly-used linear Taylor series approximations and exact solutions. The test calculations involved perturbing the height, width, cross-sectional area, tip mass, and bending inertia of the beam. The DEB method proved to be very accurate, and in most cases, was more accurate than the linear Taylor series approximation. The method is applicable to simultaneous perturbation of several design variables. Also, the approximations may be used to calculate other system response quantities. For example, the approximations for displacements are used to approximate bending stresses.

  10. Dense Stereo Matching Method Based on Local Affine Model.

    PubMed

    Li, Jie; Shi, Wenxuan; Deng, Dexiang; Jia, Wenyan; Sun, Mingui

    2013-07-01

    A new method for constructing an accurate disparity space image and performing an efficient cost aggregation in stereo matching based on local affine model is proposed in this paper. The key algorithm includes a new self-adapting dissimilarity measurement used for calculating the matching cost and a local affine model used in cost aggregation stage. Different from the traditional region-based methods, which try to change the matching window size or to calculate an adaptive weight to do the aggregation, the proposed method focuses on obtaining the efficient and accurate local affine model to aggregate the cost volume while preserving the disparity discontinuity. Moreover, the local affine model can be extended to the color space. Experimental results demonstrate that the proposed method is able to provide subpixel precision disparity maps compared with some state-of-the-art stereo matching methods. PMID:24163727

  11. [Reconstituting evaluation methods based on both qualitative and quantitative paradigms].

    PubMed

    Miyata, Hiroaki; Okubo, Suguru; Yoshie, Satoru; Kai, Ichiro

    2011-01-01

    Debate about the relationship between quantitative and qualitative paradigms is often muddled and confusing and the clutter of terms and arguments has resulted in the concepts becoming obscure and unrecognizable. In this study we conducted content analysis regarding evaluation methods of qualitative healthcare research. We extracted descriptions on four types of evaluation paradigm (validity/credibility, reliability/credibility, objectivity/confirmability, and generalizability/transferability), and classified them into subcategories. In quantitative research, there has been many evaluation methods based on qualitative paradigms, and vice versa. Thus, it might not be useful to consider evaluation methods of qualitative paradigm are isolated from those of quantitative methods. Choosing practical evaluation methods based on the situation and prior conditions of each study is an important approach for researchers.

  12. Empirical comparison of structure-based pathway methods

    PubMed Central

    Jaakkola, Maria K.

    2016-01-01

    Multiple methods have been proposed to estimate pathway activities from expression profiles, and yet, there is not enough information available about the performance of those methods. This makes selection of a suitable tool for pathway analysis difficult. Although methods based on simple gene lists have remained the most common approach, various methods that also consider pathway structure have emerged. To provide practical insight about the performance of both list-based and structure-based methods, we tested six different approaches to estimate pathway activities in two different case study settings of different characteristics. The first case study setting involved six renal cell cancer data sets, and the differences between expression profiles of case and control samples were relatively big. The second case study setting involved four type 1 diabetes data sets, and the profiles of case and control samples were more similar to each other. In general, there were marked differences in the outcomes of the different pathway tools even with the same input data. In the cancer studies, the results of a tested method were typically consistent across the different data sets, yet different between the methods. In the more challenging diabetes studies, almost all the tested methods detected as significant only few pathways if any. PMID:26197809

  13. Consistency-based ellipse detection method for complicated images

    NASA Astrophysics Data System (ADS)

    Zhang, Lijun; Huang, Xuexiang; Feng, Weichun; Liang, Shuli; Hu, Tianjian

    2016-05-01

    Accurate ellipse detection in complicated images is a challenging problem due to corruptions from image clutter, noise, or occlusion of other objects. To cope with this problem, an edge-following-based ellipse detection method is proposed which promotes the performances of the subprocesses based on consistency. The ellipse detector models edge connectivity by line segments and exploits inconsistent endpoints of the line segments to split the edge contours into smooth arcs. The smooth arcs are further refined with a novel arc refinement method which iteratively improves the consistency degree of the smooth arc. A two-phase arc integration method is developed to group disconnected elliptical arcs belonging to the same ellipse, and two constraints based on consistency are defined to increase the effectiveness and speed of the merging process. Finally, an efficient ellipse validation method is proposed to evaluate the saliency of the elliptic hypotheses. Detailed evaluation on synthetic images shows that our method outperforms other state-of-the-art ellipse detection methods in terms of effectiveness and speed. Additionally, we test our detector on three challenging real-world datasets. The F-measure score and execution time of results demonstrate that our method is effective and fast in complicated images. Therefore, the proposed method is suitable for practical applications.

  14. 16. VIEW OF THE ENRICHED URANIUM RECOVERY SYSTEM. ENRICHED URANIUM ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    16. VIEW OF THE ENRICHED URANIUM RECOVERY SYSTEM. ENRICHED URANIUM RECOVERY PROCESSED RELATIVELY PURE MATERIALS AND SOLUTIONS AND SOLID RESIDUES WITH RELATIVELY LOW URANIUM CONTENT. URANIUM RECOVERY INVOLVED BOTH SLOW AND FAST PROCESSES. (4/4/66) - Rocky Flats Plant, General Manufacturing, Support, Records-Central Computing, Southern portion of Plant, Golden, Jefferson County, CO

  15. Multi-stage combustion using nitrogen-enriched air

    DOEpatents

    Fischer, Larry E.; Anderson, Brian L.

    2004-09-14

    Multi-stage combustion technology combined with nitrogen-enriched air technology for controlling the combustion temperature and products to extend the maintenance and lifetime cycles of materials in contact with combustion products and to reduce pollutants while maintaining relatively high combustion and thermal cycle efficiencies. The first stage of combustion operates fuel rich where most of the heat of combustion is released by burning it with nitrogen-enriched air. Part of the energy in the combustion gases is used to perform work or to provide heat. The cooled combustion gases are reheated by additional stages of combustion until the last stage is at or near stoichiometric conditions. Additional energy is extracted from each stage to result in relatively high thermal cycle efficiency. The air is enriched with nitrogen using air separation technologies such as diffusion, permeable membrane, absorption, and cryogenics. The combustion method is applicable to many types of combustion equipment, including: boilers, burners, turbines, internal combustion engines, and many types of fuel including hydrogen and carbon-based fuels including methane and coal.

  16. Enrichments of Cellulolytic Communities from Diverse Natural Sources Using a Novel Selection System

    NASA Astrophysics Data System (ADS)

    Ludwig, Evan Joel

    In order to ensure a sustainable future and curb carbon dioxide emissions from the combustion of fossil fuels, it is imperative to develop a cost-competitive manufacturing process for an alternative liquid fuel with low life cycle greenhouse gas emissions. A potential route towards this sustainable future is the large-scale production of fuels derived from plant biomass, biofuels. A major step for the biological conversion of biomass to fuel is the solubilization and utilization of cellulose. However, lignocellulose is a recalcitrant material, and has evolved to resist microbial degradation. Studying cellulolytic communities from nature can reveal the mechanisms by which organisms can utilize lignocellulose, and also reveal the conditions that facilitate the fastest possible rates of cellulose utilization. This thesis used an Automated Repetitive Batch (ARB) system to perform enrichments of cellulolytic communities to test if cellulolytic communities from diverse sources could be reproducibly enriched for rapid cellulose utilization. This thesis first developed a robust method for reproducibly enriching cellulolytic communities in the ARB system with a single environmental source. Using this method, this research then investigated if cellulolytic communities could be enriched for rapid cellulose utilization from different inoculum sources. In all reproducible enrichments, this thesis then confirmed the use of carbon dioxide as a real time proxy for cellulose utilization based on end product analysis. This thesis showed that the ARB system could yield cellulolytic communities capable of rapid cellulose utilization from diverse environmental sources, and laid a strong foundation for determining whether or not these different sources can be enriched to yield functionally similar cellulolytic communities. The work from this thesis also suggests that fermentation conditions, rather than source material, play a more important role in determining enriched community

  17. Spatial clustering method based on three-dimensional cloud model

    NASA Astrophysics Data System (ADS)

    Wang, Haijun; Wang, Li; Deng, Yu; Liu, Jia

    2008-12-01

    Spatial clustering is one of those major methods applying to spatial data mining and knowledge discovery. The purpose of this paper is to set forth Spatial Clustering Method Based on Multidimensional Cloud Model, which can be widely applied to the research on classification and hierarchy in realm of spatial data mining and knowledge discovery. This paper summarizes all kinds of cloud model and analyzes the optimalizing form of spatial data-three-dimensional cloud model. The limitation which sets the weighing value subjectively in traditional way and propagation of error can be avoided. The implementation procedure of this method is advanced, and the feasibility of this method is proven through experiments effectively.

  18. A perceptual hashing method based on luminance features

    NASA Astrophysics Data System (ADS)

    Luo, Siqing

    2011-02-01

    With the rapid development of multimedia technology, content based searching and image authentication has become strong requirements. Image hashing technique has been proposed to meet them. In this paper, an RST (Rotation, Scaling, and Translation) resistant image hash algorithm is presented. In this method, the geometric distortions are extracted and adjusted by normalization. The features of the image are generated from the high-rank moments of luminance distribution. With the help of the efficient image representation capability of high-rank moments, the robustness and discrimination of proposed method are improved. The experimental results show that the proposed method is better than some existing methods in robustness under rotation attack.

  19. System and method for deriving a process-based specification

    NASA Technical Reports Server (NTRS)

    Hinchey, Michael Gerard (Inventor); Rash, James Larry (Inventor); Rouff, Christopher A. (Inventor)

    2009-01-01

    A system and method for deriving a process-based specification for a system is disclosed. The process-based specification is mathematically inferred from a trace-based specification. The trace-based specification is derived from a non-empty set of traces or natural language scenarios. The process-based specification is mathematically equivalent to the trace-based specification. Code is generated, if applicable, from the process-based specification. A process, or phases of a process, using the features disclosed can be reversed and repeated to allow for an interactive development and modification of legacy systems. The process is applicable to any class of system, including, but not limited to, biological and physical systems, electrical and electro-mechanical systems in addition to software, hardware and hybrid hardware-software systems.

  20. Enrichment and identification of glycoproteins in human saliva using lectin magnetic bead arrays.

    PubMed

    Caragata, Michael; Shah, Alok K; Schulz, Benjamin L; Hill, Michelle M; Punyadeera, Chamindie

    2016-03-15

    Aberrant glycosylation of proteins is a hallmark of tumorigenesis and could provide diagnostic value in cancer detection. Human saliva is an ideal source of glycoproteins due to the relatively high proportion of glycosylated proteins in the salivary proteome. Moreover, saliva collection is noninvasive and technically straightforward, and the sample collection and storage is relatively easy. Although differential glycosylation of proteins can be indicative of disease states, identification of differential glycosylation from clinical samples is not trivial. To facilitate salivary glycoprotein biomarker discovery, we optimized a method for differential glycoprotein enrichment from human saliva based on lectin magnetic bead arrays (saLeMBA). Selected lectins from distinct reactivity groups were used in the saLeMBA platform to enrich salivary glycoproteins from healthy volunteer saliva. The technical reproducibility of saLeMBA was analyzed with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify the glycosylated proteins enriched by each lectin. Our saLeMBA platform enabled robust glycoprotein enrichment in a glycoprotein- and lectin-specific manner consistent with known protein-specific glycan profiles. We demonstrated that saLeMBA is a reliable method to enrich and detect glycoproteins present in human saliva.