Science.gov

Sample records for based enrichment method

  1. Modeling Damage in Composite Materials Using an Enrichment Based Multiscale Method

    DTIC Science & Technology

    2015-03-01

    Multiscale Enrichment Technique The approach to implementing structural based enrichment varies depending on the governing method . In this...the two simulations. Using the enrichment method without any damaged RVEs still reduced the error by 6% over the homogenization approaches . When using...Technical Report ARWSB-TR-15002 Modeling Damage in Composite Materials Using an Enrichment Based Multiscale Method Michael F

  2. Partition enrichment of nucleotide sequences (PINS)--a generally applicable, sequence based method for enrichment of complex DNA samples.

    PubMed

    Kvist, Thomas; Sondt-Marcussen, Line; Mikkelsen, Marie Just

    2014-01-01

    The dwindling cost of DNA sequencing is driving transformative changes in various biological disciplines including medicine, thus resulting in an increased need for routine sequencing. Preparation of samples suitable for sequencing is the starting point of any practical application, but enrichment of the target sequence over background DNA is often laborious and of limited sensitivity thereby limiting the usefulness of sequencing. The present paper describes a new method, Probability directed Isolation of Nucleic acid Sequences (PINS), for enrichment of DNA, enabling the sequencing of a large DNA region surrounding a small known sequence. A 275,000 fold enrichment of a target DNA sample containing integrated human papilloma virus is demonstrated. Specifically, a sample containing 0.0028 copies of target sequence per ng of total DNA was enriched to 786 copies per ng. The starting concentration of 0.0028 target copies per ng corresponds to one copy of target in a background of 100,000 complete human genomes. The enriched sample was subsequently amplified using rapid genome walking and the resulting DNA sequence revealed not only the sequence of a the truncated virus, but also 1026 base pairs 5' and 50 base pairs 3' to the integration site in chromosome 8. The demonstrated enrichment method is extremely sensitive and selective and requires only minimal knowledge of the sequence to be enriched and will therefore enable sequencing where the target concentration relative to background is too low to allow the use of other sample preparation methods or where significant parts of the target sequence is unknown.

  3. StageTip-based HAMMOC, an efficient and inexpensive phosphopeptide enrichment method for plant shotgun phosphoproteomics.

    PubMed

    Nakagami, Hirofumi

    2014-01-01

    Phosphopeptide enrichment is the most critical step for successful LC-MS/MS-based shotgun phosphoproteomics. Recent technological improvements have made selective phosphopeptide enrichment from non-fractionated whole cell lysate digests with a single-step procedure possible. Here, a handy protocol is described for phosphopeptide enrichment from plant materials using hydroxy acid-modified metal oxide chromatography (HAMMMOC) with a stop-and-go-extraction tip (StageTip).

  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 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

  6. Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods.

    PubMed

    Bernacki, Katarzyna; Kalyanaraman, Chakrapani; Jacobson, Matthew P

    2005-10-01

    Motivated by their participation in the McMaster Data-Mining and Docking Competition, the authors developed 2 new computational technologies and applied them to docking against Escherichia coli dihydrofolate reductase: a receptor preparation procedure that incorporates rotamer optimization of side chains and a physics-based rescoring procedure for estimating relative binding affinities of the protein-ligand complexes. Both methods use the same energy function, consisting of the all-atom OPLS-AA force field and a generalized Born solvent model, which treats the protein receptor and small-molecule ligands in a consistent manner. Thus, the energy function is similar to that used in more sophisticated approaches, such as free-energy perturbation and the molecular mechanics Poisson-Boltzmann/surface area, but sampling during the rescoring procedure is limited to simple energy minimization of the ligand. The use of a highly efficient minimization algorithm permitted the authors to apply this rescoring procedure to hundreds of thousands of protein-ligand complexes during the competition, using a modest Linux cluster. To test these methods, they used the 12 competitive inhibitors identified in the training set, plus methotrexate, as positive controls in enrichment studies with both the training and test sets, each containing 50,000 compounds. The key conclusion is that combining the receptor preparation and rescoring methods makes it possible to identify most of the positive controls within the top few tenths of a percent of the rank-ordered training and test set libraries.

  7. Nonprotein Based Enrichment Method to Analyze Peptide Cross-Linking in Protein Complexes

    PubMed Central

    Yan, Funing; Che, Fa-Yun; Rykunov, Dmitry; Nieves, Edward; Fiser, Andras; Weiss, Louis M.; Angeletti, Ruth Hogue

    2009-01-01

    Cross-linking analysis of protein complexes and structures by tandem mass spectrometry (MS/MS) has advantages in speed, sensitivity, specificity, and the capability of handling complicated protein assemblies. However, detection and accurate assignment of the cross-linked peptides are often challenging due to their low abundance and complicated fragmentation behavior in collision-induced dissociation (CID). To simplify the MS analysis and improve the signal-to-noise ratio of the cross-linked peptides, we developed a novel peptide enrichment strategy that utilizes a cross-linker with a cryptic thiol group and using beads modified with a photocleavable cross-linker. The functional cross-linkers were designed to react with the primary amino groups in proteins. Human serum albumin was used as a model protein to detect intra- and intermolecular cross-linkages. Use of this protein-free selective retrieval method eliminates the contamination that can result from avidin–biotin based retrieval systems and simplifies data analysis. These features may make the method suitable to investigate protein–protein interactions in biological samples. PMID:19642656

  8. 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.

  9. A novel hypothesis-unbiased method for Gene Ontology enrichment based on transcriptome data

    PubMed Central

    Fruzangohar, Mario; Ebrahimie, Esmaeil; Adelson, David L.

    2017-01-01

    Gene Ontology (GO) classification of statistically significantly differentially expressed genes is commonly used to interpret transcriptomics data as a part of functional genomic analysis. In this approach, all significantly expressed genes contribute equally to the final GO classification regardless of their actual expression levels. Gene expression levels can significantly affect protein production and hence should be reflected in GO term enrichment. Genes with low expression levels can also participate in GO term enrichment through cumulative effects. In this report, we have introduced a new GO enrichment method that is suitable for multiple samples and time series experiments that uses a statistical outlier test to detect GO categories with special patterns of variation that can potentially identify candidate biological mechanisms. To demonstrate the value of our approach, we have performed two case studies. Whole transcriptome expression profiles of Salmonella enteritidis and Alzheimer’s disease (AD) were analysed in order to determine GO term enrichment across the entire transcriptome instead of a subset of differentially expressed genes used in traditional GO analysis. Our result highlights the key role of inflammation related functional groups in AD pathology as granulocyte colony-stimulating factor receptor binding, neuromedin U binding, and interleukin were remarkably upregulated in AD brain when all using all of the gene expression data in the transcriptome. Mitochondrial components and the molybdopterin synthase complex were identified as potential key cellular components involved in AD pathology. PMID:28199395

  10. A novel hypothesis-unbiased method for Gene Ontology enrichment based on transcriptome data.

    PubMed

    Fruzangohar, Mario; Ebrahimie, Esmaeil; Adelson, David L

    2017-01-01

    Gene Ontology (GO) classification of statistically significantly differentially expressed genes is commonly used to interpret transcriptomics data as a part of functional genomic analysis. In this approach, all significantly expressed genes contribute equally to the final GO classification regardless of their actual expression levels. Gene expression levels can significantly affect protein production and hence should be reflected in GO term enrichment. Genes with low expression levels can also participate in GO term enrichment through cumulative effects. In this report, we have introduced a new GO enrichment method that is suitable for multiple samples and time series experiments that uses a statistical outlier test to detect GO categories with special patterns of variation that can potentially identify candidate biological mechanisms. To demonstrate the value of our approach, we have performed two case studies. Whole transcriptome expression profiles of Salmonella enteritidis and Alzheimer's disease (AD) were analysed in order to determine GO term enrichment across the entire transcriptome instead of a subset of differentially expressed genes used in traditional GO analysis. Our result highlights the key role of inflammation related functional groups in AD pathology as granulocyte colony-stimulating factor receptor binding, neuromedin U binding, and interleukin were remarkably upregulated in AD brain when all using all of the gene expression data in the transcriptome. Mitochondrial components and the molybdopterin synthase complex were identified as potential key cellular components involved in AD pathology.

  11. 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.

  12. Phosphopeptide enrichment: Development of magnetic solid phase extraction method based on polydopamine coating and Ti(4+)-IMAC.

    PubMed

    Piovesana, Susy; Capriotti, Anna Laura; Cavaliere, Chiara; Ferraris, Francesca; Samperi, Roberto; Ventura, Salvatore; Laganà, Aldo

    2016-02-25

    Protein post translational modifications currently represent one of the main challenges with proteomic analysis, due to the important biological role they play within cells. Protein phosphorylation is one of the most important, with several approaches developed for phosphopeptides enrichment and analysis, essential for comprehensive phosphoproteomic analysis. However, the development of new materials for phosphopeptides enrichment may overcome previous drawbacks and improve enrichment of such peptides. In this regard, new magnetic stationary phases based on polydopamine coating and Ti(4+) immobilization exploit the potential of IMAC enrichment and couple it with the versatility of magnetic solid phase extraction. In this work the use of such stationary phase was extended from the MALDI proof of concept stage with the development of an optimized method for phosphopeptides enrichment compatible with typical shotgun proteomics experimental workflows. Different loading and elution buffers were tested to improve phosphopeptides recovery and enrichment selectivity. Finally, the analysis of isolated peptides pointed out that polydopamine alone is an ideal support matrix for polar post translational modifications because it enables to reduce unspecific binding and preferentially binds hydrophilic peptides.

  13. 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

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

    PubMed

    Rohrman, Brittany; Richards-Kortum, Rebecca

    2015-02-03

    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.

  15. A Rapid Spin Column-Based Method to Enrich Pathogen Transcripts from Eukaryotic Host Cells Prior to Sequencing

    PubMed Central

    Bent, Zachary W.; Poorey, Kunal; LaBauve, Annette E.; Hamblin, Rachelle; Williams, Kelly P.

    2016-01-01

    When analyzing pathogen transcriptomes during the infection of host cells, the signal-to-background (pathogen-to-host) ratio of nucleic acids (NA) in infected samples is very small. Despite the advancements in next-generation sequencing, the minute amount of pathogen NA makes standard RNA-seq library preps inadequate for effective gene-level analysis of the pathogen in cases with low bacterial loads. In order to provide a more complete picture of the pathogen transcriptome during an infection, we developed a novel pathogen enrichment technique, which can enrich for transcripts from any cultivable bacteria or virus, using common, readily available laboratory equipment and reagents. To evenly enrich for pathogen transcripts, we generate biotinylated pathogen-targeted capture probes in an enzymatic process using the entire genome of the pathogen as a template. The capture probes are hybridized to a strand-specific cDNA library generated from an RNA sample. The biotinylated probes are captured on a monomeric avidin resin in a miniature spin column, and enriched pathogen-specific cDNA is eluted following a series of washes. To test this method, we performed an in vitro time-course infection using Klebsiella pneumoniae to infect murine macrophage cells. K. pneumoniae transcript enrichment efficiency was evaluated using RNA-seq. Bacterial transcripts were enriched up to ~400-fold, and allowed the recovery of transcripts from ~2000–3600 genes not observed in untreated control samples. These additional transcripts revealed interesting aspects of K. pneumoniae biology including the expression of putative virulence factors and the expression of several genes responsible for antibiotic resistance even in the absence of drugs. PMID:28002481

  16. Method for laser induced isotope enrichment

    DOEpatents

    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.

  17. 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.

  18. A combined sequence and structure based method for discovering enriched motifs in RNA from in vivo binding data.

    PubMed

    Polishchuk, Maya; Paz, Inbal; Kohen, Refael; Mesika, Rona; Yakhini, Zohar; Mandel-Gutfreund, Yael

    2017-03-06

    RNA binding proteins (RBPs) play an important role in regulating many processes in the cell. RBPs often recognize their RNA targets in a specific manner. In addition to the RNA primary sequence, the structure of the RNA has been shown to play a central role in RNA recognition by RBPs. In recent years, many experimental approaches, both in vitro and in vivo, were developed and employed to identify and characterize RBP targets and extract their binding specificities. In vivo binding techniques, such as CrossLinking and ImmunoPrecipitation (CLIP)-based methods, enable the characterization of protein binding sites on RNA targets. However, these methods do not provide information regarding the structural preferences of the protein. While methods to obtain the structure of RNA are available, inferring both the sequence and the structure preferences of RBPs remains a challenge. Here we present SMARTIV, a novel computational tool for discovering combined sequence and structure binding motifs from in vivo RNA binding data relying on the sequences of the target sites, the ranking of their binding scores and their predicted secondary structure. The combined motifs are provided in a unified representation that is informative and easy for visual perception. We tested the method on CLIP-seq data from different platforms for a variety of RBPs. Overall, we show that our results are highly consistent with known binding motifs of RBPs, offering additional information on their structural preferences.

  19. 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.

  20. 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.

  1. 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.

  2. FDR-FET: an optimizing gene set enrichment analysis method

    PubMed Central

    Ji, Rui-Ru; Ott, Karl-Heinz; Yordanova, Roumyana; Bruccoleri, Robert E

    2011-01-01

    Gene set enrichment analysis for analyzing large profiling and screening experiments can reveal unifying biological schemes based on previously accumulated knowledge represented as “gene sets”. Most of the existing implementations use a fixed fold-change or P value cutoff to generate regulated gene lists. However, the threshold selection in most cases is arbitrary, and has a significant effect on the test outcome and interpretation of the experiment. We developed a new gene set enrichment analysis method, ie, FDR-FET, which dynamically optimizes the threshold choice and improves the sensitivity and selectivity of gene set enrichment analysis. The procedure translates experimental results into a series of regulated gene lists at multiple false discovery rate (FDR) cutoffs, and computes the P value of the overrepresentation of a gene set using a Fisher’s exact test (FET) in each of these gene lists. The lowest P value is retained to represent the significance of the gene set. We also implemented improved methods to define a more relevant global reference set for the FET. We demonstrate the validity of the method using a published microarray study of three protease inhibitors of the human immunodeficiency virus and compare the results with those from other popular gene set enrichment analysis algorithms. Our results show that combining FDR with multiple cutoffs allows us to control the error while retaining genes that increase information content. We conclude that FDR-FET can selectively identify significant affected biological processes. Our method can be used for any user-generated gene list in the area of transcriptome, proteome, and other biological and scientific applications. PMID:21918636

  3. FDR-FET: an optimizing gene set enrichment analysis method.

    PubMed

    Ji, Rui-Ru; Ott, Karl-Heinz; Yordanova, Roumyana; Bruccoleri, Robert E

    2011-01-01

    Gene set enrichment analysis for analyzing large profiling and screening experiments can reveal unifying biological schemes based on previously accumulated knowledge represented as "gene sets". Most of the existing implementations use a fixed fold-change or P value cutoff to generate regulated gene lists. However, the threshold selection in most cases is arbitrary, and has a significant effect on the test outcome and interpretation of the experiment. We developed a new gene set enrichment analysis method, ie, FDR-FET, which dynamically optimizes the threshold choice and improves the sensitivity and selectivity of gene set enrichment analysis. The procedure translates experimental results into a series of regulated gene lists at multiple false discovery rate (FDR) cutoffs, and computes the P value of the overrepresentation of a gene set using a Fisher's exact test (FET) in each of these gene lists. The lowest P value is retained to represent the significance of the gene set. We also implemented improved methods to define a more relevant global reference set for the FET. We demonstrate the validity of the method using a published microarray study of three protease inhibitors of the human immunodeficiency virus and compare the results with those from other popular gene set enrichment analysis algorithms. Our results show that combining FDR with multiple cutoffs allows us to control the error while retaining genes that increase information content. We conclude that FDR-FET can selectively identify significant affected biological processes. Our method can be used for any user-generated gene list in the area of transcriptome, proteome, and other biological and scientific applications.

  4. 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

  5. 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

  6. Enrichment of the finite element method with reproducing kernel particle method

    SciTech Connect

    Chen, Y.; Liu, W.K.; Uras, R.A.

    1995-07-01

    Based on the reproducing kernel particle method on enrichment procedure is introduced to enhance the effectiveness of the finite element method. The basic concepts for the reproducing kernel particle method are briefly reviewed. By adopting the well-known completeness requirements, a generalized form of the reproducing kernel particle method is developed. Through a combination of these two methods their unique advantages can be utilized. An alternative approach, the multiple field method is also introduced.

  7. Application of seismic multi-attribute fusion method based on D-S evidence theory in prediction of CBM-enriched area

    NASA Astrophysics Data System (ADS)

    Qi, Xue-Mei; Zhang, Shao-Cong

    2012-03-01

    D-S evidence theory provides a good approach to fuse uncertain information. In this article, we introduce seismic multi-attribute fusion based on D-S evidence theory to predict the coalbed methane (CBM) concentrated areas. First, we choose seismic attributes that are most sensitive to CBM content changes with the guidance of CBM content measured at well sites. Then the selected seismic attributes are fused using D-S evidence theory and the fusion results are used to predict CBM-enriched area. The application shows that the predicted CBM content and the measured values are basically consistent. The results indicate that using D-S evidence theory in seismic multi-attribute fusion to predict CBM-enriched areas is feasible.

  8. [Comparative studies of methods of salmonella enrichment (author's transl)].

    PubMed

    Pietzsch, O; Kretschmer, F J; Bulling, E

    1975-07-01

    Eight different methods of salmonella enrichment were compared in two series of experiments involving 100 samples of whole-egg powder and 80 samples of frozen whole liquid egg, respectively. 66 out of a total of 100 samples of whole-egg powder had been artificially infected with varying numbers of S. typhi-murium; 60 out of 80 samples of frozen whole liquid egg were found to be naturally infected with various salmonella species. 3 of the 8 methods (Table 1) were compared within an international collaborative study with 14 laboratories in 11 countries participating. A reduction of the pre-enrichment period from 18 to 6 hours and of volumes used in pre-enrichment and selective enrichment from 10 and 100 ml, respectively to 1 and 10 ml, respectively were found to have adverse influence upon the result of isolations, in particular in the case of weakly infected samples. In contrast, extended incubation over 48 hours as well as preparation of two sub-cultures on solid selective media following incubation of enrichment cultures over 18-24 hours and 42-48 hours, respectively always resulted in a certain increase of salmonella yield which, however, exhibited gradual differences for the individual methods examined. Preparation of a 2nd sub-culture meant, in particular, a decisive improvement of the result of isolations from artificially infected samples if selenite-cystine enrichment volumes were 10 and 100 ml, respectively. The best results could be obtained by means of the following methods of enrichment: Pre-enrichment of material in buffered peptone water at 37 degrees C over 18 hours; pipetting of 10 ml inoculated and incubated pre-enriched material into 100 ml selenite-cystine or tetrathionate enrichment medium according to MULLER-KAUFFMANN; onward incubation of the enrichment culture at 43 degrees C over 48 hours; and preparation of sub-cultures on solid selective media after 24 and 48 hours. The method using tetrathionate enrichment medium was found to be most

  9. 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.

  10. 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.

  11. Quantification of Listeria monocytogenes in minimally processed leafy vegetables using a combined method based on enrichment and 16S rRNA real-time PCR.

    PubMed

    Aparecida de Oliveira, Maria; Abeid Ribeiro, Eliana Guimarães; Morato Bergamini, Alzira Maria; Pereira De Martinis, Elaine Cristina

    2010-02-01

    Modern lifestyle markedly changed eating habits worldwide, with an increasing demand for ready-to-eat foods, such as minimally processed fruits and leafy greens. Packaging and storage conditions of those products may favor the growth of psychrotrophic bacteria, including the pathogen Listeria monocytogenes. In this work, minimally processed leafy vegetables samples (n = 162) from retail market from Ribeirão Preto, São Paulo, Brazil, were tested for the presence or absence of Listeria spp. by the immunoassay Listeria Rapid Test, Oxoid. Two L. monocytogenes positive and six artificially contaminated samples of minimally processed leafy vegetables were evaluated by the Most Probable Number (MPN) with detection by classical culture method and also culture method combined with real-time PCR (RTi-PCR) for 16S rRNA genes of L. monocytogenes. Positive MPN enrichment tubes were analyzed by RTi-PCR with primers specific for L. monocytogenes using the commercial preparation ABSOLUTE QPCR SYBR Green Mix (ABgene, UK). Real-time PCR assay presented good exclusivity and inclusivity results and no statistical significant difference was found in comparison with the conventional culture method (p < 0.05). Moreover, RTi-PCR was fast and easy to perform, with MPN results obtained in ca. 48 h for RTi-PCR in comparison to 7 days for conventional method.

  12. 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

    ... 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 a license application that proposes the construction, operation, and decommissioning of a...

  13. 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.

  14. 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.

  15. 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.

  16. Method for production of an isotopically enriched compound

    DOEpatents

    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.

  17. Evaluation of different enrichment methods for pathogenic Yersinia species detection by real time PCR

    PubMed Central

    2014-01-01

    Background Yersiniosis is a zoonotic disease reported worldwide. Culture and PCR based protocols are the most common used methods for detection of pathogenic Yersinia species in animal samples. PCR sensitivity could be increased by an initial enrichment step. This step is particularly useful in surveillance programs, where PCR is applied to samples from asymptomatic animals. The aim of this study was to evaluate the improvement in pathogenic Yersinia species detection using a suitable enrichment method prior to the real time PCR (rtPCR). Nine different enrichment protocols were evaluated including six different broth mediums (CASO, ITC, PSB, PBS, PBSMSB and PBSSSB). Results The analysis of variance showed significant differences in Yersinia detection by rtPCR according to the enrichment protocol used. These differences were higher for Y. pseudotuberculosis than for Y. enterocolitica. In general, samples incubated at lower temperatures yielded the highest detection rates. The best results were obtained with PBSMSB and PBS2. Application of PBSMSB protocol to free-ranging wild board samples improved the detection of Y. enterocolitica by 21.2% when compared with direct rtPCR. Y. pseudotuberculosis detection was improved by 10.6% when results obtained by direct rtPCR and by PBSMSB enrichment before rtPCR were analyzed in combination. Conclusions The data obtained in the present study indicate a difference in Yersinia detection by rtPCR related to the enrichment protocol used, being PBSMSB enrichment during 15 days at 4°C and PBS during 7 days at 4°C the most efficient. The use of direct rtPCR in combination with PBSMSB enrichment prior to rtPCR resulted in an improvement in the detection rates of pathogenic Yersinia in wild boar and could be useful for application in other animal samples. PMID:25168886

  18. A generalized finite element method with global-local enrichment functions for confined plasticity problems

    NASA Astrophysics Data System (ADS)

    Kim, D.-J.; Duarte, C. A.; Proenca, S. P.

    2012-11-01

    The main feature of partition of unity methods such as the generalized or extended finite element method is their ability of utilizing a priori knowledge about the solution of a problem in the form of enrichment functions. However, analytical derivation of enrichment functions with good approximation properties is mostly limited to two-dimensional linear problems. This paper presents a procedure to numerically generate proper enrichment functions for three-dimensional problems with confined plasticity where plastic evolution is gradual. This procedure involves the solution of boundary value problems around local regions exhibiting nonlinear behavior and the enrichment of the global solution space with the local solutions through the partition of unity method framework. This approach can produce accurate nonlinear solutions with a reduced computational cost compared to standard finite element methods since computationally intensive nonlinear iterations can be performed on coarse global meshes after the creation of enrichment functions properly describing localized nonlinear behavior. Several three-dimensional nonlinear problems based on the rate-independent J 2 plasticity theory with isotropic hardening are solved using the proposed procedure to demonstrate its robustness, accuracy and computational efficiency.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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

  6. Adaptive enriched Galerkin methods for miscible displacement problems with entropy residual stabilization

    NASA Astrophysics Data System (ADS)

    Lee, Sanghyun; Wheeler, Mary F.

    2017-02-01

    We present a novel approach to the simulation of miscible displacement by employing adaptive enriched Galerkin finite element methods (EG) coupled with entropy residual stabilization for transport. In particular, numerical simulations of viscous fingering instabilities in heterogeneous porous media and Hele-Shaw cells are illustrated. EG is formulated by enriching the conforming continuous Galerkin finite element method (CG) with piecewise constant functions. The method provides locally and globally conservative fluxes, which are crucial for coupled flow and transport problems. Moreover, EG has fewer degrees of freedom in comparison with discontinuous Galerkin (DG) and an efficient flow solver has been derived which allows for higher order schemes. Dynamic adaptive mesh refinement is applied in order to reduce computational costs for large-scale three dimensional applications. In addition, entropy residual based stabilization for high order EG transport systems prevents spurious oscillations. Numerical tests are presented to show the capabilities of EG applied to flow and transport.

  7. 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.

  8. 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.

  9. Novel co-enrichment method for isolation of magnetotactic bacteria.

    PubMed

    Sorty, Ajay M; Shaikh, Nasir R

    2015-04-01

    A novel co-enrichment technique was designed for enrichment of magnetotactic bacteria from soil, water, and sediments. Delayed addition of iron uptake inducer and the iron source proved amenable to induce magnetosome synthesis by MTB followed by their separation from consortium using magnetic flux. We successfully enriched and isolated both North seeking as well as South seeking magnetotactic bacteria from Lonar Lake (Buldhana), Moti Lake (Jalna), Ghanewadi Lake (Jalna), Ganesh Lake (Miraj), Rankala Lake (Kolhapur), and industrial metal-contaminated glaying soils (Jalna) and a soil (Karad), (MS, India) exposed to high-voltage electric current. The hanging drop preparations and growth under magnetic stress on low-agar media allowed conformation of magnetotactic behavior of the isolates. Both Gram positive and Gram negative MTB were isolated with diverse morphologies. South seeking population was more predominant. The soil inhabitants showed little dwelling property which was more prominent in case of aquatic inhabitants. The use of in situ pH and salt concentrations during enrichment and isolation found suited. The simultaneous growth of whole consortium in the system ensured the in situ simulation of microenvironment needful for proper growth of fastidious MTB.

  10. 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.

  11. 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.

  12. 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.

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

    PubMed Central

    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

  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. Growth of 18O isotopically enriched ZnO nanorods by two novel VPT methods

    NASA Astrophysics Data System (ADS)

    Gray, Ciarán; Trefflich, Lukas; Röder, Robert; Ronning, Carsten; Henry, Martin O.; McGlynn, Enda

    2017-02-01

    We have developed two novel vapour phase transport methods to grow ZnO nanorod arrays isotopically enriched with 18O. Firstly, a three-step process used to grow natural and Zn-enriched ZnO nanorods has been further modified, by replacing the atmospheric O2 with enriched 18O2, in order to grow 18O-enriched ZnO nanorods using this vapour-solid method on chemical bath deposited buffer layers. In addition, 18O-enriched ZnO nanorods were successfully grown using 18O isotopically enriched ZnO source powders in a vapour-liquid-solid growth method. Scanning electron microscopy studies confirmed the success of both growth methods in terms of nanorod morphology, although in the case of the vapour-liquid-solid samples, the nanorods' c-axes were not vertically aligned due to the use of a non-epitaxial substrate. Raman and PL studies indicated clearly that O-enrichment was successful in both cases, although the results indicate that the enrichment is at a lower level in our samples compared to previous reports with the same nominal enrichment levels. The results of our studies also allow us to comment on both levels of enrichment achieved and on novel effects of the high temperature growth environment on the nanorod growth, as well as suggesting possible mechanisms for such effects. Very narrow photoluminescence line widths, far narrower than those reported previously in the literature for isotopically enriched bulk ZnO, are seen in both the vapour-solid and vapour-liquid-solid nanorod samples demonstrating their excellent optical quality and their potential for use in detailed optical studies of defects and impurities using low temperature photoluminescence.

  16. A new enrichment method for isolation of Bacillus thuringiensis from diverse sample types.

    PubMed

    Patel, Ketan D; Bhanshali, Forum C; Chaudhary, Avani V; Ingle, Sanjay S

    2013-05-01

    New or more efficient methodologies having different principles are needed, as one method could not be suitable for isolation of organisms from samples of diverse types and from various environments. In present investigation, growth kinetics study revealed a higher germination rate, a higher growth rate, and maximum sporulation of Bacillus thuringiensis (Bt) compared to other Bacillus species. Considering these facts, a simple and efficient enrichment method was devised which allowed propagation of spores and vegetative cells of Bt and thereby increased Bt cell population proportionately. The new enrichment method yielded Bt from 44 out of 58 samples. Contrarily, Bt was isolated only from 16 and 18 samples by sodium acetate selection and dry heat pretreatment methods, respectively. Moreover, the percentages of Bt colonies isolated by the enrichment method were higher comparatively. Vegetative whole cell protein profile analysis indicated isolation of diverse population of Bt from various samples. Bt strains isolated by the enrichment method represented novel serovars and possibly new cry2 gene.

  17. Microdroplet-based PCR enrichment for large-scale targeted sequencing.

    PubMed

    Tewhey, Ryan; Warner, Jason B; Nakano, Masakazu; Libby, Brian; Medkova, Martina; David, Patricia H; Kotsopoulos, Steve K; Samuels, Michael L; Hutchison, J Brian; Larson, Jonathan W; Topol, Eric J; Weiner, Michael P; Harismendy, Olivier; Olson, Jeff; Link, Darren R; Frazer, Kelly A

    2009-11-01

    Targeted enrichment of specific loci of the human genome is a promising approach to enable sequencing-based studies of genetic variation in large populations. Here we describe an enrichment approach based on microdroplet PCR, which enables 1.5 million amplifications in parallel. We sequenced six samples enriched by microdroplet or traditional singleplex PCR using primers targeting 435 exons of 47 genes. Both methods generated similarly high-quality data: 84% of the uniquely mapping reads fell within the targeted sequences; coverage was uniform across approximately 90% of targeted bases; sequence variants were called with >99% accuracy; and reproducibility between samples was high (r(2) = 0.9). We scaled the microdroplet PCR to 3,976 amplicons totaling 1.49 Mb of sequence, sequenced the resulting sample with both Illumina GAII and Roche 454, and obtained data with equally high specificity and sensitivity. Our results demonstrate that microdroplet technology is well suited for processing DNA for massively parallel enrichment of specific subsets of the human genome for targeted sequencing.

  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. Does capillary racetrack-based enrichment reflect the diversity of uncultivated magnetotactic cocci in environmental samples?

    PubMed

    Lin, Wei; Tian, Lanxiang; Li, Jinhua; Pan, Yongxin

    2008-02-01

    The racetrack-based PCR approach is widely used in phylogenetic analysis of magnetotactic bacteria (MTB), which are isolated from environmental samples using the capillary racetrack method. To evaluate whether the capillary racetrack-based enrichment can truly reflect the diversity of MTB in the targeted environmental sample, phylogenetic diversity studies of MTB enriched from the Miyun lake near Beijing were carried out, using both the capillary racetrack-based PCR and a modified metagenome-based PCR approach. Magnetotactic cocci were identified in the studied sample using both approaches. Comparative studies showed that three clusters of magnetotactic cocci were revealed by the modified metagenome-based PCR approach, while only one of them (e.g. MYG-22 sequence) was detected by the racetrack-based PCR approach from the studied sample. This suggests that the result of capillary racetrack-based enrichment might have been biased by the magnetotaxis of magnetotactic bacteria. It appears that the metagenome-based PCR approach better reflects the original diversity of MTB in the environmental sample.

  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. 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.

  2. An Innovative Non-Destructive and Computational Method for Uranium Activity and Enrichment Verification of UF{sub 6} Cylinder

    SciTech Connect

    El-Mongy, Sayed A.; Allam, K.M.; Farid, Osama M.

    2006-07-01

    Verification of {sup 235}U enrichment in uranium hexafluoride (UF{sub 6}) cylinders is often achieved by destructive and non-destructive assay techniques. These techniques are time consuming, need suitable and similar standard, in addition to loss of the nuclear material in the case of destructive analysis. This paper introduce an innovative approach for verifying of {sup 235}U enrichment in UF{sub 6} cylinder. The approach is based on measuring dose rate ({mu}Sv/h) resulted from the emitted gamma rays of {sup 235}U at the surface of the cylinder and then calculating the activity of uranium and enrichment percentage inside the cylinder by a three dimensional model. Attenuation of the main {sup 235}U gamma transitions due to the cylinder wall (5A Type of Ni alloy) was also calculated and corrected for. The method was applied on UF{sub 6} cylinders enriched with 19.75% of {sup 235}U. The calculated enrichment was found to be 18% with 9% uncertainty. By the suggested method, the calculated total uranium activity inside one of the investigated UF{sub 6} cylinder was found close to the target (certified) value (5.6 GBq) with 9% uncertainty. The method is being developed by taking into consideration other parameters. (authors)

  3. Comparison of polymerase chain reaction methods and plating for analysis of enriched cultures of Listeria monocytogenes when using the ISO11290-1 method.

    PubMed

    Dalmasso, Marion; Bolocan, Andrei Sorin; Hernandez, Marta; Kapetanakou, Anastasia E; Kuchta, Tomáš; Manios, Stavros G; Melero, Beatriz; Minarovičová, Jana; Muhterem, Meryem; Nicolau, Anca Ioana; Rovira, Jordi; Skandamis, Panagiotis N; Stessl, Beatrix; Wagner, Martin; Jordan, Kieran; Rodríguez-Lázaro, David

    2014-03-01

    Analysis for Listeria monocytogenes by ISO11290-1 is time-consuming, entailing two enrichment steps and subsequent plating on agar plates, taking five days without isolate confirmation. The aim of this study was to determine if a polymerase chain reaction (PCR) assay could be used for analysis of the first and second enrichment broths, saving four or two days, respectively. In a comprehensive approach involving six European laboratories, PCR and traditional plating of both enrichment broths from the ISO11290-1 method were compared for the detection of L. monocytogenes in 872 food, raw material and processing environment samples from 13 different dairy and meat food chains. After the first and second enrichments, total DNA was extracted from the enriched cultures and analysed for the presence of L. monocytogenes DNA by PCR. DNA extraction by chaotropic solid-phase extraction (spin column-based silica) combined with real-time PCR (RTi-PCR) was required as it was shown that crude DNA extraction applying sonication lysis and boiling followed by traditional gel-based PCR resulted in fewer positive results than plating. The RTi-PCR results were compared to plating, as defined by the ISO11290-1 method. For first and second enrichments, 90% of the samples gave the same results by RTi-PCR and plating, whatever the RTi-PCR method used. For the samples that gave different results, plating was significantly more accurate for detection of positive samples than RTi-PCR from the first enrichment, but RTi-PCR detected a greater number of positive samples than plating from the second enrichment, regardless of the RTi-PCR method used. RTi-PCR was more accurate for non-food contact surface and food contact surface samples than for food and raw material samples especially from the first enrichment, probably because of sample matrix interference. Even though RTi-PCR analysis of the first enrichment showed less positive results than plating, in outbreak scenarios where a rapid result is

  4. 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.

  5. 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)

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

    SciTech Connect

    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.

  7. WaveSeq: A Novel Data-Driven Method of Detecting Histone Modification Enrichments Using Wavelets

    PubMed Central

    Mitra, Apratim; Song, Jiuzhou

    2012-01-01

    Background Chromatin immunoprecipitation followed by next-generation sequencing is a genome-wide analysis technique that can be used to detect various epigenetic phenomena such as, transcription factor binding sites and histone modifications. Histone modification profiles can be either punctate or diffuse which makes it difficult to distinguish regions of enrichment from background noise. With the discovery of histone marks having a wide variety of enrichment patterns, there is an urgent need for analysis methods that are robust to various data characteristics and capable of detecting a broad range of enrichment patterns. Results To address these challenges we propose WaveSeq, a novel data-driven method of detecting regions of significant enrichment in ChIP-Seq data. Our approach utilizes the wavelet transform, is free of distributional assumptions and is robust to diverse data characteristics such as low signal-to-noise ratios and broad enrichment patterns. Using publicly available datasets we showed that WaveSeq compares favorably with other published methods, exhibiting high sensitivity and precision for both punctate and diffuse enrichment regions even in the absence of a control data set. The application of our algorithm to a complex histone modification data set helped make novel functional discoveries which further underlined its utility in such an experimental setup. Conclusions WaveSeq is a highly sensitive method capable of accurate identification of enriched regions in a broad range of data sets. WaveSeq can detect both narrow and broad peaks with a high degree of accuracy even in low signal-to-noise ratio data sets. WaveSeq is also suited for application in complex experimental scenarios, helping make biologically relevant functional discoveries. PMID:23029045

  8. 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

  9. Comparison of direct-plating and enrichment methods for isolation of Vibrio cholerae from diarrhea patients.

    PubMed Central

    Lesmana, M; Richie, E; Subekti, D; Simanjuntak, C; Walz, S E

    1997-01-01

    A direct-plating method on thiosulfate citrate bile salts sucrose agar (DIR-TCBS) in conjunction with enrichment in alkaline peptone water (APW) incubated for both 6 h and 24 h followed by subculture onto TCBS (APW6h-TCBS and APW24h-TCBS, respectively) was performed on 16,034 rectal swab samples for isolating Vibrio cholerae. A total of 2,932 (18.3%) rectal swab samples were positive for V. cholerae O1 biotype El Tor, with the Ogawa serotype constituting 99.2% of the isolates. There were no significant differences in V. cholerae O1 isolation rates between the three culture systems nor between the combinations of any two systems. However, direct plating plus enrichment demonstrated a significantly higher V. cholerae O1 isolation rate than DIR-TCBS alone (P < 0.02). Conversely, enrichment procedure, alone or in combination with DIR-TCBS, yielded significantly more (P < 0.0001) V. cholerae non-O1 isolates than DIR-TCBS alone. The length of incubation time of the enrichment broth, 6 h, offers no significant advantages over 24 h for the isolation of V. cholerae O1 and non-O1. A 24-h enrichment broth incubation period has the practical advantage of being easy to integrate into a normal laboratory workday, whereas 6-h broth enrichment, although more commonly recommended, requires that arrangements be made for after-hours subculture. PMID:9196208

  10. 3D hierarchical interface-enriched finite element method: Implementation and applications

    NASA Astrophysics Data System (ADS)

    Soghrati, Soheil; Ahmadian, Hossein

    2015-10-01

    A hierarchical interface-enriched finite element method (HIFEM) is proposed for the mesh-independent treatment of 3D problems with intricate morphologies. The HIFEM implements a recursive algorithm for creating enrichment functions that capture gradient discontinuities in nonconforming finite elements cut by arbitrary number and configuration of materials interfaces. The method enables the mesh-independent simulation of multiphase problems with materials interfaces that are in close proximity or contact while providing a straightforward general approach for evaluating the enrichments. In this manuscript, we present a detailed discussion on the implementation issues and required computational geometry considerations associated with the HIFEM approximation of thermal and mechanical responses of 3D problems. A convergence study is provided to investigate the accuracy and convergence rate of the HIFEM and compare them with standard FEM benchmark solutions. We will also demonstrate the application of this mesh-independent method for simulating the thermal and mechanical responses of two composite materials systems with complex microstructures.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. An enriched finite element method to fractional advection-diffusion equation

    NASA Astrophysics Data System (ADS)

    Luan, Shengzhi; Lian, Yanping; Ying, Yuping; Tang, Shaoqiang; Wagner, Gregory J.; Liu, Wing Kam

    2017-03-01

    In this paper, an enriched finite element method with fractional basis [ 1,x^{α }] for spatial fractional partial differential equations is proposed to obtain more stable and accurate numerical solutions. For pure fractional diffusion equation without advection, the enriched Galerkin finite element method formulation is demonstrated to simulate the exact solution successfully without any numerical oscillation, which is advantageous compared to the traditional Galerkin finite element method with integer basis [ 1,x] . For fractional advection-diffusion equation, the oscillatory behavior becomes complex due to the introduction of the advection term which can be characterized by a fractional element Peclet number. For the purpose of addressing the more complex numerical oscillation, an enriched Petrov-Galerkin finite element method is developed by using a dimensionless fractional stabilization parameter, which is formulated through a minimization of the residual of the nodal solution. The effectiveness and accuracy of the enriched finite element method are demonstrated by a series of numerical examples of fractional diffusion equation and fractional advection-diffusion equation, including both one-dimensional and two-dimensional, steady-state and time-dependent cases.

  17. A new method to track seed dispersal and recruitment using 15N isotope enrichment.

    PubMed

    Carlo, Tomás A; Tewksbury, Joshua J; Martínez Del Río, Carlos

    2009-12-01

    Seed dispersal has a powerful influence on population dynamics, genetic structuring, evolutionary rates, and community ecology. Yet, patterns of seed dispersal are difficult to measure due to methodological shortcomings in tracking dispersed seeds from sources of interest. Here we introduce a new method to track seed dispersal: stable isotope enrichment. It consists of leaf-feeding plants with sprays of 15N-urea during the flowering stage such that seeds developed after applications are isotopically enriched. We conducted a greenhouse experiment with Solanum americanum and two field experiments with wild Capsicum annuum in southern Arizona, USA, to field-validate the method. First, we show that plants sprayed with 15N-urea reliably produce isotopically enriched progeny, and that delta 15N (i.e., the isotopic ratio) of seeds and seedlings is a linear function of the 15N-urea concentration sprayed on mothers. We demonstrate that three urea dosages can be used to distinctly enrich plants and unambiguously differentiate their offspring after seeds are dispersed by birds. We found that, with high urea dosages, the resulting delta 15N values in seedlings are 10(3) - 10(4) times higher than the delta 15N values of normal plants. This feature allows tracking not only where seeds arrive, but in locations where seeds germinate and recruit, because delta 15N enrichment is detectable in seedlings that have increased in mass by at least two orders of magnitude before fading to normal delta 15N values. Last, we tested a mixing model to analyze seed samples in bulk. We used the delta 15N values of batches (i.e., combined seedlings or seeds captured in seed traps) to estimate the number of enriched seeds coming from isotopically enriched plants in the field. We confirm that isotope enrichment, combined with batch-sampling, is a cheap, reliable, and user-friendly method for bulk-processing seeds and is thus excellent for the detection of rare dispersal events. This method could

  18. Enrichment, Amplification, and Sequence-Based Typing of Salmonella enterica and Other Foodborne Pathogens.

    PubMed

    Edlind, Tom; Brewster, Jeffrey D; Paoli, George C

    2017-01-01

    Detection of Salmonella enterica in foods typically involves microbiological enrichment, molecular-based assay, and subsequent isolation and identification of a pure culture. This is ideally followed by strain typing, which provides information critical to the investigation of outbreaks and the attribution of their sources. Pulsed-field gel electrophoresis is the "gold standard" for S. enterica strain typing, but its limitations have encouraged the search for alternative methods, including whole genome sequencing. Both methods typically require a pure culture, which adds to the cost and turnaround time. A more rapid and cost-effective method with sufficient discriminatory power would benefit food industries, regulatory agencies, and public health laboratories. To address this need, a novel enrichment, amplification, and sequence-based typing (EAST) approach was developed involving (i) overnight enrichment and total DNA preparation, (ii) amplification of polymorphic tandem repeat-containing loci with electrophoretic detection, and (iii) DNA sequencing and bioinformatic analysis to identify related strains. EAST requires 3 days or less and provides a strain resolution that exceeds serotyping and is comparable to pulsed-field gel electrophoresis. Evaluation with spiked ground turkey demonstrated its sensitivity (with a starting inoculum of ≤1 CFU/g) and specificity (with unique or nearly unique alleles relative to databases of >1,000 strains). In tests with unspiked retail chicken parts, 3 of 11 samples yielded S. enterica -specific PCR products. Sequence analysis of three distinct typing targets (SeMT1, SeCRISPR1, and SeCRISPR2) revealed consistent similarities to specific serotype Schwarzengrund, Montevideo, and Typhimurium strains. EAST provides a time-saving and cost-effective approach for detecting and typing foodborne S. enterica , and postenrichment steps can be commercially outsourced to facilitate its implementation. Initial studies with Listeria

  19. 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

  20. Electronic and optoelectronic devices based on chirality-enriched wafer-scale single-wall carbon nanotube thin films

    NASA Astrophysics Data System (ADS)

    Gao, Weilu; He, Xiaowei; Xie, Lijuan; Zhang, Qi; Haroz, Erik; Doorn, Stephen K.; Kono, Junichiro

    2015-03-01

    The unique and rich material properties of single-wall carbon nanotubes (SWCNTs) make them attractive for nano-electronic and optoelectronic applications. Slight changes in tube diameter and wrapping angle, defined by the chirality indices (n, m), can dramatically modify the bandstructure, which can be utilized for designing devices with tailored properties. However, it remains to be a challenge to fabricate macroscopic, single-chirality devices. Here, we introduce a simple way of producing chirality-enriched wafer-scale SWCNT films by combining recently developed solution-based polymer-modified sorting method and vacuum filtration. The produced thin films can be easily transferred onto any substrate to have a CMOS compatible wafer. We fabricated a transistor of (6,5)-enriched SWCNTs with an on/off ratio >103. Large-scale photothermoelectric-effect-based and photovoltaic-effect-based photodetectors made of (6,6)- and (6,5)-enriched films, respectively, will also be discussed.

  1. Cellular enrichment through microfluidic fractionation based on cell biomechanical properties.

    PubMed

    Wang, Gonghao; Turbyfield, Cory; Crawford, Kaci; Alexeev, Alexander; Sulchek, Todd

    2015-10-01

    The biomechanical properties of populations of diseased cells are shown to have differences from healthy populations of cells, yet the overlap of these biomechanical properties can limit their use in disease cell enrichment and detection. We report a new microfluidic cell enrichment technology that continuously fractionates cells through differences in biomechanical properties, resulting in highly pure cellular subpopulations. Cell fractionation is achieved in a microfluidic channel with an array of diagonal ridges that are designed to segregate biomechanically distinct cells to different locations in the channel. Due to the imposition of elastic and viscous forces during cellular compression, which are a function of cell biomechanical properties including size and viscoelasticity, larger, stiffer and less viscos cells migrate parallel to the diagonal ridges and exhibit positive lateral displacement. On the other hand, smaller, softer and more viscous cells migrate perpendicular to the diagonal ridges due to circulatory flow induced by the ridges and result in negative lateral displacement. Multiple outlets are then utilized to collect cells with finer gradation of differences in cell biomechanical properties. The result is that cell fractionation dramatically improves cell separation efficiency compared to binary outputs and enables the measurement of subtle biomechanical differences within a single cell type. As a proof-of-concept demonstration, we mix two different leukemia cell lines (K562 and HL60) and utilize cell fractionation to achieve over 45-fold enhancement of cell populations, with high purity cellular enrichment (90% to 99%) of each cell line. In addition, we demonstrate cell fractionation of a single cell type (K562 cells) into subpopulations and characterize the variations of biomechanical properties of the separated cells with atomic force microscopy. These results will be beneficial to obtaining label-free separation of cellular mixtures, or to

  2. Cellular enrichment through microfluidic fractionation based on cell biomechanical properties

    PubMed Central

    Wang, Gonghao; Turbyfield, Cory; Crawford, Kaci; Alexeev, Alexander; Sulchek, Todd

    2017-01-01

    The biomechanical properties of populations of diseased cells are shown to have differences from healthy populations of cells, yet the overlap of these biomechanical properties can limit their use in disease cell enrichment and detection. We report a new microfluidic cell enrichment technology that continuously fractionates cells through differences in biomechanical properties, resulting in highly pure cellular subpopulations. Cell fractionation is achieved in a microfluidic channel with an array of diagonal ridges that are designed to segregate biomechanically distinct cells to different locations in the channel. Due to the imposition of elastic and viscous forces during cellular compression, which are a function of cell biomechanical properties including size and viscoelasticity, larger, stiffer and less viscos cells migrate parallel to the diagonal ridges and exhibit positive lateral displacement. On the other hand, smaller, softer and more viscous cells migrate perpendicular to the diagonal ridges due to circulatory flow induced by the ridges and result in negative lateral displacement. Multiple outlets are then utilized to collect cells with finer gradation of differences in cell biomechanical properties. The result is that cell fractionation dramatically improves cell separation efficiency compared to binary outputs and enables the measurement of subtle biomechanical differences within a single cell type. As a proof-of-concept demonstration, we mix two different leukemia cell lines (K562 and HL60) and utilize cell fractionation to achieve over 45-fold enhancement of cell populations, with high purity cellular enrichment (90% to 99%) of each cell line. In addition, we demonstrate cell fractionation of a single cell type (K562 cells) into subpopulations and characterize the variations of biomechanical properties of the separated cells with atomic force microscopy. These results will be beneficial to obtaining label-free separation of cellular mixtures, or to

  3. 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

  4. Rare earth element enrichment using membrane based solvent extraction

    NASA Astrophysics Data System (ADS)

    Makertiharta, I. G. B. N.; Dharmawijaya, P. T.; Zunita, M.; Wenten, I. G.

    2017-01-01

    The chemical, catalytic, electrical, magnetic, and optical properties of rare earth elements are required in broad applications. Rare earth elements have similar physical and chemical properties thus it is difficult to separate one from each other. Rare earth element is relatively abundant in earth's crust but rarely occur in high concentrated deposits. Traditionally, ion-exchange and solvent extraction techniques have been developed to separate and purify single rare earth solutions or compounds. Recently, membrane starts to gain attention for rare earth separation by combining membrane and proven technologies such as solvent extraction. Membrane-based process offers selective, reliable, energy efficient and easy to scale up separation. During membrane-based separation process, one phase passes through membrane pores while the other phase is rejected. There is no direct mixing of two phases thus the solvent loss is very low. Membrane can also lower solvent physical properties requirement (viscosity, density) and backmixing, eliminate flooding phenomenon and provide large interfacial area for mass transfer. This paper will summarize research efforts in developing membrane technology for rare earth element separation. Special attention will be given to solvent extraction related process as the commonly used method for rare earth element separation. Furthermore, membrane configuration and its potentials will also be discussed.

  5. 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.

  6. Targeted sequencing with enrichment PCR: a novel diagnostic method for the detection of EGFR mutations

    PubMed Central

    Kang, Suki; Kim, Baek Gil; Han, Hyun Ho; Lee, Joo Hyun; Kim, Ji Eun; Shim, Hyo Sup; Cho, Nam Hoon

    2015-01-01

    Epidermal growth factor receptor (EGFR) is an important mediator of tumor cell survival and proliferation. The detection of EGFR mutations can predict prognoses and indicate when treatment with EGFR tyrosine kinase inhibitors should be used. As such, the development of highly sensitive methods for detecting EGFR mutations is important. Targeted next-generation sequencing is an effective method for diagnosing mutations. We compared the abilities of enrichment PCR followed by ultra-deep pyrosequencing (UDP), UDP alone, and PNA-mediated RT-PCR clamping to detect low-frequency EGFR mutations in tumor cell lines and tissue samples. Using enrichment PCR-UDP, we were able to detect the E19del and L858R mutations at minimum frequencies of 0.01% and 0.05%, respectively, in the PC-9 and H197 tumor cell lines. We also confirmed the sensitivity of detecting the E19del mutation by performing a titration analysis in FFPE tumor samples. The lowest mutation frequency detected was 0.0692% in tissue samples. EGFR mutations with frequencies as low as 0.01% were detected using enrichment PCR-UDP, suggesting that this method is a valuable tool for detecting rare mutations, especially in scarce tissue samples or those with small quantities of DNA. PMID:25915533

  7. 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

    2016-07-01

    "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.

  8. Methods for Determining the Statistical Significance of Enrichment or Depletion of Gene Ontology Classifications under Weighted Membership.

    PubMed

    Iacucci, Ernesto; Zingg, Hans H; Perkins, Theodore J

    2012-01-01

    High-throughput molecular biology studies, such as microarray assays of gene expression, two-hybrid experiments for detecting protein interactions, or ChIP-Seq experiments for transcription factor binding, often result in an "interesting" set of genes - say, genes that are co-expressed or bound by the same factor. One way of understanding the biological meaning of such a set is to consider what processes or functions, as defined in an ontology, are over-represented (enriched) or under-represented (depleted) among genes in the set. Usually, the significance of enrichment or depletion scores is based on simple statistical models and on the membership of genes in different classifications. We consider the more general problem of computing p-values for arbitrary integer additive statistics, or weighted membership functions. Such membership functions can be used to represent, for example, prior knowledge on the role of certain genes or classifications, differential importance of different classifications or genes to the experimenter, hierarchical relationships between classifications, or different degrees of interestingness or evidence for specific genes. We describe a generic dynamic programming algorithm that can compute exact p-values for arbitrary integer additive statistics. We also describe several optimizations for important special cases, which can provide orders-of-magnitude speed up in the computations. We apply our methods to datasets describing oxidative phosphorylation and parturition and compare p-values based on computations of several different statistics for measuring enrichment. We find major differences between p-values resulting from these statistics, and that some statistics recover "gold standard" annotations of the data better than others. Our work establishes a theoretical and algorithmic basis for far richer notions of enrichment or depletion of gene sets with respect to gene ontologies than has previously been available.

  9. Imaging based enrichment criteria using deep learning algorithms for efficient clinical trials in MCI

    PubMed Central

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

    2015-01-01

    The Mild Cognitive Impairment (MCI) stage of 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, employing multi-modal imaging-derived inclusion criteria may be especially beneficial. Here, we present a novel multi-modal 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 (MRI), based on a new deep learning algorithm (randomized denoising autoencoder marker, rDAm). Using ADNI2 MCI data, we show that employing rDAm as a trial enrichment criterion reduces the required sample estimates by at least five times compared to the no-enrichment regime, and leads to smaller trials with high statistical power, compared to existing methods. PMID:26093156

  10. Porous membrane ultrafiltration-A novel method for enrichment of the active compounds from micro-plasma samples

    NASA Astrophysics Data System (ADS)

    Liu, Qingshan; Yin, Xiaoying; Sha, Biying; You, Jingjing

    2014-10-01

    To enrich the active compounds from plasma samples, a novel and simple method has been developed using a porous membrane envelope based on the ultrafiltration technique combining with high-performance liquid chromatography. The ultrafiltration device is a sealed porous membrane envelope prepared with a polypropylene sheet to effectively separate the active small molecules and large biomolecules, and a sample carrier is held inside the envelope to load plasma samples. The enrichment of hyperoside and isoquercitrin from rat plasma was used as an example. Significant factors of this method, such as membrane types, the desorption solvent, and the desorption time were optimized for the ultrafiltration method. Under the optimal conditions, correlation coefficients of 0.999 and 0.998 were obtained for hyperoside and isoquercitrin, respectively, with a linear range between 0.5 and 100 μg/mL. The absolute extraction recoveries from 83.2% to 86.8% were achieved. The detection limits of the method for hyperoside and isoquercitrin were 0.22 and 0.20 μg/mL, respectively. Compared with protein precipitation, solid-phase extraction and commercial ultrafiltration membrane methods, our proposed method demonstrates lower detection limits and lower cost for extraction. Also, it consumes less plasma samples and is found to be applicable to biological samples.

  11. Porous membrane ultrafiltration-A novel method for enrichment of the active compounds from micro-plasma samples.

    PubMed

    Liu, Qingshan; Yin, Xiaoying; Sha, Biying; You, Jingjing

    2014-10-15

    To enrich the active compounds from plasma samples, a novel and simple method has been developed using a porous membrane envelope based on the ultrafiltration technique combining with high-performance liquid chromatography. The ultrafiltration device is a sealed porous membrane envelope prepared with a polypropylene sheet to effectively separate the active small molecules and large biomolecules, and a sample carrier is held inside the envelope to load plasma samples. The enrichment of hyperoside and isoquercitrin from rat plasma was used as an example. Significant factors of this method, such as membrane types, the desorption solvent, and the desorption time were optimized for the ultrafiltration method. Under the optimal conditions, correlation coefficients of 0.999 and 0.998 were obtained for hyperoside and isoquercitrin, respectively, with a linear range between 0.5 and 100μg/mL. The absolute extraction recoveries from 83.2% to 86.8% were achieved. The detection limits of the method for hyperoside and isoquercitrin were 0.22 and 0.20μg/mL, respectively. Compared with protein precipitation, solid-phase extraction and commercial ultrafiltration membrane methods, our proposed method demonstrates lower detection limits and lower cost for extraction. Also, it consumes less plasma samples and is found to be applicable to biological samples.

  12. Material classification and automatic content enrichment of images using supervised learning and knowledge bases

    NASA Astrophysics Data System (ADS)

    Mallepudi, Sri Abhishikth; Calix, Ricardo A.; Knapp, Gerald M.

    2011-02-01

    In recent years there has been a rapid increase in the size of video and image databases. Effective searching and retrieving of images from these databases is a significant current research area. In particular, there is a growing interest in query capabilities based on semantic image features such as objects, locations, and materials, known as content-based image retrieval. This study investigated mechanisms for identifying materials present in an image. These capabilities provide additional information impacting conditional probabilities about images (e.g. objects made of steel are more likely to be buildings). These capabilities are useful in Building Information Modeling (BIM) and in automatic enrichment of images. I2T methodologies are a way to enrich an image by generating text descriptions based on image analysis. In this work, a learning model is trained to detect certain materials in images. To train the model, an image dataset was constructed containing single material images of bricks, cloth, grass, sand, stones, and wood. For generalization purposes, an additional set of 50 images containing multiple materials (some not used in training) was constructed. Two different supervised learning classification models were investigated: a single multi-class SVM classifier, and multiple binary SVM classifiers (one per material). Image features included Gabor filter parameters for texture, and color histogram data for RGB components. All classification accuracy scores using the SVM-based method were above 85%. The second model helped in gathering more information from the images since it assigned multiple classes to the images. A framework for the I2T methodology is presented.

  13. 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,…

  14. 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.

  15. Highly sensitive and rapid detection of Pseudomonas aeruginosa based on magnetic enrichment and magnetic separation.

    PubMed

    Tang, Yongjun; Zou, Jun; Ma, Chao; Ali, Zeeshan; Li, Zhiyang; Li, Xiaolong; Ma, Ninging; Mou, Xianbo; Deng, Yan; Zhang, Liming; Li, Kai; Lu, Guangming; Yang, Haowen; He, Nongyue

    2013-01-01

    A method for highly sensitive and rapid detection of Pseudomonas aeruginosa, based on magnetic enrichment and magnetic separation, is described in this paper. The magnetic nanoparticles (MNPs) were applied to adsorb genome DNA after the sample was lysed. The DNA binding MNPs were directly subjected to polymerase chain reaction (PCR) to amplify gyrB specific sequence of Pseudomonas aeruginosa. The biotin labeled PCR products were detected by chemiluminescence when they were successively incubated with the probes-modified MNPs and alkaline phosphatase (ALP) labeled streptavidin (SA). Agarose gel electrophoresis analyses approved the method of in situ PCR to be highly reliable. The factors which could affect the chemiluminiscence were studied in detail. The results showed that the MNPs of 400 nm in diameter are beneficial to the detection. The sequence length and the binding site of the probe with a target sequence have obvious effects on the detection. The optimal concentration of the probes, hybridization temperature and hybridization time were 10 μM, 60 ºC and 60 mins, respectively. The method of in situ PCR based on MNPs can greatly improve the utilization rate of the DNA template ultimately enhancing the detection sensitivity. Experiment results proved that the primer and probe had high specificity, and Pseudomonas aeruginosa was successfully detected with detection limits as low as 10 cfu/mL by this method, while the detection of a single Pseudomonas aeruginosa can also be achieved.

  16. 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.

  17. 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.

  18. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25805860

  20. 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

  1. Machine learning approaches to supporting the identification of photoreceptor-enriched genes based on expression data

    PubMed Central

    Wang, Haiying; Zheng, Huiru; Simpson, David; Azuaje, Francisco

    2006-01-01

    Background Retinal photoreceptors are highly specialised cells, which detect light and are central to mammalian vision. Many retinal diseases occur as a result of inherited dysfunction of the rod and cone photoreceptor cells. Development and maintenance of photoreceptors requires appropriate regulation of the many genes specifically or highly expressed in these cells. Over the last decades, different experimental approaches have been developed to identify photoreceptor enriched genes. Recent progress in RNA analysis technology has generated large amounts of gene expression data relevant to retinal development. This paper assesses a machine learning methodology for supporting the identification of photoreceptor enriched genes based on expression data. Results Based on the analysis of publicly-available gene expression data from the developing mouse retina generated by serial analysis of gene expression (SAGE), this paper presents a predictive methodology comprising several in silico models for detecting key complex features and relationships encoded in the data, which may be useful to distinguish genes in terms of their functional roles. In order to understand temporal patterns of photoreceptor gene expression during retinal development, a two-way cluster analysis was firstly performed. By clustering SAGE libraries, a hierarchical tree reflecting relationships between developmental stages was obtained. By clustering SAGE tags, a more comprehensive expression profile for photoreceptor cells was revealed. To demonstrate the usefulness of machine learning-based models in predicting functional associations from the SAGE data, three supervised classification models were compared. The results indicated that a relatively simple instance-based model (KStar model) performed significantly better than relatively more complex algorithms, e.g. neural networks. To deal with the problem of functional class imbalance occurring in the dataset, two data re-sampling techniques were

  2. Wide dynamic range enrichment method of semiconducting single-walled carbon nanotubes with weak field centrifugation

    PubMed Central

    Reis, Wieland G.; Tomović, Željko; Weitz, R. Thomas; Krupke, Ralph; Mikhael, Jules

    2017-01-01

    The potential of single–walled carbon nanotubes (SWCNTs) to outperform silicon in electronic application was finally enabled through selective separation of semiconducting nanotubes from the as-synthesized statistical mix with polymeric dispersants. Such separation methods provide typically high semiconducting purity samples with narrow diameter distribution, i.e. almost single chiralities. But for a wide range of applications high purity mixtures of small and large diameters are sufficient or even required. Here we proof that weak field centrifugation is a diameter independent method for enrichment of semiconducting nanotubes. We show that the non-selective and strong adsorption of polyarylether dispersants on nanostructured carbon surfaces enables simple separation of diverse raw materials with different SWCNT diameter. In addition and for the first time, we demonstrate that increased temperature enables higher purity separation. Furthermore we show that the mode of action behind this electronic enrichment is strongly connected to both colloidal stability and protonation. By giving simple access to electronically sorted SWCNTs of any diameter, the wide dynamic range of weak field centrifugation can provide economical relevance to SWCNTs. PMID:28317942

  3. Wide dynamic range enrichment method of semiconducting single-walled carbon nanotubes with weak field centrifugation

    NASA Astrophysics Data System (ADS)

    Reis, Wieland G.; Tomović, Željko; Weitz, R. Thomas; Krupke, Ralph; Mikhael, Jules

    2017-03-01

    The potential of single–walled carbon nanotubes (SWCNTs) to outperform silicon in electronic application was finally enabled through selective separation of semiconducting nanotubes from the as-synthesized statistical mix with polymeric dispersants. Such separation methods provide typically high semiconducting purity samples with narrow diameter distribution, i.e. almost single chiralities. But for a wide range of applications high purity mixtures of small and large diameters are sufficient or even required. Here we proof that weak field centrifugation is a diameter independent method for enrichment of semiconducting nanotubes. We show that the non-selective and strong adsorption of polyarylether dispersants on nanostructured carbon surfaces enables simple separation of diverse raw materials with different SWCNT diameter. In addition and for the first time, we demonstrate that increased temperature enables higher purity separation. Furthermore we show that the mode of action behind this electronic enrichment is strongly connected to both colloidal stability and protonation. By giving simple access to electronically sorted SWCNTs of any diameter, the wide dynamic range of weak field centrifugation can provide economical relevance to SWCNTs.

  4. Size-selective separation and overall-amplification of cell-free fetal DNA fragments using PCR-based enrichment

    PubMed Central

    Yang, Qiwei; Du, Zhenwu; Song, Yang; Gao, Sujie; Yu, Shan; Zhu, He; Ren, Ming; Zhang, Guizhen

    2017-01-01

    This study aimed to establish a method for the selective amplification of cell-free fetal DNA (cffDNA) in maternal plasma and preserve the integrity of DNA fragments during amplification, thereby providing a sufficient amount of cffDNA to meet the requirement of routine non-invasive prenatal testing. We amplified DNA molecules in a one-reaction system without considering their particular sequences and lengths (overall amplification) by using PCR-based enrichment. We then modified PCR conditions to verify the effect of denaturation temperature on DNA amplification on various lengths of DNA (selective overall amplification). Finally, we used an optimum temperature range to amplify cffDNA selectively. Amplification results were validated by electrophoresis and real-time quantitative PCR. Our PCR-based enrichment efficiently amplified all DNA fragments with differing lengths within a single reaction system, as well as preserving the integrity of the DNA fragments. cffDNA was significantly amplified along with the selective amplification of small fragment maternal plasma DNA in an appropriate range of denaturation temperatures. We have established a PCR-based method for the simultaneous enrichment and amplification of cffDNA in order to meet the requirements of high cffDNA quantity for routine non-invasive prenatal testing. PMID:28102322

  5. Size-selective separation and overall-amplification of cell-free fetal DNA fragments using PCR-based enrichment.

    PubMed

    Yang, Qiwei; Du, Zhenwu; Song, Yang; Gao, Sujie; Yu, Shan; Zhu, He; Ren, Ming; Zhang, Guizhen

    2017-01-19

    This study aimed to establish a method for the selective amplification of cell-free fetal DNA (cffDNA) in maternal plasma and preserve the integrity of DNA fragments during amplification, thereby providing a sufficient amount of cffDNA to meet the requirement of routine non-invasive prenatal testing. We amplified DNA molecules in a one-reaction system without considering their particular sequences and lengths (overall amplification) by using PCR-based enrichment. We then modified PCR conditions to verify the effect of denaturation temperature on DNA amplification on various lengths of DNA (selective overall amplification). Finally, we used an optimum temperature range to amplify cffDNA selectively. Amplification results were validated by electrophoresis and real-time quantitative PCR. Our PCR-based enrichment efficiently amplified all DNA fragments with differing lengths within a single reaction system, as well as preserving the integrity of the DNA fragments. cffDNA was significantly amplified along with the selective amplification of small fragment maternal plasma DNA in an appropriate range of denaturation temperatures. We have established a PCR-based method for the simultaneous enrichment and amplification of cffDNA in order to meet the requirements of high cffDNA quantity for routine non-invasive prenatal testing.

  6. 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

  7. 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…

  8. Aptamer-based microfluidic device for enrichment, sorting, and detection of multiple cancer cells.

    PubMed

    Xu, Ye; Phillips, Joseph A; Yan, Jilin; Li, Qingge; Fan, Z Hugh; Tan, Weihong

    2009-09-01

    The ability to diagnose cancer based on the detection of rare cancer cells in blood or other bodily fluids is a significant challenge. To address this challenge, we have developed a microfluidic device that can simultaneously sort, enrich, and then detect multiple types of cancer cells from a complex sample. The device, which is made from poly(dimethylsiloxane) (PDMS), implements cell-affinity chromatography based on the selective cell-capture of immobilized DNA-aptamers and yields a 135-fold enrichment of rare cells in a single run. This enrichment is achieved because the height of the channel is on the order of a cell diameter. The sorted cells grow at the comparable rate as cultured cells and are 96% pure based on flow cytometry determination. Thus, by using our aptamer based device, cell capture is achieved simply and inexpensively, with no sample pretreatment before cell analysis. Enrichment and detection of multiple rare cancer cells can be used to detect cancers at the early stages, diagnose metastatic relapse, stratify patients for therapeutic purposes, monitor response to drugs and therapies, track tumor progression, and gain a deeper understanding of the biology of circulating tumor cells (CTCs).

  9. 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'…

  10. 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.

  11. 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

  12. Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods

    PubMed Central

    Reynès, Christelle; Host, Hélène; Camproux, Anne-Claude; Laconde, Guillaume; Leroux, Florence; Mazars, Anne; Deprez, Benoit; Fahraeus, Robin; Villoutreix, Bruno O.; Sperandio, Olivier

    2010-01-01

    Protein-protein interactions (PPIs) may represent one of the next major classes of therapeutic targets. So far, only a minute fraction of the estimated 650,000 PPIs that comprise the human interactome are known with a tiny number of complexes being drugged. Such intricate biological systems cannot be cost-efficiently tackled using conventional high-throughput screening methods. Rather, time has come for designing new strategies that will maximize the chance for hit identification through a rationalization of the PPI inhibitor chemical space and the design of PPI-focused compound libraries (global or target-specific). Here, we train machine-learning-based models, mainly decision trees, using a dataset of known PPI inhibitors and of regular drugs in order to determine a global physico-chemical profile for putative PPI inhibitors. This statistical analysis unravels two important molecular descriptors for PPI inhibitors characterizing specific molecular shapes and the presence of a privileged number of aromatic bonds. The best model has been transposed into a computer program, PPI-HitProfiler, that can output from any drug-like compound collection a focused chemical library enriched in putative PPI inhibitors. Our PPI inhibitor profiler is challenged on the experimental screening results of 11 different PPIs among which the p53/MDM2 interaction screened within our own CDithem platform, that in addition to the validation of our concept led to the identification of 4 novel p53/MDM2 inhibitors. Collectively, our tool shows a robust behavior on the 11 experimental datasets by correctly profiling 70% of the experimentally identified hits while removing 52% of the inactive compounds from the initial compound collections. We strongly believe that this new tool can be used as a global PPI inhibitor profiler prior to screening assays to reduce the size of the compound collections to be experimentally screened while keeping most of the true PPI inhibitors. PPI-HitProfiler is

  13. 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.

  14. 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.

  15. 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

  16. Isolation and enrichment of low abundant particles with insulator-based dielectrophoresis

    PubMed Central

    LaLonde, Alexandra; Romero-Creel, Maria F.; Saucedo-Espinosa, Mario A.; Lapizco-Encinas, Blanca H.

    2015-01-01

    Isolation and enrichment of low-abundant particles are essential steps in many bio-analytical and clinical applications. In this work, the capability of an insulator-based dielectrophoresis (iDEP) device for the detection and stable capture of low abundant polystyrene particles and yeast cells was evaluated. Binary and tertiary mixtures of particles and cells were tested, where the low-abundant particles had concentration ratios on the order of 1:10 000 000 compared to the other particles present in the mixture. The results demonstrated successful and stable capture and enrichment of rare particles and cells (trapping efficiencies over 99%), where particles remained trapped in a stable manner for up to 4 min. A device with four reservoirs was employed for the separation and enrichment of rare particles, where the particles of interest were first selectively concentrated and then effectively directed to a side port for future collection and analysis. The present study demonstrates that simple iDEP devices have appropriate screening capacity and can be used for handling samples containing rare particles; achieving both enrichment and isolation of low-abundant particles and cells. PMID:26674134

  17. Faith-Based Organizations and Veteran Reintegration: Enriching the Web of Support

    DTIC Science & Technology

    2015-01-01

    and others in the web of support at times limit FBOs’ work with veter- ans. Other barriers to support include resource and capacity constraints, lack...of awareness or expe- C O R P O R A T I O N Faith-Based Organizations and Veteran Reintegration Enriching the Web of Support Laura Werber, Kathryn...also address many other areas of veteran health and wellness. • FBOs are already interacting with other organizations in the web of reintegration

  18. 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.

  19. Pruned-enriched Rosenbluth method: Simulations of {theta} polymers of chain length up to 1000000

    SciTech Connect

    Grassberger, P. |

    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 {theta} polymers on the simple-cubic lattice. There it allows high statistics simulations of chains of length up to N=10{sup 6}. For storage reasons, this is feasable only for polymers in a finite volume. For free {theta} polymers in infinite volume, we present very high statistics runs with N=10000. These simulations fully agree with previous simulations made by Hegger and Grassberger [J. Chem. Phys. {bold 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 {theta} 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 {ital et al.} [Macromolecules {bold 19}, 452 (1986) and later work]. {copyright} {ital 1997} {ital The American Physical Society}

  20. Nutrient enrichment reduces constraints on material flows in a detritus-based food web.

    PubMed

    Cross, Wyatt F; Wallace, J Bruce; Rosemond, Amy D

    2007-10-01

    Most aquatic and terrestrial ecosystems are experiencing increased nutrient availability, which is affecting their structure and function. By altering community composition and productivity of consumers, enrichment can indirectly cause changes in the pathways and magnitude of material flows in food webs. These changes, in turn, have major consequences for material storage and cycling in the ecosystem. Understanding mechanisms and predicting consequences of nutrient-induced changes in material flows requires a quantitative food web approach that combines information on consumer energetics and consumer-resource stoichiometry. We examined effects of a whole-system experimental nutrient enrichment on the trophic basis of production and the magnitude and pathways of carbon (C), nitrogen (N), and phosphorus (P) flows in a detritus-based stream food web. We compared the response of the treated stream to an adjacent reference stream throughout the study. Dietary composition and elemental flows varied considerably among invertebrate functional feeding groups. During nutrient enrichment, increased flows of leaf litter and amorphous detritus to shredders and gatherers accounted for most of the altered flows of C from basal resources to consumers. Nutrient enrichment had little effect on patterns of material flows but had large positive effects on the magnitude of C, N, and P flows to consumers (mean increase of 97% for all elements). Nutrient-specific food webs revealed similar flows of N and P to multiple functional groups despite an order of magnitude difference among groups in consumption of C. Secondary production was more strongly related to consumption of nutrients than C, and increased material flows were positively related to the degree of consumer-resource C:P and C:N imbalances. Nutrient enrichment resulted in an increased proportion of detrital C inputs consumed by primary consumers (from -15% to 35%) and a decreased proportion of invertebrate prey consumed by

  1. 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

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

    PubMed Central

    Dores, Camila; Rancourt, Derrick; Dobrinski, Ina

    2015-01-01

    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 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: stirred suspension bioreactor followed by differential plating. After 66 hours of culture, germ cell enrichment in stirred suspension bioreactors 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 stirred suspension bioreactor allows enrichment of germ cells in a controlled and scalable environment providing an efficient method when handling large cell numbers while reducing variability due to handling. PMID:25877677

  3. Transversally enriched pipe element method (TEPEM): An effective numerical approach for blood flow modeling.

    PubMed

    Mansilla Alvarez, Luis; Blanco, Pablo; Bulant, Carlos; Dari, Enzo; Veneziani, Alessandro; Feijóo, Raúl

    2017-04-01

    In this work, we present a novel approach tailored to approximate the Navier-Stokes equations to simulate fluid flow in three-dimensional tubular domains of arbitrary cross-sectional shape. The proposed methodology is aimed at filling the gap between (cheap) one-dimensional and (expensive) three-dimensional models, featuring descriptive capabilities comparable with the full and accurate 3D description of the problem at a low computational cost. In addition, this methodology can easily be tuned or even adapted to address local features demanding more accuracy. The numerical strategy employs finite (pipe-type) elements that take advantage of the pipe structure of the spatial domain under analysis. While low order approximation is used for the longitudinal description of the physical fields, transverse approximation is enriched using high order polynomials. Although our application of interest is computational hemodynamics and its relevance to pathological dynamics like atherosclerosis, the approach is quite general and can be applied in any internal fluid dynamics problem in pipe-like domains. Numerical examples covering academic cases as well as patient-specific coronary arterial geometries demonstrate the potentialities of the developed methodology and its performance when compared against traditional finite element methods. Copyright © 2016 John Wiley & Sons, Ltd.

  4. 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.

  5. 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.

  6. Effect of Different Mixing and Placement Methods on the Compressive Strength of Calcium-Enriched Mixture

    PubMed Central

    Sahebi, Safoora; Sadatshojaee, Nooshin; Jafari, Zahra

    2015-01-01

    Introduction: The aim of this experimental laboratory study was to evaluate the effect of different mixing and placement techniques on compressive strength (CS) of calcium-enriched mixture (CEM) cement. Methods and Materials: CEM powder was mixed with its liquid either by hand mixing or amalgamator mixing. The mixture was loaded to cylindrical acrylic molds with 6.0±0.1 mm height and 4.0±1 mm diameter. Half of the specimens in each group were selected randomly and ultrasonic energy was applied to them for 30 sec. All samples were incubated for 7 days at 37°C. The CS test was performed by means of a universal testing machine. The data were analyzed by the two-way analysis of variance (ANOVA) and Tukey’s post hoc tests. The level of significance was set at 0.05. Results: The maximum CS was seen in the amalgamator-mixed samples that did not receive ultrasonic agitation. The CS value of amalgamator-mixed samples was significantly higher than manually-mixed ones (P=0.003). Ultrasonic vibration did not change the CS of specimens. Conclusion: According to the results, mixing with amalgamator increases the CS of CEM cement, while ultrasonic vibration had no positive effect. PMID:25834593

  7. A Convenient and Efficient Method to Enrich and Maintain Highly Proliferative Human Fetal Liver Stem Cells.

    PubMed

    Guo, Xuan; Wang, Shu; Dou, Ya-ling; Guo, Xiang-fei; Chen, Zhao-li; Wang, Xin-wei; Shen, Zhi-qiang; Qiu, Zhi-gang; Jin, Min; Li, Jun-wen

    2015-06-01

    Pluripotent human hepatic stem cells have broad research and clinical applications, which are, however, restricted by both limited resources and technical difficulties with respect to isolation of stem cells from the adult or fetal liver. In this study, we developed a convenient and efficient method involving a two-step in situ collagenase perfusion, gravity sedimentation, and Percoll density gradient centrifugation to enrich and maintain highly proliferative human fetal liver stem cells (hFLSCs). Using this method, the isolated hFLSCs entered into the exponential growth phase within 10 days and maintained sufficient proliferative activity to permit subculture for at least 20 passages without differentiation. Immunocytochemistry, immunofluorescence, and flow cytometry results showed that these cells expressed stem cell markers, such as c-kit, CD44, epithelial cell adhesion molecule (EpCAM), oval cell marker-6 (OV-6), epithelial marker cytokeratin 18 (CK18), biliary ductal marker CK19, and alpha-fetoprotein (AFP). Gene expression analysis showed that these cells had stable mRNA expression of c-Kit, EpCAM, neural cell adhesion molecule (NCAM), CK19, CK18, AFP, and claudin 3 (CLDN-3) throughout each passage while maintaining low levels of ALB, but with complete absence of cytochrome P450 3A4 (C3A4), phosphoenolpyruvate carboxykinase (PEPCK), telomeric repeat binding factor (TRF), and connexin 26 (CX26) expression. When grown in appropriate medium, these isolated liver stem cells could differentiate into hepatocytes, cholangiocytes, osteoblasts, adipocytes, or endothelial cells. Thus, we have demonstrated a more economical and efficient method to isolate hFLSCs than magnetic-activated cell sorting (MACS). This novel approach may provide an excellent tool to isolate highly proliferative hFLSCs for tissue engineering and regenerative therapies.

  8. Ceria-based nanocomposites for the enrichment and identification of phosphopeptides.

    PubMed

    Fatima, Batool; Najam-ul-Haq, Muhammad; Jabeen, Fahmida; Majeed, Saadat; Ashiq, Muhammad N; Musharraf, S Ghulam; Shad, Muhammad A; Xu, Guobao

    2013-09-07

    Nanocomposites are given preference over the individual materials due to the combined properties of the components involved. Ceria has a high efficiency in phosphopeptide enrichment as well as in dephosphorylation. Iron oxide and tin oxide are chosen as counter metal oxides to synthesize the ceria nanocomposites using a co-precipitation method. The nanocomposites are characterized by Fourier-transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). Tryptic β-casein digest shows the feasibility of phosphopeptide enrichment by the two nanocomposites. Selectivity studies show their performance in comparison to ceria. Being more selective in the extended mass range, both nanocomposites are applied to spiked human serum and non-fat milk digest. The ceria nanocomposites are also capable of being used as material-enhanced laser desorption/ionization (MELDI) carrier/affinity materials for real biological samples with varying degrees of complexity. The enriched content is analyzed by MALDI-TOF MS. All the phosphopeptides in all variants of casein are identified. The sequence coverage of caseins is also interpreted. Nanocomposites thus offer a high selectivity and sensitivity, which make them promising materials for biomarker discoveries and the identification of phosphorylation pathways for new post translational modifications (PTMs).

  9. 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.

  10. Erythrocyte Enrichment in Hematopoietic Progenitor Cell Cultures Based on Magnetic Susceptibility of the Hemoglobin

    PubMed Central

    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. PMID:22952572

  11. 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.

  12. 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

  13. An optimised version of the secretome protein enrichment with click sugars (SPECS) method leads to enhanced coverage of the secretome.

    PubMed

    Serdaroglu, Alperen; Müller, Stephan A; Schepers, Ute; Bräse, Stefan; Weichert, Wilko; Lichtenthaler, Stefan F; Kuhn, Peer-Hendrik

    2017-03-01

    The secretome, the entirety of all soluble proteins either being secreted or proteolytically released by a cell, plays a key role in inter-cellular communication of multi-cellular organisms. Pathological alterations contribute to diseases such as hypertension, cancer, autoimmune disorders or neurodegenerative diseases. Hence, studying disease-related perturbations of the secretome and the secretome itself covers an important aspect of cellular physiology. We recently developed the secretome protein enrichment with click sugars (SPECS) method that enables the analysis of secretomes of in vitro cell cultures even in the presence of FCS with MS. So far, SPECS facilitated the identification of protease substrates of BACE1, SPPL3 and ADAM10. Though, the SPECS method has already enabled deep insights into secretome biology, we aimed to improve the SPECS protocol to obtain even more information from MS-based secretome analysis and reduce the amount of input material. Here, we optimised the reaction buffer, the pH and replaced Dibenzocyclooctyne (DBCO) PEG12-biotin with the more water-soluble variant DBCO-sulpho-biotin to finally provide an optimised protocol of the recently published SPECS protocol. Overall, the number of quantified glycoproteins and their average sequence coverage was increased by 1.6- and 2.4-fold, respectively. Thus, the opzimised SPECS protocol allows reducing the input material by half without losing information. These improvements make the SPECS method more sensitive and more universal applicable to cell types with limited availability.

  14. Innovative method for the enrichment of high-polarity bioactive molecules present at low concentrations in complex matrices.

    PubMed

    Liu, Qing-Shan; He, Jie; Zhou, Wen-Bin; Gu, Yu-Long; Huang, Huoqiang; Li, Ke-Qin; Yin, Xiao-Ying

    2017-02-01

    Ginsenoside Rg1 is a valuable bioactive molecule but its high polarity and low concentration in complex mixtures makes it a challenge to separate Ginsenoside Rg1 from other saponins with similar structures, resulting in low extraction efficiency. The successful development of effective Rg1 molecularly imprinted polymers that exhibit high selectivity and adsorption may offer an improved method for the enrichment of active compounds. In this work, molecularly imprinted polymers were prepared with two different methods, precipitation polymerization or surface imprinted polymerization. Comparison of the adsorption abilities showed higher adsorption of the surface molecularly imprinted polymers prepared by surface imprinted polymerization, 46.80 mg/g, compared to the 27.74 mg/g observed for the molecularly imprinted polymers prepared by precipitation polymerization. Therefore, for higher adsorption of the highly polar Rg1, surface imprinted polymerization is a superior technique to make Rg1 molecularly imprinted polymers. The prepared surface molecularly imprinted polymers were tested as a solid-phase extraction column to directionally enrich Rg1 and its analogues from ginseng tea and total ginseng extracts. The column with surface molecularly imprinted polymers showed higher enrichment efficiency and better selectivity than a C18 solid-phase extraction column. Overall, a new, innovative method was developed to efficiently enrich high-polarity bioactive molecules present at low concentrations in complex matrices.

  15. HPOSim: An R Package for Phenotypic Similarity Measure and Enrichment Analysis Based on the Human Phenotype Ontology

    PubMed Central

    Deng, Yue; Gao, Lin; Wang, Bingbo; Guo, Xingli

    2015-01-01

    Background Phenotypic features associated with genes and diseases play an important role in disease-related studies and most of the available methods focus solely on the Online Mendelian Inheritance in Man (OMIM) database without considering the controlled vocabulary. The Human Phenotype Ontology (HPO) provides a standardized and controlled vocabulary covering phenotypic abnormalities in human diseases, and becomes a comprehensive resource for computational analysis of human disease phenotypes. Most of the existing HPO-based software tools cannot be used offline and provide only few similarity measures. Therefore, there is a critical need for developing a comprehensive and offline software for phenotypic features similarity based on HPO. Results HPOSim is an R package for analyzing phenotypic similarity for genes and diseases based on HPO data. Seven commonly used semantic similarity measures are implemented in HPOSim. Enrichment analysis of gene sets and disease sets are also implemented, including hypergeometric enrichment analysis and network ontology analysis (NOA). Conclusions HPOSim can be used to predict disease genes and explore disease-related function of gene modules. HPOSim is open source and freely available at SourceForge (https://sourceforge.net/p/hposim/). PMID:25664462

  16. 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.

  17. 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…

  18. 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

  19. 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.

  20. Bead Based Proteome Enrichment Enhances Features of the Protein Elution Plate (PEP) for Functional Proteomic Profiling

    PubMed Central

    Wang, Xing; Davies, Michael; Roy, Swapan; Kuruc, Matthew

    2015-01-01

    A novel functional proteomics technology called PEP(Protein Elution Plate) was developed to separate complex proteomes from natural sources and analyze protein functions systematically. The technology takes advantage of the powerful resolution of two-dimensional gel electrophoresis (2-D Gels). The modification of electrophoretic conditions in combination with a high-resolution protein elution plate supports the recovery of functionally active proteins. As 2DE(2-Dimensional Electrophoresis) resolution can be limited by protein load, we investigated the use of bead based enrichment technologies, called AlbuVoid™ and KinaSorb™ to determine their effect on the proteomic features which can be generated from the PEP platform. Using a variety of substrates and enzyme activity assays, we report on the benefits of combining bead based enrichment to improve the signal report and the features generated for Hexokinase, Protein Kinase, Protease, and Alkaline Phosphatase activities. As a result, the PEP technology allows systematic analysis of large enzyme families and can build a comprehensive picture of protein function from a complex proteome, providing biological insights that could otherwise not be observed if only protein abundances were analyzed. PMID:28248280

  1. Selective enrichment of the degradation products of organophosphorus nerve agents by zirconia based solid-phase extraction.

    PubMed

    Kanaujia, Pankaj K; Pardasani, Deepak; Tak, Vijay; Purohit, Ajay K; Dubey, D K

    2011-09-23

    Selective extraction and enrichment of nerve agent degradation products has been achieved using zirconia based commercial solid-phase extraction cartridges. Target analytes were O-alkyl alkylphosphonic acids and alkylphosphonic acids, the environmental markers of nerve agents such as sarin, soman and VX. Critical extraction parameters such as modifier concentration, nature and volume of washing and eluting solvents were investigated. Amongst other anionic compounds, selectivity in extraction was observed for organophosphorus compounds. Recoveries of analytes were determined by GC-MS which ranged from 80% to 115%. Comparison of zirconia based solid-phase extraction method with anion-exchange solid-phase extraction revealed its selectivity towards phosphonic acids. The limits of detection (LOD) and limit of quantification (LOQ) with selected analytes were achieved down to 4.3 and 8.5 ng mL(-1), respectively, in selected ion monitoring mode.

  2. Multiplex enrichment quantitative PCR (ME-qPCR): a high-throughput, highly sensitive detection method for GMO identification.

    PubMed

    Fu, Wei; Zhu, Pengyu; Wei, Shuang; Zhixin, Du; Wang, Chenguang; Wu, Xiyang; Li, Feiwu; Zhu, Shuifang

    2017-04-01

    Among all of the high-throughput detection methods, PCR-based methodologies are regarded as the most cost-efficient and feasible methodologies compared with the next-generation sequencing or ChIP-based methods. However, the PCR-based methods can only achieve multiplex detection up to 15-plex due to limitations imposed by the multiplex primer interactions. The detection throughput cannot meet the demands of high-throughput detection, such as SNP or gene expression analysis. Therefore, in our study, we have developed a new high-throughput PCR-based detection method, multiplex enrichment quantitative PCR (ME-qPCR), which is a combination of qPCR and nested PCR. The GMO content detection results in our study showed that ME-qPCR could achieve high-throughput detection up to 26-plex. Compared to the original qPCR, the Ct values of ME-qPCR were lower for the same group, which showed that ME-qPCR sensitivity is higher than the original qPCR. The absolute limit of detection for ME-qPCR could achieve levels as low as a single copy of the plant genome. Moreover, the specificity results showed that no cross-amplification occurred for irrelevant GMO events. After evaluation of all of the parameters, a practical evaluation was performed with different foods. The more stable amplification results, compared to qPCR, showed that ME-qPCR was suitable for GMO detection in foods. In conclusion, ME-qPCR achieved sensitive, high-throughput GMO detection in complex substrates, such as crops or food samples. In the future, ME-qPCR-based GMO content identification may positively impact SNP analysis or multiplex gene expression of food or agricultural samples. Graphical abstract For the first-step amplification, four primers (A, B, C, and D) have been added into the reaction volume. In this manner, four kinds of amplicons have been generated. All of these four amplicons could be regarded as the target of second-step PCR. For the second-step amplification, three parallels have been taken for

  3. In vivo protein quality of selected cereal-based staple foods enriched with soybean proteins

    PubMed Central

    Acevedo-Pacheco, Laura; Serna-Saldívar, Sergio O.

    2016-01-01

    Background One way to diminish protein malnutrition in children is by enriching cereal-based flours for the manufacturing of maize tortillas, wheat flour tortillas, and yeast-leavened breads, which are widely consumed among low socio-economic groups. Objective The aim was to determine and compare the essential amino acid (EAA) scores, protein digestibility corrected amino acid scores (PDCAAS), and in vivo protein quality (protein digestibility, protein efficiency ratio (PER), biological values (BV), and net protein utilization (NPU) values) of regular versus soybean-fortified maize tortillas, yeast-leavened bread, and wheat flour tortillas. Design To comparatively assess differences in protein quality among maize tortillas, wheat flour tortillas, and yeast-leavened breads, EAA compositions and in vivo studies with weanling rats were performed. The experimental diets based on regular or soybean-fortified food products were compared with a casein-based diet. Food intake, weight gains, PER, dry matter and protein digestibility, BV, NPU, and PDCAAS were assessed. The soybean-fortified tortillas contained 6% of defatted soybean flour, whereas the yeast-leavened bread flour contained 4.5% of soybean concentrate. Results The soybean-fortified tortillas and bread contained higher amounts of lysine and tryptophan, which improved their EAA scores and PDCAAS. Rats fed diets based on soybean-fortified maize or wheat tortillas gained considerably more weight and had better BV and NPU values compared with counterparts fed with respective regular products. As a result, fortified maize tortillas and wheat flour tortillas improved PER from 0.73 to 1.64 and 0.69 to 1.77, respectively. The PER improvement was not as evident in rats fed the enriched yeast-leavened bread because the formulation contained sugar that decreased lysine availability possibly to Maillard reactions. Conclusions The proposed enrichment of cereal-based foods with soybean proteins greatly improved PDCAAS, animal

  4. 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.

  5. 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.

  6. 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.

  7. [Study on the method of nanometer-size zirconium dioxide enrichment separation and inductively coupled plasma mass spectrometry determination of trace barium(II) in water].

    PubMed

    Du, Ying-Qiu; Yin, Yi-Dong; Fan, Nai-Ying; Chen, Peng-Gang; Zhang, Xiao-Bo; Ren, Hong-Bo; Chen, Guo-You; Qu, Qiu-Yao; Sun, Zhi-Bo; Chen, Yue-Xin

    2012-11-01

    Monoclinic fusiform zirconium dioxide (ZrO2) nanoparticles were synthesized by hydrothermal method, a method was established based on monoclinic fusiform nanometer-sized ZrO2 enrichment separation, and trace barium in water was determined by inductively coupled plasma mass spectrometry (ICP-MS). The detection limit for Ba(II) was 0.007 ng x mL(-1), and the relative standard deviation was 0.13% (n = 11). The optimal enrichment separation conditions of nanometer-sized ZrO2 for Ba(II) were studied in detail, it was found that the percentage of adsorbed Ba(II) was more than 99% under pH 10.0 and 2 mL 0.5 mol x L(-1) HCl was sufficient for elution of Ba(II) by more than 98%. The static adsorption capacity of ZrO2 to Ba(II) was 196.6 microg x g(-1) and enrichment factor was 250. Properties of nanometer-sized ZrO2 were discussed through regeneration experiment and effects of co-existing ions and contrast experiment to ordinary ZrO2, adsorption properties of nanometer-sized ZrO2 were applied to real samples in the analysis of Ba(II) and the determination was carried out by ICP-MS with satisfactory results.

  8. 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

  9. Processes involved in sweeping as sample enrichment method in cyclodextrin-modified micellar electrokinetic chromatography of hydrophobic basic analytes.

    PubMed

    El-Awady, Mohamed; Pyell, Ute

    2014-03-01

    Sweeping is an enrichment method in MEKC, which includes following steps: stacking/destacking of the micelles, sweeping of analyte by the stacked/destacked micelles, destacking/stacking of the swept analyte zone and additional focusing/defocusing due to the retention factor gradient effect (RFGE). In this study, we investigate additional processes, regarding online focusing in cyclodextrin-modified MEKC (CD-MEKC) of hydrophobic basic analytes: dynamic pH junction (sample with pH different from that of BGE) and adsorption of analyte onto the capillary wall within the sample zone. It is demonstrated that the developed method for the assessment of the sweeping efficiency is also applicable to CD-MEKC taking ethylparaben as an example of acidic analytes and desloratadine as an example of basic analytes using different types of β-cyclodextrin. Our previous results regarding RFGE as an additional focusing/defocusing effect in sweeping-MEKC are confirmed for the case that the apparent distribution coefficient differs for the sample and the BGE due to a different content of the complex-forming agent cyclodextrin and due to a pH difference between the sample and the BGE. Despite being significantly more hydrophobic than ethylparaben, desloratadine shows an unexpectedly low enrichment factor. This enrichment factor is nearly unaffected by the addition of CD to the BGE. This unexpected behavior is attributed to wall adsorption of the protonated hydrophobic basic analyte within the sample zone, which significantly counteracts the sweeping process. This assumption is corroborated by an improvement in the enrichment factor achieved via addition of a dynamic coating agent (triethylamine) to the sample solution.

  10. 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.

  11. 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.

  12. Multiplexed Single Intact Cell Droplet Digital PCR (MuSIC ddPCR) Method for Specific Detection of Enterohemorrhagic E. coli (EHEC) in Food Enrichment Cultures

    PubMed Central

    McMahon, Tanis C.; Blais, Burton W.; Wong, Alex; Carrillo, Catherine D.

    2017-01-01

    Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin (stx) and intimin (eae)]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae-negative STEC and eae-positive E. coli, but no EHEC with both markers in a single cell. To reduce false-positive detection of EHEC in food enrichment samples, a Multiplexed, Single Intact Cell droplet digital PCR (MuSIC ddPCR) assay capable of detecting the co-occurrence of the stx and eae genes in a single bacterial cell was developed. This method requires: (1) dispersal of intact bacteria into droplets; (2) release of genomic DNA (gDNA) by heat lysis; and (3) amplification and detection of genetic targets (stx and eae) using standard TaqMan chemistries with ddPCR. Performance of the method was tested with panels of EHEC and non-target E. coli. By determining the linkage (i.e., the proportion of droplets in which stx and eae targets were both amplified), samples containing EHEC (typically greater than 20% linkage) could be distinguished from samples containing mixtures of eae-negative STEC and eae-positive E. coli (0–2% linkage). The use of intact cells was necessary as this linkage was not observed with gDNA extracts. EHEC could be accurately identified in enrichment broth cultures containing excess amounts of background E. coli and in enrichment cultures derived from ground beef/pork and leafy-green produce samples. To our knowledge, this is the first report of dual-target detection in single bacterial cells using ddPCR. The application of MuSIC ddPCR to enrichment-culture screening would reduce false-positives, thereby improving the cost, speed, and accuracy of

  13. Multiplexed Single Intact Cell Droplet Digital PCR (MuSIC ddPCR) Method for Specific Detection of Enterohemorrhagic E. coli (EHEC) in Food Enrichment Cultures.

    PubMed

    McMahon, Tanis C; Blais, Burton W; Wong, Alex; Carrillo, Catherine D

    2017-01-01

    Foodborne illness attributed to enterohemorrhagic E. coli (EHEC), a highly pathogenic subset of Shiga toxin-producing E. coli (STEC), is increasingly recognized as a significant public health issue. Current microbiological methods for identification of EHEC in foods often use PCR-based approaches to screen enrichment broth cultures for characteristic gene markers [i.e., Shiga toxin (stx) and intimin (eae)]. However, false positives arise when complex food matrices, such as beef, contain mixtures of eae-negative STEC and eae-positive E. coli, but no EHEC with both markers in a single cell. To reduce false-positive detection of EHEC in food enrichment samples, a Multiplexed, Single Intact Cell droplet digital PCR (MuSIC ddPCR) assay capable of detecting the co-occurrence of the stx and eae genes in a single bacterial cell was developed. This method requires: (1) dispersal of intact bacteria into droplets; (2) release of genomic DNA (gDNA) by heat lysis; and (3) amplification and detection of genetic targets (stx and eae) using standard TaqMan chemistries with ddPCR. Performance of the method was tested with panels of EHEC and non-target E. coli. By determining the linkage (i.e., the proportion of droplets in which stx and eae targets were both amplified), samples containing EHEC (typically greater than 20% linkage) could be distinguished from samples containing mixtures of eae-negative STEC and eae-positive E. coli (0-2% linkage). The use of intact cells was necessary as this linkage was not observed with gDNA extracts. EHEC could be accurately identified in enrichment broth cultures containing excess amounts of background E. coli and in enrichment cultures derived from ground beef/pork and leafy-green produce samples. To our knowledge, this is the first report of dual-target detection in single bacterial cells using ddPCR. The application of MuSIC ddPCR to enrichment-culture screening would reduce false-positives, thereby improving the cost, speed, and accuracy of

  14. Abundance-based Classifier for the Prediction of Mass Spectrometric Peptide Detectability Upon Enrichment (PPA)*

    PubMed Central

    Muntel, Jan; Boswell, Sarah A.; Tang, Shaojun; Ahmed, Saima; Wapinski, Ilan; Foley, Greg; Steen, Hanno; Springer, Michael

    2015-01-01

    The function of a large percentage of proteins is modulated by post-translational modifications (PTMs). Currently, mass spectrometry (MS) is the only proteome-wide technology that can identify PTMs. Unfortunately, the inability to detect a PTM by MS is not proof that the modification is not present. The detectability of peptides varies significantly making MS potentially blind to a large fraction of peptides. Learning from published algorithms that generally focus on predicting the most detectable peptides we developed a tool that incorporates protein abundance into the peptide prediction algorithm with the aim to determine the detectability of every peptide within a protein. We tested our tool, “Peptide Prediction with Abundance” (PPA), on in-house acquired as well as published data sets from other groups acquired on different instrument platforms. Incorporation of protein abundance into the prediction allows us to assess not only the detectability of all peptides but also whether a peptide of interest is likely to become detectable upon enrichment. We validated the ability of our tool to predict changes in protein detectability with a dilution series of 31 purified proteins at several different concentrations. PPA predicted the concentration dependent peptide detectability in 78% of the cases correctly, demonstrating its utility for predicting the protein enrichment needed to observe a peptide of interest in targeted experiments. This is especially important in the analysis of PTMs. PPA is available as a web-based or executable package that can work with generally applicable defaults or retrained from a pilot MS data set. PMID:25473088

  15. Literature-Based Reading: Children's Books and Activities To Enrich the K-5 Curriculum.

    ERIC Educational Resources Information Center

    Laughlin, Mildred Knight; Swisher, Claudia Lisman

    This book helps teachers and media directors to use children's literature to enrich elementary reading programs and to pursue sound educational objectives as they share the books and stories. It provides activities designed to expand and enrich the opportunities for children to become literate. It is a tool which addresses the need for children to…

  16. An automatic method for the enrichment of DICOM metadata using biomedical ontologies.

    PubMed

    Perez, Wilson; Tello, Andres; Saquicela, Victor; Vidal, Maria-Esther; La Cruz, Alexandra

    2015-01-01

    This work is a novel contribution for enriching medical images using semantic annotations with a strategy for unifying different ontologies and instances of DICOM medical files. We present the L-MOM library (Library for Mapping of Ontological Metadata) as a tool for making an automatic mapping between instances of DICOM medical files and different medical ontologies (e.g., FMA, RadLex, MeSH). The main contributions are: i) the domain independent L-MOM library which is able to integrate DICOM metadata with ontologies from different domains; ii) a strategy to automatically annotate DICOM data with universally accepted medical ontologies, and provide values of similarity between ontologies and DICOM metadata; and iii) a framework to traverse ontological concepts that characterized clinical studies of patients registered in the framework catalog.

  17. 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.

  18. 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.

  19. Event-Based Media Enrichment Using an Adaptive Probabilistic Hypergraph Model.

    PubMed

    Liu, Xueliang; Wang, Meng; Yin, Bao-Cai; Huet, Benoit; Li, Xuelong

    2015-11-01

    Nowadays, with the continual development of digital capture technologies and social media services, a vast number of media documents are captured and shared online to help attendees record their experience during events. In this paper, we present a method combining semantic inference and multimodal analysis for automatically finding media content to illustrate events using an adaptive probabilistic hypergraph model. In this model, media items are taken as vertices in the weighted hypergraph and the task of enriching media to illustrate events is formulated as a ranking problem. In our method, each hyperedge is constructed using the K-nearest neighbors of a given media document. We also employ a probabilistic representation, which assigns each vertex to a hyperedge in a probabilistic way, to further exploit the correlation among media data. Furthermore, we optimize the hypergraph weights in a regularization framework, which is solved as a second-order cone problem. The approach is initiated by seed media and then used to rank the media documents using a transductive inference process. The results obtained from validating the approach on an event dataset collected from EventMedia demonstrate the effectiveness of the proposed approach.

  20. 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

  1. A method and software framework for enriching private biomedical sources with data from public online repositories.

    PubMed

    Anguita, Alberto; García-Remesal, Miguel; Graf, Norbert; Maojo, Victor

    2016-04-01

    Modern biomedical research relies on the semantic integration of heterogeneous data sources to find data correlations. Researchers access multiple datasets of disparate origin, and identify elements-e.g. genes, compounds, pathways-that lead to interesting correlations. Normally, they must refer to additional public databases in order to enrich the information about the identified entities-e.g. scientific literature, published clinical trial results, etc. While semantic integration techniques have traditionally focused on providing homogeneous access to private datasets-thus helping automate the first part of the research, and there exist different solutions for browsing public data, there is still a need for tools that facilitate merging public repositories with private datasets. This paper presents a framework that automatically locates public data of interest to the researcher and semantically integrates it with existing private datasets. The framework has been designed as an extension of traditional data integration systems, and has been validated with an existing data integration platform from a European research project by integrating a private biological dataset with data from the National Center for Biotechnology Information (NCBI).

  2. A Facile Method for Separating and Enriching Nano and Submicron Particles from Titanium Dioxide Found in Food and Pharmaceutical Products

    PubMed Central

    Yang, Yu; Capco, David G.; Westerhoff, Paul

    2016-01-01

    Recent studies indicate the presence of nano-scale titanium dioxide (TiO2) as an additive in human foodstuffs, but a practical protocol to isolate and separate nano-fractions from soluble foodstuffs as a source of material remains elusive. As such, we developed a method for separating the nano and submicron fractions found in commercial-grade TiO2 (E171) and E171 extracted from soluble foodstuffs and pharmaceutical products (e.g., chewing gum, pain reliever, and allergy medicine). Primary particle analysis of commercial-grade E171 indicated that 54% of particles were nano-sized (i.e., < 100 nm). Isolation and primary particle analysis of five consumer goods intended to be ingested revealed differences in the percent of nano-sized particles from 32%‒58%. Separation and enrichment of nano- and submicron-sized particles from commercial-grade E171 and E171 isolated from foodstuffs and pharmaceuticals was accomplished using rate-zonal centrifugation. Commercial-grade E171 was separated into nano- and submicron-enriched fractions consisting of a nano:submicron fraction of approximately 0.45:1 and 3.2:1, respectively. E171 extracted from gum had nano:submicron fractions of 1.4:1 and 0.19:1 for nano- and submicron-enriched, respectively. We show a difference in particle adhesion to the cell surface, which was found to be dependent on particle size and epithelial orientation. Finally, we provide evidence that E171 particles are not immediately cytotoxic to the Caco-2 human intestinal epithelium model. These data suggest that this separation method is appropriate for studies interested in isolating the nano-sized particle fraction taken directly from consumer products, in order to study separately the effects of nano and submicron particles. PMID:27798677

  3. A Facile Method for Separating and Enriching Nano and Submicron Particles from Titanium Dioxide Found in Food and Pharmaceutical Products.

    PubMed

    Faust, James J; Doudrick, Kyle; Yang, Yu; Capco, David G; Westerhoff, Paul

    2016-01-01

    Recent studies indicate the presence of nano-scale titanium dioxide (TiO2) as an additive in human foodstuffs, but a practical protocol to isolate and separate nano-fractions from soluble foodstuffs as a source of material remains elusive. As such, we developed a method for separating the nano and submicron fractions found in commercial-grade TiO2 (E171) and E171 extracted from soluble foodstuffs and pharmaceutical products (e.g., chewing gum, pain reliever, and allergy medicine). Primary particle analysis of commercial-grade E171 indicated that 54% of particles were nano-sized (i.e., < 100 nm). Isolation and primary particle analysis of five consumer goods intended to be ingested revealed differences in the percent of nano-sized particles from 32%‒58%. Separation and enrichment of nano- and submicron-sized particles from commercial-grade E171 and E171 isolated from foodstuffs and pharmaceuticals was accomplished using rate-zonal centrifugation. Commercial-grade E171 was separated into nano- and submicron-enriched fractions consisting of a nano:submicron fraction of approximately 0.45:1 and 3.2:1, respectively. E171 extracted from gum had nano:submicron fractions of 1.4:1 and 0.19:1 for nano- and submicron-enriched, respectively. We show a difference in particle adhesion to the cell surface, which was found to be dependent on particle size and epithelial orientation. Finally, we provide evidence that E171 particles are not immediately cytotoxic to the Caco-2 human intestinal epithelium model. These data suggest that this separation method is appropriate for studies interested in isolating the nano-sized particle fraction taken directly from consumer products, in order to study separately the effects of nano and submicron particles.

  4. 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.

  5. Functional connectivity decreases in autism in emotion, self, and face circuits identified by Knowledge-based Enrichment Analysis.

    PubMed

    Cheng, Wei; Rolls, Edmund T; Zhang, Jie; Sheng, Wenbo; Ma, Liang; Wan, Lin; Luo, Qiang; Feng, Jianfeng

    2017-03-01

    A powerful new method is described called Knowledge based functional connectivity Enrichment Analysis (KEA) for interpreting resting state functional connectivity, using circuits that are functionally identified using search terms with the Neurosynth database. The method derives its power by focusing on neural circuits, sets of brain regions that share a common biological function, instead of trying to interpret single functional connectivity links. This provides a novel way of investigating how task- or function-related networks have resting state functional connectivity differences in different psychiatric states, provides a new way to bridge the gap between task and resting-state functional networks, and potentially helps to identify brain networks that might be treated. The method was applied to interpreting functional connectivity differences in autism. Functional connectivity decreases at the network circuit level in 394 patients with autism compared with 473 controls were found in networks involving the orbitofrontal cortex, anterior cingulate cortex, middle temporal gyrus cortex, and the precuneus, in networks that are implicated in the sense of self, face processing, and theory of mind. The decreases were correlated with symptom severity.

  6. 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...

  7. 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.

  8. Quantitative Secretome Analysis of Activated Jurkat Cells Using Click Chemistry-Based Enrichment of Secreted Glycoproteins.

    PubMed

    Witzke, Kathrin E; Rosowski, Kristin; Müller, Christian; Ahrens, Maike; Eisenacher, Martin; Megger, Dominik A; Knobloch, Jürgen; Koch, Andrea; Bracht, Thilo; Sitek, Barbara

    2017-01-06

    Quantitative secretome analyses are a high-performance tool for the discovery of physiological and pathophysiological changes in cellular processes. However, serum supplements in cell culture media limit secretome analyses, but serum depletion often leads to cell starvation and consequently biased results. To overcome these limiting factors, we investigated a model of T cell activation (Jurkat cells) and performed an approach for the selective enrichment of secreted proteins from conditioned medium utilizing metabolic marking of newly synthesized glycoproteins. Marked glycoproteins were labeled via bioorthogonal click chemistry and isolated by affinity purification. We assessed two labeling compounds conjugated with either biotin or desthiobiotin and the respective secretome fractions. 356 proteins were quantified using the biotin probe and 463 using desthiobiotin. 59 proteins were found differentially abundant (adjusted p-value ≤0.05, absolute fold change ≥1.5) between inactive and activated T cells using the biotin method and 86 using the desthiobiotin approach, with 31 mutual proteins cross-verified by independent experiments. Moreover, we analyzed the cellular proteome of the same model to demonstrate the benefit of secretome analyses and provide comprehensive data sets of both. 336 proteins (61.3%) were quantified exclusively in the secretome. Data are available via ProteomeXchange with identifier PXD004280.

  9. 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.

  10. 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.

  11. A lectin-based isolation/enrichment strategy for improved coverage of N-glycan analysis.

    PubMed

    Guan, Feng; Tan, Zengqi; Li, Xiang; Pang, Xingchen; Zhu, Yunlin; Li, Dongliang; Yang, Ganglong

    2015-10-30

    Glycomics provides an increasingly useful research tool as the genomes and proteomes of more and more animal species are elucidated. In view of the general complexity and heterogeneity of glycans, improved depth-of-coverage and sensitivity are required for glycosylation analysis. In this study, we established the lectin-based isolation/enrichment strategy for total glycomic information. Specific lectins are added onto the filter to capture corresponding glycans prior to release of N-glycans by peptide N-glycosidase F (PNGase F). Non-bound glycans and bound glycans are released and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), respectively. Application of the strategy to chicken ovalbumin, normal mouse mammary epithelial cells (NMuMG), and human serum resulted in detection of 5, 6, and 11 additional N-glycan structures, respectively. The strategy facilitates identification of intact N-glycans in biological samples, and can be extended to detailed analysis of O-glycome or glycoproteome.

  12. 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.

  13. 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.

  14. 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.

  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. Solid-phase extraction disk based on multiwalled carbon nanotubes for the enrichment of targeted pesticides from aqueous samples.

    PubMed

    Zdolšek, Nikola; Kumrić, Ksenija; Kalijadis, Ana; Trtić-Petrović, Tatjana

    2017-04-01

    A sensitive method for the determination of six varying polarity pesticides (imidacloprid, acetamiprid, carbendazim, simazine, linuron, and tebufenozide) based on a solid-phase extraction disk with multiwalled nanotubes is proposed.A dispersion of multiwalled nanotubes in a surfactant aqueous solution (Triton X-100) was used for the preparation of the solid-phase extraction disk. The effect of surfactant on the functional groups of multiwalled nanotubes was examined by applying temperature-programmed desorption. It was found that this treatment increased the amount of oxygen groups of treated multiwalled nanotubes comparing with untreated ones. The factors that may influence the adsorption and recovery such as the kind and volume of eluent, volume, flow rate and pH of sample were investigated and optimized. Under the optimized conditions, the maximal enrichment factors for low polar pesticides are ranging from 4000 to 4985 and for more polar are 2250 and 2750. The linear range of calibration curves was 10-500 ng/L with correlation coefficient higher than 0.9960, and the detection limit was 6.2-23.7 ng/L. Finally optimized method was applied for determination trace level of five out of six pesticides in tap and river water samples with good recovery.

  18. 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.

  19. 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…

  20. 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.

  1. 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.

  2. Reliability-targeted HPLC-UV method validation--a protocol enrichment perspective.

    PubMed

    Dharuman, Joghee Gowder; Vasudevan, Mahalingam

    2014-02-01

    Method validation is important in analytical chemistry to obtain the reliability of an analytical method. Guidelines provided by the regulatory bodies can be used as a general framework to assess the validity of a method. Since these guidelines do not focus on the reliability of analytical results exclusively, this study was aimed to combine a few recently evolved strategies that may render analytical method validation more reliable and trustworthy. In this research, the analytical error function was determined by appropriate polynomial regression statistics that determine the range of analyte concentration that may lead to more accurate measurements by producing the least possible total error in the assay and can be regarded as a reliable weighting method. The reliability of the analytical results over a particular concentration range has been proposed by a Bayesian probability study. In order to ensure the applicability of this approach, it was applied for the validation of an HPLC-UV assay method dedicated to the quantification of cefepime and tazobactam in human plasma. A comparison between the newer approach and the usual method validation revealed that the application of analytical error function and Bayesian analysis at the end of the validation process can produce significant improvements in the analytical results.

  3. 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.

  4. 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.

  5. An Easy and Fast Protocol for Affinity Bead-Based Protein Enrichment and Storage of Proteome Samples.

    PubMed

    Otto, A; Maaß, S; Bonn, F; Büttner, K; Becher, D

    2017-01-01

    Analysis of dilute protein samples is a challenging task for scientific and industrial labs all over the world. Although there are different methods available that allow for protein enrichment from various biological sources, all of them have serious limitations apart from their advantages. In order to perform highly reproducible and sensitive protein analysis of lowest concentrated samples, we optimized a method to enrich proteins on affinity beads (StrataClean) recently. This chapter describes the general protocol of this strategy, thereby discussing the power as well as the limits of this technique for qualitative and quantitative proteomic studies. Moreover, additional application and protocol variants will be discussed, expanding the number of compatible up- and downstream processing techniques compared to the originally published method. Hence, we evaluated the reduction of time for sample preparation by use of preprimed affinity beads and shorter incubation durations as well as the influence of high concentration of salts or urea in the sample buffer.

  6. 10 CFR Appendix F to Part 110 - Illustrative List of Laser-Based Enrichment Plant Equipment and Components Under NRC Export...

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... uranium vaporization systems that contain high-power strip or scanning electron beam guns with a delivered... 10 Energy 2 2014-01-01 2014-01-01 false Illustrative List of Laser-Based Enrichment Plant... Appendix F to Part 110—Illustrative List of Laser-Based Enrichment Plant Equipment and Components Under...

  7. 10 CFR Appendix F to Part 110 - Illustrative List of Laser-Based Enrichment Plant Equipment and Components Under NRC Export...

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... uranium vaporization systems that contain high-power strip or scanning electron beam guns with a delivered... 10 Energy 2 2013-01-01 2013-01-01 false Illustrative List of Laser-Based Enrichment Plant... Appendix F to Part 110—Illustrative List of Laser-Based Enrichment Plant Equipment and Components Under...

  8. 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…

  9. 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

    ... laser. The laser system for MLIS usually consists of a CO2 or excimer laser and a multi-pass optical... 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...

  10. 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.

  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. 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...

  13. An enrichment, amplification, and sequence-based typing (EAST) approach for foodborne pathogen detection and surveillance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Introduction: Detection of foodborne pathogens typically involves microbiological enrichment with subsequent isolation and identification of a pure culture. This is typically followed by strain typing, which provides information critical to outbreak and source investigations. In the early 1990’s pul...

  14. 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).

  15. 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.

  16. 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.

  17. Selection based on indirect genetic effects for growth, environmental enrichment and coping style affect the immune status of pigs.

    PubMed

    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.

  18. 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

    2009-10-01

    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

  19. MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes

    PubMed Central

    Ma, Wei; Huang, Chuanbo; Zhou, Yuan; Li, Jianwei; Cui, Qinghua

    2017-01-01

    The microbiota colonized on human body is renowned as “a forgotten organ” due to its big impacts on human health and disease. Recently, microbiome studies have identified a large number of microbes differentially regulated in a variety of conditions, such as disease and diet. However, methods for discovering biological patterns in the differentially regulated microbes are still limited. For this purpose, here, we developed a web-based tool named MicroPattern to discover biological patterns for a list of microbes. In addition, MicroPattern implemented and integrated an algorithm we previously presented for the calculation of disease similarity based on disease-microbe association data. MicroPattern first grouped microbes into different sets based on the associated diseases and the colonized positions. Then, for a given list of microbes, MicroPattern performed enrichment analysis of the given microbes on all of the microbe sets. Moreover, using MicroPattern, we can also calculate disease similarity based on the shared microbe associations. Finally, we confirmed the accuracy and usefulness of MicroPattern by applying it to the changed microbes under the animal-based diet condition. MicroPattern is freely available at http://www.cuilab.cn/micropattern. PMID:28071710

  20. Application of a target enrichment-based next-generation sequencing protocol for identification and sequence-based prediction of pneumococcal serotypes

    PubMed Central

    2014-01-01

    Background The use of whole-genome sequencing in microbiology at a diagnostic level, although feasible, is still limited by the expenses associated and by the complex bioinformatics pipelines in data analyses. We describe the use of target enrichment-based next-generation sequencing for pneumococcal identification and serotyping as applied to the polysaccharide 23 valent vaccine serotypes as an affordable alternative to whole genome sequencing. Results Correct identification of Streptococcus pneumoniae and prediction of common vaccine serotypes: 12 to serotype level and the rest to serogroup levels were achieved for all serotypes with >500 reads mapped against serotypes sequences. A proportion-based criterion also enabled the identification of two serotypes present in the same sample, thus indicating the possibility of using this method in detecting co-colonizing serotypes. The results obtained were comparable to or an improvement on the currently existing molecular serotyping methods for S. pneumoniae in relation to the polysaccharide vaccine serotypes. Conclusion We propose that this method has the potential to become an affordable and adaptable alternative to whole-genome sequencing for pneumococcal identification and serotyping. PMID:24612771

  1. 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.

  2. Uncovering Arabidopsis Membrane Protein Interactome Enriched in Transporters Using Mating-Based Split Ubiquitin Assays and Classification Models

    PubMed Central

    Chen, Jin; Lalonde, Sylvie; Obrdlik, Petr; Noorani Vatani, Azam; Parsa, Saman A.; Vilarino, Cristina; Revuelta, Jose Luis; Frommer, Wolf B.; Rhee, Seung Y.

    2012-01-01

    High-throughput data are a double-edged sword; for the benefit of large amount of data, there is an associated cost of noise. To increase reliability and scalability of high-throughput protein interaction data generation, we tested the efficacy of classification to enrich potential protein–protein interactions. We applied this method to identify interactions among Arabidopsis membrane proteins enriched in transporters. We validated our method with multiple retests. Classification improved the quality of the ensuing interaction network and was effective in reducing the search space and increasing true positive rate. The final network of 541 interactions among 239 proteins (of which 179 are transporters) is the first protein interaction network enriched in membrane transporters reported for any organism. This network has similar topological attributes to other published protein interaction networks. It also extends and fills gaps in currently available biological networks in plants and allows building a number of hypotheses about processes and mechanisms involving signal-transduction and transport systems. PMID:22737156

  3. Direct PCR - A rapid method for multiplexed detection of different serotypes of Salmonella in enriched pork meat samples.

    PubMed

    Chin, Wai Hoe; Sun, Yi; Høgberg, Jonas; Quyen, Than Linh; Engelsmann, Pia; Wolff, Anders; Bang, Dang Duong

    2017-04-01

    Salmonellosis, an infectious disease caused by Salmonella spp., is one of the most common foodborne diseases. Isolation and identification of Salmonella by conventional bacterial culture method is time consuming. In response to the demand for rapid on line or at site detection of pathogens, in this study, we developed a multiplex Direct PCR method for rapid detection of different Salmonella serotypes directly from pork meat samples without any DNA purification steps. An inhibitor-resistant Phusion Pfu DNA polymerase was used to overcome PCR inhibition. Four pairs of primers including a pair of newly designed primers targeting Salmonella spp. at subtype level were incorporated in the multiplex Direct PCR. To maximize the efficiency of the Direct PCR, the ratio between sample and dilution buffer was optimized. The sensitivity and specificity of the multiplex Direct PCR were tested using naturally contaminated pork meat samples for detecting and subtyping of Salmonella spp. Conventional bacterial culture methods were used as reference to evaluate the performance of the multiplex Direct PCR. Relative accuracy, sensitivity and specificity of 98.8%; 97.6% and 100%, respectively, were achieved by the method. Application of the multiplex Direct PCR to detect Salmonella in pork meat at slaughter reduces the time of detection from 5 to 6 days by conventional bacterial culture and serotyping methods to 14 h (including 12 h enrichment time). Furthermore, the method poses a possibility of miniaturization and integration into a point-of-need Lab-on-a-chip system for rapid online pathogen detection.

  4. Halogen-enriched fragment libraries as chemical probes for harnessing halogen bonding in fragment-based lead discovery.

    PubMed

    Zimmermann, Markus O; Lange, Andreas; Wilcken, Rainer; Cieslik, Markus B; Exner, Thomas E; Joerger, Andreas C; Koch, Pierre; Boeckler, Frank M

    2014-04-01

    Halogen bonding has recently experienced a renaissance, gaining increased recognition as a useful molecular interaction in the life sciences. Halogen bonds are favorable, fairly directional interactions between an electropositive region on the halogen (the σ-hole) and a number of different nucleophilic interaction partners. Some aspects of halogen bonding are not yet understood well enough to take full advantage of its potential in drug discovery. We describe and present the concept of halogen-enriched fragment libraries. These libraries consist of unique chemical probes, facilitating the identification of favorable halogen bonds by sharing the advantages of classical fragment-based screening. Besides providing insights into the nature and applicability of halogen bonding, halogen-enriched fragment libraries provide smart starting points for hit-to-lead evolution.

  5. The occurrence of salmonellas and lactose-negative Arizonas in reptiles in The Netherlands, and a comparison of three enrichment methods used in their isolation

    PubMed Central

    Koopman, J. P.; Janssen, F. G. J.

    1973-01-01

    A survey was conducted in 1971 in healthy reptiles supplied to the Central Animal Laboratory of Nijmegen for experimental animal research. In order to determine which salmonella serotypes occur, and whether there are several serotypes per animal, several strains of each positive sample were typed. It was found that 160 of 169 samples contained salmonellas or lactose-negative Arizonas or both, and 95 different serotypes were isolated. Of 127 animals examined individually, 67 were carriers of more than one serotype, 42 animals having two types, 21 three types and 4 animals four types. Three enrichment methods were compared. These were tetrathionate broth incubated at 37° C. (T37) and at 43° C. (T43), and selenite broth incubated at 37° C. (SB). All were incubated for 48 hr. before subculture on brilliant-green agar plates. The enrichment methods T37, T43 and SB produced 99, 125 and 123 positive samples respectively, when taken separately. The combinations of T37 and T43, T37 and SB, and T43 and SB produced 145, 142 and 150 positive samples respectively. The yield of serotypes in comparable samples showed no difference between the three enrichment methods. With the use of two methods the yield increased by about 38% compared with one method, and the combination of three methods showed an increase in serotype yield of about 64% compared with one method. A distinct preference by serotypes for definite enrichment methods was not proved. PMID:4578303

  6. 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.

  7. 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.

  8. Enrichment of low molecular weight serum proteins using acetonitrile precipitation for mass spectrometry based proteomic analysis.

    PubMed

    Kay, Richard; Barton, Chris; Ratcliffe, Lucy; Matharoo-Ball, Balwir; Brown, Pamela; Roberts, Jane; Teale, Phil; Creaser, Colin

    2008-10-01

    A rapid acetonitrile (ACN)-based extraction method has been developed that reproducibly depletes high abundance and high molecular weight proteins from serum prior to mass spectrometric analysis. A nanoflow liquid chromatography/tandem mass spectrometry (nano-LC/MS/MS) multiple reaction monitoring (MRM) method for 57 high to medium abundance serum proteins was used to characterise the ACN-depleted fraction after tryptic digestion. Of the 57 targeted proteins 29 were detected and albumin, the most abundant protein in serum and plasma, was identified as the 20th most abundant protein in the extract. The combination of ACN depletion and one-dimensional nano-LC/MS/MS enabled the detection of the low abundance serum protein, insulin-like growth factor-I (IGF-I), which has a serum concentration in the region of 100 ng/mL. One-dimensional sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the depleted serum showed no bands corresponding to proteins of molecular mass over 75 kDa after extraction, demonstrating the efficiency of the method for the depletion of high molecular weight proteins. Total protein analysis of the ACN extracts showed that approximately 99.6% of all protein is removed from the serum. The ACN-depletion strategy offers a viable alternative to the immunochemistry-based protein-depletion techniques commonly used for removing high abundance proteins from serum prior to MS-based proteomic analyses.

  9. Direct analysis of δ2H and δ18O in natural and enriched human urine using laser-based, Off-Axis Integrated Cavity Output Spectroscopy

    PubMed Central

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

    2012-01-01

    The stable isotopes of hydrogen (δ2H) and oxygen (δ18O) 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 (approx. 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 (δ2H = −454 to +1702 ‰ and δ18O= −58.3 to +265 ‰). Measurements of human urine were precise to better than 0.65 ‰ 1σ for δ2H and 0.09 ‰ 1σ for δ18O for natural urines, 1.1 ‰ 1σ for δ2H and 0.13 ‰ 1σ for δ18O for low enriched urines, and 1.0 ‰ 1σ for δ2H and 0.08 ‰ 1σ for δ18O for high enriched urines. Furthermore, the accuracy of the isotope measurements of human urines was verified to better than ±0.81 ‰ in δ2H and ±0.13 ‰ in δ18O (average deviation) against three independent IRMS 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

  10. 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].

  11. 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.

  12. 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.

  13. Culture enrichment assists the diagnosis of cattle botulism by a monoclonal antibody based sandwich ELISA.

    PubMed

    Brooks, C E; Clarke, H J; Finlay, D A; McConnell, W; Graham, D A; Ball, H J

    2010-07-29

    Monoclonal antibodies (MAbs) obtained from a mouse immunised with Clostridium botulinum type D toxoid were developed into a sandwich ELISA (sELISA) format that was able to detect type D toxin and types C and D toxin complexes. The sELISA was examined for its potential to replace the mouse bioassay as an alternative in vitro assay for the diagnosis of cattle botulism. Its application directly to intestinal samples collected from suspect cattle botulism cases and prepared for testing for the standard mouse bioassay showed poor correlation and sensitivity with the mouse bioassay results. However, anaerobic pre-enrichment of the samples after heat treatment at 80 degrees C for 10 min to activate any residual C. botulinum spores greatly improved the sELISA detection rate of the toxin by increasing the sample toxin levels. All of the mouse bioassay positive cattle cases tested were detected by the sELISA from the heated and pre-enriched samples tested after 24h incubation. Toxin was detected by sELISA and subsequently confirmed by mouse bioassay in samples from an additional 3 cases that had been originally mouse bioassay negative. The results indicate that the application of this procedure for screening intestinal samples for C. botulinum strains that produce types C and D toxins from suspect cattle botulism cases would improve the diagnostic rate as well as significantly reduce the number of mice involved in diagnosis.

  14. Universal method for online enrichment of target compounds in capillary gas chromatography using in-oven cryotrapping.

    PubMed

    Chin, Sung-Tong; Maikhunthod, Bussayarat; Marriott, Philip J

    2011-09-01

    A method is described that permits automated online enrichment of injected compounds in multidimensional gas chromatography by using a microfluidic heart-cut (H-C) device to direct target compounds into a cryogenically cooled internal trap (cryotrap, CT). By performing multiple injections of a sample, selected compounds or regions of a primary column separation can be collected in the CT. Remobilizing the trapped species allows elution and further resolution on the second column. Using a well-balanced H-C device, compounds can be fully excluded from the collection step or quantitatively transferred to the CT. Peak areas of the remobilized compound correlate well with the number of sample injections. Trapping on various column phases shows the method is suited to quantitative trapping of alkanes of mass greater than about dodecane and fatty acid methyl esters greater than the C8 homologue. Caffeine and menthol standards of concentration 100 μg mL(-1) gave peak area correlation coefficients for 1-10 and 1-50 replicate split injections of 1 μL volume of 0.999 and 0.996, respectively. Peak height correlations were less favorable as a result of peak broadening on the second column, presumably due to overloading at greater collected mass. The method was applied to 0.2% solutions of peppermint oil (menthol; a major component; 44%) and 1.0% lavender oil (α-terpineol and neryl acetate; minor components of 1.05 and 0.42% abundance). The minor components gave good area and height correlations, and good recovery around 90% was observed for menthol compounds recovered from 15 accumulations. Response amplification was further demonstrated for menthol from mint oil headspace sampling using solid phase microextraction. This approach should be a valuable adjunct for improved detection specificity, for detectors of low sensitivity, and when prior sample concentration provides insufficient response of selected target analytes.

  15. Conversion and enrichment in the Soviet Union

    SciTech Connect

    1991-04-01

    In the Soviet Union, just as in the West, the civilian nuclear industry emerged from research work undertaken for nuclear weapons development. At first, researchers tried various techniques for physical separation of uranium isotopes: electromagnetic and molecular-kinetic thermo-diffusion methods; gaseous diffusion; and centrifuge methods. All of those methods, which are based primarily on differences in the atomic mass of uranium isotopes, called for extensive research and the development of new, technically unprecedented equipment. Gradually gaseous diffusion and gas centrifuge technology became recognized as most feasible for industrial use, so research on other methods was terminated. Industrial-scale uranium enrichment in the Soviet Union began in 1949 using the gaseous diffusion method; by the early 1960s, centrifuge technology was in use on an industrial scale. All Soviet production of highly-enriched, weapons-grade uranium was halted in 1987. The Soviet Union now has four enrichment plants in operation (at classified locations), solely for civilian nuclear power needs. All four enrichment plants have centrifuge modules, and enrichment provided by gaseous diffusion accounts for less than 5% of their total output. Two of the four enrichment plants also incorporate facilities for conversion to uranium hexafluoride (UF{sub 6}).

  16. 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.

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

    PubMed Central

    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 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 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 S-nitrosylation). This protocol serves as a general approach for enrichment of thiol-containing proteins or peptides derived from reversibly modified proteins. The approach utilizes 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 LC–MS/MS based quantitative site-specific analysis of cysteine-based reversible modifications. The overall approach requires a simpler workflow with increased specificity compared to the commonly used biotinylation-based assays. The procedure for selective enrichment and analyses of S-nitrosylation 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 approximately 3 days for sample processing with an additional day for LC-MS/MS and data analysis. PMID:24336471

  18. Effects of citrate-enriched bicarbonate based dialysate on anticoagulation and dialyzer reuse in maintenance hemodialysis patients.

    PubMed

    Rocha, Amanda D; Padua, Vanessa C; Oliveira, Esther; Guimaraes, Márcia M; Lugon, Jocemir R; Strogoff de Matos, Jorge P

    2014-04-01

    Systemic anticoagulation with unfractionated heparin is commonly used in maintenance hemodialysis (HD), but it increases the risk of bleeding complications. We investigated whether the use of citrate-enriched bicarbonate based dialysate (CD) would reduce systemic anticoagulation without compromising the efficacy of reprocessed dialyzers. This is a crossover study in which half of a total of 30 patients initially underwent HD with acetate-enriched bicarbonate based dialysate and a standard heparin dose of ∼ 100 IU/kg (Treatment A), whereas the remaining patients were treated with CD and a 30% reduced heparin dose (Treatment B). After 12 consecutive HD sessions in each treatment, the dialysate and heparin doses were reversed, then followed for another period of 12 HD sessions. The two treatment phases were split by a washout period of six HD sessions using acetate-enriched bicarbonate based dialysate and standard heparin dose. Systemic anticoagulation was higher in Treatment A. The activated partial thromboplastin time at the end of HD session was 68 ± 36 seconds in Treatment A and 47 ± 16 seconds in Treatment B (P = 0.005). Sixty-eight percent of the dialyzers remained adequate until the 12th use in Treatment A and 61% did so in Treatment B (P = 0.63). Patients had three and 24 cramps episodes during Treatment A and B, respectively (P < 0.001). Nine and 26 symptomatic intradialytic hypotension episodes were seen in Treatment A and B, respectively, (P = 0.003). In conclusion, the use of CD had a favorable effect on anticoagulation in the extracorporeal circuit in patients on maintenance HD, but it was also associated with more hypotension and cramps.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Project ENRICH.

    ERIC Educational Resources Information Center

    Gwaley, Elizabeth; And Others

    Project ENRICH was conceived in Beaver County, Pennsylvania, to: (1) identify preschool children with learning disabilities, and (2) to develop a program geared to the remediation of the learning disabilities within a school year, while allowing the child to be enrolled in a regular class situation for the following school year. Through…

  5. New method for GC/FID and GC-C-IRMS analysis of plasma free fatty acid concentration and isotopic enrichment.

    PubMed

    Kangani, Cyrous O; Kelley, David E; Delany, James P

    2008-09-15

    A simple, direct and accurate method for the determination of concentration and enrichment of free fatty acids (FFAs) in human plasma was developed. The validation and comparison to a conventional method are reported. Three amide derivatives, dimethyl, diethyl and pyrrolidide, were investigated in order to achieve optimal resolution of the individual fatty acids. This method involves the use of dimethylamine/Deoxo-Fluor to derivatize plasma free fatty acids to their dimethylamides. This derivatization method is very mild and efficient, and is selective only towards FFAs so that no separation from a total lipid extract is required. The direct method gave lower concentrations for palmitic acid and stearic acid and increased concentrations for oleic acid and linoleic acid in plasma as compared to methyl ester derivative after thin-layer chromatography. The [(13)C]palmitate isotope enrichment measured using direct method was significantly higher than that observed with the BF(3)/MeOH-TLC method. The present method provided accurate and precise measures of concentration as well as enrichment when analyzed with gas chromatography combustion-isotope ratio-mass spectrometry.

  6. 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.

  7. Development of functional milk desserts enriched with resistant starch based on consumers' perception.

    PubMed

    Ares, Florencia; Arrarte, Eloísa; De León, Tania; Ares, Gastón; Gámbaro, Adriana

    2012-10-01

    Sensory characteristics play a key role in determining consumers' acceptance of functional foods. In this context, the aim of the present work was to apply a combination of sensory and consumer methodologies to the development of chocolate milk desserts enriched with resistant starch. Chocolate milk desserts containing modified waxy maize starch were formulated with six different concentrations of two types of resistant starch (which are part of insoluble dietary fiber). The desserts were evaluated by trained assessors using Quantitative Descriptive Analysis. Moreover, consumers scored their overall liking and willingness to purchase and answered an open-ended question. Resistant starch caused significant changes in the sensory characteristics of the desserts and a significant decrease in consumers' overall liking and willingness to purchase. Consumer data was analyzed applying survival analysis on overall liking scores, considering the risk on consumers liking and willing to purchase the functional products less than their regular counterparts. The proposed methodologies proved to be useful to develop functional foods taking into account consumers' perception, which could increase their success in the market.

  8. Thermal reversibility of vitamin E-enriched emulsion-based delivery systems produced using spontaneous emulsification.

    PubMed

    Saberi, Amir Hossein; Fang, Yuan; McClements, David Julian

    2015-10-15

    The influence of temperature scanning and isothermal storage conditions on turbidity, particle size, and thermal reversibility of vitamin E-enriched emulsions produced by spontaneous emulsification was examined. Initially, the mini-emulsions formed were optically transparent and contained small droplets (d ≈ 44 nm). When heated (20-90 °C), emulsions exhibited a complex turbidity-temperature profile with a phase inversion temperature (PIT) at ≈ 75-80 °C. Temperature scanning rate had a major influence on emulsion thermal reversibility. Slow heating (0.5 °C/min) above the PIT followed by quench cooling (≈ 67 °C min(-1)) to 30 °C did not appreciably increase turbidity or droplet diameter (d ≈ 50 nm), suggesting these systems were thermo-reversible. However, slow heating to temperatures below the PIT followed by rapid cooling appreciably increased droplet size and turbidity (thermo-irreversible). Cooling rate also affected emulsion thermo-reversibility: the turbidity and droplet size after heating above the PIT decreased with increasing cooling rate.

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. Development of a novel stirrerliquid/solid microextraction method for the separation and enrichment of trace levels of active compounds in traditional Chinese medicine.

    PubMed

    Wang, Caiyun; Chen, Xuan; Hu, Shuang; Bai, Xiaohong

    2016-11-01

    A novel stirrer-liquid/solid microextraction method was developed for the separation and enrichment of trace levels of curcumin, bisdemethoxycurcumin, and demethoxycurcumin in Rhizoma Curcumae Longae, Radix Curcumae, and Rhizoma Curcumae before their analysis by high-performance liquid chromatography with ultraviolet detection. In the proposed approach, a magnetic stirrer was immersed in decanol to coat its surface completely with decanol, which was used as an extraction platform. The stirrer coated with decanol is not only a power to agitate the sample solution to constantly update the sample on the stirrer surface but also it can adsorb and extract the target analytes. Some effective parameters, including suitable superficial area of stirrer, extraction solvent, sample phase pH, NaCl concentration, stirring rate, extraction time, sample phase volume, were analyzed and selected. Under the optimal conditions, the linearities are 0.0044-2.20 μg/mL, detection limits are 0.3-0.6 ng/mL, and the extraction content per unit length and enrichment factors of the target analytes are 6.24-9.71/mm and 589-917, respectively. Also, the stirrer-liquid/solid microextraction mechanism for the extraction and enrichment of the target analytes was analyzed and expounded. The results showed that stirrer-liquid/solid microextraction is a simple, rapid sample pretreatment approach with a high enrichment factor.

  14. 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.

  15. 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…

  16. 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.

  17. 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.

  18. Growing Gifted Students in the Desert: Using Alternative, Community-Based Assessment and an Enriched Curriculum.

    ERIC Educational Resources Information Center

    Belcher, Rebecca Newcom; Fletcher-Carter, R.

    1999-01-01

    Describes a federally funded Javits project that involved two rural elementary schools with a primarily Hispanic population. The project was designed to develop an alternative community-based assessment procedure for identifying gifted minority students. Identified students were taught using a developed science curriculum that focused on problem…

  19. Improved data retrieval from TreeBASE via taxonomic and linguistic data enrichment

    PubMed Central

    Anwar, Nadia; Hunt, Ela

    2009-01-01

    Background TreeBASE, the only data repository for phylogenetic studies, is not being used effectively since it does not meet the taxonomic data retrieval requirements of the systematics community. We show, through an examination of the queries performed on TreeBASE, that data retrieval using taxon names is unsatisfactory. Results We report on a new wrapper supporting taxon queries on TreeBASE by utilising a Taxonomy and Classification Database (TCl-Db) we created. TCl-Db holds merged and consolidated taxonomic names from multiple data sources and can be used to translate hierarchical, vernacular and synonym queries into specific query terms in TreeBASE. The query expansion supported by TCl-Db shows very significant information retrieval quality improvement. The wrapper can be accessed at the URL The methodology we developed is scalable and can be applied to new data, as those become available in the future. Conclusion Significantly improved data retrieval quality is shown for all queries, and additional flexibility is achieved via user-driven taxonomy selection. PMID:19426482

  20. 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

  1. 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.

  2. An efficient and rapid method for enrichment of lipophilic proteins from Mycobacterium tuberculosis H37Rv for two-dimensional gel electrophoresis.

    PubMed

    Sharma, Divakar; Bisht, Deepa

    2016-05-01

    Lipophilic proteome profiling is crucial because they have an anticipated role in biological processes and pathogenesis of Mycobacterium tuberculosis. These lipophilic proteins might be used as potential targets for the development of newer diagnostic markers and drug targets due to their association with membranes and drugs. We developed an efficient and rapid method to enrich the lipophilic proteins extraction from M. tuberculosis H37Rv for 2DE. In the extraction of lipophilic proteins, nonionic detergent (Triton X-100) was added in sonication buffer that augmented the solubilization of the proteins at the time of sonication. Enriched whole cell lysate was subjected to direct phase separation using Triton X-114, without the need for preisolation of membranes. In this study, we report that our optimized extraction buffer increased the lipophilic proteins extraction and their improved resolution on 2D gel up to two- to threefolds (quantitatively and qualitatively) as compared to standard extraction buffer. Some proteins were identified by MALDI-TOF/MS.

  3. Coffee-ring effect-based simultaneous SERS substrate fabrication and analyte enrichment for trace analysis

    NASA Astrophysics Data System (ADS)

    Wang, Weidong; Yin, Yongguang; Tan, Zhiqiang; Liu, Jingfu

    2014-07-01

    Based on the ``coffee-ring effect'', we developed a highly efficient SERS platform which integrates the fabrication of SERS-active substrates and the preconcentration of analytes into one step. The high sensitivity, robustness, reproducibility and simplicity make this platform ideal for on-site analysis of small volume samples at low concentrations in complex matrices.Based on the ``coffee-ring effect'', we developed a highly efficient SERS platform which integrates the fabrication of SERS-active substrates and the preconcentration of analytes into one step. The high sensitivity, robustness, reproducibility and simplicity make this platform ideal for on-site analysis of small volume samples at low concentrations in complex matrices. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr03198a

  4. A pilot study applying the plant Anchored Hybrid Enrichment method to New World sages (Salvia subgenus Calosphace; Lamiaceae).

    PubMed

    Fragoso-Martínez, Itzi; Salazar, Gerardo A; Martínez-Gordillo, Martha; Magallón, Susana; Sánchez-Reyes, Luna; Moriarty Lemmon, Emily; Lemmon, Alan R; Sazatornil, Federico; Granados Mendoza, Carolina

    2017-02-09

    We conducted a pilot study using Anchored Hybrid Enrichment to resolve relationships among a mostly Neotropical sage lineage that may have undergone a recent evolutionary radiation. Conventional markers (ITS, trnL-trnF and trnH-psbA) have not been able to resolve the relationships among species nor within portions of the backbone of the lineage. We sampled 12 representative species of subgenus Calosphace and included one species of Salvia's s.l. closest relative, Lepechinia, as outgroup. Hybrid enrichment and sequencing were successful, yielding 448 alignments of individual loci with an average length of 704bp. The performance of the phylogenomic data in phylogenetic reconstruction was superior to that of conventional markers, increasing both support and resolution. Because the captured loci vary in the amount of net phylogenetic informativeness at different phylogenetic depths, these data are promising in phylogenetic reconstruction of this group and likely other lineages within Lamiales. However, special attention should be placed on the amount of phylogenetic noise that the data could potentially contain. A prior exploration step using phylogenetic informativeness profiles to detect loci with sites with disproportionately high substitution rates (showing "phantom" spikes) and, if required, the ensuing filtering of the problematic data is recommended. In our dataset, filtering resulted in increased support and resolution for the shallow nodes in maximum likelihood phylogenetic trees resulting from concatenated analyses of all the loci. Additionally, it is expected that an increase in sampling (loci and taxa) will aid in resolving weakly supported, short deep internal branches.

  5. 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.

  6. 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.

  7. Faith-Based Organizations and Veteran Reintegration: Enriching the Web of Support.

    PubMed

    Werber, Laura; Derose, Kathryn Pitkin; Rudnick, Mollie; Harrell, Margaret C; Naranjo, Diana

    2015-11-30

    Faith-based organizations (FBOs) are an important community-based resource for veterans as they readjust to civilian life. Through interviews with both national-level and smaller, local FBOs, the authors sought to understand better the current and potential roles for FBOs in veteran reintegration. Interviewees suggested that veterans may look to FBOs for support because they offer privacy and confidentiality, two features that may be especially critical when a potential stigma is involved. Some FBOs have also developed a reputation as safe places for veterans, providing supportive, judgment-free environments. FBOs not only help veterans with spiritual matters but address diverse areas of veteran health and wellness, including vocation, education, financial and legal stability, shelter, access to goods and services, mental health, access to health care, physical health, family, and social networks. In some cases, the support is offered to veterans directly; in other instances, the support is indirect, via training individuals to help veterans or educating the public about them. In the process of providing support, FBOs interact with varied organizations, including government entities, private nonprofits, and one another, for training, outreach, referrals, information exchange, obtaining donations, and collaboration. Yet challenges exist, including insufficient connections with chaplains working in different settings and others in the web of support, resource and capacity constraints, lack of awareness of experience with veterans, issues related to religious philosophy or orientation, and characteristics of veterans themselves. To move forward, the authors offer recommendations for policymakers, organizations that interact with FBOs, and FBOs themselves to help FBOs engage fully in the web of reintegration support.

  8. 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

  9. 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

  10. 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

  11. Status of gadolinium enrichment technology at LLNL

    SciTech Connect

    Haynam, C.; Comaskey, B.; Conway, J.; Eggert, J.; Glaser, J.; Ng, E.; Paisner, J.; Solarz, R.; Worden, E.

    1993-01-01

    A method based on,polarization selectivity and three step laser photoionization is presented for separation of the odd isotopes of gadolinium. Measurements of the spectroscopic parameters needed to quantify the excitation pathway are discussed. Model results are presented for the efficiency of photoionization. The vapor properties of electron beam vaporized gadolinium are presented which show dramatic cooling during the expansion of the hot dense vapor into a vacuum. This results in a significant increase in the efficiency of conversion of natural feed into enriched product in the AVLIS process. Production of enriched gadolinium for use in commercial power reactors appears to be economically viable using technology in use at LLNL.

  12. 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.

  13. Comparison of direct and enrichment methods for the selective isolation of vancomycin-resistant enterococci from feces of pigs and poultry.

    PubMed

    Butaye, P; Devriese, L A; Haesebrouck, F

    1999-01-01

    Isolation results of vancomycin-resistant enterococci (VRE) of fecal samples from pigs and broiler and layer chickens obtained with two vancomycin-supplemented enrichment media, kanamycin aesculin azide (KAA) broth and Enterococcosel (ECC) broth, and three isolation media, KAA agar, ECC agar, and Slanetz and Bartley (SL) agar, were compared. Direct isolation on vancomycin-containing agar plates was not efficient in swine and layer chickens, which had only low numbers of VRE. In broilers chickens, the VRE content of the samples was high, and SL as well as ECC were found to perform better than KAA agar. The same three agar media were used as selective plating media after 1 and 2 days incubation of the samples in KAA and ECC enrichment broths. Sensitivities of the 12 different enrichment-plate combinations tested ranged from 0 to 81% in layer chickens and from 5 to 44% in samples from pigs. In the high prevalence type of samples from broilers, sensitivities still varied substantially from 52 to 78%. Incubating vancomycin-containing enrichment broths for 2 days compared with 1 day was favorable for the isolation of vancomycin-resistant Enterococcus faecalis, E. gallinarum, and E. casseliflavus but not for E. faecium and E. hirae/E. durans. ECC broth and ECC plates yielded the highest number of E. gallinarum and E. casseliflavus. In layer as well as in broiler chickens, ECC broth incubated for 2 days and plated on ECC agar was the most sensitive method. In pigs, however, KAA broth incubated for 2 days and plated on ECC medium yielded the highest number of VRE.

  14. A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae1

    PubMed Central

    Mandel, Jennifer R.; Dikow, Rebecca B.; Funk, Vicki A.; Masalia, Rishi R.; Staton, S. Evan; Kozik, Alex; Michelmore, Richard W.; Rieseberg, Loren H.; Burke, John M.

    2014-01-01

    • Premise of the study: The Compositae (Asteraceae) are a large and diverse family of plants, and the most comprehensive phylogeny to date is a meta-tree based on 10 chloroplast loci that has several major unresolved nodes. We describe the development of an approach that enables the rapid sequencing of large numbers of orthologous nuclear loci to facilitate efficient phylogenomic analyses. • Methods and Results: We designed a set of sequence capture probes that target conserved orthologous sequences in the Compositae. We also developed a bioinformatic and phylogenetic workflow for processing and analyzing the resulting data. Application of our approach to 15 species from across the Compositae resulted in the production of phylogenetically informative sequence data from 763 loci and the successful reconstruction of known phylogenetic relationships across the family. • Conclusions: These methods should be of great use to members of the broader Compositae community, and the general approach should also be of use to researchers studying other families. PMID:25202605

  15. Integrated and Contextual Basic Science Instruction in Preclinical Education: Problem-Based Learning Experience Enriched with Brain/Mind Learning Principles

    ERIC Educational Resources Information Center

    Gülpinar, Mehmet Ali; Isoglu-Alkaç, Ümmühan; Yegen, Berrak Çaglayan

    2015-01-01

    Recently, integrated and contextual learning models such as problem-based learning (PBL) and brain/mind learning (BML) have become prominent. The present study aimed to develop and evaluate a PBL program enriched with BML principles. In this study, participants were 295 first-year medical students. The study used both quantitative and qualitative…

  16. 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…

  17. 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…

  18. Vitamin A Activity of Rice-based Weaning Foods Enriched with Germinated Cowpea Flour, Banana, Pumpkin and Milk Powder.

    PubMed

    Hashim, N; Pongjata, J

    2000-03-01

    The objective of this study was to identify the effect of different drying methods on vitamin A activity of formulated weaning food. Weaned foods on vitamin A activity of formulated using treated cowpea flour, locally available rice flour, banana-pumpkin, skim milk powder and sugar in the ratio 35:35:15:15:5. Treated cowpea flour consisted of original cowpea flour, 24 h germinated cowpea flour. Each treated flour was mixed separately with the other ingredients and cooked into a slurry. Each mixture was either oven-dried or freeze-dried to produce a dry flaky mixture. The carotenoid composition of the product was determined by HPLC. Vitamin A activity of oven-dried weaning food was significantly reduced (p<0.05) compared to freeze-dried weaning food. The freeze-dried weaning foods showed a higher retinol equivalent than oven-dried weaning foods for all treatments. The results of the study found that an intake of 100 g of freeze-dried weaning foods enriched with banana-pumpkin and cowpea flour provided an adequate amount of the recommended daily allowance (RDA) of vitamin A for infants.

  19. On-plate glycoproteins/glycopeptides selective enrichment and purification based on surface pattern for direct MALDI MS analysis.

    PubMed

    Zeng, Zhoufang; Wang, Yandong; Guo, Xinhua; Wang, Ling; Lu, Nan

    2013-05-21

    In this paper, a novel method has been proposed to achieve selective enrichment and purification of glycoproteins/glycopeptides on a surface patterned sample support, which consists of a hydrophobic outer layer (F-SAM) and an internal boronic acid-modified gold microspot (900 μm). Upon deposition, the sample solution is firstly concentrated in a small area by repulsion of the hydrophobic outer layer, and then the glycoproteins/glycopeptides are selectively captured through boronic acid covalently binding in the inner layer. However, the non-glycosylated proteins/peptides or high concentration salts are removed after rinsing with alkaline solution. As a result, the detection sensitivity is improved by an order of magnitude greater than when using a stainless steel MALDI plate. With surface patterned sample support, the glycoproteins/glycopeptides can be detected even under interference from the excessive existing non-glycosylated proteins/peptides (10 times more than glycoproteins/glycopeptides). Simultaneously, high-quality mass spectra can be obtained even in the presence of urea (1 M), NaCl (1 M), or NH4HCO3 (200 mM). Therefore, this novel technique may be applied to high-throughput analysis of low-abundance glycoproteins/glycopeptides in complicated proteome research.

  20. Base-compositional biases and the bat problem. II. DNA-hybridization trees based on AT- and GC-enriched tracers.

    PubMed Central

    Kirsch, J A; Pettigrew, J D

    1998-01-01

    We conducted a series of parallel DNA-hybridization experiments on a small group of bats (species of Pteropus, Rhinolophus, Noctilio and Pteronotus) and outgroups (Lemur, Cynocephalus, Didelphis), using whole-genome labels and tracers made from extracts enriched with AT and two levels of GC content. FITCH (additive phylogenetic trees) topologies were constructed from the four sets of comparisons, indexed as both delta Tmode and delta NPHs (normalized percentage of hybridization). Based on our previous work showing that the shared AT bias of pteropodids and some microchiropterans may affect the rank-ordering of taxa based on either AT- or GC-rich labels, our expectation was that the resulting trees would show differing topologies when generated from tracers made with the variously enriched DNA extracts. Whereas there was some variation among the trees, most of them grouped the bats together, and almost all paired the representative megachiropteran and rhinolophoid microchiropteran as sister-taxa in contrast to the other microchiropterans. As the pteropodid-rhinolophoid relationship is an unexpected and unlikely one, we attribute this association to an AT bias that was not obviated even by our most GC-rich labels, and suggest that such a bias may compromise the truth of some molecular trees. Accordingly, we believe the broader issue of bat monophyly remains unresolved by DNA-hybridization and probably also by gene-sequencing studies. PMID:9569431

  1. 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.

  2. 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

  3. A Novel Method for the Simultaneous Enrichment, Identification, and Quantification of Phosphopeptides and Sialylated Glycopeptides Applied to a Temporal Profile of Mouse Brain Development*

    PubMed Central

    Palmisano, Giuseppe; Parker, Benjamin L.; Engholm-Keller, Kasper; Lendal, Sara Eun; Kulej, Katarzyna; Schulz, Melanie; Schwämmle, Veit; Graham, Mark E.; Saxtorph, Henrik; Cordwell, Stuart J.; Larsen, Martin R.

    2012-01-01

    We describe a method that combines an optimized titanium dioxide protocol and hydrophilic interaction liquid chromatography to simultaneously enrich, identify and quantify phosphopeptides and formerly N-linked sialylated glycopeptides to monitor changes associated with cell signaling during mouse brain development. We initially applied the method to enriched membrane fractions from HeLa cells, which allowed the identification of 4468 unique phosphopeptides and 1809 formerly N-linked sialylated glycopeptides. We subsequently combined the method with isobaric tagging for relative quantification to compare changes in phosphopeptide and formerly N-linked sialylated glycopeptide abundance in the developing mouse brain. A total of 7682 unique phosphopeptide sequences and 3246 unique formerly sialylated glycopeptides were identified. Moreover 669 phosphopeptides and 300 formerly N-sialylated glycopeptides differentially regulated during mouse brain development were detected. This strategy allowed us to reveal extensive changes in post-translational modifications from postnatal mice from day 0 until maturity at day 80. The results of this study confirm the role of sialylation in organ development and provide the first extensive global view of dynamic changes between N-linked sialylation and phosphorylation. PMID:22843994

  4. A novel method for the simultaneous enrichment, identification, and quantification of phosphopeptides and sialylated glycopeptides applied to a temporal profile of mouse brain development.

    PubMed

    Palmisano, Giuseppe; Parker, Benjamin L; Engholm-Keller, Kasper; Lendal, Sara Eun; Kulej, Katarzyna; Schulz, Melanie; Schwämmle, Veit; Graham, Mark E; Saxtorph, Henrik; Cordwell, Stuart J; Larsen, Martin R

    2012-11-01

    We describe a method that combines an optimized titanium dioxide protocol and hydrophilic interaction liquid chromatography to simultaneously enrich, identify and quantify phosphopeptides and formerly N-linked sialylated glycopeptides to monitor changes associated with cell signaling during mouse brain development. We initially applied the method to enriched membrane fractions from HeLa cells, which allowed the identification of 4468 unique phosphopeptides and 1809 formerly N-linked sialylated glycopeptides. We subsequently combined the method with isobaric tagging for relative quantification to compare changes in phosphopeptide and formerly N-linked sialylated glycopeptide abundance in the developing mouse brain. A total of 7682 unique phosphopeptide sequences and 3246 unique formerly sialylated glycopeptides were identified. Moreover 669 phosphopeptides and 300 formerly N-sialylated glycopeptides differentially regulated during mouse brain development were detected. This strategy allowed us to reveal extensive changes in post-translational modifications from postnatal mice from day 0 until maturity at day 80. The results of this study confirm the role of sialylation in organ development and provide the first extensive global view of dynamic changes between N-linked sialylation and phosphorylation.

  5. Oil-enriched, ultra-small nanostructured lipid carriers (usNLC): a novel delivery system based on flip-flop structure.

    PubMed

    Keck, Cornelia M; Baisaeng, Nuttakorn; Durand, Philippe; Prost, Michel; Meinke, Martina C; Müller, Rainer H

    2014-12-30

    For the development of ultra-small NLC (usNLC) the determination of the required HLB (hydrophilic lipophilic balance) was found to be a suitable method, i.e., usNLC with a size below 50 nm were obtained by this method. Loading with 5% (w/w) coenzyme Q10 (Q10) led to usNLC with a size of about 85 nm. In comparison to classical NLC with a size of 230 nm and a nanoemulsion with similar size, the Q10 loaded usNLC show a higher release, a higher antioxidant capacity, and a better skin penetration for Q10. The reason for this is a flip-flop core-shell structure of the lipid matrix, i.e., the oil with dissolved active is surrounding the solid lipid based core. As the flip-flop structure was probably achieved by admixing high contents of liquid lipid, oil enriched usNLC might represent a novel and promising carrier system for the improved delivery of lipophilic actives.

  6. 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

    2011-11-07

    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.

  7. Ru-TsDPEN with formic acid/Hunig's base for asymmetric transfer hydrogenation, a practical synthesis of optically enriched N-propyl pantolactam.

    PubMed

    Zhang, Ji; Blazecka, Peter G; Bruendl, Michelle M; Huang, Yun

    2009-02-06

    The Noyori-Ikariya catalysts, Ru-TsDPEN 1 or 2, in combination with HCOOH/Hunig's base (5:2) have been successfully utilized for catalytic asymmetric transfer hydrogenation of alpha-ketopantolactam, and optically enriched N-substituted pantolactam was prepared (S/C = 500, up to 95% ee and 99% conversion in HCOOH/Hunig's base condition). More than 2 kg of this key intermediate 9 has been synthesized efficiently with excellent chemical yield and chiral purity.

  8. IgM-Enriched Human Intravenous Immunoglobulin-Based Treatment of Patients With Early Donor Specific Anti-HLA Antibodies After Lung Transplantation

    PubMed Central

    Ius, Fabio; Sommer, Wiebke; Kieneke, Daniela; Tudorache, Igor; Kühn, Christian; Avsar, Murat; Siemeni, Thierry; Salman, Jawad; Erdfelder, Carolin; Verboom, Murielle; Kielstein, Jan; Tecklenburg, Andreas; Greer, Mark; Hallensleben, Michael; Blasczyk, Rainer; Schwerk, Nicolaus; Gottlieb, Jens; Welte, Tobias; Haverich, Axel; Warnecke, Gregor

    2016-01-01

    Background At our institution, until April 2013, patients who showed early donor specific anti-HLA antibodies (DSA) after lung transplantation were preemptively treated with therapeutic plasma exchange (tPE) and a single dose of Rituximab. In April 2013, we moved to a therapy based on IgM-enriched human immunoglobulins (IVIG), repeated every 4 weeks, and a single dose of Rituximab. Methods This observational study was designed to evaluate the short-term patient and graft survival in patients who underwent IVIG-based DSA treatment (group A, n = 57) versus contemporary patients transplanted between April 2013 and January 2015 without DSA (group C, n = 180), as well as to evaluate DSA clearance in IVIG-treated patients versus historic patients who had undergone tPE-based treatment (group B, n = 56). Patient records were retrospectively reviewed. Follow-up ended on April 1, 2015. Results At 6 months and 1 year of follow-up, group A had a survival similar to group C (P = 0.81) but better than group B (P = 0.008). Group A showed statistically nonsignificant trends toward improved freedom from pulsed-steroid therapy and biopsy-confirmed rejection over groups B and C. The DSA clearance was better in group A than group B at treatment end (92% vs 64%; P = 0.002) and last DSA control (90% vs 75%; P = 0.04). Conclusions Patients with new early DSA but without graft dysfunction that are treated with IVIG and Rituximab have similarly good early survival as contemporary lung transplant recipients without early DSA. The IVIG yielded increased DSA clearance compared with historic tPE-based treatment, yet spontaneous clearance of new DSA also remains common. PMID:26714123

  9. 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.

  10. 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…

  11. 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

    2015-07-02

    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.

  12. 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

    2015-04-02

    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.

  13. 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…

  14. An alum-based water treatment residual can reduce extractable phosphorus concentrations in three phosphorus-enriched coastal plain soils.

    PubMed

    Novak, J M; Watts, D W

    2005-01-01

    The accumulation of excess soil phosphorus (P) in watersheds under intensive animal production has been linked to increases in dissolved P concentrations in rivers and streams draining these watersheds. Reductions in water dissolved P concentrations through very strong P sorption reactions may be obtainable after land application of alum-based drinking water treatment residuals (WTRs). Our objectives were to (i) evaluate the ability of an alum-based WTR to reduce Mehlich-3 phosphorus (M3P) and water-soluble phosphorus (WSP) concentrations in three P-enriched Coastal Plain soils, (ii) estimate WTR application rates necessary to lower soil M3P levels to a target 150 mg kg(-1) soil M3P concentration threshold level, and (iii) determine the effects on soil pH and electrical conductivity (EC). Three soils containing elevated M3P (145-371 mg kg(-1)) and WSP (12.3-23.5 mg kg(-1)) concentrations were laboratory incubated with between 0 and 6% WTR (w w(-1)) for 84 d. Incorporation of WTR into the three soils caused a near linear and significant reduction in soil M3P and WSP concentrations. In two soils, 6% WTR application caused a soil M3P concentration decrease to below the soil P threshold level. An additional incubation on the third soil using higher WTR to soil treatments (10-15%) was required to reduce the mean soil M3P concentration to 178 mg kg(-1). After incubation, most treatments had less than a half pH unit decline and a slight increase in soil EC values suggesting a minimal impact on soil quality properties. The results showed that WTR incorporation into soils with high P concentrations caused larger relative reductions in extractable WSP than M3P concentrations. The larger relative reductions in the extractable WSP fraction suggest that WTR can be more effective at reducing potential runoff P losses than usage as an amendment to lower M3P concentrations.

  15. 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.

  16. 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.

  17. 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.

  18. 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

    2013-08-07

    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

  19. 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.

  20. Research on BOM based composable modeling method

    NASA Astrophysics Data System (ADS)

    Zhang, Mingxin; He, Qiang; Gong, Jianxing

    2013-03-01

    Composable modeling method has been a research hotpot in the area of Modeling and Simulation for a long time. In order to increase the reuse and interoperability of BOM based model, this paper put forward a composable modeling method based on BOM, studied on the basic theory of composable modeling method based on BOM, designed a general structure of the coupled model based on BOM, and traversed the structure of atomic and coupled model based on BOM. At last, the paper introduced the process of BOM based composable modeling and made a conclusion on composable modeling method based on BOM. From the prototype we developed and accumulative model stocks, we found this method could increase the reuse and interoperability of models.

  1. MTTE: an innovative strategy for the evaluation of targeted/exome enrichment efficiency

    PubMed Central

    Klonowska, Katarzyna; Handschuh, Luiza; Swiercz, Aleksandra; Figlerowicz, Marek; Kozlowski, Piotr

    2016-01-01

    Although currently available strategies for the preparation of exome-enriched libraries are well established, a final validation of the libraries in terms of exome enrichment efficiency prior to the sequencing step is of considerable importance. Here, we present a strategy for the evaluation of exome enrichment, i.e., the Multipoint Test for Targeted-enrichment Efficiency (MTTE), PCR-based approach utilizing multiplex ligation-dependent probe amplification with capillary electrophoresis separation. We used MTTE for the analysis of subsequent steps of the Illumina TruSeq Exome Enrichment procedure. The calculated values of enrichment-associated parameters (i.e., relative enrichment, relative clearance, overall clearance, and fold enrichment) and the comparison of MTTE results with the actual enrichment revealed the high reliability of our assay. Additionally, the MTTE assay enabled the determination of the sequence-associated features that may confer bias in the enrichment of different targets. Importantly, the MTTE is low cost method that can be easily adapted to the region of interest important for a particular project. Thus, the MTTE strategy is attractive for post-capture validation in a variety of targeted/exome enrichment NGS projects. PMID:27572310

  2. High-Affinity DNA Aptamer Generation Targeting von Willebrand Factor A1-Domain by Genetic Alphabet Expansion for Systematic Evolution of Ligands by Exponential Enrichment Using Two Types of Libraries Composed of Five Different Bases.

    PubMed

    Matsunaga, Ken-Ichiro; Kimoto, Michiko; Hirao, Ichiro

    2017-01-11

    The novel evolutionary engineering method ExSELEX (genetic alphabet expansion for systematic evolution of ligands by exponential enrichment) provides high-affinity DNA aptamers that specifically bind to target molecules, by introducing an artificial hydrophobic base analogue as a fifth component into DNA aptamers. Here, we present a newer version of ExSELEX, using a library with completely randomized sequences consisting of five components: four natural bases and one unnatural hydrophobic base, 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds). In contrast to the limited number of Ds-containing sequence combinations in our previous library, the increased complexity of the new randomized library could improve the success rates of high-affinity aptamer generation. To this end, we developed a sequencing method for each clone in the enriched library after several rounds of selection. Using the improved library, we generated a Ds-containing DNA aptamer targeting von Willebrand factor A1-domain (vWF) with significantly higher affinity (KD = 75 pM), relative to those generated by the initial version of ExSELEX, as well as that of the known DNA aptamer consisting of only the natural bases. In addition, the Ds-containing DNA aptamer was stabilized by introducing a mini-hairpin DNA resistant to nucleases, without any loss of affinity (KD = 61 pM). This new version is expected to consistently produce high-affinity DNA aptamers.

  3. Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

    PubMed Central

    Thomsen, Martin Christen Frølund; Nielsen, Morten

    2012-01-01

    Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active sites, etc. in biological sequences. Accurate generation of sequence logos is often compromised by sequence redundancy and low number of observations. Moreover, most methods available for sequence logo generation focus on displaying the position-specific enrichment of amino acids, discarding the equally valuable information related to amino acid depletion. Seq2logo aims at resolving these issues allowing the user to include sequence weighting to correct for data redundancy, pseudo counts to correct for low number of observations and different logotype representations each capturing different aspects related to amino acid enrichment and depletion. Besides allowing input in the format of peptides and MSA, Seq2Logo accepts input as Blast sequence profiles, providing easy access for non-expert end-users to characterize and identify functionally conserved/variable amino acids in any given protein of interest. The output from the server is a sequence logo and a PSSM. Seq2Logo is available at http://www.cbs.dtu.dk/biotools/Seq2Logo (14 May 2012, date last accessed). PMID:22638583

  4. Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion.

    PubMed

    Thomsen, Martin Christen Frølund; Nielsen, Morten

    2012-07-01

    Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active sites, etc. in biological sequences. Accurate generation of sequence logos is often compromised by sequence redundancy and low number of observations. Moreover, most methods available for sequence logo generation focus on displaying the position-specific enrichment of amino acids, discarding the equally valuable information related to amino acid depletion. Seq2logo aims at resolving these issues allowing the user to include sequence weighting to correct for data redundancy, pseudo counts to correct for low number of observations and different logotype representations each capturing different aspects related to amino acid enrichment and depletion. Besides allowing input in the format of peptides and MSA, Seq2Logo accepts input as Blast sequence profiles, providing easy access for non-expert end-users to characterize and identify functionally conserved/variable amino acids in any given protein of interest. The output from the server is a sequence logo and a PSSM. Seq2Logo is available at http://www.cbs.dtu.dk/biotools/Seq2Logo (14 May 2012, date last accessed).

  5. An enrichment technique for auxotrophs of Agrobacterium tumefaciens using a combination of carbenicillin and lysozyme.

    PubMed

    Klapwijk, P M; de Jonge, A J; Schilperoort, R A; Rörsch, A

    1975-11-01

    A procedure to enrich for auxotrophic and fermentation mutants of Agrobacterium tumefaciens is described. The method is based on the amplification of the killing power of carbenicillin by the addition of lysozyme. Isolation frequencies of some types of mutants are presented, with and without the application of the proposed procedure. The yield of mutants is usually enhanced a hundredfold per enrichment treatment.

  6. Method of recovering oil-based fluid

    SciTech Connect

    Brinkley, H.E.

    1993-07-13

    A method is described of recovering oil-based fluid, said method comprising the steps of: applying an oil-based fluid absorbent cloth of man-made fiber to an oil-based fluid, the cloth having at least a portion thereof that is napped so as to raise ends and loops of the man-made fibers and define voids; and absorbing the oil-based fluid into the napped portion of the cloth.

  7. 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

  8. The Melt-Dilute Treatment of Al-Base Highly Enriched DOE Spent Nuclear Fuels: Principles and Practices

    SciTech Connect

    Adams, T.M.

    1998-11-25

    The melt-dilute treatment technology program is focused on the development and implementation of a treatment technology for diluting highly enriched (>20 percent 235U) aluminum spent nuclear fuel to low enriched levels (<20 percent 235U) and qualifying the LEU Al-SNF form for geologic repository storage. In order to reduce the enrichment of these assemblies prior to ultimate geologic repository disposal, the melt-dilute technology proposes to melt these SNF assemblies and then dilute with additions of depleted uranium. The benefits accrued from this treatment process include the potential for significant volume reduction, reduced criticality potential, and the potential for enhanced SNF form characteristics. The emphasis within the development program to date has been on determining the process metallurgy and off-gas system design for the treatment of all types of Al SNF (UAlx, Al-U3O8, and Al-U3Si2). In determining the process metallurgy a wide range of alloys, representative of those expected in the Al-SNF form, have been fabricated and their product characteristics, namely microstructure, homogeneity, phase composition, and "ternary" constituent effects have been analyzed. As a result of the presence of species within the melt which will possess significant vapor pressures in the desired operating temperature range an off-gas system is necessary. Of the volitile species the one of greatest concern is 137Cs.

  9. Identification of Crosslinked Peptides after Click-based Enrichment Using Sequential CID and ETD Tandem Mass Spectrometry

    PubMed Central

    Chowdhury, Saiful M.; Du, Xiuxia; Tolić, Nikola; Wu, Si; Moore, Ronald J.; Mayer, M. Uljana; Smith, Richard D.; Adkins, Joshua N.

    2010-01-01

    Chemical crosslinking combined with mass spectrometry can be a powerful approach for the identification of protein-protein interactions and for providing constraints on protein structures. However, enrichment of crosslinked peptides is crucial to reduce sample complexity before mass spectrometric analysis. In addition compact crosslinkers are often preferred to provide short spacer lengths, surface accessibility to the protein complexes, and must have reasonable solubility under condition where the native complex structure is stable. In this study, we present a novel compact crosslinker that contains two distinct features: 1) an alkyne tag and 2) a small molecule detection tag (NO2-) to maintain reasonable solubility in water. The alkyne tag enables enrichment of the crosslinked peptide after proteolytic cleavage after coupling of an affinity tag using alkyne-azido click chemistry. Neutral loss of the small NO2- moiety provides a secondary means of detecting crosslinked peptides in MS/MS analyses, providing additional confidence in peptide identifications. We show the labeling efficiency of this crosslinker, which we termed CLIP (Click-enabled Linker for Interacting Proteins) using ubiquitin. The enrichment capability of CLIP is demonstrated for crosslinked ubiquitin in highly complex E. coli cell lysates. Sequential CID-MS/MS and ETD-MS/MS of inter-crosslinked peptides (two peptides connected with a crosslinker) are also demonstrated for improved automated identification of crosslinked peptides. PMID:19496583

  10. The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus

    PubMed Central

    Shafagati, Nazly; Narayanan, Aarthi; Baer, Alan; Fite, Katherine; Pinkham, Chelsea; Bailey, Charles; Kashanchi, Fatah; Lepene, Benjamin; Kehn-Hall, Kylene

    2013-01-01

    Background Rift Valley Fever Virus (RVFV) is a zoonotic virus that is not only an emerging pathogen but is also considered a biodefense pathogen due to the threat it may cause to public health and national security. The current state of diagnosis has led to misdiagnosis early on in infection. Here we describe the use of a novel sample preparation technology, NanoTrap particles, to enhance the detection of RVFV. Previous studies demonstrated that NanoTrap particles lead to both 100 percent capture of protein analytes as well as an improvement of more than 100-fold in sensitivity compared to existing methods. Here we extend these findings by demonstrating the capture and enrichment of viruses. Results Screening of NanoTrap particles indicated that one particle, NT53, was the most efficient at RVFV capture as demonstrated by both qRT-PCR and plaque assays. Importantly, NT53 capture of RVFV resulted in greater than 100-fold enrichment from low viral titers when other diagnostics assays may produce false negatives. NT53 was also capable of capturing and enhancing RVFV detection from serum samples. RVFV that was inactivated through either detergent or heat treatment was still found bound to NT53, indicating the ability to use NanoTrap particles for viral capture prior to transport to a BSL-2 environment. Furthermore, both NP-40-lysed virus and purified RVFV RNA were bound by NT53. Importantly, NT53 protected viral RNA from RNase A degradation, which was not observed with other commercially available beads. Incubation of RVFV samples with NT53 also resulted in increased viral stability as demonstrated through preservation of infectivity at elevated temperatures. Finally, NanoTrap particles were capable of capturing VEEV and HIV, demonstrating the broad applicability of NanoTrap particles for viral diagnostics. Conclusion This study demonstrates NanoTrap particles are capable of capturing, enriching, and protecting RVFV virions. Furthermore, the use of NanoTrap particles

  11. Identification of Cross-Linked Peptides after Click-Based Enrichment Using Sequential Collision-Induced Dissociation and Electron Transfer Dissociation Tandem Mass Spectrometry

    SciTech Connect

    Chowdhury, Saiful M.; Du, Xiuxia; Tolic, Nikola; Wu, Si; Moore, Ronald J.; Mayer, M. Uljana; Smith, Richard D.; Adkins, Joshua N.

    2009-07-01

    Chemical cross-linking combined with mass spectrometric analysis is emerging as a powerful technique for protein-protein interaction and protein structure elucidation studies.1 Cross-linkers covalently link two interacting proteins, often with chemistries specific to certain amino acid side chains. After enzymatic digestion of the proteins, the resulting cross-linked peptides can be subjected to analysis by LC-MS(/MS) to identify cross-linked species.2,3 For studying protein interactions using chemical cross-linking towards global discovery-based applications, the critical needs are the development of cross-linkers that are highly specific, amenable to LC-MS/MS, and resulting spectra are interpretable by bioinformatics tools to automatically assign cross-linked peptides with high confidence.4-10 As recently mentioned by Aebersold and co-workers, due to the low relative abundances of cross-linking products compared to their unmodified counterparts, enrichment of cross-linked species is also highly desirable to improve the likelihood of unambiguous identification of cross-linked peptides.6 Most of the currently available enrichable cross-linkers are bulky and are not amenable to studying protein-protein interactions in vivo. To discover protein-protein interactions with high confidence, there is a need for chemical cross-linkers that can effectively label protein complexes, utilize mass spectrometry based bottom-up proteomics analysis pipelines and also contains enrichment functionality.

  12. A novel technology for the detection, enrichment, and separation of trace amounts of target DNA based on amino-modified fluorescent magnetic composite nanoparticles.

    PubMed

    Wang, Guannan; Su, Xingguang

    2010-06-01

    A novel, highly sensitive technology for the detection, enrichment, and separation of trace amounts of target DNA was developed on the basis of amino-modified fluorescent magnetic composite nanoparticles (AFMN). In this study, the positively charged amino-modified composite nanoparticles conjugate with the negatively charged capture DNA through electrostatic binding. The optimal combination of AFMN and capture DNA was measured by dynamic light scattering (DLS) and UV-vis absorption spectroscopy. The highly sensitive detection of trace amounts of target DNA was achieved through enrichment by means of AFMN. The detection limit for target DNA is 0.4 pM, which could be further improved by using a more powerful magnet. Because of their different melting temperatures, single-base mismatched target DNA could be separated from perfectly complementary target DNA. In addition, the photoluminescence (PL) signals of perfectly complementary target DNA and single-base mismatched DNA as well as the hybridization kinetics of different concentrations of target DNA at different reaction times have also been studied. Most importantly, the detection, enrichment, and separation ability of AFMN was further verified with milk. Simple and satisfactory results were obtained, which show the great potential in the fields of mutation identification and clinical diagnosis.

  13. 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.

  14. Heart cells with regenerative potential from pediatric patients with end stage heart failure: a translatable method to enrich and propagate.

    PubMed

    Steele, Ann; Boucek, Robert J; Jacobs, Jeffrey Phillip; Steele, Peter; Asante-Korang, Alfred; Chamizo, Wilfredo; Steele, Jasmine; Chai, Paul J; Quintessenza, James A

    2012-01-01

    Background. Human cardiac-derived progenitor cells (hCPCs) have shown promise in treating heart failure (HF) in adults. The purpose of this study was to describe derivation of hCPCs from pediatric patients with end-stage HF. Methods. At surgery, discarded right atrial tissues (hAA) were obtained from HF patients (n = 25; hAA-CHF). Minced tissues were suspended in complete (serum-containing) DMEM. Cells were selected for their tissue migration and expression of stem cell factor receptor (hc-kit). Characterization of hc-kit(positive) cells included immunohistochemical screening with a panel of monoclonal antibodies. Results. Cells, including phase-bright cells identified as hc-kit(positive), spontaneously emigrated from hAA-CHF in suspended explant cultures (SEC) after Day 7. When cocultured with tissue, emigrated hc-kit(positive) cells proliferated, first as loosely attached clones and later as multicellular clusters. At Day 21~5% of cells were hc-kit(positive). Between Days 14 and 28 hc-kit(positive) cells exhibited mesodermal commitment (GATA-4(positive) and NKX2.5(positive)); then after Day 28 cardiac lineages (flk-1(positive), smooth muscle actin(positive), troponin-I(positive), and myosin light chain(positive)). Conclusions. C-kit(positive) hCPCs can be derived from atrial tissue of pediatric patients with end-stage HF. SEC is a novel culture method for derivation of migratory hc-kit(positive) cells that favors clinical translation by reducing the need for exogenously added factors to expand hCPCs in vitro.

  15. Heart Cells with Regenerative Potential from Pediatric Patients with End Stage Heart Failure: A Translatable Method to Enrich and Propagate

    PubMed Central

    Steele, Ann; Boucek, Robert J.; Jacobs, Jeffrey Phillip; Steele, Peter; Asante-Korang, Alfred; Chamizo, Wilfredo; Steele, Jasmine; Chai, Paul J.; Quintessenza, James A.

    2012-01-01

    Background. Human cardiac-derived progenitor cells (hCPCs) have shown promise in treating heart failure (HF) in adults. The purpose of this study was to describe derivation of hCPCs from pediatric patients with end-stage HF. Methods. At surgery, discarded right atrial tissues (hAA) were obtained from HF patients (n = 25; hAA-CHF). Minced tissues were suspended in complete (serum-containing) DMEM. Cells were selected for their tissue migration and expression of stem cell factor receptor (hc-kit). Characterization of hc-kitpositive cells included immunohistochemical screening with a panel of monoclonal antibodies. Results. Cells, including phase-bright cells identified as hc-kitpositive, spontaneously emigrated from hAA-CHF in suspended explant cultures (SEC) after Day 7. When cocultured with tissue, emigrated hc-kitpositive cells proliferated, first as loosely attached clones and later as multicellular clusters. At Day 21~5% of cells were hc-kitpositive. Between Days 14 and 28 hc-kitpositive cells exhibited mesodermal commitment (GATA-4positive and NKX2.5positive); then after Day 28 cardiac lineages (flk-1positive, smooth muscle actinpositive, troponin-Ipositive, and myosin light chainpositive). Conclusions. C-kitpositive hCPCs can be derived from atrial tissue of pediatric patients with end-stage HF. SEC is a novel culture method for derivation of migratory hc-kitpositive cells that favors clinical translation by reducing the need for exogenously added factors to expand hCPCs in vitro. PMID:22936950

  16. A reliable solid phase microextraction-gas chromatography-triple quadrupole mass spectrometry method for the assay of selenomethionine and selenomethylselenocysteine in aqueous extracts: difference between selenized and not-enriched selenium potatoes.

    PubMed

    Gionfriddo, Emanuela; Naccarato, Attilio; Sindona, Giovanni; Tagarelli, Antonio

    2012-10-17

    A new analytical approach is exploited in the assay of selenium speciation in selenized and not selenium enriched potatoes based on the widely available solid-phase microextraction (SPME) coupled to-GC-triple quadrupole mass spectrometry (SPME-GC-QqQ MS) method. The assay of selenomethionine (SeMet) and selenomethylselenocysteine (SeMeSeCys) in potatoes here reported provides clues to the effectiveness of SPME technique combined with gas chromatography-tandem mass spectrometry, which could be of general use. For the exploitation of the GC method, the selected analytes were converted into their N(O,S)-alkoxycarbonyl alkyl esters derivatives by direct treatment with alkyl chloroformate in aqueous extracts. The performance of five SPME fibers and three chloroformates were tested in univariate mode and the best results were obtained using the divinylbenzene/carboxen/polydimethylsiloxane fiber and propylchloroformate. The variables affecting the efficiency of SPME analysis were optimized by the multivariate approach of design of experiment (DoE) and, in particular, a central composite design (CCD) was applied. Tandem mass spectrometry in selected reaction monitoring (SRM) has allowed the elimination of matrix interferences, providing reconstructed chromatograms with well-resolved peaks and the achievement of very satisfactory detection and quantification limits. Both precision and recovery of the proposed protocol tested at concentration of 8 and 40 μg kg(-1) (dry matter), offered values ranging from 82.3 to 116.3% and from 8.5 to 13.1% for recovery and precision, respectively. The application of the method to commercial samples of selenized and not selenium enriched potatoes proved that the Se fertilization increases significantly the concentration of these bioavailable selenoamino acids.

  17. Polymeric integrated selective enrichment target (ISET) for solid-phase-based sample preparation in MALDI-TOF MS.

    PubMed

    Ekström, Simon; Wallman, Lars; Helldin, Göran; Nilsson, Johan; Marko-Varga, György; Laurell, Thomas

    2007-11-01

    A polymer microfabricated proteomic sample preparation and MALDI MS sample presentation device, the integrated selective enrichment target (ISET), comprising an array of perforated nanovials is reported. Each perforated nanovial can be filled with selective extraction media (microbeads) for purification and concentration of protein/peptides prior to matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). The main areas covered are the influence of the molding-process-induced surface roughness and how to address the lack of inherent conductivity in the polyetheretherketone (PEEK) material for optimal MALDI MS readout. Application of the disposable polymeric ISET devices for solid-phase extraction and phosphopeptide capture is also demonstrated.

  18. Accelerated solvent-based extraction and enrichment of selected plasticisers and 4-nonylphenol, and extraction of tin from organotin sources in sediments, sludges and leachate soils.

    PubMed

    Reid, Antoinette M; Brougham, Concepta A; Fogarty, Andrew M; Roche, James J

    2009-02-23

    Enrichment techniques have become an important feature in the trace analysis of oestrogen mimicking chemicals in the environment. Recent developments such as accelerated solvent extraction (ASE) have improved extraction recoveries in a wide variety of solid matrices including sediments, sludges and leachate soils. Such samples taken from the Irish Midlands Shannon Catchment region during the winter of 2004/5 and suspected to contain certain xenooestrogens or hormonally active agents were extracted using this technique, which was then coupled with high performance liquid chromatography (HPLC) for quantification purposes. ASE was thus employed to both isolate and pre-concentrate targeted analytes using the minimum amount of solvent hence making extractions more conservational. Two simple, yet extremely sensitive liquid chromatographic methods were developed based on UV detection; one for phthalates and one for alkylphenols, with recoveries reaching up to 92.0%. Acid digestion was used for the extraction of the tin and organotin compounds with analysis by polarography. In river sediment, levels of up to 24.4 mg kg(-1) phthalate, 1.14 mg kg(-1) 4-nonylphenol and 118 mg kg(-1) tin were found. In leachate sediments, values up to 49.8 mg kg(-1) phthalate, 1.57 mg kg(-1) 4-nonylphenol, and 36.0 mg kg(-1) tin were determined. In sludge, values up to 174 mg kg(-1) phthalate and 22.8 mg kg(-1) 4-nonylphenol were quantified. The highest value of tin (118 mg kg(-1)) was found present in an area of high leisure craft activity. Typical sediment levels of tin at other river locations ranged between 1.20 and 37.5 mg kg(-1).

  19. 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.

  20. Environmental enrichment for primates in laboratories

    NASA Astrophysics Data System (ADS)

    Buchanan-Smith, H. M.

    2010-06-01

    Environmental enrichment is a critical component of Refinement, one of the 3Rs underlying humane experimentation on animals. In this paper I discuss why primates housed in laboratories, which often have constraints of space and study protocols, are a special case for enrichment. I outline a framework for categorising the different types of enrichment, using the marmoset as a case study, and summarise the methods used to determine what animals want/prefer. I briefly review the arguments that enrichment does not negatively affect experimental outcomes. Finally I focus on complexity and novelty, choice and control, the underlying features of enrichment that makes it successful, and how combined with a thorough understanding of natural history we can put effective enrichment into practice in laboratories. Throughout the paper I emphasise the need to evaluate enrichment to ensure it is having the desired effect.

  1. 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)

  2. 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

  3. Method for comparing content based image retrieval methods

    NASA Astrophysics Data System (ADS)

    Barnard, Kobus; Shirahatti, Nikhil V.

    2003-01-01

    We assume that the goal of content based image retrieval is to find images which are both semantically and visually relevant to users based on image descriptors. These descriptors are often provided by an example image--the query by example paradigm. In this work we develop a very simple method for evaluating such systems based on large collections of images with associated text. Examples of such collections include the Corel image collection, annotated museum collections, news photos with captions, and web images with associated text based on heuristic reasoning on the structure of typical web pages (such as used by Google(tm)). The advantage of using such data is that it is plentiful, and the method we propose can be automatically applied to hundreds of thousands of queries. However, it is critical that such a method be verified against human usage, and to do this we evaluate over 6000 query/result pairs. Our results strongly suggest that at least in the case of the Corel image collection, the automated measure is a good proxy for human evaluation. Importantly, our human evaluation data can be reused for the evaluation of any content based image retrieval system and/or the verification of additional proxy measures.

  4. 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.

  5. A microarray-based method to perform nucleic acid selections.

    PubMed

    Aminova, Olga; Disney, Matthew D

    2010-01-01

    This method describes a microarray-based platform to perform nucleic acid selections. Chemical ligands to which a nucleic acid binder is desired are immobilized onto an agarose microarray surface; the array is then incubated with an RNA library. Bound RNA library members are harvested directly from the array surface via gel excision at the position on the array where a ligand was immobilized. The RNA is then amplified via RT-PCR, cloned, and sequenced. This method has the following advantages over traditional resin-based Systematic Evolution of Ligands by Exponential Enrichment (SELEX): (1) multiple selections can be completed in parallel on a single microarray surface; (2) kinetic biases in the selections are mitigated since all RNA binders are harvested from an array via gel excision; (3) the amount of chemical ligand needed to perform a selection is minimized; (4) selections do not require expensive resins or equipment; and (5) the matrix used for selections is inexpensive and easy to prepare. Although this protocol was demonstrated for RNA selections, it should be applicable for any nucleic acid selection.

  6. 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.

  7. Oxidative Stability of Granola Bars Enriched with Multilayered Fish Oil Emulsion in the Presence of Novel Brown Seaweed Based Antioxidants.

    PubMed

    Hermund, Ditte B; Karadağ, Ayşe; Andersen, Ulf; Jónsdóttir, Rósa; Kristinsson, Hordur G; Alasalvar, Cesarettin; Jacobsen, Charlotte

    2016-11-09

    Fucus vesiculosus extracts that have both radical scavenging activity and metal chelating ability in vitro were used as natural antioxidant in granola bars enriched with fish oil emulsion by using primary and secondary emulsion systems stabilized by sodium caseinate alone and sodium caseinate-chitosan. The bars were stored at 20 °C and evaluated over a period of 10 weeks by measuring the development of primary and secondary oxidation products. The samples prepared with secondary emulsion system developed less oxidation products probably due to increased interfacial layer thickness that would act as a barrier to the penetration and diffusion of molecular species that promote oxidation. The positive charge of oil droplets in the secondary emulsion may also inhibit iron-lipid interaction through electrostatic repulsion. Additional protection against lipid oxidation was obtained when fish oil emulsions were added to the granola bars especially in combination with acetone and ethanol extracts of Fucus vesiculosus.

  8. High-purity, isotopically enriched bulk silicon

    SciTech Connect

    Ager III, J.W.; Beeman, J.W.; Hansen, W.L.; Haller, E.E.; Sharp, I.D.; Liao, C.; Yang, A.; Thewalt, M.L.W.; Riemann, H.

    2004-11-17

    The synthesis and characterization of dislocation-free, undoped, single crystals of Si enriched in all 3 stable isotopes is reported: {sup 28}Si (99.92%), {sup 29}Si (91.37%), and {sup 30}Si (89.8%). A silane-based process compatible with the relatively small amounts of isotopically enriched precursors that are practically available was used. The silane is decomposed to silicon on a graphite starter rod heated to 700-750 C in a recirculating flow reactor. A typical run produces 35 gm of polycrystalline Si at a growth rates of 5 {micro}m/min and conversion efficiency >95%. Single crystals are grown by the floating zone method and characterized by electrical and optical measurements. Concentrations of shallow dopants (P and B) are as low as mid-10{sup 13} cm{sup -3}. Concentrations of C and O lie below 10{sup 16} and 10{sup 15} cm{sup -3}, respectively.

  9. A Simple Method for Measuring Carbon-13 Fatty Acid Enrichment in the Major Lipid Classes of Microalgae Using GC-MS

    PubMed Central

    Elahee Doomun, Sheik Nadeem; Loke, Stella; O’Callaghan, Sean; Callahan, Damien L.

    2016-01-01

    A simple method for tracing carbon fixation and lipid synthesis in microalgae was developed using a combination of solid-phase extraction (SPE) and negative ion chemical ionisation gas chromatography mass spectrometry (NCI-GC-MS). NCI-GC-MS is an extremely sensitive technique that can produce an unfragmented molecular ion making this technique particularly useful for stable isotope enrichment studies. Derivatisation of fatty acids using pentafluorobenzyl bromide (PFBBr) allows the coupling of the high separation efficiency of GC and the measurement of unfragmented molecular ions for each of the fatty acids by single quadrupole MS. The key is that isotope spectra can be measured without interference from co-eluting fatty acids or other molecules. Pre-fractionation of lipid extracts by SPE allows the measurement of 13C isotope incorporation into the three main lipid classes (phospholipids, glycolipids, neutral lipids) in microalgae thus allowing the study of complex lipid biochemistry using relatively straightforward analytical technology. The high selectivity of GC is necessary as it allows the collection of mass spectra for individual fatty acids, including cis/trans isomers, of the PFB-derivatised fatty acids. The combination of solid-phase extraction and GC-MS enables the accurate determination of 13C incorporation into each lipid pool. Three solvent extraction protocols that are commonly used in lipidomics were also evaluated and are described here with regard to extraction efficiencies for lipid analysis in microalgae. PMID:27845718

  10. 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

  11. Design for validation, based on formal methods

    NASA Technical Reports Server (NTRS)

    Butler, Ricky W.

    1990-01-01

    Validation of ultra-reliable systems decomposes into two subproblems: (1) quantification of probability of system failure due to physical failure; (2) establishing that Design Errors are not present. Methods of design, testing, and analysis of ultra-reliable software are discussed. It is concluded that a design-for-validation based on formal methods is needed for the digital flight control systems problem, and also that formal methods will play a major role in the development of future high reliability digital systems.

  12. Enabling Enrichment Analysis with the Human Disease Ontology

    PubMed Central

    LePendu, Paea; Musen, Mark A.; Shah, Nigam H.

    2012-01-01

    Advanced statistical methods used to analyze high-throughput data such as gene-expression assays result in long lists of “significant genes.” One way to gain insight into the significance of altered expression levels is to determine whether Gene Ontology (GO) terms associated with a particular biological process, molecular function, or cellular component are over- or under-represented in the set of genes deemed significant. This process, referred to as enrichment analysis, profiles a gene-set, and is widely used to make sense of the results of high-throughput experiments. Our goal is to develop and apply general enrichment analysis methods to profile other sets of interest, such as patient cohorts from the electronic medical record, using a variety of ontologies including SNOMED CT, MedDRA, RxNorm, and others. Although it is possible to perform enrichment analysis using ontologies other than the GO, a key pre-requisite is the availability of a background set of annotations to enable the enrichment calculation. In the case of the GO, this background set is provided by the Gene Ontology Annotations. In the current work, we describe: (i) a general method that uses hand-curated GO annotations as a starting point for creating background datasets for enrichment analysis using other ontologies; and (ii) a gene–disease background annotation set—that enables disease-based enrichment—to demonstrate feasibility of our method. PMID:21550421

  13. 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).

  14. Quantitative determination of 8-isoprostaglandin F(2α) in human urine using microfluidic chip-based nano-liquid chromatography with on-chip sample enrichment and tandem mass spectrometry.

    PubMed

    Bai, Hsin-Yu; Lin, Shu-Ling; Chung, Yu-Ting; Liu, Tsung-Yun; Chan, Shan-An; Fuh, Ming-Ren

    2011-04-15

    Urinary 8-isoprostaglandin F(2α) (8-isoPGF(2α)) has been reported as an important biomarker to indicate the oxidative stress status in vivo. In order to quantitatively determine the low contents of 8-isoPGF(2α) (in sub- to low ng mL(-1) range) in physiological fluids, a sensitive detection method has become an important issue. In this study, we employed a microfluidic chip-based nano liquid chromatography (chip-nanoLC) with on-chip sample enrichment coupled to triple quadrupole mass spectrometer (QqQ-MS) for the quantitative determination of 8-isoPGF(2α) in human urine. This chip-nanoLC unit integrates a microfluidic switch, a chip column design having a pre-column (enrichment column) for sample enrichment prior to an analytical column for separation, as well as a nanospray emitter on a single polyimide chip. The introduction of enrichment column offers the advantages of online sample pre-concentration and reducing matrix influence on MS detection to improve sensitivity. In this study, the chip-nanoLC consisting of Zorbax 300A SB-C18 columns and Agilent QqQ Mass spectrometer were used for determining 8-isoPGF(2α) in human urine. Gradient elution was employed for effective LC separation and multiple reaction monitoring (MRM) was utilized for the quantitative determination of 8-isoPGF(2α) (m/z 353→193). We employed liquid-liquid extraction (LLE)/solid-phase extraction (SPE) for extracting analyte and reducing matrix effect from urine sample prior to chip-nanoLC/QqQ-MS analysis for determining urinary 8-isoPGF(2α). Good recoveries were found to be in the range of 83.0-85.3%. The linear range was 0.01-2 ng mL(-1) for urinary 8-isoPGF(2α). In addition, the proposed method showed good precision and accuracy for 8-isoPGF(2α) spiked synthetic urine samples. Intra-day and inter-day precisions were 1.8-5.0% and 4.3-5.8%, respectively. The method accuracy for intra-day and inter-day assays ranged from 99.3 to 99.9% and 99.4 to 99.7%, respectively. Due to its

  15. Comparing real-time and conventional PCR to culture-based methods for detecting and quantifying Escherichia coli O157 in cattle feces.

    PubMed

    Jacob, M E; Bai, J; Renter, D G; Rogers, A T; Shi, X; Nagaraja, T G

    2014-02-01

    Detection of Escherichia coli O157 in cattle feces has traditionally used culture-based methods; PCR-based methods have been suggested as an alternative. We aimed to determine if multiplex real-time (mq) or conventional PCR methods could reliably detect cattle naturally shedding high (≥10(4) CFU/g of feces) and low (∼10(2) CFU/g of feces) concentrations of E. coli O157. Feces were collected from pens of feedlot cattle and evaluated for E. coli O157 by culture methods. Samples were categorized as (i) high shedders, (ii) immunomagnetic separation (IMS) positive after enrichment, or (iii) culture negative. DNA was extracted pre- and postenrichment from 100 fecal samples from each category (high shedder, IMS positive, culture negative) and subjected to mqPCR and conventional PCR assays based on detecting three genes, rfbE, stx1, and stx2. In feces from cattle determined to be E. coli O157 high shedders by culture, 37% were positive by mqPCR prior to enrichment; 85% of samples were positive after enrichment. In IMS-positive samples, 4% were positive by mqPCR prior to enrichment, while 43% were positive after enrichment. In culture-negative feces, 7% were positive by mqPCR prior to enrichment, and 40% were positive after enrichment. The proportion of high shedder-positive and culture-positive (high shedder and IMS) samples were significantly different from mqPCR-positive samples before and after enrichment (P < 0.01). Similar results were observed for conventional PCR. Our data suggest that mqPCR and conventional PCR are most useful in identifying high shedder animals and may not be an appropriate substitute to culture-based methods for detection of E. coli O157 in cattle feces.

  16. 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.

  17. BioTile, A Perl based tool for the identification of differentially enriched regions in tiling microarray data

    PubMed Central

    2013-01-01

    Background Genome-wide tiling array experiments are increasingly used for the analysis of DNA methylation. Because DNA methylation patterns are tissue and cell type specific, the detection of differentially methylated regions (DMRs) with small effect size is a necessary feature of tiling microarray ‘peak’ finding algorithms, as cellular heterogeneity within a studied tissue may lead to a dilution of the phenotypically relevant effects. Additionally, the ability to detect short length DMRs is necessary as biologically relevant signal may occur in focused regions throughout the genome. Results We present a free open-source Perl application, Binding Intensity Only Tile array analysis or “BioTile”, for the identification of differentially enriched regions (DERs) in tiling array data. The application of BioTile to non-smoothed data allows for the identification of shorter length and smaller effect-size DERs, while correcting for probe specific variation by inversely weighting on probe variance through a permutation corrected meta-analysis procedure employed at identified regions. BioTile exhibits higher power to identify significant DERs of low effect size and across shorter genomic stretches as compared to other peak finding algorithms, while not sacrificing power to detect longer DERs. Conclusion BioTile represents an easy to use analysis option applicable to multiple microarray platforms, allowing for its integration into the analysis workflow of array data analysis. PMID:23452827

  18. Selective enrichment of metal-binding proteins based on magnetic core/shell microspheres functionalized with metal cations.

    PubMed

    Fang, Caiyun; Zhang, Lei; Zhang, Xiaoqin; Lu, Haojie

    2015-06-21

    Metal binding proteins play many important roles in a broad range of biological processes. Characterization of metal binding proteins is important for understanding their structure and biological functions, thus leading to a clear understanding of metal associated diseases. The present study is the first to investigate the effectiveness of magnetic microspheres functionalized with metal cations (Ca(2+), Cu(2+), Zn(2+) and Fe(3+)) as the absorbent matrix in IMAC technology to enrich metal containing/binding proteins. The putative metal binding proteins in rat liver were then globally characterized by using this strategy which is very easy to handle and can capture a number of metal binding proteins effectively. In total, 185 putative metal binding proteins were identified from rat liver including some known less abundant and membrane-bound metal binding proteins such as Plcg1, Acsl5, etc. The identified proteins are involved in many important processes including binding, catalytic activity, translation elongation factor activity, electron carrier activity, and so on.

  19. Wavelet-based Multiresolution Particle Methods

    NASA Astrophysics Data System (ADS)

    Bergdorf, Michael; Koumoutsakos, Petros

    2006-03-01

    Particle methods offer a robust numerical tool for solving transport problems across disciplines, such as fluid dynamics, quantitative biology or computer graphics. Their strength lies in their stability, as they do not discretize the convection operator, and appealing numerical properties, such as small dissipation and dispersion errors. Many problems of interest are inherently multiscale, and their efficient solution requires either multiscale modeling approaches or spatially adaptive numerical schemes. We present a hybrid particle method that employs a multiresolution analysis to identify and adapt to small scales in the solution. The method combines the versatility and efficiency of grid-based Wavelet collocation methods while retaining the numerical properties and stability of particle methods. The accuracy and efficiency of this method is then assessed for transport and interface capturing problems in two and three dimensions, illustrating the capabilities and limitations of our approach.

  20. 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

  1. 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.

  2. 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

  3. 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.

  4. The Effect of Different Mixing Methods on the pH and Solubility 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

    2015-01-01

    Introduction: The aim of this study was to evaluate the effect of different mixing techniques on the pH and solubility of mineral trioxide aggregate (MTA) and calcium-enriched mixture (CEM). Methods and Materials: Five samples were prepared from each biomaterial with different mixing techniques including hand-, amalgamator- or ultrasonic-mixing and were then placed in pre-weighted plastic tubes to determine their pH values. Each tube was then incubated in 10 mL deionized distilled water for 1 h at 37ºC. An electrode was placed in the fluid in each flask at 24ºC and the pH was recorded. In the next stage, six samples from each mixing technique/material were separately placed in glass bottles containing 50 mL of distilled water at 37ºC for 1 h and were let dry for 1 h at 37ºC. The samples’ weights were measured and recorded twice. The procedure was repeated at 1-, 7- and 21-day intervals. Data were analyzed with the repeated measures ANOVA (for solubility) and two-way ANOVA (for pH) and then the post-hoc Tukey’s test was done. Results: The pH of the materials was not significantly affected by mixing methods. (P=0.8 for CEM and P=0.1 for MTA). The solubility of all test groups was within the acceptable range (=3%). However, the solubility of CEM at 1- and 21-day intervals was significantly different (P=0.03 for 1 day and P=0.001 for 21 days). Different mixing techniques had significant effects on the solubility of MTA at the three time points (P=0.004, 0.003 and 0.002 for 1-, 7- and 21-day intervals, respectively). Conclusion: The pH of biomaterials was not influenced by the mixing technique and their solubility was within the acceptable range. PMID:25834601

  5. Autologous antibody capture to enrich immunogenic viruses for viral discovery.

    PubMed

    Oude Munnink, Bas B; Jazaeri Farsani, Seyed Mohammad; Deijs, Martin; Jonkers, Jiri; Verhoeven, Joost T P; Ieven, Margareta; Goossens, Herman; de Jong, Menno D; Berkhout, Ben; Loens, Katherine; Kellam, Paul; Bakker, Margreet; Canuti, Marta; Cotten, Matthew; van der Hoek, Lia

    2013-01-01

    Discovery of new viruses has been boosted by novel deep sequencing technologies. Currently, many viruses can be identified by sequencing without knowledge of the pathogenicity of the virus. However, attributing the presence of a virus in patient material to a disease in the patient can be a challenge. One approach to meet this challenge is identification of viral sequences based on enrichment by autologous patient antibody capture. This method facilitates identification of viruses that have provoked an immune response within the patient and may increase the sensitivity of the current virus discovery techniques. To demonstrate the utility of this method, virus discovery deep sequencing (VIDISCA-454) was performed on clinical samples from 19 patients: 13 with a known respiratory viral infection and 6 with a known gastrointestinal viral infection. Patient sera was collected from one to several months after the acute infection phase. Input and antibody capture material was sequenced and enrichment was assessed. In 18 of the 19 patients, viral reads from immunogenic viruses were enriched by antibody capture (ranging between 1.5x to 343x in respiratory material, and 1.4x to 53x in stool). Enriched reads were also determined in an identity independent manner by using a novel algorithm Xcompare. In 16 of the 19 patients, 21% to 100% of the enriched reads were derived from infecting viruses. In conclusion, the technique provides a novel approach to specifically identify immunogenic viral sequences among the bulk of sequences which are usually encountered during virus discovery metagenomics.

  6. 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

  7. 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.

  8. Treecode-based generalized Born method

    NASA Astrophysics Data System (ADS)

    Xu, Zhenli; Cheng, Xiaolin; Yang, Haizhao

    2011-02-01

    We have developed a treecode-based O(Nlog N) algorithm for the generalized Born (GB) implicit solvation model. Our treecode-based GB (tGB) is based on the GBr6 [J. Phys. Chem. B 111, 3055 (2007)], an analytical GB method with a pairwise descreening approximation for the R6 volume integral expression. The algorithm is composed of a cutoff scheme for the effective Born radii calculation, and a treecode implementation of the GB charge-charge pair interactions. Test results demonstrate that the tGB algorithm can reproduce the vdW surface based Poisson solvation energy with an average relative error less than 0.6% while providing an almost linear-scaling calculation for a representative set of 25 proteins with different sizes (from 2815 atoms to 65456 atoms). For a typical system of 10k atoms, the tGB calculation is three times faster than the direct summation as implemented in the original GBr6 model. Thus, our tGB method provides an efficient way for performing implicit solvent GB simulations of larger biomolecular systems at longer time scales.

  9. A MULTICORE BASED PARALLEL IMAGE REGISTRATION METHOD

    PubMed Central

    Yang, Lin; Gong, Leiguang; Zhang, Hong; Nosher, John L.; Foran, David J.

    2012-01-01

    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

  10. Enriching consumer health vocabulary through mining a social Q&A site: a similarity-based approach.

    PubMed

    He, Zhe; Chen, Zhiwei; Oh, Sanghee; Hou, Jinghui; Bian, Jiang

    2017-03-27

    The widely known vocabulary gap between health consumers and healthcare professionals hinders information seeking and health dialogue of consumers on end-user health applications. The Open Access and Collaborative Consumer Health Vocabulary (OAC CHV), which contains health-related terms used by lay consumers, has been created to bridge such a gap. Specifically, the OAC CHV facilitates consumers' health information retrieval by enabling consumer-facing health applications to translate between professional language and consumer friendly language. To keep up with the constantly evolving medical knowledge and language use, new terms need to be identified and added to the OAC CHV. User-generated content on social media, including social question and answer (social Q&A) sites, afford us an enormous opportunity in mining consumer health terms. Existing methods of identifying new consumer terms from text typically use ad-hoc lexical syntactic patterns and human review. Our study extends an existing method by extracting n-grams from a social Q&A textual corpus and representing them with a rich set of contextual and syntactic features. Using K-means clustering, our method, simiTerm, was able to identify terms that are both contextually and syntactically similar to the existing OAC CHV terms. We tested our method on social Q&A corpora on two disease domains: diabetes and cancer. Our method outperformed three baseline ranking methods. A post-hoc qualitative evaluation by human experts further validated that our method can effectively identify meaningful new consumer terms on social Q&A.

  11. 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.

  12. 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…

  13. 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.

  14. A cage-based training, cognitive testing and enrichment system optimized for rhesus macaques in neuroscience research.

    PubMed

    Calapai, A; Berger, M; Niessing, M; Heisig, K; Brockhausen, R; Treue, S; Gail, A

    2017-02-01

    In neurophysiological studies with awake non-human primates (NHP), it is typically necessary to train the animals over a prolonged period of time on a behavioral paradigm before the actual data collection takes place. Rhesus monkeys (Macaca mulatta) are the most widely used primate animal models in system neuroscience. Inspired by existing joystick- or touch-screen-based systems designed for a variety of monkey species, we built and successfully employed a stand-alone cage-based training and testing system for rhesus monkeys (eXperimental Behavioral Intrument, XBI). The XBI is mobile and easy to handle by both experts and non-experts; animals can work with only minimal physical restraints, yet the ergonomic design successfully encourages stereotypical postures with a consistent positioning of the head relative to the screen. The XBI allows computer-controlled training of the monkeys with a large variety of behavioral tasks and reward protocols typically used in systems and cognitive neuroscience research.

  15. The Legacy Project: A Case Study of Civic Capacity Building and Transformative Educational Leadership in a Community-Based Academic Enrichment Program

    ERIC Educational Resources Information Center

    Didlick-Davis, Celeste R.

    2016-01-01

    This study examines how a grassroots educational enrichment program in a small urban economically depressed area builds and uses civic capacity. Using qualitative data collected through a case study of the Legacy Academic Enrichment program in Middletown, Ohio, I identify factors that make Legacy sustainable and successful in a community that has…

  16. Enrichment Activities for Geometry.

    ERIC Educational Resources Information Center

    Usiskin, Zalman

    1983-01-01

    Enrichment activities that teach about geometry as they instruct in geometry are given for some significant topics. The facets of geometry included are tessellations, round robin tournaments, geometric theorems on triangles, and connections between geometry and complex numbers. (MNS)

  17. Method for extruding pitch based foam

    DOEpatents

    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.

  18. 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.

  19. 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.

  20. Enrichment of cancer cells from whole blood using a microfabricated porous filter.

    PubMed

    Kim, Eun Hye; Lee, Jong Kil; Kim, Byung Chul; Rhim, Sung Han; Kim, Jhin Wook; Kim, Kyung Hee; Jung, Sung Mok; Park, Pyeong Soo; Park, Hee Chul; Lee, Jason; Jeon, Byung Hee

    2013-09-01

    Enrichment of circulating tumor cells (CTCs) from whole blood is very challenging due to its rarity. We have developed a new CTC enrichment method using a microfabricated filter. The filter was designed to fractionate tumor cells by cell size and optimized to have high porosity and proper pore distribution. When cancer cells were spiked in whole blood, the average recovery rate was 82.0 to 86.7% and the limit of detection by filtration process was approximately 2 cancer cells in a testing volume of blood. The results indicate that the microfabricated filter-based enrichment would be useful to retrieve and analyze CTCs in practice.

  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. Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking

    PubMed Central

    Sasse, Alexander; de Vries, Sjoerd J.; Schindler, Christina E. M.; de Beauchêne, Isaure Chauvot

    2017-01-01

    Protein-protein docking protocols aim to predict the structures of protein-protein complexes based on the structure of individual partners. Docking protocols usually include several steps of sampling, clustering, refinement and re-scoring. The scoring step is one of the bottlenecks in the performance of many state-of-the-art protocols. The performance of scoring functions depends on the quality of the generated structures and its coupling to the sampling algorithm. A tool kit, GRADSCOPT (GRid Accelerated Directly SCoring OPTimizing), was designed to allow rapid development and optimization of different knowledge-based scoring potentials for specific objectives in protein-protein docking. Different atomistic and coarse-grained potentials can be created by a grid-accelerated directly scoring dependent Monte-Carlo annealing or by a linear regression optimization. We demonstrate that the scoring functions generated by our approach are similar to or even outperform state-of-the-art scoring functions for predicting near-native solutions. Of additional importance, we find that potentials specifically trained to identify the native bound complex perform rather poorly on identifying acceptable or medium quality (near-native) solutions. In contrast, atomistic long-range contact potentials can increase the average fraction of near-native poses by up to a factor 2.5 in the best scored 1% decoys (compared to existing scoring), emphasizing the need of specific docking potentials for different steps in the docking protocol. PMID:28118389

  3. The limitations of simple gene set enrichment analysis assuming gene independence.

    PubMed

    Tamayo, Pablo; Steinhardt, George; Liberzon, Arthur; Mesirov, Jill P

    2016-02-01

    Since its first publication in 2003, the Gene Set Enrichment Analysis method, based on the Kolmogorov-Smirnov statistic, has been heavily used, modified, and also questioned. Recently a simplified approach using a one-sample t-test score to assess enrichment and ignoring gene-gene correlations was proposed by Irizarry et al. 2009 as a serious contender. The argument criticizes Gene Set Enrichment Analysis's nonparametric nature and its use of an empirical null distribution as unnecessary and hard to compute. We refute these claims by careful consideration of the assumptions of the simplified method and its results, including a comparison with Gene Set Enrichment Analysis's on a large benchmark set of 50 datasets. Our results provide strong empirical evidence that gene-gene correlations cannot be ignored due to the significant variance inflation they produced on the enrichment scores and should be taken into account when estimating gene set enrichment significance. In addition, we discuss the challenges that the complex correlation structure and multi-modality of gene sets pose more generally for gene set enrichment methods.

  4. 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

  5. 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.

  6. 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.

  7. ProbCD: enrichment analysis accounting for categorization uncertainty

    PubMed Central

    Vêncio, Ricardo ZN; Shmulevich, Ilya

    2007-01-01

    Background As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as enrichment (also over-representation or enhancement) analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic information since they are mainly based on variants of the Fisher Exact Test. Results We developed an open-source R-based software to deal with probabilistic categorical data analysis, ProbCD, that does not require a static contingency table. The contingency table for the enrichment problem is built using the expectation of a Bernoulli Scheme stochastic process given the categorization probabilities. An on-line interface was created to allow usage by non-programmers and is available at: . Conclusion We present an analysis framework and software tools to address the issue of uncertainty in categorical data analysis. In particular, concerning the enrichment analysis, ProbCD can accommodate: (i) the stochastic nature of the high-throughput experimental techniques and (ii) probabilistic gene annotation. PMID:17935624

  8. Hyaluronan based porous nano-particles enriched with growth factors for the treatment of ulcers: a placebo-controlled study.

    PubMed

    Zavan, B; Vindigni, V; Vezzù, K; Zorzato, G; Luni, C; Abatangelo, G; Elvassore, N; Cortivo, R

    2009-01-01

    The present study describes the production of hyaluronan based porous microparticles by a semi-continuous gas anti-solvent (GAS) precipitation process to be used as a growth factor delivery system for in vivo treatment of ulcers. Operative process conditions, such as pressure, nozzle diameter and HYAFF11 solution concentrations, were adjusted to optimize particle production in terms of morphology and size. Scanning electron microscopy (SEM) and light scattering demonstrated that porous nano-structured particles with a size of 300 and 900 nm had a high specific surface suitable for absorption of growth factors from the aqueous environment within the polymeric matrix. Water acted as a plasticizer, enhancing growth factor absorption. Water contents within the HYAFF11 matrix were analyzed by differential scanning calorimetry (DSC). The absorption process was developed using fluorescence dyes and growth factors. Immunohistochemical analysis confirmed the high efficiency of absorption of growth factor and a mathematical model was generated to quantify and qualify the in vitro kinetics of growth factor release within the polymeric matrix. In vivo experiments were performed with the aim to optimize timed and focal release of PDGF to promote optimal tissue repair and regeneration of full-thickness wounds.

  9. 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

  10. Recovery of Listeria monocytogenes from vacuum-sealed packages of frankfurters: comparison of the U.S. Department of Agriculture (USDA) food safety and inspection service product composite enrichment method, the USDA Agricultural Research Service (ARS) product composite rinse method, and the USDA-ARS package rinse method.

    PubMed

    Luchansky, John B; Porto, Anna C S; Wallace, F Morgan; Call, Jeffrey E

    2002-03-01

    This study compared three methods for the recovery of Listeria monocytogenes from commercially prepared and vacuum-packaged frankfurters that were inoculated with a five-strain mixture of this pathogen at averages of 22 and 20,133 CFU per package over three trials. The presence and levels of the pathogen were determined by (i) the U.S. Department of Agriculture (USDA) Food Safety and Inspection Service (FSIS) product composite enrichment method, involving the selective enrichment of a 25-g composite of product and the subsequent plating of this product onto selective agar plates; (ii) the USDA Agricultural Research Service (ARS) product composite rinse method, involving the rinsing of a 25-g composite of product with 0.1% peptone water and the subsequent plating of a portion of the rinse fluid directly onto selective agar plates; and (iii) the USDA-ARS package rinse method, involving the use of 25 ml of 0.1% peptone water to rinse the entire contents of a package and the subsequent plating of a portion of the rinse fluid directly onto selective agar plates. For packages inoculated with 20,133 CFU. L. monocytogenes was recovered at a frequency (percentage of packages positive) of 100% by each of the three methods. The pathogen was recovered at efficiencies (percentages of recovery of L. monocytogenes) of 43 and 94% with the USDA-ARS product rinse method and the USDA-ARS package rinse method, respectively. For packages inoculated with 22 CFU, L. monocytogenes was recovered at frequencies of 17, 10, and 100% by the USDA-FSIS product composite enrichment method, the USDA-ARS product composite rinse method, and the USDA-ARS package rinse method, respectively. The pathogen was recovered at efficiencies of 20 and 95% with the USDA-ARS product composite rinse method and the USDA-ARS package rinse method, respectively. In a related study, the USDA-ARS package rinse method was the only method that detected the pathogen in 60 packages from each of five brands of frankfurters

  11. Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool.

    PubMed

    Clark, Neil R; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D; Jones, Matthew R; Ma'ayan, Avi

    2015-11-01

    Gene set analysis of differential expression, which identifies collectively differentially expressed gene sets, has become an important tool for biology. The power of this approach lies in its reduction of the dimensionality of the statistical problem and its incorporation of biological interpretation by construction. Many approaches to gene set analysis have been proposed, but benchmarking their performance in the setting of real biological data is difficult due to the lack of a gold standard. In a previously published work we proposed a geometrical approach to differential expression which performed highly in benchmarking tests and compared well to the most popular methods of differential gene expression. As reported, this approach has a natural extension to gene set analysis which we call Principal Angle Enrichment Analysis (PAEA). PAEA employs dimensionality reduction and a multivariate approach for gene set enrichment analysis. However, the performance of this method has not been assessed nor its implementation as a web-based tool. Here we describe new benchmarking protocols for gene set analysis methods and find that PAEA performs highly. The PAEA method is implemented as a user-friendly web-based tool, which contains 70 gene set libraries and is freely available to the community.

  12. 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.

  13. 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.

  14. Community-aware user profile enrichment in folksonomy.

    PubMed

    Xie, Haoran; Li, Qing; Mao, Xudong; Li, Xiaodong; Cai, Yi; Rao, Yanghui

    2014-10-01

    In the era of big data, collaborative tagging (a.k.a. folksonomy) systems have proliferated as a consequence of the growth of Web 2.0 communities. Constructing user profiles from folksonomy systems is useful for many applications such as personalized search and recommender systems. The identification of latent user communities is one way to better understand and meet user needs. The behavior of users is highly influenced by the behavior of their neighbors or community members, and this can be utilized in constructing user profiles. However, conventional user profiling techniques often encounter data sparsity problems as data from a single user is insufficient to build a powerful profile. Hence, in this paper we propose a method of enriching user profiles based on latent user communities in folksonomy data. Specifically, the proposed approach contains four sub-processes: (i) tag-based user profiles are extracted from a folksonomy tripartite graph; (ii) a multi-faceted folksonomy graph is constructed by integrating tag and image affinity subgraphs with the folksonomy tripartite graph; (iii) random walk distance is used to unify various relationships and measure user similarities; (iv) a novel prototype-based clustering method based on user similarities is used to identify user communities, which are further used to enrich the extracted user profiles. To evaluate the proposed method, we conducted experiments using a public dataset, the results of which show that our approach outperforms previous ones in user profile enrichment.

  15. 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.

  16. Microsatellite DNA capture from enriched libraries.

    PubMed

    Gonzalez, Elena G; Zardoya, Rafael

    2013-01-01

    Microsatellites are DNA sequences of tandem repeats of one to six nucleotides, which are highly polymorphic, and thus the molecular markers of choice in many kinship, population genetic, and conservation studies. There have been significant technical improvements since the early methods for microsatellite isolation were developed, and today the most common procedures take advantage of the hybrid capture methods of enriched-targeted microsatellite DNA. Furthermore, recent advents in sequencing technologies (i.e., next-generation sequencing, NGS) have fostered the mining of microsatellite markers in non-model organisms, affording a cost-effective way of obtaining a large amount of sequence data potentially useful for loci characterization. The rapid improvements of NGS platforms together with the increase in available microsatellite information open new avenues to the understanding of the evolutionary forces that shape genetic structuring in wild populations. Here, we provide detailed methodological procedures for microsatellite isolation based on the screening of GT microsatellite-enriched libraries, either by cloning and Sanger sequencing of positive clones or by direct NGS. Guides for designing new species-specific primers and basic genotyping are also given.

  17. 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.

  18. Imaging Earth's Interior Based Upon Adjoint Methods

    NASA Astrophysics Data System (ADS)

    Tromp, J.; Komatitsch, D.; Liu, Q.; Tape, C.; Maggi, A.

    2008-12-01

    Modern numerical methods in combination with rapid advances in parallel computing have enabled the simulation of seismic wave propagation in 3D Earth models at unpredcented resolution and accuracy. On a modest PC cluster one can now simulate global seismic wave propagation at periods of 20~s longer accounting for heterogeneity in the crust and mantle, topography, anisotropy, attenuation, fluid-solid interactions, self-gravitation, rotation, and the oceans. On the 'Ranger' system at the Texas Advanced Computing Center one can break the 2~s barrier. By drawing connections between seismic tomography, adjoint methods popular in climate and ocean dynamics, time-reversal imaging, and finite-frequency 'banana-doughnut' kernels, it has been demonstrated that Fréchet derivatives for tomographic and (finite) source inversions in complex 3D Earth models may be obtained based upon just two numerical simulations for each earthquake: one calculation for the current model and a second, 'adjoint', calculation that uses time-reversed signals at the receivers as simultaneous, fictitious sources. The adjoint wavefield is calculated while the regular wavefield is reconstructed on the fly by propagating the last frame of the wavefield saved by a previous forward simulation backward in time. This aproach has been used to calculate sensitivity kernels in regional and global Earth models for various body- and surface-wave arrivals. These kernels illustrate the sensitivity of the observations to the structural parameters and form the basis of 'adjoint tomography'. We use a non-linear conjugate gradient method in combination with a source subspace projection preconditioning technique to iterative minimize the misfit function. Using an automated time window selection algorithm, our emphasis is on matching targeted, frequency-dependent body-wave traveltimes and surface-wave phase anomalies, rather than entire waveforms. To avoid reaching a local minimum in the optimization procedure, we

  19. 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.

  20. 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.

  1. Effects of dietary almond- and olive oil-based docosahexaenoic acid- and vitamin E-enriched beverage supplementation on athletic performance and oxidative stress markers.

    PubMed

    Capó, X; Martorell, M; Busquets-Cortés, C; Sureda, A; Riera, J; Drobnic, F; Tur, J A; Pons, A

    2016-12-07

    Functional beverages based on almonds and olive oil and enriched with α-tocopherol and docosahexaenoic acid (DHA) could be useful in modulating oxidative stress and enhancing physical performance in sportsmen. The aim of this work was to evaluate the effects of supplementation with functional beverages on physical performance, plasma and erythrocyte fatty acids' and polyphenol handling, oxidative and nitrative damage, and antioxidant and mitochondrial gene expression in young and senior athletes. Athletes performed maximal exercise tests before and after one month of dietary supplementation and blood samples were taken immediately before and one hour after each test. The beverages did not alter performance parameters during maximal exercise. Supplementation increased polyunsaturated and reduced saturated plasma fatty acids while increasing the DHA erythrocyte content; it maintained basal plasma and blood polyphenol levels, but increased the blood cell polyphenol concentration in senior athletes. Supplementation protects against oxidative damage although it enhances nitrative damage in young athletes. The beverages enhance the gene expression of antioxidant enzymes in peripheral blood mononuclear cells after exercise in young athletes.

  2. 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.

  3. Selective enrichment and desalting of hydrophilic peptides using graphene oxide.

    PubMed

    Jiang, Miao; Qi, Linyu; Liu, Peiru; Wang, Zijun; Duan, Zhigui; Wang, Ying; Liu, Zhonghua; Chen, Ping

    2016-08-01

    The wide variety and low abundance of peptides in tissue brought great difficulties to the separation and identification of peptides, which is not in favor of the development of peptidomics. RP-HPLC, which could purify small molecules based on their hydrophobicity, has been widely used in the separation and enrichment of peptide due to its fast, good reproducibility and high resolution. However, RP-HPLC requires the instrument and expensive C18 column and its sample capacity is also limited. Recently, graphene oxide has been applied to the adsorption of amino acids. However, the enrichment efficiency and selectivity of graphene oxide for peptides remain unclear. In this study, the adsorption efficiency and selectivity of graphene oxide and RP-C18 matrix were compared on trypsinized α-actin and also on tissue extracts from pituitary gland and hippocampus. For α-actin, there exhibit similar elution peaks for total trypsinized products and those adsorpted by GO and C18 matrix. But peptides adsorbed by GO showed the higher hydrophilic peaks than which adsorbed by C18 matrix. The resulted RP-HPLC profile showed that most of peptides enriched by graphene oxide were eluted at low concentration of organic solvent, while peptides adsorbed by RP-C18 matrix were mostly eluted at relatively high concentration. Moreover, mass spectrometry analysis suggested that, in pituitary sample, there were 495 peptides enriched by graphene oxide, 447 peptides enriched by RP-C18 matrix while in hippocampus sample 333 and 243 peptides respectively. The GRAVY value analysis suggested that the graphene oxide has a stronger adsorption for highly hydrophilic peptides compared to the RP-C18 matrix. Furthermore, the combination of these two methods could notably increase the number of identification peptides but also the number of predicted protein precursors. Our study provided a new thought to the role of graphene oxide during the enrichment of peptides from tissue which should be useful for

  4. Adaptive Discontinuous Galerkin Methods in Multiwavelets Bases

    SciTech Connect

    Archibald, Richard K; Fann, George I; Shelton Jr, William Allison

    2011-01-01

    We use a multiwavelet basis with the Discontinuous Galerkin (DG) method to produce a multi-scale DG method. We apply this Multiwavelet DG method to convection and convection-diffusion problems in multiple dimensions. Merging the DG method with multiwavelets allows the adaptivity in the DG method to be resolved through manipulation of multiwavelet coefficients rather than grid manipulation. Additionally, the Multiwavelet DG method is tested on non-linear equations in one dimension and on the cubed sphere.

  5. 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.

  6. 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.

  7. 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…

  8. 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…

  9. Development and validation of an automated method for the liquid chromatographic determination of sotalol in plasma using dialysis and trace enrichment on a cation-exchange pre-column as on-line sample preparation.

    PubMed

    Chiap, P; Ceccato, A; Miralles Buraglia, B; Boulanger, B; Hubert, P; Crommen, J

    2001-03-01

    A fully automated method for the determination of sotalol in human plasma was developed, involving dialysis through a cellulose acetate membrane, clean-up and enrichment of the dialysate on a strong cation-exchange pre-column and subsequent liquid chromatographic (LC) analysis with UV detection. All sample handling operations were carried out by means of an ASTED system. Before starting dialysis, the trace enrichment column (TEC) was conditioned. The plasma sample, to which the internal standard (atenolol) was automatically added, was then loaded in the donor channel and was kept static while the dialysis liquid, consisting of 0.017 M acetic acid, was passed through the acceptor channel in successive pulses. After each pulse, the dialysate was dispensed onto the TEC. When dialysis was discontinued, the analytes were eluted from the TEC by the LC mobile phase by rotation of a switching valve and transferred to the analytical column packed with octyl silica. The LC mobile phase was a mixture of methanol and pH 7.0 phosphate buffer containing 1-octanesulfonate at a concentration of 7.5 x 10(-4) M (19:81; v/v). The UV detection was performed at 230 nm. The influence of several parameters of the dialysis and trace enrichment processes on analyte recovery and method selectivity was investigated. The method was then validated. The mean absolute recovery for sotalol was about 60%. The limit of quantitation was 25 ng/ml and R.S.D. for repeatability and intermediate precision obtained at a concentration level of 50 ng/ml were 4.3 and 5.8%, respectively.

  10. Comparative proteomic assessment of matrisome enrichment methodologies

    PubMed Central

    Krasny, Lukas; Paul, Angela; Wai, Patty; Howard, Beatrice A.; Natrajan, Rachael C.; Huang, Paul H.

    2016-01-01

    The matrisome is a complex and heterogeneous collection of extracellular matrix (ECM) and ECM-associated proteins that play important roles in tissue development and homeostasis. While several strategies for matrisome enrichment have been developed, it is currently unknown how the performance of these different methodologies compares in the proteomic identification of matrisome components across multiple tissue types. In the present study, we perform a comparative proteomic assessment of two widely used decellularisation protocols and two extraction methods to characterise the matrisome in four murine organs (heart, mammary gland, lung and liver). We undertook a systematic evaluation of the performance of the individual methods on protein yield, matrisome enrichment capability and the ability to isolate core matrisome and matrisome-associated components. Our data find that sodium dodecyl sulphate (SDS) decellularisation leads to the highest matrisome enrichment efficiency, while the extraction protocol that comprises chemical and trypsin digestion of the ECM fraction consistently identifies the highest number of matrisomal proteins across all types of tissue examined. Matrisome enrichment had a clear benefit over non-enriched tissue for the comprehensive identification of matrisomal components in murine liver and heart. Strikingly, we find that all four matrisome enrichment methods led to significant losses in the soluble matrisome-associated proteins across all organs. Our findings highlight the multiple factors (including tissue type, matrisome class of interest and desired enrichment purity) that influence the choice of enrichment methodology, and we anticipate that these data will serve as a useful guide for the design of future proteomic studies of the matrisome. PMID:27589945

  11. DNA-based methods of geochemical prospecting

    DOEpatents

    Ashby, Matthew [Mill Valley, CA

    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.

  12. 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

  13. An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes.

    PubMed

    Jin, Xin; He, Mingze; Ferguson, Betsy; Meng, Yuhuan; Ouyang, Limei; Ren, Jingjing; Mailund, Thomas; Sun, Fei; Sun, Liangdan; Shen, Juan; Zhuo, Min; Song, Li; Wang, Jufang; Ling, Fei; Zhu, Yuqi; Hvilsom, Christina; Siegismund, Hans; Liu, Xiaoming; Gong, Zhuolin; Ji, Fang; Wang, Xinzhong; Liu, Boqing; Zhang, Yu; Hou, Jianguo; Wang, Jing; Zhao, Hua; Wang, Yanyi; Fang, Xiaodong; Zhang, Guojie; Wang, Jian; Zhang, Xuejun; Schierup, Mikkel H; Du, Hongli; Wang, Jun; Wang, Xiaoning

    2012-01-01

    Non-human primates have emerged as an important resource for the study of human disease and evolution. The characterization of genomic variation between and within non-human primate species could advance the development of genetically defined non-human primate disease models. However, non-human primate specific reagents that would expedite such research, such as exon-capture tools, are lacking. We evaluated the efficiency of using a human exome capture design for the selective enrichment of exonic regions of non-human primates. We compared the exon sequence recovery in nine chimpanzees, two crab-eating macaques and eight Japanese macaques. Over 91% of the target regions were captured in the non-human primate samples, although the specificity of the capture decreased as evolutionary divergence from humans increased. Both intra-specific and inter-specific DNA variants were identified; Sanger-based resequencing validated 85.4% of 41 randomly selected SNPs. Among the short indels identified, a majority (54.6%-77.3%) of the variants resulted in a change of 3 base pairs, consistent with expectations for a selection against frame shift mutations. Taken together, these findings indicate that use of a human design exon-capture array can provide efficient enrichment of non-human primate gene regions. Accordingly, use of the human exon-capture methods provides an attractive, cost-effective approach for the comparative analysis of non-human primate genomes, including gene-based DNA variant discovery.

  14. 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

    2013-01-03

    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.

  15. 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

  16. 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.

  17. 6-Li enriched Cs2LiYCl6:Ce based thermal neutron detector coupled with CMOS solid-state photomultipliers for a portable detector unit

    NASA Astrophysics Data System (ADS)

    Whitney, Chad; Stapels, Christopher; Johnson, Erik; Chapman, Eric; Alberghini, Guy; Glodo, Jarek; Shah, Kanai; Christian, James

    2011-03-01

    For detecting neutrons, 3-He tubes provide sensitivity and a unique capability for detecting and discriminating neutron signals from background gamma-ray signals. A solid-state scintillation-based detector provides an alternative to 3-He for neutron detection. A real-time, portable, and low cost thermal neutron detector has been constructed from a 6Li-enriched Cs2LiYCl6:Ce (CLYC) scintillator crystal coupled with a CMOS solid-state photomultiplier (SSPM). These components are fully integrated with a miniaturized multi-channel analyzer (MCA) unit for calculation and readout of the counts and count rates. CLYC crystals and several other elpasolites including Cs2LiLaCl6:Ce (CLLC) and Cs2LiLaBr6:Ce (CLLB) have been considered for their unique properties in detecting neutrons and discriminating gamma ray events along with providing excellent energy resolution comparable to NaI(Tl) scintillators. CLYC's slower rise and decay time for neutrons (70ns and 900ns respectively) relative to a faster rise and decay time for gamma ray events (6ns and 55ns respectively) allows for pulse shape discrimination in mixed radiation fields. Light emissions from CLYC crystals are detected using an array of avalanche photodiodes referred to as solid-state photomultipliers. SSPMs are binary photon counting devices where the number of pixels activated is directly proportional to the light output of the CLYC scintillator which is proportional to the energy deposited from the radiation field. SSPMs can be fabricated using standard CMOS processes and inherently contain the low noise performance associated with ordinary photomultiplier tubes (PMT) while providing a light and compact solution for portable neutron detectors.

  18. Portable NDA equipment for enrichment measurements for the HEU transparency program

    SciTech Connect

    Decman, D J; Glaser, J; Hernandez, J M; Luke, S J

    1999-07-20

    In October 1996, the Department of Energy (DOE) and MINATOM agreed to use portable non-destructive assay (NDA) equipment to measure the {sup 235}U enrichment of material subject to the HEU Transparency agreement. A system based on the ''enrichment meter'' method and high-purity germanium (HPGe) detectors had been previously developed for this application. Instead, sodium iodide (NaI) detectors were chosen to measure {sup 235}U enrichment because HPGe systems might reveal sensitive information. Although the accuracy of the NaI systems is less than an HPGe system, it still satisfies the transparency requirements. The equipment consists of a collimated NaI detector, a Canberra Inspector Multi-channel Analyzer, and a laptop computer. The units have been used to confirm the enrichment of material at Russian facilities since January 1997. This paper compares the performance of the NaI systems with the HPGe system and discusses some significant differences.

  19. Enriching text with images and colored light

    NASA Astrophysics Data System (ADS)

    Sekulovski, Dragan; Geleijnse, Gijs; Kater, Bram; Korst, Jan; Pauws, Steffen; Clout, Ramon

    2008-01-01

    We present an unsupervised method to enrich textual applications with relevant images and colors. The images are collected by querying large image repositories and subsequently the colors are computed using image processing. A prototype system based on this method is presented where the method is applied to song lyrics. In combination with a lyrics synchronization algorithm the system produces a rich multimedia experience. In order to identify terms within the text that may be associated with images and colors, we select noun phrases using a part of speech tagger. Large image repositories are queried with these terms. Per term representative colors are extracted using the collected images. Hereto, we either use a histogram-based or a mean shift-based algorithm. The representative color extraction uses the non-uniform distribution of the colors found in the large repositories. The images that are ranked best by the search engine are displayed on a screen, while the extracted representative colors are rendered on controllable lighting devices in the living room. We evaluate our method by comparing the computed colors to standard color representations of a set of English color terms. A second evaluation focuses on the distance in color between a queried term in English and its translation in a foreign language. Based on results from three sets of terms, a measure of suitability of a term for color extraction based on KL Divergence is proposed. Finally, we compare the performance of the algorithm using either the automatically indexed repository of Google Images and the manually annotated Flickr.com. Based on the results of these experiments, we conclude that using the presented method we can compute the relevant color for a term using a large image repository and image processing.

  20. Motif enrichment tool.

    PubMed

    Blatti, Charles; Sinha, Saurabh

    2014-07-01

    The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/.

  1. 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.

  2. Chromatin enrichment for proteomics

    PubMed Central

    Kustatscher, Georg; Wills, Karen L. H.; Furlan, Cristina; Rappsilber, Juri

    2015-01-01

    During interphase, chromatin hosts fundamental cellular processes, such as gene expression, DNA replication and DNA damage repair. To analyze chromatin on a proteomic scale, we have developed chromatin enrichment for proteomics (ChEP), which is a simple biochemical procedure that enriches interphase chromatin in all its complexity. It enables researchers to take a ‘snapshot’ of chromatin and to isolate and identify even transiently bound factors. In ChEP, cells are fixed with formaldehyde; subsequently, DNA together with all cross-linked proteins is isolated by centrifugation under denaturing conditions. This approach enables the analysis of global chromatin composition and its changes, which is in contrast with existing chromatin enrichment procedures, which either focus on specific chromatin loci (e.g., affinity purification) or are limited in specificity, such as the analysis of the chromatin pellet (i.e., analysis of all insoluble nuclear material). ChEP takes half a day to complete and requires no specialized laboratory skills or equipment. ChEP enables the characterization of chromatin response to drug treatment or physiological processes. Beyond proteomics, ChEP may preclear chromatin for chromatin immunoprecipitation (ChIP) analyses. PMID:25101823

  3. 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.

  4. An affinity-based genome walking method to find transgene integration loci in transgenic genome.

    PubMed

    Thirulogachandar, V; Pandey, Prachi; Vaishnavi, C S; Reddy, Malireddy K

    2011-09-15

    Identifying a good transgenic event from the pool of putative transgenics is crucial for further characterization. In transgenic plants, the transgene can integrate in either single or multiple locations by disrupting the endogenes and/or in heterochromatin regions causing the positional effect. Apart from this, to protect the unauthorized use of transgenic plants, the signature of transgene integration for every commercial transgenic event needs to be characterized. Here we show an affinity-based genome walking method, named locus-finding (LF) PCR (polymerase chain reaction), to determine the transgene flanking sequences of rice plants transformed by Agrobacterium tumefaciens. LF PCR includes a primary PCR by a degenerated primer and transfer DNA (T-DNA)-specific primer, a nested PCR, and a method of enriching the desired amplicons by using a biotin-tagged primer that is complementary to the T-DNA. This enrichment technique separates the single strands of desired amplicons from the off-target amplicons, reducing the template complexity by several orders of magnitude. We analyzed eight transgenic rice plants and found the transgene integration loci in three different chromosomes. The characteristic illegitimate recombination of the Agrobacterium sp. was also observed from the sequenced integration loci. We believe that the LF PCR should be an indispensable technique in transgenic analysis.

  5. 10 CFR Appendix F to Part 110 - Illustrative List of Laser-Based Enrichment Plant Equipment and Components Under NRC Export...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... compound. Common nomenclature for these processes include: first category-atomic vapor laser isotope...) Desublimers (or cold traps) used to remove UF6 from the enrichment process for subsequent transfer upon... −120 °C or less; or (iii) UF6 cold traps capable of temperatures of −20 °C or less. (13) Lasers...

  6. 10 CFR Appendix F to Part 110 - Illustrative List of Laser-Based Enrichment Plant Equipment and Components Under NRC Export...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... compound. Common nomenclature for these processes include: first category-atomic vapor laser isotope...) Desublimers (or cold traps) used to remove UF6 from the enrichment process for subsequent transfer upon... −120 °C or less; or (iii) UF6 cold traps capable of temperatures of −20 °C or less. (13) Lasers...

  7. Servo Control Using Wave-Based Method

    NASA Astrophysics Data System (ADS)

    Marek, O.

    The wave-based control of flexible mechanical systems has been developed. It is based on the idea of sending waves into the mechanical system, measuring of the incoming waves and avoiding the re-sending of these waves into the continuum again. This approach actually absorbs the energy coming from the system. It has been successfully applied for the number of simulations. This paper deals with the implementation of the wave-based control for experiments using servomotor. It particularly describes the implementation on Yaskawa servo-motor and its PLC system.

  8. 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

  9. Adaptive Kernel Based Machine Learning Methods

    DTIC Science & Technology

    2012-10-15

    multiscale collocation method with a matrix compression strategy to discretize the system of integral equations and then use the multilevel...augmentation method to solve the resulting discrete system. A priori and a posteriori 1 parameter choice strategies are developed for thesemethods. The...performance of the proximity algo- rithms for the L1/TV denoising model. This leads us to a new characterization of all solutions to the L1/TV model via fixed

  10. 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.

  11. A new nonenzymatic method and device to obtain a fat tissue derivative highly enriched in pericyte-like elements by mild mechanical forces from human lipoaspirates.

    PubMed

    Bianchi, Francesca; Maioli, Margherita; Leonardi, Erika; Olivi, Elena; Pasquinelli, Gianandrea; Valente, Sabrina; Mendez, Armando J; Ricordi, Camillo; Raffaini, Mirco; Tremolada, Carlo; Ventura, Carlo

    2013-01-01

    Adipose tissue contains multipotent elements with phenotypic and gene expression profiles similar to human mesenchymal stem cells (hMSCs) and pericytes. The chance of clinical translation of the multilineage potential of these cells is delayed by the poor/negligible cell survival within cryopreserved lipoaspirates, the difficulty of ex vivo expansion, and the complexity of current Good Manufacturing Practice (cGMP) requirements for expanded cells. Hence, availability of a minimally manipulated, autologous, hMSC/pericyte-enriched fat product would have remarkable biomedical and clinical relevance. Here, we present an innovative system, named Lipogems, providing a nonexpanded, ready-to-use fat product. The system uses mild mechanical forces in a completely closed system, avoiding enzymes, additives, and other manipulations. Differently from unprocessed lipoaspirate, the nonexpanded Lipogems product encompasses a remarkably preserved vascular stroma with slit-like capillaries wedged between adipocytes and stromal stalks containing vascular channels with evident lumina. Immunohistochemistry revealed that Lipogems stromal vascular tissue included abundant cells with pericyte/hMSC identity. Flow cytometry analysis of nonexpanded, collagenase-treated Lipogems product showed that it was comprised with a significantly higher percentage of mature pericytes and hMSCs, and lower amount of hematopoietic elements, than enzymatically digested lipoaspirates. Differently from the lipoaspirate, the distinctive traits of freshly isolated Lipogems product were not altered by cryopreservation. Noteworthy, the features of fresh product were retained in the Lipogems product obtained from human cadavers, paving the way to an off-the-shelf strategy for reconstructive procedures and regenerative medicine. When placed in tissue culture medium, the Lipogems product yielded a highly homogeneous adipose tissue-derived hMSC population, exhibiting features of hMSCs isolated from other sources

  12. Capillary electrophoresis-systematic evolution of ligands by exponential enrichment selection of base- and sugar-modified DNA aptamers: target binding dominated by 2'-O,4'-C-methylene-bridged/locked nucleic acid primer.

    PubMed

    Kasahara, Yuuya; Irisawa, Yuuta; Fujita, Hiroto; Yahara, Aiko; Ozaki, Hiroaki; Obika, Satoshi; Kuwahara, Masayasu

    2013-05-21

    Chemically modified DNA aptamers specific to human α-thrombin were obtained from oligodeoxyribonucleotide (ODN) libraries by using a capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) method. These libraries contained 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides (B/L nucleotides) in the primer region and/or C5-modified thymidine bearing N(6)-ethyladenine (t) in the nonprimer region. Modified DNA aptamers showed high binding affinities to the target, with dissociation constants (Kd) values in the range of subnanomolar to several ten nanomolar levels. The introduction of base modification significantly suppressed the frequency of G-quadruplex motifs, which are often seen in thrombin-binding DNA aptamers. The resulting alternatives contained the 10-mer consensus sequence t5Gt2G2, which is frequently found in modified DNA aptamers with subnanomolar protein binding affinities. Furthermore, some base- and sugar-modified DNA aptamers with the 12-mer consensus sequence t2G2tC(A/G)A2G2t displayed binding activities that were dependent on the presence of B/L nucleotides in the primer region. Such aptamers were interestingly not recovered from a natural DNA library or from DNA libraries modified with either B/L nucleotides or t's. This emerging characteristic binding property will enable the creation of a direct selection methodology for DNA-based molecular switches that are triggered by chemical conversion of B/L nucleotides introduced to constant sequence regions in ODN libraries.

  13. 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.

  14. Detection of thermal-induced prompt fission neutrons of highly-enriched uranium: A position sensitive technique

    NASA Astrophysics Data System (ADS)

    Tartaglione, A.; Di Lorenzo, F.; Mayer, R. E.

    2009-07-01

    Cargo interrogation in search for special nuclear materials like highly-enriched uranium or 239Pu is a first priority issue of international borders security. In this work we present a thermal-pulsed neutron-based approach to a technique which combines the time-of-flight method and demonstrates a capability to detect small quantities of highly-enriched uranium shielded with high or low Z materials providing, in addition, a manner to know the approximate position of the searched material.

  15. Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data

    PubMed Central

    Wu, Qian; Won, Kyoung-Jae; Li, Hongzhe

    2015-01-01

    Chromatin immunoprecipitation sequencing (ChIP-seq) is a powerful method for analyzing protein interactions with DNA. It can be applied to identify the binding sites of transcription factors (TFs) and genomic landscape of histone modification marks (HMs). Previous research has largely focused on developing peak-calling procedures to detect the binding sites for TFs. However, these procedures may fail when applied to ChIP-seq data of HMs, which have diffuse signals and multiple local peaks. In addition, it is important to identify genes with differential histone enrichment regions between two experimental conditions, such as different cellular states or different time points. Parametric methods based on Poisson/negative binomial distribution have been proposed to address this differential enrichment problem and most of these methods require biological replications. However, many ChIP-seq data usually have a few or even no replicates. We propose a nonparametric method to identify the genes with differential histone enrichment regions even without replicates. Our method is based on nonparametric hypothesis testing and kernel smoothing in order to capture the spatial differences in histone-enriched profiles. We demonstrate the method using ChIP-seq data on a comparative epigenomic profiling of adipogenesis of murine adipose stromal cells and the Encyclopedia of DNA Elements (ENCODE) ChIP-seq data. Our method identifies many genes with differential H3K27ac histone enrichment profiles at gene promoter regions between proliferating preadipocytes and mature adipocytes in murine 3T3-L1 cells. The test statistics also correlate with the gene expression changes well and are predictive to gene expression changes, indicating that the identified differentially enriched regions are indeed biologically meaningful. PMID:25657574

  16. Hybrid Enrichment Verification Array: Module Characterization Studies

    SciTech Connect

    Zalavadia, Mital A.; Smith, Leon E.; McDonald, Benjamin S.; Kulisek, Jonathan A.; Mace, Emily K.; Deshmukh, Nikhil S.

    2016-03-01

    The work presented in this report is focused on the characterization and refinement of the Hybrid Enrichment Verification Array (HEVA) approach, which combines the traditional 186-keV 235U signature with high-energy prompt gamma rays from neutron capture in the detector and surrounding collimator material, to determine the relative enrichment and 235U mass of the cylinder. The design of the HEVA modules (hardware and software) deployed in the current field trial builds on over seven years of study and evolution by PNNL, and consists of a ø3''×3'' NaI(Tl) scintillator coupled to an Osprey digital multi-channel analyzer tube base from Canberra. The core of the HEVA methodology, the high-energy prompt gamma-ray signature, serves as an indirect method for the measurement of total neutron emission from the cylinder. A method for measuring the intrinsic efficiency of this “non-traditional” neutron signature and the results from a benchmark experiment are presented. Also discussed are potential perturbing effects on the non-traditional signature, including short-lived activation of materials in the HEVA module. Modeling and empirical results are presented to demonstrate that such effects are expected to be negligible for the envisioned implementation scenario. In comparison to previous versions, the new design boosts the high-energy prompt gamma-ray signature, provides more flexible and effective collimation, and improves count-rate management via commercially available pulse-processing electronics with a special modification prompted by PNNL.

  17. 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.

  18. 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.

  19. Alaska climate divisions based on objective methods

    NASA Astrophysics Data System (ADS)

    Angeloff, H.; Bieniek, P. A.; Bhatt, U. S.; Thoman, R.; Walsh, J. E.; Daly, C.; Shulski, M.

    2010-12-01

    Alaska is vast geographically, is located at high latitudes, is surrounded on three sides by oceans and has complex topography, encompassing several climate regions. While climate zones exist, there has not been an objective analysis to identify regions of homogeneous climate. In this study we use cluster analysis on a robust set of weather observation stations in Alaska to develop climate divisions for the state. Similar procedures have been employed in the contiguous United States and other parts of the world. Our analysis, based on temperature and precipitation, yielded a set of 10 preliminary climate divisions. These divisions include an eastern and western Arctic (bounded by the Brooks Range to the south), a west coast region along the Bering Sea, and eastern and western Interior regions (bounded to the south by the Alaska Range). South of the Alaska Range there were the following divisions: an area around Cook Inlet (also including Valdez), coastal and inland areas along Bristol Bay including Kodiak and Lake Iliamna, the Aleutians, and Southeast Alaska. To validate the climate divisions based on relatively sparse station data, additional sensitivity analysis was performed. Additional clustering analysis utilizing the gridded North American Regional Reanalysis (NARR) was also conducted. In addition, the divisions were evaluated using correlation analysis. These sensitivity tests support the climate divisions based on cluster analysis.

  20. 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.

  1. Method for producing iron-based catalysts

    SciTech Connect

    Farcasiu, M.; Kaufman, P.B.; Diehl, J.R.; Kathrein, H.

    1999-09-07

    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.

  2. Identification of cross-linked peptides after click-based enrichment using sequential collision-induced dissociation and electron transfer dissociation tandem mass spectrometry.

    PubMed

    Chowdhury, Saiful M; Du, Xiuxia; Tolić, Nikola; Wu, Si; Moore, Ronald J; Mayer, M Uljana; Smith, Richard D; Adkins, Joshua N

    2009-07-01

    Chemical cross-linking combined with mass spectrometry can be a powerful approach for the identification of protein-protein interactions and for providing constraints on protein structures. However, enrichment of cross-linked peptides is crucial to reduce sample complexity before mass spectrometric analysis. In addition compact cross-linkers are often preferred to provide short spacer lengths, surface accessibility to the protein complexes, and must have reasonable solubility under conditions where the native complex structure is stable. In this study, we present a novel compact cross-linker that contains two distinct features: (1) an alkyne tag and (2) a small molecule detection tag (NO(2)) to maintain reasonable solubility in water. The alkyne tag enables enrichment of the cross-linked peptides after proteolytic cleavage and coupling of an affinity tag using alkyne-azido click chemistry. Neutral loss of the small NO(2) moiety provides a secondary means of detecting cross-linked peptides in MS/MS analyses, providing additional confidence in peptide identifications. We show the labeling efficiency of this cross-linker, which we termed CLIP (click-enabled linker for interacting proteins) using ubiquitin. The enrichment capability of CLIP is demonstrated for cross-linked ubiquitin in highly complex E. coli cell lysates. Sequential collision-induced dissociation tandem mass spectrometry (CID-MS/MS) and electron transfer dissociation (ETD)-MS/MS of intercross-linked peptides (two peptides connected with a cross-linker) are also demonstrated for improved automated identification of cross-linked peptides.

  3. Enrichment of fetal cells from maternal blood by high gradient magnetic cell sorting (double MACS) for PCR-based genetic analysis.

    PubMed

    Büsch, J; Huber, P; Pflüger, E; Miltenyi, S; Holtz, J; Radbruch, A

    1994-12-01

    For simple and effective isolation of fetal cells from peripheral maternal blood, we combined depletion of maternal cells and enrichment of fetal cells by high-gradient magnetic cell separation (MACS). First CD45+ and CD14+ cells were depleted from maternal peripheral blood mononuclear cells by MACS. From the depleted fraction, CD71+ erythroid cells were enriched up to 80 per cent by MACS. This double-MACS' procedure yielded an average depletion rate of 780-fold and an average enrichment rate of 500-fold, with approximate recovery rates of 40-55 per cent. For paternity testing, cells from unseparated blood and the various fractions were analysed for polymorphism of the HLA-DQ-A1 locus and D1S80 locus by the polymerase chain reaction (PCR). In CD45-/CD71+ sorted cells from maternal blood, but not in unfractionated cells from maternal blood or CD45-/CD14- cells, paternal alleles could be detected. In the CD45-/CD71+ fraction, the relative frequency of paternal alleles compared with maternal alleles ranged from 1 in 20 to 1 in 200 (determined by titration and depending on the quality of separation and biological variation). In 7 out of 11 cases, between weeks 12 and 25 of gestation, we could identify paternal alleles by PCR, either HLA-DQ-A1 or D1S80. This double-MACS procedure is simple, fast, efficient, and reliable for non-invasive prenatal diagnosis.

  4. 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…

  5. 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…

  6. A power function method for estimating base flow.

    PubMed

    Lott, Darline A; Stewart, Mark T

    2013-01-01

    Analytical base flow separation techniques are often used to determine the base flow contribution to total stream flow. Most analytical methods derive base flow from discharge records alone without using basin-specific variables other than basin area. This paper derives a power function for estimating base flow, the form being aQ(b) + cQ, an analytical method calibrated against an integrated basin variable, specific conductance, relating base flow to total discharge, and is consistent with observed mathematical behavior of dissolved solids in stream flow with varying discharge. Advantages of the method are being uncomplicated, reproducible, and applicable to hydrograph separation in basins with limited specific conductance data. The power function relationship between base flow and discharge holds over a wide range of basin areas. It better replicates base flow determined by mass balance methods than analytical methods such as filters or smoothing routines that are not calibrated to natural tracers or empirical basin and gauge-specific variables. Also, it can be used with discharge during periods without specific conductance values, including separating base flow from quick flow for single events. However, it may overestimate base flow during very high flow events. Application of geochemical mass balance and power function base flow separation methods to stream flow and specific conductance records from multiple gauges in the same basin suggests that analytical base flow separation methods must be calibrated at each gauge. Using average values of coefficients introduces a potentially significant and unknown error in base flow as compared with mass balance methods.

  7. Method for hardfacing a ferrous base material

    SciTech Connect

    Sakaguchi, S.; Ito, H.; Shiroyama, M.

    1984-10-23

    Tungsten carbide and nickel-phosphorus alloy coexist in individual particles. The composite powder produced by a mechanical mix of these two substances consists of 30 about 95 percent by weight of tungsten carbide and valanced nickel-phosphorus alloy. This powder is sprayed to the ferrous base material, resulting in a uniform dispersion of both tungsten carbide and nickel-phosphorus, causing tight adhesion to the surface because the tungsten carbide and nickel-phosphorus alloy coexist in individual particles in the composite. A hard metal coating is produced having high hardness and excellent wear resistance, after the surface of the hard metal coating is heated and the high temperature of the nickel-phosphorus alloy causes a liquid phase under the condition of a nonoxidizing atmosphere. This hard metal coating is used for various kinds of the wear-resistant materials.

  8. Spatial Variation of Deuterium Enrichment in Bulk Water of Snowgum Leaves1[OA

    PubMed Central

    Šantrůček, Jiří; Květoň, Jiří; Šetlík, Jiří; Bulíčková, 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 δdeuterium. 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

  9. GoBean: a Java GUI application for visual exploration of GO term enrichments.

    PubMed

    Lee, Sanghyuk; Cha, Ji-Young; Kim, Hyeonjin; Yu, Ungsik

    2012-02-01

    We have developed a biologist-friendly, Java GUI application (GoBean) for GO term enrichment analysis. It was designed to be a comprehensive and flexible GUI tool for GO term enrichment analysis, combining the merits of other programs and incorporating extensive graphic exploration of enrichment results. An intuitive user interface with multiple panels allows for extensive visual scrutiny of analysis results. The program includes many essential and useful features, such as enrichment analysis algorithms, multiple test correction methods, and versatile filtering of enriched GO terms for more focused analyses. A unique graphic interface reflecting the GO tree structure was devised to facilitate comparisons of multiple GO analysis results, which can provide valuable insights for biological interpretation. Additional features to enhance user convenience include built in ID conversion, evidence code-based gene-GO association filtering, set operations of gene lists and enriched GO terms, and user -provided data files. It is available at http://neon.gachon.ac.kr/GoBean/.

  10. 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.

  11. FOCUS: a deconvolution method based on algorithmic complexity

    NASA Astrophysics Data System (ADS)

    Delgado, C.

    2006-07-01

    A new method for improving the resolution of images is presented. It is based on Occam's razor principle implemented using algorithmic complexity arguments. The performance of the method is illustrated using artificial and real test data.

  12. Enriching Science and Math through Engineering

    ERIC Educational Resources Information Center

    Redmond, Adrienne; Thomas, Julie; High, Karen; Scott, Margaret; Jordan, Pat; Dockers, Jean

    2011-01-01

    This case study reviewed the collaborative efforts of university engineers, teacher educators, and middle school teachers to advance sixth- and seventh-grade students' learning through a series of project-based engineering activities. This two-year project enriched regular school curricula by introducing real-world applications of science and…

  13. ParentSource: A Practice in Enrichment

    ERIC Educational Resources Information Center

    Blackwell, Patricia

    2005-01-01

    Community-based parenting education programs have a unique role to play in the promotion of infant mental health. In contrast to classes that seek to accelerate child development, the author describes enrichment programs that promote parent-child bonding and healthy social and emotional development. The ParentSource program was developed on the…

  14. Human leukocyte antigen haplotype phasing by allele-specific enrichment with peptide nucleic acid probes

    PubMed Central

    Murphy, Nicholas M; Pouton, Colin W; Irving, Helen R

    2014-01-01

    Targeted capture of large fragments of genomic DNA that enrich for human leukocyte antigen (HLA) system haplotypes has utility in haematopoietic stem cell transplantation. Current methods of HLA matching are based on inference or familial studies of inheritance; and each approach has its own inherent limitations. We have designed and tested a probe–target-extraction method for capturing specific HLA haplotypes by hybridization of peptide nucleic acid (PNA) probes to alleles of the HLA-DRB1 gene. Short target fragments contained in plasmids were initially used to optimize the method followed by testing samples of genomic DNA from human subjects with preselected HLA haplotypes and obtained approximately 10% enrichment for the specific haplotype. When performed with high-molecular-weight genomic DNA, 99.0% versus 84.0% alignment match was obtained for the specific haplotype probed. The allele-specific target enrichment that we obtained can facilitate the elucidation of haplotypes between the 65 kb separating the HLA-DRB1 and the HLA-DQA1 genes, potentially spanning a total distance of at least 130 kb. Allele-specific target enrichment with PNA probes is a straightforward technique that has the capability to improve the resolution of DNA and whole genome sequencing technologies by allowing haplotyping of enriched DNA and crucially, retaining the DNA methylation profile. PMID:24936514

  15. Advanced Neutron Source enrichment study

    SciTech Connect

    Bari, R.A.; Ludewig, H.; Weeks, J.R.

    1994-12-31

    A study has been performed of the impact on performance of using low enriched uranium (20% {sup 235}U) or medium enriched uranium (35% {sup 235}U) as an alternative fuel for the Advanced Neutron Source, which is currently designed to use uranium enriched to 93% {sup 235}U. Higher fuel densities and larger volume cores were evaluated at the lower enrichments in terms of impact on neutron flux, safety, safeguards, technical feasibility, and cost. The feasibility of fabricating uranium silicide fuel at increasing material density was specifically addressed by a panel of international experts on research reactor fuels. The most viable alternative designs for the reactor at lower enrichments were identified and discussed. Several sensitivity analyses were performed to gain an understanding of the performance of the reactor at parametric values of power, fuel density, core volume, and enrichment that were interpolations between the boundary values imposed on the study or extrapolations from known technology.

  16. Uranium enrichment management review: summary of analysis

    SciTech Connect

    Not Available

    1981-01-01

    In May 1980, the Assistant Secretary for Resource Applications within the Department of Energy requested that a group of experienced business executives be assembled to review the operation, financing, and management of the uranium enrichment enterprise as a basis for advising the Secretary of Energy. After extensive investigation, analysis, and discussion, the review group presented its findings and recommendations in a report on December 2, 1980. The following pages contain background material on which that final report was based. This report is arranged in chapters that parallel those of the uranium enrichment management review final report - chapters that contain summaries of the review group's discussion and analyses in six areas: management of operations and construction; long-range planning; marketing of enrichment services; financial management; research and development; and general management. Further information, in-depth analysis, and discussion of suggested alternative management practices are provided in five appendices.

  17. 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.

  18. 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.

  19. Gravimetric enrichment of high lipid and starch accumulating microalgae.

    PubMed

    Hassanpour, Morteza; Abbasabadi, Mahsa; Ebrahimi, Sirous; Hosseini, Maryam; Sheikhbaglou, Ahmad

    2015-11-01

    This study presents gravimetric enrichment of mixed culture to screen starch and lipid producing species separately in a sequencing batch reactor. In the enriched starch-producing mixed culture photobioreactor, the starch content at the end of steady state batch became 3.42 times the beginning of depletion. Whereas in the enriched lipid-producing photobioreactor, the lipid content at the end of steady state batch became 3 times the beginning of famine phase. The obtained results revealed that the gravimetric enrichment is a suitable screening method for specific production of storage compounds in none-sterile large-scaled condition.

  20. Uranium enrichment determination by high-energy photon interrogation

    NASA Astrophysics Data System (ADS)

    Zhu, Jianyu; Zhang, Songbai; Wu, Jun

    2011-11-01

    Uranium enrichment determination by non-destructive assay is an important method in authenticating the nuclear warhead or uranium component in deep nuclear reduction verifications. In this paper, the feasibility of applying the high-energy photon interrogation to determine the uranium enrichment is studied. Simplified models are presented which were simulated by particle Monte Carlo transport code. The results indicate that the relation curves of the released neutrons and the enrichment of uranium objects are almost linear. For a uranium object of a given shape, the uranium enrichment can be obtained with the relation curves, which could be got in advance by calibration experiments or simulations.

  1. 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.

  2. 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.

  3. 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

  4. A Summary of Actinide Enrichment Technologies and Capability Gaps

    SciTech Connect

    Patton, Bradley D.; Robinson, Sharon M.

    2017-01-01

    The evaluation performed in this study indicates that a new program is needed to efficiently provide a national actinide radioisotope enrichment capability to produce milligram-to-gram quantities of unique materials for user communities as summarized in Table 1. This program xiv should leverage past actinide enrichment, the recent advances in stable isotope enrichment, and assessments of the future requirements to cost effectively develop this capability while establishing an experience base for a new generation of researchers in this vital area. Preliminary evaluations indicate that an EMIS device would have the capability to meet the future needs of the user community for enriched actinides. The EMIS technology could be potentially coupled with other enrichment technologies, such as irradiation, as pre-enrichment and/or post-enrichment systems to increase the throughput, reduce losses of material, and/or reduce operational costs of the base EMIS system. Past actinide enrichment experience and advances in the EMIS technology applied in stable isotope separations should be leveraged with this new evaluation information to assist in the establishment of a domestic actinide radioisotope enrichment capability.

  5. 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

  6. Neuron enriched nuclear proteome isolated from human brain.

    PubMed

    Dammer, Eric B; Duong, Duc M; Diner, Ian; Gearing, Marla; Feng, Yue; Lah, James J; Levey, Allan I; Seyfried, Nicholas T

    2013-07-05

    The brain consists of diverse cell types including neurons, astrocytes, oligodendrocytes, and microglia. The isolation of nuclei from these distinct cell populations provides an opportunity to identify cell-type-specific nuclear proteins, histone modifications, and regulation networks that are altered with normal brain aging or neurodegenerative disease. In this study, we used a method by which intact neuronal and non-neuronal nuclei were purified from human post-mortem brain employing a modification of fluorescence activated cell sorting (FACS) termed fluorescence activated nuclei sorting (FANS). An antibody against NeuN, a neuron specific splicing factor, was used to isolate neuronal nuclei. Utilizing mass spectrometry (MS) based label-free quantitative proteomics, we identified 1755 proteins from sorted NeuN-positive and negative nuclear extracts. Approximately 20% of these proteins were significantly enriched or depleted in neuronal versus non-neuronal populations. Immunoblots of primary cultured rat neuron, astrocyte, and oligodendrocyte extracts confirmed that distinct members of the major nucleocytoplasmic structural linkage complex (LINC), nesprin-1 and nesprin-3, were differentially enriched in neurons and astrocytes, respectively. These comparative proteomic data sets also reveal a number of transcription and splicing factors that are selectively enriched in a cell-type-specific manner in human brain.

  7. 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.

  8. 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.

  9. Early Recovery of Salmonella from Food Using a 6-Hour Non-selective Pre-enrichment and Reformulation of Tetrathionate Broth

    PubMed Central

    Daquigan, Ninalynn; Grim, Christopher J.; White, James R.; Hanes, Darcy E.; Jarvis, Karen G.

    2016-01-01

    Culture based methods are commonly employed to detect pathogens in food and environmental samples. These methods are time consuming and complex, requiring multiple non-selective and selective enrichment broths, and usually take at least 1 week to recover and identify pathogens. Improving pathogen detection in foods is a primary goal for regulatory agencies and industry. Salmonella detection in food relies on a series of culture steps in broth formulations optimized to resuscitate Salmonella and reduce the abundance of competitive bacteria. Examples of non-selective pre-enrichment broths used to isolate Salmonella from food include Lactose, Universal Pre-enrichment, BPW, and Trypticase Soy broths. Tetrathionate (TT) and Rappaport–Vassiliadis (RV) broths are employed after a 24-h non-selective enrichment to select for Salmonella and hamper the growth of competitive bacteria. In this study, we tested a new formulation of TT broth that lacks brilliant green dye and has lower levels of TT . We employed this TT broth formulation in conjunction with a 6-h non-selective pre-enrichment period and determined that Salmonella recovery was possible one day earlier than standard food culture methods. We tested the shortened culture method in different non-selective enrichment broths, enumerated Salmonella in the non-selective enrichments, and used 16S rRNA gene sequencing to determine the proportional abundances of Salmonella in the TT and RV selective enrichments. Together these data revealed that a 6-h non-selective pre-enrichment reduces the levels of competitive bacteria inoculated into the selective TT and RV broths, enabling the recovery of Salmonella 1 day earlier than standard culture enrichment methods. PMID:28082968

  10. 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

  11. Exploring the Query Expansion Methods for Concept Based Representation

    DTIC Science & Technology

    2014-11-01

    Exploring the Query Expansion Methods for Concept Based Representation Yue Wang and Hui Fang Department of Electrical and Computer Engineering...physicians find relevant medical cases for patients they are dealing with. Concept based representation has been shown to be effective in biomedical...in this paper, we explored two external resources to perform query expansion for the basic concept based representation method, and discussed the

  12. Modeling electrokinetic flow by Lagrangian particle-based method

    NASA Astrophysics Data System (ADS)

    Pan, Wenxiao; Kim, Kyungjoo; Perego, Mauro; Tartakovsky, Alexandre; Parks, Mike

    2015-11-01

    This work focuses on mathematical models and numerical schemes based on Lagrangian particle-based method that can effectively capture mesoscale multiphysics (hydrodynamics, electrostatics, and advection-diffusion) associated in applications of micro-/nano-transport and technology. The order of accuracy is significantly improved for particle-based method with the presented implicit consistent numerical scheme. Specifically, we show simulation results on electrokinetic flows and microfluidic mixing processes in micro-/nano-channel and through semi-permeable porous structures.

  13. Oriented Connectivity-Based Method for Segmenting Solar Loops

    NASA Technical Reports Server (NTRS)

    Lee, J. K.; Newman, T. S.; Gary, G. A.

    2005-01-01

    A method based on oriented connectivity that can automatically segnient arc-like structures (solar loops) from intensity images of the Sun's corona is introduced. The method is a constructive approach that uses model-guided processing to enable extraction of credible loop structures. Since the solar loops are vestiges of the solar magnetic field, the model-guided processing exploits external estimates of this field s local orientations that are derived from a physical magnetic field model. Empirical studies of the method s effectiveness are also presented. The Oriented Connectivity- Based Method is the first automatic method for the segmentation of solar loops.

  14. 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.

  15. Profile of World Uranium Enrichment Programs-2009

    SciTech Connect

    Laughter, Mark D

    2009-04-01

    based entirely on open-source information, which is dependent on published sources and may therefore not be completely accurate or reflect the most recent developments. Consequently, readers should not assume that information cited here has the endorsement of either ORNL or the U.S. Department of Energy. We are merely reporting what's been reported. In addition, this report briefly describes some of the safeguards techniques being used at various enrichment plants, including implementation of HSP recommendations.

  16. Development Issues on Linked Data Weblog Enrichment

    NASA Astrophysics Data System (ADS)

    Ruiz-Rube, Iván; Cornejo, Carlos M.; Dodero, Juan Manuel; García, Vicente M.

    In this paper, we describe the issues found during the development of LinkedBlog, a Linked Data extension for WordPress blogs. This extension enables to enrich text-based and video information contained in blog entries with RDF triples that are suitable to be stored, managed and exploited by other web-based applications. The issues have to do with the generality, usability, tracking, depth, security, trustiness and performance of the linked data enrichment process. The presented annotation approach aims at maintaining web-based contents independent from the underlying ontological model, by providing a loosely coupled RDFa-based approach in the linked data application. Finally, we detail how the performance of annotations can be improved through a semantic reasoner.

  17. 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.

  18. IFCM Based Segmentation Method for Liver Ultrasound Images.

    PubMed

    Jain, Nishant; Kumar, Vinod

    2016-11-01

    In this paper we have proposed an iterative Fuzzy C-Mean (IFCM) method which divides the pixels present in the image into a set of clusters. This set of clusters is then used to segment a focal liver lesion from a liver ultrasound image. Advantage of IFCM methods is that n-clusters FCM method may lead to non-uniform distribution of centroids, whereas in IFCM method centroids will always be uniformly distributed. Proposed method is compared with the edge based Active contour Chan-Vese (CV) method, and MAP-MRF method by implementing the methods on MATLAB. Proposed method is also compared with region based active contour region-scalable fitting energy (RSFE) method whose MATLAB code is available in author's website. Since no comparison is available on a common database, the performance of three methods and the proposed method have been compared on liver ultrasound (US) images available with us. Proposed method gives the best accuracy of 99.8 % as compared to accuracy of 99.46 %, 95.81 % and 90.08 % given by CV, MAP-MRF and RSFE methods respectively. Computation time taken by the proposed segmentation method for segmentation is 14.25 s as compared to 44.71, 41.27 and 49.02 s taken by CV, MAP-MRF and RSFE methods respectively.

  19. Selection-by-function: efficient enrichment of cathepsin E inhibitors from a DNA library.

    PubMed

    Naimuddin, Mohammed; Kitamura, Koichirou; Kinoshita, Yasunori; Honda-Takahashi, Yoko; Murakami, Marina; Ito, Masato; Yamamoto, Kenji; Hanada, Kazunori; Husimi, Yuzuru; Nishigaki, Koichi

    2007-01-01

    A method for efficient enrichment of protease inhibitors out of a DNA library was developed by introducing SF-link technology. A two-step selection strategy was designed consisting of the initial enrichment of aptamers based on binding function while the second enrichment step was based on the inhibitory activity to a protease, cathepsin E (CE). The latter was constructed by covalently linking of a biotinylated peptide substrate to each of the ssDNA molecule contained in the preliminarily selected DNA library, generating 'SF-link'. Gradual enrichment of inhibitory DNAs was attained in the course of selection. One molecule, SFR-6-3, showed an IC(50) of around 30 nM, a K(d) of around 15 nM and high selectivity for CE. Sequence and structure analysis revealed a C-rich sequence without any guanine and possibly an i-motif structure, which must be novel to be found in in vitro-selected aptamers. SF-link technology, which is novel as the screening technology, provided a remarkable enrichment of specific protease inhibitors and has a potential to be further developed.

  20. FEMO, A FLOW AND ENRICHMENT MONITOR FOR VERIFYING COMPLIANCE WITH INTERNATIONAL SAFEGUARDS REQUIREMENTS AT A GAS CENTRIFUGE ENRICHMENT FACILITY

    SciTech Connect

    Gunning, John E; Laughter, Mark D; March-Leuba, Jose A

    2008-01-01

    A number of countries have received construction licenses or are contemplating the construction of large-capacity gas centrifuge enrichment plants (GCEPs). The capability to independently verify nuclear material flows is a key component of international safeguards approaches, and the IAEA does not currently have an approved method to continuously monitor the mass flow of 235U in uranium hexafluoride (UF6) gas streams. Oak Ridge National Laboratory is investigating the development of a flow and enrichment monitor, or FEMO, based on an existing blend-down monitoring system (BDMS). The BDMS was designed to continuously monitor both 235U mass flow and enrichment of UF6 streams at the low pressures similar to those which exists at GCEPs. BDMSs have been installed at three sites-the first unit has operated successfully in an unattended environment for approximately 10 years. To be acceptable to GCEP operators, it is essential that the instrument be installed and maintained without interrupting operations. A means to continuously verify flow as is proposed by FEMO will likely be needed to monitor safeguards at large-capacity plants. This will enable the safeguards effectiveness that currently exists at smaller plants to be maintained at the larger facilities and also has the potential to reduce labor costs associated with inspections at current and future plants. This paper describes the FEMO design requirements, operating capabilities, and development work required before field demonstration.

  1. Engaging African American men in empirically based marriage enrichment programs: lessons from two focus groups on the ProSAAM project.

    PubMed

    Hurt, Tera R; Beach, Steven R H; Stokes, LaTrena A; Bush, Perdeta L; Sheats, Kameron J; Robinson, Shayla G

    2012-07-01

    To better meet the needs of eligible African American men who were reluctant to enroll in a 5-year study called the Program for Strong African American Marriages (ProSAAM), we employed two focus groups to listen to the voices of a sample of the population being recruited and to explore their feedback about taking part in such a marriage enrichment program and how best to recruit other African American men. We explain our application of the focus group results to our recruitment of African American married couples for ProSAAM. The positive outcomes from the implementation of these results can provide potential ideas for those seeking innovative means to improve recruitment of African American men to programs that strengthen marital relationships.

  2. Targeting Colorectal Cancer Proliferation, Stemness and Metastatic Potential Using Brassicaceae Extracts Enriched in Isothiocyanates: A 3D Cell Model-Based Study.

    PubMed

    Pereira, Lucília P; Silva, Patrícia; Duarte, Marlene; Rodrigues, Liliana; Duarte, Catarina M M; Albuquerque, Cristina; Serra, Ana Teresa

    2017-04-10

    Colorectal cancer (CRC) recurrence is often attributable to circulating tumor cells and/or cancer stem cells (CSCs) that resist to conventional therapies and foster tumor progression. Isothiocyanates (ITCs) derived from Brassicaceae vegetables have demonstrated anticancer effects in CRC, however little is known about their effect in CSCs and tumor initiation properties. Here we examined the effect of ITCs-enriched Brassicaceae extracts derived from watercress and broccoli in cell proliferation, CSC phenotype and metastasis using a previously developed three-dimensional HT29 cell model with CSC-like traits. Both extracts were phytochemically characterized and their antiproliferative effect in HT29 monolayers was explored. Next, we performed cell proliferation assays and flow cytometry analysis in HT29 spheroids treated with watercress and broccoli extracts and respective main ITCs, phenethyl isothiocyanate (PEITC) and sulforaphane (SFN). Soft agar assays and relative quantitative expression analysis of stemness markers and Wnt/β-catenin signaling players were performed to evaluate the effect of these phytochemicals in stemness and metastasis. Our results showed that both Brassicaceae extracts and ITCs exert antiproliferative effects in HT29 spheroids, arresting cell cycle at G₂/M, possibly due to ITC-induced DNA damage. Colony formation and expression of LGR5 and CD133 cancer stemness markers were significantly reduced. Only watercress extract and PEITC decreased ALDH1 activity in a dose-dependent manner, as well as β-catenin expression. Our research provides new insights on CRC therapy using ITC-enriched Brassicaceae extracts, specially watercress extract, to target CSCs and circulating tumor cells by impairing cell proliferation, ALDH1-mediated chemo-resistance, anoikis evasion, self-renewal and metastatic potential.

  3. New generation enrichment monitoring technology for gas centrifuge enrichment plants

    SciTech Connect

    Ianakiev, Kiril D; Alexandrov, Boian S.; Boyer, Brian D.; Hill, Thomas R.; Macarthur, Duncan W.; Marks, Thomas; Moss, Calvin E.; Sheppard, Gregory A.; Swinhoe, Martyn T.

    2008-06-13

    The continuous enrichment monitor, developed and fielded in the 1990s by the International Atomic Energy Agency, provided a go-no-go capability to distinguish between UF{sub 6} containing low enriched (approximately 4% {sup 235}U) and highly enriched (above 20% {sup 235}U) uranium. This instrument used the 22-keV line from a {sup 109}Cd source as a transmission source to achieve a high sensitivity to the UF{sub 6} gas absorption. The 1.27-yr half-life required that the source be periodically replaced and the instrument recalibrated. The instrument's functionality and accuracy were limited by the fact that measured gas density and gas pressure were treated as confidential facility information. The modern safeguarding of a gas centrifuge enrichment plant producing low-enriched UF{sub 6} product aims toward a more quantitative flow and enrichment monitoring concept that sets new standards for accuracy stability, and confidence. An instrument must be accurate enough to detect the diversion of a significant quantity of material, have virtually zero false alarms, and protect the operator's proprietary process information. We discuss a new concept for advanced gas enrichment assay measurement technology. This design concept eliminates the need for the periodic replacement of a radioactive source as well as the need for maintenance by experts. Some initial experimental results will be presented.

  4. Hydrogen-enriched fuels

    SciTech Connect

    Roser, R.

    1998-08-01

    NRG Technologies, Inc. is attempting to develop hardware and infrastructure that will allow mixtures of hydrogen and conventional fuels to become viable alternatives to conventional fuels alone. This commercialization can be successful if the authors are able to achieve exhaust emission levels of less than 0.03 g/kw-hr NOx and CO; and 0.15 g/kw-hr NMHC at full engine power without the use of exhaust catalysts. The major barriers to achieving these goals are that the lean burn regimes required to meet exhaust emissions goals reduce engine output substantially and tend to exhibit higher-than-normal total hydrocarbon emissions. Also, hydrogen addition to conventional fuels increases fuel cost, and reduces both vehicle range and engine output power. Maintaining low emissions during transient driving cycles has not been demonstrated. A three year test plan has been developed to perform the investigations into the issues described above. During this initial year of funding research has progressed in the following areas: (a) a cost effective single-cylinder research platform was constructed; (b) exhaust gas speciation was performed to characterize the nature of hydrocarbon emissions from hydrogen-enriched natural gas fuels; (c) three H{sub 2}/CH{sub 4} fuel compositions were analyzed using spark timing and equivalence ratio sweeping procedures and finally; (d) a full size pick-up truck platform was converted to run on HCNG fuels. The testing performed in year one of the three year plan represents a baseline from which to assess options for overcoming the stated barriers to success.

  5. Magnetic graphitic carbon nitride anion exchanger for specific enrichment of phosphopeptides.

    PubMed

    Zhu, Gang-Tian; He, Xiao-Mei; Chen, Xi; Hussain, Dilshad; Ding, Jun; Feng, Yu-Qi

    2016-03-11

    Anion-exchange chromatography (AEX) is one of the chromatography-based methods effectively being used for phosphopeptide enrichment. However, the development of AEX materials with high specificity toward phosphopeptides is still less explored as compared to immobilized metal affinity chromatography (IMAC) or metal oxide affinity chromatography (MOAC). In this work, magnetic graphitic carbon nitride (MCN) was successfully prepared and introduced as a promising AEX candidate for phosphopeptide enrichment. Due to the extremely abundant content of nitrogen with basic functionality on the surface, this material kept excellent retention for phosphopeptides at pH as low as 1.8. Benefiting from the large binding capacity at such low pH, MCN showed remarkable specificity to capture phosphopeptides from tryptic digests of standard protein mixtures as well as nonfat milk and human serum. In addition, MCN was also applied to selective enrichment of phosphopeptides from the tryptic digests of rat brain lysate and 2576 unique phosphopeptides were successfully identified.

  6. Portable NDA Equipment for Enrichment Measurements in the HEU Transparency Program

    SciTech Connect

    Decman, D J; Bandong, B B; Wong, J L; Valentine, J D; Luke, S J

    2008-06-02

    The Highly Enriched Uranium (HEU) Transparency Program has used portable nondestructive assay (NDA) equipment to measure the {sup 235}U enrichment of material subject to the transparency agreement since 1997. The equipment is based on the 'enrichment meter' method and uses low-resolution sodium iodide (NaI(Tl)) detectors. Although systems using high-purity germanium (HPGe) detectors can produce more accurate results we have found that the results with NaI(Tl) detectors are quite adequate for the requirements of the transparency agreement. This paper will describe the details of the equipment's operation, calibration, testing, and deployment in Russia. We will also provide a comparison of the units originally deployed in 1997 with the upgraded systems that were deployed in 2003.

  7. Comparison of conventional staining methods and monoclonal antibody-based methods for Cryptosporidium oocyst detection.

    PubMed Central

    Arrowood, M J; Sterling, C R

    1989-01-01

    The sensitivity and specificity of seven microscopy-based Cryptosporidium oocyst detection methods were compared after application to unconcentrated fecal smears. The seven methods were as follows: (i) a commercial acid-fast (AF) stain (VOLU-SOL) method, (ii) Truant auramine-rhodamine (AR) stain method, (iii) fluorescein-conjugated C1B3 monoclonal antibody (MAb) direct fluorescence method, (iv) OW3 MAb indirect fluorescence method, (v) biotinylated OW3 indirect fluorescence method, (vi) biotinylated OW3-indirect diaminobenzidine (DAB) method, and (vii) biotinylated OW3-aminoethylcarbazole (AEC) method. A total of 281 randomly collected Formalin-fixed fecal samples (submitted to the Maricopa County Health Department, Phoenix, Ariz.) and 30 known positives (Formalin-fixed and K2Cr2O7-preserved stools from our laboratory) were examined in a blind test; 32 of 311 samples (10.3%) were confirmed positive. Of the confirmed positives, 40.6% were identified by the AF method, 93.8% were identified by the AR method, 93.8% were identified by the C1B3 method, 81.3% were identified by the OW3-DAB method, 71.9% were identified by the OW3-AEC method, 100% were identified by the OW3 indirect fluorescence method, and 100% were identified by the biotinylated OW3 indirect fluorescence method. False-positives were encountered by the AF and AR methods (52.0 and 85.7% specificity, respectively), while no false-positives encountered by the MAb-based methods. Oocysts in infected tissue sections were easily detected by the MAb-based methods. Images PMID:2475523

  8. Measurement of the enrichment of uranium in the pipework of a gas centrifuge enrichment plant

    SciTech Connect

    Packer, T.W.; Lees, E.W.; Close, D.; Nixon, K.V.; Pratt, J.C.; Strittmatter, R.

    1985-01-01

    The US and UK have been separately working on the development of a NDA instrument to determine the enrichment of gaseous UF/sub 6/ at low pressures in cascade header pipework in line with the conclusions of the Hexapartite Safeguards Project viz. the instrument is capable of making a ''go/no go'' decision of whether the enrichment is less than/greater than 20%. Recently, there has been a series of very useful technical exchanges of ideas and information between the two countries. This has led to a technical formulation for such an instrumentation based on ..gamma..-ray spectrometry which, although plant-specific in certain features, nevertheless is based on the same physical principles. Experimental results from commercially operating enrichment plants are very encouraging and indicate that a complete measurement including set up time on the pipe should be attainable in about 30 minutes when measuring pipes of diameter around 110 mm.

  9. Measurement of the enrichment of uranium in the pipework of a gas centrifuge enrichment plant

    SciTech Connect

    Packer, T W; Lees, E W; Close, D; Nixon, K V; Pratt, J C; Strittmatter, R

    1985-01-01

    The US and UK have been separately working on the development of a NDA instrument to determine the enrichment of gaseous UF/sub 6/ at low pressures in cascade header pipework in line with the conclusions of the Hexapartite Safeguards Project viz. the instrument is capable of making a ''go/no go'' decision of whether the enrichment is less than/greater than 20%. Recently, there has been a series of very useful technical exchanges of ideas and information between the two countries. This has led to a technical formulation for such an instrumentation based on ..gamma..-ray spectrometry which, although plant-specific in certain features, nevertheless is based on the same physical principles. Experimental results from commercially operating enrichment plants are very encouraging and indicate that a complete measurement including set up time on the pipe should be attainable in about 30 minutes when measuring pipes of diameter around 110 mm. 5 refs., 4 figs.

  10. Propensity Score-Based Methods versus MTE-Based Methods in Causal Inference: Identification, Estimation, and Application.

    PubMed

    Zhou, Xiang; Xie, Y U

    2016-02-01

    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.

  11. Phosphopeptide Enrichment by Immobilized Metal Affinity Chromatography.

    PubMed

    Thingholm, Tine E; Larsen, Martin R

    2016-01-01

    Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively charged metal ions such as Fe(3+), Ga(3+), Al(3+), Zr(4+), and Ti(4+) has made it possible to enrich phosphorylated peptides from peptide samples. However, the selectivity of most of the metal ions is limited, when working with highly complex samples, e.g., whole-cell extracts, resulting in contamination from nonspecific binding of non-phosphorylated peptides. This problem is mainly caused by highly acidic peptides that also share high binding affinity towards these metal ions. By lowering the pH of the loading buffer nonspecific binding can be reduced significantly, however with the risk of reducing specific binding capacity. After binding, the enriched phosphopeptides are released from the metal ions using alkaline buffers of pH 10-11, EDTA, or phosphate-containing buffers. Here we describe a protocol for IMAC using Fe(3+) for phosphopeptide enrichment. The principles are illustrated on a semi-complex peptide mixture.

  12. 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.

  13. Anthropogenic impact on the sediment record from Lake Czechowskie (N-Poland) based on heavy metal contents in combination with high-resolution pollen and varve data: Geochemical background vs enrichment history and landsurface changes

    NASA Astrophysics Data System (ADS)

    Hoelzmann, Philipp; Słowiński, Michał; Obremska, Milena; Ott, Florian; Brauer, Achim

    2016-04-01

    For Czechowskie Lake, situated in a rural environment in N-Poland, we present a detailed heavy metal enrichment history for Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn for the last two hundred years at 1 cm intervals from an annually laminated sediment core and the near-by lake sediment record of Lake Głęboczek. To determine local geogenic background values for the lake different types of Holocene lake sediments (e.g. calcareous gyttja, organic gyttja etc.) were analyzed for their heavy metal concentrations. On the base of these results enrichment factors were calculated that represent the anthropogenic heavy metal deposition. This data is supplemented by on average five year resolution pollen record for the last 700 years. Based on vegetation changes (e.g. arboreal % such as Pinus and Carpinus betulus; Cerealia %; charcoal pieces), heavy metal input (mainly Pb, Zn and Cd), varve thickness, and precise varve dating (±3a years for the last 200a and ±8a years for the last 700a) five phases of significantly lower human activity interrupted by stronger human impact were distinguished. Strongest declines in anthropogenic pressure on the landscape are related to periods following war or economic regression and subsequent regeneration. Our results provide means to calculate and quantify with sub-decadal resolution anthropogenic impact as well as to define regional measures for a state of reference, reflecting natural conditions without human impact.

  14. An entropy-based objective evaluation method for image segmentation

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Fritts, Jason E.; Goldman, Sally A.

    2003-12-01

    Accurate image segmentation is important for many image, video and computer vision applications. Over the last few decades, many image segmentation methods have been proposed. However, the results of these segmentation methods are usually evaluated only visually, qualitatively, or indirectly by the effectiveness of the segmentation on the subsequent processing steps. Such methods are either subjective or tied to particular applications. They do not judge the performance of a segmentation method objectively, and cannot be used as a means to compare the performance of different segmentation techniques. A few quantitative evaluation methods have been proposed, but these early methods have been based entirely on empirical analysis and have no theoretical grounding. In this paper, we propose a novel objective segmentation evaluation method based on information theory. The new method uses entropy as the basis for measuring the uniformity of pixel characteristics (luminance is used in this paper) within a segmentation region. The evaluation method provides a relative quality score that can be used to compare different segmentations of the same image. This method can be used to compare both various parameterizations of one particular segmentation method as well as fundamentally different segmentation techniques. The results from this preliminary study indicate that the proposed evaluation method is superior to the prior quantitative segmentation evaluation techniques, and identify areas for future research in objective segmentation evaluation.

  15. 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.

  16. 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

  17. Qualitative Assessment of Inquiry-Based Teaching Methods

    ERIC Educational Resources Information Center

    Briggs, Michael; Long, George; Owens, Katrina

    2011-01-01

    A new approach to teaching method assessment using student focused qualitative studies and the theoretical framework of mental models is proposed. The methodology is considered specifically for the advantages it offers when applied to the assessment of inquiry-based teaching methods. The theoretical foundation of mental models is discussed, and…

  18. 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…

  19. 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.

  20. 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

  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

    2016-09-14

    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.

  2. 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.

  3. 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.

  4. Effects of Almond- and Olive Oil-Based Docosahexaenoic- and Vitamin E-Enriched Beverage Dietary Supplementation on Inflammation Associated to Exercise and Age.

    PubMed

    Capó, Xavier; Martorell, Miquel; Sureda, Antoni; Riera, Joan; Drobnic, Franchek; Tur, Josep Antoni; Pons, Antoni

    2016-10-09

    n-3-polyunsaturated fatty acids and polyphenols are potential key factors for the treatment and prevention of chronic inflammation associated to ageing and non-communicable diseases. The aim was to analyse effects of an almond and olive oil beverage enriched with α-tocopherol and docosahexaenoic, exercise and age on inflammatory plasma markers, and immune gene expression in peripheral blood mononuclear cells (PBMCs). Five young and five senior athletes who were supplemented for five weeks with a functional beverage performed a stress test under controlled conditions before and after beverage supplementation. Blood samples were taken immediately before and 1 h after each test. Plasma, erythrocytes and PBMCs were isolated. Beverage supplementation increased plasmatic Tumour Necrosis Factor α (TNFα) levels depending on age and exercise. Exercise increased plasma non esterified fatty acids (NEFAs), soluble Intercellular adhesion molecule 3 (sICAM3) and soluble L-selectin (sL-Selectin), and this increase was attenuated by the supplementation. Exercise increased PGE2 plasma levels in supplemented young and in senior placebo athletes. Exercise increased NFkβ-activated levels in PBMCs, which are primed to a pro-inflammatory response increasing pro-inflammatory genes expression after the exercise mainly in the young group after the supplementation. The functional beverage supplementation to young athletes enhances a pro-inflammatory circulating environment in response to the exercise that was less evident in the senior group.

  5. Nanoliter-volume protein enrichment, tryptic digestion, and partial separation based on isoelectric points by CE for MALDI mass spectral analysis.

    PubMed

    Nesbitt, Chandra A; Jurcic, Kristina; Yeung, Ken K-C

    2008-01-01

    Sequence-specific proteolysis is an important part of protein identification by MS. Digestion of protein is commonly performed in-solution, in sample vials with volumes ranging from milli- to microliters. When digestion is performed with a sample volume below 1 microL, handling of solution and potential sample loss via adsorption become significant issues. In this report, a proof of concept for the digestion of a small volume protein solution inside a capillary was demonstrated using a discontinuous buffer system previously studied (Nesbitt, C. A., et al. J. Chromatogr. A 2005, 1073, 175-180). Upon voltage application, a pH junction was created by the discontinuous buffer. Using myoglobin as an example, the protein molecules were enriched at the junction with an estimated volume of a few nanoliters. A protease, trypsin, was then introduced to myoglobin at the junction by coenrichment to induce in-capillary digestion. The voltage application was then suspended to provide the necessary time (2 h) for the proteolysis to proceed. When completed, voltage application was resumed, and the discontinuous buffer reconcentrated the peptides formed from digestion. Importantly, the refocused peptides appeared to roughly elute according to their pIs, resulting in a partial separation. Direct sample deposition from capillary was performed to facilitate mass spectral analysis by MALDI. The partial separation, according to pI, offered the potential benefits of MALDI MS signal enhancement and provided supplementary pI information for peptide identity assignment.

  6. Use of a capture-based pathogen transcript enrichment strategy for RNA-Seq analysis of the Francisella tularensis LVS transcriptome during infection of murine macrophages.

    PubMed

    Bent, Zachary W; Brazel, David M; Tran-Gyamfi, Mary B; Hamblin, Rachelle Y; VanderNoot, Victoria A; Branda, Steven S

    2013-01-01

    Francisella tularensis is a zoonotic intracellular pathogen that is capable of causing potentially fatal human infections. Like all successful bacterial pathogens, F. tularensis rapidly responds to changes in its environment during infection of host cells, and upon encountering different microenvironments within those cells. This ability to appropriately respond to the challenges of infection requires rapid and global shifts in gene expression patterns. In this study, we use a novel pathogen transcript enrichment strategy and whole transcriptome sequencing (RNA-Seq) to perform a detailed characterization of the rapid and global shifts in F. tularensis LVS gene expression during infection of murine macrophages. We performed differential gene expression analysis on all bacterial genes at two key stages of infection: phagosomal escape, and cytosolic replication. By comparing the F. tularensis transcriptome at these two stages of infection to that of the bacteria grown in culture, we were able to identify sets of genes that are differentially expressed over the course of infection. This analysis revealed the temporally dynamic expression of a number of known and putative transcriptional regulators and virulence factors, providing insight into their role during infection. In addition, we identified several F. tularensis genes that are significantly up-regulated during infection but had not been previously identified as virulence factors. These unknown genes may make attractive therapeutic or vaccine targets.

  7. Effects of Almond- and Olive Oil-Based Docosahexaenoic- and Vitamin E-Enriched Beverage Dietary Supplementation on Inflammation Associated to Exercise and Age

    PubMed Central

    Capó, Xavier; Martorell, Miquel; Sureda, Antoni; Riera, Joan; Drobnic, Franchek; Tur, Josep Antoni; Pons, Antoni

    2016-01-01

    n-3-polyunsaturated fatty acids and polyphenols are potential key factors for the treatment and prevention of chronic inflammation associated to ageing and non-communicable diseases. The aim was to analyse effects of an almond and olive oil beverage enriched with α-tocopherol and docosahexaenoic, exercise and age on inflammatory plasma markers, and immune gene expression in peripheral blood mononuclear cells (PBMCs). Five young and five senior athletes who were supplemented for five weeks with a functional beverage performed a stress test under controlled conditions before and after beverage supplementation. Blood samples were taken immediately before and 1 h after each test. Plasma, erythrocytes and PBMCs were isolated. Beverage supplementation increased plasmatic Tumour Necrosis Factor α (TNFα) levels depending on age and exercise. Exercise increased plasma non esterified fatty acids (NEFAs), soluble Intercellular adhesion molecule 3 (sICAM3) and soluble L-selectin (sL-Selectin), and this increase was attenuated by the supplementation. Exercise increased PGE2 plasma levels in supplemented young and in senior placebo athletes. Exercise increased NFkβ-activated levels in PBMCs, which are primed to a pro-inflammatory response increasing pro-inflammatory genes expression after the exercise mainly in the young group after the supplementation. The functional beverage supplementation to young athletes enhances a pro-inflammatory circulating environment in response to the exercise that was less evident in the senior group. PMID:27735833

  8. Enriched environment induces higher CNPase positive cells in aged rat hippocampus.

    PubMed

    Zhao, Yuan-Yu; Shi, Xiao-Yan; Zhang, Lei; Wu, Hong; Chao, Feng-Lei; Huang, Chun-Xia; Gao, Yuan; Qiu, Xuan; Chen, Lin; Lu, Wei; Tang, Yong

    2013-10-25

    It had been reported that enriched environment was beneficial for the brain cognition and for the neurons and synapses in hippocampus. Previous study reported that the oligodendrocyte density in hippocampus was increased when the rats were reared in the enriched environment from weaning to adulthood. However, biological conclusions based on density were difficult to interpret because the changes in density could be due to an alteration of total quantity and/or an alteration in the reference volume. In the present study, we used unbiased stereological methods to investigate the effect of enriched environment on the total number of 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase) positive cells in CA1 and dentate gyrus (DG) of the hippocampus in aged rats. Our results indicated that there was significant difference in the total numbers of CNPase positive cells in both CA1 and DG between enriched environment group and standard environment group. The present study provided the first evidence for the protective effects of enriched environment on the CNPase positive cells in aged hippocampus.

  9. A targeted enrichment strategy for massively parallel sequencing of angiosperm plastid genomes1

    PubMed Central

    Stull, Gregory W.; Moore, Michael J.; Mandala, Venkata S.; Douglas, Norman A.; Kates, Heather-Rose; Qi, Xinshuai; Brockington, Samuel F.; Soltis, Pamela S.; Soltis, Douglas E.; Gitzendanner, Matthew A.

    2013-01-01

    • Premise of the study: We explored a targeted enrichment strategy to facilitate rapid and low-cost next-generation sequencing (NGS) of numerous complete plastid genomes from across the phylogenetic breadth of angiosperms. • Methods and Results: A custom RNA probe set including the complete sequences of 22 previously sequenced eudicot plastomes was designed to facilitate hybridization-based targeted enrichment of eudicot plastid genomes. Using this probe set and an Agilent SureSelect targeted enrichment kit, we conducted an enrichment experiment including 24 angiosperms (22 eudicots, two monocots), which were subsequently sequenced on a single lane of the Illumina GAIIx with single-end, 100-bp reads. This approach yielded nearly complete to complete plastid genomes with exceptionally high coverage (mean coverage: 717×), even for the two monocots. • Conclusions: Our enrichment experiment was highly successful even though many aspects of the capture process employed were suboptimal. Hence, significant improvements to this methodology are feasible. With this general approach and probe set, it should be possible to sequence more than 300 essentially complete plastid genomes in a single Illumina GAIIx lane (achieving ∼50× mean coverage). However, given the complications of pooling numerous samples for multiplex sequencing and the limited number of barcodes (e.g., 96) available in commercial kits, we recommend 96 samples as a current practical maximum for multiplex plastome sequencing. This high-throughput approach should facilitate large-scale plastid genome sequencing at any level of phylogenetic diversity in angiosperms. PMID:25202518

  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, 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.

  12. 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.

  13. Method of recovering oil-based fluid and apparatus

    SciTech Connect

    Brinkley, H.E.

    1993-07-20

    A method is described for recovering oil-based fluid from a surface having oil-based fluid thereon comprising the steps of: applying to the oil-based fluid on the surface an oil-based fluid absorbent cloth of man-made fibers, the cloth having at least one napped surface that defines voids therein, the nap being formed of raised ends or loops of the fibers; absorbing, with the cloth, oil-based fluid; feeding the cloth having absorbed oil-based fluid to a means for applying a force to the cloth to recover oil-based fluid; and applying force to the cloth to recover oil-based fluid therefrom using the force applying means.

  14. 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

  15. Use of boronic acid nanoparticles in glycoprotein enrichment.

    PubMed

    Xu, Yawei; Zhang, Lijuan; Lu, Haojie

    2013-01-01

    Glyco-specific enrichment methods for mass spectrometry pretreatment are invaluable for the detection of low abundant glycoproteins or glycopeptides. For example, boronic acid can specifically interact with glycans in nonaqueous or basic aqueous solutions. Here, we describe a glyco-specific enrichment method which uses a boronic acid-functionalized "core-satellite" composite nanoparticle to isolate glycoproteins or glycopeptides from complex biological samples. Furthermore, we also demonstrate detection limit improvements and show how to evaluate the percent recovery from the glycoprotein or glycopeptide enrichment process via SDS-PAGE and (16)O/(18)O labeling strategies.

  16. 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.

  17. 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.

  18. MAVTgsa: An R Package for Gene Set (Enrichment) Analysis

    DOE PAGES

    Chien, Chih-Yi; Chang, Ching-Wei; Tsai, Chen-An; ...

    2014-01-01

    Gene semore » t analysis methods aim to determine whether an a priori defined set of genes shows statistically significant difference in expression on either categorical or continuous outcomes. Although many methods for gene set analysis have been proposed, a systematic analysis tool for identification of different types of gene set significance modules has not been developed previously. This work presents an R package, called MAVTgsa, which includes three different methods for integrated gene set enrichment analysis. (1) The one-sided OLS (ordinary least squares) test detects coordinated changes of genes in gene set in one direction, either up- or downregulation. (2) The two-sided MANOVA (multivariate analysis variance) detects changes both up- and downregulation for studying two or more experimental conditions. (3) A random forests-based procedure is to identify gene sets that can accurately predict samples from different experimental conditions or are associated with the continuous phenotypes. MAVTgsa computes the P values and FDR (false discovery rate) q -value for all gene sets in the study. Furthermore, MAVTgsa provides several visualization outputs to support and interpret the enrichment results. This package is available online.« less

  19. Systematic measurements of proton-induced reactions on enriched molybdenum

    NASA Astrophysics Data System (ADS)

    Lamere, Edward; Gilardy, Gwenaelle; Meisel, Zach; Moran, Michael; Seymore, Christopher; Skulski, Michael; Simonetti, Antonio; Couder, Manoel

    2016-09-01

    Between 2008 and 2010, shortages in the world-wide supply of Mo highlighted weaknesses in the current fission-based production method of mTc, a critical medical isotope. This crisis sparked interest in developing the direct production of mTc from proton-induced reactions on enriched Mo targets as an alternative. One complication with this method is that mTc must be chemically extracted from the irradiated target. Therefore, radiopharmaceuticals produced from proton bombardment will contain a mixture of all Tc-species with open production channels, affecting radiochemical purity, specific activity and total production yield of mTc-factors critical for the feasibility of this production method. Reactions on trace impurities in the enriched targets have been shown to impact these factors dramatically. Precise cross-section measurements for all Mo +p reactions that lead to Tc or Mo species are required for proper assessment of this production technique. Cross-section measurements for the main reaction of interest, mTc(p,2n), have been performed in recent years, however, other reactions producing Tc have been mostly neglected. We will introduce a systematic study of proton-induced reactionson 92, 94-98, 100 Mo currently being performed at Notre Dame. Preliminary results will be presented. NRC-HQ-12-G-38-0073.

  20. 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.

  1. Computer based safety training: an investigation of methods

    PubMed Central

    Wallen, E; Mulloy, K

    2005-01-01

    Background: Computer based methods are increasingly being used for training workers, although our understanding of how to structure this training has not kept pace with the changing abilities of computers. Information on a computer can be presented in many different ways and the style of presentation can greatly affect learning outcomes and the effectiveness of the learning intervention. Many questions about how adults learn from different types of presentations and which methods best support learning remain unanswered. Aims: To determine if computer based methods, which have been shown to be effective on younger students, can also be an effective method for older workers in occupational health and safety training. Methods: Three versions of a computer based respirator training module were developed and presented to manufacturing workers: one consisting of text only; one with text, pictures, and animation; and one with narration, pictures, and animation. After instruction, participants were given two tests: a multiple choice test measuring low level, rote learning; and a transfer test measuring higher level learning. Results: Participants receiving the concurrent narration with pictures and animation scored significantly higher on the transfer test than did workers receiving the other two types of instruction. There were no significant differences between groups on the multiple choice test. Conclusions: Narration with pictures and text may be a more effective method for training workers about respirator safety than other popular methods of computer based training. Further study is needed to determine the conditions for the effective use of this technology. PMID:15778259

  2. Selective enrichment of STRs for applications in forensic human identification.

    PubMed

    Gadipally, Sreeja R; Sarkar, Anujit; Nandineni, Madhusudan R

    2015-08-01

    Forensic human identification (HID) is currently based on determining repeat length polymorphisms located in short tandem repeat regions in the human genome. Despite the great progress made in the area of multiplex PCR-based approaches, limitations associated with challenging forensic samples such as DNA degradation, cooccurrence of inhabited microbial DNA and PCR inhibitors significantly affect the success rate of human DNA profiling. We have developed a sequence-specific pre-PCR STR enrichment method and evaluated its efficacy using DNA samples doped with various contaminants in view of its application on compromised forensic samples. This strategy has enabled us to generate complete and reproducible DNA profiles from samples doped with fivefold excess of nonhuman DNA and three to fourfold excess of various potent PCR inhibitors than that is claimed to be tolerated by some of the widely used commercial multiplex STR kits, from as little as two nanograms of degraded human DNA. The "hybrid capture"-based STR enrichment strategy described in this study is easily adaptable and offers a sensitive, efficient, and economical approach for successful human DNA profiling from compromised and recalcitrant forensic samples that are usually encountered in mass disaster incidents and missing persons' identifications.

  3. 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