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Sample records for cell-free translation system

  1. IRES-Mediated Translation of Membrane Proteins and Glycoproteins in Eukaryotic Cell-Free Systems

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    Brödel, Andreas K.; Sonnabend, Andrei; Roberts, Lisa O.; Stech, Marlitt; Wüstenhagen, Doreen A.; Kubick, Stefan

    2013-01-01

    Internal ribosome entry site (IRES) elements found in the 5′ untranslated region of mRNAs enable translation initiation in a cap-independent manner, thereby representing an alternative to cap-dependent translation in cell-free protein expression systems. However, IRES function is largely species-dependent so their utility in cell-free systems from different species is rather limited. A promising approach to overcome these limitations would be the use of IRESs that are able to recruit components of the translation initiation apparatus from diverse origins. Here, we present a solution to this technical problem and describe the ability of a number of viral IRESs to direct efficient protein expression in different eukaryotic cell-free expression systems. The IRES from the intergenic region (IGR) of the Cricket paralysis virus (CrPV) genome was shown to function efficiently in four different cell-free systems based on lysates derived from cultured Sf21, CHO and K562 cells as well as wheat germ. Our results suggest that the CrPV IGR IRES-based expression vector is universally applicable for a broad range of eukaryotic cell lysates. Sf21, CHO and K562 cell-free expression systems are particularly promising platforms for the production of glycoproteins and membrane proteins since they contain endogenous microsomes that facilitate the incorporation of membrane-spanning proteins and the formation of post-translational modifications. We demonstrate the use of the CrPV IGR IRES-based expression vector for the enhanced synthesis of various target proteins including the glycoprotein erythropoietin and the membrane proteins heparin-binding EGF-like growth factor receptor as well as epidermal growth factor receptor in the above mentioned eukaryotic cell-free systems. CrPV IGR IRES-mediated translation will facilitate the development of novel eukaryotic cell-free expression platforms as well as the high-yield synthesis of desired proteins in already established systems. PMID

  2. IRES-mediated translation of membrane proteins and glycoproteins in eukaryotic cell-free systems.

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    Andreas K Brödel

    Full Text Available Internal ribosome entry site (IRES elements found in the 5' untranslated region of mRNAs enable translation initiation in a cap-independent manner, thereby representing an alternative to cap-dependent translation in cell-free protein expression systems. However, IRES function is largely species-dependent so their utility in cell-free systems from different species is rather limited. A promising approach to overcome these limitations would be the use of IRESs that are able to recruit components of the translation initiation apparatus from diverse origins. Here, we present a solution to this technical problem and describe the ability of a number of viral IRESs to direct efficient protein expression in different eukaryotic cell-free expression systems. The IRES from the intergenic region (IGR of the Cricket paralysis virus (CrPV genome was shown to function efficiently in four different cell-free systems based on lysates derived from cultured Sf21, CHO and K562 cells as well as wheat germ. Our results suggest that the CrPV IGR IRES-based expression vector is universally applicable for a broad range of eukaryotic cell lysates. Sf21, CHO and K562 cell-free expression systems are particularly promising platforms for the production of glycoproteins and membrane proteins since they contain endogenous microsomes that facilitate the incorporation of membrane-spanning proteins and the formation of post-translational modifications. We demonstrate the use of the CrPV IGR IRES-based expression vector for the enhanced synthesis of various target proteins including the glycoprotein erythropoietin and the membrane proteins heparin-binding EGF-like growth factor receptor as well as epidermal growth factor receptor in the above mentioned eukaryotic cell-free systems. CrPV IGR IRES-mediated translation will facilitate the development of novel eukaryotic cell-free expression platforms as well as the high-yield synthesis of desired proteins in already established

  3. Regulation of LacZ mRNA translatability in a cell-free system at heat shock by the last four sense codons.

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    Denisenko, O N; Yarchuk, O B

    1989-04-24

    Under heat shock conditions translation of Xenopus laevis normal mRNAs in a rabbit reticulocyte cell-free system is blocked whereas hsp70 mRNA is translated. mRNA for E. coli beta-galactosidase containing the last four sense codons of Drosophila hsp70 at its 3'-end was constructed. This mRNA is efficiently translated in a rabbit reticulocyte cell-free system at 43 degrees C.

  4. Production and partial purification of membrane proteins using a liposome-supplemented wheat cell-free translation system

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    Iwasaki Takahiro

    2011-04-01

    Full Text Available Abstract Background Recently, some groups have reported on cell-free synthesis of functional membrane proteins (MPs in the presence of exogenous liposomes (liposomes. Previously, we reported synthesis of a functional AtPPT1 plant phosphate transporter that was associated with liposomes during translation. However, it is unclear whether or not lipid/MP complex formation is common to all types of MPs in the wheat cell-free system. Results AtPPT1 was synthesized using a wheat cell-free system with or without liposomes. AtPPT1 synthesized with liposomes showed high transport activity, but the activity of AtPPT1 synthesized without liposomes was less than 10% activity of that with liposomes. To test whether co-translational association with liposomes is observed in the synthesis of other MPs, we used 40 mammalian MPs having one to 14 transmembrane domains (TMDs and five soluble proteins as a control. The association rate of all 40 MPs into liposomes was more than 40% (mean value: 59%, while that of the five soluble proteins was less than 20% (mean value: 12%. There were no significant differences in association rate among MPs regardless of the number of TMDs and synthesis yield. These results indicate that the wheat cell-free system is a highly productive method for lipid/MP complex formation and is suitable for large-scale preparation. The liposome association of green fluorescent protein (GFP-fusion MPs were also tested and recovered as lipid/MP complex after floatation by Accudenz density gradient ultracentrifugation (DGU. Employment of GFP-MPs revealed optimal condition for Accudenz floatation. Using the optimized Accudenz DGU condition, P2RX4/lipid complexes were partially purified and detected as a major band by Coomassie Brilliant Blue (CBB-staining after SDS-PAGE. Conclusion Formation of lipid/AtPPT1 complex during the cell-free synthesis reaction is critical for synthesis of a functional MP. The lipid/MP complex during the translation was

  5. A combined cell-free transcription-translation system from Saccharomyces cerevisiae for rapid and robust protein synthe.

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    Gan, Rui; Jewett, Michael C

    2014-05-01

    Cell-free protein synthesis (CFPS) provides a valuable platform for understanding, using, and expanding the capabilities of the translation apparatus. For example, high-throughput CFPS is helping to address the increasing discrepancy between genome sequence data and their translation products. Here, we report the development of a combined cell-free transcription-translation (Tx/Tl) system from Saccharomyces cerevisiae that is suitable for such efforts. First, we show the ability to enable translation initiation in a cap-independent manner. The performance of various genetic elements was assessed, including 5'-UTR, 3'-UTR, and length of poly(A) tail. A specific vector harboring the 5'-UTR fragment of the Ω sequence from the tobacco mosaic virus and a poly(A) tail of 50 nucleotides led to optimal performance. Second, we developed a simple, two-step polymerase chain reaction (PCR) method for high-throughput production of linear templates for yeast CFPS. This procedure allows all functional elements needed for Tx/Tl to be added to an open-reading frame directly by overlap extension PCR. Our two-step PCR method was successfully applied to three reporter proteins: luciferase, green fluorescence protein, and chloramphenicol acetyl transferase, yielding 7 to 12.5 μg mL-1 active protein after 1.5-h batch reactions. Surprisingly, the linear templates outperformed plasmid DNA by up to 60%. Hence, the presented CFPS method has the potential to rapidly prepare tens to thousands of DNA templates without time-consuming cloning work. Further, it holds promise for fast and convenient optimization of expression constructs, study of internal ribosome entry site, and production of protein libraries for genome-scale studies. See accompanying commentary by Russ and Dueber DOI: 10.1002/biot.201400071. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Artificial OFF-Riboswitches That Downregulate Internal Ribosome Entry without Hybridization Switches in a Eukaryotic Cell-Free Translation System.

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    Ogawa, Atsushi; Masuoka, Hiroki; Ota, Tsubasa

    2017-09-15

    We constructed novel artificial riboswitches that function in a eukaryotic translation system (wheat germ extract), by rationally implanting an in vitro-selected aptamer into the intergenic internal ribosome entry site (IRES) of Plautia stali intestine virus. These eukaryotic OFF-riboswitches (OFF-eRSs) ligand-dose-dependently downregulate IRES-mediated translation without hybridization switches, which typical riboswitches utilize for gene regulation. The hybridization-switch-free mechanism not only allows for easy design but also requires less energy for regulation, resulting in a higher switching efficiency than hybridization-switch-based OFF-eRSs provide. In addition, even a small ligand such as theophylline can induce satisfactory repression, in contrast to other types of OFF-eRSs that modulate the 5' cap-dependent canonical translation. Because our proposed hybridization-switch-free OFF-eRSs are based on a versatile IRES that functions well in many types of eukaryotic translation systems, they would be widely usable elements for synthetic gene circuits in both cell-free and cell-based synthetic biology.

  7. A miRNA-responsive cell-free translation system facilitates isolation of hepatitis C virus miRNP complexes

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    Bradrick, Shelton S.; Nagyal, Simardeep; Novatt, Hilary

    2013-01-01

    Micro(mi)RNAs are 21- to 23-nt RNAs that regulate multiple biological processes. In association with Argonaute (Ago) proteins and other factors that form the RNA-induced silencing complex (RISC), miRNAs typically bind mRNA 3′ untranslated regions (UTRs) and repress protein production through antagonizing translation and transcript stability. For a given mRNA–miRNA interaction, cis-acting RNA elements and trans-acting RNA-binding proteins (RBPs) may influence mRNA fate. This is particularly true of the hepatitis C virus (HCV) genome which interacts with miR-122, an abundant liver miRNA. miR-122 binding to HCV RNA considerably stimulates virus replication in cultured cells and primates, but the mechanism(s) and associated host factors required for enhancement of HCV replication have not been fully elucidated. We recapitulated miR-122–HCV RNA interactions in a cell-free translation system derived from cells that express miR-122. Specifically, lysates produced from HEK-293 cells that inducibly transcribe and process pri-miR-122 were characterized alongside those from isogenic cells lacking miR-122 expression. We observed a stimulatory effect of miR-122 on HCV reporter mRNAs in a manner that depended on expression of miR-122 and intact target sites within the HCV 5′ UTR. We took advantage of this system to affinity-purify miR-122-HCV RNP complexes. Similar to functional assays, we found that association of immobilized HCV internal ribosome entry site (IRES) RNA with endogenous Ago2 requires both miR-122 expression and intact miR-122 target sites in cis. This combined approach may be generalizable to affinity purification of miRNP complexes for selected target mRNAs, allowing identification of miRNP components and RBPs that may contribute to regulation. PMID:23793894

  8. In Vitro Translation of Oogenetic Messenger RNA of Sea Urchin Eggs and Picornavirus RNA with a Cell-Free System from Sarcoma 180

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    Jenkins, Nancy; Taylor, Milton W.; Raff, Rudolf A.

    1973-01-01

    A cell-free protein-synthesizing system prepared from mouse sarcoma 180 was characterized by use of RNA from mengo virus and sea urchin egg. In the presence of exogenous mammalian transfer RNA, total sea urchin egg RNA and mengo RNA direct incorporation of [3H]leucine into acid-insoluble material. The system is extremely efficient in that a stimulation of 100-times over background can be obtained. Studies with formylmethionyl-transfer RNA, as well as with inhibitors of initiation, indicate that multiple initiation occurs; further, 85-90% of all chains made in vitro are subsequently released from ribosomes. An average translation time of 3.5 min was determined with messenger RNA of sea urchin egg, and product analysis indicates that high-molecular-weight products (greater than 50,000 molecular weight) are being made in vitro. Sequences of sea urchin egg RNA containing poly(A) act as messenger RNA. PMID:4357864

  9. Translational active mRNPs from rabbit reticulocytes are qualitatively different from free mRNA in their translatability in cell-free system.

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    Minich, W B; Korneyeva, N L; Ovchinnikov, L P

    1989-11-06

    The translatability of polyribosomal and free mRNPs from rabbit reticulocytes and their mRNA was compared. Both classes of mRNPs turned out to be active in rabbit reticulocyte lysates. Considerable differences between mRNPs and mRNA have been revealed. The most striking feature of mRNPs was that high concentrations of mRNPs do not inhibit protein biosynthesis, whereas high concentrations of mRNA strongly inhibit this process. This inhibition is specific for mRNA and does not occur at the addition of the same amount of rRNA from E. coli. The features of mRNP translation are not the result of addition of the supplementary translation factors within particles. The specific function of mRNP proteins in the process of translation is under discussion.

  10. Localization of BiP to translating ribosomes increases soluble accumulation of secreted eukaryotic proteins in an Escherichia coli cell-free system.

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    Welsh, John P; Bonomo, Jeanne; Swartz, James R

    2011-08-01

    The endoplasmic reticulum (ER) resident Hsp70 chaperone, BiP, docks to the Sec translocon and interacts co-translationally with polypeptides entering the ER to encourage proper folding. In order to recreate this interaction in Escherichia coli cell-free protein synthesis (CFPS) reactions, a fusion protein was formed between the ribosome-binding portion of the E. coli protein trigger factor (TF) and BiP. The biophysical affinity to ribosomes as well as the characteristic Hsp70 ATPase activity were both verified for the fusion protein. When added to E. coli-based CFPS reactions, the TF-BiP fusion chaperone increased soluble yields of several protein fragments that are normally secreted through the ER and have poor solubility in typical CFPS reactions. For comparison, a fusion between TF and the native E. coli Hsp70, DnaK, was also constructed. This fusion was also biologically active and increased soluble yields of certain protein targets in CFPS. The TF-BiP fusion described in this study can be seen as a first step in reconstituting and better understanding ER folding pathways in the prokaryotic environment of E. coli CFPS. Copyright © 2011 Wiley Periodicals, Inc.

  11. Easy and Rapid Binding Assay for Functional Analysis of Disulfide-Containing Peptides by a Pull-Down Method Using a Puromycin-Linker and a Cell-Free Translation System

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    Yutaro Tanemura

    2015-03-01

    Full Text Available Constrained peptides are an attractive class as affinity reagents or drug leads owing to their excellent binding properties. Many kinds of these peptides, such as cyclic peptides containing disulfide bridges, are found in nature or designed artificially by directed evolution. However, confirming the binding properties of the disulfide-rich peptides can be generally difficult, because of oxidative folding problems in the preparation steps. Therefore, a method for evaluating the binding properties of such peptides rapidly and easily is required. Here, we report an easy and rapid method for preparing biotin-attached peptides containing disulfide bridges or a chemical cross-linker using a cell-free translation system and a puromycin-linker, which is applicable to pull-down assays for protein (or peptide molecular interaction analysis.

  12. Function of Shaker potassium channels produced by cell-free translation upon injection into Xenopus oocytes.

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    Jarecki, Brian W; Makino, Shin-ichi; Beebe, Emily T; Fox, Brian G; Chanda, Baron

    2013-01-01

    Voltage-gated ion channels are a class of membrane proteins that temporally orchestrate the ion flux critical for chemical and electrical signaling in excitable cells. Current methods to investigate the function of these channels rely on heterologous expression in living systems or reconstitution into artificial membranes; however these approaches have inherent drawbacks which limit potential biophysical applications. Here, we describe a new integrated approach combining cell-free translation of membrane proteins and in vivo expression using Xenopus laevis oocytes. In this method, proteoliposomes containing Shaker potassium channels are synthesized in vitro and injected into the oocytes, yielding functional preparations as shown by electrophysiological and fluorescence measurements within few hours. This strategy for studying eukaryotic ion channels is contrasted with existing, laborious procedures that require membrane protein extraction and reconstitution into synthetic lipid systems.

  13. Integrating stakeholder perspectives into the translation of cell-free fetal DNA testing for aneuploidy.

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    Sayres, Lauren C; Allyse, Megan; Cho, Mildred K

    2012-01-01

    The translation of novel genomic technologies from bench to bedside enjoins the comprehensive consideration of the perspectives of all stakeholders who stand to influence, or be influenced by, the translational course. Non-invasive prenatal aneuploidy testing that utilizes cell-free fetal DNA (cffDNA) circulating in maternal blood is one example of an innovative technology that promises significant benefits for its intended end users; however, it is currently uncertain whether it will achieve widespread clinical implementation. We conducted qualitative interviews with 18 diverse stakeholders in this domain, including prospective users of the technology and healthcare personnel, researchers and developers, and experts in social, legal, and regulatory aspects of genetic technology, and a pilot survey of 62 obstetric healthcare providers. Analysis of interview and survey data was combined with a review of the proceedings of a full-day, multidisciplinary conference on the topic and published scientific and ethics literature surrounding this and other relevant technologies. We constructed potential pathways for technological implementation, identified broad stakeholder classes party to these translational processes, and performed a preliminary assessment of the viewpoints and interrelations among these diverse stakeholders. Some of the stakeholders whose priorities are critical to understand and integrate into translation include pregnant women and their families; healthcare providers; scientists, their institutions or companies, and the funding agencies that support them; regulatory and judicial bodies; third-party payers; professional societies; educational systems; disability rights communities; and other representatives from civil society. Stakeholder interviews, survey findings, and conference proceedings add complexity to these envisioned pathways and also demonstrate a paramount need to incorporate an iterative stakeholder analysis early and throughout the

  14. Cell-Free Protein Synthesis: Pros and Cons of Prokaryotic and Eukaryotic Systems.

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    Zemella, Anne; Thoring, Lena; Hoffmeister, Christian; Kubick, Stefan

    2015-11-01

    From its start as a small-scale in vitro system to study fundamental translation processes, cell-free protein synthesis quickly rose to become a potent platform for the high-yield production of proteins. In contrast to classical in vivo protein expression, cell-free systems do not need time-consuming cloning steps, and the open nature provides easy manipulation of reaction conditions as well as high-throughput potential. Especially for the synthesis of difficult to express proteins, such as toxic and transmembrane proteins, cell-free systems are of enormous interest. The modification of the genetic code to incorporate non-canonical amino acids into the target protein in particular provides enormous potential in biotechnology and pharmaceutical research and is in the focus of many cell-free projects. Many sophisticated cell-free systems for manifold applications have been established. This review describes the recent advances in cell-free protein synthesis and details the expanding applications in this field. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  15. Expression Optimization and Inducible Negative Feedback in Cell-Free Systems

    Energy Technology Data Exchange (ETDEWEB)

    Karig, David K [ORNL; Iyer, Sukanya [ORNL; Simpson, Michael L [ORNL; Doktycz, Mitchel John [ORNL

    2012-01-01

    Synthetic biology offers great promise to a variety of applications through the forward engineering of biological function. Most efforts in this field have focused on employing living cells. Cell-free approaches, on the other hand, offer simpler and more flexible contexts, but few synthetic systems based on cell-free protein expression have been constructed. Here, we evaluate cell-free regulatory systems based on T7 promoter driven expression, and we demonstrate negative feedback, an essential motif in many natural and engineered systems. First, we characterize variants of TetR and LacI repressible T7 promoters in a cell-free context and examine sequence elements that determine expression efficiency. Then, we explore different approaches for composing regulatory systems, leading to the implementation of inducible negative feedback in E. coli extracts and in the minimal PURE system, which consists of purified proteins necessary for transcription and translation. Our quantitative cell-free component characterizations and demonstration of negative feedback embody important steps on the path to harnessing biological function in a bottom up fashion.

  16. Heavy Water Reduces GFP Expression in Prokaryotic Cell-Free Assays at the Translation Level While Stimulating Its Transcription

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    Luisa S. Hohlefelder

    2013-01-01

    Full Text Available The in vitro proliferation of prokaryotic and eukaryotic cells is remarkably hampered in the presence of heavy water (D2O. Impairment of gene expression at the transcription or translation level can be the base for this effect. However, insights into the underlying mechanisms are lacking. Here, we employ a cell-free expression system for the quantitative analysis of the effect of increasing percentages of D2O on the kinetics of in-vitro GFP expression. Experiments are designed to discriminate the rates of transcription, translation, and protein folding using pDNA and mRNA vectors, respectively. We find that D2O significantly stimulates GFP expression at the transcription level but acts as a suppressor at translation and maturation (folding in a linear dose-dependent manner. At a D2O concentration of 60%, the GFP expression rate was reduced to 40% of an undisturbed sample. We observed a similar inhibition of GFP expression by D2O in a recombinant Escherichia coli strain, although the inhibitory effect is less pronounced. These results demonstrate the suitability of cell-free systems for quantifying the impact of heavy water on gene expression and establish a platform to further assess the potential therapeutic use of heavy water as antiproliferative agent.

  17. In silico assessment of cell-free systems.

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    Bujara, Matthias; Panke, Sven

    2012-10-01

    Cell-free extract (CFX)-derived biocatalytic systems are usually embedded in a complex metabolic network, which makes chemical insulation of the production system necessary by removing enzymatic connections. While insulation can be performed by different methods, the identification of potentially disturbing reactions can become a rather lengthy undertaking requiring extensive experimental analysis and literature review. Therefore, a tool for network topology analysis in cell-free systems was developed based on genome scale metabolic models. Genome scale metabolic models define a potential network topology for living cells, and can be adapted to the characteristics of cell-free systems by: (i) removal of compartmentalization, (ii) application of different objective functions, (iii) enabling the accumulation of all metabolites, (iv) applying different constraints for substrate supply, and (v) constraining the reaction space through cofactor availability, microarray data, feasible reaction rates, and thermodynamics. The resulting computational tool successfully predicted for Escherichia coli-derived CFXs a previously identified undesired pathway for dihydroxyacetone phosphate (DHAP) production from adenosine phosphates. The tool was then applied to the identification of potentially interfering pathways to further insulate a DHAP-producing multi-enzyme system based on CFX. Copyright © 2012 Wiley Periodicals, Inc.

  18. Cell-Free and In Vivo Characterization of Lux, Las, and Rpa Quorum Activation Systems in E. coli.

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    Halleran, Andrew D; Murray, Richard M

    2017-11-28

    Synthetic biologists have turned toward quorum systems as a path for building sophisticated microbial consortia that exhibit group decision making. Currently, however, even the most complex consortium circuits rely on only one or two quorum sensing systems, greatly restricting the available design space. High-throughput characterization of available quorum sensing systems is useful for finding compatible sets of systems that are suitable for a defined circuit architecture. Recently, cell-free systems have gained popularity as a test-bed for rapid prototyping of genetic circuitry. We take advantage of the transcription-translation cell-free system to characterize three commonly used Lux-type quorum activators, Lux, Las, and Rpa. We then compare the cell-free characterization to results obtained in vivo. We find significant genetic crosstalk in both the Las and Rpa systems and substantial signal crosstalk in Lux activation. We show that cell-free characterization predicts crosstalk observed in vivo.

  19. Site-Specific Cleavage of Ribosomal RNA in Escherichia coli-Based Cell-Free Protein Synthesis Systems.

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    Jurek Failmezger

    Full Text Available Cell-free protein synthesis, which mimics the biological protein production system, allows rapid expression of proteins without the need to maintain a viable cell. Nevertheless, cell-free protein expression relies on active in vivo translation machinery including ribosomes and translation factors. Here, we examined the integrity of the protein synthesis machinery, namely the functionality of ribosomes, during (i the cell-free extract preparation and (ii the performance of in vitro protein synthesis by analyzing crucial components involved in translation. Monitoring the 16S rRNA, 23S rRNA, elongation factors and ribosomal protein S1, we show that processing of a cell-free extract results in no substantial alteration of the translation machinery. Moreover, we reveal that the 16S rRNA is specifically cleaved at helix 44 during in vitro translation reactions, resulting in the removal of the anti-Shine-Dalgarno sequence. These defective ribosomes accumulate in the cell-free system. We demonstrate that the specific cleavage of the 16S rRNA is triggered by the decreased concentrations of Mg2+. In addition, we provide evidence that helix 44 of the 30S ribosomal subunit serves as a point-of-entry for ribosome degradation in Escherichia coli. Our results suggest that Mg2+ homeostasis is fundamental to preserving functional ribosomes in cell-free protein synthesis systems, which is of major importance for cell-free protein synthesis at preparative scale, in order to create highly efficient technical in vitro systems.

  20. Production of G protein-coupled receptors in an insect-based cell-free system.

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    Sonnabend, Andrei; Spahn, Viola; Stech, Marlitt; Zemella, Anne; Stein, Christoph; Kubick, Stefan

    2017-10-01

    The biochemical analysis of human cell membrane proteins remains a challenging task due to the difficulties in producing sufficient quantities of functional protein. G protein-coupled receptors (GPCRs) represent a main class of membrane proteins and drug targets, which are responsible for a huge number of signaling processes regulating various physiological functions in living cells. To circumvent the current bottlenecks in GPCR studies, we propose the synthesis of GPCRs in eukaryotic cell-free systems based on extracts generated from insect (Sf21) cells. Insect cell lysates harbor the fully active translational and translocational machinery allowing posttranslational modifications, such as glycosylation and phosphorylation of de novo synthesized proteins. Here, we demonstrate the production of several GPCRs in a eukaryotic cell-free system, performed within a short time and in a cost-effective manner. We were able to synthesize a variety of GPCRs ranging from 40 to 133 kDa in an insect-based cell-free system. Moreover, we have chosen the μ opioid receptor (MOR) as a model protein to analyze the ligand binding affinities of cell-free synthesized MOR in comparison to MOR expressed in a human cell line by "one-point" radioligand binding experiments. Biotechnol. Bioeng. 2017;114: 2328-2338. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.

  1. Cell-free system for synthesizing membrane proteins cell free method for synthesizing membrane proteins

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    Laible, Philip D; Hanson, Deborah K

    2013-06-04

    The invention provides an in vitro method for producing proteins, membrane proteins, membrane-associated proteins, and soluble proteins that interact with membrane-associated proteins for assembly into an oligomeric complex or that require association with a membrane for proper folding. The method comprises, supplying intracytoplasmic membranes from organisms; modifying protein composition of intracytoplasmic membranes from organism by modifying DNA to delete genes encoding functions of the organism not associated with the formation of the intracytoplasmic membranes; generating appropriate DNA or RNA templates that encode the target protein; and mixing the intracytoplasmic membranes with the template and a transcription/translation-competent cellular extract to cause simultaneous production of the membrane proteins and encapsulation of the membrane proteins within the intracytoplasmic membranes.

  2. Gateway-compatible vectors for high-throughput protein expression in pro- and eukaryotic cell-free systems.

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    Gagoski, Dejan; Mureev, Sergey; Giles, Nichole; Johnston, Wayne; Dahmer-Heath, Mareike; Škalamera, Dubravka; Gonda, Thomas J; Alexandrov, Kirill

    2015-02-10

    Although numerous techniques for protein expression and production are available the pace of genome sequencing outstrips our ability to analyze the encoded proteins. To address this bottleneck, we have established a system for parallelized cloning, DNA production and cell-free expression of large numbers of proteins. This system is based on a suite of pCellFree Gateway destination vectors that utilize a Species Independent Translation Initiation Sequence (SITS) that mediates recombinant protein expression in any in vitro translation system. These vectors introduce C or N terminal EGFP and mCherry fluorescent and affinity tags, enabling direct analysis and purification of the expressed proteins. To maximize throughput and minimize the cost of protein production we combined Gateway cloning with Rolling Circle DNA Amplification. We demonstrate that as little as 0.1 ng of plasmid DNA is sufficient for template amplification and production of recombinant human protein in Leishmania tarentolae and Escherichia coli cell-free expression systems. Our experiments indicate that this approach can be applied to large gene libraries as it can be reliably performed in multi-well plates. The resulting protein expression pipeline provides a valuable new tool for applications of the post genomic era. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Translation-coupling systems

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    Pfleger, Brian; Mendez-Perez, Daniel

    2013-11-05

    Disclosed are systems and methods for coupling translation of a target gene to a detectable response gene. A version of the invention includes a translation-coupling cassette. The translation-coupling cassette includes a target gene, a response gene, a response-gene translation control element, and a secondary structure-forming sequence that reversibly forms a secondary structure masking the response-gene translation control element. Masking of the response-gene translation control element inhibits translation of the response gene. Full translation of the target gene results in unfolding of the secondary structure and consequent translation of the response gene. Translation of the target gene is determined by detecting presence of the response-gene protein product. The invention further includes RNA transcripts of the translation-coupling cassettes, vectors comprising the translation-coupling cassettes, hosts comprising the translation-coupling cassettes, methods of using the translation-coupling cassettes, and gene products produced with the translation-coupling cassettes.

  4. Circulating cell free DNA as a predictor of systemic lupus ...

    African Journals Online (AJOL)

    Background: Systemic lupus erythematosus (SLE) is the most heterogeneous chronic autoimmune disease; it is characterized by the presence of auto reactive B and T cells, responsible for the aberrant production of a broad and heterogeneous group of autoantibodies. Recent studies using various detection methods have ...

  5. Circulating cell free DNA as a predictor of systemic lupus ...

    African Journals Online (AJOL)

    Olfat M. Hendy

    2015-07-29

    Jul 29, 2015 ... C4;. CRP;. Procalcitonin;. RT-PCR;. Anti-nucleosome. Abstract Background: Systemic lupus erythematosus (SLE) is the most heterogeneous chronic autoimmune .... SLE can cause various tissue inflammation and damage in a ... chronic or acute inflammatory diseases were excluded from the study. 3.

  6. Anti-NO action of carvedilol in cell-free system and in vascular endothelial cells

    OpenAIRE

    Yoshioka, Toshimasa; Iwamoto, Noriko; Tsukahara, Fujiko; Irie, Kaoru; Urakawa, Ikuko; Muraki, Takamura

    2000-01-01

    Carvedilol, an adrenoceptor blocker with antioxidant activity, was studied for its ability to interact with NO in a cell-free condition and in an endothelial cell line (ECV304).In a cell-free system, carvedilol attenuated NO-dependent reduction of carboxy-2-phenyl-4,4,5,5-tetramethyl-imidazoline-1-oxyl-3-oxide induced by a NO donor, 1-hydroxy-2-oxo-3-(aminopropyl)-3-isopropyl-1-triazene (NOC5), which was determined by electron paramagnetic resonance (EPR) spectrometry. The EPR study also show...

  7. Multi-input regulation and logic with T7 promoters in cells and cell free systems

    Energy Technology Data Exchange (ETDEWEB)

    Iyer, Sukanya [ORNL; Karig, David K [ORNL; Norred, Sarah E [ORNL; Simpson, Michael L [ORNL; Doktycz, Mitchel John [ORNL

    2014-01-01

    Engineered gene circuits offer an opportunity to harness biological systems for biotechnological and biomedical applications. However, reliance on host E. coli promoters for the construction of circuit elements, such as logic gates, makes implementation of predictable, independently functioning circuits difficult. In contrast, T7 promoters offer a simple orthogonal expression system for use in a variety of cellular backgrounds and even in cell free systems. Here we develop a T7 promoter system that can be regulated by two different transcriptional repressors for the construction of a logic gate that functions in cells and in cell free systems. We first present LacI repressible T7lacO promoters that are regulated from a distal lac operator site for repression. We next explore the positioning of a tet operator site within the T7lacO framework to create T7 promoters that respond to tet and lac repressors and realize an IMPLIES gate. Finally, we demonstrate that these dual input sensitive promoters function in a commercially available E. coli cell-free protein expression system. Together, our results contribute to the first demonstration of multi-input regulation of T7 promoters and expand the utility of T7 promoters in cell based as well as cell-free gene circuits.

  8. Synthetic biology outside the cell: linking computational tools to cell-free systems.

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    Lewis, Daniel D; Villarreal, Fernando D; Wu, Fan; Tan, Cheemeng

    2014-01-01

    As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.

  9. Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems

    Directory of Open Access Journals (Sweden)

    Daniel eLewis

    2014-12-01

    Full Text Available As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo systems, with only a few examples of prominent work done on predicting the dynamics of cell-free systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the development of a new generation of biomimetic systems. In this review, we explore both in vivo and in vitro models of biochemical networks with a special focus on tools that could be applied to the construction of cell-free expression systems. We believe that quantitative studies of complex cellular mechanisms and pathways in synthetic systems can yield important insights into what makes cells different from conventional chemical systems.

  10. New bioproduction systems: from molecular circuits to novel reactor concepts in cell-free biotechnology.

    Science.gov (United States)

    Rupp, Steffen

    2013-01-01

    : The last decades witnessed a strong growth in several areas of biotechnology, especially in fields related to health, as well as in industrial biotechnology. Advances in molecular engineering now enable biotechnologists to design more efficient pathways in order to convert a larger spectrum of renewable resources into industrially used biofuels and chemicals as well as into new pharmaceuticals and therapeutic proteins. In addition material sciences advanced significantly making it more and more possible to integrate biology and engineering. One of the key questions currently is how to develop new ways of engineering biological systems to cope with the complexity and limitations given by the cell. The options to integrate biology with classical engineering advanced cell free technologies in the recent years significantly. Cell free protein production using cellular extracts is now a well-established universal technology for production of proteins derived from many organisms even at the milligram scale. Among other applications it has the potential to supply the demand for a multitude of enzymes and enzyme variants facilitating in vitro metabolic engineering. This review will briefly address the recent achievements and limitations of cell free conversions. Especially, the requirements for reactor systems in cell free biotechnology, a currently underdeveloped field, are reviewed and some perspectives are given on how material sciences and biotechnology might be able to advance these new developments in the future.

  11. Synthetic Biology Outside the Cell: Linking Computational Tools to Cell-Free Systems

    OpenAIRE

    Daniel eLewis; Villarreal, Fernando D.; Fan eWu; Cheemeng eTan

    2014-01-01

    As mathematical models become more commonly integrated into the study of biology, a common language for describing biological processes is manifesting. Many tools have emerged for the simulation of in vivo synthetic biological systems, with only a few examples of prominent work done on predicting the dynamics of cell-free synthetic systems. At the same time, experimental biologists have begun to study dynamics of in vitro systems encapsulated by amphiphilic molecules, opening the door for the...

  12. Enhanced functional expression of aquaporin Z via fusion of in situ cleavable leader peptides in Escherichia coli cell-free system.

    Science.gov (United States)

    Zhang, Xu; Lian, Jiazhang; Kai, Lei; Huang, Lei; Cen, Peilin; Xu, Zhinan

    2014-02-05

    Aquaporin Z (AqpZ) is a water channel protein from Escherichia coli and has attracted many attentions to develop the biomimetic water filtration technology. Cell-free protein synthesis (CFPS) system, one of the most complex multi-enzymatic systems, has the ability of producing the integral membrane protein in vitro. To enhance the synthesis of AqpZ in E. coli cell-free system, several natural leader peptides were respectively fused at the N-terminus and were verified to enhance the expression level significantly. Moreover, the supplementation of detergents or liposome could activate leader peptidase from the cell-free extract and provide hydrophobic environment for proper folding of AqpZ. Thus, the release of mature AqpZ via the in situ removal of leader peptide was achieved, with a specific water transport activity of (2.1 ± 0.1) × 10⁻¹⁴ cm³ s⁻¹ monomer⁻¹. Using this in situ removable leader peptide strategy, the transcription-translation, leader sequence cleavage and membrane protein folding were integrated into a simple process in the cell-free system, providing a convenient approach to enhance the expression of target proteins, especially those membrane proteins difficult to achieve. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Cell-Free Systems Based on CHO Cell Lysates: Optimization Strategies, Synthesis of "Difficult-to-Express" Proteins and Future Perspectives.

    Directory of Open Access Journals (Sweden)

    Lena Thoring

    Full Text Available Nowadays, biotechnological processes play a pivotal role in target protein production. In this context, Chinese Hamster Ovary (CHO cells are one of the most prominent cell lines for the expression of recombinant proteins and revealed as a safe host for nearly 40 years. Nevertheless, the major bottleneck of common in vivo protein expression platforms becomes obvious when looking at the production of so called "difficult-to-express" proteins. This class of proteins comprises in particular several ion channels and multipass membrane proteins as well as cytotoxic proteins. To enhance the production of "difficult-to-express" proteins, alternative technologies were developed, mainly based on translationally active cell lysates. These so called "cell-free" protein synthesis systems enable an efficient production of different classes of proteins. Eukaryotic cell-free systems harboring endogenous microsomal structures for the synthesis of functional membrane proteins and posttranslationally modified proteins are of particular interest for future applications. Therefore, we present current developments in cell-free protein synthesis based on translationally active CHO cell extracts, underlining the high potential of this platform. We present novel results highlighting the optimization of protein yields, the synthesis of various "difficult-to-express" proteins and the cotranslational incorporation of non-standard amino acids, which was exemplarily demonstrated by residue specific labeling of the glycoprotein Erythropoietin and the multimeric membrane protein KCSA.

  14. Polyvinylsulfonic acid: A Low-cost RNase inhibitor for enhanced RNA preservation and cell-free protein translation.

    Science.gov (United States)

    Earl, Conner C; Smith, Mark T; Lease, Richard A; Bundy, Bradley C

    2017-06-29

    The effectiveness and economics of polyvinyl sulfonic acid (PVSA) as a ribonuclease inhibitor for in vitro systems is reported. PVSA was shown to inhibit RNA cleavage in the presence of RNase A as well as in the presence of Escherichia coli lysate, suggesting that PVSA can act as a broader ribonuclease inhibitor. In addition, PVSA was shown to improve the integrity of mRNA transcripts by up to 5-fold in vitro as measured by their translational viability. Improved preservation of mRNA transcripts in the presence of PVSA under common RNA storage conditions is also reported. A cost comparison with commercially available RNAse inhibitors indicates the economic practicality of PVSA which is approximately 1,700 times less expensive than commonly used ribonuclease inhibitors. PVSA can also be separated from RNA by alcohol precipitation for applications that may be sensitive to the presence of PVSA.

  15. Recombinant Nox4 cytosolic domain produced by a cell or cell-free base systems exhibits constitutive diaphorase activity

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Minh Vu Chuong, E-mail: mvchuong@yahoo.fr [GREPI AGIM FRE 3405 CNRS-UJF, Universite Joseph Fourier, Grenoble (France); Zhang, Leilei [GREPI AGIM FRE 3405 CNRS-UJF, Universite Joseph Fourier, Grenoble (France); Lhomme, Stanislas; Mouz, Nicolas [PX' Therapeutics, MINATEC/Batiment de Haute Technologie, Grenoble (France); Lenormand, Jean-Luc [HumProTher Laboratory, TheReX/TIMC-IMAG UMR 5525 CNRS UJF, Universite Joseph Fourier, UFR de Medecine, Domaine de la Merci, 38706 La Tronche (France); Lardy, Bernard; Morel, Francoise [GREPI AGIM FRE 3405 CNRS-UJF, Universite Joseph Fourier, Grenoble (France)

    2012-03-16

    Highlights: Black-Right-Pointing-Pointer A comparison of two bacterial cell and cell-free protein expression systems is presented. Black-Right-Pointing-Pointer Soluble and active truncated Nox4 proteins are produced. Black-Right-Pointing-Pointer Nox4 has a constitutive diaphorase activity which is independent of cytosolic factors. Black-Right-Pointing-Pointer Isoform Nox4B is unable to initiate the first electronic transfer step. Black-Right-Pointing-Pointer Findings contribute to the understanding of the mechanism of Nox4 oxidase activity. -- Abstract: The membrane protein NADPH (nicotinamide adenine dinucleotide phosphate) oxidase Nox4 constitutively generates reactive oxygen species differing from other NADPH oxidases activity, particularly in Nox2 which needs a stimulus to be active. Although the precise mechanism of production of reactive oxygen species by Nox2 is well characterized, the electronic transfer throughout Nox4 remains unclear. Our study aims to investigate the initial electronic transfer step (diaphorase activity) of the cytosolic tail of Nox4. For this purpose, we developed two different approaches to produce soluble and active truncated Nox4 proteins. We synthesized soluble recombinant proteins either by in vitro translation or by bacteria induction. While proteins obtained by bacteria induction demonstrate an activity of 4.4 {+-} 1.7 nmol/min/nmol when measured against iodonitro tetrazolium chloride and 20.5 {+-} 2.8 nmol/min/nmol with cytochrome c, the soluble proteins produced by cell-free expression system exhibit a diaphorase activity with a turn-over of 26 {+-} 2.6 nmol/min/nmol when measured against iodonitro tetrazolium chloride and 48 {+-} 20.2 nmol/min/nmol with cytochrome c. Furthermore, the activity of the soluble proteins is constitutive and does not need any stimulus. We also show that the cytosolic tail of the isoform Nox4B lacking the first NADPH binding site is unable to demonstrate any diaphorase activity pointing out the

  16. Sodium nitrite induces acute central nervous system toxicity in guinea pigs exposed to systemic cell-free hemoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Buehler, Paul W.; Butt, Omer I. [Laboratory of Biochemistry and Vascular Biology, Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD (United States); D' Agnillo, Felice, E-mail: felice.dagnillo@fda.hhs.gov [Laboratory of Biochemistry and Vascular Biology, Division of Hematology, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD (United States)

    2011-06-10

    Highlights: {yields} Toxicological implications associated with the use of NaNO{sub 2} therapy to treat systemic cell-free Hb exposure are not well-defined. {yields} Systemic Hb exposure followed by NaNO{sub 2} infusion induces acute CNS toxicities in guinea pigs. {yields} These CNS effects were not reproduced by the infusion of cell-free Hb or NaNO{sub 2} alone. {yields} NaNO{sub 2}-mediated oxidation of cell-free Hb may play a causative role in the observed CNS changes. -- Abstract: Systemic cell-free hemoglobin (Hb) released via hemolysis disrupts vascular homeostasis, in part, through the scavenging of nitric oxide (NO). Sodium nitrite (NaNO{sub 2}) therapy can attenuate the hypertensive effects of Hb. However, the chemical reactivity of NaNO{sub 2} with Hb may enhance heme- or iron-mediated toxicities. Here, we investigate the effect of NaNO{sub 2} on the central nervous system (CNS) in guinea pigs exposed to systemic cell-free Hb. Intravascular infusion of NaNO{sub 2}, at doses sufficient to alleviate Hb-mediated blood pressure changes, reduced the expression of occludin, but not zona occludens-1 (ZO-1) or claudin-5, in cerebral tight junctions 4 h after Hb infusion. This was accompanied by increased perivascular heme oxygenase-1 expression, neuronal iron deposition, increased astrocyte and microglial activation, and reduced expression of neuron-specific nuclear protein (NeuN). These CNS changes were not observed in animals treated with Hb or NaNO{sub 2} alone. Taken together, these findings suggest that the use of nitrite salts to treat systemic Hb exposure may promote acute CNS toxicity.

  17. Scavenging of superoxide anion by phosphorylethanolamine: studies in human neutrophils and in a cell free system.

    Science.gov (United States)

    Gordon, L I; Weiss, D; Prachand, S; Weitzman, S A

    1991-01-01

    On the basis of previous observations, we attempted to characterize the effects of various products of phospholipid hydrolysis on neutrophil (PMN) respiratory burst activity. We studied the effects of phosphorylcholine (PC) and phosphorylethanoline (PE) on superoxide anion production in PMN and in cell free system. We found that PE but not PC inhibited measured superoxide anion, but that this was not due to inhibition of cellular superoxide generation but to scavenging of generated superoxide anion. Further, utilizing a system based upon the photo-oxidation of O-dianisidine sensitized by riboflavin, we were able to determine that the scavenging effect of PE was not superoxide dismutase (SOD)-like but rather a general scavenging or glutathione (GSH)-like effect. These data underscore the importance of identifying the mechanism of inhibition of superoxide generation by putative inhibitors as being due to a direct cellular effect or to a scavenging property.

  18. Replication independent formation of extrachromosomal circular DNA in mammalian cell-free system.

    Directory of Open Access Journals (Sweden)

    Zoya Cohen

    Full Text Available Extrachromosomal circular DNA (eccDNA is a pool of circular double stranded DNA molecules found in all eukaryotic cells and composed of repeated chromosomal sequences. It was proposed to be involved in genomic instability, aging and alternative telomere lengthening. Our study presents novel mammalian cell-free system for eccDNA generation. Using purified protein extract we show that eccDNA formation does not involve de-novo DNA synthesis suggesting that eccDNA is generated through excision of chromosomal sequences. This process is carried out by sequence-independent enzymes as human protein extract can produce mouse-specific eccDNA from high molecular weight mouse DNA, and vice versa. EccDNA production does not depend on ATP, requires residual amounts of Mg(2+ and is enhanced by double strand DNA breaks.

  19. Membrane protein synthesis in cell-free systems: from bio-mimetic systems to bio-membranes.

    Science.gov (United States)

    Sachse, Rita; Dondapati, Srujan K; Fenz, Susanne F; Schmidt, Thomas; Kubick, Stefan

    2014-08-25

    When taking up the gauntlet of studying membrane protein functionality, scientists are provided with a plethora of advantages, which can be exploited for the synthesis of these difficult-to-express proteins by utilizing cell-free protein synthesis systems. Due to their hydrophobicity, membrane proteins have exceptional demands regarding their environment to ensure correct functionality. Thus, the challenge is to find the appropriate hydrophobic support that facilitates proper membrane protein folding. So far, various modes of membrane protein synthesis have been presented. Here, we summarize current state-of-the-art methodologies of membrane protein synthesis in biomimetic-supported systems. The correct folding and functionality of membrane proteins depend in many cases on their integration into a lipid bilayer and subsequent posttranslational modification. We highlight cell-free systems utilizing the advantages of biological membranes. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

  20. Anti-NO action of carvedilol in cell-free system and in vascular endothelial cells.

    Science.gov (United States)

    Yoshioka, T; Iwamoto, N; Tsukahara, F; Irie, K; Urakawa, I; Muraki, T

    2000-04-01

    1. Carvedilol, an adrenoceptor blocker with antioxidant activity, was studied for its ability to interact with NO in a cell-free condition and in an endothelial cell line (ECV304). 2. In a cell-free system, carvedilol attenuated NO-dependent reduction of carboxy-2-phenyl-4,4, 5,5-tetramethyl-imidazoline-1-oxyl-3-oxide induced by a NO donor, 1-hydroxy-2-oxo-3-(aminopropyl)-3-isopropyl-1-triazene (NOC5), which was determined by electron paramagnetic resonance (EPR) spectrometry. The EPR study also showed that nitrosylhaemoglobin formation in rat red blood cells by the addition of NO-saturated solution was attenuated by prior incubation with 0.1 - 10 microM carvedilol. 3. NO-induced fluorescence in 4,5-diaminofluorescein-2 diacethyl (DAF-2DA)-loaded ECV304 cells was attenuated by carvedilol but not by labetalol. The IC(50) of carvedilol for NOC5 or sodium nitroprusside-induced fluorescence of DAF-2DA in ECV304 cells was 1. 0x10(-7) M, which was similar to the reported IC(50) of carvedilol for the antioxidant effect. 4. Cell toxicity induced by a NO donor determined by the number of viable cells after 24 h treatment with 2-2'(hydroxynitrosohydrazino)bis-ethanamine was significantly attenuated by pretreatment with 1 microM carvedilol. 5. Both free and cell-associated carvedilol quenched NO. Because NO mediates both physiological and pathophysiological processes, NO quenching by the drug may have diverse clinical implications depending upon specific functions of local NO in tissues where carvedilol is distributed.

  1. Anti-NO action of carvedilol in cell-free system and in vascular endothelial cells

    Science.gov (United States)

    Yoshioka, Toshimasa; Iwamoto, Noriko; Tsukahara, Fujiko; Irie, Kaoru; Urakawa, Ikuko; Muraki, Takamura

    2000-01-01

    Carvedilol, an adrenoceptor blocker with antioxidant activity, was studied for its ability to interact with NO in a cell-free condition and in an endothelial cell line (ECV304).In a cell-free system, carvedilol attenuated NO-dependent reduction of carboxy-2-phenyl-4,4,5,5-tetramethyl-imidazoline-1-oxyl-3-oxide induced by a NO donor, 1-hydroxy-2-oxo-3-(aminopropyl)-3-isopropyl-1-triazene (NOC5), which was determined by electron paramagnetic resonance (EPR) spectrometry. The EPR study also showed that nitrosylhaemoglobin formation in rat red blood cells by the addition of NO-saturated solution was attenuated by prior incubation with 0.1–10 μM carvedilol.NO-induced fluorescence in 4,5-diaminofluorescein-2 diacethyl (DAF-2DA)-loaded ECV304 cells was attenuated by carvedilol but not by labetalol. The IC50 of carvedilol for NOC5 or sodium nitroprusside-induced fluorescence of DAF-2DA in ECV304 cells was 1.0×10−7 M, which was similar to the reported IC50 of carvedilol for the antioxidant effect.Cell toxicity induced by a NO donor determined by the number of viable cells after 24 h treatment with 2-2′(hydroxynitrosohydrazino)bis-ethanamine was significantly attenuated by pretreatment with 1 μM carvedilol.Both free and cell-associated carvedilol quenched NO. Because NO mediates both physiological and pathophysiological processes, NO quenching by the drug may have diverse clinical implications depending upon specific functions of local NO in tissues where carvedilol is distributed. PMID:10742311

  2. Study of messenger RNA inactivation and protein degradation in an Escherichia coli cell-free expression system

    Directory of Open Access Journals (Sweden)

    Noireaux Vincent

    2010-07-01

    Full Text Available Abstract Background A large amount of recombinant proteins can be synthesized in a few hours with Escherichia coli cell-free expression systems based on bacteriophage transcription. These cytoplasmic extracts are used in many applications that require large-scale protein production such as proteomics and high throughput techniques. In recent years, cell-free systems have also been used to engineer complex informational processes. These works, however, have been limited by the current available cell-free systems, which are not well adapted to these types of studies. In particular, no method has been proposed to increase the mRNA inactivation rate and the protein degradation rate in cell-free reactions. The construction of in vitro informational processes with interesting dynamics requires a balance between mRNA and protein synthesis (the source, and mRNA inactivation and protein degradation (the sink. Results Two quantitative studies are presented to characterize and to increase the global mRNA inactivation rate, and to accelerate the degradation of the synthesized proteins in an E. coli cell-free expression system driven by the endogenous RNA polymerase and sigma factor 70. The E. coli mRNA interferase MazF was used to increase and to adjust the mRNA inactivation rate of the Firefly luciferase (Luc and of the enhanced green fluorescent protein (eGFP. Peptide tags specific to the endogenous E. coli AAA + proteases were used to induce and to adjust the protein degradation rate of eGFP. Messenger RNA inactivation rate, protein degradation rate, maturation time of Luc and eGFP were measured. Conclusions The global mRNA turnover and the protein degradation rate can be accelerated and tuned in a biologically relevant range in a cell-free reaction with quantitative procedures easy to implement. These features broaden the capabilities of cell-free systems with a better control of gene expression. This cell-free extract could find some applications in

  3. Chemical communication between bacteria and cell-free gene expression systems within linear chains of emulsion droplets.

    Science.gov (United States)

    Schwarz-Schilling, M; Aufinger, L; Mückl, A; Simmel, F C

    2016-04-18

    Position-dependent gene expression in gradients of morphogens is one of the key processes involved in cellular differentiation during development. Here, we study a simple artificial differentiation process, which is based on the diffusion of genetic inducers within one-dimensional arrangements of 50 μm large water-in-oil droplets. The droplets are filled with either bacteria or cell-free gene expression systems, both equipped with genetic constructs that produce inducers or respond to them via expression of a fluorescent protein. We quantitatively study the coupled diffusion-gene expression process and demonstrate that gene expression can be made position-dependent both within bacteria-containing and cell-free droplets. By generating diffusing quorum sensing signals in situ, we also establish communication between artificial cell-free sender cells and bacterial receivers, and vice versa.

  4. Increased death of adipose cells, a path to release cell-free DNA into systemic circulation of obese women.

    Science.gov (United States)

    Haghiac, Maricela; Vora, Neeta L; Basu, Subhabrata; Johnson, Kirby L; Presley, Larraine; Bianchi, Diana W; Hauguel-de Mouzon, Sylvie

    2012-11-01

    Remodeling of adipose tissue is required to support the expansion of adipose mass. In obesity, an increased death of adipocytes contributes to the accelerated cellular turnover. We have shown that obesity in pregnancy is associated with metabolic and immune alterations in the adipose tissue. In this study, we characterized the mechanisms responsible for increased death of adipose cells of pregnant obese women and its functional consequences. We postulated that a higher turnover of dead cells in white adipose tissue of obese women would translate into release of cell-free DNA (cfDNA) into their systemic circulation. Increase in adipose mass of obese compared to lean women results from a lesser number of hypertrophic adipocytes and an accumulation of macrophages in the stromal vascular fraction (SVF). The adipocytes of obese displayed enhanced necrosis with a loss of perilipin staining at the plasma membrane. Apoptosis was prominent in SVF cells with an increased expression of caspase 9 and caspase 3 and a higher rate of terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end-labeling (TUNEL) positive CD68 macrophages in obese vs. lean. Whereas circulating fetal cfDNA concentrations were not changed, there was a twofold increase in circulating glyceraldehyde-3-phosphate dehydrogenase (GAPDH) cfDNA and adipose tissue GAPDH mRNA in obese women. The maternal systemic GAPDH cfDNA was positively correlated with BMI and gestational weight gain. These data suggest that the active remodeling of adipose tissue of obese pregnant women results in an increased release of cfDNA of maternal origin into the circulation.

  5. A New Cell-Free System to Study BRCA1 Function

    Science.gov (United States)

    2016-06-01

    One interpretation is that fork convergence triggers a conformational change in CMG that makes it responsive to the action of BRCA1-BARD1, which is...approach (cell-free egg extracts) to interrogate genome maintenance processes and underwent rigorous training in the design and interpretation of...Protein Research in Copenhagen , Denmark. Thomas Graham will start a post-doctoral position in the laboratory of Vanessa Ruta at Rockefeller

  6. Heterotrophic nature of the cell-free protein-synthesizing system from the strict chemolithotroph, Thiobacillus thiooxidans.

    Science.gov (United States)

    Amemiya, K; Umbreit, W W

    1974-02-01

    A cell-free protein-synthesizing system prepared from the strict chemolithotroph, Thiobacillus thiooxidans, was similar to that of heterotrophs. The poly-U directed system had a temperature optimum of 37 C, but in the presence of spermidine (3 mM) the optimum shifted to 45 C. Although growth of the chemolithotroph occurs only in acid conditions, the pH optimum for the cell-free system was pH 7.2. The endogenous-directed activity in the presence or absence of spermidine was maximal at pH 7.8. Spermidine had a stimulatory effect; however, this effect was dependent on the magnesium and tris(hydroxymethyl)aminomethane (Tris) concentrations. At low Tris concentrations (10 mM), spermidine (3 to 5 mM) could completely replace magnesium. When the Tris concentration was increased (50 mM), spermidine could not replace magnesium. Supernatant and ribosomal fractions from T. thiooxidans were exchanged with those of Bacillus thuringiensis and Escherichia coli, and the ribosomal fraction from the chemolithotroph gave good to moderate stimulation when exchanged with the supernatant from the heterotrophs. On the other hand, the supernatant from T. thiooxidans gave good stimulation when mixed with ribosomes from B. thuringiensis but poor activity with ribosomes from E. coli. Both supernatant and ribosomal fractions prepared from stationary phase extracts of T. thiooxidans were inactive in the cell-free system.

  7. Functional expression of a single-chain antibody to ErbB-2 in plants and cell-free systems

    Directory of Open Access Journals (Sweden)

    Benevolo Maria

    2006-09-01

    Full Text Available Abstract Background Aberrant signaling by ErbB-2 (HER 2, Neu, a member of the human Epidermal Growth Factor (EGF receptor family, is associated with an aggressive clinical behaviour of carcinomas, particularly breast tumors. Antibodies targeting the ErbB-2 pathway are a preferred therapeutic option for patients with advanced breast cancer, but a worldwide deficit in the manufacturing capacities of mammalian cell bioreactors is foreseen. Methods Herein, we describe a multi-platform approach for the production of recombinant Single chain Fragments of antibody variable regions (ScFvs to ErbB-2 that involves their functional expression in (a bacteria, (b transient as well as stable transgenic tobacco plants, and (c a newly developed cell-free transcription-translation system. Results An ScFv (ScFv800E6 was selected by cloning immunoglobulin sequences from murine hybridomas, and was expressed and fully functional in all the expression platforms, thereby representing the first ScFv to ErbB-2 produced in hosts other than bacteria and yeast. ScFv800E6 was optimized with respect to redox synthesis conditions. Different tags were introduced flanking the ScFv800E6 backbone, with and without spacer arms, including a novel Strep II tag that outperforms conventional streptavidin-based detection systems. ScFv800E6 was resistant to standard chemical radiolabeling procedures (i.e. Chloramine T, displayed a binding ability extremely similar to that of the parental monovalent Fab' fragment, as well as a flow cytometry performance and an equilibrium binding affinity (Ka approximately 2 × 108 M-1 only slightly lower than those of the parental bivalent antibody, suggesting that its binding site is conserved as compared to that of the parental antibody molecule. ScFv800E6 was found to be compatible with routine reagents for immunohistochemical staining. Conclusion ScFv800E6 is a useful reagent for in vitro biochemical and immunodiagnostic applications in oncology

  8. Cell-free synthetic biology for in vitro prototype engineering.

    Science.gov (United States)

    Moore, Simon J; MacDonald, James T; Freemont, Paul S

    2017-06-15

    Cell-free transcription-translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells. © 2017 The Author(s).

  9. Exploiting Cell-Free Systems : Implementation and Debugging of a System of Biotransformations

    NARCIS (Netherlands)

    Bujara, Matthias; Schümperli, Michael; Billerbeck, Sonja; Heinemann, Matthias; Panke, Sven

    2010-01-01

    The orchestration of a multitude of enzyme catalysts allows cells to carry out complex and thermodynamically unfavorable chemical conversions. In an effort to recruit these advantages for in vitro biotransformations, we have assembled a 10-step catalytic system—a system of biotransformations

  10. Exploiting Cell-Free Systems: Implementation and Debugging of a System of Biotransformations

    OpenAIRE

    Bujara, Matthias; Schümperli, Michael; Billerbeck, Sonja; Heinemann, Matthias; Panke, Sven

    2010-01-01

    The orchestration of a multitude of enzyme catalysts allows cells to carry out complex and thermodynamically unfavorable chemical conversions. In an effort to recruit these advantages for in vitro biotransformations, we have assembled a 10-step catalytic system—a system of biotransformations (SBT)—for the synthesis of unnatural monosaccharides based on the versatile building block dihydroxyacetone phosphate (DHAP). To facilitate the assembly of such a network, we have insulated a production p...

  11. Exploiting cell-free systems: Implementation and debugging of a system of biotransformations.

    Science.gov (United States)

    Bujara, Matthias; Schümperli, Michael; Billerbeck, Sonja; Heinemann, Matthias; Panke, Sven

    2010-06-15

    The orchestration of a multitude of enzyme catalysts allows cells to carry out complex and thermodynamically unfavorable chemical conversions. In an effort to recruit these advantages for in vitro biotransformations, we have assembled a 10-step catalytic system-a system of biotransformations (SBT)-for the synthesis of unnatural monosaccharides based on the versatile building block dihydroxyacetone phosphate (DHAP). To facilitate the assembly of such a network, we have insulated a production pathway from Escherichia coli's central carbon metabolism. This pathway consists of the endogenous glycolysis without triose-phosphate isomerase to enable accumulation of DHAP and was completed with lactate dehydrogenase to regenerate NAD(+). It could be readily extended for the synthesis of unnatural sugar molecules, such as the unnatural monosaccharide phosphate 5,6,7-trideoxy-D-threo-heptulose-1-phosphate from DHAP and butanal. Insulation required in particular inactivation of the amn gene encoding the AMP nucleosidase, which otherwise led to glucose-independent DHAP production from adenosine phosphates. The work demonstrates that a sufficiently insulated in vitro multi-step enzymatic system can be readily assembled from central carbon metabolism pathways. 2010 Wiley Periodicals, Inc.

  12. Hemisynthesis of deuteriated adenosylhopane and conversion into bacteriohopanetetrol by a cell-free system from Methylobacterium organophilum.

    Science.gov (United States)

    Liu, Wenjun; Bodlenner, Anne; Rohmer, Michel

    2015-03-21

    Adenosylhopane is a putative precursor of the widespread bacterial C35 biohopanoids. A concise and flexible hemisynthesis of adenosylhopane has been developed including as key steps a cross metathesis between two olefins containing either the hopane moiety or a protected adenosine derivative and a subsequent diimide reduction of the resulting olefin. Reduction by deuteriated diimide allowed deuterium labelling. This synthetic protocol represents a versatile tool to access to deuteriated composite bacterial hopanoids required for biosynthetic studies. Deuteriated adenosylhopane was thus converted into bacteriohopanetetrol by a crude cell-free system from Methylobacterium organophilum in the presence of NADPH, showing for the first time the precursor to product relationship between these two bacterial metabolites.

  13. Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity.

    Science.gov (United States)

    Kamath-Rayne, Beena D; Du, Yina; Hughes, Maria; Wagner, Erin A; Muglia, Louis J; DeFranco, Emily A; Whitsett, Jeffrey A; Salomonis, Nathan; Xu, Yan

    2015-10-22

    Amniotic fluid (AF) is a proximal fluid to the fetus containing higher amounts of cell-free fetal RNA/DNA than maternal serum, thereby making it a promising source for identifying novel biomarkers that predict fetal development and organ maturation. Our aim was to compare AF transcriptomic profiles at different time points in pregnancy to demonstrate unique genetic signatures that would serve as potential biomarkers indicative of fetal maturation. We isolated AF RNA from 16 women at different time points in pregnancy: 4 from 18 to 24 weeks, 6 from 34 to 36 weeks, and 6 from 39 to 40 weeks. RNA-sequencing was performed on cell-free RNA. Gene expression and splicing analyses were performed in conjunction with cell-type and pathway predictions. Sample-level analysis at different time points in pregnancy demonstrated a strong correlation with cell types found in the intrauterine environment and fetal respiratory, digestive and external barrier tissues of the fetus, using high-confidence cellular molecular markers. While some RNAs and splice variants were present throughout pregnancy, many transcripts were uniquely expressed at different time points in pregnancy and associated with distinct neonatal co-morbidities (respiratory distress and gavage feeding), indicating fetal immaturity. The AF transcriptome exhibits unique cell/organ-selective expression patterns at different time points in pregnancy that can potentially identify fetal organ maturity and predict neonatal morbidity. Developing novel biomarkers indicative of the maturation of multiple organ systems can improve upon our current methods of fetal maturity testing which focus solely on the lung, and will better inform obstetrical decisions regarding delivery timing.

  14. Systems Biocatalysis: Development and engineering of cell-free "artificial metabolisms" for preparative multi-enzymatic synthesis.

    Science.gov (United States)

    Fessner, Wolf-Dieter

    2015-12-25

    Systems Biocatalysis is an emerging concept of organizing enzymes in vitro to construct complex reaction cascades for an efficient, sustainable synthesis of valuable chemical products. The strategy merges the synthetic focus of chemistry with the modular design of biological systems, which is similar to metabolic engineering of cellular production systems but can be realized at a far lower level of complexity from a true reductionist approach. Such operations are free from material erosion by competing metabolic pathways, from kinetic restrictions by physical barriers and regulating circuits, and from toxicity problems with reactive foreign substrates, which are notorious problems in whole-cell systems. A particular advantage of cell-free concepts arises from the inherent opportunity to construct novel biocatalytic reaction systems for the efficient synthesis of non-natural products ("artificial metabolisms") by using enzymes specifically chosen or engineered for non-natural substrate promiscuity. Examples illustrating the technology from our laboratory are discussed. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. An economical and highly productive cell-free protein synthesis system utilizing fructose-1,6-bisphosphate as an energy source.

    Science.gov (United States)

    Kim, Tae-Wan; Keum, Jung-Won; Oh, In-Seok; Choi, Cha-Yong; Kim, Ho-Cheol; Kim, Dong-Myung

    2007-07-15

    In this study, we describe the development of a cost effective and highly productive cell-free protein synthesis system derived from Escherichia coli. Through the use of an optimal energy source and cell extract, approximately 1.3mg/mL of protein was generated from a single batch reaction at greatly reduced reagent costs. Compared to previously reported systems, the described method yields approximately 14-fold higher productivity per unit reagent cost making this cell-free synthesis technique a promising alternative for more efficient protein production.

  16. Responding to chromosomal breakage during M-phase: insights from a cell-free system

    Directory of Open Access Journals (Sweden)

    Costanzo Vincenzo

    2009-07-01

    Full Text Available Abstract DNA double strand breaks (DSBs activate ATM and ATR dependent checkpoints that prevent the onset of mitosis. However, how cells react to DSBs occurring when they are already in mitosis is poorly understood. The Xenopus egg extract has been utilized to study cell cycle progression and DNA damage checkpoints. Recently this system has been successfully used to uncover an ATM and ATR dependent checkpoint affecting centrosome driven spindle assembly. These studies have led to the identification of XCEP63 as major target of this pathway. XCEP63 is a coiled-coil rich protein localized at centrosome essential for proper spindle assembly. ATM and ATR directly phosphorylate XCEP63 on serine 560 inducing its delocalization from centrosome, which in turn delays spindle assembly. This pathway might contribute to regulate DNA repair or mitotic cell survival in the presence of chromosome breakage.

  17. An economical method for producing stable-isotope labeled proteins by the E. coli cell-free system.

    Science.gov (United States)

    Yokoyama, Jun; Matsuda, Takayoshi; Koshiba, Seizo; Kigawa, Takanori

    2010-12-01

    Improvement of the cell-free protein synthesis system (CF) over the past decade have made it one of the most powerful protein production methods. The CF approach is especially useful for stable-isotope (SI) labeling of proteins for NMR analysis. However, it is less popular than expected, partly because the SI-labeled amino acids used for SI labeling by the CF are too expensive. In the present study, we developed a simple and inexpensive method for producing an SI-labeled protein using Escherichia coli cell extract-based CF. This method takes advantage of endogenous metabolic conversions to generate SI-labeled asparagine, glutamine, cysteine, and tryptophan, which are much more expensive than the other 16 kinds of SI-labeled amino acids, from inexpensive sources, such as SI-labeled algal amino acid mixture, SI-labeled indole, and sodium sulfide, during the CF reaction. As compared with the conventional method employing 20 kinds of SI-labeled amino acids, highly enriched uniform SI-labeling with similar labeling efficiency was achieved at a greatly reduced cost with the newly developed method. Therefore, our method solves the cost problem of the SI labeling of proteins using the CF.

  18. Antioxidant efficacy of iridoid and phenylethanoid glycosides from the medicinal plant Teucrium chamaedris in cell-free systems.

    Science.gov (United States)

    Pacifico, Severina; D'Abrosca, Brigida; Pascarella, Maria Teresa; Letizia, Marianna; Uzzo, Piera; Piscopo, Vincenzo; Fiorentino, Antonio

    2009-09-01

    Twelve glycosides, seven iridoids and five phenylethanoids, have been isolated from leaf and root methanolic extracts of Wall Germander (Teucrium chamaedrys), a Mediterranean species historically used as a medicinal plant. Among them, three iridoid and one phenylethanoid glycosides have been isolated and characterized for the first time. All of the structures have been elucidated on the basis of their spectral data, especially 1D and 2D NMR experiments. The antioxidative properties of pure metabolites, as well as of crude organic extracts of the plant, have been analyzed on the basis of their DPPH radical scavenging capability. The antioxidant capacity in cell-free systems of the isolated metabolites was carried out by measuring their capabilities to inhibit the synthesis of thiobarbituric acid reactive species in assay media using as oxidable substrates a vegetable fat and the pentose sugar 2-deoxyribose and to prevent oxidative damage of the hydrosoluble bovine serum albumin (BSA) protein. Phenylethanoid glycosides resulted efficacious DPPH radical, while iridoid glycosides prevent massively the 2-deoxyribose and BSA oxidations in assay media.

  19. Quasi-greedy systems of integer translates

    DEFF Research Database (Denmark)

    Nielsen, Morten; Sikic, Hrvoje

    We consider quasi-greedy systems of integer translates in a finitely generated shift invariant subspace of L2(Rd), that is systems for which the thresholding approximation procedure is well behaved. We prove that every quasi-greedy system of integer translates is also a Riesz basis for its closed...... linear span. The result shows that there are no conditional quasi-greedy basis of integer translates in a finitely generated shift invariant space....

  20. Quasi-greedy systems of integer translates

    DEFF Research Database (Denmark)

    Nielsen, Morten; Sikic, Hrvoje

    2008-01-01

    We consider quasi-greedy systems of integer translates in a finitely generated shift-invariant subspace of L2(Rd), that is systems for which the thresholding approximation procedure is well behaved. We prove that every quasi-greedy system of integer translates is also a Riesz basis for its closed...... linear span. The result shows that there are no conditional quasi-greedy bases of integer translates in a finitely generated shift-invariant space....

  1. Cell-Free Synthesis Meets Antibody Production: A Review

    Directory of Open Access Journals (Sweden)

    Marlitt Stech

    2015-01-01

    Full Text Available Engineered antibodies are key players in therapy, diagnostics and research. In addition to full size immunoglobulin gamma (IgG molecules, smaller formats of recombinant antibodies, such as single-chain variable fragments (scFv and antigen binding fragments (Fab, have emerged as promising alternatives since they possess different advantageous properties. Cell-based production technologies of antibodies and antibody fragments are well-established, allowing researchers to design and manufacture highly specific molecular recognition tools. However, as these technologies are accompanied by the drawbacks of being rather time-consuming and cost-intensive, efficient and powerful cell-free protein synthesis systems have been developed over the last decade as alternatives. So far, prokaryotic cell-free systems have been the focus of interest. Recently, eukaryotic in vitro translation systems have enriched the antibody production pipeline, as these systems are able to mimic the natural pathway of antibody synthesis in eukaryotic cells. This review aims to overview and summarize the advances made in the production of antibodies and antibody fragments in cell-free systems.

  2. Network Basic Language Translation System: Security Infrastructure

    National Research Council Canada - National Science Library

    Mittrick, Mark R

    2007-01-01

    .... The Network Basic Language Translation System (NetBLTS) was proposed and accepted as part of the U.S. Army Research Laboratory's offering of initiatives within the Horizontal Fusion portfolio in 2003...

  3. Synthesis of Bacteriophage M13-Specific Proteins in a DNA-Dependent Cell-Free System II. In Vitro Synthesis of Biologically Active Gene 5 Protein

    Science.gov (United States)

    Konings, Ruud N. H.; Jansen, Josephine; Cuypers, Theo; Schoenmakers, John G. G.

    1973-01-01

    It is shown that gene 5 protein of bacteriophage M13 is one of the major proteins synthesized in vitro under the direction of M13 replicative-form DNA. By means of DNA-cellulose chromatography, this protein has been purified to homogeneity and its biological characteristics have been compared with those of its native counterpart. Like native gene 5 protein, the purified, in vitro-synthesized protein binds tightly and selectively to single-stranded, but not to double-stranded, DNAs. These results suggest that truly functional gene 5 protein is made in the cell-free system. Images PMID:4586780

  4. Chinese-English Machine Translation System.

    Science.gov (United States)

    Wang, William S-Y; And Others

    The report documents results of a two-year R&D effort directed at the completion of a prototype system for Chinese-English machine translation of S&T literature. The system, designated QUINCE, accepts Chinese input exactly as printed, with no pre-editing of any kind, and produces English output on experimental basis. Coding of Chinese text via…

  5. Nod2-Nodosome in a Cell-Free System: Implications in Pathogenesis and Drug Discovery for Blau Syndrome and Early-Onset Sarcoidosis

    Directory of Open Access Journals (Sweden)

    Tomoyuki Iwasaki

    2016-01-01

    Full Text Available Nucleotide-binding oligomerization domain-containing protein (Nod 2 is an intracellular pattern recognition receptor, which recognizes muramyl dipeptide (N-Acetylmuramyl-L-Alanyl-D-Isoglutamine: MDP, a bacterial peptidoglycan component, and makes a NF-κB-activating complex called nodosome with adaptor protein RICK (RIP2/RIPK2. Nod2 mutants are associated with the autoinflammatory diseases, Blau syndrome (BS/early-onset sarcoidosis (EOS. For drug discovery of BS/EOS, we tried to develop Nod2-nodosome in a cell-free system. FLAG-tagged RICK, biotinylated-Nod2, and BS/EOS-associated Nod2 mutants were synthesized, and proximity signals between FLAG-tagged and biotinylated proteins were detected by amplified luminescent proximity homogeneous assay (ALPHA. Upon incubation with MDP, the ALPHA signal of interaction between Nod2-WT and RICK was increased in a dose-dependent manner. The ALPHA signal of interaction between RICK and the BS/EOS-associated Nod2 mutants was more significantly increased than Nod2-WT. Notably, the ALPHA signal between Nod2-WT and RICK was increased upon incubation with MDP, but not when incubated with the same concentrations, L-alanine, D-isoglutamic acid, or the MDP-D-isoform. Thus, we successfully developed Nod2-nodosome in a cell-free system reflecting its function in vivo, and it can be useful for screening Nod2-nodosome-targeted therapeutic molecules for BS/EOS and granulomatous inflammatory diseases.

  6. Nod2-Nodosome in a Cell-Free System: Implications in Pathogenesis and Drug Discovery for Blau Syndrome and Early-Onset Sarcoidosis.

    Science.gov (United States)

    Iwasaki, Tomoyuki; Kaneko, Naoe; Ito, Yuki; Takeda, Hiroyuki; Sawasaki, Tatsuya; Heike, Toshio; Migita, Kiyoshi; Agematsu, Kazunaga; Kawakami, Atsushi; Morikawa, Shinnosuke; Mokuda, Sho; Kurata, Mie; Masumoto, Junya

    2016-01-01

    Nucleotide-binding oligomerization domain-containing protein (Nod) 2 is an intracellular pattern recognition receptor, which recognizes muramyl dipeptide (N-Acetylmuramyl-L-Alanyl-D-Isoglutamine: MDP), a bacterial peptidoglycan component, and makes a NF-κB-activating complex called nodosome with adaptor protein RICK (RIP2/RIPK2). Nod2 mutants are associated with the autoinflammatory diseases, Blau syndrome (BS)/early-onset sarcoidosis (EOS). For drug discovery of BS/EOS, we tried to develop Nod2-nodosome in a cell-free system. FLAG-tagged RICK, biotinylated-Nod2, and BS/EOS-associated Nod2 mutants were synthesized, and proximity signals between FLAG-tagged and biotinylated proteins were detected by amplified luminescent proximity homogeneous assay (ALPHA). Upon incubation with MDP, the ALPHA signal of interaction between Nod2-WT and RICK was increased in a dose-dependent manner. The ALPHA signal of interaction between RICK and the BS/EOS-associated Nod2 mutants was more significantly increased than Nod2-WT. Notably, the ALPHA signal between Nod2-WT and RICK was increased upon incubation with MDP, but not when incubated with the same concentrations, L-alanine, D-isoglutamic acid, or the MDP-D-isoform. Thus, we successfully developed Nod2-nodosome in a cell-free system reflecting its function in vivo, and it can be useful for screening Nod2-nodosome-targeted therapeutic molecules for BS/EOS and granulomatous inflammatory diseases.

  7. Expression of proteins containing disulfide bonds in an insect cell-free system and confirmation of their arrangements by MALDI-TOF MS.

    Science.gov (United States)

    Ezure, Toru; Suzuki, Takashi; Shikata, Masamitsu; Ito, Masaaki; Ando, Eiji; Nishimura, Osamu; Tsunasawa, Susumu

    2007-12-01

    Escherichia coli alkaline phosphatase (AP) and human lysozyme (h-LYZ), which contain two and four disulfide bonds, respectively, were expressed in a cell-free protein synthesis system constructed from Spodoptera frugiperda 21 (Sf21) cells. AP was expressed in a soluble and active form using the insect cell-free system under non-reducing conditions, and h-LYZ was expressed in a soluble and active form under non-reducing conditions after addition of reduced glutathione (GSH), oxidized glutathione (GSSG), and protein disulfide isomerase (PDI). The in vitro synthesized proteins were purified by means of a Strep-tag attached to their C termini. Approximately 41 microg AP and 30 microg h-LYZ were obtained from 1 mL each of the reaction mixture. The efficiency of protein synthesis approached that measured under reducing conditions. Analysis of the disulfide bond arrangements by MALDI-TOF MS showed that disulfide linkages identical to those observed in the wild-type proteins were formed.

  8. Cotranslational incorporation of non-standard amino acids using cell-free protein synthesis.

    Science.gov (United States)

    Quast, Robert B; Mrusek, Devid; Hoffmeister, Christian; Sonnabend, Andrei; Kubick, Stefan

    2015-07-08

    Over the last years protein engineering using non-standard amino acids has gained increasing attention. As a result, improved methods are now available, enabling the efficient and directed cotranslational incorporation of various non-standard amino acids to equip proteins with desired characteristics. In this context, the utilization of cell-free protein synthesis is particularly useful due to the direct accessibility of the translational machinery and synthesized proteins without having to maintain a vital cellular host. We review prominent methods for the incorporation of non-standard amino acids into proteins using cell-free protein synthesis. Furthermore, a list of non-standard amino acids that have been successfully incorporated into proteins in cell-free systems together with selected applications is provided. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

  9. Cell-free synthetic biology: Engineering in an open world.

    Science.gov (United States)

    Lu, Yuan

    2017-03-01

    Cell-free synthetic biology emerges as a powerful and flexible enabling technology that can engineer biological parts and systems for life science applications without using living cells. It provides simpler and faster engineering solutions with an unprecedented freedom of design in an open environment than cell system. This review focuses on recent developments of cell-free synthetic biology on biological engineering fields at molecular and cellular levels, including protein engineering, metabolic engineering, and artificial cell engineering. In cell-free protein engineering, the direct control of reaction conditions in cell-free system allows for easy synthesis of complex proteins, toxic proteins, membrane proteins, and novel proteins with unnatural amino acids. Cell-free systems offer the ability to design metabolic pathways towards the production of desired products. Buildup of artificial cells based on cell-free systems will improve our understanding of life and use them for environmental and biomedical applications.

  10. Cell-free synthetic biology: Engineering in an open world

    Directory of Open Access Journals (Sweden)

    Yuan Lu

    2017-03-01

    Full Text Available Cell-free synthetic biology emerges as a powerful and flexible enabling technology that can engineer biological parts and systems for life science applications without using living cells. It provides simpler and faster engineering solutions with an unprecedented freedom of design in an open environment than cell system. This review focuses on recent developments of cell-free synthetic biology on biological engineering fields at molecular and cellular levels, including protein engineering, metabolic engineering, and artificial cell engineering. In cell-free protein engineering, the direct control of reaction conditions in cell-free system allows for easy synthesis of complex proteins, toxic proteins, membrane proteins, and novel proteins with unnatural amino acids. Cell-free systems offer the ability to design metabolic pathways towards the production of desired products. Buildup of artificial cells based on cell-free systems will improve our understanding of life and use them for environmental and biomedical applications.

  11. Developing Deployable Spoken Language Translation Systems given Limited Resources

    OpenAIRE

    Eck, Matthias

    2008-01-01

    Approaches are presented that support the deployment of spoken language translation systems. Newly developed methods allow low cost portability to new language pairs. Proposed translation model pruning techniques achieve a high translation performance even in low memory situations. The named entity and specialty vocabulary coverage, particularly on small and mobile devices, is targeted to an individual user by translation model personalization.

  12. A novel xeno-free and feeder-cell-free system for human pluripotent stem cell culture

    OpenAIRE

    Wang, Qihui; Mou, Xiaoning; Cao, Henghua; Meng, Qingzhang; Ma, Yanni; Han, Pengcheng; Jiang, Junjie; Zhang, Hao; Ma, Yue

    2012-01-01

    While human induced pluripotent stem cells (hiPSCs) have promising applications in regenerative medicine, most of the hiPSC lines available today are not suitable for clinical applications due to contamination with nonhuman materials, such as sialic acid, and potential pathogens from animal-product-containing cell culture systems. Although several xeno-free cell culture systems have been established recently, their use of human fibroblasts as feeders reduces the clinical potential of hiPSCs d...

  13. A stromal cell free culture system generates mouse pro-T cells that can reconstitute T-cell compartments in vivo.

    Science.gov (United States)

    Gehre, Nadine; Nusser, Anja; von Muenchow, Lilly; Tussiwand, Roxane; Engdahl, Corinne; Capoferri, Giuseppina; Bosco, Nabil; Ceredig, Rhodri; Rolink, Antonius G

    2015-03-01

    T-cell lymphopenia following BM transplantation or diseases such as AIDS result in immunodeficiency. Novel approaches to ameliorate this situation are urgently required. Herein, we describe a novel stromal cell free culture system in which Lineage(-) Sca1(+)c-kit(+) BM hematopoietic progenitors very efficiently differentiate into pro-T cells. This culture system consists of plate-bound Delta-like 4 Notch ligand and the cytokines SCF and IL-7. The pro-T cells developing in these cultures express CD25, CD117, and partially CD44; express cytoplasmic CD3ε; and have their TCRβ locus partially D-J rearranged. They could be expanded for over 3 months and used to reconstitute the T-cell compartments of sublethally irradiated T-cell-deficient CD3ε(-/-) mice or lethally irradiated WT mice. Pro-T cells generated in this system could partially correct the T-cell lymphopenia of pre-Tα(-/-) mice. However, reconstituted CD3ε(-/-) mice suffered from a wasting disease that was prevented by co-injection of purified CD4(+) CD25(high) WT Treg cells. In a T-cell-sufficient or T-lymphopenic setting, the development of disease was not observed. Thus, this in vitro culture system represents a powerful tool to generate large numbers of pro-T cells for transplantation and possibly with clinical applications. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Influence of Mabs on PrP(Sc formation using in vitro and cell-free systems.

    Directory of Open Access Journals (Sweden)

    Binggong Chang

    Full Text Available PrP(Sc is believed to serve as a template for the conversion of PrP(C to the abnormal isoform. This process requires contact between the two proteins and implies that there may be critical contact sites that are important for conversion. We hypothesized that antibodies binding to either PrP(cor PrP(Sc would hinder or prevent the formation of the PrP(C-PrP(Sc complex and thus slow down or prevent the conversion process. Two systems were used to analyze the effect of different antibodies on PrP(Sc formation: (i neuroblastoma cells persistently infected with the 22L mouse-adapted scrapie stain, and (ii protein misfolding cyclic amplification (PMCA, which uses PrP(Sc as a template or seed, and a series of incubations and sonications, to convert PrP(C to PrP(Sc. The two systems yielded similar results, in most cases, and demonstrate that PrP-specific monoclonal antibodies (Mabs vary in their ability to inhibit the PrP(C-PrP(Sc conversion process. Based on the numerous and varied Mabs analyzed, the inhibitory effect does not appear to be epitope specific, related to PrP(C conformation, or to cell membrane localization, but is influenced by the targeted PrP region (amino vs carboxy.

  15. Complementation of the xeroderma pigmentosum DNA repair synthesis defect with Escherichia coli UvrABC proteins in a cell-free system

    Energy Technology Data Exchange (ETDEWEB)

    Lindahl, T.; Wood, R.D. (Clare Hall Labs., South Mimms (England)); Grossman, L.; Hansson, J. (Johns Hopkins Univ., Baltimore, MD (USA))

    1990-01-11

    A newly developed cell-free system was used to study DNA repair synthesis carried out by extracts from human cell lines in vitro. Extracts from a normal human lymphoid cell line and from cell lines established from individuals with hereditary dysplastic nevus syndrome performed damage-dependent repair synthesis in plasmid DNA treated with cis- or trans-diamminedichloro-platinum(II) or irradiated with ultraviolet light. Cell extracts of xeroderma pigmentosum origin (complementation groups A, C, D, and G) are deficient in DNA repair synthesis. When damaged plasmid DNA was pretreated with purified Escherichia coli UvrABC proteins, xeroderma pigmentosum cell extracts were able to carry out DNA repair synthesis. The ability of E. coli UvrABC proteins to complement xeroderma pigmentosum cell extracts indicates that the extracts are deficient in incision, but can carry out later steps of repair. Thus the in vitro system provides results that are in agreement with the incision defect found from studies of xeroderma pigmentosum cells.

  16. A Review of Hydrogen Production by Photosynthetic Organisms Using Whole-Cell and Cell-Free Systems.

    Science.gov (United States)

    Martin, Baker A; Frymier, Paul D

    2017-10-01

    Molecular hydrogen is a promising currency in the future energy economy due to the uncertain availability of finite fossil fuel resources and environmental effects from their combustion. It also has important uses in the production of fertilizers and platform chemicals as well as in upgrading conventional fuels. Conventional methods for producing molecular hydrogen from natural gas produce carbon dioxide and use a finite resource as feedstock. However, these issues can be overcome by using light energy from the Sun combined with microorganisms and their molecular machinery capable of photosynthesis. In the presence of light, the proteins involved in photosynthesis coupled with appropriate catalysts in higher plants, algae, and cyanobacteria can produce molecular hydrogen, and optimization via genetic modifications and biomolecular engineering further improves production rates. In this review, we will discuss techniques that have been utilized to improve rates of hydrogen production in biological systems based on the protein machinery of photosynthesis coupled with appropriate catalysts. We will also suggest areas for improvement and future directions for work in the field.

  17. Semantic Processing Performance of Internet Machine Translation Systems.

    Science.gov (United States)

    Watters, Paul A.; Patel, Malti

    1999-01-01

    Discusses the performance of automatic direct machine translation systems available through the Internet and examines semantic processing errors that result in confusion when the intended meaning of sentences is not correctly translated. Suggests the need for Web-based translation systems that have an explicit cross-linguistic representation of…

  18. Wheat germ cell-free system-based production of hemagglutinin-neuraminidase protein of human parainfluenza virus type 3: generation and characterization of monoclonal antibody

    Directory of Open Access Journals (Sweden)

    Satoko eMatsunaga

    2014-05-01

    Full Text Available Human parainfluenza virus 3 (HPIV3 commonly causes respiratory disorders in infants and young children. Monoclonal antibodies (MAbs have been produced to several components of HPIV3 and commercially available. However, the utility of these antibodies for several immunological and proteomic assays for understanding the nature of HPIV3 infection remain to be characterized. Herein, we report the development and characterization of monoclonal antibodies against hemagglutinin-neuraminidase (HN of HPIV3. A recombinant full-length HPIV3-HN was successfully synthesized using the wheat-germ cell-free protein production system. After immunization and cell fusion, 36 mouse hybridomas producing MAbs to HPIV3-HN were established. The MAbs obtained were fully characterized using ELISA, immunoblotting and immunofluorescent analyses. Of the MAbs tested, single clone was found to be applicable in both flow cytometry and immunoprecipitation procedures. By utilizing the antibody, we newly identified HPIV3-HN binding host proteins via immunoprecipitation-based mass spectrometry analysis. This study provides the availability of our newly-developed MAbs as a valuable tool for the study of HPIV3 infection as well as the several diagnostic tests of this virus.

  19. Expression regulation by a methyl-CpG binding domain in an E. coli based, cell-free TX-TL system

    Science.gov (United States)

    Schenkelberger, M.; Shanak, S.; Finkler, M.; Worst, E. G.; Noireaux, V.; Helms, V.; Ott, A.

    2017-04-01

    Cytosine methylation plays an important role in the epigenetic regulation of eukaryotic gene expression. The methyl-CpG binding domain (MBD) is common to a family of eukaryotic transcriptional regulators. How MBD, a stretch of about 80 amino acids, recognizes CpGs in a methylation dependent manner, and as a function of sequence, is only partly understood. Here we show, using an Escherichia coli cell-free expression system, that MBD from the human transcriptional regulator MeCP2 performs as a specific, methylation-dependent repressor in conjunction with the BDNF (brain-derived neurotrophic factor) promoter sequence. Mutation of either base flanking the central CpG pair changes the expression level of the target gene. However, the relative degree of repression as a function of MBD concentration remains unaltered. Molecular dynamics simulations that address the DNA B fiber ratio and the handedness reveal cooperative transitions in the promoter DNA upon MBD binding that correlate well with our experimental observations. We suggest that not only steric hindrance, but also conformational changes of the BDNF promoter as a result of MBD binding are required for MBD to act as a specific inhibitory element. Our work demonstrates that the prokaryotic transcription machinery can reproduce features of epigenetic mammalian transcriptional regulatory elements.

  20. The Mystro system: A comprehensive translator toolkit

    Science.gov (United States)

    Collins, W. R.; Noonan, R. E.

    1985-01-01

    Mystro is a system that facilities the construction of compilers, assemblers, code generators, query interpretors, and similar programs. It provides features to encourage the use of iterative enhancement. Mystro was developed in response to the needs of NASA Langley Research Center (LaRC) and enjoys a number of advantages over similar systems. There are other programs available that can be used in building translators. These typically build parser tables, usually supply the source of a parser and parts of a lexical analyzer, but provide little or no aid for code generation. In general, only the front end of the compiler is addressed. Mystro, on the other hand, emphasizes tools for both ends of a compiler.

  1. Dual axis translation apparatus and system for translating an optical beam and related method

    Science.gov (United States)

    Cassidy, Kelly

    1991-01-01

    A dual axis translation device and system in accordance with this invention, for translating an optical beam along both an x-axis and a y-axis which are perpendicular to one another, has a beam directing means acting on said optical beam for directing the beam along a particular path transverse to said x and y axes. An arrangement supporting said beam directing means for movement in the x and y direction within a given plane is provided. The arrangement includes a first means for translating said beam directing means along the x-axis in said given plane in order to translate the beam along said x-axis. The arrangement comprises a second means for translating said beam directing means along the y-axis in said given plane in order to translate the beam along said y-axis.

  2. Integrated lipase production and in situ biodiesel synthesis in a recombinant Pichia pastoris yeast: an efficient dual biocatalytic system composed of cell free enzymes and whole cell catalysts

    Science.gov (United States)

    2014-01-01

    Background Lipase-catalyzed biotransformation of acylglycerides or fatty acids into biodiesel via immobilized enzymes or whole cell catalysts has been considered as one of the most promising methods to produce renewable and environmentally friendly alternative liquid fuels, thus being extensively studied so far. In all previously pursued approaches, however, lipase enzymes are prepared in an independent process separated from enzymatic biodiesel production, which would unavoidably increase the cost and energy consumption during industrial manufacture of this cost-sensitive energy product. Therefore, there is an urgent need to develop novel cost-effective biocatalysts and biocatalytic processes with genuine industrial feasibility. Result Inspired by the consolidated bioprocessing of lignocellulose to generate bioethanol, an integrated process with coupled lipase production and in situ biodiesel synthesis in a recombinant P. pastoris yeast was developed in this study. The novel and efficient dual biocatalytic system based on Thermomyces lanuginosus lipase took advantage of both cell free enzymes and whole cell catalysts. The extracellular and intracellular lipases of growing yeast cells were simultaneously utilized to produce biodiesel from waste cooking oils in situ and in one pot. This integrated system effectively achieved 58% and 72% biodiesel yield via concurrent esterified-transesterified methanolysis and stepwise hydrolysis-esterification at 3:1 molar ratio between methanol and waste cooking oils, respectively. Further increasing the molar ratio of methanol to waste cooking oils to 6:1 led to an 87% biodiesel yield using the stepwise strategy. Both water tolerance and methanol tolerance of this novel system were found to be significantly improved compared to previous non-integrated biodiesel production processes using separately prepared immobilized enzymes or whole cell catalysts. Conclusion We have proposed a new concept of integrated biodiesel production

  3. Cell-free synthetic biology: Engineering in an open world

    OpenAIRE

    Lu, Yuan

    2017-01-01

    Cell-free synthetic biology emerges as a powerful and flexible enabling technology that can engineer biological parts and systems for life science applications without using living cells. It provides simpler and faster engineering solutions with an unprecedented freedom of design in an open environment than cell system. This review focuses on recent developments of cell-free synthetic biology on biological engineering fields at molecular and cellular levels, including protein engineering, met...

  4. Cell-free extract based optimization of biomolecular circuits with droplet microfluidics.

    Science.gov (United States)

    Hori, Yutaka; Kantak, Chaitanya; Murray, Richard M; Abate, Adam R

    2017-09-12

    Engineering an efficient biomolecular circuit often requires time-consuming iterations of optimization. Cell-free protein expression systems allow rapid testing of biocircuits in vitro, speeding the design-build-test cycle of synthetic biology. In this paper, we combine this with droplet microfluidics to densely scan a transcription-translation biocircuit space. Our system assays millions of parameter combinations per hour, providing a detailed map of function. The ability to comprehensively map biocircuit parameter spaces allows accurate modeling to predict circuit function and identify optimal circuits and conditions.

  5. Refinements in hierarchical phrase-based translation systems

    OpenAIRE

    Pino, Juan Miguel

    2015-01-01

    The relatively recently proposed hierarchical phrase-based translation model for statistical machine translation (SMT) has achieved state-of-the-art performance in numerous recent translation evaluations. Hierarchical phrase-based systems comprise a pipeline of modules with complex interactions. In this thesis, we propose refinements to the hierarchical phrase-based model as well as improvements and analyses in various modules for hierarchical phrase-based systems. We too...

  6. Cell-free synthetic biology for environmental sensing and remediation.

    Science.gov (United States)

    Karig, David K

    2017-06-01

    The fields of biosensing and bioremediation leverage the phenomenal array of sensing and metabolic capabilities offered by natural microbes. Synthetic biology provides tools for transforming these fields through complex integration of natural and novel biological components to achieve sophisticated sensing, regulation, and metabolic function. However, the majority of synthetic biology efforts are conducted in living cells, and concerns over releasing genetically modified organisms constitute a key barrier to environmental applications. Cell-free protein expression systems offer a path towards leveraging synthetic biology, while preventing the spread of engineered organisms in nature. Recent efforts in the areas of cell-free approaches for sensing, regulation, and metabolic pathway implementation, as well as for preserving and deploying cell-free expression components, embody key steps towards realizing the potential of cell-free systems for environmental sensing and remediation. Copyright © 2017 The Author. Published by Elsevier Ltd.. All rights reserved.

  7. Activation of the superoxide forming NADPH oxidase in a cell-free system by sodium dodecyl sulfate. Characterization of the membrane-associated component.

    Science.gov (United States)

    Pick, E; Bromberg, Y; Shpungin, S; Gadba, R

    1987-12-05

    Sodium dodecyl sulfate (SDS) was shown to elicit NADPH-dependent superoxide (O2-) production by a cell-free system derived from sonically disrupted resting guinea pig macrophages (Bromberg, Y., and Pick, E. (1985) J. Biol. Chem. 260, 13539-13545). O2- production was absolutely dependent on the cooperation between a membrane-associated component, sedimenting with the 48,000 X g pellet and a cytosolic factor, nonsedimentable at 265,000 X g. The present report describes the solubilization and characterization of the membrane-associated component of the SDS-activable O2(-)-forming NADPH oxidase (operationally termed pi). Treatment of the 48,000 X g pellet with 30 mM octyl glucoside resulted in complete transfer of pi to the soluble fraction. The solubilized pellet produced an average of 0.92 mumol of O2-/mg of protein/min upon reduction of octyl glucoside content below the critical micellar concentration and in the presence of cytosol, 100 microM SDS, and 0.2 mM NADPH. The activity of solubilized pellet-cytosol combinations was also expressed as NADPH-dependent, azide-resistant oxygen consumption and hydrogen peroxide production. pi was inactivated by the sulfhydryl reagent p-chloromercuribenzoate. Solubilized pellet contained spectroscopically detectable cytochrome b559 (225.6 +/- 15.0 pmol/mg mg protein). Both pi and cytochrome b559 were bound by Cibacron Blue Sepharose and could be eluted by a gradient of octyl glucoside (0-30 mM) in the presence of 1 M KCl. On high performance gel filtration on Superose 12, both pi and cytochrome b559 eluted in the excluded volume; when 25 mM octyl glucoside was present in the elution buffer, pi was partially dissociated from cytochrome b559. Sequential purification of pi on Blue Sepharose followed by gel filtration on Superose 12 in the presence of 25 mM octyl glucoside lead to complete resolution of pi from cytochrome b559 (pi was found in the Mr = 28,000 - 11,000 range while the bulk of cytochrome b559 eluted in the Mr = 113

  8. Evaluation of the SYSTRAN Automatic Translation System. Report No. 5.

    Science.gov (United States)

    Chaumier, Jacques; And Others

    The Commission of the European Communities has acquired an automatic translation system (SYSTRAN), which has been put into operation on an experimental basis. The system covers translation of English into French and comprises a dictionary for food science and technology containing 25,000 words or inflections and 4,500 expressions. This report…

  9. Translating Knowledge From a Family Systems Approach to Clinical Practice: Insights From Knowledge Translation Research Experiences.

    Science.gov (United States)

    Duhamel, Fabie

    2017-11-01

    While there has been continued growth in family nursing knowledge, the complex process of implementing and sustaining family nursing in health care settings continues to be a challenge for family nursing researchers and clinicians alike. Developing knowledge and skills about how to translate family nursing theory to practice settings is a global priority to make family nursing more visible. There is a critical need for more research methods and research evidence about how to best move family nursing knowledge into action. Enhancing health care practice is a multifactorial process that calls for a systemic perspective to ensure its efficacy and sustainability. This article presents insights derived from lessons learned through recent research experiences of using a knowledge translation model to promote practice changes in health care settings. These insights aim to optimize (a) knowledge translation of a Family Systems Approach (FSA) in practice settings; (b) knowledge translation research processes; and (c) sustainability of desired changes in practice with families in health care settings.

  10. Increasing the fidelity of noncanonical amino acid incorporation in cell-free protein synthesis.

    Science.gov (United States)

    Gan, Qinglei; Fan, Chenguang

    2017-11-01

    Cell-free protein synthesis provides a robust platform for co-translational incorporation of noncanonical amino acid (ncAA) into proteins to facilitate biological studies and biotechnological applications. Recently, eliminating the activity of release factor 1 has been shown to increase ncAA incorporation in response to amber codons. However, this approach could promote mis-incorporation of canonical amino acids by near cognate suppression. We performed a facile protocol to remove near cognate tRNA isoacceptors of the amber codon from total tRNAs, and used the phosphoserine (Sep) incorporation system as validation. By manipulating codon usage of target genes and tRNA species introduced into the cell-free protein synthesis system, we increased the fidelity of Sep incorporation at a specific position. By removing three near cognate tRNA isoacceptors of the amber stop codon [tRNA Lys , tRNA Tyr , and tRNA Gln (CUG)] from the total tRNA, the near cognate suppression decreased by 5-fold without impairing normal protein synthesis in the cell-free protein synthesis system. Mass spectrometry analyses indicated that the fidelity of ncAA incorporation was improved. Removal of near cognate tRNA isoacceptors of the amber codon could increase ncAA incorporation fidelity towards the amber stop codon in release factor deficiency systems. We provide a general strategy to improve fidelity of ncAA incorporation towards stop, quadruplet and sense codons in cell-free protein synthesis systems. This article is part of a Special Issue entitled "Biochemistry of Synthetic Biology - Recent Developments" Guest Editor: Dr. Ilka Heinemann and Dr. Patrick O'Donoghue. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. The emerging age of cell-free synthetic biology.

    Science.gov (United States)

    Smith, Mark Thomas; Wilding, Kristen M; Hunt, Jeremy M; Bennett, Anthony M; Bundy, Bradley C

    2014-08-25

    The engineering of and mastery over biological parts has catalyzed the emergence of synthetic biology. This field has grown exponentially in the past decade. As increasingly more applications of synthetic biology are pursued, more challenges are encountered, such as delivering genetic material into cells and optimizing genetic circuits in vivo. An in vitro or cell-free approach to synthetic biology simplifies and avoids many of the pitfalls of in vivo synthetic biology. In this review, we describe some of the innate features that make cell-free systems compelling platforms for synthetic biology and discuss emerging improvements of cell-free technologies. We also select and highlight recent and emerging applications of cell-free synthetic biology. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  12. Cell-free carrier system for localized delivery of peripheral blood cell-derived engineered factor signaling: towards development of a one-step device for autologous angiogenic therapy.

    Science.gov (United States)

    Hadjipanayi, E; Bauer, A T; Moog, P; Salgin, B; Kuekrek, H; Fersch, B; Hopfner, U; Meissner, T; Schlüter, A; Ninkovic, M; Machens, H G; Schilling, A F

    2013-07-10

    Spatiotemporally-controlled delivery of hypoxia-induced angiogenic factor mixtures has been identified by this group as a promising strategy for overcoming the limited ability of chronically ischemic tissues to generate adaptive angiogenesis. We previously developed an implantable, as well as an injectable system for delivering fibroblast-produced factors in vivo. Here, we identify peripheral blood cells (PBCs) as the ideal factor-providing candidates, due to their autologous nature, ease of harvest and ample supply, and investigate wound-simulating biochemical and biophysical environmental parameters that can be controlled to optimize PBC angiogenic activity. It was found that hypoxia (3% O₂) significantly affected the expression of a range of angiogenesis-related factors including VEGF, angiogenin and thrombospondin-1, relative to the normoxic baseline. While all three factors underwent down-regulation over time under hypoxia, there was significant variation in the temporal profile of their expression. VEGF expression was also found to be dependent on cell-scaffold material composition, with fibrin stimulating production the most, followed by collagen and polystyrene. Cell-scaffold matrix stiffness was an additional important factor, as shown by higher VEGF protein levels when PBCs were cultured on stiff vs. compliant collagen hydrogel scaffolds. Engineered PBC-derived factor mixtures could be harvested within cell-free gel and microsphere carriers. The angiogenic effectiveness of factor-loaded carriers could be demonstrated by the ability of their releasates to induce endothelial cell tubule formation and directional migration in in vitro Matrigel assays, and microvessel sprouting in the aortic ring assay. To aid the clinical translation of this approach, we propose a device design that integrates this system, and enables one-step harvesting and delivering of angiogenic factor protein mixtures from autologous peripheral blood. This will facilitate the

  13. English to Tamil machine translation system using universal ...

    Indian Academy of Sciences (India)

    This paper proposes English to Tamil machine translation system, using the universal networking language (UNL) as the intermediate representation. The UNL approach is a hybrid approach of the rule and knowledge-based approaches to machine translation. UNL is a declarative formal language, specifically designed to ...

  14. Back to basics: the untreated rabbit reticulocyte lysate as a competitive system to recapitulate cap/poly(A) synergy and the selective advantage of IRES-driven translation.

    Science.gov (United States)

    Soto Rifo, Ricardo; Ricci, Emiliano P; Décimo, Didier; Moncorgé, Olivier; Ohlmann, Théophile

    2007-01-01

    Translation of most eukaryotic mRNAs involves the synergistic action between the 5' cap structure and the 3' poly(A) tail at the initiation step. The poly(A) tail has also been shown to stimulate translation of picornavirus internal ribosome entry sites (IRES)-directed translation. These effects have been attributed principally to interactions between eIF4G and poly(A)-binding protein (PABP) but also to the participation of PABP in other steps during translation initiation. As the rabbit reticulocyte lysate (RRL) does not recapitulate this cap/poly(A) synergy, several systems based on cellular cell-free extracts have been developed to study the effects of poly(A) tail in vitro but they generally exhibit low translational efficiency. Here, we describe that the non-nuclease-treated RRL (untreated RRL) is able to recapitulate the effects of poly(A) tail on translation in vitro. In this system, translation of a capped/polyadenylated RNA was specifically inhibited by either Paip2 or poly(rA), whereas translation directed by HCV IRES remained unaffected. Moreover, cleavage of eIF4G by FMDV L protease strongly stimulated translation directed by the EMCV IRES, thus recapitulating the competitive advantage that the proteolytic processing of eIF4G confers to IRES-driven RNAs.

  15. Structured Query Translation in Peer to Peer Database Sharing Systems

    Directory of Open Access Journals (Sweden)

    Mehedi Masud

    2009-10-01

    Full Text Available This paper presents a query translation mechanism between heterogeneous peers in Peer to Peer Database Sharing Systems (PDSSs. A PDSS combines a database management system with P2P functionalities. The local databases on peers are called peer databases. In a PDSS, each peer chooses its own data model and schema and maintains data independently without any global coordinator. One of the problems in such a system is translating queries between peers, taking into account both the schema and data heterogeneity. Query translation is the problem of rewriting a query posed in terms of one peer schema to a query in terms of another peer schema. This paper proposes a query translation mechanism between peers where peers are acquainted in data sharing systems through data-level mappings for sharing data.

  16. Biosynthesis of electron transfer flavoprotein in a cell-free system and in cultured human fibroblasts. Defect in the alpha subunit synthesis is a primary lesion in glutaric aciduria type II.

    OpenAIRE

    Ikeda, Y; Keese, S M; Tanaka, K.

    1986-01-01

    We investigated the biosynthesis of electron transfer flavoprotein (ETF) in a cell-free system. Both alpha-(alpha-ETF, 32,000 molecular weight [mol wt]) and beta-subunits (beta-ETF, 27,000 mol wt) were nuclear-coded, and synthesized in the cytosol. alpha-ETF was synthesized as a precursor (p alpha-ETF), 3,000 mol wt larger than its mature counterpart, and was translocated into the mitochondria and processed to the mature alpha-ETF. The newly synthesized beta-ETF was the same as the mature bet...

  17. Theme in Translation: A Systemic Functional Linguistic Perspective

    Directory of Open Access Journals (Sweden)

    Bo Wang

    2014-10-01

    Full Text Available Since the 1990s, discourse analysis has been applied to translation studies, and studies with this approach have become quite prominent. As one resource of discourse analysis, the SFL (Systemic Functional Linguistics model can be applied to analyze both the original text and the translated text. Following this approach, both texts are compared at the sociological, semiotic, generic, registerial, discoursal, and lexicogrammatical levels by adopting a top-down process. The applicability of Halliday’s linguistic framework has then been widely recognized within the field of translation studies. Meanwhile, different strata of Systemic Functional Grammar have shed light on a number of studies. In this paper, I have restricted the topic to one aspect only, i.e. the textual metafunction. I have first traced the development of SFL and its integration with translation studies. Some basic terms in SFL and Theme/Rheme analysis are also explained. Then, some of the existing studies involving thematic analysis and translation are reviewed. As advocated by several scholars, what we need is a more objective apparatus for descriptive translation studies. It would be beneficial to link SFL and descriptive translation studies together, as SFL serves as a tool that relates linguistic choices to the sociocultural context systematically.

  18. Development of German-English Machine Translation System.

    Science.gov (United States)

    Lehmann, Winfred P.; Stachowitz, Rolf A.

    The report presents a progress in theoretical linguistics, descriptive linguistics, lexicography, and systems design in the development of a German-English Machine Translation System. Work in the theoretical group concentrated on intrasentenial disambiguation and on improving certain parts of the system to achieve greater economy in processing.…

  19. Machine Translation as a Complex System: The Role of Esperanto

    Directory of Open Access Journals (Sweden)

    Federic Gobbo

    2015-04-01

    Full Text Available The history of machine translation and the history of Esperanto have long been connected, as they are two different ways to deal with the same problem: the problem of communication across language barriers. Language can be considered a Complex Adaptive System (CAS, and machine translation too. In fact, there are multiple agents (both natural and artificial involved, interacting with one another and committed to achieve a common goal, i.e., the machine translation task. The main characteristics of language as a CAS are also shared in machine translation, especially if we consider the example-based, statistical approach, which is nowadays paradigmatic and unavoidable. In fact, control is distributed, there is no ideal representing agent (intrinsic diversity, there are perpetual dynamics in performance, adapted through amplification and competition of new examples from the crowd of users. On the other hand, Esperanto, being a living language, can be considered a CAS, but of a special kind, because its intrinsic regularity in structure simplifies the task of machine translation, at least up to a certain level. This paper reviews how Esperanto has enhanced the development of human-machine communication in general and within machine translation in particular, tracing some prospects for further development of machine translation, where Esperanto could play a key role.

  20. INTEGRATING MACHINE TRANSLATION AND SPEECH SYNTHESIS COMPONENT FOR ENGLISH TO DRAVIDIAN LANGUAGE SPEECH TO SPEECH TRANSLATION SYSTEM

    Directory of Open Access Journals (Sweden)

    J. SANGEETHA

    2015-02-01

    Full Text Available This paper provides an interface between the machine translation and speech synthesis system for converting English speech to Tamil text in English to Tamil speech to speech translation system. The speech translation system consists of three modules: automatic speech recognition, machine translation and text to speech synthesis. Many procedures for incorporation of speech recognition and machine translation have been projected. Still speech synthesis system has not yet been measured. In this paper, we focus on integration of machine translation and speech synthesis, and report a subjective evaluation to investigate the impact of speech synthesis, machine translation and the integration of machine translation and speech synthesis components. Here we implement a hybrid machine translation (combination of rule based and statistical machine translation and concatenative syllable based speech synthesis technique. In order to retain the naturalness and intelligibility of synthesized speech Auto Associative Neural Network (AANN prosody prediction is used in this work. The results of this system investigation demonstrate that the naturalness and intelligibility of the synthesized speech are strongly influenced by the fluency and correctness of the translated text.

  1. Cell-free protein synthesis: applications come of age.

    Science.gov (United States)

    Carlson, Erik D; Gan, Rui; Hodgman, C Eric; Jewett, Michael C

    2012-01-01

    Cell-free protein synthesis has emerged as a powerful technology platform to help satisfy the growing demand for simple and efficient protein production. While used for decades as a foundational research tool for understanding transcription and translation, recent advances have made possible cost-effective microscale to manufacturing scale synthesis of complex proteins. Protein yields exceed grams protein produced per liter reaction volume, batch reactions last for multiple hours, costs have been reduced orders of magnitude, and reaction scale has reached the 100-liter milestone. These advances have inspired new applications in the synthesis of protein libraries for functional genomics and structural biology, the production of personalized medicines, and the expression of virus-like particles, among others. In the coming years, cell-free protein synthesis promises new industrial processes where short protein production timelines are crucial as well as innovative approaches to a wide range of applications. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. In vivo and in vitro translation of the RNAs of four tobamoviruses

    DEFF Research Database (Denmark)

    Beier, H; Mundry, K W; Issinger, O G

    1980-01-01

    The RNAs from four tobamoviruses [tobacco mosaic virus(TMV) vulgare, TMV dahlemense, TMV U2, and the cowpea strain of TMV (CcTMV)] were translated in a cell-free ribosome system from reticulocytes. Among the translation products found were two polypeptides with molecular weights of 170,000 and 120...

  3. Non-standard amino acid incorporation into proteins using Escherichia coli cell-free protein synthesis

    Directory of Open Access Journals (Sweden)

    Seok Hoon eHong

    2014-06-01

    Full Text Available Incorporating non-standard amino acids (NSAAs into proteins enables new chemical properties, new structures, and new functions. In recent years, improvements in cell-free protein synthesis (CFPS systems have opened the way to accurate and efficient incorporation of NSAAs into proteins. The driving force behind this development has been three-fold. First, a technical renaissance has enabled high-yielding (>1 g/L and long-lasting (>10 h in batch operation CFPS in systems derived from Escherichia coli. Second, the efficiency of orthogonal translation systems has improved. Third, the open nature of the CFPS platform has brought about an unprecedented level of control and freedom of design. Here, we review recent developments in CFPS platforms designed to precisely incorporate NSAAs. In the coming years, we anticipate that CFPS systems will impact efforts to elucidate structure/function relationships of proteins and to make biomaterials and sequence-defined biopolymers for medical and industrial applications.

  4. Machine-Aided Translation: From Terminology Banks to Interactive Translation Systems.

    Science.gov (United States)

    Greenfield, Concetta C.; Serain, Daniel

    The rapid growth of the need for technical translations in recent years has led specialists to utilize computer technology to improve the efficiency and quality of translation. The two approaches considered were automatic translation and terminology banks. Since the results of fully automatic translation were considered unsatisfactory by various…

  5. Translationally-invariant coupled-cluster method for finite systems

    Energy Technology Data Exchange (ETDEWEB)

    Guardiola, R.; Moliner, I. [Valencia Univ., Burjassot (Spain). Dept. de Fisica Atomica Molecular i Nuclear; Navarro, J.; Portesi, M. [IFIC (Centre Mixt CSIC -Universitat de Valencia), Avda. Dr. Moliner 50, E-46.100 Burjassot (Spain)

    1998-01-12

    The translational invariant formulation of the coupled-cluster method is presented here at the complete SUB(2) level for a system of nucleons treated as bosons. The correlation amplitudes are solutions of a non-linear coupled system of equations. These equations have been solved for light and medium systems, considering the central but still semi-realistic nucleon-nucleon S3 interaction. (orig.). 16 refs.

  6. An Electronic Dictionary and Translation System for Murrinh-Patha

    Science.gov (United States)

    Seiss, Melanie; Nordlinger, Rachel

    2012-01-01

    This paper presents an electronic dictionary and translation system for the Australian language Murrinh-Patha. Its complex verbal structure makes learning Murrinh-Patha very difficult. Design learning materials or a dictionary which is easy to understand and to use also presents a challenge. This paper discusses some of the difficulties posed by…

  7. Sequoyah Foreign Language Translation System - Business Case Analysis

    Science.gov (United States)

    2007-12-01

    placards, detainees, local language Standard Operating Procedures (SOP), linguist support, and teaching rudimentary English to local nationals...and BabelFish. 1. Complexities with Speech-to-text Translation MLT systems may occasionally produce incorrect pronunciation and thus introduce the...exercises being conducted annually with coalition partners where English is not the primary language of communication. Hence, language capability becomes

  8. Clinical translation of controlled protein delivery systems for tissue engineering.

    Science.gov (United States)

    Spiller, Kara L; Vunjak-Novakovic, Gordana

    2015-04-01

    Strategies that utilize controlled release of drugs and proteins for tissue engineering have enormous potential to regenerate damaged organs and tissues. The multiple advantages of controlled release strategies merit overcoming the significant challenges to translation, including high costs and long, difficult regulatory pathways. This review highlights the potential of controlled release of proteins for tissue engineering and regenerative medicine. We specifically discuss treatment modalities that have reached preclinical and clinical trials, with emphasis on controlled release systems for bone tissue engineering, the most advanced application with several products already in clinic. Possible strategies to address translational and regulatory concerns are also discussed.

  9. An Automated Translator for Model Checking Time Constrained Workflow Systems

    Science.gov (United States)

    Mashiyat, Ahmed Shah; Rabbi, Fazle; Wang, Hao; Maccaull, Wendy

    Workflows have proven to be a useful conceptualization for the automation of business processes. While formal verification methods (e.g., model checking) can help ensure the reliability of workflow systems, the industrial uptake of such methods has been slow largely due to the effort involved in modeling and the memory required to verify complex systems. Incorporation of time constraints in such systems exacerbates the latter problem. We present an automated translator, YAWL2DVE-t, which takes as input a time constrained workflow model built with the graphical modeling tool YAWL, and outputs the model in DVE, the system specification language for the distributed LTL model checker DiVinE. The automated translator, together with the graphical editor and the distributed model checker, provides a method for rapid design, verification and refactoring of time constrained workflow systems. We present a realistic case study developed through collaboration with the local health authority.

  10. Quantitative systems pharmacology: a promising approach for translational pharmacology.

    Science.gov (United States)

    Gadkar, K; Kirouac, D; Parrott, N; Ramanujan, S

    Biopharmaceutical companies have increasingly been exploring Quantitative Systems Pharmacology (QSP) as a potential avenue to address current challenges in drug development. In this paper, we discuss the application of QSP modeling approaches to address challenges in the translational of preclinical findings to the clinic, a high risk area of drug development. Three cases have been highlighted with QSP models utilized to inform different questions in translational pharmacology. In the first, a mechanism based asthma model is used to evaluate efficacy and inform biomarker strategy for a novel bispecific antibody. In the second case study, a mitogen-activated protein kinase (MAPK) pathway signaling model is used to make translational predictions on clinical response and evaluate novel combination therapies. In the third case study, a physiologically based pharmacokinetic (PBPK) model it used to guide administration of oseltamivir in pediatric patients. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Violation of Bell inequality in perfect translation-invariant systems

    Science.gov (United States)

    Sun, Zhao-Yu; Wu, Yu-Ying; Xu, Jian; Huang, Hai-Lin; Chen, Bo-Jun; Wang, Bo

    2013-11-01

    Bell inequalities and nonlocality have been widely studied in one-dimensional quantum systems. As a kind of quantum correlation, it is expected that bipartite nonlocality should be present in quantum systems, just as bipartite entanglement does. Surprisingly, for various models, two-qubit states do not violate Bell inequalities, i.e., they are local. Recently, it is realized that the results are related to the monogamy trade-off obeyed by bipartite Bell correlations, thus it is believed that for general translation invariant systems, two-qubit states should not violate the Bell inequality [Oliveira, Europhys. Lett.EULEEJ0295-507510.1209/0295-5075/100/60004 100, 60004 (2012)]. In this Brief Report, we demonstrate that in perfect translation-invariant systems with an even number of sites, the Bell inequality can be violated. A nontrivial model is constructed to confirm the conclusion.

  12. High-yield Escherichia coli-based cell-free expression of human proteins

    Energy Technology Data Exchange (ETDEWEB)

    Michel, Erich; Wuethrich, Kurt, E-mail: wuthrich@mol.biol.ethz.ch [ETH Zurich, Institute of Molecular Biology and Biophysics (Switzerland)

    2012-05-15

    Production of sufficient amounts of human proteins is a frequent bottleneck in structural biology. Here we describe an Escherichia coli-based cell-free system which yields mg-quantities of human proteins in N-terminal fusion constructs with the GB1 domain, which show significantly increased translation efficiency. A newly generated E. coli BL21 (DE3) RIPL-Star strain was used, which contains a variant RNase E with reduced activity and an excess of rare-codon tRNAs, and is devoid of lon and ompT protease activity. In the implementation of the expression system we used freshly in-house prepared cell extract. Batch-mode cell-free expression with this setup was up to twofold more economical than continuous-exchange expression, with yields of 0.2-0.9 mg of purified protein per mL of reaction mixture. Native folding of the proteins thus obtained is documented with 2D [{sup 15}N,{sup 1}H]-HSQC NMR.

  13. From translational research to open technology innovation systems.

    Science.gov (United States)

    Savory, Clive; Fortune, Joyce

    2015-01-01

    The purpose of this paper is to question whether the emphasis placed within translational research on a linear model of innovation provides the most effective model for managing health technology innovation. Several alternative perspectives are presented that have potential to enhance the existing model of translational research. A case study is presented of innovation of a clinical decision support system. The paper concludes from the case study that an extending the triple helix model of technology transfer, to one based on a quadruple helix, present a basis for improving the performance translational research. A case study approach is used to help understand development of an innovative technology within a teaching hospital. The case is then used to develop and refine a model of the health technology innovation system. The paper concludes from the case study that existing models of translational research could be refined further through the development of a quadruple helix model of heath technology innovation that encompasses greater emphasis on user-led and open innovation perspectives. The paper presents several implications for future research based on the need to enhance the model of health technology innovation used to guide policy and practice. The quadruple helix model of innovation that is proposed can potentially guide alterations to the existing model of translational research in the healthcare sector. Several suggestions are made for how innovation activity can be better supported at both a policy and operational level. This paper presents a synthesis of the innovation literature applied to a theoretically important case of open innovation in the UK National Health Service. It draws in perspectives from other industrial sectors and applies them specifically to the management and organisation of innovation activities around health technology and the services in which they are embedded.

  14. Analysing cell-free plasma DNA and SLE disease activity.

    Science.gov (United States)

    Atamaniuk, Johanna; Hsiao, Yu-Yang; Mustak, Monika; Bernhard, Duhm; Erlacher, Ludwig; Fodinger, Manuela; Tiran, Beate; Stuhlmeier, Karl M

    2011-06-01

    Over the years, the demonstration and confirmation of cell-free DNA in the circulation has increasingly been recognized as a valuable diagnostic tool. Likewise, it has been known for some time that DNA structures that are targeted by auto-antibodies play a central role in systemic lupus erythematosis (SLE) and that DNA-antibody complexes in the circulation are one of the hallmarks of SLE. Investigating whether and to what degree fluctuations in free plasma DNA levels in patients with SLE might correspond to disease severity was therefore the goal of this investigation. Blood from 13 patients with SLE and from 13 healthy controls was taken and analysed for the presence of anti-dsDNA, anti-ssDNA, anti-nucleosome, anti-histone antibodies as well as for cell-free DNA concentrations. For each patient, the SLE disease activity index (SLEDAI) was calculated. As demonstrated herein, compared to healthy subjects, cell-free DNA plasma levels in patients with SLE were significantly increased and so were anti-dsDNA, anti-ssDNA, anti-histone and anti-nucleosome antibodies. Furthermore, a statistically significant correlation was noted between cell-free DNA and anti-histone antibodies in patients with SLE. However, no correlation was noted between disease activity and anti-dsDNA, anti-ssDNA and anti-nucleosome antibody concentrations. Surprisingly, and more important in the context of this study, there was no correlation between cell-free DNA levels and SLEDAI scores.  The presented data seem to exclude measuring free plasma DNA as an inexpensive, simple and quick tool to assess disease activity in patients with SLE. Further studies on a larger patient population would be needed to confirm our results. © 2010 The Authors. European Journal of Clinical Investigation © 2010 Stichting European Society for Clinical Investigation Journal Foundation.

  15. A simple and high-sensitivity method for analysis of ubiquitination and polyubiquitination based on wheat cell-free protein synthesis

    Directory of Open Access Journals (Sweden)

    Seki Motoaki

    2009-04-01

    Full Text Available Abstract Background Ubiquitination is mediated by the sequential action of at least three enzymes: the E1 (ubiquitin-activating enzyme, E2 (ubiquitin-conjugating enzyme and E3 (ubiquitin ligase proteins. Polyubiquitination of target proteins is also implicated in several critical cellular processes. Although Arabidopsis genome research has estimated more than 1,300 proteins involved in ubiquitination, little is known about the biochemical functions of these proteins. Here we demonstrate a novel, simple and high-sensitive method for in vitro analysis of ubiquitination and polyubiquitination based on wheat cell-free protein synthesis and luminescent detection. Results Using wheat cell-free synthesis, 11 E3 proteins from Arabidopsis full-length cDNA templates were produced. These proteins were analyzed either in the translation mixture or purified recombinant protein from the translation mixture. In our luminescent method using FLAG- or His-tagged and biotinylated ubiquitins, the polyubiquitin chain on AtUBC22, UPL5 and UPL7 (HECT and CIP8 (RING was detected. Also, binding of ubiquitin to these proteins was detected using biotinylated ubiquitin and FLAG-tagged recombinant protein. Furthermore, screening of the RING 6 subgroup demonstrated that At1g55530 was capable of polyubiquitin chain formation like CIP8. Interestingly, these ubiquitinations were carried out without the addition of exogenous E1 and/or E2 proteins, indicating that these enzymes were endogenous to the wheat cell-free system. The amount of polyubiquitinated proteins in the crude translation reaction mixture was unaffected by treatment with MG132, suggesting that our system does not contain 26S proteasome-dependent protein degradation activity. Conclusion In this study, we developed a simple wheat cell-free based luminescence method that could be a powerful tool for comprehensive ubiquitination analysis.

  16. 47 CFR 74.795 - Digital low power TV and TV translator transmission system facilities.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Digital low power TV and TV translator... DISTRIBUTIONAL SERVICES Low Power TV, TV Translator, and TV Booster Stations § 74.795 Digital low power TV and TV translator transmission system facilities. (a) A digital low power TV or TV translator station shall operate...

  17. Advancing System Flexibility for High Penetration Renewable Integration (Chinese Translation)

    Energy Technology Data Exchange (ETDEWEB)

    Milligan, Michael [National Renewable Energy Lab. (NREL), Golden, CO (United States); Frew, Bethany [National Renewable Energy Lab. (NREL), Golden, CO (United States); Zhou, Ella [National Renewable Energy Lab. (NREL), Golden, CO (United States); Arent, Douglas J. [Joint Inst. for Strategic Energy Analysis, Golden, CO (United States)

    2015-10-01

    This is a Chinese translation of NREL/TP-6A20-64864. This report summarizes some of the issues discussed during the engagement on power system flexibility. By design, the focus is on flexibility options used in the United States. Exploration of whether and how U.S. experiences can inform Chinese energy planning will be part of the continuing project, and will benefit from the knowledge base provided by this report. We believe the initial stage of collaboration represented in this report has successfully started a process of mutual understanding, helping Chinese researchers to begin evaluating how lessons learned in other countries might translate to China's unique geographic, economic, social, and political contexts.

  18. Escherichia coli NemA is an efficient chromate reductase that can be biologically immobilized to provide a cell free system for remediation of hexavalent chromium.

    Directory of Open Access Journals (Sweden)

    Katherine J Robins

    Full Text Available Hexavalent chromium is a serious and widespread environmental pollutant. Although many bacteria have been identified that can transform highly water-soluble and toxic Cr(VI to insoluble and relatively non-toxic Cr(III, bacterial bioremediation of Cr(VI pollution is limited by a number of issues, in particular chromium toxicity to the remediating cells. To address this we sought to develop an immobilized enzymatic system for Cr(VI remediation. To identify novel Cr(VI reductase enzymes we first screened cell extracts from an Escherichia coli library of soluble oxidoreductases derived from a range of bacteria, but found that a number of these enzymes can reduce Cr(VI indirectly, via redox intermediates present in the crude extracts. Instead, activity assays for 15 candidate enzymes purified as His6-tagged proteins identified E. coli NemA as a highly efficient Cr(VI reductase (k(cat/K(M= 1.1×10(5 M(-1 s(-1 with NADH as cofactor. Fusion of nemA to the polyhydroxyalkanoate synthase gene phaC from Ralstonia eutropha enabled high-level biosynthesis of functionalized polyhydroxyalkanoate granules displaying stable and active NemA on their surface. When these granules were combined with either Bacillus subtilis glucose dehydrogenase or Candida boidinii formate dehydrogenase as a cofactor regenerating partner, high levels of chromate transformation were observed with only low initial concentrations of expensive NADH cofactor being required, the overall reaction being powered by consumption of the cheap sacrificial substrates glucose or formic acid, respectively. This system therefore offers promise as an economic solution for ex situ Cr(VI remediation.

  19. Autoregulatory systems controlling translation factor expression: thermostat-like control of translational accuracy.

    Science.gov (United States)

    Betney, Russell; de Silva, Eric; Krishnan, Jawahar; Stansfield, Ian

    2010-04-01

    In both prokaryotes and eukaryotes, the expression of a large number of genes is controlled by negative feedback, in some cases operating at the level of translation of the mRNA transcript. Of particular interest are those cases where the proteins concerned have cell-wide function in recognizing a particular codon or RNA sequence. Examples include the bacterial translation termination release factor RF2, initiation factor IF3, and eukaryote poly(A) binding protein. The regulatory loops that control their synthesis establish a negative feedback control mechanism based upon that protein's RNA sequence recognition function in translation (for example, stop codon recognition) without compromising the accurate recognition of that codon, or sequence during general, cell-wide translation. Here, the bacterial release factor RF2 and initiation factor IF3 negative feedback loops are reviewed and compared with similar negative feedback loops that regulate the levels of the eukaryote release factor, eRF1, established artificially by mutation. The control properties of such negative feedback loops are discussed as well as their evolution. The role of negative feedback to control translation factor expression is considered in the context of a growing body of evidence that both IF3 and RF2 can play a role in stimulating stalled ribosomes to abandon translation in response to amino acid starvation. Here, we make the case that negative feedback control serves primarily to limit the overexpression of these translation factors, preventing the loss of fitness resulting from an unregulated increase in the frequency of ribosome drop-off.

  20. Translational Systems Approaches to the Biology of Inflammation and Healing

    Science.gov (United States)

    Vodovotz, Yoram; Constantine, Gregory; Faeder, James; Mi, Qi; Rubin, Jonathan; Bartels, John; Sarkar, Joydeep; Squires, Robert H.; Okonkwo, David O.; Gerlach, Jörg; Zamora, Ruben; Luckhart, Shirley; Ermentrout, Bard; An, Gary

    2011-01-01

    Inflammation is a complex, non-linear process central to many of the diseases that affect both developed and emerging nations. A systems-based understanding of inflammation, coupled to translational applications, is therefore necessary for efficient development of drugs and devices, for streamlining analyses at the level of populations, and for the implementation of personalized medicine. We have carried out an iterative and ongoing program of literature analysis, generation of prospective data, data analysis, and computational modeling in various experimental and clinical inflammatory disease settings. These simulations have been used to gain basic insights into the inflammatory response under baseline, gene-knockout, and drug-treated experimental animals for in silico studies associated with the clinical settings of sepsis, trauma, acute liver failure, and wound healing to create patient-specific simulations in polytrauma, traumatic brain injury, and vocal fold inflammation; and to gain insight into host-pathogen interactions in malaria, necrotizing enterocolitis, and sepsis. These simulations have converged with other systems biology approaches (e.g., functional genomics) to aid in the design of new drugs or devices geared towards modulating inflammation. Since they include both circulating and tissue-level inflammatory mediators, these simulations transcend typical cytokine networks by associating inflammatory processes with tissue/organ impacts via tissue damage/dysfunction. This framework has now allowed us to suggest how to modulate acute inflammation in a rational, individually optimized fashion. This plethora of computational and intertwined experimental/engineering approaches is the cornerstone of Translational Systems Biology approaches for inflammatory diseases. PMID:20170421

  1. Machine Translation

    Institute of Scientific and Technical Information of China (English)

    张严心

    2015-01-01

    As a kind of ancillary translation tool, Machine Translation has been paid increasing attention to and received different kinds of study by a great deal of researchers and scholars for a long time. To know the definition of Machine Translation and to analyse its benefits and problems are significant for translators in order to make good use of Machine Translation, and helpful to develop and consummate Machine Translation Systems in the future.

  2. A Systems Medicine Approach: Translating Emerging Science into Individualized Wellness

    Directory of Open Access Journals (Sweden)

    J. S. Bland

    2017-01-01

    Full Text Available In today’s aging society, more people are living with lifestyle-related noncommunicable diseases (NCDs such as cardiovascular disease, type 2 diabetes, obesity, and cancer. Numerous opinion-leader organizations recommend lifestyle medicine as the first-line approach in NCD prevention and treatment. However, there is a strong need for a personalized approach as “one-size-fits-all” public health recommendations have been insufficient in addressing the interindividual differences in the diverse populations. Advancement in systems biology and the “omics” technologies has allowed comprehensive analysis of how complex biological systems are impacted upon external perturbations (e.g., nutrition and exercise, and therefore is gradually pushing personalized lifestyle medicine toward reality. Clinicians and healthcare practitioners have a unique opportunity in advocating lifestyle medicine because patients see them as a reliable source of advice. However, there are still numerous technical and logistic challenges to overcome before personal “big data” can be translated into actionable and clinically relevant solutions. Clinicians are also facing various issues prior to bringing personalized lifestyle medicine to their practice. Nevertheless, emerging ground-breaking research projects have given us a glimpse of how systems thinking and computational methods may lead to personalized health advice. It is important that all stakeholders work together to create the needed paradigm shift in healthcare before the rising epidemic of NCDs overwhelm the society, the economy, and the dated health system.

  3. IBM MASTOR SYSTEM: Multilingual Automatic Speech-to-speech Translator

    National Research Council Canada - National Science Library

    Gao, Yuqing; Gu, Liang; Zhou, Bowen; Sarikaya, Ruhi; Afify, Mohamed; Kuo, Hong-Kwang; Zhu, Wei-zhong; Deng, Yonggang; Prosser, Charles; Zhang, Wei

    2006-01-01

    .... Challenges include speech recognition and machine translation in adverse environments, lack of training data and linguistic resources for under-studied languages, and the need to rapidly develop...

  4. Cell-free synthesis of a functional G protein-coupled receptor complexed with nanometer scale bilayer discs

    Directory of Open Access Journals (Sweden)

    Peterson Todd C

    2011-05-01

    Full Text Available Abstract Background G protein coupled receptors (GPCRs represent the largest family of membrane proteins in the human genome and the richest source of targets for the pharmaceutical industry. A major limitation to characterizing GPCRs has been the difficulty in developing high-level heterologous expression systems that are cost effective. Reasons for these difficulties include inefficient transport and insertion in the plasma membrane and cytotoxicity. Additionally, GPCR purification requires detergents, which have a negative effect on receptor yields and stability. Results Here we report a detergent-free cell-free protein expression-based method to obtain pharmacologically active GPCRs in about 2 hours. Our strategy relies on the co-translational insertion of modified GPCRs into nanometer-sized planar membranes. As a model we employed an engineered β2-adrenergic receptor in which the third intracellular loop has been replaced with T4 lysozyme (β2AR -T4L. We demonstrated that nanolipoprotein particles (NLPs are necessary for expression of active β2AR -T4L in cell-free systems. The binding specificity of the NLP- β2AR-T4L complex has been determined by competitive assays. Our results demonstrate that β2AR-T4L synthesized in vitro depends on similar oxidative conditions as those required by an in vivo-expressed receptor. Conclusions Although the activation of β2AR-T4L requires the insertion of the T4 lysozyme sequence and the yield of that active protein limited, our results conceptually prove that cell-free protein expression could be used as a fast approach to express these valuable and notoriously difficult-to-express proteins.

  5. Translational and rotational dynamic analysis of a superconducting levitation system

    Energy Technology Data Exchange (ETDEWEB)

    Cansiz, A [Electric-Electronic Engineering Department, Ataturk University, Erzurum (Turkey); Hull, J R [Energy Technology Division, Argonne National Laboratory, Argonne, IL (United States); Gundogdu, Oe [Mechanical Engineering Department, Ataturk University, Erzurum (Turkey)

    2005-07-01

    The rotational dynamics of a disc-shaped permanent magnet rotor levitated over a high temperature superconductor was studied experimentally and theoretically. The interaction between the rotor magnet and the superconductor was modelled by assuming the magnet to be a magnetic dipole and the superconductor a diamagnet. In the magnetomechanical analysis of the superconductor part, the frozen image concept was combined with the diamagnetic image, and the damping in the system was neglected. The interaction potential of the system is the combination of magnetic and gravitational potentials. From the dynamical analysis the equations of motion of the permanent magnet were stated as a function of lateral, vertical, tilt, precision and rotating angles. The vibration behaviour and correlation of the vibration of one direction with that of another were determined with a numerical calculation based on the Runge-Kutta method. The various vibrational frequencies identified were vertical, radial, tilt, precession and rotation. The tests performed for experimental verifications were translational and rotational. The permanent magnet was 'spun up' under vacuum conditions to analyse the dynamics of the free 'spin down' behaviour of the permanent magnet.

  6. NMTPY: A Flexible Toolkit for Advanced Neural Machine Translation Systems

    Directory of Open Access Journals (Sweden)

    Caglayan Ozan

    2017-10-01

    Full Text Available In this paper, we present nmtpy, a flexible Python toolkit based on Theano for training Neural Machine Translation and other neural sequence-to-sequence architectures. nmtpy decouples the specification of a network from the training and inference utilities to simplify the addition of a new architecture and reduce the amount of boilerplate code to be written. nmtpy has been used for LIUM’s top-ranked submissions to WMT Multimodal Machine Translation and News Translation tasks in 2016 and 2017.

  7. Cell-free metabolic engineering: biomanufacturing beyond the cell.

    Science.gov (United States)

    Dudley, Quentin M; Karim, Ashty S; Jewett, Michael C

    2015-01-01

    Industrial biotechnology and microbial metabolic engineering are poised to help meet the growing demand for sustainable, low-cost commodity chemicals and natural products, yet the fraction of biochemicals amenable to commercial production remains limited. Common problems afflicting the current state-of-the-art include low volumetric productivities, build-up of toxic intermediates or products, and byproduct losses via competing pathways. To overcome these limitations, cell-free metabolic engineering (CFME) is expanding the scope of the traditional bioengineering model by using in vitro ensembles of catalytic proteins prepared from purified enzymes or crude lysates of cells for the production of target products. In recent years, the unprecedented level of control and freedom of design, relative to in vivo systems, has inspired the development of engineering foundations for cell-free systems. These efforts have led to activation of long enzymatic pathways (>8 enzymes), near theoretical conversion yields, productivities greater than 100 mg L(-1) h(-1) , reaction scales of >100 L, and new directions in protein purification, spatial organization, and enzyme stability. In the coming years, CFME will offer exciting opportunities to: (i) debug and optimize biosynthetic pathways; (ii) carry out design-build-test iterations without re-engineering organisms; and (iii) perform molecular transformations when bioconversion yields, productivities, or cellular toxicity limit commercial feasibility. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Determination of the potency of a novel saw palmetto supercritical CO2 extract (SPSE) for 5α-reductase isoform II inhibition using a cell-free in vitro test system.

    Science.gov (United States)

    Pais, Pilar; Villar, Agustí; Rull, Santiago

    2016-01-01

    The nicotinamide adenine dinucleotide phosphate-dependent membrane protein 5α-reductase catalyses the conversion of testosterone to the most potent androgen - 5α-dihydrotestosterone. Two 5α-reductase isoenzymes are expressed in humans: type I and type II. The latter is found primarily in prostate tissue. Saw palmetto extract (SPE) has been used extensively in the treatment of lower urinary tract symptoms secondary to benign prostatic hyperplasia (BPH). The pharmacological effects of SPE include the inhibition of 5α-reductase, as well as anti-inflammatory and antiproliferative effects. Clinical studies of SPE have been inconclusive - some have shown significant results, and others have not - possibly the result of varying bioactivities of the SPEs used in the studies. To determine the in vitro potency in a cell-free test system of a novel SP supercritical CO2 extract (SPSE), an inhibitor of the 5α-reductase isoenzyme type II. The inhibitory potency of SPSE was compared to that of finasteride, an approved 5α-reductase inhibitor, on the basis of the enzymatic conversion of the substrate androstenedione to the 5α-reduced product 5α-androstanedione. By concentration-dependent inhibition of 5α-reductase type II in vitro (half-maximal inhibitory concentration 3.58±0.05 μg/mL), SPSE demonstrated competitive binding toward the active site of the enzyme. Finasteride, the approved 5α-reductase inhibitor tested as positive control, led to 63%-75% inhibition of 5α-reductase type II. SPSE effectively inhibits the enzyme that has been linked to BPH, and the amount of extract required for activity is comparatively low. It can be confirmed from the results of this study that SPSE has bioactivity that promotes prostate health at a level that is superior to that of many other phytotherapeutic extracts. The bioactivity of SPSE corresponds favorably to that reported for the hexane extract used in a large number of positive BPH clinical trials, as well as to finasteride

  9. Determination of the potency of a novel saw palmetto supercritical CO2 extract (SPSE for 5α-reductase isoform II inhibition using a cell-free in vitro test system

    Directory of Open Access Journals (Sweden)

    Pais P

    2016-04-01

    Full Text Available Pilar Pais, Agustí Villar, Santiago Rull Euromed, Barcelona, Spain Background: The nicotinamide adenine dinucleotide phosphate-dependent membrane protein 5α-reductase catalyses the conversion of testosterone to the most potent androgen – 5α-dihydrotestosterone. Two 5α-reductase isoenzymes are expressed in humans: type I and type II. The latter is found primarily in prostate tissue. Saw palmetto extract (SPE has been used extensively in the treatment of lower urinary tract symptoms secondary to benign prostatic hyperplasia (BPH. The pharmacological effects of SPE include the inhibition of 5α-reductase, as well as anti-inflammatory and antiproliferative effects. Clinical studies of SPE have been inconclusive – some have shown significant results, and others have not – possibly the result of varying bioactivities of the SPEs used in the studies. Purpose: To determine the in vitro potency in a cell-free test system of a novel SP supercritical CO2 extract (SPSE, an inhibitor of the 5α-reductase isoenzyme type II. Materials and methods: The inhibitory potency of SPSE was compared to that of finasteride, an approved 5α-reductase inhibitor, on the basis of the enzymatic conversion of the substrate androstenedione to the 5α-reduced product 5α-androstanedione. Results: By concentration-dependent inhibition of 5α-reductase type II in vitro (half-maximal inhibitory concentration 3.58±0.05 µg/mL, SPSE demonstrated competitive binding toward the active site of the enzyme. Finasteride, the approved 5α-reductase inhibitor tested as positive control, led to 63%–75% inhibition of 5α-reductase type II. Conclusion: SPSE effectively inhibits the enzyme that has been linked to BPH, and the amount of extract required for activity is comparatively low. It can be confirmed from the results of this study that SPSE has bioactivity that promotes prostate health at a level that is superior to that of many other phytotherapeutic extracts. The

  10. Comparative Evaluation of Online Machine Translation Systems with Legal Texts

    National Research Council Canada - National Science Library

    Chunyu Kit; Tak Ming Wong

    2008-01-01

    ... answer. In this article, we will examine a number of the most commonly used online MT services and compare their translation performance on legal texts, a text genus of particular importance to law...

  11. Sequoyah Foreign Language Translation System - Business Case Analysis

    National Research Council Canada - National Science Library

    Ong, Wing S. S

    2007-01-01

    Sequoyah, which is the Department of Defense (DoD)'s Program of Record for automated foreign language translation, is to identify current and developing technologies to meet warfighter requirements for foreign language support...

  12. Machine Translation Projects for Portuguese at INESC ID's Spoken Language Systems Laboratory

    Directory of Open Access Journals (Sweden)

    Anabela Barreiro

    2014-12-01

    Full Text Available Language technologies, in particular machine translation applications, have the potential to help break down linguistic and cultural barriers, presenting an important contribution to the globalization and internationalization of the Portuguese language, by allowing content to be shared 'from' and 'to' this language. This article aims to present the research work developed at the Laboratory of Spoken Language Systems of INESC-ID in the field of machine translation, namely the automated speech translation, the translation of microblogs and the creation of a hybrid machine translation system. We will focus on the creation of the hybrid system, which aims at combining linguistic knowledge, in particular semantico-syntactic knowledge, with statistical knowledge, to increase the level of translation quality.

  13. REACH VA: Moving from Translation to System Implementation.

    Science.gov (United States)

    Nichols, Linda O; Martindale-Adams, Jennifer; Burns, Robert; Zuber, Jeffrey; Graney, Marshall J

    2016-02-01

    Resources for Enhancing All Caregivers Health in the Department of Veterans Affairs (REACH VA) has been implemented in the VA system as a national program for caregivers. We describe the trajectory of REACH VA from national randomized clinical trial through translation to national implementation. The implementation is examined through the six stages of the Fixsen and Blasé implementation process model: exploration and adoption, program installation, initial implementation, full operation, innovation, and sustainability. Different drivers that move the implementation process forward are important at each stage, including staff selection, staff training, consultation and coaching, staff evaluation, administrative support, program evaluation/fidelity, and systems interventions. Caregivers in the REACH VA 4 session intervention currently implemented in the VA had similar outcomes to longer REACH interventions, including Resources for Enhancing Alzheimer's Caregivers Health (REACH II). Caregivers experienced significant decreases in burden, depression, anxiety, number of troubling patient behaviors reported, caregiving frustrations, stress symptoms (feeling overwhelmed, feeling like crying, being frustrated as a result of caregiving, being lonely), and general stress. Effect sizes (Cohen's d) for these significant variables were between small and medium ranging from .24 to .46. The implementation of REACH VA provides a road map for implementation of other behavioral interventions in health care delivery settings. Lessons learned include the importance of implementing a proven, needed intervention, support from both leadership and clinical staff, willingness to respond to staff and organization needs and modify the intervention while preserving its integrity, and fitting the intervention into ongoing routines and practices. Published by Oxford University Press on behalf of the Gerontological Society of America 2014.

  14. Translationally invariant coupled cluster theory for simple finite systems

    Energy Technology Data Exchange (ETDEWEB)

    Bishop, R.F.; Flynn, M.F. (Department of Mathematics, University of Manchester Institute of Science and Technology, P.O. Box 88, Manchester M60 1QD (United Kingdom)); Bosca, M.C.; Buendriaaa, E.; Guardiola, R. (Departamento de Fisica Moderna, Universidad de Granada, Facultad de Ciencias, 18071 Granada (Spain))

    1990-10-01

    The widely used coupled cluster method (CCM) in quantum many-body theory has recently provided very accurate descriptions of a large number of extended systems. Although its earlier applications to closed-shell and neighboring finite nuclei were also very successful, they have been shrouded in algebraic and technical complexity. Furthermore, they are difficult to compare with more traditional calculations of generalized shell-model theory since, at least at the important level of two-body correlations, they have been largely implemented in relative-coordinate space rather than the more usual oscillator configuration space. The CCM is reviewed here in the precise context of applications to simple finite systems. Special attention is paid to formulate it in such a way that comparison may be made with generalized shell-model or configuration-interaction (CI) theories. Particular regard is paid to an exact incorporation of translational invariance, so that any spuriosity associated with the center-of-mass motion is always avoided. An important side benefit is that the number of many-body configurations in the usual oscillator basis is dramatically reduced. We are thereby able to present both CI and CCM calculations on {sup 4}He up to the essentially unprecedented level of 60{h bar}{omega} in oscillator excitation energy, for two popular and quasirealistic choices of the nucleon-nucleon interaction for which exact Monte Carlo results are available for this nucleus. Although even our simplest approximations attain about 95% of the total binding energy, the convergence in the oscillator configuration space is shown to be both very slow and of a complicated nonuniform nature. Strong implications are drawn for standard implementations of generalized shell-model techniques for heavier nuclei.

  15. Methodology for the analysis of transcription and translation in transcription-coupled-to-translation systems in vitro.

    Science.gov (United States)

    Castro-Roa, Daniel; Zenkin, Nikolay

    2015-09-15

    The various properties of RNA polymerase (RNAP) complexes with nucleic acids during different stages of transcription involve various types of regulation and different cross-talk with other cellular entities and with fellow RNAP molecules. The interactions of transcriptional apparatus with the translational machinery have been focused mainly in terms of outcomes of gene expression, whereas the study of the physical interaction of the ribosome and the RNAP remains obscure partly due to the lack of a system that allows such observations. In this article we will describe the methodology needed to set up a pure, transcription-coupled-to-translation system in which the translocation of the ribosome can be performed in a step-wise manner towards RNAP allowing investigation of the interactions between the two machineries at colliding and non-colliding distances. In the same time RNAP can be put in various types of states, such as paused, roadblocked, backtracked, etc. The experimental system thus allows studying the effects of the ribosome on different aspects of transcription elongation and the effects by RNAP on translation. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  16. Cell-free fetal DNA and cell-free total DNA levels in spontaneous abortion with fetal chromosomal aneuploidy.

    Directory of Open Access Journals (Sweden)

    Ji Hyae Lim

    Full Text Available Cell-free fetal DNA and cell-free total DNA in maternal circulation have been proposed as potential markers for noninvasive monitoring of the placental condition during the pregnancy. However, the correlation of and change in cell-free fetal DNA and cell-free total DNA in spontaneous abortion (SA with fetal chromosomal aneuploidy have not yet been reported. Therefore, we investigated cell-free fetal DNA and cell-free total DNA levels in SA women with fetal chromosomal aneuploidy.A nested case-control study was conducted with maternal plasma collected from 268 women in their first trimester of pregnancy. Subjects included 41 SA with normal fetal karyotype, 26 SA with fetal chromosomal aneuploidy, and 201 normal controls. The unmethylated PDE9A gene was used to measure the maternal plasma levels of cell-free fetal DNA. The GAPDH gene was used to measure the maternal plasma levels of cell-free total DNA. The diagnostic accuracy was measured using receiver-operating characteristic (ROC curves. Levels of cell-free fetal DNA and cell-free total DNA were significantly higher in both SA women with normal fetal karyotype and SA women with fetal chromosomal aneuploidy in comparison with the normal controls (P<0.001 in both. The correlation between cell-free fetal DNA and cell-free total DNA levels was stronger in the normal controls (r = 0.843, P<0.001 than in SA women with normal karyotype (r = 0.465, P = 0.002 and SA women with fetal chromosomal aneuploidy (r = 0.412, P = 0.037. The area under the ROC curve for cell-free fetal DNA and cell-free total DNA was 0.898 (95% CI, 0.852-0.945 and 0.939 (95% CI, 0.903-0.975, respectively.Significantly high levels of cell-free fetal DNA and cell-free total DNA were found in SA women with fetal chromosomal aneuploidy. Our findings suggest that cell-free fetal DNA and cell-free total DNA may be useful biomarkers for the prediction of SA with fetal chromosomal aneuploidy, regardless of fetal

  17. Validation of cell-free culture using scanning electron microscopy (SEM) and gene expression studies.

    Science.gov (United States)

    Yang, R; Elankumaran, Y; Hijjawi, N; Ryan, U

    2015-06-01

    A cell-free culture system for Cryptosporidium parvum was analysed using scanning electron microscopy (SEM) to characterise life cycle stages and compare gene expression in cell-free culture and cell culture using HCT-8 cells. Cryptosporidium parvum samples were harvested at 2 h, 8 h, 14 h, 26 h, 50 h, 74 h, 98 h, 122 h and 170 h, chemically fixed and specimens were observed using a Zeiss 1555 scanning electron microscope. The presence of sporozoites, trophozoites and type I merozoites were identified by SEM. Gene expression in cell culture and cell-free culture was studied using reverse transcriptase quantitative PCR (RT-qPCR) of the sporozoite surface antigen protein (cp15), the glycoprotein 900 (gp900), the Cryptosporidium oocyst wall protein (COWP) and 18S ribosomal RNA (rRNA) genes in both cell free and conventional cell culture. In cell culture, cp15 expression peaked at 74 h, gp900 expression peaked at 74 h and 98 h and COWP expression peaked at 50 h. In cell-free culture, CP15 expression peaked at 98 h, gp900 expression peaked at 74 h and COWP expression peaked at 122 h. The present study is the first to compare gene expression of C. parvum in cell culture and cell-free culture and to characterise life cycle stages of C. parvum in cell-free culture using SEM. Findings from this study showed that gene expression patterns in cell culture and cell-free culture were similar but in cell-free culture, gene expression was delayed for CP15 and COWP in cell free culture compared with the cell culture system and was lower. Although three life cycle stageswere conclusively identified, improvements in SEM methodology should lead to the detection of more life cycle stages. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. 77 FR 65049 - Privacy Act; System of Records: Translator and Interpreter Records, State-37

    Science.gov (United States)

    2012-10-24

    ... Act; System of Records: Translator and Interpreter Records, State-37 SUMMARY: Notice is hereby given... Interpreter Records, State-37, pursuant to the provisions of the Privacy Act of 1974, as amended (5 U.S.C... retain the name ``Translator and Interpreter Records'' (42 FR 49719). The system will facilitate the...

  19. Advancement in Productivity of Arabic into English Machine Translation Systems from 2008 to 2013

    Science.gov (United States)

    Abu-Al-Sha'r, Awatif M.; AbuSeileek, Ali F.

    2013-01-01

    This paper attempts to compare between the advancements in the productivity of Arabic into English Machine Translation Systems between two years, 2008 and 2013. It also aims to evaluate the progress achieved by various systems of Arabic into English electronic translation between the two years. For tracing such advancement, a comparative analysis…

  20. ILLC-UvA translation system for EMNLP-WMT 2011

    NARCIS (Netherlands)

    Khalilov, M.; Sima'an, K.

    2011-01-01

    In this paper we describe the Institute for Logic, Language and Computation (University of Amsterdam) phrase-based statistical machine translation system for Englishto- German translation proposed within the EMNLP-WMT 2011 shared task. The main novelty of the submitted system is a syntaxdriven

  1. Development of the EtsaTrans translation system prototype and its ...

    African Journals Online (AJOL)

    The issue of multilingualism at the University of the Free State (UFS) gained momentum with the development of the EtsaTrans translation system which is being developed according to the principles of example-based machine translation. In this article the development of the system prototype is described, and an ...

  2. ADAPTING HYBRID MACHINE TRANSLATION TECHNIQUES FOR CROSS-LANGUAGE TEXT RETRIEVAL SYSTEM

    Directory of Open Access Journals (Sweden)

    P. ISWARYA

    2017-03-01

    Full Text Available This research work aims in developing Tamil to English Cross - language text retrieval system using hybrid machine translation approach. The hybrid machine translation system is a combination of rule based and statistical based approaches. In an existing word by word translation system there are lot of issues and some of them are ambiguity, Out-of-Vocabulary words, word inflections, and improper sentence structure. To handle these issues, proposed architecture is designed in such a way that, it contains Improved Part-of-Speech tagger, machine learning based morphological analyser, collocation based word sense disambiguation procedure, semantic dictionary, and tense markers with gerund ending rules, and two pass transliteration algorithm. From the experimental results it is clear that the proposed Tamil Query based translation system achieves significantly better translation quality over existing system, and reaches 95.88% of monolingual performance.

  3. Danish translation and validation of the International Skin Tear Advisory Panel Skin Tear Classification System

    DEFF Research Database (Denmark)

    Skiveren, J; Bermark, S; LeBlanc, K

    2015-01-01

    OBJECTIVE: The aim of this study was to translate, validate and establish reliability of the International Skin Tear Classification System in Danish. METHOD: Phase 1 of the project involved the translation of the International Skin Tear Advisory Panel (ISTAP) Skin Tear Classification System...... and external validation by the ISTAP group. The subjects were approached in their place of work and invited to participate in the study and to attend an educational session related to skin tears. RESULTS: The Danish translation of the ISTAP classification system was tested on 270 non-wound specialists...... into Danish, using the forward-back translation method described by the principles of good practice for the translation process for patient-reported outcomes. In Phase 2, the Danish group sought to replicate the ISTAP validation study and validate the classification system with registered nurses (RN...

  4. Identification and Evaluation of Medical Translator Mobile Applications Using an Adapted APPLICATIONS Scoring System.

    Science.gov (United States)

    Khander, Amrin; Farag, Sara; Chen, Katherine T

    2017-12-22

    With an increasing number of patients requiring translator services, many providers are turning to mobile applications (apps) for assistance. However, there have been no published reviews of medical translator apps. To identify and evaluate medical translator mobile apps using an adapted APPLICATIONS scoring system. A list of apps was identified from the Apple iTunes and Google Play stores, using the search term, "medical translator." Apps not found on two different searches, not in an English-based platform, not used for translation, or not functional after purchase, were excluded. The remaining apps were evaluated using an adapted APPLICATIONS scoring system, which included both objective and subjective criteria. App comprehensiveness was a weighted score defined by the number of non-English languages included in each app relative to the proportion of non-English speakers in the United States. The Apple iTunes and Google Play stores. Medical translator apps identified using the search term "medical translator." Main Outcomes and Measures: Compilation of medical translator apps for provider usage. A total of 524 apps were initially found. After applying the exclusion criteria, 20 (8.2%) apps from the Google Play store and 26 (9.2%) apps from the Apple iTunes store remained for evaluation. The highest scoring apps, Canopy Medical Translator, Universal Doctor Speaker, and Vocre Translate, scored 13.5 out of 18.7 possible points. A large proportion of apps initially found did not function as medical translator apps. Using the APPLICATIONS scoring system, we have identified and evaluated medical translator apps for providers who care for non-English speaking patients.

  5. Machine Translation as a complex system, and the phenomenon of Esperanto

    NARCIS (Netherlands)

    Gobbo, F.

    2015-01-01

    The history of machine translation and the history of Esperanto have long been connected, as they are two different ways to deal with the same problem: the problem of communication across language barriers. Language can be considered a Complex Adaptive System (CAS), and machine translation too. In

  6. Method and system for dual resolution translation stage

    Science.gov (United States)

    Halpin, John Michael

    2014-04-22

    A dual resolution translation stage includes a stage assembly operable to receive an optical element and a low resolution adjustment device mechanically coupled to the stage assembly. The dual resolution stage also includes an adjustable pivot block mechanically coupled to the stage assembly. The adjustable pivot block includes a pivot shaft. The dual resolution stage further includes a lever arm mechanically coupled to the adjustable pivot block. The lever arm is operable to pivot about the pivot shaft. The dual resolution stage additionally includes a high resolution adjustment device mechanically coupled to the lever arm and the stage assembly.

  7. A System Level Tool for Translating Software to Reconfigurable Hardware Project

    Data.gov (United States)

    National Aeronautics and Space Administration — In this research we will develop a system level tool to translate binary code of a general-purpose processor into Register Transfer Level VHDL code to be mapped onto...

  8. Grid-translation beam deflection systems for 5-cm and 30-cm diameter Kaufman thrusters

    Science.gov (United States)

    Lathem, W. C.

    1972-01-01

    A 5-cm grid translation mechanism has been developed capable of 10 deg beam deflection. A 2026-hour endurance test was run at a preset 10 deg deflection angle and an extrapolated lifetime of better than 10,000 hours obtained. Response time data for grid translation are presented. Preliminary results for a 30-cm diameter system are given and results of a theoretical analysis of a dished grid system are discussed.

  9. Chemical Screening Using Cell-FreeXenopusEgg Extract.

    Science.gov (United States)

    Broadus, Matthew R; Lee, Ethan

    2018-02-23

    Most drug screening methods use purified proteins, cultured cells, and/or small model organisms such as Xenopus , zebrafish, flies, or nematodes. These systems have proven successes in drug discovery, but they also have weaknesses. Although purified cellular components allow for identification of compounds with activity against specific targets, such systems lack the complex biological interactions present in cellular and organismal screens. In vivo systems overcome these weaknesses, but the lack of cellular permeability, efflux by cellular pumps, and/or toxicity can be major limitations. Xenopus laevis egg extract, a concentrated and biologically active cytosol, can potentially overcome these weaknesses. Drug interactions occur in a near-physiological milieu, thereby functioning in a "truer" endogenous manner than purified components. Also, Xenopus egg extract is a cell-free system that lacks intact plasma membranes that could restrict drug access to potential targets. Finally, Xenopus egg extract is readily manipulated at the protein level: Proteins are easily depleted or added to the system, an important feature for analyzing drug effects in disease states. Thus, Xenopus egg extract offers an attractive media for screening drugs that merges strengths of both in vitro and in vivo systems. © 2018 Cold Spring Harbor Laboratory Press.

  10. The Asthma Control Scoring System: translation and cross-cultural adaptation for use in Brazil.

    Science.gov (United States)

    Tavares, Michelle Gonçalves de Souza; Pizzichini, Márcia Margaret Menezes; Steidle, Leila John Marques; Nazário, Nazaré Otília; Rocha, Cristiane Cinara; Perraro, Maíra Chiaradia; Pizzichini, Emílio

    2010-01-01

    The translation and cross-cultural adaptation of a specific scoring instrument for the comprehensive control of asthma, the Asthma Control Scoring System (ACSS), for use in Brazil. The protocol included ten steps: acquisition of written permission from the author of the ACSS; translation of the instrument to Brazilian Portuguese, carried out by three separate translators; analysis and comparison of the three versions by a review committee; literal back-translation to English; review and harmonization of the back-translation; acquisition of the approval of the original author; review of the translation by specialists; cognitive debriefing: test of clarity to, understanding by, and acceptance of the target population (evaluation of the translation by 10 health care workers); second cognitive debriefing: review of the revised version by a second group of health care workers; and reconciliation and preparation of the final version by the review committee. The Brazilian Portuguese-language version of the ACSS showed clarity, understandability, and acceptability. The instrument was considered to be comprehensive because it includes the clinical manifestations of asthma, as well as the functional and inflammatory aspects of the disease. With the use of this careful methodology in the translation and cross-cultural adaptation of the ACSS, we have ensured its cultural adequacy for Brazil. The use of this instrument could facilitate future studies on asthma control.

  11. Protein biogenesis in Archaea: addressing translation initiation using an in vitro protein synthesis system for Haloferax volcanii.

    Science.gov (United States)

    Ring, Gabriela; Londei, Paola; Eichler, Jerry

    2007-05-01

    Translation initiation in Archaea combines aspects of the parallel process in Eukarya and Bacteria alongside traits unique to this domain. To better understand translation initiation in Archaea, an in vitro translation system from the haloarchaeon Haloferax volcanii has been developed. The ability to translate individual mRNAs both under the conditions used in previously developed poly(U)-dependent poly(Phe) synthesis systems as well as under physiological conditions was shown. Using the H. volcanii system, mRNAs proceeded by either 'strong' or 'weak' Shine-Dalgarno (SD) motifs, or completely lacking leader sequences were effectively translated. The in vitro haloarchaeal system also successfully translated mRNA from Bacteria, again either presenting a SD initiation motif or completely lacking a leader sequence. Thus, the ability to translate individual mRNAs in vitro offers a system to address translation initiation as well as other aspects of protein biogenesis in Archaea.

  12. Cell-free DNA levels and correlation to stage and outcome following treatment of locally advanced rectal cancer.

    Science.gov (United States)

    Boysen, Anders Kindberg; Wettergren, Yvonne; Sorensen, Boe Sandahl; Taflin, Helena; Gustavson, Bengt; Spindler, Karen-Lise Garm

    2017-11-01

    Accurate staging of rectal cancer remains essential for optimal patient selection for combined modality treatment, including radiotherapy, chemotherapy and surgery. We aimed at examining the correlation of cell free DNA with the pathologic stage and subsequent risk of recurrence for patients with locally advanced rectal cancer undergoing preoperative chemoradiation. We examined 75 patients with locally advanced rectal cancer receiving preoperative chemoradiation. Blood samples for translational use were drawn prior to rectal surgery. The level of cell free DNA was quantified by digital droplet PCR and expressed as copy number of beta 2 microglobulin. We found a median level of cell free DNA in the AJCC stages I-III of 3100, 8300, and 10,700 copies/mL respectively. For patients with 12 sampled lymph nodes or above, the median level of cell free DNA were 2400 copies/mL and 4400 copies/mL (p = 0.04) for node negative and node positive disease respectively. The median follow-up was 39 months and 11 recurrences were detected (15%). The median level for patients with recurrent disease was 13,000 copies/mL compared to 5200 copies/mL for non-recurrent patients (p = 0.08). We have demonstrated a correlation between the level of total cell free DNA and the pathologic stage and nodal involvement. Furthermore, we have found a trend towards a correlation with the risk of recurrence following resection of localized rectal cancer.

  13. Danish translation and validation of the International Skin Tear Advisory Panel Skin Tear Classification System.

    Science.gov (United States)

    Skiveren, J; Bermark, S; LeBlanc, K; Baranoski, S

    2015-08-01

    The aim of this study was to translate, validate and establish reliability of the International Skin Tear Classification System in Danish. Phase 1 of the project involved the translation of the International Skin Tear Advisory Panel (ISTAP) Skin Tear Classification System into Danish, using the forward-back translation method described by the principles of good practice for the translation process for patient-reported outcomes. In Phase 2, the Danish group sought to replicate the ISTAP validation study and validate the classification system with registered nurses (RN) and social and health-care assistants (non-RN) from both primary health care and a Danish university hospital in Copenhagen. Thirty photographs, with equal representation of the three types of skin tears, were selected to test validity. The photographs chosen were those originally used for internal and external validation by the ISTAP group. The subjects were approached in their place of work and invited to participate in the study and to attend an educational session related to skin tears. The Danish translation of the ISTAP classification system was tested on 270 non-wound specialists. The ISTAP classification system was validated by 241 RNs, and 29 non-RN. The results indicated a moderate level of agreement on classification of skin tears by type (Fleiss' Kappa=0.460). A moderate level of agreement was demonstrated for both the RN group and the non-RN group (Fleiss' Kappa=0.464 and 0.443, respectively). The ISTAP Skin Tear Classification System was developed with the goal of establishing a global language for describing and documenting skin tears and to raise the health-care community's awareness of skin tears. The Danish translation of the ISTAP classification system supports the earlier ISTAP study and further validates the classification system. The Danish translation of the classification system is vital to the promotion of skin tears in both research and the clinical settings in Denmark.

  14. An overview of the EtsaTrans machine translation system: compilation of an administrative domain

    Directory of Open Access Journals (Sweden)

    L. Ehlers

    2008-07-01

    Full Text Available The EtsaTrans machine translation system has been in development at the University of the Free State for the last four years and is currently the only machine translation system being developed in South Africa for specialised and nongeneral translation needs. The purpose of this exposition is to present the program through its phases of development, and to report on current levels of performance. We analyse the output, the size of the database, and then propose the future implementation of a part of speech tagger and word stemmer into the program to improve its linguistic performance. Our goal with the system is not to translate all types of document, but to work in a specialised domain that will allow the system to translate documents that are repetitive in nature. This will enable translators to spend more time on non-repetitive subject matter. By capturing the nature of the language of such repetitive documents in the database, we are able to create a standardised language usage for the specialised domain.

  15. Bioinformatics analysis of circulating cell-free DNA sequencing data.

    Science.gov (United States)

    Chan, Landon L; Jiang, Peiyong

    2015-10-01

    The discovery of cell-free DNA molecules in plasma has opened up numerous opportunities in noninvasive diagnosis. Cell-free DNA molecules have become increasingly recognized as promising biomarkers for detection and management of many diseases. The advent of next generation sequencing has provided unprecedented opportunities to scrutinize the characteristics of cell-free DNA molecules in plasma in a genome-wide fashion and at single-base resolution. Consequently, clinical applications of circulating cell-free DNA analysis have not only revolutionized noninvasive prenatal diagnosis but also facilitated cancer detection and monitoring toward an era of blood-based personalized medicine. With the remarkably increasing throughput and lowering cost of next generation sequencing, bioinformatics analysis becomes increasingly demanding to understand the large amount of data generated by these sequencing platforms. In this Review, we highlight the major bioinformatics algorithms involved in the analysis of cell-free DNA sequencing data. Firstly, we briefly describe the biological properties of these molecules and provide an overview of the general bioinformatics approach for the analysis of cell-free DNA. Then, we discuss the specific upstream bioinformatics considerations concerning the analysis of sequencing data of circulating cell-free DNA, followed by further detailed elaboration on each key clinical situation in noninvasive prenatal diagnosis and cancer management where downstream bioinformatics analysis is heavily involved. We also discuss bioinformatics analysis as well as clinical applications of the newly developed massively parallel bisulfite sequencing of cell-free DNA. Finally, we offer our perspectives on the future development of bioinformatics in noninvasive diagnosis. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  16. Quantifying the Efficiency of a Translator: The Effect of Syntactical and Literal Written Translations on Language Comprehension Using the Machine Translation System FALCon

    Science.gov (United States)

    McCulloh, Ian A.; Morton, Jillian; Jantzi, Jennifer K.; Rodriguez, Amy M.; Graham, John

    2008-01-01

    This study introduces a new method of evaluating human comprehension in the context of machine translation using a language translation program known as the FALCon (Forward Area Language Converter). The participants include 48 freshmen from the United States Military Academy enrolled in the General Psychology course, PL100. Results of this study…

  17. Quantifying the Efficiency of a Translator: The Effect of Syntactical and Literal Written Translations on Language Comprehension Using the Machine Translation System FALCon (Foreign Area Language Converter)

    Science.gov (United States)

    McCulloh, Ian A.; Morton, Jillian; Jantzi, Jennifer K.; Rodriguez, Amy M.; Graham, John

    2008-01-01

    The purpose of this study is to introduce a new method of evaluating human comprehension in the context of machine translation using a language translation program known as the FALCon (Forward Area Language Converter). The FALCon works by converting documents into digital images via scanner, and then converting those images to electronic text by…

  18. A translator writing system for microcomputer high-level languages and assemblers

    Science.gov (United States)

    Collins, W. R.; Knight, J. C.; Noonan, R. E.

    1980-01-01

    In order to implement high level languages whenever possible, a translator writing system of advanced design was developed. It is intended for routine production use by many programmers working on different projects. As well as a fairly conventional parser generator, it includes a system for the rapid generation of table driven code generators. The parser generator was developed from a prototype version. The translator writing system includes various tools for the management of the source text of a compiler under construction. In addition, it supplies various default source code sections so that its output is always compilable and executable. The system thereby encourages iterative enhancement as a development methodology by ensuring an executable program from the earliest stages of a compiler development project. The translator writing system includes PASCAL/48 compiler, three assemblers, and two compilers for a subset of HAL/S.

  19. Linnaeus' restless system: translation as textual engineering in eighteenth-century botany.

    Science.gov (United States)

    Dietz, Bettina

    2016-04-01

    In this essay, translations of Linnaeus' Systema naturae into various European languages will be placed into the context of successively expanded editions of Linnaeus' writings. The ambition and intention of most translators was not only to make the Systema naturae accessible for practical botanical use by a wider readership, but also to supplement and correct it, and thus to shape it. By recruiting more users, translations made a significant contribution to keeping the Systema up to date and thus maintaining its practical value for decades. The need to incorporate countless additions and corrections into an existing text, to document their provenance, to identify inconsistencies, and to refer to relevant observations, descriptions, and illustrations in the botanical literature all helped to develop and refine techniques of textual montage. This form of textual engineering, becoming increasingly complex with each translation cycle, shaped the external appearance of new editions of the Systema, and reflected the modular architecture of a botanical system designed for expansion.

  20. Impact and Estimation of Balance Coordinate System Rotations and Translations in Wind-Tunnel Testing

    Science.gov (United States)

    Toro, Kenneth G.; Parker, Peter A.

    2017-01-01

    Discrepancies between the model and balance coordinate systems lead to biases in the aerodynamic measurements during wind-tunnel testing. The reference coordinate system relative to the calibration coordinate system at which the forces and moments are resolved is crucial to the overall accuracy of force measurements. This paper discusses sources of discrepancies and estimates of coordinate system rotation and translation due to machining and assembly differences. A methodology for numerically estimating the coordinate system biases will be discussed and developed. Two case studies are presented using this methodology to estimate the model alignment. Examples span from angle measurement system shifts on the calibration system to discrepancies in actual wind-tunnel data. The results from these case-studies will help aerodynamic researchers and force balance engineers to better the understand and identify potential differences in calibration systems due to coordinate system rotation and translation.

  1. Complement system activation in ANCA vasculitis : A translational success story?

    NARCIS (Netherlands)

    Kallenberg, Cees G. M.; Heeringa, Peter

    2015-01-01

    The ANCA-associated vasculitides (AAV) are characterized by pauci-immune necrotizing small to medium size vessel vasculitis frequently including necrotizing crescentric glomerulonephritis. Neutrophil activation by ANCA appears a primary pathogenic event. More recently, the complement system has been

  2. The protein invasion: a broad review on the origin of the translational system.

    Science.gov (United States)

    Morgens, David W

    2013-10-01

    Translation, coded peptide synthesis, arguably exists at the heart of modern cellular life. By orchestrating an incredibly complex interaction between tRNAs, mRNAs, aaRSs, the ribosome, and numerous other small molecules, the translational system allows the interpretation of data in the form of DNA to create massively complex proteins which control and enact almost every cellular function. A natural question then, is how did this system evolve? Here we present a broad review of the existing theories of the last two decades on the origin of the translational system. We attempt to synthesize the wide variety of ideas as well as organize them into modular components, addressing the evolution of the peptide-RNA interaction, tRNA, mRNA, the ribosome, and the first proteins separately. We hope to provide both a comprehensive overview of the literature as well as a framework for future discussions and novel theories.

  3. Translation system engineering in Escherichia coli enhances non-canonical amino acid incorporation into proteins.

    Science.gov (United States)

    Gan, Rui; Perez, Jessica G; Carlson, Erik D; Ntai, Ioanna; Isaacs, Farren J; Kelleher, Neil L; Jewett, Michael C

    2017-05-01

    The ability to site-specifically incorporate non-canonical amino acids (ncAAs) into proteins has made possible the study of protein structure and function in fundamentally new ways, as well as the bio synthesis of unnatural polymers. However, the task of site-specifically incorporating multiple ncAAs into proteins with high purity and yield continues to present a challenge. At the heart of this challenge lies the lower efficiency of engineered orthogonal translation system components compared to their natural counterparts (e.g., translation elements that specifically use a ncAA and do not interact with the cell's natural translation apparatus). Here, we show that evolving and tuning expression levels of multiple components of an engineered translation system together as a whole enhances ncAA incorporation efficiency. Specifically, we increase protein yield when incorporating multiple p-azido-phenylalanine(pAzF) residues into proteins by (i) evolving the Methanocaldococcus jannaschii p-azido-phenylalanyl-tRNA synthetase anti-codon binding domain, (ii) evolving the elongation factor Tu amino acid-binding pocket, and (iii) tuning the expression of evolved translation machinery components in a single vector. Use of the evolved translation machinery in a genomically recoded organism lacking release factor one enabled enhanced multi-site ncAA incorporation into proteins. We anticipate that our approach to orthogonal translation system development will accelerate and expand our ability to site-specifically incorporate multiple ncAAs into proteins and biopolymers, advancing new horizons for synthetic and chemical biotechnology. Biotechnol. Bioeng. 2017;114: 1074-1086. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  4. Ontology Translation: The Semiotic Engineering of Content Management Systems

    Directory of Open Access Journals (Sweden)

    Alejandro Villamarin M.

    2015-12-01

    Full Text Available The present paper proposes the application of Semiotic Engineering theory to Content Management Systems (CMS focusing on the analysis of how the use of different ontologies can affect the user’s efficiency when performing tasks in a CMS. The analysis is performed using the theoretical semiotic model Web-Semiotic Interface Design Evaluation (W-SIDE model.

  5. Translating addictions research into evidence-based practice: the Polaris CD outcomes management system.

    Science.gov (United States)

    Toche-Manley, L; Grissom, G; Dietzen, L; Sangsland, S

    2011-06-01

    Converting the findings from addictions studies into information actionable by (non-research) treatment programs is important to improving program outcomes. This paper describes the translation of the findings of studies on Patient-Services matching, prediction of patient response to treatment (Expected Treatment Response) and prediction of dropout to provide evidence-based decision support in routine treatment. The findings of the studies and their application to the development of an outcomes management system are described. Implementation issues in a network of addictions treatment programs are discussed. The work illustrates how outcomes management systems can play an important role in translating research into practice. Copyright © 2011 Elsevier Ltd. All rights reserved.

  6. Preparative scale production of functional mouse aquaporin 4 using different cell-free expression modes.

    Directory of Open Access Journals (Sweden)

    Lei Kai

    Full Text Available The continuous progress in the structural and functional characterization of aquaporins increasingly attracts attention to study their roles in certain mammalian diseases. Although several structures of aquaporins have already been solved by crystallization, the challenge of producing sufficient amounts of functional proteins still remains. CF (cell free expression has emerged in recent times as a promising alternative option in order to synthesize large quantities of membrane proteins, and the focus of this report was to evaluate the potential of this technique for the production of eukaryotic aquaporins. We have selected the mouse aquaporin 4 as a representative of mammalian aquaporins. The protein was synthesized in an E. coli extract based cell-free system with two different expression modes, and the efficiencies of two modes were compared. In both, the P-CF (cell-free membrane protein expression as precipitate mode generating initial aquaporin precipitates as well as in the D-CF (cell-free membrane protein expression in presence of detergent mode, generating directly detergent solubilized samples, we were able to obtain mg amounts of protein per ml of cell-free reaction. Purified aquaporin samples solubilized in different detergents were reconstituted into liposomes, and analyzed for the water channel activity. The calculated P(f value of proteoliposome samples isolated from the D-CF mode was 133 µm/s at 10°C, which was 5 times higher as that of the control. A reversible inhibitory effect of mercury chloride was observed, which is consistent with previous observations of in vitro reconstituted aquaporin 4. In this study, a fast and convenient protocol was established for functional expression of aquaporins, which could serve as basis for further applications such as water filtration.

  7. Translator awareness Translator awareness

    Directory of Open Access Journals (Sweden)

    Wolfram Wilss

    2008-04-01

    Full Text Available If we want to encompass adequately the wide-ranging field of human translation, it is necessary to include in translation studies (TS the concept of translator awareness (or translator consciousness, for that matter. However, this is more easily said than done, because this concept does not easily lend itself to definition, let alone to measurement, e. g., by investigating translator behaviour. To put it bluntly: Translator awareness is a fuzzy concept. Like many obviously difficult-to-define concepts, with which dialogue in TS is burdened, translator awareness lacks an articulated theory within which different forms of translator behaviour can be convincingly related to, or distinguished from, one another. Hence, TS has so far not tackled, at least not systematically, the issue of translator awareness. If we want to encompass adequately the wide-ranging field of human translation, it is necessary to include in translation studies (TS the concept of translator awareness (or translator consciousness, for that matter. However, this is more easily said than done, because this concept does not easily lend itself to definition, let alone to measurement, e. g., by investigating translator behaviour. To put it bluntly: Translator awareness is a fuzzy concept. Like many obviously difficult-to-define concepts, with which dialogue in TS is burdened, translator awareness lacks an articulated theory within which different forms of translator behaviour can be convincingly related to, or distinguished from, one another. Hence, TS has so far not tackled, at least not systematically, the issue of translator awareness.

  8. Complex biomedical systems: from basic science to translation.

    Science.gov (United States)

    Grzywacz, Norberto M

    2012-07-01

    The Department of Biomedical Engineering (BME) of the University of Southern California (BME@USC) has a longstanding tradition of advancing biomedicine through the development and application of novel engineering ideas. More than 80 primary and affiliated faculty members conduct cutting-edge research in a wide variety of areas, such as neuroengineering, biosystems and biosignal analysis, medical devices (including biomicroelectromechanical systems (bioMEMS) and bionanotechnology), biomechanics, bioimaging, and imaging informatics. Currently, the department hosts six internationally recognized research centers: the Biomimetic MicroElectronic Systems Engineering Research Center (funded by the National Science Foundation), the Biomedical Simulations Resource [funded by the National Institutes of Health (NIH)], the Medical Ultrasonic Transducer Center (funded by NIH), the Center for Neural Engineering, the Center for Vision Science and Technology (funded by an NIH Bioengineering Research Partnership Grant), and the Center for Genomic and Phenomic Studies in Autism (funded by NIH). BME@USC ranks in the top tier of all U.S. BME departments in terms of research funding per faculty.

  9. A translational platform for prototyping closed-loop neuromodulation systems

    Directory of Open Access Journals (Sweden)

    Pedram eAfshar

    2013-01-01

    Full Text Available While modulating neural activity through stimulation is an effective treatment for neurological diseases such as Parkinson’s disease and essential tremor, an opportunity for improving neuromodulation therapy remains in automatically adjusting therapy to continuously optimize patient outcomes. Practical issues associated with achieving this include the paucity of human data related to disease states, poorly validated estimators of patient state, and unknown dynamic mappings of optimal stimulation parameters based on estimated states. To overcome these challenges, we present an investigational platform including: an implanted sensing and stimulation device to collect data and run automated closed-loop algorithms; an external tool to prototype classifier and control-policy algorithms; and real-time telemetry to update the implanted device firmware and monitor its state. The prototyping system was demonstrated in a chronic large animal model studying hippocampal dynamics. We used the platform to find biomarkers of the observed states and transfer functions of different stimulation amplitudes. Data showed that moderate levels of stimulation suppress hippocampal beta activity, while high levels of stimulation produce seizure-like after-discharge activity. The biomarker and transfer function observations were mapped into classifier and control-policy algorithms, which were downloaded to the implanted device to continuously titrate stimulation amplitude for the desired network effect. The platform is designed to be a flexible prototyping tool and could be used to develop improved mechanistic models and automated closed-loop systems for a variety of neurological disorders.

  10. Deflection and translation of a ray traversing an optical system, nodal rays and the optical axis

    Directory of Open Access Journals (Sweden)

    W. F. Harris

    2009-12-01

    Full Text Available Expressions are derived for the deflection and transverse translation of a ray as it traverses an arbitrary optical system.  The system may be astigmatic and have relatively decentred refracting elements.  The expressions are in terms of the fundamental properties of the system.  Because nodal rays are rays that undergo no deflection the results lead immediately to expressions that define nodal rays through the system.  An optical axis of an optical system is a nodal ray that is a straight line through the system.  This allows one to write an expression that determines the optical axis of an arbitrary optical system.

  11. In vitro evaluation of translating and rotating plates using a robot testing system under follower load.

    Science.gov (United States)

    Yan, Y; Bell, K M; Hartman, R A; Hu, J; Wang, W; Kang, J D; Lee, J Y

    2017-01-01

    Various modifications to standard "rigid" anterior cervical plate designs (constrained plate) have been developed that allow for some degree of axial translation and/or rotation of the plate (semi-constrained plate)-theoretically promoting proper load sharing with the graft and improved fusion rates. However, previous studies about rigid and dynamic plates have not examined the influence of simulated muscle loading. The objective of this study was to compare rigid, translating, and rotating plates for single-level corpectomy procedures using a robot testing system with follower load. In-vitro biomechanical test. N = 15 fresh-frozen human (C3-7) cervical specimens were biomechanically tested. The follower load was applied to the specimens at the neutral position from 0 to 100 N. Specimens were randomized into a rigid plate group, a translating plate group and a rotating plate group and then tested in flexion, extension, lateral bending and axial rotation to a pure moment target of 2.0 Nm under 100N of follower load. Range of motion, load sharing, and adjacent level effects were analyzed using a repeated measures analysis of variance (ANOVA). No significant differences were observed between the translating plate and the rigid plate on load sharing at neutral position and C4-6 ROM, but the translating plate was able to maintain load through the graft at a desired level during flexion. The rotating plate shared less load than rigid and translating plates in the neutral position, but cannot maintain the graft load during flexion. This study demonstrated that, in the presence of simulated muscle loading (follower load), the translating plate demonstrated superior performance for load sharing compared to the rigid and rotating plates.

  12. A two-cassette reporter system for assessing target gene translation and target gene product inclusion body formation

    DEFF Research Database (Denmark)

    2016-01-01

    The present invention relates to a dual cassette reporter system capable of assessing target gene translation and target gene product folding. The present invention further relates to vectors and host cells comprising the dual cassette reporter system. In addition the invention relates to the use...... of the dual cassette reporter system for assessing target gene translation and target gene product folding....

  13. Subnanometer Translation of Microelectromechanical Systems Measured by Discrete Fourier Analysis of CCD Images

    NARCIS (Netherlands)

    Yamahata, Christophe; Sarajlic, Edin; Krijnen, Gijsbertus J.M.; Gijs, Martin A.M.

    2010-01-01

    Abstract—In-plane linear displacements of microelectromechanical systems are measured with subnanometer accuracy by observing the periodic micropatterns with a charge-coupled device camera attached to an optical microscope. The translation of the microstructure is retrieved from the video by

  14. Burden of Circulatory System Diseases and Ignored Barriers ofKnowledge Translation

    Directory of Open Access Journals (Sweden)

    Hamed-Basir Ghafouri

    2012-10-01

    Full Text Available Circulatory system disease raise third highest disability-adjusted life years among Iranians and ischemic cardiac diseases are main causes for such burden. Despite available evidences on risk factors of the disease, no effective intervention was implemented to control and prevent the disease. This paper non-systematically reviews available literature on the problem, solutions, and barriers of implementation of knowledge translation in Iran. It seems that there are ignored factors such as cultural and motivational issues in knowledge translation interventions but there are hopes for implementation of started projects and preparation of students as next generation of knowledge transferors.

  15. Applications of cell-free protein synthesis in synthetic biology: Interfacing bio-machinery with synthetic environments.

    Science.gov (United States)

    Lee, Kyung-Ho; Kim, Dong-Myung

    2013-11-01

    Synthetic biology is built on the synthesis, engineering, and assembly of biological parts. Proteins are the first components considered for the construction of systems with designed biological functions because proteins carry out most of the biological functions and chemical reactions inside cells. Protein synthesis is considered to comprise the most basic levels of the hierarchical structure of synthetic biology. Cell-free protein synthesis has emerged as a powerful technology that can potentially transform the concept of bioprocesses. With the ability to harness the synthetic power of biology without many of the constraints of cell-based systems, cell-free protein synthesis enables the rapid creation of protein molecules from diverse sources of genetic information. Cell-free protein synthesis is virtually free from the intrinsic constraints of cell-based methods and offers greater flexibility in system design and manipulability of biological synthetic machinery. Among its potential applications, cell-free protein synthesis can be combined with various man-made devices for rapid functional analysis of genomic sequences. This review covers recent efforts to integrate cell-free protein synthesis with various reaction devices and analytical platforms. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. A Rule-Based System Implementing a Method for Translating FOL Formulas into NL Sentences

    Science.gov (United States)

    Mpagouli, Aikaterini; Hatzilygeroudis, Ioannis

    In this paper, we mainly present the implementation of a system that translates first order logic (FOL) formulas into natural language (NL) sentences. The motivation comes from an intelligent tutoring system teaching logic as a knowledge representation language, where it is used as a means for feedback to the students-users. FOL to NL conversion is achieved by using a rule-based approach, where we exploit the pattern matching capabilities of rules. So, the system consists of rule-based modules corresponding to the phases of our translation methodology. Facts are used in a lexicon providing lexical and grammatical information that helps in producing the NL sentences. The whole system is implemented in Jess, a java-implemented rule-based programming tool. Experimental results confirm the success of our choices.

  17. Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry.

    Science.gov (United States)

    Harris, D Calvin; Jewett, Michael C

    2012-10-01

    Just as synthetic organic chemistry once revolutionized the ability of chemists to build molecules (including those that did not exist in nature) following a basic set of design rules, cell-free synthetic biology is beginning to provide an improved toolbox and faster process for not only harnessing but also expanding the chemistry of life. At the interface between chemistry and biology, research in cell-free synthetic systems is proceeding in two different directions: using synthetic biology for synthetic chemistry and using synthetic chemistry to reprogram or mimic biology. In the coming years, the impact of advances inspired by these approaches will make possible the synthesis of nonbiological polymers having new backbone compositions, new chemical properties, new structures, and new functions. Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. Systems of Phraseological Machine Translation of Polythematic Texts from Russian into English and from English into Russian (RETRANS and ERTRANS Systems).

    Science.gov (United States)

    Belonogov, G. G.; And Others

    1995-01-01

    Discusses the development of phraseological machine translation based on the theory that in natural languages, phraseological units cannot always be reduced to words. Describes the phraseological translation process of computer software and machine dictionary systems that translate Russian into English and English into Russian. (JMV)

  19. 5' cap-independent translation of dengue virus genomic RNA

    OpenAIRE

    Pérez Dominguez, Mariela; Facultad de Odontología. Universidad de Carabobo. Valencia, Venezuela. Instituto de Investigaciones Biomédicas “Dr. Francisco J. Triana Alonso”, Facultad de Ciencias de la Salud, Universidad de Carabobo. Sede Aragua, Maracay, Venezuela.; Rojas, Roselbis; Instituto de Investigaciones Biomédicas “Dr. Francisco J. Triana Alonso”, Facultad de Ciencias de la Salud, Universidad de Carabobo. Sede Aragua, Maracay, Venezuela.; Requena, Dayana; Instituto de Investigaciones Biomédicas “Dr. Francisco J. Triana Alonso”, Facultad de Ciencias de la Salud, Universidad de Carabobo. Sede Aragua, Maracay, Venezuela.; Ferreras, Ana C.; Instituto de Investigaciones Biomédicas “Dr. Francisco J. Triana Alonso”, Facultad de Ciencias de la Salud, Universidad de Carabobo. Sede Aragua, Maracay, Venezuela.; Triana, Juana L.; Instituto de Investigaciones Biomédicas “Dr. Francisco J. Triana Alonso”, Facultad de Ciencias de la Salud, Universidad de Carabobo. Sede Aragua, Maracay, Venezuela.; Triana-Alonso, Francisco; Instituto de Investigaciones Biomédicas “Dr. Francisco J. Triana Alonso”, Facultad de Ciencias de la Salud, Universidad de Carabobo. Sede Aragua, Maracay, Venezuela.

    2015-01-01

    Objetives. To analyze the involvement of methyl guanosine triphosphate cap (5’cap) and the start site of the genomic RNA ofDengue virus serotype 2 (DENV-2) American genotype in translation, using a cell-free system prepared from human placenta.Materials and methods. The recombinant plasmid pTZ18R-D2 was prepared containing DNA encoding the 5’UTR and thefirst 201 nucleotides of the viral capsid. This plasmid was used to transcribe the corresponding RNA (RNA-D2) without the 5’cap. The RNA-D2 wa...

  20. Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment.

    Science.gov (United States)

    Ichihashi, Norikazu; Usui, Kimihito; Kazuta, Yasuaki; Sunami, Takeshi; Matsuura, Tomoaki; Yomo, Tetsuya

    2013-01-01

    The ability to evolve is a key characteristic that distinguishes living things from non-living chemical compounds. The construction of an evolvable cell-like system entirely from non-living molecules has been a major challenge. Here we construct an evolvable artificial cell model from an assembly of biochemical molecules. The artificial cell model contains artificial genomic RNA that replicates through the translation of its encoded RNA replicase. We perform a long-term (600-generation) replication experiment using this system, in which mutations are spontaneously introduced into the RNA by replication error, and highly replicable mutants dominate the population according to Darwinian principles. During evolution, the genomic RNA gradually reinforces its interaction with the translated replicase, thereby acquiring competitiveness against selfish (parasitic) RNAs. This study provides the first experimental evidence that replicating systems can be developed through Darwinian evolution in a cell-like compartment, even in the presence of parasitic replicators.

  1. Probing the biology of cell boundary conditions through confinement of Xenopus cell-free cytoplasmic extracts.

    Science.gov (United States)

    Bermudez, Jessica G; Chen, Hui; Einstein, Lily C; Good, Matthew C

    2017-01-01

    Cell-free cytoplasmic extracts prepared from Xenopus eggs and embryos have for decades provided a biochemical system with which to interrogate complex cell biological processes in vitro. Recently, the application of microfabrication and microfluidic strategies in biology has narrowed the gap between in vitro and in vivo studies by enabling formation of cell-size compartments containing functional cytoplasm. These approaches provide numerous advantages over traditional biochemical experiments performed in a test tube. Most notably, the cell-free cytoplasm is confined using a two- or three-dimensional boundary, which mimics the natural configuration of a cell. This strategy enables characterization of the spatial organization of a cell, and the role that boundaries play in regulating intracellular assembly and function. In this review, we describe the marriage of Xenopus cell-free cytoplasm and confinement technologies to generate synthetic cell-like systems, the recent biological insights they have enabled, and the promise they hold for future scientific discovery. © 2017 Wiley Periodicals, Inc.

  2. In Vitro Evolution of Bovine Foamy Virus Variants with Enhanced Cell-Free Virus Titers and Transmission

    Directory of Open Access Journals (Sweden)

    Qiuying Bao

    2015-11-01

    Full Text Available Virus transmission is essential for spreading viral infections and is a highly coordinated process which occurs by cell-free transmission or cell–cell contact. The transmission of Bovine Foamy Virus (BFV is highly cell-associated, with undetectable cell-free transmission. However, BFV particle budding can be induced by overexpression of wild-type (wt BFV Gag and Env or artificial retargeting of Gag to the plasma membrane via myristoylation membrane targeting signals, closely resembling observations in other foamy viruses. Thus, the particle release machinery of wt BFV appears to be an excellent model system to study viral adaption to cell-free transmission by in vitro selection and evolution. Using selection for BFV variants with high cell-free infectivity in bovine and non-bovine cells, infectivity dramatically increased from almost no infectious units to about 105–106 FFU (fluorescent focus forming units/mL in both cell types. Importantly, the selected BFV variants with high titer (HT cell-free infectivity could still transmit via cell-cell contacts and were neutralized by serum from naturally infected cows. These selected HT–BFV variants will shed light into virus transmission and potential routes of intervention in the spread of viral infections. It will also allow the improvement or development of new promising approaches for antiretroviral therapies.

  3. Codon usage regulates protein structure and function by affecting translation elongation speed in Drosophila cells.

    Science.gov (United States)

    Zhao, Fangzhou; Yu, Chien-Hung; Liu, Yi

    2017-08-21

    Codon usage biases are found in all eukaryotic and prokaryotic genomes and have been proposed to regulate different aspects of translation process. Codon optimality has been shown to regulate translation elongation speed in fungal systems, but its effect on translation elongation speed in animal systems is not clear. In this study, we used a Drosophila cell-free translation system to directly compare the velocity of mRNA translation elongation. Our results demonstrate that optimal synonymous codons speed up translation elongation while non-optimal codons slow down translation. In addition, codon usage regulates ribosome movement and stalling on mRNA during translation. Finally, we show that codon usage affects protein structure and function in vitro and in Drosophila cells. Together, these results suggest that the effect of codon usage on translation elongation speed is a conserved mechanism from fungi to animals that can affect protein folding in eukaryotic organisms. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. The AFRL-MITLL WMT16 News-Translation Task Systems

    Science.gov (United States)

    2016-08-11

    Inf. Errors Pct. Hyp. Words Baseline 5823 9.349% Annotated 5994 9.351% Table 1: Hjerson performance The verb annotation technique aims to increase the...baseline system, so the room for improvement in translation quality is small (shown in Table 2.) Error Type Instances Pct. Hyp. Words Word Choice 30031...nouns use case inflections, multiple Russian word forms may map to a single English spelling . For this reason, we tried rescoring with a unigram

  5. Biochemical Preparation of Cell Extract for Cell-Free Protein Synthesis without Physical Disruption.

    Directory of Open Access Journals (Sweden)

    Kei Fujiwara

    Full Text Available Cell-free protein synthesis (CFPS is a powerful tool for the preparation of toxic proteins, directed protein evolution, and bottom-up synthetic biology. The transcription-translation machinery for CFPS is provided by cell extracts, which usually contain 20-30 mg/mL of proteins. In general, these cell extracts are prepared by physical disruption; however, this requires technical experience and special machinery. Here, we report a method to prepare cell extracts for CFPS using a biochemical method, which disrupts cells through the combination of lysozyme treatment, osmotic shock, and freeze-thaw cycles. The resulting cell extracts showed similar features to those obtained by physical disruption, and was able to synthesize active green fluorescent proteins in the presence of appropriate chemicals to a concentration of 20 μM (0.5 mg/mL.

  6. MSC exosome as a cell-free MSC therapy for cartilage regeneration: Implications for osteoarthritis treatment.

    Science.gov (United States)

    Toh, Wei Seong; Lai, Ruenn Chai; Hui, James Hoi Po; Lim, Sai Kiang

    2017-07-01

    Mesenchymal stem cell (MSC) therapies have demonstrated efficacy in cartilage repair in animal and clinical studies. The efficacy of MSC-based therapies which was previously predicated on the chondrogenic potential of MSC is increasingly attributed to the paracrine secretion, particularly exosomes. Exosomes are thought to function primarily as intercellular communication vehicles to transfer bioactive lipids, nucleic acids (mRNAs and microRNAs) and proteins between cells to elicit biological responses in recipient cells. For MSC exosomes, many of these biological responses translated to a therapeutic outcome in injured or diseased cells. Here, we review the current understanding of MSC exosomes, discuss the possible mechanisms of action in cartilage repair within the context of the widely reported immunomodulatory and regenerative potency of MSC exosomes, and provide new perspectives for development of an off-the-shelf and cell-free MSC therapy for treatment of cartilage injuries and osteoarthritis. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Cell-Free DNA in Metastatic Colorectal Cancer

    DEFF Research Database (Denmark)

    Spindler, Karen-Lise G; Boysen, Anders K; Pallisgård, Niels

    2017-01-01

    of tumor-specific mutations, whereas the use of total cell-free DNA (cfDNA) quantification is somehow controversial and sparsely described in the literature, but holds important clinical information in itself. The purpose of the present report was to present a systematic review and meta...... independent investigators. Eligibility criteria were (a) total cfDNA analysis, (b) mCRC, and (c) prognostic value during palliative treatment. The preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines were followed, and meta-analysis applied on both aggregate data extraction...... therapy. Small fragments of circulating cell-free DNA (cfDNA) can be measured in a simple blood sample. This report presents the first meta-analysis of the prognostic value of total cfDNA measurement in patients with metastatic colorectal cancer. Data from 1,076 patients confirmed that patients...

  8. Biotinylated-sortase self-cleavage purification (BISOP method for cell-free produced proteins

    Directory of Open Access Journals (Sweden)

    Endo Yaeta

    2010-06-01

    Full Text Available Abstract Background Technology used for the purification of recombinant proteins is a key issue for the biochemical and structural analyses of proteins. In general, affinity tags, such as glutathione-S-transferase or six-histidines, are used to purify recombinant proteins. Since such affinity tags often interfere negatively with the structural and functional analyses of proteins, they are usually removed by treatment with proteases. Previously, Dr. H. Mao reported self-cleavage purification of a target protein by fusing the sortase protein to its N-terminal end, and subsequently obtained tag-free recombinant protein following expression in Escherichia coli. This method, however, is yet to be applied to the cell-free based protein production. Results The histidine tag-based self-cleavage method for purifying proteins produced by the wheat cell-free protein synthesis system showed high background, low recovery, and unexpected cleavage between the N-terminally fused sortase and target protein during the protein synthesis. Addition of calcium chelator BAPTA to the cell-free reaction inhibited the cleavage. In order to adapt the sortase-based purification method to the cell-free system, we next used biotin as the affinity tag. The biotinylated sortase self-cleavage purification (BISOP method provided tag-free, highly purified proteins due to improved recovery of proteins from the resin. The N-terminal sequence analysis of the GFP produced by the BISOP method revealed that the cleavage indeed occurred at the right cleavage site. Using this method, we also successfully purified the E2 heterocomplex of USE2N and USE2v1. The c-terminal src kinase (CSK obtained by the BISOP method showed high activity in phosphorylating the Src protein. Furthermore, we demonstrated that this method is suitable for automatically synthesizing and purifying proteins using robots. Conclusion We demonstrated that the newly developed BISOP method is very useful for obtaining

  9. The species translation challenge-a systems biology perspective on human and rat bronchial epithelial cells.

    Science.gov (United States)

    Poussin, Carine; Mathis, Carole; Alexopoulos, Leonidas G; Messinis, Dimitris E; Dulize, Rémi H J; Belcastro, Vincenzo; Melas, Ioannis N; Sakellaropoulos, Theodore; Rhrissorrakrai, Kahn; Bilal, Erhan; Meyer, Pablo; Talikka, Marja; Boué, Stéphanie; Norel, Raquel; Rice, John J; Stolovitzky, Gustavo; Ivanov, Nikolai V; Peitsch, Manuel C; Hoeng, Julia

    2014-01-01

    The biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and in the field of toxicology, and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and attempted to 'translate' the results to humans. In this context, the SBV IMPROVER (Systems Biology Verification for Industrial Methodology for PROcess VErification in Research) collaborative initiative, which uses crowd-sourcing techniques to address fundamental questions in systems biology, invited scientists to deploy their own computational methodologies to make predictions on species translatability. A multi-layer systems biology dataset was generated that was comprised of phosphoproteomics, transcriptomics and cytokine data derived from normal human (NHBE) and rat (NRBE) bronchial epithelial cells exposed in parallel to more than 50 different stimuli under identical conditions. The present manuscript describes in detail the experimental settings, generation, processing and quality control analysis of the multi-layer omics dataset accessible in public repositories for further intra- and inter-species translation studies.

  10. Milk—A Nutrient System of Mammalian Evolution Promoting mTORC1-Dependent Translation

    Science.gov (United States)

    Melnik, Bodo C.

    2015-01-01

    Based on own translational research of the biochemical and hormonal effects of cow’s milk consumption in humans, this review presents milk as a signaling system of mammalian evolution that activates the nutrient-sensitive kinase mechanistic target of rapamycin complex 1 (mTORC1), the pivotal regulator of translation. Milk, a mammary gland-derived secretory product, is required for species-specific gene-nutrient interactions that promote appropriate growth and development of the newborn mammal. This signaling system is highly conserved and tightly controlled by the lactation genome. Milk is sufficient to activate mTORC1, the crucial regulator of protein, lipid, and nucleotide synthesis orchestrating anabolism, cell growth and proliferation. To fulfill its mTORC1-activating function, milk delivers four key metabolic messengers: (1) essential branched-chain amino acids (BCAAs); (2) glutamine; (3) palmitic acid; and (4) bioactive exosomal microRNAs, which in a synergistical fashion promote mTORC1-dependent translation. In all mammals except Neolithic humans, postnatal activation of mTORC1 by milk intake is restricted to the postnatal lactation period. It is of critical concern that persistent hyperactivation of mTORC1 is associated with aging and the development of age-related disorders such as obesity, type 2 diabetes mellitus, cancer, and neurodegenerative diseases. Persistent mTORC1 activation promotes endoplasmic reticulum (ER) stress and drives an aimless quasi-program, which promotes aging and age-related diseases. PMID:26225961

  11. A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants.

    Science.gov (United States)

    Yus, Eva; Yang, Jae-Seong; Sogues, Adrià; Serrano, Luis

    2017-08-28

    Quantitative analysis of the sequence determinants of transcription and translation regulation is relevant for systems and synthetic biology. To identify these determinants, researchers have developed different methods of screening random libraries using fluorescent reporters or antibiotic resistance genes. Here, we have implemented a generic approach called ELM-seq (expression level monitoring by DNA methylation) that overcomes the technical limitations of such classic reporters. ELM-seq uses DamID (Escherichia coli DNA adenine methylase as a reporter coupled with methylation-sensitive restriction enzyme digestion and high-throughput sequencing) to enable in vivo quantitative analyses of upstream regulatory sequences. Using the genome-reduced bacterium Mycoplasma pneumoniae, we show that ELM-seq has a large dynamic range and causes minimal toxicity. We use ELM-seq to determine key sequences (known and putatively novel) of promoter and untranslated regions that influence transcription and translation efficiency. Applying ELM-seq to other organisms will help us to further understand gene expression and guide synthetic biology.Quantitative analysis of how DNA sequence determines transcription and translation regulation is of interest to systems and synthetic biologists. Here the authors present ELM-seq, which uses Dam activity as reporter for high-throughput analysis of promoter and 5'-UTR regions.

  12. Effect of scalings and translations on the supersymmetric quantum mechanical structure of soliton systems

    Science.gov (United States)

    Arancibia, Adrián; Guilarte, Juan Mateos; Plyushchay, Mikhail S.

    2013-02-01

    We investigate a peculiar supersymmetry of the pairs of reflectionless quantum mechanical systems described by n-soliton potentials of a general form that depends on n scaling and n translation parameters. We show that if all the discrete energy levels of the subsystems are different, the superalgebra, being insensitive to translation parameters, is generated by two supercharges of differential order 2n, two supercharges of order 2n+1, and two bosonic integrals of order 2n+1 composed from Lax integrals of the partners. The exotic supersymmetry undergoes a reduction when r discrete energy levels of one subsystem coincide with any r discrete levels of the partner; the total order of the two independent intertwining generators reduces then to 4n-2r+1, and the nonlinear superalgebraic structure acquires a dependence on r relative translations. For a complete pairwise coincidence of the scaling parameters which control the energies of the bound states and the transmission scattering amplitudes, the emerging isospectrality is detected by a transmutation of one of the Lax integrals into a bosonic central charge. Within the isospectral class, we reveal a special case giving a new family of finite-gap first order Bogoliubov-de Gennes systems related to the Ablowitz-Kaup-Newell-Segur integrable hierarchy.

  13. Immunohistochemical localization of translationally controlled tumor protein in the mouse digestive system.

    Science.gov (United States)

    Sheverdin, Vadim; Jung, Jiwon; Lee, Kyunglim

    2013-09-01

    Translationally controlled tumor protein (TCTP) is a housekeeping protein, highly conserved among various species. It plays a major role in cell differentiation, growth, proliferation, apoptosis and carcinogenesis. Studies reported so far on TCTP expression in different digestive organs have not led to any understanding of the role of TCTP in digestion, so we localized TCTP in organs of the mouse digestive system employing immunohistochemical techniques. Translationally controlled tumor protein was found expressed in all organs studied: tongue, salivary glands, esophagus, stomach, small and large intestines, liver and pancreas. The expression of TCTP was found to be predominant in epithelia and neurons of myenteric nerve ganglia; high in serous glands (parotid, submandibular, gastric, intestinal crypts, pancreatic acini) and in neurons of myenteric nerve ganglia, and moderate to low in epithelia. In epithelia, expression of TCTP varied depending on its type and location. In enteric neurons, TCTP was predominantly expressed in the processes. Translationally controlled tumor protein expression in the liver followed porto-central gradient with higher expression in pericentral hepatocytes. In the pancreas, TCTP was expressed in both acini and islet cells. Our finding of nearly universal localization and expression of TCTP in mouse digestive organs points to the hitherto unrecognized functional importance of TCTP in the digestive system and suggests the need for further studies of the possible role of TCTP in the proliferation, secretion, absorption and neural regulation of the digestive process and its importance in the physiology and pathology of digestive process. © 2013 Anatomical Society.

  14. Milk—A Nutrient System of Mammalian Evolution Promoting mTORC1-Dependent Translation

    Directory of Open Access Journals (Sweden)

    Bodo C. Melnik

    2015-07-01

    Full Text Available Based on own translational research of the biochemical and hormonal effects of cow’s milk consumption in humans, this review presents milk as a signaling system of mammalian evolution that activates the nutrient-sensitive kinase mechanistic target of rapamycin complex 1 (mTORC1, the pivotal regulator of translation. Milk, a mammary gland-derived secretory product, is required for species-specific gene-nutrient interactions that promote appropriate growth and development of the newborn mammal. This signaling system is highly conserved and tightly controlled by the lactation genome. Milk is sufficient to activate mTORC1, the crucial regulator of protein, lipid, and nucleotide synthesis orchestrating anabolism, cell growth and proliferation. To fulfill its mTORC1-activating function, milk delivers four key metabolic messengers: (1 essential branched-chain amino acids (BCAAs; (2 glutamine; (3 palmitic acid; and (4 bioactive exosomal microRNAs, which in a synergistical fashion promote mTORC1-dependent translation. In all mammals except Neolithic humans, postnatal activation of mTORC1 by milk intake is restricted to the postnatal lactation period. It is of critical concern that persistent hyperactivation of mTORC1 is associated with aging and the development of age-related disorders such as obesity, type 2 diabetes mellitus, cancer, and neurodegenerative diseases. Persistent mTORC1 activation promotes endoplasmic reticulum (ER stress and drives an aimless quasi-program, which promotes aging and age-related diseases.

  15. Translation, cultural adaptation and validation into portuguese (Brazil) in Systemic Sclerosis Questionnaire (SySQ).

    Science.gov (United States)

    Machado, Roberta Ismael Lacerda; Souto, Lais Medeiros; Freire, Eutilia Andrade Medeiros

    2014-01-01

    Systemic sclerosis (SSc) is a multisystem disease, autoimmune disorder characterized by a fibroblastic disfunction, with significant impact on quality of life (QoL), measured by instruments or questionnaires that usually were formulated in other languages and in different cultural contexts. Translate into Brazilian Portuguese, cross cultural adaptation and assess the reliability and validity of the Systemic Sclerosis Questionnaire (SySQ). Translation and adaptation: into Portuguese and cross-cultural adaptation was performed in accordance with studies on questionnaire translation methodology into other languages. Reliability: it was analyzed using three interviews with different interviewers, two on the same day (interobserver) and the third within 14 days of the first assessment (intraobserver).Validity was assessed by correlating clinical and quality of life parameters with the domain scores of Sysc. a descriptive analysis of the study sample. Reproducibility was assessed using an intraclass correlation coefficient (ICC). Internal consistency was assessed using Cronbach's alpha coefficient. To assess validity we used Spearman correlation coefficient. Five percent was the level of significance adopted for all statistical tests. In the evaluation of the questionnaires, the results were similar to the original questionnaire, the internal consistency ranging between 0.73 and 0.93 for each item. The interobserver reproducibility was very good for all domains (α = 0.786 to 0.983) and intraobserver agreement was considered very good for general symptoms domain (ICC = 0.916), good for musculoskeletal symptoms domain (ICC = 0.897) and cardiopulmonary domain (ICC = 0.842) and reasonable for gastrointestinal symptoms domain (ICC = 0.686). The Brazilian Portuguese version of SySQ proved to be reproducible and valid for our population, using a recognized methodology for translation and cultural adaptation of questionnaires, as well as to assess the reproducibility and

  16. Operational characteristics of a translation screen grid beam deflection system for a 5-cm Kaufman thruster

    Science.gov (United States)

    Lathem, W. C.; Hudson, W. R.

    1972-01-01

    Measurements of beam deflection angle with respect to spring positioning power and accelerator impingement current as a function of deflection angle were made on a 5-cm diameter system. Response time measurements on the translational grid beam deflection system showed that the time for the maximum deflection angle analyzed (+16.4 deg to -16.4 deg) could be reduced by a factor of nine by increasing the heating power applied to the positioning spring from 4 to 16 watts. At 14 watts the response time for maximum deflection was about 1 minute.

  17. Word translation entropy in translation

    DEFF Research Database (Denmark)

    Schaeffer, Moritz; Dragsted, Barbara; Hvelplund, Kristian Tangsgaard

    2016-01-01

    This study reports on an investigation into the relationship between the number of translation alternatives for a single word and eye movements on the source text. In addition, the effect of word order differences between source and target text on eye movements on the source text is studied...... language activation during source text reading in translation, i.e. co-activation of the two linguistic systems, employed late eye movement measures or reaction times. The current study therefore aims to investigate if and to what extent earlier eye movement measures in reading for translation show...... evidence of co-activation. Results show that the number of translation alternatives for a single word and differences between source and target text in terms of word order have an effect on very early and late eye movement measures. Results are interpreted in terms of semantic and structural cross...

  18. Translation Theory 'Translated'

    DEFF Research Database (Denmark)

    Wæraas, Arild; Nielsen, Jeppe

    2016-01-01

    common theoretical approaches to translation within the organization and management discipline: actor-network theory, knowledge-based theory, and Scandinavian institutionalism. Although each of these approaches already has borne much fruit in research, the literature is diverse and somewhat fragmented......, but also overlapping. We discuss the ways in which the three versions of translation theory may be combined and enrich each other so as to inform future research, thereby offering a more complete understanding of translation in and across organizational settings....

  19. Oncological translational research in the Spanish national health system: the INTRO study.

    Science.gov (United States)

    Caballero, C; Jantus-Lewintre, E; Carrato, A; García-Foncillas, J; Gascón, P; Blasco, A; Moreno-Nogueira, J A; Guillem, V; López, R; Codes, M; Antón, A; Díaz-Rubio, E; Camps, C

    2014-08-01

    Under the auspices of the Foundation for Excellence and Quality in Oncology (ECO), the Translational Research in Oncology Medical Services Study (INTRO) was conducted with the aim of describing the current state of, and future expectations for translational cancer research in Spanish medical centres. The first step in the investigation was intended to analyse the current condition of the national Medical Oncology Services network by examining different aspects of the oncology research field. A descriptive and observational multicentre study was performed at a statewide level; information was collected by surveying a cross-section of all those responsible for Medical Oncology Services in Spain. The survey was completed by key informants, who were selected independently by each service, between September 2010 and April 2011. We were able to gather comprehensive data from a total of 27 Spanish hospitals. These data enabled us to describe the allocation of human and material resources devoted to clinical and translational research across the Medical Oncology Services and to describe the organisational and functional components of these services and units. These data included information pertaining to the activities developed, their funding sources, and their functional dependence on other internal or external bodies. Finally, we explored the degree of dissemination and use of some specific techniques used for the genetic diagnosis of cancer, which have recently been introduced in Medical Oncology within the Spanish healthcare system. A wide range of variability exists between different oncology services in Spanish hospitals. Time should be spent reflecting on the need and opportunities for improvement in the development of translational research within the field of oncology.

  20. Multimodal Translation System Using Texture-Mapped Lip-Sync Images for Video Mail and Automatic Dubbing Applications

    Directory of Open Access Journals (Sweden)

    Nakamura Satoshi

    2004-01-01

    Full Text Available We introduce a multimodal English-to-Japanese and Japanese-to-English translation system that also translates the speaker's speech motion by synchronizing it to the translated speech. This system also introduces both a face synthesis technique that can generate any viseme lip shape and a face tracking technique that can estimate the original position and rotation of a speaker's face in an image sequence. To retain the speaker's facial expression, we substitute only the speech organ's image with the synthesized one, which is made by a 3D wire-frame model that is adaptable to any speaker. Our approach provides translated image synthesis with an extremely small database. The tracking motion of the face from a video image is performed by template matching. In this system, the translation and rotation of the face are detected by using a 3D personal face model whose texture is captured from a video frame. We also propose a method to customize the personal face model by using our GUI tool. By combining these techniques and the translated voice synthesis technique, an automatic multimodal translation can be achieved that is suitable for video mail or automatic dubbing systems into other languages.

  1. COGNITIVE TECHNOLOGIES OF DEVELOPMENT, TRANSLATING AND PERCEPTION OF CONCEPTUAL SYSTEMS OF MULTIMODAL INTERACTION PARTICIPANTS

    Directory of Open Access Journals (Sweden)

    Korobova Olga Valeryevna

    2014-11-01

    Full Text Available The article deals with the cognitive technologies and translating techniques, as well as the literal perception and construction of conceptual systems of participants of TV political talk shows in the process of multimodal interaction. It is shown that cognitive technologies and techniques aim at effecting the processes of acquiring, assimilating and storing the human knowledge in different forms within a personal conceptual system which is formed in the human consciousness in the process of the reality being mentally acquired. The communication between TV political talk show participants is based on such effect. The basic intention of such communication is translating and construction of conceptual systems of participants of TV political talk show in multimodal interaction. It is realized with the help of verbal and non- verbal cognitive factors which are actualized by means of different modalities. The communicants who find themselves in the united media scene of TV political talk show, rather than interactants (actual show participants are the main objects of the effect. Thus, the authors determine that the interaction of communicants in multimodal communication is possible due to the correspondence of fragments of their conceptual systems.

  2. Screw-System-Based Mobility Analysis of a Family of Fully Translational Parallel Manipulators

    Directory of Open Access Journals (Sweden)

    Ernesto Rodriguez-Leal

    2013-01-01

    Full Text Available This paper investigates the mobility of a family of fully translational parallel manipulators based on screw system analysis by identifying the common constraint and redundant constraints, providing a case study of this approach. The paper presents the branch motion-screws for the 3-RP̲C-Y parallel manipulator, the 3-RCC-Y (or 3-RP̲RC-Y parallel manipulator, and a newly proposed 3-RP̲C-T parallel manipulator. Then the paper determines the sets of platform constraint-screws for each of these three manipulators. The constraints exerted on the platforms of the 3-RP̲C architectures and the 3-RCC-Y manipulators are analyzed using the screw system approach and have been identified as couples. A similarity has been identified with the axes of couples: they are perpendicular to the R joint axes, but in the former the axes are coplanar with the base and in the latter the axes are perpendicular to the limb. The remaining couples act about the axis that is normal to the base. The motion-screw system and constraint-screw system analysis leads to the insightful understanding of the mobility of the platform that is then obtained by determining the reciprocal screws to the platform constraint screw sets, resulting in three independent instantaneous translational degrees-of-freedom. To validate the mobility analysis of the three parallel manipulators, the paper includes motion simulations which use a commercially available kinematics software.

  3. Translation Theory and Translation Studies in China

    Science.gov (United States)

    Guo, Qin

    2012-01-01

    This dissertation is a comparative study of "translation theory" and "translation studies" in China and the West. Its focus is to investigate whether there is translation theory in the Chinese tradition. My study begins with an examination of the debate in China over whether there has already existed a system of translation…

  4. Cell-free nucleic acids as potential markers for preeclampsia.

    Science.gov (United States)

    Hahn, S; Rusterholz, C; Hösli, I; Lapaire, O

    2011-02-01

    Preeclampsia is one of the leading causes of maternal and fetal/neonatal mortality and morbidity worldwide. Therefore, widely applicable and affordable tests are needed to make an early diagnosis before the occurrence of the clinical symptoms. Circulating cell-free nucleic acids in plasma and serum are novel biomarkers with promising clinical applications in different medical fields, including prenatal diagnosis. Quantitative changes of cell-free fetal (cff)DNA in maternal plasma as an indicator for impending preeclampsia have been reported in different studies, using real-time quantitative PCR for the male-specific SRY or DYS 14 loci. In case of early onset preeclampsia, elevated levels may be already seen in the first trimester. The increased levels of cffDNA before the onset of symptoms may be due to hypoxia/reoxygenation within the intervillous space leading to tissue oxidative stress and increased placental apoptosis and necrosis. In addition to the evidence for increased shedding of cffDNA into the maternal circulation, there is also evidence for reduced renal clearance of cffDNA in preeclampsia. As the amount of fetal DNA is currently determined by quantifying Y-chromosome specific sequences, alternative approaches such as the measurement of total cell-free DNA or the use of gender-independent fetal epigenetic markers, such as DNA methylation, offer a promising alternative. Cell-free RNA of placental origin might be another potentially useful biomarker for screening and diagnosis of preeclampsia in clinical practice. Fetal RNA is associated with subcellular placental particles that protect it from degradation. Its levels are ten-fold higher in pregnant women with preeclampsia compared to controls. In conclusion, through the use of gender-independent sequences, the universal incorporation of fetal nucleic acids into routine obstetric care and into screening or diagnostic settings using combined markers may soon become a reality. Effort has now to be put into

  5. Patient-Centered Network of Learning Health Systems: Developing a resource for clinical translational research.

    Science.gov (United States)

    Finney Rutten, L J; Alexander, A; Embi, P J; Flores, G; Friedman, C; Haller, I V; Haug, P; Jensen, D; Khosla, S; Runger, G; Shah, N D; Winden, T; Roger, V L

    2017-02-01

    The Learning Health System Network clinical data research network includes academic medical centers, health-care systems, public health departments, and health plans, and is designed to facilitate outcomes research, pragmatic trials, comparative effectiveness research, and evaluation of population health interventions. The Learning Health System Network is 1 of 13 clinical data research networks assembled to create, in partnership with 20 patient-powered research networks, a National Patient-Centered Clinical Research Network. Herein, we describe the Learning Health System Network as an emerging resource for translational research, providing details on the governance and organizational structure of the network, the key milestones of the current funding period, and challenges and opportunities for collaborative science leveraging the network.

  6. V2S: Voice to Sign Language Translation System for Malaysian Deaf People

    Science.gov (United States)

    Mean Foong, Oi; Low, Tang Jung; La, Wai Wan

    The process of learning and understand the sign language may be cumbersome to some, and therefore, this paper proposes a solution to this problem by providing a voice (English Language) to sign language translation system using Speech and Image processing technique. Speech processing which includes Speech Recognition is the study of recognizing the words being spoken, regardless of whom the speaker is. This project uses template-based recognition as the main approach in which the V2S system first needs to be trained with speech pattern based on some generic spectral parameter set. These spectral parameter set will then be stored as template in a database. The system will perform the recognition process through matching the parameter set of the input speech with the stored templates to finally display the sign language in video format. Empirical results show that the system has 80.3% recognition rate.

  7. Synthesizing Marketing, Community Engagement, and Systems Science Approaches for Advancing Translational Research.

    Science.gov (United States)

    Kneipp, Shawn M; Leeman, Jennifer; McCall, Pamela; Hassmiller-Lich, Kristen; Bobashev, Georgiy; Schwartz, Todd A; Gilmore, Robert; Riggan, Scott; Gil, Benjamin

    2015-01-01

    The adoption and implementation of evidence-based interventions (EBIs) are the goals of translational research; however, potential end-users' perceptions of an EBI value have contributed to low rates of adoption. In this article, we describe our application of emerging dissemination and implementation science theoretical perspectives, community engagement, and systems science principles to develop a novel EBI dissemination approach. Using consumer-driven, graphics-rich simulation, the approach demonstrates predicted implementation effects on health and employment outcomes for socioeconomically disadvantaged women at the local level and is designed to increase adoption interest of county program managers accountable for improving these outcomes in their communities.

  8. A Simple and Rapid Method for Preparing a Cell-Free Bacterial Lysate for Protein Synthesis.

    Directory of Open Access Journals (Sweden)

    Nitzan Krinsky

    Full Text Available Cell-free protein synthesis (CFPS systems are important laboratory tools that are used for various synthetic biology applications. Here, we present a simple and inexpensive laboratory-scale method for preparing a CFPS system from E. coli. The procedure uses basic lab equipment, a minimal set of reagents, and requires less than one hour to process the bacterial cell mass into a functional S30-T7 extract. BL21(DE3 and MRE600 E. coli strains were used to prepare the S30-T7 extract. The CFPS system was used to produce a set of fluorescent and therapeutic proteins of different molecular weights (up to 66 kDa. This system was able to produce 40-150 μg-protein/ml, with variations depending on the plasmid type, expressed protein and E. coli strain. Interestingly, the BL21-based CFPS exhibited stability and increased activity at 40 and 45°C. To the best of our knowledge, this is the most rapid and affordable lab-scale protocol for preparing a cell-free protein synthesis system, with high thermal stability and efficacy in producing therapeutic proteins.

  9. Machine Translation Project

    Science.gov (United States)

    Bajis, Katie

    1993-01-01

    The characteristics and capabilities of existing machine translation systems were examined and procurement recommendations were developed. Four systems, SYSTRAN, GLOBALINK, PC TRANSLATOR, and STYLUS, were determined to meet the NASA requirements for a machine translation system. Initially, four language pairs were selected for implementation. These are Russian-English, French-English, German-English, and Japanese-English.

  10. Gender issues in translation

    OpenAIRE

    ERGASHEVA G.I.

    2015-01-01

    The following research is done regarding gender in translation dealing specifically with the issue of the translators’ gender identity and its effect on their translations, as well as on how gender itself is translated and produced. We will try to clarify what gender is, how gender manifests itself in the system of language, and what problems translators encounter when translating or producing gender-related materials

  11. Dutch-Flemish translation of 17 item banks from the patient-reported outcomes measurement information system (PROMIS).

    Science.gov (United States)

    Terwee, C B; Roorda, L D; de Vet, H C W; Dekker, J; Westhovens, R; van Leeuwen, J; Cella, D; Correia, H; Arnold, B; Perez, B; Boers, M

    2014-08-01

    The Patient-Reported Outcomes Measurement Information System (PROMIS(®)) is a new, state-of-the-art assessment system for measuring patient-reported health and well-being of adults and children that has the potential to be more valid, reliable and responsive than existing PROMs. The PROMIS items can be administered in short forms or, more efficiently, through computerized adaptive testing. This paper describes the translation of 563 items from 17 PROMIS item banks (domains) for adults from the English source into Dutch-Flemish. The translation was performed by FACITtrans using standardized methodology and approved by the PROMIS Statistical Center. The translation included four forward translations, two back-translations, three to five independent reviews (at least two Dutch, one Flemish) and pre-testing in 70 adults (age range 20-77) from the Netherlands and Flanders. A small number of items required separate translations for Dutch and Flemish: physical function (five items), pain behaviour (two items), pain interference (one item), social isolation (one item) and global health (one item). Challenges faced in the translation process included: scarcity or overabundance of possible translations, unclear item descriptions, constructs broader/smaller in the target language, difficulties in rank ordering items, differences in unit of measurement, irrelevant items or differences in performance of activities. By addressing these challenges, acceptable translations were obtained for all items. The methodology used and experience gained in this study can be used as an example for researchers in other countries interested in translating PROMIS. The Dutch-Flemish PROMIS items are linguistically equivalent. Short forms will soon be available for use and entire item banks are ready for cross-cultural validation in the Netherlands and Flanders.

  12. The Ovine Cerebral Venous System: Comparative Anatomy, Visualization, and Implications for Translational Research

    Science.gov (United States)

    Nitzsche, Björn; Lobsien, Donald; Seeger, Johannes; Schneider, Holm; Boltze, Johannes

    2014-01-01

    Cerebrovascular diseases are significant causes of death and disability in humans. Improvements in diagnostic and therapeutic approaches strongly rely on adequate gyrencephalic, large animal models being demanded for translational research. Ovine stroke models may represent a promising approach but are currently limited by insufficient knowledge regarding the venous system of the cerebral angioarchitecture. The present study was intended to provide a comprehensive anatomical analysis of the intracranial venous system in sheep as a reliable basis for the interpretation of experimental results in such ovine models. We used corrosion casts as well as contrast-enhanced magnetic resonance venography to scrutinize blood drainage from the brain. This combined approach yielded detailed and, to some extent, novel findings. In particular, we provide evidence for chordae Willisii and lateral venous lacunae, and report on connections between the dorsal and ventral sinuses in this species. For the first time, we also describe venous confluences in the deep cerebral venous system and an ‘anterior condylar confluent’ as seen in humans. This report provides a detailed reference for the interpretation of venous diagnostic imaging findings in sheep, including an assessment of structure detectability by in vivo (imaging) versus ex vivo (corrosion cast) visualization methods. Moreover, it features a comprehensive interspecies-comparison of the venous cerebral angioarchitecture in man, rodents, canines and sheep as a relevant large animal model species, and describes possible implications for translational cerebrovascular research. PMID:24736654

  13. The species translation challenge—A systems biology perspective on human and rat bronchial epithelial cells

    Science.gov (United States)

    Poussin, Carine; Mathis, Carole; Alexopoulos, Leonidas G; Messinis, Dimitris E; Dulize, Rémi H J; Belcastro, Vincenzo; Melas, Ioannis N; Sakellaropoulos, Theodore; Rhrissorrakrai, Kahn; Bilal, Erhan; Meyer, Pablo; Talikka, Marja; Boué, Stéphanie; Norel, Raquel; Rice, John J; Stolovitzky, Gustavo; Ivanov, Nikolai V; Peitsch, Manuel C; Hoeng, Julia

    2014-01-01

    The biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and in the field of toxicology, and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and attempted to ‘translate’ the results to humans. In this context, the SBV IMPROVER (Systems Biology Verification for Industrial Methodology for PROcess VErification in Research) collaborative initiative, which uses crowd-sourcing techniques to address fundamental questions in systems biology, invited scientists to deploy their own computational methodologies to make predictions on species translatability. A multi-layer systems biology dataset was generated that was comprised of phosphoproteomics, transcriptomics and cytokine data derived from normal human (NHBE) and rat (NRBE) bronchial epithelial cells exposed in parallel to more than 50 different stimuli under identical conditions. The present manuscript describes in detail the experimental settings, generation, processing and quality control analysis of the multi-layer omics dataset accessible in public repositories for further intra- and inter-species translation studies. PMID:25977767

  14. The ovine cerebral venous system: comparative anatomy, visualization, and implications for translational research.

    Directory of Open Access Journals (Sweden)

    Anke Hoffmann

    Full Text Available Cerebrovascular diseases are significant causes of death and disability in humans. Improvements in diagnostic and therapeutic approaches strongly rely on adequate gyrencephalic, large animal models being demanded for translational research. Ovine stroke models may represent a promising approach but are currently limited by insufficient knowledge regarding the venous system of the cerebral angioarchitecture. The present study was intended to provide a comprehensive anatomical analysis of the intracranial venous system in sheep as a reliable basis for the interpretation of experimental results in such ovine models. We used corrosion casts as well as contrast-enhanced magnetic resonance venography to scrutinize blood drainage from the brain. This combined approach yielded detailed and, to some extent, novel findings. In particular, we provide evidence for chordae Willisii and lateral venous lacunae, and report on connections between the dorsal and ventral sinuses in this species. For the first time, we also describe venous confluences in the deep cerebral venous system and an 'anterior condylar confluent' as seen in humans. This report provides a detailed reference for the interpretation of venous diagnostic imaging findings in sheep, including an assessment of structure detectability by in vivo (imaging versus ex vivo (corrosion cast visualization methods. Moreover, it features a comprehensive interspecies-comparison of the venous cerebral angioarchitecture in man, rodents, canines and sheep as a relevant large animal model species, and describes possible implications for translational cerebrovascular research.

  15. Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems.

    Science.gov (United States)

    Lam, Maggie P Y; Venkatraman, Vidya; Xing, Yi; Lau, Edward; Cao, Quan; Ng, Dominic C M; Su, Andrew I; Ge, Junbo; Van Eyk, Jennifer E; Ping, Peipei

    2016-11-04

    Amidst the proteomes of human tissues lie subsets of proteins that are closely involved in conserved pathophysiological processes. Much of biomedical research concerns interrogating disease signature proteins and defining their roles in disease mechanisms. With advances in proteomics technologies, it is now feasible to develop targeted proteomics assays that can accurately quantify protein abundance as well as their post-translational modifications; however, with rapidly accumulating number of studies implicating proteins in diseases, current resources are insufficient to target every protein without judiciously prioritizing the proteins with high significance and impact for assay development. We describe here a data science method to prioritize and expedite assay development on high-impact proteins across research fields by leveraging the biomedical literature record to rank and normalize proteins that are popularly and preferentially published by biomedical researchers. We demonstrate this method by finding priority proteins across six major physiological systems (cardiovascular, cerebral, hepatic, renal, pulmonary, and intestinal). The described method is data-driven and builds upon the collective knowledge of previous publications referenced on PubMed to lend objectivity to target selection. The method and resulting popular protein lists may also be useful for exploring biological processes associated with various physiological systems and research topics, in addition to benefiting ongoing efforts to facilitate the broad translation of proteomics technologies.

  16. Research Networking Systems: The State of Adoption at Institutions Aiming to Augment Translational Research Infrastructure

    Science.gov (United States)

    Obeid, Jihad S; Johnson, Layne M; Stallings, Sarah; Eichmann, David

    2015-01-01

    Fostering collaborations across multiple disciplines within and across institutional boundaries is becoming increasingly important with the growing emphasis on translational research. As a result, Research Networking Systems that facilitate discovery of potential collaborators have received significant attention by institutions aiming to augment their research infrastructure. We have conducted a survey to assess the state of adoption of these new tools at the Clinical and Translational Science Award (CTSA) funded institutions. Survey results demonstrate that most CTSA funded institutions have either already adopted or were planning to adopt one of several available research networking systems. Moreover a good number of these institutions have exposed or plan to expose the data on research expertise using linked open data, an established approach to semantic web services. Preliminary exploration of these publically-available data shows promising utility in assessing cross-institutional collaborations. Further adoption of these technologies and analysis of the data are needed, however, before their impact on cross-institutional collaboration in research can be appreciated and measured. PMID:26491707

  17. Understanding Translation

    DEFF Research Database (Denmark)

    Schjoldager, Anne Gram; Gottlieb, Henrik; Klitgård, Ida

    Understanding Translation is designed as a textbook for courses on the theory and practice of translation in general and of particular types of translation - such as interpreting, screen translation and literary translation. The aim of the book is to help you gain an in-depth understanding of the...... - translators, language teachers, translation users and literary, TV and film critics, for instance. Discussions focus on translation between Danish and English....

  18. Danish translation of a physical function item bank from the Patient-Reported Outcome Measurement Information System (PROMIS).

    Science.gov (United States)

    Schnohr, Christina W; Rasmussen, Charlotte L; Langberg, Henning; Bjørner, Jakob B

    2017-01-01

    The Patient-Reported Outcome Measurement Information System (PROMIS) is an assessment system that aims to provide more valid, reliable, responsive, and precise patient-reported outcome (PRO) measures than has been previously available. This paper documents the translation of the Physical Function item bank into Danish. We followed the PROMIS standard procedure, including: 1) two independent translations, 2) back translation, 3) independent reviews of translation quality, and 4) cognitive interviews with a representative sample of the adult population from the municipality of Copenhagen. After each phase, the new information was reviewed and the Danish version of the PROMIS Physical Function items was revised, if warranted. Relatively few problems were related to translation in itself and such problems could be fixed by changes in item wordings to fit the Danish context. Cognitive testing revealed problem of a general issue: annoyance in case of mismatch between respondents' functional level and question difficulty, problems imagining performance on activities that the respondents did not usually do, and uncertainty whether mobility aids (e.g., canes and walkers) should be considered when performing an activity. Solutions to the more general issues would require revisions to the original items. The standard translation methodology was successful in eliminating problems in translation, and pointed to problems of a general issue in some of the original questions, producing translated Danish versions of the PROMIS Physical Functioning items. Translation and validation studies provide a valuable source when revising and improving PROs in a clinical setting or for research. The present paper exemplifies this with experiences from Denmark. The study describes how the use of PROs when measuring physical functioning in a Danish context can be improved-hence improving the items used for research, future trials and in clinical settings.

  19. Towards improving English-Latvian translation: a system comparison and a new rescoring feature

    NARCIS (Netherlands)

    Khalilov, M.; Fonollosa, J.A.R.; Skadiņa, I.; Brālītis, E.; Pretkalniņa, L.; Calzolari, N.; Choukri, K.; Maegaard, B.; Mariani, J.; Odijk, J.; Piperidis, S.; Rosner, M.; Tapias, D.

    2010-01-01

    Translation into the languages with relatively free word order has received a lot less attention than translation into fixed word order languages (English), or into analytical languages (Chinese). At the same time this translation task is found among the most difficult challenges for machine

  20. Divide and conquer the Hilbert space of translation-symmetric spin systems.

    Science.gov (United States)

    Weisse, Alexander

    2013-04-01

    Iterative methods that operate with the full Hamiltonian matrix in the untrimmed Hilbert space of a finite system continue to be important tools for the study of one- and two-dimensional quantum spin models, in particular in the presence of frustration. To reach sensible system sizes such numerical calculations heavily depend on the use of symmetries. We describe a divide-and-conquer strategy for implementing translation symmetries of finite spin clusters, which efficiently uses and extends the "sublattice coding" of H. Q. Lin [Phys. Rev. B 42, 6561 (1990)]. With our method, the Hamiltonian matrix can be generated on-the-fly in each matrix vector multiplication, and problem dimensions beyond 10^{11} become accessible.

  1. I-TNT: PHONE NUMBER EXPANSION AND TRANSLATION SYSTEM FOR MANAGING INTERCONNECTIVITY ADDRESSING IN SIP PEERING

    Directory of Open Access Journals (Sweden)

    A. A. KHUDHER

    2015-02-01

    Full Text Available Voice over IP (VoIP subscribers is growing vastly in the recent years due to the ever increase in smartphones, 3G, WiFi, etc. This growth leads the VoIP service providers to peer with each other through Session Initiation Protocol (SIP peering for low/free cost of voice communication. Naturally, this growth is not without challenges, especially in phone addressing. This paper proposes an I-TNT (Infrastructure-Phone Number Translation numbering system to expand the range of the existing E.164 numbers and mapping between private and public number at the edge of the signalling path. As a result, I-TNT numbering system is successfully implemented and able to allocate the expanded phone numbers to end-users in one service provider.

  2. Application of a systems pharmacology model for translational prediction of hERG-mediated QTc prolongation.

    Science.gov (United States)

    Gotta, Verena; Yu, Zhiyi; Cools, Frank; van Ammel, Karel; Gallacher, David J; Visser, Sandra A G; Sannajust, Frederick; Morissette, Pierre; Danhof, Meindert; van der Graaf, Piet H

    2016-12-01

    Drug-induced QTc interval prolongation (Δ QTc) is a main surrogate for proarrhythmic risk assessment. A higher in vivo than in vitro potency for hERG-mediated QTc prolongation has been suggested. Also, in vivo between-species and patient populations' sensitivity to drug-induced QTc prolongation seems to differ. Here, a systems pharmacology model integrating preclinical in vitro (hERG binding) and in vivo (conscious dog Δ QTc) data of three hERG blockers (dofetilide, sotalol, moxifloxacin) was applied (1) to compare the operational efficacy of the three drugs in vivo and (2) to quantify dog-human differences in sensitivity to drug-induced QTc prolongation (for dofetilide only). Scaling parameters for translational in vivo extrapolation of drug effects were derived based on the assumption of system-specific myocardial ion channel densities and transduction of ion channel block: the operational efficacy (transduction of hERG block) in dogs was drug specific (1-19% hERG block corresponded to ≥10 msec Δ QTc). System-specific maximal achievable Δ QTc was estimated to 28% from baseline in both dog and human, while %hERG block leading to half-maximal effects was 58% lower in human, suggesting a higher contribution of hERG-mediated potassium current to cardiac repolarization. These results suggest that differences in sensitivity to drug-induced QTc prolongation may be well explained by drug- and system-specific differences in operational efficacy (transduction of hERG block), consistent with experimental reports. The proposed scaling approach may thus assist the translational risk assessment of QTc prolongation in different species and patient populations, if mediated by the hERG channel.

  3. Deliberative dialogues as a strategy for system-level knowledge translation and exchange.

    Science.gov (United States)

    Boyko, Jennifer A; Lavis, John N; Dobbins, Maureen

    2014-05-01

    We undertook a case study in order to explore deliberative dialogue as a system-level knowledge translation and exchange (KTE) strategy and to describe the design features and intended effects of this dialogue. Our data included observations made during the dialogue, evaluations completed by dialogue participants and interviews. We placed these data in the context of our broader experience. We learned that (a) all the design elements we examined could be maintained in future dialogues, but organizers of dialogues that address similar issues and take place in similar contexts should consider the relative importance of these features and (b) the intended effects of a deliberative dialogue that addresses a low-priority policy issue are mainly apparent at the individual level among dialogue participants. Further research is required to explore the key features and intended effects of deliberative dialogues used to address other issues or in different contexts. Copyright © 2014 Longwoods Publishing.

  4. Why Translation Is Difficult

    DEFF Research Database (Denmark)

    Carl, Michael; Schaeffer, Moritz Jonas

    2017-01-01

    The paper develops a definition of translation literality that is based on the syntactic and semantic similarity of the source and the target texts. We provide theoretical and empirical evidence that absolute literal translations are easy to produce. Based on a multilingual corpus of alternative...... translations we investigate the effects of cross-lingual syntactic and semantic distance on translation production times and find that non-literality makes from-scratch translation and post-editing difficult. We show that statistical machine translation systems encounter even more difficulties with non-literality....

  5. Why Translation Is Difficult

    DEFF Research Database (Denmark)

    Carl, Michael; Schaeffer, Moritz Jonas

    2017-01-01

    translations we investigate the effects of cross-lingual syntactic and semantic distance on translation production times and find that non-literality makes from-scratch translation and post-editing difficult. We show that statistical machine translation systems encounter even more difficulties with non-literality.......The paper develops a definition of translation literality that is based on the syntactic and semantic similarity of the source and the target texts. We provide theoretical and empirical evidence that absolute literal translations are easy to produce. Based on a multilingual corpus of alternative...

  6. Cell-free expression of protein kinase a for rapid activity assays.

    Science.gov (United States)

    Leippe, Donna M; Zhao, Kate Qin; Hsiao, Kevin; Slater, Michael R

    2010-05-19

    Functional protein analysis often calls for lengthy, laborious in vivo protein expression and purification, and can be complicated by the lack of stability of the purified protein. In this study, we demonstrate the feasibility of a simplified procedure for functional protein analysis on magnetic particles using cell-free protein synthesis of the catalytic subunit of human cAMP-dependent protein kinase as a HaloTag((R)) fusion protein. The cell-free protein synthesis systems provide quick access to the protein of interest, while the HaloTag technology provides efficient, covalent protein immobilization of the fusion protein, eliminating the need for further protein purification and minimizing storage-related stability issues. The immobilized cPKA fusion protein is assayed directly on magnetic beads and can be used in inhibitor analyses. The combination of rapid protein synthesis and capture technologies can greatly facilitate the process of protein expression and activity screening, and therefore, can become a valuable tool for functional proteomics studies.

  7. Cell-Free Expression of Protein Kinase a for Rapid Activity Assays

    Directory of Open Access Journals (Sweden)

    Donna M. Leippe

    2010-01-01

    Full Text Available Functional protein analysis often calls for lengthy, laborious in vivo protein expression and purification, and can be complicated by the lack of stability of the purified protein. In this study, we demonstrate the feasibility of a simplified procedure for functional protein analysis on magnetic particles using cell-free protein synthesis of the catalytic subunit of human cAMP-dependent protein kinase as a HaloTag ® fusion protein. The cell-free protein synthesis systems provide quick access to the protein of interest, while the HaloTag technology provides efficient, covalent protein immobilization of the fusion protein, eliminating the need for further protein purification and minimizing storage-related stability issues. The immobilized cPKA fusion protein is assayed directly on magnetic beads and can be used in inhibitor analyses. The combination of rapid protein synthesis and capture technologies can greatly facilitate the process of protein expression and activity screening, and therefore, can become a valuable tool for functional proteomics studies.

  8. Cell-Free Expression of Protein Kinase A for Rapid Activity Assays

    Directory of Open Access Journals (Sweden)

    Donna M. Leippe

    2010-05-01

    Full Text Available Functional protein analysis often calls for lengthy, laborious in vivo protein expression and purification, and can be complicated by the lack of stability of the purified protein. In this study, we demonstrate the feasibility of a simplified procedure for functional protein analysis on magnetic particles using cell-free protein synthesis of the catalytic subunit of human cAMP-dependent protein kinase as a HaloTag® fusion protein. The cell-free protein synthesis systems provide quick access to the protein of interest, while the HaloTag technology provides efficient, covalent protein immobilization of the fusion protein, eliminating the need for further protein purification and minimizing storage-related stability issues. The immobilized cPKA fusion protein is assayed directly on magnetic beads and can be used in inhibitor analyses. The combination of rapid protein synthesis and capture technologies can greatly facilitate the process of protein expression and activity screening, and therefore, can become a valuable tool for functional proteomics studies.

  9. Understanding Translation

    DEFF Research Database (Denmark)

    Schjoldager, Anne Gram; Gottlieb, Henrik; Klitgård, Ida

    Understanding Translation is designed as a textbook for courses on the theory and practice of translation in general and of particular types of translation - such as interpreting, screen translation and literary translation. The aim of the book is to help you gain an in-depth understanding...... of the phenomenon of translation and to provide you with a conceptual framework for the analysis of various aspects of professional translation. Intended readers are students of translation and languages, but the book will also be relevant for others who are interested in the theory and practice of translation...

  10. For "Translation and Theories"

    Science.gov (United States)

    Ni, Lili

    2009-01-01

    Translation studies stem from comparative literature and contrastive analysis. It involves the transfer of messages between two different language systems and cultures, and Munday (2001, p.1) notes that translation "by its nature" "is multilingual and also interdisciplinary". Translation subjects are the texts in various…

  11. Understanding Translation

    DEFF Research Database (Denmark)

    Schjoldager, Anne Gram; Gottlieb, Henrik; Klitgård, Ida

    Understanding Translation is designed as a textbook for courses on the theory and practice of translation in general and of particular types of translation - such as interpreting, screen translation and literary translation. The aim of the book is to help you gain an in-depth understanding...... of the phenomenon of translation and to provide you with a conceptual framework for the analysis of various aspects of professional translation. Intended readers are students of translation and languages, but the book will also be relevant for others who are interested in the theory and practice of translation...... - translators, language teachers, translation users and literary, TV and film critics, for instance. Discussions focus on translation between Danish and English....

  12. Cell-free nucleic acids as noninvasive biomarkers for colorectal cancer detection

    KAUST Repository

    Mansour, Hicham

    2014-08-27

    Cell-free nucleic acids (CFNA) have been reported by several authors in blood, stool, and urine of patients with colorectal cancer (CRC). These genetic biomarkers can be an indication of neoplastic colorectal epithelial cells, and can thus potentially be used as noninvasive tests for the detection of the disease in CRC patients and monitor their staging, without the need to use heavier and invasive tools. In a number of test-trials, these genetic tests have shown the advantage of non-invasiveness, making them well accepted by most of the patients, without major side effects. They have also shown a promising sensitivity and specificity in the detection of malignant and premalignant neoplasms. Moreover, costs for performing such tests are very low. Several studies reported and confirmed the proof of the principle for these genetic tests for screening, diagnosis, and prognosis; the main challenge of translating this approach from research to clinical laboratory is the validation from large and long-term randomized trials to prove sustainable high sensitivity and specificity. In this paper, we present a review on the noninvasive genetics biomarkers for CRC detection described in the literature and the challenges that can be encountered for validation processes.

  13. Membrane integration of in vitro-translated gap junctional proteins: co- and post-translational mechanisms.

    Science.gov (United States)

    Zhang, J T; Chen, M; Foote, C I; Nicholson, B J

    1996-03-01

    Connexins (Cx) are protein components of gap junction channels that permit the passage of small molecules between neighboring cells. cDNAs of a large family of connexins have been isolated and sequenced. A gap junction channel consists of two connexons, one from each cell in contact, composed of six connexin subunits. It has been suggested by Musil and coworkers that the oligomerization of formation of a connexon occurs at the level of the trans-Golgi network. In the present study, we initiated an analysis of the early stages of protein synthesis and membrane insertion of Cx32 and Cx26, two connexins that we have demonstrated are co-expressed in the same junctions in hepatocytes. Using an in vitro transcription and a coupled cell-free translation and translocation system, we observed that both Cx32 and Cx26 could insert into microsome membranes co-translationally, producing a topological structure indistinguishable from that in isolated gap junctions. To our surprise, Cx26 could also insert into membranes post-translationally with a native orientation. This post-translational membrane insertion process is dependent on nucleotides but not their hydrolysis. Cx32, on the other hand, could not insert into membranes post-translationally. These disparate properties of Cx32 and Cx26 are not due to the significant difference in the lengths of their C-terminal domains, but rather to their internal amino acid sequences. These observations raise the possibility that there may be another pathway for Cx26 to insert into membranes in cells and this feature may be important for the regulation of its functions. These findings may also lead us to a new approach to reconstitution without detergent extraction.

  14. Radio-modification by caffeine alone and in combination with phosphorothioates: in vivo and cell-free studies

    Energy Technology Data Exchange (ETDEWEB)

    Swenberg, C.E.; Landauer, M.R. [Armed Forces Radiobiology Research Institute, Bethesda (United States); Weiss, J.F. [Office of International Health Programs, Department of Energy, Germantown (United States)

    1997-03-01

    Caffeine is generally considered to result in radiosensitization by affecting the cell cycle. Data from in vivo studies, however, do not suggest sensitization; caffeine administration did not adversely affect survival of mice irradiated at doses causing hematopoietic injury, or gastrointestinal injury, or when administered in combination with phosphorothioates. For example, caffeine administration (20 mg/kg IP) in combination with the radioprotector WR-151327, S-2-(3-methyl-amino-propyl-amino)propyl-phosphoro-thioic acid. (200 mg/kg IP) resulted in a dose modification factor of 1.54 in comparison to 1.51 for WR-151327 treatment alone. In a cell-free system, the active metabolites of phosphorothiotates, i.e. free thiols and disulfides, appear to mimic polyamines and modulate enzymes involves in DNA structure and synthesis. The free thiol of WR-151327 (WR-151326) actively enhanced topoisomerase I-mediated unwinding of supercoiled plB130 DNA and super-coiling of DNA mediated by DNA gyrase (topoisomerase II). Caffeine, in general, had opposite effects on potoisomerase activities compared to WR-151326. When caffeine was added to the cell-free system together with WR-151326, the stimulatory effects of WR-151326 were suppressed. Further studies are needed in cell-free systems, cells, and animals to elucidate the potential utility of caffeine administration in combination with radiation and other therapeutic agents. (authors)

  15. Circulating Cell Free DNA in the Diagnosis of Trophoblastic Tumors

    Science.gov (United States)

    Openshaw, Mark R.; Harvey, Richard A.; Sebire, Neil J.; Kaur, Baljeet; Sarwar, Naveed; Seckl, Michael J.; Fisher, Rosemary A.

    2015-01-01

    Gestational trophoblastic neoplasia (GTN) represents a group of diseases characterized by production of human chorionic gonadotropin (hCG). Since non-gestational tumors may occasionally secrete hCG, histopathological diagnosis is important for appropriate clinical management. However, a histopathological diagnosis is not always available. We therefore investigated the feasibility of extracting cell free DNA (cfDNA) from the plasma of women with GTN for use as a “liquid biopsy” in patients without histopathological diagnosis. cfDNA was prepared from the plasma of 20 women with a diagnosis of GTN and five with hCG-secreting tumors of unknown origin. Genotyping of cfDNA from the patient, genomic DNA from her and her partner and DNA from the tumor tissue identified circulating tumor DNA (ctDNA) (from 9% to 53% of total cfDNA) in 12 of 20 patients with GTN. In one case without a tissue diagnosis, ctDNA enabled a diagnosis of GTN originating in a non-molar conception and in another a diagnosis of non-gestational tumor, based on the high degree of allelic instability and loss of heterozygosity in the ctDNA. In summary ctDNA can be detected in the plasma of women with GTN and can facilitate the diagnosis of both gestational and non-gestational trophoblastic tumors in cases without histopathological diagnosis. PMID:26981554

  16. Cell-Free Production of Protein Biologics Within 24 H.

    Science.gov (United States)

    Sullivan, Challise J; Pendleton, Erik D; Dresios, John

    2018-01-01

    Protein biologics have emerged as a safe and effective group of drug products that can be used in a variety of medical disorders and clinical settings, including treatment of orphan diseases, personalized medicine, and point-of-care applications. However, the full potential of protein biologics for such applications will not be realized until there are methods available for rapid and cost-effective production of small scale products for individual needs. Here, we describe a modular and scalable method for rapid and adaptable production of protein-based medical products at small doses. The method includes cell-free synthesis of the protein target in a reactor module followed by a fluidic process for protein purification. As a proof of concept, we describe the application of this method for expression and purification of a bioactive pharmaceutically relevant protein biologic, recombinant human erythropoietin, at a single dose within 24 h. This method can be applied toward the development of automated platforms for rapid and adaptive production of protein biologics at the point of care in response to specific medical needs.

  17. Circulating Cell Free DNA in the Diagnosis of Trophoblastic Tumors

    Directory of Open Access Journals (Sweden)

    Mark R. Openshaw

    2016-02-01

    Full Text Available Gestational trophoblastic neoplasia (GTN represents a group of diseases characterized by production of human chorionic gonadotropin (hCG. Since non-gestational tumors may occasionally secrete hCG, histopathological diagnosis is important for appropriate clinical management. However, a histopathological diagnosis is not always available. We therefore investigated the feasibility of extracting cell free DNA (cfDNA from the plasma of women with GTN for use as a “liquid biopsy” in patients without histopathological diagnosis. cfDNA was prepared from the plasma of 20 women with a diagnosis of GTN and five with hCG-secreting tumors of unknown origin. Genotyping of cfDNA from the patient, genomic DNA from her and her partner and DNA from the tumor tissue identified circulating tumor DNA (ctDNA (from 9% to 53% of total cfDNA in 12 of 20 patients with GTN. In one case without a tissue diagnosis, ctDNA enabled a diagnosis of GTN originating in a non-molar conception and in another a diagnosis of non-gestational tumor, based on the high degree of allelic instability and loss of heterozygosity in the ctDNA. In summary ctDNA can be detected in the plasma of women with GTN and can facilitate the diagnosis of both gestational and non-gestational trophoblastic tumors in cases without histopathological diagnosis.

  18. Probiotic Properties of Lyophilized Cell Free Extract of Lactobacillus casei.

    Science.gov (United States)

    Saadatzadeh, Afrooz; Fazeli, Mohamma Reza; Jamalifar, Hossein; Dinarvand, Rassoul

    2013-08-01

    In recent years there have been considerable interests in the use of probiotic live cells for nutritional and therapeutic purposes. This strategy can be concomitant with some limitations such as survival of live cell during the GI-transit and their effective delivery to target tissues upon ingestion. Several attempts have been made to overcome these limitations such as their microencapsulation, spray-drying and lyophilization. In this study extract of cultured probiotics without cells was evaluated for its antimicrobial effects, antioxidant activity, and its stability. In this work the potential of lyophilized-cell-free-probiotic-extract (LPE) as a suitable alternative strategy for the preparation of probiotic-products was investigated. The main aim of this study was to find out the antibacterial and antioxidant activity of LPE and also its stability. LPE was obtained by centrifugation and subsequent lyophilization of the collected supernatant from culture media of Lactobacillus casei. An enzymatic reagent-kit was used for detection of its content of lactic acid. Antibacterial test was performed using agar cup-plat-method, the DPPH scavenging -assay was used to determine its antioxidant activity and during a storage course, LPE was under a long-term stability study. Results showed that, LPE had more antipathogenic effects, antioxidant activity, and stability during storage-time when compared to fresh probiotic-extract. Employing the LPE as a new approach, gives novel concept of probiotic-products in food and medical marketing.

  19. Translational genomics

    Directory of Open Access Journals (Sweden)

    Martin Kussmann

    2014-09-01

    Full Text Available The term “Translational Genomics” reflects both title and mission of this new journal. “Translational” has traditionally been understood as “applied research” or “development”, different from or even opposed to “basic research”. Recent scientific and societal developments have triggered a re-assessment of the connotation that “translational” and “basic” are either/or activities: translational research nowadays aims at feeding the best science into applications and solutions for human society. We therefore argue here basic science to be challenged and leveraged for its relevance to human health and societal benefits. This more recent approach and attitude are catalyzed by four trends or developments: evidence-based solutions; large-scale, high dimensional data; consumer/patient empowerment; and systems-level understanding.

  20. From Function to System: Advances in Choosing a Matrix Structure of the Translation Process

    Directory of Open Access Journals (Sweden)

    Ирина Николаевна Ремхе

    2016-12-01

    Full Text Available This article presents the authors’ view on the transition towards a new paradigm in the study of the translation process based on synergy, collaboration, networking and the cognitive structure of the translator’s mind. In the search for a hypothetical cognitive model of translation, a matrix model is represented to further enrich the interdisciplinary platform through understanding the conglomerate of the many sources involved in the act of translation and focusing on the role of the individual human being in translational cognition. The Map-Matrix Model comprises three levels of the translator’s mental space: Neurological, Representational and Conceptual. Each level corresponds to the inheritance relations between mapping patterns, clusters and frames. The model will be presented and interrogated through the results of a practical Think-aloud protocols experiment in order to give a better insight into the translation efficiency in terms of information processing and a clearer assumption of the feasibility of the concept.

  1. Translational systems biology: introduction of an engineering approach to the pathophysiology of the burn patient.

    Science.gov (United States)

    An, Gary; Faeder, James; Vodovotz, Yoram

    2008-01-01

    The pathophysiology of the burn patient manifests the full spectrum of the complexity of the inflammatory response. In the acute phase, inflammation may have negative effects via capillary leak, the propagation of inhalation injury, and development of multiple organ failure. Attempts to mediate these processes remain a central subject of burn care research. Conversely, inflammation is a necessary prologue and component in the later stage processes of wound healing. Despite the volume of information concerning the cellular and molecular processes involved in inflammation, there exists a significant gap between the knowledge of mechanistic pathophysiology and the development of effective clinical therapeutic regimens. Translational systems biology (TSB) is the application of dynamic mathematical modeling and certain engineering principles to biological systems to integrate mechanism with phenomenon and, importantly, to revise clinical practice. This study will review the existing applications of TSB in the areas of inflammation and wound healing, relate them to specific areas of interest to the burn community, and present an integrated framework that links TSB with traditional burn research.

  2. Bridging the gap between clinicians and systems biologists: from network biology to translational biomedical research.

    Science.gov (United States)

    Jinawath, Natini; Bunbanjerdsuk, Sacarin; Chayanupatkul, Maneerat; Ngamphaiboon, Nuttapong; Asavapanumas, Nithi; Svasti, Jisnuson; Charoensawan, Varodom

    2016-11-22

    With the wealth of data accumulated from completely sequenced genomes and other high-throughput experiments, global studies of biological systems, by simultaneously investigating multiple biological entities (e.g. genes, transcripts, proteins), has become a routine. Network representation is frequently used to capture the presence of these molecules as well as their relationship. Network biology has been widely used in molecular biology and genetics, where several network properties have been shown to be functionally important. Here, we discuss how such methodology can be useful to translational biomedical research, where scientists traditionally focus on one or a small set of genes, diseases, and drug candidates at any one time. We first give an overview of network representation frequently used in biology: what nodes and edges represent, and review its application in preclinical research to date. Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. These types of inhibitors have the potential to be more specific, resulting in high efficacy treatments with less side effects, compared to the conventional treatments such as chemotherapy. Global analysis may provide better insight into the overall picture of human diseases, as well as identify previously overlooked problems, leading to rapid advances in medicine. From the clinicians' point of view, it is necessary to bridge the gap between theoretical network biology and practical biomedical research, in order to improve the diagnosis, prevention, and treatment of the world's major diseases.

  3. Translatress, Translator, Translation

    OpenAIRE

    Margala, Miriam

    2009-01-01

    I still manage to surprise a few scholars from other fields when they hear that there is such a thing as research of gender issues within the field of translation studies. It may seem as such a narrow niche – but only deceivingly so. It is language, linguistics, pragmatics, culture, history, literature, anthropology, gender metaphorics, communication, interpreting, cultural politics, social studies and politics, psychology and I can go on and on. History seems to be a very appropriate startin...

  4. Televaluation and usability assessment of the human-machine interface for a novel adaptive health knowledge translation system.

    Science.gov (United States)

    Copen, John; Kushniruk, Andre

    2009-01-01

    We describe results from usability assessment of a novel adaptive health knowledge translation system interface. Search or retrieval logic, navigation, and presentation elements are crucial to delivering best content. Design requirements have been enhanced by assessing participant needs and desired features.

  5. Coping with complexity: machine learning optimization of cell-free protein synthesis.

    Science.gov (United States)

    Caschera, Filippo; Bedau, Mark A; Buchanan, Andrew; Cawse, James; de Lucrezia, Davide; Gazzola, Gianluca; Hanczyc, Martin M; Packard, Norman H

    2011-09-01

    Biological systems contain complex metabolic pathways with many nonlinearities and synergies that make them difficult to predict from first principles. Protein synthesis is a canonical example of such a pathway. Here we show how cell-free protein synthesis may be improved through a series of iterated high-throughput experiments guided by a machine-learning algorithm implementing a form of evolutionary design of experiments (Evo-DoE). The algorithm predicts fruitful experiments from statistical models of the previous experimental results, combined with stochastic exploration of the experimental space. The desired experimental response, or evolutionary fitness, was defined as the yield of the target product, and new experimental conditions were discovered to have ∼ 350% greater yield than the standard. An analysis of the best experimental conditions discovered indicates that there are two distinct classes of kinetics, thus showing how our evolutionary design of experiments is capable of significant innovation, as well as gradual improvement. Copyright © 2011 Wiley Periodicals, Inc.

  6. Identification of minimal sequences of the Rhopalosiphum padi virus 5' untranslated region required for internal initiation of protein synthesis in mammalian, plant and insect translation systems

    DEFF Research Database (Denmark)

    Groppelli, Elisabetta; Belsham, Graham; Roberts, Lisa O.

    2007-01-01

    Rhopalosiphum padi virus (RhPV) is a member of the family Dicistroviridae. The genomes of viruses in this family contain two open reading frames, each preceded by distinct internal ribosome entry site (IRES) elements. The RhPV 5' IRES is functional in mammalian, insect and plant translation systems...... (rabbit reticulocyte lysate), plant (wheatgerm extract) and insect (Sf21 cells) translation systems have now been defined. A fragment (nt 426–579) from the 3' portion of the 5' UTR can direct translation in each of these translation systems. In addition, a distinct region (nt 300–429) is also active. Thus...

  7. A functional renormalization group approach to electronic structure calculations for systems without translational symmetry

    CERN Document Server

    Seiler, Christian

    2016-01-01

    A formalism for electronic-structure calculations is presented that is based on the functional renormalization group (FRG). The traditional FRG has been formulated for systems that exhibit a translational symmetry with an associated Fermi surface, which can provide the organization principle for the renormalization group (RG) procedure. We here advance an alternative formulation, where the RG-flow is organized in the energy-domain rather than in k-space. This has the advantage that it can also be applied to inhomogeneous matter lacking a band-structure, such as disordered metals or molecules. The energy-domain FRG ({\\epsilon}FRG) presented here accounts for Fermi-liquid corrections to quasi-particle energies and particle-hole excitations. It goes beyond the state of the art GW-BSE, because in {\\epsilon}FRG the Bethe-Salpeter equation (BSE) is solved in a self-consistent manner. An efficient implementation of the approach that has been tested against exact diagonalization calculations and calculations based on...

  8. Emerging Utility of Urinary Cell-free Nucleic Acid Biomarkers for Prostate, Bladder, and Renal Cancers.

    Science.gov (United States)

    Lin, Selena Y; Linehan, Jennifer A; Wilson, Timothy G; Hoon, Dave S B

    2017-04-01

    By 2020 the estimated incidence of genitourinary (GU) cancers (prostate, bladder, and kidney) will be over 2 million worldwide and responsible for ∼800 000 deaths. Current diagnosis and monitoring methods of GU cancer patients are often invasive and/or lack sensitivity and specificity. Given the utility of blood-based cell-free nucleic acid (cfNA) biomarkers, the development of urinary cfNA biomarkers may improve the sensitivity of urine assays utilizing urine sediment for GU cancers. This review of urinary cfNA in GU cancers identifies the current stage of research, potential clinical utility, and the next steps needed to enter clinical use. To critically evaluate the literature of urinary cfNA in GU cancers for clinical utility in diagnosis, screening, and precision medicine. Furthermore, the strategy for future efforts to discover potential new urinary cfNA biomarkers will be described. A PubMed database (2006 to current) search was performed according to Preferred Reporting Items for Systemic Review and Meta-analysis using key Medical Subject Headings terms. Additional studies were obtained by cross-referencing from the literature. The collective research publications in urinary cfNA of GU cancers present a promising alternative liquid biopsy approach compared with blood biopsies and urine sediment, particularly for early-stage GU diseases. Urinary cfNA as a liquid biopsy holds potential for a more sensitive alternative to blood biopsies and urine sediment-based tests for clinical use in GU cancers. Not only does urinary cfNA offer advantages including the potential for more frequent testing, monitoring, and home use, but also has applications in early-stage GU cancers. In this review, we evaluated the current status of urinary cell-free nucleic acid in genitourinary cancers. We identified the potential advantages of urinary cell-free nucleic acid over blood and urine sediment and its clinical use in genitourinary cancer. Copyright © 2017 European

  9. Committee Opinion No. 640: Cell-Free DNA Screening For Fetal Aneuploidy.

    Science.gov (United States)

    2015-09-01

    Noninvasive prenatal screening that uses cell-free DNA from the plasma of pregnant women offers tremendous potential as a screening method for fetal aneuploidy. A number of laboratories have validated different techniques for the use of cell-free DNA as a screening test for fetal aneuploidy. All tests have a high sensitivity and specificity for trisomy 18 and trisomy 21, regardless of which molecular technique is used. Women whose results are not reported, indeterminate, or uninterpretable (a "no call" test result) from cell-free DNA screening should receive further genetic counseling and be offered comprehensive ultrasound evaluation and diagnostic testing because of an increased risk of aneuploidy. Patients should be counseled that cell-free DNA screening does not replace the precision obtained with diagnostic tests, such as chorionic villus sampling or amniocentesis and, therefore, is limited in its ability to identify all chromosome abnormalities. Cell-free DNA screening does not assess risk of fetal anomalies such as neural tube defects or ventral wall defects. Patients who are undergoing cell-free DNA screening should be offered maternal serum alpha-fetoprotein screening or ultrasound evaluation for risk assessment. The cell-free DNA screening test should not be considered in isolation from other clinical findings and test results. Management decisions, including termination of the pregnancy, should not be based on the results of the cell-free DNA screening alone. Patients should be counseled that a negative cell-free DNA test result does not ensure an unaffected pregnancy. Given the performance of conventional screening methods, the limitations of cell-free DNA screening performance, and the limited data on cost-effectiveness in the low-risk obstetric population, conventional screening methods remain the most appropriate choice for first-line screening for most women in the general obstetric population.

  10. Committee Opinion Summary No. 640: Cell-Free DNA Screening For Fetal Aneuploidy.

    Science.gov (United States)

    2015-09-01

    Noninvasive prenatal screening that uses cell-free DNA from the plasma of pregnant women offers tremendous potential as a screening method for fetal aneuploidy. A number of laboratories have validated different techniques for the use of cell-free DNA as a screening test for fetal aneuploidy. All tests have a high sensitivity and specificity for trisomy 18 and trisomy 21, regardless of which molecular technique is used. Women whose results are not reported, indeterminate, or uninterpretable (a "no call" test result) from cell-free DNA screening should receive further genetic counseling and be offered comprehensive ultrasound evaluation and diagnostic testing because of an increased risk of aneuploidy. Patients should be counseled that cell-free DNA screening does not replace the precision obtained with diagnostic tests, such as chorionic villus sampling or amniocentesis and, therefore, is limited in its ability to identify all chromosome abnormalities. Cell-free DNA screening does not assess risk of fetal anomalies such as neural tube defects or ventral wall defects. Patients who are undergoing cell-free DNA screening should be offered maternal serum alpha-fetoprotein screening or ultrasound evaluation for risk assessment. The cell-free DNA screening test should not be considered in isolation from other clinical findings and test results. Management decisions, including termination of the pregnancy, should not be based on the results of the cell-free DNA screening alone. Patients should be counseled that a negative cell-free DNA test result does not ensure an unaffected pregnancy. Given the performance of conventional screening methods, the limitations of cell-free DNA screening performance, and the limited data on cost-effectiveness in the low-risk obstetric population, conventional screening methods remain the most appropriate choice for first-line screening for most women in the general obstetric population.

  11. Temperature and UV light affect the activity of marine cell-free enzymes

    Directory of Open Access Journals (Sweden)

    B. Thomson

    2017-09-01

    Full Text Available Microbial extracellular enzymatic activity (EEA is the rate-limiting step in the degradation of organic matter in the oceans. These extracellular enzymes exist in two forms: cell-bound, which are attached to the microbial cell wall, and cell-free, which are completely free of the cell. Contrary to previous understanding, cell-free extracellular enzymes make up a substantial proportion of the total marine EEA. Little is known about these abundant cell-free enzymes, including what factors control their activity once they are away from their sites (cells. Experiments were run to assess how cell-free enzymes (excluding microbes respond to ultraviolet radiation (UVR and temperature manipulations, previously suggested as potential control factors for these enzymes. The experiments were done with New Zealand coastal waters and the enzymes studied were alkaline phosphatase (APase, β-glucosidase, (BGase, and leucine aminopeptidase (LAPase. Environmentally relevant UVR (i.e. in situ UVR levels measured at our site reduced cell-free enzyme activities by up to 87 % when compared to controls, likely a consequence of photodegradation. This effect of UVR on cell-free enzymes differed depending on the UVR fraction. Ambient levels of UV radiation were shown to reduce the activity of cell-free enzymes for the first time. Elevated temperatures (15 °C increased the activity of cell-free enzymes by up to 53 % when compared to controls (10 °C, likely by enhancing the catalytic activity of the enzymes. Our results suggest the importance of both UVR and temperature as control mechanisms for cell-free enzymes. Given the projected warming ocean environment and the variable UVR light regime, it is possible that there could be major changes in the cell-free EEA and in the enzymes contribution to organic matter remineralization in the future.

  12. Temperature and UV light affect the activity of marine cell-free enzymes

    Science.gov (United States)

    Thomson, Blair; Hepburn, Christopher David; Lamare, Miles; Baltar, Federico

    2017-09-01

    Microbial extracellular enzymatic activity (EEA) is the rate-limiting step in the degradation of organic matter in the oceans. These extracellular enzymes exist in two forms: cell-bound, which are attached to the microbial cell wall, and cell-free, which are completely free of the cell. Contrary to previous understanding, cell-free extracellular enzymes make up a substantial proportion of the total marine EEA. Little is known about these abundant cell-free enzymes, including what factors control their activity once they are away from their sites (cells). Experiments were run to assess how cell-free enzymes (excluding microbes) respond to ultraviolet radiation (UVR) and temperature manipulations, previously suggested as potential control factors for these enzymes. The experiments were done with New Zealand coastal waters and the enzymes studied were alkaline phosphatase (APase), β-glucosidase, (BGase), and leucine aminopeptidase (LAPase). Environmentally relevant UVR (i.e. in situ UVR levels measured at our site) reduced cell-free enzyme activities by up to 87 % when compared to controls, likely a consequence of photodegradation. This effect of UVR on cell-free enzymes differed depending on the UVR fraction. Ambient levels of UV radiation were shown to reduce the activity of cell-free enzymes for the first time. Elevated temperatures (15 °C) increased the activity of cell-free enzymes by up to 53 % when compared to controls (10 °C), likely by enhancing the catalytic activity of the enzymes. Our results suggest the importance of both UVR and temperature as control mechanisms for cell-free enzymes. Given the projected warming ocean environment and the variable UVR light regime, it is possible that there could be major changes in the cell-free EEA and in the enzymes contribution to organic matter remineralization in the future.

  13. Pro-B cells propagated in stromal cell-free cultures reconstitute functional B-cell compartments in immunodeficient mice.

    Science.gov (United States)

    von Muenchow, Lilly; Tsapogas, Panagiotis; Albertí-Servera, Llucia; Capoferri, Giuseppina; Doelz, Marianne; Rolink, Hannie; Bosco, Nabil; Ceredig, Rhodri; Rolink, Antonius G

    2017-02-01

    Up to now long-term in vitro growth of pro-B cells was thought to require stromal cells. However, here we show that fetal liver (FL) and bone marrow (BM) derived pro-B cells can be propagated long-term in stromal cell-free cultures supplemented with IL-7, stem cell factor and FLT3 ligand. Within a week, most cells expressed surface CD19, CD79A, λ5, and VpreB antigens and had rearranged immunoglobulin D-J heavy chain genes. Both FL and BM pro-B cells reconstituted the B-cell compartments of immuno-incompetent Rag2-deficient mice, with FL pro-B cells generating follicular, marginal zone (MZB) and B1a B cells, and BM pro-B cells giving rise mainly to MZB cells. Reconstituted Rag2-deficient mice generated significant levels of IgM and IgG antibodies to a type II T-independent antigen; mice reconstituted with FL pro-B cells generated surprisingly high IgG1 titers. Finally, we show for the first time that mice reconstituted with mixtures of pro-B and pro-T cells propagated in stromal cell-free in vitro cultures mounted a T-cell-dependent antibody response. This novel stromal cell-free culture system facilitates our understanding of B-cell development and might be applied clinically. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. The fine structure of sexual stage development and sporogony of Cryptosporidium parvum in cell-free culture.

    Science.gov (United States)

    Aldeyarbi, Hebatalla M; Karanis, Panagiotis

    2016-05-01

    The sexual stages and new oocysts development of Cryptosporidium parvum were investigated in a cell-free culture system using transmission electron microscopy (TEM). Sexual development was extremely rapid after inoculation of oocysts into the medium. The process began within 1/2-12 h and was completed with new oocyst formation 120 h post-inoculation. The macrogamonts were bounded by two membranes and had amylopectin granules and two distinct types of wall-forming bodies. The microgamonts had a large nucleus showing lobe projections and condensation of chromatin, giving rise to peripherally budding microgametes. The microgametes contained a large area of granular substance containing groups of microtubules surrounding the electron-dense nucleus. In some instances, the dividing microgamy was observed in cell-free cultures with no preceding merogonic process. Fertilization was observed with the bullet-shaped microgamete penetrating an immature macrogamont at 24 and 216 h. The new thin- and thick-walled oocysts had a large residuum with polysaccharide granules and sporogony noted inside these oocysts. Novel immature four-layer walled thick oocysts with irregular knob-like protrusions on the outer layer resembling the immature Eimeria oocysts were also observed. The present study confirms the gametogony and sporogony of C. parvum in cell-free culture and describes their ultra-structure for the first time.

  15. Animal models in psychiatric research: The RDoC system as a new framework for endophenotype-oriented translational neuroscience

    Directory of Open Access Journals (Sweden)

    Elmira Anderzhanova

    2017-12-01

    Full Text Available The recently proposed Research Domain Criteria (RDoC system defines psychopathologies as phenomena of multilevel neurobiological existence and assigns them to 5 behavioural domains characterizing a brain in action. We performed an analysis on this contemporary concept of psychopathologies in respect to a brain phylogeny and biological substrates of psychiatric diseases. We found that the RDoC system uses biological determinism to explain the pathogenesis of distinct psychiatric symptoms and emphasises exploration of endophenotypes but not of complex diseases. Therefore, as a possible framework for experimental studies it allows one to evade a major challenge of translational studies of strict disease-to-model correspondence. The system conforms with the concept of a normality and pathology continuum, therefore, supports basic studies. The units of analysis of the RDoC system appear as a novel matrix for model validation. The general regulation and arousal, positive valence, negative valence, and social interactions behavioural domains of the RDoC system show basic construct, network, and phenomenological homologies between human and experimental animals. The nature and complexity of the cognitive behavioural domain of the RDoC system deserve further clarification. These homologies in the 4 domains justifies the validity, reliably and translatability of animal models appearing as endophenotypes of the negative and positive affect, social interaction and general regulation and arousal systems’ dysfunction. Keywords: RDoC, Translational research, Animal models, Endophenotypes, Basic studies, Normality and psychopathology continuum

  16. A Novel String Grammar Unsupervised Possibilistic C-Medians Algorithm for Sign Language Translation Systems

    Directory of Open Access Journals (Sweden)

    Atcharin Klomsae

    2017-12-01

    Full Text Available Sign language is a basic method for solving communication problems between deaf and hearing people. In order to communicate, deaf and hearing people normally use hand gestures, which include a combination of hand positioning, hand shapes, and hand movements. Thai Sign Language is the communication method for Thai hearing-impaired people. Our objective is to improve the dynamic Thai Sign Language translation method with a video captioning technique that does not require prior hand region detection and segmentation through using the Scale Invariant Feature Transform (SIFT method and the String Grammar Unsupervised Possibilistic C-Medians (sgUPCMed algorithm. This work is the first to propose the sgUPCMed algorithm to cope with the unsupervised generation of multiple prototypes in the possibilistic sense for string data. In our experiments, the Thai Sign Language data set (10 isolated sign language words was collected from 25 subjects. The best average result within the constrained environment of the blind test data sets of signer-dependent cases was 89–91%, and the successful rate of signer semi-independent cases was 81–85%, on average. For the blind test data sets of signer-independent cases, the best average classification rate was 77–80%. The average result of the system without a constrained environment was around 62–80% for the signer-independent experiments. To show that the proposed algorithm can be implemented in other sign languages, the American sign language (RWTH-BOSTON-50 data set, which consists of 31 isolated American Sign Language words, is also used in the experiment. The system provides 88.56% and 91.35% results on the validation set alone, and for both the training and validation sets, respectively.

  17. Pattern-based Automatic Translation of Structured Power System Data to Functional Models for Decision Support Applications

    DEFF Research Database (Denmark)

    Heussen, Kai; Weckesser, Johannes Tilman Gabriel; Kullmann, Daniel

    2013-01-01

    Improved information and insight for decision support in operations and design are central promises of a smart grid. Well-structured information about the composition of power systems is increasingly becoming available in the domain, e.g. due to standard information models (e.g. CIM or IEC61850) ....... This paper presents an approach to link available structured power system data directly to a functional representation suitable for diagnostic reasoning. The translation method is applied to test cases also illustrating decision support....

  18. Translational Creativity

    DEFF Research Database (Denmark)

    Nielsen, Sandro

    2010-01-01

    A long-established approach to legal translation focuses on terminological equivalence making translators strictly follow the words of source texts. Recent research suggests that there is room for some creativity allowing translators to deviate from the source texts. However, little attention...... is given to genre conventions in source texts and the ways in which they can best be translated. I propose that translators of statutes with an informative function in expert-to-expert communication may be allowed limited translational creativity when translating specific types of genre convention....... This creativity is a result of translators adopting either a source-language or a target-language oriented strategy and is limited by the pragmatic principle of co-operation. Examples of translation options are provided illustrating the different results in target texts. The use of a target-language oriented...

  19. A knowledge translation intervention to enhance clinical application of a virtual reality system in stroke rehabilitation.

    Science.gov (United States)

    Levac, Danielle; Glegg, Stephanie M N; Sveistrup, Heidi; Colquhoun, Heather; Miller, Patricia A; Finestone, Hillel; DePaul, Vincent; Harris, Jocelyn E; Velikonja, Diana

    2016-10-06

    Despite increasing evidence for the effectiveness of virtual reality (VR)-based therapy in stroke rehabilitation, few knowledge translation (KT) resources exist to support clinical integration. KT interventions addressing known barriers and facilitators to VR use are required. When environmental barriers to VR integration are less amenable to change, KT interventions can target modifiable barriers related to therapist knowledge and skills. A multi-faceted KT intervention was designed and implemented to support physical and occupational therapists in two stroke rehabilitation units in acquiring proficiency with use of the Interactive Exercise Rehabilitation System (IREX; GestureTek). The KT intervention consisted of interactive e-learning modules, hands-on workshops and experiential practice. Evaluation included the Assessing Determinants of Prospective Take Up of Virtual Reality (ADOPT-VR) Instrument and self-report confidence ratings of knowledge and skills pre- and post-study. Usability of the IREX was measured with the System Usability Scale (SUS). A focus group gathered therapist experiences. Frequency of IREX use was recorded for 6 months post-study. Eleven therapists delivered a total of 107 sessions of VR-based therapy to 34 clients with stroke. On the ADOPT-VR, significant pre-post improvements in therapist perceived behavioral control (p = 0.003), self-efficacy (p = 0.005) and facilitating conditions (p =0.019) related to VR use were observed. Therapist intention to use VR did not change. Knowledge and skills improved significantly following e-learning completion (p = 0.001) and was sustained 6 months post-study. Below average perceived usability of the IREX (19(th) percentile) was reported. Lack of time was the most frequently reported barrier to VR use. A decrease in frequency of perceived barriers to VR use was not significant (p = 0.159). Two therapists used the IREX sparingly in the 6 months following the study. Therapists reported

  20. The National Institutes of Health's Biomedical Translational Research Information System (BTRIS): design, contents, functionality and experience to date.

    Science.gov (United States)

    Cimino, James J; Ayres, Elaine J; Remennik, Lyubov; Rath, Sachi; Freedman, Robert; Beri, Andrea; Chen, Yang; Huser, Vojtech

    2014-12-01

    The US National Institutes of Health (NIH) has developed the Biomedical Translational Research Information System (BTRIS) to support researchers' access to translational and clinical data. BTRIS includes a data repository, a set of programs for loading data from NIH electronic health records and research data management systems, an ontology for coding the disparate data with a single terminology, and a set of user interface tools that provide access to identified data from individual research studies and data across all studies from which individually identifiable data have been removed. This paper reports on unique design elements of the system, progress to date and user experience after five years of development and operation. Published by Elsevier Inc.

  1. Knowledge management for systems biology a general and visually driven framework applied to translational medicine

    Directory of Open Access Journals (Sweden)

    Falciani Francesco

    2011-03-01

    Full Text Available Abstract Background To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the

  2. Cell-free DNA induced apoptosis of granulosa cells by oxidative stress.

    Science.gov (United States)

    Guan, Yichun; Zhang, Wenjuan; Wang, Xingling; Cai, Pengfei; Jia, Qi; Zhao, Wenjie

    2017-10-01

    Cell-free DNA is a DNA fragment that is produced by cell apoptosis which can affect the micro-environment of cell apoptosis. The levels of Cell-free DNA have been associated with successful rate of in vitro fertilization-embryo transfer (IVF-ET) and embryonic development. Our aim is to determine the relationship between cell-free DNA and embryo quality. The mechanisms of cell-free DNA in granulose and the apoptosis will be determined also. The study enrolled patients who were undergone IVF for the first time and grouped the patients as pregnant (n=130) and non-pregnant (n=59). The relationship was determined by statistical analysis between the levels of cell-free DNA in the follicular fluid and clinical data of IVF patients. Flow cytometry was done to detect the rate of granulosa cell apoptosis and intracellular reactive oxygen species (ROS) level. Western blotting and fluorescent quantitative PCR detected the apoptosis-related gene expressions. Clinical data statistics showed that cell-free DNA levels were positively correlated with granulosa cell apoptosis and negatively correlated with embryo quality and pregnancy rates. High levels of cell-free DNA lead to increased ROS in granulosa cells and activated caspase through Fas/FasL that induced apoptosis. High levels of cell-free DNA triggers granulosa cell apoptosis and influences oocyte maturation embryo development and pregnancy rates in IVF treatments. Cell-free DNA can be as a secondary criteria and predictive marker for the quality control of IVF embryo. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Translating Europe

    Directory of Open Access Journals (Sweden)

    Yves Chevrel

    2007-07-01

    Europe thinks in many languages and Europe is a land of translation. Translation is a means of transmitting culture, a means of making it available to others and an invitation to share. It is a cement which binds Europe together.

  4. "Keeping our mission, changing our system": translation and organizational change in natural foods co-ops.

    Science.gov (United States)

    Haedicke, Michael A

    2012-01-01

    Institutional theory has played a central role in the study of organizations for over half a century, but it often overlooks the actions of the people who bring organizations to life. This article advances an inhabited approach to institutional analysis that foregrounds the creativity of organizational members. It argues that people use local cultures to translate and respond to institutional pressures. The article analyzes qualitative data from countercultural co-op stores that have been pushed to conform to mainstream forms of business organization by a competitive market and demonstrates that translation explains why outcomes that institutional theory would not predict have come to pass.

  5. A set of ligation-independent in vitro translation vectors for eukaryotic protein production

    Directory of Open Access Journals (Sweden)

    Endo Yaeta

    2008-03-01

    Full Text Available Abstract Background The last decade has brought the renaissance of protein studies and accelerated the development of high-throughput methods in all aspects of proteomics. Presently, most protein synthesis systems exploit the capacity of living cells to translate proteins, but their application is limited by several factors. A more flexible alternative protein production method is the cell-free in vitro protein translation. Currently available in vitro translation systems are suitable for high-throughput robotic protein production, fulfilling the requirements of proteomics studies. Wheat germ extract based in vitro translation system is likely the most promising method, since numerous eukaryotic proteins can be cost-efficiently synthesized in their native folded form. Although currently available vectors for wheat embryo in vitro translation systems ensure high productivity, they do not meet the requirements of state-of-the-art proteomics. Target genes have to be inserted using restriction endonucleases and the plasmids do not encode cleavable affinity purification tags. Results We designed four ligation independent cloning (LIC vectors for wheat germ extract based in vitro protein translation. In these constructs, the RNA transcription is driven by T7 or SP6 phage polymerase and two TEV protease cleavable affinity tags can be added to aid protein purification. To evaluate our improved vectors, a plant mitogen activated protein kinase was cloned in all four constructs. Purification of this eukaryotic protein kinase demonstrated that all constructs functioned as intended: insertion of PCR fragment by LIC worked efficiently, affinity purification of translated proteins by GST-Sepharose or MagneHis particles resulted in high purity kinase, and the affinity tags could efficiently be removed under different reaction conditions. Furthermore, high in vitro kinase activity testified of proper folding of the purified protein. Conclusion Four newly

  6. TRANSLATING FEMINISM

    OpenAIRE

    Gajewska, Agnieszka

    2012-01-01

    Translating feminism Pointing to manifold and long-lasting connections between feminism and translation, the article first presents a selection of multilingual writers (Narcyza Żmichowska and Deborah Vogel), translators (Zofia Żeleńska and Kazimiera Iłłakowiczówna) and translation commentators (Joanna Lisek and Karolina Szymaniak) to ponder why the work of early Polish feminists is neglected. It seems that one of the reasons might be the current colonization of Polish femini...

  7. TRANSLATION TECHNIQUE OF MODALITY ON INAUGURATION SPEECH OF UNITED STATE OF AMERICA ELECTED PRESIDENT (A SYSTEMIC FUNCTIONAL LINGUISTICS PERSPECTIVE

    Directory of Open Access Journals (Sweden)

    Siti Nuraisiah

    2017-12-01

    Full Text Available The study deals with the United State of America elected president‘s attitude on inauguration speech revealed through the use of modality. It investigates category, level and orientation of modality and its translation technique used by two different news media. It employed descriptive qualitative approach. Its data were obtained through content analysis and analyzed by Systemic Functional Linguistics (SFL perspective as proposed by Halliday (1994 and translation technique as proposed by Molina and Albir (2002. The result indicates the followings. First, inauguration speech states inclination, probablity, obligation and usuality. It is dominated by median level of modality, then followed by high and low level. Its attitudes are expressed through subjective implicit, as the most frequent orientation, objective implicit, subjective explicit and objective explicit. Second, the first news media uses some translation techniques including established equivalent, reduction, combination and transposition. Third, the second news media uses some translation techniques including established equivalent, combination, reduction and transposition. It is argued that established equivalent produces the same category, level and orientation of modality. Besides, reduction and transposition tend to change modality into another linguistic entities.

  8. ARABIC TRANSLATION AND ADAPTATION OF THE HOSPITAL CONSUMER ASSESSMENT OF HEALTHCARE PROVIDERS AND SYSTEMS (HCAHPS) PATIENT SATISFACTION SURVEY INSTRUMENT.

    Science.gov (United States)

    Dockins, James; Abuzahrieh, Ramzi; Stack, Martin

    2015-01-01

    To translate and adapt an effective, validated, benchmarked, and widely used patient satisfaction measurement tool for use with an Arabic-speaking population. Translation of survey's items, survey administration process development, evaluation of reliability, and international benchmarking Three hundred-bed tertiary care hospital in Jeddah, Saudi Arabia. 645 patients discharged during 2011 from the hospital's inpatient care units. INTERVENTIONS; The Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) instrument was translated into Arabic, a randomized weekly sample of patients was selected, and the survey was administered via telephone during 2011 to patients or their relatives. Scores were compiled for each of the HCAHPS questions and then for each of the six HCAHPS clinical composites, two non-clinical items, and two global items. Clinical composite scores, as well as the two non-clinical and two global items were analyzed for the 645 respondents. Clinical composites were analyzed using Spearman's correlation coefficient and Cronbach's alpha to demonstrate acceptable internal consistency for these items and scales demonstrated acceptable internal consistency for the clinical composites. (Spearman's correlation coefficient = 0.327 - 0.750, P translation and adaptation of the HCAHPS is a valid, reliable, and feasible tool for evaluation and benchmarking of inpatient satisfaction in Arabic speaking populations.

  9. Cell-free DNA in a three-dimensional spheroid cell culture model: A preliminary study.

    Science.gov (United States)

    Aucamp, Janine; Calitz, Carlemi; Bronkhorst, Abel J; Wrzesinski, Krzysztof; Hamman, Sias; Gouws, Chrisna; Pretorius, Piet J

    2017-08-01

    Investigating the biological functions of cell-free DNA (cfDNA) is limited by the interference of vast numbers of putative sources and causes of DNA release into circulation. Utilization of three-dimensional (3D) spheroid cell cultures, models with characteristics closer to the in vivo state, may be of significant benefit for cfDNA research. CfDNA was isolated from the growth medium of C3A spheroid cultures in rotating bioreactors during both normal growth and treatment with acetaminophen. Spheroid growth was monitored via planimetry, lactate dehydrogenase activity and glucose consumption and was related to isolated cfDNA characteristics. Changes in spheroid growth and stability were effectively mirrored by cfDNA characteristics. CfDNA characteristics correlated with that of previous two-dimensional (2D) cell culture and human plasma research. 3D spheroid cultures can serve as effective, simplified in vivo-simulating "closed-circuit" models since putative sources of cfDNA are limited to only the targeted cells. In addition, cfDNA can also serve as an alternative or auxiliary marker for tracking spheroid growth, development and culture stability. 3D cell cultures can be used to translate "closed-circuit" in vitro model research into data that is relevant for in vivo studies and clinical applications. In turn, the utilization of cfDNA during 3D culture research can optimize sample collection without affecting the stability of the growth environment. Combining 3D culture and cfDNA research could, therefore, optimize both research fields. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Optimizing Immobilized Enzyme Performance in Cell-Free Environments to Produce Liquid Fuels

    Energy Technology Data Exchange (ETDEWEB)

    Belfort, Georges [Rensselaer Polytechnic Inst., Troy, NY (United States). Dept. of Chemical and Biological Engineering; Grimaldi, Joseph J. [Rensselaer Polytechnic Inst., Troy, NY (United States). Dept. of Chemical and Biological Engineering

    2015-01-27

    Limitations on biofuel production using cell culture (Escherichia coli, Clostridium, Saccharomyces cerevisiae, brown microalgae, blue-green algae and others) include low product (alcohol) concentrations (≤0.2 vol%) due to feedback inhibition, instability of cells, and lack of economical product recovery processes. To overcome these challenges, an alternate simplified biofuel production scheme was tested based on a cell-free immobilized enzyme system. Using this cell free system, we were able to obtain about 2.6 times higher concentrations of iso-butanol using our non-optimized system as compared with live cell systems. This process involved two steps: (i) converts acid to aldehyde using keto-acid decarboxylase (KdcA), and (ii) produces alcohol from aldehyde using alcohol dehydrogenase (ADH) with a cofactor (NADH) conversion from inexpensive formate using a third enzyme, formate dehydrogenase (FDH). To increase stability and conversion efficiency with easy separations, the first two enzymes were immobilized onto methacrylate resin. Fusion proteins of labile KdcA (fKdcA) were expressed to stabilize the covalently immobilized KdcA. Covalently immobilized ADH exhibited long-term stability and efficient conversion of aldehyde to alcohol over multiple batch cycles without fusions. High conversion rates and low protein leaching were achieved by covalent immobilization of enzymes on methacrylate resin. The complete reaction scheme was demonstrated by immobilizing both ADH and fKdcA and using FDH free in solution. The new system without in situ removal of isobutanol achieved a 55% conversion of ketoisovaleric acid to isobutanol at a concentration of 0.5 % (v/v). Further increases in titer will require continuous removal of the isobutanol using our novel brush membrane system that exhibits a 1.5 fold increase in the separation factor of isobutanol from water versus that obtained for commercial silicone rubber membranes. These bio-inspired brush membranes are based on the

  11. Effects of translational symmetry breaking induced by the boundaries in a driven diffusive system

    DEFF Research Database (Denmark)

    Andersen, Jørgen Vitting; Leung, Kwan-tai

    1991-01-01

    We study the effects of the boundary conditions in a driven diffusive lattice-gas model which is known to display kinetic phase transitions. We find, in the case of attractive interaction, that a boundary-condition-induced symmetry breaking of the translational invariance, along the direction of ...

  12. Mission Profile Translation to Capacitor Stresses in Grid-Connected Photovoltaic Systems

    DEFF Research Database (Denmark)

    Yang, Yongheng; Ma, Ke; Wang, Huai

    2014-01-01

    capacitors are varying along with the intermittent solar PV energy (i.e. of weather-dependency) and also the grid conditions (e.g. voltage fault transients). This paper serves to translate real-field mission profiles (i.e. solar irradiance and ambient temperature) into voltage, current, and temperature...

  13. THE MOUSE THERMOREGULATORY SYSTEM:ITS IMPACT ON TRANSLATING BIOMEDICAL DATA TO HUMANS

    Science.gov (United States)

    The laboratory mouse has become the predominant test species in biomedical research. The number of papers that translate or extrapolate data from mouse to human has grown exponentially since the year 2000. There are many physiological and anatomical factors to consider in the pro...

  14. Automatic translation among spoken languages

    Science.gov (United States)

    Walter, Sharon M.; Costigan, Kelly

    1994-01-01

    The Machine Aided Voice Translation (MAVT) system was developed in response to the shortage of experienced military field interrogators with both foreign language proficiency and interrogation skills. Combining speech recognition, machine translation, and speech generation technologies, the MAVT accepts an interrogator's spoken English question and translates it into spoken Spanish. The spoken Spanish response of the potential informant can then be translated into spoken English. Potential military and civilian applications for automatic spoken language translation technology are discussed in this paper.

  15. Machine translation

    Energy Technology Data Exchange (ETDEWEB)

    Nagao, M.

    1982-04-01

    Each language has its own structure. In translating one language into another one, language attributes and grammatical interpretation must be defined in an unambiguous form. In order to parse a sentence, it is necessary to recognize its structure. A so-called context-free grammar can help in this respect for machine translation and machine-aided translation. Problems to be solved in studying machine translation are taken up in the paper, which discusses subjects for semantics and for syntactic analysis and translation software. 14 references.

  16. Oligodeoxynucleotide decoy therapy blocks type 1 procollagen transcription and the prolyl hydroxylase beta subunit translation.

    Science.gov (United States)

    Lok, Chun-Nam; Ehrlich, H Paul; White, Sheryl L; Buttolph, Thomas R; Cutroneo, Kenneth R; Chiu, Jen-Fu

    2008-03-01

    Persistent transforming growth factor-beta1 (TGF-beta1) exposure to lungs increases type 1 collagen synthesis and deposition resulting in excess fibrosis which leads to morbidity and possibly death. We now report using human embryonic lung fibroblasts in the presence of TGF-beta1, a novel double-stranded (ds) DNA decoy with phosphorothioate (PT) linkages, containing the TGF-beta cis-element found in the distal promoter region of the COL1A1 gene which silences COL1A1 gene expression. In a cell-free protein translation system, we have previously reported that collagen synthesis was inhibited by disulfide isomerase, the prolyl-4-hydroxylase (P-4-H) beta subunit. By comparative proteomics dsdecoy therapy increased the levels of disulfide isomerase, the P-4-H beta subunit. These findings taken together support the notion that the dsdecoy inhibits type 1 collagen synthesis at both the transcriptional and translational levels.

  17. Cardiopulmonary bypass in the newborn: effects of circulatory cell-free hemoglobin and hyperoxia evaluated in a novel rat pup model.

    Science.gov (United States)

    Jungner, Åsa; Vallius, Suvi; Bruschettini, Matteo; Romantsik, Olga; Gram, Magnus; Ley, David

    2017-10-04

    Infants with congenital heart defects (CHD) are at risk for white matter brain injury. This novel rat pup model characterizes the systemic effects of intravasal cell-free hemoglobin and hyperoxia, hypothesizing that immature endogenous scavenging systems relate to increased vulnerability to conditions present during cardiopulmonary bypass (CPB). Plasma pharmacokinetics of cell-free human hemoglobin (Hb) was determined after intraperitoneal (i.p.) administration in postnatal day 6 (P6) rat pups. Cell-free hemoglobin degradation, scavenger- and oxidative stress responses in altered oxygen environments were evaluated in P6 rat pups exposed to i.p. cell-free Hb or vehicle and subjected to hyperoxia or normoxia for 24 h. Plasma and liver were analyzed for free heme, haptoglobin, hemopexin, heme-oxygenase 1, and 8-OHdG at 3-120 h post-injection. Baseline scavenging properties were evaluated in P0-P12 rat pups. Cell-free Hb displayed peak plasma concentrations of 3.6 ± 0.5 mg/mL (mean ± SD) at 3 h post-administration. Animals exposed to cell-free Hb demonstrated a 30-fold increase in plasma haptoglobin and a decrease in plasma hemopexin to 1/6 of concentrations observed in pups exposed to vehicle. Exposure to cell-free Hb and hyperoxia mediated increased plasma concentrations of free heme (72.7 ± 19.5 μM, mean ± SD) compared to exposure to cell-free Hb and normoxia (49.3 ± 13.1 μM) at 3 h, and an elevated hepatic mRNA expression of heme-oxygenase 1. mRNA expression of haptoglobin and hemopexin was increased in animals exposed to hemoglobin with a mitigated response in pups exposed to hemoglobin and hyperoxia. Animals exposed to hyperoxia displayed an increase in hepatic transcription of scavenger proteins at 24 h. Combined exposure to cell-free Hb and hyperoxia mediated an increased DNA-oxidation at 6 h, whereas all insults conveyed a decrease in DNA-oxidation at 120 h. In this study, we present a novel rat pup model with scavenging

  18. Study on bioactivity of cell-free filtrates from dairy propionibacteria.

    Science.gov (United States)

    Filippone, Alfonso; Sinigaglia, Milena; Altieri, Clelia

    2014-12-01

    In this paper, the bioactivity of cell-free extracts obtained by dairy propionibacteria strains was investigated. Probiotic bifidobacteria and lactobacilli were used as microbial targets. The extracellular filtrates were added as ingredient (1% v/v) into the growth medium; the effect of cell-free filtrates was evaluated through viable count of microbial targets on appropriate media, monitoring the response of target microorganisms both in growth and death phase. The Gompertz equation was used to model the experimental data. Kinetics and time parameters were estimated in order to quantify the effectiveness of cell-free filtrates effect. To emphasize the results about the bioactivity of cell-free extract, supporting a complete picture of response, a new approach was developed: Probiotic Stability Time was calculated. This temporal parameter, defined as the time over that the cell load preserve a living value upper than 10(7) cfu ml(-1), was very useful to evaluate the probiotic capability and effectiveness. A stimulant effect was registered on growth and a positive one was recordered on survival of both bifidobacteria and lactobacilli strains, and the results obtained suggest that a prebiotic activity by dairy propionibacteria cell-free filtrates could be supposed. The cell-free filtrate obtained from Propionibacterium freudenreichii subsp. shermanii was the most effective, in our experimental conditions. Although bifidobacteria were the most sensitive to the effect of cell-free filtrates, lactobacilli have been showed a similar probiotic stability time, showing a high sensitivity to the filtrates. This paper is the first report of a positive bioactivity by propionibacteria cell-free filtrates on lactobacilli. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Dynamic Modeling of Cell-Free Biochemical Networks Using Effective Kinetic Models

    Science.gov (United States)

    2015-03-03

    1984, 26, 203–216. 3. Steinmeyer, D.; Shuler, M. Structured model for Saccharomyces cerevisiae . Chem. Eng. Sci. 1989, 44, 2017–2030. 4. Wu, P.; Ray...consider cell growth . Thus, cell-free operation holds several significant advantages for model development, identification The views, opinions and/or...longer have to consider cell growth . Thus, cell-free operation holds several significant advantages for model development, identification and validation

  20. Evaluating Arabic to English Machine Translation

    OpenAIRE

    Laith S. Hadla; Taghreed M. Hailat; Mohammed N. Al-Kabi

    2014-01-01

    Online text machine translation systems are widely used throughout the world freely. Most of these systems use statistical machine translation (SMT) that is based on a corpus full with translation examples to learn from them how to translate correctly. Online text machine translation systems differ widely in their effectiveness, and therefore we have to fairly evaluate their effectiveness. Generally the manual (human) evaluation of machine translation (MT) systems is better than the automatic...

  1. Translational recoding as a feedback controller: systems approaches reveal polyamine-specific effects on the antizyme ribosomal frameshift

    Science.gov (United States)

    Rato, Claudia; Amirova, Svetlana R.; Bates, Declan G.; Stansfield, Ian; Wallace, Heather M.

    2011-01-01

    The antizyme protein, Oaz1, regulates synthesis of the polyamines putrescine, spermidine and spermine by controlling stability of the polyamine biosynthetic enzyme, ornithine decarboxylase. Antizyme mRNA translation depends upon a polyamine-stimulated +1 ribosomal frameshift, forming a complex negative feedback system in which the translational frameshifting event may be viewed in engineering terms as a feedback controller for intracellular polyamine concentrations. In this article, we present the first systems level study of the characteristics of this feedback controller, using an integrated experimental and modeling approach. Quantitative analysis of mutant yeast strains in which polyamine synthesis and interconversion were blocked revealed marked variations in frameshift responses to the different polyamines. Putrescine and spermine, but not spermidine, showed evidence of co-operative stimulation of frameshifting and the existence of multiple ribosome binding sites. Combinatorial polyamine treatments showed polyamines compete for binding to common ribosome sites. Using concepts from enzyme kinetics and control engineering, a mathematical model of the translational controller was developed to describe these complex ribosomal responses to combinatorial polyamine effects. Each one of a range of model predictions was successfully validated against experimental frameshift frequencies measured in S-adenosylmethionine-decarboxylase and antizyme mutants, as well as in the wild-type genetic background. PMID:21303766

  2. Progress in Documentation: Machine Translation and Machine-Aided Translation.

    Science.gov (United States)

    Hutchins, W. J.

    1978-01-01

    Discusses the prospects for fully automatic machine translation of good quality. Sections include history and background, operational and experimental machine translation systems of recent years, descriptions of interactive systems and machine-assisted translation, and a general survey of present problems and future possibilities. (VT)

  3. Vascularisation to improve translational potential of tissue engineering systems for cardiac repair.

    Science.gov (United States)

    Dilley, Rodney J; Morrison, Wayne A

    2014-11-01

    Cardiac tissue engineering is developing as an alternative approach to heart transplantation for treating heart failure. Shortage of organ donors and complications arising after orthotopic transplant remain major challenges to the modern field of heart transplantation. Engineering functional myocardium de novo requires an abundant source of cardiomyocytes, a biocompatible scaffold material and a functional vasculature to sustain the high metabolism of the construct. Progress has been made on several fronts, with cardiac cell biology, stem cells and biomaterials research particularly promising for cardiac tissue engineering, however currently employed strategies for vascularisation have lagged behind and limit the volume of tissue formed. Over ten years we have developed an in vivo tissue engineering model to construct vascularised tissue from various cell and tissue sources, including cardiac tissue. In this article we review the progress made with this approach and others, together with their potential to support a volume of engineered tissue for cardiac tissue engineering where contractile mass impacts directly on functional outcomes in translation to the clinic. It is clear that a scaled-up cardiac tissue engineering solution required for clinical treatment of heart failure will include a robust vascular supply for successful translation. This article is part of a directed issue entitled: Regenerative Medicine: the challenge of translation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Translating Inclusion

    DEFF Research Database (Denmark)

    Fallov, Mia Arp; Birk, Rasmus

    2018-01-01

    The purpose of this paper is to explore how practices of translation shape particular paths of inclusion for people living in marginalized residential areas in Denmark. Inclusion, we argue, is not an end-state, but rather something which must be constantly performed. Active citizenship, today......, is not merely a question of participation, but of learning to become active in all spheres of life. The paper draws on empirical examples from a multi-sited field work in 6 different sites of local community work in Denmark, to demonstrate how different dimensions of translation are involved in shaping active...... citizenship. We propose the following different dimensions of translation: translating authority, translating language, translating social problems. The paper takes its theoretical point of departure from assemblage urbanism, arguing that cities are heterogeneous assemblages of socio-material interactions...

  5. Translation project adaptation for MT-enhanced computer assisted translation

    OpenAIRE

    Cettolo, Mauro; Bertoldi, Nicola; Federico, Marcello; Schwenk, Holger; Barrault, loïc; Servan, Christophe

    2014-01-01

    International audience; The effective integration of MT technology into computer-assisted translation tools is a challenging topic both for academic research and the translation industry. Particularly, professional translators feel crucial the ability of MT systems to adapt to their feedback. In this paper, we propose an adaptation scheme to tune a statistical MT system to a translation project using small amounts of post-edited texts, like those generated by a single user in even just one da...

  6. On Yao's method of translation

    NARCIS (Netherlands)

    Liu, X; Hoede, C.

    2002-01-01

    Machine Translation, i.e., translating one kind of natural language to another kind of natural language by using a computer system, is a very important research branch in Artificial Intelligence. Yao developed a method of translation that he called ``Lexical-Semantic Driven". In his system he

  7. Lessons learned in applying the International Society for Pharmacoeconomics and Outcomes Research methodology to translating Canadian Emergency Department Information System Presenting Complaints List into German.

    Science.gov (United States)

    Brammen, Dominik; Greiner, Felix; Dormann, Harald; Mach, Carsten; Wrede, Christian; Ballaschk, Anne; Stewart, Declan; Walker, Steven; Oesterling, Christine; Kulla, Martin

    2017-03-02

    The patient's presenting complaint guides diagnosis and treatment in the emergency department, but there is no classification system available in German. The Canadian Emergency Department Information System (CEDIS) Presenting Complaint List (PCL) is available only in English and French. As translation risks the altering of meaning, the International Society for Pharmacoeconomics and Outcomes Research (ISPOR) has set guidelines to ensure translational accuracy. The aim of this paper is to describe our experiences of using the ISPOR guidelines to translate the CEDIS PCL into German. The CEDIS PCL (version 3.0) was forward-translated and back-translated in accordance with the ISPOR guidelines using bilingual clinicians/translators and an occupationally mixed evaluation group that completed a self-developed questionnaire. The CEDIS PCL was forward-translated (four emergency physicians) and back-translated (three mixed translators). Back-translation uncovered eight PCL items requiring amendment. In total, 156 comments were received from 32 evaluators, six of which resulted in amendments. The ISPOR guidelines facilitated adaptation of a PCL into German, but the process required time, language skills and clinical knowledge. The current methodology may be applicable to translating the CEDIS PCL into other languages, with the aim of developing a harmonized, multilingual PCL.This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc-nd/4.0/.

  8. Precision calibration method for binocular vision measurement systems based on arbitrary translations and 3D-connection information

    Science.gov (United States)

    Yang, Jinghao; Jia, Zhenyuan; Liu, Wei; Fan, Chaonan; Xu, Pengtao; Wang, Fuji; Liu, Yang

    2016-10-01

    Binocular vision systems play an important role in computer vision, and high-precision system calibration is a necessary and indispensable process. In this paper, an improved calibration method for binocular stereo vision measurement systems based on arbitrary translations and 3D-connection information is proposed. First, a new method for calibrating the intrinsic parameters of binocular vision system based on two translations with an arbitrary angle difference is presented, which reduces the effect of the deviation of the motion actuator on calibration accuracy. This method is simpler and more accurate than existing active-vision calibration methods and can provide a better initial value for the determination of extrinsic parameters. Second, a 3D-connection calibration and optimization method is developed that links the information of the calibration target in different positions, further improving the accuracy of the system calibration. Calibration experiments show that the calibration error can be reduced to 0.09%, outperforming traditional methods for the experiments of this study.

  9. [Portuguese-language translation and cross-cultural adaptation of the Fatigue domain of Patient-Reported-Outcomes Measurement Information System (PROMIS)].

    Science.gov (United States)

    Alves, Flávio Sérgio Marques; Pinto, Rogério de Melo Costa; Mendonça, Tânia Maria Silva; Silva, Carlos Henrique Martins da

    2014-05-01

    The items bank of the Fatigue domain is part of an American system developed for evaluation of results reported by patients, called Patient-Reported-Outcomes Measurement Information System (PROMIS). This study aimed to translate and cross-culturally adapt this item bank for the Brazilian population, as a promising new tool for evaluating health-related quality of life. The items in this bank were translated using rigorous translation and back-translation protocols. The translated version was pre-tested in twenty Brazilians with a brief cognitive and retrospective interview in order to test the items' conceptual, cultural, and semantic equivalences. In the translation and back-translation process, only three of the 82 items had to be reworded due to the culturally inadequate content. In the pretest, only four items needed to be reworded, but without conceptual and semantic alterations. The results showed that the translated version of this item bank is conceptually, culturally, and semantically equivalent to the original version.

  10. Health related quality of life measure in systemic pediatric rheumatic diseases and its translation to different languages: an international collaboration.

    Science.gov (United States)

    Moorthy, Lakshmi Nandini; Roy, Elizabeth; Kurra, Vamsi; Peterson, Margaret G E; Hassett, Afton L; Lehman, Thomas J A; Scott, Christiaan; El-Ghoneimy, Dalia; Saad, Shereen; El Feky, Reem; Al-Mayouf, Sulaiman; Dolezalova, Pavla; Malcova, Hana; Herlin, Troels; Nielsen, Susan; Wulffraat, Nico; van Royen, Annet; Marks, Stephen D; Belot, Alexandre; Brunner, Jurgen; Huemer, Christian; Foeldvari, Ivan; Horneff, Gerd; Saurenman, Traudel; Schroeder, Silke; Pratsidou-Gertsi, Polyxeni; Trachana, Maria; Uziel, Yosef; Aggarwal, Amita; Constantin, Tamas; Cimaz, Rolando; Giani, Theresa; Cantarini, Luca; Falcini, Fernanda; Manzoni, Silvia Magni; Ravelli, Angelo; Rigante, Donato; Zulian, Fracnceso; Miyamae, Takako; Yokota, Shumpei; Sato, Juliana; Magalhaes, Claudia S; Len, Claudio A; Appenzeller, Simone; Knupp, Sheila Oliveira; Rodrigues, Marta Cristine; Sztajnbok, Flavio; de Almeida, Rozana Gasparello; de Jesus, Adriana Almeida; de Arruda Campos, Lucia Maria; Silva, Clovis; Lazar, Calin; Susic, Gordana; Avcin, Tadej; Cuttica, Ruben; Burgos-Vargas, Ruben; Faugier, Enrique; Anton, Jordi; Modesto, Consuelo; Vazquez, Liza; Barillas, Lilliana; Barinstein, Laura; Sterba, Gary; Maldonado, Irama; Ozen, Seza; Kasapcopur, Ozgur; Demirkaya, Erkan; Benseler, Susa

    2014-01-01

    Rheumatic diseases in children are associated with significant morbidity and poor health-related quality of life (HRQOL). There is no health-related quality of life (HRQOL) scale available specifically for children with less common rheumatic diseases. These diseases share several features with systemic lupus erythematosus (SLE) such as their chronic episodic nature, multi-systemic involvement, and the need for immunosuppressive medications. HRQOL scale developed for pediatric SLE will likely be applicable to children with systemic inflammatory diseases. We adapted Simple Measure of Impact of Lupus Erythematosus in Youngsters (SMILEY©) to Simple Measure of Impact of Illness in Youngsters (SMILY©-Illness) and had it reviewed by pediatric rheumatologists for its appropriateness and cultural suitability. We tested SMILY©-Illness in patients with inflammatory rheumatic diseases and then translated it into 28 languages. Nineteen children (79% female, n=15) and 17 parents participated. The mean age was 12±4 years, with median disease duration of 21 months (1-172 months). We translated SMILY©-Illness into the following 28 languages: Danish, Dutch, French (France), English (UK), German (Germany), German (Austria), German (Switzerland), Hebrew, Italian, Portuguese (Brazil), Slovene, Spanish (USA and Puerto Rico), Spanish (Spain), Spanish (Argentina), Spanish (Mexico), Spanish (Venezuela), Turkish, Afrikaans, Arabic (Saudi Arabia), Arabic (Egypt), Czech, Greek, Hindi, Hungarian, Japanese, Romanian, Serbian and Xhosa. SMILY©-Illness is a brief, easy to administer and score HRQOL scale for children with systemic rheumatic diseases. It is suitable for use across different age groups and literacy levels. SMILY©-Illness with its available translations may be used as useful adjuncts to clinical practice and research.

  11. Watch Out for the “Living Dead”: Cell-Free Enzymes and Their Fate

    Directory of Open Access Journals (Sweden)

    Federico Baltar

    2018-01-01

    Full Text Available Microbes are the engines driving biogeochemical cycles. Microbial extracellular enzymatic activities (EEAs are the “gatekeepers” of the carbon cycle. The total EEA is the sum of cell-bound (i.e., cell-attached, and dissolved (i.e., cell-free enzyme activities. Cell-free enzymes make up a substantial proportion (up to 100% of the total marine EEA. Although we are learning more about how microbial diversity and function (including total EEA will be affected by environmental changes, little is known about what factors control the importance of the abundant cell-free enzymes. Since cell-attached EEAs are linked to the cell, their fate will likely be linked to the factors controlling the cell’s fate. In contrast, cell-free enzymes belong to a kind of “living dead” realm because they are not attached to a living cell but still are able to perform their function away from the cell; and as such, the factors controlling their activity and fate might differ from those affecting cell-attached enzymes. This article aims to place cell-free EEA into the wider context of hydrolysis of organic matter, deal with recent studies assessing what controls the production, activity and lifetime of cell-free EEA, and what their fate might be in response to environmental stressors. This perspective article advocates the need to go “beyond the living things,” studying the response of cells/organisms to different stressors, but also to study cell-free enzymes, in order to fully constrain the future and evolution of marine biogeochemical cycles.

  12. Evaluation du systeme de traduction automatique SYSTRAN anglais-Francais, version 1978, de la Commission des Communautes Europeennes (Evaluation of the English-French SYSTRAN Machine Translation System, 19 version, of the Commission of European Communities).

    Science.gov (United States)

    Van Slype, Georges

    1979-01-01

    Describes the French-English version of the SYSTRAN machine translation system, used by the Commission of European Communities, and an evaluation study which examined the quality, cost, and weaknesses of the system. The study concluded that this type of system is useful for "pretranslation" and "rough" translation only. (AM)

  13. Synthetic Biology for Cell-Free Biosynthesis: Fundamentals of Designing Novel In Vitro Multi-Enzyme Reaction Networks.

    Science.gov (United States)

    Morgado, Gaspar; Gerngross, Daniel; Roberts, Tania M; Panke, Sven

    2018-01-01

    Cell-free biosynthesis in the form of in vitro multi-enzyme reaction networks or enzyme cascade reactions emerges as a promising tool to carry out complex catalysis in one-step, one-vessel settings. It combines the advantages of well-established in vitro biocatalysis with the power of multi-step in vivo pathways. Such cascades have been successfully applied to the synthesis of fine and bulk chemicals, monomers and complex polymers of chemical importance, and energy molecules from renewable resources as well as electricity. The scale of these initial attempts remains small, suggesting that more robust control of such systems and more efficient optimization are currently major bottlenecks. To this end, the very nature of enzyme cascade reactions as multi-membered systems requires novel approaches for implementation and optimization, some of which can be obtained from in vivo disciplines (such as pathway refactoring and DNA assembly), and some of which can be built on the unique, cell-free properties of cascade reactions (such as easy analytical access to all system intermediates to facilitate modeling).

  14. Assessing the Quality of MT Systems for Hindi to English Translation

    Science.gov (United States)

    Kalyani, Aditi; Kumud, Hemant; Pal Singh, Shashi; Kumar, Ajai

    2014-03-01

    Evaluation plays a vital role in checking the quality of MT output. It is done either manually or automatically. Manual evaluation is very time consuming and subjective, hence use of automatic metrics is done most of the times. This paper evaluates the translation quality of different MT Engines for Hindi-English (Hindi data is provided as input and English is obtained as output) using various automatic metrics like BLEU, METEOR etc. Further the comparison automatic evaluation results with Human ranking have also been given.

  15. Translation of Hecker's 1922 "the occipital-atlanto-axial ligament system": A study in comparative anatomy.

    Science.gov (United States)

    Oakes, Peter C; Sardi, Juan Pablo; Iwanaga, Joe; Topale, Nitsa; Oskouian, Rod J; Tubbs, R Shane

    2017-04-01

    In 1922, Paul Hecker, a French physician and Head of Anatomy at the Medical College of Strasbourg, published a sentinel thesis on the ligaments of the craniocervical junction based on a study of comparative anatomy. Unfortunately, this dissertation has been lost to history and until now, was unavailable in the English language. Herein, we present a translation of Hecker's work with an update in its nomenclature, which with modern imaging capabilities of the craniocervical junction is germane and timely. Clin. Anat. 30:322-329, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  16. tmRNA-mediated trans-translation as the major ribosome rescue system in a bacterial cell

    Directory of Open Access Journals (Sweden)

    Hyouta eHimeno

    2014-04-01

    Full Text Available tmRNA (transfer messenger RNA; also known as 10Sa RNA or SsrA RNA is a small RNA molecule that is conserved among bacteria. It has structural and functional similarities to tRNA: it has an upper half of the tRNA-like structure, its 5’ end is processed by RNase P, it has typical tRNA-specific base modifications, it is aminoacylated with alanine, it binds to EF-Tu after aminoacylation and it enters the ribosome with EF-Tu and GTP. However, tmRNA lacks an anticodon, and instead it has a coding sequence for a short peptide called tag-peptide. An elaborate interplay of actions of tmRNA as both tRNA and mRNA with the help of a tmRNA-binding protein, SmpB, facilitates trans-translation, which produces a single polypeptide from two mRNA molecules. Initially alanyl-tmRNA in complex with EF-Tu and SmpB enters the vacant A-site of the stalled ribosome like aminoacyl-tRNA but without a codon-anticodon interaction, and subsequently truncated mRNA is replaced with the tag-encoding region of tmRNA. During these processes, not only tmRNA but also SmpB structurally and functionally mimics both tRNA and mRNA. Thus trans-translation rescues the stalled ribosome, thereby allowing recycling of the ribosome. Since the tag-peptide serves as a target of AAA+ proteases, the trans-translation products are preferentially degraded so that they do not accumulate in the cell. Although alternative rescue systems have recently been revealed, trans-translation is the only system that universally exists in bacteria. Furthermore, it is unique in that it employs a small RNA and that it prevents accumulation of nonfunctional proteins from truncated mRNA in the cell. It might play the major role in rescuing the stalled translation in the bacterial cell.

  17. BioBankWarden: A web-based system to support translational cancer research by managing clinical and biomaterial data.

    Science.gov (United States)

    Ferretti, Yuri; Miyoshi, Newton Shydeo Brandão; Silva, Wilson Araújo; Felipe, Joaquim Cezar

    2017-05-01

    Researchers of translational medicine face numerous challenges in attempting to bring research results to the bedside. This field of research covers a wide range of resources, including blood and tissue samples, which are processed for isolation of RNA and DNA to study cancer omics data (genomics, proteomics and metabolomics). Clinical information about patients׳ habits, family history, physical examinations, remissions, etc., is also important to underpin studies aimed at identifying patterns that lead to the development of cancer and to its successful treatment. Development of a web-based computer system-BioBankWarden-to manage, consolidate and integrate these diversified data, enabling cancer research groups to retrieve and analyze clinical and biomolecular data within an integrative environment. The system has a three-tier architecture comprising database, logic and user-interface layers. The system׳s integrated database and user-friendly interface allow for the control of patient records, biomaterial storage, research groups, research projects, users and biomaterial exchange. BioBankWarden can be used to store and retrieve specific information from different clinical fields linked to biomaterials collected from patients, providing the functionalities required to support translational research in the field of cancer. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Translation Competence

    DEFF Research Database (Denmark)

    Vandepitte, Sonia; Mousten, Birthe; Maylath, Bruce

    2014-01-01

    at different stages in the translation processes in the Trans-Atlantic and Pacific Project, a long-term cross-cultural virtual team. It describes the forms of collaborative learning practised in this multilateral international project in technical communication and translator training programmes and explores...

  19. Unique and concise system translation matrices for evaluating optical aberration variations.

    Science.gov (United States)

    Chen, Chaohsien

    2017-08-01

    New unique and concise translation matrices are derived for evaluating the aberration variations of conceptual and real lenses when the paraxial marginal and chief ray paths are arbitrarily changed. They are helpful in investigating the general behaviors of lenses and optimizing the balanced aberrations of lens components in prime and zoom lenses. These new matrices, with a dimension of 9×9 for monochromatic aberrations and a dimension of 4×4 for chromatic aberrations, are derived based on our earlier algorithms of which four cases with distinct translation factors and matrices are required according to the relationships of the original and new positions of the object and pupil; otherwise, division-by-zero errors or insufficient numerical accuracy will be encountered. As a comparison, the new matrices have several advantages. First, by introducing four meaningful equivalent optical invariants, multiplying the old matrices, and simplifying the new matrices, they have concise expressions to significantly reduce the calculation time. Second, they are unique and always accurate to apply for all kinds of object and pupil positions without suffering any mathematical problems, i.e., four separated algorithms are no longer necessary. Third, due to the unique property, the component contributions of original aberrations to new aberrations can be directly evaluated and analyzed.

  20. Detection of Infertility-related Neutralizing Antibodies with a Cell-free Microfluidic Method

    Science.gov (United States)

    Eyer, Klaus; Root, Katharina; Verboket, Pascal E.; Dittrich, Petra S.

    2015-11-01

    The unwanted emergence of neutralizing antibodies (nAbs) against an endogenous or a therapeutic protein can result in deficiency diseases or therapy failure. Here, we developed a cell-free microfluidic method for the sensitive detection and quantification of nAbs in human serum that are associated with infertility. We used cell-derived vesicles containing the luteinizing hormone (LH)/choriogonadotropin receptor (LHHCGR) to detect nAbs against LH. The method exploits the entire cellular signal amplification mechanism, and facilitates the detection of as little as 0.44 nM of LH-nAb (Kd 1.5 nM) in human serum matrix within only 15 minutes. In addition, dose-response curves can be generated in less than 2 hours to evaluate the nAB concentration and dissociation constant. The developed system is devoid of problems associated with cell-based assays and we believe that this simple effect-directed analysis can be used in clinical environments, and is adaptable to other hormones or cytokines and their respective nAbs.

  1. Cholesterol: A modulator of the phagocyte NADPH oxidase activity - A cell-free study

    Directory of Open Access Journals (Sweden)

    Rawand Masoud

    2014-01-01

    Full Text Available The NADPH oxidase Nox2, a multi-subunit enzyme complex comprising membrane and cytosolic proteins, catalyzes a very intense production of superoxide ions O2•−, which are transformed into other reactive oxygen species (ROS. In vitro, it has to be activated by addition of amphiphiles like arachidonic acid (AA. It has been shown that the membrane part of phagocyte NADPH oxidase is present in lipid rafts rich in cholesterol. Cholesterol plays a significant role in the development of cardio-vascular diseases that are always accompanied by oxidative stress. Our aim was to investigate the influence of cholesterol on the activation process of NADPH oxidase. Our results clearly show that, in a cell-free system, cholesterol is not an efficient activator of NADPH oxidase like arachidonic acid (AA, however it triggers a basal low superoxide production at concentrations similar to what found in neutrophile. A higher concentration, if present during the assembly process of the enzyme, has an inhibitory role on the production of O2•−. Added cholesterol acts on both cytosolic and membrane components, leading to imperfect assembly and decreasing the affinity of cytosolic subunits to the membrane ones. Added to the cytosolic proteins, it retains their conformations but still allows some conformational change induced by AA addition, indispensable to activation of NADPH oxidase.

  2. Biological Synthesis of Silver Nanoparticles by Cell-Free Extract of Spirulina platensis

    Directory of Open Access Journals (Sweden)

    Gaurav Sharma

    2015-01-01

    Full Text Available The present study explores biological synthesis of silver nanoparticles (AgNPs using the cell-free extract of Spirulina platensis. Biosynthesised AgNPs were characterised by UV-Vis spectroscopy, SEM, TEM, and FTIR analysis and finally evaluated for antibacterial activity. Extracellular synthesis using aqueous extract of S. platensis showed the formation of well scattered, highly stable, spherical AgNPs with an average size of 30–50 nm. The size and morphology of the nanoparticles were confirmed by SEM and TEM analysis. FTIR and UV-Vis spectra showed that biomolecules, proteins and peptides, are mainly responsible for the formation and stabilisation of AgNPs. Furthermore, the synthesised nanoparticles exhibited high antibacterial activity against pathogenic Gram-negative, that is, Escherichia coli, MTCC-9721; Proteus vulgaris, MTCC-7299; Klebsiella pneumoniae, MTCC-9751, and Gram-positive, that is, Staphylococcus aureus, MTCC-9542; S. epidermidis, MTCC-2639; Bacillus cereus, MTCC-9017, bacteria. The AgNPs had shown maximum zone of inhibition (ZOI that is 31.3±1.11 in P. vulgaris. Use of such a microalgal system provides a simple, cost-effective alternative template for the biosynthesis of nanomaterials of silver in a large scale that could be of great use in biomedical applications.

  3. A 5000-hour test of a grid-translation beam-deflection system for a 5-cm diameter Kaufman thruster

    Science.gov (United States)

    Lathem, W. C.

    1973-01-01

    A grid-translation type beam deflection system was tested on a 5-cm diameter mercury ion thruster for 5000 hours at a thrust level of about 0.36 mlb. During the first 2000 hours the beam was vectored 10 degrees in one direction. No erosion damage attributable to beam deflection was detected. Results indicate a possible lifetime of 15,000 to 20,000 hours. An optimized neutralizer position was used which eliminated the sputter erosion groove observed on the SERT 2 thrusters.

  4. Maternal urinary cell free fetal DNA in relation to gestational age

    Directory of Open Access Journals (Sweden)

    Mona Mohamed Shaban

    2016-12-01

    Full Text Available Objectives: To evaluate the presence of cell-free fetal DNA in the maternal urine in relation to gestational age as a potential source for non-invasive prenatal diagnosis. Material and methods: One hundred and sixty normal pregnant women were included in the study; 80 women pregnant with male fetuses and 80 women pregnant with female fetuses. Maternal urine of all patients was examined at 12, 16 and 20 wks’ gestation for the SRY gene (sex-determining region Y as a cffDNA (cell free fetal DNA marker and Ribonuclease P RNA component H1 (RPPH1 as a total cfDNA (cell free DNA marker using a quantitative real-time PCR assay. Results: SRY gene was detected in maternal urine of those pregnant with male fetuses starting from 16 weeks in 25% (20/80 of cases only and in 80% of cases (64/80 at 20 weeks, but it was not detected at 12 weeks. All women female fetuses were negative for SRY gene. Conclusions: Cell free fetal DNA in maternal urine was not detected in early gestational age using SRY gene alone despite the use of extraction kit specific for extraction of Free-circulating nucleic acids and highly sensitive reported PCR technique. Further studies should be done to evaluate whether cell free fetal DNA in maternal urine can be detected after reaching a certain threshold in blood.

  5. Rapid Detection of Cell-Free Mycobacterium tuberculosis DNA in Tuberculous Pleural Effusion.

    Science.gov (United States)

    Che, Nanying; Yang, Xinting; Liu, Zichen; Li, Kun; Chen, Xiaoyou

    2017-05-01

    Tuberculous pleurisy is one of the most common types of extrapulmonary tuberculosis, but its diagnosis remains difficult. In this study, we report for the first time on the detection of cell-free Mycobacterium tuberculosis DNA in pleural effusion and an evaluation of a newly developed molecular assay for the detection of cell-free Mycobacterium tuberculosis DNA. A total of 78 patients with pleural effusion, 60 patients with tuberculous pleurisy, and 18 patients with alternative diseases were included in this study. Mycobacterial culture, the Xpert MTB/RIF assay, the adenosine deaminase assay, the T-SPOT.TB assay, and the cell-free Mycobacterium tuberculosis DNA assay were performed on all the pleural effusion samples. The cell-free Mycobacterium tuberculosis DNA assay and adenosine deaminase assay showed significantly higher sensitivities of 75.0% and 68.3%, respectively, than mycobacterial culture and the Xpert MTB/RIF assay, which had sensitivities of 26.7% and 20.0%, respectively (P Mycobacterium tuberculosis DNA assay detected as few as 1.25 copies of IS6110 per ml of pleural effusion and showed good accordance of the results between repeated tests (r = 0.978, P = 2.84 × 10-10). These data suggest that the cell-free Mycobacterium tuberculosis DNA assay is a rapid and accurate molecular test which provides direct evidence of Mycobacterium tuberculosis etiology. Copyright © 2017 American Society for Microbiology.

  6. Cerebellar Exposure to Cell-Free Hemoglobin Following Preterm Intraventricular Hemorrhage: Causal in Cerebellar Damage?

    Science.gov (United States)

    Agyemang, Alex Adusei; Sveinsdóttir, Kristbjörg; Vallius, Suvi; Sveinsdóttir, Snjolaug; Bruschettini, Matteo; Romantsik, Olga; Hellström, Ann; Smith, Lois E H; Ohlsson, Lennart; Holmqvist, Bo; Gram, Magnus; Ley, David

    2017-06-10

    Decreased cerebellar volume is associated with intraventricular hemorrhage (IVH) in very preterm infants and may be a principal component in neurodevelopmental impairment. Cerebellar deposition of blood products from the subarachnoid space has been suggested as a causal mechanism in cerebellar underdevelopment following IVH. Using the preterm rabbit pup IVH model, we evaluated the effects of IVH induced at E29 (3 days prior to term) on cerebellar development at term-equivalent postnatal day 0 (P0), term-equivalent postnatal day 2 (P2), and term-equivalent postnatal day 5 (P5). Furthermore, the presence of cell-free hemoglobin (Hb) in cerebellar tissue was characterized, and cell-free Hb was evaluated as a causal factor in the development of cerebellar damage following preterm IVH. IVH was associated with a decreased proliferative (Ki67-positive) portion of the external granular layer (EGL), delayed Purkinje cell maturation, and activated microglia in the cerebellar white matter. In pups with IVH, immunolabeling of the cerebellum at P0 demonstrated a widespread presence of cell-free Hb, primarily distributed in the white matter and the molecular layer. Intraventricular injection of the Hb scavenger haptoglobin (Hp) resulted in a corresponding distribution of immunolabeled Hp in the cerebellum and a partial reversal of the damaging effects observed following IVH. The results suggest that cell-free Hb is causally involved in cerebellar damage following IVH and that blocking cell-free Hb may have protective effects.

  7. High-throughput, cell-free, liposome-based approach for assessing in vitro activity of lipid kinases.

    Science.gov (United States)

    Demian, Douglas J; Clugston, Susan L; Foster, Meta M; Rameh, Lucia; Sarkes, Deborah; Townson, Sharon A; Yang, Lily; Zhang, Melvin; Charlton, Maura E

    2009-08-01

    Lipid kinases are central players in lipid signaling pathways involved in inflammation, tumorigenesis, and metabolic syndrome. A number of these kinase targets have proven difficult to investigate in higher throughput cell-free assay systems. This challenge is partially due to specific substrate interaction requirements for several of the lipid kinase family members and the resulting incompatibility of these substrates with most established, homogeneous assay formats. Traditional, cell-free in vitro investigational methods for members of the lipid kinase family typically involve substrate incorporation of [gamma-32P] and resolution of signal by thin-layer chromatography (TLC) and autoradiograph densitometry. This approach, although highly sensitive, does not lend itself to high-throughput testing of large numbers of small molecules (100 s to 1 MM+). The authors present the development and implementation of a fully synthetic, liposome-based assay for assessing in vitro activity of phosphatidylinositol-5-phosphate-4-kinase isoforms (PIP4KIIbeta and alpha) in 2 commonly used homogeneous technologies. They have validated these assays through compound testing in both traditional TLC and radioactive filterplate approaches as well as binding validation using isothermic calorimetry. A directed library representing known kinase pharmacophores was screened against type IIbeta phosphatidylinositol-phosphate kinase (PIPK) to identify small-molecule inhibitors. This assay system can be applied to other types and isoforms of PIPKs as well as a variety of other lipid kinase targets.

  8. Typologically robust statistical machine translation : Understanding and exploiting differences and similarities between languages in machine translation

    NARCIS (Netherlands)

    Daiber, J.

    2018-01-01

    Machine translation systems often incorporate modeling assumptions motivated by properties of the language pairs they initially target. When such systems are applied to language families with considerably different properties, translation quality can deteriorate. Phrase-based machine translation

  9. Translation-Memory (TM) Research

    DEFF Research Database (Denmark)

    Schjoldager, Anne Gram; Christensen, Tina Paulsen

    2010-01-01

      It is no exaggeration to say that the advent of translation-memory (TM) systems in the translation profession has led to drastic changes in translators' processes and workflow, and yet, though many professional translators nowadays depend on some form of TM system, this has not been the object...... of much research. Our paper attempts to find out what we know about the nature, applications and influences of TM technology, including translators' interaction with TMs, and also how we know it. An essential part of the analysis is based on a selection of empirical TM studies, which we assume...... to be representative of the research field as a whole. Our analysis suggests that, while considerable knowledge is available about the technical side of TMs, more research is needed to understand how translators interact with TM technology and how TMs influence translators' cognitive translation processes....

  10. Flexible programming of cell-free protein synthesis using magnetic bead-immobilized plasmids.

    Directory of Open Access Journals (Sweden)

    Ka-Young Lee

    Full Text Available The use of magnetic bead-immobilized DNA as movable template for cell-free protein synthesis has been investigated. Magnetic microbeads containing chemically conjugated plasmids were used to direct cell-free protein synthesis, so that protein generation could be readily programmed, reset and reprogrammed. Protein synthesis by using this approach could be ON/OFF-controlled through repeated addition and removal of the microbead-conjugated DNA and employed in sequential expression of different genes in a same reaction mixture. Since the incubation periods of individual template plasmids are freely controllable, relative expression levels of multiple proteins can be tuned to desired levels. We expect that the presented results will find wide application to the flexible design and execution of synthetic pathways in cell-free chassis.

  11. Binary translation using peephole translation rules

    Science.gov (United States)

    Bansal, Sorav; Aiken, Alex

    2010-05-04

    An efficient binary translator uses peephole translation rules to directly translate executable code from one instruction set to another. In a preferred embodiment, the translation rules are generated using superoptimization techniques that enable the translator to automatically learn translation rules for translating code from the source to target instruction set architecture.

  12. Cell-Free DNA Modulates Clot Structure and Impairs Fibrinolysis in Sepsis.

    Science.gov (United States)

    Gould, Travis J; Vu, Trang T; Stafford, Alan R; Dwivedi, Dhruva J; Kim, Paul Y; Fox-Robichaud, Alison E; Weitz, Jeffrey I; Liaw, Patricia C

    2015-12-01

    Sepsis is characterized by systemic activation of inflammation and coagulation in response to infection. In sepsis, activated neutrophils extrude neutrophil extracellular traps composed of cell-free DNA (CFDNA) that not only trap pathogens but also provide a stimulus for clot formation. Although the effect of CFDNA on coagulation has been extensively studied, much less is known about the impact of CFDNA on fibrinolysis. To address this, we (1) investigated the relationship between CFDNA levels and fibrinolytic activity in sepsis and (2) determined the mechanisms by which CFDNA modulates fibrinolysis. Plasma was collected from healthy and septic individuals, and CFDNA was quantified. Clot lysis assays were performed in plasma and purified systems, and lysis times were determined by monitoring absorbance. Clot morphology was assessed using scanning electron microscopy. Clots formed in plasma from septic patients containing >5 µg/mL CFDNA were dense in structure and resistant to fibrinolysis, a phenomenon overcome by deoxyribonuclease addition. These effects were recapitulated in control plasma supplemented with CFDNA. In a purified system, CFDNA delayed fibrinolysis but did not alter tissue-type plasminogen activator-induced plasmin generation. Using surface plasmon resonance, CFDNA bound plasmin with a Kd value of 4.2±0.3 µmol/L, and increasing concentrations of CFDNA impaired plasmin-mediated degradation of fibrin clots via the formation of a nonproductive ternary complex between plasmin, CFDNA, and fibrin. Our studies suggest that the increased levels of CFDNA in sepsis impair fibrinolysis by inhibiting plasmin-mediated fibrin degradation, thereby identifying CFDNA as a potential therapeutic target for sepsis treatment. © 2015 American Heart Association, Inc.

  13. Machine Translation Effect on Communication

    DEFF Research Database (Denmark)

    Jensen, Mika Yasuoka; Bjørn, Pernille

    2011-01-01

    Intercultural collaboration facilitated by machine translation has gradually spread in various settings. Still, little is known as for the practice of machine-translation mediated communication. This paper investigates how machine translation affects intercultural communication in practice. Based...... on communication in which multilingual communication system is applied, we identify four communication types and its’ influences on stakeholders’ communication process, especially focusing on establishment and maintenance of common ground. Different from our expectation that quality of machine translation results...

  14. Experiment and quantitative modeling of cell-free gene expression dynamics

    OpenAIRE

    Stögbauer, Tobias Roland

    2012-01-01

    Genexpression that is the cellular synthesis of proteins is comprised of the sub-steps tran- scription (mRNA synthesis based on the DNA master), translation (protein synthesis based on the mRNA) and protein folding. Owing to the large number of interactions between individual components this process is very complex in vivo and therefore mathematical modeling is extremely laborious. By means of simpli�ed in vitro model systems individual aspects of cellular gene expression can be studied...

  15. Cell-free (RNA and cell-associated (DNA HIV-1 and postnatal transmission through breastfeeding.

    Directory of Open Access Journals (Sweden)

    James Ndirangu

    Full Text Available Transmission through breastfeeding remains important for mother-to-child transmission (MTCT in resource-limited settings. We quantify the relationship between cell-free (RNA and cell-associated (DNA shedding of HIV-1 virus in breastmilk and the risk of postnatal HIV-1 transmission in the first 6 months postpartum.Thirty-six HIV-positive mothers who transmitted HIV-1 by breastfeeding were matched to 36 non-transmitting HIV-1 infected mothers in a case-control study nested in a cohort of HIV-infected women. RNA and DNA were quantified in the same breastmilk sample taken at 6 weeks and 6 months. Cox regression analysis assessed the association between cell-free and cell-associated virus levels and risk of postnatal HIV-1 transmission.There were higher median levels of cell-free than cell-associated HIV-1 virus (per ml in breastmilk at 6 weeks and 6 months. Multivariably, adjusting for antenatal CD4 count and maternal plasma viral load, at 6 weeks, each 10-fold increase in cell-free or cell-associated levels (per ml was significantly associated with HIV-1 transmission but stronger for cell-associated than cell-free levels [2.47 (95% CI 1.33-4.59 vs. aHR 1.52 (95% CI, 1.17-1.96, respectively]. At 6 months, cell-free and cell-associated levels (per ml in breastmilk remained significantly associated with HIV-1 transmission but was stronger for cell-free than cell-associated levels [aHR 2.53 (95% CI 1.64-3.92 vs. 1.73 (95% CI 0.94-3.19, respectively].The findings suggest that cell-associated virus level (per ml is more important for early postpartum HIV-1 transmission (at 6 weeks than cell-free virus. As cell-associated virus levels have been consistently detected in breastmilk despite antiretroviral therapy, this highlights a potential challenge for resource-limited settings to achieve the UNAIDS goal for 2015 of eliminating vertical transmission. More studies would further knowledge on mechanisms of HIV-1 transmission and help develop more effective

  16. Defective thymine dimer excision by cell-free extracts of xeroderma pigmentosum cells.

    Science.gov (United States)

    Mortelmans, K; Friedberg, E C; Slor, H; Thomas, G; Cleaver, J E

    1976-01-01

    Crude extracts of normal human diploid fibroblasts and of human peripheral blood lymphocytes excise thymine dimers from purified ultraviolet-irradiated DNA, or from the DNA presumably present as chromatin in unfractionated cell-free preparations of cells that had been labeled with [3H]thymidine. Extracts of xeroderma pigmentosum cells from complementation groups A, C, and D also excise thymine dimers from purified DNA, but extracts of group A cells do not excise dimers from the DNA of radioactively labeled unfractionated cell-free preparations. PMID:1066689

  17. Revising Translations

    DEFF Research Database (Denmark)

    Rasmussen, Kirsten Wølch; Schjoldager, Anne

    2011-01-01

    survey. Results clearly show that most translation companies regard both unilingual and comparative revisions as essential components of professional quality assurance. Data indicate that revision is rarely fully comparative, as the preferred procedure seems to be a unilingual revision followed by a more...... or less comparative rereading. Though questionnaire data seem to indicate that translation companies use linguistic correctness and presentation as the only revision parameters, interview data reveal that textual and communicative aspects are also considered. Generally speaking, revision is not carried...... out by specialised revisers, but by staff translators, who revise the work of colleagues and freelancers on an ad hoc basis. Corrections are mostly given in a peer-to-peer fashion, though the work of freelancers and inexperienced in-house translators is often revised in an authoritative (nonnegotiable...

  18. A multilingual set exploration of interpersonal grammar in Brazilian Portuguese/English under a Translation Studies and Systemic Functional Theory Framework

    Directory of Open Access Journals (Sweden)

    Giacomo Patrocinio Figueredo

    2015-04-01

    Full Text Available The paper explores translation in interpersonal grammar systems of Brazilian Portuguese and English, identifying its behavior in a multilingual environment. It aims at deploying translation equivalence, correspondence and shift at the grammar stratum in the multilingual environment to model interpersonal clause grammar. The multilingual environment is as a result modeled as the power set of resources in both languages and translation equivalence, formal correspondence and shifts are taken as tools for such modeling. Subsets of language-specific resources and their intersections – i.e., multilingual – between them can then be described. Language contact behavior is described through translation equivalence and shift, since it is a variation of language deployment. Through such modeling this paper shows how equivalence, correspondence and shift can be used as tools to model a multilingual environment. Moreover, it suggests the notion of ‘multilingual’ may refer both to the pervasive nature of grammar systems and grammar behavior of languages when in contact.

  19. A multilingual set exploration of interpersonal grammar in Brazilian Portuguese/English under a Translation Studies and Systemic Functional Theory Framework

    Directory of Open Access Journals (Sweden)

    Giacomo Patrocinio Figueredo

    2015-06-01

    Full Text Available The paper explores translation in interpersonal grammar systems of Brazilian Portuguese and English, identifying its behavior in a multilingual environment. It aims at deploying translation equivalence, correspondence and shift at the grammar stratum in the multilingual environment to model interpersonal clause grammar. The multilingual environment is as a result modeled as the power set of resources in both languages and translation equivalence, formal correspondence and shifts are taken as tools for such modeling. Subsets of language-specific resources and their intersections – i.e., multilingual – between them can then be described. Language contact behavior is described through translation equivalence and shift, since it is a variation of language deployment. Through such modeling this paper shows how equivalence, correspondence and shift can be used as tools to model a multilingual environment. Moreover, it suggests the notion of ‘multilingual’ may refer both to the pervasive nature of grammar systems and grammar behavior of languages when in contact.

  20. Beyond Translation

    DEFF Research Database (Denmark)

    Olwig, Mette Fog

    2013-01-01

    This article contributes to the growing scholarship on local development practitioners by re-examining conceptualizations of practitioners as ‘brokers’ strategically translating between ‘travelling’ (development institution) rationalities and ‘placed’ (recipient area) rationalities in relation to...... rationalities. This is shown to have important implications for theory, research and practice concerning disaster risk reduction and climate change adaptation in which such translation is often expected....

  1. Engineering artificial cells by combining HeLa-based cell-free expression and ultrathin double emulsion template.

    Science.gov (United States)

    Ho, Kenneth K Y; Murray, Victoria L; Liu, Allen P

    2015-01-01

    Generation of artificial cells provides the bridge needed to cover the gap between studying the complexity of biological processes in whole cells and studying these same processes in an in vitro reconstituted system. Artificial cells are defined as the encapsulation of biologically active material in a biological or synthetic membrane. Here, we describe a robust and general method to produce artificial cells for the purpose of mimicking one or more behaviors of a cell. A microfluidic double emulsion system is used to encapsulate a mammalian cell-free expression system that is able to express membrane proteins into the bilayer or soluble proteins inside the vesicles. The development of a robust platform that allows the assembly of artificial cells is valuable in understanding subcellular functions and emergent behaviors in a more cell-like environment as well as for creating novel signaling pathways to achieve specific cellular behaviors. Copyright © 2015 Elsevier Inc. All rights reserved.

  2. The Pharmacogenomics Research Network Translational Pharmacogenetics Program: Outcomes and Metrics of Pharmacogenetic Implementations Across Diverse Healthcare Systems.

    Science.gov (United States)

    Luzum, J A; Pakyz, R E; Elsey, A R; Haidar, C E; Peterson, J F; Whirl-Carrillo, M; Handelman, S K; Palmer, K; Pulley, J M; Beller, M; Schildcrout, J S; Field, J R; Weitzel, K W; Cooper-DeHoff, R M; Cavallari, L H; O'Donnell, P H; Altman, R B; Pereira, N; Ratain, M J; Roden, D M; Embi, P J; Sadee, W; Klein, T E; Johnson, J A; Relling, M V; Wang, L; Weinshilboum, R M; Shuldiner, A R; Freimuth, R R

    2017-09-01

    Numerous pharmacogenetic clinical guidelines and recommendations have been published, but barriers have hindered the clinical implementation of pharmacogenetics. The Translational Pharmacogenetics Program (TPP) of the National Institutes of Health (NIH) Pharmacogenomics Research Network was established in 2011 to catalog and contribute to the development of pharmacogenetic implementations at eight US healthcare systems, with the goal to disseminate real-world solutions for the barriers to clinical pharmacogenetic implementation. The TPP collected and normalized pharmacogenetic implementation metrics through June 2015, including gene-drug pairs implemented, interpretations of alleles and diplotypes, numbers of tests performed and actionable results, and workflow diagrams. TPP participant institutions developed diverse solutions to overcome many barriers, but the use of Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines provided some consistency among the institutions. The TPP also collected some pharmacogenetic implementation outcomes (scientific, educational, financial, and informatics), which may inform healthcare systems seeking to implement their own pharmacogenetic testing programs. © 2017, The American Society for Clinical Pharmacology and Therapeutics.

  3. Diurnal Variations of Human Circulating Cell-Free Micro-RNA.

    Science.gov (United States)

    Heegaard, Niels H H; Carlsen, Anting Liu; Lilje, Berit; Ng, Kim Lee; Rønne, Mette E; Jørgensen, Henrik L; Sennels, Henriette; Fahrenkrug, Jan

    2016-01-01

    A 24-hour light and dark cycle-dependent rhythmicity pervades physiological processes in virtually all living organisms including humans. These regular oscillations are caused by external cues to endogenous, independent biological time-keeping systems (clocks). The rhythm is reflected by gene expression that varies in a circadian and specific fashion in different organs and tissues and is regulated largely by dynamic epigenetic and post-transcriptional mechanisms. This leads to well-documented oscillations of specific electrolytes, hormones, metabolites, and plasma proteins in blood samples. An emerging, important class of gene regulators is short single-stranded RNA (micro-RNA, miRNA) that interferes post-transcriptionally with gene expression and thus may play a role in the circadian variation of gene expression. MiRNAs are promising biomarkers by virtue of their disease-specific tissue expression and because of their presence as stable entities in the circulation. However, no studies have addressed the putative circadian rhythmicity of circulating, cell-free miRNAs. This question is important both for using miRNAs as biological markers and for clues to miRNA function in the regulation of circadian gene expression. Here, we investigate 92 miRNAs in plasma samples from 24 young male, healthy volunteers repeatedly sampled 9 times during a 24-hour stay in a regulated environment. We demonstrate that a third (26/79) of the measurable plasma miRNAs (using RT-qPCR on a microfluidic system) exhibit a rhythmic behavior and are distributed in two main phase patterns. Some of these miRNAs weakly target known clock genes and many have strong targets in intracellular MAPK signaling pathways. These novel findings highlight the importance of considering bio-oscillations in miRNA biomarker studies and suggest the further study of a set of specific circulating miRNAs in the regulation and functioning of biological clocks.

  4. Diurnal Variations of Human Circulating Cell-Free Micro-RNA.

    Directory of Open Access Journals (Sweden)

    Niels H H Heegaard

    Full Text Available A 24-hour light and dark cycle-dependent rhythmicity pervades physiological processes in virtually all living organisms including humans. These regular oscillations are caused by external cues to endogenous, independent biological time-keeping systems (clocks. The rhythm is reflected by gene expression that varies in a circadian and specific fashion in different organs and tissues and is regulated largely by dynamic epigenetic and post-transcriptional mechanisms. This leads to well-documented oscillations of specific electrolytes, hormones, metabolites, and plasma proteins in blood samples. An emerging, important class of gene regulators is short single-stranded RNA (micro-RNA, miRNA that interferes post-transcriptionally with gene expression and thus may play a role in the circadian variation of gene expression. MiRNAs are promising biomarkers by virtue of their disease-specific tissue expression and because of their presence as stable entities in the circulation. However, no studies have addressed the putative circadian rhythmicity of circulating, cell-free miRNAs. This question is important both for using miRNAs as biological markers and for clues to miRNA function in the regulation of circadian gene expression. Here, we investigate 92 miRNAs in plasma samples from 24 young male, healthy volunteers repeatedly sampled 9 times during a 24-hour stay in a regulated environment. We demonstrate that a third (26/79 of the measurable plasma miRNAs (using RT-qPCR on a microfluidic system exhibit a rhythmic behavior and are distributed in two main phase patterns. Some of these miRNAs weakly target known clock genes and many have strong targets in intracellular MAPK signaling pathways. These novel findings highlight the importance of considering bio-oscillations in miRNA biomarker studies and suggest the further study of a set of specific circulating miRNAs in the regulation and functioning of biological clocks.

  5. Antioxidant Systems are Regulated by Nitric Oxide-Mediated Post-translational Modifications (NO-PTMs)

    Science.gov (United States)

    Begara-Morales, Juan C.; Sánchez-Calvo, Beatriz; Chaki, Mounira; Valderrama, Raquel; Mata-Pérez, Capilla; Padilla, María N.; Corpas, Francisco J.; Barroso, Juan B.

    2016-01-01

    Nitric oxide (NO) is a biological messenger that orchestrates a plethora of plant functions, mainly through post-translational modifications (PTMs) such as S-nitrosylation or tyrosine nitration. In plants, hundreds of proteins have been identified as potential targets of these NO-PTMs under physiological and stress conditions indicating the relevance of NO in plant-signaling mechanisms. Among these NO protein targets, there are different antioxidant enzymes involved in the control of reactive oxygen species (ROS), such as H2O2, which is also a signal molecule. This highlights the close relationship between ROS/NO signaling pathways. The major plant antioxidant enzymes, including catalase, superoxide dismutases (SODs) peroxiredoxins (Prx) and all the enzymatic components of the ascorbate-glutathione (Asa-GSH) cycle, have been shown to be modulated to different degrees by NO-PTMs. This mini-review will update the recent knowledge concerning the interaction of NO with these antioxidant enzymes, with a special focus on the components of the Asa-GSH cycle and their physiological relevance. PMID:26909095

  6. Caenorhabditis elegans as a model system to study post-translational modifications of human transthyretin

    Science.gov (United States)

    Henze, Andrea; Homann, Thomas; Rohn, Isabelle; Aschner, Michael; Link, Christopher D.; Kleuser, Burkhard; Schweigert, Florian J.; Schwerdtle, Tanja; Bornhorst, Julia

    2016-11-01

    The visceral protein transthyretin (TTR) is frequently affected by oxidative post-translational protein modifications (PTPMs) in various diseases. Thus, better insight into structure-function relationships due to oxidative PTPMs of TTR should contribute to the understanding of pathophysiologic mechanisms. While the in vivo analysis of TTR in mammalian models is complex, time- and resource-consuming, transgenic Caenorhabditis elegans expressing hTTR provide an optimal model for the in vivo identification and characterization of drug-mediated oxidative PTPMs of hTTR by means of matrix assisted laser desorption/ionization - time of flight - mass spectrometry (MALDI-TOF-MS). Herein, we demonstrated that hTTR is expressed in all developmental stages of Caenorhabditis elegans, enabling the analysis of hTTR metabolism during the whole life-cycle. The suitability of the applied model was verified by exposing worms to D-penicillamine and menadione. Both drugs induced substantial changes in the oxidative PTPM pattern of hTTR. Additionally, for the first time a covalent binding of both drugs with hTTR was identified and verified by molecular modelling.

  7. Application of systems thinking in health: opportunities for translating theory into practice

    Science.gov (United States)

    Malik, Asmat Ullah

    2015-01-01

    Systems thinking is not a new concept to health system strengthening; however, one question remains unanswered: How policy-makers, system designers and consultants with a system thinking philosophy should act (have acted) as potential change agents in actually gaining opportunities to introduce systems thinking? Development of Comprehensive Multi-Year Plans (cMYPs) for Immunization System is one such opportunity because almost all Low- and Middle-Income Countries (LMICs) develop and implement cMYPs every five years. Without building upon examples and showing practical application, the discussions and deliberations on systems thinking may fade away with passage of time. There are opportunities that exist around us in our existing health systems that we can benefit from starting with an incremental approach and generating evidence for longer lasting system-wide changes. PMID:26340394

  8. Translators and Machines--Can They Cooperate?

    Science.gov (United States)

    Melby, Alan K.

    1981-01-01

    Discusses fundamental questions about the nature of machine translation and outlines its history. Also describes an experiment in cooperative translation called ITS (Interactive Translation System), evaluating the system's capabilities and predicting future developments. Finally, offers suggestions for translators interested in preparing to use…

  9. The Clinical Utilization of Circulating Cell Free DNA (CCFDNA) in Blood of Cancer Patients

    Science.gov (United States)

    Elshimali, Yahya I.; Khaddour, Husseina; Sarkissyan, Marianna; Wu, Yanyuan; Vadgama, Jaydutt V.

    2013-01-01

    Qualitative and quantitative testing of circulating cell free DNA (CCFDNA) can be applied for the management of malignant and benign neoplasms. Detecting circulating DNA in cancer patients may help develop a DNA profile for early stage diagnosis in malignancies. The technical issues of obtaining, using, and analyzing CCFDNA from blood will be discussed. PMID:24065096

  10. Plasma HER2 amplification in cell-free DNA during neoadjuvant chemotherapy in breast cancer

    DEFF Research Database (Denmark)

    Bechmann, Troels; Andersen, Rikke Fredslund; Pallisgaard, Niels

    2013-01-01

    Measurement of human epidermal growth factor receptor 2 (HER2) gene amplification in cell-free DNA (cfDNA) is an evolving technique in breast cancer, enabling liquid biopsies and treatment monitoring. The present study investigated the dynamics of plasma HER2 gene copy number and amplification...

  11. A plasmonic nanosensor with inverse sensitivity for circulating cell-free DNA quantification.

    Science.gov (United States)

    Pallares, Roger M; Kong, Say Li; Ru, Tan Hui; Thanh, Nguyên T K; Lu, Yi; Su, Xiaodi

    2015-10-04

    A plasmonic nanosensor (using gold nanorods) with inverse sensitivity is presented for circulating cell-free DNA quantification. The inverse sensitivity (i.e. the lower the analyte concentration, the higher the response intensity) is achieved by the unusual DNA concentration-dependent gold nanorod aggregation. This assay method can adjust the dynamic range by controlling the concentration of nanoparticles in solution.

  12. Post-Translational Nitric Oxide-Dependent Modifications In Immune System.

    Science.gov (United States)

    Martínez-Ruiz, Antonio

    2015-08-01

    Nitric oxide non classical signalling is exerted through a series of covalent protein post-translational modifications, which include modification of cysteine residues by S-nitrosylation and S-glutathionylation. A key process in adaptive immunity is the immune synapse that tightly couples T cells with antigen presenting cells, triggering antigen recognition by T cells. In this highly regulated process, we have shown that eNOS is activated, inducing protein S-nitrosylation. While both N-Ras and K-Ras are present in T cells, only N-Ras, which colocalizes in the Golgi with eNOS, is S-nitrosylated and activated during the immune synapse, providing an example of short-range selectivity of NO signalling through S-nitrosylation. We have developed proteomic methods to detect S-nitrosylation and reversible cysteine oxidations. We have applied them to detecting S-nitrosylated proteins in macrophage activation, highlighting the role of denitrosylase mechanism, particularly the thioredoxin pathway, in protecting macrophages from self-modification. We have also applied these proteomic methods to studying protein modification in acute hypoxia. In endothelial cells, there is an increase in cysteine oxidation in several proteins that can mediate acute responses to hypoxia prior to the activation of the HIF pathway, and we are currently studying in more detail the role of protein S-nitrosylation. We have also recently shown that acute hypoxia produces a superoxide burst in cells, which can be converted in an oxidative signal through protein cysteine modification, and we are unraveling the molecular mechanisms producing this superoxide burst in mitochondria. Copyright © 2015. Published by Elsevier B.V.

  13. Bundling in Place: Translating the NGSS into Place-Based Earth-System Science Curricula

    Science.gov (United States)

    Semken, S. C.

    2016-12-01

    Bundling is the process of grouping Performance Expectations (PEs) from the Next Generation Science Standards (NGSS) into coherent units based on a defined topic, idea, question, or phenomenon. Bundling sorts the PEs for a given grade or grade band into a teachable narrative: a key stage in building curriculum, instruction, and assessment from the NGSS. To encourage and facilitate this, bundling guidelines have recently been released on the NGSS website (nextgenscience.org/glossary/bundlesbundling), and example bundles for different grade bands and disciplines are also being developed and posted there. According to these guidelines the iterative process of bundling begins with organization of PEs according to natural connections among them, and alignment of the three NGSS dimensions (Disciplinary Core Ideas, Cross-Cutting Concepts, and Science and Engineering Practices) that underpin each PE. Bundles are grouped by coherence and increasing complexity into courses, and courses into course sets that should encompass all PEs for a grade band. Bundling offers a natural way to translate the NGSS into highly contextualized curricula such as place-based (PB) teaching, which is situated in specific places or regions and focused on natural and cultural features, processes, phenomena, history, and challenges to sustainability therein. Attributes of place and our individual and collective connections to place (sense of place) directly inform PB curriculum, pedagogy, and assessment. PEs can be bundled by their relevance to these themes. Following the NGSS guidelines, I model the process for PB instruction by bundling PEs around the themes of Paleozoic geology and carbonate deposition and their relationships to mining and calcining of limestone in Anthropocene cement production for developing communities. The bundles integrate aspects of Earth history, the carbon cycle, mineral resources, climate change, and sustainability using specific local examples and narratives. They are

  14. A translational continuum of model systems for evaluating treatment strategies in Alzheimer’s disease: isradipine as a candidate drug

    Directory of Open Access Journals (Sweden)

    Philip F. Copenhaver

    2011-09-01

    A growing body of evidence supports the ‘calcium hypothesis’ of Alzheimer’s disease (AD, which postulates that a variety of insults might disrupt the homeostatic regulation of neuronal calcium (Ca2+ in the brain, resulting in the progressive symptoms that typify the disease. However, despite ongoing efforts to develop new methods for testing therapeutic compounds that might be beneficial in AD, no single bioassay permits both rapid screening and in vivo validation of candidate drugs that target specific components of the Ca2+ regulatory machinery. To address this issue, we have integrated four distinct model systems that provide complementary information about a trial compound: the human neuroblastoma MC65 line, which provides an in vitro model of amyloid toxicity; a transgenic Drosophila model, which develops age-dependent pathologies associated with AD; the 3×TgAD transgenic mouse, which recapitulates many of the neuropathological features that typify AD; and the embryonic nervous system of Manduca, which provides a novel in vivo assay for the acute effects of amyloid peptides on neuronal motility. To demonstrate the value of this ‘translational suite’ of bioassays, we focused on a set of clinically approved dihydropyridines (DHPs, a class of well-defined inhibitors of L-type calcium channels that have been suggested to be neuroprotective in AD. Among the DHPs tested in this study, we found that isradipine reduced the neurotoxic consequences of β-amyloid accumulation in all four model systems without inducing deleterious side effects. Our results provide new evidence in support of the Ca2+ hypothesis of AD, and indicate that isradipine represents a promising drug for translation into clinical trials. In addition, these studies also demonstrate that this continuum of bioassays (representing different levels of complexity provides an effective means of evaluating other candidate compounds that target specific components of the Ca2+ regulatory machinery

  15. Establishment of a Wheat Cell-Free Synthesized Protein Array Containing 250 Human and Mouse E3 Ubiquitin Ligases to Identify Novel Interaction between E3 Ligases and Substrate Proteins.

    Directory of Open Access Journals (Sweden)

    Hirotaka Takahashi

    Full Text Available Ubiquitination is a key post-translational modification in the regulation of numerous biological processes in eukaryotes. The primary roles of ubiquitination are thought to be the triggering of protein degradation and the regulation of signal transduction. During protein ubiquitination, substrate specificity is mainly determined by E3 ubiquitin ligase (E3. Although more than 600 genes in the human genome encode E3, the E3s of many target proteins remain unidentified owing to E3 diversity and the instability of ubiquitinated proteins in cell. We demonstrate herein a novel biochemical analysis for the identification of E3s targeting specific proteins. Using wheat cell-free protein synthesis system, a protein array containing 227 human and 23 mouse recombinant E3s was synthesized. To establish the high-throughput binding assay using AlphaScreen technology, we selected MDM2 and p53 as the model combination of E3 and its target protein. The AlphaScreen assay specifically detected the binding of p53 and MDM2 in a crude translation mixture. Then, a comprehensive binding assay using the E3 protein array was performed. Eleven of the E3s showed high binding activity, including four previously reported E3s (e.g., MDM2, MDM4, and WWP1 targeting p53. This result demonstrated the reliability of the assay. Another interactors, RNF6 and DZIP3-which there have been no report to bind p53-were found to ubiquitinate p53 in vitro. Further analysis showed that RNF6 decreased the amount of p53 in H1299 cells in E3 activity-dependent manner. These results suggest the possibility that the RNF6 ubiquitinates and degrades p53 in cells. The novel in vitro screening system established herein is a powerful tool for finding novel E3s of a target protein.

  16. Can neural machine translation do simultaneous translation?

    OpenAIRE

    Cho, Kyunghyun; Esipova, Masha

    2016-01-01

    We investigate the potential of attention-based neural machine translation in simultaneous translation. We introduce a novel decoding algorithm, called simultaneous greedy decoding, that allows an existing neural machine translation model to begin translating before a full source sentence is received. This approach is unique from previous works on simultaneous translation in that segmentation and translation are done jointly to maximize the translation quality and that translating each segmen...

  17. [Brazilian-Portuguese translation and cultural adaptation of the sleep and wake disturbances domains of the Patient-Reported-Outcomes Measurement Information System (PROMIS)].

    Science.gov (United States)

    Silva E Costa, Zilma Maria Severino; Pinto, Rogério de Melo Costa; Mendonça, Tânia Maria da Silva; Silva, Carlos Henrique Martins da

    2014-07-01

    Altered sleep and wakefulness affect individuals' mood, memory, and psychomotor performance and thus directly impact their quality of life. Tools to analyze the quality of these factors should be available for clinical evaluation. This study aimed to translate into Brazilian Portuguese and culturally adapt the Patient-Reported Outcomes Measurement Information System (PROMIS), specifically the sleep and wake disturbances domains. The translation and cultural adaptation processes followed the guidelines proposed by the Functional Assessment of Chronic Illness Therapy (FACIT) organization. The methodology included translation, reconciliation, back-translation, review by PROMIS, review by independent reviewers, pretest, and incorporation of the results into the final version. The Portuguese version of the sleep and wake disturbances domains presents semantic, idiomatic, cultural, and conceptual equivalence with the items in the source language.

  18. In vivo reduction of cell-free methemoglobin to oxyhemoglobin results in vasoconstriction in canines.

    Science.gov (United States)

    Wang, Dong; Piknova, Barbora; Solomon, Steven B; Cortes-Puch, Irene; Kern, Steven J; Sun, Junfeng; Kanias, Tamir; Gladwin, Mark T; Helms, Christine; Kim-Shapiro, Daniel B; Schechter, Alan N; Natanson, Charles

    2013-12-01

    Cell-free hemoglobin (Hb) in the vasculature leads to vasoconstriction and injury. Proposed mechanisms have been based on nitric oxide (NO) scavenging by oxyhemoglobin (oxyHb) or processes mediated by oxidative reactions of methemoglobin (metHb). To clarify this, we tested the vascular effect and fate of oxyHb or metHb infusions. Twenty beagles were challenged with 1-hour similar infusions of (200 μmol/L) metHb (n = 5), oxyHb (n = 5), albumin (n = 5), or saline (n = 5). Measurements were taken over 3 hours. Infusions of the two pure Hb species resulted in increases in mean arterial blood pressure (MAP), systemic vascular resistance index, and NO consumption capacity of plasma (all p < 0.05) with the effects of oxyHb being greater than that from metHb (MAP; increase 0 to 3 hr; 27 ± 6% vs. 7 ± 2%, respectively; all p < 0.05). The significant vasoconstrictive response of metHb (vs. albumin and saline controls) was related to in vivo autoreduction of metHb to oxyHb, and the vasoactive Hb species that significantly correlated with MAP was always oxyHb, either from direct infusion or after in vivo reduction from metHb. Clearance of total Hb from plasma was faster after metHb than oxyHb infusion (p < 0.0001). These findings indicate that greater NO consumption capacity makes oxyHb more vasoactive than metHb. Additionally, metHb is reduced to oxyHb after infusion and cleared faster or is less stable than oxyHb. Although we found no direct evidence that metHb itself is involved in acute vascular effects, in aggregate, these studies suggest that metHb is not inert and its mechanism of vasoconstriction is due to its delayed conversion to oxyHb by plasma-reducing agents. © 2013 American Association of Blood Banks.

  19. Rapid Electrokinetic Isolation of Cancer-Related Circulating Cell-Free DNA Directly from Blood

    Science.gov (United States)

    Sonnenberg, Avery; Marciniak, Jennifer Y.; Rassenti, Laura; Ghia, Emanuela M.; Skowronski, Elaine A.; Manouchehri, Sareh; McCanna, James; Widhopf, George F.; Kipps, Thomas J.; Heller, Michael J.

    2014-01-01

    BACKGROUND Circulating cell-free DNA (ccf-DNA) is becoming an important biomarker for cancer diagnostics and therapy monitoring. The isolation of ccf-DNA from plasma as a “liquid biopsy” may begin to replace more invasive tissue biopsies for the detection and analysis of cancer-related mutations. Conventional methods for the isolation of ccf-DNA from plasma are costly, time-consuming, and complex, preventing the use of ccf-DNA biomarkers for point-of-care diagnostics and limiting other biomedical research applications. METHODS We used an AC electrokinetic device to rapidly isolate ccf-DNA from 25 μL unprocessed blood. ccf-DNA from 15 chronic lymphocytic leukemia (CLL) patients and 3 healthy individuals was separated into dielectrophoretic (DEP) high-field regions, after which other blood components were removed by a fluidic wash. Concentrated ccf-DNA was detected by fluorescence and eluted for quantification,PCR,and DNA sequencing. The complete process, blood to PCR, required <10 min. ccf-DNA was amplified by PCR with immunoglobulin heavy chain variable region (IGHV)-specific primers to identify the unique IGHV gene expressed by the leukemic B-cell clone, and then sequenced. RESULTS PCR and DNA sequencing results obtained by DEP from 25 μL CLL blood matched results obtained by use of conventional methods for ccf-DNA isolation from 1 mL plasma and for genomic DNA isolation from CLL patient leukemic B cells isolated from 15–20 mL blood. CONCLUSIONS Rapid isolation of ccf-DNA directly from a drop of blood will advance disease-related biomarker research, accelerate the transition from tissue to liquid biopsies, and enable point-of-care diagnostic systems for patient monitoring. PMID:24270796

  20. Plasma cell-free mitochondrial DNA declines in response to prolonged moderate aerobic exercise.

    Science.gov (United States)

    Shockett, Penny E; Khanal, Januka; Sitaula, Alina; Oglesby, Christopher; Meachum, William A; Castracane, V Daniel; Kraemer, Robert R

    2016-01-01

    Increased plasma cell-free mitochondrial DNA (cf-mDNA), a damage-associated molecular pattern (DAMP) produced by cellular injury, contributes to neutrophil activation/inflammation in trauma patients and arises in cancer and autoimmunity. To further understand relationships between cf-mDNA released by tissue injury, inflammation, and health benefits of exercise, we examined cf-mDNA response to prolonged moderate aerobic exercise. Seven healthy moderately trained young men (age = 22.4 ± 1.2) completed a treadmill exercise trial for 90 min at 60% VO2 max and a resting control trial. Blood was sampled immediately prior to exercise (0 min = baseline), during (+18, +54 min), immediately after (+90 min), and after recovery (R40). Plasma was analyzed for cf-mDNA, IL-6, and lactate. A significant difference in cf-mDNA response was observed between exercise and control trials, with cf-mDNA levels reduced during exercise at +54 and +90 (with or without plasma volume shift correction). Declines in cf-mDNA were accompanied by increased lactate and followed by an increase in IL-6, suggesting a temporal association with muscle stress and inflammatory processes. Our novel finding of cf-mDNA decline with prolonged moderate treadmill exercise provides evidence for increased clearance from or reduced release of cf-mDNA into the blood with prolonged exercise. These studies contrast with previous investigations involving exhaustive short-term treadmill exercise, in which no change in cf-mDNA levels were reported, and contribute to our understanding of differences between exercise- and trauma-induced inflammation. We propose that transient declines in cf-mDNA may induce health benefits, by reducing systemic inflammation. © 2016 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of the American Physiological Society and The Physiological Society.

  1. Rapid electrokinetic isolation of cancer-related circulating cell-free DNA directly from blood.

    Science.gov (United States)

    Sonnenberg, Avery; Marciniak, Jennifer Y; Rassenti, Laura; Ghia, Emanuela M; Skowronski, Elaine A; Manouchehri, Sareh; McCanna, James; Widhopf, George F; Kipps, Thomas J; Heller, Michael J

    2014-03-01

    Circulating cell-free DNA (ccf-DNA) is becoming an important biomarker for cancer diagnostics and therapy monitoring. The isolation of ccf-DNA from plasma as a "liquid biopsy" may begin to replace more invasive tissue biopsies for the detection and analysis of cancer-related mutations. Conventional methods for the isolation of ccf-DNA from plasma are costly, time-consuming, and complex, preventing the use of ccf-DNA biomarkers for point-of-care diagnostics and limiting other biomedical research applications. We used an AC electrokinetic device to rapidly isolate ccf-DNA from 25 μL unprocessed blood. ccf-DNA from 15 chronic lymphocytic leukemia (CLL) patients and 3 healthy individuals was separated into dielectrophoretic (DEP) high-field regions, after which other blood components were removed by a fluidic wash. Concentrated ccf-DNA was detected by fluorescence and eluted for quantification, PCR, and DNA sequencing. The complete process, blood to PCR, required B-cell clone, and then sequenced. PCR and DNA sequencing results obtained by DEP from 25 μL CLL blood matched results obtained by use of conventional methods for ccf-DNA isolation from 1 mL plasma and for genomic DNA isolation from CLL patient leukemic B cells isolated from 15-20 mL blood. Rapid isolation of ccf-DNA directly from a drop of blood will advance disease-related biomarker research, accelerate the transition from tissue to liquid biopsies, and enable point-of-care diagnostic systems for patient monitoring.

  2. Tuberculosis-Diagnostic Expert System: an architecture for translating patients information from the web for use in tuberculosis diagnosis.

    Science.gov (United States)

    Osamor, Victor C; Azeta, Ambrose A; Ajulo, Oluseyi O

    2014-12-01

    Over 1.5-2 million tuberculosis deaths occur annually. Medical professionals are faced with a lot of challenges in delivering good health-care with unassisted automation in hospitals where there are several patients who need the doctor's attention. To automate the pre-laboratory screening process against tuberculosis infection to aid diagnosis and make it fast and accessible to the public via the Internet. The expert system we have built is designed to also take care of people who do not have access to medical experts, but would want to check their medical status. A rule-based approach has been used, and unified modeling language and the client-server architecture technique were applied to model the system and to develop it as a web-based expert system for tuberculosis diagnosis. Algorithmic rules in the Tuberculosis-Diagnosis Expert System necessitate decision coverage where tuberculosis is either suspected or not suspected. The architecture consists of a rule base, knowledge base, and patient database. These units interact with the inference engine, which receives patient' data through the Internet via a user interface. We present the architecture of the Tuberculosis-Diagnosis Expert System and its implementation. We evaluated it for usability to determine the level of effectiveness, efficiency and user satisfaction. The result of the usability evaluation reveals that the system has a usability of 4.08 out of a scale of 5. This is an indication of a more-than-average system performance. Several existing expert systems have been developed for the purpose of supporting different medical diagnoses, but none is designed to translate tuberculosis patients' symptomatic data for online pre-laboratory screening. Our Tuberculosis-Diagnosis Expert System is an effective solution for the implementation of the needed web-based expert system diagnosis. © The Author(s) 2013.

  3. Machine Translation and Other Translation Technologies.

    Science.gov (United States)

    Melby, Alan

    1996-01-01

    Examines the application of linguistic theory to machine translation and translator tools, discusses the use of machine translation and translator tools in the real world of translation, and addresses the impact of translation technology on conceptions of language and other issues. Findings indicate that the human mind is flexible and linguistic…

  4. Lost in Translation

    Science.gov (United States)

    Lass, Wiebke; Reusswig, Fritz

    2014-05-01

    Lost in Translation? Introducing Planetary Boundaries into Social Systems. Fritz Reusswig, Wiebke Lass Potsdam Institute for Climate Impact Research, Potsdam, Germany Identifying and quantifying planetary boundaries by interdisciplinary science efforts is a challenging task—and a risky one, as the 1972 Limits to Growth publication has shown. Even if we may be assured that scientific understanding of underlying processes of the Earth system has significantly improved since then, the challenge of translating these findings into the social systems of the planet remains crucial for any kind of action, and in many respects far more challenging. We would like to conceptualize what could also be termed a problem of coupling social and natural systems as a nested set of social translation processes, well aware of the limited applicability of the language-related translation metaphor. Societies must, first, perceive these boundaries, and they have to understand their relevance. This includes, among many other things, the organization of transdisciplinary scientific cooperation. They will then have to translate this understood perception into possible actions, i.e. strategies for different local bodies, actors, and institutional settings. This implies a lot of 'internal' translation processes, e.g. from the scientific subsystem to the mass media, the political and the economic subsystem. And it implies to develop subsystem-specific schemes of evaluation for these alternatives, e.g. convincing narratives, cost-benefit analyses, or ethical legitimacy considerations. And, finally, societies do have to translate chosen action alternatives into monitoring and evaluation schemes, e.g. for agricultural production or renewable energies. This process includes the continuation of observing and re-analyzing the planetary boundary concept itself, as a re-adjustment of these boundaries in the light of new scientific insights cannot be excluded. Taken all together, societies may well

  5. Weyl-Heisenberg frames, translation invariant systems, and the Walnut representation

    DEFF Research Database (Denmark)

    Casazza, P.G.; Christensen, Ole; Janssen, A. J. E. M.

    2001-01-01

    We present a comprehensive analysis of the convergence properties of the frame operators of Weyl-Heisenberg systems and shift-invariant systems, and relate these to the convergence of the Walnut representation. We give a deep analysis of necessary conditions and sufficient conditions for converge...

  6. 5D quantum dynamics of the H{sub 2}@SWNT system: Quantitative study of the rotational-translational coupling

    Energy Technology Data Exchange (ETDEWEB)

    Mondelo-Martell, M.; Huarte-Larrañaga, F., E-mail: fermin.huarte@ub.edu [Departament de Química Física and Institut de Química Teòrica i Computacional (IQTCUB),Universitat de Barcelona, C/ Martí i Franqués 1, 08028 Barcelona (Spain)

    2015-02-28

    The dynamics of the dihydrogen molecule when confined in carbon nanotubes with different chiralities and diameters are studied by using a 5 dimensional model considering the most relevant degrees of freedom of the system. The nuclear eigenstates are calculated for an (8,0) and a (5,0) carbon nanotubes by the State-Average Multiconfigurational Time-dependent Hartree, and then studied using qualitative tools (mapping of the total wave functions onto given subspaces) and more rigorous analysis (different kinds of overlaps with reference functions). The qualitative analysis is seen to fail due to a strong coupling between the internal and translational degrees of freedom. Using more accurate tools allows us to gain a deeper insight into the behaviour of confined species.

  7. Histaminergic system in brain disorders: lessons from the translational approach and future perspectives.

    Science.gov (United States)

    Baronio, Diego; Gonchoroski, Taylor; Castro, Kamila; Zanatta, Geancarlo; Gottfried, Carmem; Riesgo, Rudimar

    2014-01-01

    Histamine and its receptors were first described as part of immune and gastrointestinal systems, but their presence in the central nervous system and importance in behavior are gaining more attention. The histaminergic system modulates different processes including wakefulness, feeding, and learning and memory consolidation. Histamine receptors (H1R, H2R, H3R, and H4R) belong to the rhodopsin-like family of G protein-coupled receptors, present constitutive activity, and are subjected to inverse agonist action. The involvement of the histaminergic system in brain disorders, such as Alzheimer's disease, schizophrenia, sleep disorders, drug dependence, and Parkinson's disease, is largely studied. Data obtained from preclinical studies point antagonists of histamine receptors as promising alternatives to treat brain disorders. Thus, clinical trials are currently ongoing to assess the effects of these drugs on humans. This review summarizes the role of histaminergic system in brain disorders, as well as the effects of different histamine antagonists on animal models and humans.

  8. Specialised Translation Dictionaries for Learners

    DEFF Research Database (Denmark)

    Nielsen, Sandro

    2010-01-01

    Specialised translation dictionaries for learners are reference tools that can help users with domain discourse in a foreign language in connection with translation. The most common type is the business dictionary covering several more or less related subject fields. However, business dictionaries....... The result is that the traditional focus on language system will be extended to usage because the central unit of translation is not the word but the text....... treat one or few fields extensively thereby neglecting the discourse of the other fields. Furthermore, recent research shows that specialised translation is not limited to terms but also concerns domain-specific syntactic structures and genre conventions using various translation strategies. To meet...

  9. Translation, cross-cultural adaptation, and validation of the Mouth Handicap in Systemic Sclerosis questionnaire (MHISS) into the Dutch language.

    Science.gov (United States)

    Schouffoer, A A; Strijbos, E; Schuerwegh, A J M; Mouthon, L; Vliet Vlieland, T P M

    2013-11-01

    The Mouth Handicap in Systemic Sclerosis (MHISS) is a French-generic questionnaire evaluating mouth-opening restriction, dryness, and esthetic concerns. The aim of this study was to translate and adapt the MHISS questionnaire into the Dutch language and evaluate its psychometric properties. The MHISS was translated according to international guidelines, field-tested among 16 systemic sclerosis (SSc) patients, and adapted. Subsequently, the Dutch MHISS was administered to 52 SSc patients visiting the outpatient or day patient clinic of a university hospital and readministered after 2 weeks. Internal consistency was tested by computing Cronbach's alpha. Test-retest reliability was determined by computing the intraclass correlation coefficient (ICC) and validity by determining associations with measures of overall functioning (Health Assessment Questionnaire (HAQ)), maximum mouth opening (MMO, in millimeter), subjective xerostomia (visual analog scale), and objective xerostomia (Saxon test). Patients had mean ± standard deviation (SD) age and disease duration of 55 ± 21 and 7.2 ± 7.3 years. Twenty-seven (52 %) patients had diffuse cutaneous SSc. The mean Dutch MHISS score was 17.5 (SD 10.0) with Cronbach's alpha being 0.862. Dutch MHISS scores differed significantly between patients with high and low disability levels (HAQ, MMO, and subjective and objective xerostomia divided according to the median; paired t test). Spearman rank correlations with HAQ (r = 0.599, p = 0.000), MMO (r = -0.518, p = 0.000), and subjective xerostomia (r = 0.536, p = 0.000) were moderate; correlation with objective xerostomia did not reach statistical significance. The ICC was 0.94. The Dutch version of the MHISS demonstrated good psychometric properties and is useful in assessing mouth disability in SSc patients.

  10. Word Translation Entropy

    DEFF Research Database (Denmark)

    Schaeffer, Moritz; Dragsted, Barbara; Hvelplund, Kristian Tangsgaard

    language activation during source text reading in translation, i.e. co-activation of the two linguistic systems, employed late eye movement measures or reaction times. The current study therefore aims to investigate if and to what extent earlier eye movement measures in reading for translation show......This study reports on an investigation into the relationship between the number of translation alternatives for a single word and eye movements on the source text. In addition, the effect of word order differences between source and target text on eye movements on the source text is studied...... evidence of co-activation. Results show that the number of translation alternatives for a single word and differences between source and target text in terms of word order have an effect on very early and late eye movement measures. Results are interpreted in terms of semantic and structural cross...

  11. Immune regulation of systemic hypertension, pulmonary arterial hypertension, and preeclampsia: shared disease mechanisms and translational opportunities.

    Science.gov (United States)

    Jafri, Salema; Ormiston, Mark L

    2017-12-01

    Systemic hypertension, preeclampsia, and pulmonary arterial hypertension (PAH) are diseases of high blood pressure in the systemic or pulmonary circulation. Beyond the well-defined contribution of more traditional pathophysiological mechanisms, such as changes in the renin-angiotensin-aldosterone system, to the development of these hypertensive disorders, there is substantial clinical evidence supporting an important role for inflammation and immunity in the pathogenesis of each of these three conditions. Over the last decade, work in small animal models, bearing targeted deficiencies in specific cytokines or immune cell subsets, has begun to clarify the immune-mediated mechanisms that drive changes in vascular structure and tone in hypertensive disease. By summarizing the clinical and experimental evidence supporting a contribution of the immune system to systemic hypertension, preeclampsia, and PAH, the current review highlights the cellular and molecular pathways that are common to all three hypertensive disorders. These mechanisms are centered on an imbalance in CD4+ helper T cell populations, defined by excessive Th17 responses and impaired Treg activity, as well as the excessive activation or impairment of additional immune cell types, including macrophages, dendritic cells, CD8+ T cells, B cells, and natural killer cells. The identification of common immune mechanisms in systemic hypertension, preeclampsia, and PAH raises the possibility of new therapeutic strategies that target the immune component of hypertension across multiple disorders. Copyright © 2017 the American Physiological Society.

  12. Solar tracker motor having a fixed caliper and a translating caliper each with an electromagnetic brake system

    Science.gov (United States)

    Rau, Scott James

    2013-01-29

    Concepts and technologies described herein provide for an accurate and cost-effective method for rotating a solar array disk for tracking the movement of the sun. According to various aspects, a motor includes a fixed caliper and a translating caliper positioned adjacent to one another. Electromagnetically controlled brakes on the translating caliper grip the solar array disk while adjacent, but spaced apart, electromagnets on the fixed caliper and the translating caliper are energized to create an attractive force that pulls the translating caliper with the solar array disk toward the fixed caliper. After reaching the fixed caliper, brakes on the fixed caliper are engaged with the disk, brakes on the translating caliper are released from the disk, and the translating caliper is pushed back to the starting location where the process repeats until the desired rotation is completed.

  13. Circulating cell-free DNA-based epigenetic assay can detect early breast cancer.

    Science.gov (United States)

    Uehiro, Natsue; Sato, Fumiaki; Pu, Fengling; Tanaka, Sunao; Kawashima, Masahiro; Kawaguchi, Kosuke; Sugimoto, Masahiro; Saji, Shigehira; Toi, Masakazu

    2016-12-19

    Circulating cell-free DNA (cfDNA) has recently been recognized as a resource for biomarkers of cancer progression, treatment response, and drug resistance. However, few have demonstrated the usefulness of cfDNA for early detection of cancer. Although aberrant DNA methylation in cfDNA has been reported for more than a decade, its diagnostic accuracy remains unsatisfactory for cancer screening. Thus, the aim of the present study was to develop a highly sensitive cfDNA-based system for detection of primary breast cancer (BC) using epigenetic biomarkers and digital PCR technology. Array-based genome-wide DNA methylation analysis was performed using 56 microdissected breast tissue specimens, 34 cell lines, and 29 blood samples from healthy volunteers (HVs). Epigenetic markers for BC detection were selected, and a droplet digital methylation-specific PCR (ddMSP) panel with the selected markers was established. The detection model was constructed by support vector machine and evaluated using cfDNA samples. The methylation array analysis identified 12 novel epigenetic markers (JAK3, RASGRF1, CPXM1, SHF, DNM3, CAV2, HOXA10, B3GNT5, ST3GAL6, DACH1, P2RX3, and chr8:23572595) for detecting BC. We also selected four internal control markers (CREM, GLYATL3, ELMOD3, and KLF9) that were identified as infrequently altered genes using a public database. A ddMSP panel using these 16 markers was developed and detection models were constructed with a training dataset containing cfDNA samples from 80 HVs and 87 cancer patients. The best detection model adopted four methylation markers (RASGRF1, CPXM1, HOXA10, and DACH1) and two parameters (cfDNA concentration and the mean of 12 methylation markers), and, and was validated in an independent dataset of 53 HVs and 58 BC patients. The area under the receiver operating characteristic curve for cancer-normal discrimination was 0.916 and 0.876 in the training and validation dataset, respectively. The sensitivity and the specificity of the

  14. Danish translation of a physical function item bank from the Patient-Reported Outcome Measurement Information System (PROMIS)

    DEFF Research Database (Denmark)

    Schnohr, Christina W.; Rasmussen, Charlotte L.; Langberg, Henning

    2017-01-01

    of the Physical Function item bank into Danish. METHODS: We followed the PROMIS standard procedure, including: 1) two independent translations, 2) back translation, 3) independent reviews of translation quality, and 4) cognitive interviews with a representative sample of the adult population from the municipality...... the use of PROs when measuring physical functioning in a Danish context can be improved-hence improving the items used for research, future trials and in clinical settings....

  15. How the Organic Food System Supports Sustainable Diets and Translates These into Practice.

    Science.gov (United States)

    Strassner, Carola; Cavoski, Ivana; Di Cagno, Raffaella; Kahl, Johannes; Kesse-Guyot, Emmanuelle; Lairon, Denis; Lampkin, Nicolas; Løes, Anne-Kristin; Matt, Darja; Niggli, Urs; Paoletti, Flavio; Pehme, Sirli; Rembiałkowska, Ewa; Schader, Christian; Stolze, Matthias

    2015-01-01

    Organic production and consumption provide a delineated food system that can be explored for its potential contribution to sustainable diets. While organic agriculture improves the sustainability performance on the production side, critical reflections are made on how organic consumption patterns, understood as the practice of people consuming significant amounts of organic produce, may also be taken as an example for sustainable food consumption. The consumption patterns of regular organic consumers seem to be close to the sustainable diet concept of FAO. Certain organic-related measures might therefore be useful in the sustainability assessment of diets, e.g., organic production and organic consumption. Since diets play a central role in shaping food systems and food systems shape diets, the role of organic consumption emerges as an essential topic to be addressed. This role may be based on four important organic achievements: organic agriculture and food production has a definition, well-established principles, public standards, and useful metrics. By 2015, data for organic production and consumption are recorded annually from more than 160 countries, and regulations are in force in more than 80 countries or regions. The organic food system puts the land (agri-cultura) back into the diet; it is the land from which the diet in toto is shaped. Therefore, the organic food system provides essential components of a sustainable diet.

  16. How the Organic Food System Supports Sustainable Diets and Translates These into Practice

    Science.gov (United States)

    Strassner, Carola; Cavoski, Ivana; Di Cagno, Raffaella; Kahl, Johannes; Kesse-Guyot, Emmanuelle; Lairon, Denis; Lampkin, Nicolas; Løes, Anne-Kristin; Matt, Darja; Niggli, Urs; Paoletti, Flavio; Pehme, Sirli; Rembiałkowska, Ewa; Schader, Christian; Stolze, Matthias

    2015-01-01

    Organic production and consumption provide a delineated food system that can be explored for its potential contribution to sustainable diets. While organic agriculture improves the sustainability performance on the production side, critical reflections are made on how organic consumption patterns, understood as the practice of people consuming significant amounts of organic produce, may also be taken as an example for sustainable food consumption. The consumption patterns of regular organic consumers seem to be close to the sustainable diet concept of FAO. Certain organic-related measures might therefore be useful in the sustainability assessment of diets, e.g., organic production and organic consumption. Since diets play a central role in shaping food systems and food systems shape diets, the role of organic consumption emerges as an essential topic to be addressed. This role may be based on four important organic achievements: organic agriculture and food production has a definition, well-established principles, public standards, and useful metrics. By 2015, data for organic production and consumption are recorded annually from more than 160 countries, and regulations are in force in more than 80 countries or regions. The organic food system puts the land (agri-cultura) back into the diet; it is the land from which the diet in toto is shaped. Therefore, the organic food system provides essential components of a sustainable diet. PMID:26176912

  17. Diabetes mellitus disease management in a safety net hospital system: translating evidence into practice.

    Science.gov (United States)

    Butler, Michael K; Kaiser, Michael; Johnson, Jolene; Besse, Jay; Horswell, Ronald

    2010-12-01

    The Louisiana State University Health Care Services Division system assessed the effectiveness of implementing a multisite disease management program targeting diabetes mellitus in an indigent patient population. A population-based disease management program centered on evidence-based clinical care guidelines was applied from the system level. Specific clinic modifications and models were used, as well as ancillary services such as medication assistance and equipment subsidies. Marked improvement in process goals led to improved clinical outcomes. From 2001 to 2008, the percentage of patients with a hemoglobin A1c management programs can be successfully implemented and achieve statistically significant results.

  18. Clinical relevance of circulating cell-free microRNAs in ovarian cancer.

    Science.gov (United States)

    Nakamura, Koji; Sawada, Kenjiro; Yoshimura, Akihiko; Kinose, Yasuto; Nakatsuka, Erika; Kimura, Tadashi

    2016-06-24

    Ovarian cancer is the leading cause of death among gynecologic malignancies. Since ovarian cancer develops asymptomatically, it is often diagnosed at an advanced and incurable stage. Despite many years of research, there is still a lack of reliable diagnostic markers and methods for early detection and screening. Recently, it was discovered that cell-free microRNAs (miRNAs) circulate in the body fluids of healthy and diseased patients, suggesting that they may serve as a novel diagnostic marker. This review summarizes the current knowledge regarding the potential clinical relevance of circulating cell-free miRNA for ovarian cancer diagnosis, prognosis, and therapeutics. Despite the high levels of ribonucleases in many types of body fluids, most of the circulating miRNAs are packaged in microvesicles, exosomes, or apoptotic bodies, are binding to RNA-binding protein such as argonaute 2 or lipoprotein complexes, and are thus highly stable. Cell-free miRNA signatures are known to be parallel to those from the originating tumor cells, indicating that circulating miRNA profiles accurately reflect the tumor profiles. Since it is well established that the dysregulation of miRNAs is involved in the tumorigenesis of ovarian cancer, cell-free miRNAs circulating in body fluids such as serum, plasma, whole blood, and urine may reflect not only the existence of ovarian cancer but also tumor histology, stage, and prognoses of the patients. Several groups have successfully demonstrated that serum or plasma miRNAs are able to discriminate patients with ovarian cancer patients from healthy controls, suggesting that the addition of these miRNAs to current testing regimens may improve diagnosis accuracies for ovarian cancer. Furthermore, recent studies have revealed that changes in levels of cell-free circulating miRNAs are associated with the condition of cancer patients. Discrepancies between the results across studies due to the lack of an established endogenous miRNA control to

  19. Systems for the expression of orthogonal translation components in eubacterial host cells

    Science.gov (United States)

    Ryu, Youngha [San Diego, CA; Schultz, Peter G [La Jolla, CA

    2011-06-14

    The invention relates to compositions and methods for the in vivo production of polypeptides comprising one or more unnatural amino acids. Specifically, the invention provides plasmid systems for the efficient eubacterial expression of polypeptides comprising one or more unnatural amino acids at genetically-programmed positions.

  20. Systems for the expression of orthogonal translation components eubacterial host cells

    Science.gov (United States)

    Ryu, Youngha [San Diego, CA; Schultz, Peter G [La Jolla, CA

    2012-06-12

    The invention relates to compositions and methods for the in vivo production of polypeptides comprising one or more unnatural amino acids. Specifically, the invention provides plasmid systems for the efficient eubacterial expression of polypeptides comprising one or more unnatural amino acids at genetically-programmed positions.

  1. Evaluation of bipartite entanglement between two optical multi-mode systems using mode translation symmetry

    Science.gov (United States)

    Wu, Jun-Yi; Hofmann, Holger F.

    2017-10-01

    Optical multi-mode systems provide large scale Hilbert spaces that can be accessed and controlled using single photon sources, linear optics and photon detection. Here, we consider the bipartite entanglement generated by coherently distributing M photons in M modes to two separate locations, where linear optics and photon detection is used to verify the non-classical correlations between the two M-mode systems. We show that the entangled state is symmetric under mode shift operations performed in the two systems and use this symmetry to derive correlations between photon number distributions detected after a discrete Fourier transform (DFT) of the modes. The experimentally observable correlations can be explained by a simple and intuitive rule that relates the sum of the output mode indices to the eigenvalue of the input state under the mode shift operation. Since the photon number operators after the DFT do not commute with the initial photon number operators, entanglement is necessary to achieve strong correlations in both the initial mode photon numbers and the photon numbers observed after the DFT. We can therefore derive entanglement witnesses based on the experimentally observable correlations in both photon number distributions, providing a practical criterion for the evaluation of large scale entanglement in optical multi-mode systems. Our method thus demonstrates how non-classical signatures in large scale optical quantum circuits can be accessed experimentally by choosing an appropriate combination of modes in which to detect the photon number distributions that characterize the quantum coherences of the state.

  2. Found in Translation: Applying Lessons from Model Systems to Strigolactone Signaling in Parasitic Plants.

    Science.gov (United States)

    Lumba, Shelley; Subha, Asrinus; McCourt, Peter

    2017-07-01

    Strigolactones (SLs) are small molecules that act as endogenous hormones to regulate plant development as well as exogenous cues that help parasitic plants to infect their hosts. Given that parasitic plants are experimentally challenging systems, researchers are using two approaches to understand how they respond to host-derived SLs. The first involves extrapolating information on SLs from model genetic systems to dissect their roles in parasitic plants. The second uses chemicals to probe SL signaling directly in the parasite Striga hermonthica. These approaches indicate that parasitic plants have co-opted a family of α/β hydrolases to perceive SLs. The importance of this genetic and chemical information cannot be overstated since parasitic plant infestations are major obstacles to food security in the developing world. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Alcohol Use Disorders: Translational Utility of DSM-IV Liabilities to the DSM-5 System.

    Science.gov (United States)

    Kiselica, Andrew M; Cohn, Amy M; Hagman, Brett T

    2015-03-01

    Young adults have some of the highest rates of problem drinking and alcohol use disorders (AUDs) relative to any other age. However, recent evidence suggests that the DSM-IV hierarchical classification system of AUDs does not validly represent symptoms in the population; instead, it evinces a unitary, dimensional classification scheme. The DSM-5 has been altered to fit this changing, evidence-based conceptualization. Nevertheless, little is understood about the degree to which known risk factors for DSM-IV AUD diagnoses will transfer to the new DSM-5 guidelines in this group of high-risk drinkers. The current study built a coherent model of liabilities for DSM-IV AUDs in young adults and tested for transferability to DSM-5. N = 496 college students (51.10% male) were assessed on a variety of factors related to AUD risk, including demographics, substance use (past 90-days), and drinking motives. Liability models were created using all variables in Structural Equation Modeling to test direct and indirect effects on DSM diagnostic status. The best model under the DSM-IV was chosen based on fit and parsimony. This model was then applied to the DSM-5 system to test for transferability. The best the fitting model for DSM-IV included direct influences of drug use, quantity-frequency of alcohol consumption, and social and coping drinking motives. Improved model fit was found when the DSM-5 system was the outcome. Knowledge of risk factors for AUDs appear to transfer well to the new diagnostic system.

  4. Translating place identity into transmedia communication systems: Communication design process and methods

    OpenAIRE

    Scuri, Sabrina; Chiodo, Elisa; Calabi, Daniela

    2016-01-01

    [EN] The paper discusses the role of Communication Design in promoting cultural heritage and enhancing local identity. It deals with the need of designing communication systems able to increase people's understanding and engagement with a given place. We argue that a communication strategy able to leverage on both tangible and intangible aspects of place identity leads to a more mindful tourism consumption, and it is a means to strengthen citizens' sense of belonging as well. T...

  5. How the organic food system supports sustainable diets and translates these into practice

    Directory of Open Access Journals (Sweden)

    Carola eStrassner

    2015-06-01

    Full Text Available Organic production and consumption provide a delineated food system that can be explored for its potential contribution to sustainable diets. While organic agriculture improves the sustainability performance on the production side, critical reflections are made on how organic consumption patterns, understood as the practice of people consuming significant amounts of organic produce, may also be taken as an example for sustainable food consumption. The consumption patterns of regular organic consumers seem to be close to the sustainable diet concept of FAO. Certain organic-related measures might therefore be useful in the sustainability assessment of diets, e.g. organic production and organic consumption. Since diets play a central role in shaping food systems and food systems shape diets, the role of organic consumption emerges as an essential topic to be addressed. This role may be based on four important organic achievements: organic agriculture and food production has a definition, well-established principles, public standards and useful metrics. By 2015 data for organic production and consumption is recorded annually from more than 160 countries, and regulations are in force in more than 80 countries or regions. The organic fo

  6. Word translation entropy in translation

    DEFF Research Database (Denmark)

    Dragsted, Barbara; Hvelplund, Kristian Tangsgaard; Balling, Laura Winther

    2016-01-01

    This study reports on an investigation into the relationship between the number of translation alternatives for a single word and eye movements on the source text. In addition, the effect of word order differences between source and target text on eye movements on the source text is studied. In p...

  7. Not lost in translation: generalization of the primary systems hypothesis to Japanese-specific language processes.

    Science.gov (United States)

    Ueno, Taiji; Saito, Satoru; Saito, Akie; Tanida, Yuki; Patterson, Karalyn; Lambon Ralph, Matthew A

    2014-02-01

    The emergentist-connectionist approach assumes that language processing reflects interaction between primary neural systems (Primary Systems Hypothesis). This idea offers an overarching framework that generalizes to various kinds of (English) language and nonverbal cognitive activities. The current study advances this approach with respect to language in two new and important ways. The first is the provision of a neuroanatomically constrained implementation of the theory. The second is a test of its ability to generalize to a language other than English (in this case Japanese) and, in particular, to a feature of that language (pitch accent) for which there is no English equivalent. A corpus analysis revealed the presence and distribution of typical and atypical accent forms in Japanese vocabulary, forming a quasiregular domain. Consequently, according to the Primary Systems Hypothesis, there should be a greater semantic impact on the processing of words with an atypical pitch accent. In turn, when word meaning is intrinsically less rich (e.g., abstract words), speakers should be prone to regularization errors of pitch accent. We explored these semantic-phonological interactions, first, in a neuroanatomically constrained, parallel-distributed processing model of spoken language processing. This model captured the accent typicality effect observed in nonword repetition in Japanese adults and children and exhibited the predicted semantic impact on repetition of words with atypical accent patterns. Second, also as predicted, in word repetition and immediate serial recall of spoken words, human participants exhibited reduced pitch-accent accuracy and/or slower RT for low imageability words with atypical accent patterns, and they generated accent errors reflecting the more typical accent patterns found in Japanese.

  8. Pre-analytical conditions in non-invasive prenatal testing of cell-free fetal RHD.

    Directory of Open Access Journals (Sweden)

    Frederik Banch Clausen

    Full Text Available BACKGROUND: Non-invasive prenatal testing of cell-free fetal DNA (cffDNA in maternal plasma can predict the fetal RhD type in D negative pregnant women. In Denmark, routine antenatal screening for the fetal RhD gene (RHD directs the administration of antenatal anti-D prophylaxis only to women who carry an RhD positive fetus. Prophylaxis reduces the risk of immunization that may lead to hemolytic disease of the fetus and the newborn. The reliability of predicting the fetal RhD type depends on pre-analytical factors and assay sensitivity. We evaluated the testing setup in the Capital Region of Denmark, based on data from routine antenatal RHD screening. METHODS: Blood samples were drawn at gestational age 25 weeks. DNA extracted from 1 mL of plasma was analyzed for fetal RHD using a duplex method for exon 7/10. We investigated the effect of blood sample transportation time (n = 110 and ambient outdoor temperatures (n = 1539 on the levels of cffDNA and total DNA. We compared two different quantification methods, the delta Ct method and a universal standard curve. PCR pipetting was compared on two systems (n = 104. RESULTS: The cffDNA level was unaffected by blood sample transportation for up to 9 days and by ambient outdoor temperatures ranging from -10 °C to 28 °C during transport. The universal standard curve was applicable for cffDNA quantification. Identical levels of cffDNA were observed using the two automated PCR pipetting systems. We detected a mean of 100 fetal DNA copies/mL at a median gestational age of 25 weeks (range 10-39, n = 1317. CONCLUSION: The setup for real-time PCR-based, non-invasive prenatal testing of cffDNA in the Capital Region of Denmark is very robust. Our findings regarding the transportation of blood samples demonstrate the high stability of cffDNA. The applicability of a universal standard curve facilitates easy cffDNA quantification.

  9. Pre-Analytical Conditions in Non-Invasive Prenatal Testing of Cell-Free Fetal RHD

    Science.gov (United States)

    Rieneck, Klaus; Krog, Grethe Risum; Nielsen, Leif Kofoed; Tabor, Ann; Dziegiel, Morten Hanefeld

    2013-01-01

    Background Non-invasive prenatal testing of cell-free fetal DNA (cffDNA) in maternal plasma can predict the fetal RhD type in D negative pregnant women. In Denmark, routine antenatal screening for the fetal RhD gene (RHD) directs the administration of antenatal anti-D prophylaxis only to women who carry an RhD positive fetus. Prophylaxis reduces the risk of immunization that may lead to hemolytic disease of the fetus and the newborn. The reliability of predicting the fetal RhD type depends on pre-analytical factors and assay sensitivity. We evaluated the testing setup in the Capital Region of Denmark, based on data from routine antenatal RHD screening. Methods Blood samples were drawn at gestational age 25 weeks. DNA extracted from 1 mL of plasma was analyzed for fetal RHD using a duplex method for exon 7/10. We investigated the effect of blood sample transportation time (n = 110) and ambient outdoor temperatures (n = 1539) on the levels of cffDNA and total DNA. We compared two different quantification methods, the delta Ct method and a universal standard curve. PCR pipetting was compared on two systems (n = 104). Results The cffDNA level was unaffected by blood sample transportation for up to 9 days and by ambient outdoor temperatures ranging from -10°C to 28°C during transport. The universal standard curve was applicable for cffDNA quantification. Identical levels of cffDNA were observed using the two automated PCR pipetting systems. We detected a mean of 100 fetal DNA copies/mL at a median gestational age of 25 weeks (range 10–39, n = 1317). Conclusion The setup for real-time PCR-based, non-invasive prenatal testing of cffDNA in the Capital Region of Denmark is very robust. Our findings regarding the transportation of blood samples demonstrate the high stability of cffDNA. The applicability of a universal standard curve facilitates easy cffDNA quantification. PMID:24204719

  10. The cell-free fetal DNA fraction in maternal blood decreases after physical activity

    DEFF Research Database (Denmark)

    Schlütter, Jacob Mørup; Hatt, Lotte; Bach, Cathrine

    2014-01-01

    of cycling with a pulse-rate of 150 beats per minute. The concentrations of cffDNA (DYS14) and cfDNA (RASSF1A) were assessed using quantitative real-time polymerase chain reaction. RESULTS: The fetal fraction decreased significantly in all participants after physical activity (p ...OBJECTIVE: If noninvasive prenatal testing using next generation sequencing is to be effective for pregnant women, a cell-free fetal DNA (cffDNA) fraction above 4% is essential unless the depth of sequencing is increased. This study's objective is to determine whether physical activity has...... an effect on the proportion of cell-free DNA (cfDNA) arising from the fetus (fetal fraction). METHODS: Nine pregnant women carrying male fetuses at gestational age 12(+0)  weeks to 14(+6)  weeks were included. Plasma from nine pregnant women was drawn prior to, immediately after, and 30 min after 30 min...

  11. LimsPortal and BonsaiLIMS: development of a lab information management system for translational medicine

    Directory of Open Access Journals (Sweden)

    Afzal Vackar

    2011-05-01

    Full Text Available Abstract Background Laboratory Information Management Systems (LIMS are an increasingly important part of modern laboratory infrastructure. As typically very sophisticated software products, LIMS often require considerable resources to select, deploy and maintain. Larger organisations may have access to specialist IT support to assist with requirements elicitation and software customisation, however smaller groups will often have limited IT support to perform the kind of iterative development that can resolve the difficulties that biologists often have when specifying requirements. Translational medicine aims to accelerate the process of treatment discovery by bringing together multiple disciplines to discover new approaches to treating disease, or novel applications of existing treatments. The diverse set of disciplines and complexity of processing procedures involved, especially with the use of high throughput technologies, bring difficulties in customizing a generic LIMS to provide a single system for managing sample related data within a translational medicine research setting, especially where limited IT support is available. Results We have designed and developed a LIMS, BonsaiLIMS, around a very simple data model that can be easily implemented using a variety of technologies, and can be easily extended as specific requirements dictate. A reference implementation using Oracle 11 g database and the Python framework, Django is presented. Conclusions By focusing on a minimal feature set and a modular design we have been able to deploy the BonsaiLIMS system very quickly. The benefits to our institute have been the avoidance of the prolonged implementation timescales, budget overruns, scope creep, off-specifications and user fatigue issues that typify many enterprise software implementations. The transition away from using local, uncontrolled records in spreadsheet and paper formats to a centrally held, secured and backed-up database brings the

  12. LimsPortal and BonsaiLIMS: development of a lab information management system for translational medicine.

    Science.gov (United States)

    Bath, Timothy G; Bozdag, Selcuk; Afzal, Vackar; Crowther, Daniel

    2011-05-13

    Laboratory Information Management Systems (LIMS) are an increasingly important part of modern laboratory infrastructure. As typically very sophisticated software products, LIMS often require considerable resources to select, deploy and maintain. Larger organisations may have access to specialist IT support to assist with requirements elicitation and software customisation, however smaller groups will often have limited IT support to perform the kind of iterative development that can resolve the difficulties that biologists often have when specifying requirements. Translational medicine aims to accelerate the process of treatment discovery by bringing together multiple disciplines to discover new approaches to treating disease, or novel applications of existing treatments. The diverse set of disciplines and complexity of processing procedures involved, especially with the use of high throughput technologies, bring difficulties in customizing a generic LIMS to provide a single system for managing sample related data within a translational medicine research setting, especially where limited IT support is available. We have designed and developed a LIMS, BonsaiLIMS, around a very simple data model that can be easily implemented using a variety of technologies, and can be easily extended as specific requirements dictate. A reference implementation using Oracle 11 g database and the Python framework, Django is presented. By focusing on a minimal feature set and a modular design we have been able to deploy the BonsaiLIMS system very quickly. The benefits to our institute have been the avoidance of the prolonged implementation timescales, budget overruns, scope creep, off-specifications and user fatigue issues that typify many enterprise software implementations. The transition away from using local, uncontrolled records in spreadsheet and paper formats to a centrally held, secured and backed-up database brings the immediate benefits of improved data visibility, audit and

  13. Translating democracy

    DEFF Research Database (Denmark)

    Doerr, Nicole

    2012-01-01

    grassroots activists in social movements use translation as a novel practice to debate political alternatives in the European Union's (EU) multilingual public sphere. In recent years, new cross-European protest movements have created the multilingual discursive democracy arena known as the European Social...... Forum (ESF). I compare deliberative practices in the multilingual ESF preparatory meetings with those in monolingual national Social Forum meetings in three Western European countries. My comparison shows that multilingualism does not reduce the inclusivity of democratic deliberation as compared...... in institutionalized habits and norms of deliberation. Addressing democratic theorists, my findings suggest that translation could be a way to think about difference not as a hindrance but as a resource for democracy in linguistically heterogeneous societies and public spaces, without presupposing a shared language...

  14. Recent advances in cell-free PrPSc amplification technique.

    Science.gov (United States)

    Atarashi, Ryuichiro

    2009-01-01

    The development of amplification technology for abnormal forms of prion protein in vitro has had a great impact on the field of prion research. This novel technology has generated new possibilities for understanding the molecular basis of prions and for developing an early diagnostic test for prion diseases. This review provides an overview of recent progress in cell-free PrPSc amplification techniques.

  15. Circulating cell-free DNA and its integrity as a prognostic marker for breast cancer

    OpenAIRE

    Iqbal, Sobuhi; Vishnubhatla, Sreenivas; Raina, Vinod; Sharma, Surabhi; Gogia, Ajay; Deo, Suryanarayana S V; Mathur, Sandeep; Shukla, Nutan Kumar

    2015-01-01

    The aim of our study was to look for alternative predictive biomarkers for breast cancer management in limited resource setup. A comprehensive analysis of circulating cell-free DNA (CCFD) in serum at baseline was performed to assess its prognostic potential. Quantitative polymerase chain reaction (qPCR) of ALU sequences using ALU115 and ALU247 primers was carried out in patients (N: baseline 148, postoperative 47) and 51 healthy controls. Mean serum DNA integrity, levels of ALU 247 and levels...

  16. Enzymatic cyanide degradation by cell-free extract of Rhodococcus UKMP-5M.

    Science.gov (United States)

    Nallapan Maniyam, Maegala; Sjahrir, Fridelina; Latif Ibrahim, Abdul; Cass, Anthony E G

    2015-01-01

    The cell-free extract of locally isolated Rhodococcus UKMP-5M strain was used as an alternative to develop greener and cost effective cyanide removal technology. The present study aims to assess the viability of the cell-free extract to detoxify high concentrations of cyanide which is measured through the monitoring of protein concentration and specific cyanide-degrading activity. When cyanide-grown cells were subjected to grinding in liquid nitrogen which is relatively an inexpressive and fast cell disruption method, highest cyanide-degrading activity of 0.63 mM min(-1) mg(-1) protein was obtained in comparison to enzymatic lysis and agitation with fine glass beads. The cell-free extracts managed to degrade 80% of 20 mM KCN within 80 min and the rate of cyanide consumption increased linearly as the concentration of protein was raised. In both cases, the addition of co-factor was not required which proved to be advantageous economically. The successful formation of ammonia and formate as endproducts indicated that the degradation of cyanide by Rhodococcus UKMP-5M proceeded via the activity of cyanidase and the resulting non-toxic products are safe for disposal into the environment. Further verification with SDS-PAGE revealed that the molecular weight of the active enzyme was estimated to be 38 kDa, which is consistent with previously reported cyanidases. Thus, the utilization of cell-free extracts as an alternative to live microbial in cyanide degradation offers numerous advantageous such as the potential to tolerate and degrade higher concentration of cyanide and total reduction in the overall cost of operation since the requirement for nutrient support is irrelevant.

  17. Percutaneous Mitral Valve Repair in Mitral Regurgitation Reduces Cell-Free Hemoglobin and Improves Endothelial Function.

    Directory of Open Access Journals (Sweden)

    Christos Rammos

    Full Text Available Endothelial dysfunction is predictive for cardiovascular events and may be caused by decreased bioavailability of nitric oxide (NO. NO is scavenged by cell-free hemoglobin with reduction of bioavailable NO up to 70% subsequently deteriorating vascular function. While patients with mitral regurgitation (MR suffer from an impaired prognosis, mechanisms relating to coexistent vascular dysfunctions have not been described yet. Therapy of MR using a percutaneous mitral valve repair (PMVR approach has been shown to lead to significant clinical benefits. We here sought to investigate the role of endothelial function in MR and the potential impact of PMVR.Twenty-seven patients with moderate-to-severe MR treated with the MitraClip® device were enrolled in an open-label single-center observational study. Patients underwent clinical assessment, conventional echocardiography, and determination of endothelial function by measuring flow-mediated dilation (FMD of the brachial artery using high-resolution ultrasound at baseline and at 3-month follow-up. Patients with MR demonstrated decompartmentalized hemoglobin and reduced endothelial function (cell-free plasma hemoglobin in heme 28.9±3.8 μM, FMD 3.9±0.9%. Three months post-procedure, PMVR improved ejection fraction (from 41±3% to 46±3%, p = 0.03 and NYHA functional class (from 3.0±0.1 to 1.9±1.7, p<0.001. PMVR was associated with a decrease in cell free plasma hemoglobin (22.3±2.4 μM, p = 0.02 and improved endothelial functions (FMD 4.8±1.0%, p<0.0001.We demonstrate here that plasma from patients with MR contains significant amounts of cell-free hemoglobin, which is accompanied by endothelial dysfunction. PMVR therapy is associated with an improved hemoglobin decompartmentalization and vascular function.

  18. Numerical simulations of the mutual effect among the superconducting constituents in a levitation system with translational symmetry

    Science.gov (United States)

    Ma, Guang-Tong; Liu, Huan; Li, Xing-Tian; Zhang, Han; Xu, Yuan-Yuan

    2014-02-01

    By the introduction of a generalized magnetic vector potential, which contains the contributions of both the magnetic and electric parts, and the use of the Ampere's law within the quasistatic approximation as the state equation, the partial differential equations for governing the electromagnetic properties of superconductors as well as the surrounding coolant were established and numerically discretized by resorting to the finite-element technique and finite-difference scheme, respectively, in the spatial and temporal domain. In conjunction with an analytic method to calculate the magnetic field generated by permanent magnet, we compiled a numerical tool for performing an intricate study of the mutual effect among the superconducting constituents in a superconducting levitation system with translational symmetry. Taking a superconducting unit with three constituents inside as a practice, we simulated the electromagnetic responses of this unit while moving in the nonuniform magnetic field generated by permanent magnet guideway and, identified the influences of the mutual effect on the levitation force as well as on the distributions of the magnetic flux density, the supercurrent density, and the levitation force density by comparing to an envisaged reference, one constituent was simulated with all the rest absent to remove the mutual effect. The insights attained by the present study, mostly being inaccessible from the experiments, are aimed to provide useful implications for the design of a superconducting levitation system for the transit and analogous purposes, which usually employ multiple superconductors to achieve the desired capability.

  19. Characterization of dye decolorization in cell-free culture broth of Trametes versicolor CBR43.

    Science.gov (United States)

    Ryu, Hyun; Ryu, Hee Wook; Cho, Kyung Suk

    2016-09-23

    The dye decolorization rate in a cell-free culture broth of the white rot fungus Trametes versicolor CBR43 was studied, including the effects of inhibitors of NaCl, Zn(II), and Cd(II) on dye decolorization activity. The maximum rates of dye decolorization in cell-free culture broth were 1410, 44.7, 41.2, and 0.19 μmol L-1 min-1 for Acid Blue 62, Acid Black 175, Reactive Blue 4, and Acid Red 114, respectively. The inhibition effects of NaCl, Zn(II), and Cd(II) on dye decolorization were quantitatively compared using the half maximal inhibition concentration (IC50), which indicates the concentration of an inhibitor required for 50% inhibition. Based on IC50 values, dye decolorization in the cell-free culture broth of CBR43 was most potently inhibited by Cd(II), whereas the inhibitory effect of NaCl was relatively low. The dye decolorization rates and IC50 data can be used in the design and development of a dye-wastewater treatment process using T. versicolor CBR43 and its operating factors.

  20. Stability of cell-free DNA from maternal plasma isolated following a single centrifugation step.

    Science.gov (United States)

    Barrett, Angela N; Thadani, Henna A; Laureano-Asibal, Cecille; Ponnusamy, Sukumar; Choolani, Mahesh

    2014-12-01

    Cell-free fetal DNA can be used for prenatal testing with no procedure-related risk to the fetus. However, yield of fetal DNA is low compared with maternal cell-free DNA fragments, resulting in technical challenges for some downstream applications. To maximize the fetal fraction, careful blood processing procedures are essential. We demonstrate that fetal fraction can be preserved using a single centrifugation step followed by postage of plasma to the laboratory for further processing. Digital PCR was used to quantify copies of total, maternal, and fetal DNA present in single-spun plasma at time points over a two-week period, compared with immediately processed double-spun plasma, with storage at room temperature, 4°C, and -80°C representing different postage scenarios. There was no significant change in total, maternal, or fetal DNA copy numbers when single-spun plasma samples were stored for up to 1 week at room temperature and 2 weeks at -80°C compared with plasma processed within 4 h. Following storage at 4°C no change in composition of cell-free DNA was observed. Single-spun plasma can be transported at room temperature if the journey is expected to take one week or less; shipping on dry ice is preferable for longer journeys. © 2014 John Wiley & Sons, Ltd.

  1. Characterisation of the changing genomic landscape of metastatic melanoma using cell free DNA.

    Science.gov (United States)

    Cutts, Anthony; Venn, Oliver; Dilthey, Alexander; Gupta, Avinash; Vavoulis, Dimitris; Dreau, Helene; Middleton, Mark; McVean, Gil; Taylor, Jenny C; Schuh, Anna

    2017-09-04

    Cancer is characterised by complex somatically acquired genetic aberrations that manifest as intra-tumour and inter-tumour genetic heterogeneity and can lead to treatment resistance. In this case study, we characterise the genome-wide somatic mutation dynamics in a metastatic melanoma patient during therapy using low-input (50 ng) PCR-free whole genome sequencing of cell-free DNA from pre-treatment and post-relapse blood samples. We identify de novo tumour-specific somatic mutations from cell-free DNA, while the sequence context of single nucleotide variants showed the characteristic UV-damage mutation signature of melanoma. To investigate the behaviour of individual somatic mutations during proto-oncogene B-Raf -targeted and immune checkpoint inhibition, amplicon-based deep sequencing was used to verify and track frequencies of 212 single nucleotide variants at 10 distinct time points over 13 months of treatment. Under checkpoint inhibition therapy, we observed an increase in mutant allele frequencies indicating progression on therapy 88 days before clinical determination of non-response positron emission tomogrophy-computed tomography. We also revealed mutations from whole genome sequencing of cell-free DNA that were not present in the tissue biopsy, but that later contributed to relapse. Our findings have potential clinical applications where high quality tumour-tissue derived DNA is not available.

  2. Monitoring of organ transplants through genomic analyses of circulating cell-free DNA

    Science.gov (United States)

    de Vlaminck, Iwijn

    Solid-organ transplantation is the preferred treatment for patients with end-stage organ diseases, but complications due to infection and acute rejection undermine its long-term benefits. While clinicians strive to carefully monitor transplant patients, diagnostic options are currently limited. My colleagues and I in the lab of Stephen Quake have found that a combination of next-generation sequencing with a phenomenon called circulating cell-free DNA enables non-invasive diagnosis of both infection and rejection in transplantation. A substantial amount of small fragments of cell-free DNA circulate in blood that are the debris of dead cells. We discovered that donor specific DNA is released in circulation during injury to the transplant organ and we show that the proportion of donor DNA in plasma is predictive of acute rejection in heart and lung transplantation. We profiled viral and bacterial DNA sequences in plasma of transplant patients and discovered that the relative representation of different viruses and bacteria is informative of immunosuppression. This discovery suggested a novel biological measure of a person's immune strength, a finding that we have more recently confirmed via B-cell repertoire sequencing. Lastly, our studies highlight applications of shotgun sequencing of cell-free DNA in the broad, hypothesis free diagnosis of infection.

  3. Translation of EMS: clinical practice and system oversight from core content study guide to best practices implementation in an Urban EMS system.

    Science.gov (United States)

    Tataris, Katie; Mercer, Mary; Brown, John

    2015-01-01

    Since 2009, the seminal text in emergency medical services (EMS) medicine has been used to guide the academic development of the new subspecialty but direct application of the material into EMS oversight has not been previously described. The EMS/Disaster Medicine fellowship program at our institution scheduled a monthly meeting to systematically review the text and develop a study guide to assist the fellow and affiliated faculty in preparation for the board examination. In addition to the summary of chapter content, the review included an assessment of areas from each chapter subject where our EMS system did not exhibit recommended characteristics. A matrix was developed in the form of a gap analysis to include specific recommendations based on each perceived gap. Initial review and completion dates for each identified gap enable tracking and a responsible party. This matrix assisted the fellow with development of projects for EMS system improvement in addition to focusing and prioritizing the work of other interested physicians working in the system. By discussing expert recommendations in the setting of an actual EMS system, the faculty can teach the fellow how to approach system improvements based on prior experiences and current stakeholders. This collaborative environment facilitates system-based practice and practice-based learning, aligning with ACGME core competencies. Our educational model has demonstrated the success of translating the text into action items for EMS systems. This model may be useful in other systems and could contribute to the development of EMS system standards nationwide.

  4. Pharmacometrics and systems pharmacology of immune checkpoint inhibitor nivolumab in cancer translational medicine

    Directory of Open Access Journals (Sweden)

    Sujit Nair

    2016-02-01

    Full Text Available Nivolumab, a fully human immunoglobulin G4 (IgG4 monoclonal antibody (mAb that targets the programmed cell death-1 (PD-1 inhibitory receptor expressed on lymphocytes and dendritic cells, has been approved for metastatic melanoma, advanced squamous non-small cell lung cancer (NSCLC and metastatic renal cell carcinoma. In this review, pharmacology and pharmacometrics systems of this immunopharmaceutical are discussed. Mechanistic actions of T-cell biology with respect to both “priming phase” (anti-cytotoxic T-lymphocyte associated antigen 4 (anti-CTLA-4 mAb; ipilimumab and “effector phase” (anti-PD-1 mAb; nivolumab was discussed, respectively. Key pharmacometric variables in anticancer efficacy of nivolumab such as target engagement, metabolism, pharmacology systems and clearance are elucidated with an emphasis on current knowledge from pre-clinical as well as phase 1, 2 and 3 clinical trials information, including the data presented at the American Society of Clinical Oncology (ASCO 2015 and European Cancer Congress 2015. Nivolumab biomarkers, safety, and synergistic combination immunotherapies are delineated. Nivolumab, administered via intravenous infusion, has an acceptable safety profile and good efficacy. Indeed, the way forward to leverage maximum benefits for the cancer patient may be to synergize anti-PD-1 blockade with complementary targets in immune checkpoint pathways or other oncogenic signal transduction pathways. The encouraging results with nivolumab lend credence to the promise of immune checkpoint blockade as a therapeutic strategy that has been come-of-age in clinical oncology. Of necessity, the burden of “financial toxicity” on cancer patients and families must be factored in considering nivolumab therapy. The problem of ligand PD-L1 being a weak biomarker in clinical practice was discussed. Appropriate patient selection methods including immunopharmacogenomics may be used to identify those patients who are most

  5. Automatic Evaluation of Machine Translation

    DEFF Research Database (Denmark)

    Martinez, Mercedes Garcia; Koglin, Arlene; Mesa-Lao, Bartolomé

    2015-01-01

    The availability of systems capable of producing fairly accurate translations has increased the popularity of machine translation (MT). The translation industry is steadily incorporating MT in their workflows engaging the human translator to post-edit the raw MT output in order to comply with a set...... of quality criteria in as few edits as possible. The quality of MT systems is generally measured by automatic metrics, producing scores that should correlate with human evaluation.In this study, we investigate correlations between one of such metrics, i.e. Translation Edit Rate (TER), and actual post......-editing effort as it is shown in post-editing process data collected under experimental conditions. Using the CasMaCat workbench as a post-editing tool, process data were collected using keystrokes and eye-tracking data from five professional translators under two different conditions: i) traditional post...

  6. Using example-based machine translation to translate DVD subtitles

    DEFF Research Database (Denmark)

    Flanagan, Marian

    Audiovisual Translation (AVT), and in particular subtitling, has been recognised as an area that could potentially benefit from the introduction of machine translation (followed by post-editing). In recent years the demands on subtitlers have increased, while the payment to subtitlers and time...... allotted to produce the subtitles have both decreased. Therefore, this market is recognised as a potential real-world application of MT. Recent publications have introduced Corpus-Based MT approaches to translate subtitles. An SMT system has been implemented in a Swedish subtitling company to translate...... is not fully known. In this paper we report on the success to date of using this hybrid system to translate English-German DVD subtitles, based on a human evaluation of the system output using real end-users of the subtitles. We then comment on the developments that are required to make the EBMT/SMT system...

  7. Translation Method and Computer Programme for Assisting the Same

    DEFF Research Database (Denmark)

    2013-01-01

    , a machine translation system translating the written source text into a set of translations hypotheses in the target language, and an integration module combining the set of spoken word hypotheses and the set of machine translation hypotheses obtaining a text in the target language. Thereby obtaining......The present invention relates to a translation method comprising the steps of: a translator speaking a translation of a written source text in a target language, an automatic speech recognition system converting the spoken translation into a set of phone and word hypotheses in the target language...... a significantly improved and faster translation compared to what is achieved by known translation methods....

  8. Imposed Environmental Stresses Facilitate Cell-Free Nanoparticle Formation by Deinococcus radiodurans.

    Science.gov (United States)

    Chen, Angela; Contreras, Lydia M; Keitz, Benjamin K

    2017-09-15

    The biological synthesis of metal nanoparticles has been examined in a wide range of organisms, due to increased interest in green synthesis and environmental remediation applications involving heavy metal ion contamination. Deinococcus radiodurans is particularly attractive for environmental remediation involving metal reduction, due to its high levels of resistance to radiation and other environmental stresses. However, few studies have thoroughly examined the relationships between environmental stresses and the resulting effects on nanoparticle biosynthesis. In this work, we demonstrate cell-free nanoparticle production and study the effects of metal stressor concentrations and identity, temperature, pH, and oxygenation on the production of extracellular silver nanoparticles by D. radiodurans R1. We also report the synthesis of bimetallic silver and gold nanoparticles following the addition of a metal stressor (silver or gold), highlighting how production of these particles is enabled through the application of environmental stresses. Additionally, we found that both the morphology and size of monometallic and bimetallic nanoparticles were dependent on the environmental stresses imposed on the cells. The nanoparticles produced by D. radiodurans exhibited antimicrobial activity comparable to that of pure silver nanoparticles and displayed catalytic activity comparable to that of pure gold nanoparticles. Overall, we demonstrate that biosynthesized nanoparticle properties can be partially controlled through the tuning of applied environmental stresses, and we provide insight into how their application may affect nanoparticle production in D. radiodurans during bioremediation.IMPORTANCE Biosynthetic production of nanoparticles has recently gained prominence as a solution to rising concerns regarding increased bacterial resistance to antibiotics and a desire for environmentally friendly methods of bioremediation and chemical synthesis. To date, a range of organisms

  9. The V-Cycle for system innovation translating a broad societal need into concrete product service solutions: the multifunctional centre Apeldoorn case

    NARCIS (Netherlands)

    Joore, J.P.

    2008-01-01

    In this paper a system innovation project is presented in which a sustainable future vision with a long-term perspective was developed and translated into short-term commercial innovation opportunities, which in turn can benefit the longer-term vision of society. The case described is a three-year

  10. Machine Translations of Chinese Mathematical Articles.

    Science.gov (United States)

    Loh, Shiu-Chang; And Others

    1978-01-01

    A practical machine translation system called CULT (Chinese University Language Translator), capable of translating Chinese mathematical texts into readable English, has been developed during the period 1969-1977 at the Chinese University of Hong Kong. Programs for the system are written in Standard FORTRAN and run on the ICL1904A computer system.…

  11. Random-lattice models and simulation algorithms for the phase equilibria in two-dimensional condensed systems of particles with coupled internal and translational degrees of freedom

    DEFF Research Database (Denmark)

    Nielsen, Morten; Miao, Ling; Ipsen, John Hjorth

    1996-01-01

    In this work we concentrate on phase equilibria in two-dimensional condensed systems of particles where both translational and internal degrees of freedom are present and coupled through microscopic interactions, with a focus on the manner of the macroscopic coupling between the two types...... where the spin degrees of freedom are slaved by the translational degrees of freedom and develop a first-order singularity in the order-disorder transition that accompanies the lattice-melting transition. The internal degeneracy of the spin states in model III implies that the spin order...... transitional properties for model III are discussed in relation to experiments on planar bilayers of lipid-chain molecules whose properties are determined by a subtle coupling between the translational variables and the intrachain conformational states....

  12. An Evaluation of Output Quality of Machine Translation (Padideh Software vs. Google Translate

    Directory of Open Access Journals (Sweden)

    Haniyeh Sadeghi Azer

    2015-08-01

    Full Text Available This study aims to evaluate the translation quality of two machine translation systems in translating six different text-types, from English to Persian. The evaluation was based on criteria proposed by Van Slype (1979. The proposed model for evaluation is a black-box type, comparative and adequacy-oriented evaluation. To conduct the evaluation, a questionnaire was assigned to end-users to evaluate the outputs to examine and determine, if the machine-generated translations are intelligible and acceptable from their point of view and which one of the machine-generated translations produced by Padideh software and Google Translate is more acceptable and useful from the end-users point of view. The findings indicate that, the machine-generated translations are intelligible and acceptable in translating certain text-types, for end-users and Google Translate is more acceptable from end-users point of view. Keywords: Machine Translation, Machine Translation Evaluation, Translation Quality

  13. A translational and systemic approach to transferring liver transplant recipients from pediatric to adult-oriented care settings.

    Science.gov (United States)

    Annunziato, Rachel A; Hogan, Brittany; Barton, Codette; Miloh, Tamir; Arnon, Ronen; Iyer, Kishore; Kerkar, Nanda

    2010-11-01

    The purpose of this review is to (i) describe systemic changes made in our clinical practice to facilitate transfer of transplant recipients from the pediatric to the adult service and (ii) provide the rationale for instituting these organizational changes. To determine specific areas patients struggle to master, a survey assessing behaviors indicative of health care management was administered in pediatrics. Based on the results of the survey, all liver transplant recipients who transfer out of pediatrics are given a comprehensive clinical protocol, which includes a transfer checklist containing prerequisite items derived from our prior work. Patients are furthermore invited to enroll in a research study prospectively tracking both medical and psychosocial outcomes at six-month intervals. Data are discussed by the pediatric and adult teams, and additional adjustments to the transfer process are implemented in response. A summary of our clinical interventions and the resources required for implementation are presented. In conclusion, preliminary studies have demonstrated that transplant recipients are vulnerable to disruptions in health care management when they transfer out of pediatrics. This study describes one site's translational efforts to improve the transfer process for both the recipients and the clinicians, thus improving outcomes. © 2010 John Wiley & Sons A/S.

  14. A Systems Biology Overview on Human Diabetic Nephropathy: From Genetic Susceptibility to Post-Transcriptional and Post-Translational Modifications.

    Science.gov (United States)

    Conserva, Francesca; Gesualdo, Loreto; Papale, Massimo

    2016-01-01

    Diabetic nephropathy (DN), a microvascular complication occurring in approximately 20-40% of patients with type 2 diabetes mellitus (T2DM), is characterized by the progressive impairment of glomerular filtration and the development of Kimmelstiel-Wilson lesions leading to end-stage renal failure (ESRD). The causes and molecular mechanisms mediating the onset of T2DM chronic complications are yet sketchy and it is not clear why disease progression occurs only in some patients. We performed a systematic analysis of the most relevant studies investigating genetic susceptibility and specific transcriptomic, epigenetic, proteomic, and metabolomic patterns in order to summarize the most significant traits associated with the disease onset and progression. The picture that emerges is complex and fascinating as it includes the regulation/dysregulation of numerous biological processes, converging toward the activation of inflammatory processes, oxidative stress, remodeling of cellular function and morphology, and disturbance of metabolic pathways. The growing interest in the characterization of protein post-translational modifications and the importance of handling large datasets using a systems biology approach are also discussed.

  15. Machine Aids to Translation.

    Science.gov (United States)

    Brinkmann, Karl-Heinz

    1981-01-01

    Describes the TEAM Program System of the Siemens Language Services Department, particularly the main features of its terminology data bank. Discusses criteria to which stored terminology must conform and methods of data bank utilization. Concludes by summarizing the consequences that machine-aided translation development has had for the…

  16. Detection of polycistronic and overlapping bacteriophage T7 late transcripts by in vitro translation.

    Science.gov (United States)

    Pachl, C A; Young, E T

    1976-01-01

    Bacteriphage T7 RNAs have been fractionated on preparative polyacrylamide gels. The in vitro coding capacities of the RNAs have been determined by translation of the RNAs in a cell-free system and analysis of the polypeptide products on sodium dodecyl sulfate polyacrylamide slab gels. The T7 early RNAs are fractionated according to their molecular weight and without intermolecular aggregation. Fractionation of the late T7 RNAs gives rise to 10 major RNAs, ranging in size from 0.29 X 10(6) daltons to 2.05 X 10(6) daltons. Five of these RNAs are polycistronic and overlapping species are present for some T7 proteins. In particular, the gene 10 protein, the major capsid protein, is translated from at least three mRNAs. The smallest of these gene 10 mRNAs is monocistronic. A second gene 10 mRNA also codes for the gene 9 protein, and a third gene 10 mRNA codes for both gene 8 and gene 9 proteins. The T7 gene 3.5 protein, a T7 lytic enzyme, is also translated from several differently sized mRNAs. Comparison with published data on in vitro transcription by T7 RNA polymerase suggestes that transcription from multiple initiation sites and cleavage of larger precursors are both involved in generating the late T7 transcripts we observe. The overlapping mode of transcription could serve to amplify certain gene products. Images PMID:1061135

  17. Translational Molecular Nuclear Cardiology.

    Science.gov (United States)

    Thackeray, James T; Bengel, Frank M

    2016-02-01

    Increased rollout and availability of preclinical imaging provides a foundation for development of novel molecular nuclear imaging agents. The current armamentarium of radiotracers available for nuclear cardiology allows for the interrogation of critical molecular processes involved in a myriad of cardiovascular disorders, including altered metabolism, ventricular remodeling, sympathetic neuronal activation, and systemic inflammation. Effective translational molecular imaging requires coordination of clinical need with tracer development and molecular biology, leading to the identification of ideal translational imaging compounds. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Computer-aided translation tools

    DEFF Research Database (Denmark)

    Christensen, Tina Paulsen; Schjoldager, Anne

    2016-01-01

    in Denmark is rather high in general, but limited in the case of machine translation (MT) tools: While most TSPs use translation-memory (TM) software, often in combination with a terminology management system (TMS), only very few have implemented MT, which is criticised for its low quality output, especially......The paper reports on a questionnaire survey from 2013 of the uptake and use of computer-aided translation (CAT) tools by Danish translation service providers (TSPs) and discusses how these tools appear to have impacted on the Danish translation industry. According to our results, the uptake...... when Danish is one of the languages, though some also express willingness to consider using MT (more) when output quality improves. Most respondents report that CAT has changed the translation industry, mentioning that the technology facilitates improved productivity and consistency, but also...

  19. The RNA Helicase DeaD Stimulates ExsA Translation To Promote Expression of the Pseudomonas aeruginosa Type III Secretion System

    Science.gov (United States)

    Intile, Peter J.; Balzer, Grant J.; Wolfgang, Matthew C.

    2015-01-01

    ABSTRACT The Pseudomonas aeruginosa type III secretion system (T3SS) is a primary virulence factor important for phagocytic avoidance, disruption of host cell signaling, and host cell cytotoxicity. ExsA is the master regulator of T3SS transcription. The expression, synthesis, and activity of ExsA is tightly regulated by both intrinsic and extrinsic factors. Intrinsic regulation consists of the well-characterized ExsECDA partner-switching cascade, while extrinsic factors include global regulators that alter exsA transcription and/or translation. To identify novel extrinsic regulators of ExsA, we conducted a transposon mutagenesis screen in the absence of intrinsic control. Transposon disruptions within gene PA2840, which encodes a homolog of the Escherichia coli RNA-helicase DeaD, significantly reduced T3SS gene expression. Recent studies indicate that E. coli DeaD can promote translation by relieving inhibitory secondary structures within target mRNAs. We report here that PA2840, renamed DeaD, stimulates ExsA synthesis at the posttranscriptional level. Genetic experiments demonstrate that the activity of an exsA translational fusion is reduced in a deaD mutant. In addition, exsA expression in trans fails to restore T3SS gene expression in a deaD mutant. We hypothesized that DeaD relaxes mRNA secondary structure to promote exsA translation and found that altering the mRNA sequence of exsA or the native exsA Shine-Dalgarno sequence relieved the requirement for DeaD in vivo. Finally, we show that purified DeaD promotes ExsA synthesis using in vitro translation assays. Together, these data reveal a novel regulatory mechanism for P. aeruginosa DeaD and add to the complexity of global regulation of T3SS. IMPORTANCE Although members of the DEAD box family of RNA helicases are appreciated for their roles in mRNA degradation and ribosome biogenesis, an additional role in gene regulation is now emerging in bacteria. By relaxing secondary structures in mRNAs, DEAD box

  20. Whole resting cells vs. cell free extracts of Candida parapsilosis ATCC 7330 for the synthesis of gold nanoparticles

    National Research Council Canada - National Science Library

    Krishnan, Saravanan; Narayan, Shoba; Chadha, Anju

    2016-01-01

    The cell free extracts of Candida parapsilosis ATCC 7330 are more efficient than the whole resting cells of the yeast in the synthesis of directly usable gold nanoparticles as revealed by this systematic study...

  1. Translation and linguistic validation of the Pediatric Patient-Reported Outcomes Measurement Information System measures into simplified Chinese using cognitive interviewing methodology.

    Science.gov (United States)

    Liu, Yanyan; Hinds, Pamela S; Wang, Jichuan; Correia, Helena; Du, Shizheng; Ding, Jian; Gao, Wen Jun; Yuan, Changrong

    2013-01-01

    The Pediatric Patient-Reported Outcomes Measurement Information System (PROMIS) measures were developed using modern measurement theory and tested in a variety of settings to assess the quality of life, function, and symptoms of children and adolescents experiencing a chronic illness and its treatment. Developed in English, this set of measures had not been translated into Chinese. The objective of this study was to develop the Chinese version of the Pediatric PROMIS measures (C-Ped-PROMIS), specifically 8 short forms, and to pretest the translated measures in children and adolescents through cognitive interviewing methodology. The C-Ped-PROMIS was developed following the standard Functional Assessment of Chronic Illness Therapy Translation Methodology. Bilingual teams from the United States and China reviewed the translation to develop a provisional version, which was then pretested with cognitive interview by probing 10 native Chinese-speaking children aged 8 to 17 years in China. The translation was finalized by the bilingual teams. Most items, response options, and instructions were well understood by the children, and some revisions were made to address patient's comments during the cognitive interview. The results indicated that the C-Ped-PROMIS items were semantically and conceptually equivalent to the original. Children aged 8 to 17 years in China were able to comprehend these measures and express their experience and feelings about illness or their life. The C-Ped-PROMIS is available for psychometric validation. Future work will be directed at translating the rest of the item banks, calibrating them and creating a Chinese final version of the short forms.

  2. Folding of newly translated membrane protein CCR5 is assisted by the chaperonin GroEL-GroES

    Science.gov (United States)

    Chi, Haixia; Wang, Xiaoqiang; Li, Jiqiang; Ren, Hao; Huang, Fang

    2015-11-01

    The in vitro folding of newly translated human CC chemokine receptor type 5 (CCR5), which belongs to the physiologically important family of G protein-coupled receptors (GPCRs), has been studied in a cell-free system supplemented with the surfactant Brij-35. The freshly synthesized CCR5 can spontaneously fold into its biologically active state but only slowly and inefficiently. However, on addition of the GroEL-GroES molecular chaperone system, the folding of the nascent CCR5 was significantly enhanced, as was the structural stability and functional expression of the soluble form of CCR5. The chaperonin GroEL was partially effective on its own, but for maximum efficiency both the GroEL and its GroES lid were necessary. These results are direct evidence for chaperone-assisted membrane protein folding and therefore demonstrate that GroEL-GroES may be implicated in the folding of membrane proteins.

  3. Assessment of EGFR mutation status using cell-free DNA from bronchoalveolar lavage fluid.

    Science.gov (United States)

    Park, Sojung; Hur, Jae Young; Lee, Kye Young; Lee, Jae Cheol; Rho, Jin Kyung; Shin, Sun Hwa; Choi, Chang-Min

    2017-08-28

    Much attention has been focused on epidermal growth factor receptor (EGFR) mutation testing since the introduction of EGFR-tyrosine kinase inhibitors have improved survival in EGFR-positive lung cancer patients. Liquid biopsy using circulating tumor cells or cell-free DNA (cfDNA) has enabled less invasive testing, but requires a highly sensitive method. To date, liquid biopsy using bronchoalveolar lavage (BAL) fluid has rarely been used. From 20 patients with lung adenocarcinoma, we isolated cfDNA from 20 samples of cell-free BAL fluid and 19 cell-free bronchial washing samples. cfDNA was examined for EGFR mutations using peptide nucleic acid (PNA)-mediated PCR clamping method. In cases where the results from the tumor biopsy and BAL-derived cfDNA test were not consistent, PANAMutyper™ R EGFR kit was used along with PNA clamping-assisted fluorescence melting curve analysis. We included 17 patients with advanced stage disease and three with non-advanced stage disease. Tumor biopsy detected EGFR mutations in 12 of the patients. One patient had a p.L858R mutation and a de novo p.T790M mutation. The results from PNA-mediated PCR clamping were 75.0% (9/12) concordant with the tumor biopsy results for EGFR mutation status. PANAMutyper with fluorescence melting curve analysis was performed in three cases, which detected EGFR mutations in two more patients (11/12, 91.7%). EGFR mutations were detected in the cfDNA extracted from two bronchial washing samples. cfDNA from BAL fluid could be used for molecular testing of EGFR mutations and identification of p.T790M mutations, with an easily applicable method.

  4. Translator's preface.

    Science.gov (United States)

    Lamiell, James T

    2013-08-01

    Presents a preface from James T. Lamiell, who translates Wilhelm Wundt's Psychology's Struggle for Existence (Die Psychologie im Kampf ums Dasein), in which Wundt advised against the impending divorce of psychology from philosophy, into English. Lamiell comments that more than a decade into the 21st century, it appears that very few psychologists have any interest at all in work at the interface of psychology and philosophy. He notes that one clear indication of this is that the Society for Theoretical and Philosophical Psychology, which is Division 24 of the American Psychological Association (APA), remains one of the smallest of the APA's nearly 60 divisions. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

  5. Translating Harbourscapes

    DEFF Research Database (Denmark)

    Diedrich, Lisa Babette

    This thesis investigates site-specific design approaches in contemporary harbour transformation. The integration into the urban fabric of disused harbour areas, those spatial leftovers of late 19th- and 20th-century heavy industry, is a major task of contemporary urban planning. Common solutions...... for these areas feature generic office complexes, luxury housing, shopping centres and leisure facilities, built on the tabula rasa of the former harbours, only preserving the occasional old object from a harbour for folkloristic reasons. This research explores more site-specific ways to transform harbours, where......-specific design are proposed for all actors involved in harbour transformation. The study ends with an invitation to further investigate translation as a powerful metaphor for the way existing qualities of a site can be transformed, rather than erased or rewritten, and to explore how this metaphor can foster new...

  6. Whole resting cells vs. cell free extracts of Candida parapsilosis ATCC 7330 for the synthesis of gold nanoparticles

    OpenAIRE

    Krishnan, Saravanan; Narayan, Shoba; Chadha, Anju

    2016-01-01

    The cell free extracts of Candida parapsilosis ATCC 7330 are more efficient than the whole resting cells of the yeast in the synthesis of directly usable gold nanoparticles as revealed by this systematic study. Cell free extracts yielded gold nanoparticles of hydrodynamic diameter (50?200?nm). In this study, the total protein concentration influences the nanofabrication and not only the reductase enzymes as originally thought. Powder X-ray diffraction studies confirm the crystalline nature of...

  7. Mapping Translation Technology Research in Translation Studies

    DEFF Research Database (Denmark)

    Schjoldager, Anne; Christensen, Tina Paulsen; Flanagan, Marian

    2017-01-01

    Due to the growing uptake of translation technology in the language industry and its documented impact on the translation profession, translation students and scholars need in-depth and empirically founded knowledge of the nature and influences of translation technology (e.g. Christensen....../Schjoldager 2010, 2011; Christensen 2011). Unfortunately, the increasing professional use of translation technology has not been mirrored within translation studies (TS) by a similar increase in research projects on translation technology (Munday 2009: 15; O’Hagan 2013; Doherty 2016: 952). The current thematic...... section aims to improve this situation by presenting new and innovative research papers that reflect on recent technological advances and their impact on the translation profession and translators from a diversity of perspectives and using a variety of methods. In Section 2, we present translation...

  8. Mapping Translation Technology Research in Translation Studies

    DEFF Research Database (Denmark)

    Schjoldager, Anne; Christensen, Tina Paulsen; Flanagan, Marian

    2017-01-01

    Due to the growing uptake of translation technology in the language industry and its documented impact on the translation profession, translation students and scholars need in-depth and empirically founded knowledge of the nature and influences of translation technology (e.g. Christensen...... section aims to improve this situation by presenting new and innovative research papers that reflect on recent technological advances and their impact on the translation profession and translators from a diversity of perspectives and using a variety of methods. In Section 2, we present translation....../Schjoldager 2010, 2011; Christensen 2011). Unfortunately, the increasing professional use of translation technology has not been mirrored within translation studies (TS) by a similar increase in research projects on translation technology (Munday 2009: 15; O’Hagan 2013; Doherty 2016: 952). The current thematic...

  9. Circulating Cell-Free Tumour DNA in the Management of Cancer

    Directory of Open Access Journals (Sweden)

    Glenn Francis

    2015-06-01

    Full Text Available With the development of new sensitive molecular techniques, circulating cell-free tumour DNA containing mutations can be identified in the plasma of cancer patients. The applications of this technology may result in significant changes to the care and management of cancer patients. Whilst, currently, these “liquid biopsies” are used to supplement the histological diagnosis of cancer and metastatic disease, in the future these assays may replace the need for invasive procedures. Applications include the monitoring of tumour burden, the monitoring of minimal residual disease, monitoring of tumour heterogeneity, monitoring of molecular resistance and early diagnosis of tumours and metastatic disease.

  10. Construction of a Sequencing Library from Circulating Cell-Free DNA.

    Science.gov (United States)

    Fang, Nan; Löffert, Dirk; Akinci-Tolun, Rumeysa; Heitz, Katja; Wolf, Alexander

    2016-04-01

    Circulating DNA is cell-free DNA (cfDNA) in serum or plasma that can be used for non-invasive prenatal testing, as well as cancer diagnosis, prognosis, and stratification. High-throughput sequence analysis of the cfDNA with next-generation sequencing technologies has proven to be a highly sensitive and specific method in detecting and characterizing mutations in cancer and other diseases, as well as aneuploidy during pregnancy. This unit describes detailed procedures to extract circulating cfDNA from human serum and plasma and generate sequencing libraries from a wide concentration range of circulating DNA. Copyright © 2016 John Wiley & Sons, Inc.

  11. Pre-Analytical Conditions in Non-Invasive Prenatal Testing of Cell-Free Fetal RHD

    DEFF Research Database (Denmark)

    Clausen, Frederik Banch; Jakobsen, Tanja Roien; Rieneck, Klaus

    2013-01-01

    Non-invasive prenatal testing of cell-free fetal DNA (cffDNA) in maternal plasma can predict the fetal RhD type in D negative pregnant women. In Denmark, routine antenatal screening for the fetal RhD gene (RHD) directs the administration of antenatal anti-D prophylaxis only to women who carry an Rh......D positive fetus. Prophylaxis reduces the risk of immunization that may lead to hemolytic disease of the fetus and the newborn. The reliability of predicting the fetal RhD type depends on pre-analytical factors and assay sensitivity. We evaluated the testing setup in the Capital Region of Denmark, based...

  12. caTIES: a grid based system for coding and retrieval of surgical pathology reports and tissue specimens in support of translational research.

    Science.gov (United States)

    Crowley, Rebecca S; Castine, Melissa; Mitchell, Kevin; Chavan, Girish; McSherry, Tara; Feldman, Michael

    2010-01-01

    The authors report on the development of the Cancer Tissue Information Extraction System (caTIES)--an application that supports collaborative tissue banking and text mining by leveraging existing natural language processing methods and algorithms, grid communication and security frameworks, and query visualization methods. The system fills an important need for text-derived clinical data in translational research such as tissue-banking and clinical trials. The design of caTIES addresses three critical issues for informatics support of translational research: (1) federation of research data sources derived from clinical systems; (2) expressive graphical interfaces for concept-based text mining; and (3) regulatory and security model for supporting multi-center collaborative research. Implementation of the system at several Cancer Centers across the country is creating a potential network of caTIES repositories that could provide millions of de-identified clinical reports to users. The system provides an end-to-end application of medical natural language processing to support multi-institutional translational research programs.

  13. Establishment and Application of a High Throughput Screening System Targeting the Interaction between HCV Internal Ribosome Entry Site and Human Eukaryotic Translation Initiation Factor 3

    Directory of Open Access Journals (Sweden)

    Yuying Zhu

    2017-05-01

    Full Text Available Viruses are intracellular obligate parasites and the host cellular machinery is usually recruited for their replication. Human eukaryotic translation initiation factor 3 (eIF3 could be directly recruited by the hepatitis C virus (HCV internal ribosome entry site (IRES to promote the translation of viral proteins. In this study, we establish a fluorescence polarization (FP based high throughput screening (HTS system targeting the interaction between HCV IRES and eIF3. By screening a total of 894 compounds with this HTS system, two compounds (Mucl39526 and NP39 are found to disturb the interaction between HCV IRES and eIF3. And these two compounds are further demonstrated to inhibit the HCV IRES-dependent translation in vitro. Thus, this HTS system is functional to screen the potential HCV replication inhibitors targeting human eIF3, which is helpful to overcome the problem of viral resistance. Surprisingly, one compound HP-3, a kind of oxytocin antagonist, is discovered to significantly enhance the interaction between HCV IRES and eIF3 by this HTS system. HP-3 is demonstrated to directly interact with HCV IRES and promote the HCV IRES-dependent translation both in vitro and in vivo, which strongly suggests that HP-3 has potentials to promote HCV replication. Therefore, this HTS system is also useful to screen the potential HCV replication enhancers, which is meaningful for understanding the viral replication and screening novel antiviral drugs. To our knowledge, this is the first HTS system targeting the interaction between eIF3 and HCV IRES, which could be applied to screen both potential HCV replication inhibitors and enhancers.

  14. Systems Level Analysis of Histone H3 Post-translational Modifications (PTMs) Reveals Features of PTM Crosstalk in Chromatin Regulation*

    Science.gov (United States)

    Schwämmle, Veit; Sidoli, Simone; Ruminowicz, Chrystian; Wu, Xudong; Lee, Chung-Fan; Helin, Kristian; Jensen, Ole N.

    2016-01-01

    Histones are abundant chromatin constituents carrying numerous post-translational modifications (PTMs). Such PTMs mediate a variety of biological functions, including recruitment of enzymatic readers, writers and erasers that modulate DNA replication, transcription and repair. Individual histone molecules contain multiple coexisting PTMs, some of which exhibit crosstalk, i.e. coordinated or mutually exclusive activities. Here, we present an integrated experimental and computational systems level molecular characterization of histone PTMs and PTM crosstalk. Using wild type and engineered mouse embryonic stem cells (mESCs) knocked out in components of the Polycomb Repressive Complex 2 (PRC2, Suz12−/−), PRC1 (Ring1A/B−/−) and (Dnmt1/3a/3b−/−) we performed comprehensive PTM analysis of histone H3 tails (50 aa) by utilizing quantitative middle-down proteome analysis by tandem mass spectrometry. We characterized combinatorial PTM features across the four mESC lines and then applied statistical data analysis to predict crosstalk between histone H3 PTMs. We detected an overrepresentation of positive crosstalk (codependent marks) between adjacent mono-methylated and acetylated marks, and negative crosstalk (mutually exclusive marks) among most of the seven characterized di- and tri-methylated lysine residues in the H3 tails. We report novel features of PTM interplay involving hitherto poorly characterized arginine methylation and lysine methylation sites, including H3R2me, H3R8me and H3K37me. Integration of the H3 data with RNAseq data by coabundance clustering analysis of histone PTMs and histone modifying enzymes revealed correlations between PTM and enzyme levels. We conclude that middle-down proteomics is a powerful tool to determine conserved or dynamic interdependencies between histone marks, which paves the way for detailed investigations of the histone code. Histone H3 PTM data is publicly available in the CrossTalkDB repository at http

  15. Systems Level Analysis of Histone H3 Post-translational Modifications (PTMs) Reveals Features of PTM Crosstalk in Chromatin Regulation.

    Science.gov (United States)

    Schwämmle, Veit; Sidoli, Simone; Ruminowicz, Chrystian; Wu, Xudong; Lee, Chung-Fan; Helin, Kristian; Jensen, Ole N

    2016-08-01

    Histones are abundant chromatin constituents carrying numerous post-translational modifications (PTMs). Such PTMs mediate a variety of biological functions, including recruitment of enzymatic readers, writers and erasers that modulate DNA replication, transcription and repair. Individual histone molecules contain multiple coexisting PTMs, some of which exhibit crosstalk, i.e. coordinated or mutually exclusive activities. Here, we present an integrated experimental and computational systems level molecular characterization of histone PTMs and PTM crosstalk. Using wild type and engineered mouse embryonic stem cells (mESCs) knocked out in components of the Polycomb Repressive Complex 2 (PRC2, Suz12(-/-)), PRC1 (Ring1A/B(-/-)) and (Dnmt1/3a/3b(-/-)) we performed comprehensive PTM analysis of histone H3 tails (50 aa) by utilizing quantitative middle-down proteome analysis by tandem mass spectrometry. We characterized combinatorial PTM features across the four mESC lines and then applied statistical data analysis to predict crosstalk between histone H3 PTMs. We detected an overrepresentation of positive crosstalk (codependent marks) between adjacent mono-methylated and acetylated marks, and negative crosstalk (mutually exclusive marks) among most of the seven characterized di- and tri-methylated lysine residues in the H3 tails. We report novel features of PTM interplay involving hitherto poorly characterized arginine methylation and lysine methylation sites, including H3R2me, H3R8me and H3K37me. Integration of the H3 data with RNAseq data by coabundance clustering analysis of histone PTMs and histone modifying enzymes revealed correlations between PTM and enzyme levels. We conclude that middle-down proteomics is a powerful tool to determine conserved or dynamic interdependencies between histone marks, which paves the way for detailed investigations of the histone code. Histone H3 PTM data is publicly available in the CrossTalkDB repository at http

  16. Institutional capacity for health systems research in East and Central African schools of public health: knowledge translation and effective communication.

    Science.gov (United States)

    Ayah, Richard; Jessani, Nasreen; Mafuta, Eric M

    2014-06-02

    Local health systems research (HSR) provides policymakers and practitioners with contextual, evidence-based solutions to health problems. However, producers and users of HSR rarely understand the complexities of the context within which each operates, leading to the "know-do" gap. Universities are well placed to conduct knowledge translation (KT) integrating research production with uptake. The HEALTH Alliance Africa Hub, a consortium of seven schools of public health (SPHs) in East and Central Africa, was formed to build capacity in HSR. This paper presents information on the capacity of the various SPHs to conduct KT activities. In 2011, each member of the Africa Hub undertook an institutional HSR capacity assessment using a context-adapted and modified self-assessment tool. KT capacity was measured by several indicators including the presence of a KT strategy, an organizational structure to support KT activities, KT skills, and institutional links with stakeholders and media. Respondents rated their opinions on the various indicators using a 5-point Likert scale. Averages across all respondents for each school were calculated. Thereafter, each school held a results validation workshop. A total of 123 respondents from all seven SPHs participated. Only one school had a clear KT strategy; more commonly, research was disseminated at scientific conferences and workshops. While most respondents perceived their SPH as having strong institutional ties with organizations interested in HSR as well as strong institutional leadership, the organizational structures required to support KT activities were absent. Furthermore, individual researchers indicated that they had little time or skills to conduct KT. Additionally, institutional and individual links with policymakers and media were reported as weak. Few SPHs in Africa have a clear KT strategy. Strengthening the weak KT capacity of the SPHs requires working with institutional leadership to develop KT strategies designed

  17. Translating Translations: Selecting and Using Translated Early Childhood Materials.

    Science.gov (United States)

    Santos, Rosa Milagros; Lee, Sung Yoon; Valdivia, Rebeca; Zhang, Chun

    2001-01-01

    This article provides early intervention professionals with strategies for selecting and using translated materials. It stresses the importance of considering both the intended audience of the material and the quality of the translation itself. The article notes that many Web-based translator programs fail to capture the idiomatic usage or…

  18. False Negative Cell-Free DNA Screening Result in a Newborn with Trisomy 13

    Directory of Open Access Journals (Sweden)

    Yang Cao

    2016-01-01

    Full Text Available Background. Noninvasive prenatal screening (NIPS is revolutionizing prenatal screening as a result of its increased sensitivity, specificity. NIPS analyzes cell-free fetal DNA (cffDNA circulating in maternal plasma to detect fetal chromosome abnormalities. However, cffDNA originates from apoptotic placental trophoblast; therefore cffDNA is not always representative of the fetus. Although the published data for NIPS testing states that the current technique ensures high sensitivity and specificity for aneuploidy detection, false positives are possible due to isolated placental mosaicism, vanishing twin or cotwin demise, and maternal chromosome abnormalities or malignancy. Results. We report a case of false negative cell-free DNA (cfDNA screening due to fetoplacental mosaicism. An infant male with negative cfDNA screening result was born with multiple congenital abnormalities. Postnatal chromosome and FISH studies on a blood specimen revealed trisomy 13 in 20/20 metaphases and 100% interphase nuclei, respectively. FISH analysis on tissues collected after delivery revealed extraembryonic mosaicism. Conclusions. Extraembryonic tissue mosaicism is likely responsible for the false negative cfDNA screening result. This case illustrates that a negative result does not rule out the possibility of a fetus affected with a trisomy, as cffDNA is derived from the placenta and therefore may not accurately represent the fetal genetic information.

  19. Cell-free DNA in healthy individuals, noncancerous disease and strong prognostic value in colorectal cancer

    DEFF Research Database (Denmark)

    Spindler, Karen-Lise Garm; Appelt, Ane L; Pallisgaard, Niels

    2014-01-01

    The purpose was to investigate total cell-free DNA (cfDNA) in colorectal cancer (CRC) patients during treatment with second-line chemotherapy and in healthy controls and patients with different comorbidities. Patient treated with second-line irinotecan for metastatic CRC (n = 100), a cohort of he...... mutations added further prognostic impact, which was consistent when performed on the samples drawn at time of progression. In conclusion, cfDNA measurement holds important clinical information and could become a useful tool for prediction of outcome from chemotherapy in mCRC.......The purpose was to investigate total cell-free DNA (cfDNA) in colorectal cancer (CRC) patients during treatment with second-line chemotherapy and in healthy controls and patients with different comorbidities. Patient treated with second-line irinotecan for metastatic CRC (n = 100), a cohort...... of healthy controls with and without comorbidity (n = 70 and 100, respectively) were included. cfDNA was quantified by an in-house developed quantitative polymerase chain reaction from plasma samples drawn prior to the first cycle of chemotherapy and at time of progression. cfDNA levels were significantly...

  20. Mechanically stable solvent-free lipid bilayers in nano- and micro-tapered apertures for reconstitution of cell-free synthesized hERG channels.

    Science.gov (United States)

    Tadaki, Daisuke; Yamaura, Daichi; Araki, Shun; Yoshida, Miyu; Arata, Kohei; Ohori, Takeshi; Ishibashi, Ken-Ichi; Kato, Miki; Ma, Teng; Miyata, Ryusuke; Tozawa, Yuzuru; Yamamoto, Hideaki; Niwano, Michio; Hirano-Iwata, Ayumi

    2017-12-18

    The self-assembled bilayer lipid membrane (BLM) is the basic component of the cell membrane. The reconstitution of ion channel proteins in artificially formed BLMs represents a well-defined system for the functional analysis of ion channels and screening the effects of drugs that act on them. However, because BLMs are unstable, this limits the experimental throughput of BLM reconstitution systems. Here we report on the formation of mechanically stable solvent-free BLMs in microfabricated apertures with defined nano- and micro-tapered edge structures. The role of such nano- and micro-tapered structures on the stability of the BLMs was also investigated. Finally, this BLM system was combined with a cell-free synthesized human ether-a-go-go-related gene channel, a cardiac potassium channel whose relation to arrhythmic side effects following drug treatment is well recognized. Such stable BLMs as these, when combined with a cell-free system, represent a potential platform for screening the effects of drugs that act on various ion-channel genotypes.

  1. An exploratory investigation of the translation of Pacific Northwest Laboratory`s print manuals system to an on-line manuals system

    Energy Technology Data Exchange (ETDEWEB)

    Heubach, J.G.; Hunt, S.T.; Pond, L.R.

    1992-06-01

    Information management technology has proliferated in the past decade in response to the information explosion. As documentation accumulates, the need to access information residing in manuals, handbooks and regulations conveniently, accurately, and quickly has increased. However, studies show that only fractions of the available information is read (Martin, 1978). Consequently, one of the biggest challenges in linking information and electronic management of information is to use the power of communication technology to meet the information needs of the audience. Pacific Northwest Laboratories` (PNL) investigation of translating its print manual system to an on-line system fits this challenge precisely. PNL`s manuals contain a tremendous amount of information for which manual holders are responsible. To perform their tasks in compliance with policy and procedure guidelines, users need to access information accurately, conveniently, and quickly. In order to select and use information management tools wisely, answers must be sought to a few basic questions. Communication experts cite four key questions: What do users want? What do users need? What characteristics of an on-line information system affect its usefulness? Who are the users whose wants and needs are to be met? Once these questions are answered, attention can be focused on finding the best match between user requirements and technology characteristics and weighing the costs and benefits of proposed options.

  2. An exploratory investigation of the translation of Pacific Northwest Laboratory's print manuals system to an on-line manuals system

    Energy Technology Data Exchange (ETDEWEB)

    Heubach, J.G.; Hunt, S.T.; Pond, L.R.

    1992-06-01

    Information management technology has proliferated in the past decade in response to the information explosion. As documentation accumulates, the need to access information residing in manuals, handbooks and regulations conveniently, accurately, and quickly has increased. However, studies show that only fractions of the available information is read (Martin, 1978). Consequently, one of the biggest challenges in linking information and electronic management of information is to use the power of communication technology to meet the information needs of the audience. Pacific Northwest Laboratories' (PNL) investigation of translating its print manual system to an on-line system fits this challenge precisely. PNL's manuals contain a tremendous amount of information for which manual holders are responsible. To perform their tasks in compliance with policy and procedure guidelines, users need to access information accurately, conveniently, and quickly. In order to select and use information management tools wisely, answers must be sought to a few basic questions. Communication experts cite four key questions: What do users want What do users need What characteristics of an on-line information system affect its usefulness Who are the users whose wants and needs are to be met Once these questions are answered, attention can be focused on finding the best match between user requirements and technology characteristics and weighing the costs and benefits of proposed options.

  3. Cell-free reconstitution of vacuole membrane fragmentation reveals regulation of vacuole size and number by TORC1.

    Science.gov (United States)

    Michaillat, Lydie; Baars, Tonie Luise; Mayer, Andreas

    2012-03-01

    Size and copy number of organelles are influenced by an equilibrium of membrane fusion and fission. We studied this equilibrium on vacuoles-the lysosomes of yeast. Vacuole fusion can readily be reconstituted and quantified in vitro, but it had not been possible to study fission of the organelle in a similar way. Here we present a cell-free system that reconstitutes fragmentation of purified yeast vacuoles (lysosomes) into smaller vesicles. Fragmentation in vitro reproduces physiological aspects. It requires the dynamin-like GTPase Vps1p, V-ATPase pump activity, cytosolic proteins, and ATP and GTP hydrolysis. We used the in vitro system to show that the vacuole-associated TOR complex 1 (TORC1) stimulates vacuole fragmentation but not the opposing reaction of vacuole fusion. Under nutrient restriction, TORC1 is inactivated, and the continuing fusion activity then dominates the fusion/fission equilibrium, decreasing the copy number and increasing the volume of the vacuolar compartment. This result can explain why nutrient restriction not only induces autophagy and a massive buildup of vacuolar/lysosomal hydrolases, but also leads to a concomitant increase in volume of the vacuolar compartment by coalescence of the organelles into a single large compartment.

  4. Scaling-up impact in perinatology through systems science: Bridging the collaboration and translational divides in cross-disciplinary research and public policy.

    Science.gov (United States)

    Munar, Wolfgang; Hovmand, Peter S; Fleming, Carrie; Darmstadt, Gary L

    2015-08-01

    Despite progress over the past decade in reducing the global burden of newborn deaths, gaps in the knowledge base persist, and means of translating empirical findings into effective policies and programs that deliver life-saving interventions remain poorly understood. Articles in this issue highlight the relevance of transdisciplinary research in perinatology and calls for increased efforts to translate research into public policy and to integrate interventions into existing primary care delivery systems. Given the complexity and multi-causality of many of the remaining challenges in newborn health, and the effects that social and economic factors have over many newborn conditions, it has further been proposed that integrated, multi-sector public policies are also required. In this article, we discuss the application of systems science methods to advance transdisciplinary research and public policy-making in perinatology. Such approaches to research and public policy have been used to address various global challenges but have rarely been implemented in developing country settings. We propose that they hold great promise to improve not only our understanding of complex perinatology problems but can also help translate research-based insights into effective, multi-pronged solutions that deliver positive, intended effects. Examples of successful transdisciplinary science exist, but successes and failures are context specific, and there are no universal blueprints or formulae to reproduce what works in a specific context into different social system settings. Group model building is a tool, based in the field of System Dynamics, that we have used to facilitate transdisciplinary research and, to a lesser extent, policy formulation in a systematic and replicable way. In this article, we describe how group model building can be used and argue for scaling its use to further the translation of empirical evidence and insights into policy and action that increase maternal

  5. A rule driven bi-directional translation system for remapping queries and result sets between a mediated schema and heterogeneous data sources.

    OpenAIRE

    Shaker, R.; Mork, P.; Barclay, M; Tarczy-Hornoch, P.

    2002-01-01

    As the number of online biomedical data sources increases, so too do the number of ways to access such data. The research described herein focuses on creating a data access system that provides bi-directional translation and mapping of data between heterogeneous databases and a mediated schema. Semantic mapping rules stored in a knowledge base are used by our generalized software to convert XML query results obtained from each data source to a common schema representing a single ontology. We ...

  6. Technological Devices Improving System of Translating Languages: What About their Usefulness on the Applicability in Medicine and Health Sciences?

    Directory of Open Access Journals (Sweden)

    Adilia Maria Pires Sciarra

    2015-12-01

    Full Text Available ABSTRACT INTRODUCTION: In a world in which global communication is becoming ever more important and in which English is increasingly positioned as the pre-eminent international language, that is, English as a Lingua Franca refers to the use of English as a medium of communication between peoples of different languages. It is important to highlight the positive advances in communication in health, provided by technology. OBJECTIVE: To present an overview on some technological devices of translating languages provided by the Web as well as to point out some advantages and disadvantages specially using Google Translate in Medicine and Health Sciences. METHODS: A bibliographical survey was performed to provide an overview on the usefulness of online translators for applicability using written and spoken languages. RESULTS: As we have to consider this question to be further surely answered, this study could present some advantages and disadvantages in using translating online devices. CONCLUSION: Considering Medicine and Health Sciences as expressive into the human scientific knowledge to be spread worldwidely; technological devices available on communication should be used to overcome some language barriers either written or spoken, but with some caution depending on the context of their applicability.

  7. Technological Devices Improving System of Translating Languages: What About their Usefulness on the Applicability in Medicine and Health Sciences?

    Science.gov (United States)

    Sciarra, Adilia Maria Pires; Batigália, Fernando; Oliveira, Marcos Aurélio Barboza de

    2015-01-01

    In a world in which global communication is becoming ever more important and in which English is increasingly positioned as the pre-eminent international language, that is, English as a Lingua Franca refers to the use of English as a medium of communication between peoples of different languages. It is important to highlight the positive advances in communication in health, provided by technology. To present an overview on some technological devices of translating languages provided by the Web as well as to point out some advantages and disadvantages specially using Google Translate in Medicine and Health Sciences. A bibliographical survey was performed to provide an overview on the usefulness of online translators for applicability using written and spoken languages. As we have to consider this question to be further surely answered, this study could present some advantages and disadvantages in using translating online devices. Considering Medicine and Health Sciences as expressive into the human scientific knowledge to be spread worldwidely; technological devices available on communication should be used to overcome some language barriers either written or spoken, but with some caution depending on the context of their applicability.

  8. Quorum quenching activity in cell-free lysate of endophytic bacteria isolated from Pterocarpus santalinus Linn., and its effect on quorum sensing regulated biofilm in Pseudomonas aeruginosa PAO1.

    Science.gov (United States)

    Rajesh, P S; Ravishankar Rai, V

    2014-01-01

    Quorum sensing mechanism allows the microorganisms to resist the antibiotic treatment by forming biofilms. Quorum quenching is one of the mechanisms to control the development of drug resistance in microbes. Endophyte bacteria are beneficial to plant growth as they support the immune system against the pathogen attack. The endophytic bacteria present in Pterocarpus santalinus were screened for the presence of N-acyl homoserine lactones (AHLs) degrading bacteria using biosensor strains and further confirmed by quantifying the violacein production. Cell-free lysate of endophytic bacteria, Bacillus firmus PT18 and Enterobacter asburiae PT39 exhibited potent AHL degrading ability by inhibiting about 80% violacein production in biosensor strain. Furthermore, when the cell-free lysate was applied to Pseudomonas aeruginosa PAO1 and PAO1-JP2 biofilm it resulted in significant (p<0.01) inhibition of biofilm formation. The biofilm inhibition was confirmed by visualization of biofilm slides under fluorescence microscopy, which showed decrease in total biomass formation in treated slides. Isolation and amplification of the gene (aiiA) indicated that the presence of AHL lactonase in cell-free lysate and sequence alignment indicated that AiiA contains a "HXHXDH" zinc-binding motif that is being conserved in several groups of metallohydrolases. Therefore, the study shows the potential of AHLs degradation by AHL lactonase present in cell-free lysate of isolated endophytic bacteria and inhibition of quorum sensing regulated biofilm formation in P. aeruginosa PAO1. Copyright © 2013 Elsevier GmbH. All rights reserved.

  9. Cell-Free Total and Fetal DNA in First Trimester Maternal Serum and Subsequent Development of Preeclampsia.

    Science.gov (United States)

    Silver, Robert M; Myatt, Leslie; Hauth, John C; Leveno, Kenneth J; Peaceman, Alan M; Ramin, Susan M; Samuels, Philip; Saade, George; Sorokin, Yoram; Clifton, Rebecca G; Reddy, Uma M

    2017-01-01

    Objective The objective of this study was to assess the relationship between first trimester cell-free total and fetal DNA in maternal plasma and the subsequent development of preeclampsia. Study Design Nested case-control study of patients enrolled in the Combined Antioxidant and Preeclampsia Prediction Studies prediction study of 175 women who did and 175 women who did not develop preeclampsia. The predictive values of cell-free total and fetal DNA and the subsequent development of preeclampsia were measured using receiver operating characteristic curves. Results Cell-free total DNA was higher in African American (median; 25-75%; 6.15; 0.14-28.73; p = 0.02) and Hispanic (4.95; 0.20-26.82; p = 0.037) compared with white women (2.33; 0.03-13.10). Levels of cell-free total DNA were also associated with maternal body mass index (BMI) (p = 0.02). Cell-free total DNA levels were similar between women who later developed preeclampsia (3.52; 0.11-25.3) and controls (3.74; 0.12-21.14, p = 0.96). Conclusion There is no significant difference in levels of cell-free total DNA in the first trimester in women who subsequently develop preeclampsia. Levels of cell-free total DNA in the first trimester are increased in African American and Hispanic compared with white women, and levels increase with increasing BMI. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  10. Efficacy of bacteriocin-containing cell-free culture supernatants from lactic acid bacteria to control Listeria monocytogenes in food.

    Science.gov (United States)

    Hartmann, H Andreas; Wilke, Thomas; Erdmann, Ralf

    2011-03-30

    Consumer demands have led to an increased interest in the use of natural antimicrobials for food protection. With the objective of developing novel products for enhancing the microbial safety of food, we have tested cell-free culture supernatants (CFS's) of eight antagonistic bacterial strains for their efficacy to inhibit Listeria monocytogenes in different food matrices. The antagonistic strains represented different members of the order Lactobacillales as well as one isolate of Staphylococcus sciuri and all showed strong inhibition of L. monocytogenes on agar plates. Cell-free supernatants were obtained after growing the bacteria in a yeast extract-glucose broth. In six of the CFS's, different class IIa bacteriocins, namely leucocin A, leucocin B, mundticin L, pediocin PA-1, sakacin A, and sakacin X, were identified as the major anti-listerial compounds. For the other two strains, the active substances could not be ascertained conclusively. The minimal effective concentration (MEC) of the individual CFS's to achieve a 2.3 log(10) reduction of L. monocytogenes was determined in culture broth, whole milk, and ground beef at 4°C. While all bacteriocin-containing CFS's were effective in broth at concentrations from 52 to 205 AU/ml, significant higher concentrations were needed when applied in food. Best results were obtained using CFS's containing pediocin PA-1, that displayed only three- and ten-times higher MEC's in milk (307 AU/ml) and ground meat (1024 AU/g) compared to broth, respectively. A twenty-fold increase in the MEC (2048 AU/ml) was observed for a mundticin L-containing fermentate, and a CFS containing leucocin A and B was inactivated more than fifty-fold (>1280 AU/ml) in both food matrices. Remarkably, the sakacin A and sakacin X containing CFS's displayed very selective inactivation rates, in which sakacin A was only effective in meat (512 AU/g), while sakacin X was only effective in milk (2048 AU/ml). In all cases, inhibition of L. monocytogenes was

  11. Evaluating English to Arabic Machine Translation Using BLEU

    OpenAIRE

    Mohammed N. Al-Kabi; Taghreed M. Hailat; Emad M. Al-Shawakfa; Alsmadi, Izzat M.

    2013-01-01

    This study aims to compare the effectiveness of two popular machine translation systems (Google Translate and Babylon machine translation system) used to translate English sentences into Arabic relative to the effectiveness of English to Arabic human translation. There are many automatic methods used to evaluate different machine translators, one of these methods; Bilingual Evaluation Understudy (BLEU) method, which was adopted and implemented to achieve the main goal of this study. BLEU meth...

  12. Statistical machine translation for biomedical text: are we there yet?

    Science.gov (United States)

    Wu, Cuijun; Xia, Fei; Deleger, Louise; Solti, Imre

    2011-01-01

    In our paper we addressed the research question: "Has machine translation achieved sufficiently high quality to translate PubMed titles for patients?". We analyzed statistical machine translation output for six foreign language - English translation pairs (bi-directionally). We built a high performing in-house system and evaluated its output for each translation pair on large scale both with automated BLEU scores and human judgment. In addition to the in-house system, we also evaluated Google Translate's performance specifically within the biomedical domain. We report high performance for German, French and Spanish -- English bi-directional translation pairs for both Google Translate and our system.

  13. A GRAMMATICAL ADJUSTMENT ANALYSIS OF STATISTICAL MACHINE TRANSLATION METHOD USED BY GOOGLE TRANSLATE COMPARED TO HUMAN TRANSLATION IN TRANSLATING ENGLISH TEXT TO INDONESIAN

    Directory of Open Access Journals (Sweden)

    Eko Pujianto

    2017-04-01

    Full Text Available Google translate is a program which provides fast, free and effortless translating service. This service uses a unique method to translate. The system is called ―Statistical Machine Translation‖, the newest method in automatic translation. Machine translation (MT is an area of many kinds of different subjects of study and technique from linguistics, computers science, artificial intelligent (AI, translation theory, and statistics. SMT works by using statistical methods and mathematics to process the training data. The training data is corpus-based. It is a compilation of sentences and words of the languages (SL and TL from translation done by human. By using this method, Google let their machine discovers the rules for themselves. They do this by analyzing millions of documents that have already been translated by human translators and then generate the result based on the corpus/training data. However, questions arise when the results of the automatic translation prove to be unreliable in some extent. This paper questions the dependability of Google translate in comparison with grammatical adjustment that naturally characterizes human translators' specific advantage. The attempt is manifested through the analysis of the TL of some texts translated by the SMT. It is expected that by using the sample of TL produced by SMT we can learn the potential flaws of the translation. If such exists, the partial of more substantial undependability of SMT may open more windows to the debates of whether this service may suffice the users‘ need.

  14. Discriminative syntactic reranking for statistical machine translation

    NARCIS (Netherlands)

    Carter, S.; Monz, C.

    2010-01-01

    This paper describes a method that successfully exploits simple syntactic features for n-best translation candidate reranking using perceptrons. Our approach uses discriminative language modelling to rerank the n-best translations generated by a statistical machine translation system. The

  15. Induction of inflammatory responses from THP-1 cells by cell-free filtrates from clinical isolates of Alloiococcus otitidis.

    Science.gov (United States)

    Ashhurst-Smith, Christopher; Hall, Sharron T; Burns, Christine J; Stuart, John; Blackwell, C Caroline

    2014-04-01

    In our model system using the THP-1 monocytic cell line, whole heat-killed cells of Alloiococcus otitidis elicited several pro-inflammatory cytokines identified in ear effusions of children with otitis media (OM). Levels of these cytokines were equivalent to or greater than those elicited by a standard Gram-positive otopathogen, Streptococcus pneumoniae. The current study examined the hypothesis that extracellular material produced by A. otitidis might also contribute to the inflammatory responses in OM. Cell-free culture filtrates of recent A. otitidis isolates (n = 39) were tested for induction of pro-inflammatory cytokines from THP-1 cells primed with IFN-γ. The highest responses were from IL-8 followed by IL-1β, and the lowest from IL-6. Filtrates from nine isolates were treated with lysozyme or proteinase K to assess the nature of the extracellular stimulants. Peptidoglycan was not a major component eliciting the responses. There was no correlation between colony type or β-haemolysin production. Proteinase K treatment indicated extracellular proteins might induce the inflammatory responses, particularly the 70-75 ku band. Further studies on the role of the extracellular proteins of A. otitidis and cytokine responses in pathogenesis of ear infections are needed.

  16. The curious case of legal translation

    Directory of Open Access Journals (Sweden)

    E. Cornelius

    2011-06-01

    Full Text Available This article explores the nature and scope of legal translation which is an under-researched area in South Africa. In this article the author predicts that the demand for competent legal translators will increase in the future, evidenced by a recent call by the Department of Justice and Constitutional Development(DoJ&CD, inviting applications for ten positions for “legislative language practitioners”. However, legal translation differs substantially from general translation in the sense that legal translation is subject to heavy restrictions at all levels and legal considerations are of paramount importance in a country such as South Africa, which provides for eleven official languages. Legal translation involves different legal languages, different legal systems and different cultural systems that require specialised knowledge and skills of the translator. The aim of this article is to investigate the core competencies and skills the legal translator must have; to consider the balance between legal competence and translation or linguistic competence; and to propose a discourse-analytical method of source text analysis, developed by Bhatia as a simplification strategy, as this may be a powerful tool in the training of legal translators in South Africa. Recent developments in South Africa relating to the Department of Arts and Culture’s obligation to translate legislation into all official languages, have important consequences for legal translation in general and the training of legal translators in particular.

  17. Translator Attitudes towards Translator-Computer Interaction – Findings from a Workplace Study

    DEFF Research Database (Denmark)

    Bundgaard, Kristine

    2017-01-01

    ), referred to as MT-assisted TM translation, and in this type of tool, translators switch between editing TM matches and post-editing MT matches. It is generally assumed that translators’ attitudes towards technology impact on this interaction with the technology. Drawing on Eagly/ Chaiken’s (1995) de nition......Today technology is part and parcel of professional translation, and translation has therefore been characterised as Translator-Computer Interaction (TCI) (O’Brien 2012). Translation is increasingly carried out using Translation Memory (TM) systems which incorporate machine translation (MT...... resistances offered by the tool. The study shows that the translators express disfavour towards MT in many respects, but also acknowledge positive aspects of the technology and expect MT to play a signi cant role in their future working lives. The translators do not make many positive or negative comments...

  18. Producing cell-free culture broth of rhamnolipids as a cost-effective fungicide against plant pathogens.

    Science.gov (United States)

    Sha, Ruyi; Jiang, Lifang; Meng, Qin; Zhang, Guoliang; Song, Zhirong

    2012-08-01

    Biosurfactants of rhamnolipids have been enthusiastically investigated for substitutes of synthetic agrochemicals against plant pathogens. However, all such studies have been conducted on rhamnolipids with high purity which have limitations due to high costs. This paper focused on the applicability of rhamnolipid-containing cell-free culture broth. It was found that rhamnolipids in cell-free culture broth of Pseudomonas aeruginosa ZJU211 were largely composed of di-rhamnolipid and mono-rhamnolipid with the ratio varying with culture time. After 96 h of fermentation, the mass ratio of di-rhamnolipid over mono-rhamnolipid increased to 2.6:1. Crude rhamnolipids in a form of cell-free culture broth showed high antifungal activity against colony growth and biomass accumulation of seven plant pathogens comprising two Oomycetes, three Ascomycota and two Mucor spp. fungi, among which three plant pathogens were firstly reported in this paper showing inhibition to rhamnolipids. Particularly, rhamnolipids showed potent activity against two Oomycetes that acquire resistance to commercial compound of metalaxyal. Furthermore, di-rhamnolipid was elucidated to dominate the antifungal activity of crude rhamnolipids by in vitro studies. At last, the efficacy and safety of cell-free culture broth was preliminarily illustrated on plants in vivo. So cell-free culture broth as a crude rhamnolipid product could be served as a potential cost-effective and environmental-friendly fungicide in agriculture. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Culture in Translation and Translation Studies.

    Science.gov (United States)

    Schaffner, Christina

    1994-01-01

    Reviews the evolution of translation from an exchange of information within and across cultural boundaries to its current status as a scholarly endeavor. Translations may have far-reaching effects in the target and source culture. Translators should be cognizant of the foreign language and culture in order to successfully realize their role as…

  20. Bidirectional American Sign Language to English Translation

    OpenAIRE

    Cate, Hardie; Hussain, Zeshan

    2017-01-01

    We outline a bidirectional translation system that converts sentences from American Sign Language (ASL) to English, and vice versa. To perform machine translation between ASL and English, we utilize a generative approach. Specifically, we employ an adjustment to the IBM word-alignment model 1 (IBM WAM1), where we define language models for English and ASL, as well as a translation model, and attempt to generate a translation that maximizes the posterior distribution defined by these models. T...

  1. Applicability of Ion Torrent Colon and Lung sequencing panel on circulating cell-free DNA

    DEFF Research Database (Denmark)

    Demuth, Christina; Tranberg Madsen, Anne; Larsen, Anne Winther

    Background: Identifying tumor-specific mutations in plasma from cancer patients serves as a non-invasive supplement to taking biopsies. Targeted sequencing of the circulating cell-free DNA (cfDNA) is an efficient method, for screening for a number of relevant mutations. Different approaches......: We used the Horizon multiplex cfDNA standard with eight known mutations at concentrations of 5 % (5-6.3 %), 1 % (1-1.3 %) , 0.1 % (0.1-0.13 %) and no mutations (wild type), respectively, to test the reproducibility of the panel. We obtained plasma from healthy donors from the danish Blood Bank to set...... a baseline for the panel. Lastly, the panel was tested on 52 patient samples. Patient plasma samples are from a previously collected cohort of EGFR wild-type non-small cell lung cancer patients (ClinicalTrial.gov: NCT02043002) All samples were sequenced using the Ion Torrent Oncomine Solid Tumor DNA kit...

  2. Extraction of cell-free DNA from urine, using polylysine-coated silica particles.

    Science.gov (United States)

    Takano, Sho; Hu, Qingjiang; Amamoto, Takaki; Refinetti, Paulo; Mimori, Koshi; Funatsu, Takashi; Kato, Masaru

    2017-06-01

    DNA analysis is used for a variety of purposes, including disease diagnosis and DNA profiling; this involves extracting DNA from living organisms. In this study, we prepared polycationic silica particles to extract DNA that has the negatively charged phosphate backbone from solution. The coated particles were prepared by mixing conventional silica gel particles and poly-Lys; these particles could efficiently extract 1.3 μg of cell-free DNA from 50 mL of (male) urine. It is expected that these easily prepared particles (just a mixture of two commercially available chemicals) can be used as a noninvasive diagnostic tool for genetic disorders such as cancer, diabetes, and hypertension. Graphical abstract Effective extraction method of cfDNA from urine was developed that used commercially available silica gel particles and poly-Lys.

  3. Osteochondritis dissecans of the medial femoral condyle : New cell-free scaffold as a treatment option.

    Science.gov (United States)

    Stadler, N; Trieb, K

    2016-08-01

    There is no gold standard in treating osteochondral lesions, which is why the treatment remains very challenging. Osteochondral defects can occur in any joint, but the most common locations are the knee and the ankle. Trauma, repeated microtrauma, avascular necrosis and osteochondritis dissecans (a special type of avascular necrosis) are blamed for the cartilage damage and the damage of adjacent subchondral bone. The self-healing ability of the cartilage is unfortunately very poor; thus, it is necessary to develop new methods of cartilage repair. Unfortunately, few data and long-term survival rates for these new scaffolds are available. We report a case of osteochondritis dissecans treated with a new cell-free scaffold MaioRegen® (Fin-Ceramica Faenza Spa, Faenza, Italy).

  4. More than Tiny Sacks: Stem Cell Exosomes as Cell-free Modality for Cardiac Repair

    Science.gov (United States)

    Kishore, Raj; Khan, Mohsin

    2015-01-01

    Stem cell therapy provides immense hope for regenerating the pathological heart yet has been marred by issues surrounding the effectiveness, unclear mechanisms and survival of the donated cell population in the ischemic myocardial milieu. Poor survival and engraftment coupled to inadequate cardiac commitment of the adoptively transferred stem cells compromises the improvement in cardiac function. Various alternative approaches to enhance the efficacy of stem cell therapies and to overcome issues with cell therapy have been employed with varied success. Cell free components such as exosomes enriched in proteins, mRNAs and miRs characteristic of parental stem cells represent a potential approach for treating cardiovascular diseases. Recently, exosomes from different kinds of stem cells have been effectively employed to promote cardiac function in the pathological heart. The aim of this review is to summarize current research efforts on stem cell exosomes including their potential benefits and limitations in order to develop a potentially viable therapy for cardiovascular problems. PMID:26838317

  5. Kinetics of Circulating Plasma Cell-Free DNA in Paediatric Classical Hodgkin Lymphoma

    Science.gov (United States)

    Primerano, Simona; Burnelli, Roberta; Carraro, Elisa; Pillon, Marta; Elia, Caterina; Farruggia, Piero; Sala, Alessandra; Vinti, Luciana; Buffardi, Salvatore; Basso, Giuseppe; Mascarin, Maurizio; Mussolin, Lara

    2016-01-01

    Levels of plasma cell-free DNA (cfDNA) of a large series of children with classical Hodgkin lymphoma (cHL) were evaluated and analyzed at diagnosis and during chemotherapy treatment in relation with clinical characteristics. CfDNA levels in cHL patients were significantly higher compared with controls (p=0.002). CfDNA at diagnosis was correlated with presence of B symptoms (p=0.027) and high erythrocyte sedimentation rate (p=0.049). We found that the increasing of plasma cfDNA after first chemotherapy cycle seems to be associated with a worse prognosis (p=0.049). Levels of plasma cfDNA might constitute an interesting non-invasive tool in cHL patients' management. PMID:26918050

  6. Detection of copy number alterations in cell-free tumor DNA from plasma

    DEFF Research Database (Denmark)

    Østrup, Olga; Ahlborn, Lise Barlebo; Lassen, Ulrik

    2017-01-01

    purposes, however specify and reliability of methods have to be tested. METHODS: SNP microarrays (Affymetrix) were used to generate whole-genome copy number profiles from plasma ccfDNA (OncoScan) and paired tumor biopsies (CytoScan) from ten patients with metastatic cancers. Numerical, segmental and focal......BACKGROUND: Somatic copy number alterations (SCNAs) occurring in tumors can provide information about tumor classification, patient's outcome or treatment targets. Liquid biopsies, incl. plasma samples containing circulating cell-free tumor DNA (ccfDNA) can be used to assess SCNAs for clinical...... of SCNAs changes during the treatment course of one patient also indicated that apoptosis/necrosis of non-cancerous cells presumably induced by treatment can influence ccfDNA composition and introduce false-negative findings into the analysis of liquid biopsies. CONCLUSIONS: Genomic alterations detected...

  7. Regulation of cancer metastasis by cell-free miRNAs

    Science.gov (United States)

    Alečković, Maša; Kang, Yibin

    2014-01-01

    MicroRNAs (miRNAs) are integral molecules in the regulation of numerous physiological cellular processes that have emerged as critical players in cancer initiation and metastatic progression, both by promoting and suppressing metastasis. Recently, cell-free miRNAs shed from cancer cells into circulation have been reported in cancer patients, raising hope for development of novel biomarkers that can be routinely measured in easily accessible samples. In fact, establishing miRNA expression in the circulation likely has advantages over determination in primary tumor tissue, further augmenting the potential applications of miRNA detection in oncological practice. In addition, secretion of miRNAs impacting distant cell signaling or promoting the formation of a niche that sustains a distant tumor microenvironment allows for new treatment approaches to thwart cancer progression. PMID:25450578

  8. In-Situ Observation of Membrane Protein Folding during Cell-Free Expression.

    Science.gov (United States)

    Baumann, Axel; Kerruth, Silke; Fitter, Jörg; Büldt, Georg; Heberle, Joachim; Schlesinger, Ramona; Ataka, Kenichi

    2016-01-01

    Proper insertion, folding and assembly of functional proteins in biological membranes are key processes to warrant activity of a living cell. Here, we present a novel approach to trace folding and insertion of a nascent membrane protein leaving the ribosome and penetrating the bilayer. Surface Enhanced IR Absorption Spectroscopy selectively monitored insertion and folding of membrane proteins during cell-free expression in a label-free and non-invasive manner. Protein synthesis was performed in an optical cell containing a prism covered with a thin gold film with nanodiscs on top, providing an artificial lipid bilayer for folding. In a pilot experiment, the folding pathway of bacteriorhodopsin via various secondary and tertiary structures was visualized. Thus, a methodology is established with which the folding reaction of other more complex membrane proteins can be observed during protein biosynthesis (in situ and in operando) at molecular resolution.

  9. In-Situ Observation of Membrane Protein Folding during Cell-Free Expression.

    Directory of Open Access Journals (Sweden)

    Axel Baumann

    Full Text Available Proper insertion, folding and assembly of functional proteins in biological membranes are key processes to warrant activity of a living cell. Here, we present a novel approach to trace folding and insertion of a nascent membrane protein leaving the ribosome and penetrating the bilayer. Surface Enhanced IR Absorption Spectroscopy selectively monitored insertion and folding of membrane proteins during cell-free expression in a label-free and non-invasive manner. Protein synthesis was performed in an optical cell containing a prism covered with a thin gold film with nanodiscs on top, providing an artificial lipid bilayer for folding. In a pilot experiment, the folding pathway of bacteriorhodopsin via various secondary and tertiary structures was visualized. Thus, a methodology is established with which the folding reaction of other more complex membrane proteins can be observed during protein biosynthesis (in situ and in operando at molecular resolution.

  10. [Advance in clinical application of non-invasive prenatal screening using cell-free fetal DNA].

    Science.gov (United States)

    Hu, Jilin; Zhu, Baosheng

    2017-12-10

    Non-invasive prenatal screening using cell-free fetal DNA (NIPS) has been integrated into the prenatal health care only in a short span of five years, and the guidelines provided by professional bodies have been continuously updated. The American College of Medical Genetics and Genomics has made a statement on NIPS in July, 2016, suggesting that the NIPS can replace conventional screening for Patau, Edwards and Down syndromes in a continuum of gestational age and for any maternal age, except those who are significantly obese. The scope of target diseases of NIPS are also growing. Meanwhile, pre- and post-test counseling for NIPS has put forward a greater challenge for medical professionals.

  11. From Polarity to Plurality in Translation Scholarship

    Directory of Open Access Journals (Sweden)

    Abdolla Karimzadeh

    2012-09-01

    Full Text Available Review of the literature in translation studies shows that translation scholarship can be discussed in 3 Macro-levels including 1 Corpus-based studies, 2 Protocol-based studies, and 3 Systems- based studies. Researchers in the corpus-based studies test the hypothesis about the universals of translation. They also try to identify translation norms and regular linguistic patterns. This scholarship aims at showing that the language of translation is different from that of non-translation. The other purpose is to identify the techniques and strategies adopted by the translators. In protocol –based studies, the researchers study the mental activities and the individual behaviors of the translators while translating. They aim to describe the behavior of professional translators (versus translator trainees during the process of translation in a bid to identify how they chunk the source text (unit of translation and to describe how the translation trainees develop their translation competence. These studies are longitudinal for the reason that they aim to investigate the change of intended behaviors in the subjects of the study. Like corpus-based studies, they are experimental and data for analysis are collected by various methods including the translators’ verbal report, keystroke logging, eye tracking, and so on. Recently, in a method called “triangulation”, they combine the above-mentioned methods of data collection to test their hypotheses on a stronger experimental basis. To collect the data, they also employ the methods used in neurology (for example the technology of Electroencephalogram in order to obtain information on the physiological processes in the brains of the translators while translating. And finally in the systems-based studies, the researchers analyze more extended systems of production, distribution, and consumption of translations and their impacts on the target culture in a specific socio-cultural context. Differentiating

  12. Prediction of clear cell renal cell carcinoma by integrity of cell-free DNA in serum.

    Science.gov (United States)

    Gang, Feng; Guorong, Li; An, Zhao; Anne, Gentil-Perret; Christian, Genin; Jacques, Tostain

    2010-02-01

    To hypothesize that serum cell-free DNA integrity may be clinically useful for prediction of clear cell renal cell carcinoma (cRCC). The integrity of cell-free DNA released from cancer cells was different from that released from apoptotic cells. We collected peripheral blood samples from 78 patients before surgery; among these patients, 22 with tumor, both pre- and postoperation, and 42 controls without tumor. After the column extraction of DNA, we performed conventional polymerase chain reaction using different sizes of primers (size of products: 109, 193, 397, and 456 bp) of the housekeeping gene, glyceraldehyde-3-phosphate dehydrogenase for measurement of serum cf-DNA integrity. Age and gender were not associated with cf-DNA integrity in controls (P = .136 and P = .345). Among the cRCC patients, we observed no significant association between cf-DNA integrity and gender, age, tumor grade (P = .510, P = .618 and P = .052), except tumor stage and size (P = .001 and P = .001). All specimens contained 109 bp products. The 193 bp product was detected in 75 of 78 cRCCs and 37 of 42 controls (P = .091), 21 of 22 patients preoperation and 19 of 22 postoperation (P = .294). The 397 bp product was detected in 71 of 78 cRCCs and 0 of 42 of controls (P = .001), 18 of 22 patients preoperation- and 7 of 22 postoperation (P = .003). The 456 bp product was detected in 69 of 78 of cRCCs and 0 of 42 of controls (P = .001), 18 of 22 preoperation and 3 of 22 postoperation (P = .002). Serum cf-DNA integrity may be a potential tool for the detection of clear cRCC. 2010 Elsevier Inc. All rights reserved.

  13. Accurate quantitation of circulating cell-free mitochondrial DNA in plasma by droplet digital PCR.

    Science.gov (United States)

    Ye, Wei; Tang, Xiaojun; Liu, Chu; Wen, Chaowei; Li, Wei; Lyu, Jianxin

    2017-04-01

    To establish a method for accurate quantitation of circulating cell-free mitochondrial DNA (ccf-mtDNA) in plasma by droplet digital PCR (ddPCR), we designed a ddPCR method to determine the copy number of ccf-mtDNA by amplifying mitochondrial ND1 (MT-ND1). To evaluate the sensitivity and specificity of the method, a recombinant pMD18-T plasmid containing MT-ND1 sequences and mtDNA-deleted (ρ 0 ) HeLa cells were used, respectively. Subsequently, different plasma samples were prepared for ddPCR to evaluate the feasibility of detecting plasma ccf-mtDNA. In the results, the ddPCR method showed high sensitivity and specificity. When the DNA was extracted from plasma prior to ddPCR, the ccf-mtDNA copy number was higher than that measured without extraction. This difference was not due to a PCR inhibitor, such as EDTA-Na 2 , an anti-coagulant in plasma, because standard EDTA-Na 2 concentration (5 mM) did not significantly inhibit ddPCR reactions. The difference might be attributable to plasma exosomal mtDNA, which was 4.21 ± 0.38 copies/μL of plasma, accounting for ∼19% of plasma ccf-mtDNA. Therefore, ddPCR can quickly and reliably detect ccf-mtDNA from plasma with a prior DNA extraction step, providing for a more accurate detection of ccf-mtDNA. The direct use of plasma as a template in ddPCR is suitable for the detection of exogenous cell-free nucleic acids within plasma, but not of nucleic acids that have a vesicle-associated form, such as exosomal mtDNA. Graphical Abstract Designs of the present work. *: Module 1, #: Module 2, &: Module 3.

  14. Concise Review: MSC-Derived Exosomes for Cell-Free Therapy.

    Science.gov (United States)

    Phinney, Donald G; Pittenger, Mark F

    2017-04-01

    Mesenchymal stem cell transplantation is undergoing extensive evaluation as a cellular therapy in human clinical trials. Because MSCs are easily isolated and amenable to culture expansion in vitro there is a natural desire to test MSCs in many diverse clinical indications. This is exemplified by the rapidly expanding literature base that includes many in vivo animal models. More recently, MSC-derived extracellular vesicles (EVs), which include exosomes and microvesicles (MV), are being examined for their role in MSC-based cellular therapy. These vesicles are involved in cell-to-cell communication, cell signaling, and altering cell or tissue metabolism at short or long distances in the body. The exosomes and MVs can influence tissue responses to injury, infection, and disease. MSC-derived exosomes have a content that includes cytokines and growth factors, signaling lipids, mRNAs, and regulatory miRNAs. To the extent that MSC exosomes can be used for cell-free regenerative medicine, much will depend on the quality, reproducibility, and potency of their production, in the same manner that these parameters dictate the development of cell-based MSC therapies. However, the MSC exosome's contents are not static, but rather a product of the MSC tissue origin, its activities and the immediate intercellular neighbors of the MSCs. As such, the exosome content produced by MSCs appears to be altered when MSCs are cultured with tumor cells or in the in vivo tumor microenvironment. Therefore, careful attention to detail in producing MSC exosomes may provide a new therapeutic paradigm for cell-free MSC-based therapies with decreased risk. Stem Cells 2017;35:851-858. © 2017 AlphaMed Press.

  15. An Advanced Model to Precisely Estimate the Cell-Free Fetal DNA Concentration in Maternal Plasma.

    Directory of Open Access Journals (Sweden)

    Xiongbin Kang

    Full Text Available With the speedy development of sequencing technologies, noninvasive prenatal testing (NIPT has been widely applied in clinical practice for testing for fetal aneuploidy. The cell-free fetal DNA (cffDNA concentration in maternal plasma is the most critical parameter for this technology because it affects the accuracy of NIPT-based sequencing for fetal trisomies 21, 18 and 13. Several approaches have been developed to calculate the cffDNA fraction of the total cell-free DNA in the maternal plasma. However, most approaches depend on specific single nucleotide polymorphism (SNP allele information or are restricted to male fetuses.In this study, we present an innovative method to accurately deduce the concentration of the cffDNA fraction using only maternal plasma DNA. SNPs were classified into four maternal-fetal genotype combinations and three boundaries were added to capture effective SNP loci in which the mother was homozygous and the fetus was heterozygous. The median value of the concentration of the fetal DNA fraction was estimated using the effective SNPs. A depth-bias correction was performed using simulated data and corresponding regression equations for adjustments when the depth of the sequencing data was below 100-fold or the cffDNA fraction is less than 10%.Using our approach, the median of the relative bias was 0.4% in 18 maternal plasma samples with a median sequencing depth of 125-fold. There was a significant association (r = 0.935 between our estimations and the estimations inferred from the Y chromosome. Furthermore, this approach could precisely estimate a cffDNA fraction as low as 3%, using only maternal plasma DNA at the targeted region with a sequencing depth of 65-fold. We also used PCR instead of parallel sequencing to calculate the cffDNA fraction. There was a significant association (r = 98.2% between our estimations and those inferred from the Y chromosome.

  16. TRANSLATION TECHNIQUES ON INDONESIAN SWORN TRANSLATOR’S LEGAL TEXTS TRANSLATION

    OpenAIRE

    Wuryantoro, Aris; Edi Subroto, H.D.; Nababan, M. R

    2016-01-01

    Legal translation is the transferring the meaning from source language text into target language which not only consists of language system but also legal system. This research aims to analyze the translation  techniques  used  by  the  Indonesian  sworn  translators  in  translating  legal  texts  from English into Indonesian. This research uses descriptive qualitative method. Data obtained through content analysis on translations of the Indonesian sworn translators containing Certificate of...

  17. Speaking your Translation

    DEFF Research Database (Denmark)

    Dragsted, Barbara; Mees, Inger M.; Gorm Hansen, Inge

    2011-01-01

    In this article we discuss the translation processes and products of 14 MA students who produced translations from Danish (L1) into English (L2) under different working conditions: (1) written translation, (2) sight translation, and (3) sight translation with a speech recognition (SR) tool. Audio...... output and keystrokes were recorded. Oral and written translation data were examined in order to investigate if task times and translation quality differed in the three modalities. Although task times were found to be highest in written translation, the quality was not consistently better. In addition...

  18. 2-Guanidino-quinazolines as a novel class of translation inhibitors.

    Science.gov (United States)

    Komarova Andreyanova, E S; Osterman, I A; Pletnev, P I; Ivanenkov, Y A; Majouga, A G; Bogdanov, A A; Sergiev, P V

    2017-02-01

    A variety of structurally unrelated organic compounds has been reported to have antibacterial activity. Among these, certain small-molecule translation inhibitors have attracted a great deal of attention, due to their relatively high selectivity against prokaryotes, and an appropriate therapeutic index with minor "off target" effects. However, ribosomes are being considered as poorly druggable biological targets, thereby making some routine computational-based approaches to rational drug design and its development rather ineffective. Taking this into account, diversity-oriented biological screening can reasonably be considered as the most advantageous strategy. Thus, using a high-throughput screening (HTS) platform, we applied a unique biological assay for in vitro evaluation of thousands of organic molecules, especially targeted against bacterial ribosomes and translation. As a result, we have identified a series of structurally diverse small-molecule compounds that induce a reporter strain sensitive to translation and DNA biosynthesis inhibitors. In a cell free system, several molecules were found to strongly inhibit protein biosynthesis. Among them, compounds bearing a 2-guanidino-quinazoline core demonstrated the most promising antibacterial activity. With regard to the preliminary structure-activity relationship (SAR) study, we revealed that relatively small substituents at positions 4, 6 and 8 of the quinazoline ring significantly enhance the target activity whereas modification of the guanidine group leads to decrease or loss of antibacterial potency. This novel class of translation inhibitors can properly be regarded as a promising starting point for the development of novel antibacterial therapeutic or screening tools. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  19. Messenger RNA during early embryogenesis in Artemia salina: altered translatability and sequence complexity.

    Science.gov (United States)

    James, T C; Tata, J R

    1980-02-01

    RNA from developing embryos of Artemia salina (5, 10, and 20 h after re-initiation of development) was translated 3-10 times more efficiently in a rabbit reticulocyte lysate cell-free protein synthesizing system than RNA from dormant gastrulae. The latter did not appear to contain any significant amount of translation inhibitor activity. Ninety percent of the translatable activity in dormant gastrulae was recovered as poly(A)--RNA, whereas 80% of that in post-gastrular developing embryos was present as poly(A)+-RNA. The size of most polypeptides coded for by dormant gastrular RNA was less than 130,000 daltons whereas the size of those coded for by developing embryonic RNA was up to 200,000 daltons, which correlated with a corresponding shift to poly A-containing RNA of higher molecular weight. Two major polypeptides of about 37,000 daltons coded for by dormant gastrular RNA disappeared at 20 h after resumption of development. Hybridization of complementary DNA (cDNA) to a 1000-fold excess of the homologous poly(A)+-RNA revealed the presence of three complexity classes of mRNA. Forty-five percent, 30%, and 25% of RNA in dormant gastrulae were present as high, middle, and low abundance classes comprising about 10, 80, and 9700 species, respectively whereas in the nauplii there were 10, 150, and 7900 species of high, middle, and low abundancy sequences, respectively. Heterologous hybridizations using cDNA complementary to highly abundant messenger population of nauplii (isolated by chromatography on hydroxyapatite) to poly(A)+-RNA from dormant cysts showed considerably divergence in this class of messengers from the two developmental stages. Re-initiation of development of dormant Artemia gastrulae is thus characterized by a "re-programming" seen as a simultaneous and rapid increase in the polyadenylation and translatability of poly(A)+-RNA accompanied by a qualitative change in its sequence complexity.

  20. Structural Coupling and Translation

    DEFF Research Database (Denmark)

    Tække, Jesper

    formations. After presenting the two theories the article put forward Twitter as an example making it possible to compare the two theories. Hereby the article also provides two analysis of how Twitter changes the communication milieu of modern society. In systems theory media can be seen as the mechanisms...... and translations the social medium of Twitter opens for. The second, but most prioritized, aim of the paper is to present, compare and discuss the two theories: How do they understand what becomes visible in their different optics, which observations become possible in the one or the other – and is it possible...... creating networks consisting in both humans and non-humans. Then the two appearing frameworks are used to observe Twitter and discuss which structural couplings and translations are made possible by this medium. In the end of the paper the two theories are discussed and compared....

  1. Circulating cell free DNA as a predictor of systemic lupus erythematosus severity and monitoring of therapy

    Directory of Open Access Journals (Sweden)

    Olfat M. Hendy

    2016-01-01

    Conclusion: Our findings support that the measurement of cf-DNA appears to be a useful marker in addition to laboratory tests used in SLE diagnosis. High correlation with markers of disease severity suggesting its role in disease pathogenesis and decreasing its level after therapy makes it to be a marker of treatment follow-up.

  2. Machine Translation

    Indian Academy of Sciences (India)

    These components incorporate a lot of knowledge about words (lexical knowledge), and about the language (linguistic knowledge). Such knowledge is stored in one or more lexicons, and possibly other sources of . linguistic knowledge, such as grammar. The user interface is invariably a crucial part of most MT systems.

  3. On automatic machine translation evaluation

    Directory of Open Access Journals (Sweden)

    Darinka Verdonik

    2013-05-01

    Full Text Available An important task of developing machine translation (MT is evaluating system performance. Automatic measures are most commonly used for this task, as manual evaluation is time-consuming and costly. However, to perform an objective evaluation is not a trivial task. Automatic measures, such as BLEU, TER, NIST, METEOR etc., have their own weaknesses, while manual evaluations are also problematic since they are always to some extent subjective. In this paper we test the influence of a test set on the results of automatic MT evaluation for the subtitling domain. Translating subtitles is a rather specific task for MT, since subtitles are a sort of summarization of spoken text rather than a direct translation of (written text. Additional problem when translating language pair that does not include English, in our example Slovene-Serbian, is that commonly the translations are done from English to Serbian and from English to Slovenian, and not directly, since most of the TV production is originally filmed in English. All this poses additional challenges to MT and consequently to MT evaluation. Automatic evaluation is based on a reference translation, which is usually taken from an existing parallel corpus and marked as a test set. In our experiments, we compare the evaluation results for the same MT system output using three types of test set. In the first round, the test set are 4000 subtitles from the parallel corpus of subtitles SUMAT. These subtitles are not direct translations from Serbian to Slovene or vice versa, but are based on an English original. In the second round, the test set are 1000 subtitles randomly extracted from the first test set and translated anew, from Serbian to Slovenian, based solely on the Serbian written subtitles. In the third round, the test set are the same 1000 subtitles, however this time the Slovene translations were obtained by manually correcting the Slovene MT outputs so that they are correct translations of the

  4. Study of the functionality of the Helicobacter pylori trans-translation components SmpB and SsrA in an heterologous system

    Directory of Open Access Journals (Sweden)

    Ecobichon Chantal

    2010-03-01

    Full Text Available Abstract Background Trans-translation is a ubiquitous bacterial quality control-mechanism for both transcription and translation. With its two major partners, SsrA a small stable RNA and the SmpB protein, it promotes the release of ribosomes stalled on defective mRNAs and directs the corresponding truncated proteins to degradation pathways. We have recently shown that trans-translation is an essential function in the gastric pathogen Helicobacter pylori. Our results suggested that some properties of the H. pylori trans-translation machinery distinguishes it from the well known system in E. coli. Therefore, we decided to test the functionality of the SmpB and SsrA molecules of H. pylori in the E. coli heterologous system using two established phenotypic tests. Results H. pylori SmpB protein was found to successfully restore the E. coli ΔsmpB mutant growth defect and its capacity to propagate λimmP22 phage. We showed that in E. coli, H. pylori SsrA (Hp-SsrA was stably expressed and maturated and that this molecule could restore wild type growth to the E. coli ΔssrA mutant. Hp-SsrA mutants affected in the ribosome rescue function were not able to restore normal growth to E. coli ΔssrA supporting a major role of ribosome rescue in this phenotype. Surprisingly, Hp-SsrA did not restore the phage λimmP22 propagation capacity to the E. coli ΔssrA mutant. Conclusions These data suggest an additional role of the tag sequence that presents specific features in Hp-SsrA. Our interpretation is that a secondary role of protein tagging in phage propagation is revealed by heterologous complementation because ribosome rescue is less efficient. In conclusion, tmRNAs present in all eubacteria, have coevolved with the translational machinery of their host and possess specific determinants that can be revealed by heterologous complementation studies.

  5. Translation technology fills important niche.

    Science.gov (United States)

    2007-06-01

    Software systems that can interpret and translate foreign languages can augment existing services and be available immediately, when live interpreters or even phone services may not be. Knowledge of their capabilities and cost can help you narrow your decision. Systems will take you from registration process through triage to diagnosis. All systems will provide text and audio translation. The more sophisticated systems also offer video services and sign language for deaf patients. The cost can be more than $100,000, but local foundations may offer grants that will cover your expenses.

  6. Literature in Translation.

    Science.gov (United States)

    Snodgrass, Mary Ellen

    An examination of literature in translation is vital to literary interpretation and, ultimately, essential to mutual understanding among peoples from different cultures. Teaching translations requires consideration of linguistic, social, and temporal areas. Translations require alterations in language since languages never translate precisely from…

  7. Theoretical Aspects of Translation.

    Science.gov (United States)

    House, Juliane M.

    This study attempts to bring some clarification into the concept of translation, especially into the theoretical problems presented by the difficulties of translation. The following aspects of the question are treated: (1) translation in the past and present, including the controversy over translation as an art or a science, the relevance of…

  8. Narcissism lost: on translating and being translated.

    Science.gov (United States)

    Carneiro, Maria Inês N E; Brakel, Arthur

    2010-08-01

    The authors present a detailed account of the experiences shared in translating and having one's work translated. Carneiro maintains that, in order to communicate with their readers, writers should relinquish the narcissistic satisfaction they derive from their texts in the original. Beyond this, she feels that, owing to a good understanding between her and her translator, the creativity in her original text persists in the translation. Brakel introduces himself to the IJPA readership and shows how he works when translating the cultural and linguistic nuances and peculiarities of Brazilian Portuguese. He concludes with some thoughts about the affect he experiences from his original work and the work he has translated. Copyright © 2009 Institute of Psychoanalysis.

  9. Some Major Steps to Translation and Translator

    Directory of Open Access Journals (Sweden)

    Mohammad Reza Hojat Shamami

    2012-09-01

    Full Text Available This work is an overview of the main issues at the core of theorizing translation practice and the features of a good translator or how to be a good translator and of course what are the Skills to become a Freelance Translator and Translation process. In this world of science and technology there is knowledge explosion every day. This knowledge which is generally written in the English language needs to be transmitted in various languages so that people who do not know how to speak and write the original language can get the knowledge necessary for industrial development and technological innovation to keep up with the rest of the world. To transmit this knowledge effectively, there is a need for competent translators in various languages.

  10. A comparative study of protein synthesis in in vitro systems: from the prokaryotic reconstituted to the eukaryotic extract-based

    Directory of Open Access Journals (Sweden)

    Hillebrecht Jason R

    2008-07-01

    Full Text Available Abstract Background Cell-free protein synthesis is not only a rapid and high throughput technology to obtain proteins from their genes, but also provides an in vitro platform to study protein translation and folding. A detailed comparison of in vitro protein synthesis in different cell-free systems may provide insights to their biological differences and guidelines for their applications. Results Protein synthesis was investigated in vitro in a reconstituted prokaryotic system, a S30 extract-based system and a eukaryotic system. Compared to the S30 system, protein synthesis in the reconstituted system resulted in a reduced yield, and was more cold-sensitive. Supplementing the reconstituted system with fractions from a size-exclusion separation of the S30 extract significantly increased the yield and activity, to a level close to that of the S30 system. Though protein synthesis in both prokaryotic and eukaryotic systems showed no significant differences for eukaryotic reporter proteins, drastic differences were observed when an artificial fusion protein was synthesized in vitro. The prokaryotic systems failed to synthesize and correctly fold a significant amount of the full-length fusion protein, even when supplemented with the eukaryotic lysate. The active full-length fusion protein was synthesized only in the eukaryotic system. Conclusion The reconstituted bacterial system is sufficient but not efficient in protein synthesis. The S30 system by comparison contains additional cellular factors capable of enhancing protein translation and folding. The eukaryotic translation machinery may have evolved from its prokaryotic counterpart in order to translate more complex (difficult-to-translate templates into active proteins.

  11. Ten Guidelines for Translating Legal Texts

    Directory of Open Access Journals (Sweden)

    Alenka Kocbek

    2017-12-01

    Full Text Available The paper proposes a targeted model for translating legal texts, developed by the author by combining translation science (i.e. functionalist approaches with the findings of comparative law and legal linguistics. It consists of ten guidelines directing the translator from defining the intended function of the target text and selecting the corresponding translation type, through comparing the legal systems involved in the translation and analysing the memetic structure of the source text and parallel texts in the target culture to designing the target text as a cultureme and ensuring its legal security.

  12. Phraseological comptence and the translation of phrasemes

    DEFF Research Database (Denmark)

    Hallsteinsdóttir, Erla

    2011-01-01

    In this article, that is based on my contribution to the workshop Multilingual phraseology and translation, I’ll focus on the aspects and the role of language competence in the translation of phrasemes, i.a. the phraseological competence. At first, I’ll describe the context of language competence...... in translation. Secondly, I’ll define and illustrate some aspects of the phraseological competence that are relevant in the act of translating, and finally, I’ll discuss the difference between phraseology in system and the conception of the translation as a text in relation to the praseological competence...

  13. Cell-free DNA promoter hypermethylation in plasma as a diagnostic marker for pancreatic adenocarcinoma.

    Science.gov (United States)

    Henriksen, Stine Dam; Madsen, Poul Henning; Larsen, Anders Christian; Johansen, Martin Berg; Drewes, Asbjørn Mohr; Pedersen, Inge Søkilde; Krarup, Henrik; Thorlacius-Ussing, Ole

    2016-01-01

    Pancreatic cancer has a 5-year survival rate of only 5-7%. Difficulties in detecting pancreatic cancer at early stages results in the high mortality and substantiates the need for additional diagnostic tools. Surgery is the only curative treatment and unfortunately only possible in localized tumours. A diagnostic biomarker for pancreatic cancer will have a major impact on patient survival by facilitating early detection and the possibility for curative treatment. DNA promoter hypermethylation is a mechanism of early carcinogenesis, which can cause inactivation of tumour suppressor genes. The aim of this study was to examine promoter hypermethylation in a panel of selected genes from cell-free DNA, as a diagnostic marker for pancreatic adenocarcinoma. Patients with suspected or biopsy-verified pancreatic cancer were included prospectively and consecutively. Patients with chronic/acute pancreatitis were included as additional benign control groups. Based on an optimized accelerated bisulfite treatment protocol, methylation-specific PCR of a 28 gene panel was performed on plasma samples. A diagnostic prediction model was developed by multivariable logistic regression analysis using backward stepwise elimination. Patients with pancreatic adenocarcinoma ( n  = 95), chronic pancreatitis ( n  = 97) and acute pancreatitis ( n  = 59) and patients screened, but negative for pancreatic adenocarcinoma ( n  = 27), were included. The difference in mean number of methylated genes in the cancer group (8.41 (95% CI 7.62-9.20)) vs the total control group (4.74 (95% CI 4.40-5.08)) was highly significant ( p  diagnostic prediction model (age >65, BMP3 , RASSF1A , BNC1 , MESTv2 , TFPI2 , APC , SFRP1 and SFRP2 ) had an area under the curve of 0.86 (sensitivity 76%, specificity 83%). The model performance was independent of cancer stage. Cell-free DNA promoter hypermethylation has the potential to be a diagnostic marker for pancreatic adenocarcinoma and differentiate

  14. Machine Translation in a Modern Languages Curriculum.

    Science.gov (United States)

    Lewis, Derek

    1997-01-01

    Reviews the current state of Machine Translation (MT), i.e., computer systems attempting automatic natural language translation. Describes the experiences of teaching MT to modern language college students using a commercially available system and overviews the main features of the system. (Nine references) (Author/CK)

  15. The controversy about controls for fetal blood group genotyping by cell-free fetal DNA in maternal plasma

    NARCIS (Netherlands)

    Scheffer, Peter G.; de Haas, Masja; van der Schoot, C. Ellen

    2011-01-01

    Fetal blood group genotyping using cell-free fetal DNA from maternal plasma is routinely performed in alloimmunized women and has been introduced for targeted antenatal anti-D prophylaxis. The necessity to control for extraction of fetal DNA in these tests is questioned by many. This review

  16. Circulating Tumor Cells (CTC and Cell-Free DNA (cfDNA Workshop 2016: Scientific Opportunities and Logistics for Cancer Clinical Trial Incorporation

    Directory of Open Access Journals (Sweden)

    Lori E. Lowes

    2016-09-01

    Full Text Available Despite the identification of circulating tumor cells (CTCs and cell-free DNA (cfDNA as potential blood-based biomarkers capable of providing prognostic and predictive information in cancer, they have not been incorporated into routine clinical practice. This resistance is due in part to technological limitations hampering CTC and cfDNA analysis, as well as a limited understanding of precisely how to interpret emergent biomarkers across various disease stages and tumor types. In recognition of these challenges, a group of researchers and clinicians focused on blood-based biomarker development met at the Canadian Cancer Trials Group (CCTG Spring Meeting in Toronto, Canada on 29 April 2016 for a workshop discussing novel CTC/cfDNA technologies, interpretation of data obtained from CTCs versus cfDNA, challenges regarding disease evolution and heterogeneity, and logistical considerations for incorporation of CTCs/cfDNA into clinical trials, and ultimately into routine clinical use. The objectives of this workshop included discussion of the current barriers to clinical implementation and recent progress made in the field, as well as fueling meaningful collaborations and partnerships between researchers and clinicians. We anticipate that the considerations highlighted at this workshop will lead to advances in both basic and translational research and will ultimately impact patient management strategies and patient outcomes.

  17. Writing Through: Practising Translation

    Directory of Open Access Journals (Sweden)

    Joel Scott

    2010-05-01

    Full Text Available This essay exists as a segment in a line of study and writing practice that moves between a critical theory analysis of translation studies conceptions of language, and the practical questions of what those ideas might mean for contemporary translation and writing practice. Although the underlying preoccupation of this essay, and my more general line of inquiry, is translation studies and practice, in many ways translation is merely a way into a discussion on language. For this essay, translation is the threshold of language. But the two trails of the discussion never manage to elude each other, and these concatenations have informed two experimental translation methods, referred to here as Live Translations and Series Translations. Following the essay are a number of poems in translation, all of which come from Blanco Nuclear by the contemporary Spanish poet, Esteban Pujals Gesalí. The first group, the Live Translations consist of transcriptions I made from audio recordings read in a public setting, in which the texts were translated in situ, either off the page of original Spanish-language poems, or through a process very much like that carried out by simultaneous translators, for which readings of the poems were played back to me through headphones at varying speeds to be translated before the audience. The translations collected are imperfect renderings, attesting to a moment in language practice rather than language objects. The second method involves an iterative translation process, by which three versions of any one poem are rendered, with varying levels of fluency, fidelity and servility. All three translations are presented one after the other as a series, with no version asserting itself as the primary translation. These examples, as well as the translation methods themselves, are intended as preliminary experiments within an endlessly divergent continuum of potential methods and translations, and not as a complete representation of

  18. Translational approach for gene therapy in epilepsy: Model system and unilateral overexpression of neuropeptide Y and Y2 receptors.

    Science.gov (United States)

    Ledri, Litsa Nikitidou; Melin, Esbjörn; Christiansen, Søren H; Gøtzsche, Casper R; Cifra, Alessandra; Woldbye, David P D; Kokaia, Mérab

    2016-02-01

    Although novel treatment strategies based on the gene therapy approach for epilepsy has been encouraging, there is still a gap in demonstrating a proof-of-concept in a clinically relevant animal model and study design. In the present study, a conceptually novel framework reflecting a plausible clinical trial for gene therapy of temporal lobe epilepsy was explored: We investigated (i) whether the post intrahippocampal kainate-induced status epilepticus (SE) model of chronic epilepsy in rats could be clinically relevant; and (ii) whether a translationally designed neuropeptide Y (NPY)/Y2 receptor-based gene therapy approach targeting only the seizure-generating focus unilaterally can decrease seizure frequency in this chronic model of epilepsy. Our data suggest that the intrahippocampal kainate model resembles the disease development of human chronic mesial temporal lobe epilepsy (mTLE): (i) spontaneous seizures originate in the sclerotic hippocampus; (ii) only a part of the animals develops chronic epilepsy; (iii) animals show largely variable seizure frequency that (iv) tends to progressively increase over time. Despite significant hippocampal degeneration caused by the kainate injection, the use of MRI allowed targeting the recombinant adeno-associated viral (rAAV) vectors encoding NPY and Y2 receptor genes to the remaining dorsal and ventral hippocampal areas ipsilateral to the kainate injection. Continuous video-EEG monitoring demonstrated not only prevention of the progressive increase in seizure frequency in rAAV-NPY/Y2 treated animals as compared to the controls, but even 45% decrease of seizure frequency in 80% of the epileptic animals. This translationally designed study in a clinically relevant model of epilepsy suggests that simultaneous overexpression of NPY and Y2 receptors unilaterally in the seizure focus is a relevant and promising approach that can be further validated in more extensive preclinical studies to develop a future treatment strategy for

  19. Hyperthermia does not affect rejoining of DNA double-strand breaks in a cell-free assay.

    Science.gov (United States)

    Wachsberger, P R; Iliakis, G

    2000-03-01

    Heat radiosensitization is poorly understood but is believed to be caused by an inhibition in the repair of radiation-induced DNA lesions. This inhibition in DNA repair may be caused either by direct heat inactivation of repair enzymes, or by heat-induced protein denaturation that leads to their precipitation onto nuclear chromatin structures, generating a barrier that prevents repair enzymes from reaching the damage sites. A previously described (Ganguly and Iliakis, Int J Radiat Biol 1995, 68, 447-457) cell-free assay was introduced to evaluate rejoining of radiation-induced DNA double-strand breaks (dsb) in heated (45.5 degrees C, 20 min) nuclei prepared from A549 cells, in reactions assembled with extracts of non-heated and non-irradiated HeLa cells. The assay allowed the functional evaluation of the effect of precipitated nuclear protein on dsb rejoining. By combining heated nuclei with extracts of non-heated cells the assay avoided complications that would otherwise arise when intact cells are studied, where both nuclear structures and repair factors are heated and therefore potentially altered. It was observed that exposure of A549 cells to 45.5 degrees C for 20 min caused a 50% increase in the relative protein content of isolated nuclei but had no effect on the in vitro rejoining of dsb. In agreement with earlier reports, a greatly reduced rate of dsb rejoining was observed either in intact A549 or HeLa cells after exposure to heat. The results indicate that an increased retention of proteins in heated nuclei is not necessarily associated with an inhibition of dsb rejoining. While the in vitro system may only reproduce certain aspects of the in vivo conditions, the results suggest that protein accretion as a mechanism of heat radiosensitization requires further testing using functional assays.

  20. Production of monoclonal antibodies against GPCR using cell-free synthesized GPCR antigen and biotinylated liposome-based interaction assay.

    Science.gov (United States)

    Takeda, Hiroyuki; Ogasawara, Tomio; Ozawa, Tatsuhiko; Muraguchi, Atsushi; Jih, Pei-Ju; Morishita, Ryo; Uchigashima, Motokazu; Watanabe, Masahiko; Fujimoto, Toyoshi; Iwasaki, Takahiro; Endo, Yaeta; Sawasaki, Tatsuya

    2015-06-10

    G-protein-coupled receptors (GPCRs) are one of the most important drug targets, and anti-GPCR monoclonal antibody (mAb) is an essential tool for functional analysis of GPCRs. However, it is very difficult to develop GPCR-specific mAbs due to difficulties in production of recombinant GPCR antigens, and lack of efficient mAb screening method. Here we describe a novel approach for the production of mAbs against GPCR using two original methods, bilayer-dialysis method and biotinylated liposome-based interaction assay (BiLIA), both of which are developed using wheat cell-free protein synthesis system and liposome technology. Using bilayer-dialysis method, various GPCRs were successfully synthesized with quality and quantity sufficient for immunization. For selection of specific mAb, we designed BiLIA that detects interaction between antibody and membrane protein on liposome. BiLIA prevented denaturation of GPCR, and then preferably selected conformation-sensitive antibodies. Using this approach, we successfully obtained mAbs against DRD1, GHSR, PTGER1 and T1R1. With respect to DRD1 mAb, 36 mouse mAbs and 6 rabbit mAbs were obtained which specifically recognized native DRD1 with high affinity. Among them, half of the mAbs were conformation-sensitive mAb, and two mAbs recognized extracellular loop 2 of DRD1. These results indicated that this approach is useful for GPCR mAb production.

  1. An Economic Analysis of Cell-Free DNA Non-Invasive Prenatal Testing in the US General Pregnancy Population.

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    Peter Benn

    Full Text Available Analyze the economic value of replacing conventional fetal aneuploidy screening approaches with non-invasive prenatal testing (NIPT in the general pregnancy population.Using decision-analysis modeling, we compared conventional screening to NIPT with cell-free DNA (cfDNA analysis in the annual US pregnancy population. Sensitivity and specificity for fetal aneuploidies, trisomy 21, trisomy 18, trisomy 13, and monosomy X, were estimated using published data and modeling of both first- and second trimester screening. Costs were assigned for each prenatal test component and for an affected birth. The overall cost to the healthcare system considered screening costs, the number of aneuploid cases detected, invasive procedures performed, procedure-related euploid losses, and affected pregnancies averted. Sensitivity analyses evaluated the effect of variation in parameters. Costs were reported in 2014 US Dollars.Replacing conventional screening with NIPT would reduce healthcare costs if it can be provided for $744 or less in the general pregnancy population. The most influential variables were timing of screening entry, screening costs, and pregnancy termination rates. Of the 13,176 affected pregnancies undergoing screening, NIPT detected 96.5% (12,717/13,176 of cases, compared with 85.9% (11,314/13,176 by conventional approaches. NIPT reduced invasive procedures by 60.0%, with NIPT and conventional methods resulting in 24,596 and 61,430 invasive procedures, respectively. The number of procedure-related euploid fetal losses was reduced by 73.5% (194/264 in the general screening population.Based on our analysis, universal application of NIPT would increase fetal aneuploidy detection rates and can be economically justified. Offering this testing to all pregnant women is associated with substantial prenatal healthcare benefits.

  2. An Economic Analysis of Cell-Free DNA Non-Invasive Prenatal Testing in the US General Pregnancy Population.

    Science.gov (United States)

    Benn, Peter; Curnow, Kirsten J; Chapman, Steven; Michalopoulos, Steven N; Hornberger, John; Rabinowitz, Matthew

    2015-01-01

    Analyze the economic value of replacing conventional fetal aneuploidy screening approaches with non-invasive prenatal testing (NIPT) in the general pregnancy population. Using decision-analysis modeling, we compared conventional screening to NIPT with cell-free DNA (cfDNA) analysis in the annual US pregnancy population. Sensitivity and specificity for fetal aneuploidies, trisomy 21, trisomy 18, trisomy 13, and monosomy X, were estimated using published data and modeling of both first- and second trimester screening. Costs were assigned for each prenatal test component and for an affected birth. The overall cost to the healthcare system considered screening costs, the number of aneuploid cases detected, invasive procedures performed, procedure-related euploid losses, and affected pregnancies averted. Sensitivity analyses evaluated the effect of variation in parameters. Costs were reported in 2014 US Dollars. Replacing conventional screening with NIPT would reduce healthcare costs if it can be provided for $744 or less in the general pregnancy population. The most influential variables were timing of screening entry, screening costs, and pregnancy termination rates. Of the 13,176 affected pregnancies undergoing screening, NIPT detected 96.5% (12,717/13,176) of cases, compared with 85.9% (11,314/13,176) by conventional approaches. NIPT reduced invasive procedures by 60.0%, with NIPT and conventional methods resulting in 24,596 and 61,430 invasive procedures, respectively. The number of procedure-related euploid fetal losses was reduced by 73.5% (194/264) in the general screening population. Based on our analysis, universal application of NIPT would increase fetal aneuploidy detection rates and can be economically justified. Offering this testing to all pregnant women is associated with substantial prenatal healthcare benefits.

  3. Lost in translation? Theory, policy and practice in systems-based environmental approaches to obesity prevention in the Healthy Towns programme in England.

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    Sautkina, Elena; Goodwin, Denise; Jones, Andy; Ogilvie, David; Petticrew, Mark; White, Martin; Cummins, Steven

    2014-09-01

    This paper explores how system-wide approaches to obesity prevention were 'theorised' and translated into practice in the 'Healthy Towns' programme implemented in nine areas in England. Semi-structured interviews with 20 informants, purposively selected to represent national and local programme development, management and delivery were undertaken. Results suggest that informants articulated a theoretical understanding of a system-wide approach to obesity prevention, but simplifying this complex task in the context of uncertainty over programme aims and objectives, and absence of a clear direction from the central government, resulted in local programmes relying on traditional multi-component approaches to programme delivery. The development of clear, practical guidance on implementation should form a central part of future system-wide approaches to obesity prevention. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Urine cell-free DNA integrity as a marker for early bladder cancer diagnosis: preliminary data.

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    Casadio, Valentina; Calistri, Daniele; Tebaldi, Michela; Bravaccini, Sara; Gunelli, Roberta; Martorana, Giuseppe; Bertaccini, Alessandro; Serra, Luigi; Scarpi, Emanuela; Amadori, Dino; Silvestrini, Rosella; Zoli, Wainer

    2013-11-01

    Urine cell-free (UCF) DNA has recently been proposed as a potential marker for early bladder cancer diagnosis. It is known that normal apoptotic cells produce highly fragmented DNA while cancer cells release longer DNA. Therefore, we verified the potential role of UCF DNA integrity in early bladder cancer diagnosis. UCF DNA was isolated from 51 bladder cancer patients, 46 symptomatic patients, and 32 healthy volunteers. To verify UCF DNA integrity, sequences longer than 250 bp, c-Myc, BCAS1, and HER2, were quantified by real time PCR. At the best cutoff value of 0.1 ng/μl, UCF DNA integrity analysis showed a sensitivity of 0.73 (95% CI 0.61-0.85), and a specificity of 0.84 (95% CI 0.71-0.97) in healthy individuals and 0.83 (95% CI 0.72-0.94) in symptomatic patients. Receiver operating characteristic (ROC) curve analysis revealed an area under the curve of 0.834 (95% CI 0.739-0.930) for healthy individuals and 0.796 (95% CI 0.707-0.885) for symptomatic patients. These preliminary data suggest that UCF DNA integrity is a potentially good marker for early noninvasive diagnosis of bladder cancer. Its diagnostic performance does not seem to vary significantly, even in an "at risk" population of symptomatic individuals. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. Urine Cell-Free DNA Integrity Analysis for Early Detection of Prostate Cancer Patients

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    Gurioli, Giorgia; Martignano, Filippo; Foca, Flavia; Gunelli, Roberta; Cicchetti, Giacomo; De Giorgi, Ugo; Zoli, Wainer; Calistri, Daniele

    2015-01-01

    Introduction. The detection of tumor-specific markers in urine has paved the way for new early noninvasive diagnostic approaches for prostate cancer. We evaluated the DNA integrity in urine supernatant to verify its capacity to discriminate between prostate cancer and benign diseases of the urogenital tract. Patients and Methods. A total of 131 individuals were enrolled: 67 prostate cancer patients and 64 patients with benign diseases of the urogenital tract (control group). Prostate-specific antigen (PSA) levels were determined. Urine cell-free (UCF) DNA was isolated and sequences longer than 250 bp corresponding to 3 genes (c-MYC, HER2, and AR) were quantified by Real-Time PCR to assess UCF-DNA integrity. Results. UCF-DNA was quantifiable in all samples, while UCF-DNA integrity was evaluable in all but 16 samples. Receiver operating characteristic analysis showed an area under the curve of 0.5048 for UCF-DNA integrity and 0.8423 for PSA. Sensitivity was 0.58 and 0.95 for UCF-DNA integrity and PSA, respectively. Specificity was 0.44 and 0.69, respectively. Conclusions. UCF-DNA integrity showed lower accuracy than PSA and would not seem to be a reliable marker for early prostate cancer diagnosis. Despite this, we believe that UCF-DNA could represent a source of other biomarkers and could detect gene alterations. PMID:26412928

  6. Green Synthesis and Antimicrobial Activities of Silver Nanoparticles using Cell Free-Extracts of Enterococcus species

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    Iyabo C. OLADIPO

    2017-06-01

    Full Text Available Cell-free extracts of six strains of Enterococcus species obtained from fermented foods were used for the green synthesis of silver nanoparticles (AgNPs, which was characterized by UV-Vis spectroscopy, Fourier-transform infrared spectroscopy (FTIR and transmission electron microscopy (TEM. The biosynthesized AgNPs were dark brown in colour having surface plasmon resonance in the range of 420-442 nm. The spherical shaped AgNPs had sizes of 4-55 nm, whose formations were facilitated by proteins as indicated by the presence of peaks 1,635-1,637 and 3,275-3,313 cm-1 in the FTIR spectra. The energy dispersive x-ray (EDX showed prominent presence of silver in the AgNPs colloidal solution, while the selected area electron diffraction was typified by the face-centred crystalline nature of silver. The particles inhibited the growth of multi-drug resistant clinical isolates of Escherichia coli, Klebsiella pneumoniae and Proteus vulgaris, and also potentiated the activities of ampicillin, ciprofloxacin and cefuroxime in the AgNPs-antibiotic synergy studies. In addition, the prospective relevance of the particles as nanopreservative in paints was demonstrated with the inhibition of growth of Staphylococcus aureus, Pseudomonas aeruginosa, Aspergillus niger and A. flavus in AgNPs-paint admixture. This report further demonstrates the green synthesis of AgNPs by strains of Enterococcus species.

  7. Multi-marker analysis of circulating cell-free DNA toward personalized medicine for colorectal cancer.

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    Mouliere, Florent; El Messaoudi, Safia; Pang, Dalong; Dritschilo, Anatoly; Thierry, Alain R

    2014-07-01

    Development of a Q-PCR-based assay for the high-performance analysis of circulating cell-free DNA (ccfDNA) requires good knowledge of its structure and size. In this work, we present the first visual determination of ccfDNA by Atomic Force Microscopy (AFM) on plasma samples from colorectal cancer (CRC) patients and healthy donors. In addition to the examination of fragment size distribution profile as performed by Q-PCR, this analysis confirms that ccfDNA is highly fragmented and that more than 80% of ccfDNA fragments in CRC plasma are below 145 bp. We adapted an Allele-Specific Blocker (ASB) Q-PCR to small ccfDNA fragments to determine simultaneously the total ccfDNA concentration, the presence of point mutation, the proportion of mutated allele, and a ccfDNA integrity index. The data validated analytically these four parameters in 124 CRC clinical samples and 71 healthy individuals. The multi-marker method, termed Intplex, enables sensitive and specific non-invasive analysis of tumor ccfDNA, which has great potential in terms of cost, quality control, and easy implementation in every clinical center laboratory. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  8. Effects of polymorphisms in ovine and caprine prion protein alleles on cell-free conversion

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    Eiden Martin

    2011-02-01

    Full Text Available Abstract In sheep polymorphisms of the prion gene (PRNP at the codons 136, 154 and 171 strongly influence the susceptibility to scrapie and bovine spongiform encephalopathy (BSE infections. In goats a number of other gene polymorphisms were found which are suspected to trigger similar effects. However, no strong correlation between polymorphisms and TSE susceptibility in goats has yet been obtained from epidemiological studies and only a low number of experimental challenge data are available at present. We have therefore studied the potential impact of these polymorphisms in vitro by cell-free conversion assays using mouse scrapie strain Me7. Mouse scrapie brain derived PrPSc served as seeds and eleven recombinant single mutation variants of sheep and goat PrPC as conversion targets. With this approach it was possible to assign reduced conversion efficiencies to specific polymorphisms, which are associated to low frequency in scrapie-affected goats or found only in healthy animals. Moreover, we could demonstrate a dominant-negative inhibition of prion polymorphisms associated with high susceptibility by alleles linked to low susceptibility in vitro.

  9. Cell-free DNA testing after combined test: factors affecting the uptake.

    Science.gov (United States)

    Maiz, Nerea; Alzola, Irune; Murua, Emerson J; Rodríguez Santos, Javier

    2016-11-01

    First, to assess what was the uptake of cell free DNA (cfDNA) testing after a combined test and the maternal and fetal factors that influenced this decision, and second, to assess the uptake and factors that influence the choice of invasive testing. This observational retrospective study included 1083 singleton pregnancies who had a combined test for screening for Down syndrome between 11 (+) (0) and 13 (+) (6) weeks. Multivariate logistic regression analysis was used to determine which factors affected the uptake of cfDNA test and invasive testing among risk for trisomies 21, 18, and 13, maternal characteristics and fetal nuchal translucency (NT) thickness. Two-hundred fifty-seven (23.7%) women had a cfDNA test, 89 (8.2%) had an invasive test, and 737 (68.1%) had no further test. The uptake of cfDNA increased with the risk for trisomies (p < 0.001), maternal age (p = 0.013), and was higher in nulliparous women (p = 0.004). The uptake of invasive test increased with the risk for trisomies (p < 0.001) and NT thickness (p < 0.001). This study shows that the uptake of cfDNA testing increases with the risk for trisomies, maternal age, and is higher in nulliparous, whereas the uptake of invasive testing increases with the risk for trisomies and NT thickness.

  10. Cell-Free DNA Next-Generation Sequencing in Pancreatobiliary Carcinomas.

    Science.gov (United States)

    Zill, Oliver A; Greene, Claire; Sebisanovic, Dragan; Siew, Lai Mun; Leng, Jim; Vu, Mary; Hendifar, Andrew E; Wang, Zhen; Atreya, Chloe E; Kelley, Robin K; Van Loon, Katherine; Ko, Andrew H; Tempero, Margaret A; Bivona, Trever G; Munster, Pamela N; Talasaz, AmirAli; Collisson, Eric A

    2015-10-01

    Patients with pancreatic and biliary carcinomas lack personalized treatment options, in part because biopsies are often inadequate for molecular characterization. Cell-free DNA (cfDNA) sequencing may enable a precision oncology approach in this setting. We attempted to prospectively analyze 54 genes in tumor and cfDNA for 26 patients. Tumor sequencing failed in 9 patients (35%). In the remaining 17, 90.3% (95% confidence interval, 73.1%-97.5%) of mutations detected in tumor biopsies were also detected in cfDNA. The diagnostic accuracy of cfDNA sequencing was 97.7%, with 92.3% average sensitivity and 100% specificity across five informative genes. Changes in cfDNA correlated well with tumor marker dynamics in serial sampling (r = 0.93). We demonstrate that cfDNA sequencing is feasible, accurate, and sensitive in identifying tumor-derived mutations without prior knowledge of tumor genotype or the abundance of circulating tumor DNA. cfDNA sequencing should be considered in pancreatobiliary cancer trials where tissue sampling is unsafe, infeasible, or otherwise unsuccessful. Precision medicine efforts in biliary and pancreatic cancers have been frustrated by difficulties in obtaining adequate tumor tissue for next-generation sequencing. cfDNA sequencing reliably and accurately detects tumor-derived mutations, paving the way for precision oncology approaches in these deadly diseases. ©2015 American Association for Cancer Research.

  11. Mesenchymal Stem Cell-derived Extracellular Vesicles: Toward Cell-free Therapeutic Applications.

    Science.gov (United States)

    Rani, Sweta; Ryan, Aideen E; Griffin, Matthew D; Ritter, Thomas

    2015-05-01

    Mesenchymal stem (stromal) cells (MSCs) are multipotent cells with the ability to differentiate into several cell types, thus serving as a cell reservoir for regenerative medicine. Much of the current interest in therapeutic application of MSCs to various disease settings can be linked to their immunosuppressive and anti-inflammatory properties. One of the key mechanisms of MSC anti-inflammatory effects is the secretion of soluble factors with paracrine actions. Recently it has emerged that the paracrine functions of MSCs could, at least in part, be mediated by extracellular vesicles (EVs). EVs are predominantly released from the endosomal compartment and contain a cargo that includes miRNA, mRNA, and proteins from their cells of origin. Recent animal model-based studies suggest that EVs have significant potential as a novel alternative to whole cell therapies. Compared to their parent cells, EVs may have a superior safety profile and can be safely stored without losing function. In this article, we review current knowledge related to the potential use of MSC-derived EVs in various diseases and discuss the promising future for EVs as an alternative, cell-free therapy.

  12. Stable corneal regeneration four years after implantation of a cell-free recombinant human collagen scaffold.

    Science.gov (United States)

    Fagerholm, Per; Lagali, Neil S; Ong, Jeb A; Merrett, Kimberley; Jackson, W Bruce; Polarek, James W; Suuronen, Erik J; Liu, Yuwen; Brunette, Isabelle; Griffith, May

    2014-03-01

    We developed cell-free implants, comprising carbodiimide crosslinked recombinant human collagen (RHC), to enable corneal regeneration by endogenous cell recruitment, to address the worldwide shortage of donor corneas. Patients were grafted with RHC implants. Over four years, the regenerated neo-corneas were stably integrated without rejection, without the long immunosuppression regime needed by donor cornea patients. There was no recruitment of inflammatory dendritic cells into the implant area, whereas, even with immunosuppression, donor cornea recipients showed dendritic cell migration into the central cornea and a rejection episode was observed. Regeneration as evidenced by continued nerve and stromal cell repopulation occurred over the four years to approximate the micro-architecture of healthy corneas. Histopathology of a regenerated, clear cornea from a regrafted patient showed normal corneal architecture. Donor human cornea grafted eyes had abnormally tortuous nerves and stromal cell death was found. Implanted patients had a 4-year average corrected visual acuity of 20/54 and gained more than 5 Snellen lines of vision on an eye chart. The visual acuity can be improved with more robust materials for better shape retention. Nevertheless, these RHC implants can achieve stable regeneration and therefore, represent a potentially safe alternative to donor organ transplantation. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

  13. Circulating cell-free DNA mutation patterns in early and late stage colon and pancreatic cancer.

    Science.gov (United States)

    Vietsch, Eveline E; Graham, Garrett T; McCutcheon, Justine N; Javaid, Aamir; Giaccone, Giuseppe; Marshall, John L; Wellstein, Anton

    2017-12-01

    Cancer is a heterogeneous disease harboring diverse subclonal populations that can be discriminated by their DNA mutations. Environmental pressure selects subclones that ultimately drive disease progression and tumor relapse. Circulating cell-free DNA (ccfDNA) can be used to approximate the mutational makeup of cancer lesions and can serve as a marker for monitoring disease progression at the molecular level without the need for invasively acquired samples from primary or metastatic lesions. This potential for molecular analysis makes ccfDNA attractive for the study of clonal evolution and for uncovering emerging therapeutic resistance or sensitivity. We assessed ccfDNA from colon and pancreatic adenocarcinoma patients using next generation sequencing of 56 cancer-associated genes at the time of primary resectable disease and metastatic progression and compared this to the mutational patterns of the primary tumor. 28%-47% of non-synonymous mutations in the primary tumors were also detected in the ccfDNA while 71%-78% mutations found in ccfDNA were not detected in the primary tumors. ccfDNA collected at the time of progression harbored 3-5 new mutations not detected in ccfDNA at the earlier collection time points. We conclude that incorporation of ccfDNA analysis provides crucial insights into the changing molecular makeup of progressive colon and pancreatic cancer. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype.

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    Eilon Sharon

    2017-08-01

    Full Text Available Quantification of cell-free DNA (cfDNA in circulating blood derived from a transplanted organ is a powerful approach to monitoring post-transplant injury. Genome transplant dynamics (GTD quantifies donor-derived cfDNA (dd-cfDNA by taking advantage of single-nucleotide polymorphisms (SNPs distributed across the genome to discriminate donor and recipient DNA molecules. In its current implementation, GTD requires genotyping of both the transplant recipient and donor. However, in practice, donor genotype information is often unavailable. Here, we address this issue by developing an algorithm that estimates dd-cfDNA levels in the absence of a donor genotype. Our algorithm predicts heart and lung allograft rejection with an accuracy that is similar to conventional GTD. We furthermore refined the algorithm to handle closely related recipients and donors, a scenario that is common in bone marrow and kidney transplantation. We show that it is possible to estimate dd-cfDNA in bone marrow transplant patients that are unrelated or that are siblings of the donors, using a hidden Markov model (HMM of identity-by-descent (IBD states along the genome. Last, we demonstrate that comparing dd-cfDNA to the proportion of donor DNA in white blood cells can differentiate between relapse and the onset of graft-versus-host disease (GVHD. These methods alleviate some of the barriers to the implementation of GTD, which will further widen its clinical application.

  15. A multiplex PCR for non-invasive fetal RHD genotyping using cell-free fetal DNA.

    Science.gov (United States)

    Tounta, Georgia; Vrettou, Christina; Kolialexi, Aggeliki; Papantoniou, Nikolas; Destouni, Aspasia; Tsangaris, George T; Antsaklis, Aris; Kanavakis, Emmanuel; Mavrou, Ariadni

    2011-01-01

    To design a protocol for non-invasive prenatal diagnosis of fetal Rhesus D (RhD) status. A total of 112 single lymphocytes were used to test the efficiency of the assay. The protocol was validated using blood samples from 84 RhD-negative pregnant women at 7-24 weeks of gestation. Cell-free DNA (cfDNA) was enzymatically digested using AciI and analyzed by a polymerase chain reaction (PCR) that allowed simultaneous amplification of RHD exons 7 and 10, SRY, RASFF1A and ACTB. On the one genome-equivalent level, the efficiency of the protocol was ≥ 94.6% for each locus amplified. Conclusive results from the first set of PCRs were obtained for 79 cases with one false-positive. In five cases the analysis was repeated and, subsequently, all cases were accurately diagnosed. The proposed protocol is rapid, applicable in most molecular diagnostic laboratories and provides the basis for non-invasive examination of fetal RhD with 96.7% specificity and 100% sensitivity.

  16. Cell free fetal DNA testing in maternal blood of Romanian pregnant women

    Directory of Open Access Journals (Sweden)

    Viorica E Radoi

    2015-10-01

    Full Text Available Background: The discovery of circulating fetal DNA in maternal blood led to the discovery of new strategies to perform noninvasive testing for prenatal diagnosis. Objective: The purpose of the study was to detect fetal aneuploidy at chromosomes 13, 18, 21, X, and Y by analysis of fetal cell-free DNA from maternal blood, without endangering pregnancy. Materials and Methods: This retrospective study has been performed in Bucharest at Medlife Maternal and Fetal Medicine Department between 2013-2014. In total 201 women were offered noninvasive prenatal test. Maternal plasma samples were collected from women at greater than 9 weeks of gestation after informed consent and genetics counseling. Results: From 201 patients; 28 (13.93% had screening test with high risk for trisomy 21, 116 (57.71% had advanced maternal age, 1 (0.49% had second trimester ultrasound markers and the remaining 56 patients (27.86% performed the test on request. Of those patients, 189 (94.02% had a “low risk” result (99% risk all for trisomy 21 (T21. T21 was confirmed by amniocentesis in 1 patient and the other 4 patients declined confirmation. The 7 remaining patients (3.48% had a low fetal fraction of DNA. Conclusion: It is probably that prenatal diagnosis using fetal DNA in maternal blood would play an increasingly role in the future practice of prenatal testing because of high accuracy.

  17. Photoinactivation of cell-free human immunodeficiency virus by hematoporphyrin monomethyl ether.

    Science.gov (United States)

    Yin, Huijuan; Li, Yingxin; Zheng, Yongtang; Ye, Xuying; Zheng, Liqing; Li, Chunyan; Xue, Zhixiao

    2012-09-01

    Human immunodeficiency virus (HIV) particles that remain in the blood of patients are frequently ignored as targets for AIDS treatment. We therefore investigated the use of photodynamic therapy (PDT) with hematoporphyrin monomethyl ether (HMME) as a means of inactivating cell-free HIV in vitro. Virus particles including HIV-1(IIIB), resistant HIV-1 variants, HIV-1 clinical variants, and HIV-2 variants were incubated with HMME for 40 min, followed by irradiation with a 630-nm semiconductor laser at an energy density of 0.3 J/cm(2). The antiviral effects were evaluated by counting syncytium formation or measuring p24 antigen expression levels in supernatants by enzyme-linked immunosorbent assay. The relationships between photoinactivation and HMME concentrations, energy density, power density and antioxidants (NaN(3) and D: -mannitol) were also assessed using the above methods. All the tested virus particles were completely responsive to HMME-PDT. HMME concentration and energy density were positively correlated with photoinactivation of HIV, while power density was negatively correlated. Both sodium azide and D: -mannitol weakened the inhibitory effect of PDT on virus-induced membrane fusion, with D: -mannitol having a stronger effect. HMME-PDT can inactivate HIV particles, and may therefore represent a promising treatment for AIDS patients.

  18. Factors affecting cell-free DNA fetal fraction and the consequences for test accuracy.

    Science.gov (United States)

    Scott, Fergus Perry; Menezes, Melody; Palma-Dias, Ricardo; Nisbet, Debbie; Schluter, Philip; da Silva Costa, Fabricio; McLennan, Andrew Cameron

    2017-06-08

    Biological factors are known to influence the fetal fraction (FF) of cell-free DNA and may also influence the accuracy of non-invasive prenatal testing. NIPT from 5267 mixed risk women across three specialist clinics in Australia were analyzed. Multivariable regression analysis was used to determine whether maternal characteristics, ultrasound, and placental biomarkers affect FF and test accuracy. FF ranged from 4% to 37% (mean 11.6%). Body mass index (BMI), gestation, and placental biomarkers were found to be significant factors associated with FF. For each unit increase in BMI, the logarithmically transformed FF, (lnFF), mean value decreased by 0.027. Each week increases in gestation, lnFF increased by 0.023. Each unit increase in free BhCG, PAPPA, and PlGF, the lnFF increased by 0.065, 0.050, and 0.17, respectively. There was no significant association between FF with either maternal age or nuchal translucency. The false-positive cases and one false-negative case did not have lower FF than the true-positive cases. The fetal fraction in maternal plasma cfDNA increased with gestational age, serum pregnancy-associated plasma protein A (PAPP-A), β-hCG, and PlGF and decreased with increasing maternal BMI. There was no significant correlation between low FF and test accuracy, when FF was above 4%.

  19. An Evaluation of Output Quality of Machine Translation (Padideh Software vs. Google Translate)

    Science.gov (United States)

    Azer, Haniyeh Sadeghi; Aghayi, Mohammad Bagher

    2015-01-01

    This study aims to evaluate the translation quality of two machine translation systems in translating six different text-types, from English to Persian. The evaluation was based on criteria proposed by Van Slype (1979). The proposed model for evaluation is a black-box type, comparative and adequacy-oriented evaluation. To conduct the evaluation, a…

  20. Bean Soup Translation: Flexible, Linguistically-Motivated Syntax for Machine Translation

    Science.gov (United States)

    Mehay, Dennis Nolan

    2012-01-01

    Machine translation (MT) systems attempt to translate texts from one language into another by translating words from a "source language" and rearranging them into fluent utterances in a "target language." When the two languages organize concepts in very different ways, knowledge of their general sentence structure, or…