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Sample records for chimerism analysis post

  1. Chimerism analysis in peripheral blood using indel quantitative real-time PCR is a useful tool to predict post-transplant relapse in acute leukemia.

    PubMed

    Jacque, N; Nguyen, S; Golmard, J-L; Uzunov, M; Garnier, A; Leblond, V; Vernant, J-P; Bories, D; Dhédin, N

    2015-02-01

    Detection of increasing mixed chimerism (IMC) using standard PCR correlates with relapse after allo-SCT for acute leukemias (ALs). Quantitative real-time PCR of insertion/deletion polymorphism (indel qrtPCR) is a much more sensitive method, which can be performed on peripheral blood. We studied the significance of low increases of recipient cells (0.1%) detected by indel qrtPCR in a cohort of 89 transplants. We did not observe relapse among the 32 patients with no IMC. Fifty-seven patients presented a first IMC, which was followed by four different scenarios: a decreasing MC (26 cases, no relapse), a stable MC (1 case, 1 relapse), a second IMC (24 cases, 15 relapse) or no control of chimerism (6 cases, 5 relapses). In multivariate analysis, detection of two successive IMCs was strongly associated with relapse (hazard ratio (HR): 9.4, 95% confidence interval (CI): 3.8-23; P<0.0001). Among the 57 patients who presented at least one IMC, 27 underwent immunomodulation (tapering of immunosuppression or donor lymphocyte injection), leading to a 1-year relapse rate of 15.7% vs 57.6% in the 30 other patients (P=0.0007). Altogether, these results indicate that chimerism analysis using indel qrtPCR in peripheral blood is a useful tool for detection of relapse in patients transplanted for AL.

  2. The impact of chimerism in DNA-based forensic sex determination analysis.

    PubMed

    George, Renjith; Donald, Preethy Mary; Nagraj, Sumanth Kumbargere; Idiculla, Jose Joy; Hj Ismail, Rashid

    2013-01-01

    Sex determination is the most important step in personal identification in forensic investigations. DNA-based sex determination analysis is comparatively more reliable than the other conventional methods of sex determination analysis. Advanced technology like real-time polymerase chain reaction (PCR) offers accurate and reproducible results and is at the level of legal acceptance. But still there are situations like chimerism where an individual possess both male and female specific factors together in their body. Sex determination analysis in such cases can give erroneous results. This paper discusses the phenomenon of chimerism and its impact on sex determination analysis in forensic investigations.

  3. The impact of chimerism in DNA-based forensic sex determination analysis

    PubMed Central

    George, Renjith; Donald, Preethy Mary; Nagraj, Sumanth Kumbargere; Idiculla, Jose Joy; Hj Ismail, Rashid

    2013-01-01

    Sex determination is the most important step in personal identification in forensic investigations. DNA-based sex determination analysis is comparatively more reliable than the other conventional methods of sex determination analysis. Advanced technology like real-time polymerase chain reaction (PCR) offers accurate and reproducible results and is at the level of legal acceptance. But still there are situations like chimerism where an individual possess both male and female specific factors together in their body. Sex determination analysis in such cases can give erroneous results. This paper discusses the phenomenon of chimerism and its impact on sex determination analysis in forensic investigations. PMID:23785258

  4. Structure-function analysis of peroxisomal ATP-binding cassette transporters using chimeric dimers.

    PubMed

    Geillon, Flore; Gondcaille, Catherine; Charbonnier, Soëli; Van Roermund, Carlo W; Lopez, Tatiana E; Dias, Alexandre M M; Pais de Barros, Jean-Paul; Arnould, Christine; Wanders, Ronald J; Trompier, Doriane; Savary, Stéphane

    2014-08-29

    ABCD1 and ABCD2 are two closely related ATP-binding cassette half-transporters predicted to homodimerize and form peroxisomal importers for fatty acyl-CoAs. Available evidence has shown that ABCD1 and ABCD2 display a distinct but overlapping substrate specificity, although much remains to be learned in this respect as well as in their capability to form functional heterodimers. Using a cell model expressing an ABCD2-EGFP fusion protein, we first demonstrated by proximity ligation assay and co-immunoprecipitation assay that ABCD1 interacts with ABCD2. Next, we tested in the pxa1/pxa2Δ yeast mutant the functionality of ABCD1/ABCD2 dimers by expressing chimeric proteins mimicking homo- or heterodimers. For further structure-function analysis of ABCD1/ABCD2 dimers, we expressed chimeric dimers fused to enhanced GFP in human skin fibroblasts of X-linked adrenoleukodystrophy patients. These cells are devoid of ABCD1 and accumulate very long-chain fatty acids (C26:0 and C26:1). We checked that the chimeric proteins were correctly expressed and targeted to the peroxisomes. Very long-chain fatty acid levels were partially restored in transfected X-linked adrenoleukodystrophy fibroblasts regardless of the chimeric construct used, thus demonstrating functionality of both homo- and heterodimers. Interestingly, the level of C24:6 n-3, the immediate precursor of docosahexaenoic acid, was decreased in cells expressing chimeric proteins containing at least one ABCD2 moiety. Our data demonstrate for the first time that both homo- and heterodimers of ABCD1 and ABCD2 are functionally active. Interestingly, the role of ABCD2 (in homo- and heterodimeric forms) in the metabolism of polyunsaturated fatty acids is clearly evidenced, and the chimeric dimers provide a novel tool to study substrate specificity of peroxisomal ATP-binding cassette transporters. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Structure-Function Analysis of Peroxisomal ATP-binding Cassette Transporters Using Chimeric Dimers*

    PubMed Central

    Geillon, Flore; Gondcaille, Catherine; Charbonnier, Soëli; Van Roermund, Carlo W.; Lopez, Tatiana E.; Dias, Alexandre M. M.; Pais de Barros, Jean-Paul; Arnould, Christine; Wanders, Ronald J.; Trompier, Doriane; Savary, Stéphane

    2014-01-01

    ABCD1 and ABCD2 are two closely related ATP-binding cassette half-transporters predicted to homodimerize and form peroxisomal importers for fatty acyl-CoAs. Available evidence has shown that ABCD1 and ABCD2 display a distinct but overlapping substrate specificity, although much remains to be learned in this respect as well as in their capability to form functional heterodimers. Using a cell model expressing an ABCD2-EGFP fusion protein, we first demonstrated by proximity ligation assay and co-immunoprecipitation assay that ABCD1 interacts with ABCD2. Next, we tested in the pxa1/pxa2Δ yeast mutant the functionality of ABCD1/ABCD2 dimers by expressing chimeric proteins mimicking homo- or heterodimers. For further structure-function analysis of ABCD1/ABCD2 dimers, we expressed chimeric dimers fused to enhanced GFP in human skin fibroblasts of X-linked adrenoleukodystrophy patients. These cells are devoid of ABCD1 and accumulate very long-chain fatty acids (C26:0 and C26:1). We checked that the chimeric proteins were correctly expressed and targeted to the peroxisomes. Very long-chain fatty acid levels were partially restored in transfected X-linked adrenoleukodystrophy fibroblasts regardless of the chimeric construct used, thus demonstrating functionality of both homo- and heterodimers. Interestingly, the level of C24:6 n-3, the immediate precursor of docosahexaenoic acid, was decreased in cells expressing chimeric proteins containing at least one ABCD2 moiety. Our data demonstrate for the first time that both homo- and heterodimers of ABCD1 and ABCD2 are functionally active. Interestingly, the role of ABCD2 (in homo- and heterodimeric forms) in the metabolism of polyunsaturated fatty acids is clearly evidenced, and the chimeric dimers provide a novel tool to study substrate specificity of peroxisomal ATP-binding cassette transporters. PMID:25043761

  6. Assessment of the purity of isolated cell populations for lineage-specific chimerism monitoring post haematopoietic stem cell transplantation.

    PubMed

    Hanson, V; Adams, B; Lord, J; Barker, A; Poulton, K; Lee, H

    2013-10-01

    Following haematopoietic stem cell transplantation, monitoring the proportion of donor and recipient haematopoiesis in the patient (chimerism) is an influential tool in directing further treatment choices. Short tandem repeat (STR) analysis is a method of chimerism monitoring using DNA isolated from peripheral blood, bone marrow or specific isolated cell lineages such as CD3+ T cells. For lineage-specific STR analysis on cell populations isolated from peripheral blood, a qualitative estimation of the purity of each isolated population is essential for the correct interpretation of the test data. We describe a rapid, inexpensive method for the determination of purity using a simple flow cytometry method. The method described for assessing the purity of sorted CD3+ cells can be applied to any cell population isolated using the same technology. Data obtained were comparable to results from a commercial polymerase chain reaction (PCR)-based method for the assessment of purity (Non-T Genomic Detection Kit, Accumol, Calgary, AB, Canada) (P = 0.59). Of the 303 samples tested by flow cytometry, 290 (95.7%) exceeded 90% purity, and 215 (70.95%) were over 99% pure. There were some outlying samples, showing diversity between samples and the unpredictability of purity of isolated cell populations. This flow cytometry method can be easily assimilated into routine testing protocols, allowing purity assessment in multiple-sorted cell populations for lineage-specific chimerism monitoring using a single secondary antibody and giving results comparable to a PCR-based method. As purity of isolated cell lineages is affected by time after venepuncture and storage temperature, assessment of each sample is recommended to give a reliable indication of sample quality and confidence in the interpretation of the results. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  7. Follow-up of post-transplant minimal residual disease and chimerism in childhood lymphoblastic leukaemia: 90 d to react.

    PubMed

    Pochon, Cécile; Oger, Emmanuel; Michel, Gérard; Dalle, Jean-Hugues; Salmon, Alexandra; Nelken, Brigitte; Bertrand, Yves; Cavé, Hélène; Cayuela, Jean-Michel; Grardel, Nathalie; Macintyre, Elizabeth; Margueritte, Geneviève; Méchinaud, Françoise; Rohrlich, Pierre; Paillard, Catherine; Demeocq, François; Schneider, Pascale; Plantaz, Dominique; Poirée, Marilyne; Eliaou, Jean-François; Semana, Gilbert; Drunat, Séverine; Jonveaux, Philippe; Bordigoni, Pierre; Gandemer, Virginie

    2015-04-01

    Relapse after transplantation is a major cause of treatment failure in paediatric acute lymphoblastic leukaemia (ALL). Here, we report the findings of a prospective national study designed to investigate the feasibility of immune intervention in children in first or subsequent remission following myeloablative conditioning. This study included 133 children who received a transplant for ALL between 2005 and 2008. Minimal Residual Disease (MRD) based on T cell receptor/immunoglobulin gene rearrangements was measured on days -30, 30, 90 and 150 post-transplantation. Ciclosporin treatment was rapidly discontinued and donor lymphocyte infusions (DLI) were programmed for patients with a pre- or post-transplant MRD status ≥10(-3) . Only nine patients received DLI. Pre- and post-transplant MRD status, and the duration of ciclosporin were independently associated with 5-year overall survival (OS), which was 62·07% for the whole cohort. OS was substantially higher in patients cleared of MRD than in those with persistent MRD (52·3% vs. 14·3%, respectively). Only pre-transplant MRD status (Hazard Ratio 2·57, P = 0·04) and duration of ciclosporin treatment (P < 0·001) were independently associated with relapse. The kinetics of chimerism were not useful for predicting relapse, whereas MRD monitoring up to 90 d post-transplantation was a valuable prognostic tool to guide therapeutic intervention. © 2014 John Wiley & Sons Ltd.

  8. Understanding Zika Virus Stability and Developing a Chimeric Vaccine through Functional Analysis

    PubMed Central

    Yang, Yujiao; Muruato, Antonio E.; Zou, Jing; Shan, Chao; Nunes, Bruno T. D.; Medeiros, Daniele B. A.; Vasconcelos, Pedro F. C.; Weaver, Scott C.; Rossi, Shannan L.

    2017-01-01

    ABSTRACT Compared with other flaviviruses, Zika virus (ZIKV) is uniquely associated with congenital diseases in pregnant women. One recent study reported that (i) ZIKV has higher thermostability than dengue virus (DENV [a flavivirus closely related to ZIKV]), which might contribute to the disease outcome; (ii) the higher thermostability of ZIKV could arise from an extended loop structure in domain III of the viral envelope (E) protein and an extra hydrogen-bond interaction between E molecules (V. A. Kostyuchenko, E. X. Y. Lim, S. Zhang, G. Fibriansah, T.-S. Ng, J. S. G. Ooi, J. Shi, and S.-M. Lok, Nature 533:425–428, 2016, https://doi.org/10.1038/nature17994). Here we report the functional analysis of the structural information in the context of complete ZIKV and DENV-2 virions. Swapping the prM-E genes between ZIKV and DENV-2 switched the thermostability of the chimeric viruses, identifying the prM-E proteins as the major determinants for virion thermostability. Shortening the extended loop of the E protein by 1 amino acid was lethal for ZIKV assembly/release. Mutations (Q350I and T351V) that abolished the extra hydrogen-bond interaction between the E proteins did not reduce ZIKV thermostability, indicating that the extra interaction does not increase the thermostability. Interestingly, mutant T351V was attenuated in A129 mice defective in type I interferon receptors, even though the virus retained the wild-type thermostability. Furthermore, we found that a chimeric ZIKV with the DENV-2 prM-E and a chimeric DENV-2 with the ZIKV prM-E were highly attenuated in A129 mice; these chimeric viruses were highly immunogenic and protective against DENV-2 and ZIKV challenge, respectively. These results indicate the potential of these chimeric viruses for vaccine development. PMID:28174309

  9. Understanding Zika Virus Stability and Developing a Chimeric Vaccine through Functional Analysis.

    PubMed

    Xie, Xuping; Yang, Yujiao; Muruato, Antonio E; Zou, Jing; Shan, Chao; Nunes, Bruno T D; Medeiros, Daniele B A; Vasconcelos, Pedro F C; Weaver, Scott C; Rossi, Shannan L; Shi, Pei-Yong

    2017-02-07

    Compared with other flaviviruses, Zika virus (ZIKV) is uniquely associated with congenital diseases in pregnant women. One recent study reported that (i) ZIKV has higher thermostability than dengue virus (DENV [a flavivirus closely related to ZIKV]), which might contribute to the disease outcome; (ii) the higher thermostability of ZIKV could arise from an extended loop structure in domain III of the viral envelope (E) protein and an extra hydrogen-bond interaction between E molecules (V. A. Kostyuchenko, E. X. Y. Lim, S. Zhang, G. Fibriansah, T.-S. Ng, J. S. G. Ooi, J. Shi, and S.-M. Lok, Nature 533:425-428, 2016, https://doi.org/10.1038/nature17994). Here we report the functional analysis of the structural information in the context of complete ZIKV and DENV-2 virions. Swapping the prM-E genes between ZIKV and DENV-2 switched the thermostability of the chimeric viruses, identifying the prM-E proteins as the major determinants for virion thermostability. Shortening the extended loop of the E protein by 1 amino acid was lethal for ZIKV assembly/release. Mutations (Q350I and T351V) that abolished the extra hydrogen-bond interaction between the E proteins did not reduce ZIKV thermostability, indicating that the extra interaction does not increase the thermostability. Interestingly, mutant T351V was attenuated in A129 mice defective in type I interferon receptors, even though the virus retained the wild-type thermostability. Furthermore, we found that a chimeric ZIKV with the DENV-2 prM-E and a chimeric DENV-2 with the ZIKV prM-E were highly attenuated in A129 mice; these chimeric viruses were highly immunogenic and protective against DENV-2 and ZIKV challenge, respectively. These results indicate the potential of these chimeric viruses for vaccine development. Analysis of a recently observed high-resolution structure of ZIKV led to a hypothesis that its unusual stability may contribute to the associated, unique disease outcomes. Here we performed a functional

  10. [Chimerism analysis after allogeneic haematopoietic stem cell transplantation. Interest of cell sorting: general review].

    PubMed

    Mollet, I; Giannoli, C; Rigal, D; Dubois, V

    2012-04-01

    Haematopoietic stem cells transplantation, widely used these last decades, represent the ultimate treatment resource for patients with haematological malignancies. Long range success of this treatment is particularly affected by relapse of the initial disease, graft rejection or graft versus host disease. Chimerism analysis after transplantation had been used since several years to document engraftment, to determine the risk of relapse and to adapt therapy promptly when necessary. Usefulness of this analysis for the outcome of transplanted patients, as well as the impact of using high sensitive techniques coupled with specific cell populations sorted have been demonstrated by retrospective studies. Follow-up of chimerism would allow to operate efficiently before the onset of clinical signs in leukaemic patients with high risk of relapse and to control the expression of minimal residual disease when specific molecular markers could not be monitored. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

  11. Transcriptome analysis revealed chimeric RNAs, single nucleotide polymorphisms and allele-specific expression in porcine prenatal skeletal muscle

    PubMed Central

    Yang, Yalan; Tang, Zhonglin; Fan, Xinhao; Xu, Kui; Mu, Yulian; Zhou, Rong; Li, Kui

    2016-01-01

    Prenatal skeletal muscle development genetically determines postnatal muscle characteristics such as growth and meat quality in pigs. However, the molecular mechanisms underlying prenatal skeletal muscle development remain unclear. Here, we performed the first genome-wide analysis of chimeric RNAs, single nuclear polymorphisms (SNPs) and allele-specific expression (ASE) in prenatal skeletal muscle in pigs. We identified 14,810 protein coding genes and 163 high-confidence chimeric RNAs expressed in prenatal skeletal muscle. More than 94.5% of the chimeric RNAs obeyed the canonical GT/AG splice rule and were trans-splicing events. Ten and two RNAs were aligned to human and mouse chimeric transcripts, respectively. We detected 106,457 high-quality SNPs (6,955 novel), which were mostly (89.09%) located within QTLs for production traits. The high proportion of non-exonic SNPs revealed the incomplete annotation status of the current swine reference genome. ASE analysis revealed that 11,300 heterozygous SNPs showed allelic imbalance, whereas 131 ASE variants were located in the chimeric RNAs. Moreover, 4 ASE variants were associated with various economically relevant traits of pigs. Taken together, our data provide a source for studies of chimeric RNAs and biomarkers for pig breeding, while illuminating the complex transcriptional events underlying prenatal skeletal muscle development in mammals. PMID:27352850

  12. The Relationship between STR-PCR Chimerism Analysis and Chronic GvHD Following Hematopoietic Stem Cell Transplantation

    PubMed Central

    Mousavi, Seyed Asadollah; Javadimoghadam, Mina; Ghavamzadeh, Ardeshir; Alimoghaddam, Kamran; Sayarifard, Azadeh; Ghaffari, Seyed-Hamidollah; Chahardouli, Bahram; Basi, Ali

    2017-01-01

    Background: The study attempts to assess the relationship between chimerism analysis using polymerase chain reaction of short tandem repeat (STR) and the incidence of chronic graft versus host disease (GvHD) as well as survival. Subjects and Methods: The retrospective cohort included all patients who received allo-HSCT during 2005-2013. Data collected by day +100 were reviewed in terms of the incidence of chronic GvHD and survival. Chimerism was evaluated for whole blood, T-cell and PMN cells on days 15, 30 and 60, respectively using polymerase chain reaction of short tandem repeat (STR). Results: Forty (69%) patients developed chronic GvHD, 11 (19%) relapsed and 22 (39.7%) expired during the study. There was a significant relationship between chronic GvHD and chimerism analysis including whole blood on day 60 (p=0.001), Polymorphonuclear neutrophil (PMN) on day 60 (p=0.05), T-cell on days 15 (p=0.028), 30 (p=0.01) and 60 (p=0.004). Patients with chronic GvHD showed a long-term survival as compared with those without chronic GvHD (p=0.0013). Conclusion: Conducting continuous analysis of chimerism provides an opportunity to initiate immediate measures in order to prevent complications. PMID:28286611

  13. Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis

    PubMed Central

    Conlin, Laura K.; Thiel, Brian D.; Bonnemann, Carsten G.; Medne, Livija; Ernst, Linda M.; Zackai, Elaine H.; Deardorff, Matthew A.; Krantz, Ian D.; Hakonarson, Hakon; Spinner, Nancy B.

    2010-01-01

    Mosaic aneuploidy and uniparental disomy (UPD) arise from mitotic or meiotic events. There are differences between these mechanisms in terms of (i) impact on embryonic development; (ii) co-occurrence of mosaic trisomy and UPD and (iii) potential recurrence risks. We used a genome-wide single nucleotide polymorphism (SNP) array to study patients with chromosome aneuploidy mosaicism, UPD and one individual with XX/XY chimerism to gain insight into the developmental mechanism and timing of these events. Sixteen cases of mosaic aneuploidy originated mitotically, and these included four rare trisomies and all of the monosomies, consistent with the influence of selective factors. Five trisomies arose meiotically, and three of the five had UPD in the disomic cells, confirming increased risk for UPD in the case of meiotic non-disjunction. Evidence for the meiotic origin of aneuploidy and UPD was seen in the patterns of recombination visible during analysis with 1–3 crossovers per chromosome. The mechanisms of formation of the UPD included trisomy rescue, with and without concomitant trisomy, monosomy rescue, and mitotic formation of a mosaic segmental UPD. UPD was also identified in an XX/XY chimeric individual, with one cell line having complete maternal UPD consistent with a parthenogenetic origin. Utilization of SNP arrays allows simultaneous evaluation of genomic alterations and insights into aneuploidy and UPD mechanisms. Differentiation of mitotic and meiotic origins for aneuploidy and UPD supports existence of selective factors against full trisomy of some chromosomes in the early embryo and provides data for estimation of recurrence and disease mechanisms. PMID:20053666

  14. Functional analysis of aldehyde oxidase using expressed chimeric enzyme between monkey and rat.

    PubMed

    Itoh, Kunio; Asakawa, Tasuku; Hoshino, Kouichi; Adachi, Mayuko; Fukiya, Kensuke; Watanabe, Nobuaki; Tanaka, Yorihisa

    2009-01-01

    Aldehyde oxidase (AO) is a homodimer with a subunit molecular mass of approximately 150 kDa. Each subunit consists of about 20 kDa 2Fe-2S cluster domain storing reducing equivalents, about 40 kDa flavine adenine dinucleotide (FAD) domain and about 85 kDa molybdenum cofactor (MoCo) domain containing a substrate binding site. In order to clarify the properties of each domain, especially substrate binding domain, chimeric cDNAs were constructed by mutual exchange of 2Fe-2S/FAD and MoCo domains between monkey and rat. Chimeric monkey/rat AO was referred to one with monkey type 2Fe-2S/FAD domains and a rat type MoCo domain. Rat/monkey AO was vice versa. AO-catalyzed 2-oxidation activities of (S)-RS-8359 were measured using the expressed enzyme in Escherichia coli. Substrate inhibition was seen in rat AO and chimeric monkey/rat AO, but not in monkey AO and chimeric rat/monkey AO, suggesting that the phenomenon might be dependent on the natures of MoCo domain of rat. A biphasic Eadie-Hofstee profile was observed in monkey AO and chimeric rat/monkey AO, but not rat AO and chimeric monkey/rat AO, indicating that the biphasic profile might be related to the properties of MoCo domain of monkey. Two-fold greater V(max) values were observed in monkey AO than in chimeric rat/monkey AO, and in chimeric monkey/rat AO than in rat AO, suggesting that monkey has the more effective electron transfer system than rat. Thus, the use of chimeric enzymes revealed that 2Fe-2S/FAD and MoCo domains affect the velocity and the quantitative profiles of AO-catalyzed (S)-RS-8359 2-oxidation, respectively.

  15. Clinical utility of chimerism status assessed by lineage-specific short tandem repeat analysis: experience from four cases of allogeneic stem cell transplantation.

    PubMed

    Goh, Ri-Young; Cho, Sung-Suk; Song, Yoo-Jeong; Heo, Kyeong; Oh, Sung-Yong; Kim, Sung-Hyun; Kwon, Hyeok-Chan; Kim, Hyo-Jin; Han, Jin-Yeong

    2009-08-01

    Chimerism testing permits early prediction and documentation of successful engraftment, and also facilitates detection of impending graft rejection. In this study, we serially monitored chimerism status by short tandem repeat-based PCR in nucleated cells (NC), T cells and natural killer (NK) cells after myeloablative allogeneic stem cell transplantation (SCT). Four patients with myeloid malignancies showed discrepant chimerism results among those three fractions. Three patients had mixed chimerism (MC) of donor/host T cells at a time point around the onset of chronic graft-versus-host disease (GVHD). In two patients with disease relapse, MC of NK cells preceded a morphological relapse or NK cells showed a higher percentage of patient cells compared to NC. Therefore, our study shows that chimerism analysis in lineage-specific cells might be useful in predicting clinical outcome after allogeneic SCT in certain patients.

  16. Real-Time PCR Analysis of Chimerism in T Cell Subsets as an Early Predictor of Graft-Versus-Host Disease Following Allogeneic Stem Cell Transplantation.

    PubMed

    Guz, Katarzyna; Nasiłowska, Barbara; Tomaszewska, Agnieszka; Orzińska, Agnieszka; Smolarczyk-Wodzyńska, Justyna; Krzemienowska, Magdalen; Hałaburda, Kazimierz; Przybylski, Maciej; Jędrzejczak, Wiesław Wiktor; Mariańska, Bożena; Brojer, Ewa

    2015-12-03

    Graft-versus-host-disease (GvHD) is the major cause of morbidity and mortality after stem cell transplantation. The development of early prediction methods is therefore of importance. Our aim was to analyze the usefulness of early donor chimerism monitoring after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in T cells and in CD4+ and CD8+ (lineage chimerism) for GvHD prediction. Chimerism was analyzed in 76 consecutive adult patients using RQ-PCR TaqMan technology on DNA extracted from Pan T, CD4+, and CD8+ cell subsets on Day 5, 10, 15 and 30 after allo-HSCT. The threshold of chimerism predictive for GvHD was the same for all tested cell subsets. In acute myeloid leukemia (AML) patients treated with myeloablative conditioning (MAC), the threshold predictive for acute graft versus host disease was 95% and 99% for Day 10 and Day 15, respectively. In patients treated with reduced intensity conditioning (RIC), the threshold predictive for chronic graft versus host disease was 98% on Day 10. The differences were statistically significant. Chimerism analysis in T cell subsets by RQ-PCR on Day 10 and Day 15 after transplantation is useful for prediction of aGvHD (AML patients after MAC) and cGvHD (patients after RIC). However, there was no difference in the results between chimerism in the T cell subsets. Our RQ-PCR protocol was highly sensitive and proved effective for analysis of lineage chimerism.

  17. ReX: A suite of computational tools for the design, visualization, and analysis of chimeric protein libraries.

    PubMed

    Huang, Weiliang; Johnston, Wayne A; Boden, Mikael; Gillam, Elizabeth M J

    2016-02-01

    Directed evolution has greatly facilitated protein engineering and provided new insights into protein structure-function relationships. DNA shuffling using restriction enzymes is a particularly simple and cost-effective means of recombinatorial evolution that is well within the capability of most molecular biologists, but tools for the design and analysis of such experiments are limited. Here we introduce a suite of freely available online tools to make the construction and analysis of chimeric libraries readily accessible to the novice. REcut (http://qpmf.rx.umaryland.edu/REcut.html) facilitates the choice of DNA fragmentation strategy, while Xover (http://qpmf.rx.umaryland.edu/Xover.html) analyzes chimeric mutants to reveal recombination patterns and extract quantitative data.

  18. IVGEN Post Flight Analysis

    NASA Technical Reports Server (NTRS)

    Mcquillen, John; Brown, Dan; Hussey, Sam; Zoldak, John

    2014-01-01

    The Intravenous Fluid Generation (IVGEN) Experiment was a technology demonstration experiment that purified ISS potable water, mixed it with salt, and transferred it through a sterilizing filter. On-orbit performance was verified as appropriate and two 1.5 l bags of normal saline solution were returned to earth for post-flight testing by a FDA certified laboratory for compliance with United States Pharmacopiea (USP) standards. Salt concentration deviated from required values and an analysis identified probable causes. Current efforts are focused on Total Organic Content (TOC) testing, and shelf life.The Intravenous Fluid Generation (IVGEN) Experiment demonstrated the purification of ISS potable water, the mixing of the purified water with sodium chloride, and sterilization of the solution via membrane filtration. On-orbit performance was monitored where feasible and two 1.5-liter bags of normal saline solution were returned to earth for post-flight testing by a FDA-registered laboratory for compliance with United States Pharmacopeia (USP)standards [1]. Current efforts have been focused on challenge testing with identified [2] impurities (total organic-carbon), and shelf life testing. The challenge testing flowed known concentrations of contaminants through the IVGEN deionizing cartridge and membrane filters to test their effectiveness. One finding was that the filters and DI-resin themselves contribute to the contaminant load during initial startup, suggesting that the first 100 ml of fluid be discarded. Shelf life testing is ongoing and involves periodic testing of stored DI cartridges and membrane filters that are capped and sealed in hermetic packages. The testing is conducted at six month intervals measuring conductivity and endotoxins in the effluent. Currently, the packaging technique has been successfully demonstrated for one year of storage testing. The USP standards specifies that the TOC be conducted at point of generation as opposed to point of

  19. Design and kinetic analysis of hammerhead ribozyme and DNAzyme that specifically cleave TEL-AML1 chimeric mRNA

    SciTech Connect

    Choi, Woo-Hyung; Choi, Bo-Ra; Kim, Jae Hyun; Yeo, Woon-Seok; Oh, Sangtaek; Kim, Dong-Eun

    2008-09-12

    In order to develop the oligonucleotides to abolish an expression of TEL-AML1 chimeric RNA, which is a genetic aberration that causes the acute lymphoblastic leukemia (ALL), hammerhead ribozymes and deoxyoligoribozymes that can specifically cleave TEL-AML1 fusion RNA were designed. Constructs of the deoxyribozyme with an asymmetric substrate binding arm (Dz26) and the hammerhead ribozyme with a 4 nt-bulged substrate binding arm in the stem III (buRz28) were able to cleave TEL-AML1 chimeric RNA specifically at sites close to the junction in vitro, without cleaving the normal TEL and AML1 RNA. Single-turnover kinetic analysis under enzyme-excess condition revealed that the buRz28 is superior to the Dz26 in terms of substrate binding and RNA-cleavage. In conjunction with current progress in a gene-delivery technology, the designed oligonucleotides that specifically cleave the TEL-AML1 chimeric mRNA are hoped to be applicable for the treatment of ALL in vivo.

  20. The Evolution and Analysis of the Functional Domains of the Chimeric Proteins that Initiate Pyrimidine Biosynthesis

    DTIC Science & Technology

    1989-10-15

    proteins in eubacteria , but are consolidated in a single 243 kDa chimeric plypeptide in mrnmals and other higher eukaryotes. We have shown previously that...and regulatory properties, have been identified in eubacteria . E. coli aspartate transcarbamylase, a well characterized class B enzyme, Is a

  1. Complex chimerism

    PubMed Central

    Ma, Kimberly K.; Petroff, Margaret G.; Coscia, Lisa A.; Armenti, Vincent T.; Adams Waldorf, Kristina M.

    2013-01-01

    Thousands of women with organ transplantation have undergone successful pregnancies, however little is known about how the profound immunologic changes associated with pregnancy might influence tolerance or rejection of the allograft. Pregnant women with a solid organ transplant are complex chimeras with multiple foreign cell populations from the donor organ, fetus, and mother of the pregnant woman. We consider the impact of complex chimerism and pregnancy-associated immunologic changes on tolerance of the allograft both during pregnancy and the postpartum period. Mechanisms of allograft tolerance are likely dynamic during pregnancy and affected by the influx of fetal microchimeric cells, HLA relationships (between the fetus, pregnant woman and/or donor), peripheral T cell tolerance to fetal cells, and fetal minor histocompatibility antigens. Further research is necessary to understand the complex immunology during pregnancy and the postpartum period of women with a solid organ transplant. PMID:23974274

  2. CRISPR/Cas9 mediated genome editing in ES cells and its application for chimeric analysis in mice

    PubMed Central

    Oji, Asami; Noda, Taichi; Fujihara, Yoshitaka; Miyata, Haruhiko; Kim, Yeon Joo; Muto, Masanaga; Nozawa, Kaori; Matsumura, Takafumi; Isotani, Ayako; Ikawa, Masahito

    2016-01-01

    Targeted gene disrupted mice can be efficiently generated by expressing a single guide RNA (sgRNA)/CAS9 complex in the zygote. However, the limited success of complicated genome editing, such as large deletions, point mutations, and knockins, remains to be improved. Further, the mosaicism in founder generations complicates the genotypic and phenotypic analyses in these animals. Here we show that large deletions with two sgRNAs as well as dsDNA-mediated point mutations are efficient in mouse embryonic stem cells (ESCs). The dsDNA-mediated gene knockins are also feasible in ESCs. Finally, we generated chimeric mice with biallelic mutant ESCs for a lethal gene, Dnajb13, and analyzed their phenotypes. Not only was the lethal phenotype of hydrocephalus suppressed, but we also found that Dnajb13 is required for sperm cilia formation. The combination of biallelic genome editing in ESCs and subsequent chimeric analysis provides a useful tool for rapid gene function analysis in the whole organism. PMID:27530713

  3. Possible Formation of Mitochondrial-RNA Containing Chimeric or Trimeric RNA Implies a Post-Transcriptional and Post-Splicing Mechanism for RNA Fusion

    PubMed Central

    Yang, Wei; Wu, Jian-min; Bi, An-ding; Ou-yang, Yong-chang; Shen, Hai-hong; Chirn, Gung-wei; Zhou, Jian-hua; Weiss, Emily; Holman, Emily Pauline; Liao, D. Joshua

    2013-01-01

    Human cells are known to express many chimeric RNAs, i.e. RNAs containing two genes' sequences. Wondering whether there also is trimeric RNA, i.e. an RNA containing three genes' sequences, we wrote simple computer code to screen human expression sequence tags (ESTs) deposited in different public databases, and obtained hundreds of putative trimeric ESTs. We then used NCBI Blast and UCSC Blat browsers to further analyze their sequences, and identified 61 trimeric and two tetrameric ESTs (one EST containing four different sequences). We also identified 57 chimeric, trimeric or teterameric ESTs that contained both mitochondrial (mt) RNA and nuclear RNA (nRNA), i.e. were mtRNA-nRNA fusions. In some trimeric ESTs, the downstream partner was fused to the poly-A tail of the upstream partner, which, together with the mtRNA-nRNA fusions, suggests a possible new mechanism for RNA fusion that occurs after both transcription and splicing have been terminated, and possibly outside the nucleus, in contrast to the two current hypothetical mechanisms, trans-splicing and transcriptional-slippage, that occur in the nucleus. The mt-sequences in the mtRNA-nRNA fusions had pseudogenes in the nucleus but, surprisingly, localized mainly in chromosomes 1 and 5. In some mtRNA-nRNA fusions, as well as in some ESTs that were derived only from mtRNA, the mt-sequences might be cis- or trans-spliced. Actually, we cloned a new cis-spliced mtRNA, coined as 16SrRNA-s. Hence, mtDNA may not always be intron-less. Fusion of three or more RNAs to one, fusion of nRNA to mtRNA, and cis- or trans-splicing of mtRNA should all enlarge the cellular RNA repertoire, in turn enlarging the cellular functions. Therefore, future experimental verification of the existence of these novel classes of fusion RNAs and spliced mtRNAs in human cells should significantly advance our understanding of biology and medicine. PMID:24204722

  4. Possible formation of mitochondrial-RNA containing chimeric or trimeric RNA implies a post-transcriptional and post-splicing mechanism for RNA fusion.

    PubMed

    Yang, Wei; Wu, Jian-min; Bi, An-ding; Ou-Yang, Yong-chang; Shen, Hai-hong; Chirn, Gung-wei; Zhou, Jian-hua; Weiss, Emily; Holman, Emily Pauline; Liao, D Joshua

    2013-01-01

    Human cells are known to express many chimeric RNAs, i.e. RNAs containing two genes' sequences. Wondering whether there also is trimeric RNA, i.e. an RNA containing three genes' sequences, we wrote simple computer code to screen human expression sequence tags (ESTs) deposited in different public databases, and obtained hundreds of putative trimeric ESTs. We then used NCBI Blast and UCSC Blat browsers to further analyze their sequences, and identified 61 trimeric and two tetrameric ESTs (one EST containing four different sequences). We also identified 57 chimeric, trimeric or teterameric ESTs that contained both mitochondrial (mt) RNA and nuclear RNA (nRNA), i.e. were mtRNA-nRNA fusions. In some trimeric ESTs, the downstream partner was fused to the poly-A tail of the upstream partner, which, together with the mtRNA-nRNA fusions, suggests a possible new mechanism for RNA fusion that occurs after both transcription and splicing have been terminated, and possibly outside the nucleus, in contrast to the two current hypothetical mechanisms, trans-splicing and transcriptional-slippage, that occur in the nucleus. The mt-sequences in the mtRNA-nRNA fusions had pseudogenes in the nucleus but, surprisingly, localized mainly in chromosomes 1 and 5. In some mtRNA-nRNA fusions, as well as in some ESTs that were derived only from mtRNA, the mt-sequences might be cis- or trans-spliced. Actually, we cloned a new cis-spliced mtRNA, coined as 16SrRNA-s. Hence, mtDNA may not always be intron-less. Fusion of three or more RNAs to one, fusion of nRNA to mtRNA, and cis- or trans-splicing of mtRNA should all enlarge the cellular RNA repertoire, in turn enlarging the cellular functions. Therefore, future experimental verification of the existence of these novel classes of fusion RNAs and spliced mtRNAs in human cells should significantly advance our understanding of biology and medicine.

  5. Biochemical and Functional Analysis of Drosophila-Sciara Chimeric Sex-Lethal Proteins

    PubMed Central

    Ruiz, María Fernanda; Sarno, Francesca; Zorrilla, Silvia; Rivas, Germán; Sánchez, Lucas

    2013-01-01

    Background The Drosophila SXL protein controls sex determination and dosage compensation. It is a sex-specific factor controlling splicing of its own Sxl pre-mRNA (auto-regulation), tra pre-mRNA (sex determination) and msl-2 pre-mRNA plus translation of msl-2 mRNA (dosage compensation). Outside the drosophilids, the same SXL protein has been found in both sexes so that, in the non-drosophilids, SXL does not appear to play the key discriminating role in sex determination and dosage compensation that it plays in Drosophila. Comparison of SXL proteins revealed that its spatial organisation is conserved, with the RNA-binding domains being highly conserved, whereas the N- and C-terminal domains showing significant variation. This manuscript focuses on the evolution of the SXL protein itself and not on regulation of its expression. Methodology Drosophila-Sciara chimeric SXL proteins were produced. Sciara SXL represents the non-sex-specific function of ancient SXL in the non-drosophilids from which presumably Drosophila SXL evolved. Two questions were addressed. Did the Drosophila SXL protein have affected their functions when their N- and C-terminal domains were replaced by the corresponding ones of Sciara? Did the Sciara SXL protein acquire Drosophila sex-specific functions when the Drosophila N- and C-terminal domains replaced those of Sciara? The chimeric SXL proteins were analysed in vitro to study their binding affinity and cooperative properties, and in vivo to analyse their effect on sex determination and dosage compensation by producing Drosophila flies that were transgenic for the chimeric SXL proteins. Conclusions The sex-specific properties of extant Drosophila SXL protein depend on its global structure rather than on a specific domain. This implies that the modifications, mainly in the N- and C-terminal domains, that occurred in the SXL protein during its evolution within the drosophilid lineage represent co-evolutionary changes that determine the appropriate

  6. [The immune-enzyme analysis based on chimeric molecule and oligopeptide fragmentations to detect autoantibodies to beta-adrenergic receptor in patients with dilation cardiomyopathy].

    PubMed

    Afanas'eva, O I; Klesareva, E A; Efremov, E E; Sidorova, M V; Bespalova, Zh D; Levashov, P A; Ezhov, M V; Adamova, I Iu; Pokrovskiĭ, S N

    2013-04-01

    The article deals with specification of technique of immune-enzyme analysis to detect autoantibodies to beta-adrenergic receptors (beta1-AP) using compound of oligopeptids representing the fragmentations of extracellular sites beta1-AP and chimeric molecule of extracellular section of receptor This technique significantly exceeds the analogues defined in publications by its sensitivity and correlation with diagnosis.

  7. Isolated extramedullary cutaneous relapse despite concomitant severe graft-vs.-host disease and tissue chimerism analysis in a patient with acute lymphoblastic leukemia after allogeneic hematopoietic stem cell transplantation: A case report

    PubMed Central

    Kantarcioglu, Bulent; Bekoz, Huseyin Saffet; Ogret, Yeliz Duvarci; Cakir, Asli; Kivanc, Demet; Oguz, Fatma Savran; Sargin, Deniz

    2016-01-01

    Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a potentially curative treatment option for patients with acute lymphoblastic leukemia (ALL). The curative potential of allo-HSCT for ALL is, in part, due to the graft-vs.-leukemia (GVL) effect, in addition to the intensive conditioning chemo-radiotherapy. However, relapse remains the major cause of treatment failure following allo-HSCT for ALL. In the allo-HSCT setting, testing for genetic markers of hematopoietic chimerism has become a part of the routine diagnostic program. Routine chimerism analysis is usually performed in peripheral blood or bone marrow; in fact, little is known about the value of tissue chimerism in patients with extramedullary relapse (EMR) after the allo-HSCT setting. The present study reports on, a case of a patient with ALL who experienced isolated cutaneous EMR despite ongoing graft-vs.-host disease (GVHD), and the results of peripheral blood and skin tissue chimerism studies using multiplex polymerase chain reaction (PCR) of short tandem repeats (STR-PCR). The present case demonstrates that, although complete remission and/or chimerism may be achieved in the bone marrow, chimerism achieved at the tissue level, and the subsequent GVL effect, may be limited, despite concomitant severe GVHD following allo-HSCT. Our tissue chimerism analysis results provide a good example of how skin tissue may be a ‘sanctuary’ site for effector cells of GVL, despite active GVHD and complete hematopoetic chimerism. PMID:28105353

  8. Post-Newtonian Jeans Analysis

    NASA Astrophysics Data System (ADS)

    Nazari, Elham; Kazemi, Ali; Roshan, Mahmood; Abbassi, Shahram

    2017-04-01

    The Jeans analysis is studied in the first post-Newtonian limit. In other words, the relativistic effects on local gravitational instability are considered for systems whose characteristic velocities and corresponding gravitational fields are higher than those permitted in the Newtonian limit. The dispersion relation for the propagation of small perturbations is found in the post-Newtonian approximation using two different techniques. A new Jeans mass is derived and compared to the standard Jeans mass. In this limit, the relativistic effects make the new Jeans mass smaller than the Newtonian Jeans mass. Furthermore, the fractional difference between these two masses increases when the temperature/pressure of the system increases. Interestingly, in this limit, pressure can enhance gravitational instability instead of preventing it. Finally, the results are applied to high-temperature astrophysical systems, and the possibility of local fragmentation in some relativistic systems is investigated.

  9. Genotypic analysis at multiple loci across Kaposi's sarcoma herpesvirus (KSHV) DNA molecules: clustering patterns, novel variants and chimerism.

    PubMed

    Zong, Jianchao; Ciufo, Dolores M; Viscidi, Raphael; Alagiozoglou, Lee; Tyring, Stephen; Rady, Peter; Orenstein, Jan; Boto, William; Kalumbuja, Henry; Romano, Nino; Melbye, Mads; Kang, Gyeong H; Boshoff, Chris; Hayward, Gary S

    2002-01-01

    The genomes of human Kaposi's sarcoma-associated herpesvirus (KSHV) display several levels of DNA sequence heterogeneity and subgrouping that show distinctive clustering patterns in related human populations. The four major subtype patterns for the hypervariable ORF-K1 protein correlate closely with the principal diasporas resulting from the migration of modern humans out of East Africa and suggest that KSHV is an ancient human virus that is transmitted primarily in a familial fashion with consequent very low recombination rates. However, chimeric genomes have also been detected, especially with regard to the presence of P versus M alleles of the ORF-K15 gene. To understand further the genetic organization and evolutionary history of KSHV, especially with regard to possible new subtypes, recombinant genomes, constant region loci and clustering in particular ethnic groups or among classic versus epidemic cases in the same geographic area. Direct PCR DNA sequencing was carried out on the ORF-K1 and ORF-K15 genes at the extreme left and right hand sides, as well as on six other internal loci of diagnostic samples collected from 70 new KSHV-positive patients in Israel, South Korea, Sicily, Scandinavia, Brazil, Uganda, South Africa and the US. Our overall results from more than 135 KSHV genomes from many different human population groups now provides evidence for seven distinct subtypes of KSHV genomes (referred to as A/P, B/P, C/P, D/P, M, N and Q). However, the two most closely related subtypes (A/P and C/P) are only differentiated at the LHS side of the genome, and the three most distantly related forms (M, N and Q) appear to exist only as small chimeric segments that are remnants from the RHS of more ancient forms of the virus. By analyzing multiple conserved loci across the B subtype genomes that predominate in sub-Saharan Africa, we can also now recognize three to four distinct B genome subgroups with varying patterns of inter and intratypic mosaicism. Analysis of

  10. Chimeric analysis of Notch2 function: a role for Notch2 in the development of the roof plate of the mouse brain.

    PubMed

    Kadokawa, Yuzo; Marunouchi, Tohru

    2002-10-01

    Notch proteins are transmembrane receptors involved in cell-fate determination throughout development. Targeted disruption of either the Notch1 or Notch2 gene in mice results in embryonic lethality around embryonic day (E) 10.5 with widespread cell death. Although Notch1-deficient mice show disorganized somitogenesis, Notch2 mutants did not show definitive abnormalities in any tissue expressing high levels of the Notch2 gene, including the central nervous system. To study Notch2 function in development beyond the embryonic lethal stage, we performed chimeric analysis between Notch2 mutant and wild-type mouse embryos. Chimeric embryos developed normally and homozygous Notch2 mutant-specific cell death was not observed. Although chimeric embryos showed normal mosaicism until E9.5 in all tissues studied to date, Notch2 homozygous mutant cells failed to contribute to formation of the roof plate of the diencephalon and mesencephalon at later developmental stages, when Notch2 is normally expressed at high levels at there. Furthermore, Notch2 heterozygous mutant cells were also excluded from the roof plate of the chimera, however, Notch2 heterozygous mutant mice developed normally. We also showed that Wnt-1 and Mash1 expression patterns at the roof plate were disorganized in Notch2 homozygous mutant embryos. These results indicate that Notch2 plays an important role in development of the roof plate of the diencephalon and mesencephalon, and suggest that cellular rearrangement is involved in this process.

  11. Processing of chimeric mammalian cytochrome b5 precursors in Escherichia coli: reaction specificity of signal peptidase and identification of an aminopeptidase in post-translocational processing.

    PubMed Central

    Harding, V; Karim, A; Kaderbhai, N; Jones, A; Evans, A; Kaderbhai, M A

    1993-01-01

    A chimeric precursor interlinked by an arginine residue between the full-length signal sequence of alkaline phosphatase and the eukaryotic cytoplasmic cytochrome b5 was constructed. Expression of the chimeric precursor protein in Escherichia coli resulted in efficient export of spectrally authentic cytochrome b5 into the periplasm [Karim, Harding, Evans, Kaderbhai and Kaderbhai (1993) Bio/Technology 11, 612-618]. On sequencing, the apparent absence of arginine at the N-terminus of the secreted cytochrome b5 implied that the chimera was either miscleaved by signal peptidase or further processed following signal excision by an uncharacterized peptidase. The influence of the N-terminal region of cytochrome b5 on the unusual processing of the chimeric precursor was investigated by engineering a number of variant forms in which the region between Arg+1 and the mature portion of cytochrome b5 was extended and varied. Observations of the in vivo processed patterns of these variant cytochrome b5 forms exported into the periplasm revealed that the absence of arginine was due to neither miscleavage of the translocated precursor by the signal peptidase nor the nature of the early region of cytochrome b5. In fact, the selective excision of the arginine residue occurred subsequent to signal sequence deletion by an aminopeptidase which was sensitive to the metal chelator o-phenanthroline. We show that this aminopeptidase also participates in the trimming of the N-terminal arginine residue of the bacterial alkaline phosphatase to generate the three isoenzymes in the periplasm. Images Figure 4 Figure 5 Figure 6 PMID:8352742

  12. [Post-mortem microbiology analysis].

    PubMed

    Fernández-Rodríguez, Amparo; Alberola, Juan; Cohen, Marta Cecilia

    2013-12-01

    Post-mortem microbiology is useful in both clinical and forensic autopsies, and allows a suspected infection to be confirmed. Indeed, it is routinely applied to donor studies in the clinical setting, as well as in sudden and unexpected death in the forensic field. Implementation of specific sampling techniques in autopsy can minimize the possibility of contamination, making interpretation of the results easier. Specific interpretation criteria for post-mortem cultures, the use of molecular diagnosis, and its fusion with molecular biology and histopathology have led to post-mortem microbiology playing a major role in autopsy. Multidisciplinary work involving microbiologists, pathologists, and forensic physicians will help to improve the achievements of post-mortem microbiology, prevent infectious diseases, and contribute to a healthier population.

  13. Detection and quantification of in vitro-culture induced chimerism using simple sequence repeat (SSR) analysis in Theobroma cacao (L.).

    PubMed

    Rodríguez López, Carlos M; Wetten, Andrew C; Wilkinson, Michael J

    2004-12-01

    Mutation rates are often elevated in plants regenerated from in vitro culture, giving rise to so-called 'somaclonal variation'. Detailed characterisation of mutation profiles that arise during culture should improve our understanding of processes influencing mutation and allow the selection of protocols yielding the fewest/least severe changes. Somatic mutations will usually produce genetic chimeras where unchanged alleles are retained by some cells. Such chimeras are difficult to detect but likely to form a significant proportion of any regenerant population. We present a simple protocol that enables the provisional diagnosis of both homogenous and chimeric mutants among large regenerant populations, together with a semi-quantitative means of estimating the proportion of mutant cells. The assay exploits consistent differential amplification of alternate simple sequence repeat alleles at heterozygous loci. Calibration of the relative amplification of alleles from two genotypes-and the synthetic chimeras created from them-revealed a strong linear relationship between 'peak heights' representing alternate alleles following capillary electrophoresis. The assay predicts chimeric composition to a reasonable level of confidence (+/-5%) so long as the infrequent allele exceeds 15% of the template. The system was applied to 233 regenerants of cocoa somatic embryogenesis and identified 72 (31%) putative chimeric mutants for slippage mutation or allele loss across two loci.

  14. Crystal Structure of PG16 and Chimeric Dissection with Somatically Related PG9: Structure-Function Analysis of Two Quaternary-Specific Antibodies That Effectively Neutralize HIV-1

    SciTech Connect

    Pancera, Marie; McLellan, Jason S.; Wu, Xueling; Zhu, Jiang; Changela, Anita; Schmidt, Stephen D.; Yang, Yongping; Zhou, Tongqing; Phogat, Sanjay; Mascola, John R.; Kwong, Peter D.

    2010-11-03

    HIV-1 resists neutralization by most antibodies. Two somatically related human antibodies, PG9 and PG16, however, each neutralize 70 to 80% of circulating HIV-1 isolates. Here we present the structure of the antigen-binding fragment of PG16 in monoclinic and orthorhombic lattices at 2.4 and 4.0 {angstrom}, respectively, and use a combination of structural analysis, paratope dissection, and neutralization assessment to determine the functional relevance of three unusual PG9/PG16 features: N-linked glycosylation, extensive affinity maturation, and a heavy chain-third complementarity-determining region (CDR H3) that is one of the longest observed in human antibodies. Glycosylation extended off the side of the light chain variable domain and was not required for neutralization. The CDR H3 formed an axe-shaped subdomain, which comprised 42% of the CDR surface, with the axe head looming {approx}20 {angstrom} above the other combining loops. Comprehensive sets of chimeric swaps between PG9 and PG16 of light chain, heavy chain, and CDR H3 were employed to decipher structure-function relationships. Chimeric swaps generally complemented functionally, with differences in PG9/PG16 neutralization related primarily to residue differences in CDR H3. Meanwhile, chimeric reversions to genomic V genes showed isolate-dependent effects, with affinity maturation playing a significant role in augmenting neutralization breadth (P = 0.036) and potency (P < 0.0001). The structural and functional details of extraordinary CDR H3 and extensive affinity maturation provide insights into the neutralization mechanism of and the elicitation pathway for broadly neutralizing antibodies like PG9 and PG16.

  15. Bone marrow cell migration to the heart in a chimeric mouse model of acute chagasic disease

    PubMed Central

    Irion, Camila Iansen; Paredes, Bruno Diaz; Brasil, Guilherme Visconde; da Cunha, Sandro Torrentes; Paula, Luis Felipe; Carvalho, Alysson Roncally; de Carvalho, Antonio Carlos Campos; Carvalho, Adriana Bastos; Goldenberg, Regina Coeli dos Santos

    2017-01-01

    BACKGROUND Chagas disease is a public health problem caused by infection with the protozoan Trypanosoma cruzi. There is currently no effective therapy for Chagas disease. Although there is some evidence for the beneficial effect of bone marrow-derived cells in chagasic disease, the mechanisms underlying their effects in the heart are unknown. Reports have suggested that bone marrow cells are recruited to the chagasic heart; however, studies using chimeric mouse models of chagasic cardiomyopathy are rare. OBJECTIVES The aim of this study was to investigate the migration of bone marrow cells to the heart after T. cruzi infection in a model of chagasic disease in chimeric mice. METHODS To obtain chimerical mice, wild-type (WT) C57BL6 mice were exposed to full body irradiation (7 Gy), causing bone marrow ablation. Then, bone marrow cells from green fluorescent protein (GFP)-transgenic mice were infused into the mice. Graft effectiveness was confirmed by flow cytometry. Experimental mice were divided into four groups: (i) infected chimeric (iChim) mice; (ii) infected WT (iWT) mice, both of which received 3 × 104 trypomastigotes of the Brazil strain; (iii) non-infected chimeric (Chim) mice; and (iv) non-infected WT mice. FINDINGS At one-month post-infection, iChim and iWT mice showed first degree atrioventricular block with decreased heart rate and treadmill exercise parameters compared to those in the non-infected groups. MAIN CONCLUSIONS iChim mice showed an increase in parasitaemia, myocarditis, and the presence of amastigote nests in the heart tissue compared to iWT mice. Flow cytometry analysis did not detect haematopoietic progenitor cells in the hearts of infected mice. Furthermore, GFP+ cardiomyocytes were not detected in the tissues of chimeric mice. PMID:28767980

  16. Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes.

    PubMed

    Brzozowski, A M; Lawson, D M; Turkenburg, J P; Bisgaard-Frantzen, H; Svendsen, A; Borchert, T V; Dauter, Z; Wilson, K S; Davies, G J

    2000-08-08

    Several chimeric alpha-amylases genes were constructed by an in vivo recombination technique from the Bacillus amyloliquefaciens and Bacillus licheniformis genes. One of the fusion amylases (hereafter BA2), consisting of residues 1-300 from B. amyloliquefaciens and 301-483 from B. licheniformis, has been extensively studied by X-ray crystallography at resolutions between 2.2 and 1.7 A. The 3-dimensional structure of the native enzyme was solved by multiple isomorphous replacement, and refined at a resolution of 1.7 A. It consists of 483 amino acids, organized similarly to the known B. lichiniformis alpha-amylase structure [Machius et al. (1995) J. Mol. Biol. 246, 545-559], but features 4 bound calcium ions. Two of these form part of a linear cluster of three ions, the central ion being attributed to sodium. This cluster lies at the junction of the A and B domains with one calcium of the cluster structurally equivalent to the major Ca(2+) binding site of fungal alpha-amylases. The third calcium ion is found at the interface of the A and C domains. BA2 contains a fourth calcium site, not observed in the B. licheniformis alpha-amylase structure. It is found on the C domain where it bridges the two beta-sheets. Three acid residues (Glu261, Asp328, and Asp231) form an active site similar to that seen in other amylases. In the presence of TRIS buffer, a single molecule of TRIS occupies the -1 subsite of the enzyme where it is coordinated by the three active-center carboxylates. Kinetic data reveal that BA2 displays properties intermediate to those of its parents. Data for crystals soaked in maltooligosaccharides reveal the presence of a maltotriose binding site on the N-terminal face of the (beta/alpha)(8) barrel of the molecule, not previously described for any alpha-amylase structure, the biological function of which is unclear. Data for a complex soaked with the tetrasaccharide inhibitor acarbose, at 1.9 A, reveal a decasaccharide moiety, spanning the -7 to +3

  17. A multivariate morphometric analysis of hippocampal anatomical variation in C57BL/6 in equilibrium BALB/c chimeric mice.

    PubMed

    Crusio, W E; Bär, I M; Schwegler, H; Buselmaier, W

    1990-12-10

    We investigated hippocampal anatomy in artificially-produced chimeras derived by the aggregation of embryos from two widely-studied inbred mouse strains, C57BL/6J and BALB/cJ. Contrary to expectations, the chimeras were not always intermediate between the parental strains. For a number of characters, the chimeras exceeded qualitatively as well as quantitatively the phenotypical range displayed by both inbred parental strains. These findings imply that if only one parent is available for comparison, for instance, in studies involving a normally inviable genotype, separating effects of this genotype from idiosyncratic effects inherent to the chimeric model will be very difficult, if not impossible.

  18. Chimeric Pestivirus Experimental Vaccines.

    PubMed

    Reimann, Ilona; Blome, Sandra; Beer, Martin

    2016-01-01

    Chimeric pestiviruses have shown great potential as marker vaccine candidates against pestiviral infections. Exemplarily, we describe here the construction and testing of the most promising classical swine fever vaccine candidate "CP7_E2alf" in detail. The description is focused on classical cloning technologies in combination with reverse genetics.

  19. Long-Term Stable Mixed Chimerism after Hematopoietic Stem Cell Transplantation in Patients with Non-Malignant Disease, Shall We Be Tolerant?

    PubMed Central

    Stikvoort, Arwen; Sundin, Mikael; Uzunel, Mehmet; Gertow, Jens; Sundberg, Berit; Schaffer, Marie; Mattsson, Jonas; Uhlin, Michael

    2016-01-01

    Long-term stable mixed chimerism is a rare and poorly understood phenomenon post hematopoietic stem cell transplantation. This study aims to shed light on whether the two hematopoietic systems in patients with mixed chimerism remain functional. Additionally, we investigate possible immunologic differences in these individuals compared to patients with only donor derived immune cells. Patients with donor and mixed chimerism, at median 10 (5–16) years post-HSCT for non-malignant diseases, were assessed regarding clinical situation and immune system (phenotypical and functional). No difference in long-term outcome was seen in terms of general wellbeing, central phenotypic immune system features (e.g., differentiation status, CD4/CD8 ratio, B and NK-cell frequency) and antibody responses to immunizations. At a median of 10 years post transplantation, patients with mixed chimerism had significantly higher IgG3 and platelet levels. Additionally, these patients had higher NKT-cell levels (CD94+CD8+ and CD56+CD8+) than patients with donor chimerism. In depth phenotypic analysis of patients with mixed chimerism demonstrated recipient-derived fractions in most immune cell lineages (e.g., T-cell, B-cell and NK-cell subsets). Recipient cells were also capable of responding to mitogenic stimulation with production of several cytokines. In conclusion, long-term mixed chimerism did not negatively affect patient wellbeing and long-term outcome. Moreover, recipient-derived immunity may still be functional in these patients, suggesting an active state of tolerance and immunologic dependence on both hematopoietic systems. PMID:27152621

  20. Acute GVHD is a strong predictor of full donor CD3+ T cell chimerism after reduced intensity conditioning allogeneic stem cell transplantation.

    PubMed

    El-Cheikh, Jean; Vazquez, Alberto; Crocchiolo, Roberto; Furst, Sabine; Calmels, Boris; Castagna, Luca; Lemarie, Claude; Granata, Angela; Ladaique, Patrick; Oudin, Claire; Faucher, Catherine; Chabannon, Christian; Blaise, Didier

    2012-12-01

    The monitoring of chimerism is a standard procedure to assess engraftment and achievement of full donor lymphoid cells after reduced intensity conditioning (RIC) stem cell transplantation (Allo-SCT). However, there is no consensus on when and how often to monitor post-transplant chimerism. We retrospectively analyzed our experience regarding the impact of acute graft versus host disease (GVHD) for the prediction of allograft chimerism. One-hundred-and-fifteen patients transplanted between 2001 and 2010 were identified. This group included 57 females and 58 males with a median age of 50 years (range: 26-68). Patients evaluated in this study were adult patients with hematologic malignancies, who received transplants from an HLA-matched sibling donor or matched unrelated donor (MUD) at allele level so-called 10/10, and received the RIC regimen including fludarabine/busulfan and anti-thymoglobulin (ATG). Mixed T-cell chimerism was defined as between 5 and 94% recipient cells, and full chimerism was defined as the presence of more than 95% donor T-cell chimerism (TCC). Full donor TCC was achieved in 93 patients (81%) at a median of 77 days (range: 30-120) post-transplant. The cumulative incidence of Grade 2-4 GVHD in our population was 25% (95% CI 17-34). The analysis of the population of patients with acute GVHD grade ≥2 showed that at day 120 after Allo-SCT they all had a total full donor TCC. On the other hand, 78 (68%) patients without acute GVHD grade ≥2 presented with mixed chimerism (p = 0.002) on day 120 post-transplant. Interestingly, patients who received ATG 5 mg/kg obtained a higher probability of complete chimerism compared with those receiving 2.5 mg/kg (p = 0.03). In conclusion, our study demonstrates that acute GVHD was predictive of full donor TCC after RIC Allo-SCT. Therefore, our data may challenge the concept of the frequent or close monitoring of donor chimerism in some patients with ongoing acute GVHD. However, chimerism testing could represent

  1. Content analysis of cancer blog posts*

    PubMed Central

    Kim, Sujin

    2009-01-01

    Objectives: The efficacy of user-defined subject tagging and software-generated subject tagging for describing and organizing cancer blog contents was explored. Methods: The Technorati search engine was used to search the blogosphere for cancer blog postings generated during a two-month period. Postings were mined for relevant subject concepts, and blogger-defined tags and Text Analysis Portal for Research (TAPoR) software–defined tags were generated for each message. Descriptive data were collected, and the blogger-defined tags were compared with software-generated tags. Three standard vocabularies (Opinion Templates, Basic Resource, and Medical Subject Headings [MeSH] Resource) were used to assign subject terms to the blogs, with results compared for efficacy in information retrieval. Results: Descriptive data showed that most of the studied cancer blogs (80%) contained fewer than 500 words each. The numbers of blogger-defined tags per posting (M = 4.49 per posting) were significantly smaller than the TAPoR keywords (M = 23.55 per posting). Both blogger-defined subject tags and software-generated subject tags were often overly broad or overly narrow in focus, producing less than effective search results for those seeking to extract information from cancer blogs. Conclusions: Additional exploration into methods for systematically organizing cancer blog postings is necessary if blogs are to become stable and efficacious information resources for cancer patients, friends, families, or providers. PMID:19851489

  2. Content analysis of cancer blog posts.

    PubMed

    Kim, Sujin

    2009-10-01

    The efficacy of user-defined subject tagging and software-generated subject tagging for describing and organizing cancer blog contents was explored. The Technorati search engine was used to search the blogosphere for cancer blog postings generated during a two-month period. Postings were mined for relevant subject concepts, and blogger-defined tags and Text Analysis Portal for Research (TAPoR) software-defined tags were generated for each message. Descriptive data were collected, and the blogger-defined tags were compared with software-generated tags. Three standard vocabularies (Opinion Templates, Basic Resource, and Medical Subject Headings [MeSH] Resource) were used to assign subject terms to the blogs, with results compared for efficacy in information retrieval. Descriptive data showed that most of the studied cancer blogs (80%) contained fewer than 500 words each. The numbers of blogger-defined tags per posting (M = 4.49 per posting) were significantly smaller than the TAPoR keywords (M = 23.55 per posting). Both blogger-defined subject tags and software-generated subject tags were often overly broad or overly narrow in focus, producing less than effective search results for those seeking to extract information from cancer blogs. Additional exploration into methods for systematically organizing cancer blog postings is necessary if blogs are to become stable and efficacious information resources for cancer patients, friends, families, or providers.

  3. Engineering Chimeric Antigen Receptors

    PubMed Central

    Kulemzin, S. V.; Kuznetsova, V. V.; Mamonkin, M.; Taranin, A. V.; Gorchakov, A. A.

    2017-01-01

    Chimeric antigen receptors (CARs) are recombinant protein molecules that redirect cytotoxic lymphocytes toward malignant and other target cells. The high feasibility of manufacturing CAR-modified lymphocytes for the therapy of cancer has spurred the development and optimization of new CAR T cells directed against a broad range of target antigens. In this review, we describe the main structural and functional elements constituting a CAR, discuss the roles of these elements in modulating the anti-tumor activity of CAR T cells, and highlight alternative approaches to CAR engineering. PMID:28461969

  4. Post Treatment With an FGF Chimeric Growth Factor Enhances Epithelial Cell Proliferation to Improve Recovery From Radiation-Induced Intestinal Damage

    SciTech Connect

    Nakayama, Fumiaki; Hagiwara, Akiko; Umeda, Sachiko; Asada, Masahiro; Goto, Megumi; Oki, Junko; Suzuki, Masashi; Imamura, Toru; Akashi, Makoto

    2010-11-01

    Purpose: A fibroblast growth factor (FGF) 1-FGF2 chimera (FGFC) was created previously and showed greater structural stability than FGF1. This chimera was capable of stimulating epithelial cell proliferation much more strongly than FGF1 or FGF2 even without heparin. Therefore FGFC was expected to have greater biologic activity in vivo. This study evaluated and compared the protective activity of FGFC and FGF1 against radiation-induced intestinal injuries. Methods and Materials: We administered FGFC and FGF1 intraperitoneally to BALB/c mice 24 h before or after total-body irradiation (TBI). The numbers of surviving crypts were determined 3.5 days after TBI with gamma rays at doses ranging from 8 to 12 Gy. Results: The effect of FGFC was equal to or slightly superior to FGF1 with heparin. However, FGFC was significantly more effective in promoting crypt survival than FGF1 (p < 0.01) when 10 {mu}g of each FGF was administered without heparin before irradiation. In addition, FGFC was significantly more effective at promoting crypt survival (p < 0.05) than FGF1 even when administered without heparin at 24 h after TBI at 10, 11, or 12 Gy. We found that FGFC post treatment significantly promoted 5-bromo-2'-deoxyuridine incorporation into crypts and increased crypt depth, resulting in more epithelial differentiation. However, the number of apoptotic cells in FGFC-treated mice decreased to almost the same level as that in FGF1-treated mice. Conclusions: These findings suggest that FGFC strongly enhanced radioprotection with the induction of epithelial proliferation without exogenous heparin after irradiation and is useful in clinical applications for both the prevention and post treatment of radiation injuries.

  5. Vectors expressing chimeric Japanese encephalitis dengue 2 viruses.

    PubMed

    Wei, Y; Wang, S; Wang, X

    2014-01-01

    Vectors based on self-replicating RNAs (replicons) of flaviviruses are becoming powerful tool for expression of heterologous genes in mammalian cells and development of novel antiviral and anticancer vaccines. We constructed two vectors expressing chimeric viruses consisting of attenuated SA14-14-2 strain of Japanese encephalitis virus (JEV) in which the PrM/M-E genes were replaced fully or partially with those of dengue 2 virus (DENV-2). These vectors, named pJED2 and pJED2-1770 were transfected to BHK-21 cells and produced chimeric viruses JED2V and JED2-1770V, respectively. The chimeric viruses could be passaged in C6/36 but not BHK-21 cells. The chimeric viruses produced in C6/36 cells CPE 4-5 days after infection and RT-PCR, sequencing, immunofluorescence assay (IFA) and Western blot analysis confirmed the chimeric nature of produced viruses. The immunogenicity of chimeric viruses in mice was proved by detecting DENV-2 E protein-specific serum IgG antibodies with neutralization titer of 10. Successful preparation of infectious clones of chimeric JEV-DENV-2 viruses showed that JEV-based expression vectors are fully functional.

  6. Long-term follow-up of patients receiving allogeneic stem cell transplant for chronic lymphocytic leukaemia: mixed T-cell chimerism is associated with high relapse risk and inferior survival.

    PubMed

    Thompson, Philip A; Stingo, Francesco; Keating, Michael J; Wierda, William G; O'Brien, Susan M; Estrov, Zeev; Ledesma, Celina; Rezvani, Katayoun; Qazilbash, Muzaffar; Shah, Nina; Parmar, Simrit; Popat, Uday; Anderlini, Paolo; Yago, Nieto; Ciurea, Stefan O; Kebriaei, Partow; Champlin, Richard; Shpall, Elizabeth J; Hosing, Chitra M

    2017-05-01

    There is limited information regarding the immunological predictors of post-allogeneic stem cell transplant (alloSCT) outcome in chronic lymphocytic leukaemia (CLL), such as mixed T-cell chimerism. We analysed 143 consecutive patients with relapsed/refractory CLL, transplanted between 2000 and 2012, to determine the prognostic relevance of mixed chimerism post-alloSCT and the ability of post-transplant immunomodulation to treat relapse. Mixed T-cell chimerism occurred in 50% of patients at 3 months and 43% at 6 months post-alloSCT; upon 3- and 6-month landmark analysis, this was associated with inferior progression-free survival (PFS) [Hazard ratio (HR) 1·93, P = 0·003 and HR 2·58, P < 0·001] and survival (HR 1·66, P = 0·05 and HR 2·17, P < 0·001), independent of baseline patient characteristics, and a lower rate of grade II-IV acute graft-versus-host disease (GHVD) (16% vs. 52%, P < 0·001). Thirty-three patients were treated with immunomodulation for relapse post-alloSCT (immunosuppression withdrawal, n = 6, donor lymphocyte infusion, n = 27); 17 achieved complete response (CR), which predicted superior PFS (53 months vs. 10 months, P < 0·001) and survival (117 months vs. 30 months, P = 0·006). Relapsed patients with mixed chimerism had inferior response to immunomodulation; conversion to full donor chimerism was highly correlated both with CR and with the development of severe acute GVHD, which was fatal in 3/8 patients. Novel therapeutic strategies are required for patients with mixed T-cell chimerism post-alloSCT for CLL. © 2017 John Wiley & Sons Ltd.

  7. Mixed Chimerism, Lymphocyte Recovery and Evidence for Early Donor-Specific Unresponsiveness in Patients Receiving CKBMT to Induce Tolerance

    PubMed Central

    LoCascio, Samuel A.; Morokata, Tatsuaki; Chittenden, Meredith; Preffer, Frederic I.; Dombkowski, David M.; Andreola, Giovanna; Crisalli, Kerry; Kawai, Tatsuo; Saidman, Susan L.; Spitzer, Thomas R.; Tolkoff-Rubin, Nina; Cosimi, A. Benedict; Sachs, David H.; Sykes, Megan

    2011-01-01

    Background We have previously reported operational tolerance in patients receiving HLA-mismatched combined kidney and bone marrow transplantation (CKBMT). We now report on transient multilineage hematopoietic chimerism and lymphocyte recovery in five patients receiving a modified CKBMT protocol, and evidence for early donor-specific unresponsiveness in one of these patients. Methods Five patients with end-stage renal disease received CKBMT from HLA-mismatched, haploidentical living related donors following modified non-myeloablative conditioning. Polychromatic flow cytometry (FCM) was used to assess multilineage chimerism where evaluable and lymphocyte recovery post-transplant. Limiting dilution analysis was used to assess helper-T-lymphocyte reactivity to donor antigens. Results Transient multilineage mixed chimerism was observed in all patients but chimerism became undetectable by 2 weeks post-CKBMT. A marked decrease in T and B lymphocyte counts immediately following transplant was followed by gradual recovery. Initially recovering T cells were depleted of CD45RA+/CD45RO− “naïve-like” cells, which have shown strong recovery in two patients and CD4/CD8 ratios increased immediately following transplant but then declined markedly. NK cells were enriched in the peripheral blood of all patients following transplant. For Subject 2, a pre-transplant limiting dilution assay revealed T helper cells recognizing both donor and third-party PBMCs. However, the anti-donor response was completely undetectable by Day 24, while third-party reactivity persisted. Conclusion These results characterize the transient multilineage mixed hematopoietic chimerism and recovery of lymphocyte subsets in patients receiving a modified CKBMT protocol. The observations are relevant to the mechanisms of donor-specific tolerance in this patient group. PMID:21085064

  8. POST-PROCESSING ANALYSIS FOR THC SEEPAGE

    SciTech Connect

    Y. SUN

    2004-09-29

    This report describes the selection of water compositions for the total system performance assessment (TSPA) model of results from the thermal-hydrological-chemical (THC) seepage model documented in ''Drift-Scale THC Seepage Model'' (BSC 2004 [DIRS 169856]). The selection has been conducted in accordance with ''Technical Work Plan for: Near-Field Environment and Transport: Coupled Processes (Mountain-Scale TH/THC/THM, Drift-Scale THC Seepage, and Post-Processing Analysis for THC Seepage) Report Integration'' (BSC 2004 [DIRS 171334]). This technical work plan (TWP) was prepared in accordance with AP-2.27Q, ''Planning for Science Activities''. Section 1.2.3 of the TWP describes planning information pertaining to the technical scope, content, and management of this report. The post-processing analysis for THC seepage (THC-PPA) documented in this report provides a methodology for evaluating the near-field compositions of water and gas around a typical waste emplacement drift as these relate to the chemistry of seepage, if any, into the drift. The THC-PPA inherits the conceptual basis of the THC seepage model, but is an independently developed process. The relationship between the post-processing analysis and other closely related models, together with their main functions in providing seepage chemistry information for the Total System Performance Assessment for the License Application (TSPA-LA), are illustrated in Figure 1-1. The THC-PPA provides a data selection concept and direct input to the physical and chemical environment (P&CE) report that supports the TSPA model. The purpose of the THC-PPA is further discussed in Section 1.2. The data selection methodology of the post-processing analysis (Section 6.2.1) was initially applied to results of the THC seepage model as presented in ''Drift-Scale THC Seepage Model'' (BSC 2004 [DIRS 169856]). Other outputs from the THC seepage model (DTN: LB0302DSCPTHCS.002 [DIRS 161976]) used in the P&CE (BSC 2004 [DIRS 169860

  9. A semi-nested real-time PCR method to detect low chimerism percentage in small quantity of hematopoietic stem cell transplant DNA samples.

    PubMed

    Aloisio, Michelangelo; Bortot, Barbara; Gandin, Ilaria; Severini, Giovanni Maria; Athanasakis, Emmanouil

    2017-02-01

    Chimerism status evaluation of post-allogeneic hematopoietic stem cell transplantation samples is essential to predict post-transplant relapse. The most commonly used technique capable of detecting small increments of chimerism is quantitative real-time PCR. Although this method is already used in several laboratories, previously described protocols often lack sensitivity and the amount of the DNA required for each chimerism analysis is too high. In the present study, we compared a novel semi-nested allele-specific real-time PCR (sNAS-qPCR) protocol with our in-house standard allele-specific real-time PCR (gAS-qPCR) protocol. We selected two genetic markers and analyzed technical parameters (slope, y-intercept, R2, and standard deviation) useful to determine the performances of the two protocols. The sNAS-qPCR protocol showed better sensitivity and precision. Moreover, the sNAS-qPCR protocol requires, as input, only 10 ng of DNA, which is at least 10-fold less than the gAS-qPCR protocols described in the literature. Finally, the proposed sNAS-qPCR protocol could prove very useful for performing chimerism analysis with a small amount of DNA, as in the case of blood cell subsets.

  10. Interspecies Chimerism with Mammalian Pluripotent Stem Cells.

    PubMed

    Wu, Jun; Platero-Luengo, Aida; Sakurai, Masahiro; Sugawara, Atsushi; Gil, Maria Antonia; Yamauchi, Takayoshi; Suzuki, Keiichiro; Bogliotti, Yanina Soledad; Cuello, Cristina; Morales Valencia, Mariana; Okumura, Daiji; Luo, Jingping; Vilariño, Marcela; Parrilla, Inmaculada; Soto, Delia Alba; Martinez, Cristina A; Hishida, Tomoaki; Sánchez-Bautista, Sonia; Martinez-Martinez, M Llanos; Wang, Huili; Nohalez, Alicia; Aizawa, Emi; Martinez-Redondo, Paloma; Ocampo, Alejandro; Reddy, Pradeep; Roca, Jordi; Maga, Elizabeth A; Esteban, Concepcion Rodriguez; Berggren, W Travis; Nuñez Delicado, Estrella; Lajara, Jeronimo; Guillen, Isabel; Guillen, Pedro; Campistol, Josep M; Martinez, Emilio A; Ross, Pablo Juan; Izpisua Belmonte, Juan Carlos

    2017-01-26

    Interspecies blastocyst complementation enables organ-specific enrichment of xenogenic pluripotent stem cell (PSC) derivatives. Here, we establish a versatile blastocyst complementation platform based on CRISPR-Cas9-mediated zygote genome editing and show enrichment of rat PSC-derivatives in several tissues of gene-edited organogenesis-disabled mice. Besides gaining insights into species evolution, embryogenesis, and human disease, interspecies blastocyst complementation might allow human organ generation in animals whose organ size, anatomy, and physiology are closer to humans. To date, however, whether human PSCs (hPSCs) can contribute to chimera formation in non-rodent species remains unknown. We systematically evaluate the chimeric competency of several types of hPSCs using a more diversified clade of mammals, the ungulates. We find that naïve hPSCs robustly engraft in both pig and cattle pre-implantation blastocysts but show limited contribution to post-implantation pig embryos. Instead, an intermediate hPSC type exhibits higher degree of chimerism and is able to generate differentiated progenies in post-implantation pig embryos.

  11. Comparative Genome Analysis Provides Insights into Both the Lifestyle of Acidithiobacillus ferrivorans Strain CF27 and the Chimeric Nature of the Iron-Oxidizing Acidithiobacilli Genomes

    PubMed Central

    Tran, Tam T. T.; Mangenot, Sophie; Magdelenat, Ghislaine; Payen, Emilie; Rouy, Zoé; Belahbib, Hassiba; Grail, Barry M.; Johnson, D. Barrie; Bonnefoy, Violaine; Talla, Emmanuel

    2017-01-01

    The iron-oxidizing species Acidithiobacillus ferrivorans is one of few acidophiles able to oxidize ferrous iron and reduced inorganic sulfur compounds at low temperatures (<10°C). To complete the genome of At. ferrivorans strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a comparative analysis with other Acidithiobacillus species whose genomes are publically available. The At. ferrivorans CF27 genome comprises a 3,409,655 bp chromosome and a 46,453 bp plasmid. At. ferrivorans CF27 possesses genes allowing its adaptation to cold, metal(loid)-rich environments, as well as others that enable it to sense environmental changes, allowing At. ferrivorans CF27 to escape hostile conditions and to move toward favorable locations. Interestingly, the genome of At. ferrivorans CF27 exhibits a large number of genomic islands (mostly containing genes of unknown function), suggesting that a large number of genes has been acquired by horizontal gene transfer over time. Furthermore, several genes specific to At. ferrivorans CF27 have been identified that could be responsible for the phenotypic differences of this strain compared to other Acidithiobacillus species. Most genes located inside At. ferrivorans CF27-specific gene clusters which have been analyzed were expressed by both ferrous iron-grown and sulfur-attached cells, indicating that they are not pseudogenes and may play a role in both situations. Analysis of the taxonomic composition of genomes of the Acidithiobacillia infers that they are chimeric in nature, supporting the premise that they belong to a particular taxonomic class, distinct to other proteobacterial subgroups. PMID:28659871

  12. Peptidoglycan: a post-genomic analysis

    PubMed Central

    2012-01-01

    Background To derive post-genomic, neutral insight into the peptidoglycan (PG) distribution among organisms, we mined 1,644 genomes listed in the Carbohydrate-Active Enzymes database for the presence of a minimal 3-gene set that is necessary for PG metabolism. This gene set consists of one gene from the glycosyltransferase family GT28, one from family GT51 and at least one gene belonging to one of five glycoside hydrolase families (GH23, GH73, GH102, GH103 and GH104). Results None of the 103 Viruses or 101 Archaea examined possessed the minimal 3-gene set, but this set was detected in 1/42 of the Eukarya members (Micromonas sp., coding for GT28, GT51 and GH103) and in 1,260/1,398 (90.1%) of Bacteria, with a 100% positive predictive value for the presence of PG. Pearson correlation test showed that GT51 family genes were significantly associated with PG with a value of 0.963 and a p value less than 10-3. This result was confirmed by a phylogenetic comparative analysis showing that the GT51-encoding gene was significantly associated with PG with a Pagel’s score of 60 and 51 (percentage of error close to 0%). Phylogenetic analysis indicated that the GT51 gene history comprised eight loss and one gain events, and suggested a dynamic on-going process. Conclusions Genome analysis is a neutral approach to explore prospectively the presence of PG in uncultured, sequenced organisms with high predictive values. PMID:23249425

  13. Invasiveness, chimerism and genetic diversity.

    PubMed

    Ben-Shlomo, Rachel

    2017-09-26

    Adaptation for invasiveness should comprise the capability to exploit and prosper in a wide range of ecological conditions, and is therefore expected to be associated with a certain level of genetic diversity. Paradoxically, however, invasive populations are established by only a few founders, resulting in low genetic diversity. As a conceivable way of attaining high genetic diversity and high variance of gene expression even when a small number of founders is involved in invasiveness, I suggest here chimerism, a fusion between different individuals-a common phenomenon found in numerous phyla. The composite entity offers the chimeric organism genetic flexibility and higher inclusive fitness that depends on the joint genomic fitness of the original partners. The ability to form a chimeric entity is also applied to subsequent generations and, consequently, the level of genetic diversity does not decline over generations of population establishment following invasion. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  14. Expression and purification of toxic anti-breast cancer p28-NRC chimeric protein

    PubMed Central

    Soleimani, Meysam; Mirmohammad-Sadeghi, Hamid; Sadeghi-Aliabadi, Hojjat; Jahanian-Najafabadi, Ali

    2016-01-01

    Background: Chimeric proteins consisting of a targeting moiety and a cytotoxic moiety are now under intense research focus for targeted therapy of cancer. Here, we report cloning, expression, and purification of such a targeted chimeric protein made up of p28 peptide as both targeting and anticancer moiety fused to NRC peptide as a cytotoxic moiety. However, since the antimicrobial activity of the NRC peptide would intervene expression of the chimeric protein in Escherichia coli, we evaluated the effects of two fusion tags, that is, thioredoxin (Trx) and 6x-His tags, and various expression conditions, on the expression of p28-NRC chimeric protein. Materials and Methods: In order to express the chimeric protein with only 6x-His tag, pET28 expression plasmid was used. Cloning in pET32 expression plasmid was performed to add both Trx and 6x-His tags to the chimeric protein. Expression of the chimeric protein with both plasmids was evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot analysis following optimization of expression conditions and host strains. Results: Expression of the chimeric protein in pET28a was performed. However, expression yield of the chimeric protein was low. Optimization of culture conditions and host strains led to reasonable expression yield of the toxic chimeric protein in pET32a vector. In cases of both plasmids, approximately 10 kDa deviation of the apparent molecular weight from the theoretical one was seen in SDS-PAGE of purified chimeric proteins. Conclusions: The study leads to proper expression and purification yield of p28-NRC chimeric protein with Trx tag following optimizing culture conditions and host strains. PMID:27169101

  15. How should chimerism be decoded?

    PubMed

    Ferrand, Christophe; Perruche, Sylvain; Robinet, Eric; Martens, Anton; Tiberghien, Pierre; Saas, Philippe

    2003-05-15

    To date, the significance of chimerism has not been fully understood. In particular, microchimerism can be associated with allograft acceptance or rejection. Several factors may influence the immunologic consequences of chimerism. In this review, the major factors influencing these consequences are briefly described. Subsequently, the different methods available for detecting and tracking donor-derived cells are listed. These techniques have been mainly developed concomitantly with nonmyeloablative hematopoietic allografts to monitor immunosuppression. Finally, the authors suggest how these methods may help to improve the understanding of microchimerism in solid organ transplantation.

  16. Bidirectional Brush Seals: Post-Test Analysis

    NASA Technical Reports Server (NTRS)

    Hendricks, Robert C.; Wilson, Jack; Wu, Tom Y.; Flower, Ralph; Mullen, Robert L.

    1997-01-01

    A post-test analysis of a set of inside-diameter/outside-diameter (ID/OD) bidirectional brush seals used in three-port wave rotor tests was undertaken to determine brush bristle and configuration wear, pullout, and rotor coating wear. The results suggest that sharp changes in the pressure profiles were not well reflected in bristle tip configuration patterns or wear. Also, positive-to-negative changes in axial pressure gradients appeared to have little effect on the backing plates. Although the brushes had similar porosities, they had very different unpacked arrays. This difference could explain the departure of experimental data from computational fluid dynamics flow predictions for well-packed arrays at higher pressure drops. The rotor wear led to "car-track" scars (upper and lower wear bands) with a whipped surface between the bands. Those bands may have resulted from bristle stiffening at the fence and gap plates during alternate portions of the rotor cycle. Within the bristle response range the wear surface reflected the pressure distribution effect on bristle motion. No sacrificial metallurgical data were taken. The bristles did wear, with correspondingly more wear on the ID brush configurations than on the OD configurations; the complexity in constructing the ID brush was a factor.

  17. Kinematic analysis of post office employees' workstations.

    PubMed

    Draicchio, Francesco; Silvetti, Alessio; Forzano, Federico; Iavicoli, Sergio; Ranavolo, Alberto

    2012-01-01

    This study analyzed a post office clerk's tasks, comparing two workstation models. The clerk was facing the client in one, and seated at 45 degrees to the counter in the other. We analyzed the most frequent tasks and those presenting the most critical points: 1) payment of a postal order; 2) accepting a registered letter, breaking them down into subtasks. We used an optoelectronic system for kinematic analysis, and calculated the range of motion of the trunk and arms in the three spatial planes. The 45( position required less torsion of the trunk and head when using the printer, placed to the left of the employee. A larger worktop improved the workstation, leaving more room for equipment and allowing the worker to sit frontally to the monitor. However, this solution involved a shorter distance between the worker and the client with longer extension of the shoulder and elbow and less trunk flexion. These findings suggested a modification in the layout that shortens the distance between the worker and client.

  18. Chimeric enzymes with improved cellulase activities

    DOEpatents

    Xu, Qi; Baker, John O; Himmel, Michael E

    2015-03-31

    Nucleic acid molecules encoding chimeric cellulase polypeptides that exhibit improved cellulase activities are disclosed herein. The chimeric cellulase polypeptides encoded by these nucleic acids and methods to produce the cellulases are also described, along with methods of using chimeric cellulases for the conversion of cellulose to sugars such as glucose.

  19. Assessment of chimerism in epithelial cancers in transplanted patients.

    PubMed

    Leboeuf, Christophe; Ratajczak, Philippe; Vérine, Jérôme; Elbouchtaoui, Morad; Plassa, François; Legrès, Luc; Ferreira, Irmine; Sandid, Wissam; Varna, Mariana; Bousquet, Guilhem; Verneuil, Laurence; Janin, Anne

    2014-01-01

    Cancer is now the most severe complication in the long term in transplant recipients. As most solid-organ or hematopoietic stem-cell transplantations are allogeneic, chimerism studies can be performed on cancers occurring in recipients. We summarize here the different methods used to study chimerism in cancers developing in allogeneic-transplant recipients, analyze their respective advantages and report the main results obtained from these studies. Chimerism analyses of cancers in transplant recipients require methods suited to tissue samples. In the case of gender-mismatched transplantation, the XY chromosomes can be explored using fluorescent in situ hybridization on whole-tissue sections or Y-sequence-specific PCR after the laser microdissection of tumor cells. For cancers occurring after gender-matched transplantation, laser microdissection of tumor cells enables studies of microsatellite markers and high-resolution melting analysis of mitochondrial DNA on genes with marked polymorphism, provided these are different in the donor and the recipient. The results of different studies address the cancers that develop in both recipients and in transplants. The presence of chimeric cells in these two types of cancer implies an exchange of progenitor/stem-cells between transplant and recipient, and the plasticity of these progenitor/stem-cells contributes to epithelial cancers. The presence of chimeric cells in concomitant cancers and preneoplastic lesions implies that the oncogenesis of these cancers progresses through a multistep process.

  20. An integrative analysis of post-translational histone modifications in the marine diatom Phaeodactylum tricornutum.

    PubMed

    Veluchamy, Alaguraj; Rastogi, Achal; Lin, Xin; Lombard, Bérangère; Murik, Omer; Thomas, Yann; Dingli, Florent; Rivarola, Maximo; Ott, Sandra; Liu, Xinyue; Sun, Yezhou; Rabinowicz, Pablo D; McCarthy, James; Allen, Andrew E; Loew, Damarys; Bowler, Chris; Tirichine, Leïla

    2015-05-20

    Nucleosomes are the building blocks of chromatin where gene regulation takes place. Chromatin landscapes have been profiled for several species, providing insights into the fundamental mechanisms of chromatin-mediated transcriptional regulation of gene expression. However, knowledge is missing for several major and deep-branching eukaryotic groups, such as the Stramenopiles, which include the diatoms. Diatoms are highly diverse and ubiquitous species of phytoplankton that play a key role in global biogeochemical cycles. Dissecting chromatin-mediated regulation of genes in diatoms will help understand the ecological success of these organisms in contemporary oceans. Here, we use high resolution mass spectrometry to identify a full repertoire of post-translational modifications on histones of the marine diatom Phaeodactylum tricornutum, including eight novel modifications. We map five histone marks coupled with expression data and show that P. tricornutum displays both unique and broadly conserved chromatin features, reflecting the chimeric nature of its genome. Combinatorial analysis of histone marks and DNA methylation demonstrates the presence of an epigenetic code defining activating or repressive chromatin states. We further profile three specific histone marks under conditions of nitrate depletion and show that the histone code is dynamic and targets specific sets of genes. This study is the first genome-wide characterization of the histone code from a stramenopile and a marine phytoplankton. The work represents an important initial step for understanding the evolutionary history of chromatin and how epigenetic modifications affect gene expression in response to environmental cues in marine environments.

  1. The Pharmacokinetics and Metabolism of Lumiracoxib in Chimeric Humanized and Murinized FRG Mice.

    PubMed

    Dickie, A P; Wilson, C E; Schreiter, K; Wehr, R; Wilson, E M; Bial, J; Scheer, N; Wilson, I D; Riley, R J

    2017-03-25

    The pharmacokinetics and metabolism of lumiracoxib were studied, after administration of single 10 mg/kg oral doses to chimeric liver-humanized and murinized FRG mice. In the chimeric humanized mice, lumiracoxib reached peak observed concentrations in the blood of 1.10 ± 0.08 μg/mL at 0.25-0.5 h post-dose with an AUCinf of 1.74 ± 0.52 μg h/mL and an effective half-life for the drug of 1.42 ± 0.72 h (n=3). In the case of the murinized animals peak observed concentrations in the blood were determined as 1.15 ± 0.08 μg/mL at 0.25 h post-dose with an AUCinf of 1.94 ± 0.22 μg h/mL and an effective half-life of 1.28 ± 0.02 h (n=3). Analysis of blood indicated only the presence of unchanged lumiracoxib. Metabolic profiling of urine, bile and faecal extracts revealed a complex pattern of metabolites for both humanized and murinized animals with, in addition to unchanged parent drug, a variety of hydroxylated and conjugated metabolites detected. The profiles obtained in humanized mice were different compared to murinized animals with e.g., a higher proportion of the dose detected in the form of acyl glucuronide metabolites and much reduced amounts of taurine conjugates. Comparison of the metabolic profiles obtained from the present study with previously published data from C57bl/6J mice and humans, revealed a greater though not complete match between chimeric humanized mice and humans, such that the liver-humanized FRG model may represent a useful approach to assessing the biotransformation of such compounds in humans.

  2. Frequency analysis of cytotoxic T lymphocyte precursors in chimeric mice. Evidence for intrathymic maturation of clonally distinct self- major histocompatibility complex- and allo-major histocompatiblilty complex-restricted virus-specific T cells

    PubMed Central

    1981-01-01

    To study whether the thymic major histocompatibility complex (MHC) imposes a constraint on the receptor repertoire of maturating cytotoxic T lymphocyte (CTL) precursors, the restriction phenotypes of virus- specific CTL of MHC-compatible and of MHC-incompatible thymus- and bone marrow-grafted (A X B)F1 chimeric mice were compared. Dependent on the mode of in vitro sensitization, thymocytes or splenocytes of both types of chimeric mice generated Sendai virus-specific, self-MHC-or allo-MHC- restricted CTL. By applying the limiting-dilution technique, the CTL- precursor (CTL-P) frequencies of self-MHC-restricted and allo-MHC- restricted virus-specific T cells as well as of alloreactive T cells were determined. The data obtained revealed that independent of MHC differences between thymus and bone marrow, the frequencies of self-MHC- restricted and allo-MHC-restricted CTL-P were comparable, and in the same older of magnitude as those previously determined in conventionally reared mice. Self-MHC-restricted, virus-specific CTL-P were in a three- to fivefold excess over allo-MHC-restricted CTL-P. A segregation analysis revealed that clonally distinct CTL-P give rise to either self-restricted or allo-MHC-restricted, virus-specific CTL. Both sets were found not only in the spleen, but also in the thymus of chimeric mice, formally demonstrating the intrathymic differentiation pathway of self-MHC as well of allo-MHC-restricted CTL-P. These data reveal no major constraint of the thymic MHC on the capacity of T cells to recognize viral antigens either in the context of self-MHC or of allogeneic MHC products. PMID:6265587

  3. Early Chimerism After Liver Transplantation Reflects the Clinical Course of Recurrent Hepatitis C.

    PubMed

    Utsumi, Masashi; Takaki, Akinobu; Umeda, Yuzo; Koike, Kazuko; Napier, Stephanie C; Watanabe, Nobukazu; Shinoura, Susumu; Yoshida, Ryuichi; Nobuoka, Daisuke; Yasunaka, Tetsuya; Oto, Takahiro; Araki, Motoo; Yamamoto, Kazuhide; Fujiwara, Toshiyoshi; Yagi, Takahito

    2017-03-24

    BACKGROUND Human leukocyte antigen (HLA) mismatch is a characteristic feature of post-orthotopic liver transplantation (OLT) hepatitis C. To investigate the importance of donor HLA-restricted immune cells in post-OLT hepatitis C recurrence, we analyzed the frequency of donor chimerism and the clinical course of post-OLT hepatitis C. MATERIAL AND METHODS We analyzed peripheral blood chimerism in 11 HCV-reinfected patients with post-HLA mismatched OLT. Patients were divided into 2 groups: the OLT chronic hepatitis C (CHC) group (n=8), exhibiting active hepatitis C recurrence; and the OLT-persistently normal ALT (PNALT) group (n=3), without active hepatitis. Chimerism was analyzed by flow cytometry using donor-specific anti-HLA antibodies in peripheral blood mononuclear cells from 1-100 days after OLT. Kidney (n=7) and lung (n=7) transplant recipients were also analyzed for comparison. As immune cells from the donor liver might contribute to post-OLT chimerism, the characteristics of perfusates from donor livers (n=10) were analyzed and defined. RESULTS Donor-derived cells were frequently observed in liver and lung transplant recipients. The frequency of donor-derived cells from the B cell subset was significantly higher in peripheral blood from OLT-CHC group than in that of the OLT-PNALT group. B cells, however, were not the predominant subset in the perfusates, indicating that inflow of donor-derived cells alone did not cause the chimerism. CONCLUSIONS Chimerism of B cells is frequent in liver transplant patients with early recurrence of hepatitis C. We propose that monitoring of early chimerism could facilitate early detection of chronic hepatitis C recurrence, although we need more cases to investigate.

  4. The concept of the eudicot shoot apical meristem as it applies to four Spiraea (Rosaceae), one Mentha (Lamiaceae) and one Euonymus (Celastraceae) cultivars based on chimeric analysis

    PubMed Central

    Korn, Robert W.

    2013-01-01

    Background and Aims Eversporting eudicots were sought to see if they behave like gymnosperms. Behaviour of eversporting gymnosperm chimeras indicates a single apical cell is present in SAM and it would be of interest to see if eudicot chimeras have the same behaviour. Methods Four eversporting spireas, the pineapple mint and the Silver King euonymus were inspected for the fate of the yellow (mutant)–green (wild type) chimeras. Key Results As with gymnosperms, unstable eudicot chimeras in the four spireas, the pineapple mint and the Silver King euonymus became stable yellow about 80 % or more of the time and 20 % or less became stable green. Conclusions The statistically significant preponderance of chimeric fates becoming all yellow suggests that a single apical cell resides in the yellow tunica. As with gymnosperms, descendent cells of the yellow replacement corpus cell eventually take over the corpus. Here is the first chimeric set of data to support the hypothesis of a one-celled meristem in eudicots rather than the traditional view of a muticellular meristem. PMID:23482330

  5. The concept of the eudicot shoot apical meristem as it applies to four Spiraea (Rosaceae), one Mentha (Lamiaceae) and one Euonymus (Celastraceae) cultivars based on chimeric analysis.

    PubMed

    Korn, Robert W

    2013-05-01

    Eversporting eudicots were sought to see if they behave like gymnosperms. Behaviour of eversporting gymnosperm chimeras indicates a single apical cell is present in SAM and it would be of interest to see if eudicot chimeras have the same behaviour. Four eversporting spireas, the pineapple mint and the Silver King euonymus were inspected for the fate of the yellow (mutant)-green (wild type) chimeras. As with gymnosperms, unstable eudicot chimeras in the four spireas, the pineapple mint and the Silver King euonymus became stable yellow about 80 % or more of the time and 20 % or less became stable green. The statistically significant preponderance of chimeric fates becoming all yellow suggests that a single apical cell resides in the yellow tunica. As with gymnosperms, descendent cells of the yellow replacement corpus cell eventually take over the corpus. Here is the first chimeric set of data to support the hypothesis of a one-celled meristem in eudicots rather than the traditional view of a muticellular meristem.

  6. Tolerance of Lung Allografts Achieved in Nonhuman Primates via Mixed Hematopoietic Chimerism

    PubMed Central

    Tonsho, M.; Lee, S.; Aoyama, A.; Boskovic, S.; Nadazdin, O.; Capetta, K.; Smith, R.-N.; Colvin, R. B.; Sachs, D. H.; Cosimi, A. B.; Kawai, T.; Madsen, J. C.; Benichou, G.; Allan, J. S.

    2015-01-01

    While the induction of transient mixed chimerism has tolerized MHC-mismatched renal grafts in nonhuman primates and patients, this approach has not been successful for more immunogenic organs. Here, we describe a modified delayed-tolerance-induction protocol resulting in three out of four monkeys achieving long-term lung allograft survival without ongoing immunosuppression. Two of the tolerant monkeys displayed stable mixed lymphoid chimerism, and the other showed transient chimerism. Serial biopsies and post-mortem specimens from the tolerant monkeys revealed no signs of chronic rejection. The tolerant recipients also exhibited T cell unresponsiveness and a lack of alloantibody. This is the first report of durable mixed chimerism and successful tolerance induction of MHC-mismatched lungs in primates. PMID:25904524

  7. Pre/Post Data Analysis - Simple or Is It?

    NASA Technical Reports Server (NTRS)

    Feiveson, Al; Fiedler, James; Ploutz-Snyder, Robert

    2011-01-01

    This slide presentation reviews some of the problems of data analysis in analyzing pre and post data. Using as an example, ankle extensor strength (AES) experiments, to measure bone density loss during bed rest, the presentation discusses several questions: (1) How should we describe change? (2) Common analysis methods for comparing post to pre results. (3) What do we mean by "% change"? and (4) What are we testing when we compare % changes?

  8. Mechanisms of tolerance induced via mixed chimerism.

    PubMed

    Sykes, Megan

    2007-05-01

    Mixed hematopoietic chimerism provides a powerful means of inducing robust, donor-specific tolerance. In this article, the minimal requirements for achieving mixed chimerism, the development of new reagents that promote its achievement, and the mechanisms by which peripheral and intrathymic tolerance are achieved via mixed chimerism are discussed. An emerging understanding of these mechanisms, along with the development of new immunosuppressive reagents, is allowing advancement toward clinical application of this approach.

  9. Donor Chimerism Early after Reduced-intensity Conditioning Hematopoietic Stem Cell Transplantation Predicts Relapse and Survival

    PubMed Central

    Koreth, John; Kim, Haesook T.; Nikiforow, Sarah; Milford, Edgar L.; Armand, Philippe; Cutler, Corey; Glotzbecker, Brett; Ho, Vincent T.; Antin, Joseph H.; Soiffer, Robert J.; Ritz, Jerome; Alyea, Edwin P.

    2015-01-01

    The impact of early donor cell chimerism on outcomes of T-replete reduced-intensity conditioning (RIC) hematopoietic stem cell transplantation (HSCT) is ill-defined. We evaluated day 30 (D30) and 100 (D100) total donor cell chimerism after RIC HSCT undertaken between 2002 and 2010 at our institution, excluding patients who died or relapsed before D30. When available, donor T-cell chimerism was also assessed. The primary outcome was overall survival (OS). Secondary outcomes included progression-free survival (PFS), relapse and non-relapse mortality (NRM). 688 patients with hematologic malignancies (48% myeloid; 52% lymphoid) and a median age of 57 years (range, 18-74) undergoing RIC HSCT with T-replete donor grafts (97% peripheral blood; 92% HLA-matched) and median follow-up of 58.2 months (range, 12.6-120.7) were evaluated. In multivariable analysis total donor cell and T-cell chimerism at D30 and D100 each predicted RIC HSCT outcomes, with D100 total donor cell chimerism most predictive. D100 total donor cell chimerism <90% was associated with increased relapse (HR 2.54, 95% CI 1.83-3.51, p<0.0001), impaired PFS (HR 2.01, 95% CI 1.53-2.65, p<0.0001) and worse OS (1.50, 95% CI 1.11-2.04, p=0.009), but not NRM (HR 0.76; 95% CI 0.44-2.27, p=0.33). There was no additional utility of incorporating sustained D30-D100 total donor cell chimerism, or T-cell chimerism. Low donor chimerism early after RIC HSCT is an independent risk factor for relapse and impaired survival. Donor chimerism assessment early after RIC HSCT can prognosticate for long-term outcomes and help identify high-risk patient cohorts that may benefit from additional therapeutic interventions. PMID:24907627

  10. Generating chimeric mice from embryonic stem cells via vial coculturing or hypertonic microinjection.

    PubMed

    Lee, Kun-Hsiung

    2014-01-01

    The generation of a fertile embryonic stem cell (ESC)-derived or F0 (100 % coat color chimerism) mice is the final criterion in proving that the ESC is truly pluripotent. Many methods have been developed to produce chimeric mice. To date, the most popular methods for generating chimeric embryos is well sandwich aggregation between zona pellucida (ZP) removed (denuded) 2.5-day post-coitum (dpc) embryos and ESC clumps, or direct microinjection of ESCs into the cavity (blastocoel) of 3.5-dpc blastocysts. However, due to systemic limitations and the disadvantages of conventional microinjection, aggregation, and coculturing, two novel methods (vial coculturing and hypertonic microinjection) were developed in recent years at my laboratory.Coculturing 2.5-dpc denuded embryos with ESCs in 1.7-mL vials for ~3 h generates chimeras that have significantly high levels of chimerism (including 100 % coat color chimerism) and germline transmission. This method has significantly fewer instrumental and technological limitations than existing methods, and is an efficient, simple, inexpensive, and reproducible method for "mass production" of chimeric embryos. For laboratories without a microinjection system, this is the method of choice for generating chimeric embryos. Microinjecting ESCs into a subzonal space of 2.5-dpc embryos can generate germline-transmitted chimeras including 100 % coat color chimerism. However, this method is adopted rarely due to the very small and tight space between ZP and blastomeres. Using a laser pulse or Piezo-driven instrument/device to help introduce ESCs into the subzonal space of 2.5-dpc embryos demonstrates the superior efficiency in generating ESC-derived (F0) chimeras. Unfortunately, due to the need for an expensive instrument/device and extra fine skill, not many studies have used either method. Recently, ESCs injected into the large subzonal space of 2.5-dpc embryos in an injection medium containing 0.2-0.3 M sucrose very efficiently generated

  11. ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining

    PubMed Central

    Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; Jang, Ye Eun; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk

    2017-01-01

    Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/. PMID:27899563

  12. ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.

    PubMed

    Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; Jang, Ye Eun; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk

    2017-01-04

    Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Chimeric honeybees (Apis mellifera) produced by transplantation of embryonic cells into pre-gastrula stage embryos and detection of chimerism by use of microsatellite markers.

    PubMed

    Bergem, M; Norberg, K; Roseth, A; Meuwissen, T; Lien, S; Aamodt, R H

    2006-04-01

    The production of chimeras, by use of cell transplantation, has proved to be highly valuable in studies of development by providing insights into cell fate, differentiation, and developmental potential. So far, chimeric honeybees have been created by nuclear transfer technologies. We have developed protocols to produce chimeric honeybees by use of cell transplantation. Embryonic cells were transplanted between pre-gastrula stage embryos (32-34 hr after oviposition) and hatched larvae were reared in vitro for 4 days. Chimeric individuals were detected by use of microsatellite analysis and a conservative estimation approach. 4.8% of embryos, posteriorly injected with embryonic cells, developed into chimeric honeybee larvae. By injection of cells pre-stained with fluorescent cell tracer dye, we studied the integration of transplanted cells in the developing embryos. Number of injected cells varied from 0 to 50 and cells remained and multiplied mainly in the area of injection.

  14. A technical application of quantitative next generation sequencing for chimerism evaluation

    PubMed Central

    Aloisio, Michelangelo; Licastro, Danilo; Caenazzo, Luciana; Torboli, Valentina; D'eustacchio, Angela; Severini, Giovanni Maria; Athanasakis, Emmanouil

    2016-01-01

    At present, the most common genetic diagnostic method for chimerism evaluation following hematopoietic stem cell transplantation is microsatellite analysis by capillary electrophoresis. The main objective was to establish, through repeated analysis over time, if a complete chimerism was present, or if the mixed chimerism was stable, increasing or decreasing over time. Considering the recent introduction of next generation sequencing (NGS) in clinical diagnostics, a detailed study evaluating an NGS protocol was conducted, coupled with a custom bioinformatics pipeline, for chimerism quantification. Based on the technology of Ion AmpliSeq, a 44-amplicon custom chimerism panel was designed, and a custom bioinformatics pipeline dedicated to the genotyping and quantification of NGS data was coded. The custom chimerism panel allowed identification of an average of 16 informative recipient alleles. The limit of detection of the protocol was fixed at 1% due to the NGS background (<1%). The protocol followed the standard Ion AmpliSeq library preparation and Ion Torrent Personal Genome Machine guidelines. Overall, the present study added to the scientific literature, identifying novel technical details for a possible future application of NGS for chimerism quantification. PMID:27499173

  15. T-Shaped Frame Critical and Post-Critical Analysis

    NASA Astrophysics Data System (ADS)

    Doicheva, Albena

    2016-03-01

    The paper shows solution of a T-shaped frame, strength- ened with two linear springs, regarding critical and post-critical analysis. The solution is exact using the Euler elastic approach and the frame of reference, originated in the point of column axis inflexion. The derived Numerical results show the effect of the springs strengthening for the crit- ical and the post-critical system behaviour. The influence of the geometry change is analyzed, as well.

  16. Rats and mice immunised with chimeric human/mouse proteinase 3 produce autoantibodies to mouse Pr3 and rat granulocytes

    PubMed Central

    van der Geld, Ymke M; Hellmark, Thomas; Selga, Daina; Heeringa, Peter; Huitema, Minke G; Limburg, Pieter C; Kallenberg, Cees G M

    2007-01-01

    Aim In this study, we employed chimeric human/mouse Proteinase 3 (PR3) proteins as tools to induce an autoantibody response to PR3 in rats and mice. Method Rats and mice were immunised with recombinant human PR3 (HPR3), recombinant murine PR3 (mPR3), single chimeric human/mouse PR3 (HHm, HmH, mHH, mmH, mHm, Hmm) or pools of chimeric proteins. Antibodies to mPR3 and HPR3 were measured by ELISA. Antibodies to rat PR3 were determined by indirect immunofluorescence (IIF) on rat white blood cells. Urinalysis was performed by dipstick analysis. Kidney and lung tissue was obtained for pathological examination. Results In mice, immunisation with the chimeric human/mouse PR3 Hmm led to an autoantibody response to mPR3. Rats immunised with the chimeric human/mouse PR3 Hmm, HmH and mmH, or a pool of the chimeric human/mouse PR3 proteins, produced antibodies selectively binding to rat granulocytes as detected by IIF. No gross pathological abnormalities could be detected in kidney or lungs of mice or rats immunised with chimeric human/mouse PR3. Conclusion Immunisation with chimeric human/mouse proteins induces autoantibodies to PR3 in rats and mice. Chimeric proteins can be instrumental in developing experimental models for autoimmune diseases. PMID:17644551

  17. Frequency of chimerism in populations of the kelp Lessonia spicata in central Chile

    PubMed Central

    2017-01-01

    Chimerism occurs when two genetically distinct conspecific individuals fuse together generating a single entity. Coalescence and chimerism in red seaweeds has been positively related to an increase in body size, and the consequent reduction in susceptibility to mortality factors, thus increasing survival, reproductive potential and tolerance to stress in contrast to genetically homogeneous organisms. In addition, they showed that a particular pattern of post-fusion growth maintains higher genetic diversity and chimerism in the holdfast but homogenous axes. In Chilean kelps (brown seaweeds), intraorganismal genetic heterogeneity (IGH) and holdfast coalescence has been described in previous research, but the extent of chimerism in wild populations and the patterns of distribution of the genetically heterogeneous thallus zone have scarcely been studied. Since kelps are under continuous harvesting, with enormous social, ecological and economic importance, natural chimerism can be considered a priceless in-situ reservoir of natural genetic resources and variability. In this study, we therefore examined the frequency of IGH and chimerism in three harvested populations of Lessonia spicata. We then evaluated whether chimeric wild-type holdfasts show higher genetic diversity than erect axes (stipe and lamina) and explored the impact of this on the traditional estimation of genetic diversity at the population level. We found a high frequency of IGH (60–100%) and chimerism (33.3–86.7%), varying according to the studied population. We evidenced that chimerism occurs mostly in holdfasts, exhibiting heterogeneous tissues, whereas stipes and lamina were more homogeneous, generating a vertical gradient of allele and genotype abundance as well as divergence, constituting the first time “within- plant” genetic patterns have been reported in kelps. This is very different from the chimeric patterns described in land plants and animals. Finally, we evidenced that IGH affected

  18. Frequency of chimerism in populations of the kelp Lessonia spicata in central Chile.

    PubMed

    González, Alejandra V; Santelices, Bernabé

    2017-01-01

    Chimerism occurs when two genetically distinct conspecific individuals fuse together generating a single entity. Coalescence and chimerism in red seaweeds has been positively related to an increase in body size, and the consequent reduction in susceptibility to mortality factors, thus increasing survival, reproductive potential and tolerance to stress in contrast to genetically homogeneous organisms. In addition, they showed that a particular pattern of post-fusion growth maintains higher genetic diversity and chimerism in the holdfast but homogenous axes. In Chilean kelps (brown seaweeds), intraorganismal genetic heterogeneity (IGH) and holdfast coalescence has been described in previous research, but the extent of chimerism in wild populations and the patterns of distribution of the genetically heterogeneous thallus zone have scarcely been studied. Since kelps are under continuous harvesting, with enormous social, ecological and economic importance, natural chimerism can be considered a priceless in-situ reservoir of natural genetic resources and variability. In this study, we therefore examined the frequency of IGH and chimerism in three harvested populations of Lessonia spicata. We then evaluated whether chimeric wild-type holdfasts show higher genetic diversity than erect axes (stipe and lamina) and explored the impact of this on the traditional estimation of genetic diversity at the population level. We found a high frequency of IGH (60-100%) and chimerism (33.3-86.7%), varying according to the studied population. We evidenced that chimerism occurs mostly in holdfasts, exhibiting heterogeneous tissues, whereas stipes and lamina were more homogeneous, generating a vertical gradient of allele and genotype abundance as well as divergence, constituting the first time "within- plant" genetic patterns have been reported in kelps. This is very different from the chimeric patterns described in land plants and animals. Finally, we evidenced that IGH affected genetic

  19. Probabilistic structural analysis of space propulsion system LOX post

    NASA Technical Reports Server (NTRS)

    Newell, J. F.; Rajagopal, K. R.; Ho, H. W.; Cunniff, J. M.

    1990-01-01

    The probabilistic structural analysis program NESSUS (Numerical Evaluation of Stochastic Structures Under Stress; Cruse et al., 1988) is applied to characterize the dynamic loading and response of the Space Shuttle main engine (SSME) LOX post. The design and operation of the SSME are reviewed; the LOX post structure is described; and particular attention is given to the generation of composite load spectra, the finite-element model of the LOX post, and the steps in the NESSUS structural analysis. The results are presented in extensive tables and graphs, and it is shown that NESSUS correctly predicts the structural effects of changes in the temperature loading. The probabilistic approach also facilitates (1) damage assessments for a given failure model (based on gas temperature, heat-shield gap, and material properties) and (2) correlation of the gas temperature with operational parameters such as engine thrust.

  20. A development of chimeric VEGFR2 TK inhibitor based on two ligand conformers from PDB: 1Y6A complex--medicinal chemistry consequences of a TKs analysis.

    PubMed

    Lintnerová, Lucia; García-Caballero, Melissa; Gregáň, Fridrich; Melicherčík, Milan; Quesada, Ana R; Dobiaš, Juraj; Lác, Ján; Sališová, Marta; Boháč, Andrej

    2014-01-24

    VEGFR2 is an important mediator of angiogenesis and influences fate of some cancer stem cells. Here we analysed all 34 structures of VEGFR2 TK available from PDB database. From them a complex PDB: 1Y6A has an exceptional AAZ ligand bound to TK in form of two conformers (U- and S-shaped). This observation inspired us to develop three chimeric bispyridyl VEGFR2 inhibitors by combining structural features of both AAZ conformers and/or their relative ligand AAX (PDB: 1Y6B). Our most interesting inhibitor 22SYM has an enzymatic VEGFR2 TK activity (IC50: 15.1 nM) comparable or better to the active compounds from clinical drugs Nexavar and Sutent. 22SYM inhibits growth, migration and tube formation of endothelial cells (EC) and selectively induces EC apoptosis. 22SYM also inhibits in vivo angiogenesis in Zebrafish embryo assay. Additionally to the above results, we proved here that tyrosine kinases in an inactive form possessing Type I inhibitors can adopt both a closed or an opened conformation of kinase A-loop independently on their DFG-out arrangement. We proposed here that an activity of certain Type I inhibitors (e.g. 22SYM-like) in complex with DFG-out TK can be negatively influenced by collisions with a dynamically moving TK A-loop.

  1. Analysis of the Relevance of Posts in Asynchronous Discussions

    ERIC Educational Resources Information Center

    Azevedo, Breno T.; Reategui, Eliseo; Behar, Patrícia A.

    2014-01-01

    This paper presents ForumMiner, a tool for the automatic analysis of students' posts in asynchronous discussions. ForumMiner uses a text mining system to extract graphs from texts that are given to students as a basis for their discussion. These graphs contain the most relevant terms found in the texts, as well as the relationships between them.…

  2. Analysis of the Relevance of Posts in Asynchronous Discussions

    ERIC Educational Resources Information Center

    Azevedo, Breno T.; Reategui, Eliseo; Behar, Patrícia A.

    2014-01-01

    This paper presents ForumMiner, a tool for the automatic analysis of students' posts in asynchronous discussions. ForumMiner uses a text mining system to extract graphs from texts that are given to students as a basis for their discussion. These graphs contain the most relevant terms found in the texts, as well as the relationships between them.…

  3. Computer Aided Modeling and Post Processing with NASTRAN Analysis

    NASA Technical Reports Server (NTRS)

    Boroughs, R. R.

    1984-01-01

    Computer aided engineering systems are invaluable tools in performing NASTRAN finite element analysis. These techniques are implemented in both the pre-processing and post-processing phases of the NASTRAN analysis. The finite element model development, or pre-processing phase, was automated with a computer aided modeling program called Supertabl, and the review and interpretation of the results of the NASTRAN analysis, or post-processing phase, was automated with a computer aided plotting program called Output Display. An intermediate program, Nasplot, which was developed in-house, has also helped to cut down on the model checkout time and reduce errors in the model. An interface has been established between the finite element computer aided engineering system and the Learjet computer aided design system whereby data can be transferred back and forth between the two. These systems have significantly improved productivity and the ability to perform NASTRAN analysis in response to product development requests.

  4. Engineering and characterization of a chimeric anti-platelet glycoprotein Ibalpha monoclonal antibody and preparation of its Fab fragment.

    PubMed

    Yang, Jianfeng; Ji, Shundong; Dong, Ningzheng; Zhao, Yiming; Ruan, Changgeng

    2010-04-01

    Glycoprotein Ibalpha (GPIbalpha) is a platelet-specific membrane protein. It mediates platelet adhesion to collagen exposed at the vascular injury site by binding to von Willebrand factor (VWF) in plasma. This process is crucial for arterial thrombus formation. Blocking interaction between GPIbalpha and VWF may prevent platelet adhesion and thrombus formation. We previously generated a high affinity monoclonal antibody against human platelet GPIbalpha, SZ2, which inhibits both ristocetin- and botrocetin-induced platelet aggregation in vitro. To convert SZ2 into mouse/human chimeric antibody for anti-platelet therapy in humans, in this study, we constructed a mouse/human chimeric antibody derived from the hybridoma cells producing murine antibody against platelet glycoprotein Ibalpha, conducted its expression in dihydrofolate reductase-deficient Chinese hamster ovary (CHO) cells, and prepared its chimeric Fab fragment. Results from ELISA and Western blot analysis showed that the chimeric antibody was secreted from the cells and that the heavy and light chains were assembled correctly. Flow cytometry analysis confirmed specific binding of the chimeric antibody to the GPIb-expressing CHO cells. In vitro functional studies revealed that the chimeric antibody and its Fab fragment prevented platelet adhesion to VWF under high shear stress and inhibited ristocetin-induced platelet aggregation in a dose-dependent manner. These results demonstrated that the chimeric antibody was successfully engineered and suggested that the Fab fragment of chimeric antibody against GPIbalpha is a promising therapeutic antibody more suitable for prevention and treatment of human arterial thrombosis.

  5. Mapping of low-frequency chimeric yeast artificial chromosome libraries from human chromosomes 16 and 21 by fluorescence in situ hybridization and quantitative image analysis

    SciTech Connect

    Marrone, B.L.; Campbell, E.W.; Anzick, S.L.; Shera, K.; Campbell, M.; Yoshida, T.M.; McCormick, M.K.; Deaven, L. )

    1994-05-01

    Yeast artificial chromosome (YAC) clones from low-frequency chimeric libraries of human chromosomes 16 and 21 were mapped onto human diploid fibroblast metaphase chromosomes using fluorescence in situ hybridization (FISH) and digital imaging microscopy. YACs mapped onto chromosome 21 were selected to provide subregional location and ordering of known and unknown markers on the long arm of chromosome 21, particularly in the Down syndrome region (q22). YACs mapped onto chromosome 16 were selected to overlap regions spanning chromosome 16 cosmid maps. YAC clones were indirectly labeled with fluorescein, and the total DNA of the chromosome was counterstained with propidium iodide. A single image containing both the FISH signal and the whole chromosome was acquired for each chromosome of interest containing the fluorescent probe signal in a metaphase spread. From the digitized image, the fluorescence intensity profile through the long axis of the chromosome gave the total chromosome length and the probe position. The map position of the probe was expressed as the fractional length (FL) of the total chromosome relative to the end of the short arm (Flpter). From each clone hybridized, 20-40 chromosome images were analyzed. Thirty-eight YACs were mapped onto chromosome 16, and their FLs were distributed along the short and long arms. On chromosome 21, 47 YACs were mapped, including 12 containing known markers. To confirm the order of a dense population of YACs within the Down syndrome region, a two-color mapping strategy was used in which an anonymous YAC was located relative to one or two known markers on the metaphase chromosome. The chromosome FL maps have a 1- to 2-Mb resolution, and the FL measurement of each probe has a typical standard error of 0.5-1 Mb. 14 refs., 3 figs., 3 tabs.

  6. Construction of chimeric cyclodextrin glucanotransferases from Bacillus circulans A11 and Paenibacillus macerans IAM1243 and analysis of their product specificity.

    PubMed

    Rimphanitchayakit, Vichien; Tonozuka, Takashi; Sakano, Yoshiyuki

    2005-10-17

    Three DNA fragments of 7919 base pairs containing genes for beta-cyclodextrin glucanotransferase (CGTase, EC 2.4.1.19), an iron III dicitrate transport protein-like protein and a partial coding sequence for putative ferrichrome ABC transporter from Bacillus circulans A11 were cloned and sequenced (GenBank Accession AF302787). The DNA sequence contained a CGTase open reading frame of 2139 base pairs, which encoded a polypeptide of 713 amino acid residues. The signal peptide constituted the N-terminal 27 amino acid residues. The amino acid sequence was highly homologous to that of Bacillus sp. 1011 with 98.7% identity. The cloned CGTase gene contained its own promoter that directed the expression of the gene in Escherichia coli host cells. Chimeric construction against the alpha-CGTase from B. macerans IAM1243 was carried out by means of three created restriction sites, XhoI, SpeI, and MfeI, introduced by mutagenesis in between domains A/B and C, C and D, and D and E, respectively, and the NdeI site within the domains A/B. The various chimeras with different combinations of domains and part of domains A/B were analyzed for their dextrinizing and CD-forming activities. Their activities were of three groups: chimeras with no dextrinizing and cyclization activities, chimeras with only dextrinizing activity, and chimeras with both dextrinizing and cyclization activities. Two chimeras in the latter group showed altered product specificity. The results located the amino acid segment essential for the product specificity at the C-terminal half of domains A/B. Further, the function of domains C and D in positioning domain E in the correct orientation and proximity to domains A/B is implicated.

  7. Mixed donor chimerism in non-malignant haematological diseases after allogeneic bone marrow transplantation.

    PubMed

    Shamshad, Ghassan Umair; Ahmed, Suhaib; Bhatti, Farhat Abbas; Ali, Nadir

    2012-12-01

    To determine the frequency of mixed donor chimerism in patients of non-malignant haematological diseases after allogeneic bone marrow transplant. A cross-sectional, observational study. Department of Haematology, Armed Forces Institute of Pathology (AFIP), Rawalpindi, from July 2010 to June 2011. Donor chimerism was assessed in patients of aplastic anaemia and beta-thalassaemia major who underwent allogeneic bone marrow transplantation (BMT). Peripheral blood samples were used to assess chimerism status by analysis of short tandem repeats (STR). In patients where pre-transplant blood sample was not available, swab of buccal mucosa was used for pre-transplant STR profile. A standard set of primers for STR markers were used and the amplified DNA was resolved by gel electrophoresis and stained with silver nitrate. The percentage of donor origin DNA was estimated by densitometer. Out of 84 patients, 52 (62%) were males, while 32 (38%) were females. In patients of beta-thalassaemia major, 31 (62%) developed mixed donor chimerism (MC), 13 (26%) developed complete donor chimerism (CC) and 6 (12%) had graft failure. In aplastic anaemia, 17 patients (50%) achieved MC, 13 (38.2%) had CC and 4 (11.8%) developed graft failure. The combined frequency of mixed donor chimerism for both the diseases was 58.3%. D3S1358 was the most informative STR marker in these patients. Majority of the studied patients developed mixed donor chimerism following bone marrow transplantation, whereas only a minor percentage of the patients had graft failure. Analysis of D3S1358 was the most informative in assessing donor chimerism in patients who underwent BMT.

  8. Advanced Post-Irradiation Examination Capabilities Alternatives Analysis Report

    SciTech Connect

    Jeff Bryan; Bill Landman; Porter Hill

    2012-12-01

    An alternatives analysis was performed for the Advanced Post-Irradiation Capabilities (APIEC) project in accordance with the U.S. Department of Energy (DOE) Order DOE O 413.3B, “Program and Project Management for the Acquisition of Capital Assets”. The Alternatives Analysis considered six major alternatives: ? No Action ? Modify Existing DOE Facilities – capabilities distributed among multiple locations ? Modify Existing DOE Facilities – capabilities consolidated at a few locations ? Construct New Facility ? Commercial Partnership ? International Partnerships Based on the alternatives analysis documented herein, it is recommended to DOE that the advanced post-irradiation examination capabilities be provided by a new facility constructed at the Materials and Fuels Complex at the Idaho National Laboratory.

  9. Radiopacity of Esthetic Post Materials: Evaluation with Digital Analysis Technique.

    PubMed

    Kaval, Mehmet Emin; Akin, Hakan; Guneri, Pelin

    2017-07-01

    To evaluate the radiopacity of five post materials using a digital image analysis method. Twelve specimens from each post type (two zirconia and three fiber based) of 2 mm in thickness were obtained using a diamond blade mounted on a cutting machine, and digital radiographs were taken along with aluminum step-wedge and dentin discs under standard exposure conditions. The mean gray-values of specimens were measured using a computer graphics program. Data were analyzed using one-way ANOVA followed by Holm-Sidak multicomparison test (p = 0.05). The highest radiopacity was observed in custom zirconia (5.842 millimeters of equivalent Al [mmAl]), and the lowest value was detected with FRC-Postec (Ivoclar Vivadent) (1.716 mmAl). Significant differences were revealed between the radiopacity values among all groups (p < 0.05), except the Zr post materials (p = 0.56). All tested post materials had higher radiopacity than dentin. Further studies will be required to clarify optimum radiopacity properties of the post materials to provide a precise clinical observation. © 2015 by the American College of Prosthodontists.

  10. Birth of two chimeric genes in the Hominidae lineage.

    PubMed

    Courseaux, A; Nahon, J L

    2001-02-16

    How genes with newly characterized functions originate remains a fundamental question. PMCHL1 and PMCHL2, two chimeric genes derived from the melanin-concentrating hormone (MCH) gene, offer an opportunity to examine such an issue in the human lineage. Detailed structural, expression, and phylogenetic analysis showed that the PMCHL1 gene was created near 25 million years ago (Ma) by a complex mechanism of exon shuffling through retrotransposition of an antisense MCH messenger RNA coupled to de novo creation of splice sites. PMCHL2 arose 5 to 10 Ma by an event of duplication involving a large chromosomal region encompassing the PMCHL1 locus. The RNA expression patterns of those chimeric genes suggest that they have been submitted to strong regulatory constraints during primate evolution.

  11. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires.

    PubMed

    Shugay, Mikhail; Bagaev, Dmitriy V; Turchaninova, Maria A; Bolotin, Dmitriy A; Britanova, Olga V; Putintseva, Ekaterina V; Pogorelyy, Mikhail V; Nazarov, Vadim I; Zvyagin, Ivan V; Kirgizova, Vitalina I; Kirgizov, Kirill I; Skorobogatova, Elena V; Chudakov, Dmitriy M

    2015-11-01

    Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at https://github.com/mikessh/vdjtools.

  12. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

    PubMed Central

    Bolotin, Dmitriy A.; Britanova, Olga V.; Putintseva, Ekaterina V.; Pogorelyy, Mikhail V.; Nazarov, Vadim I.; Zvyagin, Ivan V.; Kirgizova, Vitalina I.; Kirgizov, Kirill I.; Skorobogatova, Elena V.; Chudakov, Dmitriy M.

    2015-01-01

    Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at https://github.com/mikessh/vdjtools. PMID:26606115

  13. Functional analysis of chimeric lysin motif domain receptors mediating Nod factor-induced defense signaling in Arabidopsis thaliana and chitin-induced nodulation signaling in Lotus japonicus.

    PubMed

    Wang, Wei; Xie, Zhi-Ping; Staehelin, Christian

    2014-04-01

    The expression of chimeric receptors in plants is a way to activate specific signaling pathways by corresponding signal molecules. Defense signaling induced by chitin from pathogens and nodulation signaling of legumes induced by rhizobial Nod factors (NFs) depend on receptors with extracellular lysin motif (LysM) domains. Here, we constructed chimeras by replacing the ectodomain of chitin elicitor receptor kinase 1 (AtCERK1) of Arabidopsis thaliana with ectodomains of NF receptors of Lotus japonicus (LjNFR1 and LjNFR5). The hybrid constructs, named LjNFR1-AtCERK1 and LjNFR5-AtCERK1, were expressed in cerk1-2, an A. thaliana CERK1 mutant lacking chitin-induced defense signaling. When treated with NFs from Rhizobium sp. NGR234, cerk1-2 expressing both chimeras accumulated reactive oxygen species, expressed chitin-responsive defense genes and showed increased resistance to Fusarium oxysporum. In contrast, expression of a single chimera showed no effects. Likewise, the ectodomains of LjNFR1 and LjNFR5 were replaced by those of OsCERK1 (Oryza sativa chitin elicitor receptor kinase 1) and OsCEBiP (O. sativa chitin elicitor-binding protein), respectively. The chimeras, named OsCERK1-LjNFR1 and OsCEBiP-LjNFR5, were expressed in L. japonicus NF receptor mutants (nfr1-1; nfr5-2) carrying a GUS (β-glucuronidase) gene under the control of the NIN (nodule inception) promoter. Upon chitin treatment, GUS activation reflecting nodulation signaling was observed in the roots of NF receptor mutants expressing both chimeras, whereas a single construct was not sufficient for activation. Hence, replacement of ectodomains in LysM domain receptors provides a way to specifically trigger NF-induced defense signaling in non-legumes and chitin-induced nodulation signaling in legumes. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

  14. Post-Optimality Analysis In Aerospace Vehicle Design

    NASA Technical Reports Server (NTRS)

    Braun, Robert D.; Kroo, Ilan M.; Gage, Peter J.

    1993-01-01

    This analysis pertains to the applicability of optimal sensitivity information to aerospace vehicle design. An optimal sensitivity (or post-optimality) analysis refers to computations performed once the initial optimization problem is solved. These computations may be used to characterize the design space about the present solution and infer changes in this solution as a result of constraint or parameter variations, without reoptimizing the entire system. The present analysis demonstrates that post-optimality information generated through first-order computations can be used to accurately predict the effect of constraint and parameter perturbations on the optimal solution. This assessment is based on the solution of an aircraft design problem in which the post-optimality estimates are shown to be within a few percent of the true solution over the practical range of constraint and parameter variations. Through solution of a reusable, single-stage-to-orbit, launch vehicle design problem, this optimal sensitivity information is also shown to improve the efficiency of the design process, For a hierarchically decomposed problem, this computational efficiency is realized by estimating the main-problem objective gradient through optimal sep&ivity calculations, By reducing the need for finite differentiation of a re-optimized subproblem, a significant decrease in the number of objective function evaluations required to reach the optimal solution is obtained.

  15. Reversible Heat-Induced Inactivation of Chimeric β-Glucuronidase in Transgenic Plants1

    PubMed Central

    Almoguera, Concepción; Rojas, Anabel; Jordano, Juan

    2002-01-01

    We compared the expression patterns in transgenic tobacco (Nicotiana tabacum) of two chimeric genes: a translational fusion to β-glucuronidase (GUS) and a transcriptional fusion, both with the same promoter and 5′-flanking sequences of Ha hsp17.7 G4, a small heat shock protein (sHSP) gene from sunflower (Helianthus annuus). We found that immediately after heat shock, the induced expression from the two fusions in seedlings was similar, considering chimeric mRNA or GUS protein accumulation. Surprisingly, we discovered that the chimeric GUS protein encoded by the translational fusion was mostly inactive in such conditions. We also found that this inactivation was fully reversible. Thus, after returning to control temperature, the GUS activity was fully recovered without substantial changes in GUS protein accumulation. In contrast, we did not find differences in the in vitro heat inactivation of the respective GUS proteins. Insolubilization of the chimeric GUS protein correlated with its inactivation, as indicated by immunoprecipitation analyses. The inclusion in another chimeric gene of the 21 amino-terminal amino acids from a different sHSP lead to a comparable reversible inactivation. That effect not only illustrates unexpected post-translational problems, but may also point to sequences involved in interactions specific to sHSPs and in vivo heat stress conditions. PMID:12011363

  16. Reversible heat-induced inactivation of chimeric beta-glucuronidase in transgenic plants.

    PubMed

    Almoguera, Concepción; Rojas, Anabel; Jordano, Juan

    2002-05-01

    We compared the expression patterns in transgenic tobacco (Nicotiana tabacum) of two chimeric genes: a translational fusion to beta-glucuronidase (GUS) and a transcriptional fusion, both with the same promoter and 5'-flanking sequences of Ha hsp17.7 G4, a small heat shock protein (sHSP) gene from sunflower (Helianthus annuus). We found that immediately after heat shock, the induced expression from the two fusions in seedlings was similar, considering chimeric mRNA or GUS protein accumulation. Surprisingly, we discovered that the chimeric GUS protein encoded by the translational fusion was mostly inactive in such conditions. We also found that this inactivation was fully reversible. Thus, after returning to control temperature, the GUS activity was fully recovered without substantial changes in GUS protein accumulation. In contrast, we did not find differences in the in vitro heat inactivation of the respective GUS proteins. Insolubilization of the chimeric GUS protein correlated with its inactivation, as indicated by immunoprecipitation analyses. The inclusion in another chimeric gene of the 21 amino-terminal amino acids from a different sHSP lead to a comparable reversible inactivation. That effect not only illustrates unexpected post-translational problems, but may also point to sequences involved in interactions specific to sHSPs and in vivo heat stress conditions.

  17. Early mixed T-cell chimerism is predictive of pediatric AML or MDS relapse after hematopoietic stem cell transplant.

    PubMed

    Broglie, Larisa; Helenowski, Irene; Jennings, Lawrence J; Schafernak, Kristian; Duerst, Reggie; Schneiderman, Jennifer; Tse, William; Kletzel, Morris; Chaudhury, Sonali

    2017-03-07

    Patients with acute myeloid leukemia (AML) who relapse after hematopoietic stem cell transplantation (HCT) have dismal outcomes. Our ability to predict those at risk for relapse is limited. We examined chimerism trends post-HCT in 63 children who underwent HCT for AML or myelodysplastic syndrome (MDS). Mixed T-cell chimerism at engraftment and absence of chronic graft versus host disease (cGVHD) were associated with relapse (P = 0.04 and P = 0.02, respectively). Mixed T-cell chimerism at engraftment was predictive in patients without cGVHD (P = 0.03). Patients with engraftment mixed T-cell chimerism may warrant closer disease monitoring and consideration for early intervention.

  18. FARO base case post-test analysis by COMETA code

    SciTech Connect

    Annunziato, A.; Addabbo, C.

    1995-09-01

    The paper analyzes the COMETA (Core Melt Thermal-Hydraulic Analysis) post test calculations of FARO Test L-11, the so-called Base Case Test. The FARO Facility, located at JRC Ispra, is used to simulate the consequences of Severe Accidents in Nuclear Power Plants under a variety of conditions. The COMETA Code has a 6 equations two phase flow field and a 3 phases corium field: the jet, the droplets and the fused-debris bed. The analysis shown that the code is able to pick-up all the major phenomena occurring during the fuel-coolant interaction pre-mixing phase.

  19. Orion Exploration Flight Test Post-Flight Inspection and Analysis

    NASA Technical Reports Server (NTRS)

    Miller, J. E.; Berger, E. L.; Bohl, W. E.; Christiansen, E. L.; Davis, B. A.; Deighton, K. D.; Enriquez, P. A.; Garcia, M. A.; Hyde, J. L.; Oliveras, O. M.

    2017-01-01

    The principal mechanism for developing orbital debris environment models, is to make observations of larger pieces of debris in the range of several centimeters and greater using radar and optical techniques. For particles that are smaller than this threshold, breakup and migration models of particles to returned surfaces in lower orbit are relied upon to quantify the flux. This reliance on models to derive spatial densities of particles that are of critical importance to spacecraft make the unique nature of the EFT-1's return surface a valuable metric. To this end detailed post-flight inspections have been performed of the returned EFT-1 backshell, and the inspections identified six candidate impact sites that were not present during the pre-flight inspections. This paper describes the post-flight analysis efforts to characterize the EFT-1 mission craters. This effort included ground based testing to understand small particle impact craters in the thermal protection material, the pre- and post-flight inspection, the crater analysis using optical, X-ray computed tomography (CT) and scanning electron microscope (SEM) techniques, and numerical simulations.

  20. Generating chimeric zebrafish embryos by transplantation.

    PubMed

    Kemp, Hilary A; Carmany-Rampey, Amanda; Moens, Cecilia

    2009-07-17

    One of the most powerful tools used to gain insight into complex developmental processes is the analysis of chimeric embryos. A chimera is defined as an organism that contains cells from more than one animal; mosaics are one type of chimera in which cells from more than one genotype are mixed, usually wild-type and mutant. In the zebrafish, chimeras can be readily made by transplantation of cells from a donor embryo into a host embryo at the appropriate embryonic stage. Labeled donor cells are generated by injection of a lineage marker, such as a fluorescent dye, into the one-cell stage embryo. Labeled donor cells are removed from donor embryos and introduced into unlabeled host embryos using an oil-controlled glass pipette mounted on either a compound or dissecting microscope. Donor cells can in some cases be targeted to a specific region or tissue of the developing blastula or gastrula stage host embryo by choosing a transplantation site in the host embryo based on well-established fate maps.

  1. Differentials of post-partum amenorrhea: a survival analysis.

    PubMed

    Aryal, T R

    2007-01-01

    Post-partum amenorrhea is an important event for females' reproductive life and their health. It is the time period between the end of pregnancy and the resumption of menstruation after delivery, and it is considered to be the temporary infecundable period of women's reproductive life-span. The main aim of this article is to examine the differentials of post-partum amenorrhea by using current status reporting data according to the characteristics of the mother and her child. The data are utilized from a sample survey of Palpa and Rupandehi districts of western rural Nepal. A life-table based technique of survival analysis has been used. Important summary measures have been computed in order to see the differentials of duration of post-partum amenorrhea. The study revealed that parity of mothers, age of mothers, breast-feeding practices and survival status of the child were found to be the main differentials of the duration of post-partum amenorrhea. Amenorrhea period was found shorter for lower parity and younger mothers. Amenorrheic period was found to be increased with increased birth-interval and duration of breast-feeding practices. A strong positive association was found between the duration of post-partum amenorrhea and breast-feeding. The study also revealed that an inverse association was found between the duration of post-partum amenorrhea and socio-economic status of mothers. The survival status of the child showed a strong effect for the timing of amenorrhea. This study investigated the important differentials of amenorrhea by using current status reporting data according to the characteristics of mother and her child. The estimated values of mean, median and trimean duration of amenorrhea were compared. For instance, trimean of amenorrheic period was found to be 9.6 months while median was 8.4 months and mean was 10.4 months. This finding indicates that the trimean provided the most consistent and best estimates of the duration of amenorrhea than other

  2. Regression analysis exploring teacher impact on student FCI post scores

    NASA Astrophysics Data System (ADS)

    Mahadeo, Jonathan V.; Manthey, Seth R.; Brewe, Eric

    2013-01-01

    High School Modeling Workshops are designed to improve high school physics teachers' understanding of physics and how to teach using the Modeling method. The basic assumption is that the teacher plays a critical role in their students' physics education. This study investigated teacher impacts on students' Force Concept Inventory scores, (FCI), with the hopes of identifying quantitative differences between teachers. This study examined student FCI scores from 18 teachers with at least a year of teaching high school physics. This data was then evaluated using a General Linear Model (GLM), which allowed for a regression equation to be fitted to the data. This regression equation was used to predict student post FCI scores, based on: teacher ID, student pre FCI score, gender, and representation. The results show 12 out of 18 teachers significantly impact their student post FCI scores. The GLM further revealed that of the 12 teachers only five have a positive impact on student post FCI scores. Given these differences among teachers it is our intention to extend our analysis to investigate pedagogical differences between them.

  3. Boundary element analysis of post-tensioned slabs

    NASA Astrophysics Data System (ADS)

    Rashed, Youssef F.

    2015-06-01

    In this paper, the boundary element method is applied to carry out the structural analysis of post-tensioned flat slabs. The shear-deformable plate-bending model is employed. The effect of the pre-stressing cables is taken into account via the equivalent load method. The formulation is automated using a computer program, which uses quadratic boundary elements. Verification samples are presented, and finally a practical application is analyzed where results are compared against those obtained from the finite element method. The proposed method is efficient in terms of computer storage and processing time as well as the ease in data input and modifications.

  4. Expression of a Chimeric Gene Encoding Insecticidal Crystal Protein Cry1Aabc of Bacillus thuringiensis in Chickpea (Cicer arietinum L.) Confers Resistance to Gram Pod Borer (Helicoverpa armigera Hubner.).

    PubMed

    Das, Alok; Datta, Subhojit; Thakur, Shallu; Shukla, Alok; Ansari, Jamal; Sujayanand, G K; Chaturvedi, Sushil K; Kumar, P A; Singh, N P

    2017-01-01

    Domain swapping and generation of chimeric insecticidal crystal protein is an emerging area of insect pest management. The lepidopteran insect pest, gram pod borer (Helicoverpa armigera H.) wreaks havoc to chickpea crop affecting production. Lepidopteran insects were reported to be controlled by Bt (cryI) genes. We designed a plant codon optimized chimeric Bt gene (cry1Aabc) using three domains from three different cry1A genes (domains I, II, and III from cry1Aa, cry1Ab, and cry1Ac, respectively) and expressed it under the control of a constitutive promoter in chickpea (cv. DCP92-3) to assess its effect on gram pod borer. A total of six transgenic chickpea shoots were established by grafting into mature fertile plants. The in vitro regenerated (organogenetic) shoots were selected based on antibiotic kanamycin monosulfate (100 mg/L) with transformation efficiency of 0.076%. Three transgenic events were extensively studied based on gene expression pattern and insect mortality across generations. Protein expression in pod walls, immature seeds and leaves (pre- and post-flowering) were estimated and expression in pre-flowering stage was found higher than that of post-flowering. Analysis for the stable integration, expression and insect mortality (detached leaf and whole plant bioassay) led to identification of efficacious transgenic chickpea lines. The chimeric cry1Aabc expressed in chickpea is effective against gram pod borer and generated events can be utilized in transgenic breeding program.

  5. Expression of a Chimeric Gene Encoding Insecticidal Crystal Protein Cry1Aabc of Bacillus thuringiensis in Chickpea (Cicer arietinum L.) Confers Resistance to Gram Pod Borer (Helicoverpa armigera Hubner.)

    PubMed Central

    Das, Alok; Datta, Subhojit; Thakur, Shallu; Shukla, Alok; Ansari, Jamal; Sujayanand, G. K.; Chaturvedi, Sushil K.; Kumar, P. A.; Singh, N. P.

    2017-01-01

    Domain swapping and generation of chimeric insecticidal crystal protein is an emerging area of insect pest management. The lepidopteran insect pest, gram pod borer (Helicoverpa armigera H.) wreaks havoc to chickpea crop affecting production. Lepidopteran insects were reported to be controlled by Bt (cryI) genes. We designed a plant codon optimized chimeric Bt gene (cry1Aabc) using three domains from three different cry1A genes (domains I, II, and III from cry1Aa, cry1Ab, and cry1Ac, respectively) and expressed it under the control of a constitutive promoter in chickpea (cv. DCP92-3) to assess its effect on gram pod borer. A total of six transgenic chickpea shoots were established by grafting into mature fertile plants. The in vitro regenerated (organogenetic) shoots were selected based on antibiotic kanamycin monosulfate (100 mg/L) with transformation efficiency of 0.076%. Three transgenic events were extensively studied based on gene expression pattern and insect mortality across generations. Protein expression in pod walls, immature seeds and leaves (pre- and post-flowering) were estimated and expression in pre-flowering stage was found higher than that of post-flowering. Analysis for the stable integration, expression and insect mortality (detached leaf and whole plant bioassay) led to identification of efficacious transgenic chickpea lines. The chimeric cry1Aabc expressed in chickpea is effective against gram pod borer and generated events can be utilized in transgenic breeding program. PMID:28871265

  6. Chimeric polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    DOEpatents

    Wogulis, Mark; Sweeney, Matthew; Heu, Tia

    2017-06-14

    The present invention relates to chimeric GH61 polypeptides having cellulolytic enhancing activity. The present invention also relates to polynucleotides encoding the chimeric GH61 polypeptides; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the chimeric GH61 polypeptides.

  7. [DNA analysis for the post genome-sequencing era].

    PubMed

    Kambara, Hideki

    2002-05-01

    With the completion of the human genome sequencing, the new post genome-sequencing era has started. The major subjects are clarifying the function of genes to apply this information to medical as well as various industrial fields. Various DNA analysis methods and instruments for gene expression profiling as well as genetic diversity including SNPs typing are required and have been developed. Here, the history and technologies related to DNA analysis including the Wada project in the early 1980's, and the Human genome project from 1990 are described. Various new technologies have developed in this decade. They include a capillary gel array DNA sequencer, DNA chips, bead probe arrays, a new DNA sequencing method using pyrosequencing and an efficient SNP typing method by BAMPER.

  8. Growth and long-term somatic and germline chimerism following fusion of juvenile Botryllus schlosseri.

    PubMed

    Carpenter, Meredith A; Powell, John H; Ishizuka, Katherine J; Palmeri, Karla J; Rendulic, Snjezana; De Tomaso, Anthony W

    2011-02-01

    The colonial ascidian Botryllus schlosseri undergoes a histocompatibility reaction that can result in vascular fusion of distinct genotypes, creating a chimera. Chimerism has both potential benefits, such as an immediate increase in size that may enhance growth rates, and costs. For the latter, the presence of multiple genotypes in a chimera can lead to competition between genetically distinct stem cell lineages, resulting in complete replacement of somatic and germline tissues by a single genotype. Although fusion can occur at any point after metamorphosis, previous studies have focused on chimeras created from sexually mature adults, where no benefit to chimerism has been documented. Here we focus on the costs and benefits of fusion between juveniles, characterizing growth rates and patterns of somatic and germline chimerism after natural and controlled fusion events. We also compared outcomes between low- and high-density growth conditions, the latter more likely representative of what occurs in natural populations. We found that growth rates were density-dependent, and that only chimeras grew under high-density conditions. We also observed a positional component to a post-fusion event called resorption, indicating that extrinsic factors were important in this process. Patterns of germline and somatic chimerism and dominance in chimeras made from fused juveniles were equivalent to those after fusion of sexually mature adults, and there were no age-related differences in these processes. Finally, by using genetic markers that could retrospectively assign genotypes, we also found that the majority of individual testes in a chimera were clonally derived.

  9. Flow cytometric evaluation of red blood cell chimerism after bone marrow transplantation in Iranian patients: a preliminary study.

    PubMed

    Shaiegan, Mojgan; Hadjati, Esmerdis; Aghaiipour, Mahnaz; Iravani, Masoud; David, Gaelle; Bernard, Daniel

    2006-10-01

    The aim of this study was to evaluate mixed red cells population and red blood cell chimerism after hematopoietic stem cell transplantation. Red blood cell chimerism after hematopoietic stem cell transplantation was analyzed using a series of fluorescein isothiocyanate-conjugated monoclonal antibodies (BioAtlantic, France) directed against ABH, Rh (D, C, E, c, e), Kell, Duffy, Kidd, and Ss antigens on blood samples of 14 patients with hematologic disorders undergoing hematopoietic stem cell transplantation, by flow cytometric method on days 15, 30, and 60 after transplantation. All patients showed expression of donor red cell antigens within days 15 - 30 after hematopoietic stem cell transplantation. Graft versus host disease and ABO incompatibility did not affect the expression of chimerism. Flow cytometric analysis is a simple, accurate, and valuable test which is of significant help in monitoring chimerism in allogeneic hematopoietic stem cell transplantation.

  10. Cost analysis of post-polio certification immunization policies.

    PubMed Central

    Sangrujee, Nalinee; Cáceres, Victor M.; Cochi, Stephen L.

    2004-01-01

    OBJECTIVE: An analysis was conducted to estimate the costs of different potential post-polio certification immunization policies currently under consideration, with the objective of providing this information to policy-makers. METHODS: We analyzed three global policy options: continued use of oral poliovirus vaccine (OPV); OPV cessation with optional inactivated poliovirus vaccine (IPV); and OPV cessation with universal IPV. Assumptions were made on future immunization policy decisions taken by low-, middle-, and high-income countries. We estimated the financial costs of each immunization policy, the number of vaccine-associated paralytic poliomyelitis (VAPP) cases, and the global costs of maintaining an outbreak response capacity. The financial costs of each immunization policy were based on estimates of the cost of polio vaccine, its administration, and coverage projections. The costs of maintaining outbreak response capacity include those associated with developing and maintaining a vaccine stockpile in addition to laboratory and epidemiological surveillance. We used the period 2005-20 as the time frame for the analysis. FINDINGS: OPV cessation with optional IPV, at an estimated cost of US$ 20,412 million, was the least costly option. The global cost of outbreak response capacity was estimated to be US$ 1320 million during 2005-20. The policy option continued use of OPV resulted in the highest number of VAPP cases. OPV cessation with universal IPV had the highest financial costs, but it also had the least number of VAPP cases. Sensitivity analyses showed that global costs were sensitive to assumptions on the cost of the vaccine. Analysis also showed that if the price per dose of IPV was reduced to US$ 0.50 for low-income countries, the cost of OPV cessation with universal IPV would be the same as the costs of continued use of OPV. CONCLUSION: Projections on the vaccine price per dose and future coverage rates were major drivers of the global costs of post

  11. SHEFEX II Flight Instrumentation And Preparation Of Post Flight Analysis

    NASA Astrophysics Data System (ADS)

    Thiele, Thomas; Siebe, Frank; Gulhan, Ali

    2011-05-01

    A main disadvantage of modern TPS systems for re- entry vehicles is the expensive manufacturing and maintenance process due to the complex geometry of these blunt nose configurations. To reduce the costs and to improve the aerodynamic performance the German Aerospace Center (DLR) is following a different approach using TPS structures consisting of flat ceramic tiles. To test these new sharp edged TPS structures the SHEFEX I flight experiment was designed and successfully performed by DLR in 2005. To further improve the reliability of the sharp edged TPS design at even higher Mach numbers, a second flight experiment SHEFEX II will be performed in September 2011. In comparison to SHEFEX I the second flight experiment has a fully symmetrical shape and will reach a maximum Mach number of about 11. Furthermore the vehicle has an active steering system using four canards to control the flight attitude during re-entry, e.g. roll angle, angle of attack and sideslip. After a successful flight the evaluation of the flight data will be performed using a combination of numerical and experimental tools. The data will be used for the improvement of the present numerical analysis tools and to get a better understanding of the aerothermal behaviour of sharp TPS structures. This paper presents the flight instrumentation of the SHEFEX II TPS. In addition the concept of the post flight analysis is presented.

  12. Emoting infertility online: A qualitative analysis of men's forum posts.

    PubMed

    Hanna, Esmée; Gough, Brendan

    2016-07-01

    Relatively little research on infertility focuses exclusively or significantly on men's experiences, particularly in relation to emotional aspects. Evidence that does exist around male infertility suggests that it is a distressing experience for men, due to stigma, threats to masculinity and the perceived need to suppress emotions, and that men and women experience infertility differently. Using thematic analysis, this article examines the online emoting of men in relation to infertility via forum posts from a men-only infertility discussion board. It was noted that men 'talked' to each other about the emotional burdens of infertility, personal coping strategies and relationships with others. Three major themes were identified following in-depth analysis: 'the emotional rollercoaster', 'the tyranny of infertility' and 'infertility paranoia'. This article then offers insights into how men experience infertility emotionally, negotiate the emotional challenges involved (especially pertaining to diagnosis, treatment outcomes and their intimate relationships) and how they share (and find value in doing so) with other men the lived experience of infertility.

  13. Production of Chimeric Acidic α-Amylase by the Recombinant Pichia pastoris and Its Applications

    PubMed Central

    Parashar, Deepak; Satyanarayana, Tulasi

    2017-01-01

    Recombinant chimeric α-amylase (Ba-Gt-amy) has been produced extracellularly in Pichia pastoris under AOX promoter. Clones of P. pastoris with multiple gene copies have been generated by multiple transformations and post-transformational vector amplification, which led to 10.7-fold enhancement in α-amylase titre as compared to a clone with a copy of the gene. The recombinant P. pastoris integrated eight copies of Ba-Gt-amy in the genome of P. pastoris, as revealed by real time PCR data analysis. Heterologous protein expression as well as mRNA level of Ba-Gt-amy was higher in multi-copy clone than that with single copy. The pure Ba-Gt-amy expressed in P. pastoris is a glycoprotein of 75 kDa, which is optimally active at pH 4.0 and 60°C with T1/2 of 40 min at 70°C. The Kinetic parameters and end product analysis suggested that glycosylation has no effect on catalytic properties of Ba-Gt-amy. The enzyme saccharifies soluble as well as raw starches efficiently and generates maltose and maltooligosaccharides, thus, useful in baking and sugar syrup industries. The strategy for generating multi-copy clones is being reported for the first time, which could be useful in enhancing the production of other recombinant proteins. PMID:28382032

  14. Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms

    NASA Technical Reports Server (NTRS)

    Kopczynski, E. D.; Bateson, M. M.; Ward, D. M.

    1994-01-01

    When PCR was used to recover small-subunit (SSU) rRNA genes from a hot spring cyanobacterial mat community, chimeric SSU rRNA sequences which exhibited little or no secondary structural abnormality were recovered. They were revealed as chimeras of SSU rRNA genes of uncultivated species through separate phylogenetic analysis of short sequence domains.

  15. Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms

    NASA Technical Reports Server (NTRS)

    Kopczynski, E. D.; Bateson, M. M.; Ward, D. M.

    1994-01-01

    When PCR was used to recover small-subunit (SSU) rRNA genes from a hot spring cyanobacterial mat community, chimeric SSU rRNA sequences which exhibited little or no secondary structural abnormality were recovered. They were revealed as chimeras of SSU rRNA genes of uncultivated species through separate phylogenetic analysis of short sequence domains.

  16. Post-operative antibiotics after appendectomy and post-operative abscess development: a retrospective analysis.

    PubMed

    Hughes, Michael J; Harrison, Ewen; Paterson-Brown, Simon

    2013-02-01

    Appendectomy is one of the most common emergency operations. Prophylaxis against infective complications involves post-operative antibiotics. There is no consensus as to the optimum antibiotic regimen. This study aimed to assess the relation between the duration of the post-operative antibiotic administration and intra-abdominal infections (IAIs). All patients who underwent appendectomy between September 1, 2009, and August 31, 2010, were identified. The appearance of the appendix at operation, post-operative antibiotics, white blood cell count, and temperature at the time of conversion of intravenous (IV) to oral antibiotics were compiled. IAIs were assessed as the final outcome. Two hundred sixty six patients underwent appendectomy-188 for simple appendicitis and 78 for complicated appendicitis. There were 18 IAIs (6.8%) overall, 10 (12.8%) after complicated appendicitis and eight (4.2%) after simple appendicitis. Prolonging antibiotics beyond the operation in the simple appendicitis group did not alter the incidence of IAI. Similarly, in the complicated appendicitis group, prolonging antibiotics beyond five days did not alter the incidence of IAI. Furthermore, in patients with complicated appendicitis, the presence of leukocytosis, fever, or both when IV antibiotics were converted to oral drugs was associated with the development of IAI (p=0.013). In simple appendicitis, post-operative antibiotics may not be beneficial at all. In complicated appendicitis, prolonging the course of antibiotics was not associated with a reduced IAI rate. However, cessation of IV antibiotics when fever or leukocytosis was present was associated with IAI development.

  17. [Neutralizing Monoclonal and Chimeric Antibodies to Human IFN-γ].

    PubMed

    Larina, M V; Aliev, T K; Solopova, O N; Pozdnyakova, L P; Korobova, S V; Yakimov, S A; Sveshnikov, P G; Dolgikh, D A; Kirpichnikov, M P

    2015-01-01

    Autoiminune disorders are chronic diseases characterized by abnormal immune response directed against self-antigens that leads to tissue damage and violation of its normal functioning. Such diseases often result in disability or even death of patients. Nowadays a number of monoclonal antibodies to pro-inflammatory cytokines and their receptors are successfully used for the targeted treatment of autoimmune diseases. One of the perspective targets in autoimmune disease therapy is interferon gamma, a key cytokine in Th1 cells differentiation, activation of macrophages, and inflammation. In the present work, 5 monoclonal antibodies to human IFN-γ were obtained. For the development of potential therapeutic agent, we have performed neutralizing activity and affinity analysis of the antibodies. Based on the data obtained, the monoclonal antibody F1 was selected. This antibody has a dissociation constant 1.7 x 10(-9) M and IC90 = 8.9 ± 2.0 nM measured upon antibody inhibition of the IFN-γ-induced HLA-DR expression on the surface of U937 cells. We have constructed a bicistronic vector for the production of recombinant chimeric Fab fragment F1 chim in E. coli cells. The recombinant chimeric Fab fragment Fl chim neutralizes IFN-γ activity in vitro and has a dissociation constant 1.8 x 10(-9) M.

  18. Designing a recombinant chimeric construct contain MUC1 and HER2 extracellular domain for prediagnostic breast cancer.

    PubMed

    Gheybi, Elaheh; Amani, Jafar; Salmanian, Ali Hatef; Mashayekhi, Farhad; Khodi, Samaneh

    2014-11-01

    Breast cancer is the most common cancer among women in the world. One of the approaches for diagnosis of breast cancer is detection of its tumor-associated markers. Mucin 1 (MUC1), a tumor-associated antigen, is a transmembrane glycoprotein expressed by normal epithelial cells and overexpressed by carcinomas of epithelial origin. Also, human epidermal growth factor receptor-2 (HER2/erbB-2) belongs to the one of four members of tyrosin kinase type 1 family in which overexpression of HER2 is associated with malignancy in breast cancer. This study was aimed to bioinformatics analysis and designing a recombinant chimeric protein containing MUC1 and HER2 antigens to express in prokaryotic host (Escherichia coli) as breast cancer diagnosis tools. The immunogenic sequences of MUC1 and HER2 were extracted and fused together by a linker. The chimeric construct was analyzed by bioinformatics softwares. The optimization and purification, evaluation of the expression of chimeric protein was performed using Western blotting, ELISA, and immunohistochemistry. The results showed that the chimeric construct was stable and immunogenic domains were exposed. The pET-28a vector containing chimeric gene had high level of protein expression. The recombinant chimeric protein was confirmed using Western blotting, and it was investigated using ELISA and IHC. Then, the MUC1 and HER2 combined peptides can be used as coating antigens in ELISA for detection of antibodies against MUC1 or HER2 in human serum.

  19. Proteomic analysis of post translational modifications in cyanobacteria.

    PubMed

    Xiong, Qian; Chen, Zhuo; Ge, Feng

    2016-02-16

    Cyanobacteria are a diverse group of Gram-negative bacteria and the only prokaryotes capable of oxygenic photosynthesis. Recently, cyanobacteria have attracted great interest due to their crucial roles in global carbon and nitrogen cycles and their ability to produce clean and renewable biofuels. To survive in various environmental conditions, cyanobacteria have developed a complex signal transduction network to sense environmental signals and implement adaptive changes. The post-translational modifications (PTMs) systems play important regulatory roles in the signaling networks of cyanobacteria. The systematic investigation of PTMs could contribute to the comprehensive description of protein species and to elucidate potential biological roles of each protein species in cyanobacteria. Although the proteomic studies of PTMs carried out in cyanobacteria were limited, these data have provided clues to elucidate their sophisticated sensing mechanisms that contribute to their evolutionary and ecological success. This review aims to summarize the current status of PTM studies and recent publications regarding PTM proteomics in cyanobacteria, and discuss the novel developments and applications for the analysis of PTMs in cyanobacteria. Challenges, opportunities and future perspectives in the proteomics studies of PTMs in cyanobacteria are also discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. CRES-T, an effective gene silencing system utilizing chimeric repressors.

    PubMed

    Mitsuda, Nobutaka; Matsui, Kyoko; Ikeda, Miho; Nakata, Masaru; Oshima, Yoshimi; Nagatoshi, Yukari; Ohme-Takagi, Masaru

    2011-01-01

    Chimeric REpressor gene Silencing Technology (CRES-T) is a useful tool for functional analysis of plant transcription factors. In this system, a chimeric repressor that is produced by fusion of a transcription factor to the plant-specific EAR-motif repression domain (SRDX) suppresses target genes of a transcription factor dominantly over the activity of endogenous and functionally redundant transcription factors. As a result, the transgenic plants that express a chimeric repressor exhibit phenotypes similar to loss-of-function of the alleles of the gene encoding the transcription factor. This system is simple and effective and can be used as a powerful tool not only for functional analysis of redundant transcription factors but also for the manipulation of plant traits by active suppression of the gene expression. Strategies for construction of the chimeric repressors and their expression in transgenic plants are described. Transient effector-reporter assays for functional analysis of transcription factors and detection of protein-protein interactions using the trans-repressive activity of SRDX repression domain are also described.

  1. Use of CTLA4Ig for Induction of Mixed Chimerism and Renal Allograft Tolerance in Nonhuman Primates

    PubMed Central

    Yamada, Yohei; Ochiai, Takanori; Boskovic, Svjetlan; Nadazdin, Ognjenka; Oura, Tetsu; Schoenfeld, David; Cappetta, Kate; Smith, Rex-Neal; Colvin, Robert B; Madsen, Joren C.; Sachs, David H.; Benichou, Gilles; Cosimi, A. Benedict; Kawai, Tatsuo

    2014-01-01

    We have previously reported successful induction of renal allograft tolerance via a mixed chimerism approach in nonhuman primates (NHP). In those studies, we found that costimulatory blockade with anti-CD154 mAb was an effective adjunctive therapy for induction of renal allograft tolerance. However, since anti-CD154 mAb is not clinically available, we have evaluated CTLA4Ig as an alternative agent for effecting costimulation blockade in this treatment protocol. Two CTLA4-Igs, Abatacept and Belatacept, were substituted for anti-CD154 mAb in the conditioning regimen (low dose total body irradiation, thymic irradiation, ATG and a one month post-transplant course of cyclosporine (CyA)). Three recipients treated with the Abatacept regimen failed to develop comparable lymphoid chimerism to that achieved with anti-CD154 mAb treatment and these recipients rejected their kidney allografts early. With the Belatacept regimen, four of five recipients developed chimerism and three of these achieved long-term renal allograft survival (>861, >796 and >378 days) without maintenance immunosuppression. Neither chimerism nor long-term allograft survival were achieved in two recipients treated with the Belatacept regimen but with a lower, subtherapeutic dose of CyA. This study indicates that CD28/B7 blockade with Belatacept can provide a clinically applicable alternative to anti-CD154 mAb for promoting chimerism and renal allograft tolerance. PMID:25394378

  2. Mixed chimerism renders residual host dendritic cells incapable of alloimmunization of the marrow donor in the canine model of allogeneic marrow transplantation.

    PubMed

    Rosinski, Steven L; Graves, Scott S; Higginbotham, Deborah A; Storb, Rainer

    2015-10-02

    This study tested whether an alloimmune response can occur in the marrow donor when infused or injected with leukocytes from their mixed chimeric transplant recipient. Two mixed chimeras were produced after conditioning with three Gray total body irradiation, donor marrow infusion, and post-grafting immunosuppression. The marrow donors were then repeatedly infused and injected with leukocytes from their respective chimeric recipient. A donor lymphocyte infusion (DLI) into their mixed chimeras had no effect, even after the experiments were repeated. The presence of blood dendritic cells (DCs) of recipient origin was confirmed in chimeric recipients, as well as the presence of microchimerism in the marrow donors. Donor sensitization did occur following placement of a recipient skin graft that was confirmed following DLI into recipients that changed the mixed chimeras into full donor chimeras. These observations suggest that mixed chimerism renders recipient peripheral blood DCs incapable of inducing a donor T cell response.

  3. Finite element analysis and fracture resistance testing of a new intraradicular post

    PubMed Central

    YAMAMOTO, Eron Toshio Colauto; PAGANI, Clovis; da SILVA, Eduardo Galera; NORITOMI, Pedro Yoshito; UEHARA, André Yugou; KEMMOKU, Daniel Takanori

    2012-01-01

    Objectives The objective of the present study was to evaluate a prefabricated intraradicular threaded pure titanium post, designed and developed at the São José dos Campos School of Dentistry - UNESP, Brazil. This new post was designed to minimize stresses observed with prefabricated post systems and to improve cost-benefits. Material and methods Fracture resistance testing of the post/core/root complex, fracture analysis by microscopy and stress analysis by the finite element method were used for post evaluation. The following four prefabricated metal post systems were analyzed: group 1, experimental post; group 2, modification of the experimental post; group 3, Flexi Post, and group 4, Para Post. For the analysis of fracture resistance, 40 bovine teeth were randomly assigned to the four groups (n=10) and used for the fabrication of test specimens simulating the situation in the mouth. The test specimens were subjected to compressive strength testing until fracture in an EMIC universal testing machine. After fracture of the test specimens, their roots were sectioned and analyzed by microscopy. For the finite element method, specimens of the fracture resistance test were simulated by computer modeling to determine the stress distribution pattern in the post systems studied. Results The fracture test presented the following averages and standard deviation: G1 (45.63±8.77), G2 (49.98±7.08), G3 (43.84±5.52), G4 (47.61±7.23). Stress was homogenously distributed along the body of the intraradicular post in group 1, whereas high stress concentrations in certain regions were observed in the other groups. These stress concentrations in the body of the post induced the same stress concentration in root dentin. Conclusions The experimental post (original and modified versions) presented similar fracture resistance and better results in the stress analysis when compared with the commercial post systems tested (08/2008-PA/CEP). PMID:23032204

  4. Transcriptome Sequencing for the Detection of Chimeric Transcripts.

    PubMed

    Chu, Hsueh-Ting

    2016-01-01

    The occurrence of chimeric transcripts has been reported in many cancer cells and seen as potential biomarkers and therapeutic targets. Modern high-throughput sequencing technologies offer a way to investigate individual chimeric transcripts and the systematic information of associated gene expressions about underlying genome structural variations and genomic interactions. The detection methods of finding chimeric transcripts from massive amount of short read sequence data are discussed here. Both assembly-based and alignment-based methods are used for the investigation of chimeric transcripts.

  5. Humanization of excretory pathway in chimeric mice with humanized liver.

    PubMed

    Okumura, Hirotoshi; Katoh, Miki; Sawada, Toshiro; Nakajima, Miki; Soeno, Yoshinori; Yabuuchi, Hikaru; Ikeda, Toshihiko; Tateno, Chise; Yoshizato, Katsutoshi; Yokoi, Tsuyoshi

    2007-06-01

    The liver of a chimeric urokinase-type plasminogen activator (uPA)(+/+)/severe combined immunodeficient (SCID) mouse line recently established in Japan could be replaced by more than 80% with human hepatocytes. We previously reported that the chimeric mice with humanized liver could be useful as a human model in studies on drug metabolism and pharmacokinetics. In the present study, the humanization of an excretory pathway was investigated in the chimeric mice. Cefmetazole (CMZ) was used as a probe drug. The CMZ excretions in urine and feces were 81.0 and 5.9% of the dose, respectively, in chimeric mice and were 23.7 and 59.4% of the dose, respectively, in control uPA(-/-)/SCID mice. Because CMZ is mainly excreted in urine in humans, the excretory profile of chimeric mice was demonstrated to be similar to that of humans. In the chimeric mice, the hepatic mRNA expression of human drug transporters could be quantified. On the other hand, the hepatic mRNA expression of mouse drug transporters in the chimeric mice was significantly lower than in the control uPA(-/-)/SCID mice. In conclusion, chimeric mice exhibited a humanized profile of drug excretion, suggesting that this chimeric mouse line would be a useful animal model in excretory studies.

  6. Blood ties: chimerism can mask twin discordance in high-throughput sequencing.

    PubMed

    Erlich, Yaniv

    2011-04-01

    Twin studies have long provided a means to separate the contributions of genetic and environmental factors. A recent pioneering report by Baranzini et al. presented an analysis of the complete genomes and epigenomes of a monozygotic (MZ) twin pair discordant for multiple sclerosis. This failed to find any difference between the twins, raising doubts regarding the value of whole-genome twin studies for defining disease susceptibility alleles. However, the study was carried out with DNA extracted from blood. In many cases, the hematopoietic lineages of MZ twins are chimeric due to twin-to-twin exchange of hematopoietic stem cells during embryogenesis. We therefore wondered how chimerism might impact the ability to identify genetic differences. We inferred the blood chimerism rates and profiles of more than 30 discordant twin cases from a wide variety of medical conditions. We found that the genotype compositions of the twins were highly similar. We then benchmarked the performance of SNP callers to detect discordant variations using high-throughput sequencing data. Our analysis revealed that chimerism patterns, well within the range normally observed in MZ twins, greatly reduce the sensitivity of SNP calls. This raises questions regarding any conclusions of genomic homogeneity that might be drawn from studies of blood-derived twin DNA.

  7. reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

    PubMed Central

    Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

    2016-01-01

    Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contributes to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), that enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the following iterations. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. PMID:26419769

  8. reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

    NASA Astrophysics Data System (ADS)

    Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

    2015-11-01

    Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website.

  9. An Analysis of Access Barriers to Post-Secondary Education

    ERIC Educational Resources Information Center

    Vaccaro, Angelo

    2012-01-01

    Post-Secondary Education (PSE) in Ontario and in Canada has expanded on both the demand and supply sides in the last couple of decades. As of 2007, 50% of the population aged 18 to 24 was enrolled in post-secondary institutions. Enrolment in Ontario universities grew from 10,000 in 1960 to approximately 400,000 in 2007 (Clark, Moran, Skolnik,…

  10. Stress analysis of different post-luting systems: a three-dimensional finite element analysis.

    PubMed

    Romeed, S A; Dunne, S M

    2013-03-01

    The longevity of endodontically treated teeth is usually determined by the adequacy of root canal treatments, coronal seal and favourable stress distribution within the remaining tooth tissues. The aim of this study was to investigate the influence of post material and luting cement on the biomechanics of endodontically treated teeth using three-dimensional finite element analysis (3-D FEA). A 3 mm section of endodontically treated canine tooth was scanned and reconstructed for 3-D modelling and FE analyses. A metal post (MP) and a glass fibre post (GFP) were tested individually with four luting cements [zinc phosphate (ZPH), glass ionomer (GI), resin modified glass ionomer (RMGI) and resin based cements (RC)]. A push-out test was conducted by subjecting all models to 100 N perpendicular loading at the post. The maximum stresses generated along the MP-cement interface were significantly higher than corresponding stresses in the GFP-cement interface regardless of the cement type. GFP generated seven times higher stresses within the root dentine than metal posts when ZPH and GI were used, and three times higher when RMGI and RC were used. The displacement of GFP was double (50 μ) the displacement of MP (20 μ) in all groups. The low elastic modulus of GFP generated lower stresses along its interface and higher stresses within the root dentine, therefore the probability of debonding and root fracture in the GFP group was lower. © 2013 Australian Dental Association.

  11. Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

    PubMed Central

    Borel, Christelle; Mudge, Jonathan M.; Howald, Cédric; Foissac, Sylvain; Ucla, Catherine; Chrast, Jacqueline; Ribeca, Paolo; Martin, David; Murray, Ryan R.; Yang, Xinping; Ghamsari, Lila; Lin, Chenwei; Bell, Ian; Dumais, Erica; Drenkow, Jorg; Tress, Michael L.; Gelpí, Josep Lluís; Orozco, Modesto; Valencia, Alfonso; van Berkum, Nynke L.; Lajoie, Bryan R.; Vidal, Marc; Stamatoyannopoulos, John; Batut, Philippe; Dobin, Alex; Harrow, Jennifer; Hubbard, Tim; Dekker, Job; Frankish, Adam; Salehi-Ashtiani, Kourosh; Reymond, Alexandre; Antonarakis, Stylianos E.; Guigó, Roderic; Gingeras, Thomas R.

    2012-01-01

    The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast to human has blurred the definition and physical boundaries of genes. Using multiple analysis approaches we have characterized individual gene boundaries mapping on human chromosomes 21 and 22. Analyses of the locations of the 5′ and 3′ transcriptional termini of 492 protein coding genes revealed that for 85% of these genes the boundaries extend beyond the current annotated termini, most often connecting with exons of transcripts from other well annotated genes. The biological and evolutionary importance of these chimeric transcripts is underscored by (1) the non-random interconnections of genes involved, (2) the greater phylogenetic depth of the genes involved in many chimeric interactions, (3) the coordination of the expression of connected genes and (4) the close in vivo and three dimensional proximity of the genomic regions being transcribed and contributing to parts of the chimeric RNAs. The non-random nature of the connection of the genes involved suggest that chimeric transcripts should not be studied in isolation, but together, as an RNA network. PMID:22238572

  12. The rapid generation of chimerical genes expanding protein diversity in zebrafish.

    PubMed

    Fu, Beide; Chen, Ming; Zou, Ming; Long, Manyuan; He, Shunping

    2010-11-24

    Variation of gene number among species indicates that there is a general process of new gene origination. One of the major mechanism providing raw materials for the origin of new genes is gene duplication. Retroposition, as a special type of gene duplication- the RNA-based duplication, has been found to play an important role in new gene evolution in mammals and plants, but little is known about the process in the teleostei genome. Here we screened the zebrafish genome for identification of retrocopies and new chimerical retrogenes and investigated their origination and evolution. We identified 652 retrocopies, of which 440 are intact retrogenes and 212 are pseudogenes. Retrocopies have long been considered evolutionary dead ends without functional significance due to the presumption that retrocopies lack the regulatory element needed for expression. However, 437 transcribed retrocopies were identified from all of the retrocopies. This discovery combined with the substitution analysis suggested that the majority of all retrocopies are subject to negative selection, indicating that most of the retrocopies may be functional retrogenes. Moreover, we found that 95 chimerical retrogenes had recruited new sequences from neighboring genomic regions that formed de novo splice sites, thus generating new intron-containing chimeric genes. Based on our analysis of 38 pairs of orthologs between Cyprinus carpio and Danio rerio, we found that the synonymous substitution rate of zebrafish genes is 4.13×10⁻⁹ substitution per silent site per year. We also found 10 chimerical retrogenes that were created in the last 10 million years, which is 7.14 times the rate of 0.14 chimerical retrogenes per million years in the primate lineage toward human and 6.25 times the rate of 0.16 chimerical genes per million years in Drosophila. This is among the most rapid rates of generation of chimerical genes, just next to the rice. There is compelling evidence that much of the extensive

  13. Finite element analysis of stress distribution in four different endodontic post systems in a model canine.

    PubMed

    Chen, Aijie; Feng, Xiaoli; Zhang, Yanli; Liu, Ruoyu; Shao, Longquan

    2015-01-01

    To investigate the stress distribution in a maxillary canine restored with each of four different post systems at different levels of alveolar bone loss. Two-dimensional finite element analysis (FEA) was performed by modeling a severely damaged canine with four different post systems: CAD/CAM zirconia, CAD/CAM glass fiber, cast titanium, and cast gold. A force of 100 N was applied to the crown, and the von Mises stresses were obtained. FEA revealed that the CAD/CAM zirconia post system produced the lowest maximum von Mises stress in the dentin layer at 115.8 MPa, while the CAD/CAM glass fiber post produced the highest stress in the dentin at 518.2 MPa. For a severely damaged anterior tooth, a zirconia post system is the best choice while a cast gold post ranks second. The CAD/CAM glass fiber post is least recommended in terms of stress level in the dentin.

  14. Lung rejection occurs in lung transplant recipients with blood chimerism.

    PubMed

    Knoop, C; Andrien, M; Defleur, V; Antoine, M; de Francquen, P; Goldman, M; Estenne, M

    1997-07-15

    It has been postulated that chimerism after transplantation might promote graft acceptance. In the present study, we prospectively assessed blood chimerism in 10 lung transplant recipients during the first posttransplant year and investigated whether chimerism was associated with an immunologically stable situation of the graft. The recipients' peripheral blood mononuclear cells were obtained before transplantation and at various time points during the first postoperative year. Donor cells were detected using nested polymerase chain reaction amplification of a donor-specific HLA-DRB1 allele. Clinical graft acceptance was determined by the number of rejection episodes. The incidence of blood chimerism was high during the first 3 postoperative months and then decreased over time. All patients experienced at least one acute rejection episode, and three patients developed chronic rejection. We, thus, conclude that rejection of the lung allograft may occur in the presence of blood chimerism.

  15. Selective targeting of human cells by a chimeric adenovirus vector containing a modified fiber protein.

    PubMed Central

    Stevenson, S C; Rollence, M; Marshall-Neff, J; McClelland, A

    1997-01-01

    The adenovirus fiber protein is responsible for attachment of the virion to unidentified cell surface receptors. There are at least two distinct adenovirus fiber receptors which interact with the group B (Ad3) and group C (Ad5) adenoviruses. We have previously shown by using expressed adenovirus fiber proteins that it is possible to change the specificity of the fiber protein by exchanging the head domain with another serotype which recognizes a different receptor (S. C. Stevenson et al., J. Virol. 69:2850-2857, 1995). A chimeric fiber cDNA containing the Ad3 fiber head domain fused to the Ad5 fiber tail and shaft was incorporated into the genome of an adenovirus vector with E1 and E3 deleted encoding beta-galactosidase to generate Av9LacZ4, an adenovirus particle which contains a chimeric fiber protein. Western blot analysis of the chimeric fiber vector confirmed expression of the chimeric fiber protein and its association with the adenovirus capsid. Transduction experiments with fiber protein competitors demonstrated the altered receptor tropism of the chimeric fiber vector compared to that of the parental Av1LacZ4 vector. Transduction of a panel of human cell lines with the chimeric and parental vectors provided evidence for a different cellular distribution of the Ad5 and Ad3 receptors. Three cell lines (THP-1, MRC-5, and FaDu) were more efficiently transduced by the vector containing the Ad3 fiber head than by the Ad5 fiber vector. In contrast, human coronary artery endothelial cells were transduced more readily with the vector containing the Ad5 fiber than with the chimeric fiber vector. HeLa and human umbilical vein endothelial cells were transduced at equivalent levels compared with human diploid fibroblasts, which were refractory to transduction with both vectors. These results provide evidence for the differential expression of the Ad5 and Ad3 receptors on human cell lines derived from clinically relevant target tissues. Furthermore, we show that exchange

  16. Ethical acceptability of research on human-animal chimeric embryos: summary of opinions by the Japanese Expert Panel on Bioethics.

    PubMed

    Mizuno, Hiroshi; Akutsu, Hidenori; Kato, Kazuto

    2015-01-01

    Human-animal chimeric embryos are embryos obtained by introducing human cells into a non-human animal embryo. It is envisaged that the application of human-animal chimeric embryos may make possible many useful research projects including producing three-dimensional human organs in animals and verification of the pluripotency of human ES cells or iPS cells in vivo. The use of human-animal chimeric embryos, however, raises several ethical and moral concerns. The most fundamental one is that human-animal chimeric embryos possess the potential to develop into organisms containing human-derived tissue, which may lead to infringing upon the identity of the human species, and thus impairing human dignity. The Japanese Expert Panel on Bioethics in the Cabinet Office carefully considered the scientific significance and ethical acceptability of the issue and released its "Opinions regarding the handling of research using human-animal chimeric embryos". The Panel proposed a framework of case-by-case review, and suggested that the following points must be carefully reviewed from the perspective of ethical acceptability: (a) Types of animal embryos and types of animals receiving embryo transfers, particularly in dealing with non-human primates; (b) Types of human cells and organs intended for production, particularly in dealing with human nerve or germ cells; and (c) Extent of the period required for post-transfer studies. The scientific knowledge that can be gained from transfer into an animal uterus and from the production of an individual must be clarified to avoid unnecessary generation of chimeric animals. The time is ripe for the scientific community and governments to start discussing the ethical issues for establishing a global consensus.

  17. [Discussion on the building of post market risk analysis method in hemodialysis device].

    PubMed

    Xu, Honglei; Peng, Xiaolong; Tian, Xiaojun; Wang, Peilian

    2014-09-01

    This paper discussed the building of post market risk analysis method in hemodialysis device from the point of government supervision. By proposing practical research methods for post market risk identification and estimation on hemodialysis device, providing technical guidance for government to put risk management of hemodialysis device into effect, and offering reference for enterprises to carry out post market risk evaluation on their products as well.

  18. Hybridization accompanying FRET event in labeled natural nucleoside-unnatural nucleoside containing chimeric DNA duplexes.

    PubMed

    Bag, Subhendu Sekhar; Das, Suman K; Pradhan, Manoj Kumar; Jana, Subhashis

    2016-09-01

    Förster resonance energy transfer (FRET) is a highly efficient strategy in illuminating the structures, structural changes and dynamics of DNA, proteins and other biomolecules and thus is being widely utilized in studying such phenomena, in designing molecular/biomolecular probes for monitoring the hybridization event of two single stranded DNA to form duplex, in gene detection and in many other sensory applications in chemistry, biology and material sciences. Moreover, FRET can give information about the positional status of chromophores within the associated biomolecules with much more accuracy than other methods can yield. Toward this end, we want to report here the ability of fluorescent unnatural nucleoside, triazolylphenanthrene ((TPhen)BDo) to show FRET interaction upon hybridization with fluorescently labeled natural nucleosides, (Per)U or (OxoPy)U or (Per)U, forming two stable chimeric DNA duplexes. The pairing selectivity and the thermal duplex stability of the chimeric duplexes are higher than any of the duplexes with natural nucleoside formed. The hybridization results in a Förster resonance energy transfer (FRET) from donor triazolylphenanthrene of (TPhen)BDo to acceptor oxopyrene of (OxoPy)U and/or to perylene chromophore of (Per)U, respectively, in two chimeric DNA duplexes. Therefore, we have established the FRET process in two chimeric DNA duplexes wherein a fluorescently labeled natural nucleoside ((OxoPy)U or (Per)U) paired against an unnatural nucleoside ((TPhen)BDo) without sacrificing the duplex stability and B-DNA conformation. The hybridization accompanying FRET event in these classes of interacting fluorophores is new. Moreover, there is no report of such designed system of chimeric DNA duplex. Our observed phenomenon and the design can potentially be exploited in designing more of such efficient FRET pairs for useful application in the detection and analysis of biomolecular interactions and in material science application. Copyright

  19. Design and analysis of post-marketing research.

    PubMed

    Zhou, Xiao-Hua Andrew; Yang, Wei

    2013-07-01

    A post-marketing study is an integral part of research that helps to ensure a favorable risk-benefit profile for approved drugs used in the market. Because most of post-marketing studies use observational designs, which are liable to confounding, estimation of the causal effect of a drug versus a comparative one is very challenging. This article focuses on methodological issues of importance in designing and analyzing studies to evaluate the safety of marketed drugs, especially marketed traditional Chinese medicine (TCM) products. Advantages and limitations of the current designs and analytic methods for postmarketing studies are discussed, and recommendations are given for improving the validity of postmarketing studies in TCM products.

  20. Zygotes segregate entire parental genomes in distinct blastomere lineages causing cleavage-stage chimerism and mixoploidy

    PubMed Central

    Destouni, Aspasia; Zamani Esteki, Masoud; Catteeuw, Maaike; Tšuiko, Olga; Dimitriadou, Eftychia; Smits, Katrien; Kurg, Ants; Salumets, Andres; Van Soom, Ann; Voet, Thierry; Vermeesch, Joris R.

    2016-01-01

    Dramatic genome dynamics, such as chromosome instability, contribute to the remarkable genomic heterogeneity among the blastomeres comprising a single embryo during human preimplantation development. This heterogeneity, when compatible with life, manifests as constitutional mosaicism, chimerism, and mixoploidy in live-born individuals. Chimerism and mixoploidy are defined by the presence of cell lineages with different parental genomes or different ploidy states in a single individual, respectively. Our knowledge of their mechanistic origin results from indirect observations, often when the cell lineages have been subject to rigorous selective pressure during development. Here, we applied haplarithmisis to infer the haplotypes and the copy number of parental genomes in 116 single blastomeres comprising entire preimplantation bovine embryos (n = 23) following in vitro fertilization. We not only demonstrate that chromosome instability is conserved between bovine and human cleavage embryos, but we also discovered that zygotes can spontaneously segregate entire parental genomes into different cell lineages during the first post-zygotic cleavage division. Parental genome segregation was not exclusively triggered by abnormal fertilizations leading to triploid zygotes, but also normally fertilized zygotes can spontaneously segregate entire parental genomes into different cell lineages during cleavage of the zygote. We coin the term “heterogoneic division” to indicate the events leading to noncanonical zygotic cytokinesis, segregating the parental genomes into distinct cell lineages. Persistence of those cell lines during development is a likely cause of chimerism and mixoploidy in mammals. PMID:27197242

  1. Market segmentation and analysis of Japan's residential post and beam construction market.

    Treesearch

    Joseph A. Roos; Ivan L. Eastin; Hisaaki. Matsuguma

    2005-01-01

    A mail survey of Japanese post and beam builders was conducted to measure their level of ethnocentrism, market orientation, risk aversion, and price consciousness. The data were analyzed utilizing factor and cluster analysis. The results showed that Japanese post and beam builders can be divided into three distinct market segments: open to import...

  2. Chimeric conundra: are nucleomorphs and chromists monophyletic or polyphyletic?

    PubMed Central

    Cavalier-Smith, T; Allsopp, M T; Chao, E E

    1994-01-01

    All algae with chloroplasts located not freely in the cytosol, but inside two extra membranes, probably arose chimerically by the permanent fusion of two different eukaryote cells: a protozoan host and a eukaryotic algal symbiont. Two such groups, cryptomonads (phylum Cryptista) and Chlorarachniophyta, still retain a DNA-containing relic of the nucleus of the algal endosymbiont, known as the nucleomorph, as well as the host nucleus. These two phyla were traditionally assumed to have obtained their chloroplasts separately by two independent symbioses. We have sequenced the nuclear and the nucleomorph 18S rRNA genes of the nonphotosynthetic cryptomonad Chilomonas paramecium. Our phylogenetic analysis suggests that cryptomonad and chlorarachniophyte nucleomorphs may be related to each other and raises the possibility that both phyla may have diverged from a common ancestral chimeric cell that originated by a single endosymbiosis involving an algal endosymbiont related to the ancestor of red algae. But, because of the instability of the molecular trees when different taxa are added, there is insufficient evidence to overturn the traditional view that Chlorarachnion nucleomorphs evolved separately from a relative of green algae. The four phyla that contain chromophyte algae (those with chlorophyll c--i.e., Cryptista, Heterokonta, Haptophyta, Dinozoa) are distantly related to each other and to Chlorarachniophyta on our trees. However, all of the photosynthetic taxa within each of these four phyla radiate from each other very substantially after the radiation of the four phyla themselves. This favors the view that the common ancestor of these four phyla was not photosynthetic and that chloroplasts were implanted separately into each much more recently. This probable polyphyly of the chromophyte algae, if confirmed, would make it desirable to treat Cryptista, Heterokonta, and Haptophyta as separate kingdoms, rather than to group them together in the single kingdom

  3. Novel fusion genes and chimeric transcripts in ependymal tumors.

    PubMed

    Olsen, Thale Kristin; Panagopoulos, Ioannis; Gorunova, Ludmila; Micci, Francesca; Andersen, Kristin; Kilen Andersen, Hege; Meling, Torstein R; Due-Tønnessen, Bernt; Scheie, David; Heim, Sverre; Brandal, Petter

    2016-12-01

    We have previously identified two ALK rearrangements in a subset of ependymal tumors using a combination of cytogenetic data and RNA sequencing. The aim of this study was to perform an unbiased search for fusion transcripts in our entire series of ependymal tumors. Fusion analysis was performed using the FusionCatcher algorithm on 12 RNA-sequenced ependymal tumors. Candidate transcripts were prioritized based on the software's filtering and manual visualization using the BLAST (Basic Local Alignment Search Tool) and BLAT (BLAST-like alignment tool) tools. Genomic and reverse transcriptase PCR with subsequent Sanger sequencing was used to validate the potential fusions. Fluorescent in situ hybridization (FISH) using locus-specific probes was also performed. A total of 841 candidate chimeric transcripts were identified in the 12 tumors, with an average of 49 unique candidate fusions per tumor. After algorithmic and manual filtering, the final list consisted of 24 potential fusion events. Raw RNA-seq read sequences and PCR validation supports two novel fusion genes: a reciprocal fusion gene involving UQCR10 and C1orf194 in an adult spinal ependymoma and a TSPAN4-CD151 fusion gene in a pediatric infratentorial anaplastic ependymoma. Our previously reported ALK rearrangements and the RELA and YAP1 fusions found in supratentorial ependymomas were until now the only known fusion genes present in ependymal tumors. The chimeric transcripts presented here are the first to be reported in infratentorial or spinal ependymomas. Further studies are required to characterize the genomic rearrangements causing these fusion genes, as well as the frequency and functional importance of the fusions. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  4. chimeraviz: a tool for visualizing chimeric RNA.

    PubMed

    Lågstad, Stian; Zhao, Sen; Hoff, Andreas M; Johannessen, Bjarne; Lingjærde, Ole Christian; Skotheim, Rolf I

    2017-09-15

    Advances in high-throughput RNA sequencing have enabled more efficient detection of fusion transcripts, but the technology and associated software used for fusion detection from sequencing data often yield a high false discovery rate. Good prioritization of the results is important, and this can be helped by a visualization framework that automatically integrates RNA data with known genomic features. Here we present chimeraviz , a Bioconductor package that automates the creation of chimeric RNA visualizations. The package supports input from nine different fusion-finder tools: deFuse, EricScript, InFusion, JAFFA, FusionCatcher, FusionMap, PRADA, SOAPfuse and STAR-FUSION. chimeraviz is an R package available via Bioconductor ( https://bioconductor.org/packages/release/bioc/html/chimeraviz.html ) under Artistic-2.0. Source code and support is available at GitHub ( https://github.com/stianlagstad/chimeraviz ). rolf.i.skotheim@rr-research.no. Supplementary data are available at Bioinformatics online.

  5. Stress distribution of endodontically treated teeth with titanium alloy post and carbon fiber post with different alveolar bone height: A three-dimensional finite element analysis.

    PubMed

    Singh, S Vijay; Bhat, Manohar; Gupta, Saurabh; Sharma, Deepak; Satija, Harsha; Sharma, Sumeet

    2015-01-01

    A three-dimensional (3D) finite element analysis (FEA) on the stress distribution of endodontically treated teeth with titanium alloy post and carbon fiber post with different alveolar bone height. The 3D model was fabricated using software to represent an endodontically treated mandibular second premolar with post and restored with a full ceramic crown restoration, which was then analyzed using FEA using FEA ANSYS Workbench V13.0 (ANSYS Inc., Canonsburg, Pennsylvania, U.S.A) software. The FEA showed the maximum stresses of 137.43 Mpa in dentin with alveolar bone height of 4 mm when the titanium post was used, 138.48 Mpa when carbon fiber post was used as compared to 105.91 Mpa in the model with alveolar bone height of 2 mm from the cement enamel junction (CEJ) when the titanium post was used and 107.37 Mpa when the carbon fiber post was used. Stress was observed more in alveolar bone height level of 4 mm from CEJ than 2 mm from CEJ. Stresses in the dentin were almost similar when the carbon fiber post was compared to titanium post. However, stresses in the post and the cement were much higher when titanium post was used as compared to carbon fiber post.

  6. Stress distribution of endodontically treated teeth with titanium alloy post and carbon fiber post with different alveolar bone height: A three-dimensional finite element analysis

    PubMed Central

    Singh, S. Vijay; Bhat, Manohar; Gupta, Saurabh; Sharma, Deepak; Satija, Harsha; Sharma, Sumeet

    2015-01-01

    Objective: A three-dimensional (3D) finite element analysis (FEA) on the stress distribution of endodontically treated teeth with titanium alloy post and carbon fiber post with different alveolar bone height. Materials and Methods: The 3D model was fabricated using software to represent an endodontically treated mandibular second premolar with post and restored with a full ceramic crown restoration, which was then analyzed using FEA using FEA ANSYS Workbench V13.0 (ANSYS Inc., Canonsburg, Pennsylvania, U.S.A) software. Results: The FEA showed the maximum stresses of 137.43 Mpa in dentin with alveolar bone height of 4 mm when the titanium post was used, 138.48 Mpa when carbon fiber post was used as compared to 105.91 Mpa in the model with alveolar bone height of 2 mm from the cement enamel junction (CEJ) when the titanium post was used and 107.37 Mpa when the carbon fiber post was used. Conclusions: Stress was observed more in alveolar bone height level of 4 mm from CEJ than 2 mm from CEJ. Stresses in the dentin were almost similar when the carbon fiber post was compared to titanium post. However, stresses in the post and the cement were much higher when titanium post was used as compared to carbon fiber post. PMID:26430375

  7. Post Buckling Progressive Failure Analysis of Composite Laminated Stiffened Panels

    NASA Astrophysics Data System (ADS)

    Anyfantis, Konstantinos N.; Tsouvalis, Nicholas G.

    2012-06-01

    The present work deals with the numerical prediction of the post buckling progressive and final failure response of stiffened composite panels based on structural nonlinear finite element methods. For this purpose, a progressive failure model (PFM) is developed and applied to predict the behaviour of an experimentally tested blade-stiffened panel found in the literature. Failure initiation and propagation is calculated, owing to the accumulation of the intralaminar failure modes induced in fibre reinforced composite materials. Hashin failure criteria have been employed in order to address the fiber and matrix failure modes in compression and tension. On the other hand, the Tsai-Wu failure criterion has been utilized for addressing shear failure. Failure detection is followed with the introduction of corresponding material degradation rules depending on the individual failure mechanisms. Failure initiation and failure propagation as well as the post buckling ultimate attained load have been numerically evaluated. Final failure behaviour of the simulated stiffened panel is due to sudden global failure, as concluded from comparisons between numerical and experimental results being in good agreement.

  8. Utility of saliva and hair follicles in donor selection for hematopoietic stem cell transplantation and chimerism monitoring.

    PubMed

    Kaur, Gurvinder; Kumar, Neeraj; Nandakumar, Ramya; Rapthap, Chowphi C; Sharma, Gaurav; Neolia, Shekhar; Kumra, Heena; Mahalwar, Prateek; Garg, Abhinav; Kumar, Sunil; Kaur, Jasmeet; Hakim, Mrinali; Kumar, Lalit; Mehra, Narinder K

    2012-01-01

    Selection of an HLA identical donor is a critical pre-requisite for successful hematopoietic stem cell transplantation (HSCT). Most transplant centers utilize blood as the most common source of DNA for HLA testing. However, obtaining blood through phlebotomy is often challenging in patients with conditions like severe leucopenia or hemophilia, pediatric and elderly patients. We have used a simple in-house protocol and shown that HLA genotypes obtained on DNA extracted from saliva or hair are concordant with blood and hence can be used for selection of donors for HSCT or organ transplantation. Similarly, for post-HSCT chimerism monitoring, non-availability of pre-transplant DNA samples poses a major limitation of reference STR fingerprints. This study shows that DNA obtained post-HSCT from hair follicles can be used to generate pre-transplant patient specific fingerprints while the STR profiles obtained in saliva samples cannot as these display a mixed state of chimerism.

  9. Association of mixed hematopoietic chimerism with elevated circulating autoantibodies and chronic graft-versus-host disease occurrence

    PubMed Central

    Perruche, Sylvain; Marandin, Aliette; Kleinclauss, François M.; Angonin, Régis; Fresnay, Stéphanie; Baron, Marie Hélène; Tiberghien, Pierre; Saas, Philippe

    2006-01-01

    Background Use of a reduced intensity conditioning regimen before an allogeneic hematopoietic cell transplantation is frequently associated with an early state of mixed hematopoietic chimerism. Such a co-existence of both host and donor hematopoietic cells may influence post-transplant alloreactivity and may affect the occurrence and severity of acute and chronic graft-versus-host disease (GVHD) as well as the intensity of the graft-versus-leukemia effect. Here we evaluated the relation between chimerism state after reduced intensity conditioning transplantation (RICT), auto-antibody production and chronic GVHD (cGVHD)-related pathology. Methods Chimerism state, circulating anti-cardiolipin and anti-double stranded DNA auto-antibody (Ab) titers as well as occurrence of cGVHD-like lesions were investigated in a murine RICT model. Results We observed a novel association between mixed chimerism state, high levels of pathogenic IgG auto-Abs and subsequent development of cGVHD-like lesions. Furthermore, we found that the persistence of host B cells, but not dendritic cell origin or subset, was a factor associated with the appearance of cGVHD-like lesions. The implication of host B cells was confirmed by a host origin of auto-Abs. Conclusions Recipient B cell persistence may therefore contribute to the frequency and/or severity of cGVHD after RICT. PMID:16495806

  10. [Monitoring of chimerism in myeloid cells sorting of transplanted patients with acute myeloid leukaemia: a study from Lyon (France)].

    PubMed

    Mollet, I; Giannoli, C; Rigal, D; Michallet, M; Dubois, V

    2012-04-01

    Chimerism analysis after allogeneic haematopoietic stem cell transplantation has been used to document engraftment and to adapt therapy promptly. The aim of this study was to document engraftment and to detect as soon as possible relapse in patients with acute myeloid leukaemia who underwent stem cell transplantation. Real-time quantitative polymerase chain reaction is a highly sensitive and reproducible technology. It is useful in some disease to target selected sub-populations in order to have an earlier detection of relapse on cell fractions. In the acute myeloid leukaemia (n=65), analysis of the chimerism on whole peripheral blood cells and bone marrow cells, CD3+ cells, specific myeloid CD33+ cells (from blood) and CD34+ cells (from bone marrow) is of importance. After transplant, 25 patients relapsed (38%), three massively, with chimerism detection in whole blood and bone marrow and 22 insidiously following two different schemes (GRI and GRII). In GRI, (n=13): chimerism of CD33+ and CD34+ cellular fractions allowed an early detection of relapse in 100% of cases undetected in whole cells whereas in GRII (n=9): myeloid cells could identified relapse in 89% of cases when whole blood cells and CD3+ cells expressed a mixed chimerism. This study highlighted the importance of sub-cellular population chimerism documentation enable to ascertain a stable engraftment and to detect early relapse. The selection of sub-cellular population studied with high sensitive technology allows a rapid and efficient intervention before the onset of clinical signs in patient with acute myeloid leukaemia and could improve the patient's follow-up. Copyright © 2010 Elsevier Masson SAS. All rights reserved.

  11. Stable mixed chimerism and tolerance to human organ transplants.

    PubMed

    Strober, Samuel

    2015-04-03

    Tolerance to combined kidney and hematopoietic cell transplant has been achieved in humans after establishment of mixed chimerism allowing for the withdrawal of immunosuppressive drugs. The seminal contributions of Ray Owen provided the scientific basis for the human protocol.

  12. Chimeric alignment by dynamic programming: Algorithm and biological uses

    SciTech Connect

    Komatsoulis, G.A.; Waterman, M.S.

    1997-12-01

    A new nearest-neighbor method for detecting chimeric 16S rRNA artifacts generated during PCR amplification from mixed populations has been developed. The method uses dynamic programming to generate an optimal chimeric alignment, defined as the highest scoring alignment between a query and a concatenation of a 5{prime} and a 3{prime} segment from two separate entries from a database of related sequences. Chimeras are detected by studying the scores and form of the chimeric and global sequence alignments. The chimeric alignment method was found to be marginally more effective than k-tuple based nearest-neighbor methods in simulation studies, but its most effective use is in concert with k-tuple methods. 15 refs., 3 figs., 1 tab.

  13. Trends in Post-mastectomy Reconstruction: A SEER Database Analysis

    PubMed Central

    Lang, Julie E.; Summers, Danielle E.; Cui, Haiyan; Carey, Joseph N.; Viscusi, Rebecca K.; Hurst, Craig A.; Waer, Amy L.; Ley, Michele L B.; Sener, Stephen F.; Vijayasekaran, Aparna

    2014-01-01

    Background and Objectives This study was performed to investigate recent trends and factors associated with immediate breast reconstruction (IBR) using a large population-based registry. We hypothesized that rates of IBR have increased since passage of the Women’s Health and Cancer Rights Act of 1998. Methods The SEER (Surveillance, Epidemiology and End Results) database was used to evaluate Stage I–III breast cancer (BC) patients who underwent total mastectomy from 1998–2008. Univariate and multivariate analyses were performed to study predictors of IBR. Results Of 112,348 patients with BC treated by mastectomy, 18,001 (16%) had IBR. Rates of IBR increased significantly from 1998–2008 (p<0.0001). Use of IBR significantly decreased as patient age increased (p<0.0001), as stage increased (p<0.0001), and as the number of positive lymph nodes increased (p<0.0001). Estrogen receptor +/progesterone receptor + (ER+/PR+) patients had significantly higher IBR rates than ER−/PR− patients (p<0.0001). IBR was used in 3615 of 25,823 (14.0%) of patients having post-mastectomy radiation (XRT) and in 14,188 of 86,513 (16.4%) of those not having XRT (p<0.0001). Conclusions The utilization of IBR has increased significantly over the last decade. IBR was found to be significantly associated with age, race, geographical region, stage, ER, grade, LN status, and XRT (p<0.0001). PMID:23861196

  14. Orion Exploration Flight Test Post-Flight Inspection and Analysis

    NASA Technical Reports Server (NTRS)

    Miller, J. E.; Berger, E. L.; Bohl, W. E.; Christiansen, E. L.; Davis, B. A.; Deighton, K. D.; Enriquez, P. A.; Garcia, M. A.; Hyde, J. L.; Oliveras, O. M.

    2017-01-01

    The multipurpose crew vehicle, Orion, is being designed and built for NASA to handle the rigors of crew launch, sustainment and return from scientific missions beyond Earth orbit. In this role, the Orion vehicle is meant to operate in the space environments like the naturally occurring meteoroid and the artificial orbital debris environments (MMOD) with successful atmospheric reentry at the conclusion of the flight. As a result, Orion's reentry module uses durable porous, ceramic tiles on almost thirty square meters of exposed surfaces to accomplish both of these functions. These durable, non-ablative surfaces maintain their surface profile through atmospheric reentry; thus, they preserve any surface imperfections that occur prior to atmospheric reentry. Furthermore, Orion's launch abort system includes a shroud that protects the thermal protection system while awaiting launch and during ascent. The combination of these design features and a careful pre-flight inspection to identify any manufacturing imperfections results in a high confidence that damage to the thermal protection system identified post-flight is due to the in-flight solid particle environments. These favorable design features of Orion along with the unique flight profile of the first exploration flight test of Orion (EFT-1) have yielded solid particle environment measurements that have never been obtained before this flight.

  15. Digital PCR Panel for Sensitive Hematopoietic Chimerism Quantification after Allogeneic Stem Cell Transplantation

    PubMed Central

    Stahl, Tanja; Rothe, Caroline; Böhme, Manja U.; Kohl, Aloisa; Kröger, Nicolaus; Fehse, Boris

    2016-01-01

    Accurate and sensitive determination of hematopoietic chimerism is a crucial diagnostic measure after allogeneic stem cell transplantation to monitor engraftment and potentially residual disease. Short tandem repeat (STR) amplification, the current “gold standard” for chimerism assessment facilitates reliable accuracy, but is hampered by its limited sensitivity (≥1%). Digital PCR (dPCR) has been shown to combine exact quantification and high reproducibility over a very wide measurement range with excellent sensitivity (routinely ≤0.1%) and thus represents a promising alternative to STR analysis. We here aimed at developing a whole panel of digital-PCR based assays for routine diagnostic. To this end, we tested suitability of 52 deletion/insertion polymorphisms (DIPs) for duplex analysis in combination with either a reference gene or a Y-chromosome specific PCR. Twenty-nine DIPs with high power of discrimination and good performance were identified, optimized and technically validated. We tested the newly established assays on retrospective patient samples that were in parallel also measured by STR amplification and found excellent correlation. Finally, a screening plate for initial genotyping with DIP-specific duplex dPCR assays was designed for convenient assay selection. In conclusion, we have established a comprehensive dPCR system for precise and high-sensitivity measurement of hematopoietic chimerism, which should be highly useful for clinical routine diagnostics. PMID:27618030

  16. Chimeric mitochondrial peptides from contiguous regular and swinger RNA.

    PubMed

    Seligmann, Hervé

    2016-01-01

    Previous mass spectrometry analyses described human mitochondrial peptides entirely translated from swinger RNAs, RNAs where polymerization systematically exchanged nucleotides. Exchanges follow one among 23 bijective transformation rules, nine symmetric exchanges (X ↔ Y, e.g. A ↔ C) and fourteen asymmetric exchanges (X → Y → Z → X, e.g. A → C → G → A), multiplying by 24 DNA's protein coding potential. Abrupt switches from regular to swinger polymerization produce chimeric RNAs. Here, human mitochondrial proteomic analyses assuming abrupt switches between regular and swinger transcriptions, detect chimeric peptides, encoded by part regular, part swinger RNA. Contiguous regular- and swinger-encoded residues within single peptides are stronger evidence for translation of swinger RNA than previously detected, entirely swinger-encoded peptides: regular parts are positive controls matched with contiguous swinger parts, increasing confidence in results. Chimeric peptides are 200 × rarer than swinger peptides (3/100,000 versus 6/1000). Among 186 peptides with > 8 residues for each regular and swinger parts, regular parts of eleven chimeric peptides correspond to six among the thirteen recognized, mitochondrial protein-coding genes. Chimeric peptides matching partly regular proteins are rarer and less expressed than chimeric peptides matching non-coding sequences, suggesting targeted degradation of misfolded proteins. Present results strengthen hypotheses that the short mitogenome encodes far more proteins than hitherto assumed. Entirely swinger-encoded proteins could exist.

  17. Trends in post-mastectomy reconstruction: a SEER database analysis.

    PubMed

    Lang, Julie E; Summers, Danielle E; Cui, Haiyan; Carey, Joseph N; Viscusi, Rebecca K; Hurst, Craig A; Waer, Amy L; Ley, Michele L B; Sener, Stephen F; Vijayasekaran, Aparna

    2013-09-01

    This study was performed to investigate recent trends and factors associated with immediate breast reconstruction (IBR) using a large population-based registry. We hypothesized that rates of IBR have increased since passage of the Women's Health and Cancer Rights Act of 1998. The SEER (surveillance, epidemiology and end results) database was used to evaluate Stage I-III breast cancer (BC) patients who underwent total mastectomy from 1998 to 2008. Univariate and multivariate analyses were performed to study predictors of IBR. Of 112,348 patients with BC treated by mastectomy 18,001 (16%) had IBR. Rates of IBR increased significantly from 1998 to 2008 (P < 0.0001). Use of IBR significantly decreased as patient age increased (P < 0.0001), as stage increased (P < 0.0001), and as the number of positive lymph nodes increased (P < 0.0001). Estrogen receptor+/progesterone receptor+ (ER+/PR+) patients had significantly higher IBR rates than ER-/PR-patients (P < 0.0001). IBR was used in 3,615 of 25,823 (14.0%) of patients having post-mastectomy radiation (XRT) and in 14,188 of 86,513 (16.4%) of those not having XRT (P < 0.0001). The utilization of IBR has increased significantly over the last decade. IBR was found to be significantly associated with age, race, geographical region, stage, ER, grade, LN status, and XRT (P < 0.0001). Copyright © 2013 Wiley Periodicals, Inc.

  18. Calcium-stimulated autophosphorylation site of plant chimeric calcium/calmodulin-dependent protein kinase

    NASA Technical Reports Server (NTRS)

    Sathyanarayanan, P. V.; Siems, W. F.; Jones, J. P.; Poovaiah, B. W.

    2001-01-01

    The existence of two molecular switches regulating plant chimeric Ca(2+)/calmodulin-dependent protein kinase (CCaMK), namely the C-terminal visinin-like domain acting as Ca(2+)-sensitive molecular switch and calmodulin binding domain acting as Ca(2+)-stimulated autophosphorylation-sensitive molecular switch, has been described (Sathyanarayanan, P. V., Cremo, C. R., and Poovaiah, B. W. (2000) J. Biol. Chem. 275, 30417-30422). Here we report the identification of Ca(2+)-stimulated autophosphorylation site of CCaMK by matrix-assisted laser desorption ionization time of flight-mass spectrometry. Thr(267) was confirmed as the Ca(2+)-stimulated autophosphorylation site by post-source decay experiments and by site-directed mutagenesis. The purified T267A mutant form of CCaMK did not show Ca(2+)-stimulated autophosphorylation, autophosphorylation-dependent variable calmodulin affinity, or Ca(2+)/calmodulin stimulation of kinase activity. Sequence comparison of CCaMK from monocotyledonous plant (lily) and dicotyledonous plant (tobacco) suggests that the autophosphorylation site is conserved. This is the first identification of a phosphorylation site specifically responding to activation by second messenger system (Ca(2+) messenger system) in plants. Homology modeling of the kinase and calmodulin binding domain of CCaMK with the crystal structure of calcium/calmodulin-dependent protein kinase 1 suggests that the Ca(2+)-stimulated autophosphorylation site is located on the surface of the kinase and far from the catalytic site. Analysis of Ca(2+)-stimulated autophosphorylation with increasing concentration of CCaMK indicates the possibility that the Ca(2+)-stimulated phosphorylation occurs by an intermolecular mechanism.

  19. Calcium-stimulated autophosphorylation site of plant chimeric calcium/calmodulin-dependent protein kinase

    NASA Technical Reports Server (NTRS)

    Sathyanarayanan, P. V.; Siems, W. F.; Jones, J. P.; Poovaiah, B. W.

    2001-01-01

    The existence of two molecular switches regulating plant chimeric Ca(2+)/calmodulin-dependent protein kinase (CCaMK), namely the C-terminal visinin-like domain acting as Ca(2+)-sensitive molecular switch and calmodulin binding domain acting as Ca(2+)-stimulated autophosphorylation-sensitive molecular switch, has been described (Sathyanarayanan, P. V., Cremo, C. R., and Poovaiah, B. W. (2000) J. Biol. Chem. 275, 30417-30422). Here we report the identification of Ca(2+)-stimulated autophosphorylation site of CCaMK by matrix-assisted laser desorption ionization time of flight-mass spectrometry. Thr(267) was confirmed as the Ca(2+)-stimulated autophosphorylation site by post-source decay experiments and by site-directed mutagenesis. The purified T267A mutant form of CCaMK did not show Ca(2+)-stimulated autophosphorylation, autophosphorylation-dependent variable calmodulin affinity, or Ca(2+)/calmodulin stimulation of kinase activity. Sequence comparison of CCaMK from monocotyledonous plant (lily) and dicotyledonous plant (tobacco) suggests that the autophosphorylation site is conserved. This is the first identification of a phosphorylation site specifically responding to activation by second messenger system (Ca(2+) messenger system) in plants. Homology modeling of the kinase and calmodulin binding domain of CCaMK with the crystal structure of calcium/calmodulin-dependent protein kinase 1 suggests that the Ca(2+)-stimulated autophosphorylation site is located on the surface of the kinase and far from the catalytic site. Analysis of Ca(2+)-stimulated autophosphorylation with increasing concentration of CCaMK indicates the possibility that the Ca(2+)-stimulated phosphorylation occurs by an intermolecular mechanism.

  20. Prospective Analysis of Risk Factors Related to Depression and Post Traumatic Stress Disorder in Deployed United States Navy Personnel

    DTIC Science & Technology

    2011-03-28

    34Prospective Analysis of Risk Factors Related to Depression and Post Traumatic Stress Disorder in Deployed United States Navy Personnel" Name of...Risk Factors Related to Depression and Post Traumatic Stress Disorder in Deployed United States...Dissertation: Prospective Analysis of Risk Factors Related to Depression and Post Traumatic Stress Disorder in Deployed United States Navy Personnel

  1. Analysis and experiments of a waveguide post's influence on photocathode RF gun

    NASA Astrophysics Data System (ADS)

    Qian, Houjun; Tang, Chuanxiang; Zheng, Shuxin; Tong, Dechun; Chen, Huaibi; Huang, Wenhui; Guan, Xin

    2008-12-01

    Several BNL/KEK/SHI type photocathode RF guns have been fabricated for high-quality electron beams in Accelerator Laboratory of Tsinghua University. This paper describes how the characteristics of a waveguide post can be chosen to correct for a mismatch in power coupling without affecting the pi-mode resonant frequency and the balance of fields between the two cells. Microwave circuit theories are used to analyze how to select the proper location and depth of the waveguide post. The tolerance on the post positioning is evaluated based on gun field quality requirements. MAFIA simulations and RF experiments have been done to confirm the theoretical analysis.

  2. MITG post-test analysis and design improvements

    SciTech Connect

    Schock, A.

    1983-01-01

    The design, performance analysis, and key attributes of the Modular Isotopic Thermoelectric Generator (MITG) were described in a 1981 IECEC paper; and the design, fabrication, and testing of prototypical MITG test assemblies were described in preceding papers in these proceedings. Each test assembly simulated a typical modular slice of the flight generator. The present paper describes a detailed thermal-stress analysis, which identified the causes of stress-related problems observed during the tests. It then describes how additional analyses were used to evaluate design changes to alleviate those problems. Additional design improvements are discussed in the next paper in these proceedings, which also describes revised fabrication procedures and updated performance estimates for the generator.

  3. Analysis of cost regression and post-accident absence

    NASA Astrophysics Data System (ADS)

    Wojciech, Drozd

    2017-07-01

    The article presents issues related with costs of work safety. It proves the thesis that economic aspects cannot be overlooked in effective management of occupational health and safety and that adequate expenditures on safety can bring tangible benefits to the company. Reliable analysis of this problem is essential for the description the problem of safety the work. In the article attempts to carry it out using the procedures of mathematical statistics [1, 2, 3].

  4. Chimeric Antigen Receptor Therapy for Cancer

    PubMed Central

    Barrett, David M.; Singh, Nathan; Porter, David L.; Grupp, Stephan A.; June, Carl H.

    2014-01-01

    Improved outcomes for patients with cancer hinge on the development of new targeted therapies with acceptable short-term and long-term toxicity. Progress in basic, preclinical, and clinical arenas spanning cellular immunology, synthetic biology, and cell-processing technologies has paved the way for clinical applications of chimeric antigen receptor– based therapies. This new form of targeted immunotherapy merges the exquisite targeting specificity of monoclonal antibodies with the potent cytotoxicity and long-term persistence provided by cytotoxic T cells. Although this field is still in its infancy, clinical trials have already shown clinically significant antitumor activity in neuroblastoma, chronic lymphocytic leukemia, and B cell lymphoma, and trials targeting a variety of other adult and pediatric malignancies are under way. Ongoing work is focused on identifying optimal tumor targets and on elucidating and manipulating both cell- and host-associated factors to support expansion and persistence of the genetically engineered cells in vivo. The potential to target essentially any tumor-associated cell-surface antigen for which a monoclonal antibody can be made opens up an entirely new arena for targeted therapy of cancer. PMID:24274181

  5. Structure aided design of chimeric antibiotics.

    PubMed

    Karoli, Tomislav; Mamidyala, Sreeman K; Zuegg, Johannes; Fry, Scott R; Tee, Ernest H L; Bradford, Tanya A; Madala, Praveen K; Huang, Johnny X; Ramu, Soumya; Butler, Mark S; Cooper, Matthew A

    2012-04-01

    The rise of antibiotic resistance is of great clinical concern. One approach to reducing the development of resistance is to co-administer two or more antibiotics with different modes of action. However, it can be difficult to control the distribution and pharmacokinetics of two drugs to ensure both concentrations remain within the range of therapeutic efficacy whilst avoiding adverse effects. Hybrid drugs, where two drugs are linked together with a flexible linker, have been explored, but the resultant large, flexible molecules can have poor bioavailability. We have developed a chimeric approach using click chemistry where the pharmacophores of two drugs are overlapped into a single smaller, more drug-like molecule. Design and selection of compounds were assisted by in silico structural docking. We prepared a series of compounds that include candidates showing activity against the targets of both trimethoprim; dihydrofolate reductase, and ciprofloxacin; DNA gyrase and topoisomerase IV. The resultant triazole containing molecules show modest, but broad spectrum activities against drug sensitive and resistant Gram-negative and Gram-positive bacteria, with no observable cytotoxicity.

  6. Syngeneic Transplants with Modified Chimeric Hematopoietic Tumors.

    PubMed

    Hemann, Michael

    2015-08-03

    This protocol describes strategies to rapidly transduce tumor cells ex vivo and then transplant modified cells into immunocompetent-recipient mice. Inherent in the definition of a bona fide murine hematopoietic malignancy, unlike a myelo- or lympho-proliferative disease, is the ability to transplant tumors and give rise to a malignancy in recipient animals. This characteristic of hematopoietic disease makes these tumors a tractable model for examining the role of specific genes in tumor growth, dissemination, or therapeutic response. Additionally, because of the systemic nature of hematopoietic malignancies, transplanted tumors are frequently pathologically indistinguishable from donor malignancies-allowing one to perform decisive therapy studies on large cohorts of transplant recipients. Finally, following ex vivo manipulation, transplanted tumors can be made chimeric for the presence of defined retrovirally induced alterations. Thus, these malignancies can be made to resemble genetically heterogeneous human tumors that are in the process of acquiring new capabilities. In these experiments, fluorescent markers serve as a surrogate marker for the expression of a defined alteration, and the change in the percentage of fluorescent cells in a tumor population over time or in response to therapy can be used to gauge the impact of specific alterations on tumor behavior.

  7. 4-1BB chimeric antigen receptors.

    PubMed

    Campana, Dario; Schwarz, Herbert; Imai, Chihaya

    2014-01-01

    In addition to T-cell receptor signals, T lymphocytes require costimulatory signals for robust activation. Among these, those mediated by 4-1BB (CD137, TNFRSF9) are critical for tumor immunity. 4-1BB is expressed in T-cell receptor-activated lymphocytes as well as natural killer cells and other hematopoietic and nonhematopoietic cells. 4-1BB ligation induces a signaling cascade that results in cytokine production, expression of antiapoptotic molecules, and enhanced immune responses. In line with the described function of 4-1BB, its addition to CD3ζ chimeric antigen receptors (CARs) increases their capacity to provoke T-cell expansion and antitumor activity. The results of preclinical studies with 4-1BB CARs have been corroborated by encouraging results from clinical trials. Advantages and disadvantages of 4-1BB CARs versus CARs bearing other costimulatory components remain to be fully elucidated. In this review, we discuss the properties of 4-1BB, the design of 4-1BB CARs, and the function of T lymphocytes and natural killer cells expressing them.

  8. Moving beyond Univariate Post-Hoc Testing in Exercise Science: A Primer on Descriptive Discriminate Analysis

    ERIC Educational Resources Information Center

    Barton, Mitch; Yeatts, Paul E.; Henson, Robin K.; Martin, Scott B.

    2016-01-01

    There has been a recent call to improve data reporting in kinesiology journals, including the appropriate use of univariate and multivariate analysis techniques. For example, a multivariate analysis of variance (MANOVA) with univariate post hocs and a Bonferroni correction is frequently used to investigate group differences on multiple dependent…

  9. Moving beyond Univariate Post-Hoc Testing in Exercise Science: A Primer on Descriptive Discriminate Analysis

    ERIC Educational Resources Information Center

    Barton, Mitch; Yeatts, Paul E.; Henson, Robin K.; Martin, Scott B.

    2016-01-01

    There has been a recent call to improve data reporting in kinesiology journals, including the appropriate use of univariate and multivariate analysis techniques. For example, a multivariate analysis of variance (MANOVA) with univariate post hocs and a Bonferroni correction is frequently used to investigate group differences on multiple dependent…

  10. Finite element analysis of weakened roots restored with composite resin and posts.

    PubMed

    Coelho, Carla Santina de Miranda; Biffi, João Carlos Gabrielli; Silva, Gisele Rodrigues da; Abrahão, Anthony; Campos, Roberto Elias; Soares, Carlos José

    2009-11-01

    Finite element analysis (FEA) was used to investigate the influence of different post systems on the stress distribution of weakened teeth under oblique-load application. A maxillary central incisor root obtained from a sound tooth was weakened by partial removal of dentin inside the root canal. Seven two-dimensional numerical models, one from the sound tooth and six from the weakened root restored with composite resin and post systems were created as follows - ST: sound tooth; CPC: cast CuAl post and core; SSP: stainless steel post + composite core; GP: fiberglass + composite core; CP: carbon fiber + composite core; ZP: zirconium dioxide post + composite core; TP: titanium post + composite core. The numerical models were considered to be restored with a leucite-reinforced all-ceramic crown and received a 45 masculine occlusal load (10 N) on the lingual surface.All the materials and structures were considered linear elastic, homogeneous, and isotropic, with the exception of fiberglass and carbon fiber posts which assumed orthotropic behavior. The numerical models were plotted and meshed with isoparametric elements, and the results were analyzed using von Mises and Sy stress criteria. When compared with the sound tooth, FEA revealed differences in stress distribution when post systems were used. Among the restored teeth, the use of CPC, SSP, ZP, and TP resulted in higher stress concentration in the post itself when compared to GP and CP. Therefore, results from the FEA images suggested that the use of non-metallic post systems could result in improved mechanical behavior for the weakened restored teeth.

  11. Practical post-calibration uncertainty analysis: Yucca Mountain, Nevada, USA

    NASA Astrophysics Data System (ADS)

    James, S. C.; Doherty, J.; Eddebbarh, A.

    2009-12-01

    The values of parameters in a groundwater flow model govern the precision of predictions of future system behavior. Predictive precision, thus, typically depends on an ability to infer values of system properties from historical measurements through calibration. When such data are scarce, or when their information content with respect to parameters that are most relevant to predictions of interest is weak, predictive uncertainty may be high, even if the model is “calibrated.” Recent advances help recognize this condition, quantitatively evaluate predictive uncertainty, and suggest a path toward improved predictive accuracy by identifying sources of predictive uncertainty and by determining what observations will most effectively reduce this uncertainty. We demonstrate linear and nonlinear predictive error/uncertainty analyses as applied to a groundwater flow model of Yucca Mountain, Nevada, the US’s proposed site for disposal of high-level radioactive waste. Both of these types uncertainty analysis are readily implemented as an adjunct to model calibration with medium to high parameterization density. Linear analysis yields contributions made by each parameter to a prediction’s uncertainty and the worth of different observations, both existing and yet-to-be-gathered, toward reducing this uncertainty. Nonlinear analysis provides more accurate characterization of the uncertainty of model predictions while yielding their (approximate) probability distribution functions. This paper applies the above methods to a prediction of specific discharge and confirms the uncertainty bounds on specific discharge supplied in the Yucca Mountain Project License Application. Furthermore, Monte Carlo simulations confirm that hydrogeologic units thought to be flow barriers have probability distributions skewed toward lower permeabilities.

  12. Non-Chimeric HLA-Identical Renal Transplant Tolerance: Regulatory Immunophenotypic/Genomic Biomarkers

    PubMed Central

    Leventhal, J.R.; Mathew, J.M.; Salomon, D.R.; Kurian, S.M.; Friedewald, J.J.; Gallon, L.; Konieczna, I.; Tambur, A.R.; charette, j.; Levitsky, J.; Jie, C.; Kanwar, Y. S.; Abecassis, M. M.; Miller, J.

    2015-01-01

    We previously described early results of a non-chimeric operational tolerance protocol in HLA identical living donor renal transplants and now update these results. Recipients given alemtuzumab, tacrolimus/MPA with early sirolimus conversion were multiply infused with donor hematopoietic CD34+ stem cells. Immunosuppression was withdrawn by 24 months. Twelve months later operational tolerance was confirmed by rejection-free transplant biopsies. Five of the first 8 enrollees were initially tolerant one year off immunosuppression. Biopsies of 3 others after total withdrawal showed Banff 1A acute cellular rejection without renal dysfunction. With longer follow-up including 5 year post-transplant biopsies 4 of the 5 tolerant recipients remain without rejection while one developed Banff 1A without renal dysfunction. We now add 7 new subjects (2 operationally tolerant), and demonstrate time-dependent increases of circulating CD4+CD25+++CD127−FOXP3+ Tregs vs. losses of Tregs in non-tolerant subjects (p< 0.001). Gene expression signatures, developed using global RNA expression profiling of sequential whole blood and protocol biopsy samples, were highly associative with operational tolerance as early as 1 year post-transplant. The blood signature was validated by an external ITN data set. Our approach to non-chimeric operational HLA identical tolerance reveals association with Treg immunophenotypes and serial gene expression profiles. PMID:26227106

  13. Fate of donor cells in vascularized bone grafts: identification of systemic chimerism by the polymerase chain reaction.

    PubMed

    Muramatsu, Keiichi; Bishop, Allen T; Sunagawa, Toru; Valenzuela, Richard G

    2003-02-01

    Systemic chimerism, or the movement of cells from a transplanted tissue into host organs, is a phenomenon known to occur in association with development of immunological tolerance in allotransplantation. However, little is known about the fate and movement of cells into or out of autogenous free tissue transfers, including vascularized bone grafts. The purpose of this study was to identify systemic chimerism in vascularized bone grafts by transplantation of a vascularized tibiofibular graft from isogenous (inbred) male Lewis rats to female recipients. Donor (male) cells could be identified in the recipient (female) tissues by semiquantitative polymerase chain reaction analysis for a Y chromosome-specific DNA sequence. Chimerism was assessed at 1, 12, 18, and 24 weeks after transplantation. Competitive polymerase chain reaction study using the specific primers for a Y-chromosome marker ( gene) and an autosomal gene (GAPDH) allowed detection of small amounts of male cells in a large pool of female cells and measurement of their relative proportions as a function of time. Of 19 nonimmunosuppressed recipients, nine animals (47 percent) showed low-level chimerism (<0.1 percent) in the peripheral blood. Nine (47 percent), three (16 percent), and two (11 percent) recipients showed high-level chimerism (>1 percent) in the spleen, liver, and thymus, respectively, at final assessment. Donor cells were detected in all bone grafts and in six contralateral tibial bones (i.e., 67 percent of sampled contralateral tibial bones) at 18 and 24 weeks after transplantation. Twenty-four recipients were immunosuppressed with FK506 (tacrolimus) to suppress reaction to a minor histocompatibility barrier present on the Y chromosome. In this group, 14 animals (58 percent) showed low-level chimerism in peripheral blood and 12 (50 percent), eight (33 percent), and one (4 percent) recipients showed high-level chimerism in the spleen, thymus, and liver, respectively. Transplanted cells were

  14. A chimeric human-mouse model of Sjögren's syndrome.

    PubMed

    Young, Nicholas A; Wu, Lai-Chu; Bruss, Michael; Kaffenberger, Benjamin H; Hampton, Jeffrey; Bolon, Brad; Jarjour, Wael N

    2015-01-01

    Despite recent advances in the understanding of Sjögren's Syndrome (SjS), the pathogenic mechanisms remain elusive and an ideal model for early drug discovery is not yet available. To establish a humanized mouse model of SjS, peripheral blood mononuclear cells (PBMCs) from healthy volunteers or patients with SjS were transferred into immunodeficient NOD-scid IL-2rγ(null) mouse recipients to produce chimeric mice. While no difference was observed in the distribution of cells, chimeric mice transferred with PBMCs from SjS patients produced enhanced cytokine levels, most significantly IFN-γ and IL-10. Histological examination revealed enhanced inflammatory responses in the lacrimal and salivary glands of SjS chimeras, as measured by digital image analysis and blinded histopathological scoring. Infiltrates were primarily CD4+, with minimal detection of CD8+ T-cells and B-cells. These results demonstrate a novel chimeric mouse model of human SjS that provides a unique in vivo environment to test experimental therapeutics and investigate T-cell disease pathology.

  15. Protein-Protein Interactions, Not Substrate Recognition, Dominate the Turnover of Chimeric Assembly Line Polyketide Synthases*

    PubMed Central

    Klaus, Maja; Ostrowski, Matthew P.; Austerjost, Jonas; Robbins, Thomas; Lowry, Brian; Cane, David E.; Khosla, Chaitan

    2016-01-01

    The potential for recombining intact polyketide synthase (PKS) modules has been extensively explored. Both enzyme-substrate and protein-protein interactions influence chimeric PKS activity, but their relative contributions are unclear. We now address this issue by studying a library of 11 bimodular and 8 trimodular chimeric PKSs harboring modules from the erythromycin, rifamycin, and rapamycin synthases. Although many chimeras yielded detectable products, nearly all had specific activities below 10% of the reference natural PKSs. Analysis of selected bimodular chimeras, each with the same upstream module, revealed that turnover correlated with the efficiency of intermodular chain translocation. Mutation of the acyl carrier protein (ACP) domain of the upstream module in one chimera at a residue predicted to influence ketosynthase-ACP recognition led to improved turnover. In contrast, replacement of the ketoreductase domain of the upstream module by a paralog that produced the enantiomeric ACP-bound diketide caused no changes in processing rates for each of six heterologous downstream modules compared with those of the native diketide. Taken together, these results demonstrate that protein-protein interactions play a larger role than enzyme-substrate recognition in the evolution or design of catalytically efficient chimeric PKSs. PMID:27246853

  16. Hotspot Selective Preference of the Chimeric Sequences Formed in Multiple Displacement Amplification

    PubMed Central

    Tu, Jing; Lu, Na; Duan, Mengqin; Huang, Mengting; Chen, Liang; Li, Junji; Guo, Jing; Lu, Zuhong

    2017-01-01

    Multiple displacement amplification (MDA) is considered to be a conventional approach to comprehensive amplification from low input DNA. The chimeric reads generated in MDA lead to severe disruption in some studies, including those focusing on heterogeneity, structural variation, and genetic recombination. Meanwhile, the generation of by-products gives a new approach to gain insights into the reaction process of φ29 polymerase. Here, we analyzed 36.7 million chimeras and screened 196 billion chimeric hotspots in the human genome, as well as evaluating the hotspot selective preference of chimeras. No significant preference was captured in the distributions of chimeras and hotspots among chromosomes. Hotspots with overlaps for 12–13 nucleotides (nt) were most likely to be selected as templates in chimera generation. Meanwhile, a regularly selective preference was noticed in overlap GC content. The preferences in overlap length and GC content was shown to be pertinent to the sequence denaturation temperature, which pointed out the optimization direction for reducing chimeras. Distance preference between two segments of chimeras was 80–280 nt. The analysis is beneficial for reducing the chimeras in MDA, and the characterization of MDA chimeras is helpful in distinguishing MDA chimeras from chimeric sequences caused by disease. PMID:28245591

  17. Overexpression of a Chimeric Gene, OsDST-SRDX, Improved Salt Tolerance of Perennial Ryegrass

    PubMed Central

    Cen, Huifang; Ye, Wenxing; Liu, Yanrong; Li, Dayong; Wang, Kexin; Zhang, Wanjun

    2016-01-01

    The Drought and Salt Tolerance gene (DST) encodes a C2H2 zinc finger transcription factor, which negatively regulates salt tolerance in rice (Oryza sativa). Phylogenetic analysis of six homologues of DST genes in different plant species revealed that DST genes were conserved evolutionarily. Here, the rice DST gene was linked to an SRDX domain for gene expression repression based on the Chimeric REpressor gene-Silencing Technology (CRES-T) to make a chimeric gene (OsDST-SRDX) construct and introduced into perennial ryegrass by Agrobacterium-mediated transformation. Integration and expression of the OsDST-SRDX in transgenic plants were tested by PCR and RT-PCR, respectively. Transgenic lines overexpressing the OsDST-SRDX fusion gene showed obvious phenotypic differences and clear resistance to salt-shock and to continuous salt stresses compared to non-transgenic plants. Physiological analyses including relative leaf water content, electrolyte leakage, proline content, malondialdehyde (MDA) content, H2O2 content and sodium and potassium accumulation indicated that the OsDST-SRDX fusion gene enhanced salt tolerance in transgenic perennial ryegrass by altering a wide range of physiological responses. To our best knowledge this study is the first report of utilizing Chimeric Repressor gene-Silencing Technology (CRES-T) in turfgrass and forage species for salt-tolerance improvement. PMID:27251327

  18. Confined blood chimerism in a monochorionic dizygotic sex discordant twin pregnancy conceived after induced ovulation.

    PubMed

    Mayeur Le Bras, Anne; Petit, François; Benachi, Alexandra; Bedel, Bettina; Oucherif, Salima; Martinovic, Jelena; Armanet, Narjes; Tosca, Lucie; Gautier, Valérie; Parisot, Frédéric; Labrune, Philippe; Tachdjian, Gérard; Brisset, Sophie

    2016-04-01

    Monochorionic twins are generally considered as a monozygotic twin pregnancy. However, several cases of monochorial dizygotic twin pregnancies have been reported. We report on a rare case of monochorionic dizygotic twin pregnancy conceived after induced ovulation in a 32-year-old woman. The diagnosis was made on morphological ultrasound examination at 18+4 weeks of gestation, showing two fetuses with discordant sex. The amniocentesis was declined by the patient. The monochorionic status was confirmed after a histopathalogical study of the placenta. At delivery, both a phenotypically normal boy and a phenotypically normal girl without sexual abnormality were observed. This analysis also revealed the presence of vascular anastomoses between both fetal circulations. Postnatal cytogenetic analyses indicated the presence of a chimerism in peripheral blood lymphocytes. This chimerism was not observed in cells obtained from a buccal swab. Molecular determination of zygosity confirmed the existence of the confined peripheral blood chimerism with the presence of four parental alleles. We report on a case of monochorionic dizygotic twin pregnancy. This observation underlies the need to carefully assess twin pregnancies, especially when obtained after assisted reproductive technology. © 2016 Wiley Periodicals, Inc.

  19. Prediction of hospital failure: a post-PPS analysis.

    PubMed

    Gardiner, L R; Oswald, S L; Jahera, J S

    1996-01-01

    This study investigates the ability of discriminant analysis to provide accurate predictions of hospital failure. Using data from the period following the introduction of the Prospective Payment System, we developed discriminant functions for each of two hospital ownership categories: not-for-profit and proprietary. The resulting discriminant models contain six and seven variables, respectively. For each ownership category, the variables represent four major aspects of financial health (liquidity, leverage, profitability, and efficiency) plus county marketshare and length of stay. The proportion of closed hospitals misclassified as open one year before closure does not exceed 0.05 for either ownership type. Our results show that discriminant functions based on a small set of financial and nonfinancial variables provide the capability to predict hospital failure reliably for both not-for-profit and proprietary hospitals.

  20. An analysis of post-event processing in social anxiety disorder.

    PubMed

    Brozovich, Faith; Heimberg, Richard G

    2008-07-01

    Research has demonstrated that self-focused thoughts and negative affect have a reciprocal relationship [Mor, N., Winquist, J. (2002). Self-focused attention and negative affect: A meta-analysis. Psychological Bulletin, 128, 638-662]. In the anxiety disorder literature, post-event processing has emerged as a specific construction of repetitive self-focused thoughts that pertain to social anxiety disorder. Post-event processing can be defined as an individual's repeated consideration and potential reconstruction of his performance following a social situation. Post-event processing can also occur when an individual anticipates a social or performance event and begins to brood about other, past social experiences. The present review examined the post-event processing literature in an attempt to organize and highlight the significant results. The methodologies employed to study post-event processing have included self-report measures, daily diaries, social or performance situations created in the laboratory, and experimental manipulations of post-event processing or anticipation of an upcoming event. Directions for future research on post-event processing are discussed.

  1. Radionuclide fourier amplitude analysis to predict post-aneurysmectomy ejection fraction

    SciTech Connect

    McCarthy, D.M.; Kleaveland, J.P.; Makler, P.T. Jr.; Alavi, A.

    1984-01-01

    Post-operative LV ejection fraction (EF) is an important determinant of outcome following aneurysmectomy but is difficult to predict noninvasively. First harmonic Fourier analysis of radionuclide angiography (RNA) in patients with aneurysms gives characteristic phase and amplitude images which delineate contractile and dyskinetic regions. Since pixel amplitude is proportional to stroke counts, the summed amplitude values from the contractile region (CR) and the aneurysm should reflect regional stroke volumes. A predicted post-operative LVEF may be determined from the pre-operative global LVEF and the proportion of the total amplitude located in the CR. The authors studied 19 patients undergoing LV aneurysmectomy with pre- and post-operative RNA. Three patients were excluded for technical reasons, leaving 16 patients for analysis. There were 13 males, and the mean age was 56.8 yrs (range 45-78). All patients had a history of anterior myocardial infarction and were undergoing surgery for recurrent sustained ventricular tachycardia. The global LVEF increased from 0.25 +- .13 (sd) pre-operatively to 0.38+-.11 following surgery (p<.001). The predicted post-operative LVEF (from amplitude analysis of the pre-operative RNA) averaged 0.35 +- .13 and correlated significantly with the actual post-operative LVEf (r=0.87, SEE=.06, p<.01). The results suggest that the LVEF following aneurysmectomy can be predicted from Fourier amplitude analysis of the pre-operative RNA.

  2. Three-dimensional finite element analysis of the stress distribution in the endodontically treated maxillary central incisor by glass fiber post and dentin post

    PubMed Central

    Memon, Sarfaraz; Mehta, Sonal; Malik, Salim; Nirmal, Narendra; Sharma, Deeksha; Arora, Himanshu

    2016-01-01

    Introduction: From the point of dental practice, the restoration of endodontically treated teeth has become an important aspect as it involves a range of treatment options of variable complexity. Restoring teeth with insufficient coronal tooth structure, it is always indicated to use the post to retain a core for definitive restoration. Fiber post has a modulus of elasticity in analogs to dentin structure, thus reducing the stress areas at the dowel dentin interface. However, the only material that can substantiate all these properties can be none other than dentin itself. Materials and Methodology: Three-dimensional (3D) models of the maxillary central incisor were developed incorporating all the nonlinearities. Continuum 3D elements were used in three dimensions. Maxillary central incisor was laser scanned, duplicated with the help of reverse engineering into STL format, and it was converted into 3D model for finite element analysis (FEA). For the model, fixed boundary conditions were applied at the outer bone, while 100 N static vertical occlusal loads were prescribed at 135° on the loading component of the simulated tooth. The stress distribution was evaluated using dentin and fiber post with prescribed materials, loading and boundary conditions in endontically treated teeth by 3D FEA. Results: The analysis for von Misses stress for dentin post showed that the stress in the dentin post at the cervical area was 127 MPa. The displacement in the dentin post was <0.025 mm. Von Misses stress for the fiber post at the cervical area was approximately 182 MPa and the displacement was <0.035 mm. Conclusion: The FEA results showed that the stress in the cervical area of the dentin was more for fiber post when compared to dentin post, and maximum displacement values were less for dentin post in comparison to fiber post. PMID:27134431

  3. Post-column labeling techniques in amino acid analysis by liquid chromatography.

    PubMed

    Rigas, Pantelis G

    2013-10-01

    Amino acid analysis (AAA) has always presented an analytical challenge in terms of sample preparation, separation, and detection. Because of the vast number of amino acids, various separation methods have been applied taking into consideration the large differences in their chemical structures, which span from nonpolar to highly polar side chains. Numerous separation methods have been developed in the past 60 years, and impressive achievements have been made in the fields of separation, derivatization, and detection of amino acids (AAs). Among the separation methods, liquid chromatography (LC) prevailed in the AAA field using either pre-column or post-column labeling techniques in order to improve either separation of AAs or selectivity and sensitivity of AAA. Of the two approaches, the post-column technique is a more rugged and reproducible method and provides excellent AAs separation relatively free from interferences. This review considers current separations combined with post-column labeling techniques for AAA, comparison with the pre-column methods, and the strategies used to develop effective post-column methodology. The focus of the article is on LC methods coupled with post-column labeling techniques and studying the reactions to achieve optimum post-column derivatization (PCD) conditions in order to increase sensitivity and selectivity using various types of detectors (UV-Vis, fluorescence, electrochemical etc.) and illustrating the versatility of the PCD methods for practical analysis.

  4. Assessing the technical efficiency of health posts in rural Guatemala: a data envelopment analysis.

    PubMed

    Hernández, Alison R; San Sebastián, Miguel

    2014-01-01

    Strengthening health service delivery to the rural poor is an important means of redressing inequities. Meso-level managers can help enhance efficiency in the utilization of existing resources through the application of practical tools to analyze routinely collected data reflecting inputs and outputs. This study aimed to assess the efficiency and change in productivity of health posts over two years in a rural department of Guatemala. Data envelopment analysis was used to measure health posts' technical efficiency and productivity change for 2008 and 2009. Input/output data were collected from the regional health office of Alta Verapaz for 34 health posts from the 19 districts comprising the health region. Technical efficiency varied widely across health posts, with mean scores of 0.78 (SD=0.24) and 0.75 (SD=0.21) in 2008 and 2009, respectively. Overall, productivity increased by 4%, though 47% of health posts experienced a decline in productivity. Results were combined on a bivariate plot to identify health posts at the high and low extremes of efficiency, which should be followed up to determine how and why their production processes are operating differently. Assessing efficiency using the data that are available at the meso-level can serve as a first step in strengthening performance. Further work is required to support managers in the routine application of efficiency analysis and putting the results to use in guiding efforts to improve service delivery and increase utilization.

  5. Assessing the technical efficiency of health posts in rural Guatemala: a data envelopment analysis.

    PubMed

    Hernández, Alison R; Sebastián, Miguel San

    2014-12-01

    Introduction Strengthening health service delivery to the rural poor is an important means of redressing inequities. Meso-level managers can help enhance efficiency in the utilization of existing resources through the application of practical tools to analyze routinely collected data reflecting inputs and outputs. This study aimed to assess the efficiency and change in productivity of health posts over two years in a rural department of Guatemala. Methods Data envelopment analysis was used to measure health posts' technical efficiency and productivity change for 2008 and 2009. Input/output data were collected from the regional health office of Alta Verapaz for 34 health posts from the 19 districts comprising the health region. Results Technical efficiency varied widely across health posts, with mean scores of 0.78 (SD=0.24) and 0.75 (SD=0.21) in 2008 and 2009, respectively. Overall, productivity increased by 4%, though 47% of health posts experienced a decline in productivity. Results were combined on a bivariate plot to identify health posts at the high and low extremes of efficiency, which should be followed up to determine how and why their production processes are operating differently. Conclusions Assessing efficiency using the data that are available at the meso-level can serve as a first step in strengthening performance. Further work is required to support managers in the routine application of efficiency analysis and putting the results to use in guiding efforts to improve service delivery and increase utilization.

  6. Chimeric foot-and-mouth disease viruses: evaluation of their efficacy as potential marker vaccines in cattle.

    PubMed

    Fowler, V L; Paton, D J; Rieder, E; Barnett, P V

    2008-04-07

    Previous work in pigs, has demonstrated that full protection against foot-and-mouth disease (FMD) can be achieved following vaccination with chimeric foot-and-mouth disease virus (FMDV) vaccines, in which the VP1 G-H loop had been substituted with that from another serotype. If proven to be effective in other economically important species such as cattle, such vaccine constructs could be trialed as potential marker vaccines. Here, we determine if G-H loop chimera FMDV vaccines can: (i) protect cattle from virus challenge and (ii) induce an antibody response that would enable the identification of infection, regardless of vaccination status. Inactivated, oil adjuvanated, chimeric vaccine constructs, based on the backbone sequence of the A(12)119 serotype virus, fully protected cattle from challenge 21 days post-vaccination. Differentiation assays developed for use in this study were able to identify sub-clinical infection, which in one vaccinated animal, persisted beyond day 32 post-challenge. This paper emphasises the importance of epitopes outside of the VP1 G-H loop for protective immunity in cattle, and demonstrates that chimeric FMDV vaccines could prove to be useful marker vaccines for the future.

  7. Space Shuttle Columbia Post-Accident Analysis and Investigation

    NASA Technical Reports Server (NTRS)

    McDanels, Steven J.

    2006-01-01

    Although the loss of the Space Shuttle Columbia and its crew was tragic, the circumstances offered a unique opportunity to examine a multitude of components which had experienced one of the harshest environments ever encountered by engineered materials: a break up at a velocity in excess of Mach 18 and an altitude exceeding 200,000 feet (63 KM), resulting in a debris field 645 miles/l,038 KM long and 10 miles/16 KM wide. Various analytical tools were employed to ascertain the sequence of events leading to the disintegration of the Orbiter and to characterize the features of the debris. The testing and analyses all indicated that a breach in a left wing reinforced carbon/carbon composite leading edge panel was the access point for hot gasses generated during re-entry to penetrate the structure of the vehicle and compromise the integrity of the materials and components in that area of the Shuttle. The analytical and elemental testing utilized such techniques as X-Ray Diffraction (XRD), Energy Dispersive X-Ray (EDX) dot mapping, Electron Micro Probe Analysis (EMPA), and X-Ray Photoelectron Spectroscopy (XPS) to characterize the deposition of intermetallics adjacent to the suspected location of the plasma breach in the leading edge of the left wing, Fig. 1.

  8. Chimeric cDNA Sequences from Citrus tristeza virus Confer RNA Silencing-Mediated Resistance in Transgenic Nicotiana benthamiana Plants.

    PubMed

    Roy, Gourgopal; Sudarshana, Mysore R; Ullman, Diane E; Ding, Shou-Wei; Dandekar, Abhaya M; Falk, Bryce W

    2006-08-01

    ABSTRACT RNA silencing has been shown to be an important mechanism for conferring resistance in transgenic, virus-resistant plants. We used this approach to evaluate resistance in Nicotiana benthamiana plants transformed with chimeric coding and noncoding sequences from Citrus tristeza virus (CTV). Several independent transgenic plant lines were generated, using two constructs (pCTV1 and pCTV2) designed to produce self-complementary transcripts. The pCTV1 contained cDNA sequences from the CTV capsid protein (CP), p20, and 3' untranslated region (UTR); and pCTV2 contained CP, p23, and 3' UTR sequences. Heterologous recombinant Potato virus X (PVX) containing either homologous or heterologous CTV sequences was used to challenge plants and resistance was evaluated phenotypically and validated with reverse-transcriptase polymerase chain reaction and northern hybridization analysis. Transgenic plants (T1 generation) for each construct showed resistance to recombinant PVX constructs used for challenge experiments when PVX contained p20 or UTR (for CTV1 plants), or p23 or UTR (for CTV2 plants). However, no resistance was seen when plants were challenged with PVX containing the CTV CP. T2 generation plants also showed resistance even when challenged with PVX containing the cognate CTV sequences obtained from heterologous CTV isolates. The presence of transgene-specific small interfering RNAs in the resistant CTV1 and CTV2 plants indicated that resistance was mediated by post-transcriptional gene silencing.

  9. Post-traumatic stress disorder in the perinatal period: A concept analysis.

    PubMed

    Vignato, Julie; Georges, Jane M; Bush, Ruth A; Connelly, Cynthia D

    2017-03-15

    To report an analysis of the concept of perinatal post-traumatic stress disorder. Prevalence of perinatal post-traumatic stress disorder is rising in the USA, with 9% of the U.S. perinatal population diagnosed with the disorder and an additional 18% being at risk for the condition. Left untreated, adverse maternal-child outcomes result in increased morbidity, mortality and healthcare costs. Concept analysis via Walker and Avant's approach. The databases Cumulative Index to Nursing and Allied Health Literature (CINAHL), Medline, Academic Search Premier and PsychINFO were searched for articles, written in English, published between 2006-2015, containing the terms perinatal and post-traumatic stress disorder. Perinatal post-traumatic stress disorder owns unique attributes, antecedents and outcomes when compared to post-traumatic stress disorder in other contexts, and may be defined as a disorder arising after a traumatic experience, diagnosed any time from conception to 6 months postpartum, lasting longer than 1 month, leading to specific negative maternal symptoms and poor maternal-infant outcomes. Attributes include a diagnostic time frame (conception to 6 months postpartum), harmful prior or current trauma and specific diagnostic symptomatology defined in the Diagnostic and Statistical Manual of Mental Disorders, 5th edition. Antecedents were identified as trauma (perinatal complications and abuse), postpartum depression and previous psychiatric history. Consequences comprised adverse maternal-infant outcomes. Further research on perinatal post-traumatic stress disorder antecedents, attributes and outcomes in ethnically diverse populations may provide clinicians a more comprehensive framework for identifying and treating perinatal post-traumatic stress disorder. Nurses are encouraged to increase their awareness of perinatal post-traumatic stress disorder for early assessment and intervention, and prevention of adverse maternal-infant outcomes. © 2017 John Wiley

  10. Steroid metabolism in chimeric mice with humanized liver.

    PubMed

    Lootens, Leen; Van Eenoo, Peter; Meuleman, Philip; Pozo, Oscar J; Van Renterghem, Pieter; Leroux-Roels, Geert; Delbeke, Frans T

    2009-11-01

    Anabolic androgenic steroids are considered to be doping agents and are prohibited in sports. Their metabolism needs to be elucidated to allow for urinary detection by gas chromatography-mass spectrometry (GC-MS) or liquid chromatography-tandem mass spectrometry (LC-MS/MS). Steroid metabolism was assessed using uPA(+/+) SCID mice with humanized livers (chimeric mice). This study presents the results of 19-norandrost-4-ene-3,17-dione (19-norAD) administration to these in vivo mice. As in humans, 19-norandrosterone and 19-noretiocholanolone are the major detectable metabolites of 19-norAD in the urine of chimeric mice.A summary is given of the metabolic pathways found in chimeric mice after administration of three model steroid compounds (methandienone, androst-4-ene-3,17-dione and 19-norandrost-4-ene-3,17-dione). From these studies we can conclude that all major metabolic pathways for anabolic steroids in humans are present in the chimeric mouse. It is hoped that, in future, this promising chimeric mouse model might assist the discovery of new and possible longer detectable metabolites of (designer) steroids.

  11. Post2 End-to-End Descent and Landing Simulation for ALHAT Design Analysis Cycle 2

    NASA Technical Reports Server (NTRS)

    Davis, Jody L.; Striepe, Scott A.; Maddock, Robert W.; Johnson, Andrew E.; Paschall, Stephen C., II

    2010-01-01

    The ALHAT project is an agency-level program involving NASA centers, academia, and industry, with a primary goal to develop a safe, autonomous, precision-landing system for robotic and crew-piloted lunar and planetary descent vehicles. POST2 is used as the 6DOF descent and landing trajectory simulation for determining integrated system performance of ALHAT landing-system models and lunar environment models. This paper presents updates in the development of the ALHAT POST2 simulation, as well as preliminary system performance analysis for ALDAC-2 used for the testing and assessment of ALHAT system models. The ALDAC-2 POST2 Monte Carlo simulation results have been generated and focus on HRN model performance with the fully integrated system, as well performance improvements of AGNC and TSAR model since the previous design analysis cycle

  12. FEM analysis of the mandibular first premolar with different post diameters.

    PubMed

    Du, Je-Kang; Lin, Wei-Ko; Wang, Chau-Hsiang; Lee, Huey-Er; Li, Hung-Yuan; Wu, Ju-Hui

    2011-07-01

    Several reports have pointed out that endodontically treated teeth can lack strength, and that the teeth can be reinforced using posts. However, it has not been clear how to select posts that meet the needs of most clinical situations, particularly in terms of the post diameter, which has a major influence on the occurrence of root fracture. The purpose of this study was to analyze the stress distributions of posts of various diameters during masticatory loads using a finite element method. A 3-dimensional (3D) finite element model of a lower first premolar was developed. We used the image software Geomagic Studio (3D Digital 2002; Geomagic, Research Triangle Park, NC, USA) to reduce the post diameter by 6 ratios to a root diameter of 20, 30, 40, 50, 60, and 80% and then individually implemented them into the root of a tooth. A chewing static force of 100 N was applied as a 45° diagonal load on the buccal cusp tip, and the σ(von Mises) and σ(max) stresses were calculated. Analysis of the σ(von Mises) values revealed that the stresses were concentrated in the middle 1/3 of both the post and the root surface for all models, as were the σ(max) values. The results also indicated that when the diameter of the post was 50% of that of the root, the stress distributions of the post and the root surface were most favorable. In conclusion, the clinical implications of the results will need to be further studied and discussed.

  13. Finite element analysis of strength and adhesion of cast posts compared to glass fiber-reinforced composite resin posts in anterior teeth.

    PubMed

    Dejak, Beata; Młotkowski, Andrzej

    2011-02-01

    Previous studies on the strength of teeth restored with posts have not resolved the controversy as to which post systems provide the greatest strength and longevity. The purpose of this study was to compare the strength of teeth restored using cast posts with those restored using glass fiber-reinforced composite resin posts and to evaluate the bond strength of the posts to dentin. The investigation was conducted by using finite element analysis, combined with the application of contact elements. Three-dimensional (3-D) models of the maxillary central incisors were generated: IT, an intact tooth; CC, a tooth with a ceramic crown; FP, a tooth restored with an FRC (glass fiber-reinforced composite resin) post; CPAu, a tooth restored with a gold alloy cast post; and CPNi, a tooth restored with an NiCr (nickel chromium alloy) cast post. Each model was subjected to vertical and oblique loads with a force of 100 N. To evaluate the strength of the restored tooth, ceramics, and composite resin, the modified von Mises failure criterion was used, the Tsai-Wu criterion for FRC, and the von Mises criterion for gold and NiCr alloy. The equivalent stresses found in the tested models were compared with the tensile strength of the respective materials. Contact stresses in the luting cement-dentin interface were calculated. The maximum mvM (modified von Mises failure criterion) stresses in the dentin of the teeth restored with FRC posts were reduced by 21%, and in those restored with cast NiCr posts, stresses were reduced by 25% when compared to the stresses in the intact tooth. The equivalent stresses in metal posts were several times higher than in FRC posts, but did not exceed the tensile strength of the materials. The highest mvM stress in the luting resin cement around the FRC post was 55% higher than in the luting resin cement around the metal post, under an oblique load. In the ceramic crown, which covered the composite resin post and core, the highest mvM stress was 30.7 MPa

  14. Campus Sustainability Governance in Canada: A Content Analysis of Post-Secondary Institutions' Sustainability Policies

    ERIC Educational Resources Information Center

    Vaughter, Philip; McKenzie, Marcia; Lidstone, Lauri; Wright, Tarah

    2016-01-01

    Purpose: This paper aims to provide an overview of a content analysis of sustainability policies from Canadian post-secondary education institutions. The paper reports findings on the orientations to sustainability evident in the policies; references to other policies within the documents; and other key themes on how sustainability is engaged in…

  15. The Impact of Guided Notes on Post-Secondary Student Achievement: A Meta-Analysis

    ERIC Educational Resources Information Center

    Larwin, Karen H.; Larwin, David A.

    2013-01-01

    The common practice of using of guided notes in the post-secondary classroom is not fully appreciated or understood. In an effort to add to the existing research about this phenomenon, the current investigation expands on previously published research and one previously published meta-analysis that examined the impact of guided notes on…

  16. Campus Sustainability Governance in Canada: A Content Analysis of Post-Secondary Institutions' Sustainability Policies

    ERIC Educational Resources Information Center

    Vaughter, Philip; McKenzie, Marcia; Lidstone, Lauri; Wright, Tarah

    2016-01-01

    Purpose: This paper aims to provide an overview of a content analysis of sustainability policies from Canadian post-secondary education institutions. The paper reports findings on the orientations to sustainability evident in the policies; references to other policies within the documents; and other key themes on how sustainability is engaged in…

  17. An Analysis of Foster Care Placement History and Post-Secondary Graduation Rates

    ERIC Educational Resources Information Center

    Day, Angelique; Dworsky, Amy; Feng, Wenning

    2013-01-01

    Prior research has document significant disparities in post-secondary educational attainment between young adults who had been in foster care and their peers in the general population. This study uses survival analysis to compare the four-year college graduation rate of students who had been in foster care to the graduation rate of first…

  18. Assessing the technical efficiency of health posts in rural Guatemala: a data envelopment analysis

    PubMed Central

    Hernández, Alison R.; Sebastián, Miguel San

    2014-01-01

    Introduction Strengthening health service delivery to the rural poor is an important means of redressing inequities. Meso-level managers can help enhance efficiency in the utilization of existing resources through the application of practical tools to analyze routinely collected data reflecting inputs and outputs. This study aimed to assess the efficiency and change in productivity of health posts over two years in a rural department of Guatemala. Methods Data envelopment analysis was used to measure health posts’ technical efficiency and productivity change for 2008 and 2009. Input/output data were collected from the regional health office of Alta Verapaz for 34 health posts from the 19 districts comprising the health region. Results Technical efficiency varied widely across health posts, with mean scores of 0.78 (SD=0.24) and 0.75 (SD=0.21) in 2008 and 2009, respectively. Overall, productivity increased by 4%, though 47% of health posts experienced a decline in productivity. Results were combined on a bivariate plot to identify health posts at the high and low extremes of efficiency, which should be followed up to determine how and why their production processes are operating differently. Conclusions Assessing efficiency using the data that are available at the meso-level can serve as a first step in strengthening performance. Further work is required to support managers in the routine application of efficiency analysis and putting the results to use in guiding efforts to improve service delivery and increase utilization. PMID:24461356

  19. Post-exercise heart rate variability recovery: a time-frequency analysis.

    PubMed

    Peçanha, Tiago; de Paula-Ribeiro, Marcelle; Nasario-Junior, Olivassé; de Lima, Jorge Roberto Perrout

    2013-12-01

    Most studies investigating the effects of non-pharmacological interventions, such as physical training (PT), on cardiac autonomic control, assessed the HRV only in resting conditions. Recently, a new time-frequency mathematical approach based on the short-time Fourier transform (STFT) method has been validated for the assessment of HRV in non-stationary conditions such as the immediate post-exercise period. The aim of this study was to evaluate the effects of the PT on post-exercise cardiac autonomic control using the time-frequency STFT analysis of the HRV. Twenty-one healthy male volunteers participated in this study. The subjects were initially evaluated for their physical exercise/sport practice and allocated to groups of low physical training ((Low)PT, n = 13) or high physical training (H(igh)PT, n = 8). The post-exercise HRV was assessed by the STFT method, which provides the analysis of dynamic changes in the power of the low- and high-frequency spectral components (LF and HF, respectively) of the HRV during the whole recovery period. Greater LF (from the min 5 to 10) and HF (from the min 6 to 10) in the post-exercise period in the H(igh)PT compared to the (Low)PT group (P < 0.05) was observed. These results indicate that exercise training exerts beneficial effects on post-exercise cardiac autonomic control.

  20. Prevention of post-endoscopic retrograde cholangiopancreatography pancreatitis: a cost-effectiveness analysis.

    PubMed

    Nicolás-Pérez, David; Castilla-Rodríguez, Iván; Gimeno-García, Antonio Z; Romero-García, Rafael; Núñez-Díaz, Venancio; Quintero, Enrique

    2015-03-01

    The aim of the present study was to perform a comparative cost-effectiveness analysis of the different strategies used to prevent post-endoscopic retrograde cholangiopancreatography (ERCP) acute pancreatitis. We performed a cost-effectiveness decision analysis of 4 prophylactic strategies (nonsteroidal anti-inflammatory drugs or NSAIDs, pancreatic stent, stent plus rectal indomethacin, and no prophylaxis) in a simulated cohort of 300 patients during 1 year. Treatment effectiveness was defined as the number of patients who did not develop post-ERCP pancreatitis. The baseline costs of each strategy were as follows: rectal NSAID $359,098, pancreatic stent $426,504, stent plus rectal indomethacin $479,153, and no prophylaxis $491,275. The mean number of cases developing post-ERCP pancreatitis was 16, 21, 23, and 37 for the strategies rectal NSAID, pancreatic stent, stent plus rectal indomethacin, and no prophylaxis, respectively. Taking rectal NSAID prophylaxis as the reference strategy, the odds ratio of an episode of post-ERCP acute pancreatitis after pancreatic stent placement was 1.33 (95% confidence interval [CI], 0.68-2.61); after stent plus indomethacin, it was 1.40 (95% CI, 0.72-2.73), and after no prophylaxis, it was 2.49 (95% CI, 1.35-4.59). Rectal NSAID administration proved to be the most cost-effective prophylactic strategy used to prevent post-ERCP pancreatitis. The strategy of no prophylaxis for this complication should be avoided.

  1. Facilitating cells: Translation of hematopoietic chimerism to achieve clinical tolerance

    PubMed Central

    Ildstad, Suzanne T.; Leventhal, Joseph; Wen, Yujie; Yolcu, Esma

    2015-01-01

    ABSTRACT For over 50 y the association between hematopoietic chimerism and tolerance has been recognized. This originated with the brilliant observation by Dr. Ray Owen that freemartin cattle twins that shared a common placental blood supply were red blood cell chimeras, which led to the discovery that hematopoietic chimerism resulted in actively acquired tolerance. This was first confirmed in neonatal mice by Medawar et al. and subsequently in adult rodents. Fifty years later this concept has been successfully translated to solid organ transplant recipients in the clinic. The field is new, but cell-based therapies are being used with increasing frequency to induce tolerance and immunomodulation. The future is bright. This review focuses on chimerism and tolerance: past, present and prospects for the future. PMID:26745761

  2. High frequency of donor chimerism after allogeneic transplantation of CD34+-selected peripheral blood cells.

    PubMed

    Briones, J; Urbano-Ispizua, A; Lawler, M; Rozman, C; Gardiner, N; Marín, P; Salgado, C; Féliz, P; McCann, S; Montserrat, E

    1998-05-01

    Ex vivo T cell depletion of allogeneic grafts is associated with a high (up to 80%) rate of mixed chimerism (MC) posttransplantation. The number of transplanted progenitor cells is an important factor in achieving complete donor chimerism in the T cell depletion setting. Use of granulocyte colony-stimulating factor (G-CSF) peripheral blood allografts allows the administration of large numbers of CD34+ cells. We studied the chimeric status of 13 patients who received allogeneic CD34+-selected peripheral blood progenitor cell transplants (allo-PBPCTs/CD34+) from HLA-identical sibling donors. Patients were conditioned with cyclophosphamide (120 mg/kg) and total-body irradiation (13 Gy in four fractions). Apheresis products were T cell-depleted by the immunoadsorption avidin-biotin method. The median number of CD34+ and CD3+ cells infused was 2.8x10(6)/kg (range 1.9-8.6x10(6)/kg) and 0.4x10(6)/kg (range 0.3-1x10(6)/kg), respectively. Molecular analysis of the engraftment was performed using polymerase chain reaction (PCR) amplification of highly polymorphic short tandem repeat (PCR-STR) sequences in peripheral blood samples. MC was detected in two (15%) of 13 patients. These two patients relapsed at 8 and 10 months after transplant, respectively. The remaining 11 patients showed complete donor chimerism and were in clinical remission after a maximum follow-up period of 24 months (range 6-24 months). These results were compared with those obtained in 10 patients who were treated with T cell-depleted bone marrow transplantation by means of elutriation and who received the same conditioning treatment and similar amounts of CD3+ cells (median 0.45x10(6)/kg; not significant) but a lower number of CD34+ cells (median 0.8x10(6)/kg; p = 0.001). MC was documented in six of 10 patients (60%), which was significantly higher than in the allo-PBPCT/CD34+ group (p = 0.04). We conclude that a high frequency of complete donor chimerism is achieved in patients receiving allo-PBPCT/CD34

  3. Influence of different post design and composition on stress distribution in maxillary central incisor: Finite element analysis.

    PubMed

    Silva, Natércia R; Castro, Carolina G; Santos-Filho, Paulo C F; Silva, Gisele R; Campos, Roberto E; Soares, Paulo Vinicins; Soares, Carlos José

    2009-01-01

    Post design and material has very important effects on dentinal stress distribution since the post placement can create stresses that lead to root fracture. In this study we use finite element analysis (FEA) to evaluate stress distribution on endodontically treated maxillary central incisors that have been restored with different prefabricated posts. Six models were generated from the image of anatomical plate: Four metallic posts (ParaPost XH, ParaPost XT, ParaPost XP, and Flexi-Flange) and one fiberglass post (ParaPost Fiber Lux). The sixth model was a control-a sound maxillary central incisor. We used CAD software and exported the models to ANSYS 9.0. All the materials and structures were considered elastic, isotropic, homogeneous, and linear except the fiberglass post which was considered orthotropic. The values for the mechanical properties were obtained by a review of the literature and the model was meshed with 8-node tetrahedral elements. A load of 2N was applied to the lingual surface at an angle of 135 degrees. The stress results were recorded by shear stress and von Mises criteria; it was observed that there was no difference for stress distribution among the titanium posts in the radicular portions and into posts. There was higher stress concentration on the coronary portion with the titanium posts than with the glass fiber post. It seems that the metallic posts' external configuration does not influence the stress distribution. Fiber posts show more homogeneous stress distribution than metallic posts. The post material seems to be more relevant for the stress distribution in endodontically treated teeth than the posts' external configuration.

  4. Influence of fiber post cementation length on coronal microleakage values in vitro and finite element analysis.

    PubMed

    Bergoli, Cásar Dalmolin; de Carvalho, Rodrigo Furtado; Balducci, Ivan; Meira, Josete Barbosa Cruz; de Araújo, Maria Amália Méximo; Valera, Marcia Carneiro

    2014-07-01

    This study aims to evaluate, the Influence of different fiber posts cementation lengths by finite element analysis (FEA) and coronal microleakage. Fifty anterior bovine teeth were sectioned to obtain roots with 16 mm length. The coronal length of the post was 6 mm for all groups, while the radicular length were varied 6, 8, 10 or 12 mm. The fiber posts surfaces were cleaned with alcohol and silanized. Then the posts were cemented using a two steps total etch-and-rinse adhesive system + conventional resin cement. Forty teeth were submitted to mechanical cycling (45°; 2.000.000 cycles; 90N; 4Hz; 37°C) and ten teeth with radicular length of 12 mm was not submitted, ser ving as c ontrol. So, the experimental design was composed by different ratios of post coronal length/post radicular length and mechanical cycling (MC): Gr1- 1/1 + MC; Gr2- 3/4 + MC; Gr3- 3/5 + MC; Gr4- 1/2 + MC. All groups were immersed in a 1% toluidine blue solution. After 24 hours, the teeth were longitudinally sectioned and the microleakage scores was given by a blind operator. Data were submitted to Kruskal-Wallis test (p = 0.05). The experimental variables were simulated in two-dimensional finite element analysis (2D-FEA). The maximum principal stress distributions were compared. No difference was observed in microleakage values between the cycled groups, whilst the control groups showed the lowest values. FEA analysis showed similar maximum principal stress distribution between the groups. Mechanical cycling affected the values of coronal microleakage and different cementation length generated similar values of coronal microleakage and stress distribution. These results showed that from the microleakage point of view, more conservative cementation lengths have the same effect as longer cementation lengths.

  5. TOPP: A post-processor for TOPAZ, the one dimensional pipe flow analysis code

    SciTech Connect

    Martin, R.W.

    1987-07-01

    TOPP is a Lawrence Livermore National Laboratory (LLNL) post-processor for producing graphical results from the one dimensional pipe flow analysis code, TOPAZ. TOPAZ was written by W. S. Winters of Sandia National Laboratory, Livermore (SNLL) and is available on the CRAY computers at LLNL. The SNLL version of TOPAZ produces a very limited set of variables that can be used as input to a post-processor. The version at LLNL has been modified to output every time-dependent variable to an absolute binary file at the user specified minor edit frequency. TOPP reads this absolute binary file and produces a variety of graphical results. 2 refs.

  6. Failure mode analysis of a post-tension anchored dam using linear finite element analysis

    NASA Astrophysics Data System (ADS)

    Corn, Aimee

    There are currently over 84,000 dams in the United States, and the average age of those dams is 52 years. Concrete gravity dams are the second most common dam type, with more than 3,000 in the United States. Current engineering technology and technical understanding of hydrologic and seismic events has resulted in significant increases to the required design loads for most dams; therefore, many older dams do not have adequate safety for extreme loading events. Concrete gravity dams designed and constructed in the early 20th century did not consider uplift pressures beneath the dam, which reduces the effective weight of the structure. One method that has been used to enhance the stability of older concrete gravity dams includes the post-tension anchor (PTA) system. Post-tensioning infers modifying cured concrete and using self-equilibrating elements to increase the weight of the section, which provides added stability. There is a lack of historical evidence regarding the potential failure mechanisms for PTA concrete gravity dams. Of particular interest, is how these systems behave during large seismic events. The objective of this thesis is to develop a method by which the potential failure modes during a seismic event for a PTA dam can be evaluated using the linear elastic finite element method of analysis. The most likely potential failure modes (PFM) for PTA designs are due to tensile failure and shear failure. A numerical model of a hypothetical project was developed to simulate PTAs in the dam. The model was subjected to acceleration time-history motions that simulated the seismic loads. The results were used to evaluate the likelihood of tendon failure due to both tension and shear. The results from the analysis indicated that the PTA load increased during the seismic event; however, the peak load in the tendons was less than the gross ultimate tensile strength (GUTS) and would not be expected to result in tensile failure at the assumed project. The analysis

  7. Long duration exposure facility post-flight thermal analysis, part 1

    NASA Technical Reports Server (NTRS)

    Berrios, William M.; Sampair, Thomas R.

    1992-01-01

    Results of the post-flight thermal analysis of the Long Duration Exposure Facility (LDEF) mission are presented. The LDEF mission thermal analysis was verified by comparing the thermal model results to flight data from the LDEF Thermal Measurements System (THERM). Post-flight calculated temperature uncertainties have been reduced to under +/- 18 F from the pre-flight uncertainties of +/- 40 F. The THERM consisted of eight temperature sensors, a shared tape recorder, a standard LDEF flight battery, and an electronics control box. The temperatures were measured at selected locations on the LDEF structure interior during the first 390 days of flight and recorded for post-flight analysis. After the LDEF retrieval from Space on 12 Jan. 1990, the tape recorder was recovered from the spacecraft and the data reduced for comparison to the LDEF predicted temperatures. The LDEF mission temperatures were calculated prior to the LDEF deployment on 7 Apr. 1980, and updated after the LDEF retrieval with the following actual flight parameter data: including thermal fluxes, spacecraft attitudes, thermal coatings degradation, and contamination effects. All updated data used for the calculation of post-flight temperatures is also presented in this document.

  8. Long duration exposure facility post-flight thermal analysis, part 2

    NASA Technical Reports Server (NTRS)

    Berrios, William M.; Sampair, Thomas R.

    1992-01-01

    Results of the post-flight thermal analysis for the Long Duration Exposure Facility (LDEF) mission are presented. The LDEF mission thermal analysis was verified by comparing the thermal model results to flight data from the LDEF Thermal Measurements System (THERM). Post-flight calculated temperature uncertainties have been reduced to under +/- 18 F from the pre-flight uncertainties of +/- 40 F. The THERM consisted of eight temperature sensors, a shared tape recorder, a standard LDEF flight battery, and an electronics control box. The temperatures were measured at selected locations on the LDEF structure interior during the first 390 days of flight and recorded for post-flight analysis. After the LDEF retrieval from Space on 12 Jan. 1990, the tape recorder was recovered from the spacecraft and the data reduced for comparison to the LDEF predicted temperatures. The LDEF mission temperatures were calculated prior to the LDEF deployment on 7 Apr. 1980, and updated after the LDEF retrieval with the following actual flight parameter data: thermal fluxes, spacecraft attitudes, thermal coatings degradation, and contamination effects. All updated data used for calculation of post-flight temperatures is also presented in this document.

  9. Uncertainty characterization and quantification in air pollution models. Application to the CHIMERE model

    NASA Astrophysics Data System (ADS)

    Debry, Edouard; Mallet, Vivien; Garaud, Damien; Malherbe, Laure; Bessagnet, Bertrand; Rouïl, Laurence

    2010-05-01

    probability density function (PDF) is associated with an input parameter, according to its assumed uncertainty. Then the combined PDFs are propagated into the model, by means of several simulations with randomly perturbed input parameters. One may then obtain an approximation of the PDF of modeled concentrations, provided the Monte Carlo process has reasonably converged. The uncertainty analysis with CHIMERE has been led with a Monte Carlo method on the French domain and on two periods : 13 days during January 2009, with a focus on particles, and 28 days during August 2009, with a focus on ozone. The results show that for the summer period and 500 simulations, the time and space averaged standard deviation for ozone is 16 µg/m3, to be compared with an averaged concentration of 89 µg/m3. It is noteworthy that the space averaged standard deviation for ozone is relatively constant over time (the standard deviation of the timeseries itself is 1.6 µg/m3). The space variation of the ozone standard deviation seems to indicate that emissions have a significant impact, followed by western boundary conditions. Monte Carlo simulations are then post-processed by both ensemble [4] and Bayesian [5] methods in order to assess the quality of the uncertainty estimation. (1) Rao, K.S. Uncertainty Analysis in Atmospheric Dispersion Modeling, Pure and Applied Geophysics, 2005, 162, 1893-1917. (2) Beekmann, M. and Derognat, C. Monte Carlo uncertainty analysis of a regional-scale transport chemistry model constrained by measurements from the Atmospheric Pollution Over the Paris Area (ESQUIF) campaign, Journal of Geophysical Research, 2003, 108, 8559-8576. (3) Hanna, S.R. and Lu, Z. and Frey, H.C. and Wheeler, N. and Vukovich, J. and Arunachalam, S. and Fernau, M. and Hansen, D.A. Uncertainties in predicted ozone concentrations due to input uncertainties for the UAM-V photochemical grid model applied to the July 1995 OTAG domain, Atmospheric Environment, 2001, 35, 891-903. (4) Mallet, V., and B

  10. Analysis of Post-Deployment Cognitive Performance and Symptom Recovery in U.S. Marines

    PubMed Central

    Haran, F. J.; Alphonso, Aimee L.; Creason, Alia; Campbell, Justin S.; Johnson, Dagny; Young, Emily; Tsao, Jack W.

    2013-01-01

    Background Computerized neurocognitive testing (NCAT) has been proposed to be useful as a screening tool for post-deployment cognitive deficits in the setting of mild traumatic brain injury (mTBI). We assessed the clinical utility of post-injury/post-deployment Automated Neurocognitive Assessment Metric (ANAM) testing, using a longitudinal design to compare baseline ANAM tests with two post-deployment ANAM tests in a group of Marines who experienced combat during deployment. Methods and Findings Post-deployment cognitive performance and symptom recovery were compared in a subsample of 1324 U.S. Marines with high rates of combat exposure during deployment. Of the sample, 169 Marines had available baseline and twice repeated post-deployment ANAM results. A retrospective analysis of the ANAM data, which consisted of a self-report questionnaire about deployment-related blast exposure, recent history of mTBI, current clinical symptoms, and cognitive performance. Self-reported concussion sustained anytime during deployment was associated with a decrease in cognitive performance measured between 2–8 weeks post-deployment. At the second post-deployment test conducted on average eight months later, performance on the second simple reaction time test, in particular, remained impaired and was the most consistent and sensitive indicator of the cognitive decrements. Additionally, post-concussive symptoms were shown to persist in injured Marines with a self-reported history of concussion for an additional five months after most cognitive deficits resolved. Results of this study showed a measurable deployment effect on cognitive performance, although this effect appears to resolve without lasting clinical sequelae in those without history of deployment-related concussion. Conclusions These results highlight the need for a detailed clinical examination for service members with history of concussion and persistent clinical symptoms. Reliance solely upon computerized

  11. Intron retention and transcript chimerism conserved across mammals: Ly6g5b and Csnk2b-Ly6g5b as examples

    PubMed Central

    2013-01-01

    Background Alternative splicing (AS) is a major mechanism for modulating gene expression of an organism, allowing the synthesis of several structurally and functionally distinct mRNAs and protein isoforms from a unique gene. Related to AS is the Transcription Induced Chimerism (TIC) or Tandem Chimerism, by which chimeric RNAs between adjacent genes can be found, increasing combinatorial complexity of the proteome. The Ly6g5b gene presents particular behaviours in its expression, involving an intron retention event and being capable to form RNA chimera transcripts with the upstream gene Csnk2b. We wanted to characterise these events more deeply in four tissues in six different mammals and analyse their protein products. Results While canonical Csnk2b isoform was widely expressed, Ly6g5b canonical isoform was less ubiquitous, although the Ly6g5b first intron retained transcript was present in all the tissues and species analysed. Csnk2b-Ly6g5b chimeras were present in all the samples analysed, but with restricted expression patterns. Some of these chimeric transcripts maintained correct structural domains from Csnk2b and Ly6g5b. Moreover, we found Csnk2b, Ly6g5b, and Csnk2b-Ly6g5b transcripts that present exon skipping, alternative 5' and 3' splice site and intron retention events. These would generate truncated or aberrant proteins whose role remains unknown. Some chimeric transcripts would encode CSNK2B proteins with an altered C-terminus, which could affect its biological function broadening its substrate specificity. Over-expression of human CSNK2B, LY6G5B, and CSNK2B-LY6G5B proteins, show different patterns of post-translational modifications and cell distribution. Conclusions Ly6g5b intron retention and Csnk2b-Ly6g5b transcript chimerism are broadly distributed in tissues of different mammals. PMID:23521802

  12. A qualitative analysis of the nursing documentation of post-operative pain management.

    PubMed

    Briggs, M; Dean, K L

    1998-03-01

    As part of trust-wide practice development project to improve post-operative pain management, a descriptive study was conducted in the orthopaedic directorate of a large teaching hospital in the north of England. Sixty-five patients were included in this prospective study. Patients were interviewed post-operatively about their pain experience, and present and worst pain scores were recorded. The nursing documentation relating to pain management was also transcribed and a content analysis of this nursing documentation is reported. Findings indicate that individual assessment of pain was poorly documented and that the nurses' record of the patient's post-operative pain experience differed from the patient report. Reliance on pharmacological methods of pain relief was evident and interventions to help patients cope with night time pain were rarely documented. The results are discussed in light of a theoretical framework for acute pain management and current research. Implications for practice are discussed and areas for further research are suggested.

  13. 78 FR 16505 - Prospective Grant of Exclusive License: Chimeric West Nile/Dengue Viruses

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-15

    ...: Chimeric West Nile/Dengue Viruses AGENCY: Centers for Disease Control and Prevention (CDC), Department of... Application 61/049,342, filed 4/30/2008, entitled ``Engineered, Chimeric West Nile/Dengue Viruses;'' PCT..., filed 10/29/2010, entitled ``Chimeric West Nile/Dengue Viruses;'' and all related continuing and foreign...

  14. Use of ubiquitous, highly heterozygous copy number variants and digital droplet polymerase chain reaction to monitor chimerism after allogeneic haematopoietic stem cell transplantation.

    PubMed

    Whitlam, John B; Ling, Ling; Swain, Michael; Harrington, Tom; Mirochnik, Oksana; Brooks, Ian; Cronin, Sara; Challis, Jackie; Petrovic, Vida; Bruno, Damien L; Mechinaud, Francoise; Conyers, Rachel; Slater, Howard

    2017-05-01

    Chimerism analysis has an important role in the management of allogeneic hematopoietic stem cell transplantation. It informs response to disease relapse, graft rejection, and graft-versus-host disease. We have developed a method for chimerism analysis using ubiquitous copy number variation (CNV), which has the benefit of a "negative background" against which multiple independent informative markers are quantified using digital droplet polymerase chain reaction. A panel of up to 38 CNV markers with homozygous deletion frequencies of approximately 0.4-0.6 were used. Sensitivity, precision, reproducibility, and informativity were assessed. CNV chimerism results were compared against established fluorescence in situ hybridization, single nucleotide polymorphism, and short tandem repeat-based methods with excellent correlation. Using 30 ng of input DNA per well, the limit of detection was 0.05% chimerism and the limit of quantification was 0.5% chimerism. High informativity was seen with a median of four informative markers detectable per individual in 39 recipients and 43 donor genomes studied. The strength of this approach was exemplified in a multiple donor case involving four genomes (three related). The precision, sensitivity, and informativity of this approach recommend it for use in clinical practice. Copyright © 2017 ISEH - International Society for Experimental Hematology. Published by Elsevier Inc. All rights reserved.

  15. Prophylactic clipping and post-polypectomy bleeding: a meta-analysis and systematic review

    PubMed Central

    Boumitri, Christine; Mir, Fazia A.; Ashraf, Imran; Matteson-Kome, Michelle L.; Nguyen, Douglas L.; Puli, Srinivas R.; Bechtold, Matthew L.

    2016-01-01

    Background Bleeding after polypectomy is a common issue associated with colonoscopy. To help prevent post-polypectomy bleeding, many endoscopists place clips at the site. However, this practice remains controversial. Therefore, we performed a meta-analysis of the efficacy of clip placement in the prevention of post-polypectomy bleeding. Methods Multiple databases, including Embase, Scopus, MEDLINE/PubMed, CINAHL, Cochrane databases, and recent abstracts from major American meetings were searched in April 2016. Using the DerSimonian and Laird (random effects) model with odds ratio (OR), a meta-analysis was performed of post-polypectomy bleeding with prophylactic clip versus no prophylactic clip. Results Five hundred and thirty potential articles and abstracts were discovered. Thirty-five articles were reviewed, with 12 studies satisfying the inclusion criteria. No statistically significant difference in prophylactic clipping versus no prophylactic clipping for post-polypectomy bleeding in all polyps was found when all studies (OR 1.49; 95% CI: 0.56–4.00; P=0.42), only peer-reviewed studies where abstracts were excluded (OR 0.84; 95% CI: 0.42–1.69; P=0.63), and only randomized controlled trials (OR 1.24; 95% CI: 0.69–2.24; P=0.47) were analyzed. Conclusions The use of prophylactic clipping for all polypectomies does not seem to prevent post-polypectomy bleeding and should not be a routine practice. However, for large polyps (>2 cm), prophylactic clipping may or may not be beneficial in preventing post-polypectomy bleeding. Further studies are required to fully evaluate this subgroup. PMID:27708518

  16. Genetic analysis of post-weaning growth traits of Thalli sheep under tropical conditions.

    PubMed

    Hussain, Asghar; Akhtar, Pervez; Ali, Safdar; Javed, Khalid; Younas, Muhammad; Shakoor, Abdul; Waheed, Usman

    2014-12-01

    Present investigation was carried out to study the influence of genetic and non-genetic factors affecting post-weaning performance traits in Thalli sheep. Data on post-weaning growth of Thalli sheep maintained at Livestock Experiment Station, Rakh Ghulaman, District Bhakkar-Punjab, Pakistan during 1977-2003 were subjected to genetic analysis. The average values for weight at 180 and 270 days of age, yearling weight and post-weaning average daily gain were 22.37 ± 4.21, 25.96 ± 4.90 and 28.93 ± 5.20 kg and 28 ± 0.01 g/day, respectively. Weight at 180, 270 and 365 days of age and post-weaning average daily gain were significantly affected by year of birth, sex, type of birth and weaning weight (covariable) whereas season of birth was a significant source of variation for 180 and 270 days of age. The heritability estimates for 180 and 270 days, yearling weight and post-weaning average daily gain were 0.07 ± 0.02, 0.08 ± 0.02, 0.07 ± 0.02 and 0.07 ± 0.02, respectively.

  17. [Analysis of prognostic factors in Chinese patients with post-polycythemia vera myelofibrosis and post-essential thrombocythemia myelofibrosis].

    PubMed

    Chen, M; Xu, Z F; Xu, J Q; Li, B; Zhang, P H; Qin, T J; Zhang, Y; Wang, J Y; Zhang, H L; Fang, L W; Pan, L J; Hu, N B; Qu, S Q; Xiao, Z J

    2016-10-14

    Objective: To evaluate the performances of the prognostic scoring systems devised for primary myelofibrosis(PMF)and the new developed MYSEC- PM(Mysec Prognostic Model)and investigate the risk factors in Chinese patients with post-polycythemia vera myelofibrosis and post-essential thrombocythemia myelofibrosis(post- PV/ET MF). The most widely used prognostic scoring systems in PMF included the International Prognostic Scoring System(IPSS), dynamic International Prognostic Scoring System(DIPSS), refined DIPSS(DIPSS plus), modified IPSS for Chinese(IPSS-Chinese), and modified DIPSS for Chinese(DIPSS- Chinese). Methods: The clinical and hematologic information of 55 consecutive patients diagnosed with post- PV/ET MF from March 1984 to December 2013 were retrospectively collected. All post-PV/ET MF patients were categorized according to IPSS, DIPSS, DIPSS plus, IPSS-Chinese, DIPSS-Chinese and MYSEC-PM, and the possible prognostic factors were statistically analyzed. Results: Fifty five patients diagnosed with post-PV MF(n=32)or post-ET MF(n=23)were analyzed with a median age of 59(range: 20- 88)years old, including 20 males and 35 females. Median time from original diagnosis to myelofibrosis was 7.8(range: 1.1- 23.4)years. With a median follow up from post-PV/ET MF diagnosis of 37(range: 1-156)months, 44(80.0%)patients were censored alive, 11(20.0%)patients died. Median survival was 110(95% CI 87.5-132.8)months. Using IPSS, DIPSS, DIPSS plus, IPSS- Chinese and MYSEC- PM criteria, there were no statistically significances in survival among different risk groups(P>0.05). In univariate analyses HGB<100 g/L(P=0.003)was the only factor associated with poorer overall survival. The prognosis in subjects with HGB≥100 g/L was significantly better than that with HGB<100 g/L(median OS: not reached vs 47 months, P=0.003). Conclusion: IPSS, DIPSS, DIPSS plus, IPSS- Chinese and MYSEC- PM did not accurately discriminate different risk categories in post PV/ET MF patients. HGB< 100 g

  18. SSME LOX post flow analysis/fluid structure interaction. Volume 1: Flow analysis

    NASA Technical Reports Server (NTRS)

    Burke, Roger W.

    1989-01-01

    The realization of measures to improve the performance of the Space Shuttle is, to a large extent, dependent on an improved understanding of the fluid flow phenomena occurring in the main engine. The overall arrangement of the primary components of the Space Shuttle Main Engine (SSME) are presented. The impingement of the hot gases from the transfer ducts onto the LOX posts causes them to be subjected to severe thermal and gas dynamic loads, which in the past have resulted in the occasional breakage of some elements of the outer row of posts during test firings of the engine, particularly at higher power levels. Large velocities in the gap between the LOX posts may also be a contributing factor in causing dynamic stability problems. The deforming structural response of the posts to the pressure loading may likely affect the gas flowfield by producing a moving flowfield boundary, thereby creating a dynamically coupled unsteady fluid-structure system. The objective was to investigate the three-dimensional, turbulent flow around a simplified SSME LOX post array using an existing Reynolds averaged Navier-Stokes flow solver and a suitable turbulence model to parameterize the turbulent shear stresses. Numerical computations were performed to analyze the effect on the flowfield of varying the spacing between the LOX posts, which were modeled as rigid, three-dimensional circular cylinders. The methodology used in the computations is described. Results are presented.

  19. Quality of post-operative patient handover in the post-anaesthesia care unit: a prospective analysis.

    PubMed

    Milby, A; Böhmer, A; Gerbershagen, M U; Joppich, R; Wappler, F

    2014-02-01

    Anaesthesiology plays a key role in promoting safe perioperative care. This includes the perioperative phase in the post-anaesthesia care unit (PACU) where problems with incomplete information transfer may have a negative impact on patient safety and can lead to patient harm. The objective of this study was to analyse information transfer during post-operative handovers in the PACU. With a self-developed checklist including 59 items the information transfer during post-operative handovers was documented and subsequently compared with patient information in anaesthesia records during a 2-month period. A total number of 790 handovers with duration of 73 ± 49 s was analysed. Few items were transferred in most of the cases such as type of surgery (97% of the cases), regional anaesthesia (94% of the cases) and cardiac instability (93% of the cases). However, some items were rarely transferred, such as American Society of Anesthesiologists physical status (7% of the cases), initiation of post-operative pain management (12% of the cases), antibiotic therapy (14% of the cases) and fluid management (15% of the cases). There was a slight correlation between amount of information transferred and duration of post-operative handovers (r = 0.5). The study shows that post-operative handovers in the PACU are in most cases incomplete. It appears useful to optimise the post-operative handover process, for example by implementing a standardised handover checklist. © 2013 The Acta Anaesthesiologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

  20. The effects of post-persulfate-digestion procedures on total phosphorus analysis in water.

    PubMed

    Zhou, Meifang; Struve, David M

    2004-11-01

    There are differences between the EPA Method 365 and the APHA-AWWA-WEF's Standard Method 4500 with respect to the post-digestion treatment procedures of the persulfate-digested water. The effects on total phosphorus analysis of different post-digestion treatment procedures, such as neutralization and reacidification, and shaking/settling, were investigated in this study using the total phosphorus measurements of water samples from the Everglades Round Robin (ERR) study and comparing the results with the ERR study. The effects of the insoluble particles or phosphorus adsorption/precipitation on/with Al and Fe hydroxides in different post-digestion treatment procedures adequately accounted for the differences between the most probable value and the higher or lower total phosphorus measurements reported in the ERR study. Based on the results of this investigation we recommend that a clearly defined set of digestion and post-digestion treatment procedures be adopted as the standard for total phosphorus analysis using the ascorbic acid method.

  1. A postprocessor system for the data reduction and post analysis of NASTRAN results

    NASA Technical Reports Server (NTRS)

    Raibstein, A. I.; Emil, S.; Pipano, A.

    1976-01-01

    NASTRAN analysis results are scanned to determine maximum and minimum displacements, forces and stresses. Allowables and margins of safety are computed, and in the case of multiple loading conditions, envelopes for displacements, forces, stresses and margins of safety are also produced for specified element sets. Graphical plots of the reduced or the regular NASTRAN results may be obtained superimposed either of a developed fuselage strip or on a projection of any specified part of the finite element model. The use of the data reduction, post analysis and graphical plotting capabilities provide the analyst with a fast and convenient tool for the study of NASTRAN analysis results and their presentation for project documentation.

  2. Integrated proteomic analysis of post-translational modifications by serial enrichment

    PubMed Central

    Mertins, Philipp; Qiao, Jana W; Patel, Jinal; Udeshi, Namrata D; Clauser, Karl R; Mani, D R; Burgess, Michael W; Gillette, Michael A; Jaffe, Jacob D; Carr, Steven A

    2014-01-01

    We report a mass spectrometry–based method for the integrated analysis of protein expression, phosphorylation, ubiquitination and acetylation by serial enrichments of different post-translational modifications (SEPTM) from the same biological sample. this technology enabled quantitative analysis of nearly 8,000 proteins and more than 20,000 phosphorylation, 15,000 ubiquitination and 3,000 acetylation sites per experiment, generating a holistic view of cellular signal transduction pathways as exemplified by analysis of bortezomib-treated human leukemia cells. PMID:23749302

  3. Therapeutic use of chimeric bacteriophage (phage) lysins in staphylococcal endophthalmitis

    USDA-ARS?s Scientific Manuscript database

    Purpose: Phage endolysins are peptidoglycan hydrolases that are produced at the end of the phage lytic cycle to digest the host bacterial cell wall, facilitating the release of mature phage progeny. The aim of this study is to determine the antimicrobial activity of chimeric phage lysins against cli...

  4. Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster.

    PubMed

    Rogers, Rebekah L; Bedford, Trevor; Lyons, Ana M; Hartl, Daniel L

    2010-06-15

    Chimeric genes, which form through the genomic fusion of two protein-coding genes, are a significant source of evolutionary novelty in Drosophila melanogaster. However, the propensity of chimeric genes to produce adaptive phenotypic changes is not fully understood. Here, we describe the chimeric gene Quetzalcoatl (Qtzl; CG31864), which formed in the recent past and swept to fixation in D. melanogaster. Qtzl arose through a duplication on chromosome 2L that united a portion of the mitochondrially targeted peptide CG12264 with a segment of the polycomb gene escl. The 3' segment of the gene, which is derived from escl, is inherited out of frame, producing a unique peptide sequence. Nucleotide diversity is drastically reduced and site frequency spectra are significantly skewed surrounding the duplicated region, a finding consistent with a selective sweep on the duplicate region containing Qtzl. Qtzl has an expression profile that largely resembles that of escl, with expression in early pupae, adult females, and male testes. However, expression patterns appear to have been decoupled from both parental genes during later embryonic development and in head tissues of adult males, indicating that Qtzl has developed a distinct regulatory profile through the rearrangement of different 5' and 3' regulatory domains. Furthermore, misexpression of Qtzl suppresses defects in the formation of the neuromuscular junction in larvae, demonstrating that Qtzl can produce phenotypic effects in cells. Together, these results show that chimeric genes can produce structural and regulatory changes in a single mutational step and may be a major factor in adaptive evolution.

  5. Ray Owen and the history of naturally acquired chimerism

    PubMed Central

    Martin, Aryn

    2015-01-01

    abstract This article interweaves a history of Ray Owen's early work with a broader account of the conceptual landscape of immunology in the mid 1950's. In particular, Owen's openness to the very possibility of chimeric phenomena is recognized. PMID:27093621

  6. Systematic evaluation of atmospheric chemistry-transport model CHIMERE

    NASA Astrophysics Data System (ADS)

    Khvorostyanov, Dmitry; Menut, Laurent; Mailler, Sylvain; Siour, Guillaume; Couvidat, Florian; Bessagnet, Bertrand; Turquety, Solene

    2017-04-01

    Regional-scale atmospheric chemistry-transport models (CTM) are used to develop air quality regulatory measures, to support environmentally sensitive decisions in the industry, and to address variety of scientific questions involving the atmospheric composition. Model performance evaluation with measurement data is critical to understand their limits and the degree of confidence in model results. CHIMERE CTM (http://www.lmd.polytechnique.fr/chimere/) is a French national tool for operational forecast and decision support and is widely used in the international research community in various areas of atmospheric chemistry and physics, climate, and environment (http://www.lmd.polytechnique.fr/chimere/CW-articles.php). This work presents the model evaluation framework applied systematically to the new CHIMERE CTM versions in the course of the continuous model development. The framework uses three of the four CTM evaluation types identified by the Environmental Protection Agency (EPA) and the American Meteorological Society (AMS): operational, diagnostic, and dynamic. It allows to compare the overall model performance in subsequent model versions (operational evaluation), identify specific processes and/or model inputs that could be improved (diagnostic evaluation), and test the model sensitivity to the changes in air quality, such as emission reductions and meteorological events (dynamic evaluation). The observation datasets currently used for the evaluation are: EMEP (surface concentrations), AERONET (optical depths), and WOUDC (ozone sounding profiles). The framework is implemented as an automated processing chain and allows interactive exploration of the results via a web interface.

  7. Chimeric Genes in Deletions and Duplications Associated with Intellectual Disability

    PubMed Central

    Monfort, Sandra; Roselló, Mónica; Oltra, Silvestre; Caro-Llopis, Alfonso

    2017-01-01

    We report on three nonrelated patients with intellectual disability and CNVs that give rise to three new chimeric genes. All the genes forming these fusion transcripts may have an important role in central nervous system development and/or in gene expression regulation, and therefore not only their deletion or duplication but also the resulting chimeric gene may contribute to the phenotype of the patients. Deletions and duplications are usually pathogenic when affecting dose-sensitive genes. Alternatively, a chimeric gene may also be pathogenic by different gain-of-function mechanisms that are not restricted to dose-sensitive genes: the emergence of a new polypeptide that combines functional domains from two different genes, the deregulated expression of any coding sequence by the promoter region of a neighboring gene, and/or a putative dominant-negative effect due to the preservation of functional domains of partially truncated proteins. Fusion oncogenes are well known, but in other pathologies, the search for chimeric genes is disregarded. According to our findings, we hypothesize that the frequency of fusion transcripts may be much higher than suspected, and it should be taken into account in the array-CGH analyses of patients with intellectual disability. PMID:28630856

  8. Synthesis of a heterogeneous artificial metallolipase with chimeric catalytic activity.

    PubMed

    Filice, M; Romero, O; Gutiérrez-Fernández, J; de Las Rivas, B; Hermoso, J A; Palomo, J M

    2015-06-07

    A solid-phase strategy using lipase as a biomolecular scaffold to produce a large amount of Cu(2+)-metalloenzyme is proposed here. The application of this protocol on different 3D cavities of the enzyme allows creating a heterogeneous artificial metallolipase showing chimeric catalytic activity. The artificial catalyst was assessed in Diels-Alder cycloaddition reactions and cascade reactions showing excellent catalytic properties.

  9. Construction of yellow fever-influenza A chimeric virus particles.

    PubMed

    Oliveira, B C E P D; Liberto, M I M; Barth, O M; Cabral, M C

    2002-12-01

    In order to obtain a better understanding of the functional mechanisms involved in the fusogenesis of enveloped viruses, the influenza A (X31) and the yellow fever (17DD) virus particles were used to construct a chimeric structure based on their distinct pH requirements for fusion, and the distinct malleability of their nucleocapsids. The malleable nucleocapsid of the influenza A virus particle is characterized by a pleomorphic configuration when observed by electron microscopy. A heat inactivated preparation of X31 virus was used as a lectin to interact with the sialic acid domains present in the 17DD virus envelope. The E spikes of 17DD virus were induced to promote fusion of both envelopes, creating a double genome enveloped structure, the chimeric yellow fever-influenza A virus particle. These chimeric viral particles, originally denominated 'partículas virais quiméricas' (PVQ), were characterized by their infectious capacity for different biological systems. Cell inoculation with PVQ resulted in viral products that showed similar characteristics to those obtained after 17DD virus infections. Our findings open new opportunities towards the understanding of both virus particles and aspects of cellular physiologic quality control. The yellow fever-influenza A chimeric particles, by means of their hybrid composition, should be a valuable tool in the study of cell biology and the function of viral components.

  10. Blog Posting After Lung Cancer Notification: Content Analysis of Blogs Written by Patients or Their Families.

    PubMed

    Sato, Akira; Aramaki, Eiji; Shimamoto, Yumiko; Tanaka, Shiro; Kawakami, Koji

    2015-05-18

    The advent and spread of the Internet has changed the way societies communicate. A portion of information on the Internet may constitute an important source of information concerning the experiences and thoughts of patients and their families. Patients and their families use blogs to obtain updated information, search for alternative treatments, facilitate communication with other patients, and receive emotional support. However, much of this information has yet to be actively utilized by health care professionals. We analyzed health-related information in blogs from Japan, focusing on the feelings and satisfaction levels of lung cancer patients or their family members after being notified of their disease. We collected 100 blogs written in Japanese by patients (or their families) who had been diagnosed with lung cancer by a physician. These 100 blogs posts were searchable between June 1 and June 30, 2013. We focused on blog posts that addressed the lung cancer notification event. We analyzed the data using two different approaches (Analysis A and Analysis B). Analysis A was blog content analysis in which we analyzed the content addressing the disease notification event in each blog. Analysis B was patient's dissatisfaction and anxiety analysis. Detailed blog content regarding patient's dissatisfaction and anxiety at the individual sentence level was coded and analyzed. The 100 blog posts were written by 48 men, 46 women, and 6 persons whose sex was undisclosed. The average age of the blog authors was 52.4 years. With regard to cancer staging, there were 5 patients at Stage I, 3 patients at Stage II, 14 patients at Stage III, 21 patients at Stage IV, and 57 patients without a disclosed cancer stage. The results of Analysis A showed that the proportion of patients who were dissatisfied with the level of health care exceeded that of satisfied patients (22% vs 8%). From the 2499 sentences in the 100 blog posts analyzed, we identified expressions of dissatisfaction and

  11. Attitudes of Crohn's Disease Patients: Infodemiology Case Study and Sentiment Analysis of Facebook and Twitter Posts.

    PubMed

    Roccetti, Marco; Marfia, Gustavo; Salomoni, Paola; Prandi, Catia; Zagari, Rocco Maurizio; Gningaye Kengni, Faustine Linda; Bazzoli, Franco; Montagnani, Marco

    2017-08-09

    Data concerning patients originates from a variety of sources on social media. The aim of this study was to show how methodologies borrowed from different areas including computer science, econometrics, statistics, data mining, and sociology may be used to analyze Facebook data to investigate the patients' perspectives on a given medical prescription. To shed light on patients' behavior and concerns, we focused on Crohn's disease, a chronic inflammatory bowel disease, and the specific therapy with the biological drug Infliximab. To gain information from the basin of big data, we analyzed Facebook posts in the time frame from October 2011 to August 2015. We selected posts from patients affected by Crohn's disease who were experiencing or had previously been treated with the monoclonal antibody drug Infliximab. The selected posts underwent further characterization and sentiment analysis. Finally, an ethnographic review was carried out by experts from different scientific research fields (eg, computer science vs gastroenterology) and by a software system running a sentiment analysis tool. The patient feeling toward the Infliximab treatment was classified as positive, neutral, or negative, and the results from computer science, gastroenterologist, and software tool were compared using the square weighted Cohen's kappa coefficient method. The first automatic selection process returned 56,000 Facebook posts, 261 of which exhibited a patient opinion concerning Infliximab. The ethnographic analysis of these 261 selected posts gave similar results, with an interrater agreement between the computer science and gastroenterology experts amounting to 87.3% (228/261), a substantial agreement according to the square weighted Cohen's kappa coefficient method (w2K=0.6470). A positive, neutral, and negative feeling was attributed to 36%, 27%, and 37% of posts by the computer science expert and 38%, 30%, and 32% by the gastroenterologist, respectively. Only a slight agreement was

  12. Dystrophic Muscle in Mice Chimeric for Expression of α5 Integrin

    PubMed Central

    Taverna, Daniela; Disatnik, Marie-Helene; Rayburn, Helen; Bronson, Roderick T.; Yang, Joy; Rando, Thomas A.; Hynes, Richard O.

    1998-01-01

    α5-deficient mice die early in embryogenesis (Yang et al., 1993). To study the functions of α5 integrin later in mouse embryogenesis and during adult life we generated α5 −/−;+/+ chimeric mice. These animals contain α5-negative and positive cells randomly distributed. Analysis of the chimerism by glucose- 6-phosphate isomerase (GPI) assay revealed that α5 −/− cells contributed to all the tissues analyzed. High contributions were observed in the skeletal muscle. The perinatal survival of the mutant chimeras was lower than for the controls, however the subsequent life span of the survivors was only slightly reduced compared with controls (Taverna et al., 1998). Histological analysis of α5 −/−;+/+ mice from late embryogenesis to adult life revealed an alteration in the skeletal muscle structure resembling a typical muscle dystrophy. Giant fibers, increased numbers of nuclei per fiber with altered position and size, vacuoli and signs of muscle degeneration–regeneration were observed in head, thorax and limb muscles. Electron microscopy showed an increase in the number of mitochondria in some muscle fibers of the mutant mice. Increased apoptosis and immunoreactivity for tenascin-C were observed in mutant muscle fibers. All the alterations were already visible at late stages of embryogenesis. The number of altered muscle fibers varied in different animals and muscles and was often increased in high percentage chimeric animals. Differentiation of α5 −/− ES cells or myoblasts showed that in vitro differentiation into myotubes was achieved normally. However proper adhesion and survival of myoblasts on fibronectin was impaired. Our data suggest that a novel form of muscle dystrophy in mice is α5-integrin-dependent. PMID:9813102

  13. Evaluation of Trichodysplasia Spinulosa-Associated Polyomavirus Capsid Protein as a New Carrier for Construction of Chimeric Virus-Like Particles Harboring Foreign Epitopes

    PubMed Central

    Gedvilaite, Alma; Kucinskaite-Kodze, Indre; Lasickiene, Rita; Timinskas, Albertas; Vaitiekaite, Ausra; Ziogiene, Danguole; Zvirbliene, Aurelija

    2015-01-01

    Recombinant virus-like particles (VLPs) represent a promising tool for protein engineering. Recently, trichodysplasia spinulosa-associated polyomavirus (TSPyV) viral protein 1 (VP1) was efficiently produced in yeast expression system and shown to self-assemble to VLPs. In the current study, TSPyV VP1 protein was exploited as a carrier for construction of chimeric VLPs harboring selected B and T cell-specific epitopes and evaluated in comparison to hamster polyomavirus VP1 protein. Chimeric VLPs with inserted either hepatitis B virus preS1 epitope DPAFR or a universal T cell-specific epitope AKFVAAWTLKAAA were produced in yeast Saccharomyces cerevisiae. Target epitopes were incorporated either at the HI or BC loop of the VP1 protein. The insertion sites were selected based on molecular models of TSPyV VP1 protein. The surface exposure of the insert positions was confirmed using a collection of monoclonal antibodies raised against the intact TSPyV VP1 protein. All generated chimeric proteins were capable to self-assemble to VLPs, which induced a strong immune response in mice. The chimeric VLPs also activated dendritic cells and T cells as demonstrated by analysis of cell surface markers and cytokine production profiles in spleen cell cultures. In conclusion, TSPyV VP1 protein represents a new potential carrier for construction of chimeric VLPs harboring target epitopes. PMID:26230706

  14. Mapping Viral DNA Specificity to the Central Region of Integrase by Using Functional Human Immunodeficiency Virus Type 1/Visna Virus Chimeric Proteins

    PubMed Central

    Katzman, Michael; Sudol, Malgorzata

    1998-01-01

    We previously described the construction and analysis of the first set of functional chimeric lentivirus integrases, involving exchange of the N-terminal, central, and C-terminal regions of the human immunodeficiency virus type 1 (HIV-1) and visna virus integrase (IN) proteins. Based on those results, additional HIV-1/visna virus chimeric integrases were designed and purified. Each of the chimeric enzymes was functional in at least one oligonucleotide-based IN assay. Of a total of 12 chimeric IN proteins, 3 exhibit specific viral DNA processing, 9 catalyze insertion of viral DNA ends, 12 can reverse that reaction, and 11 are active for nonspecific alcoholysis. Functional data obtained with the processing assay indicate that the central region of the protein is responsible for viral DNA specificity. Target site selection for nonspecific alcoholysis again mapped to the central domain of IN, confirming our previous data indicating that this region can position nonviral DNA for nucleophilic attack. However, the chimeric proteins created patterns of viral DNA insertion distinct from that of either wild-type IN, suggesting that interactions between regions of IN influence target site selection for viral DNA integration. The results support a new model for the functional organization of IN in which viral DNA initially binds nonspecifically to the C-terminal portion of IN but the catalytic central region of the enzyme has a prominent role both in specific recognition of viral DNA ends and in positioning the host DNA for viral DNA integration. PMID:9499023

  15. Histological analysis of tonsillectomies: relationship with surgical technique, post-operative pain and haemorrhage.

    PubMed

    Magdalena, M L; Solé, A; Blanco, V; Rodrigo, J P

    2016-12-01

    There is no consensus on the optimal technique to decrease post-tonsillectomy morbidity. Histopathological analysis can estimate collateral tissue damage. This study compared histological findings for tonsils removed by cold or electrocautery dissection and their relationship with post-operative complications. Two adult out-patient groups were included in the study: 37 who underwent cold dissection and 37 who underwent electrocautery dissection. Histological analysis was used to assess tissue damage. Tissue damage was significantly higher in the electrocautery dissection group (p = 0.002), as were the number of emergency department visits (p = 0.01) and the need for supplemental analgesia (p = 0.013). Patients in the cold dissection group experienced less pain (p = 0.001) and fewer secondary haemorrhage episodes. Cold dissection produces less tissue damage, which is associated with lower incidence of complications. This study suggests that cold dissection is the technique of choice for tonsillectomy.

  16. Chimeric aptamers in cancer cell-targeted drug delivery

    PubMed Central

    Kanwar, Jagat R; Roy, Kislay; Kanwar, Rupinder K

    2011-01-01

    Aptamers are single-stranded structured oligonucleotides (DNA or RNA) that can bind to a wide range of targets ("apatopes") with high affinity and specificity. These nucleic acid ligands, generated from pools of random-sequence by an in vitro selection process referred to as systematic evolution of ligands by exponential enrichment (SELEX), have now been identified as excellent tools for chemical biology, therapeutic delivery, diagnosis, research, and monitoring therapy in real-time imaging. Today, aptamers represent an interesting class of modern Pharmaceuticals which with their low immunogenic potential mimic extend many of the properties of monoclonal antibodies in diagnostics, research, and therapeutics. More recently, chimeric aptamer approach employing many different possible types of chimerization strategies has generated more stable and efficient chimeric aptamers with aptamer-aptamer, aptamer-nonaptamer biomacromolecules (siRNAs, proteins) and aptamer-nanoparticle chimeras. These chimeric aptamers when conjugated with various biomacromolecules like locked nucleic acid (LNA) to potentiate their stability, biodistribution, and targeting efficiency, have facilitated the accurate targeting in preclinical trials. We developed LNA-aptamer (anti-nucleolin and EpCAM) complexes which were loaded in iron-saturated bovine lactofeerin (Fe-blf)-coated dopamine modified surface of superparamagnetic iron oxide (Fe3O4) nanoparticles (SPIONs). This complex was used to deliver the specific aptamers in tumor cells in a co-culture model of normal and cancer cells. This review focuses on the chimeric aptamers, currently in development that are likely to find future practical applications in concert with other therapeutic molecules and modalities. PMID:21955150

  17. TC-2 post Helios experiment data review. [postflight systems analysis of spacecraft performance

    NASA Technical Reports Server (NTRS)

    1975-01-01

    Data are presented from a systems postflight analysis of the Centaur Launch Vehicle and Helios. Also given is a comparison of data from preflight analyses. Topics examined are: (1) propellant behavior; (2) helium usage; (3) propellant tank pressurization; (4) propellant tank thermodynamics; (5) component heating; thermal control; and thermal protection system; (6) main engine system; (7) H2O2 consumption; (8) boost pump post-meco performance; and (9) an overview of other systems.

  18. Post-Traumatic Stress Innovations: U.S. Military Enterprise Analysis

    DTIC Science & Technology

    2011-01-26

    does not display a currently valid OMB control number. 1. REPORT DATE 26 JAN 2011 2 . REPORT TYPE 3. DATES COVERED 00-00-2011 to 00-00-2011 4...dx ( COSC / OSCAR) Family Advocacy / Family Support Readiness General Education on PH (All SM &FM) Substance Abuse Aftercare OT for Non-PH...of the continuum of services in preventing and managing Post Traumatic Stress and related conditions. Three Phases: 1. Current state analysis 2

  19. Outcome and survival analysis of surgical repair of post-infarction ventricular septal rupture.

    PubMed

    Pang, Philip Y K; Sin, Yoong Kong; Lim, Chong Hee; Tan, Teing Ee; Lim, See Lim; Chao, Victor T T; Su, Jang Wen; Chua, Yeow Leng

    2013-03-09

    To review the experience of surgical repair of post-infarction ventricular septal rupture (VSR) and analyze the associated outcomes and prognostic factors. Following approval from the Singhealth Centralised Institutional Review Board (reference: 2011/881/C), a retrospective review was performed on 38 consecutive patients who had undergone surgical repair of post-infarction VSR between 1999 and 2011. Continuous variables were expressed as either mean ± standard deviation or median with 25th and 75th percentiles. These were compared using two-tailed t-test or Mann-Whitney U test respectively. Categorical variables were compared using chi-square or Fisher's exact test. To identify predictors of operative mortality, univariate analysis of perioperative variables followed by multivariate analysis of significant univariate risk factors was performed. A two-tailed p-value < 0.05 was used to indicate statistical significance. Mean age was 65.7 ± 9.4 years with 52.6% males. The VSR was anterior in 28 (73.7%) and posterior in 10 patients. Median interval from myocardial infarction to VSR was 1 day (1, 4). Pre-operative intra-aortic balloon pump was inserted in 37 patients (97.8%). Thirty-six patients (94.7%) underwent coronary angiography.Thirty-five patients (92.1%) underwent patch repair. Mean aortic cross clamp time was 82 ± 40 minutes and mean cardiopulmonary bypass time was 152 ± 52 minutes. Coronary artery bypass grafting (CABG) was performed in 19 patients (50%), with a mean of 1.5 ± 0.7 distal anastomoses. Operative mortality within 30 days was 39.5%.Univariate analysis identified emergency surgery, New York Heart Association (NYHA) class, inotropic support, right ventricular dysfunction, EuroSCORE II, intra-operative red cell transfusion, post-operative renal failure and renal replacement therapy (RRT) as predictors of operative mortality. Multivariate analysis identified NYHA class and post-operative RRT as predictors of operative mortality.Ten year overall

  20. Micromechanics Analysis Code Post-Processing (MACPOST) User Guide. 1.0

    NASA Technical Reports Server (NTRS)

    Goldberg, Robert K.; Comiskey, Michele D.; Bednarcyk, Brett A.

    1999-01-01

    As advanced composite materials have gained wider usage. the need for analytical models and computer codes to predict the thermomechanical deformation response of these materials has increased significantly. Recently, a micromechanics technique called the generalized method of cells (GMC) has been developed, which has the capability to fulfill this -oal. Tc provide a framework for GMC, the Micromechanics Analysis Code with Generalized Method of Cells (MAC/GMC) has been developed. As MAC/GMC has been updated, significant improvements have been made to the post-processing capabilities of the code. Through the MACPOST program, which operates directly within the MSC/PATRAN graphical pre- and post-processing package, a direct link between the analysis capabilities of MAC/GMC and the post-processing capabilities of MSC/PATRAN has been established. MACPOST has simplified the production, printing. and exportation of results for unit cells analyzed by MAC/GMC. MACPOST allows different micro-level quantities to be plotted quickly and easily in contour plots. In addition, meaningful data for X-Y plots can be examined. MACPOST thus serves as an important analysis and visualization tool for the macro- and micro-level data generated by MAC/GMC. This report serves as the user's manual for the MACPOST program.

  1. Molecular analysis of post-harvest withering in grape by AFLP transcriptional profiling

    PubMed Central

    Zamboni, Anita; Minoia, Leone; Ferrarini, Alberto; Tornielli, Giovanni Battista; Zago, Elisa; Delledonne, Massimo; Pezzotti, Mario

    2008-01-01

    Post-harvest withering of grape berries is used in the production of dessert and fortified wines to alter must quality characteristics and increase the concentration of simple sugars. The molecular processes that occur during withering are poorly understood, so a detailed transcriptomic analysis of post-harvest grape berries was carried out by AFLP-transcriptional profiling analysis. This will help to elucidate the molecular mechanisms of berry withering and will provide an opportunity to select markers that can be used to follow the drying process and evaluate different drying techniques. AFLP-TP identified 699 withering-specific genes, 167 and 86 of which were unique to off-plant and on-plant withering, respectively. Although similar molecular events were revealed in both withering processes, it was apparent that off-plant withering induced a stronger dehydration stress response resulting in the high level expression of genes involved in stress protection mechanisms, such as dehydrin and osmolite accumulation. Genes involved in hexose metabolism and transport, cell wall composition, and secondary metabolism (particularly the phenolic and terpene compound pathways) were similarly regulated in both processes. This work provides the first comprehensive analysis of the molecular events underpinning post-harvest withering and could help to define markers for different withering processes. PMID:19010774

  2. Using reliability of change analysis to evaluate post-acute neuro-rehabilitation.

    PubMed

    Palmer, Christina; Kneebone, Ian I; Strauss, Clara; Jones, Anna-Marie

    2016-01-01

    It is important to evaluate change in order to re-assure commissioners, staff and patients of the effectiveness of interventions, but also in order to identify areas for improvement. To consider whether analysis of improvement at the level of the individual, taking into account measurement error, may offer a further valuable way to assess change and inform service development over considering change at the group level in a post-acute neuro-rehabilitation unit. Pre and post intervention Scores on the FIM+FAM Full Scale and Cognitive and Motor subscales were considered for eighteen patients aged between 35 and 81 with mixed diagnoses who attended a post-acute inpatient neuro-rehabilitation unit for treatment. Statistically significant improvements were achieved on the FIM+FAM Full Scale and Cognitive and Motor subscales in a whole group analysis. Reliable change analyses for each patient within each subscale however identified only half of the sample achieved reliable improvement within the Motor domain and just one person within the Cognitive domain (5.6%). Findings are consistent with the emphasis of the rehabilitation unit on physical/motor function, and unsurprising as many of those assessed had multiple sclerosis, an often deteriorative condition. Use of reliable change analysis allowed a more detailed understanding of intervention impact, potentially identifying what services reliably work for whom, thereby informing future planning.

  3. High risk of urinary tract infections in post-operative gynaecology patients: a retrospective case analysis.

    PubMed

    Crosby-Nwaobi, R R; Faithfull, S

    2011-11-01

    This study was undertaken to determine the incidence and risk factors related to the occurrence of urinary tract infections (UTIs), post surgery, in women being treated for a gynaecological cancer. A retrospective case analysis of 215 women was conducted using data collected via case review with domains covering known risk factors for the occurrence of urinary infections. Bacteriuria was defined as greater than 10(5) colony-forming units per millilitre. A total of 30.7% of women had a UTI post-operatively. Among these, 75.7% infections were Escherichia coli. Having a catheter in situ for ≤3 days was found to be slightly significant in the formation of a UTI post-operatively (U= 3878, P < 0.05). Having a catheter in situ for ≥7 days was found to be highly significant (χ(2) (1) = 6.602, P < 0.01), with an odds ratio of 2.44. A positive correlation was found between the duration of the catheter in situ and type of UTI (τ= .251, P < 0.01). Although urinary catheterisation is known to be related to hospital-acquired infection, a shorter duration of catheterisation may reduce the risk of possible infection post surgery. Oncology teams need to be more aware of this risk, identify women more likely to be catheterised for longer and use preventative strategies for managing infection, such as silver nitrite-lined catheters.

  4. Predictors of birth-related post-traumatic stress symptoms: secondary analysis of a cohort study.

    PubMed

    Furuta, Marie; Sandall, Jane; Cooper, Derek; Bick, Debra

    2016-12-01

    This study aimed to identify factors associated with birth-related post-traumatic stress symptoms during the early postnatal period. Secondary analysis was conducted using data from a prospective cohort study of 1824 women who gave birth in one large hospital in England. Post-traumatic stress symptoms were measured by the Impact of Event Scale at 6 to 8 weeks postpartum. Zero-inflated negative binomial regression models were developed for analyses. Results showed that post-traumatic stress symptoms were more frequently observed in black women and in women who had a higher pre-pregnancy BMI compared to those with a lower BMI. Women who have a history of mental illness as well as those who gave birth before arriving at the hospital, underwent an emergency caesarean section or experienced severe maternal morbidity or neonatal complications also showed symptoms. Women's perceived control during labour and birth significantly reduced the effects of some risk factors. A higher level of perceived social support during the postnatal period also reduced the risk of post-traumatic stress symptoms. From the perspective of clinical practice, improving women's sense of control during labour and birth appears to be important, as does providing social support following the birth.

  5. Measurement uncertainty analysis of low-dose-rate prostate seed brachytherapy: post-implant dosimetry.

    PubMed

    Gregory, Kent J; Pattison, John E; Bibbo, Giovanni

    2015-03-01

    The minimal dose covering 90 % of the prostate volume--D 90--is arguably the most important dosimetric parameter in low-dose-rate prostate seed brachytherapy. In this study an analysis of the measurement uncertainties in D 90 from low-dose-rate prostate seed brachytherapy was conducted for two common treatment procedures with two different post-implant dosimetry methods. The analysis was undertaken in order to determine the magnitude of D 90 uncertainty, how the magnitude of the uncertainty varied when D 90 was calculated using different dosimetry methods, and which factors were the major contributors to the uncertainty. The analysis considered the prostate as being homogeneous and tissue equivalent and made use of published data, as well as original data collected specifically for this analysis, and was performed according to the Guide to the expression of uncertainty in measurement (GUM). It was found that when prostate imaging and seed implantation were conducted in two separate sessions using only CT images for post-implant analysis, the expanded uncertainty in D 90 values were about 25 % at the 95 % confidence interval. When prostate imaging and seed implantation were conducted during a single session using CT and ultrasound images for post-implant analysis, the expanded uncertainty in D 90 values were about 33 %. Methods for reducing these uncertainty levels are discussed. It was found that variations in contouring the target tissue made the largest contribution to D 90 uncertainty, while the uncertainty in seed source strength made only a small contribution. It is important that clinicians appreciate the overall magnitude of D 90 uncertainty and understand the factors that affect it so that clinical decisions are soundly based, and resources are appropriately allocated.

  6. The minimum required level of donor chimerism in hereditary hemophagocytic lymphohistiocytosis

    PubMed Central

    Hartz, Bernd; Marsh, Rebecca; Rao, Kanchan; Henter, Jan-Inge; Jordan, Michael; Filipovich, Lisa; Bader, Peter; Beier, Rita; Burkhardt, Birgit; Meisel, Roland; Schulz, Ansgar; Winkler, Beate; Albert, Michael H.; Greil, Johann; Karasu, Gülsün; Woessmann, Wilhelm; Corbacioglu, Selim; Gruhn, Bernd; Holter, Wolfgang; Kühl, Jörn-Sven; Lang, Peter; Seidel, Markus G.; Veys, Paul; Löfstedt, Alexandra; Ammann, Sandra; Ehl, Stephan; Janka, Gritta; Müller, Ingo

    2016-01-01

    Reduced-intensity conditioning has improved survival after hematopoietic stem cell transplantation (HSCT) for hemophagocytic lymphohistiocytosis (HLH) at the cost of more frequent mixed chimerism. The minimum level of donor chimerism (DC) required to prevent HLH reactivation in humans remains to be determined. In a multicenter retrospective study, 103 patients transplanted for hereditary HLH (2000-2013) and DC permanently or transiently <75% (overall, CD3+, CD56+) were analyzed regarding DC, specific immunologic function, occurrence of systemic reactivations (≥5/8 HLH criteria), partial systemic flares (<5 criteria and HLH-directed treatment), isolated central nervous system reactivations, and management. Recurrence was reported in 18 patients (systemic reactivation n = 11, partial flare n = 3, isolated central nervous system reactivation n = 4). Ten events occurred during profound immune suppression before day 180 (median DC, 10%; range, 1-100%; CD3+ if available, otherwise overall DC), which renders a differentiation between secondary post-HSCT HLH and HLH related to the genetic defect difficult. Eight events occurred between 0.5 and 6.7 years post-HSCT (median DC, 13%; range, 0-30%). In 5 patients, overall and lineage-specific DC were ≤10% for >6 months (median, 5.1; range, 1.1-10 years) without reactivation. A second HSCT was performed in 18 patients (median, DC 4%; range, 0-19%). Death from reactivation occurred in 4 patients (22% of recurrences). Six patients died of transplant complications following a second HSCT (33% of second HSCT). We conclude that a DC >20%-30% is protective against late reactivation. Lower levels do not, however, inescapably result in recurrences. The decision for or against second HSCT must be based on a thorough risk assessment. PMID:27099148

  7. Design and Construction of Chimeric VP8-S2 Antigen for Bovine Rotavirus and Bovine Coronavirus

    PubMed Central

    Nasiri, Khadijeh; Nassiri, Mohammadreza; Tahmoorespur, Mojtaba; Haghparast, Alireza; Zibaee, Saeed

    2016-01-01

    Purpose: Bovine Rotavirus and Bovine Coronavirus are the most important causes of diarrhea in newborn calves and in some other species such as pigs and sheep. Rotavirus VP8 subunit is the major determinant of the viral infectivity and neutralization. Spike glycoprotein of coronavirus is responsible for induction of neutralizing antibody response. Methods: In the present study, several prediction programs were used to predict B and T-cells epitopes, secondary and tertiary structures, antigenicity ability and enzymatic degradation sites. Finally, a chimeric antigen was designed using computational techniques. The chimeric VP8-S2 antigen was constructed. It was cloned and sub-cloned into pGH and pET32a(+) expression vector. The recombinant pET32a(+)-VP8-S2 vector was transferred into E.oli BL21CodonPlus (DE3) as expression host. The recombinant VP8-S2 protein was purified by Ni-NTA chromatography column. Results: The results of colony PCR, enzyme digestion and sequencing showed that the VP8-S2 chimeric antigen has been successfully cloned and sub-cloned into pGH and pET32a(+).The results showed that E.coli was able to express VP8-S2 protein appropriately. This protein was expressed by induction of IPTG at concentration of 1mM and it was confirmed by Ni–NTA column, dot-blotting analysis and SDS-PAGE electrophoresis. Conclusion: The results of this study showed that E.coli can be used as an appropriate host to produce the recombinant VP8-S2 protein. This recombinant protein may be suitable to investigate to produce immunoglobulin, recombinant vaccine and diagnostic kit in future studies after it passes biological activity tests in vivo in animal model and or other suitable procedure. PMID:27123423

  8. Role of minimal residual disease and chimerism after reduced-intensity and myeloablative allo-transplantation in acute myeloid leukemia and high-risk myelodysplastic syndrome.

    PubMed

    Bernal, Teresa; Diez-Campelo, María; Godoy, Vicky; Rojas, Silvia; Colado, Enrique; Alcoceba, Miguel; González, Marcos; Vidriales, Belén; Sánchez-Guijo, Fermín M; López-Corral, Lucía; Luño, Elisa; del Cañizo, Consuelo

    2014-05-01

    We evaluated the impact of detection of minimal residual disease by flow cytometry (FCMRD) and CD3 chimerism in relapse in a cohort of 87 patients with acute myeloid leukemia or myelodysplastic syndrome undergoing stem cell transplantation. Patients with a positive FCMRD at day +100 after transplantation showed higher relapse rates and worse overall survival. In multivariate analysis, a positive FCMRD after transplantation was a significant predictor of relapse. Mixed chimerism showed a trend to statistical signification. We conclude that FCMRD at day 100 after SCT is the best predictor of relapse after SCT in patients with aggressive myeloid malignancies.

  9. Survival analysis of pure seminoma at post-chemotherapy retroperitoneal lymph node dissection.

    PubMed

    Rice, Kevin R; Beck, Stephen D W; Bihrle, Richard; Cary, K Clint; Einhorn, Lawrence H; Foster, Richard S

    2014-11-01

    Viable seminoma encountered at post-chemotherapy retroperitoneal lymph node dissection for pure testicular seminoma is rare due to the chemosensitivity of this germ cell tumor. In this study we define the natural history of viable seminoma at post-chemotherapy retroperitoneal lymph node dissection. The Indiana University testis cancer database was queried from 1988 to 2011 to identify all patients with primary testicular or retroperitoneal pure seminoma and who were found to have pure seminoma at post-chemotherapy retroperitoneal lymph node dissection. Clinical characteristics were reviewed and survival analysis was performed. A total of 36 patients met the study inclusion criteria. All patients received standard first line cisplatin based chemotherapy and 17 received salvage chemotherapy. The decision to proceed to retroperitoneal lymph node dissection was based on enlarging retroperitoneal mass and/or positron emission positivity in the majority of cases. Seven patients had undergone previous retroperitoneal lymph node dissection. Additional surgical procedures were required in 19 patients to achieve a complete resection. The 5-year cancer specific survival rate was 54%. However, only 9 of 36 patients remained continuously free of disease and of these patients 4 received adjuvant chemotherapy. Mean time from post-chemotherapy retroperitoneal lymph node dissection to death was 6.9 months. Second line chemotherapy, reoperative retroperitoneal lymph node dissection and earlier era of treatment were associated with poorer cancer specific survival. A total of 36 patients with pure seminoma were found to have viable pure seminoma at post-chemotherapy retroperitoneal lymph node dissection. While 5-year cancer specific survival was 54%, these surgeries are technically demanding and only a minority of patients achieves a durable cure from surgery alone. Copyright © 2014 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights

  10. Analysis of Sawtooth Post-Cursor Oscillations in Low Safety Factor DIII-D Plasmas

    NASA Astrophysics Data System (ADS)

    Cabrera, J. D.; Paz-Soldan, C.; Strait, E. J.; Shiraki, D.

    2014-10-01

    Large sawtooth oscillations are a commonly observed phenomenon in very low safety factor (q95 ~ 2) plasmas. Following the sawtooth crash phase, low frequency (~200 Hz) post-cursor oscillations in the magnetic field, with amplitudes ~2 G decaying in time, are excited. These post-cursor oscillations do not exhibit the usual m = odd poloidal structures of sawtooth oscillation, but instead are found to be m = even in structure, suggesting the excitation of global kink modes. A novel means of modeling such post-cursor oscillations is presented via computational analysis of data obtained from high-resolution magnetic sensors installed at the DIII-D tokamak facility. Nonlinear regression analysis is used to obtain modeling parameters such as rates of decay and rotation. Trends in parameters over many oscillations are then compared with equilibrium plasma parameters. The impact of measured parameters on global instability onset and disruption prediction is considered. Supported by the National Undergraduate Fellowship Program in Plasma Physics and Fusion Energy Sciences and the US DOE under DE-FC02-04ER54698.

  11. Clinical relevance of post-transplant pharmacodynamic analysis of cyclosporine in renal transplantation.

    PubMed

    Kurata, Yoko; Kuzuya, Takafumi; Miwa, Yuko; Iwasaki, Kenta; Haneda, Masataka; Amioka, Katsuo; Yamada, Kiyofumi; Watarai, Yoshihiko; Katayama, Akio; Uchida, Kazuharu; Kobayashi, Takaaki

    2014-10-01

    Although therapeutic drug monitoring based on blood concentration has been widely implemented in transplant recipients treated with immunosuppressive agents, clinical adverse events such as rejection, infection or drug-induced toxicity caused by inappropriate dosage cannot be completely controlled. Development of an effective assay for optimized immunosuppression would be desirable, which can potentially lead to personalized medicine in renal transplantation. Cyclosporine (CSA) pharmacodynamic analysis using carboxyfluorescein diacetate succinimidyl ester (CFSE)-based T cell proliferation assay was examined in 66 kidney transplant recipients before and after transplantation. Two parameters, the 50% inhibitory concentration (IC50) and the percentage of T-cell proliferation values at the lower plateau (bottom), were compared with clinical events. A significant relation in CSA pharmacodynamic parameters was observed between pre- and post-transplantation. Analysis of the association between clinical outcomes and pharmacodynamic parameters in post-transplant samples demonstrated the following findings: (i) cytomegalovirus (CMV)/varicella zoster virus (VZV) reactivation and CSA-induced nephrotoxicity were significantly associated with high sensitivity to CSA (low bottom or low IC50), (ii) acute T cell-mediated rejection (ATMR) was significantly related to low sensitivity to CSA (high bottom), and (iii) de novo human leukocyte antigen (HLA) antibody production was associated with lower bottom and IC50 values, although the elucidation of those mechanisms is still in progress. It was suggested that CSA pharmacodynamics applied at post-transplantation would be useful for optimizing immunosuppressive therapy. Copyright © 2014 Elsevier B.V. All rights reserved.

  12. The United States Air Force in Europe: An Analysis within the Post-Cold War Security Environment

    DTIC Science & Technology

    1992-12-01

    ANALYSIS WITHIN THE POST-COLD WAR SECURITY ENVIRONMENT by Matthew K. Moeller December 1992 Thesis Advisor: R. Mitchell Brown III Second Reader: Rodney...WORK UNIT ELEMENT NO. NO. NO. ACCESSION NO. 11. I ITLE (Include Security Classification) The United States Air Force in Europe: An Analysis within... Analysis Within the Post-Cold War Security Environment by Matthew K. Moeller Lieutenant, United States Air Force B.S., San Jose State University, 1989

  13. Post-Buckling and Ultimate Strength Analysis of Stiffened Composite Panel Base on Progressive Damage

    NASA Astrophysics Data System (ADS)

    Zhang, Guofan; Sun, Xiasheng; Sun, Zhonglei

    Stiffened composite panel is the typical thin wall structure applied in aerospace industry, and its main failure mode is buckling subjected to compressive loading. In this paper, the development of an analysis approach using Finite Element Method on post-buckling behavior of stiffened composite structures under compression was presented. Then, the numerical results of stiffened panel are obtained by FE simulations. A thorough comparison were accomplished by comparing the load carrying capacity and key position strains of the specimen with test. The comparison indicates that the FEM results which adopted developed methodology could meet the demand of engineering application in predicting the post-buckling behavior of intact stiffened structures in aircraft design stage.

  14. Effectiveness of Prophylactic Antibiotics against Post-Ureteroscopic Lithotripsy Infections: Systematic Review and Meta-Analysis.

    PubMed

    Lo, Chi-Wen; Yang, Stephen Shei-Dei; Hsieh, Cheng-Hsing; Chang, Shang-Jen

    2015-08-01

    To evaluate the effectiveness of prophylactic antibiotic therapy in reducing the incidence of post-ureteroscopic lithotripsy (URL) infections. A systemic search of PubMED was performed to identify all randomized trials that compared the incidence of post-operative infections in patients without pre-operative urinary tract infections who underwent URL with and without a single dose of prophylactic antibiotics. The data were analyzed using Cochrane Collaboration Review Manager (RevMan, version 5.2). The endpoints of the analysis were pyuria (>10 white blood cells/high-power field), bacteriuria (urine culture with bacteria >10(5) colony-forming units/mL), and febrile urinary tract infections (fUTIs), defined as a body temperature of >38°C with pyuria or meaningful bacteriuria within 1 wk after the operation. In total, four trials enrolling 500 patients met the inclusion criteria and were subjected to meta-analysis. Prophylactic antibiotics significantly reduced post-URL pyuria (risk ratios [RR] 0.65; 95% confidence interval [CI] 0.51-0.82) and bacteriuria (RR 0.26; 95% CI 0.12-0.60; p=0.001). Patients who received prophylactic antibiotics tended to have lower rates of fUTI, although the difference was not statistically significant. Prophylactic antibiotic therapy can reduce the incidence of pyuria and bacteriuria after URL. However, because of the low incidence of post-URL fUTIs, we failed to show that a single dose of prophylactic antibiotics can reduce the rate of such infections significantly.

  15. A Replication-incompetent Rift Valley Fever Vaccine: Chimeric Virus-like Particles Protect Mice and Rats Against Lethal Challenge

    PubMed Central

    Mandell, Robert B.; Koukuntla, Ramesh; Mogler, Laura J. K.; Carzoli, Andrea K.; Freiberg, Alexander N.; Holbrook, Michael R.; Martin, Brian K.; Staplin, William R.; Vahanian, Nicholas N.; Link, Charles J.; Flick, Ramon

    2009-01-01

    Virus-like particles (VLPs) present viral antigens in a native conformation and are effectively recognized by the immune system and therefore are considered as suitable and safe vaccine candidates against many viral diseases. Here we demonstrate that chimeric VLPs containing Rift Valley fever virus (RVFV) glycoproteins GN and GC, nucleoprotein N and the gag protein of Moloney murine leukemia virus represent an effective vaccine candidate against Rift Valley fever, a deadly disease in humans and livestock. Long-lasting humoral and cellular immune responses are demonstrated in a mouse model by the analysis of neutralizing antibody titers and cytokine secretion profiles. Vaccine efficacy studies were performed in mouse and rat lethal challenge models resulting in high protection rates. Taken together, these results demonstrate that replication-incompetent chimeric RVF VLPs are an efficient RVFV vaccine candidate. PMID:19932911

  16. Correlative scanning-transmission electron microscopy reveals that a chimeric flavivirus is released as individual particles in secretory vesicles.

    PubMed

    Burlaud-Gaillard, Julien; Sellin, Caroline; Georgeault, Sonia; Uzbekov, Rustem; Lebos, Claude; Guillaume, Jean-Marc; Roingeard, Philippe

    2014-01-01

    The intracellular morphogenesis of flaviviruses has been well described, but flavivirus release from the host cell remains poorly documented. We took advantage of the optimized production of an attenuated chimeric yellow fever/dengue virus for vaccine purposes to study this phenomenon by microscopic approaches. Scanning electron microscopy (SEM) showed the release of numerous viral particles at the cell surface through a short-lived process. For transmission electron microscopy (TEM) studies of the intracellular ultrastructure of the small number of cells releasing viral particles at a given time, we developed a new correlative microscopy method: CSEMTEM (for correlative scanning electron microscopy - transmission electron microscopy). CSEMTEM analysis suggested that chimeric flavivirus particles were released as individual particles, in small exocytosis vesicles, via a regulated secretory pathway. Our morphological findings provide new insight into interactions between flaviviruses and cells and demonstrate that CSEMTEM is a useful new method, complementary to SEM observations of biological events by intracellular TEM investigations.

  17. Correlative Scanning-Transmission Electron Microscopy Reveals that a Chimeric Flavivirus Is Released as Individual Particles in Secretory Vesicles

    PubMed Central

    Burlaud-Gaillard, Julien; Sellin, Caroline; Georgeault, Sonia; Uzbekov, Rustem; Lebos, Claude; Guillaume, Jean-Marc; Roingeard, Philippe

    2014-01-01

    The intracellular morphogenesis of flaviviruses has been well described, but flavivirus release from the host cell remains poorly documented. We took advantage of the optimized production of an attenuated chimeric yellow fever/dengue virus for vaccine purposes to study this phenomenon by microscopic approaches. Scanning electron microscopy (SEM) showed the release of numerous viral particles at the cell surface through a short-lived process. For transmission electron microscopy (TEM) studies of the intracellular ultrastructure of the small number of cells releasing viral particles at a given time, we developed a new correlative microscopy method: CSEMTEM (for correlative scanning electron microscopy - transmission electron microscopy). CSEMTEM analysis suggested that chimeric flavivirus particles were released as individual particles, in small exocytosis vesicles, via a regulated secretory pathway. Our morphological findings provide new insight into interactions between flaviviruses and cells and demonstrate that CSEMTEM is a useful new method, complementary to SEM observations of biological events by intracellular TEM investigations. PMID:24681578

  18. Characterization of oligosaccharide structures on a chimeric respiratory syncytial virus protein expressed in insect cell line Sf9

    SciTech Connect

    Wathen, M.W.; Aeed, P.A.; Elhammer, A.P. )

    1991-03-19

    The oligosaccharide structures added to a chimeric protein (FG) composed of the extracellular domains of respiratory syncytial virus F and G proteins, expressed in the insect cell line Sf9, were investigated. Cells were labeled in vivo with ({sup 3}H)glucosamine and infected wit a recombinant baculovirus containing the FG gene. The secreted chimeric protein was isolated by immunoprecipitation and subjected to oligosaccharide analysis. The FG protein contains two types of O-linked oligosaccharides: GalNAc and Gal{beta}1-3GalNAc constituting 17 and 66% of the total number of structures respectively. Only one type of N-linked oligosaccharide, constituting the remaining 17% of the structures on FG, was detected: a trimannosyl core structure with a fucose residue linked {alpha}1-6 to the asparagine-linked N-acetylglucosamine.

  19. Online communication as a potential travel medicine research tool: analysis of messages posted on the TravelMed listserv.

    PubMed

    Macdonald, Liane; MacPherson, Douglas W; Gushulak, Brian D

    2009-01-01

    Access to the Internet and electronic mail has created opportunities for online discussion that can facilitate medical education and clinical problem solving. Research into the use of these information technologies is increasing and the analysis of these tools can support and guide the activities of professional organizations, including educational endeavors. The initial objective was to analyze patterns of information exchange on the International Society of Travel Medicine's (ISTM) travel health electronic mailing list related to a specific area of society interest. Secondary objectives included the analysis of listserv use in relation to subscriber demographics and rates of participation to support travel health educational activities. This study examined the use of the ISTM TravelMed listserv over an 8-month period from January 1, 2006, to July 31, 2006. Descriptive data analysis included TravelMed user demographics, the type of posting, the topic and frequency of postings, and the source of information provided. During the study period, 911 (47%) of the eligible ISTM members subscribed to the TravelMed listserv. About 369 of these subscribers posted 1,710 individual messages. About 1,506 (88%) postings were educational; 207 (12%) postings were administrative. A total of 389 (26%) of the educational postings were primary queries and 1,120 (74%) were responses, with a mean string length of 2.9 responses per query (range: 1-51). Twenty participants contributed 40% of the educational postings. The topics with the most frequent postings were vaccines and vaccine-preventable diseases (473/31%) and malaria (258/17%). Postings focused on special populations, including pregnant women or immigrants, comprised a total of 14 postings (<1%). During the study period, a limited number of ISTM members (19%) authored postings on the listserv. Regular discussion centered on a limited number of recurring topics. The analysis provides several opportunities for the support of

  20. Novel Antiproliferative Chimeric Compounds with Marked Histone Deacetylase Inhibitory Activity

    PubMed Central

    2014-01-01

    Given our interest in finding potential antitumor agents and in view of the multifactorial mechanistic nature of cancer, in the present work, taking advantage of the multifunctional ligands approach, new chimeric molecules were designed and synthesized by combining in single chemical entities structural features of SAHA, targeting histone deacetylases (HDACs), with substituted stilbene or terphenyl derivatives previously obtained by us and endowed with antiproliferative and pro-apoptotic activity. The new chimeric derivatives were characterized with respect to their cytotoxic activity and their effects on cell cycle progression on different tumor cell lines, as well as their HDACs inhibition. Among the other, trans-6 showed the most interesting biological profile, as it exhibited a strong pro-apoptotic activity in tumor cell lines in comparison with both of its parent compounds and a marked HDAC inhibition. PMID:25221651

  1. Chimeric antigen receptors: driving immunology towards synthetic biology

    PubMed Central

    Sadelain, Michel

    2017-01-01

    The advent of second generation CARs and the CD19 paradigm have ushered a new therapeutic modality in oncology. In contrast to earlier forms of adoptive cell therapy, which were based on the isolation and expansion of naturally occurring T cells, CAR therapy is based on the design and manufacture of engineered T cells with optimized properties. A new armamentarium, comprising not only CARs but also chimeric costimulatory receptors, chimeric cytokine receptors, inhibitory receptors and synthetic Notch receptors, expressed in naïve, central memory or stem cell-like memory T cells, is being developed for clinical use in a wide range of cancers. Immunological principles are thus finding a new purpose thanks to advances in genetic engineering, synthetic biology and cell manufacturing sciences. PMID:27372731

  2. Blood Chimerism in Dizygotic Monochorionic Twins During 5 Years Observation.

    PubMed

    Dziegiel, M H; Hansen, M H; Haedersdal, S; Barrett, A N; Rieneck, K; Main, K M; Hansen, A T; Clausen, F B

    2017-04-19

    Dizygotic monochorionic twin pregnancies can result in blood chimerism due to in utero twin-to-twin exchange of stem cells. In this case, we examined the proportion of allogeneic red blood cells by flow cytometry and the proportion of allogeneic nucleated cells by digital polymerase chain reaction at 7 months and again at 5 years. We found an increase in the proportion of allogeneic cells from 63% to 89% in one twin, and a similar increase in autologous cells in the other twin from 57% to 84%. A paradigm for stem cell therapy could be modeled on this case: induction of tolerance and chimerism by antenatal transfusion of donor stem cells. The procedure would hold the promise of transplantation and tolerance induction without myeloablative conditioning for inheritable benign hematological diseases such as sickle cell disease and thalassemia. © 2017 The American Society of Transplantation and the American Society of Transplant Surgeons.

  3. Characterization of chimeric plasmid cloning vehicles in Bacillus subtilis.

    PubMed

    Gryczan, T; Shivakumar, A G; Dubnau, D

    1980-01-01

    Restriction endonuclease cleavage maps of seven chimeric plasmids that may be used for molecular cloning in Bacillus subtilis are presented. These plasmids all carry multiple antibiotic resistance markers and were constructed by in vitro molecular cloning techniques. Several of the antibiotic resistance markers were shown to undergo insertional inactivation at specific restriction endonuclease sites. Kanamycin inactivation occurred at the BglII site of pUB110 derivatives, erythromycin inactivation occurred at the HpaI and BclI sites of pE194 derivatives, and streptomycin inactivation occurred at the HindIII site of pSA0501 derivatives. A stable mini-derivative of pBD12 was isolated and characterized. By using these plasmids, we identified proteins involved in plasmid-coded kanamycin and erythromycin resistance. The properties and uses of these chimeric plasmids in the further development of recombinant deoxyribonucleic acid technology in B. subtilis are discussed.

  4. Mechanisms of Tolerance Induction by Hematopoietic Chimerism: The Immune Perspective.

    PubMed

    Yolcu, Esma S; Shirwan, Haval; Askenasy, Nadir

    2017-03-01

    Hematopoietic chimerism is one of the effective approaches to induce tolerance to donor-derived tissue and organ grafts without administration of life-long immunosuppressive therapy. Although experimental efforts to develop such regimens have been ongoing for decades, substantial cumulative toxicity of combined hematopoietic and tissue transplants precludes wide clinical implementation. Tolerance is an active immunological process that includes both peripheral and central mechanisms of mutual education of coresident donor and host immune systems. The major stages include sequential suppression of early alloreactivity, establishment of hematopoietic chimerism and suppressor cells that sustain the state of tolerance, with significant mechanistic and temporal overlap along the tolerization process. Efforts to devise less toxic transplant strategies by reduction of preparatory conditioning focus on modulation rather than deletion of residual host immunity and early reinstitution of regulatory subsets at the central and peripheral levels. Stem Cells Translational Medicine 2017;6:700-712.

  5. Construction and immunogenic properties of a chimeric protein comprising CfaE, CfaB and LTB against Enterotoxigenic Escherichia coli.

    PubMed

    Gheibi Hayat, Seyed-Mohammad; Mousavi Gargari, Seyed-Latif; Nazarian, Shahram

    2016-11-01

    ETEC (Enterotoxigenic Escherichia coli) is a major cause of diarrhea in developing countries and children. ETEC has two virulence factors including colonization factors antigen (CFA) and labile enterotoxins (LTs). CFA/I consists the major pilin subunit CfaB and a minor adhesive subunit, CfaE. In this study a tripartite fusion protein containing CfaB, CfaE and LTB was designed. In silico analysis of the tertiary structure of the chimeric protein showed a protein with three main domains linked together with linkers. Linear and conformational B-cell epitopes were identified. A chimera consisting cfaB, cfaE and ltB(BET)was then synthesized with E. coli codon bias in pUC57 and sub cloned into pET32 vector. Recombinant protein was expressed and purified by affinity chromatography and confirmed by western blotting. Mice were immunized with recombinant protein and the antibody titer and specificity of the sera were analyzed by ELISA. The efficiency of the immune sera against ETEC was evaluated by binding assay and GM1-ELISA. VaxiJen analysis of the protein showed high antigenicity. Post-immune sera contained high titers of anti-BET IgG. Pretreatment of ETEC cells with sera from immunized mice decreased their ability to adhere to cells of the human colon adenocarcinoma cell line HT29.

  6. Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster

    PubMed Central

    Rogers, Rebekah L.; Bedford, Trevor; Lyons, Ana M.; Hartl, Daniel L.

    2010-01-01

    Chimeric genes, which form through the genomic fusion of two protein-coding genes, are a significant source of evolutionary novelty in Drosophila melanogaster. However, the propensity of chimeric genes to produce adaptive phenotypic changes is not fully understood. Here, we describe the chimeric gene Quetzalcoatl (Qtzl; CG31864), which formed in the recent past and swept to fixation in D. melanogaster. Qtzl arose through a duplication on chromosome 2L that united a portion of the mitochondrially targeted peptide CG12264 with a segment of the polycomb gene escl. The 3′ segment of the gene, which is derived from escl, is inherited out of frame, producing a unique peptide sequence. Nucleotide diversity is drastically reduced and site frequency spectra are significantly skewed surrounding the duplicated region, a finding consistent with a selective sweep on the duplicate region containing Qtzl. Qtzl has an expression profile that largely resembles that of escl, with expression in early pupae, adult females, and male testes. However, expression patterns appear to have been decoupled from both parental genes during later embryonic development and in head tissues of adult males, indicating that Qtzl has developed a distinct regulatory profile through the rearrangement of different 5′ and 3′ regulatory domains. Furthermore, misexpression of Qtzl suppresses defects in the formation of the neuromuscular junction in larvae, demonstrating that Qtzl can produce phenotypic effects in cells. Together, these results show that chimeric genes can produce structural and regulatory changes in a single mutational step and may be a major factor in adaptive evolution. PMID:20534482

  7. Cord blood chimerism and relapse after haplo-cord transplantation.

    PubMed

    van Besien, Koen; Koshy, Nebu; Gergis, Usama; Mayer, Sebastian; Cushing, Melissa; Rennert, Hannah; Reich-Slotky, Ronit; Mark, Tomer; Pearse, Roger; Rossi, Adriana; Phillips, Adrienne; Vasovic, Liljana; Ferrante, Rosanna; Hsu, Yen-Michael; Shore, Tsiporah

    2017-02-01

    Haplo-cord stem cell transplantation combines the infusion of CD34 selected hematopoietic progenitors from a haplo-identical donor with an umbilical cord blood (UCB) graft from an unrelated donor and allows faster count recovery, with low rates of disease recurrence and chronic graft-versus-host disease (GVHD). But the contribution of the umbilical cord blood graft to long-term transplant outcome remains unclear. We analyzed 39 recipients of haplo-cord transplants with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS), engrafted and in remission at 2 months. Median age was 66 (18-72) and all had intermediate, high, or very-high risk disease. Less than 20% UCB chimerism in the CD33 lineage was associated with an increased rate of disease recurrence (54% versus 11% p < 0.0001) and decrease in one year progression-free (20% versus 55%, p = 0.004) and overall survival (30% versus 62%, p = 0.02). Less than 100% UCB chimerism in the CD3 lineage was associated with increase rate of disease recurrence (46% versus 12%, p = 0.007). Persistent haplo-chimerism in the CD3 lineage was associated with an increased rate of disease recurrence (40% versus 15%, p = 0.009) Chimerism did not predict for treatment related mortality. The cumulative incidence of acute GVHD by day 100 was 43%. The cumulative incidence of moderate/severe chronic GVHD was only 5%. Engraftment of the umbilical cord blood grafts provides powerful graft-versus-leukemia (GVL) effects which protect against disease recurrence and is associated with low risk of chronic GVHD. Engraftment of CD34 selected haplo-identical cells can lead to rapid development of circulating T-cells, but when these cells dominate, GVL-effects are limited and rates of disease recurrence are high.

  8. Immunogenicity of candidate chimeric DNA vaccine against tuberculosis and leishmaniasis.

    PubMed

    Dey, Ayan; Kumar, Umesh; Sharma, Pawan; Singh, Sarman

    2009-08-13

    Mycobacterium tuberculosis and Leishmania donovani are important intracellular pathogens, especially in Indian context. In India and other South East Asian countries, both these infections are highly endemic and in about 20% cases co-infection of these pathogens is reported. For both these pathogens cell mediated immunity plays most important role. The available treatment of these infections is either prolonged or cumbersome or it is ineffective in controlling the outbreaks and spread. Therefore, potentiation of a common host defense mechanism can be used to prevent both the infections simultaneously. In this study we have developed a novel chimeric DNA vaccine candidate comprising the esat-6 gene of M. tuberculosis and kinesin motor domain gene of L. donovani. After developing this novel chimera, its immunogenicity was studied in mouse model. The immune response was compared with individual constructs of esat-6 and kinesin motor domain. The results showed that immunization with chimeric DNA vaccine construct resulted in stronger IFN-gamma and IL-2 response against kinesin (3012+/-102 and 367.5+/-8.92pg/ml) and ESAT-6 (1334+/-46.5 and 245.1+/-7.72pg/ml) in comparison to the individual vaccine constructs. The reciprocal immune response (IFN-gamma and IL-2) against individual construct was lower (kinesin motor domain: 1788+/-36.48 and 341.8+/-9.801pg/ml and ESAT-6: 867.0+/-47.23 and 170.8+/-4.578pg/ml, respectively). The results also suggest that using the chimeric construct both proteins yielded a reciprocal adjuvant affect over each other as the IFN-gamma production against chimera vaccination is statistically significant (p<0.0001) than individual construct vaccination. From this pilot study we could envisage that the chimeric DNA vaccine construct may offer an attractive strategy in controlling co-infection of leishmaniasis and tuberculosis and have important implication in future vaccine design.

  9. Chimeric Protein Complexes in Hybrid Species Generate Novel Phenotypes

    PubMed Central

    Piatkowska, Elzbieta M.; Naseeb, Samina; Knight, David; Delneri, Daniela

    2013-01-01

    Hybridization between species is an important mechanism for the origin of novel lineages and adaptation to new environments. Increased allelic variation and modification of the transcriptional network are the two recognized forces currently deemed to be responsible for the phenotypic properties seen in hybrids. However, since the majority of the biological functions in a cell are carried out by protein complexes, inter-specific protein assemblies therefore represent another important source of natural variation upon which evolutionary forces can act. Here we studied the composition of six protein complexes in two different Saccharomyces “sensu stricto” hybrids, to understand whether chimeric interactions can be freely formed in the cell in spite of species-specific co-evolutionary forces, and whether the different types of complexes cause a change in hybrid fitness. The protein assemblies were isolated from the hybrids via affinity chromatography and identified via mass spectrometry. We found evidence of spontaneous chimericity for four of the six protein assemblies tested and we showed that different types of complexes can cause a variety of phenotypes in selected environments. In the case of TRP2/TRP3 complex, the effect of such chimeric formation resulted in the fitness advantage of the hybrid in an environment lacking tryptophan, while only one type of parental combination of the MBF complex allowed the hybrid to grow under respiratory conditions. These phenotypes were dependent on both genetic and environmental backgrounds. This study provides empirical evidence that chimeric protein complexes can freely assemble in cells and reveals a new mechanism to generate phenotypic novelty and plasticity in hybrids to complement the genomic innovation resulting from gene duplication. The ability to exchange orthologous members has also important implications for the adaptation and subsequent genome evolution of the hybrids in terms of pattern of gene loss. PMID

  10. Chimeric plantibody passively protects mice against aerosolized ricin challenge.

    PubMed

    Sully, Erin K; Whaley, Kevin J; Bohorova, Natasha; Bohorov, Ognian; Goodman, Charles; Kim, Do H; Pauly, Michael H; Velasco, Jesus; Hiatt, Ernie; Morton, Josh; Swope, Kelsi; Roy, Chad J; Zeitlin, Larry; Mantis, Nicholas J

    2014-05-01

    Recent incidents in the United States and abroad have heightened concerns about the use of ricin toxin as a bioterrorism agent. In this study, we produced, using a robust plant-based platform, four chimeric toxin-neutralizing monoclonal antibodies that were then evaluated for the ability to passively protect mice from a lethal-dose ricin challenge. The most effective antibody, c-PB10, was further evaluated in mice as a therapeutic following ricin exposure by injection and inhalation.

  11. Prism adaptation changes perceptual awareness for chimeric visual objects but not for chimeric faces in spatial neglect after right-hemisphere stroke.

    PubMed

    Sarri, Margarita; Kalra, Lalit; Greenwood, Richard; Driver, Jon

    2006-06-01

    Prism adaptation can ameliorate some symptoms of left spatial neglect after right-hemisphere stroke. The mechanisms behind this remain unclear. Prism therapy may increase exploration towards the contralesional side, yet without improving perceptual awareness, as apparently for the left side of chimeric face stimuli (Ferber et al. 2003). However, other prism studies suggest that perceptual awareness might be improved (e.g., Maravita et al., 2003). We tested the impact of prism therapy on visual awareness for the left side of chimeric objects as well as chimeric faces, in three neglect patients. Prism therapy dramatically improved awareness for the identity of the left side of chimeric non-face objects, but had no effect on judging expressions for chimeric faces. The latter may thus be unique in showing no prism benefit.

  12. Mixed T Lymphocyte Chimerism after Allogeneic Hematopoietic Transplantation Is Predictive for Relapse of Acute Myeloid Leukemia and Myelodysplastic Syndromes.

    PubMed

    Lee, Hans C; Saliba, Rima M; Rondon, Gabriela; Chen, Julianne; Charafeddine, Yasmeen; Medeiros, L Jeffrey; Alatrash, Gheath; Andersson, Borje S; Popat, Uday; Kebriaei, Partow; Ciurea, Stefan; Oran, Betul; Shpall, Elizabeth; Champlin, Richard

    2015-11-01

    Chimerism testing after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in patients with acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) represents a promising tool for predicting disease relapse, although its precise role in this setting remains unclear. We investigated the predictive value of T lymphocyte chimerism analysis at 90 to 120 days after allo-HSCT in 378 patients with AML/MDS who underwent busulfan/fludarabine-based myeloablative preparative regimens. Of 265 (70%) patients with available T lymphocyte chimerism data, 43% of patients in first or second complete remission (CR1/CR2) at the time of transplantation had complete (100%) donor T lymphocytes at day +90 to +120 compared with 60% of patients in the non-CR1/CR2 cohort (P = .005). In CR1/CR2 patients, donor T lymphocyte chimerism ≤ 85% at day +90 to +120 was associated with a higher frequency of 3-year disease progression (29%; 95% confidence interval [CI], 18% to 46% versus 15%; 95% CI, 9% to 23%; hazard ratio [HR], 2.1; P = .04). However, in the more advanced, non-CR1/CR2 cohort, mixed T lymphocyte chimerism was not associated with relapse (37%; 95% CI, 20% to 66% versus 34%; 95% CI, 25% to 47%; HR, 1.3; P = .60). These findings demonstrate that early T lymphocyte chimerism testing at day +90 to +120 is a useful approach for predicting AML/MDS disease recurrence in patients in CR1/CR2 at the time of transplantation.

  13. Viability of Poliovirus/Rhinovirus VPg Chimeric Viruses and Identification of an Amino Acid Residue in the VPg Gene Critical for Viral RNA Replication

    PubMed Central

    Cheney, I. Wayne; Naim, Suhaila; Shim, Jae Hoon; Reinhardt, Meghan; Pai, Bharati; Wu, Jim Z.; Hong, Zhi; Zhong, Weidong

    2003-01-01

    Picornaviral RNA replication utilizes a small virus-encoded protein, termed 3B or VPg, as a primer to initiate RNA synthesis. This priming step requires uridylylation of the VPg peptide by the viral polymerase protein 3Dpol, in conjunction with other viral or host cofactors. In this study, we compared the viral specificity in 3Dpol-catalyzed uridylylation reactions between poliovirus (PV) and human rhinovirus 16 (HRV16). It was found that HRV16 3Dpol was able to uridylylate PV VPg as efficiently as its own VPg, but PV 3Dpol could not uridylylate HRV16 VPg. Two chimeric viruses, PV containing HRV16 VPg (PV/R16-VPg) and HRV16 containing PV VPg (R16/PV-VPg), were constructed and tested for replication capability in H1-HeLa cells. Interestingly, only PV/R16-VPg chimeric RNA produced infectious virus particles upon transfection. No viral RNA replication or cytopathic effect was observed in cells transfected with R16/PV-VPg chimeric RNA, despite the ability of HRV16 3Dpol to uridylylate PV VPg in vitro. Sequencing analysis of virion RNA isolated from the virus particles generated by PV/R16-VPg chimeric RNA identified a single residue mutation in the VPg peptide (Glu6 to Val). Reverse genetics confirmed that this mutation was highly compensatory in enhancing replication of the chimeric viral RNA. PV/R16-VPg RNA carrying this mutation replicated with similar kinetics and magnitude to wild-type PV RNA. This cell culture-induced mutation in HRV16 VPg moderately increased its uridylylation by PV 3Dpol in vitro, suggesting that it might be involved in other function(s) in addition to the direct uridylylation reaction. This study demonstrated the use of chimeric viruses to characterize viral specificity and compatibility in vivo between PV and HRV16 and to identify critical amino acid residue(s) for viral RNA replication. PMID:12805442

  14. Minimising post-operative risk using a Post-Anaesthetic Care Tool (PACT): protocol for a prospective observational study and cost-effectiveness analysis

    PubMed Central

    Phillips, Nicole M; Kent, Bridie; Colgan, Stephen; Mohebbi, Mohammadreza

    2015-01-01

    Introduction While the risk of adverse events following surgery has been identified, the impact of nursing care on early detection of these events is not well established. A systematic review of the evidence and an expert consensus study in post-anaesthetic care identified essential criteria for nursing assessment of patient readiness for discharge from the post-anaesthetic care unit (PACU). These criteria were included in a new nursing assessment tool, the Post-Anaesthetic Care Tool (PACT), and incorporated into the post-anaesthetic documentation at a large health service. The aim of this study is to test the clinical reliability of the PACT and evaluate whether the use of PACT will (1) enhance the recognition and response to patients at risk of deterioration in PACU; (2) improve documentation for handover from PACU nurse to ward nurse; (3) result in improved patient outcomes and (4) reduce healthcare costs. Methods and analysis A prospective, non-randomised, pre-implementation and post-implementation design comparing: (1) patients (n=750) who have surgery prior to the implementation of the PACT and (2) patients (n=750) who have surgery after PACT. The study will examine the use of the tool through the observation of patient care and nursing handover. Patient outcomes and cost-effectiveness will be determined from health service data and medical record audit. Descriptive statistics will be used to describe the sample and compare the two patient groups (pre-intervention and post-intervention). Differences in patient outcomes between the two groups will be compared using the Cochran-Mantel-Haenszel test and regression analyses and reported as ORs with the corresponding 95% CIs. Conclusions This study will test the clinical reliability and cost-effectiveness of the PACT. It is hypothesised that the PACT will enable nurses to recognise and respond to patients at risk of deterioration, improve handover to ward nurses, improve patient outcomes, and reduce healthcare

  15. Xenobiotics, chimerism and the induction of tolerance following organ transplantation

    PubMed Central

    Delaney, C. P.; Thomson, A. W.; Demetris, A. J.; Starzl, T. E.

    2010-01-01

    Summary The successful results seen after organ transplantation are largely attributable to the potency and specificity of modern immunosuppressive agents. Although drug-free unresponsiveness to graft alloantigens has not been routinely achieved in clinical practice, recent appreciation of the importance of cell chimerism, which develops after the migration from donor to host of leukocytes contained in solid organ grafts, has introduced a concept which may explain the mechanism of graft tolerance. Recent evidence has indicated that immunosuppressive drugs may have a common potential to induce graft tolerance, even though they act through diverse mechanisms, and that this potential may be mediated by a permissive effect on the migration and survival of donor-derived leukocytes. This review briefly examines the mechanisms by which immunosuppressive drugs function and analyses the different methods which these agents might use to induce chimerism associated with graft tolerance. Furthermore, we describe ongoing clinical studies in which the chimerism produced after solid organ transplantation is augmented with donor bone marrow in an attempt to facilitate the induction of tolerance. PMID:7584491

  16. Chimeric antibodies with extended half-life in ferrets

    PubMed Central

    Nesspor, Thomas C; Scallon, Bernard

    2014-01-01

    Background Ferrets have long been used as a disease model for the study of influenza vaccines, but a more recent use has been for the study of human monoclonal antibodies directed against influenza viruses. Published data suggest that human antibodies are cleared unusually quickly from the ferret and that immune responses may be partially responsible. This immunogenicity increases variability within groups and may present an obstacle to long-term studies. Objective Our aim was to identify an antibody design with reduced immunogenicity and longer circulating half-life in ferrets. Methods The constant region coding sequences for ferret immunoglobulin G were cloned, and chimeric human/ferret antibodies were expressed and purified. Some of the chimeric antibodies included substitutions that have been shown to extend the half-life of human IgG antibodies. These chimeric antibodies were tested for binding to recombinant ferret FcRn receptor and then evaluated in pharmacokinetic studies in ferrets. Results A one-residue substitution in the ferret Fc domain, S252Y, was identified that increased binding affinity to the ferret neonatal receptor by 24-fold and extended half-life from 65 ± 27 to 206 ± 28 hours or ∼9 days. Ferrets dosed twice with this surrogate antibody showed no indications of an immune response. Conclusion Expressing the variable region of a candidate human therapeutic antibody with ferret constant regions containing the S252Y substitution can offer long half-life and limit immunogenicity. PMID:25074755

  17. Chimeric creatures in Greek mythology and reflections in science.

    PubMed

    Bazopoulou-Kyrkanidou, E

    2001-04-15

    "The Chimaera" in Homer's Iliad, "was of divine stock, not of men, in the forepart a lion, in the hinder a serpent, and in the midst a goat, ellipsis Bellerophon slew her, trusting in the signs of the gods." In Hesiod's Theogony it is emphasized that "Chimaera ellipsis had three heads, one of a grim-eyed lion, another of a goat, and another of a snakeellipsis". In addition to this interspecies animal chimera, human/animal chimeras are referred to in Greek mythology, preeminent among them the Centaurs and the Minotaur. The Centaurs, as horse/men, first appear in Geometric and early Archaic art, but in the literature not until early in the fifth century B.C. The bullheaded-man Minotaur, who is not certainly attested in the literary evidence until circa 500 B.C., first appears in art about 650 B.C. Attempts, in the fourth century B.C. and thereafter, to rationalize their mythical appearance were in vain; their chimeric nature retained its fascinating and archetypal form over the centuries. Early in the 1980s, experimental sheep/goat chimeras were produced removing the reproductive barrier between these two animal species. Late in the 1990s, legal, political, ethical, and moral fights loomed over a patent bid on human/animal chimeras. Chimeric technology is recently developed; however, the concept of chimerism has existed in literary and artistic form in ancient mythology. This is yet another example where art and literature precede scientific research and development.

  18. A modular strategy for engineering orthogonal chimeric RNA transcription regulators

    PubMed Central

    Takahashi, Melissa K.; Lucks, Julius B.

    2013-01-01

    Antisense RNA transcription attenuators are a key component of the synthetic biology toolbox, with their ability to serve as building blocks for both signal integration logic circuits and transcriptional cascades. However, a central challenge to building more sophisticated RNA genetic circuitry is creating larger families of orthogonal attenuators that function independently of each other. Here, we overcome this challenge by developing a modular strategy to create chimeric fusions between the engineered transcriptional attenuator from plasmid pT181 and natural antisense RNA translational regulators. Using in vivo gene expression assays in Escherichia coli, we demonstrate our ability to create chimeric attenuators by fusing sequences from five different translational regulators. Mutagenesis of these functional attenuators allowed us to create a total of 11 new chimeric attenutaors. A comprehensive orthogonality test of these culminated in a 7 × 7 matrix of mutually orthogonal regulators. A comparison between all chimeras tested led to design principles that will facilitate further engineering of orthogonal RNA transcription regulators, and may help elucidate general principles of non-coding RNA regulation. We anticipate that our strategy will accelerate the development of even larger families of orthogonal RNA transcription regulators, and thus create breakthroughs in our ability to construct increasingly sophisticated RNA genetic circuitry. PMID:23761434

  19. Factor Analysis of Persistent Post-Concussive Symptoms within a Military Sample with Blast Exposure

    PubMed Central

    Franke, L.M.; Czarnota, J.N.; Ketchum, J.M.; Walker, W.C.

    2014-01-01

    Objective To determine the factor structure of persistent post-concussive syndrome (PPCS) symptoms in a blast-exposed military sample and validate factors against objective and symptom measures. Setting Veterans Affairs medical center and military bases. Participants One hundred eighty-one service members and veterans with at least one significant exposure to blast during deployment within the two years prior to study enrollment. Design Confirmatory and exploratory factor analysis of the Rivermead Post-concussion Questionnaire (RPQ). Main Measures RPQ, PTSD Symptom Checklist-Civilian, Center for Epidemiologic Studies Depression inventory, Sensory Organization Test, Paced Auditory Serial Addition Test, California Verbal Learning Test, Delis-Kaplan Executive Function System subtests. Results The three-factor structure of PPCS was not confirmed. A four-factor structure was extracted, and factors were interpreted as reflecting emotional, cognitive, visual, and vestibular functions. All factors were associated with scores on psychological symptom inventories; visual and vestibular factors were also associated with balance performance. There was no significant association between the cognitive factor and neuropsychological performance, nor between a history of mTBI and factor scores. Conclusion Persistent post-concussive symptoms observed months after blast exposure seem to be related to four distinct forms of distress, but not to mTBI per se, with vestibular and visual factors possibly related to injury of sensory organs by blast. PMID:24695267

  20. Analysis of bond strength by pull out test on fiber glass posts cemented in different lengths.

    PubMed

    Webber, Mariana Benedetti Ferreira; Michida, Silvia Masae de Araújo; Marson, Fabiano Carlos; de Oliveira, Giovani Corrêa; Silva, Cleverson de Oliveira E

    2015-04-01

    The aim of this study was to evaluate, by means of pull-out test, the bond strength of fiberglass posts when cemented with different lengths in endodontically treated teeth. Sixty single-rooted bovine roots were cut in the cementoenamel junction with 21 mm length. They were endodontically treated and randomly divided into three groups (n = 20). Group 1 - Preparation of 2/3 of the remaining roots; Group 2 - Preparation of ½ of the remaining roots and Group 3 - Preparation of ¼ of remaining roots. For all groups it were used posts n = 3 (Exacto, Angelus, Brazil), and cemented with self-etching resin cement (RelyXU200). After cementing posts, the samples were thermocycled (10.000 cycles/5°C and 55°C). The pull-out test was performed on a universal testing machine (EMIC - DL500) and the values obtained were statistically analyzed by analysis of variance (one-factor ANOVA) and multiple comparison test of Tukey, with level of significance of 5%. The mean values ± standard deviation in Newtons (N) were: Group 1 = 120.5 (±42.8) A, Group 2 = 103.1 (±31.2) AB, Group 3 = 41.2 (±22.4) C, P < 0.005. The preparation of ½ of remaining root appears to be a viable alternative when 2/3 of the preparation of the remaining root is not possible, but more results are needed for clinical validation.

  1. Pre and post PET-CT impact on oesophageal cancer management: a retrospective analysis.

    NASA Astrophysics Data System (ADS)

    Azmi, NA; Razak, HRA; Vinjamuri, S.

    2017-05-01

    Assessment of the retrospective cancer incidence, prevalence and crude survival rates of oesophageal cancer to allow comparison between pre and post PET-CT introduction are part of 4 phase cost effectiveness research. It will provide baseline data for to assess PET or PET-CT cost effective potential for staging. A total of 849 patient’s data received from NWCIS databases with various stages of oesophageal cancer between 2001 and 2008. The fundamental activities are retrospective analysis of patient data. In most cases where appropriate, results are presented with 95 percent confidence intervals (CI). Variances between patient groups and variables are assessed using chi-square test. In cases where it deems vital, multiple logistic regression are used to modify for potential confounder such as age and sex. All p-values are two-sided and any value lower than 0.05 were considered to suggest a statistically significant result. Retrospective analysis were categorised into two categories, patients from 2001-2003 considered as pre PET and post PET for 2004-2008. This categorisation allows better comparison of patients’ survival trend to be made between both groups. Rates are presented in percentages and being grouped by tumour characteristics and other variables associated with demographic profile, diagnosis, staging and treatment. Results allowed comparison of oesophageal cancer trends between the pre and post PET-CT introduction such as changes in incidence rate or changes in survival. These data were used to normalise the decision tree model so that cost-effectiveness analysis can be performed across the whole population.

  2. PEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis.

    PubMed

    Nickchi, Payman; Jafari, Mohieddin; Kalantari, Shiva

    2015-01-01

    Conventional proteomics has discovered a wide gap between protein sequences and biological functions. The third generation of proteomics was provoked to bridge this gap. Targeted and untargeted post-translational modification (PTM) studies are the most important parts of today's proteomics. Considering the expensive and time-consuming nature of experimental methods, computational methods are developed to study, analyze, predict, count and compute the PTM annotations on proteins. The enrichment analysis softwares are among the common computational biology and bioinformatic software packages. The focus of such softwares is to find the probability of occurrence of the desired biological features in any arbitrary list of genes/proteins. We introduce Post-translational modification Enrichment Integration and Matching Analysis (PEIMAN) software to explore more probable and enriched PTMs on proteins. Here, we also represent the statistics of detected PTM terms used in enrichment analysis in PEIMAN software based on the latest released version of UniProtKB/Swiss-Prot. These results, in addition to giving insight to any given list of proteins, could be useful to design targeted PTM studies for identification and characterization of special chemical groups. Database URL: http://bs.ipm.ir/softwares/PEIMAN/ © The Author(s) 2015. Published by Oxford University Press.

  3. Analysis of nonstandard and home-made explosives and post-blast residues in forensic practice

    NASA Astrophysics Data System (ADS)

    Kotrlý, Marek; Turková, Ivana

    2014-05-01

    Nonstandard and home-made explosives may constitute a considerable threat and as well as a potential material for terrorist activities. Mobile analytical devices, particularly Raman, or also FTIR spectrometers are used for the initial detection. Various sorts of phlegmatizers (moderants) to decrease sensitivity of explosives were tested, some kinds of low viscosity lubricants yielded very good results. If the character of the substance allows it, phlegmatized samples are taken in the amount of approx.0.3g for a laboratory analysis. Various separation methods and methods of concentrations of samples from post-blast scenes were tested. A wide range of methods is used for the laboratory analysis. XRD techniques capable of a direct phase identification of the crystalline substance, namely in mixtures, have highly proved themselves in practice for inorganic and organic phases. SEM-EDS/WDS methods are standardly employed for the inorganic phase. In analysing post-blast residues, there are very important techniques allowing analysis at the level of separate particles, not the overall composition in a mixed sample.

  4. PEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis

    PubMed Central

    Nickchi, Payman; Jafari, Mohieddin; Kalantari, Shiva

    2015-01-01

    Conventional proteomics has discovered a wide gap between protein sequences and biological functions. The third generation of proteomics was provoked to bridge this gap. Targeted and untargeted post-translational modification (PTM) studies are the most important parts of today’s proteomics. Considering the expensive and time-consuming nature of experimental methods, computational methods are developed to study, analyze, predict, count and compute the PTM annotations on proteins. The enrichment analysis softwares are among the common computational biology and bioinformatic software packages. The focus of such softwares is to find the probability of occurrence of the desired biological features in any arbitrary list of genes/proteins. We introduce Post-translational modification Enrichment Integration and Matching Analysis (PEIMAN) software to explore more probable and enriched PTMs on proteins. Here, we also represent the statistics of detected PTM terms used in enrichment analysis in PEIMAN software based on the latest released version of UniProtKB/Swiss-Prot. These results, in addition to giving insight to any given list of proteins, could be useful to design targeted PTM studies for identification and characterization of special chemical groups. Database URL: http://bs.ipm.ir/softwares/PEIMAN/ PMID:25911152

  5. Detachably assembled microfluidic device for perfusion culture and post-culture analysis of a spheroid array.

    PubMed

    Sakai, Yusuke; Hattori, Koji; Yanagawa, Fumiki; Sugiura, Shinji; Kanamori, Toshiyuki; Nakazawa, Kohji

    2014-07-01

    Microfluidic devices permit perfusion culture of three-dimensional (3D) tissue, mimicking the flow of blood in vascularized 3D tissue in our body. Here, we report a microfluidic device composed of a two-part microfluidic chamber chip and multi-microwell array chip able to be disassembled at the culture endpoint. Within the microfluidic chamber, an array of 3D tissue aggregates (spheroids) can be formed and cultured under perfusion. Subsequently, detailed post-culture analysis of the spheroids collected from the disassembled device can be performed. This device facilitates uniform spheroid formation, growth analysis in a high-throughput format, controlled proliferation via perfusion flow rate, and post-culture analysis of spheroids. We used the device to culture spheroids of human hepatocellular carcinoma (HepG2) cells under two controlled perfusion flow rates. HepG2 spheroids exhibited greater cell growth at higher perfusion flow rates than at lower perfusion flow rates, and exhibited different metabolic activity and mRNA and protein expression under the different flow rate conditions. These results show the potential of perfusion culture to precisely control the culture environment in microfluidic devices. The construction of spheroid array chambers allows multiple culture conditions to be tested simultaneously, with potential applications in toxicity and drug screening. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Continuous versus group sequential analysis for post-market drug and vaccine safety surveillance.

    PubMed

    Silva, I R; Kulldorff, M

    2015-09-01

    The use of sequential statistical analysis for post-market drug safety surveillance is quickly emerging. Both continuous and group sequential analysis have been used, but consensus is lacking as to when to use which approach. We compare the statistical performance of continuous and group sequential analysis in terms of type I error probability; statistical power; expected time to signal when the null hypothesis is rejected; and the sample size required to end surveillance without rejecting the null. We present a mathematical proposition to show that for any group sequential design there always exists a continuous sequential design that is uniformly better. As a consequence, it is shown that more frequent testing is always better. Additionally, for a Poisson based probability model and a flat rejection boundary in terms of the log likelihood ratio, we compare the performance of various continuous and group sequential designs. Using exact calculations, we found that, for the parameter settings used, there is always a continuous design with shorter expected time to signal than the best group design. The two key conclusions from this article are (i) that any post-market safety surveillance system should attempt to obtain data as frequently as possible, and (ii) that sequential testing should always be performed when new data arrives without deliberately waiting for additional data.

  7. Computational Biomechanical Analysis of Asymmetric Ectasia Risk in Unilateral Post-LASIK Ectasia.

    PubMed

    Vahdati, Ali; Seven, Ibrahim; Mysore, Naveen; Randleman, J Bradley; Dupps, William J

    2016-12-01

    To develop a computational approach to corneal biomechanical risk analysis in refractive surgery and to investigate its utility in an enigmatic case of unilateral ectasia after bilateral LASIK. Preoperative corneal elevation datasets from both eyes of a patient who developed unilateral post-LASIK ectasia were used to construct geometrically patient-specific, microstructurally motivated finite element models. Models were assessed before and after implementation of case-specific treatment parameters for interocular differences in corneal geometry and strain behavior under physiological loading conditions. Standard clinical predictors of post-LASIK ectasia risk were similar for the affected and contralateral eyes, and no risk factor asymmetry was identified in tomographic screening that included posterior corneal elevation analysis. However, differences in the magnitude and distribution of strain and stress were observed that are consistent with greater predisposition to biomechanical instability in the affected eye. Load testing with simulated intraocular pressure increases provoked opposite trends in curvature change in the preoperative models representing affected and unaffected eyes, with steepening in the ectatic eye and flattening in the clinically stable eye. Patient-specific computational analyses revealed differences in intrinsic biomechanical behaviors that may predispose a cornea to instability after refractive surgery. Strain and stress analyses elucidated differential risk not ascertained with current refractive surgery screening paradigms. This pilot study illustrates a risk analysis approach that implicitly considers the entire corneal three-dimensional geometry and can be performed a priori in a screening setting. [J Refract Surg. 2016;32(12):811-820.]. Copyright 2016, SLACK Incorporated.

  8. Lesson Learned from AGILE and LARES ASI Projects About MATED Data Collection and Post Analysis

    NASA Astrophysics Data System (ADS)

    Carpentiero, Rita; Mrchetti, Ernesto; Natalucci, Silvia; Portelli, Claudio

    2012-07-01

    ASI has managed and collected data on project development of two scientific all-Italian missions: AGILE and LARES. Collection of the Model And Test Effectiveness Database (MATED) data, concerning Project, AIV (Assembly Integration and Verification) and NCR (Non Conformance Report) aspects has been performed by the Italian Space Agency (ASI), using available technical documentation of both AGILE e LARES projects. In this paper some consideration on the needs of 'real time' data collection is made, together with proposal of front end improvement of this tool. In addition a preliminary analysis of MATED effectiveness related to the above ASI projects will be presented in a bottom-up and post verification approach.

  9. Application of the Post-Boiling-Transition Standard to Licensing Analysis

    SciTech Connect

    Mizokami, Shinya; Kitamura, Hideya; Kudo, Yoshiro; Komura, Seiichi; Nagata, Yoshifumi; Morooka, Shinichi

    2005-10-15

    To ensure fuel integrity, light water reactor cores are designed to avoid the onset of boiling transition (BT) inside the fuel assembly that leads to a deterioration of the heat transfer characteristics and subsequent excessive rise of the fuel-cladding temperature in the anticipated operational occurrences (AOOs). However, some boiling water reactors' AOO events result in immediate scram or suppression of the reactor power due to an increase in the reactor coolant void fraction. Recent studies show that a short duration of dryout inside the fuel assembly only leads to a small rise in the fuel-cladding temperature and thus does not pose a threat to fuel integrity. Many tests on BT and an improved comprehension of its mechanism have led to the development of a methodology to appropriately assess the fuel-cladding temperature after BT has been reached. The Standards Committee of the Atomic Energy Society of Japan has therefore proposed a cladding temperature criterion after BT. Applying the post-BT standard enables the value of the operating limit minimum critical power ratio (OLMCPR) to be decreased by allowing for a short duration of dryout. We calculated the fuel-cladding temperature and dryout duration in the load rejection condition without a bypass event. The calculated results show that both the fuel-cladding temperature and dryout duration meet the post-BT standard in the case of a small OLMCPR, which is determined by the loss of feedwater heating. This enables a more efficient reactor core to be designed by applying the post-BT standard to licensing analysis. The possibility of applying a post-BT standard is demonstrated from the results of this work.

  10. Cognitive Training for Post-Acute Traumatic Brain Injury: A Systematic Review and Meta-Analysis

    PubMed Central

    Hallock, Harry; Collins, Daniel; Lampit, Amit; Deol, Kiran; Fleming, Jennifer; Valenzuela, Michael

    2016-01-01

    Objective: To quantitatively aggregate effects of cognitive training (CT) on cognitive and functional outcome measures in patients with traumatic brain injury (TBI) more than 12-months post-injury. Design: We systematically searched six databases for non-randomized and randomized controlled trials of CT in TBI patients at least 12-months post-injury reporting cognitive and/or functional outcomes. Main Measures: Efficacy was measured as standardized mean difference (Hedges’ g) of post-training change. We investigated heterogeneity across studies using subgroup analyses and meta-regressions. Results: Fourteen studies encompassing 575 patients were included. The effect of CT on overall cognition was small and statistically significant (g = 0.22, 95%CI 0.05 to 0.38; p = 0.01), with low heterogeneity (I2 = 11.71%) and no evidence of publication bias. A moderate effect size was found for overall functional outcomes (g = 0.32, 95%CI 0.08 to 0.57, p = 0.01) with low heterogeneity (I2 = 14.27%) and possible publication bias. Statistically significant effects were also found only for executive function (g = 0.20, 95%CI 0.02 to 0.39, p = 0.03) and verbal memory (g = 0.32, 95%CI 0.14 to 0.50, p < 0.01). Conclusion: Despite limited studies in this field, this meta-analysis indicates that CT is modestly effective in improving cognitive and functional outcomes in patients with post-acute TBI and should therefore play a more significant role in TBI rehabilitation. PMID:27833541

  11. [NMR structure and dynamics of the chimeric protein SH3-F2].

    PubMed

    Kutyshenko, V P; Gushchina, L V; Khristoforov, V S; Prokhorov, D A; Timchenko, M A; Kudrevatykh, Iu A; Fediukina, D V; Filimonov, V V

    2010-01-01

    For the further elucidation of structural and dynamic principles of protein self-organization and protein-ligand interactions the design of new chimeric protein SH3-F2 was made and genetically engineered construct was created. The SH3-F2 amino acid sequence consists of polyproline ligand mgAPPLPPYSA, GG linker and the sequence of spectrin SH3 domain circular permutant S19-P20s. Structural and dynamics properties of the protein were studied by high-resolution NMR. According to NMR data the tertiary structure of the chimeric protein SH3-F2 has the topology which is typical of SH3 domains in the complex with the ligand, forming polyproline type II helix, located in the conservative region of binding in the orientation II. The polyproline ligand closely adjoins with the protein globule and is stabilized by hydrophobic interactions. However the interaction of ligand and the part of globule relative to SH3 domain is not too large because the analysis of protein dynamic characteristics points to the low amplitude, high-frequency ligand tumbling in relation to the slow intramolecular motions of the main globule. The constructed chimera permits to carry out further structural and thermodynamic investigations of polyproline helix properties and its interaction with regulatory domains.

  12. AID-GFP chimeric protein increases hypermutation of Ig genes with no evidence of nuclear localization

    PubMed Central

    Rada, Cristina; Jarvis, John M.; Milstein, César

    2002-01-01

    Somatic hypermutation generates variants of antibody genes and underpins the affinity maturation of antibodies. It is restricted to the V-gene segments, and although it decays exponentially toward the 3′end, it includes recognizable hot spots. Although the detailed mechanism of hypermutation remains elusive, the process may take place in two separate stages, preferentially targeting G/Cs in the first and A/Ts in the second stage. It seems that MSH2 is involved in the second stage, and that activation induced deaminase (AID) is implicated in the control of hypermutation. The constitutively hypermutating cell line Ramos expresses AID, and we have prepared transfectants that express a chimeric AID-green fluorescent protein. The fluorescence is strongly detected in the cytoplasm but not in the nucleus. Yet, the chimeric protein increases the hypermutation rate either directly or, more likely, indirectly, by favoring the transport of AID into the nucleus. Thus, in Ramos, AID seems to be rate limiting. Unexpectedly, the proportion of deletions also is increased. The increase in mutation rate detected by a fast cytofluorimetric method based on the accumulation of sIgM-loss mutants correlates with the increase measured by mutations defined by sequence analysis. The higher mutation rate is largely explained by the higher proportion of mutated clones, indicating that AID controls the number of cells that undergo hypermutation but not the number of mutations that are incorporated in each mutation round. PMID:12011459

  13. Human natural chimerism: an acquired character or a vestige of evolution?

    PubMed

    Rinkevich, B

    2001-06-01

    Analysis on five common classes of human natural chimeras (cytomictical, whole body, fetal-maternal, germ cell, and tumor chimeras) reveals that (1) they initiate only during pregnancy, (2) the most common class are chimeras which contain maternal cells, and (3) the primary mechanisms that are involved in their formation and establishment are still elusive. These classes of natural chimerism, are involved only with maladaptive phenomena such as malignancy and autoimmune diseases and without any documented benefit. A recent review has challenged the accepted dogma that the evolution of immunity is pathogen-directed and asserted that preserving individuality from littering the soma and the germline by conspecific alien cells might have been the original function of the innate immunity. Following this tenet, I propose here that human natural chimerism is a by-product of the new role evolved from primitive components of immunity to "educate" the developing embryo with the armamentarium of effector mechanisms, dedicated to purge the individual from pervasive somatic and germline variants, and is not a vestige of evolution.

  14. The 2005 meta-analysis of homeopathy: the importance of post-publication data.

    PubMed

    Rutten, A L B; Stolper, C F

    2008-10-01

    There is a discrepancy between the outcome of a meta-analysis published in 1997 of 89 trials of homeopathy by Linde et al and an analysis of 110 trials by Shang et al published in 2005, these reached opposite conclusions. Important data were not mentioned in Shang et al's paper, but only provided subsequently. What was the outcome of Shang et al's predefined hypotheses? Were the homeopathic and conventional trials comparable? Was subgroup selection justified? The possible role of ineffective treatments. Was the conclusion about effect justified? Were essential data missing in the original article? Analysis of post-publication data. Re-extraction and analysis of 21 higher quality trials selected by Shang et al with sensitivity analysis for the influence of single indications. Analysis of comparability. Sensitivity analysis of influence of subjective choices, like quality of single indications and of cut-off values for 'larger samples'. The quality of trials of homeopathy was better than of conventional trials. Regarding smaller trials, homeopathy accounted for 14 out of 83 and conventional medicine 2 out of 78 good quality trials with n<100. There was selective inclusion of unpublished trials only for homeopathy. Quality was assessed differently from previous analyses. Selecting subgroups on sample size and quality caused incomplete matching of homeopathy and conventional trials. Cut-off values for larger trials differed between homeopathy and conventional medicine without plausible reason. Sensitivity analyses for the influence of heterogeneity and the cut-off value for 'larger higher quality studies' were missing. Homeopathy is not effective for muscle soreness after long distance running, OR=1.30 (95% CI 0.96-1.76). The subset of homeopathy trials on which the conclusion was based was heterogeneous, comprising 8 trials on 8 different indications, and was not matched on indication with those of conventional medicine. Essential data were missing in the original

  15. Lassa-vesicular stomatitis chimeric virus safely destroys brain tumors.

    PubMed

    Wollmann, Guido; Drokhlyansky, Eugene; Davis, John N; Cepko, Connie; van den Pol, Anthony N

    2015-07-01

    High-grade tumors in the brain are among the deadliest of cancers. Here, we took a promising oncolytic virus, vesicular stomatitis virus (VSV), and tested the hypothesis that the neurotoxicity associated with the virus could be eliminated without blocking its oncolytic potential in the brain by replacing the neurotropic VSV glycoprotein with the glycoprotein from one of five different viruses, including Ebola virus, Marburg virus, lymphocytic choriomeningitis virus (LCMV), rabies virus, and Lassa virus. Based on in vitro infections of normal and tumor cells, we selected two viruses to test in vivo. Wild-type VSV was lethal when injected directly into the brain. In contrast, a novel chimeric virus (VSV-LASV-GPC) containing genes from both the Lassa virus glycoprotein precursor (GPC) and VSV showed no adverse actions within or outside the brain and targeted and completely destroyed brain cancer, including high-grade glioblastoma and melanoma, even in metastatic cancer models. When mice had two brain tumors, intratumoral VSV-LASV-GPC injection in one tumor (glioma or melanoma) led to complete tumor destruction; importantly, the virus moved contralaterally within the brain to selectively infect the second noninjected tumor. A chimeric virus combining VSV genes with the gene coding for the Ebola virus glycoprotein was safe in the brain and also selectively targeted brain tumors but was substantially less effective in destroying brain tumors and prolonging survival of tumor-bearing mice. A tropism for multiple cancer types combined with an exquisite tumor specificity opens a new door to widespread application of VSV-LASV-GPC as a safe and efficacious oncolytic chimeric virus within the brain. Many viruses have been tested for their ability to target and kill cancer cells. Vesicular stomatitis virus (VSV) has shown substantial promise, but a key problem is that if it enters the brain, it can generate adverse neurologic consequences, including death. We tested a series of

  16. Lassa-Vesicular Stomatitis Chimeric Virus Safely Destroys Brain Tumors

    PubMed Central

    Wollmann, Guido; Drokhlyansky, Eugene; Davis, John N.; Cepko, Connie

    2015-01-01

    ABSTRACT High-grade tumors in the brain are among the deadliest of cancers. Here, we took a promising oncolytic virus, vesicular stomatitis virus (VSV), and tested the hypothesis that the neurotoxicity associated with the virus could be eliminated without blocking its oncolytic potential in the brain by replacing the neurotropic VSV glycoprotein with the glycoprotein from one of five different viruses, including Ebola virus, Marburg virus, lymphocytic choriomeningitis virus (LCMV), rabies virus, and Lassa virus. Based on in vitro infections of normal and tumor cells, we selected two viruses to test in vivo. Wild-type VSV was lethal when injected directly into the brain. In contrast, a novel chimeric virus (VSV-LASV-GPC) containing genes from both the Lassa virus glycoprotein precursor (GPC) and VSV showed no adverse actions within or outside the brain and targeted and completely destroyed brain cancer, including high-grade glioblastoma and melanoma, even in metastatic cancer models. When mice had two brain tumors, intratumoral VSV-LASV-GPC injection in one tumor (glioma or melanoma) led to complete tumor destruction; importantly, the virus moved contralaterally within the brain to selectively infect the second noninjected tumor. A chimeric virus combining VSV genes with the gene coding for the Ebola virus glycoprotein was safe in the brain and also selectively targeted brain tumors but was substantially less effective in destroying brain tumors and prolonging survival of tumor-bearing mice. A tropism for multiple cancer types combined with an exquisite tumor specificity opens a new door to widespread application of VSV-LASV-GPC as a safe and efficacious oncolytic chimeric virus within the brain. IMPORTANCE Many viruses have been tested for their ability to target and kill cancer cells. Vesicular stomatitis virus (VSV) has shown substantial promise, but a key problem is that if it enters the brain, it can generate adverse neurologic consequences, including death. We

  17. Utilizing chimeric proteins for exploring the cellular fate of endogenous proteins.

    PubMed

    Ben-Yehudah, Ahmi; Aqeilan, Rami; Belostotsky, Ruth; Azar, Yehudith; Lorberboum-Galski, Haya

    2002-01-11

    We recently designed and constructed chimeric proteins for the elimination of specific cell populations. These chimeric proteins are composed of a targeting component fused to an apoptotic protein as the killing moiety. However, chimeric proteins can serve not only to eliminate cell populations, but also as "biological tools" for studying the fate of endogenous proteins. We show here that upon entering their target cell, a variety of chimeric proteins composed of an endogenous protein as their killing moiety reach the subcellular location of their endogenous counterpart. In contrast, bacterial-based killing domains head for the subcellular site of their substrate. Moreover, the chimeric protein acts similarly to the endogenous protein, while causing the cell to die. Therefore, chimeric proteins may serve as a unique tool for investigating cellular proteins and their intracellular localization, without the need to overexpress them.

  18. Rotavirus VP7 epitope chimeric proteins elicit cross-immunoreactivity in guinea pigs.

    PubMed

    Zhao, Bingxin; Pan, Xiaoxia; Teng, Yumei; Xia, Wenyue; Wang, Jing; Wen, Yuling; Chen, Yuanding

    2015-10-01

    VP7 of group A rotavirus (RVA) contains major neutralizing epitopes. Using the antigenic protein VP6 as the vector, chimeric proteins carrying foreign epitopes have been shown to possess good immunoreactivity and immunogenicity. In the present study, using modified VP6 as the vector, three chimeric proteins carrying epitopes derived from VP7 of RVA were constructed. The results showed that the chimeric proteins reacted with anti-VP6 and with SA11 and Wa virus strains. Antibodies from guinea pigs inoculated with the chimeric proteins recognized VP6 and VP7 of RVA and protected mammalian cells from SA11 and Wa infection in vitro. The neutralizing activities of the antibodies against the chimeric proteins were significantly higher than those against the vector protein VP6F. Thus, development of chimeric vaccines carrying VP7 epitopes using VP6 as a vector could be a promising alternative to enhance immunization against RVAs.

  19. Ex post power economic analysis of record of decision operational restrictions at Glen Canyon Dam.

    SciTech Connect

    Veselka, T. D.; Poch, L. A.; Palmer, C. S.; Loftin, S.; Osiek, B; Decision and Information Sciences; Western Area Power Administration

    2010-07-31

    On October 9, 1996, Bruce Babbitt, then-Secretary of the U.S. Department of the Interior signed the Record of Decision (ROD) on operating criteria for the Glen Canyon Dam (GCD). Criteria selected were based on the Modified Low Fluctuating Flow (MLFF) Alternative as described in the Operation of Glen Canyon Dam, Colorado River Storage Project, Arizona, Final Environmental Impact Statement (EIS) (Reclamation 1995). These restrictions reduced the operating flexibility of the hydroelectric power plant and therefore its economic value. The EIS provided impact information to support the ROD, including an analysis of operating criteria alternatives on power system economics. This ex post study reevaluates ROD power economic impacts and compares these results to the economic analysis performed prior (ex ante) to the ROD for the MLFF Alternative. On the basis of the methodology used in the ex ante analysis, anticipated annual economic impacts of the ROD were estimated to range from approximately $15.1 million to $44.2 million in terms of 1991 dollars ($1991). This ex post analysis incorporates historical events that took place between 1997 and 2005, including the evolution of power markets in the Western Electricity Coordinating Council as reflected in market prices for capacity and energy. Prompted by ROD operational restrictions, this analysis also incorporates a decision made by the Western Area Power Administration to modify commitments that it made to its customers. Simulated operations of GCD were based on the premise that hourly production patterns would maximize the economic value of the hydropower resource. On the basis of this assumption, it was estimated that economic impacts were on average $26.3 million in $1991, or $39 million in $2009.

  20. Enhancement by dimethyl myleran of donor type chimerism in murine recipients of bone marrow allografts

    SciTech Connect

    Lapidot, T.; Terenzi, A.; Singer, T.S.; Salomon, O.; Reisner, Y. )

    1989-05-15

    A major problem in using murine models for studies of bone marrow allograft rejection in leukemia patients is the narrow margin in which graft rejection can be analyzed. In mice irradiated with greater than 9 Gy total body irradiation (TBI) rejection is minimal, whereas after administration of 8 Gy TBI, which spares a significant number of clonable T cells, a substantial frequency of host stem cells can also be detected. In current murine models, unlike in humans, bone marrow allograft rejection is generally associated with full autologous hematopoietic reconstitution. In the present study, we investigated the effect of the myeloablative drug dimethyl myleran (DMM) on chimerism status following transplantation of T cell-depleted allogenic bone marrow (using C57BL/6 donors and C3H/HeJ recipients, conditioned with 8 Gy TBI). Donor type chimerism 1 to 2 months post-transplant of 1 to 3 x 10(6) bone marrow cells was markedly enhanced by using DMM one day after TBI and prior to transplantation. Conditioning with cyclophosphamide instead of DMM, in combination with 8 Gy TBI, did not enhance engraftment of donor type cells. Artificial reconstitution of T cells, after conditioning with TBI plus DMM, by adding mature thymocytes, or presensitization with irradiated donor type spleen cells 1 week before TBI and DMM, led to strong graft rejection and consequently to severe anemia. The anti-donor responses in these models were proportional to the number of added T cells and to the number of cells used for presensitization, and they could be neutralized by increasing the bone marrow inoculum.

  1. Updated SO2 Emission Estimates over China using OMI/Aura Observations and the CHIMERE CTM

    NASA Astrophysics Data System (ADS)

    van der A, R. J.; Balis, D.; Koukouli, M.; Theys, N.; Ding, J.; Zyrichidou, I.; Mijling, B.

    2016-12-01

    As part of EU FP7 Monitoring and Assessment of Regional air quality in China using space Observations, Project Of Long-term sino-european co-Operation, MarcoPolo, project, http://www.marcopolo.eu/, updated sulphur dioxide, SO2, emissions for the time period 2005 to 2015 inclusive are presented here. Monthly mean OMI/Aura anthropogenic SO2, observations over Eastern China for the domain 102°E to 132°E and from 15°N to 55°N form the basis of the new emission inventory, which is provided on a spatial resolution of 0.25°x0.25°. The 2010 Multi-resolution Emission Inventory for China (MEIC), http://www.meicmodel.org/. SO2 emissions, in Mg/month, form the baseline apriori inventory, coupled with the multi-scale model for air quality forecasting and simulation, CHIMERE, http://www.lmd.polytechnique.fr/chimere/, v2013b, which is providing the SO2 field. The pre-2010 trend in resulting emissions show that these appear to be stable in time, with a slight negative, possibly not significant, trend nonetheless; from the monthly mean aposteriori emissions, for the entire domain, pre-2010, the change appears to be of the order of -0.51±0.38Tg, whereas post-2010, -1.64±0.37Tg. From the seasonal emissions, those estimates remain similar at -0.34±0.49Tg and -1.26±0.33Tg respectively. The largest differences between apriori and aposteriori become vastly significant from year 2014 onwards, confirming similar studies that monitor the decrease in SO2 emissions over China from space.

  2. Chimeric Proteins to Detect DNA Damage and Mismatches

    SciTech Connect

    McCutchen-Maloney, S; Malfatti, M; Robbins, K M

    2002-01-14

    The goal of this project was to develop chimeric proteins composed of a DNA mismatch or damage binding protein and a nuclease, as well as methods to detect DNA mismatches and damage. We accomplished this through protein engineering based on using polymerase chain reactions (PCRs) to create chimeras with novel functions for damage and mismatch detection. This project addressed fundamental questions relating to disease susceptibility and radiation-induced damage in cells. It also supported and enhanced LLNL's competency in the emerging field of proteomics. In nature, DNA is constantly being subjected to damaging agents such as exposure to ultraviolet (UV) radiation and various environmental and dietary carcinogens. If DNA damage is not repaired however, mutations in DNA result that can eventually manifest in cancer and other diseases. In addition to damage-induced DNA mutations, single nucleotide polymorphisms (SNPs), which are variations in the genetic sequence between individuals, may predispose some to disease. As a result of the Human Genome Project, the integrity of a person's DNA can now be monitored. Therefore, methods to detect DNA damage, mutations, and SNPs are useful not only in basic research but also in the health and biotechnology industries. Current methods of detection often use radioactive labeling and rely on expensive instrumentation that is not readily available in many research settings. Our methods to detect DNA damage and mismatches employ simple gel electrophoresis and flow cytometry, thereby alleviating the need for radioactive labeling and expensive equipment. In FY2001, we explored SNP detection by developing methods based on the ability of the chimeric proteins to detect mismatches. Using multiplex assays with flow cytometry and fluorescent beads to which the DNA substrates where attached, we showed that several of the chimeras possess greater affinity for damaged and mismatched DNA than for native DNA. This affinity was demonstrated in

  3. Voxel-Based Analysis of Fractional Anisotropy in Post-Stroke Apathy

    PubMed Central

    Yang, Song-ran; Shang, Xin-yuan; Tao, Jun; Liu, Jian-yang; Hua, Ping

    2015-01-01

    Objective To explore the structural basis of post-stroke apathy by using voxel-based analysis (VBA) of fractional anisotropy (FA) maps. Methods We enrolled 54 consecutive patients with ischemic stroke during convalescence, and divided them into apathy (n = 31) and non-apathy (n = 23) groups. We obtained magnetic resonance images of their brains, including T1, T2 and DTI sequences. Age, sex, education level, Hamilton Depression Scale (HAMD) scores, Mini-Mental State Examination (MMSE) scores, National Institutes of Health Stroke Scale (NIHSS) scores, and infarct locations for the two groups were compared. Finally, to investigate the structural basis of post-stroke apathy, VBA of FA maps was performed in which we included the variables that a univariate analysis determined had P-values less than 0.20 as covariates. Results HAMD (P = 0.01) and MMSE (P<0.01) scores differed significantly between the apathy and non-apathy groups. After controlling for age, education level, HAMD scores, and MMSE scores, significant FA reduction was detected in four clusters with peak voxels at the genu of the corpus callosum (X = −16, Y = 30, Z = 8), left anterior corona radiata (−22, 30, 10), splenium of the corpus callosum (−24, −56, 18), and right inferior frontal gyrus white matter (52, 24, 18), after family-wise error correction for multiple comparisons. Conclusions Post-stroke apathy is related to depression and cognitive decline. Damage to the genu of the corpus callosum, left anterior corona radiata, splenium of the corpus callosum, and white matter in the right inferior frontal gyrus may lead to apathy after ischemic stroke. PMID:25555189

  4. Voxel-based analysis of fractional anisotropy in post-stroke apathy.

    PubMed

    Yang, Song-ran; Shang, Xin-yuan; Tao, Jun; Liu, Jian-yang; Hua, Ping

    2015-01-01

    To explore the structural basis of post-stroke apathy by using voxel-based analysis (VBA) of fractional anisotropy (FA) maps. We enrolled 54 consecutive patients with ischemic stroke during convalescence, and divided them into apathy (n = 31) and non-apathy (n = 23) groups. We obtained magnetic resonance images of their brains, including T1, T2 and DTI sequences. Age, sex, education level, Hamilton Depression Scale (HAMD) scores, Mini-Mental State Examination (MMSE) scores, National Institutes of Health Stroke Scale (NIHSS) scores, and infarct locations for the two groups were compared. Finally, to investigate the structural basis of post-stroke apathy, VBA of FA maps was performed in which we included the variables that a univariate analysis determined had P-values less than 0.20 as covariates. HAMD (P = 0.01) and MMSE (P<0.01) scores differed significantly between the apathy and non-apathy groups. After controlling for age, education level, HAMD scores, and MMSE scores, significant FA reduction was detected in four clusters with peak voxels at the genu of the corpus callosum (X = -16, Y = 30, Z = 8), left anterior corona radiata (-22, 30, 10), splenium of the corpus callosum (-24, -56, 18), and right inferior frontal gyrus white matter (52, 24, 18), after family-wise error correction for multiple comparisons. Post-stroke apathy is related to depression and cognitive decline. Damage to the genu of the corpus callosum, left anterior corona radiata, splenium of the corpus callosum, and white matter in the right inferior frontal gyrus may lead to apathy after ischemic stroke.

  5. Patient-specific Finite Element Analysis of Fiber Post and Ferrule Design.

    PubMed

    Rodrigues, Monise de Paula; Soares, Priscilla Barbosa Ferreira; Valdivia, Andréa Dollores Correia Miranda; Pessoa, Roberto Sales; Veríssimo, Crisnicaw; Versluis, Antheunis; Soares, Carlos José

    2017-09-01

    A ferrule on anterior endodontic-treated teeth has been evaluated using clinical trials, in vitro tests, and finite element analysis (FEA). The patient-specific FEA with a nonuniform ferrule and nonlinear contact biting load associated with clinical validation can be used to predict failure. A patient was selected with both maxillary central incisors with different ferrule designs who received endodontic treatment and restoration using a fiber post, composite core, and computer aided design and computer aided manufacturing lithium disilicate ceramic crowns. Strain gauges were attached to the buccal surfaces of both teeth to record ceramic strain during bite force recording for FEA validation. Cone-beam computed tomographic imaging was performed, and the Digital Imaging and Communication in Medicine files were exported to Mimics, 3-Matic (Materialise, Leuven, Belgium) and Patran (MSC Software, Santa Ana, CA) software to create a patient-specific FEA model. Bite load was applied using contact load applied by antagonist teeth (155 N). Mechanical properties were obtained from the literature. Modified von Mises equivalent stress was used for stress evaluation. Stresses on the dentin and fiber post on the left incisor, which had a nonuniform ferrule, were higher compared with the right incisor. The strain values recorded for the right central incisor (strain gauge =79.9 ± 3.8 μS and FEA = 69.5 μS) and the left central incisor (strain gauge = 83.5 ± 5.3 μS and FEA = 73.9 μS) validate the FEA analysis. FEA was validated with in vivo strain values measured at the buccal crown surfaces, supporting that the stress levels were realistic for investigation of the clinical performance of fiber posts. Maintaining a uniform ferrule was more favorable than a localized higher ferrule. Copyright © 2017 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  6. Effect of IL-2-Bax, a novel interleukin-2-receptor-targeted chimeric protein, on bleomycin lung injury.

    PubMed

    Segel, Michael J; Aqeilan, Rami; Zilka, Keren; Lorberboum-Galski, Haya; Wallach-Dayan, Shulamit B; Conner, Michael W; Christensen, Thomas G; Breuer, Raphael

    2005-10-01

    The role of lymphocytes in the pathogenesis of lung fibrosis is not clear, but the weight of the evidence supports a pro-fibrotic effect for lymphocytes. The high-affinity interleukin-2 receptor (haIL-2R) is expressed on activated, but not quiescent, T lymphocytes. This selective expression of haIL-2R provides the basis for therapeutic strategies that target IL-2R-expressing cells. We hypothesized that elimination of activated lymphocytes by IL-2R-targeted chimeric proteins might ameliorate lung fibrosis. We investigated the effects of IL-2-Bax, a novel apoptosis-inducing IL-2R-targeted chimeric protein, on bleomycin-induced lung injury in mice. Treatment groups included (i) a single intratracheal instillation of bleomycin and twice-daily intraperitoneal injections of IL-2-Bax; (ii) intratracheal bleomycin and intraperitoneal IL-2-PE66(4Glu), an older-generation chimeric protein; (iii) intratracheal bleomycin/intraperitoneal PBS; (iv) intratracheal saline/intraperitoneal PBS. Lung injury was evaluated 14 days after intratracheal instillation by cell count in bronchoalveolar lavage (BAL) fluid, semi-quantitative and quantitative histomorphological measurements and by biochemical analysis of lung hydroxyproline. Bleomycin induced a BAL lymphocytosis that was significantly attenuated by IL-2-Bax and IL-2-PE66(4Glu). However, morphometric parameters and lung hydroxyproline were unaffected by the chimeric proteins. These results show that IL-2-Bax reduces the lymphocytic infiltration of the lungs in response to bleomycin, but this effect is not accompanied by a decrease in lung fibrosis.

  7. An in silico chimeric multi subunit vaccine targeting virulence factors of enterotoxigenic Escherichia coli (ETEC) with its bacterial inbuilt adjuvant.

    PubMed

    Nazarian, Shahram; Mousavi Gargari, Seyed Latif; Rasooli, Iraj; Amani, Jafar; Bagheri, Samane; Alerasool, Masoome

    2012-07-01

    Enteric infections resulting in diarrheal diseases remain as major global health problems. Among bacteria, enterotoxigenic Escherichia coli (ETEC) causes the largest number of diarrheal cases. There is a great interest in developing an effective ETEC vaccine. An ETEC vaccine could focus on virulence factors present in ETEC pathogens and nontoxic Heat-labile B subunit (LTB). Chimeric proteins carrying epitopes, or adjuvant sequences increase the possibility of eliciting a broad cellular or humoral immune response. In-silico tools are highly suited to study, design and evaluate vaccine strategies. Colonization factors are among the virulence factor studied in the present work employing bioinformatic tools. A synthetic chimeric gene, encoding CfaB, CstH, CotA, and LTB was designed. Modeling was done to predict the 3D structure of protein. This model was validated using Ramachandran plot statistics. The predicted B-cell epitopes were mapped on the surface of the model. Validation result showed that 97.2% residues lie in favored or additional allowed region of Ramachandran plot. VaxiJen analysis of the protein showed high antigenicity. Linear and conformational B-cell epitopes were identified. The identified T-cell epitopes are apt to bind MHC molecules. The epitopes in the chimeric protein are likely to induce both the B-cell and T-cell mediated immune responses.

  8. Identification of breed-specific DNA polymorphisms for a simple and unambiguous screening system in germline chimeric chickens.

    PubMed

    Choi, Jin Won; Lee, Eun Young; Shin, Ji Hye; Zheng, Yinghui; Cho, Byung Wook; Kim, Jin-Kyoo; Kim, Heebal; Han, Jae Yong

    2007-04-01

    In the chicken, Dominant white is one of the major loci affecting feather color. Germline chimeric chickens are identified by testcross analysis using this genetic marker. The testcross, however, is a time-consuming and laborious procedure, resulting in the need for a faster and simpler molecular method. A recent study showed that Dominant white was exclusively associated with a 9-bp insertion in the PMEL17 gene. We searched for breed-specific sequence polymorphisms in the PMEL17 gene among White Leghorn (WL) (white feather), Korean Ogol Chicken (KOC) (black feather), and Barred Plymouth Rock (grayish-white, each feather regularly crossed with parallel blue-black bars). In addition to the 9-bp insertion, WLs and KOCs have unique bases in single nucleotide polymorphisms (SNPs) at the 1,777th and 3,118th bases in the PMEL17 gene. To detect these sequence polymorphisms, allele-specific polymerase chain reaction (AS-PCR) was performed, which successfully distinguished the different breeds. We confirmed the ability of the AS primers to detect germline chimerism. This simple method can be widely used for the screening of germline chimeric chickens.

  9. Stress distribution of oval and circular fiber posts in amandibular premolar: a three-dimensional finite element analysis

    PubMed Central

    Kilic, Kerem; Esim, Emir; Aslan, Tugrul; Kilinc, Halil Ibrahim; Yildirim, Sahin

    2013-01-01

    PURPOSE The aim of the present study was to evaluate the effects of posts with different morphologies on stress distribution in an endodontically treated mandibular premolar by using finite element models (FEMs). MATERIALS AND METHODS A mandibular premolar was modeled using the ANSYS software program. Two models were created to represent circular and oval fiber posts in this tooth model. An oblique force of 300 N was applied at an angle of 45° to the occlusal plane and oriented toward the buccal side. von Mises stress was measured in three regions each for oval and circular fiber posts. RESULTS FEM analysis showed that the von Mises stress of the circular fiber post (426.81 MPa) was greater than that of the oval fiber post (346.34 MPa). The maximum distribution of von Mises stress was in the luting agent in both groups. Additionally, von Mises stresses accumulated in the coronal third of root dentin, close to the post space in both groups. CONCLUSION Oval fiber posts are preferable to circular fiber posts in oval-shaped canals given the stress distribution at the post-dentin interface. PMID:24353882

  10. Establishment of Donor Chimerism Using Allogeneic Bone Marrow with AMP Cell Co-infusion

    DTIC Science & Technology

    2016-09-01

    AWARD NUMBER: W81XWH-15-1-0234 TITLE: “Establishment of donor Chimerism Using Allogeneic Bone Marrow with AMP Cell Co-infusion” PRINCIPAL...Form 298 (Rev. 8-98) Prescribed by ANSI Std. Z39.18 Megan.sykes@columbia.edu Establishment of donor Chimerism Using Allogeneic Bone Marrow with AMP...promote the induction of durable mixed allogeneic chimerism in non-human primates. To this end, we have performed bone marrow transplantation in two

  11. Comparison of automated pre-column and post-column analysis of amino acid oligomers

    NASA Technical Reports Server (NTRS)

    Chow, J.; Orenberg, J. B.; Nugent, K. D.

    1987-01-01

    It has been shown that various amino acids will polymerize under plausible prebiotic conditions on mineral surfaces, such as clays and soluble salts, to form varying amounts of oligomers (n = 2-6). The investigations of these surface reactions required a quantitative method for the separation and detection of these amino acid oligomers at the picomole level in the presence of nanomole levels of the parent amino acid. In initial high-performance liquid chromatography (HPLC) studies using a classical postcolumn o-phthalaldehyde (OPA) derivatization ion-exchange HPLC procedure with fluorescence detection, problems encountered included lengthy analysis time, inadequate separation and large relative differences in sensitivity for the separated species, expressed as a variable fluorescent yield, which contributed to poor quantitation. We have compared a simple, automated, pre-column OPA derivatization and reversed-phase HPLC method with the classical post-column OPA derivatization and ion-exchange HPLC procedure. A comparison of UV and fluorescent detection of the amino acid oligomers is also presented. The conclusion reached is that the pre-column OPA derivatization, reversed-phase HPLC and UV detection produces enhanced separation, improved sensitivity and faster analysis than post-column OPA derivatization, ion-exchange HPLC and fluorescence detection.

  12. Analysis of hyponatraemia associated post-operative mortality in 3897 hip fracture patients.

    PubMed

    Tinning, Craig G; Cochrane, Lynda A; Singer, Brian R

    2015-07-01

    Hyponatraemia is common in hospitalised patients. In recent years the relationship between hyponatraemia and bone metabolism, falls and fractures has become more established. This study evaluates the prevalence of hyponatraemia (plasma sodium<135mmol/l) in 3897 patients undergoing operative treatment for hip fracture and the relationship between hyponatraemia and mortality in these patients. Hyponatraemia was an independent risk factor for increased post-operative mortality on multivariate analysis. Median age at admission was 83 years. Hyponatraemia was present in 19.1% of patients with hip fracture on admission, 29.5% of patients in the first 24h post-operatively and 20% of patients at discharge. There was a significant association between hyponatraemia and time from admission to surgery indicating that patients admitted with hyponatraemia waited longer. The median follow-up time was 863 (range 0-4352) days. There were 2460 deaths (63.1% of the original 3897 patients) prior to the censor date. A total of 1144 patients (29.4% of the original 3897 patients) died within 12 months of discharge. Median time to death for patients with and without hyponatraemia on admission was 34 months (SE 1.7 months) and 41 months (SE 2.5 months) respectively (p=0.003). Median time to death for patients with and without hyponatraemia within 24h post-operatively was 35 months (SE 2.5 months) and 42 months (SE 1.7 months) respectively (p=0.004). Following elimination of other independent variables associated with increased mortality, hyponatraemia on admission was associated with an increased risk of death (adjusted HR 1.15, p=0.005). Post-operative hyponatraemia was also associated with an increased risk of death (adjusted HR 1.15, p=0.006). Trends suggested that hyponatraemia within 48h of discharge was associated with an increased risk of death (adjusted HR 1.15, p=0.636). Hyponatraemia is common in elderly patients with hip fractures both at initial presentation and during

  13. Analysis of DNA from post-blast pipe bomb fragments for identification and determination of ancestry.

    PubMed

    Tasker, Esiri; LaRue, Bobby; Beherec, Charity; Gangitano, David; Hughes-Stamm, Sheree

    2017-05-01

    Improvised explosive devices (IEDs) such as pipe bombs are weapons used to detrimentally affect people and communities. A readily accessible brand of exploding targets called Tannerite® has been identified as a potential material for abuse as an explosive in pipe bombs. The ability to recover and genotype DNA from such weapons may be vital in the effort to identify suspects associated with these devices. While it is possible to recover DNA from post-blast fragments using short tandem repeat markers (STRs), genotyping success can be negatively affected by low quantities of DNA, degradation, and/or PCR inhibitors. Alternative markers such as insertion/null (INNULs) and single nucleotide polymorphisms (SNPs) are bi-allelic genetic markers that are shorter genomic targets than STRs for amplification, which are more likely to resist degradation. In this study, we constructed pipe bombs that were spiked with known amounts of biological material to: 1) recover "touch" DNA from the surface of the device, and 2) recover traces of blood from the ends of wires (simulated finger prick). The bombs were detonated with the binary explosive Tannerite® using double-base smokeless powder to initiate the reaction. DNA extracted from the post-blast fragments was quantified with the Quantifiler® Trio DNA Quantification Kit. STR analysis was conducted using the GlobalFiler® Amplification Kit, INNULs were amplified using an early-access version of the InnoTyper™ 21 Kit, and SNP analysis via massively parallel sequencing (MPS) was performed using the HID-Ion Ampliseq™ Identity and Ancestry panels using the Ion Chef and Ion PGM sequencing system. The results of this study showed that INNUL markers resulted in the most complete genetic profiles when compared to STR and SNP profiles. The random match probabilities calculated for samples using INNULs were lower than with STRs when less than 14 STR alleles were reported. These results suggest that INNUL analysis may be well suited for

  14. Post-buckling and Large Amplitude Free Vibration Analysis of Composite Beams: Simple Intuitive Formulation

    NASA Astrophysics Data System (ADS)

    Gunda, Jagadish Babu; Venkateswara Rao, Gundabathula

    2016-04-01

    Post-buckling and large amplitude free vibration analysis of composite beams with axially immovable ends is investigated in the present study using a simple intuitive formulation. Geometric nonlinearity of Von-Karman type is considered in the analysis which accounts for mid-plane stretching action of the beam. Intuitive formulation uses only two parameters: the critical bifurcation point and the axial stretching force developed due to membrane stretching action of the beam. Hinged-hinged, clamped-clamped and clamped-hinged boundary conditions are considered. Numerical accuracy of the proposed analytical closed-form solutions obtained from the intuitive formulation are compared to available finite element solutions for symmetric and asymmetric layup schemes of laminated composite beam which indicates the confidence gained on the present formulation.

  15. Modified Delphi survey for decision analysis for prophylaxis of post-radiation osteonecrosis.

    PubMed

    Cramer, Carl K; Epstein, Joel B; Sheps, Samuel B; Schechter, Martin T; Busser, James R

    2002-09-01

    to augment epidemiological data from the literature, assist Bayesian perspectives and a decision analytic framework for the minimization of post-radiation osteonecrosis (PRON; osteoradionecrosis) and its impacts in irradiated head and neck cancer patients. a modified Delphi process survey of 15 international clinical experts was used to identify and assess outcome data and factors related to PRON risk, extraction, and factor suitability for formal decision analysis. Clinimetric pain and function outcome scales were created and assessed for relevance to quality of life. expert opinion qualitative assessments were generally adequate and consistent between open- and close-ended items, but many quantitative (e.g. PRON risk rate) estimates were not. A research agenda advocated to validate the epidemiological database for minimization of PRON and decision analysis includes: adoption of a uniform definition of PRON, and ICD code for non-experimental databases; more detailed, consistent data reporting in articles; and quality of life studies.

  16. Analysis of post-blood meal flight distances in mosquitoes utilizing zoo animal blood meals.

    PubMed

    Greenberg, Jacob A; DiMenna, Mark A; Hanelt, Ben; Hofkin, Bruce V

    2012-06-01

    We assessed the post-blood meal flight distance of four mosquito species in a unique environment using blood meal analysis. Mosquitoes were trapped at the Rio Grande Zoo in Albuquerque, NM, and the blood source of blood-engorged mosquitoes was identified. The distance from the enclosure of the animal serving as a blood source to the trap site was then determined. We found that mosquitoes captured at the zoo flew no more than 170 m with an average distance of 106.7 m after taking a blood meal. This is the first study in which the flight distance of wild mosquitoes has been assessed using blood meal analysis and the first in which zoo animals have served as the exclusive source of blood meals. © 2012 The Society for Vector Ecology.

  17. Post-game analysis: An initial experiment for heuristic-based resource management in concurrent systems

    NASA Technical Reports Server (NTRS)

    Yan, Jerry C.

    1987-01-01

    In concurrent systems, a major responsibility of the resource management system is to decide how the application program is to be mapped onto the multi-processor. Instead of using abstract program and machine models, a generate-and-test framework known as 'post-game analysis' that is based on data gathered during program execution is proposed. Each iteration consists of (1) (a simulation of) an execution of the program; (2) analysis of the data gathered; and (3) the proposal of a new mapping that would have a smaller execution time. These heuristics are applied to predict execution time changes in response to small perturbations applied to the current mapping. An initial experiment was carried out using simple strategies on 'pipeline-like' applications. The results obtained from four simple strategies demonstrated that for this kind of application, even simple strategies can produce acceptable speed-up with a small number of iterations.

  18. Germ-line chimerism and paternal care in marmosets (Callithrix kuhlii).

    PubMed

    Ross, C N; French, J A; Ortí, G

    2007-04-10

    The formation of viable genetic chimeras in mammals through the transfer of cells between siblings in utero is rare. Using microsatellite DNA markers, we show here that chimerism in marmoset (Callithrix kuhlii) twins is not limited to blood-derived hematopoietic tissues as was previously described. All somatic tissue types sampled were found to be chimeric. Notably, chimerism was demonstrated to be present in germ-line tissues, an event never before documented as naturally occurring in a primate. In fact, we found that chimeric marmosets often transmit sibling alleles acquired in utero to their own offspring. Thus, an individual that contributes gametes to an offspring is not necessarily the genetic parent of that offspring. The presence of somatic and germ-line chimerism may have influenced the evolution of the extensive paternal and alloparental care system of this taxon. Although the exact mechanisms of sociobiological change associated with chimerism have not been fully explored, we show here that chimerism alters relatedness between twins and may alter the perceived relatedness between family members, thus influencing the allocation of parental care. Consistent with this prediction, we found a significant correlation between paternal care effort and the presence of epithelial chimerism, with males carrying chimeric infants more often than nonchimeric infants. Therefore, we propose that the presence of placental chorionic fusion and the exchange of cell lines between embryos may represent a unique adaptation affecting the evolution of cooperative care in this group of primates.

  19. Thionin-D4E1 chimeric protein protects plants against bacterial infections

    DOEpatents

    Stover, Eddie W; Gupta, Goutam; Hao, Guixia

    2017-08-08

    The generation of a chimeric protein containing a first domain encoding either a pro-thionon or thionin, a second domain encoding D4E1 or pro-D4E1, and a third domain encoding a peptide linker located between the first domain and second domain is described. Either the first domain or the second domain is located at the amino terminal of the chimeric protein and the other domain (second domain or first domain, respectively) is located at the carboxyl terminal. The chimeric protein has antibacterial activity. Genetically altered plants and their progeny expressing a polynucleotide encoding the chimeric protein resist diseases caused by bacteria.

  20. Fluctuating lymphocyte chimerism, tolerance and anti-tumor response in a patient with refractory lymphoma receiving nonmyeloablative conditioning and a haploidentical related allogeneic bone marrow transplant.

    PubMed

    Toh, Han C; Spitzer, Thomas R; Preffer, Frederic; Alexander, Stephen I; McAfee, Steve; Dombkowski, David; Clark, Jeffrey S; Colby, Christine; Saidman, Susan; Sackstein, Robert; Sykes, Megan

    2002-12-01

    A 51-year-old patient with refractory non-Hodgkin lymphoma (NHL) received non-myeloablative conditioning and a two of six (A, B, DR) human leucocyte antigen (HLA) mismatched donor BMT. Post-BMT lymphocytes showed fluctuating T- and natural killer (NK)-cell chimerism, which culminated in mainly donor lymphocytes by Day + 100. Changes in lymphocyte chimerism correlated with anti-donor and anti-host responses in mixed lymphocyte reaction (MLR). On Day + 100, a strong anti-host response was observed in MLR in the absence of graft-versus-host disease (GVHD), together with near complete regression of the patient's lymphoma. A mild chronic GVHD later developed and, eventually, by 680 days post-BMT, the lymphoma had relapsed and MLR reflected a state of global immune unresponsiveness. These observations demonstrate evolving host-versus-graft and graft-versus-host tolerance that correlates with fluctuating lymphoid chimerism and graft-versus-lymphoma (GVL) effects, in the absence of severe GVHD. Eventual lymphoma relapse temporally correlated with a generalised immunosuppressed state.

  1. Case of 46,XX/47,XY, +21 chimerism in a newborn infant with ambiguous genitalia

    SciTech Connect

    Sawai, Tomoko; Yoshimoto, Masaaki; Kinoshita, Ei-ichi; Baba, Tsuneyoshi; Matsumoto, Tadashi; Tsuji, Yoshiro, Niikawa, Norio; Fukuda, Shinpei; Harada, Naoki

    1994-02-15

    The authors describe the whole-body chimerism in a newborn infant with small phallus, pseudo-vaginal perineal hypospadias, and a bifid scrotum containing gonads. The human testis determining factor gene (SRY) was detected by PCR amplification. GTG-banding chromosome analysis in peripheral blood lymphocytes and cultured fibroblasts derived from right cubital skin showed a 46,XX/47,XY, +21 karyotype. Their ratios in each cell line were 294:5 and 178:7, respectively. QFQ-banding chromosome analysis documented 3 heteromorphic satellites on trisomic chromsomes 21 in the 47,XY,+21 cell line and a homozygous satellite pattern in the 46,XX cell line. Heteromorphic patterns of chromsomes 4, 13, 14, and 22 were also different between the two cell lines. To our knowledge, such disomy/trisomy chimeras have not been described previously. 10 refs., 3 figs.

  2. Case of 46,XX/47,XY, +21 chimerism in a newborn infant with ambiguous genitalia.

    PubMed

    Sawai, T; Yoshimoto, M; Kinoshita, E; Baba, T; Matsumoto, T; Tsuji, Y; Fukuda, S; Harada, N; Niikawa, N

    1994-02-15

    We describe whole-body chimerism in a newborn infant with small phallus, pseudo-vaginal perineal hypospadias, and a bifid scrotum containing gonads. The human testis determining factor gene (SRY) was detected by PCR amplification. GTG-banding chromosome analysis in peripheral blood lymphocytes and cultured fibroblasts derived from right cubital skin showed a 46,XX/47,XY, +21 karyotype. Their ratios in each cell line were 294:5 and 178:7, respectively. QFQ-banding chromosome analysis documented 3 heteromorphic satellites on trisomic chromosomes 21 in the 47,XY, +21 cell line and a homozygous satellite pattern in the 46,XX cell line. Heteromorphic patterns of chromosomes 4, 13, 14, and 22 were also different between the two cell lines. To our knowledge, such disomy/trisomy chimeras have not been described previously.

  3. [Reliability of venous blood gas analysis and radionuclide angiography in post-traumatic dystrophy].

    PubMed

    Scola, A; Scola, E

    2017-06-01

    The diagnosis "post-traumatic dystrophy" (PTD) was first defined with clinical and paraclinical criteria by Scola et al. in 2013. The objectivity and reliability of the paraclinical criteria (venous blood gas analysis [vBGA], radionuclide angiography [RNA]), and recommendations for therapy should be assessed in a prospective study. In five patients with clinical signs of post-traumatic nonbacterial inflammation of the hand, both diagnosis and a 3‑week hospital treatment were carried out in accordance with the publication mentioned above. The primary traumata (four fractures and one soft-tissue injury) were located in either the hand or the forearm. Unsuccessful outpatient treatment always led to hospital admission. One patient with severe osteopenia in the hand skeleton was treated with bisphosphonates for 6 months. All patients fulfilled the clinical and paraclinical criteria for the diagnosis of PTD. On admission, an elevated venous partial pressure of oxygen was found by vBGA in the affected hand (∆pO2 mean 22 ± 3 mm Hg) and a hyperperfusion due to arteriovenous shunts was measured using RNA (mean 75 ± 47%). The symptomatic treatment was extremely well tolerated; by the time of discharge, all patients achieved full functioning of the hand with minor loss of strength (venous ∆pO2 mean 5 ± 3 mm Hg). The osteopenia in the one patient treated with bisphosphonates showed recalcification after 6 months. The reliability of clinical and paraclinical criteria for PTD were confirmed. vBGA and RNA seem to be good parameters for confirming the diagnosis of PTD. "Rubor," a symptom traditionally interpreted as "hyperemia," contradicts the paraclinical findings and leads to the assumption that the cause of this post-traumatic syndrome is microvascular dysfunction.

  4. Finite element analysis of quasistatic and fatigue failure of post and cores.

    PubMed

    Huysmans, M C; Van der Varst, P G

    1993-02-01

    Finite element (FE) analysis of the mechanical behaviour of materials and structures facilitates the investigation of their internal stress distributions. However, the validity of the model is not always ascertained. In this study a three-dimensional (3D) FE model was developed, representing a laboratory set-up of direct post and core restored upper premolars. These restorations, using either composite or amalgam for core material, have been the subject of study in previous quasistatic and fatigue strength tests. The aim of this study was to validate the FE model for prefailure and failure modelling, by comparing the computational results with the laboratory observations and failure results. Two failure criteria were selected for investigation: Modified Von Mises and Drücker-Prager equivalent stress. Four model variations were carried out, representing different conditions at the core-tooth interface. Prefailure modelling was found to be adequate. The calculated failure results could only partly be fitted to the quasistatic tests. The best fit was effected with a model using partial bonding of the core, for the composite core. Fatigue failure was reproduced somewhat better by a model using no bonding at all, again to a higher degree for the composite core. Calculations of post stress using a model simulating increased core mobility supported an observation made previously (M. C. D. N. J. M. Huysmans et al., in press; Int. Endodont. J. XX, XXX-XXX), implying that a composite core raises the demands made on the post. The conclusion is made that validation of FE calculations is essential. A 3D model as presented here shows a satisfactory fit to fatigue data but not to quasistatic results.(ABSTRACT TRUNCATED AT 250 WORDS)

  5. Analysis of Bond Strength by Pull Out Test on Fiber Glass Posts Cemented in Different Lengths

    PubMed Central

    Webber, Mariana Benedetti Ferreira; Michida, Silvia Masae de Araújo; Marson, Fabiano Carlos; de Oliveira, Giovani Corrêa; Silva, Cleverson de Oliveira e

    2015-01-01

    Background: The aim of this study was to evaluate, by means of pull-out test, the bond strength of fiberglass posts when cemented with different lengths in endodontically treated teeth. Materials and Methods: Sixty single-rooted bovine roots were cut in the cementoenamel junction with 21 mm length. They were endodontically treated and randomly divided into three groups (n = 20). Group 1 - Preparation of 2/3 of the remaining roots; Group 2 - Preparation of ½ of the remaining roots and Group 3 - Preparation of ¼ of remaining roots. For all groups it were used posts n = 3 (Exacto, Angelus, Brazil), and cemented with self-etching resin cement (RelyXU200). After cementing posts, the samples were thermocycled (10.000 cycles/5°C and 55°C). The pull-out test was performed on a universal testing machine (EMIC - DL500) and the values obtained were statistically analyzed by analysis of variance (one-factor ANOVA) and multiple comparison test of Tukey, with level of significance of 5%. Results: The mean values ± standard deviation in Newtons (N) were: Group 1 = 120.5 (±42.8) A, Group 2 = 103.1 (±31.2) AB, Group 3 = 41.2 (±22.4) C, P < 0.005. Conclusion: The preparation of ½ of remaining root appears to be a viable alternative when 2/3 of the preparation of the remaining root is not possible, but more results are needed for clinical validation. PMID:25954063

  6. Comparing Social Network Analysis of Posts with Counting of Posts as a Measurement of Learners' Participation in Facebook Discussions

    ERIC Educational Resources Information Center

    Lee, Hye Yeon; Lee, Hyeon Woo

    2016-01-01

    With the currently growing interest in social network services, many college courses use social network services as platforms for discussions, and a number of studies have been conducted on the use of social network analysis to measure students' participation in online discussions. This study aims to demonstrate the difference between counting…

  7. Single-cell analysis reveals lineage segregation in early post-implantation mouse embryos.

    PubMed

    Wen, Jing; Zeng, Yanwu; Fang, Zhuoqing; Gu, Junjie; Ge, Laixiang; Tang, Fan; Qu, Zepeng; Hu, Jing; Cui, Yaru; Zhang, Kunshan; Wang, Junbang; Li, Siguang; Sun, Yi; Jin, Ying

    2017-03-15

    The mammalian post-implantation embryo has been extensively investigated at the tissue level. However, to unravel the molecular basis for the cell-fate plasticity and determination, it is essential to study the characteristics of individual cells. Especially, the individual definitive endoderm (DE) cells have not been characterized in vivo. Here, we report gene expression patterns in single cells freshly isolated from mouse embryos on days 5.5 and 6.5. Initial transcriptome data from 124 single cells yielded signature genes for the epiblast, visceral endoderm, and extra-embryonic ectoderm and revealed a unique distribution pattern of fibroblast growth factor (Fgf) ligands and receptors. Further analysis indicated that early-stage epiblast cells do not segregate into lineages of the major germ layers. Instead, some cells began to diverge from epiblast cells, displaying molecular features of the pre-mesendoderm by expressing higher levels of mesendoderm markers and lower levels of Sox3 transcripts. Analysis of single-cell high-throughput quantitative RT-PCR data from 441 cells identified a late stage of the day 6.5 embryo in which mesoderm and DE cells emerge, with many of them coexpressing Oct4 and Gata6. Analysis of single-cell RNA-seq data from 112 cells of the late-stage day 6.5 embryos revealed differentially expressed signaling genes and networks of transcription factors that might underlie the segregation of the mesoderm and DE lineages. Moreover, we discovered a subpopulation of mesoderm cells that possess molecular features of the extraembryonic mesoderm. This study provides fundamental insight into the molecular basis for lineage segregation in post-implantation mouse embryos.

  8. Chimeric antigen receptor T cell therapy in AML: How close are we?

    PubMed

    Gill, Saar

    2016-12-01

    The majority of patients presenting with acute myeloid leukemia (AML) initially respond to chemotherapy but post-remission therapy is required to consolidate this response and achieve long-term disease-free survival. The most effective form of post-remission therapy relies on T cell immunotherapy in the form of allogeneic hematopoietic cell transplantation (HCT). However, patients with active disease cannot usually expect to be cured with HCT. This inherent dichotomy implies that traditional T cell-based immunotherapy in the form of allogeneic HCT stops being efficacious somewhere between the measurable residual disease (MRD) and the morphologically obvious range. This is in part because the full power of T cells must be restrained in order to avoid lethal graft-versus-host disease (GVHD) and partly because only a sub-population of donor T cells are expected to be able to recognize AML cells via their T cell receptor. Chimeric antigen receptor (CAR) T cell therapy, most advanced in the treatment of patients with B-cell malignancies, may circumvent some of these limitations. However, major challenges remain to be overcome before CAR T cell therapy can be safely applied to AML.

  9. Host-Bacterial Interactions in Post-treatment Apical Periodontitis: A Metaproteome Analysis.

    PubMed

    Provenzano, José Claudio; Antunes, Henrique S; Alves, Flávio R F; Rôças, Isabela N; Alves, Wilber S; Silva, Márcia R S; Siqueira, José F

    2016-06-01

    This study evaluated the bacterial and human metaproteome of root apexes and the matched inflammatory lesions from teeth with post-treatment apical periodontitis. Root apexes and matched inflammatory lesions from root canal-treated teeth with apical periodontitis were obtained during periradicular surgery. All root canal fillings were rated as adequate on the basis of radiographs and cone-beam computed tomography. The specimens were cryopulverized and subjected to metaproteomic analysis for human and bacterial proteins by using a mass spectrometry platform that is based on nanoflow liquid chromatography coupled with linear ion trap quadrupole Velos Orbitrap. The metaproteome analyses revealed the presence of viable and metabolically active human and bacterial cells in both apexes and lesions. Several bacterial proteins of interest for pathogenicity and therapeutics were identified in both apexes and lesions, including proteins related to antibiotic resistance, proteolytic function, stress response, adhesion, and virulence. Many human proteins related to immune defense mechanisms were also detected in both root apex and lesion specimens, including immunoglobulins, complement system, and proteins linked to T-cell and B-cell activation, neutrophil microbicidal processes, antigen recognition/presentation, bone resorption, and protection against tissue damage. Occurrence of host defense factors from the innate and adaptive immune responses and bacterial virulence, survival, and resistance proteins in matched root apexes/periradicular inflammatory lesions indicates a complex and dynamic host-pathogen interaction in teeth with post-treatment apical periodontitis. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  10. The Orion Exploration Flight Test Post Flight Solid Particle Flight Environment Inspection and Analysis

    NASA Technical Reports Server (NTRS)

    Miller, Joshua E.

    2016-01-01

    Orbital debris in the millimeter size range can pose a hazard to current and planned spacecraft due to the high relative impact speeds in Earth orbit. Fortunately, orbital debris has a relatively short life at lower altitudes due to atmospheric effects; however, at higher altitudes orbital debris can survive much longer and has resulted in a band of high flux around 700 to 1,500 km above the surface of the Earth. While large orbital debris objects are tracked via ground based observation, little information can be gathered about small particles except by returned surfaces, which until the Orion Exploration Flight Test number one (EFT-1), has only been possible for lower altitudes (400 to 500 km). The EFT-1 crew module backshell, which used a porous, ceramic tile system with surface coatings, has been inspected post-flight for potential micrometeoroid and orbital debris (MMOD) damage. This paper describes the pre- and post-flight activities of inspection, identification and analysis of six candidate MMOD impact craters from the EFT-1 mission.

  11. Genetic analysis in post-mortem samples with micro-ischemic alterations.

    PubMed

    Campuzano, Oscar; Sanchez-Molero, Olallo; Mademont-Soler, Irene; Coll, Monica; Allegue, Catarina; Ferrer-Costa, Carles; Mates, Jesus; Perez-Serra, Alexandra; Del Olmo, Bernat; Iglesias, Anna; Sarquella-Brugada, Georgia; Brugada, Josep; Borondo, Juan Carlos; Castella, Josep; Medallo, Jordi; Brugada, Ramon

    2017-02-01

    Sudden cardiac arrest is a leading cause of death worldwide. Most cardiac arrests happen in patients who have previously suffered a myocardial infarct. The risk of sudden death after infarction may increase in people who carry a pathogenic genetic alteration in cardiac ion channels. We hypothesized that micro-ischemia could trigger lethal arrhythmogenesis, thus we sought to identify genetic alterations in cardiac ion channels in patients with micro-ischemic disease. We studied a cohort of 56 post-mortem samples. Autopsy studies identified myocardial infarction as the cause of death in each case. We used both Sanger sequencing and next-generation sequencing to screen candidate genes associated with sudden cardiac death. We identified six rare missense genetic variations in five unrelated patients. Two variants have been previously reported; one is associated with atrial fibrillation (SCN5A_p.H445D), and the other is predicted to be benign (ANK2_p.T2059M). The novel variants were predicted in silico as benign, except for one (RyR2_p.M4019T), which was classified as deleterious. Our post-mortem, micro-infarction cohort displayed a rate of nearly 10% non-common genetic variants. However, the clinical significance of most of the identified variants remains unknown due to lack of family assessment. Further analyses should be performed in large cohorts to clarify the role of ion-channel gene analysis in samples showing microscopic ischemic alterations.

  12. Physical rehabilitation in post-conflict settings: analysis of public policy and stakeholder networks.

    PubMed

    Blanchet, Karl; Girois, Susan; Urseau, Isabelle; Smerdon, Christine; Drouet, Yann; Jama, Ali

    2014-01-01

    Physical rehabilitation plays a determinant role in post-conflict contexts to restore disabled citizens' mobility and independence. While the main objectives of any physical rehabilitation programme are to ensure that the services provided are accessible and of good quality to meet existing needs, it is intended that the services need to be supported over the long term by public health and social welfare authorities. This article presents the results of a study conducted in three post-conflict countries on the relationships between the level of commitment of national governments to rehabilitation services and the influence of social networks on national policy related to physical rehabilitation. From a policy and resource standpoint, the environment in Nepal is the most favourable for creating leverage at the national level to influence the commitment of ministries in the rehabilitation sector, compared with Cambodia and Somaliland. Stakeholder network analysis in Nepal, furthermore, reveals a dominant civil society and private sector supporting rehabilitation services, including intense involvement of local organisations and user groups. Implications for Rehabilitation Physical rehabilitation is not on the top of the agenda of governments in fragile states. The commitment and involvement of national authorities in the rehabilitation sector is positively influenced by civil society and international organisations. The denser the social network of the rehabilitation sector is, the more influence the actors can exert influence over national authorities.

  13. Analysis of phenazepam and 3-hydroxyphenazepam in post-mortem fluids and tissues.

    PubMed

    Crichton, Megan L; Shenton, Catriona F; Drummond, Gail; Beer, Lewis J; Seetohul, L Nitin; Maskell, Peter D

    2015-10-01

    Phenazepam is a benzodiazepine that is predominantly used clinically in the former Soviet states but is being abused throughout the wider world. This study reports the tissue distribution and concentration of both phenazepam and 3-hydroxyphenazepam in 29 cases quantitated by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in a variety of post-mortem fluids (subclavian blood, femoral blood, cardiac blood, urine, vitreous humour) and tissues (thalamus, liver and psoas muscle). In 27 cases, the cause of death was not directly related to phenazepam (preserved (fluoride/oxalate) femoral blood phenazepam concentrations 0.007 mg/L to 0.360 mg/L (median 0.097 mg/L). In two cases, phenazepam was either a contributing factor to, or the certified cause of death (preserved (fluoride/oxalate) femoral blood 0.97 mg/L and 1.64 mg/L). The analysis of phenazepam and 3-hydroxyphenazepam in this study suggests that they are unlikely to be subject to large post-mortem redistribution and that there is no direct correlation between tissues/fluid and femoral blood concentrations. Preliminary investigations of phenazepam stability comparing femoral blood phenazepam concentrations in paired preserved (2.5% fluoride/oxalate) and unpreserved blood show that unpreserved samples show on average a 14% lower concentration of phenazepam and we recommend that phenazepam quantitation is carried out using preserved samples wherever possible. Copyright © 2015 John Wiley & Sons, Ltd.

  14. Sharing feelings online: studying emotional well-being via automated text analysis of Facebook posts

    PubMed Central

    Settanni, Michele; Marengo, Davide

    2015-01-01

    Digital traces of activity on social network sites represent a vast source of ecological data with potential connections with individual behavioral and psychological characteristics. The present study investigates the relationship between user-generated textual content shared on Facebook and emotional well-being. Self-report measures of depression, anxiety, and stress were collected from 201 adult Facebook users from North Italy. Emotion-related textual indicators, including emoticon use, were extracted form users’ Facebook posts via automated text analysis. Correlation analyses revealed that individuals with higher levels of depression, anxiety expressed negative emotions on Facebook more frequently. In addition, use of emoticons expressing positive emotions correlated negatively with stress level. When comparing age groups, younger users reported higher frequency of both emotion-related words and emoticon use in their posts. Also, the relationship between online emotional expression and self-report emotional well-being was generally stronger in the younger group. Overall, findings support the feasibility and validity of studying individual emotional well-being by means of examination of Facebook profiles. Implications for online screening purposes and future research directions are discussed. PMID:26257692

  15. Forest Fires and Post - Fire Regeneration in Algeria Analysis with Satellite Data

    NASA Astrophysics Data System (ADS)

    Zegrar, Ahmed

    2016-07-01

    The Algerian forests are characterized by a particularly flammable material and fuel. The wind, the relief and the slope facilitates the propagation of fire. The use of remote sensing data multi-­dates, combined with other types of data of various kinds on the environment and forest burned, opens up interesting perspectives for the management of post-­fire regeneration. In this study the use of multi-­temporal remote sensing image Alsat-­1 and Landsat combined with other types of data concerning both background and burned down forest appears to be promising in evaluating and spatial and temporal effects of post fire regeneration. A spatial analysis taking into consideration the characteristics of the burned down site in the North West of Algeria, allowed to better account new factors to explain the regeneration and its temporal and spatial variation. We intended to show the potential use of remote sensing data from satellite ALSAT-­1, of spatial resolution of 32 m. . This approach allows showing the contribution of the data of Algerian satellite ALSAT in the detection and the well attended some forest fires in Algeria.

  16. An evaluation of computer-aided disproportionality analysis for post-marketing signal detection.

    PubMed

    Lehman, H P; Chen, J; Gould, A L; Kassekert, R; Beninger, P R; Carney, R; Goldberg, M; Goss, M A; Kidos, K; Sharrar, R G; Shields, K; Sweet, A; Wiholm, B E; Honig, P K

    2007-08-01

    To understand the value of computer-aided disproportionality analysis (DA) in relation to current pharmacovigilance signal detection methods, four products were retrospectively evaluated by applying an empirical Bayes method to Merck's post-marketing safety database. Findings were compared with the prior detection of labeled post-marketing adverse events. Disproportionality ratios (empirical Bayes geometric mean lower 95% bounds for the posterior distribution (EBGM05)) were generated for product-event pairs. Overall (1993-2004 data, EBGM05> or =2, individual terms) results of signal detection using DA compared to standard methods were sensitivity, 31.1%; specificity, 95.3%; and positive predictive value, 19.9%. Using groupings of synonymous labeled terms, sensitivity improved (40.9%). More of the adverse events detected by both methods were detected earlier using DA and grouped (versus individual) terms. With 1939-2004 data, diagnostic properties were similar to those from 1993 to 2004. DA methods using Merck's safety database demonstrate sufficient sensitivity and specificity to be considered for use as an adjunct to conventional signal detection methods.

  17. Sharing feelings online: studying emotional well-being via automated text analysis of Facebook posts.

    PubMed

    Settanni, Michele; Marengo, Davide

    2015-01-01

    Digital traces of activity on social network sites represent a vast source of ecological data with potential connections with individual behavioral and psychological characteristics. The present study investigates the relationship between user-generated textual content shared on Facebook and emotional well-being. Self-report measures of depression, anxiety, and stress were collected from 201 adult Facebook users from North Italy. Emotion-related textual indicators, including emoticon use, were extracted form users' Facebook posts via automated text analysis. Correlation analyses revealed that individuals with higher levels of depression, anxiety expressed negative emotions on Facebook more frequently. In addition, use of emoticons expressing positive emotions correlated negatively with stress level. When comparing age groups, younger users reported higher frequency of both emotion-related words and emoticon use in their posts. Also, the relationship between online emotional expression and self-report emotional well-being was generally stronger in the younger group. Overall, findings support the feasibility and validity of studying individual emotional well-being by means of examination of Facebook profiles. Implications for online screening purposes and future research directions are discussed.

  18. Analysis of questions regarding morbidity coding posted to the online coding clinic of the Korean Medical Record Association.

    PubMed

    Boo, Yookyung; Han, Whiejong M; Lim, Hyunsook; Choi, Youngjin

    2014-01-01

    Accuracy and consistency in morbidity coding are important in both clinical research and practice. However,Health Information Managers (HIMs) sometimes face difficulties in assigning morbidity codes. To assist them,the Korean Medical Record Association operates an online coding clinic bulletin board, on which HIMs can post questions and receive answers. Frequency analysis and Fisher's exact testing were performed to identify differences among the types of questions posted and the characteristics of the HIMs who posted them. Through statistical analysis, it was found that HIMs working at hospitals with fewer than 500 beds and those with more than 10 years of work experience were found to post more questions than other HIMs. The study also identified the characteristics of HIMs who require more coding education and particular diagnoses for which further training is required. Our findings will assist the development of coding procedures, guidelines, education programs, and a more user-friendly database.

  19. Glycoprotein analysis by delayed extraction and post-source decay MALDI-TOF-MS

    NASA Astrophysics Data System (ADS)

    Tsarbopoulos, A.; Bahr, U.; Pramanik, B. N.; Karas, M.

    1997-12-01

    Matrix-assisted laser desorption-ionization (MALDI)-MS analysis of glycoprotein samples is usually affected by metastable fragmentation, particularly in reflectron instruments. Use of delayed extraction (DE) is shown to minimize the observed metastable fragmentation. In the case of the CHO IL-4, which contains complex-type N-linked glycans, the disialylated component gives the most abundant MALDI signal with a dramatically improved resolution and mass accuracy over the non-DE linear TOF analysis. This increased resolution is advantageous for the 30 kDa Sf9-derived IL-4 receptor, where it is possible to differentiate the individual glycans, but not for higher mass and more heterogeneous glycoproteins. It is also shown that MALDI analysis of proteins with labile functional groups is more superior and reliable with linear DE-TOF systems rather than reflectron TOF analyzers. Further structural information on the sequence and disulfide mapping, as well as glycopeptide identification can be obtained by post-source decay (PSD) analysis of peptide and glycopeptide isolated fractions. The PSD formation of a characteristic triplet of ions separated by 33 Da in mass can be used to identify disulfide-paired peptides, even from complex digest mixtures of proteins.

  20. Novel nanocomposites from spider silk–silica fusion (chimeric) proteins

    PubMed Central

    Wong Po Foo, Cheryl; Patwardhan, Siddharth V.; Belton, David J.; Kitchel, Brandon; Anastasiades, Daphne; Huang, Jia; Naik, Rajesh R.; Perry, Carole C.; Kaplan, David L.

    2006-01-01

    Silica skeletal architectures in diatoms are characterized by remarkable morphological and nanostructural details. Silk proteins from spiders and silkworms form strong and intricate self-assembling fibrous biomaterials in nature. We combined the features of silk with biosilica through the design, synthesis, and characterization of a novel family of chimeric proteins for subsequent use in model materials forming reactions. The domains from the major ampullate spidroin 1 (MaSp1) protein of Nephila clavipes spider dragline silk provide control over structural and morphological details because it can be self-assembled through diverse processing methods including film casting and fiber electrospinning. Biosilica nanostructures in diatoms are formed in aqueous ambient conditions at neutral pH and low temperatures. The R5 peptide derived from the silaffin protein of Cylindrotheca fusiformis induces and regulates silica precipitation in the chimeric protein designs under similar ambient conditions. Whereas mineralization reactions performed in the presence of R5 peptide alone form silica particles with a size distribution of 0.5–10 μm in diameter, reactions performed in the presence of the new fusion proteins generate nanocomposite materials containing silica particles with a narrower size distribution of 0.5–2 μm in diameter. Furthermore, we demonstrate that composite morphology and structure could be regulated by controlling processing conditions to produce films and fibers. These results suggest that the chimeric protein provides new options for processing and control over silica particle sizes, important benefits for biomedical and specialty materials, particularly in light of the all aqueous processing and the nanocomposite features of these new materials. PMID:16769898

  1. Novel nanocomposites from spider silk-silica fusion (chimeric) proteins.

    PubMed

    Wong Po Foo, Cheryl; Patwardhan, Siddharth V; Belton, David J; Kitchel, Brandon; Anastasiades, Daphne; Huang, Jia; Naik, Rajesh R; Perry, Carole C; Kaplan, David L

    2006-06-20

    Silica skeletal architectures in diatoms are characterized by remarkable morphological and nanostructural details. Silk proteins from spiders and silkworms form strong and intricate self-assembling fibrous biomaterials in nature. We combined the features of silk with biosilica through the design, synthesis, and characterization of a novel family of chimeric proteins for subsequent use in model materials forming reactions. The domains from the major ampullate spidroin 1 (MaSp1) protein of Nephila clavipes spider dragline silk provide control over structural and morphological details because it can be self-assembled through diverse processing methods including film casting and fiber electrospinning. Biosilica nanostructures in diatoms are formed in aqueous ambient conditions at neutral pH and low temperatures. The R5 peptide derived from the silaffin protein of Cylindrotheca fusiformis induces and regulates silica precipitation in the chimeric protein designs under similar ambient conditions. Whereas mineralization reactions performed in the presence of R5 peptide alone form silica particles with a size distribution of 0.5-10 microm in diameter, reactions performed in the presence of the new fusion proteins generate nanocomposite materials containing silica particles with a narrower size distribution of 0.5-2 microm in diameter. Furthermore, we demonstrate that composite morphology and structure could be regulated by controlling processing conditions to produce films and fibers. These results suggest that the chimeric protein provides new options for processing and control over silica particle sizes, important benefits for biomedical and specialty materials, particularly in light of the all aqueous processing and the nanocomposite features of these new materials.

  2. Characterization of chimeric Bacillus thuringiensis Vip3 toxins.

    PubMed

    Fang, Jun; Xu, Xiaoli; Wang, Ping; Zhao, Jian-Zhou; Shelton, Anthony M; Cheng, Jiaan; Feng, Ming-Guang; Shen, Zhicheng

    2007-02-01

    Bacillus thuringiensis vegetative insecticidal proteins (Vip) are potential alternatives for B. thuringiensis endotoxins that are currently utilized in commercial transgenic insect-resistant crops. Screening a large number of B. thuringiensis isolates resulted in the cloning of vip3Ac1. Vip3Ac1 showed high insecticidal activity against the fall armyworm Spodoptera frugiperda and the cotton bollworm Helicoverpa zea but very low activity against the silkworm Bombyx mori. The host specificity of this Vip3 toxin was altered by sequence swapping with a previously identified toxin, Vip3Aa1. While both Vip3Aa1 and Vip3Ac1 showed no detectable toxicity against the European corn borer Ostrinia nubilalis, the chimeric protein Vip3AcAa, consisting of the N-terminal region of Vip3Ac1 and the C-terminal region of Vip3Aa1, became insecticidal to the European corn borer. In addition, the chimeric Vip3AcAa had increased toxicity to the fall armyworm. Furthermore, both Vip3Ac1 and Vip3AcAa are highly insecticidal to a strain of cabbage looper (Trichoplusia ni) that is highly resistant to the B. thuringiensis endotoxin Cry1Ac, thus experimentally showing for the first time the lack of cross-resistance between B. thuringiensis Cry1A proteins and Vip3A toxins. The results in this study demonstrated that vip3Ac1 and its chimeric vip3 genes can be excellent candidates for engineering a new generation of transgenic plants for insect pest control.

  3. Chimeric antibodies with extended half-life in ferrets.

    PubMed

    Nesspor, Thomas C; Scallon, Bernard

    2014-09-01

    Ferrets have long been used as a disease model for the study of influenza vaccines, but a more recent use has been for the study of human monoclonal antibodies directed against influenza viruses. Published data suggest that human antibodies are cleared unusually quickly from the ferret and that immune responses may be partially responsible. This immunogenicity increases variability within groups and may present an obstacle to long-term studies. Our aim was to identify an antibody design with reduced immunogenicity and longer circulating half-life in ferrets. The constant region coding sequences for ferret immunoglobulin G were cloned, and chimeric human/ferret antibodies were expressed and purified. Some of the chimeric antibodies included substitutions that have been shown to extend the half-life of human IgG antibodies. These chimeric antibodies were tested for binding to recombinant ferret FcRn receptor and then evaluated in pharmacokinetic studies in ferrets. A one-residue substitution in the ferret Fc domain, S252Y, was identified that increased binding affinity to the ferret neonatal receptor by 24-fold and extended half-life from 65 ± 27 to 206 ± 28 hours or ~9 days. Ferrets dosed twice with this surrogate antibody showed no indications of an immune response. Expressing the variable region of a candidate human therapeutic antibody with ferret constant regions containing the S252Y substitution can offer long half-life and limit immunogenicity. © 2014 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

  4. Electroencephalography reactivity for prognostication of post-anoxic coma after cardiopulmonary resuscitation: A comparison of quantitative analysis and visual analysis.

    PubMed

    Liu, Gang; Su, Yingying; Jiang, Mengdi; Chen, Weibi; Zhang, Yan; Zhang, Yunzhou; Gao, Daiquan

    2016-07-28

    Electroencephalogram reactivity (EEG-R) is a positive predictive factor for assessing outcomes in comatose patients. Most studies assess the prognostic value of EEG-R utilizing visual analysis; however, this method is prone to subjectivity. We sought to categorize EEG-R with a quantitative approach. We retrospectively studied consecutive comatose patients who had an EEG-R recording performed 1-3 days after cardiopulmonary resuscitation (CPR) or during normothermia after therapeutic hypothermia. EEG-R was assessed via visual analysis and quantitative analysis separately. Clinical outcomes were followed-up at 3-month and dichotomized as recovery of awareness or no recovery of awareness. A total of 96 patients met the inclusion criteria, and 38 (40%) patients recovered awareness at 3-month followed-up. Of 27 patients with EEG-R measured with visual analysis, 22 patients recovered awareness; and of the 69 patients who did not demonstrated EEG-R, 16 patients recovered awareness. The sensitivity and specificity of visually measured EEG-R were 58% and 91%, respectively. The area under the receiver operating characteristic curve for the quantitative analysis was 0.92 (95% confidence interval, 0.87-0.97), with the best cut-off value of 0.10. EEG-R through quantitative analysis might be a good method in predicting the recovery of awareness in patients with post-anoxic coma after CPR.

  5. Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

    PubMed Central

    Frenkel-Morgenstern, Milana; Lacroix, Vincent; Ezkurdia, Iakes; Levin, Yishai; Gabashvili, Alexandra; Prilusky, Jaime; del Pozo, Angela; Tress, Michael; Johnson, Rory; Guigo, Roderic; Valencia, Alfonso

    2012-01-01

    Chimeric RNAs comprise exons from two or more different genes and have the potential to encode novel proteins that alter cellular phenotypes. To date, numerous putative chimeric transcripts have been identified among the ESTs isolated from several organisms and using high throughput RNA sequencing. The few corresponding protein products that have been characterized mostly result from chromosomal translocations and are associated with cancer. Here, we systematically establish that some of the putative chimeric transcripts are genuinely expressed in human cells. Using high throughput RNA sequencing, mass spectrometry experimental data, and functional annotation, we studied 7424 putative human chimeric RNAs. We confirmed the expression of 175 chimeric RNAs in 16 human tissues, with an abundance varying from 0.06 to 17 RPKM (Reads Per Kilobase per Million mapped reads). We show that these chimeric RNAs are significantly more tissue-specific than non-chimeric transcripts. Moreover, we present evidence that chimeras tend to incorporate highly expressed genes. Despite the low expression level of most chimeric RNAs, we show that 12 novel chimeras are translated into proteins detectable in multiple shotgun mass spectrometry experiments. Furthermore, we confirm the expression of three novel chimeric proteins using targeted mass spectrometry. Finally, based on our functional annotation of exon organization and preserved domains, we discuss the potential features of chimeric proteins with illustrative examples and suggest that chimeras significantly exploit signal peptides and transmembrane domains, which can alter the cellular localization of cognate proteins. Taken together, these findings establish that some chimeric RNAs are translated into potentially functional proteins in humans. PMID:22588898

  6. Bioengineered Chimeric Spider Silk-Uranium Binding Proteins

    PubMed Central

    Krishnaji, Sreevidhya Tarakkad; Kaplan, David L.

    2014-01-01

    Heavy metals constitute a source of environmental pollution. Here, novel functional hybrid biomaterials for specific interactions with heavy metals are designed by bioengineering consensus sequence repeats from spider silk of Nephila clavipes with repeats of a uranium peptide recognition motif from a mutated 33-residue of calmodulin protein from Paramecium tetraurelia. The self-assembly features of the silk to control nanoscale organic/inorganic material interfaces provides new biomaterials for uranium recovery. With subsequent enzymatic digestion of the silk to concentrate the sequestered metals, options can be envisaged to use these new chimeric protein systems in environmental engineering, including to remediate environments contaminated by uranium. PMID:23212989

  7. Chimeric transcripts resulting from complex duplications in chromosome Xq28.

    PubMed

    Zuccherato, Luciana W; Alleva, Benjamin; Whiters, Marjorie A; Carvalho, Claudia M B; Lupski, James R

    2016-02-01

    Gene fusions have been observed in somatic alterations in cancer and in schizophrenia. However, the underlying mechanism(s) for their formation are poorly understood. We experimentally demonstrated the expression of splicing variants of in silico predicted chimeric genes F8/CSAG1 and BCAP31/TEX28 in two individuals with de novo complex genomic rearrangements of Xq28; F8/CSAG1 includes exonization of an ERVL-MaLR intronic repetitive element. We provide evidence that replicative repair may contribute to exon shuffling processes and diversify the repertoire of expressed transcripts.

  8. The basic principles of chimeric antigen receptor (CAR) design

    PubMed Central

    Sadelain, Michel; Brentjens, Renier; Riviere, Isabelle

    2013-01-01

    CARs are recombinant receptors that provide both antigen-binding and T cell activating functions. A multitude of CARs has been reported over the past decade, targeting an array of cell surface tumor antigens. Their biological functions have dramatically changed following the introduction of tri-partite receptors comprising a costimulatory domain, termed second generation CARs. These have recently demonstrated clinical benefit in patients treated with CD19-targeted autologous T cells. CARs may be combined with costimulatory ligands, chimeric costimulatory receptors or cytokines to further enhance T cell potency, specificity and safety. CARs represent a new class of drugs with exciting potential for cancer immunotherapy. PMID:23550147

  9. Combination of liquid-chromatography tandem mass spectrometry in different scan modes with human and chimeric mouse urine for the study of steroid metabolism.

    PubMed

    Pozo, Oscar J; Lootens, Leen; Van Eenoo, Peter; Deventer, Koen; Meuleman, Philip; Leroux-Roels, Geert; Parr, Maria K; Schänzer, Wilhelm; Delbeke, Frans T

    2009-11-01

    Anabolic steroids are among the most frequently detected compounds in doping analysis. They are extensively metabolized and therefore an in-depth knowledge about steroid metabolism is needed. In this study, a liquid chromatography tandem mass spectometry (LC-MS/MS) method based on a precursor ion scan with a uPA-SCID mouse with humanized liver (a chimeric mouse) was explored for the detection of steroid metabolism. Methandienone was used as a model compound. The application of the precursor ion scan method in positive human samples and chimeric mice samples after methandienone administration allowed the detection of most steroid metabolites without any structural restriction. Three hitherto unreported metabolites were found using this approach. These metabolites were characterized using LC-MS/MS and feasible structures were proposed. The structure of one of them, 6-ene-epimethandienone, was confirmed by the synthesis of the reference compound. A selected reaction monitoring (SRM) method for the specific detection of all these metabolites has been developed. The application of this method to several human and chimeric mouse samples confirmed that more than 80% of the steroid metabolites were found in both samples. Only metabolites that are poorly detectable by LC-MS/MS were not detected in some urine samples. The metabolic nature of the unreported metabolites was also confirmed. A global strategy for the detection of steroid metabolites combining both human and chimeric mouse urine is proposed.

  10. At most three ES cells contribute to the somatic lineages of chimeric mice and of mice produced by ES-tetraploid complementation.

    PubMed

    Wang, Zhongde; Jaenisch, Rudolf

    2004-11-01

    Chimeric or entirely embryonic stem (ES) cell-derived mice ("ES mice") can be produced by injecting ES cells into diploid (2n) or tetraploid (4n) host blastocysts, respectively. Usually, between 10 and 15 ES cells are injected into the host blastocyst, but it is not clear how many of the injected cells contribute to the somatic lineages, thus serve as "founder cells" of the embryo proper. We have used genetically labeled ES cells to retrospectively determine the number of founder ES cells that generate the somatic lineages of chimeric and of ES mice. ES cell clones individually labeled with provirus were mixed in equal numbers and injected into 2n or 4n blastocysts to generate chimeric or ES mice. Southern analysis of DNA from the resulting animals indicated that the somatic lineages were most often derived from one or two and sometimes from up to three founder ES cells. The number of founder cells was independent of the total number of cells injected into the host blastocysts. Our results are consistent with the notion that constraints of the host embryo restrict the number of ES cells that can contribute to a chimeric or an ES mouse.

  11. A guide to genome-wide association analysis and post-analytic interrogation.

    PubMed

    Reed, Eric; Nunez, Sara; Kulp, David; Qian, Jing; Reilly, Muredach P; Foulkes, Andrea S

    2015-12-10

    This tutorial is a learning resource that outlines the basic process and provides specific software tools for implementing a complete genome-wide association analysis. Approaches to post-analytic visualization and interrogation of potentially novel findings are also presented. Applications are illustrated using the free and open-source R statistical computing and graphics software environment, Bioconductor software for bioinformatics and the UCSC Genome Browser. Complete genome-wide association data on 1401 individuals across 861,473 typed single nucleotide polymorphisms from the PennCATH study of coronary artery disease are used for illustration. All data and code, as well as additional instructional resources, are publicly available through the Open Resources in Statistical Genomics project: http://www.stat-gen.org.

  12. A pilot DTI analysis in patients with recent onset post-traumatic stress disorder

    NASA Astrophysics Data System (ADS)

    Liu, Yang; Li, Liang; Li, Baojuan; Zhang, Xi; Lu, Hongbing

    2016-03-01

    To explore the alteration in white matter between survivors with recent onset post-traumatic stress disorder (PTSD) and without PTSD, who survived from the same coal mine flood disaster, the diffusion tensor imaging (DTI) sequences were analyzed using DTI studio and statistical parametric mapping (SPM) packages in this paper. From DTI sequence, the fractional anisotropy (FA) value describes the degree of anisotropy of a diffusion process, while the apparent diffusion coefficient (ADC) value reflects the magnitude of water diffusion. The DTI analyses between PTSD and non-PTSD indicate lower FA values in the right caudate nucleus, right middle temporal gyrus, right fusiform gyrus, and right superior temporal gyrus, and higher ADC values in the right superior temporal gyrus and right corpus callosum of the subjects with PTSD. These results are partly in line with our previous volume and cortical thickness analyses, indicating the importance of multi-modality analysis for PTSD.

  13. Estimating the return on investment in disease management programs using a pre-post analysis.

    PubMed

    Fetterolf, Donald; Wennberg, David; Devries, Andrea

    2004-01-01

    Disease management programs have become increasingly popular over the past 5-10 years. Recent increases in overall medical costs have precipitated new concerns about the cost-effectiveness of medical management programs that have extended to the program directors for these programs. Initial success of the disease management movement is being challenged on the grounds that reported results have been the result of the application of faulty, if intuitive, methodologies. This paper discusses the use of "pre-post" methodology approaches in the analysis of disease management programs, and areas where application of this approach can result in spurious results and incorrect financial outcome assessments. The paper includes a checklist of these items for use by operational staff working with the programs, and a comprehensive bibliography that addresses many of the issues discussed.

  14. Error analysis in post linac to driver linac transport beam line of RAON

    NASA Astrophysics Data System (ADS)

    Kim, Chanmi; Kim, Eun-San

    2016-07-01

    We investigated the effects of magnet errors in the beam transport line connecting the post linac to the driver linac (P2DT) in the Rare Isotope Accelerator in Korea (RAON). The P2DT beam line is bent by 180-degree to send the radioactive Isotope Separation On-line (ISOL) beams accelerated in Linac-3 to Linac-2. This beam line transports beams with multi-charge state 132Sn45,46,47. The P2DT beam line includes 42 quadrupole, 4 dipole and 10 sextupole magnets. We evaluate the effects of errors on the trajectory of the beam by using the TRACK code, which includes the translational and the rotational errors of the quadrupole, dipole and sextupole magnets in the beam line. The purpose of this error analysis is to reduce the rate of beam loss in the P2DT beam line. The distorted beam trajectories can be corrected by using six correctors and seven monitors.

  15. Orion Post-Landing Crew Thermal Control Modeling and Analysis Results

    NASA Technical Reports Server (NTRS)

    Cross, Cynthia D.; Bue, Grant; Rains, George E.

    2009-01-01

    In a vehicle constrained by mass and power, it is necessary to ensure that during the process of reducing hardware mass and power that the health and well being of the crew is not compromised in the design process. To that end, it is necessary to ensure that in the final phase of flight - recovery, that the crew core body temperature remains below the crew cognitive deficit set by the Constellation program. This paper will describe the models used to calculate the thermal environment of the spacecraft after splashdown as well as the human thermal model used to calculate core body temperature. Then the results of these models will be examined to understand the key drivers for core body temperature. Finally, the analysis results will be used to show that additional cooling capability must be added to the vehicle to ensure crew member health post landing.

  16. Post-16 Physics and Chemistry Uptake: Combining Large-Scale Secondary Analysis with In-Depth Qualitative Methods

    ERIC Educational Resources Information Center

    Hampden-Thompson, Gillian; Lubben, Fred; Bennett, Judith

    2011-01-01

    Quantitative secondary analysis of large-scale data can be combined with in-depth qualitative methods. In this paper, we discuss the role of this combined methods approach in examining the uptake of physics and chemistry in post compulsory schooling for students in England. The secondary data analysis of the National Pupil Database (NPD) served…

  17. Post-16 Physics and Chemistry Uptake: Combining Large-Scale Secondary Analysis with In-Depth Qualitative Methods

    ERIC Educational Resources Information Center

    Hampden-Thompson, Gillian; Lubben, Fred; Bennett, Judith

    2011-01-01

    Quantitative secondary analysis of large-scale data can be combined with in-depth qualitative methods. In this paper, we discuss the role of this combined methods approach in examining the uptake of physics and chemistry in post compulsory schooling for students in England. The secondary data analysis of the National Pupil Database (NPD) served…

  18. Factors influencing patients' recovery and the efficacy of a psychosocial post-discharge intervention: post hoc analysis of a randomized controlled trial.

    PubMed

    Hengartner, Michael P; Passalacqua, Silvia; Heim, Gisela; Andreae, Andreas; Rössler, Wulf; von Wyl, Agnes

    2016-12-01

    The aim of this post hoc analysis was to examine self-reported recovery following a post-discharge intervention and to focus on the moderators of this intervention programme. RCT using parallel group block randomisation, including 151 patients with ≤3 hospitalisations within the last 3 years, a GAF score ≤60, and aged 18-64 years, assessed at two psychiatric hospitals from Zurich, Switzerland, between September 2011 and February 2014. In the present study, the main outcome was the OQ-45 as assessed prior to discharge from the index hospitalisation and at 12-month follow-up. Participants received either the post-discharge intervention provided by a social worker or treatment as usual (TAU). Patients in the intervention group showed substantially less recovery over the 12-month observation period than controls (d = 0.44). In the TAU group, 15.6 % remained clinically impaired at 12-month follow-up as opposed to 48.1 % in the intervention group (p = 0.001). Among participants in the intervention group, an interdisciplinary meeting of significant network members was associated with less recovery (d = 0.46). Involuntary index admission (d = 0.42) and high educational degree (d = 0.52) were significant moderators of the intervention. Both factors related to less recovery over time in the intervention group relative to TAU. According to the OQ-45, this psychosocial post-discharge intervention revealed an unintended negative effect on self-reported recovery over time. Specifically, the meeting of significant network members related to a moderate deteriorating effect, suggesting that the involvement of some carers, relatives, or friends may cause harm to the patient. Considering with reservation pending replication, these findings could have important implications for brief interventions targeted at patients' social networks. This study was supported by a private foundation. ISRCTN58280620.

  19. Expression and secretion of fungal endoglucanase II and chimeric cellobiohydrolase I in the oleaginous yeast Lipomyces starkeyi

    DOE PAGES

    Xu, Qi; Knoshaug, Eric P.; Wang, Wei; ...

    2017-07-24

    Lipomyces starkeyi is one of the leading lipid-producing microorganisms reported to date; its genetic transformation was only recently reported. Our aim is to engineer L. starkeyi to serve in consolidated bioprocessing (CBP) to produce lipid or fatty acid-related biofuels directly from abundant and low-cost lignocellulosic substrates. To evaluate L. starkeyi in this role, we first conducted a genome analysis, which revealed the absence of key endo- and exocellulases in this yeast, prompting us to select and screen four signal peptides for their suitability for the overexpression and secretion of cellulase genes. To compensate for the cellulase deficiency, we chose twomore » prominent cellulases, Trichoderma reesei endoglucanase II (EG II) and a chimeric cellobiohydrolase I (TeTrCBH I) formed by fusion of the catalytic domain from Talaromyces emersonii CBH I with the linker peptide and cellulose-binding domain from T. reesei CBH I. The systematically tested signal peptides included three peptides from native L. starkeyi and one from Yarrowia lipolytica. We found that all four signal peptides permitted secretion of active EG II. We also determined that three of these signal peptides worked for expression of the chimeric CBH I; suggesting that our design criteria for selecting these signal peptides was effective. Encouragingly, the Y. lipolytica signal peptide was able to efficiently guide secretion of the chimeric TeTrCBH I protein from L. starkeyi. The purified chimeric TeTrCBH I showed high activity against the cellulose in pretreated corn stover and the purified EG II showed high endocellulase activity measured by the CELLG3 (Megazyme) method. Our results suggest that L. starkeyi is capable of expressing and secreting core fungal cellulases. Moreover, the purified EG II and chimeric TeTrCBH I displayed significant and potentially useful enzymatic activities, demonstrating that engineered L. starkeyi has the potential to function as an oleaginous CBP strain for

  20. Generation of Novel Chimeric Mice with Humanized Livers by Using Hemizygous cDNA-uPA/SCID Mice.

    PubMed

    Tateno, Chise; Kawase, Yosuke; Tobita, Yoshimi; Hamamura, Satoko; Ohshita, Hiroki; Yokomichi, Hiroshi; Sanada, Harumi; Kakuni, Masakazu; Shiota, Akira; Kojima, Yuha; Ishida, Yuji; Shitara, Hiroshi; Wada, Naoko A; Tateishi, Hiromi; Sudoh, Masayuki; Nagatsuka, Shin-Ichiro; Jishage, Kou-Ichi; Kohara, Michinori

    2015-01-01

    producing chimeric mice for use in future long-term studies, including hepatitis virus infection analysis or drug toxicity studies.

  1. Expression and secretion of fungal endoglucanase II and chimeric cellobiohydrolase I in the oleaginous yeast Lipomyces starkeyi.

    PubMed

    Xu, Qi; Knoshaug, Eric P; Wang, Wei; Alahuhta, Markus; Baker, John O; Yang, Shihui; Vander Wall, Todd; Decker, Stephen R; Himmel, Michael E; Zhang, Min; Wei, Hui

    2017-07-24

    Lipomyces starkeyi is one of the leading lipid-producing microorganisms reported to date; its genetic transformation was only recently reported. Our aim is to engineer L. starkeyi to serve in consolidated bioprocessing (CBP) to produce lipid or fatty acid-related biofuels directly from abundant and low-cost lignocellulosic substrates. To evaluate L. starkeyi in this role, we first conducted a genome analysis, which revealed the absence of key endo- and exocellulases in this yeast, prompting us to select and screen four signal peptides for their suitability for the overexpression and secretion of cellulase genes. To compensate for the cellulase deficiency, we chose two prominent cellulases, Trichoderma reesei endoglucanase II (EG II) and a chimeric cellobiohydrolase I (TeTrCBH I) formed by fusion of the catalytic domain from Talaromyces emersonii CBH I with the linker peptide and cellulose-binding domain from T. reesei CBH I. The systematically tested signal peptides included three peptides from native L. starkeyi and one from Yarrowia lipolytica. We found that all four signal peptides permitted secretion of active EG II. We also determined that three of these signal peptides worked for expression of the chimeric CBH I; suggesting that our design criteria for selecting these signal peptides was effective. Encouragingly, the Y. lipolytica signal peptide was able to efficiently guide secretion of the chimeric TeTrCBH I protein from L. starkeyi. The purified chimeric TeTrCBH I showed high activity against the cellulose in pretreated corn stover and the purified EG II showed high endocellulase activity measured by the CELLG3 (Megazyme) method. Our results suggest that L. starkeyi is capable of expressing and secreting core fungal cellulases. Moreover, the purified EG II and chimeric TeTrCBH I displayed significant and potentially useful enzymatic activities, demonstrating that engineered L. starkeyi has the potential to function as an oleaginous CBP strain for biofuel

  2. A parametric analysis of fixation post shape in tibial knee prostheses.

    PubMed

    Au, Anthony G; Liggins, Adrian B; Raso, V James; Amirfazli, A

    2005-03-01

    A primary concern of total knee replacement (TKR) is aseptic loosening of the tibial component, which may be caused by shielding of mechanical stresses in the bone and may require subsequent revision surgery. A three-dimensional (3D) finite element (FE) model has been developed to study bone and interface stresses for four different tibial prosthesis designs. The model described here incorporates orthotropic and heterogeneous bone properties with physiologically representative loading conditions. Results from this model indicate that stress distribution is affected by the incorporation of anisotropy and spatial variation of bone properties. All bone properties were mapped from published data to characterize their anisotropy and heterogeneity. Physiological loading was incorporated by mapping experimentally determined contact patterns. Convergence testing was performed to ensure model accuracy. In terms of interface forces, a tapered post decreased post shear while slightly increasing post compression compared to a cylindrical post; a post of elliptical cross-section increased post shear and decreased post compression. In terms of cancellous bone stress, tapered and elliptical posts both relieved compression compared to a cylindrical post, while a tapered post also produced increased peripheral stress. The inclusion of medial and lateral pegs in addition to a central fixation post caused localized stress shielding in the periphery of the pegs. In general, all implant models caused a reduction of cancellous bone stress plus high compression beneath the central fixation posts.

  3. Autoregressive spectral analysis of cortical electroencephalographic signals in a rat model of post-traumatic epilepsy.

    PubMed

    Wu, Yupeng; Jiao, Baohua; Wu, Zhendong; Zhen, Junli; Jia, Qingzhong; Zhang, Hailin; Guan, Bingcai; Wang, Shuai

    2015-11-01

    Post-traumatic epilepsy (PTE) is a common consequence of traumatic brain injury (TBI) and significant predictor of poor prognosis in TBI patients. To develop clinical interventions for PTE risk reduction, there is a need to elucidate the epileptogenic mechanisms induced by brain injury. The iron-induced rat model of epilepsy used here mimics many aspects of human PTE. Intracortical injection of iron results in local neuronal damage and the establishment of an epileptic focus, leading to chronic spontaneous electroencephalographic (EEG) signals and motor seizures, with progressively increasing frequency over many months. Identifying unique aspects of PTE seizure semiology for prognosis and treatment may be aided by novel methods of EEG analysis. Here, autoregressive (AR) methods were compared to the conventional fast Fourier transform (FFT) for processing EEG signals in iron-induced epilepsy. Power spectra obtained using AR showed higher frequency resolution over a given epoch than the spectra obtained using FFT. Moreover, changes in total AR spectral power and frequency distribution over brief successive periods provided convenient indexes for long-term monitoring of seizures. Autoregression analysis may prove complementary to FFT for EEG analysis in PTE patients.

  4. Cochlear neuropathy in human presbycusis: Confocal analysis of hidden hearing loss in post-mortem tissue.

    PubMed

    Viana, Lucas M; O'Malley, Jennifer T; Burgess, Barbara J; Jones, Dianne D; Oliveira, Carlos A C P; Santos, Felipe; Merchant, Saumil N; Liberman, Leslie D; Liberman, M Charles

    2015-09-01

    Recent animal work has suggested that cochlear synapses are more vulnerable than hair cells in both noise-induced and age-related hearing loss. This synaptopathy is invisible in conventional histopathological analysis, because cochlear nerve cell bodies in the spiral ganglion survive for years, and synaptic analysis requires special immunostaining or serial-section electron microscopy. Here, we show that the same quadruple-immunostaining protocols that allow synaptic counts, hair cell counts, neuronal counts and differentiation of afferent and efferent fibers in mouse can be applied to human temporal bones, when harvested within 9 h post-mortem and prepared as dissected whole mounts of the sensory epithelium and osseous spiral lamina. Quantitative analysis of five "normal" ears, aged 54-89 yrs, without any history of otologic disease, suggests that cochlear synaptopathy and the degeneration of cochlear nerve peripheral axons, despite a near-normal hair cell population, may be an important component of human presbycusis. Although primary cochlear nerve degeneration is not expected to affect audiometric thresholds, it may be key to problems with hearing in noise that are characteristic of declining hearing abilities in the aging ear. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Analysis of a vibration isolation table comprising post-buckled Γ-shaped beam isolators

    NASA Astrophysics Data System (ADS)

    Sasaki, T.; Waters, T. P.

    2016-09-01

    In this paper, the static and dynamic characteristics of a nonlinear passive vibration isolation table is investigated through finite element analysis. The intended application is specifically isolation in the vertical direction where the isolator is required to be sufficiently stiff statically to bear the weight of the isolated object and soft dynamically for small oscillations about its equilibrium position. The modelled configuration consists of a rigid isolation table mounted on two Γ-shaped beam isolators which are loaded to their post-buckled state in their unstable buckling mode by the weight of the isolated mass. A nonlinear static analysis is presented to establish the negative stiffness provided by the buckled beams, and two linear springs are then added in parallel which are chosen to have just sufficient stiffness to restore stability. Modal analysis of the linearized system about its statically deformed position (1mm) gives a natural frequency of just 1Hz which is considerably lower than is achievable by a linear isolator. Motion transmissibility of the linearized system shows a non-resonant isolation region spanning two decades when the system is perfectly symmetric but additional resonance peaks appear when asymmetries are included in either the mass or stiffness distribution. Several strategies are explored for reducing the prominence of these resonances.

  6. Chimeric Genes as a Source of Rapid Evolution in Drosophila melanogaster

    PubMed Central

    Rogers, Rebekah L.; Hartl, Daniel L.

    2012-01-01

    Chimeric genes form through the combination of portions of existing coding sequences to create a new open reading frame. These new genes can create novel protein structures that are likely to serve as a strong source of novelty upon which selection can act. We have identified 14 chimeric genes that formed through DNA-level mutations in Drosophila melanogaster, and we investigate expression profiles, domain structures, and population genetics for each of these genes to examine their potential to effect adaptive evolution. We find that chimeric gene formation commonly produces mid-domain breaks and unites portions of wholly unrelated peptides, creating novel protein structures that are entirely distinct from other constructs in the genome. These new genes are often involved in selective sweeps. We further find a disparity between chimeric genes that have recently formed and swept to fixation versus chimeric genes that have been preserved over long periods of time, suggesting that preservation and adaptation are distinct processes. Finally, we demonstrate that chimeric gene formation can produce qualitative expression changes that are difficult to mimic through duplicate gene formation, and that extremely young chimeric genes (dS < 0.03) are more likely to be associated with selective sweeps than duplicate genes of the same age. Hence, chimeric genes can serve as an exceptional source of genetic novelty that can have a profound influence on adaptive evolution in D. melanogaster. PMID:21771717

  7. Development of a chimeric DNA-RNA hammerhead ribozyme targeting SARS virus.

    PubMed

    Fukushima, Akiko; Fukuda, Noboru; Lai, Yimu; Ueno, Takahiro; Moriyama, Mitsuhiko; Taguchi, Fumihiro; Iguchi, Akifumi; Shimizu, Kazushi; Kuroda, Kazumichi

    2009-01-01

    Severe acute respiratory syndrome (SARS) is a severe pulmonary infectious disease caused by a novel coronavirus. To develop an effective and specific medicine targeting the SARS-coronavirus (CoV), a chimeric DNA-RNA hammerhead ribozyme was designed and synthesized using a sequence homologous with the mouse hepatitis virus (MHV). Chimeric DNA-RNA hammerhead ribozyme targeting MHV and SARS-CoV were designed and synthesized.To confirm its activity, in vitro cleavage reactions were performed with the synthesized ribozyme. Effects of the chimeric ribozyme were evaluated on multiplication of MHV. Effects of the chimeric ribozyme on expression of SARS-CoV were evaluated in cultured 3T3 cells. The synthetic ribozyme cleaved the synthetic target MHV and SARS-CoV RNA into fragments of predicted length. The chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV significantly inhibited multiplication of MHV in DBT cells by about 60%. The chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV significantly inhibited the expression of SARS-CoV RNA in 3T3 cells transfected with the recombinant plasmid. The chimeric DNA-RNA ribozyme targeting SARS-CoV significantly inhibited MHV viral activity and expression of recombinant SARS RNA in vitro. These findings indicate that the synthetic chimeric DNA-RNA ribozyme could provide a feasible treatment for SARS. Copyright (c) 2009 S. Karger AG, Basel.

  8. Post-analysis report on Chesapeake Bay data processing. [spectral analysis and recognition computer signature extension

    NASA Technical Reports Server (NTRS)

    Thomson, F.

    1972-01-01

    The additional processing performed on data collected over the Rhode River Test Site and Forestry Site in November 1970 is reported. The techniques and procedures used to obtain the processed results are described. Thermal data collected over three approximately parallel lines of the site were contoured, and the results color coded, for the purpose of delineating important scene constituents and to identify trees attacked by pine bark beetles. Contouring work and histogram preparation are reviewed and the important conclusions from the spectral analysis and recognition computer (SPARC) signature extension work are summarized. The SPARC setup and processing records are presented and recommendations are made for future data collection over the site.

  9. Post-mastectomy Radiation Therapy for T3N0: A SEER Analysis

    PubMed Central

    Johnson, Matthew E.; Handorf, Elizabeth A.; Martin, Jeffrey M.; Hayes, Shelly B.

    2015-01-01

    Background There is conflicting evidence regarding the benefit of post-mastectomy radiation therapy (PMRT) for pathologic stage T3N0M0 breast cancers. We analyzed data from the Surveillance, Epidemiology, and End Results (SEER) database to investigate the benefit of PMRT in these patients. Methods We queried the SEER database for T3N0M0 breast cancer patients diagnosed from 2000–2010 who underwent modified radical mastectomy. We excluded males, patients with unknown radiation timing/type, other primary tumors, or survival <6 months. 2525 patients were included in this analysis. We performed univariate and multivariate statistical analysis using Chi-squared tests, log rank test, and Cox proportional hazards regression. Primary endpoints were overall survival (OS) and breast cancer-specific survival (CSS). Results Of the 2525 patients identified, 1063 received PMRT. The median follow-up was 56 months (range: 6–131). On univariate analysis, PMRT improved OS (76.5% vs. 61.8%, p<0.01) and CSS (85.0% vs. 82.4%, p<0.01) at 8 years. The use of PMRT remained significant on multivariate analysis: PMRT improved OS (HR 0.63, p<0.001) and CSS (HR 0.77, p=0.045). Low tumor grade (p<0.01) and marital status "married" (p=0.01) also predicted for improved CSS on multivariate analysis. Conclusion(s) PMRT was associated with significant improvements in both CSS and OS in patients with T3N0M0 breast cancers treated with modified radical mastectomy from 2000 to 2010. PMRT should be strongly considered in T3N0M0 patients. PMID:24985911

  10. Nitrogen Species in the Post-Pinatubo Stratosphere: Model Analysis Utilizing UARS Measurements. Appendix F

    NASA Technical Reports Server (NTRS)

    Danilin, Michael Y.; Rodriguez, Jose M.; Hu, Wenjie; Ko, Malcolm K. W.; Weisenstein, Debra K.; Kumer, John B.; Mergenthaler, John L.; Russell, James M., III; Koike, Makoto; Yue, Glenn K.

    1999-01-01

    We present an analysis of the impact of heterogeneous chemistry on the partitioning of nitrogen species measured by the Upper Atmosphere Research Satellite (UARS) instruments. The UARS measurements utilized include N2O, HNO3, and ClONO2 from the cryogenic limb array etalon spectrometer (CLAES), version 7 (v.7), and temperature, methane, ozone, H2O, HCl, NO and NO2 from the halogen occultation experiment (HALOE), version 18. The analysis is carried out for the UARS data obtained between January 1992 and September 1994 in the 100- to 1-mbar (approx. 17-47 km) altitude range and over 10 deg latitude bins from 70 deg S to 70 deg N. The spatiotemporal evolution of aerosol surface area density (SAD) is adopted from analysis of the Stratospheric Aerosol and Gas Experiment (SAGE) II data. A diurnal steady state photochemical box model, constrained by the temperature, ozone, H2O, CH4, aerosol SAD, and columns of O2 and O3 above the point of interest, has been used as the main tool to analyze these data. Total inorganic nitrogen (NOY) is obtained by three different methods: (1) as a sum of the UARS-measured NO, NO2, HNO3, and ClONO2; (2) from the N2O-NOY correlation; and (3) from the CH4-NOY correlation. To validate our current understanding of stratospheric heterogeneous chemistry for post-Pinatubo conditions, the model-calculated monthly averaged NO(x)/NO(y) ratios and the NO, NO2, and HNO3 profiles are compared with the UARS-derived data. In general, the UARS-constrained box model captures the main features of nitrogen species partitioning in the post-Pinatubo years, such as recovery of NO(x) after the eruption, their seasonal variability and vertical profiles. However, the model underestimates the NO2 content, particularly in the 30- to 7-mbar (approx. 23-32 km) range. Comparisons of the calculated temporal behavior of the partial columns of NO2 and HNO3 and ground-based measurements at 45 deg S and 45 deg N are also presented. Our analysis indicates that ground

  11. Nitrogen Species in the Post-Pinatubo Stratosphere: Model Analysis Utilizing UARS Measurements

    NASA Technical Reports Server (NTRS)

    Danilin, Michael Y.; Rodriguez, Jose M.; Hu, Wen-Jie; Ko, Malcolm K. W.; Weisenstein, Debra K.; Kumer, John B.; Mergenthaler, John L.; Russel, James M., III; Koike, Makoto; Yue, Glenn K.

    1999-01-01

    We present an analysis of the impact of heterogeneous chemistry on the partitioning of nitrogen species measured by the Upper Atmosphere Research Satellite (UARS) instruments. The UARS measurements utilized include N2O, HNO3, and ClONO2 from the cryogenic limb array etalon spectrometer (CLAES), version 7 (v.7), and temperature, methane, ozone, H2O, HCl, NO and NO2 from the halogen occultation experiment (HALOE), version 18. The analysis is carried out for the UARS data obtained between January 1992 and September 1994 in the 100-to 1-mbar (approx. 17-47 km) altitude range and over 10 degrees latitude bins from 70 S to 70 N. The spatiotemporal evolution of aerosol surface area density (SAD) is adopted from analysis of the Stratospheric Aerosol and Gas Experiment (SAGE) II data. A diurnal steady state photochemical box model, constrained by the temperature, ozone, H2O, CH4, aerosol SAD, and columns of O2 and O3 above the point of interest, has been used as the main tool to analyze these data. Total inorganic nitrogen (NOy) is obtained by three different methods: (1) as a sum of the UARS-measured NO, NO2, HNO3, and ClONO2; (2) from the N2O-NOy correlation, and (3) from the CH4-NOy correlation. To validate our current understanding of stratospheric heterogeneous chemistry for post-Pinatubo conditions, the model-calculated monthly averaged NOx/NOy ratios and the NO, NO2, and HNO3 profiles are compared with the UARS-derived data. In general, the UARS-constrained box model captures the main features of nitrogen species partitioning in the post-Pinatubo years, such as recovery of NOx after the eruption, their seasonal variability and vertical profiles. However, the model underestimates the NO2 content, particularly in the 30- to 7-mbar (approx.23-32 km) range. Comparisons of the calculated temporal behavior of the partial columns of NO2 and HNO3 and ground-based measurements at 45 S and 45 N are also presented. Our analysis indicates that ground-based and HALOE v.18

  12. Advanced timing analysis based on post-OPC patterning process simulations

    NASA Astrophysics Data System (ADS)

    Yang, Jie; Capodieci, Luigi; Sylvester, Dennis

    2005-05-01

    For current and upcoming technology nodes (90, 65, 45 nm and beyond) one of the fundamental enablers of Moore's Law is the use of Resolution Enhancement Techniques (RET) in optical lithography. While RETs allow for continuing reduction in integrated circuits" critical dimensions (CD), layout distortions are introduced as an undesired consequence due to proximity effects. Complex and costly Optical Proximity Correction (OPC) is then deployed to compensate for CD variations and loss of pattern fidelity, in an effort to improve yield. This, together with other sources for CD variations, causes the actual on-silicon chip performance to be quite different from sign-off expectations. In current design optimization methodologies, process variation modeling, aimed at providing guardbands for performance analysis, is based on "worst-case scenarios" (corner cases) and yields overly pessimistic simulation results which makes meeting design targets unnecessarily difficult. Assumptions of CD distributions in Monte Carlo simulations, and statistical timing analysis in general, can be made more rigorous by considering realistic systematic and random contributions to the overall process variation. A novel methodology is presented in this paper for extracting residual OPC errors from a placed and routed full chip layout and for deriving actual (i.e., calibrated to silicon) CD values, to be used in timing analysis and speed path characterization. The implementation of this automated flow is achieved through a combination of tagging critical gates, post-OPC layout back-annotation, and selective extraction from the global circuit netlist. This approach improves upon traditional design flow practices where ideal (i.e., drawn) CD values are employed, which leads to poor performance predictability of the as-fabricated design. With this more accurate timing analysis, we are able to highlight the necessity of a post-OPC verification embedded design flow by showing substantial differences

  13. Nitrogen species in the post-Pinatubo stratosphere: Model analysis utilizing UARS measurements

    NASA Astrophysics Data System (ADS)

    Danilin, Michael Y.; Rodriguez, Jose M.; Hu, Wenjie; Ko, Malcolm K. W.; Weisenstein, Debra K.; Kumer, John B.; Mergenthaler, John L.; Russell, James M.; Koike, Makoto; Yue, Glenn K.; Jones, Nicholas B.; Johnston, Paul V.

    1999-04-01

    We present an analysis of the impact of heterogeneous chemistry on the partitioning of nitrogen species measured by the Upper Atmosphere Research Satellite (UARS) instruments. The UARS measurements utilized include N2O, HNO3, and ClONO2 from the cryogenic limb array etalon spectrometer (CLAES), version 7 (v.7), and temperature, methane, ozone, H2O, HCl, NO and NO2 from the halogen occultation experiment (HALOE), version 18. The analysis is carried out for the UARS data obtained between January 1992 and September 1994 in the 100- to 1-mbar (˜17-47 km) altitude range and over 10° latitude bins from 70°S to 70°N. The spatiotemporal evolution of aerosol surface area density (SAD) is adopted from analysis of the Stratospheric Aerosol and Gas Experiment (SAGE) II data. A diurnal steady state photochemical box model, constrained by the temperature, ozone, H2O, CH4, aerosol SAD, and columns of O2 and O3 above the point of interest, has been used as the main tool to analyze these data. Total inorganic nitrogen (NOy) is obtained by three different methods: (1) as a sum of the UARS-measured NO, NO2, HNO3, and ClONO2; (2) from the N2O-NOy correlation, and (3) from the CH4-NOy correlation. To validate our current understanding of stratospheric heterogeneous chemistry for post-Pinatubo conditions, the model-calculated monthly averaged NOx/NOy ratios and the NO, NO2, and HNO3 profiles are compared with the UARS-derived data. In general, the UARS-constrained box model captures the main features of nitrogen species partitioning in the post-Pinatubo years, such as recovery of NOx after the eruption, their seasonal variability and vertical profiles. However, the model underestimates the NO2 content, particularly in the 30- to 7-mbar (˜23-32 km) range. Comparisons of the calculated temporal behavior of the partial columns of NO2 and HNO3 and ground-based measurements at 45°S and 45°N are also presented. Our analysis indicates that ground-based and HALOE v. 18 measurements of

  14. Nitrogen Species in the Post-Pinatubo Stratosphere: Model Analysis Utilizing UARS Measurements. Appendix F

    NASA Technical Reports Server (NTRS)

    Danilin, Michael Y.; Rodriguez, Jose M.; Hu, Wenjie; Ko, Malcolm K. W.; Weisenstein, Debra K.; Kumer, John B.; Mergenthaler, John L.; Russell, James M., III; Koike, Makoto; Yue, Glenn K.

    1999-01-01

    We present an analysis of the impact of heterogeneous chemistry on the partitioning of nitrogen species measured by the Upper Atmosphere Research Satellite (UARS) instruments. The UARS measurements utilized include N2O, HNO3, and ClONO2 from the cryogenic limb array etalon spectrometer (CLAES), version 7 (v.7), and temperature, methane, ozone, H2O, HCl, NO and NO2 from the halogen occultation experiment (HALOE), version 18. The analysis is carried out for the UARS data obtained between January 1992 and September 1994 in the 100- to 1-mbar (approx. 17-47 km) altitude range and over 10 deg latitude bins from 70 deg S to 70 deg N. The spatiotemporal evolution of aerosol surface area density (SAD) is adopted from analysis of the Stratospheric Aerosol and Gas Experiment (SAGE) II data. A diurnal steady state photochemical box model, constrained by the temperature, ozone, H2O, CH4, aerosol SAD, and columns of O2 and O3 above the point of interest, has been used as the main tool to analyze these data. Total inorganic nitrogen (NOY) is obtained by three different methods: (1) as a sum of the UARS-measured NO, NO2, HNO3, and ClONO2; (2) from the N2O-NOY correlation; and (3) from the CH4-NOY correlation. To validate our current understanding of stratospheric heterogeneous chemistry for post-Pinatubo conditions, the model-calculated monthly averaged NO(x)/NO(y) ratios and the NO, NO2, and HNO3 profiles are compared with the UARS-derived data. In general, the UARS-constrained box model captures the main features of nitrogen species partitioning in the post-Pinatubo years, such as recovery of NO(x) after the eruption, their seasonal variability and vertical profiles. However, the model underestimates the NO2 content, particularly in the 30- to 7-mbar (approx. 23-32 km) range. Comparisons of the calculated temporal behavior of the partial columns of NO2 and HNO3 and ground-based measurements at 45 deg S and 45 deg N are also presented. Our analysis indicates that ground

  15. Nitrogen Species in the Post-Pinatubo Stratosphere: Model Analysis Utilizing UARS Measurements

    NASA Technical Reports Server (NTRS)

    Danilin, Michael Y.; Rodriguez, Jose M.; Hu, Wen-Jie; Ko, Malcolm K. W.; Weisenstein, Debra K.; Kumer, John B.; Mergenthaler, John L.; Russel, James M., III; Koike, Makoto; Yue, Glenn K.

    1999-01-01

    We present an analysis of the impact of heterogeneous chemistry on the partitioning of nitrogen species measured by the Upper Atmosphere Research Satellite (UARS) instruments. The UARS measurements utilized include N2O, HNO3, and ClONO2 from the cryogenic limb array etalon spectrometer (CLAES), version 7 (v.7), and temperature, methane, ozone, H2O, HCl, NO and NO2 from the halogen occultation experiment (HALOE), version 18. The analysis is carried out for the UARS data obtained between January 1992 and September 1994 in the 100-to 1-mbar (approx. 17-47 km) altitude range and over 10 degrees latitude bins from 70 S to 70 N. The spatiotemporal evolution of aerosol surface area density (SAD) is adopted from analysis of the Stratospheric Aerosol and Gas Experiment (SAGE) II data. A diurnal steady state photochemical box model, constrained by the temperature, ozone, H2O, CH4, aerosol SAD, and columns of O2 and O3 above the point of interest, has been used as the main tool to analyze these data. Total inorganic nitrogen (NOy) is obtained by three different methods: (1) as a sum of the UARS-measured NO, NO2, HNO3, and ClONO2; (2) from the N2O-NOy correlation, and (3) from the CH4-NOy correlation. To validate our current understanding of stratospheric heterogeneous chemistry for post-Pinatubo conditions, the model-calculated monthly averaged NOx/NOy ratios and the NO, NO2, and HNO3 profiles are compared with the UARS-derived data. In general, the UARS-constrained box model captures the main features of nitrogen species partitioning in the post-Pinatubo years, such as recovery of NOx after the eruption, their seasonal variability and vertical profiles. However, the model underestimates the NO2 content, particularly in the 30- to 7-mbar (approx.23-32 km) range. Comparisons of the calculated temporal behavior of the partial columns of NO2 and HNO3 and ground-based measurements at 45 S and 45 N are also presented. Our analysis indicates that ground-based and HALOE v.18

  16. Chimeric antigen receptor engineered stem cells: a novel HIV therapy.

    PubMed

    Zhen, Anjie; Carrillo, Mayra A; Kitchen, Scott G

    2017-03-01

    Despite the success of combination antiretroviral therapy (cART) for suppressing HIV and improving patients' quality of life, HIV persists in cART-treated patients and remains an incurable disease. Financial burdens and health consequences of lifelong cART treatment call for novel HIV therapies that result in a permanent cure. Cellular immunity is central in controlling HIV replication. However, HIV adopts numerous strategies to evade immune surveillance. Engineered immunity via genetic manipulation could offer a functional cure by generating cells that have enhanced antiviral activity and are resistant to HIV infection. Recently, encouraging reports from several human clinical trials using an anti-CD19 chimeric antigen receptor (CAR) modified T-cell therapy for treating B-cell malignancies have provided valuable insights and generated remarkable enthusiasm in engineered T-cell therapy. In this review, we discuss the development of HIV-specific chimeric antigen receptors and the use of stem cell based therapies to generate lifelong anti-HIV immunity.

  17. Chimeric behavior of excited thioxanthone in protic solvents: II. Theory.

    PubMed

    Rai-Constapel, Vidisha; Villnow, Torben; Ryseck, Gerald; Gilch, Peter; Marian, Christel M

    2014-12-18

    The chimeric behavior of thioxanthone in protic solvents has been investigated employing computational chemistry methods. In particular, methanol and 2,2,2-trifluoroethanol have been chosen in this study. The solvent environment has been modeled using microsolvation in combination with a conductor-like screening model. The vertical excitation spectrum within the same solvent is seen to depend on the number of specific bonds formed between the chromophore and the solvent molecules. Two different models have been discussed in this work, namely, one and two H-bond models. In particular, the formation of the second H-bond causes the energy gap between the πHπL* and nOπL* states to increase further. Excited-state absorption spectra for the photophysically relevant electronic states have been theoretically determined for comparison with the time-resolved spectra recorded experimentally [Villnow, T.; Ryseck, G.; Rai-Constapel, V.; Marian, C. M.; Gilch, P. J. Phys. Chem. A 2014]. The equilibration of the 1(πHπL*) and 3(nOπL*) states holds responsible for the chimeric behavior. This equilibrium sets in with a calculated time constant of 23 ps in methanol and 14 ps in TFE (5 and 10 ps in experiment, respectively). The radiative decay from the optically bright 1(πHπL*) state is computed to occur with a time constant of 25 ns in both solvents (14–25 ns in experiment).

  18. Preliminary analgesic properties of deltorphin-5-methoxytryptamine chimeric opioid peptides.

    PubMed

    Wang, Jing; Wang, Li; Li, Meixing; Jin, Qiaoying; Dong, Shouliang

    2011-05-01

    To further understand the relationship between melatonin (MT) and deltorphins (Dels) in pain modulation, two chimeric peptides (Del I-5-methoxytryptamine and Del II-5-methoxytryptamine) both containing 5-methoxytryptamine at the carboxyl-terminal of Dels mimicking MT were designed, synthesized and characterized by tail-flick assay in mice. Results showed that intracerebroventricular (i.c.v.) administration of Del I-5-methoxytryptamine (YaFDVVG-X, X is 5-methoxytryptamine, 5, 50 nmol/kg) or Del II-5-methoxytryptamine (YaFEVVG-X, X is 5-methoxytryptamine, 5, 50 nmol/kg) produced stronger analgesia than deltorphins (Del I or Del II alone), and acting even longer and stronger than cocktails containing Del I or Del II (50 nmol/kg) and MT (50 nmol/kg). Naloxone (i.p., 100 nmol/kg) could totally block the analgesic effects induced by the chimeric peptides, while luzindole (specific antagonist of melatonin receptor, i.p., 250 nmol/kg) could only partially inhibit the effects down to that induced by Dels alone. Interestingly, Del I-5-methoxytryptamine and Del II-5-methoxytryptamine act weaker with δ receptor than Dels in vitro but could induce much longer analgesia through co-activating δ opioid receptor and melatonin receptor.

  19. Mixed chimerism to induce tolerance for solid organ transplantation

    SciTech Connect

    Wren, S.M.; Nalesnik, M.; Hronakes, M.L.; Oh, E.; Ildstad, S.T. )

    1991-04-01

    Chimerism, or the coexistence of tissue elements from more than one genetically different strain or species in an organism, is the only experimental state that results in the induction of donor-specific transplantation tolerance. Transplantation of a mixture of T-cell-depleted syngeneic (host-type) plus T-cell-depleted allogeneic (donor) bone marrow into a normal adult recipient mouse (A + B----A) results in mixed allogeneic chimerism. Recipient mice exhibit donor-specific transplantation tolerance, yet have full immunocompetence to recognize and respond to third-party transplantation antigens. After complete hematolymphopoietic repopulation at 28 days, animals accept a donor-specific skin graft but reject major histocompatibility complex (MHC) locus-disparate third-party grafts. We now report that permanent graft acceptance can also be achieved when the graft is placed at the time of bone marrow transplantation. Histologically, grafts were viable and had only minimal inflammatory changes. This model may have potential future clinical application for the induction of donor-specific transplantation tolerance.

  20. Chimeric Antisense Oligonucleotide Conjugated to α-Tocopherol

    PubMed Central

    Nishina, Tomoko; Numata, Junna; Nishina, Kazutaka; Yoshida-Tanaka, Kie; Nitta, Keiko; Piao, Wenying; Iwata, Rintaro; Ito, Shingo; Kuwahara, Hiroya; Wada, Takeshi; Mizusawa, Hidehiro; Yokota, Takanori

    2015-01-01

    We developed an efficient system for delivering short interfering RNA (siRNA) to the liver by using α-tocopherol conjugation. The α-tocopherol–conjugated siRNA was effective and safe for RNA interference–mediated gene silencing in vivo. In contrast, when the 13-mer LNA (locked nucleic acid)-DNA gapmer antisense oligonucleotide (ASO) was directly conjugated with α-tocopherol it showed markedly reduced silencing activity in mouse liver. Here, therefore, we tried to extend the 5′-end of the ASO sequence by using 5′-α-tocopherol–conjugated 4- to 7-mers of unlocked nucleic acid (UNA) as a “second wing.” Intravenous injection of mice with this α-tocopherol–conjugated chimeric ASO achieved more potent silencing than ASO alone in the liver, suggesting increased delivery of the ASO to the liver. Within the cells, the UNA wing was cleaved or degraded and α-tocopherol was released from the 13-mer gapmer ASO, resulting in activation of the gapmer. The α-tocopherol–conjugated chimeric ASO showed high efficacy, with hepatic tropism, and was effective and safe for gene silencing in vivo. We have thus identified a new, effective LNA-DNA gapmer structure in which drug delivery system (DDS) molecules are bound to ASO with UNA sequences. PMID:25584900

  1. CHIMERE-2017: from urban to hemispheric chemistry-transport modeling

    NASA Astrophysics Data System (ADS)

    Mailler, Sylvain; Menut, Laurent; Khvorostyanov, Dmitry; Valari, Myrto; Couvidat, Florian; Siour, Guillaume; Turquety, Solène; Briant, Régis; Tuccella, Paolo; Bessagnet, Bertrand; Colette, Augustin; Létinois, Laurent; Markakis, Kostantinos; Meleux, Frédérik

    2017-06-01

    CHIMERE is a chemistry-transport model designed for regional atmospheric composition. It can be used at a variety of scales from local to continental domains. However, due to the model design and its historical use as a regional model, major limitations had remained, hampering its use at hemispheric scale, due to the coordinate system used for transport as well as to missing processes that are important in regions outside Europe. Most of these limitations have been removed in the CHIMERE-2017 version, allowing its use in any region of the world and at any scale, from the scale of a single urban area up to hemispheric scale, with or without polar regions included. Other important improvements have been made in the treatment of the physical processes affecting aerosols and the emissions of mineral dust. From a computational point of view, the parallelization strategy of the model has also been updated in order to improve model numerical performance and reduce the code complexity. The present article describes all these changes. Statistical scores for a model simulation over continental Europe are presented, and a simulation of the circumpolar transport of volcanic ash plume from the Puyehue volcanic eruption in June 2011 in Chile provides a test case for the new model version at hemispheric scale.

  2. Regional analysis of distribution of pre and post 2015 Nepal Earthquake landslides

    NASA Astrophysics Data System (ADS)

    Valagussa, Andrea; Frattini, Paolo; Crosta, Giovanni; Valbuzzi, Elena

    2016-04-01

    A magnitude 7.8 earthquake struck Nepal on April 25, 2015. Three landslide inventories have been prepared in four districts: Dhading (1885 km2), Sindhupalchok (2488 km2), Rasuwa (1522 km2) and Nuwakot (1194 km2), that are located north of Kathmandu. These inventories extend 14 to 138 km SE from the epicenter of the main shock (April 25, 2015), 4.5 to 143 km NW from the epicenter of the main aftershock (May 12, 2015), and 34 to 136 km from the Main Frontal Thrust. The first inventory is a coseismic and post-seismic landslide inventory based on multi-temporal images (Google Earth, Google Crisis maps, Bing maps), and helicopter-based video. The second one is a pre-event shallow landslide inventory. In these two inventories the most abundant landslide types are: debris flows, shallow translational slides, and rockfalls. The third is a deep seated landslide inventory, in which the most represented landslide types are rock avalanches, slumps, rockslides and deep-seated gravitational slope deformations (DSGSD). All the landslides have been mapped as individual polygons. For the analysis we focus our attention on four districts: First we studied how the landslide frequency density changes as a function of topographic parameters (i.e. slope gradient, slope aspect, and elevation). The analyses have been based on the ASTER Global Digital Elevation Model (ASTER GDEM). For coseismic and post-seismic landslides we observed that the mean slope gradient at which the landslide occurs is higher with respect to the two other inventories (50° and 30/40° respectively). The slope aspect of coseismic and post-seismic landslides is also different, with a larger frequency of landslides towards SW, whereas in pre-event landslides the most common slope aspect is SE. This could be related to the direction of the seismic wave. At least the coseismic and post-seismic landslides occur, in mean, at an elevation lower than the pre-event landslides. We also analyzed the relationship between the

  3. Chimeric Autofluorescent Proteins as Photophysical Model System for Multicolor Bimolecular Fluorescence Complementation.

    PubMed

    Peter, Sébastien; Oven-Krockhaus, Sven Zur; Veerabagu, Manikandan; Rodado, Virtudes Mira; Berendzen, Kenneth W; Meixner, Alfred J; Harter, Klaus; Schleifenbaum, Frank E

    2017-03-10

    The yellow fluorescent protein (YFP) is frequently used in a protein complementation assay called bimolecular fluorescence complementation (BiFC), and is employed to visualize protein-protein interactions. In this analysis, two different, nonfluorescent fragments of YFP are genetically attached to proteins of interest. Upon interaction of these proteins, the YFP fragments are brought into proximity close enough to reconstitute their original structure, enabling fluorescence. BiFC allows for a straightforward readout of protein-protein interactions and furthermore facilitates their functional investigation by in vivo imaging. Furthermore, it has been observed that the available color range in BiFC can be extended upon complementing fragments of different proteins that are, like YFP, derived from the Aequorea victoria green fluorescent protein, thereby allowing for a multiplexed investigation of protein-protein interactions. Some spectral characteristics of "multicolor" BiFC (mcBiFC) complexes have been reported before; however, no in-depth analysis has been performed yet. Therefore, little is known about the photophysical characteristics of these mcBiFC complexes because a proper characterization essentially relies on in vitro data. This is particularly difficult for fragments of autofluorescent proteins (AFPs) because they show a very strong tendency to form supramolecular aggregates which precipitate ex vivo. In this study, this intrinsic difficulty is overcome by directly fusing the coding DNA of different AFP fragments. Translation of the genetic sequence in Escherichia coli leads to fully functional, highly soluble fluorescent proteins with distinct properties. On the basis of their construction, they are designated chimeric AFPs, or BiFC chimeras, here. Comparison of their spectral characteristics with experimental in vivo BiFC data confirmed the utility of the chimeric proteins as a BiFC model system. In this study, nine different chimeras were thoroughly

  4. A chimeric Sindbis-based vaccine protects cynomolgus macaques against a lethal aerosol challenge of eastern equine encephalitis virus

    PubMed Central

    Roy, Chad J.; Adams, A. Paige; Wang, Eryu; Leal, Grace; Seymour, Robert L.; Sivasubramani, Satheesh K.; Mega, William; Frolov, Ilya; Didier, Peter J.; Weaver, Scott C.

    2013-01-01

    Eastern equine encephalitis virus (EEEV) is a mosquito-borne alphavirus that causes sporadic, often fatal disease outbreaks in humans and equids, and is also a biological threat agent. Two chimeric vaccine candidates were constructed using a cDNA clone with a Sindbis virus (SINV) backbone and structural protein genes from either a North (SIN/NAEEEV) or South American (SIN/SAEEEV) strain of EEEV. The vaccine candidates were tested in a nonhuman primate (NHP) model of eastern equine encephalitis (EEE). Cynomolgus macaques were either sham-vaccinated, or vaccinated with a single dose of either SIN/NAEEEV or SIN/SAEEEV. After vaccination, animals were challenged by aerosol with a virulent North American strain of EEEV (NA EEEV). The SIN/NAEEEV vaccine provided significant protection, and most vaccinated animals survived EEEV challenge (82%) with little evidence of disease, whereas most SIN/SAEEEV-vaccinated (83%) and control (100%) animals died. Protected animals exhibited minimal changes in temperature and cardiovascular rhythm, whereas unprotected animals showed profound hyperthermia and changes in heart rate post-exposure. Acute inflammation and neuronal necrosis were consistent with EEEV-induced encephalitis in unprotected animals, whereas no encephalitis-related histopathologic changes were observed in the SIN/NAEEEV-vaccinated animals. These results demonstrate that the chimeric SIN/NAEEEV vaccine candidate protects against an aerosol EEEV exposure. PMID:23333212

  5. PTMScout, a Web resource for analysis of high throughput post-translational proteomics studies.

    PubMed

    Naegle, Kristen M; Gymrek, Melissa; Joughin, Brian A; Wagner, Joel P; Welsch, Roy E; Yaffe, Michael B; Lauffenburger, Douglas A; White, Forest M

    2010-11-01

    The rate of discovery of post-translational modification (PTM) sites is increasing rapidly and is significantly outpacing our biological understanding of the function and regulation of those modifications. To help meet this challenge, we have created PTMScout, a web-based interface for viewing, manipulating, and analyzing high throughput experimental measurements of PTMs in an effort to facilitate biological understanding of protein modifications in signaling networks. PTMScout is constructed around a custom database of PTM experiments and contains information from external protein and post-translational resources, including gene ontology annotations, Pfam domains, and Scansite predictions of kinase and phosphopeptide binding domain interactions. PTMScout functionality comprises data set comparison tools, data set summary views, and tools for protein assignments of peptides identified by mass spectrometry. Analysis tools in PTMScout focus on informed subset selection via common criteria and on automated hypothesis generation through subset labeling derived from identification of statistically significant enrichment of other annotations in the experiment. Subset selection can be applied through the PTMScout flexible query interface available for quantitative data measurements and data annotations as well as an interface for importing data set groupings by external means, such as unsupervised learning. We exemplify the various functions of PTMScout in application to data sets that contain relative quantitative measurements as well as data sets lacking quantitative measurements, producing a set of interesting biological hypotheses. PTMScout is designed to be a widely accessible tool, enabling generation of multiple types of biological hypotheses from high throughput PTM experiments and advancing functional assignment of novel PTM sites. PTMScout is available at http://ptmscout.mit.edu.

  6. The need for complementary hydraulic analysis in post-restoration monitoring of river restoration projects

    NASA Astrophysics Data System (ADS)

    Endreny, T. A.; Soulman, M. M.

    2011-03-01

    River restoration design methods are incrementally improved by studying and learning from monitoring data in previous projects. In this paper, we report post-restoration monitoring data for a Natural Channel Design (NCD) restoration project along 1600 m (10 channel wavelengths) of the Batavia Kill in the Catskill Mountains, NY, implemented in 2001 and 2002. The NCD project used a reference-reach to determine channel form, empirical relations between the project site and reference site bankfull dimensions to size channel geometry, and hydraulic and sediment computations to test channel capacity and sediment stability. In addition 12 cross-vanes and 48 j-hook vanes used in NCD for river training were installed to protect against bank erosion and maintain scour pools for fish habitat. Changes in pool depths were monitored with surveys from 2002-2004, and then after the channel-altering April 2005 flood. Aggradation in pools was attributed to cross-vane arms not concentrating flow in the center of the channel, which subsequently caused flow splitting and 4 partial point bar avulsions during the 2005 flood. Hydrodynamic simulation at the 18 m3s-1 bankfull flow suggested avulsions occurred where vanes allowed erosive bank scour to initiate the avulsion cut, and once the flow was split, the diminished in-channel flow caused more aggradation in the pools. In this project post-restoration monitoring had detected aggradation and considered it a problem. The lesson for the larger river restoration community is monitoring protocol should include complementary hydraulic and sediment analysis to comprehend potential consequences and develop preventative maintenance. River restoration and monitoring teams should be trained in robust hydraulic and sediment analytical methods that help them extend project restoration goals.

  7. Evaluation of a post-processing approach for multiscale analysis of biphasic mechanics of chondrocytes.

    PubMed

    Sibole, Scott C; Maas, Steve; Halloran, Jason P; Weiss, Jeffrey A; Erdemir, Ahmet

    2013-10-01

    Understanding the mechanical behaviour of chondrocytes as a result of cartilage tissue mechanics has significant implications for both evaluation of mechanobiological function and to elaborate on damage mechanisms. A common procedure for prediction of chondrocyte mechanics (and of cell mechanics in general) relies on a computational post-processing approach where tissue-level deformations drive cell-level models. Potential loss of information in this numerical coupling approach may cause erroneous cellular-scale results, particularly during multiphysics analysis of cartilage. The goal of this study was to evaluate the capacity of first- and second-order data passing to predict chondrocyte mechanics by analysing cartilage deformations obtained for varying complexity of loading scenarios. A tissue-scale model with a sub-region incorporating representation of chondron size and distribution served as control. The post-processing approach first required solution of a homogeneous tissue-level model, results of which were used to drive a separate cell-level model (same characteristics as the sub-region of control model). The first-order data passing appeared to be adequate for simplified loading of the cartilage and for a subset of cell deformation metrics, for example, change in aspect ratio. The second-order data passing scheme was more accurate, particularly when asymmetric permeability of the tissue boundaries was considered. Yet, the method exhibited limitations for predictions of instantaneous metrics related to the fluid phase, for example, mass exchange rate. Nonetheless, employing higher order data exchange schemes may be necessary to understand the biphasic mechanics of cells under lifelike tissue loading states for the whole time history of the simulation.

  8. Genetic analysis of post-mating reproductive barriers in hybridizing European Populus species

    PubMed Central

    Macaya-Sanz, D; Suter, L; Joseph, J; Barbará, T; Alba, N; González-Martínez, S C; Widmer, A; Lexer, C

    2011-01-01

    Molecular genetic analyses of experimental crosses provide important information on the strength and nature of post-mating barriers to gene exchange between divergent populations, which are topics of great interest to evolutionary geneticists and breeders. Although not a trivial task in long-lived organisms such as trees, experimental interspecific recombinants can sometimes be created through controlled crosses involving natural F1's. Here, we used this approach to understand the genetics of post-mating isolation and barriers to introgression in Populus alba and Populus tremula, two ecologically divergent, hybridizing forest trees. We studied 86 interspecific backcross (BC1) progeny and >350 individuals from natural populations of these species for up to 98 nuclear genetic markers, including microsatellites, indels and single nucleotide polymorphisms, and inferred the origin of the cytoplasm of the cross with plastid DNA. Genetic analysis of the BC1 revealed extensive segregation distortions on six chromosomes, and >90% of these (12 out of 13) favored P. tremula donor alleles in the heterospecific genomic background. Since selection was documented during early diploid stages of the progeny, this surprising result was attributed to epistasis, cyto-nuclear coadaptation, heterozygote advantage at nuclear loci experiencing introgression or a combination of these. Our results indicate that gene flow across ‘porous' species barriers affects these poplars and aspens beyond neutral, Mendelian expectations and suggests the mechanisms responsible. Contrary to expectations, the Populus sex determination region is not protected from introgression. Understanding the population dynamics of the Populus sex determination region will require tests based on natural interspecific hybrid zones. PMID:21587301

  9. Adult survivors' lived experience of burns and post-burn health: A qualitative analysis.

    PubMed

    Abrams, Thereasa E; Ogletree, Roberta J; Ratnapradipa, Dhitinut; Neumeister, Michael W

    2016-02-01

    The individual implications of major burns are likely to affect the full spectrum of patients' physical, emotional, psychological, social, environmental, spiritual and vocational health. Yet, not all of the post-burn health implications are inevitably negative. Utilizing a qualitative approach, this heuristic phenomenological study explores the experiences and perceptions early (ages 18-35) and midlife (ages 36-64) adults providing insight for how participants perceived their burns in relationship to their post-burn health. Participants were interviewed using semi-structured interview questions framed around seven domains of health. Interview recordings were transcribed verbatim then coded line by line, identifying dominant categories related to health. Categories were analyzed identifying shared themes among the study sample. Participants were Caucasian, seven males and one female. Mean age at time of interviews was 54.38 and 42.38 at time of burns. Mean time since burns occurred was 9.38 years with a minimum of (20%) total body surface area (TBSA) burns. Qualitative content analysis rendered three emergent health-related categories and associated themes that represented shared meanings within the participant sample. The category of "Physical Health" reflected the theme physical limitations, pain and sensitivity to temperature. Within the category of "Intellectual Health" were themes of insight, goal setting and self-efficacy, optimism and humor and within "Emotional Health" were the themes empathy and gratitude. By exploring subjective experiences and perceptions of health shared through dialog with experienced burned persons, there are opportunities to develop a more complete picture of how holistic health may be affected by major burns that in turn could support future long-term rehabilitative trajectories of early and midlife adult burn patients. Copyright © 2015 Elsevier Ltd and ISBI. All rights reserved.

  10. Nitrogen Species in the Post-Pinatubo Stratosphere: Model Analysis Utilizing UARS Measurements

    NASA Technical Reports Server (NTRS)

    Danilin, M. Y.; Rodriquez, J. M.; Hu, W.; Ko, M. K. W.; Weisenstein, D. K.; Mergenthaler, J. L.; Russell, J. M., III; Koike, M.; Yue, G. K.

    1998-01-01

    We present an analysis of the impact of heterogeneous chemistry on the partitioning of nitrogen species measured by the Upper Atmosphere Research Satellite (UARS) instruments. The UARS measurements utilized include: N2O, HNO3 and ClONO2 (Cryogen Limb Array Etalon Spectrometer (CLAES), version 7), temperature, methane, ozone, H2O, HCl, NO and NO2 (HALogen Occultation Experiment (HALOE), version 18). The analysis is carried out for the data from January 1992 to September 1994 in the 100-1 mbar (approx.17-47 km) altitude range and over 10 degree latitude bins from 70degS to 70degN. Temporal-spatial evolution of aerosol surface area density (SAD) is adopted according to the Stratospheric Aerosol and Gas Experiment (SAGE) 11 data. A diurnal steady-state photochemical box model, constrained by the temperature, ozone, H2O, CH4, aerosol SAD and columns of O2 and O3 above the point of interest, has been used as the main tool to analyze these data. Total inorganic nitrogen (NO(y)) is obtained by three different methods: (1) as a sum of the UARS measured NO, NO2, HNO3, and ClONO2; (2) from the N2O-NO(y) correlation, and (3) from the CH4-NO(y) correlation. To validate our current understanding of stratospheric heterogeneous chemistry for post-Pinatubo conditions, the model-calculated NO(x)/NO(y) ratios and the NO, NO2, and HNO3 profiles are compared to the UARS-derived data. In general, the UARS-constrained box model captures the main features of nitrogen species partitioning in the post-Pinatubo years. However, the model underestimates the NO2 content, particularly, in the 30-7 mbar (approx. 23-32 km) range. Comparisons of the calculated temporal behavior of the partial columns of NO2 and HNO3 and ground based measurements at 45degS and 45degN are also presented. Our analysis indicates that ground-based and HALOE v. 18 measurements of the NO2 vertical columns are consistent within the range of their uncertainties and are systematically higher (up to 50%) than the model

  11. Nitrogen Species in the Post-Pinatubo Stratosphere: Model Analysis Utilizing UARS Measurements

    NASA Technical Reports Server (NTRS)

    Danilin, M. Y.; Rodriguez, J. M.; Hu, W.; Ko, M. K. W.; Weisenstein, D. K.; Kumer, J. B.; Mergenthaler, J. L.; Russell, J. M., III; Koike, M.; Yue, G. K.

    1998-01-01

    We present an analysis of the impact of heterogeneous chemistry on the partitioning of nitrogen species measured by the Upper Atmosphere Research Satellite (UARS) instruments. The UARS measurements utilized include: N2O, HNO3 and ClONO2 (Cryogen Limb Array Etalon Spectrometer (CLAES), version 7), temperature, methane, ozone, H2O, HCI, NO and NO2 (HALogen Occultation Experiment (HALOE), version 18). The analysis is carried out for the data from January 1992 to September 1994 in the 100-1 mbar (approximately 17-47 km) altitude range and over 10 degree latitude bins from 70 deg S to 70 deg N. Temporal-spatial evolution of aerosol surface area density (SAD) is adopted according to the Stratospheric Aerosol and Gas Experiment (SAGE) II data. A diurnal steady-state photochemical box model, constrained by the temperature, ozone, H2O, CH4, aerosol SAD and columns of O2 and O3 above the point of interest, has been used as the main tool to analyze these data. Total inorganic nitrogen (NOy) is obtained by three different methods: (1) as a sum of the UARS measured NO, NO2, HNO3, and CIONO2; (2) from the N2O-NOy correlation, (3) from the CH4-NOy correlation. To validate our current understanding of stratospheric heterogeneous chemistry for post-Pinatubo conditions, the model-calculated NOx/NOy ratios and the NO, NO2, and HNO3 profiles are compared to the UARS-derived data. In general, the UARS-constrained box model captures the main features of nitrogen species partitioning in the post-Pinatubo years. However, the model underestimates the NO2 content, particularly, in the 30-7 mbar (approximately 23-32 km) range. Comparisons of the calculated temporal behavior of the partial columns of NO2 and HNO3 and ground based measurements at 45 deg S and 45 deg N are also presented. Our analysis indicates that ground-based and HALOE v.18 measurements of the NO2 vertical columns are consistent within the range of their uncertainties and are systematically higher (up to 50%) than the model

  12. Gait analysis in a pre- and post-ischemic stroke biomedical pig model.

    PubMed

    Duberstein, Kylee Jo; Platt, Simon R; Holmes, Shannon P; Dove, C Robert; Howerth, Elizabeth W; Kent, Marc; Stice, Steven L; Hill, William D; Hess, David C; West, Franklin D

    2014-02-10

    Severity of neural injury including stroke in human patients, as well as recovery from injury, can be assessed through changes in gait patterns of affected individuals. Similar quantification of motor function deficits has been measured in rodent animal models of such injuries. However, due to differences in fundamental structure of human and rodent brains, there is a need to develop a large animal model to facilitate treatment development for neurological conditions. Porcine brain structure is similar to that of humans, and therefore the pig may make a more clinically relevant animal model. The current study was undertaken to determine key gait characteristics in normal biomedical miniature pigs and dynamic changes that occur post-neural injury in a porcine middle cerebral artery (MCA) occlusion ischemic stroke model. Yucatan miniature pigs were trained to walk through a semi-circular track and were recorded with high speed cameras to detect changes in key gait parameters. Analysis of normal pigs showed overall symmetry in hindlimb swing and stance times, forelimb stance time, along with step length, step velocity, and maximum hoof height on both fore and hindlimbs. A subset of pigs were again recorded at 7, 5 and 3 days prior to MCA occlusion and then at 1, 3, 5, 7, 14 and 30 days following surgery. MRI analysis showed that MCA occlusion resulted in significant infarction. Gait analysis indicated that stroke resulted in notable asymmetries in both temporal and spatial variables. Pigs exhibited lower maximum front hoof height on the paretic side, as well as shorter swing time and longer stance time on the paretic hindlimb. These results support that gait analysis of stroke injury is a highly sensitive detection method for changes in gait parameters in pig.

  13. Analysis of the real EADGENE data set: Multivariate approaches and post analysis (Open Access publication)

    PubMed Central

    Sørensen, Peter; Bonnet, Agnès; Buitenhuis, Bart; Closset, Rodrigue; Déjean, Sébastien; Delmas, Céline; Duval, Mylène; Glass, Liz; Hedegaard, Jakob; Hornshøj, Henrik; Hulsegge, Ina; Jaffrézic, Florence; Jensen, Kirsty; Jiang, Li; de Koning, Dirk-Jan; Cao, Kim-Anh Lê; Nie, Haisheng; Petzl, Wolfram; Pool, Marco H; Robert-Granié, Christèle; San Cristobal, Magali; Lund, Mogens Sandø; van Schothorst, Evert M; Schuberth, Hans-Joachim; Seyfert, Hans-Martin; Tosser-Klopp, Gwenola; Waddington, David; Watson, Michael; Yang, Wei; Zerbe, Holm

    2007-01-01

    The aim of this paper was to describe, and when possible compare, the multivariate methods used by the participants in the EADGENE WP1.4 workshop. The first approach was for class discovery and class prediction using evidence from the data at hand. Several teams used hierarchical clustering (HC) or principal component analysis (PCA) to identify groups of differentially expressed genes with a similar expression pattern over time points and infective agent (E. coli or S. aureus). The main result from these analyses was that HC and PCA were able to separate tissue samples taken at 24 h following E. coli infection from the other samples. The second approach identified groups of differentially co-expressed genes, by identifying clusters of genes highly correlated when animals were infected with E. coli but not correlated more than expected by chance when the infective pathogen was S. aureus. The third approach looked at differential expression of predefined gene sets. Gene sets were defined based on information retrieved from biological databases such as Gene Ontology. Based on these annotation sources the teams used either the GlobalTest or the Fisher exact test to identify differentially expressed gene sets. The main result from these analyses was that gene sets involved in immune defence responses were differentially expressed. PMID:18053574

  14. Fatigue surviving, fracture resistance, shear stress and finite element analysis of glass fiber posts with different diameters.

    PubMed

    Wandscher, Vinícius Felipe; Bergoli, César Dalmolin; de Oliveira, Ariele Freitas; Kaizer, Osvaldo Bazzan; Souto Borges, Alexandre Luiz; Limberguer, Inácio da Fontoura; Valandro, Luiz Felipe

    2015-03-01

    This study evaluated the shear stress presented in glass fiber posts with parallel fiber (0°) and different coronal diameters under fatigue, fracture resistance and FEA. 160 glass-fiber posts (N=160) with eight different coronal diameters were used (DT=double tapered, number of the post=coronal diameter and W=Wider - fiber post with coronal diameter wider than the conventional): DT1.4; DT1.8W; DT1.6; DT2W; DT1.8; DT2.2W; DT2; DT2.2. Eighty posts were submitted to mechanical cycling (3×10(6) cycles; inclination: 45°; load: 50N; frequency: 4Hz; temperature: 37°C) to assess the surviving under intermittent loading and other eighty posts were submitted to fracture resistance testing (resistance [N] and shear-stress [MPa] values were obtained). The eight posts types were 3D modeled (Rhinoceros 4.0) and the shear-stress (MPa) evaluated using FEA (Ansys 13.0). One-way ANOVA showed statistically differences to fracture resistance (DT2.2W and DT2.2 showed higher values) and shear stress values (DT1.4 showed lower values). Only the DT1.4 fiber posts failed after mechanical cycling. FEA showed similar values of shear stress between the groups and these values were similar to those obtained by shear stress testing. The failure analysis showed that 95% of specimens failed by shear. Posts with parallel fiber (0°) may suffer fractures when an oblique shear load is applied on the structure; except the thinner group, greater coronal diameters promoted the same shear stresses.

  15. Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications.

    PubMed

    Pascal, Bruce D; West, Graham M; Scharager-Tapia, Catherina; Flefil, Ricardo; Moroni, Tina; Martinez-Acedo, Pablo; Griffin, Patrick R; Carvalloza, Anthony C

    2015-12-01

    The goal in proteomics to identify all peptides in a complex mixture has been largely addressed using various LC MS/MS approaches, such as data dependent acquisition, SRM/MRM, and data independent acquisition instrumentation. Despite these developments, many peptides remain unsequenced, often due to low abundance, poor fragmentation patterns, or data analysis difficulties. Many of the unidentified peptides exhibit strong evidence in high resolution MS(1) data and are frequently post-translationally modified, playing a significant role in biological processes. Proteomics Workbench (PWB) software was developed to automate the detection and visualization of all possible peptides in MS(1) data, reveal candidate peptides not initially identified, and build inclusion lists for subsequent MS(2) analysis to uncover new identifications. We used this software on existing data on the autophagy regulating kinase Ulk1 as a proof of concept for this method, as we had already manually identified a number of phosphorylation sites Dorsey, F. C. et al (J. Proteome. Res. 8(11), 5253-5263 (2009)). PWB found all previously identified sites of phosphorylation. The software has been made freely available at http://www.proteomicsworkbench.com . Graphical Abstract ᅟ.

  16. Glycoproteomic Analysis of Seven Major Allergenic Proteins Reveals Novel Post-translational Modifications*

    PubMed Central

    Halim, Adnan; Carlsson, Michael C.; Madsen, Caroline Benedicte; Brand, Stephanie; Møller, Svenning Rune; Olsen, Carl Erik; Vakhrushev, Sergey Y.; Brimnes, Jens; Wurtzen, Peter Adler; Ipsen, Henrik; Petersen, Bent L.; Wandall, Hans H.

    2015-01-01

    Allergenic proteins such as grass pollen and house dust mite (HDM) proteins are known to trigger hypersensitivity reactions of the immune system, leading to what is commonly known as allergy. Key allergenic proteins including sequence variants have been identified but characterization of their post-translational modifications (PTMs) is still limited. Here, we present a detailed PTM1 characterization of a series of the main and clinically relevant allergens used in allergy tests and vaccines. We employ Orbitrap-based mass spectrometry with complementary fragmentation techniques (HCD/ETD) for site-specific PTM characterization by bottom-up analysis. In addition, top-down mass spectrometry is utilized for targeted analysis of individual proteins, revealing hitherto unknown PTMs of HDM allergens. We demonstrate the presence of lysine-linked polyhexose glycans and asparagine-linked N-acetylhexosamine glycans on HDM allergens. Moreover, we identified more complex glycan structures than previously reported on the major grass pollen group 1 and 5 allergens, implicating important roles for carbohydrates in allergen recognition and response by the immune system. The new findings are important for understanding basic disease-causing mechanisms at the cellular level, which ultimately may pave the way for instigating novel approaches for targeted desensitization strategies and improved allergy vaccines. PMID:25389185

  17. Discriminant Context Information Analysis for Post-Ranking Person Re-Identification.

    PubMed

    Garcia, Jorge; Martinel, Niki; Gardel, Alfredo; Bravo, Ignacio; Foresti, Gian Luca; Micheloni, Christian

    2017-01-16

    Existing approaches for person re-identification are mainly based on creating distinctive representations or on learning optimal metrics. The achieved results are then provided in form of a list of ranked matching persons. It often happens that the true match is not ranked first but it is in the first positions. This is mostly due to the visual ambiguities shared between the true match and other "similar" persons. At the current state, there is a lack of a study of such visual ambiguities which limit the re-identification performance within the first ranks. We believe that an analysis of the similar appearances of the first ranks can be helpful in detecting, hence removing, such visual ambiguities. We propose to achieve such a goal by introducing an unsupervised post-ranking framework. Once the initial ranking is available, content and context sets are extracted. Then, these are exploited to remove the visual ambiguities and to obtain the discriminant feature space which is finally exploited to compute the new ranking. An in-depth analysis of the performance achieved on three public benchmark datasets support our believes. For every dataset, the proposed method remarkably improves the first ranks results and outperforms state-of-the-art approaches.

  18. Nonlinear Analysis and Post-Test Correlation for a Curved PRSEUS Panel

    NASA Technical Reports Server (NTRS)

    Gould, Kevin; Lovejoy, Andrew E.; Jegley, Dawn; Neal, Albert L.; Linton, Kim, A.; Bergan, Andrew C.; Bakuckas, John G., Jr.

    2013-01-01

    The Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS) concept, developed by The Boeing Company, has been extensively studied as part of the National Aeronautics and Space Administration's (NASA s) Environmentally Responsible Aviation (ERA) Program. The PRSEUS concept provides a light-weight alternative to aluminum or traditional composite design concepts and is applicable to traditional-shaped fuselage barrels and wings, as well as advanced configurations such as a hybrid wing body or truss braced wings. Therefore, NASA, the Federal Aviation Administration (FAA) and The Boeing Company partnered in an effort to assess the performance and damage arrestments capabilities of a PRSEUS concept panel using a full-scale curved panel in the FAA Full-Scale Aircraft Structural Test Evaluation and Research (FASTER) facility. Testing was conducted in the FASTER facility by subjecting the panel to axial tension loads applied to the ends of the panel, internal pressure, and combined axial tension and internal pressure loadings. Additionally, reactive hoop loads were applied to the skin and frames of the panel along its edges. The panel successfully supported the required design loads in the pristine condition and with a severed stiffener. The panel also demonstrated that the PRSEUS concept could arrest the progression of damage including crack arrestment and crack turning. This paper presents the nonlinear post-test analysis and correlation with test results for the curved PRSEUS panel. It is shown that nonlinear analysis can accurately calculate the behavior of a PRSEUS panel under tension, pressure and combined loading conditions.

  19. Meta-analysis of Dropout in Treatments for Post-traumatic Stress Disorder

    PubMed Central

    Imel, Zac E.; Laska, Kevin; Jakcupcak, Matthew; Simpson, Tracy L.

    2013-01-01

    Objective Many patients dropout of treatments for Post-traumatic stress disorder (PTSD) and some clinicians believe that ‘trauma focused’ treatments increase dropout. Method We conducted a meta-analysis of dropout among active treatments in clinical trials for PTSD (42 studies; 17 direct comparisons). Results The average dropout rate was 18%, but it varied significantly across studies. Group modality and greater number of sessions, but not trauma focus, predicted increased dropout. When the meta-analysis was restricted to direct comparisons of active treatments, there were no differences in dropout. Differences in trauma focus between treatments in the same study did not predict dropout. However, trauma focused treatments resulted in higher dropout as compared to Present Centered Therapy (PCT) – a treatment originally designed as a control, but now listed as a research supported intervention for PTSD. Conclusion Dropout varies between active interventions for PTSD across studies, but differences are primarily driven by differences between studies. There do not appear to be systematic differences across active interventions when they are directly compared in the same study. The degree of clinical attention placed on the traumatic event does not appear to be a primary cause of dropout from active treatments. However comparisons of PCT may be an exception to this general pattern, perhaps due to a restriction of variability in trauma focus among comparisons of active treatments. More research is needed comparing trauma focused interventions to trauma avoidant treatments such as PCT. PMID:23339535

  20. Efficacy response in CF patients treated with ivacaftor: post-hoc analysis.

    PubMed

    Konstan, Michael W; Plant, Barry J; Elborn, J Stuart; Rodriguez, Sally; Munck, Anne; Ahrens, Richard; Johnson, Charles

    2015-05-01

    Clinical studies in patients with cystic fibrosis and G551D-CFTR showed that the group treated with ivacaftor had improved clinical outcomes. To better understand the effect of ivacaftor therapy across the distribution of individual FEV(1) responses, data from Phase 3 studies (STRIVE/ENVISION) were re-examined. In this post-hoc analysis of patients (n = 209) who received 48 weeks of ivacaftor or placebo, patients were assigned to tertiles according to FEV(1) response. These groups were then used to evaluate response (FEV(1), sweat chloride, weight, CFQ-R, and pulmonary exacerbation). The number needed to treat (NNT) was calculated for specific thresholds for each outcome. Across all tertiles, numerical improvements in FEV(1), sweat chloride, CFQ-R and the frequency of pulmonary exacerbations were observed in ivacaftor-treated patients: the treatment difference versus placebo was statistically significant for all outcomes in the upper tertile and for some outcomes in the lower and middle tertiles. The NNT for a ≥ 5% improvement in %predicted FEV(1) was 1.90, for a ≥ 5% body weight increase was 5.74, and to prevent a pulmonary exacerbation was 3.85. This analysis suggests that the majority of patients with clinical characteristics similar to STRIVE/ENVISION patients have the potential to benefit from ivacaftor therapy.

  1. Struggles for recognition: a content analysis of messages posted on the Internet

    PubMed Central

    Andersen, Anders Johan W; Svensson, Tommy

    2012-01-01

    Background The Internet has enlarged the possibilities of human communication and opened new ways of exploring perceptions of mental health. This study is part of a research project aiming to explore, describe, and analyze different discourses of mental health in Norway and Sweden, using material from Internet-based services. Aim To examine messages posed by users of publicly available question-and-answer services and to describe their content. Methods A Web search was used to identify Norwegian and Swedish Websites offering mental health services by email or posted messages. A total of 601 messages from 20 services, 10 Norwegian and 10 Swedish, were analyzed by means of qualitative content analysis and further interpreted in light of the social theory of recognition by Honneth. Results Eight categories emerged from the analysis: family life, couples, others, violence, the ungovernable, self-image, negotiating normality, and life struggles. These categories were then grouped into three themes: (1) relationship to significant others, (2) relationship to self, and (3) relationship to the social community. The themes promoted an understanding of mental health as closely connected to political and social factors. Conclusions The results showed a variety of concerns from various parts of life and empowered the view that mental health should be understood broadly, at a conceptual level. Mental health emerged as a deeply relational concept that emphasized the equal distribution of chances in life. It strengthened the moral grammar of social inclusion and the acceptance of plurality in social life. PMID:22888257

  2. Software Analysis of Uncorrelated MS1 Peaks for Discovery of Post-Translational Modifications

    NASA Astrophysics Data System (ADS)

    Pascal, Bruce D.; West, Graham M.; Scharager-Tapia, Catherina; Flefil, Ricardo; Moroni, Tina; Martinez-Acedo, Pablo; Griffin, Patrick R.; Carvalloza, Anthony C.

    2015-12-01

    The goal in proteomics to identify all peptides in a complex mixture has been largely addressed using various LC MS/MS approaches, such as data dependent acquisition, SRM/MRM, and data independent acquisition instrumentation. Despite these developments, many peptides remain unsequenced, often due to low abundance, poor fragmentation patterns, or data analysis difficulties. Many of the unidentified peptides exhibit strong evidence in high resolution MS1 data and are frequently post-translationally modified, playing a significant role in biological processes. Proteomics Workbench (PWB) software was developed to automate the detection and visualization of all possible peptides in MS1 data, reveal candidate peptides not initially identified, and build inclusion lists for subsequent MS2 analysis to uncover new identifications. We used this software on existing data on the autophagy regulating kinase Ulk1 as a proof of concept for this method, as we had already manually identified a number of phosphorylation sites Dorsey, F. C. et al (J. Proteome. Res. 8(11), 5253-5263 (2009)). PWB found all previously identified sites of phosphorylation. The software has been made freely available at http://www.proteomicsworkbench.com .

  3. Qualifications and Competencies for Population Health Management Positions: A Content Analysis of Job Postings.

    PubMed

    Meyer, Melanie

    2017-04-06

    The need for population health management expertise has increased as the health care industry shifts toward value-based care. However, many organizations report hiring gaps as they seek to fill positions. The purpose of this study was to analyze the types of population health management positions for which health care organizations are hiring, including qualifications and competencies required for these positions. A content analysis was conducted on 271 job postings collected during a 2-month period. A typology of qualifications and competencies was developed based on the content analysis. Profiles were generated for the top 5 job title classifications: directors, coordinators, care managers, analysts, and specialists. This study highlights the investment health care organizations are making in population health management and the prominent role these positions are playing in the health care environment today. Many organizations are building out population health management teams resulting in multiple positions at different levels being added. As the market demands competent candidates who are equipped with specialized population health expertise as well as practical experience in program development, technology applications, care management, and analytics, professional education programs will need to adapt curricula to address the required areas. Competencies for specific job title classifications may need further evaluation and refinement over time. Study results can be used by organizations for strategic planning, by educators to target needed qualifications and competencies, and by researchers and policy advisors to assess progress toward value-based care.

  4. Reaction flow chromatography for rapid post column derivatisations: the analysis of antioxidants in natural products.

    PubMed

    Camenzuli, M; Ritchie, H J; Dennis, G R; Shalliker, R A

    2013-08-16

    The analysis of antioxidants from complex samples is conveniently achieved using liquid chromatography, which provides sample fraction, coupled with an on-line antioxidant assay, which provides detection. One particularly useful on-line antioxidant assay that has routinely been coupled with HPLC involves the diphenylpicrylhydrazyl radical (DPPH), which provides a positive test for phenolic antioxidants through a decolorisation of the DPPH reagent. A limitation of this assay, however, is the need to employ a reaction coil, which is often large with respect to the peak volume, consequently adding substantial band broadening to the separation. In this study we introduce a new concept that can be employed for systems requiring post column derivatisations, such as the DPPH assay. We have termed this 'reaction flow' chromatography, whereby, the derivatisation reagent can be added directly into one of the outlet ports of a parallel segmented flow column. Subsequently, the mixing between the derivatising reagent and the solute is very efficient removing the need to employ reaction coils. The concept is tested here using the DPPH assay for the analysis of antioxidants in samples derived from natural origin. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Analysis of Orbital Lifetime Prediction Parameters in Preparation for Post-Mission Disposal

    NASA Astrophysics Data System (ADS)

    Choi, Ha-Yeon; Kim, Hae-Dong; Seong, Jae-Dong

    2015-12-01

    Atmospheric drag force is an important source of perturbation of Low Earth Orbit (LEO) orbit satellites, and solar activity is a major factor for changes in atmospheric density. In particular, the orbital lifetime of a satellite varies with changes in solar activity, so care must be taken in predicting the remaining orbital lifetime during preparation for post-mission disposal. In this paper, the System Tool Kit (STK®) Long-term Orbit Propagator is used to analyze the changes in orbital lifetime predictions with respect to solar activity. In addition, the STK® Lifetime tool is used to analyze the change in orbital lifetime with respect to solar flux data generation, which is needed for the orbital lifetime calculation, and its control on the drag coefficient control. Analysis showed that the application of the most recent solar flux file within the Lifetime tool gives a predicted trend that is closest to the actual orbit. We also examine the effect of the drag coefficient, by performing a comparative analysis between varying and constant coefficients in terms of solar activity intensities.

  6. Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast

    PubMed Central

    Zampieri, Mattia; Sauer, Uwe

    2017-01-01

    Cells react to extracellular perturbations with complex and intertwined responses. Systematic identification of the regulatory mechanisms that control these responses is still a challenge and requires tailored analyses integrating different types of molecular data. Here we acquired time-resolved metabolomics measurements in yeast under salt and pheromone stimulation and developed a machine learning approach to explore regulatory associations between metabolism and signal transduction. Existing phosphoproteomics measurements under the same conditions and kinase-substrate regulatory interactions were used to in silico estimate the enzymatic activity of signalling kinases. Our approach identified informative associations between kinases and metabolic enzymes capable of predicting metabolic changes. We extended our analysis to two studies containing transcriptomics, phosphoproteomics and metabolomics measurements across a comprehensive panel of kinases/phosphatases knockouts and time-resolved perturbations to the nitrogen metabolism. Changes in activity of transcription factors, kinases and phosphatases were estimated in silico and these were capable of building predictive models to infer the metabolic adaptations of previously unseen conditions across different dynamic experiments. Time-resolved experiments were significantly more informative than genetic perturbations to infer metabolic adaptation. This difference may be due to the indirect nature of the associations and of general cellular states that can hinder the identification of causal relationships. This work provides a novel genome-scale integrative analysis to propose putative transcriptional and post-translational regulatory mechanisms of metabolic processes. PMID:28072816

  7. Surface topography analysis and performance on post-CMP images (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Lee, Jusang; Bello, Abner F.; Kakita, Shinichiro; Pieniazek, Nicholas; Johnson, Timothy A.

    2017-03-01

    again be calculated and used as yet another quantifiable parameter for SPC. In this work we measured the post Cu CMP of a die designed for 14nm technology. A region of interest (ROI) known to be indicative of the CMP processing is chosen for the topography analysis. The ROI, of size 1800 x 2500 pixels where each pixel represents 2um, was repeatably measured. We show the sensitivity based on measurements and the comparison between center and edge die measurements. The topography measurements and surface patch analysis were applied to hundreds of images representing the periodic process qualification runs required to control and verify CMP performance and tool matching. The analysis is shown to be sensitive to process conditions that vary in polishing time, type of slurry, CMP tool manufacturer, and CMP pad lifetime. Keywords: Keywords: CMP, Topography, Image Processing, Metrology, Interference microscopy, surface processing [1] De Lega, Xavier Colonna, and Peter De Groot. "Optical topography measurement of patterned wafers." Characterization and Metrology for ULSI Technology 2005 788 (2005): 432-436. [2] de Groot, Peter. "Coherence scanning interferometry." Optical Measurement of Surface Topography. Springer Berlin Heidelberg, 2011. 187-208. [3] Watson, Layne T., Thomas J. Laffey, and Robert M. Haralick. "Topographic classification of digital image intensity surfaces using generalized splines and the discrete cosine transformation." Computer Vision, Graphics, and Image Processing 29.2 (1985): 143-167. [4] Wang, Jun, et al. "3D facial expression recognition based on primitive surface feature distribution." Computer Vision and Pattern Recognition, 2006 IEEE Computer Society Conference on. Vol. 2. IEEE, 2006.

  8. Brain structure in post-traumatic stress disorder: A voxel-based morphometry analysis

    PubMed Central

    Tan, Liwen; Zhang, Li; Qi, Rongfeng; Lu, Guangming; Li, Lingjiang; Liu, Jun; Li, Weihui

    2013-01-01

    This study compared the difference in brain structure in 12 mine disaster survivors with chronic post-traumatic stress disorder, 7 cases of improved post-traumatic stress disorder symptoms, and 14 controls who experienced the same mine disaster but did not suffer post-traumatic stress disorder, using the voxel-based morphometry method. The correlation between differences in brain structure and post-traumatic stress disorder symptoms was also investigated. Results showed that the gray matter volume was the highest in the trauma control group, followed by the symptoms-improved group, and the lowest in the chronic post-traumatic stress disorder group. Compared with the symptoms-improved group, the gray matter volume in the lingual gyrus of the right occipital lobe was reduced in the chronic post-traumatic stress disorder group. Compared with the trauma control group, the gray matter volume in the right middle occipital gyrus and left middle frontal gyrus was reduced in the symptoms-improved group. Compared with the trauma control group, the gray matter volume in the left superior parietal lobule and right superior frontal gyrus was reduced in the chronic post-traumatic stress disorder group. The gray matter volume in the left superior parietal lobule was significantly positively correlated with the State-Trait Anxiety Inventory subscale score in the symptoms-improved group and chronic post-traumatic stress disorder group (r = 0.477, P = 0.039). Our findings indicate that (1) chronic post-traumatic stress disorder patients have gray matter structural damage in the prefrontal lobe, occipital lobe, and parietal lobe, (2) after post-traumatic stress, the disorder symptoms are improved and gray matter structural damage is reduced, but cannot recover to the trauma-control level, and (3) the superior parietal lobule is possibly associated with chronic post-traumatic stress disorder. Post-traumatic stress disorder patients exhibit gray matter abnormalities. PMID:25206550

  9. Brain structure in post-traumatic stress disorder: A voxel-based morphometry analysis.

    PubMed

    Tan, Liwen; Zhang, Li; Qi, Rongfeng; Lu, Guangming; Li, Lingjiang; Liu, Jun; Li, Weihui

    2013-09-15

    This study compared the difference in brain structure in 12 mine disaster survivors with chronic post-traumatic stress disorder, 7 cases of improved post-traumatic stress disorder symptoms, and 14 controls who experienced the same mine disaster but did not suffer post-traumatic stress disorder, using the voxel-based morphometry method. The correlation between differences in brain structure and post-traumatic stress disorder symptoms was also investigated. Results showed that the gray matter volume was the highest in the trauma control group, followed by the symptoms-improved group, and the lowest in the chronic post-traumatic stress disorder group. Compared with the symptoms-improved group, the gray matter volume in the lingual gyrus of the right occipital lobe was reduced in the chronic post-traumatic stress disorder group. Compared with the trauma control group, the gray matter volume in the right middle occipital gyrus and left middle frontal gyrus was reduced in the symptoms-improved group. Compared with the trauma control group, the gray matter volume in the left superior parietal lobule and right superior frontal gyrus was reduced in the chronic post-traumatic stress disorder group. The gray matter volume in the left superior parietal lobule was significantly positively correlated with the State-Trait Anxiety Inventory subscale score in the symptoms-improved group and chronic post-traumatic stress disorder group (r = 0.477, P = 0.039). Our findings indicate that (1) chronic post-traumatic stress disorder patients have gray matter structural damage in the prefrontal lobe, occipital lobe, and parietal lobe, (2) after post-traumatic stress, the disorder symptoms are improved and gray matter structural damage is reduced, but cannot recover to the trauma-control level, and (3) the superior parietal lobule is possibly associated with chronic post-traumatic stress disorder. Post-traumatic stress disorder patients exhibit gray matter abnormalities.

  10. Performance Assessment of a Trypanosoma cruzi Chimeric Antigen in Multiplex Liquid Microarray Assays.

    PubMed

    Santos, Fred Luciano Neves; Celedon, Paola Alejandra Fiorani; Zanchin, Nilson Ivo Tonin; Leitolis, Amanda; Crestani, Sandra; Foti, Leonardo; de Souza, Wayner Vieira; Gomes, Yara de Miranda; Krieger, Marco Aurélio

    2017-10-01

    Diagnosing chronic Chagas disease (CD) requires antibody-antigen detection methods, which are traditionally based on enzymatic assay techniques whose performance depend on the type and quality of antigen used. Previously, 4 recombinant chimeric proteins from the Instituto de Biologia Molecular do Paraná (IBMP-8.1 to 8.4) comprising immuno-dominant regions of diverse Trypanosoma cruzi antigens showed excellent diagnostic performance in enzyme-linked immunosorbent assays. Considering that next-generation platforms offer improved CD diagnostic accuracy with different T. cruzi-specific recombinant antigens, we assessed the performance of these chimeras in liquid microarrays (LMAs). The chimeric proteins were expressed in Escherichia coli and purified by chromatography. Sera from 653 chagasic and 680 healthy individuals were used to assess the performance of these chimeras in detecting specific anti-T. cruzi antibodies. Accuracies ranged from 98.1 to 99.3%, and diagnostic odds ratio values were 3,548 for IBMP-8.3, 4,826 for IBMP-8.1, 7,882 for IBMP-8.2, and 25,000 for IBMP-8.4. A separate sera bank (851 samples) was employed to assess cross-reactivity with other tropical diseases. Leishmania, a pathogen with high similarity to T. cruzi, showed cross-reactivity rates ranging from 0 to 2.17%. Inconclusive results were negligible (0 to 0.71%). Bland-Altman and Deming regression analysis based on 200 randomly selected CD-positive and negative samples demonstrated interchangeability with respect to CD diagnostic performance in both singleplex and multiplex assays. Our results suggested that these chimeras can potentially replace antigens currently used in commercially available assay kits. Moreover, the use of multiplex platforms, such as LMA assays employing 2 or more IBMP antigens, would abrogate the need for 2 different testing techniques when diagnosing CD. Copyright © 2017 American Society for Microbiology.

  11. Repeated Evolution of Chimeric Fusion Genes in the β-Globin Gene Family of Laurasiatherian Mammals

    PubMed Central

    Gaudry, Michael J.; Storz, Jay F.; Butts, Gary Tyler; Campbell, Kevin L.; Hoffmann, Federico G.

    2014-01-01

    The evolutionary fate of chimeric fusion genes may be strongly influenced by their recombinational mode of origin and the nature of functional divergence between the parental genes. In the β-globin gene family of placental mammals, the two postnatally expressed δ- and β-globin genes (HBD and HBB, respectively) have a propensity for recombinational exchange via gene conversion and unequal crossing-over. In the latter case, there are good reasons to expect differences in retention rates for the reciprocal HBB/HBD and HBD/HBB fusion genes due to thalassemia pathologies associated with the HBD/HBB “Lepore” deletion mutant in humans. Here, we report a comparative genomic analysis of the mammalian β-globin gene cluster, which revealed that chimeric HBB/HBD fusion genes originated independently in four separate lineages of laurasiatherian mammals: Eulipotyphlans (shrews, moles, and hedgehogs), carnivores, microchiropteran bats, and cetaceans. In cases where an independently derived “anti-Lepore” duplication mutant has become fixed, the parental HBD and/or HBB genes have typically been inactivated or deleted, so that the newly created HBB/HBD fusion gene is primarily responsible for synthesizing the β-type subunits of adult and fetal hemoglobin (Hb). Contrary to conventional wisdom that the HBD gene is a vestigial relict that is typically inactivated or expressed at negligible levels, we show that HBD-like genes often encode a substantial fraction (20–100%) of β-chain Hbs in laurasiatherian taxa. Our results indicate that the ascendancy or resuscitation of genes with HBD-like coding sequence requires the secondary acquisition of HBB-like promoter sequence via unequal crossing-over or interparalog gene conversion. PMID:24814285

  12. Repeated evolution of chimeric fusion genes in the β-globin gene family of laurasiatherian mammals.

    PubMed

    Gaudry, Michael J; Storz, Jay F; Butts, Gary Tyler; Campbell, Kevin L; Hoffmann, Federico G

    2014-05-09

    The evolutionary fate of chimeric fusion genes may be strongly influenced by their recombinational mode of origin and the nature of functional divergence between the parental genes. In the β-globin gene family of placental mammals, the two postnatally expressed δ- and β-globin genes (HBD and HBB, respectively) have a propensity for recombinational exchange via gene conversion and unequal crossing-over. In the latter case, there are good reasons to expect differences in retention rates for the reciprocal HBB/HBD and HBD/HBB fusion genes due to thalassemia pathologies associated with the HBD/HBB "Lepore" deletion mutant in humans. Here, we report a comparative genomic analysis of the mammalian β-globin gene cluster, which revealed that chimeric HBB/HBD fusion genes originated independently in four separate lineages of laurasiatherian mammals: Eulipotyphlans (shrews, moles, and hedgehogs), carnivores, microchiropteran bats, and cetaceans. In cases where an independently derived "anti-Lepore" duplication mutant has become fixed, the parental HBD and/or HBB genes have typically been inactivated or deleted, so that the newly created HBB/HBD fusion gene is primarily responsible for synthesizing the β-type subunits of adult and fetal hemoglobin (Hb). Contrary to conventional wisdom that the HBD gene is a vestigial relict that is typically inactivated or expressed at negligible levels, we show that HBD-like genes often encode a substantial fraction (20-100%) of β-chain Hbs in laurasiatherian taxa. Our results indicate that the ascendancy or resuscitation of genes with HBD-like coding sequence requires the secondary acquisition of HBB-like promoter sequence via unequal crossing-over or interparalog gene conversion. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  13. Recombinant chimeric vaccine composed of PRRSV antigens and truncated Pseudomonas exotoxin A (PE-K13).

    PubMed

    Yang, Hsin-Ping; Wang, Tsan-Chih; Wang, Shiou-Jen; Chen, Shih-Ping; Wu, Eva; Lai, Shao-Qun; Chang, Hsueh-Wei; Liao, Chao-Wei

    2013-10-01

    A Pseudomonas exotoxin (PE-KDEL)-based chimeric subunit vaccine system was recently developed using a reverse vaccinology technique. In this study, the plasmids containing PE-PRRS chimeric subunits were constructed that composed of porcine reproductive and respiratory syndrome virus (PRRSV) antigen moieties, a ligand moiety and a Pseudomonas exotoxin A deleted domain III (PE (ΔIII)), and a carboxyl terminal moiety that includes a polypeptide with amino acid sequence KDEL (K3). The PE-PRRS combination vaccine can effectively induce not only PRRSV-specific INF-γ cellular immunity but also a slow-reacting and complement-requiring type serum neutralizing antibody in pigs. In a specific pathogen free (SPF) pig challenge model, body temperature (colonic temperature), occurrence of PRRSV viremia, nasal excretions, gross and histopathological appearances of pneumonia, and serum antibody activity (IFA and SN) titers significantly differed between the immunized group and the control group. The survey showed that a 0.3mg/dose PE-PRRS vaccine formula conferred protection against PRRSV. A field trial of PE-PRRS vaccine was performed to study the immune response of pregnant sows after vaccination in a PRRSV persist farm. The RT-PCR analysis of viremia and serological titers showed that the PE-PRRS vaccine not only increased sow reproductive performance and evoked its immune response to PRRS viremia, it also activated maternal immune protections to prevent piglets from inflicting viremia. In conclusion, we developed a novel and effective PRRS cytotoxic T-cells (CTLs)-based vaccine containing Pseudomonas exotoxin (PE-KDEL) carrier in combination with PRRSV conserved epitopes against PRRS virus.

  14. Analysis of measured post-coupler fields in a ramped-gradient drift-tube linac

    SciTech Connect

    Billen, J.H.

    1988-01-01

    Post couplers longitudinally stabilize the axial electric field in a drift-tube linac (DTL) against tuning errors. Displacing the post couplers toward one end of the structure results in a ramped field that increases toward the other end. Such a ramped-gradient DTL is also stable, but some of the cavity power is dissipated on the post couplers to maintain the ramp. This paper reports bead-perturbation measurements of the post-coupler magnetic fields near the tank well. A simple physical model reproduces the measured fields with an accuracy of about 2% and yields current-density distributions on the post couplers in terms of the current density on the cavity wall. The peak power density occurs on the sides of the post couplers where the TM/sub 010/ magnetic field adds to the post-coupler magnetic field. In the Los Alamos Ramped-Gradient DTL (RGDTL), the peak power densities on post couplers located in the steepest part of the ramp exceed by more than 10 times the maximum power density on the tank wall far from any post couplers. Methods to reduce such power losses to levels comparable to a flat-gradient DTL will be discussed. 2 refs. , 6 figs., 1 tab.

  15. Understanding Impact and Implications of Data Standards on Post Disaster Risk Analysis

    NASA Astrophysics Data System (ADS)

    Stevenson, Robert

    2010-05-01

    Although the physical and humanitarian effects of a natural catastrophe are often bound to the locality of the event the financial impacts can have global effects. This is particularly prominent in the re/insurance community, where through a number of market mechanisms and re/insurance structures financial loss is mitigated amongst many companies across the globe. The level of risk a company wishes to retain, given an event, represents the level of risk decision makers deem acceptable. Catastrophe risk modelling tools aid the estimation of risk retention and transfer mechanisms, and increasingly the level of capital required to withstand a catastrophic event. These tools rely on appropriate representations hazard, exposure, vulnerability and insurance conditions that reflect the reality of risk. In addition, accurate estimation of loss potential in the aftermath of a catastrophic event equally relies on the data available to assess the scale of damages experienced and to provide views on the likely scale of loss. A coherent and focussed data and modelling strategy is required to ensure that the risk assessment made is as accurate as possible. A fundamental factor in determining the accuracy of catastrophe output, is the quality of data entered. It is of vital importance, therefore, to have an understanding of both the data used as well as the standard of this data, which will so powerfully impact upon the decision making process. This is perhaps best illustrated through the study of historical events, such as Hurricane Katrina and Ike. The extent of data variance in post disaster analysis clearly demonstrates issues of data discrepancies, vintage, resolution and uncertainty propagation, and reflects on the standard of the original data utilized for modelling purposes and decision making. Using experience gained from recent events, this paper will explore current data variabilities, and the impacts on effective loss estimation, both in relation to reinsurance

  16. Chimeric Antigen Receptor T Cells for Sustained Remissions in Leukemia

    PubMed Central

    Maude, Shannon L.; Frey, Noelle; Shaw, Pamela A.; Aplenc, Richard; Barrett, David M.; Bunin, Nancy J.; Chew, Anne; Gonzalez, Vanessa E.; Zheng, Zhaohui; Lacey, Simon F.; Mahnke, Yolanda D.; Melenhorst, Jan J.; Rheingold, Susan R.; Shen, Angela; Teachey, David T.; Levine, Bruce L.; June, Carl H.; Porter, David L.; Grupp, Stephan A.

    2014-01-01

    BACKGROUND Relapsed acute lymphoblastic leukemia (ALL) is difficult to treat despite the availability of aggressive therapies. Chimeric antigen receptor–modified T cells targeting CD19 may overcome many limitations of conventional therapies and induce remission in patients with refractory disease. METHODS We infused autologous T cells transduced with a CD19-directed chimeric antigen receptor (CTL019) lentiviral vector in patients with relapsed or refractory ALL at doses of 0.76×106 to 20.6×106 CTL019 cells per kilogram of body weight. Patients were monitored for a response, toxic effects, and the expansion and persistence of circulating CTL019 T cells. RESULTS A total of 30 children and adults received CTL019. Complete remission was achieved in 27 patients (90%), including 2 patients with blinatumomab-refractory disease and 15 who had undergone stem-cell transplantation. CTL019 cells proliferated in vivo and were detectable in the blood, bone marrow, and cerebrospinal fluid of patients who had a response. Sustained remission was achieved with a 6-month event-free survival rate of 67% (95% confidence interval [CI], 51 to 88) and an overall survival rate of 78% (95% CI, 65 to 95). At 6 months, the probability that a patient would have persistence of CTL019 was 68% (95% CI, 50 to 92) and the probability that a patient would have relapse-free B-cell aplasia was 73% (95% CI, 57 to 94). All the patients had the cytokine-release syndrome. Severe cytokine-release syndrome, which developed in 27% of the patients, was associated with a higher disease burden before infusion and was effectively treated with the anti–interleukin-6 receptor antibody tocilizumab. CONCLUSIONS Chimeric antigen receptor–modified T-cell therapy against CD19 was effective in treating relapsed and refractory ALL. CTL019 was associated with a high remission rate, even among patients for whom stem-cell transplantation had failed, and durable remissions up to 24 months were observed. (Funded by

  17. Chimeric antigen receptor T cells for sustained remissions in leukemia.

    PubMed

    Maude, Shannon L; Frey, Noelle; Shaw, Pamela A; Aplenc, Richard; Barrett, David M; Bunin, Nancy J; Chew, Anne; Gonzalez, Vanessa E; Zheng, Zhaohui; Lacey, Simon F; Mahnke, Yolanda D; Melenhorst, Jan J; Rheingold, Susan R; Shen, Angela; Teachey, David T; Levine, Bruce L; June, Carl H; Porter, David L; Grupp, Stephan A

    2014-10-16

    Relapsed acute lymphoblastic leukemia (ALL) is difficult to treat despite the availability of aggressive therapies. Chimeric antigen receptor-modified T cells targeting CD19 may overcome many limitations of conventional therapies and induce remission in patients with refractory disease. We infused autologous T cells transduced with a CD19-directed chimeric antigen receptor (CTL019) lentiviral vector in patients with relapsed or refractory ALL at doses of 0.76×10(6) to 20.6×10(6) CTL019 cells per kilogram of body weight. Patients were monitored for a response, toxic effects, and the expansion and persistence of circulating CTL019 T cells. A total of 30 children and adults received CTL019. Complete remission was achieved in 27 patients (90%), including 2 patients with blinatumomab-refractory disease and 15 who had undergone stem-cell transplantation. CTL019 cells proliferated in vivo and were detectable in the blood, bone marrow, and cerebrospinal fluid of patients who had a response. Sustained remission was achieved with a 6-month event-free survival rate of 67% (95% confidence interval [CI], 51 to 88) and an overall survival rate of 78% (95% CI, 65 to 95). At 6 months, the probability that a patient would have persistence of CTL019 was 68% (95% CI, 50 to 92) and the probability that a patient would have relapse-free B-cell aplasia was 73% (95% CI, 57 to 94). All the patients had the cytokine-release syndrome. Severe cytokine-release syndrome, which developed in 27% of the patients, was associated with a higher disease burden before infusion and was effectively treated with the anti-interleukin-6 receptor antibody tocilizumab. Chimeric antigen receptor-modified T-cell therapy against CD19 was effective in treating relapsed and refractory ALL. CTL019 was associated with a high remission rate, even among patients for whom stem-cell transplantation had failed, and durable remissions up to 24 months were observed. (Funded by Novartis and others; CART19 Clinical

  18. Comparison of different blood sample processing methods for sensitive detection of low level chimerism by RHD real-time PCR assay.

    PubMed

    Javadi, Ahmad; Verduin, Esther P; Brand, Anneke; Schonewille, Henk

    2013-01-01

    The rhesus D blood group, which is expressed on the red blood cells (RBC) of 85% of the Caucasian population, is one of the most immunogenic RBC antigens, inducing D antibody formation in up to 20-80% of D-negative transfusion recipients and about 10% of pregnancies at risk. Pregnancy-induced D-antibodies can persist for many years, but the mechanisms underlying this persistence are unclear. The LOTUS study, a long-term follow-up study of mothers from severely affected children with hemolytic disease of the fetus and newborn investigates, among other endpoints, whether persistent feto-maternal chimerism is associated with long-term maternal anti-D persistence. We questioned which blood sample processing method should be used to detect low levels of RHD chimerism with the highest sensitivity and specificity using qPCR. After optimization of primer and probe concentrations for singleplex RHD exon 5 and 7 qPCR, sensitivity, specificity and efficiency of RHD and DYS1 qPCR were investigated in artificial chimeric samples. Sensitivity of DYS1 was one log higher (0.0001%) in enriched mononuclear cell fractions as compared with whole blood. Comparable linear sensitivity (0.007%) and mean efficiency (84-99%) for RHD qPCR were observed in all samples regardless whether whole blood or pre- or post-mixing of cellular fractions had been used. We conclude that RHD chimerism using singleplex exon 5 and 7 qPCR is linearly detectable down to 1.0 GE, without an advantage of fraction enrichment.

  19. Expression of the leukemia-associated CBF{beta}/SMMHC chimeric gene causes transformation of 3T3 cells

    SciTech Connect

    Hajra, A.; Liu, P.; Collins, E.S.

    1994-09-01

    A pericentric inversion of chromosome 16 (inv(16)(p13;q22)) is consistently seen in acute myeloid leukemia of the M4Eo subtype. This inversion fuses almost the entire coding region of the gene encoding of the {beta} subunit of the heterodimeric transcription factor CBF/PEBP2 to the region of the MYH11 gene encoding the rod domain for the smooth muscle myosin heavy chain (SMMHC). To investigate the biological properties of the CBF{beta}/SMMHC fusion protein, we have generated 3T3 cell lines that stably express the CBF{beta}/SMMHC chimeric cDNA or the normal, nonchimeric CBF{beta} and SMMHC cDNAs. 3T3 cells expressing CBF{beta}/SMMHC acquire a transformed phenotype, as indicated by altered cell morphology, formation of foci, and growth in soft agar. Cells constitutively overexpressing the normal CBF{beta} cDNA or the rod region of SMMHC remain nontransformed. Western blot analysis using antibodies to CBF{beta} and the SMMHC rod demonstrates that stably transfected cells express the appropriate chimeric or normal protein. Electrophoretic mobility shift assays reveal that cells transformed by the chimeric cDNA do not have a CBF-DNA complex of the expected mobility, but instead contain a large complex with CBF DNA-binding activity that fails to migrate out of the gel wells. In order to define the regions of CBF{beta}/SMMHC necessary for 3T3 transformation, we have stably transfected cells with mutant CBF{beta}/SMMHC cDNAs containing various deletions of the coding region. Analysis of these cell lines indicates that the transformation property of CBF{beta}/SMMHC requires regions of CBF{beta} known to be necessary for association with the DNA-binding CBF{alpha} subunit, and also requires an intact SMMHC carboxyl terminus, which is necessary for formation of the coiled coil domain of the myosin rod.

  20. Long-term follow-up of donor chimerism and tolerance after human liver transplantation.

    PubMed

    Ayala, Rosa; Grande, Silvia; Albizua, Enriqueta; Crooke, Almudena; Meneu, Juan Carlos; Moreno, Almudena; Pérez, Baltasar; Gilsanz, Florinda; Moreno, Enrique; Martínez-Lopez, Joaquín

    2009-06-01

    We aimed to quantify peripheral donor chimerism (DC) and to analyze its association with graft and recipient outcome. Forty-two liver transplant recipients and their respective donors were studied, providing a total of 148 posttransplantation serum samples. DC was assessed with real-time quantitative polymerase chain reaction (qPCR) to detect polymorphic markers. DC did not decrease with time post-transplantation and was higher in child recipients versus adults and in recipients of deceased donor liver transplants versus recipients of live donor liver transplants. Higher levels of DC were detected in Rh-positive blood group donors, in O blood group recipients versus A blood group recipients, and in recipients with hepatitis C virus versus recipients with alcoholic cirrhosis. High DC was associated with patients with organ damage due to recurrent disease and rejection. Stable, high levels of DC, in the absence of other major clinical events, may thus be a marker of transplantation tolerance, and this knowledge may help to tailor immunosuppressive treatment. In conclusion, qPCR is a useful technique for DC follow-up in liver transplantation, although the evolution of DC levels should be analyzed in accordance with the clinical outcome of the patient.

  1. The History of Post-Secondary Finance in Alberta - An Analysis

    ERIC Educational Resources Information Center

    Hauserman, Calvin P.; Stick, Sheldon L.

    2005-01-01

    Post-secondary systems throughout Canada and the United States have struggled with funding issues during most of the last decade of the 20th Century, and the new millennium did not open with great enthusiasm for change. This article examines the impact of post-secondary education funding changes in Alberta, Canada, by tracing the historical…

  2. A COMPARATIVE ANALYSIS OF ELECTRONIC CONTENT IN PUBLIC POST-HIGH SCHOOL TECHNICAL INSTITUTES AND ELECTRONICS TECHNOLOGY REQUIREMENTS OF INDUSTRY.

    ERIC Educational Resources Information Center

    VASEK, RICHARD J.

    THE PURPOSE OF THIS STUDY WAS TO ASCERTAIN THE EXTENT TO WHICH POST-HIGH SCHOOL TECHNICAL EDUCATION PROGRAMS, THROUGH ELECTRONICS CONTENT OFFERING, WERE MEETING INDUSTRY'S NEEDS IN ELECTRONICS TECHNOLOGY. A CHECKLIST OF 435 INSTRUCTIONAL UNITS OR ITEMS, PREPARED FROM AN ANALYSIS OF 31 ELECTRONICS BOOKS AND 13 MANUALS USED BY ELECTRONICS TEACHERS,…

  3. Identifying Multimedia Production Competencies and Skills of Instructional Design and Technology Professionals: An Analysis of Recent Job Postings

    ERIC Educational Resources Information Center

    Sugar, William; Hoard, Brent; Brown, Abbie; Daniels, Lee

    2012-01-01

    In an effort to document necessary multimedia production competencies of Instructional Design and Technology graduates, a recent analysis of over 7 months' worth of Instructional Design and Technology job advertisements (n = 615) were conducted. Specific job skills from these postings were categorized and analyzed. The data set includes three job…

  4. Identifying Multimedia Production Competencies and Skills of Instructional Design and Technology Professionals: An Analysis of Recent Job Postings

    ERIC Educational Resources Information Center

    Sugar, William; Hoard, Brent; Brown, Abbie; Daniels, Lee

    2012-01-01

    In an effort to document necessary multimedia production competencies of Instructional Design and Technology graduates, a recent analysis of over 7 months' worth of Instructional Design and Technology job advertisements (n = 615) were conducted. Specific job skills from these postings were categorized and analyzed. The data set includes three job…

  5. An analysis of Social Work Oncology Network Listserv Postings on the Commission of Cancer's distress screening guidelines.

    PubMed

    Burg, Mary Ann; Adorno, Gail; Hidalgo, Jorge

    2012-01-01

    This is a qualitative study of listserv postings by members of the Social Work Oncology Network (SWON) in response to the Commission on Cancer's 2011 guidelines for distress screening of cancer patients. Archived listserv postings for the period of December 2010 to November 2011 were deidentified and a sample was derived by a list of keywords for the analysis. Aims of the study included describing the general categories and themes of the postings devoted to the new distress screening standard and examining the process of facilitation of mutual support and information exchange by oncology social workers in response to the new screening standards. During the 12-month timeframe there were 242 unique listserv postings sampled for the analysis. Oncology social worker (OSW) discussion of the distress screening guidelines remained a constant topic over the 12 months, and major themes that emerged from the data included processes of implementation of distress screening in cancer centers, screening policies and protocols, screening tool choice, and oncology social worker professional identity. The SWON listserv members used the listserv as a mechanism to post their requests for information on screening, to share their experiences in the beginning stages of implementing the guidelines, and to build support for legitimizing oncology social workers as the lead profession in the implementation of the guidelines in member cancer centers.

  6. In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae

    PubMed Central

    Kurotani, Atsushi; Sakurai, Tetsuya

    2015-01-01

    Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups. PMID:26307970

  7. Post-Test Analysis of a 10-Year Sodium Heat Pipe Life Test

    NASA Technical Reports Server (NTRS)

    Rosenfeld, John H.; Locci, Ivan E.; Sanzi, James L.; Hull, David R.; Geng, Steven M.

    2011-01-01

    High-temperature heat pipes are being evaluated for use in energy conversion applications such as fuel cells, gas turbine re-combustors, Stirling cycle heat sources; and with the resurgence of space nuclear power both as reactor heat removal elements and as radiator elements. Long operating life and reliable performance are critical requirements for these applications. Accordingly, long-term materials compatibility is being evaluated through the use of high-temperature life test heat pipes. Thermacore, Inc., has carried out a sodium heat pipe 10-year life test to establish long-term operating reliability. Sodium heat pipes have demonstrated favorable materials compatibility and heat transport characteristics at high operating temperatures in air over long time periods. A representative one-tenth segment Stirling Space Power Converter heat pipe with an Inconel 718 envelope and a stainless steel screen wick has operated for over 87,000 hr (10 years) at nearly 700 C. These life test results have demonstrated the potential for high-temperature heat pipes to serve as reliable energy conversion system components for power applications that require long operating lifetime with high reliability. Detailed design specifications, operating history, and post-test analysis of the heat pipe and sodium working fluid are described. Lessons learned and future life test plans are also discussed.

  8. Comparing pre- and post-copulatory mate competition using social network analysis in wild crickets

    PubMed Central

    Fisher, David N.; Rodríguez-Muñoz, Rolando

    2016-01-01

    Sexual selection results from variation in success at multiple stages in the mating process, including competition before and after mating. The relationship between these forms of competition, such as whether they trade-off or reinforce one another, influences the role of sexual selection in evolution. However, the relationship between these 2 forms of competition is rarely quantified in the wild. We used video cameras to observe competition among male field crickets and their matings in the wild. We characterized pre- and post-copulatory competition as 2 networks of competing individuals. Social network analysis then allowed us to determine 1) the effectiveness of precopulatory competition for avoiding postcopulatory competition, 2) the potential for divergent mating strategies, and 3) whether increased postcopulatory competition reduces the apparent reproductive benefits of male promiscuity. We found 1) limited effectiveness of precopulatory competition for avoiding postcopulatory competition; 2) males do not specifically engage in only 1 type of competition; and 3) promiscuous individuals tend to mate with each other, which will tend to reduce variance in reproductive success in the population and highlights the trade-off inherent in mate guarding. Our results provide novel insights into the works of sexual competition in the wild. Furthermore, our study demonstrates the utility of using network analyses to study competitive interactions, even in species lacking obvious social structure. PMID:27174599

  9. Comparing pre- and post-copulatory mate competition using social network analysis in wild crickets.

    PubMed

    Fisher, David N; Rodríguez-Muñoz, Rolando; Tregenza, Tom

    2016-01-01

    Sexual selection results from variation in success at multiple stages in the mating process, including competition before and after mating. The relationship between these forms of competition, such as whether they trade-off or reinforce one another, influences the role of sexual selection in evolution. However, the relationship between these 2 forms of competition is rarely quantified in the wild. We used video cameras to observe competition among male field crickets and their matings in the wild. We characterized pre- and post-copulatory competition as 2 networks of competing individuals. Social network analysis then allowed us to determine 1) the effectiveness of precopulatory competition for avoiding postcopulatory competition, 2) the potential for divergent mating strategies, and 3) whether increased postcopulatory competition reduces the apparent reproductive benefits of male promiscuity. We found 1) limited effectiveness of precopulatory competition for avoiding postcopulatory competition; 2) males do not specifically engage in only 1 type of competition; and 3) promiscuous individuals tend to mate with each other, which will tend to reduce variance in reproductive success in the population and highlights the trade-off inherent in mate guarding. Our results provide novel insights into the works of sexual competition in the wild. Furthermore, our study demonstrates the utility of using network analyses to study competitive interactions, even in species lacking obvious social structure.

  10. Liquid chromatographic analysis of aflatoxin using post-column photochemical derivatization: collaborative study.

    PubMed

    Waltking, Arthur E; Wilson, David

    2006-01-01

    Aflatoxin analysis, with post-column derivatization using a photochemical reactor for enhanced detection (PHRED) system for derivatization, has been compared to the officially recognized iodine and Kobra cell derivatization systems. This photochemical system has been extensively used for screening peanuts by some U.S. Department of Agriculture laboratories for many years. From their periodic method checks, using standard spiked samples, an 80 sample series with each of the 3 derivatization methods was statistically analyzed. Paired comparisons, using the same sample extract, were also made between the PHRED and one of the other 2 methods, among laboratories in 4 different countries, on a variety of naturally contaminated commodity products. The differences between the techniques were not significant for peanuts, but for corn the photochemical system consistently gave slightly higher values for aflatoxins B1 and B2 than the Kobra cell method. However, a comparison of all sample results showed no significant differences between methods. The Pearson correlation coefficients for aflatoxin B1 in 102 test samples and aflatoxin B2 in 94 test samples were 0.9994 and 0.9874, respectively. The probability factor was P < 0.0001, and the t-tests were not significantly different except for the corn. These indicated that the PHRED system is equivalent to the iodine and Kobra cell methods for peanuts relative to the current official procedures, but the PHRED system has a slightly high bias for corn compared to the iodine and Kobra cell systems.

  11. Post-test thermomechanical calculations and preliminary data analysis for the Spent Fuel Test: Climax

    SciTech Connect

    Butkovich, T.R.; Patrick, W.C.

    1985-09-01

    The Spent Fuel Test - Climax (SFT-C) was conducted to evaluate the feasibility of retrievable deep geologic storage of commercially generated, spent nuclear-reactor fuel assemblies. Thermomechanical response of the SFT-C was calculated before the test began using the finite-element structural analysis code ADINA and its companion heat transfer code ADINAT. While we found that the level of agreement between measured and calculated rock displacements was quite good, we needed to revise certain aspects of the heat transfer calculation, material properties, and in situ stresses to incorporate information obtained during and after the heated phase of the test. The post-test calculations reported here were performed using the best available input parameters, thermal and mechanical properties, and power levels that were directly measured or inferred from measurements made during the test. This report documents the results of these calculations and compares those results with selected measurements made during the 3-year heating phase and 6-month cooling phase of the SFT-C.

  12. Bioinformatic Analysis and Post-Translational Modification Crosstalk Prediction of Lysine Acetylation

    PubMed Central

    Lu, Zhike; Cheng, Zhongyi; Zhao, Yingming; Volchenboum, Samuel L.

    2011-01-01

    Recent proteomics studies suggest high abundance and a much wider role for lysine acetylation (K-Ac) in cellular functions. Nevertheless, cross influence between K-Ac and other post-translational modifications (PTMs) has not been carefully examined. Here, we used a variety of bioinformatics tools to analyze several available K-Ac datasets. Using gene ontology databases, we demonstrate that K-Ac sites are found in all cellular compartments. KEGG analysis indicates that the K-Ac sites are found on proteins responsible for a diverse and wide array of vital cellular functions. Domain structure prediction shows that K-Ac sites are found throughout a wide variety of protein domains, including those in heat shock proteins and those involved in cell cycle functions and DNA repair. Secondary structure prediction proves that K-Ac sites are preferentially found in ordered structures such as alpha helices and beta sheets. Finally, by mutating K-Ac sites in silico and predicting the effect on nearby phosphorylation sites, we demonstrate that the majority of lysine acetylation sites have the potential to impact protein phosphorylation, methylation, and ubiquitination status. Our work validates earlier smaller-scale studies on the acetylome and demonstrates the importance of PTM crosstalk for regulation of cellular function. PMID:22164248

  13. In Silico Analysis of Correlations between Protein Disorder and Post-Translational Modifications in Algae.

    PubMed

    Kurotani, Atsushi; Sakurai, Tetsuya

    2015-08-20

    Recent proteome analyses have reported that intrinsically disordered regions (IDRs) of proteins play important roles in biological processes. In higher plants whose genomes have been sequenced, the correlation between IDRs and post-translational modifications (PTMs) has been reported. The genomes of various eukaryotic algae as common ancestors of plants have also been sequenced. However, no analysis of the relationship to protein properties such as structure and PTMs in algae has been reported. Here, we describe correlations between IDR content and the number of PTM sites for phosphorylation, glycosylation, and ubiquitination, and between IDR content and regions rich in proline, glutamic acid, serine, and threonine (PEST) and transmembrane helices in the sequences of 20 algae proteomes. Phosphorylation, O-glycosylation, ubiquitination, and PEST preferentially occurred in disordered regions. In contrast, transmembrane helices were favored in ordered regions. N-glycosylation tended to occur in ordered regions in most of the studied algae; however, it correlated positively with disordered protein content in diatoms. Additionally, we observed that disordered protein content and the number of PTM sites were significantly increased in the species-specific protein clusters compared to common protein clusters among the algae. Moreover, there were specific relationships between IDRs and PTMs among the algae from different groups.

  14. A targeted change-detection procedure by combining change vector analysis and post-classification approach

    NASA Astrophysics Data System (ADS)

    Ye, Su; Chen, Dongmei; Yu, Jie

    2016-04-01

    In remote sensing, conventional supervised change-detection methods usually require effective training data for multiple change types. This paper introduces a more flexible and efficient procedure that seeks to identify only the changes that users are interested in, here after referred to as ;targeted change detection;. Based on a one-class classifier ;Support Vector Domain Description (SVDD);, a novel algorithm named ;Three-layer SVDD Fusion (TLSF); is developed specially for targeted change detection. The proposed algorithm combines one-class classification generated from change vector maps, as well as before- and after-change images in order to get a more reliable detecting result. In addition, this paper introduces a detailed workflow for implementing this algorithm. This workflow has been applied to two case studies with different practical monitoring objectives: urban expansion and forest fire assessment. The experiment results of these two case studies show that the overall accuracy of our proposed algorithm is superior (Kappa statistics are 86.3% and 87.8% for Case 1 and 2, respectively), compared to applying SVDD to change vector analysis and post-classification comparison.

  15. Direct visual internal urethrotomy for isolated, post-urethroplasty strictures: a retrospective analysis

    PubMed Central

    Brown, Elizabeth Timbrook; Mock, Stephen; Dmochowski, Roger; Reynolds, W. Stuart; Milam, Douglas; Kaufman, Melissa R.

    2016-01-01

    Background: Urethroplasty is often successful for the treatment of male urethral stricture disease, but limited data exists on recurrence management. Our goal was to evaluate direct visual internal urethrotomy (DVIU) as a treatment option for isolated, recurrent strictures after urethroplasty. Methods: We retrospectively identified male patients who underwent urethroplasty from 1999 to 2013 and developed an isolated, recurrent stricture at the urethroplasty site treated with DVIU. Success was defined as lack of symptomatology and no subsequent intervention. Comparative analysis identified characteristics and stricture properties associated with success. Results: A total of 436 urethroplasties were performed in 401 patients at our institution between 1999 and 2013. Stricture recurrence was noted in 64 (16%) patients. Of these, 47 (73%) underwent a DVIU. A total of 37 patients met inclusion criteria and underwent 50 DVIU procedures at the urethroplasty site. A single DVIU was successful in 13 of 37 patients (35%). A total of 4 of 6 patients required a second DVIU (67%). Overall, 17 of 43 (40%) of the total DVIUs were successful after urethroplasty. Success did not differ by age, stricture length or location, surgical technique, radiation history, prior urethroplasty or DVIU, time to failure, or etiology. Conclusions: Post-urethroplasty DVIU for isolated, recurrent strictures may be offered as a minimally invasive treatment option. Approximately 40% of patients were spared further intervention. PMID:28203286

  16. Post-transplantation lymphoproliferative disease of natural killer cell lineage: a clinicopathological and molecular analysis.

    PubMed

    Kwong, Y L; Lam, C C; Chan, T M

    2000-07-01

    Post-transplantation lymphoproliferative disorders (PTLD) occur after solid organ and bone marrow transplantation. They are predominantly of B-cell and occasionally of T-cell lineage. We report a case of PTLD of natural killer (NK) cell lineage. A renal allograft recipient developed progressive pancytopenia 1 year after transplantation. Serial bone marrow biopsies showed an increasing infiltration by large granular lymphoid cells. A subsequent leukaemic phase also developed with systemic infiltration of other organs. Immunophenotyping showed that these cells were CD2+, CD3-, CD3epsilon+, CD56+, CD94+, CD158a- and CD158b-. In situ hybridization showed Epstein-Barr virus (EBV) infection of the neoplastic cells. Genotypical analysis showed the T-cell receptor gene in germline configuration and clonal EBV episomal integration. The overall features were consistent with NK cell lymphoma/leukaemia. The patient did not respond to cessation of immunosuppression or anti-EBV treatment. Combination chemotherapy was given, but the patient died ultimately of disseminated fungal infection. In conclusion, we have demonstrated that NK cell lymphoma is another rare type of PTLD that appears to be highly aggressive and therefore may require early chemotherapy to improve treatment outcome.

  17. Integrated Post-GWAS Analysis Sheds New Light on the Disease Mechanisms of Schizophrenia.

    PubMed

    Lin, Jhih-Rong; Cai, Ying; Zhang, Quanwei; Zhang, Wen; Nogales-Cadenas, Rubén; Zhang, Zhengdong D

    2016-12-01

    Schizophrenia is a severe mental disorder with a large genetic component. Recent genome-wide association studies (GWAS) have identified many schizophrenia-associated common variants. For most of the reported associations, however, the underlying biological mechanisms are not clear. The critical first step for their elucidation is to identify the most likely disease genes as the source of the association signals. Here, we describe a general computational framework of post-GWAS analysis for complex disease gene prioritization. We identify 132 putative schizophrenia risk genes in 76 risk regions spanning 120 schizophrenia-associated common variants, 78 of which have not been recognized as schizophrenia disease genes by previous GWAS. Even more significantly, 29 of them are outside the risk regions, likely under regulation of transcriptional regulatory elements contained therein. These putative schizophrenia risk genes are transcriptionally active in both brain and the immune system, and highly enriched among cellular pathways, consistent with leading pathophysiological hypotheses about the pathogenesis of schizophrenia. With their involvement in distinct biological processes, these putative schizophrenia risk genes, with different association strengths, show distinctive temporal expression patterns, and play specific biological roles during brain development. Copyright © 2016 by the Genetics Society of America.

  18. Impact of endotracheal intubation on septic shock outcome: A post hoc analysis of the SEPSISPAM trial.

    PubMed

    Delbove, Agathe; Darreau, Cédric; Hamel, Jean François; Asfar, Pierre; Lerolle, Nicolas

    2015-12-01

    The objective of the study to is to determine the characteristics associated with endotracheal intubation in septic shock patients. This is a post hoc analysis of the database of the SEPSISPAM study, including patients with septic shock. Among the 776 patients, 633 (82%) were intubated within 12 hours of study inclusion (early intubation), 113 (15%) were never intubated, and 30 (4%) had delayed intubation. Intensive care units (ICUs) were classified according to frequency of early intubation: early intubation less than 80% of patients (lowest frequency: 7 ICUs, 254 patients), 80% to 90% (middle frequency: 5 ICUs, 170 patients), and greater than 90% (highest frequency: 6 ICUs, 297 patients). Type of ICU, pulmonary infection, lactate greater than 2 mmol/L, lower Pao2/fraction of inspired oxygen ratio, lower Glasgow score, and absence of immunosuppression were independently associated with early intubation. Patients never intubated had a lower initial severity and a low mortality rate. In comparison to patients intubated early, patients with delayed intubation had had fewer days alive without organ support by day 28. Intensive care units with the highest frequency of early intubation had a higher mortality rate in comparison to ICUs with middle frequency of early intubation. A nonsignificant increased mortality was observed in ICU with lowest frequency of early intubation. Practices regarding the place of endotracheal intubation in septic shock may impact outcome. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Stress generated by customized glass fiber posts and other types by photoelastic analysis.

    PubMed

    Bosso, Kátia; Gonini Júnior, Alcides; Guiraldo, Ricardo Danil; Berger, Sandrine Bittencourt; Lopes, Murilo Baena

    2015-01-01

    Endodontic posts are necessary to provide adequate retention and support when no sufficient remaining structure is available to retain the core. There are different materials and techniques to construct post-and-core, but there is no consensus about which one promotes better stress distribution on the remaining tooth structure. This study aimed to quantify and evaluate the distribution of stress in the root produced by customized glass fiber posts compared to different endodontic posts. Twenty-five simulated roots from photoelastic resin were made and divided into 5 groups: CPC, cast post-and-core; SP, screw post; CF, carbon fiber post; GF, glass fiber post; and CGF, customized glass fiber post. After cementing CPC and SP posts with zinc phosphate cement, and CF, GF and CGF posts with resin cement, resin cores were made for groups 2-5. Specimens were evaluated with vertical or 45° oblique loading. To analyze the fringes, the root was divided into 6 parts: palatal cervical, palatal middle, palatal apical, vestibular cervical, vestibular middle, and vestibular apical. The formed fringes were photographed and quantified. Data were recorded and subjected to two-way ANOVA and Tukey's test (5%). SP (1.95±0.60) showed higher stress (p<0.05) compared to the others (CPC-0.52±0.74; CF-0.50±0.75, GF-0.23±0.48 and CGF-0.45±0.83). All posts showed high stress in apical third (CPC-1.40±0.65; SP-2.30±0.44, CF-1.80±0.45, GF-1.20±0.45, CGF-1.70±1.03) Low stress was found in cervical third (CPC-0.20±0.45; CF-0.00±0.00, GF-0.00±0.00, CGF-0.00±0.00), except by SP (1.90±0.65), which showed statistical difference (p<0.05). Customized post showed high stress concentration at the root and conventional glass fiber posts showed more favorable biomechanical behavior.

  20. Chimeric Antigen Receptors Modified T-Cells for Cancer Therapy

    PubMed Central

    Dai, Hanren; Wang, Yao; Lu, Xuechun

    2016-01-01

    The genetic modification and characterization of T-cells with chimeric antigen receptors (CARs) allow functionally distinct T-cell subsets to recognize specific tumor cells. The incorporation of costimulatory molecules or cytokines can enable engineered T-cells to eliminate tumor cells. CARs are generated by fusing the antigen-binding region of a monoclonal antibody (mAb) or other ligand to membrane-spanning and intracellular-signaling domains. They have recently shown clinical benefit in patients treated with CD19-directed autologous T-cells. Recent successes suggest that the modification of T-cells with CARs could be a powerful approach for developing safe and effective cancer therapeutics. Here, we briefly review early studies, consider strategies to improve the therapeutic potential and safety, and discuss the challenges and future prospects for CAR T-cells in cancer therapy. PMID:26819347

  1. Humanized chimeric mouse models of hepatitis B virus infection.

    PubMed

    Sun, Suwan; Li, Jun

    2017-06-01

    Hepatitis B virus (HBV) infection is associated with an increased risk of hepatic cirrhosis, hepatocellular carcinoma, fulminant hepatitis and end-stage hepatic failure. Despite the availability of anti-HBV therapies, HBV infection remains a major global public health problem. Developing an ideal animal model of HBV infection to clarify the details of the HBV replication process, the viral life cycle, the resulting immunoresponse and the precise pathogenesis of HBV is difficult because HBV has an extremely narrow host range and almost exclusively infects humans. In this review, we summarize and evaluate animal models available for studying HBV infection, especially focusing on humanized chimeric mouse models, and we discuss future development trends regarding immunocompetent humanized mouse models that can delineate the natural history and immunopathophysiology of HBV infection. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  2. Chimeric Antigen Receptors Modified T-Cells for Cancer Therapy.

    PubMed

    Dai, Hanren; Wang, Yao; Lu, Xuechun; Han, Weidong

    2016-07-01

    The genetic modification and characterization of T-cells with chimeric antigen receptors (CARs) allow functionally distinct T-cell subsets to recognize specific tumor cells. The incorporation of costimulatory molecules or cytokines can enable engineered T-cells to eliminate tumor cells. CARs are generated by fusing the antigen-binding region of a monoclonal antibody (mAb) or other ligand to membrane-spanning and intracellular-signaling domains. They have recently shown clinical benefit in patients treated with CD19-directed autologous T-cells. Recent successes suggest that the modification of T-cells with CARs could be a powerful approach for developing safe and effective cancer therapeutics. Here, we briefly review early studies, consider strategies to improve the therapeutic potential and safety, and discuss the challenges and future prospects for CAR T-cells in cancer therapy.

  3. The pharmacology of second-generation chimeric antigen receptors.

    PubMed

    van der Stegen, Sjoukje J C; Hamieh, Mohamad; Sadelain, Michel

    2015-07-01

    Second-generation chimeric antigen receptors (CARs) retarget and reprogramme T cells to augment their antitumour efficacy. The combined activating and co-stimulatory domains incorporated in these CARs critically determine the function, differentiation, metabolism and persistence of engineered T cells. CD19-targeted CARs that incorporate CD28 or 4-1BB signalling domains are the best known to date. Both have shown remarkable complete remission rates in patients with refractory B cell malignancies. Recent data indicate that CD28-based CARs direct a brisk proliferative response and boost effector functions, whereas 4-1BB-based CARs induce a more progressive T cell accumulation that may compensate for less immediate potency. These distinct kinetic features can be exploited to further develop CAR-based T cell therapies for a variety of cancers. A new field of immunopharmacology is emerging.

  4. Chimeric Antigen Receptor T Cell Therapy in Hematology.

    PubMed

    Ataca, Pınar; Arslan, Önder

    2015-12-01

    It is well demonstrated that the immune system can control and eliminate cancer cells. Immune-mediated elimination of tumor cells has been discovered and is the basis of both cancer vaccines and cellular therapies including hematopoietic stem cell transplantation. Adoptive T cell transfer has been improved to be more specific and potent and to cause less off-target toxicity. Currently, there are two forms of engineered T cells being tested in clinical trials: T cell receptor (TCR) and chimeric antigen receptor (CAR) modified T cells. On 1 July 2014, the United States Food and Drug Administration granted 'breakthrough therapy' designation to anti-CD19 CAR T cell therapy. Many studies were conducted to evaluate the benefits of this exciting and potent new treatment modality. This review summarizes the history of adoptive immunotherapy, adoptive immunotherapy using CARs, the CAR manufacturing process, preclinical and clinical studies, and the effectiveness and drawbacks of this strategy.

  5. Chimeric antigen receptor T-cell therapy for ALL.

    PubMed

    Maude, Shannon L; Shpall, Elizabeth J; Grupp, Stephan A

    2014-12-05

    Relapsed and refractory leukemias pose substantial challenges in both children and adults, with very little progress being made in more than a decade. Targeted immunotherapy using chimeric antigen receptor (CAR)-modified T cells has emerged as a potent therapy with an innovative mechanism. Dramatic clinical responses with complete remission rates as high as 90% have been reported using CAR-modified T cells directed against the B-cell-specific antigen CD19 in patients with relapsed/refractory acute lymphoblastic leukemia. Supraphysiologic T-cell proliferation, a hallmark of this therapy, contributes to both efficacy and the most notable toxicity, cytokine release syndrome, posing a unique challenge for toxicity management. Further studies are necessary to identify additional targets, standardize approaches to cytokine release syndrome management, and determine the durability of remissions. © 2014 by The American Society of Hematology. All rights reserved.

  6. How Chimeric Antigen Receptor Design Affects Adoptive T Cell Therapy.

    PubMed

    Gacerez, Albert T; Arellano, Benjamine; Sentman, Charles L

    2016-12-01

    Chimeric antigen receptor (CAR) T cells have been developed to treat tumors and have shown great success against B cell malignancies. Exploiting modular designs and swappable domains, CARs can target an array of cell surface antigens and, upon receptor-ligand interactions, direct signaling cascades, thereby driving T cell effector functions. CARs have been designed using receptors, ligands, or scFv binding domains. Different regions of a CAR have each been found to play a role in determining the overall efficacy of CAR T cells. Therefore, this review provides an overview of CAR construction and common designs. Each CAR region is discussed in the context of its importance to a CAR's function. Additionally, the review explores how various engineering strategies have been applied to CAR T cells in order to regulate CAR T cell function and activity. J. Cell. Physiol. 231: 2590-2598, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. [Raman spectroscopic analysis of post-cement-root canal dentin interface].

    PubMed

    Li, Zhen-Chun; Wu, Xuan; Chen, Xiao-Dong; Ma, Hong-Mei; Hao, Feng-Yu

    2007-06-01

    To examine the compositions of those adhesion modes between luting cements and canal dentin, and to evaluate the dentin-cement-post interface by Laser-Ranian spectroscopy. Three representative luting cements (zinc phosphate, glass ionomer and resin cements), two kinds of prefabricated posts (titanium and fiber-glass), six extracted intact human maxillary anterior teeth were used canal dentin after endodontic treatment. Laser-Raman spectroscopy measure of cement, post and canal dentin before and after luting together. There are no evident Raman spectra change cross the ZPC/dentin interface and glass ionomer/dentin interface, while cross the resin/dentin interface and resin/glass fiber post interface can be seen special Raman spectra. Laser-Raman microspectroscopy is a useful analytical technique for evaluation interface between dentin and luting cements. Resin cement may interact with dentin and glass fiber post.

  8. Modeling cognition and disease using human glial chimeric mice.

    PubMed

    Goldman, Steven A; Nedergaard, Maiken; Windrem, Martha S

    2015-08-01

    As new methods for producing and isolating human glial progenitor cells (hGPCs) have been developed, the disorders of myelin have become especially compelling targets for cell-based therapy. Yet as animal modeling of glial progenitor cell-based therapies has progressed, it has become clear that transplanted hGPCs not only engraft and expand within murine hosts, but dynamically outcompete the resident progenitors so as to ultimately dominate the host brain. The engrafted human progenitor cells proceed to generate parenchymal astrocytes, and when faced with a hypomyelinated environment, oligodendrocytes as well. As a result, the recipient brains may become inexorably humanized with regards to their resident glial populations, yielding human glial chimeric mouse brains. These brains provide us a fundamentally new tool by which to assess the species-specific attributes of glia in modulating human cognition and information processing. In addition, the cellular humanization of these brains permits their use in studying glial infectious and inflammatory disorders unique to humans, and the effects of those disorders on the glial contributions to cognition. Perhaps most intriguingly, by pairing our ability to construct human glial chimeras with the production of patient-specific hGPCs derived from pluripotential stem cells, we may now establish mice in which a substantial proportion of resident glia are both human and disease-derived. These mice in particular may provide us new opportunities for studying the human-specific contributions of glia to psychopathology, as well as to higher cognition. As such, the assessment of human glial chimeric mice may provide us new insight into the species-specific contributions of glia to human cognitive evolution, as well as to the pathogenesis of human neurological and neuropsychiatric disease.

  9. Chimeric elk/mouse prion proteins in transgenic mice.

    PubMed

    Tamgüney, Gültekin; Giles, Kurt; Oehler, Abby; Johnson, Natrina L; DeArmond, Stephen J; Prusiner, Stanley B

    2013-02-01

    Chronic wasting disease (CWD) of deer and elk is a highly communicable neurodegenerative disorder caused by prions. Investigations of CWD are hampered by slow bioassays in transgenic (Tg) mice. Towards the development of Tg mice that will be more susceptible to CWD prions, we created a series of chimeric elk/mouse transgenes that encode the N terminus of elk PrP (ElkPrP) up to residue Y168 and the C terminus of mouse PrP (MoPrP) beyond residue 169 (mouse numbering), designated Elk3M(SNIVVK). Between codons 169 and 219, six residues distinguish ElkPrP from MoPrP: N169S, T173N, V183I, I202V, I214V and R219K. Using chimeric elk/mouse PrP constructs, we generated 12 Tg mouse lines and determined incubation times after intracerebral inoculation with the mouse-passaged RML scrapie or Elk1P CWD prions. Unexpectedly, one Tg mouse line expressing Elk3M(SNIVVK) exhibited incubation times of <70 days when inoculated with RML prions; a second line had incubation times of <90 days. In contrast, mice expressing full-length ElkPrP had incubation periods of >250 days for RML prions. Tg(Elk3M,SNIVVK) mice were less susceptible to CWD prions than Tg(ElkPrP) mice. Changing three C-terminal mouse residues (202, 214 and 219) to those of elk doubled the incubation time for mouse RML prions and rendered the mice resistant to Elk1P CWD prions. Mutating an additional two residues from mouse to elk at codons 169 and 173 increased the incubation times for mouse prions to >300 days, but made the mice susceptible to CWD prions. Our findings highlight the role of C-terminal residues in PrP that control the susceptibility and replication of prions.

  10. Chimeric elk/mouse prion proteins in transgenic mice

    PubMed Central

    Tamgüney, Gültekin; Giles, Kurt; Oehler, Abby; Johnson, Natrina L.; DeArmond, Stephen J.

    2013-01-01

    Chronic wasting disease (CWD) of deer and elk is a highly communicable neurodegenerative disorder caused by prions. Investigations of CWD are hampered by slow bioassays in transgenic (Tg) mice. Towards the development of Tg mice that will be more susceptible to CWD prions, we created a series of chimeric elk/mouse transgenes that encode the N terminus of elk PrP (ElkPrP) up to residue Y168 and the C terminus of mouse PrP (MoPrP) beyond residue 169 (mouse numbering), designated Elk3M(SNIVVK). Between codons 169 and 219, six residues distinguish ElkPrP from MoPrP: N169S, T173N, V183I, I202V, I214V and R219K. Using chimeric elk/mouse PrP constructs, we generated 12 Tg mouse lines and determined incubation times after intracerebral inoculation with the mouse-passaged RML scrapie or Elk1P CWD prions. Unexpectedly, one Tg mouse line expressing Elk3M(SNIVVK) exhibited incubation times of <70 days when inoculated with RML prions; a second line had incubation times of <90 days. In contrast, mice expressing full-length ElkPrP had incubation periods of >250 days for RML prions. Tg(Elk3M,SNIVVK) mice were less susceptible to CWD prions than Tg(ElkPrP) mice. Changing three C-terminal mouse residues (202, 214 and 219) to those of elk doubled the incubation time for mouse RML prions and rendered the mice resistant to Elk1P CWD prions. Mutating an additional two residues from mouse to elk at codons 169 and 173 increased the incubation times for mouse prions to >300 days, but made the mice susceptible to CWD prions. Our findings highlight the role of C-terminal residues in PrP that control the susceptibility and replication of prions. PMID:23100369

  11. Pooled assembly of marine metagenomic datasets: enriching annotation through chimerism.

    PubMed

    Magasin, Jonathan D; Gerloff, Dietlind L

    2015-02-01

    Despite advances in high-throughput sequencing, marine metagenomic samples remain largely opaque. A typical sample contains billions of microbial organisms from thousands of genomes and quadrillions of DNA base pairs. Its derived metagenomic dataset underrepresents this complexity by orders of magnitude because of the sparseness and shortness of sequencing reads. Read shortness and sequencing errors pose a major challenge to accurate species and functional annotation. This includes distinguishing known from novel species. Often the majority of reads cannot be annotated and thus cannot help our interpretation of the sample. Here, we demonstrate quantitatively how careful assembly of marine metagenomic reads within, but also across, datasets can alleviate this problem. For 10 simulated datasets, each with species complexity modeled on a real counterpart, chimerism remained within the same species for most contigs (97%). For 42 real pyrosequencing ('454') datasets, assembly increased the proportion of annotated reads, and even more so when datasets were pooled, by on average 1.6% (max 6.6%) for species, 9.0% (max 28.7%) for Pfam protein domains and 9.4% (max 22.9%) for PANTHER gene families. Our results outline exciting prospects for data sharing in the metagenomics community. While chimeric sequences should be avoided in other areas of metagenomics (e.g. biodiversity analyses), conservative pooled assembly is advantageous for annotation specificity and sensitivity. Intriguingly, our experiment also found potential prospects for (low-cost) discovery of new species in 'old' data. dgerloff@ffame.org Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  12. Speech coding strategies and revised cochlear implant candidacy: an analysis of post-implant performance.

    PubMed

    David, Eytan E; Ostroff, Jodi M; Shipp, David; Nedzelski, Julian M; Chen, Joseph M; Parnes, Lorne S; Zimmerman, Kim; Schramm, David; Seguin, Christiane

    2003-03-01

    Technological advances in cochlear implant systems on which a sequence of speech coding strategies have been implemented seem to have resulted in improved speech perception. However, changing selection criteria for implantation have coincided with evolving technology and may confound post-implantation speech perception performance. This study compares speech coding strategy with speech perception performance in severe and profound postlingually deafened adults using one of three successive generations of Nucleus Cochlear Implant speech processors (i.e., Mini Speech Processor, Spectra 22, and SPrint) implementing three speech coding strategies (i.e., MPEAK, SPEAK, and Advanced Combination Encoders; Cochlear Corporation, Englewood, CO, U.S.A.). Four cohorts of patients were retrospectively reviewed. Multicenter, tertiary referral cochlear implant programs in Ontario, Canada. Four cohorts of patients (n = 139) were identified based on preimplant audiological measures, duration of deafness, device type, and speech coding strategy. Word and sentence recognition scores at 12 months after implantation were compared using MPEAK with SPEAK22 implemented on the Nucleus 22 speech processors (Mini Speech Processor and Spectra22, respectively) and SPEAK24 as well as Advanced Combination Encoders implemented on the Nucleus 24 SPrint processor. Open-set speech recognition batteries revealed significant improvements in word and sentence scores as advancing technology implemented new speech coding strategies. Subgroup analysis of profoundly deafened patients supported this. Analysis of covariance confirmed that the measured differences could not be accounted for by changing selection criteria for implantation. Improvements in performance can be attributed to evolving speech coding strategies and speech processors rather than to differences in preimplant candidacy.

  13. Hydraulic analysis of river training cross-vanes as part of post-restoration monitoring

    NASA Astrophysics Data System (ADS)

    Endreny, T. A.; Soulman, M. M.

    2011-07-01

    River restoration design methods are incrementally improved by studying and learning from monitoring data in previous projects. In this paper we report post-restoration monitoring data and simulation analysis for a Natural Channel Design (NCD) restoration project along 1600 m of the Batavia Kill (14 km2 watershed) in the Catskill Mountains, NY. The restoration project was completed in 2002 with goals to reduce bank erosion and determine the efficacy of NCD approaches for restoring headwater streams in the Catskill Mountains, NY. The NCD approach used a reference-reach to determine channel form, empirical relations between the project site and reference site bankfull dimensions to size channel geometry, and hydraulic and sediment computations based on a bankfull (1.3 yr return interval) discharge to test channel capacity and sediment stability. The NCD project included 12 cross-vanes and 48 j-hook vanes as river training structures along 19 meander bends to protect against bank erosion and maintain scour pools for fish habitat. Monitoring data collected from 2002 to 2004 were used to identify aggradation of pools in meander bends and below some structures. Aggradation in pools was attributed to the meandering riffle-pool channel trending toward step-pool morphology and cross-vane arms not concentrating flow in the center of the channel. The aggradation subsequently caused flow splitting and 4 partial point bar avulsions during a spring 2005 flood with a 25-yr return interval. Processing the pre-flood monitoring data with hydraulic analysis software provided clues the reach was unstable and preventative maintenance was needed. River restoration and monitoring teams should be trained in robust hydraulic analytical methods that help them extend project restoration goals and structure stability.

  14. The aetiology of post-traumatic stress following childbirth: a meta-analysis and theoretical framework.

    PubMed

    Ayers, S; Bond, R; Bertullies, S; Wijma, K

    2016-04-01

    There is evidence that 3.17% of women report post-traumatic stress disorder (PTSD) after childbirth. This meta-analysis synthesizes research on vulnerability and risk factors for birth-related PTSD and refines a diathesis-stress model of its aetiology. Systematic searches were carried out on PsycINFO, PubMed, Scopus and Web of Science using PTSD terms crossed with childbirth terms. Studies were included if they reported primary research that examined factors associated with birth-related PTSD measured at least 1 month after birth. In all, 50 studies (n = 21 429) from 15 countries fulfilled inclusion criteria. Pre-birth vulnerability factors most strongly associated with PTSD were depression in pregnancy (r = 0.51), fear of childbirth (r = 0.41), poor health or complications in pregnancy (r = 0.38), and a history of PTSD (r = 0.39) and counselling for pregnancy or birth (r = 0.32). Risk factors in birth most strongly associated with PTSD were negative subjective birth experiences (r = 0.59), having an operative birth (assisted vaginal or caesarean, r = 0.48), lack of support (r = -0.38) and dissociation (r = 0.32). After birth, PTSD was associated with poor coping and stress (r = 0.30), and was highly co-morbid with depression (r = 0.60). Moderator analyses showed that the effect of poor health or complications in pregnancy was more apparent in high-risk samples. The results of this meta-analysis are used to update a diathesis-stress model of the aetiology of postpartum PTSD and can be used to inform screening, prevention and intervention in maternity care.

  15. Post-Messinian evolution of the Florence Ridge area (Western Cyprus Arc), Part I: Morphostructural analysis

    NASA Astrophysics Data System (ADS)

    Sellier, N. C.; Loncke, L.; Vendeville, B. C.; Mascle, J.; Zitter, T.; Woodside, J.; Loubrieu, B.

    2013-04-01

    The Florence Ridge, part of the western Cyprus arc, is a compressional relief that was eroded during the Messinian salinity crisis while deposition of salt occurred North (Antalya basin) and South (Herodotus abyssal plain). In order to better assess the impact of salt-tectonics in the Florence Ridge region deformations, we conducted a morpho-structural analysis of available multibeam and seismic data (Simed and Prismed II campaigns). It is indeed a crucial issue to distinguish crustal and gravity driven structures in the compressional to strike-slip belts of the eastern Mediterranean. Along the Antalya basin, we mainly observed multi-directional tectonic rafts typical of gravity gliding above salt. On the Florence Ridge itself, the base of salt evolves laterally to a Messinian erosional surface that erodes a series of stacked nappes. This surface is involved in recent faulting. South of the Florence Ridge, a nearly 100 km wide fold belt characterizes the Herodotus abyssal plain. Three different zones parallel to the Florence Ridge appear within this fold belt. Those are respectively from North to South zones A, B and C. Zone A is characterized mainly by small-wavelength folding and faulting. Approaching Zone B, a long extensional graben deforms the seafloor. Zone B stands ~ 100 to 200 m higher than zones A and C. There, salt welding seems common. In the easternmost zone B deep sub-circular bathymetric depressions are associated with extremely thick and fan-shaped depocenters probably emplaced in relation with active sub-salt thrusts. Many evidences suggest post-Messinian uplift in this zone. Zone C shows medium to high wavelength salt-cored folds. Wavelength of those folds increase approaching the distal Nile deep-sea fan. Within zone C, a nearly undeformed domain exists approaching the Eratosthenes seamount. 'En echelon' folds bound this flat domain suggesting lateral salt extrusion at the junction between zone C and the distal Nile deep-sea fan. To conclude

  16. Gas-phase detection of solid-state fission product complexes for post-detonation nuclear forensic analysis.

    PubMed

    Stratz, S Adam; Jones, Steven A; Oldham, Colton J; Mullen, Austin D; Jones, Ashlyn V; Auxier, John D; Hall, Howard L

    2016-01-01

    This study presents the first known detection of fission products commonly found in post-detonation nuclear debris samples using solid sample introduction and a uniquely coupled gas chromatography inductively-coupled plasma time-of-flight mass spectrometer. Rare earth oxides were chemically altered to incorporate a ligand that enhances the volatility of the samples. These samples were injected (as solids) into the aforementioned instrument and detected for the first time. Repeatable results indicate the validity of the methodology, and this capability, when refined, will prove to be a valuable asset for rapid post-detonation nuclear forensic analysis.

  17. Dualism of mixed chimerism between hematopoiesis and stroma in chronic idiopathic myelofibrosis after allogeneic stem cell transplantation.

    PubMed

    Thiele, J; Varus, E; Siebolts, U; Kvasnicka, H M; Wickenhauser, C; Metz, K A; Beelen, D W; Ditschkowski, M; Zander, A; Kröger, N

    2007-04-01

    Scant knowledge exists concerning lineage-restricted mixed chimerism (mCh) after allogeneic peripheral blood stem cell transplantation (PSCT) in patients with chronic idiopathic myelofibrosis (CIMF). Following a sex-mismatched PSCT, a combined immunopheno- and genotyping by fluorescence in-situ hybridization (FISH) was performed on sequential bone marrow (BM) biopsies at standardized intervals. Results were compared with PCR analysis of corresponding peripheral blood samples in five patients. According to FISH, pretransplant specimens revealed a gender congruence of more than 99%, while in the first three months the total BM exhibited a persistent fraction of host cells (30% to 40%) with a tendency to decline after about one year. It is noteworthy that the majority of endothelial cells maintained a recipient origin, whereas CD34+ progenitors and especially CD61+ megakaryocytes exhibited only very few host-derived cells. In keeping with the prevalence of donor cells in the hematopoietic compartment, PCR analysis of peripheral blood cells displayed a non-significant degree of mCh. In conclusion, according to FISH and PCR analysis, successful PSCT in CIMF results in an almost complete chimeric (donor-derived) state of the hematopoietic cell population. The non-transplantable stromal compartment includes the vascular endothelium with a predominance of recipient cells. The minimal mCh of this population implies probably a donor-derived origin (endothelial progenitor cells).

  18. Sex Differences in Hookah-Related Images Posted on Tumblr: A Content Analysis.

    PubMed

    Primack, Brian A; Carroll, Mary V; Shensa, Ariel; Davis, Wesley; Levine, Michele D

    2016-01-01

    Hookah tobacco smoking is prevalent, widespread, and associated with large amounts of toxicants. Hookah tobacco smoking may be viewed differently by males and females. For example, females have been drawn to types of tobacco that are flavored, milder, and marketed as more social and exotic. Individuals often use the growing segment of anonymous social networking sites, such as Tumblr, to learn about potentially dangerous or harmful behaviors. We used a systematic process involving stratification by time of day, day of week, and search term to gather a sample of 140 Tumblr posts related to hookah tobacco smoking. After a structured codebook development process, 2 coders independently assessed all posts in their entirety, and all disagreements were easily adjudicated. When data on poster sex and age were available, we found that 77% of posts were posted by females and 35% were posted by individuals younger than 18. The most prominent features displayed in all posts were references to or images of hookahs themselves, sexuality, socializing, alcohol, hookah smoke, and tricks performed with hookah smoke. Compared with females, males more frequently posted images of hookahs and alcohol-related images or references. This information may help guide future research in this area and the development of targeted interventions to curb this behavior.

  19. Evidence for Anger Saliency during the Recognition of Chimeric Facial Expressions of Emotions in Underage Ebola Survivors.

    PubMed

    Ardizzi, Martina; Evangelista, Valentina; Ferroni, Francesca; Umiltà, Maria A; Ravera, Roberto; Gallese, Vittorio

    2017-01-01

    One of the crucial features defining basic emotions and their prototypical facial expressions is their value for survival. Childhood traumatic experiences affect the effective recognition of facial expressions of negative emotions, normally allowing the recruitment of adequate behavioral responses to environmental threats. Specifically, anger becomes an extraordinarily salient stimulus unbalancing victims' recognition of negative emotions. Despite the plethora of studies on this topic, to date, it is not clear whether this phenomenon reflects an overall response tendency toward anger recognition or a selective proneness to the salience of specific facial expressive cues of anger after trauma exposure. To address this issue, a group of underage Sierra Leonean Ebola virus disease survivors (mean age 15.40 years, SE 0.35; years of schooling 8.8 years, SE 0.46; 14 males) and a control group (mean age 14.55, SE 0.30; years of schooling 8.07 years, SE 0.30, 15 males) performed a forced-choice chimeric facial expressions recognition task. The chimeric facial expressions were obtained pairing upper and lower half faces of two different negative emotions (selected from anger, fear and sadness for a total of six different combinations). Overall, results showed that upper facial expressive cues were more salient than lower facial expressive cues.