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Sample records for cell cycle-dependent variations

  1. Cell-Cycle-Dependent Variations in the FTIR Spectroscopy of HeLa Cells Treated with Trichostatin A

    Institute of Scientific and Technical Information of China (English)

    ZHANG Feng-qiu; QI Jian; YANG Zhan-guo

    2011-01-01

    It is quite complex to evaluate the mechanism of action for antitumor drugs on cancer cells.Studies have pointed out that there is an unique advantage of Fourier transform infrared spectrum to obtain a fingerprint of all molecules present in the cells when cancer cells were exposed to anti-cancer drugs.Trichostatin A (TSA) is a most potent reversible inhibitor of mammalian histone deacetylases.It can inhibit cancer cell growth in vitro and in vivo.In the present study,HeLa cells were exposed to 0,50,100,200,300 and 400 nmol · L-1 TSA,and FTIR spectra were applied to evaluate the effect of TSA on cancer cells.Results show that there is some significant relationship between the changes in FTIR absorption and cell cycle arresting.On the other hand,this investigation shows that the concentration of TSA had to be more than 200 nmol · L-1 in order to ensure A1080 cm-1/A1540cm-1 ≥1 for inhibiting cell proliferation.

  2. Cell cycle-dependent microtubule-based dynamic transport of cytoplasmic dynein in mammalian cells.

    Directory of Open Access Journals (Sweden)

    Takuya Kobayashi

    Full Text Available BACKGROUND: Cytoplasmic dynein complex is a large multi-subunit microtubule (MT-associated molecular motor involved in various cellular functions including organelle positioning, vesicle transport and cell division. However, regulatory mechanism of the cell-cycle dependent distribution of dynein has not fully been understood. METHODOLOGY/PRINCIPAL FINDINGS: Here we report live-cell imaging of cytoplasmic dynein in HeLa cells, by expressing multifunctional green fluorescent protein (mfGFP-tagged 74-kDa intermediate chain (IC74. IC74-mfGFP was successfully incorporated into functional dynein complex. In interphase, dynein moved bi-directionally along with MTs, which might carry cargos such as transport vesicles. A substantial fraction of dynein moved toward cell periphery together with EB1, a member of MT plus end-tracking proteins (+TIPs, suggesting +TIPs-mediated transport of dynein. In late-interphase and prophase, dynein was localized at the centrosomes and the radial MT array. In prometaphase and metaphase, dynein was localized at spindle MTs where it frequently moved from spindle poles toward chromosomes or cell cortex. +TIPs may be involved in the transport of spindle dyneins. Possible kinetochore and cortical dyneins were also observed. CONCLUSIONS AND SIGNIFICANCE: These findings suggest that cytoplasmic dynein is transported to the site of action in preparation for the following cellular events, primarily by the MT-based transport. The MT-based transport may have greater advantage than simple diffusion of soluble dynein in rapid and efficient transport of the limited concentration of the protein.

  3. Cell cycle-dependent alteration in NAC1 nuclear body dynamics and morphology

    Science.gov (United States)

    Wu, Pei-Hsun; Hung, Shen-Hsiu; Ren, Tina; Shih, Ie-Ming; Tseng, Yiider

    2011-02-01

    NAC1, a BTB/POZ family member, has been suggested to participate in maintaining the stemness of embryonic stem cells and has been implicated in the pathogenesis of human cancer. In ovarian cancer, NAC1 upregulation is associated with disease aggressiveness and with the development of chemoresistance. Like other BTB/POZ proteins, NAC1 forms discrete nuclear bodies in non-dividing cells. To investigate the biological role of NAC1 nuclear bodies, we characterized the expression dynamics of NAC1 nuclear bodies during different phases of the cell cycle. Fluorescence recovery after photobleaching assays revealed that NAC1 was rapidly exchanged between the nucleoplasm and NAC1 nuclear bodies in interphase cells. The number of NAC1 bodies significantly increased and their size decreased in the S phase as compared to the G0/G1 and G2 phases. NAC1 nuclear bodies disappeared and NAC1 became diffuse during mitosis. NAC1 nuclear bodies reappeared immediately after completion of mitosis. These results indicate that a cell cycle-dependent regulatory mechanism controls NAC1 body formation in the nucleus and suggest that NAC1 body dynamics are associated with mitosis or cytokinesis.

  4. Cell cycle-dependent alteration in NAC1 nuclear body dynamics and morphology

    International Nuclear Information System (INIS)

    NAC1, a BTB/POZ family member, has been suggested to participate in maintaining the stemness of embryonic stem cells and has been implicated in the pathogenesis of human cancer. In ovarian cancer, NAC1 upregulation is associated with disease aggressiveness and with the development of chemoresistance. Like other BTB/POZ proteins, NAC1 forms discrete nuclear bodies in non-dividing cells. To investigate the biological role of NAC1 nuclear bodies, we characterized the expression dynamics of NAC1 nuclear bodies during different phases of the cell cycle. Fluorescence recovery after photobleaching assays revealed that NAC1 was rapidly exchanged between the nucleoplasm and NAC1 nuclear bodies in interphase cells. The number of NAC1 bodies significantly increased and their size decreased in the S phase as compared to the G0/G1 and G2 phases. NAC1 nuclear bodies disappeared and NAC1 became diffuse during mitosis. NAC1 nuclear bodies reappeared immediately after completion of mitosis. These results indicate that a cell cycle-dependent regulatory mechanism controls NAC1 body formation in the nucleus and suggest that NAC1 body dynamics are associated with mitosis or cytokinesis

  5. RNF4 regulates DNA double-strand break repair in a cell cycle-dependent manner.

    Science.gov (United States)

    Kuo, Ching-Ying; Li, Xu; Stark, Jeremy M; Shih, Hsiu-Ming; Ann, David K

    2016-03-18

    Both RNF4 and KAP1 play critical roles in the response to DNA double-strand breaks (DSBs), but the functional interplay of RNF4 and KAP1 in regulating DNA damage response remains unclear. We have previously demonstrated the recruitment and degradation of KAP1 by RNF4 require the phosphorylation of Ser824 (pS824) and SUMOylation of KAP1. In this report, we show the retention of DSB-induced pS824-KAP1 foci and RNF4 abundance are inversely correlated as cell cycle progresses. Following irradiation, pS824-KAP1 foci predominantly appear in the cyclin A (-) cells, whereas RNF4 level is suppressed in the G0-/G1-phases and then accumulates during S-/G2-phases. Notably, 53BP1 foci, but not BRCA1 foci, co-exist with pS824-KAP1 foci. Depletion of KAP1 yields opposite effect on the dynamics of 53BP1 and BRCA1 loading, favoring homologous recombination repair. In addition, we identify p97 is present in the RNF4-KAP1 interacting complex and the inhibition of p97 renders MCF7 breast cancer cells relatively more sensitive to DNA damage. Collectively, these findings suggest that combined effect of dynamic recruitment of RNF4 to KAP1 regulates the relative occupancy of 53BP1 and BRCA1 at DSB sites to direct DSB repair in a cell cycle-dependent manner. PMID:26766492

  6. The CHR Promoter Element Controls Cell Cycle-Dependent Gene Transcription and Binds the DREAM and MMB Complexes

    OpenAIRE

    Müller, Gerd A.; Quaas, Marianne; Schümann, Michael; Krause, Eberhard; Fischer, Martin; Engeland, Kurt; Padi, Megha; Litovchick, Larisa; DeCaprio, James A.

    2011-01-01

    Cell cycle-dependent gene expression is often controlled on the transcriptional level. Genes like \\(cyclin B, CDC2\\) and \\(CDC25C\\) are regulated by cell cycle-dependent element (CDE) and cell cycle genes homology region (CHR) promoter elements mainly through repression in \\(G_0/G_1\\). It had been suggested that E2F4 binding to CDE sites is central to transcriptional regulation. However, some promoters are only controlled by a CHR. We identify the DREAM complex binding to the CHR of mouse and...

  7. Cell cycle-dependent SUMO-1 conjugation to nuclear mitotic apparatus protein (NuMA)

    Energy Technology Data Exchange (ETDEWEB)

    Seo, Jae Sung; Kim, Ha Na; Kim, Sun-Jick; Bang, Jiyoung; Kim, Eun-A; Sung, Ki Sa [Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Yoon, Hyun-Joo [TissueGene Inc. 9605 Medical Center Dr., Rockville, MD 20850 (United States); Yoo, Hae Yong [Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Center, Sungkyunkwan University, Seoul 135-710 (Korea, Republic of); Choi, Cheol Yong, E-mail: choicy@skku.ac.kr [Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of)

    2014-01-03

    Highlights: •NuMA is modified by SUMO-1 in a cell cycle-dependent manner. •NuMA lysine 1766 is the primary target site for SUMOylation. •SUMOylation-deficient NuMA induces multiple spindle poles during mitosis. •SUMOylated NuMA induces microtubule bundling. -- Abstract: Covalent conjugation of proteins with small ubiquitin-like modifier 1 (SUMO-1) plays a critical role in a variety of cellular functions including cell cycle control, replication, and transcriptional regulation. Nuclear mitotic apparatus protein (NuMA) localizes to spindle poles during mitosis, and is an essential component in the formation and maintenance of mitotic spindle poles. Here we show that NuMA is a target for covalent conjugation to SUMO-1. We find that the lysine 1766 residue is the primary NuMA acceptor site for SUMO-1 conjugation. Interestingly, SUMO modification of endogenous NuMA occurs at the entry into mitosis and this modification is reversed after exiting from mitosis. Knockdown of Ubc9 or forced expression of SENP1 results in impairment of the localization of NuMA to mitotic spindle poles during mitosis. The SUMOylation-deficient NuMA mutant is defective in microtubule bundling, and multiple spindles are induced during mitosis. The mitosis-dependent dynamic SUMO-1 modification of NuMA might contribute to NuMA-mediated formation and maintenance of mitotic spindle poles during mitosis.

  8. Cell cycle-dependent SUMO-1 conjugation to nuclear mitotic apparatus protein (NuMA)

    International Nuclear Information System (INIS)

    Highlights: •NuMA is modified by SUMO-1 in a cell cycle-dependent manner. •NuMA lysine 1766 is the primary target site for SUMOylation. •SUMOylation-deficient NuMA induces multiple spindle poles during mitosis. •SUMOylated NuMA induces microtubule bundling. -- Abstract: Covalent conjugation of proteins with small ubiquitin-like modifier 1 (SUMO-1) plays a critical role in a variety of cellular functions including cell cycle control, replication, and transcriptional regulation. Nuclear mitotic apparatus protein (NuMA) localizes to spindle poles during mitosis, and is an essential component in the formation and maintenance of mitotic spindle poles. Here we show that NuMA is a target for covalent conjugation to SUMO-1. We find that the lysine 1766 residue is the primary NuMA acceptor site for SUMO-1 conjugation. Interestingly, SUMO modification of endogenous NuMA occurs at the entry into mitosis and this modification is reversed after exiting from mitosis. Knockdown of Ubc9 or forced expression of SENP1 results in impairment of the localization of NuMA to mitotic spindle poles during mitosis. The SUMOylation-deficient NuMA mutant is defective in microtubule bundling, and multiple spindles are induced during mitosis. The mitosis-dependent dynamic SUMO-1 modification of NuMA might contribute to NuMA-mediated formation and maintenance of mitotic spindle poles during mitosis

  9. The one-cell mouse embryo: cell cycle-dependent radiosensitivity and development of chromosomal anomalies in postradiation cell cycles

    International Nuclear Information System (INIS)

    One-cell mouse embryos were irradiated with X-rays at different cell cycle stages. Examination of structural chromosomal anomalies and micronucleus formation in postradiation mitoses and interphases demonstrated cell cycle-dependent radiosensitivities in the order: late G2 phase > G1 phase > S phase > early G2 phase > stage of decondensing nuclei. Comparison of the quality and quantity of chromosomal aberrations from the first to third mitosis led to the conclusion that new chromosomal anomalies were formed in the course of postirradiation cell cycles. This hypothesis was supported by an increasing number of micronuclei from 24 to 48 h post-conception. In addition to structural chromosomal aberrations, radiation-induced chromosome loss was observed with a frequency that was obviously independent of the exposed cell cycle phase. Loss of acentric chromosome fragments and of single chromosomes contributed to the micronucleus formation. (author)

  10. The CHR promoter element controls cell cycle-dependent gene transcription and binds the DREAM and MMB complexes.

    Science.gov (United States)

    Müller, Gerd A; Quaas, Marianne; Schümann, Michael; Krause, Eberhard; Padi, Megha; Fischer, Martin; Litovchick, Larisa; DeCaprio, James A; Engeland, Kurt

    2012-02-01

    Cell cycle-dependent gene expression is often controlled on the transcriptional level. Genes like cyclin B, CDC2 and CDC25C are regulated by cell cycle-dependent element (CDE) and cell cycle genes homology region (CHR) promoter elements mainly through repression in G(0)/G(1). It had been suggested that E2F4 binding to CDE sites is central to transcriptional regulation. However, some promoters are only controlled by a CHR. We identify the DREAM complex binding to the CHR of mouse and human cyclin B2 promoters in G(0). Association of DREAM and cell cycle-dependent regulation is abrogated when the CHR is mutated. Although E2f4 is part of the complex, a CDE is not essential but can enhance binding of DREAM. We show that the CHR element is not only necessary for repression of gene transcription in G(0)/G(1), but also for activation in S, G(2) and M phases. In proliferating cells, the B-myb-containing MMB complex binds the CHR of both promoters independently of the CDE. Bioinformatic analyses identify many genes which contain conserved CHR elements in promoters binding the DREAM complex. With Ube2c as an example from that screen, we show that inverse CHR sites are functional promoter elements that can bind DREAM and MMB. Our findings indicate that the CHR is central to DREAM/MMB-dependent transcriptional control during the cell cycle. PMID:22064854

  11. The CHR promoter element controls cell cycle-dependent gene transcription and binds the DREAM and MMB complexes

    Science.gov (United States)

    Müller, Gerd A.; Quaas, Marianne; Schümann, Michael; Krause, Eberhard; Padi, Megha; Fischer, Martin; Litovchick, Larisa; DeCaprio, James A.; Engeland, Kurt

    2012-01-01

    Cell cycle-dependent gene expression is often controlled on the transcriptional level. Genes like cyclin B, CDC2 and CDC25C are regulated by cell cycle-dependent element (CDE) and cell cycle genes homology region (CHR) promoter elements mainly through repression in G0/G1. It had been suggested that E2F4 binding to CDE sites is central to transcriptional regulation. However, some promoters are only controlled by a CHR. We identify the DREAM complex binding to the CHR of mouse and human cyclin B2 promoters in G0. Association of DREAM and cell cycle-dependent regulation is abrogated when the CHR is mutated. Although E2f4 is part of the complex, a CDE is not essential but can enhance binding of DREAM. We show that the CHR element is not only necessary for repression of gene transcription in G0/G1, but also for activation in S, G2 and M phases. In proliferating cells, the B-myb-containing MMB complex binds the CHR of both promoters independently of the CDE. Bioinformatic analyses identify many genes which contain conserved CHR elements in promoters binding the DREAM complex. With Ube2c as an example from that screen, we show that inverse CHR sites are functional promoter elements that can bind DREAM and MMB. Our findings indicate that the CHR is central to DREAM/MMB-dependent transcriptional control during the cell cycle. PMID:22064854

  12. Cell-cycle dependent micronucleus formation and mitotic disturbances induced by 5-azacytidine in mammalian cells

    OpenAIRE

    Stopper, Helga; Körber, C.; Schiffmann, D; Caspary, W J

    2012-01-01

    5-Azacytidine was originally developed to treat human myelogenous leukemia. However, interest in this compound has expanded because of reports of its ability to affect cell differentiation and to alter eukaryotic gene expression. In an ongoing attempt to understand the biochemical effects of this compound, we examined the effects of 5-azacytidine on mitosis and on micronucleus formation in mammalian cells. In L5178Y mouse cells, 5-azacytidine induced micronuclei at concentrations at which we ...

  13. Backup pathways of NHEJ in cells of higher eukaryotes: Cell cycle dependence

    International Nuclear Information System (INIS)

    DNA double-strand breaks (DSBs) induced by ionizing radiation (IR) in cells of higher eukaryotes are predominantly repaired by a pathway of non-homologous end joining (NHEJ) utilizing Ku, DNA-PKcs, DNA ligase IV, XRCC4 and XLF/Cernunnos (D-NHEJ) as central components. Work carried out in our laboratory and elsewhere shows that when this pathway is chemically or genetically compromised, cells do not shunt DSBs to homologous recombination repair (HRR) but instead use another form of NHEJ operating as a backup (B-NHEJ). Here I review our efforts to characterize this repair pathway and discuss its dependence on the cell cycle as well as on the growth conditions. I present evidence that B-NHEJ utilizes ligase III, PARP-1 and histone H1. When B-NHEJ is examined throughout the cell cycle, significantly higher activity is observed in G2 phase that cannot be attributed to HRR. Furthermore, the activity of B-NHEJ is compromised when cells enter the plateau phase of growth. Together, these observations uncover a repair pathway with unexpected biochemical constitution and interesting cell cycle and growth factor regulation. They generate a framework for investigating the mechanistic basis of HRR contribution to DSB repair.

  14. Backup pathways of NHEJ in cells of higher eukaryotes: cell cycle dependence.

    Science.gov (United States)

    Iliakis, George

    2009-09-01

    DNA double-strand breaks (DSBs) induced by ionizing radiation (IR) in cells of higher eukaryotes are predominantly repaired by a pathway of non-homologous end joining (NHEJ) utilizing Ku, DNA-PKcs, DNA ligase IV, XRCC4 and XLF/Cernunnos (D-NHEJ) as central components. Work carried out in our laboratory and elsewhere shows that when this pathway is chemically or genetically compromised, cells do not shunt DSBs to homologous recombination repair (HRR) but instead use another form of NHEJ operating as a backup (B-NHEJ). Here I review our efforts to characterize this repair pathway and discuss its dependence on the cell cycle as well as on the growth conditions. I present evidence that B-NHEJ utilizes ligase III, PARP-1 and histone H1. When B-NHEJ is examined throughout the cell cycle, significantly higher activity is observed in G2 phase that cannot be attributed to HRR. Furthermore, the activity of B-NHEJ is compromised when cells enter the plateau phase of growth. Together, these observations uncover a repair pathway with unexpected biochemical constitution and interesting cell cycle and growth factor regulation. They generate a framework for investigating the mechanistic basis of HRR contribution to DSB repair. PMID:19604590

  15. Cdc6 localizes to S- and G2-phase centrosomes in a cell cycle-dependent manner

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Gwang Su; Kang, Jeeheon; Bang, Sung Woong; Hwang, Deog Su, E-mail: dshwang@snu.ac.kr

    2015-01-16

    Highlights: • Cdc6 protein is a component of the pre-replicative complex required for chromosomal replication initiation. • Cdc6 localized to centrosomes of S and G2 phases in a cell cycle-dependent manner. • The centrosomal localization was governed by centrosomal localization signal sequences of Cdc6. • Deletions or substitution mutations on the centrosomal localization signal interfered with centrosomal localization of the Cdc6 proteins. - Abstract: The Cdc6 protein has been primarily investigated as a component of the pre-replicative complex for the initiation of chromosome replication, which contributes to maintenance of chromosomal integrity. Here, we show that Cdc6 localized to the centrosomes during S and G2 phases of the cell cycle. The centrosomal localization was mediated by Cdc6 amino acid residues 311–366, which are conserved within other Cdc6 homologues and contains a putative nuclear export signal. Deletions or substitutions of the amino acid residues did not allow the proteins to localize to centrosomes. In contrast, DsRed tag fused to the amino acid residues localized to centrosomes. These results indicated that a centrosome localization signal is contained within amino acid residues 311–366. The cell cycle-dependent centrosomal localization of Cdc6 in S and G2 phases suggest a novel function of Cdc6 in centrosomes.

  16. Differential regulation of survivin by p53 contributes to cell cycle dependent apoptosis

    Institute of Scientific and Technical Information of China (English)

    Yan JIN; Yong WEI; Lei XIONG; Ying YANG; Jia Rui WU

    2005-01-01

    Recent studies indicate that cell-cycle checkpoints are tightly correlated with the regulation of apoptosis, in which p53 plays an important role. Our present works show that the expression of E6/E7 oncogenes of human papillomavirus in HeLa cells is inhibited in the presence of anti-tumor reagent tripchlorolide (TC), which results in the up-regulation of p53 in HeLa cells. Interestingly, under the same TC-treatment, the cells at the early S-phase are more susceptible to apoptosis than those at the middle S-phase although p53 protein is stabilized to the same level in both situations.Significant difference is exhibited between the two specified expression profiles. Further analysis demonstrates that anti-apoptotic gene survivin is up-regulated by p53 in the TC-treated middle-S cells, whereas it is down-regulated by p53 in the TC-treated early-S cells. Taken together, the present study indicates that the differential p53-regulated expression of survivin at different stages of the cell cycle results in different cellular outputs under the same apoptosis-inducer.

  17. Cell cycle dependence of mitotic delay in X-irradiated normal and ataxia-telangiectasia fibroblasts

    International Nuclear Information System (INIS)

    An investigation has been made of the relationship between suppression in the mitotic index and inhibition of DNA synthesis in normal (N) and ataxia-telangiectasia (A-T) skin fibroblasts, using tritiated thymidine as a marker of the cell cycle. The delay in progression of X-irradiated cells through the cell cycle, which is more pronounced in normal than in A-T fibroblasts, was greatest for cells in G2 at the time of irradiation. The greater effect of radiation on the initiation of DNA synthesis in N than in A-T cells was reflected in the shape of the percent labelled mitosis curves after 3H-thymidine treatment. The duration of the S phase in unirradiated A-T cells was greater than in N cells. It is pointed out that any explanation of the underlying defect in A-T must account not only for the reduced radiosensitivity of DNA synthesis but for the lesser delay in G2. The authors claim that their data support the hypothesis that DNA is the principal target for radiation-induced G2 delay. (U.K.)

  18. Phosphorylation of TPP1 regulates cell cycle-dependent telomerase recruitment

    OpenAIRE

    Zhang, Yi; Chen, Liuh-Yow; Han, Xin; XIE, Wei; Kim, Hyeung; Yang, Dong; Liu, Dan; Songyang, Zhou

    2013-01-01

    Telomere maintenance is essential for organisms with linear chromosomes and is carried out by telomerase during cell cycle. The precise mechanism by which cell cycle controls telomeric access of telomerase and telomere elongation in mammals remains largely unknown. Previous work has established oligonucleotide/oligosaccharide binding (OB) fold-containing telomeric protein TPP1, formerly known as TINT1, PTOP, and PIP1, as a key factor that regulates telomerase recruitment and activity. However...

  19. Cell cycle-dependent differentiation dynamics balances growth and endocrine differentiation in the pancreas

    DEFF Research Database (Denmark)

    Kim, Yung Hae; Larsen, Hjalte List; Rué, Paul;

    2015-01-01

    Organogenesis relies on the spatiotemporal balancing of differentiation and proliferation driven by an expanding pool of progenitor cells. In the mouse pancreas, lineage tracing at the population level has shown that the expanding pancreas progenitors can initially give rise to all endocrine...

  20. Identification of Cell Cycle Dependent Interaction Partners of the Septins by Quantitative Mass Spectrometry.

    Science.gov (United States)

    Renz, Christian; Oeljeklaus, Silke; Grinhagens, Sören; Warscheid, Bettina; Johnsson, Nils; Gronemeyer, Thomas

    2016-01-01

    The septins are a conserved family of GTP-binding proteins that, in the baker's yeast, assemble into a highly ordered array of filaments at the mother bud neck. These filaments undergo significant structural rearrangements during the cell cycle. We aimed at identifying key components that are involved in or regulate the transitions of the septins. By combining cell synchronization and quantitative affinity-purification mass-spectrometry, we performed a screen for specific interaction partners of the septins at three distinct stages of the cell cycle. A total of 83 interaction partners of the septins were assigned. Surprisingly, we detected DNA-interacting/nuclear proteins and proteins involved in ribosome biogenesis and protein synthesis predominantly present in alpha-factor arrested that do not display an assembled septin structure. Furthermore, two distinct sets of regulatory proteins that are specific for cells at S-phase with a stable septin collar or at mitosis with split septin rings were identified. Complementary methods like SPLIFF and immunoprecipitation allowed us to more exactly define the spatial and temporal characteristics of selected hits of the AP-MS screen. PMID:26871441

  1. Cell cycle-dependent mobility of Cdc45 determined in vivo by fluorescence correlation spectroscopy.

    Directory of Open Access Journals (Sweden)

    Ronan Broderick

    Full Text Available Eukaryotic DNA replication is a dynamic process requiring the co-operation of specific replication proteins. We measured the mobility of eGFP-Cdc45 by Fluorescence Correlation Spectroscopy (FCS in vivo in asynchronous cells and in cells synchronized at the G1/S transition and during S phase. Our data show that eGFP-Cdc45 mobility is faster in G1/S transition compared to S phase suggesting that Cdc45 is part of larger protein complex formed in S phase. Furthermore, the size of complexes containing Cdc45 was estimated in asynchronous, G1/S and S phase-synchronized cells using gel filtration chromatography; these findings complemented the in vivo FCS data. Analysis of the mobility of eGFP-Cdc45 and the size of complexes containing Cdc45 and eGFP-Cdc45 after UVC-mediated DNA damage revealed no significant changes in diffusion rates and complex sizes using FCS and gel filtration chromatography analyses. This suggests that after UV-damage, Cdc45 is still present in a large multi-protein complex and that its mobility within living cells is consistently similar following UVC-mediated DNA damage.

  2. Cell Cycle Dependent Expression of Plk1 in Synchronized Porcine Fetal Fibroblasts

    Czech Academy of Sciences Publication Activity Database

    Anger, Martin; Kues, W. A.; Klíma, Jiří; Mielenz, M.; Kubelka, Michal; Motlík, Jan; Ešner, M.; Dvořák, P.; Carnwath, J. W.; Niemann, H.

    2003-01-01

    Roč. 65, č. 3 (2003), s. 245-253. ISSN 1040-452X R&D Projects: GA MŠk LN00A065 Grant ostatní: FIRCA(XX) R03-TW-05530-01 Institutional research plan: CEZ:AV0Z5045916 Keywords : Plk1 * serum deprivation * cell cycle Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.543, year: 2003

  3. The DREAM complex: master coordinator of cell cycle-dependent gene expression.

    Science.gov (United States)

    Sadasivam, Subhashini; DeCaprio, James A

    2013-08-01

    The dimerization partner, RB-like, E2F and multi-vulval class B (DREAM) complex provides a previously unsuspected unifying role in the cell cycle by directly linking p130, p107, E2F, BMYB and forkhead box protein M1. DREAM mediates gene repression during the G0 phase and coordinates periodic gene expression with peaks during the G1/S and G2/M phases. Perturbations in DREAM complex regulation shift the balance from quiescence towards proliferation and contribute to the increased mitotic gene expression levels that are frequently observed in cancers with a poor prognosis. PMID:23842645

  4. The DREAM complex: Master coordinator of cell cycle dependent gene expression

    Science.gov (United States)

    Sadasivam, Subhashini; DeCaprio, James A.

    2014-01-01

    Preface The dimerization partner (DP), retinoblastoma (RB)-like, E2F and MuvB (DREAM) complex provides a previously unsuspected unifying role in the cell cycle by directly linking p130, p107, E2F, BMYB and FOXM1. DREAM mediates gene repression during G0 and coordinates periodic gene expression with peaks during G1/S and G2/M. Perturbations in DREAM regulation shift the balance from quiescence towards proliferation and contribute to increased mitotic gene expression levels frequently observed in cancers with poor prognosis. PMID:23842645

  5. The DREAM complex: Master coordinator of cell cycle dependent gene expression

    OpenAIRE

    Sadasivam, Subhashini; DeCaprio, James A.

    2013-01-01

    The dimerization partner (DP), retinoblastoma (RB)-like, E2F and MuvB (DREAM) complex provides a previously unsuspected unifying role in the cell cycle by directly linking p130, p107, E2F, BMYB and FOXM1. DREAM mediates gene repression during G0 and coordinates periodic gene expression with peaks during G1/S and G2/M. Perturbations in DREAM regulation shift the balance from quiescence towards proliferation and contribute to increased mitotic gene expression levels frequently observed in cance...

  6. Cell cycle-dependent DNA damage signaling induced by ICRF-193 involves ATM, ATR, CHK2, and BRCA1

    International Nuclear Information System (INIS)

    Topoisomerase II is essential for cell proliferation and survival and has been a target of various anticancer drugs. ICRF-193 has long been used as a catalytic inhibitor to study the function of topoisomerase II. Here, we show that ICRF-193 treatment induces DNA damage signaling. Treatment with ICRF-193 induced G2 arrest and DNA damage signaling involving γ-H2AX foci formation and CHK2 phosphorylation. DNA damage by ICRF-193 was further demonstrated by formation of the nuclear foci of 53BP1, NBS1, BRCA1, MDC1, and FANCD2 and increased comet tail moment. The DNA damage signaling induced by ICRF-193 was mediated by ATM and ATR and was restricted to cells in specific cell cycle stages such as S, G2, and mitosis including late and early G1 phases. Downstream signaling of ATM and ATR involved the phosphorylation of CHK2 and BRCA1. Altogether, our results demonstrate that ICRF-193 induces DNA damage signaling in a cell cycle-dependent manner and suggest that topoisomerase II might be essential for the progression of the cell cycle at several stages including DNA decondensation

  7. HIV-1 Vpr-induced apoptosis is cell cycle dependent and requires Bax but not ANT.

    Directory of Open Access Journals (Sweden)

    Joshua L Andersen

    2006-12-01

    Full Text Available The HIV-1 accessory protein viral protein R (Vpr causes G2 arrest and apoptosis in infected cells. We previously identified the DNA damage-signaling protein ATR as the cellular factor that mediates Vpr-induced G2 arrest and apoptosis. Here, we examine the mechanism of induction of apoptosis by Vpr and how it relates to induction of G2 arrest. We find that entry into G2 is a requirement for Vpr to induce apoptosis. We investigated the role of the mitochondrial permeability transition pore by knockdown of its essential component, the adenine nucleotide translocator. We found that Vpr-induced apoptosis was unaffected by knockdown of ANT. Instead, apoptosis is triggered through a different mitochondrial pore protein, Bax. In support of the idea that checkpoint activation and apoptosis induction are functionally linked, we show that Bax activation by Vpr was ablated when ATR or GADD45alpha was knocked down. Certain mutants of Vpr, such as R77Q and I74A, identified in long-term nonprogressors, have been proposed to inefficiently induce apoptosis while activating the G2 checkpoint in a normal manner. We tested the in vitro phenotypes of these mutants and found that their abilities to induce apoptosis and G2 arrest are indistinguishable from those of HIV-1NL4-3 vpr, providing additional support to the idea that G2 arrest and apoptosis induction are mechanistically linked.

  8. Effects of coronary artery occlusion and reperfusion on cardiac cycle-dependent variation of myocardial ultrasonic backscatter

    International Nuclear Information System (INIS)

    We have recently reported a systematic variation in integrated ultrasonic backscatter throughout the cardiac cycle in canine hearts. This study was performed to determine whether the pattern of such variation is modified systematically by ischemia. Measurements of integrated ultrasonic backscatter in selected regions of normal, ischemic, and reperfused hearts were compared in view of known differences in systolic function of myocardium in each of these regions. Integrated ultrasonic backscatter (3-7 MHz) gated to the first derivative of left ventricular pressure was measured at the apex, midwall, and base in 10 dogs and at the apex before and during transient ischemia and reperfusion in four dogs. Quantitative integrated ultrasonic backscatter was referenced to a steel reflector. Cyclic variation of integrated ultrasonic backscatter was greatest at the apex [peak to trough variation 5.5 +/- 0.9 dB (mean +/- SE)] with the maximum near end diastole (-52.9 +/- 0.9 dB) and minimum near end systole (-58.4 +/- 1.0 dB). Variation at the apex (5.5 +/- 0.9 dB) and the midwall (4.3 +/- 0.8 dB) was greater than at the base (0.5 +/- 1.0 dB) (P less than 0.01 for either region compared with base). Left anterior descending coronary occlusion for 10 minutes in four of 10 dogs reduced variation at the apex to 0.4 +/- 1.5 dB (P less than 0.02 compared with preocclusion). Reperfusion for 2 hours restored apical cyclic variation to 3.9 +/- 1.7 dB, i.e., to values not significantly different from those before occlusion

  9. Neutron-induced cell cycle-dependent oncogenic transformation of C3H 10T1/2 cells

    International Nuclear Information System (INIS)

    Exposure of synchronized populations of mouse C3H 10T1/2 cells to a single dose (0.6 Gy) of 5.9 MeV neutrons at intervals after mitotic shake-off results in a distinctive variation in the oncogenic transformation frequency through the cell cycle. Previous findings show a sensitive window for X-ray-induced oncogenic transformants at late times after mitotic shake-off (14-16 h). Optimal sensitivity to neutrons was observed for cell populations irradiated soon after mitotic shake-off (4-6 h), where the majority of cells would be in the G1 phase of the cell cycle. Additionally, enhanced sensitivity was also found for that period after shake-off (14-16 h) which was maximally sensitive to X rays corresponding to cell populations with a high proportion of G2-phase cells. That is, low-LET radiation (250 kVp X rays) largely appears to produce oncogenic transformants in G2-phase cells, while intermediate-LET radiation (5.9 MeV neutrons) is effective principally on G1- and, to a somewhat lesser extent, G2-phase cells. Cells irradiated with neutrons showed less variation for lethality through the cell cycle than those irradiated with X rays, in agreement with previous findings. The mechanistic basis for the differences in the response of cells in the different phases of the cell cycle to radiations of different quality is unknown but is suggestive of distinct (open-quotes signatureclose quotes) molecular changes leading to the observed oncogenic transformation response. 30 refs., 1 fig., 2 tabs

  10. Cell-Cycle-Dependent Reconfiguration of the DNA Methylome during Terminal Differentiation of Human B Cells into Plasma Cells

    Directory of Open Access Journals (Sweden)

    Gersende Caron

    2015-11-01

    Full Text Available Molecular mechanisms underlying terminal differentiation of B cells into plasma cells are major determinants of adaptive immunity but remain only partially understood. Here we present the transcriptional and epigenomic landscapes of cell subsets arising from activation of human naive B cells and differentiation into plasmablasts. Cell proliferation of activated B cells was linked to a slight decrease in DNA methylation levels, but followed by a committal step in which an S phase-synchronized differentiation switch was associated with an extensive DNA demethylation and local acquisition of 5-hydroxymethylcytosine at enhancers and genes related to plasma cell identity. Downregulation of both TGF-β1/SMAD3 signaling and p53 pathway supported this final step, allowing the emergence of a CD23-negative subpopulation in transition from B cells to plasma cells. Remarkably, hydroxymethylation of PRDM1, a gene essential for plasma cell fate, was coupled to progression in S phase, revealing an intricate connection among cell cycle, DNA (hydroxymethylation, and cell fate determination.

  11. Cell cycle-dependent expression of Ki-67 antigen in human melanoma cells subjected to irradiation and/or hyperthermia

    International Nuclear Information System (INIS)

    The proliferation of human melanoma cells in vitro during the first 3 days after irradiation and/or hyperthermia was followed by two-parameter flow cytometry combining cell cycle analysis on the basis of DNA content with Ki-67 antibody labeling. It was found that cells arrested or delayed in the S and G2 phases of the cell cycle were Ki-67-positive in spite of the antigen's very short half-life. Thus Ki-67 staining failed to reflect those changes in cell proliferation which typically occur in the course of a fractionated radiotherapy as well as those expected in the case of hyperthermia or a combined treatment. 24 refs., 3 figs., 1 tab

  12. Using a GFP-gene fusion technique to study the cell cycle-dependent distribution of calmodulin in living cells

    Institute of Scientific and Technical Information of China (English)

    李朝军; 吕品; 张东才

    1999-01-01

    In this study, a green fluorescent protein (GFP)-calmodulin (CaM) fusion gene method was used to examine the distribution of calmodulin during various stages of cell cycle. First, it was found that the distribution of CaM in living cells changes with the cell cycle. CaM was found mainly in the cytoplasm during G1 phase. It began to move into the nucleus when the cell entered S phase. At G2 phase, CaM became more concentrated in the nucleus than in cytoplasm. Second, the accumulation of CaM in the nucleus during G2 phase appeared to be related to the onset of mitosis, since inhibiting the activation of CaM at this stage resulted in blocking the nuclear membrane breakdown and chromatin condensation. Finally, after the cell entered mitosis, a high concentration of CaM was found at the polar regions of the mitotic spindle. At this time, inhibiting the activity of CaM would cause a disruption of the spindle structure. The relationship between the stage-specific distribution of CaM and its function in regulat

  13. Cell-cycle dependent radiation-induced transformations of C3H 10T1/2 cells

    International Nuclear Information System (INIS)

    Studies of the temporal distribution of dose have shown that low doses and low dose-rates of certain radiations of intermediate LET result in a higher incidence of oncogenic transformation than the same dose delivered in an acute exposure. To account for this anomalous effect, a biophysical model was proposed by Rossi and Kellerer, which postulated the existence of a narrow 'window' of sensitivity. Subsequently, in fitting all available transformation data to this model, Brenner and Hall estimated that the window of sensitivity may have a duration of about 1 hour and went on to postulate that it may correspond to cells near mitosis. A series of experiments was designed to test this hypothesis. (author). 6 refs., 2 figs

  14. The Human Papillomavirus Type 18 E2 Protein Is a Cell Cycle-Dependent Target of the SCFSkp2 Ubiquitin Ligase▿

    OpenAIRE

    Bellanger, Sophie; Tan, Chye Ling; Nei, Wenlong; He, Ping Ping; Thierry, Françoise

    2009-01-01

    The human papillomavirus type 18 (HPV-18) E2 gene is inactivated in cervical carcinoma after integration of the viral DNA into the host cellular genome. Since E2 represses the transcription of the two viral oncogenes E6 and E7, integration which allows their strong expression is considered a major step in transformation by HPV. We show here that E2 is specifically degraded at the end of the G1 phase in a Brd4-independent manner, implying that its regulatory functions are cell cycle dependent....

  15. FasL and FADD delivery by a glioma-specific and cell cycle-dependent HSV-1 amplicon virus enhanced apoptosis in primary human brain tumors

    Directory of Open Access Journals (Sweden)

    Lam Paula Y

    2010-10-01

    Full Text Available Abstract Background Glioblastoma multiforme is the most malignant cancer of the brain and is notoriously difficult to treat due to the highly proliferative and infiltrative nature of the cells. Herein, we explored the combination treatment of pre-established human glioma xenograft using multiple therapeutic genes whereby the gene expression is regulated by both cell-type and cell cycle-dependent transcriptional regulatory mechanism conferred by recombinant HSV-1 amplicon vectors. Results We demonstrated for the first time that Ki67-positive proliferating primary human glioma cells cultured from biopsy samples were effectively induced into cell death by the dual-specific function of the pG8-FasL amplicon vectors. These vectors were relatively stable and exhibited minimal cytotoxicity in vivo. Intracranial implantation of pre-transduced glioma cells resulted in better survival outcome when compared with viral vectors inoculated one week post-implantation of tumor cells, indicating that therapeutic efficacy is dependent on the viral spread and mode of viral vectors administration. We further showed that pG8-FasL amplicon vectors are functional in the presence of commonly used treatment regimens for human brain cancer. In fact, the combined therapies of pG8-FasL and pG8-FADD in the presence of temozolomide significantly improved the survival of mice bearing intracranial high-grade gliomas. Conclusion Taken together, our results showed that the glioma-specific and cell cycle-dependent HSV-1 amplicon vector is potentially useful as an adjuvant therapy to complement the current gene therapy strategy for gliomas.

  16. Cell Cycle-dependent Expression of Thyroid Hormone Receptor-β Is a Mechanism for Variable Hormone SensitivityD⃞

    OpenAIRE

    Maruvada, Padma; Dmitrieva, Natalia I.; East-Palmer, Joyce; Yen, Paul M.

    2004-01-01

    Thyroid hormone receptors (TRs) are ligand-regulatable transcription factors. Currently, little is known about the expression of TRs or other nuclear hormone receptors during the cell cycle. We thus developed a stable expression system to express green fluorescent protein-TRβ in HeLa cells under tetracycline regulation, and studied TR expression during the cell cycle by laser scanning cytometry. Only ∼9-15% of the nonsynchronized cell population expressed TR because the majority of cells were...

  17. Cell Cycle-dependent Regulation of the Forkhead Transcription Factor FOXK2 by CDK·Cyclin Complexes*

    OpenAIRE

    Marais, Anett; Ji, Zongling; Child, Emma S.; Krause, Eberhard; Mann, David J.; Sharrocks, Andrew D.

    2010-01-01

    Several mammalian forkhead transcription factors have been shown to impact on cell cycle regulation and are themselves linked to cell cycle control systems. Here we have investigated the little studied mammalian forkhead transcription factor FOXK2 and demonstrate that it is subject to control by cell cycle-regulated protein kinases. FOXK2 exhibits a periodic rise in its phosphorylation levels during the cell cycle, with hyperphosphorylation occurring in mitotic cells. Hyperphosphorylation occ...

  18. Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels

    DEFF Research Database (Denmark)

    Frenkel-Morgenstern, Milana; Danon, Tamar; Christian, Thomas;

    2012-01-01

    The cell cycle is a temporal program that regulates DNA synthesis and cell division. When we compared the codon usage of cell cycle-regulated genes with that of other genes, we discovered that there is a significant preference for non-optimal codons. Moreover, genes encoding proteins that cycle at...... the protein level exhibit non-optimal codon preferences. Remarkably, cell cycle-regulated genes expressed in different phases display different codon preferences. Here, we show empirically that transfer RNA (tRNA) expression is indeed highest in the G2 phase of the cell cycle, consistent with the non......-optimal codon usage of genes expressed at this time, and lowest toward the end of G1, reflecting the optimal codon usage of G1 genes. Accordingly, protein levels of human glycyl-, threonyl-, and glutamyl-prolyl tRNA synthetases were found to oscillate, peaking in G2/M phase. In light of our findings, we propose...

  19. Cell-cycle dependent expression of a translocation-mediated fusion oncogene mediates checkpoint adaptation in rhabdomyosarcoma.

    Science.gov (United States)

    Kikuchi, Ken; Hettmer, Simone; Aslam, M Imran; Michalek, Joel E; Laub, Wolfram; Wilky, Breelyn A; Loeb, David M; Rubin, Brian P; Wagers, Amy J; Keller, Charles

    2014-01-01

    Rhabdomyosarcoma is the most commonly occurring soft-tissue sarcoma in childhood. Most rhabdomyosarcoma falls into one of two biologically distinct subgroups represented by alveolar or embryonal histology. The alveolar subtype harbors a translocation-mediated PAX3:FOXO1A fusion gene and has an extremely poor prognosis. However, tumor cells have heterogeneous expression for the fusion gene. Using a conditional genetic mouse model as well as human tumor cell lines, we show that that Pax3:Foxo1a expression is enriched in G2 and triggers a transcriptional program conducive to checkpoint adaptation under stress conditions such as irradiation in vitro and in vivo. Pax3:Foxo1a also tolerizes tumor cells to clinically-established chemotherapy agents and emerging molecularly-targeted agents. Thus, the surprisingly dynamic regulation of the Pax3:Foxo1a locus is a paradigm that has important implications for the way in which oncogenes are modeled in cancer cells. PMID:24453992

  20. Cell-cycle dependent expression of a translocation-mediated fusion oncogene mediates checkpoint adaptation in rhabdomyosarcoma.

    Directory of Open Access Journals (Sweden)

    Ken Kikuchi

    2014-01-01

    Full Text Available Rhabdomyosarcoma is the most commonly occurring soft-tissue sarcoma in childhood. Most rhabdomyosarcoma falls into one of two biologically distinct subgroups represented by alveolar or embryonal histology. The alveolar subtype harbors a translocation-mediated PAX3:FOXO1A fusion gene and has an extremely poor prognosis. However, tumor cells have heterogeneous expression for the fusion gene. Using a conditional genetic mouse model as well as human tumor cell lines, we show that that Pax3:Foxo1a expression is enriched in G2 and triggers a transcriptional program conducive to checkpoint adaptation under stress conditions such as irradiation in vitro and in vivo. Pax3:Foxo1a also tolerizes tumor cells to clinically-established chemotherapy agents and emerging molecularly-targeted agents. Thus, the surprisingly dynamic regulation of the Pax3:Foxo1a locus is a paradigm that has important implications for the way in which oncogenes are modeled in cancer cells.

  1. Curcumin and trans-resveratrol exert cell cycle-dependent radioprotective or radiosensitizing effects as elucidated by the PCC and G2-assay

    Energy Technology Data Exchange (ETDEWEB)

    Sebastià, N., E-mail: natividad.sebastia@uv.es [Radiation Protection Service, IIS La Fe, Health Research Institute La Fe, Valencia (Spain); Montoro, A. [Radiation Protection Service, Universitary and Politechnic Hospital La Fe, Valencia (Spain); Grupo de Investigación Biomédica en Imagen GIBI230, IIS La Fe, Health Research Institute La Fe, Valencia (Spain); Unidad Mixta de Investigación en Endocrinología, Nutrición y Dietética Clínica, IIS La Fe, Health Research Institute La Fe, Valencia (Spain); Hervás, D. [Biostatistics Unit, IIS La Fe, Health Research Institute La Fe, Valencia (Spain); Pantelias, G.; Hatzi, V.I. [Institute of Nuclear and Radiological Sciences and Technology, Energy and Safety, National Centre for Scientific Research “Demokritos”, Aghia Paraskevi, Athens (Greece); Soriano, J.M. [Grupo de Investigación Biomédica en Imagen GIBI230, IIS La Fe, Health Research Institute La Fe, Valencia (Spain); Unidad Mixta de Investigación en Endocrinología, Nutrición y Dietética Clínica, IIS La Fe, Health Research Institute La Fe, Valencia (Spain); Department of Preventive Medicine and Public Health, Faculty of Pharmacy, University of Valencia, Burjassot, Valencia (Spain); Villaescusa, J.I. [Radiation Protection Service, Universitary and Politechnic Hospital La Fe, Valencia (Spain); and others

    2014-08-15

    Highlights: • Curcumin and trans-resveratrol can exert radioprotective or radiosensitizing effects. • The mechanisms underlying such dual action were elucidated using the PCC and G2-assay. • Radioprotection occurs in non-cycling cells exposed to curcumin and resveratrol. • Radiosensitization occurs in cycling cells exposed to the chemicals. • G2-checkpoint abrogation by the chemicals underlies the radiosensitizing mechanism. - Abstract: Curcumin and trans-resveratrol are well-known antioxidant polyphenols with radiomodulatory properties, radioprotecting non-cancerous cells while radiosensitizing tumor cells. This dual action may be the result of their radical scavenging properties and their effects on cell-cycle checkpoints that are activated in response to radiation-induced chromosomal damage. It could be also caused by their effect on regulatory pathways with impact on detoxification enzymes, the up-regulation of endogenous protective systems, and cell-cycle-dependent processes of DNA damage. This work aims to elucidate the mechanisms underlying the dual action of these polyphenols and investigates under which conditions they exhibit radioprotecting or radiosensitizing properties. The peripheral blood lymphocyte test system was used, applying concentrations ranging from 1.4 to 140 μM curcumin and 2.2 to 220 μM trans-resveratrol. The experimental design focuses first on their radioprotective effects in non-cycling lymphocytes, as uniquely visualized using cell fusion-mediated premature chromosome condensation, excluding, thus, cell-cycle interference to repair processes and activation of checkpoints. Second, the radiosensitizing potential of these chemicals on the induction of chromatid breaks in cultured lymphocytes following G2-phase irradiation was evaluated by a standardized G2-chromosomal radiosensitivity predictive assay. This assay uses caffeine for G2-checkpoint abrogation and it was applied to obtain an internal control for radiosensitivity

  2. Curcumin and trans-resveratrol exert cell cycle-dependent radioprotective or radiosensitizing effects as elucidated by the PCC and G2-assay

    International Nuclear Information System (INIS)

    Highlights: • Curcumin and trans-resveratrol can exert radioprotective or radiosensitizing effects. • The mechanisms underlying such dual action were elucidated using the PCC and G2-assay. • Radioprotection occurs in non-cycling cells exposed to curcumin and resveratrol. • Radiosensitization occurs in cycling cells exposed to the chemicals. • G2-checkpoint abrogation by the chemicals underlies the radiosensitizing mechanism. - Abstract: Curcumin and trans-resveratrol are well-known antioxidant polyphenols with radiomodulatory properties, radioprotecting non-cancerous cells while radiosensitizing tumor cells. This dual action may be the result of their radical scavenging properties and their effects on cell-cycle checkpoints that are activated in response to radiation-induced chromosomal damage. It could be also caused by their effect on regulatory pathways with impact on detoxification enzymes, the up-regulation of endogenous protective systems, and cell-cycle-dependent processes of DNA damage. This work aims to elucidate the mechanisms underlying the dual action of these polyphenols and investigates under which conditions they exhibit radioprotecting or radiosensitizing properties. The peripheral blood lymphocyte test system was used, applying concentrations ranging from 1.4 to 140 μM curcumin and 2.2 to 220 μM trans-resveratrol. The experimental design focuses first on their radioprotective effects in non-cycling lymphocytes, as uniquely visualized using cell fusion-mediated premature chromosome condensation, excluding, thus, cell-cycle interference to repair processes and activation of checkpoints. Second, the radiosensitizing potential of these chemicals on the induction of chromatid breaks in cultured lymphocytes following G2-phase irradiation was evaluated by a standardized G2-chromosomal radiosensitivity predictive assay. This assay uses caffeine for G2-checkpoint abrogation and it was applied to obtain an internal control for radiosensitivity

  3. The steady-state level and stability of TLS polymerase eta are cell cycle dependent in the yeast S. cerevisiae.

    Science.gov (United States)

    Plachta, Michal; Halas, Agnieszka; McIntyre, Justyna; Sledziewska-Gojska, Ewa

    2015-05-01

    Polymerase eta (Pol eta) is a ubiquitous translesion DNA polymerase that is capable of bypassing UV-induced pyrimidine dimers in an error-free manner. However, this specialized polymerase is error prone when synthesizing through an undamaged DNA template. In Saccharomyces cerevisiae, both depletion and overproduction of Pol eta result in mutator phenotypes. Therefore, regulation of the cellular abundance of this enzyme is of particular interest. However, based on the investigation of variously tagged forms of Pol eta, mutually contradictory conclusions have been reached regarding the stability of this polymerase in yeast. Here, we optimized a protocol for the detection of untagged yeast Pol eta and established that the half-life of the native enzyme is 80 ± 14 min in asynchronously growing cultures. Experiments with synchronized cells indicated that the cellular abundance of this translesion polymerase changes throughout the cell cycle. Accordingly, we show that the stability of Pol eta, but not its mRNA level, is cell cycle stage dependent. The half-life of the polymerase is more than fourfold shorter in G1-arrested cells than in those at G2/M. Our results, in concert with previous data for Rev1, indicate that cell cycle regulation is a general property of Y family TLS polymerases in S. cerevisiae. PMID:25766643

  4. βTrCP-mediated ubiquitylation regulates protein stability of Mis18β in a cell cycle-dependent manner.

    Science.gov (United States)

    Kim, Ik Soo; Lee, Minkyoung; Park, Joo Hyeon; Jeon, Raok; Baek, Sung Hee; Kim, Keun Il

    2014-01-01

    Ubiquitin E3 ligases including SCF complex are key regulators of cell cycle. Here, we show that Mis18β, a component of Mis18 complex governing CENP-A localization, is a new substrate of βTrCP-containing SCF complex. βTrCP interacted with Mis18β exclusively during interphase but not during mitosis and mediated proteasomal degradation of Mis18β leading to the inactivation of Mis18 complex during interphase. In addition, uncontrolled stabilization of Mis18β caused cell death. Together, we propose that βTrCP-mediated regulation of Mis18β stability is a mechanism to restrict centromere function of Mis18 complex from late mitosis to early G1 phase. PMID:24269809

  5. Cell cycle-dependent deposition of CENP-A requires the Dos1/2-Cdc20 complex.

    Science.gov (United States)

    Gonzalez, Marlyn; He, Haijin; Sun, Siyu; Li, Chen; Li, Fei

    2013-01-01

    Centromeric histone CENP-A, a variant of canonical histone H3, plays a central role in proper chromosome segregation. Loading of CENP-A at centromeres is cell cycle-regulated: parental CENP-A is deposited at centromeres during S phase, whereas newly synthesized CENP-A is deposited during later stages of the cell cycle. The mechanisms involved in deposition of CENP-A at centromeres during S phase remain poorly understood. In fission yeast, loading of CENP-A during S phase is regulated by the GATA-type factor, Ams2. Here we show that the Dos1/2-Cdc20 complex, previously characterized as a silencing complex essential for inheritance of H3K9 methylation during S phase, is also required for localization of CENP-A(cnp1) at centromeres at this stage. Disruption of Dos1 (also known as Raf1/Clr8/Cmc1), Dos2 (also known as Raf2/Clr7/Cmc2), or Cdc20, a DNA polymerase epsilon subunit, results in dissociation of CENP-A from centromeres and mislocalization of the protein to noncentromeric sites. All three mutants display spindle disorganization and mitotic defects. Inactivation of Dos1 or Cdc20 also results in accumulation of noncoding RNA transcripts from centromeric cores, a feature common to mutants affecting kinetochore integrity. We further find that Dos1 physically associates with Ams2 and is required for the association of Ams2 with centromeric cores during S phase. Finally, we show that Dos2 associates with centromeric cores during S phase and that its recruitment to centromeric cores depends on Cdc20. This study identifies a physical link between DNA replication and CENP-A assembly machinery and provides mechanistic insight into how CENP-A is faithfully inherited during S phase. PMID:23267073

  6. Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence.

    Science.gov (United States)

    Litovchick, Larisa; Sadasivam, Subhashini; Florens, Laurence; Zhu, Xiaopeng; Swanson, Selene K; Velmurugan, Soundarapandian; Chen, Runsheng; Washburn, Michael P; Liu, X Shirley; DeCaprio, James A

    2007-05-25

    The mammalian Retinoblastoma (RB) family including pRB, p107, and p130 represses E2F target genes through mechanisms that are not fully understood. In D. melanogaster, RB-dependent repression is mediated in part by the multisubunit protein complex Drosophila RBF, E2F, and Myb (dREAM) that contains homologs of the C. elegans synthetic multivulva class B (synMuvB) gene products. Using an integrated approach combining proteomics, genomics, and bioinformatic analyses, we identified a p130 complex termed DP, RB-like, E2F, and MuvB (DREAM) that contains mammalian homologs of synMuvB proteins LIN-9, LIN-37, LIN-52, LIN-54, and LIN-53/RBBP4. DREAM bound to more than 800 human promoters in G0 and was required for repression of E2F target genes. In S phase, MuvB proteins dissociated from p130 and formed a distinct submodule that bound MYB. This work reveals an evolutionarily conserved multisubunit protein complex that contains p130 and E2F4, but not pRB, and mediates the repression of cell cycle-dependent genes in quiescence. PMID:17531812

  7. Cell-cycle dependent localization of MELK and its new partner RACK1 in epithelial versus mesenchyme-like cells in Xenopus embryo

    Directory of Open Access Journals (Sweden)

    Isabelle Chartrain

    2013-08-01

    Maternal Embryonic Leucine zipper Kinase (MELK was recently shown to be involved in cell division of Xenopus embryo epithelial cells. The cytokinetic furrow of these cells ingresses asymmetrically and is developmentally regulated. Two subpopulations of xMELK, the mMELK (for “mitotic” xMELK and iMELK (“interphase” xMELK, which differ in their spatial and temporal regulation, are detected in Xenopus embryo. How cells regulate these two xMELK populations is unknown. In this study we show that, in epithelial cells, xMELK is present at a higher concentration at the apical junctional complex, in contrast to mesenchyme-like cells, which have uniform distribution of cortical MELK. Interestingly, mMELK and iMELK also differ by their requirements towards cell–cell contacts to establish their proper cortical localization both in epithelial and mesenchyme-like cells. Receptor for Activated protein Kinase C (RACK1, which we identified as an xMELK partner, co-localizes with xMELK at the tight junction. Moreover, a truncated RACK1 construct interferes with iMELK localization at cell–cell contacts. Collectively, our results suggest that iMELK and RACK1 are present in the same complex and that RACK1 is involved in the specific recruitment of iMELK at the apical junctional complex in epithelial cells of Xenopus embryos.

  8. Regulation of store-operated Ca2+ entry activity by cell cycle dependent up-regulation of Orai2 in brain capillary endothelial cells

    International Nuclear Information System (INIS)

    Store-operated Ca2+ entry (SOCE) via Orai1 and STIM1 complex is supposed to have obligatory roles in the regulation of cellular functions of vascular endothelial cells, while little is known about the contribution of Orai2. Quantitative PCR and Western blot analyses indicated the expression of Orai2 and STIM2, in addition to Orai1 and STIM1 in bovine brain capillary endothelial cell line, t-BBEC117. During the exponential growth of t-BBEC117, the knockdown of Orai1 and STIM1 significantly reduced the SOCE activity, whereas Orai2 and STIM2 siRNAs had no effect. To examine whether endogenous SOCE activity contributes to the regulation of cell cycle progression, t-BBEC117 were synchronized using double thymidine blockage. At the G2/M phase, Ca2+ influx via SOCE was decreased and Orai2 expression was increased compared to the G0/G1 phase. When Orai2 was knocked down at the G2/M phase, the decrease in SOCE was removed, and cell proliferation was partly attenuated. Taken together, Orai1 significantly contributes to cell proliferation via the functional expression, which is presumably independent of the cell cycle phases. In construct, Orai2 is specifically up-regulated during the G2/M phase, negatively modulates the SOCE activity, and may contribute to the regulation of cell cycle progression in brain capillary endothelial cells. - Highlights: • Orai1 is essential for SOCE activity in brain capillary endothelial cells (BCECs). • Cell cycle independent expression of Orai1 regulated SOCE and cell proliferation. • Orai2 was up-regulated only at G2/M phase and this consequently reduced SOCE. • Orai2 as well as Orai1 is a key player controlling SOCE and proliferation in BCECs

  9. Regulation of store-operated Ca{sup 2+} entry activity by cell cycle dependent up-regulation of Orai2 in brain capillary endothelial cells

    Energy Technology Data Exchange (ETDEWEB)

    Kito, Hiroaki [Department of Molecular & Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya (Japan); Department of Pharmacology, Division of Pathological Sciences, Kyoto Pharmaceutical University, Kyoto (Japan); Yamamura, Hisao; Suzuki, Yoshiaki; Yamamura, Hideto [Department of Molecular & Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya (Japan); Ohya, Susumu [Department of Molecular & Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya (Japan); Department of Pharmacology, Division of Pathological Sciences, Kyoto Pharmaceutical University, Kyoto (Japan); Asai, Kiyofumi [Department of Molecular Neurobiology, Graduate School of Medical Sciences, Nagoya City University, Nagoya (Japan); Imaizumi, Yuji, E-mail: yimaizum@phar.nagoya-cu.ac.jp [Department of Molecular & Cellular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya (Japan)

    2015-04-10

    Store-operated Ca{sup 2+} entry (SOCE) via Orai1 and STIM1 complex is supposed to have obligatory roles in the regulation of cellular functions of vascular endothelial cells, while little is known about the contribution of Orai2. Quantitative PCR and Western blot analyses indicated the expression of Orai2 and STIM2, in addition to Orai1 and STIM1 in bovine brain capillary endothelial cell line, t-BBEC117. During the exponential growth of t-BBEC117, the knockdown of Orai1 and STIM1 significantly reduced the SOCE activity, whereas Orai2 and STIM2 siRNAs had no effect. To examine whether endogenous SOCE activity contributes to the regulation of cell cycle progression, t-BBEC117 were synchronized using double thymidine blockage. At the G2/M phase, Ca{sup 2+} influx via SOCE was decreased and Orai2 expression was increased compared to the G0/G1 phase. When Orai2 was knocked down at the G2/M phase, the decrease in SOCE was removed, and cell proliferation was partly attenuated. Taken together, Orai1 significantly contributes to cell proliferation via the functional expression, which is presumably independent of the cell cycle phases. In construct, Orai2 is specifically up-regulated during the G2/M phase, negatively modulates the SOCE activity, and may contribute to the regulation of cell cycle progression in brain capillary endothelial cells. - Highlights: • Orai1 is essential for SOCE activity in brain capillary endothelial cells (BCECs). • Cell cycle independent expression of Orai1 regulated SOCE and cell proliferation. • Orai2 was up-regulated only at G2/M phase and this consequently reduced SOCE. • Orai2 as well as Orai1 is a key player controlling SOCE and proliferation in BCECs.

  10. Decreased radioiodine uptake of FRTL-5 cells after 131I incubation in vitro: molecular biological investigations indicate a cell cycle-dependent pathway

    International Nuclear Information System (INIS)

    In radioiodine therapy the ''stunning phenomenon'' is defined as a reduction of radioiodine uptake after diagnostic application of 131I. In the current study, we established an in vitro model based on the ''Fisher rat thyrocyte cell line no. 5'' (FRTL-5) to investigate the stunning. TSH-stimulated FRTL-5 cells were incubated with 131I. Time-dependent 131I uptake and the viability of FRTL-5 cells were evaluated at 4-144 h after radioiodine application. All data was corrected for number of viable cells, half life and 131I concentration. Sodium iodide symporter (NIS) and the housekeeping gene (β-actin, GAPDH) levels were quantified by quantitative polymerase chain reaction (qPCR). Additionally, immunohistochemical staining (IHC) of NIS on the cell membrane was carried out. FRTL-5 monolayer cell cultures showed a specific maximum uptake of 131I 24-48 h after application. Significantly decreased 131I uptake values were observed after 72-144 h. The decrease in radioiodine uptake was correlated with decreasing mRNA levels of NIS and housekeeping genes. In parallel, unlike in controls, IHC staining of NIS on FRTL-5 cells declined significantly after 131I long-term incubation. It could be demonstrated that during 131I incubation of FRTL-5 cells, radioiodine uptake decreased significantly. Simultaneously decreasing levels of NIS mRNA and protein expression suggest a NIS-associated mechanism. Since mRNA levels of housekeeping genes decreased, too, the reduced NIS expression might be provoked by a cell cycle arrest. Our investigations recommend the FRTL-5 model as a valuable tool for further molecular biological investigations of the stunning phenomenon. (orig.)

  11. The mammalian Cut homeodomain protein functions as a cell-cycle-dependent transcriptional repressor which downmodulates p21WAF1/CIP1/SDI1 in S phase.

    OpenAIRE

    Coqueret, O; Bérubé, G; Nepveu, A

    1998-01-01

    Cut is a homeodomain transcription factor which has the unusual property of containing several DNA-binding domains: three regions called Cut repeats and the Cut homeodomain. Genetic studies in Drosophila melanogaster indicate that cut plays important roles in the determination and maintenance of cell-type specificity. In the present study, we show that mammalian Cut proteins may yet play another biological role, specifically in proliferating cells. We found that the binding of Cut to a consen...

  12. Distinct kinetics of DNA repair protein accumulation at DNA lesions and cell cycle-dependent formation of gammaH2AX- and NBS1-positive repair foci

    Czech Academy of Sciences Publication Activity Database

    Suchánková, Jana; Kozubek, Stanislav; Legartová, Soňa; Sehnalová, Petra; Kuntzinger, T.; Bártová, Eva

    2015-01-01

    Roč. 107, č. 12 (2015), s. 440-454. ISSN 0248-4900 R&D Projects: GA ČR(CZ) GBP302/12/G157; GA ČR(CZ) GA13-07822S Institutional support: RVO:68081707 Keywords : Cell cycle * DNA repair * Interphase Subject RIV: BO - Biophysics Impact factor: 3.506, year: 2014

  13. Proximal and distal regulatory elements that influence in vivo expression of a cell cycle-dependent human H4 histone gene

    International Nuclear Information System (INIS)

    The authors have examined the sequences required in vivo to promote transcription of a cell cycle-regulated human H4 histone gene. Deletion mutants of the 5' flanking region were assayed in mouse cells or fused with the chloramphenicol acetyltransferase (CAT) gene for assay in HeLa cells. The functional limits of the regulatory sequences were shown to extend at least 6.5 kilobases (kb) upstream. Sequences sufficient for correctly initiated transcription were found in the 70 base pairs (bp) immediately 5' to the cap site. A proximal element located 200-400 bp upstream increased the level of transcription several times above the basal level, although not to maximal levels. Maximal levels of expression were achieved with 6.5 kb of 5' flanking sequence adjacent to the proximal promoter sequences or when a distal enhancer element with both position- and orientation-independent function was moved proximal to the promoter. The results indicate that a series of 5' cis-acting sequences are functionally related to the fidelity and level of expression of this human H4 histone gene

  14. Cell cycle-dependent regulation of RNA polymerase I transcription: The nucleolar transcription factor UBF is inactive in mitosis and early G1

    OpenAIRE

    Klein, Joachim; Grummt, Ingrid

    1999-01-01

    Transcription of ribosomal RNA genes by RNA polymerase (pol) I oscillates during the cell cycle, being maximal in S and G2 phase, repressed during mitosis, and gradually recovering during G1 progression. We have shown that transcription initiation factor (TIF)-IB/SL1 is inactivated during mitosis by cdc2/cyclin B-directed phosphorylation of TAFI110. In this study, we have monitored reactivation of transcription after exit from mitosis. We demonstrate that the pol I factor UBF is also inactiva...

  15. Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors.

    Science.gov (United States)

    Vallejos, Maricarmen; Deforges, Jules; Plank, Terra-Dawn M; Letelier, Alejandro; Ramdohr, Pablo; Abraham, Christopher G; Valiente-Echeverría, Fernando; Kieft, Jeffrey S; Sargueil, Bruno; López-Lastra, Marcelo

    2011-08-01

    The 5' leader of the human immunodeficiency virus type 1 (HIV-1) genomic RNA harbors an internal ribosome entry site (IRES) that is functional during the G2/M phase of the cell cycle. Here we show that translation initiation mediated by the HIV-1 IRES requires the participation of trans-acting cellular factors other than the canonical translational machinery. We used 'standard' chemical and enzymatic probes and an 'RNA SHAPE' analysis to model the structure of the HIV-1 5' leader and we show, by means of a footprinting assay, that G2/M extracts provide protections to regions previously identified as crucial for HIV-1 IRES activity. We also assessed the impact of mutations on IRES function. Strikingly, mutations did not significantly affect IRES activity suggesting that the requirement for pre-formed stable secondary or tertiary structure within the HIV-1 IRES may not be as strict as has been described for other viral IRESes. Finally, we used a proteomic approach to identify cellular proteins within the G2/M extracts that interact with the HIV-1 5' leader. Together, data show that HIV-1 IRES-mediated translation initiation is modulated by cellular proteins. PMID:21482538

  16. Uptake of host cell transforming growth factor-ß by Trypanosoma cruzi amastigotes in cardiomyocytes: potential role in parasite cycle completion. : Cycle-dependent uptake of TGF-ß by T. cruzi

    OpenAIRE

    Waghabi, Mariana,; Keramidas, Michelle; Bailly, Sabine; Degrave, Wim,; Mendonça-Lima, Leila; Soeiro, Maria De Nazaré,; Meirelles, Maria De Nazareth,; Paciornik, Sidnei; Araújo-Jorge, Tania,; Feige, Jean-Jacques

    2005-01-01

    Transforming growth factor-β (TGF-β) is a cytokine that plays various functions in the control of Trypanosoma cruzi infectivity and in the progression of Chagas disease. When we immunostained Trypanosoma cruzi-infected cardiomyocytes (following either in vivo or in vitro infections) for TGF-β, we observed stronger immunoreactivity in parasites than in host cells. TGF-β immunoreactivity evolved during parasite cycle progression: intense staining in amastigotes versus very faint staining in try...

  17. A new analysis of radiation-induced cytogenetic damage in human lymphocytes using the PCC technique, and its implications for biological dosimetry and the understanding of cell-cycle-dependent radiosensitivity fluctuations

    International Nuclear Information System (INIS)

    The objectives of the project are: to develop a sensitive biological dosemeter, based on the analysis of C-banded peripheral blood lymphocyte prematurely condensed chromosomes (PCCs), for the early assessment of radiation injury and the establishment of absorbed dose estimates in accidental overexposures; and to elucidate the mechanisms of radiation action at the molecular, chromosomal and cellular levels by the study of the effects of DNA repair inhibitors on the repair of radiation damage, effects of BrdUrd incorporation on radiation damage, effects of hyperthermia on the induction and repair of radiation-induced damage, and induction and repair of radiation damage in an X-ray sensitive CHO mutant cell line. (authors) 16 refs., 1 fig

  18. Quantifying Cell-to-Cell Variations in Lithium Ion Batteries

    Directory of Open Access Journals (Sweden)

    Shriram Santhanagopalan

    2012-01-01

    Full Text Available Lithium ion batteries have conventionally been manufactured in small capacities but large volumes for consumer electronics applications. More recently, the industry has seen a surge in the individual cell capacities, as well as the number of cells used to build modules and packs. Reducing cell-to-cell and lot-to-lot variations has been identified as one of the major means to reduce the rejection rate when building the packs as well as to improve pack durability. The tight quality control measures have been passed on from the pack manufactures to the companies building the individual cells and in turn to the components. This paper identifies a quantitative procedure utilizing impedance spectroscopy, a commonly used tool, to determine the effects of material variability on the cell performance, to compare the relative importance of uncertainties in the component properties, and to suggest a rational procedure to set quality control specifications for the various components of a cell, that will reduce cell-to-cell variability, while preventing undue requirements on uniformity that often result in excessive cost of manufacturing but have a limited impact on the cells' performance.

  19. Investigation of spatial variations in collection efficiency of solar cells

    Science.gov (United States)

    Hiltner, Jason Fredrick

    2001-11-01

    In an effort to investigate spatial variations in solar cells, an apparatus which is capable of mapping collection efficiency with micron resolution and near- solar intensity has been developed. Local reductions in collection are observed in CdTe- and Cu(In1- xGax)Se2- based devices, and are characterized by measuring the response as a function of cell bias and incident laser intensity. By modeling this data with an equivalent circuit, it is clear that the majority of local variations in the response are due to series resistance variations. Further, direct evidence is given for bandgap variations in CdTe solar cells, which are correlated with high resistance regions in some devices. The bandgap variation is attributed to diffusion of S into CdTe, forming the lower bandgap CdTe1- xSx, during the post-deposition CdCl2 treatment commonly used to improve performance. Investigation of the impact of CdCl2 on a CdTe solar cell indicates that the treatment reduces the number of variations seen with above-bandgap photon energies, but also increases local variations in bandgap. The latter effect has been attributed to non-uniform penetration of CdCl2 to the device interface. Finally, elevated-temperature stress on CdTe devices is shown to preferentially degrade regions which exhibit decreases in bandgap, and hence increased S alloying.

  20. Batch variation between branchial cell cultures: An analysis of variance

    DEFF Research Database (Denmark)

    Hansen, Heinz Johs. Max; Grosell, M.; Kristensen, L.

    2003-01-01

    We present in detail how a statistical analysis of variance (ANOVA) is used to sort out the effect of an unexpected batch-to-batch variation between cell cultures. Two separate cultures of rainbow trout branchial cells were grown on permeable filtersupports ("inserts"). They were supposed to be...

  1. The Variation of Electrochemical Cell Potentials with Temperature

    Science.gov (United States)

    Peckham, Gavin D.; McNaught, Ian J.

    2011-01-01

    Electrochemical cell potentials have no simple relationship with temperature but depend on the interplay between the sign and magnitude of the isothermal temperature coefficient, dE[degrees]/dT, and on the magnitude of the reaction quotient, Q. The variations in possible responses of standard and non-standard cell potentials to changes in the…

  2. Measuring and modelling cell-to-cell variation in uptake of gold nanoparticles

    OpenAIRE

    Jeynes, JCG; Jeynes, C.; Merchant, MJ; Kirkby, KJ

    2013-01-01

    The cell-to-cell variation of gold nanoparticle (GNP) uptake is important for therapeutic applications. We directly counted the GNPs in hundreds of individual cells, and showed that the large variation from cell-to-cell could be directly modelled by assuming log-normal distributions of both cell mass and GNP rate of uptake. This was true for GNPs non-specifically bound to fetal bovine serum or conjugated to a cell penetrating peptide. Within a population of cells, GNP content varied naturally...

  3. Mitochondrial DNA sequence variation in single cells from leukemia patients

    OpenAIRE

    Yao, Yong-Gang; Ogasawara, Yoji; Kajigaya, Sachiko; Molldrem, Jeffrey J.; Falcão, Roberto P; Pintão, Maria-Carolina; McCoy, J. Philip; Rizzatti, Edgar Gil; Young, Neal S

    2007-01-01

    A high frequency of mtDNA somatic mutation has been observed in many tumors as well as in aging tissues. In this study, we analyzed the mtDNA control region sequence variation in 3534 single normal cells and individual blasts from 18 patients with leukemia and 10 healthy donors, to address the mutation process in leukemic cells. We found significant differences in mtDNA sequence, as represented by the number of haplotypes and the mean number of cells with each nonaggregate haplotype in a popu...

  4. Robust Inference of Cell-to-Cell Expression Variations from Single- and K-Cell Profiling.

    Science.gov (United States)

    Narayanan, Manikandan; Martins, Andrew J; Tsang, John S

    2016-07-01

    Quantifying heterogeneity in gene expression among single cells can reveal information inaccessible to cell-population averaged measurements. However, the expression level of many genes in single cells fall below the detection limit of even the most sensitive technologies currently available. One proposed approach to overcome this challenge is to measure random pools of k cells (e.g., 10) to increase sensitivity, followed by computational "deconvolution" of cellular heterogeneity parameters (CHPs), such as the biological variance of single-cell expression levels. Existing approaches infer CHPs using either single-cell or k-cell data alone, and typically within a single population of cells. However, integrating both single- and k-cell data may reap additional benefits, and quantifying differences in CHPs across cell populations or conditions could reveal novel biological information. Here we present a Bayesian approach that can utilize single-cell, k-cell, or both simultaneously to infer CHPs within a single condition or their differences across two conditions. Using simulated as well as experimentally generated single- and k-cell data, we found situations where each data type would offer advantages, but using both together can improve precision and better reconcile CHP information contained in single- and k-cell data. We illustrate the utility of our approach by applying it to jointly generated single- and k-cell data to reveal CHP differences in several key inflammatory genes between resting and inflammatory cytokine-activated human macrophages, delineating differences in the distribution of 'ON' versus 'OFF' cells and in continuous variation of expression level among cells. Our approach thus offers a practical and robust framework to assess and compare cellular heterogeneity within and across biological conditions using modern multiplexed technologies. PMID:27438699

  5. Business Cycle Dependent Unemployment Benefits with Wealth Heterogeneity and Precautionary Savings

    DEFF Research Database (Denmark)

    Kristoffersen, Mark Strøm

    In the wake of the financial and economic crisis the discussion about social insurance and optimal stabilization policies has re-blossomed. This paper adds to the literature by studying the effects of a business cycle dependent level of unemployment benefits in a model with labor market matching...... of the distortionary effect (on job creation) from providing unemployment insurance, whereas countercyclical benefits facilitate consumption smoothing....

  6. Respiratory Cycle-Dependent Atrial Trachycardia; its Unique Characteristics and Relation with Autonomic Nerve System

    Directory of Open Access Journals (Sweden)

    Teppei Yamamoto, MD

    2012-12-01

    Full Text Available Respiration influences the sinus heart rate, however, little is still known about the tachyarrhythmias related to respiration. Atrial tachycardia (AT rarely emerges during inspiration and it also ceases during expiration. This type of AT is thus called respiratory cycle-dependent atrial tachycardia (RCAT, and it demonstrates a centrifugal activation pattern. Based on these peculiar P wave morphologies, the foci converged either around the right superior pulmonary vein (RSPV or inside the superior vena cava where the anterior right ganglionated plexi (ARGP is considered to be located. The mechanism of such AT is therefore thought to be related to the activity of the autonomic system.

  7. Cell cycle dependent expression of Plk 1 in synchronized porcine fetal fibroblasts

    Czech Academy of Sciences Publication Activity Database

    Anger, M.; Kues, W. A.; Klíma, J.; Mielenz, M.; Kubelka, M.; Motlík, J.; Ešner, M.; Dvořák, Petr; Carnwath, J. W.; Niemann, H.

    2003-01-01

    Roč. 65, - (2003), s. 245-253. ISSN 1040-452X R&D Projects: GA MŠk LN00A065 Institutional research plan: CEZ:AV0Z5039906 Keywords : serum deprivation Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.543, year: 2003

  8. Systematic regional variations in Purkinje cell spiking patterns.

    Directory of Open Access Journals (Sweden)

    Jianqiang Xiao

    Full Text Available In contrast to the uniform anatomy of the cerebellar cortex, molecular and physiological studies indicate that significant differences exist between cortical regions, suggesting that the spiking activity of Purkinje cells (PCs in different regions could also show distinct characteristics. To investigate this possibility we obtained extracellular recordings from PCs in different zebrin bands in crus IIa and vermis lobules VIII and IX in anesthetized rats in order to compare PC firing characteristics between zebrin positive (Z+ and negative (Z- bands. In addition, we analyzed recordings from PCs in the A2 and C1 zones of several lobules in the posterior lobe, which largely contain Z+ and Z- PCs, respectively. In both datasets significant differences in simple spike (SS activity were observed between cortical regions. Specifically, Z- and C1 PCs had higher SS firing rates than Z+ and A2 PCs, respectively. The irregularity of SS firing (as assessed by measures of interspike interval distribution was greater in Z+ bands in both absolute and relative terms. The results regarding systematic variations in complex spike (CS activity were less consistent, suggesting that while real differences can exist, they may be sensitive to other factors than the cortical location of the PC. However, differences in the interactions between SSs and CSs, including the post-CS pause in SSs and post-pause modulation of SSs, were also consistently observed between bands. Similar, though less strong trends were observed in the zonal recordings. These systematic variations in spontaneous firing characteristics of PCs between zebrin bands in vivo, raises the possibility that fundamental differences in information encoding exist between cerebellar cortical regions.

  9. Variation of DNA Methylome of Zebrafish Cells under Cold Pressure

    Science.gov (United States)

    Xu, Qiongqiong; Luo, Juntao; Shi, Yingdi; Li, Xiaoxia; Yan, Xiaonan; Zhang, Junfang

    2016-01-01

    DNA methylation is an essential epigenetic mechanism involved in multiple biological processes. However, the relationship between DNA methylation and cold acclimation remains poorly understood. In this study, Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) was performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cells (ZF4) and its variation under cold pressure. MeDIP-seq assay was conducted with ZF4 cells cultured at appropriate temperature of 28°C and at low temperature of 18°C for 5 (short-term) and 30 (long-term) days, respectively. Our data showed that DNA methylation level of whole genome increased after a short-term cold exposure and decreased after a long-term cold exposure. It is interesting that metabolism of folate pathway is significantly hypomethylated after short-term cold exposure, which is consistent with the increased DNA methylation level. 21% of methylation peaks were significantly altered after cold treatment. About 8% of altered DNA methylation peaks are located in promoter regions, while the majority of them are located in non-coding regions. Methylation of genes involved in multiple cold responsive biological processes were significantly affected, such as anti-oxidant system, apoptosis, development, chromatin modifying and immune system suggesting that those processes are responsive to cold stress through regulation of DNA methylation. Our data indicate the involvement of DNA methylation in cellular response to cold pressure, and put a new insight into the genome-wide epigenetic regulation under cold pressure. PMID:27494266

  10. A Technique for Designing Variation Resilient Subthreshold Sram Cell

    Directory of Open Access Journals (Sweden)

    Aminul Islam

    2013-04-01

    Full Text Available This paper presents a technique for designing a variability aware subthreshold SRAM cell. The architecture of the proposed cell is similar to the standard read-decoupled 8-transistor (RD8T SRAM cell with the exception that the access FETS are replaced with transmission gates (TGs. In this work, various design metrics are assessed and compared with RD8T SRAM cell. The proposed design offers 2.14× and 1.75× improvement in TRA (read access time and TWA (write access time respectively compared with RD8T. It proves its robustness against process variations by featuring narrower spread in TRA distribution (2.35× and TWA distribution (3.79× compared with RD8T. The proposed bitcell offers 1.16× higher read current (IREAD and 1.64× lower bitline leakage current (ILEAK respectively compared with RD8T. It also shows its robustness by offering 1.34× (1.58× tighter spread in IREAD (ILEAK compared with RD8T. It exhibits 1.42× larger IREAD to ILEAK ratio. It shows 2.2× higher frequency @ 250 mV with read bitline capacitance of 10 fF. Besides, the proposed bitcell achieves same read stability and write-ability as that of RD8T at the cost of 3 extra transistors. The leakage power of the proposed design is close to that of RD8T.   ABSTRAK: Kertas kerja ini membentangkan teknik merekabentuk sel bawah ambang SRAM yang bolehubah. Senibina sel yang dicadangkan adalah sama dengan sel SRAM 8-transistor (RD8T “pisahan-bacaan” piawai kecuali FET akses  digantikan dengan sel pintu transmisi (TGs. Di dalam kajian ini, beberapa metrik rekabentuk dinilai dan dibandingkan dengan sel RD8T SRAM. Rekabentuk yang dicadangkan menawarkan  peningkatan 2.14× dan 1.75×  dalam TRA (masa akses baca dan TWA (masa akses tulis berbanding dengan RD8T. Ia membuktikan kekukuhan variasi proses dengan menampilkan tebaran yang lebih sempit dalam pengagihan TRA (2.35 × dan pengagihan TWA (3.79 × berbanding dengan RD8T. Sel-Bit yang dicadangkan mempunyai arus baca 1.16

  11. Cell cycle variation in x-ray survival for cells from spheroids measured by volume cell sorting

    International Nuclear Information System (INIS)

    Considerable work has been done studying the variation in cell survival as a function of cell cycle position for monolayers or single cells exposed to radiation. Little is known about the effects of multicellular growth on the relative radiation sensitivity of cells in different cell cycle stages. The authors have developed a new technique for measuring the response of cells, using volume cell sorting, which is rapid, non-toxic, and does not require cell synchronization. By combining this technique with selective spheroid dissociation,they have measured the age response of cells located at various depths in EMT6 and Colon 26 spheroids. Although cells in the inner region had mostly G1-phase DNA contents, 15-20% had S- and G2-phase DNA contents. Analysis of these cells using BrdU labeling and flow cytometric analysis with a monoclonal antibody to BrdU indicated that the inner region cells were not synthesizing DNA. Thus, the authors were able to measure the radiation response of cells arrested in G1, S and G2 cell cycle phases. Comparison of inner and outer spheroid regions, and monolayer cultures, indicates that it is improper to extrapolate age response data in standard culture conditions to the situation in spheroids

  12. Ion-swimming speed variation of Vibrio cholerae cells

    Indian Academy of Sciences (India)

    Anindito Sen; Ranjan K Nandi; Amar N Ghosh

    2005-09-01

    In the present work we report the variation in swimming speed of Vibrio cholerae with respect to the change in concentration of sodium ions in the medium. We have also studied the variation in swimming speed with respect to temperature. We find that the swimming speed initially shows a linear increase with the increase of the sodium ions in the medium and then plateaus. The range within which the swimming speed attains saturation is approximately the same at different temperatures.

  13. Lithium-ion cell-to-cell variation during battery electric vehicle operation

    Science.gov (United States)

    Schuster, Simon F.; Brand, Martin J.; Berg, Philipp; Gleissenberger, Markus; Jossen, Andreas

    2015-11-01

    484 new and 1908 aged lithium-ion cells out of two identical battery electric vehicles (i.e. 954 cells each) were characterized by capacity and impedance measurements to yield a broad set of data for distribution fit analysis. Results prove alteration from normal to Weibull distribution for the parameters of lithium-ion cells with the progress of aging. Cells with abnormal characteristics in the aged state mostly exhibit lower capacities as compared to the distribution mode which is typical for the left-skewed Weibull shape. In addition, the strength of variation and the amount of outliers both are generally increased with the aging progress. Obtained results are compared to vehicles' operational data to provide recommendations with the aim to minimize the increasing parameter spread. However, neither temperature gradients in the battery pack nor an insufficient balancing procedure were determined. As the appearance of cells with suspicious parameters could not be assigned to local weak spots of the battery pack, a random and inevitable type of origin is assumed. Hence, the battery management system must ensure to detect outliers in a reliable manner and to balance resulting drifts of cells' states of charge to guarantee a safe battery storage operation.

  14. Variations in cell morphology in the canine cruciate ligament complex.

    Science.gov (United States)

    Smith, K D; Vaughan-Thomas, A; Spiller, D G; Clegg, P D; Innes, J F; Comerford, E J

    2012-08-01

    Cell morphology may reflect the mechanical environment of tissues and influence tissue physiology and response to injury. Normal cruciate ligaments (CLs) from disease-free stifle joints were harvested from dog breeds with a high (Labrador retriever) and low (Greyhound) risk of cranial cruciate ligament (CCL) rupture. Antibodies against the cytoskeletal components vimentin and alpha tubulin were used to analyse cell morphology; nuclei were stained with 4',6-diamidino-2-phenylindole, and images were collected using conventional and confocal microscopy. Both cranial and caudal CLs contained cells of heterogenous morphologies. Cells were arranged between collagen bundles and frequently had cytoplasmic processes. Some of these processes were long (type A cells), others were shorter, thicker and more branched (type B cells), and some had no processes (type C cells). Processes were frequently shown to contact other cells, extending longitudinally and transversely through the CLs. Cells with longer processes had fusiform nuclei, and those with no processes had rounded nuclei and were more frequent in the mid-substance of both CLs. Cells with long processes were more commonly noted in the CLs of the Greyhound. As contact between cells may facilitate direct communication, variances in cell morphology between breeds at a differing risk of CCL rupture may reflect differences in CL physiology. PMID:22465617

  15. A new method for decreasing cell-load variation in dynamic cellular manufacturing systems

    OpenAIRE

    Aidin Delgoshaei; Mohd Khairol Mohd Ariffin,; Btht Hang Tuah Bin Baharudin; Zulkiflle Leman

    2016-01-01

    Cell load variation is considered a significant shortcoming in scheduling of cellular manufacturing systems. In this article, a new method is proposed for scheduling dynamic cellular manufacturing systems in the presence of bottleneck and parallel machines. The aim of this method is to control cell load variation during the process of determining the best trading off values between in-house manufacturing and outsourcing. A genetic algorithm (GA) is developed because of the high potential of t...

  16. Somaclonal variation: a morphogenetic and biochemical analysis of Mandevilla velutina cultured cells

    Directory of Open Access Journals (Sweden)

    M. Maraschin

    2002-06-01

    Full Text Available Cell cultures of Mandevilla velutina have proved to be an interesting production system for biomass and secondary metabolites able to inhibit the hypotensive activity of bradykinin, a nonapeptide generated in plasma during tissue trauma. The crude ethyl acetate extract of cultured cells contains about 31- to 79-fold more potent anti-bradykinin compounds (e.g., velutinol A than that obtained with equivalent extracts of tubers. Somaclonal variation may be an explanation for the wide range of inhibitor activity found in the cell cultures. The heterogeneity concerning morphology, differentiation, carbon dissimilation, and velutinol A production in M. velutina cell cultures is reported. Cell cultures showed an asynchronous growth and cells in distinct developmental stages. Meristematic cells were found as the major type, with several morphological variations. Cell aggregates consisting only of meristematic cells, differentiated cells containing specialized cell structures such as functional chloroplasts (cytodifferentiation and cells with embryogenetic characteristics were observed. The time course for sucrose metabolism indicated cell populations with significant differences in growth and metabolic rates, with the highest biomass-producing cell line showing a cell cycle 60% shorter and a metabolic rate 33.6% higher than the control (F2 cell population. MALDI-TOF mass spectrometric analysis of velutinol A in selected cell lines demonstrated the existence of velutinol A producing and nonproducing somaclones. These results point to a high genetic heterogeneity in general and also in terms of secondary metabolite content.

  17. Variation in RNA virus mutation rates across host cells.

    Directory of Open Access Journals (Sweden)

    Marine Combe

    2014-01-01

    Full Text Available It is well established that RNA viruses exhibit higher rates of spontaneous mutation than DNA viruses and microorganisms. However, their mutation rates vary amply, from 10(-6 to 10(-4 substitutions per nucleotide per round of copying (s/n/r and the causes of this variability remain poorly understood. In addition to differences in intrinsic fidelity or error correction capability, viral mutation rates may be dependent on host factors. Here, we assessed the effect of the cellular environment on the rate of spontaneous mutation of the vesicular stomatitis virus (VSV, which has a broad host range and cell tropism. Luria-Delbrück fluctuation tests and sequencing showed that VSV mutated similarly in baby hamster kidney, murine embryonic fibroblasts, colon cancer, and neuroblastoma cells (approx. 10(-5 s/n/r. Cell immortalization through p53 inactivation and oxygen levels (1-21% did not have a significant impact on viral replication fidelity. This shows that previously published mutation rates can be considered reliable despite being based on a narrow and artificial set of laboratory conditions. Interestingly, we also found that VSV mutated approximately four times more slowly in various insect cells compared with mammalian cells. This may contribute to explaining the relatively slow evolution of VSV and other arthropod-borne viruses in nature.

  18. Variational method for the minimization of entropy generation in solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Smit, Sjoerd; Kessels, W. M. M., E-mail: w.m.m.kessels@tue.nl [Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven (Netherlands)

    2015-04-07

    In this work, a method is presented to extend traditional solar cell simulation tools to make it possible to calculate the most efficient design of practical solar cells. The method is based on the theory of nonequilibrium thermodynamics, which is used to derive an expression for the local entropy generation rate in the solar cell, making it possible to quantify all free energy losses on the same scale. The framework of non-equilibrium thermodynamics can therefore be combined with the calculus of variations and existing solar cell models to minimize the total entropy generation rate in the cell to find the most optimal design. The variational method is illustrated by applying it to a homojunction solar cell. The optimization results in a set of differential algebraic equations, which determine the optimal shape of the doping profile for given recombination and transport models.

  19. Variation of DNA damage levels in peripheral blood mononuclear cells isolated in different laboratories

    DEFF Research Database (Denmark)

    Godschalk, Roger W L; Ersson, Clara; Stępnik, Maciej;

    2014-01-01

    This study investigated the levels of DNA strand breaks and formamidopyrimidine DNA glycosylase (FPG) sensitive sites, as assessed by the comet assay, in peripheral blood mononuclear cells (PBMC) from healthy women from five different countries in Europe. The laboratory in each country (referred to...... as 'centre') collected and cryopreserved PBMC samples from three donors, using a standardised cell isolation protocol. The samples were analysed in 13 different laboratories for DNA damage, which is measured by the comet assay. The study aim was to assess variation in DNA damage in PBMC samples that...... were collected in the same way and processed using the same blood isolation procedure. The inter-laboratory variation was the prominent contributor to the overall variation. The inter-laboratory coefficient of variation decreased for both DNA strand breaks (from 68 to 26%) and FPG sensitive sites (from...

  20. Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

    DEFF Research Database (Denmark)

    Hou, Yong; Wu, Kui; Shi, Xulian;

    2015-01-01

    -oligonucleotide-primed PCR (DOP-PCR) and multiple annealing and looping-based amplification cycles (MALBAC). However, a comprehensive comparison of variations detection performance between these WGA methods has not yet been performed. RESULTS: We systematically compared the advantages and disadvantages of different WGA...... methods, focusing particularly on variations detection. Low-coverage whole-genome sequencing revealed that DOP-PCR had the highest duplication ratio, but an even read distribution and the best reproducibility and accuracy for detection of copy-number variations (CNVs). However, MDA had significantly......BACKGROUND: Single-cell resequencing (SCRS) provides many biomedical advances in variations detection at the single-cell level, but it currently relies on whole genome amplification (WGA). Three methods are commonly used for WGA: multiple displacement amplification (MDA), degenerate...

  1. Life cycle-dependent cytoskeletal modifications in Plasmodium falciparum infected erythrocytes.

    Directory of Open Access Journals (Sweden)

    Hui Shi

    Full Text Available Plasmodium falciparum infection of human erythrocytes is known to result in the modification of the host cell cytoskeleton by parasite-coded proteins. However, such modifications and corresponding implications in malaria pathogenesis have not been fully explored. Here, we probed the gradual modification of infected erythrocyte cytoskeleton with advancing stages of infection using atomic force microscopy (AFM. We reported a novel strategy to derive accurate and quantitative information on the knob structures and their connections with the spectrin network by performing AFM-based imaging analysis of the cytoplasmic surface of infected erythrocytes. Significant changes on the red cell cytoskeleton were observed from the expansion of spectrin network mesh size, extension of spectrin tetramers and the decrease of spectrin abundance with advancing stages of infection. The spectrin network appeared to aggregate around knobs but also appeared sparser at non-knob areas as the parasite matured. This dramatic modification of the erythrocyte skeleton during the advancing stage of malaria infection could contribute to the loss of deformability of the infected erythrocyte.

  2. Donor Dependent Variations in Hematopoietic Differentiation among Embryonic and Induced Pluripotent Stem Cell Lines

    Science.gov (United States)

    Féraud, Olivier; Valogne, Yannick; Melkus, Michael W.; Zhang, Yanyan; Oudrhiri, Noufissa; Haddad, Rima; Daury, Aurélie; Rocher, Corinne; Larbi, Aniya; Duquesnoy, Philippe; Divers, Dominique; Gobbo, Emilie; Brunet de la Grange, Philippe; Louache, Fawzia; Bennaceur-Griscelli, Annelise; Mitjavila-Garcia, Maria Teresa

    2016-01-01

    Hematopoiesis generated from human embryonic stem cells (ES) and induced pluripotent stem cells (iPS) are unprecedented resources for cell therapy. We compared hematopoietic differentiation potentials from ES and iPS cell lines originated from various donors and derived them using integrative and non-integrative vectors. Significant differences in differentiation toward hematopoietic lineage were observed among ES and iPS. The ability of engraftment of iPS or ES-derived cells in NOG mice varied among the lines with low levels of chimerism. iPS generated from ES cell-derived mesenchymal stem cells (MSC) reproduce a similar hematopoietic outcome compared to their parental ES cell line. We were not able to identify any specific hematopoietic transcription factors that allow to distinguish between good versus poor hematopoiesis in undifferentiated ES or iPS cell lines. There is a relatively unpredictable variation in hematopoietic differentiation between ES and iPS cell lines that could not be predicted based on phenotype or gene expression of the undifferentiated cells. These results demonstrate the influence of genetic background in variation of hematopoietic potential rather than the reprogramming process. PMID:26938212

  3. Seasonal variations of group-specific phytoplankton cell death in Xiamen Bay, China

    Science.gov (United States)

    Huang, Xiaozhou; Liu, Xin; Chen, Jixin; Xiao, Wupeng; Cao, Zhen; Huang, Bangqin

    2016-05-01

    The importance of phytoplankton cell death is being increasingly recognized, however, there are still no published reports on this in Xiamen Bay. In this study, the proportion of dead phytoplankton cells associated with environmental factors was assessed at a station in Xiamen Bay from December 2012 to December 2013, using a cell digestion assay, which is an eff ective method to analyze dead/ living cells in complex natural phytoplankton communities. The percentages of dead cells (% DC) in the total phytoplankton in summer (16%±6%) were lower than those in winter (27%±16%). Six groups of phytoplankton (G1-G6) were categorized by flow cytometry. These phytoplankton communities with diverse seasonal variations in % DC had different responses to environmental constraints. The main factors aff ecting mortality were temperature and salinity, while nutrient concentration showed little influence on phytoplankton death. Additionally, our results provide evidence that chlorophyll a concentrations had an inverse relationship with total phytoplankton % DC and viable cell abundance was more meaningful than total cells to explain variations in environmental parameters (such as Chl a ). Moreover, the lowest mean % DC in total phytoplankton was 16%±6% at our sample site, which is in a subtropical area with high water temperatures, full solar radiation, and rich nutrients. This indicates that phytoplankton cell death is a process that cannot be ignored. In summary, phytoplankton cell death is important in understanding the dynamics of phytoplankton communities and the functioning of subtropical ecosystems.

  4. False Operation of Static Random Access Memory Cells under Alternating Current Power Supply Voltage Variation

    Science.gov (United States)

    Sawada, Takuya; Takata, Hidehiro; Nii, Koji; Nagata, Makoto

    2013-04-01

    Static random access memory (SRAM) cores exhibit susceptibility against power supply voltage variation. False operation is investigated among SRAM cells under sinusoidal voltage variation on power lines introduced by direct RF power injection. A standard SRAM core of 16 kbyte in a 90 nm 1.5 V technology is diagnosed with built-in self test and on-die noise monitor techniques. The sensitivity of bit error rate is shown to be high against the frequency of injected voltage variation, while it is not greatly influenced by the difference in frequency and phase against SRAM clocking. It is also observed that the distribution of false bits is substantially random in a cell array.

  5. Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells

    Directory of Open Access Journals (Sweden)

    Tebaldi Toma

    2012-06-01

    Full Text Available Abstract Background The classical view on eukaryotic gene expression proposes the scheme of a forward flow for which fluctuations in mRNA levels upon a stimulus contribute to determine variations in mRNA availability for translation. Here we address this issue by simultaneously profiling with microarrays the total mRNAs (the transcriptome and the polysome-associated mRNAs (the translatome after EGF treatment of human cells, and extending the analysis to other 19 different transcriptome/translatome comparisons in mammalian cells following different stimuli or undergoing cell programs. Results Triggering of the EGF pathway results in an early induction of transcriptome and translatome changes, but 90% of the significant variation is limited to the translatome and the degree of concordant changes is less than 5%. The survey of other 19 different transcriptome/translatome comparisons shows that extensive uncoupling is a general rule, in terms of both RNA movements and inferred cell activities, with a strong tendency of translation-related genes to be controlled purely at the translational level. By different statistical approaches, we finally provide evidence of the lack of dependence between changes at the transcriptome and translatome levels. Conclusions We propose a model of diffused independency between variation in transcript abundances and variation in their engagement on polysomes, which implies the existence of specific mechanisms to couple these two ways of regulating gene expression.

  6. Variations of X chromosome inactivation occur in early passages of female human embryonic stem cells.

    Directory of Open Access Journals (Sweden)

    Tamar Dvash

    Full Text Available X chromosome inactivation (XCI is a dosage compensation mechanism essential for embryonic development and cell physiology. Human embryonic stem cells (hESCs derived from inner cell mass (ICM of blastocyst stage embryos have been used as a model system to understand XCI initiation and maintenance. Previous studies of undifferentiated female hESCs at intermediate passages have shown three possible states of XCI; 1 cells in a pre-XCI state, 2 cells that already exhibit XCI, or 3 cells that never undergo XCI even upon differentiation. In this study, XCI status was assayed in ten female hESC lines between passage 5 and 15 to determine whether XCI variations occur in early passages of hESCs. Our results show that three different states of XCI already exist in the early passages of hESC. In addition, we observe one cell line with skewed XCI and preferential expression of X-linked genes from the paternal allele, while another cell line exhibits random XCI. Skewed XCI in undifferentiated hESCs may be due to clonal selection in culture instead of non-random XCI in ICM cells. We also found that XIST promoter methylation is correlated with silencing of XIST transcripts in early passages of hESCs, even in the pre-XCI state. In conclusion, XCI variations already take place in early passages of hESCs, which may be a consequence of in vitro culture selection during the derivation process. Nevertheless, we cannot rule out the possibility that XCI variations in hESCs may reflect heterogeneous XCI states in ICM cells that stochastically give rise to hESCs.

  7. Detection of Cell Wall Chemical Variation in Zea Mays Mutants Using Near-Infrared Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Buyck, N.; Thomas, S.

    2001-01-01

    Corn stover is regarded as the prime candidate feedstock material for commercial biomass conversion in the United States. Variations in chemical composition of Zea mays cell walls can affect biomass conversion process yields and economics. Mutant lines were constructed by activating a Mu transposon system. The cell wall chemical composition of 48 mutant families was characterized using near-infrared (NIR) spectroscopy. NIR data were analyzed using a multivariate statistical analysis technique called Principal Component Analysis (PCA). PCA of the NIR data from 349 maize leaf samples reveals 57 individuals as outliers on one or more of six Principal Components (PCs) at the 95% confidence interval. Of these, 19 individuals from 16 families are outliers on either PC3 (9% of the variation) or PC6 (1% of the variation), the two PCs that contain information about cell wall polymers. Those individuals for which altered cell wall chemistry is confirmed with wet chemical analysis will then be subjected to fermentation analysis to determine whether or not biomass conversion process kinetics, yields and/or economics are significantly affected. Those mutants that provide indications for a decrease in process cost will be pursued further to identify the gene(s) responsible for the observed changes in cell wall composition and associated changes in process economics. These genes will eventually be incorporated into maize breeding programs directed at the development of a truly dual use crop.

  8. Detection and Measurement of the Intracellular Calcium Variation in Follicular Cells

    Directory of Open Access Journals (Sweden)

    Ana M. Herrera-Navarro

    2014-01-01

    Full Text Available This work presents a new method for measuring the variation of intracellular calcium in follicular cells. The proposal consists in two stages: (i the detection of the cell’s nuclei and (ii the analysis of the fluorescence variations. The first stage is performed via watershed modified transformation, where the process of labeling is controlled. The detection process uses the contours of the cells as descriptors, where they are enhanced with a morphological filter that homogenizes the luminance variation of the image. In the second stage, the fluorescence variations are modeled as an exponential decreasing function, where the fluorescence variations are highly correlated with the changes of intracellular free Ca2+. Additionally, it is introduced a new morphological called medium reconstruction process, which helps to enhance the data for the modeling process. This filter exploits the undermodeling and overmodeling properties of reconstruction operators, such that it preserves the structure of the original signal. Finally, an experimental process shows evidence of the capabilities of the proposal.

  9. Effects of common germ-line genetic variation in cell cycle genes on ovarian cancer survival

    DEFF Research Database (Denmark)

    Song, H.; Hogdall, E.; Ramus, S.J.;

    2008-01-01

    PURPOSE: Somatic alterations have been shown to correlate with ovarian cancer prognosis and survival, but less is known about the effects on survival of common inherited genetic variation. Of particular interest are genes involved in cell cycle pathways, which regulate cell division and could...... plausibly influence clinical characteristics of multiple tumors types. EXPERIMENTAL DESIGN: We examined associations between common germ-line genetic variation in 14 genes involved in cell cycle pathway (CCND1, CCND2, CCND3, CCNE1, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CDKN2D, CDK2, CDK4, CDK6, and RB1......) and survival among women with invasive ovarian cancer participating in a multicenter case-control study from United Kingdom, Denmark, and United States. DNAs from up to 1,499 women were genotyped for 97 single-nucleotide polymorphisms that tagged the known common variants (minor allele frequency > or = 0...

  10. Seasonal and Milking-to-Milking Variations in Cow Milk Fat, Protein and Somatic Cell Counts

    OpenAIRE

    Elena Raluca PAVEL; Constantin GAVAN

    2011-01-01

    The first objective of this study was to examine milking-to-milking variations in milk fat, protein and SCC (somatic cell count). The second objective of this study was to examine variations of milk components (fat, protein and SCC) over a period of six months (April-September 2010) at Agricultural Research Development Station Simnic. A total of 128 milk samples (64 morning milking and 64 evening milking ones) from milk bulk tank commingled from 90�4 Holstein cows, were collected and analyzed...

  11. Sex and estrous cycle-dependent rapid protein kinase signaling actions of estrogen in distal colonic cells.

    LENUS (Irish Health Repository)

    O'Mahony, Fiona

    2008-10-01

    Previous studies from our laboratory demonstrated that 17beta-estradiol (E2) rapidly inhibits Cl(-) secretion in rat and human distal colonic epithelium. The inhibition has been shown to occur via targeting of a basolateral K(+) channel identified as the KCNQ1 (KvLQT1) channel. E2 indirectly modulates the channel activity via a cascade of second messengers which are rapidly phosphorylated in response to E2. The anti-secretory mechanism may be the manner by which E2 induces fluid retention in the intestine during periods of high circulating plasma E2. Here we review the sex-dependent and estrous cycle regulation of this novel rapid response to E2. The inhibition of KCNQ1 channel activity and Cl(-) secretion will be of interest in the future in the investigation of the retentive effects of estrogen in female tissue and also in the study of secretory disorders and drugable targets of the intestine.

  12. A new epigenetic marker: The replication-coupled, cell cycle-dependent, dual modification of the histone H4 tail

    Czech Academy of Sciences Publication Activity Database

    Fidlerová, Helena; Kalinová, Jana; Blechová, Miroslava; Velek, Jiří; Raška, Ivan

    2009-01-01

    Roč. 167, č. 1 (2009), s. 76-82. ISSN 1047-8477 R&D Projects: GA ČR(CZ) GA304/06/1691 Grant ostatní: GA MŠk(CZ) LC535 Institutional research plan: CEZ:AV0Z50110509; CEZ:AV0Z40550506 Keywords : epigenetics * H4K16 * H4K20 Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.673, year: 2009

  13. Achilles' heel of pluripotent stem cells: genetic, genomic and epigenetic variations during prolonged culture.

    Science.gov (United States)

    Rebuzzini, Paola; Zuccotti, Maurizio; Redi, Carlo Alberto; Garagna, Silvia

    2016-07-01

    Pluripotent stem cells differentiate into almost any specialized adult cell type of an organism. PSCs can be derived either from the inner cell mass of a blastocyst-giving rise to embryonic stem cells-or after reprogramming of somatic terminally differentiated cells to obtain ES-like cells, named induced pluripotent stem cells. The potential use of these cells in the clinic, for investigating in vitro early embryonic development or for screening the effects of new drugs or xenobiotics, depends on capability to maintain their genome integrity during prolonged culture and differentiation. Both human and mouse PSCs are prone to genomic and (epi)genetic instability during in vitro culture, a feature that seriously limits their real potential use. Culture-induced variations of specific chromosomes or genes, are almost all unpredictable and, as a whole, differ among independent cell lines. They may arise at different culture passages, suggesting the absence of a safe passage number maintaining genome integrity and rendering the control of genomic stability mandatory since the very early culture passages. The present review highlights the urgency for further studies on the mechanisms involved in determining (epi)genetic and chromosome instability, exploiting the knowledge acquired earlier on other cell types. PMID:26961132

  14. Regulatory T cells, inherited variation, and clinical outcome in epithelial ovarian cancer.

    Science.gov (United States)

    Knutson, Keith L; Maurer, Matthew J; Preston, Claudia C; Moysich, Kirsten B; Goergen, Krista; Hawthorne, Kieran M; Cunningham, Julie M; Odunsi, Kunle; Hartmann, Lynn C; Kalli, Kimberly R; Oberg, Ann L; Goode, Ellen L

    2015-12-01

    The immune system constitutes one of the host factors modifying outcomes in ovarian cancer. Regulatory T cells (Tregs) are believed to be a major factor in preventing the immune response from destroying ovarian cancers. Understanding mechanisms that regulate Tregs in the tumor microenvironment could lead to the identification of novel targets aimed at reducing their influence. In this study, we used immunofluorescence-based microscopy to enumerate Tregs, total CD4 T cells, and CD8(+) cytotoxic T cells in fresh frozen tumors from over 400 patients with ovarian cancer (>80 % high-grade serous). We sought to determine whether Tregs were associated with survival and genetic variation in 79 genes known to influence Treg induction, trafficking, or function. We used Cox regression, accounting for known prognostic factors, to estimate hazard ratios (HRs) associated with T cell counts and ratios. We found that the ratios of CD8 T cells and total CD4 T cells to Tregs were associated with improved overall survival (CD8/Treg HR 0.84, p = 0.0089; CD4/Treg HR 0.88, p = 0.046) and with genetic variation in IL-10 (p = 0.0073 and 0.01, respectively). In multivariate analyses, the associations between the ratios and overall survival remained similar (IL-10 and clinical covariate-adjusted CD8/Treg HR 0.85, p = 0.031; CD4/Treg HR 0.87, p = 0.093), suggesting that this association was not driven by variation in IL-10. Thus, integration of novel tumor phenotyping measures with extensive clinical and genetic information suggests that the ratio of T cells to Tregs may be prognostic of outcome in ovarian cancer, regardless of inherited genotype in genes related to Tregs. PMID:26298430

  15. Antigenic variation of pilin regulates adhesion of Neisseria meningitidis to human epithelial cells.

    Science.gov (United States)

    Nassif, X; Lowy, J; Stenberg, P; O'Gaora, P; Ganji, A; So, M

    1993-05-01

    Pili have been shown to play an essential role in the adhesion of Neisseria meningitidis to epithelial cells. However, among piliated strains, both inter- and intrastrain variability exist with respect to their degree of adhesion to epithelial cells in vitro (Virji et al., 1992). This suggests that factors other than the presence of pili per se are involved in this process. The N. meningitidis pilin subunit undergoes extensive antigenic variation. Piliated low- and high-adhesive derivatives of the same N. meningitidis strain were selected and the nucleotide sequence of the pilin gene expressed in each was determined. The highly adhesive derivatives had the same pilin sequence. The alleles encoding the pilin subunit of the low-adhesive derivatives were completely different from the one found in the high-adhesive isolates. Using polyclonal antibodies raised against one hyperadhesive variant, it was confirmed that the low-adhesive piliated derivatives expressed pilin variants antigenically different from the highly adhesive strains. The role of antigenic variation in the adhesive process of N. meningitidis was confirmed by performing allelic exchanges of the pilE locus between low- and high-adhesive isolates. Antigenic variation has been considered a means by which virulent bacteria evade the host immune system. This work provides genetic proof that a bacterial pathogen, N. meningitidis, can use antigenic variation to modulate their degree of virulence. PMID:8332064

  16. Peripheral blood cell variations in cirrhotic portal hypertension patients with hypersplenism

    Institute of Scientific and Technical Information of China (English)

    Yun-Fu Lu; Xin-Qiu Li; Xiao-Yu Han; Xiao-Guang Gong; Shun-Wu Chang

    2013-01-01

    Objective:To explore peripheral blood cell variations in hepatic cirrhosis portal hypertension patients with hypersplenism. Methods: Clinical data of 322 hypersplenism patients with decreased peripheral blood cells, admitted with cirrhotic portal hypertension, was retrospectively studied over the last 17 years. Results:In 64% (206/322) of patients, more than 2 kinds of blood cell were decreased, including 89 cases of pancytopenia (43.2%), 52 cases of WBC+PLT decrease (25.2%), 29 cases of RBC + PLT decrease (14.1%), and 36 cases of WBC + RBC decrease (17.5%);in 36% (116/322) of patients, single type blood cell decrease occurred, including 31 cases of PLT decrease (26.7%), 29 cases of WBC decrease (25%) and 56 cases of RBC decrease (48.3%). Of 227 routine bone marrow examinations, bone marrow hyperplasia was observed in 118 cases (52.0%), the remainder showed no hyperplasia. For the distinct scope and extent of peripheralblood cell decreases, preoperative blood component transfusions were carried out, then treated by surgery, after whole group splenectomy, the peripheral blood cell count was significantly higher (P<0.05). Conclusions: Of portal hypertensive patients with splenomegaly and hypersplenism, 64%have simultaneous decrease in various blood cells, 36%have decrease in single type blood cells, 52%of patients have bone marrow hyperplasia. A splenectomy can significantly increase the reduction of peripheral blood cells.

  17. Positional variation of antipodal cells in polyembryonic rice ApⅢ before and after fertilization

    Institute of Scientific and Technical Information of China (English)

    YUAN Liangchen; CHEN Yongzhe; MU Xijin; LIN Jinxing

    2003-01-01

    The variation in the position of antipodal cells before and after fertilization in polyembryonic rice strain ApⅢ was studied by using conventional sectioning technique. It was shown that initially the three antipodal cells lie at the chalazal end of the young embryo sacs. Along with the development of embryo sac, the antipodal cells proliferate into a multicellular structure containing up to about 20 cells. Most of the cells migrate to its dorsal side when the embryo sacs turn into mature. In a few embryo sacs the antipodal cells are situated in the positions adjacent to the egg apparatus at the micropylar end, while in other sacs, they spread from the midst of the embryo sac to the micropylar end clinging to the nucellar tissue. Furthermore, it is reported for the first time that cells of some egg apparatus or proembryos disorganize when antipodal cells lie at the micropylar end, indicating that the function of the antipodal cells may vary during the embryogenesis in rice ApⅢ.

  18. Geometric Integration Of The Valsov-Maxwell System With A Variational Particle-in-cell Scheme

    International Nuclear Information System (INIS)

    A fully variational, unstructured, electromagnetic particle-in-cell integrator is developed for integration of the Vlasov-Maxwell equations. Using the formalism of Discrete Exterior Calculus [1], the field solver, interpolation scheme and particle advance algorithm are derived through minimization of a single discrete field theory action. As a consequence of ensuring that the action is invariant under discrete electromagnetic gauge transformations, the integrator exactly conserves Gauss's law.

  19. Genetic Variation in Cell Cycle Regulatory Gene AURKA and Association With Intrinsic Breast Cancer Subtype

    OpenAIRE

    Taylor, Nicholas J.; Bensen, Jeannette T.; Poole, Charles; Troester, Melissa A.; Gammon, Marilie D.; Luo, Jingchun; Millikan, Robert C.; Olshan, Andrew F.

    2014-01-01

    AURKA is a putative low-penetrance tumor susceptibility gene due to its prominent role in cell cycle regulation and centrosomal function. Germline variation in AURKA was evaluated for association with breast cancer and intrinsic breast cancer subtypes in the Carolina Breast Cancer Study (CBCS), a population-based case-control study of African Americans (AA) and Caucasians (Cau). Tag and candidate single nucleotide polymorphisms (SNPs) on AURKA were genotyped in 1946 cases and 1747 controls. I...

  20. Fractional variational problems and particle in cell gyrokinetic simulations with fuzzy logic approach for tokamaks

    Directory of Open Access Journals (Sweden)

    Rastović Danilo

    2009-01-01

    Full Text Available In earlier Rastovic's papers [1] and [2], the effort was given to analyze the stochastic control of tokamaks. In this paper, the deterministic control of tokamak turbulence is investigated via fractional variational calculus, particle in cell simulations, and fuzzy logic methods. Fractional integrals can be considered as approximations of integrals on fractals. The turbulent media could be of the fractal structure and the corresponding equations should be changed to include the fractal features of the media.

  1. Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells

    OpenAIRE

    Tebaldi Toma; Re Angela; Viero Gabriella; Pegoretti Ilaria; Passerini Andrea; Blanzieri Enrico; Quattrone Alessandro

    2012-01-01

    Abstract Background The classical view on eukaryotic gene expression proposes the scheme of a forward flow for which fluctuations in mRNA levels upon a stimulus contribute to determine variations in mRNA availability for translation. Here we address this issue by simultaneously profiling with microarrays the total mRNAs (the transcriptome) and the polysome-associated mRNAs (the translatome) after EGF treatment of human cells, and extending the analysis to other 19 different transcriptome/tran...

  2. Variation of Neisseria gonorrhoeae lipooligosaccharide directs dendritic cell-induced T helper responses.

    Directory of Open Access Journals (Sweden)

    Sandra J van Vliet

    2009-10-01

    Full Text Available Gonorrhea is one of the most prevalent sexually transmitted diseases in the world. A naturally occurring variation of the terminal carbohydrates on the lipooligosaccharide (LOS molecule correlates with altered disease states. Here, we investigated the interaction of different stable gonoccocal LOS phenotypes with human dendritic cells and demonstrate that each variant targets a different set of receptors on the dendritic cell, including the C-type lectins MGL and DC-SIGN. Neisseria gonorrhoeae LOS phenotype C constitutes the first bacterial ligand to be described for the human C-type lectin receptor MGL. Both MGL and DC-SIGN are locally expressed at the male and female genital area, the primary site of N. gonorrhoeae infection. We show that targeting of different C-type lectins with the N. gonorrhoeae LOS variants results in alterations in dendritic cell cytokine secretion profiles and the induction of distinct adaptive CD4(+ T helper responses. Whereas N. gonorrhoeae variant A with a terminal N-acetylglucosamine on its LOS was recognized by DC-SIGN and induced significantly more IL-10 production, phenotype C, carrying a terminal N-acetylgalactosamine, primarily interacted with MGL and skewed immunity towards the T helper 2 lineage. Together, our results indicate that N. gonorrhoeae LOS variation allows for selective manipulation of dendritic cell function, thereby shifting subsequent immune responses in favor of bacterial survival.

  3. Regional variations in HDL metabolism in human fat cells: effect of cell size

    International Nuclear Information System (INIS)

    Abdominal obesity is related to reduced plasma high-density lipoprotein (HDL) cholesterol, and both are associated with cardiovascular disease risk. The authors have observed that plasma membranes from abdominal subcutaneous adipocytes have a greater HDL binding capacity than omental fat cell plasma membranes. The present study examined whether these binding characteristics could be due to differences in fat cell size or cholesterol concentration between the two adipose depots. Abdominal subcutaneous and deep omental fat were obtained from massively obese patients at surgery. Subcutaneous abdominal fat cells were significantly larger and their cellular cholesterol content greater than omental adipocytes. The uptake of HDL by collagenase-isolated fat cells was studied by incubating the cells for 2 h at 370C with 10 μg/ml 125I-HDL2 or 125I-HDL3. In both depots, the cellular uptake of 125I-HDL2 and 125I-HDL3 was specifically inhibited by addition of 25-fold excess unlabeled HDL and a close correlation was observed between the cellular uptake of 125I-HDL2 and 125I-HDL3. In obese patients, the uptake of 125I-HDL was higher in subcutaneous cells than in omental cells. The cellular 125I-HDL uptake was significantly correlated with adipocyte size and fat cell cholesterol content but not with adipocyte cholesterol concentration. These results suggest that the higher HDL uptake observed in subcutaneous cells compared with omental cells in obesity is the result of differences in adipocyte size rather than differences in the cholesterol concentration (cholesterol-to-triglyceride ratio). The increased interaction of HDL with hypertrophied abdominal adipocytes may play an important role in determining the lipid composition of HDL in obesity

  4. Regional variations in HDL metabolism in human fat cells: effect of cell size

    Energy Technology Data Exchange (ETDEWEB)

    Despres, J.; Fong, B.S.; Julien, P.; Jimenez, J.; Angel, A.

    1987-05-01

    Abdominal obesity is related to reduced plasma high-density lipoprotein (HDL) cholesterol, and both are associated with cardiovascular disease risk. The authors have observed that plasma membranes from abdominal subcutaneous adipocytes have a greater HDL binding capacity than omental fat cell plasma membranes. The present study examined whether these binding characteristics could be due to differences in fat cell size or cholesterol concentration between the two adipose depots. Abdominal subcutaneous and deep omental fat were obtained from massively obese patients at surgery. Subcutaneous abdominal fat cells were significantly larger and their cellular cholesterol content greater than omental adipocytes. The uptake of HDL by collagenase-isolated fat cells was studied by incubating the cells for 2 h at 37/sup 0/C with 10 ..mu..g/ml /sup 125/I-HDL/sub 2/ or /sup 125/I-HDL/sub 3/. In both depots, the cellular uptake of /sup 125/I-HDL/sub 2/ and /sup 125/I-HDL/sub 3/ was specifically inhibited by addition of 25-fold excess unlabeled HDL and a close correlation was observed between the cellular uptake of /sup 125/I-HDL/sub 2/ and /sup 125/I-HDL/sub 3/. In obese patients, the uptake of /sup 125/I-HDL was higher in subcutaneous cells than in omental cells. The cellular /sup 125/I-HDL uptake was significantly correlated with adipocyte size and fat cell cholesterol content but not with adipocyte cholesterol concentration. These results suggest that the higher HDL uptake observed in subcutaneous cells compared with omental cells in obesity is the result of differences in adipocyte size rather than differences in the cholesterol concentration (cholesterol-to-triglyceride ratio). The increased interaction of HDL with hypertrophied abdominal adipocytes may play an important role in determining the lipid composition of HDL in obesity.

  5. Impact of process variations and long term degradation on 6T-SRAM cells

    Directory of Open Access Journals (Sweden)

    Th. Fischer

    2007-06-01

    Full Text Available In modern deep-submicron CMOS technologies voltage scaling can not keep up with the scaling of the dimensions of transistors. Therefore the electrical fields inside the transistors are not constant anymore, while scaling down the device area. The rising electrical fields bring up reliability problems, such as hot carrier injection. Also other long term degradation mechanisms like Negative Bias Temperature Instability (NBTI come into the focus of circuit design.

    Along with process device parameter variations (threshold voltage, mobility, variations due to the degradation of devices form a big challenge for designers to build circuits that both yield high under the influence of process variations and remain functional with respect to long term device drift.

    In this work we present the influence of long term degradation and process variations on the performance of SRAM core-cells and parametric yield of SRAM arrays. For different use cases we show the performance degradation depending on temperature and supply voltage.

  6. Variation in the uptake of nanoparticles by monolayer cultured cells using high resolution MeV ion beam imaging

    International Nuclear Information System (INIS)

    Gold nanoparticle uptake by cells is being increasingly studied because of its potential in biomedical applications. In this work, we show how scanning transmission ion microscopy can be employed to visualize and quantify 50 nm gold nanoparticles taken up by individual cells. Preliminary studies have indicated that the cellular content of gold nanoparticles exhibits a wide variation (up to a factor of 10) among individual cells. This cell-to-cell variation can affect the efficiency of utilizing gold nanoparticles for therapeutic or diagnostic purposes

  7. Genetic Variation Influences the B-Cell Response to Immunization with a Pneumococcal Polysaccharide Conjugate Vaccine

    OpenAIRE

    McCool, T. L.; Schreiber, J R; Greenspan, N S

    2003-01-01

    CBA/J mice immunized with pneumococcal 23F-CRM197 vaccine produce significantly lower titers of 23F-specific antibodies and fewer 23F-specific antibody-secreting cells (ASC) than did BALB/c or (CBA/J × BALB/c)F1 (CCBAF1) mice. The reduced 23F-specific titers of CBA/J versus BALB/c or CCBAF1 mice are presumably related to lower frequencies of 23F-specific ASC influenced by genetic variation.

  8. Copper variation in Cu(In,Ga)Se2 solar cells with indium sulphide buffer layer

    International Nuclear Information System (INIS)

    In the manufacturing of Cu(In,Ga)Se2 (CIGS) thin film solar cells the application of a buffer layer on top of the absorber is essential to obtain high efficiency devices. Regarding the roll-to-roll production of CIGS cells and modules a vacuum deposition process for the buffer is preferable to the conventional cadmium sulphide buffer deposited in a chemical bath. Promising results have already been achieved for the deposition of indium sulphide buffer by different vacuum techniques. The solar device performance is very sensitive to the conditions at the absorber-buffer heterojunction. In view of optimization we investigated the influence of the Cu content in the absorber on the current-voltage characteristics. In this work the integral copper content was varied between 19 and 23 at.% in CIGS on glass substrates. An improvement of the cell performance by enhanced open circuit voltage was observed for a reduction to ~ 21 at.% when thermally evaporated indium sulphide was applied as the buffer layer. The influence of stoichiometry deviations on the transport mechanism and secondary barriers in the device was studied using detailed dark and light current-voltage analysis and admittance spectroscopy and compared to the reference CdS-buffered cells. We conclude that the composition of the absorber in the interface region affects current transport in InxSy-buffered and CdS-buffered cells in different ways hence optimal Cu content in those two types of devices is different. - Highlights: • Influence of Cu-variation in CIGS cells with InxSy buffer layer on cell performance • Enhanced efficiency by slight reduction of Cu-content to 21 at.% • Contribution of tunnelling-enhanced interface recombination for higher Cu-content

  9. Few single nucleotide variations in exomes of human cord blood induced pluripotent stem cells.

    Directory of Open Access Journals (Sweden)

    Rui-Jun Su

    Full Text Available The effect of the cellular reprogramming process per se on mutation load remains unclear. To address this issue, we performed whole exome sequencing analysis of induced pluripotent stem cells (iPSCs reprogrammed from human cord blood (CB CD34(+ cells. Cells from a single donor and improved lentiviral vectors for high-efficiency (2-14% reprogramming were used to examine the effects of three different combinations of reprogramming factors: OCT4 and SOX2 (OS, OS and ZSCAN4 (OSZ, OS and MYC and KLF4 (OSMK. Five clones from each group were subject to whole exome sequencing analysis. We identified 14, 11, and 9 single nucleotide variations (SNVs, in exomes, including untranslated regions (UTR, in the five clones of OSMK, OS, and OSZ iPSC lines. Only 8, 7, and 4 of these, respectively, were protein-coding mutations. An average of 1.3 coding mutations per CB iPSC line is remarkably lower than previous studies using fibroblasts and low-efficiency reprogramming approaches. These data demonstrate that point nucleotide mutations during cord blood reprogramming are negligible and that the inclusion of genome stabilizers like ZSCAN4 during reprogramming may further decrease reprogramming-associated mutations. Our findings provide evidence that CB is a superior source of cells for iPSC banking.

  10. Plasticity in variation of xylem and phloem cell characteristics of Norway spruce under different local conditions

    Directory of Open Access Journals (Sweden)

    Jozica eGricar

    2015-09-01

    Full Text Available There is limited information on intra-annual plasticity of secondary tissues of tree species growing under different environmental conditions. To increase the knowledge about the plasticity of secondary growth, which allows trees to adapt to specific local climatic regimes, we examined climate–radial growth relationships of Norway spruce (Picea abies (L. H. Karst. from three contrasting locations in the temperate climatic zone by analyzing tree-ring widths for the period 1932–2010, and cell characteristics in xylem and phloem increments formed in the years 2009–2011. Variation in the structure of xylem and phloem increments clearly shows that plasticity in seasonal dynamics of cambial cell production and cell differentiation exists on xylem and phloem sides. Anatomical characteristics of xylem and phloem cells are predominantly site-specific characteristics, because they varied among sites but were fairly uniform among years in trees from the same site. Xylem and phloem tissues formed in the first part of the growing season seemed to be more stable in structure, indicating their priority over latewood and late phloem for tree performance. Long-term climate and radial growth analyses revealed that growth was in general less dependent on precipitation than on temperature; however, growth sensitivity to local conditions differed among the sites. Only partial dependence of radial growth of spruce on climatic factors on the selected sites confirms its strategy to adapt the structure of wood and phloem increments to function optimally in local conditions.

  11. Variation in genomic landscape of clear cell renal cell carcinoma across Europe.

    Science.gov (United States)

    Scelo, Ghislaine; Riazalhosseini, Yasser; Greger, Liliana; Letourneau, Louis; Gonzàlez-Porta, Mar; Wozniak, Magdalena B; Bourgey, Mathieu; Harnden, Patricia; Egevad, Lars; Jackson, Sharon M; Karimzadeh, Mehran; Arseneault, Madeleine; Lepage, Pierre; How-Kit, Alexandre; Daunay, Antoine; Renault, Victor; Blanché, Hélène; Tubacher, Emmanuel; Sehmoun, Jeremy; Viksna, Juris; Celms, Edgars; Opmanis, Martins; Zarins, Andris; Vasudev, Naveen S; Seywright, Morag; Abedi-Ardekani, Behnoush; Carreira, Christine; Selby, Peter J; Cartledge, Jon J; Byrnes, Graham; Zavadil, Jiri; Su, Jing; Holcatova, Ivana; Brisuda, Antonin; Zaridze, David; Moukeria, Anush; Foretova, Lenka; Navratilova, Marie; Mates, Dana; Jinga, Viorel; Artemov, Artem; Nedoluzhko, Artem; Mazur, Alexander; Rastorguev, Sergey; Boulygina, Eugenia; Heath, Simon; Gut, Marta; Bihoreau, Marie-Therese; Lechner, Doris; Foglio, Mario; Gut, Ivo G; Skryabin, Konstantin; Prokhortchouk, Egor; Cambon-Thomsen, Anne; Rung, Johan; Bourque, Guillaume; Brennan, Paul; Tost, Jörg; Banks, Rosamonde E; Brazma, Alvis; Lathrop, G Mark

    2014-01-01

    The incidence of renal cell carcinoma (RCC) is increasing worldwide, and its prevalence is particularly high in some parts of Central Europe. Here we undertake whole-genome and transcriptome sequencing of clear cell RCC (ccRCC), the most common form of the disease, in patients from four different European countries with contrasting disease incidence to explore the underlying genomic architecture of RCC. Our findings support previous reports on frequent aberrations in the epigenetic machinery and PI3K/mTOR signalling, and uncover novel pathways and genes affected by recurrent mutations and abnormal transcriptome patterns including focal adhesion, components of extracellular matrix (ECM) and genes encoding FAT cadherins. Furthermore, a large majority of patients from Romania have an unexpected high frequency of A:T>T:A transversions, consistent with exposure to aristolochic acid (AA). These results show that the processes underlying ccRCC tumorigenesis may vary in different populations and suggest that AA may be an important ccRCC carcinogen in Romania, a finding with major public health implications. PMID:25351205

  12. Co-variation of metabolic rates and cell-size in coccolithophores

    Directory of Open Access Journals (Sweden)

    G. Aloisi

    2015-04-01

    , the model is able to reproduce the co-variation of growth rate and cell size observed in the laboratory when these nutrients become limiting. These results support ongoing efforts to interpret coccosphere and coccolith size measurements in the context of climate change.

  13. Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines

    Science.gov (United States)

    Chhibber, Aparna; French, Courtney E.; Yee, Sook Wah; Gamazon, Eric R.; Theusch, Elizabeth; Qin, Xiang; Webb, Amy; Papp, Audrey C.; Wang, Ann; Simmons, Christine Q.; Konkashbaev, Anuar; Chaudhry, Amarjit S.; Mitchel, Katrina; Stryke, Doug; Ferrin, Thomas E.; Weiss, Scott T.; Kroetz, Deanna L.; Sadee, Wolfgang; Nickerson, Deborah A.; Krauss, Ronald M.; George, Alfred L.; Schuetz, Erin G.; Medina, Marisa W.; Cox, Nancy J.; Scherer, Steven E.; Giacomini, Kathleen M.; Brenner, Steven E

    2015-01-01

    Variation in the expression level and activity of genes involved in drug disposition and action (“pharmacogenes”) can affect drug response and toxicity, especially when in tissues of pharmacological importance. Previous studies have relied primarily on microarrays to understand gene expression differences, or have focused on a single tissue or small number of samples. The goal of this study was to use RNA-seq to determine the expression levels and alternative splicing of 389 PGRN pharmacogenes across four tissues (liver, kidney, heart and adipose) and lymphoblastoid cell lines (LCLs), which are used widely in pharmacogenomics studies. Analysis of RNA-seq data from 139 different individuals across the 5 tissues (20–45 individuals per tissue type) revealed substantial variation in both expression levels and splicing across samples and tissue types. This in-depth exploration also revealed 183 splicing events in pharmacogenes that were previously not annotated. Overall, this study serves as a rich resource for the research community to inform biomarker and drug discovery and use. PMID:26856248

  14. Variation in blood cell DNA content in fish from Chernobyl-contaminated ponds in Ukraine

    International Nuclear Information System (INIS)

    To assess responses of fish to chronic exposure to radionuclides, the authors sampled blood from about 300 crucian carp Carassius carrasius collected from 10 ponds in the Ukraine. The ponds were located 20--30 km from the Chernobyl reactor in areas which received 1--10 Ci 137Cs/km2 as well as other contaminants. Flow cytometric analysis of DNA content of whole blood revealed aneuploid-like patterns in some of the fish, as well as hyperdiploid shoulders. The fish populations consisted of both diploid and triploid individuals. Changes in the coefficient of variation (CV) around the G0/G1 peak have been used in previous studies as an indication of abnormal DNA content; the CV was increased in a number of the fish examined. Some fish had uninterpretable DNA histograms, with a typical diploid or triploid cell population present along with a smaller haploid population. Variations in cellular DNA content similar to those reported here have been associated with exposure to radiation and other genotoxic agents in laboratory studies. While further work is needed, these results suggest that the Chernobyl accident may have long term genetic consequences for wild organisms in the contaminated areas

  15. Power optimized variation aware dual-threshold SRAM cell design technique

    Directory of Open Access Journals (Sweden)

    Aminul Islam

    2011-02-01

    Full Text Available Aminul Islam1, Mohd Hasan21Department of Electronics and Communication Engineering, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India; 2Department of Electronics Engineering, Aligarh Muslim University, Aligarh, Uttar Pradesh, IndiaAbstract: Bulk complementary metal-oxide semiconductor (CMOS technology is facing enormous challenges at channel lengths below 45 nm, such as gate tunneling, device mismatch, random dopant fluctuations, and mobility degradation. Although multiple gate transistors and strained silicon devices overcome some of the bulk CMOS problems, it is sensible to look for revolutionary new materials and devices to replace silicon. It is obvious that future technology materials should exhibit higher mobility, better channel electrostatics, scalability, and robustness against process variations. Carbon nanotube-based technology is very promising because it has most of these desired features. There is a need to explore the potential of this emerging technology by designing circuits based on this technology and comparing their performance with that of existing bulk CMOS technology. In this paper, we propose a low-power variation-immune dual-threshold voltage carbon nanotube field effect transistor (CNFET-based seven-transistor (7T static random access memory (SRAM cell. The proposed CNFET-based 7T SRAM cell offers ~1.2× improvement in standby power, ~1.3× improvement in read delay, and ~1.1× improvement in write delay. It offers narrower spread in write access time (1.4× at optimum energy point [OEP] and 1.2× at 1 V. It features 56.3% improvement in static noise margin and 40% improvement in read static noise margin. All the simulation measurements are taken at proposed OEP decided by the optimum results obtained after extensive simulation on HSPICE (high-performance simulation program with integrated circuit emphasis environment.Keywords: carbon nanotube field effect transistor (CNFET, chirality vector, random dopant

  16. Pilus phase variation switches gonococcal adherence to invasion by caveolin-1-dependent host cell signaling.

    Science.gov (United States)

    Faulstich, Michaela; Böttcher, Jan-Peter; Meyer, Thomas F; Fraunholz, Martin; Rudel, Thomas

    2013-01-01

    Many pathogenic bacteria cause local infections but occasionally invade into the blood stream, often with fatal outcome. Very little is known about the mechanism underlying the switch from local to invasive infection. In the case of Neisseria gonorrhoeae, phase variable type 4 pili (T4P) stabilize local infection by mediating microcolony formation and inducing anti-invasive signals. Outer membrane porin PorB(IA), in contrast, is associated with disseminated infection and facilitates the efficient invasion of gonococci into host cells. Here we demonstrate that loss of pili by natural pilus phase variation is a prerequisite for the transition from local to invasive infection. Unexpectedly, both T4P-mediated inhibition of invasion and PorB(IA)-triggered invasion utilize membrane rafts and signaling pathways that depend on caveolin-1-Y14 phosphorylation (Cav1-pY14). We identified p85 regulatory subunit of PI3 kinase (PI3K) and phospholipase Cγ1 as new, exclusive and essential interaction partners for Cav1-pY14 in the course of PorBIA-induced invasion. Active PI3K induces the uptake of gonococci via a new invasion pathway involving protein kinase D1. Our data describe a novel route of bacterial entry into epithelial cells and offer the first mechanistic insight into the switch from local to invasive gonococcal infection. PMID:23717204

  17. Pilus phase variation switches gonococcal adherence to invasion by caveolin-1-dependent host cell signaling.

    Directory of Open Access Journals (Sweden)

    Michaela Faulstich

    Full Text Available Many pathogenic bacteria cause local infections but occasionally invade into the blood stream, often with fatal outcome. Very little is known about the mechanism underlying the switch from local to invasive infection. In the case of Neisseria gonorrhoeae, phase variable type 4 pili (T4P stabilize local infection by mediating microcolony formation and inducing anti-invasive signals. Outer membrane porin PorB(IA, in contrast, is associated with disseminated infection and facilitates the efficient invasion of gonococci into host cells. Here we demonstrate that loss of pili by natural pilus phase variation is a prerequisite for the transition from local to invasive infection. Unexpectedly, both T4P-mediated inhibition of invasion and PorB(IA-triggered invasion utilize membrane rafts and signaling pathways that depend on caveolin-1-Y14 phosphorylation (Cav1-pY14. We identified p85 regulatory subunit of PI3 kinase (PI3K and phospholipase Cγ1 as new, exclusive and essential interaction partners for Cav1-pY14 in the course of PorBIA-induced invasion. Active PI3K induces the uptake of gonococci via a new invasion pathway involving protein kinase D1. Our data describe a novel route of bacterial entry into epithelial cells and offer the first mechanistic insight into the switch from local to invasive gonococcal infection.

  18. Assessment of interpatient heterogeneity in tumor radiosensitivity for nonsmall cell lung cancer using tumor-volume variation data

    Energy Technology Data Exchange (ETDEWEB)

    Chvetsov, Alexei V., E-mail: chvetsov2@gmail.com; Schwartz, Jeffrey L.; Mayr, Nina [Department of Radiation Oncology, University of Washington, 1959 NE Pacific Street, Seattle, Washington 98195-6043 (United States); Yartsev, Slav [London Regional Cancer Program, London Health Sciences Centre, 790 Commissioners Road East, London, Ontario 46A 4L6 (Canada)

    2014-06-15

    Purpose: In our previous work, the authors showed that a distribution of cell surviving fractionsS{sub 2} in a heterogeneous group of patients could be derived from tumor-volume variation curves during radiotherapy for head and neck cancer. In this research study, the authors show that this algorithm can be applied to other tumors, specifically in nonsmall cell lung cancer. This new application includes larger patient volumes and includes comparison of data sets obtained at independent institutions. Methods: Our analysis was based on two data sets of tumor-volume variation curves for heterogeneous groups of 17 patients treated for nonsmall cell lung cancer with conventional dose fractionation. The data sets were obtained previously at two independent institutions by using megavoltage computed tomography. Statistical distributions of cell surviving fractionsS{sub 2} and clearance half-lives of lethally damaged cells T{sub 1/2} have been reconstructed in each patient group by using a version of the two-level cell population model of tumor response and a simulated annealing algorithm. The reconstructed statistical distributions of the cell surviving fractions have been compared to the distributions measured using predictive assays in vitro. Results: Nonsmall cell lung cancer presents certain difficulties for modeling surviving fractions using tumor-volume variation curves because of relatively large fractional hypoxic volume, low gradient of tumor-volume response, and possible uncertainties due to breathing motion. Despite these difficulties, cell surviving fractionsS{sub 2} for nonsmall cell lung cancer derived from tumor-volume variation measured at different institutions have similar probability density functions (PDFs) with mean values of 0.30 and 0.43 and standard deviations of 0.13 and 0.18, respectively. The PDFs for cell surviving fractions S{sub 2} reconstructed from tumor volume variation agree with the PDF measured in vitro. Conclusions: The data obtained

  19. Variation of Red Blood Cell Distribution Width and Mean Platelet Volume after Moderate Endurance Exercise

    Directory of Open Access Journals (Sweden)

    Giuseppe Lippi

    2014-01-01

    Full Text Available Although physical exercise strongly influences several laboratory parameters, data about the hematological changes after medium distance running are scarce. We studied 31 middle-trained athletes (mean training regimen 217±32 min/week who performed a 21.1 km, half-marathon run. Blood samples were collected before the run, at the end, and 3 and 20 hours thereafter. The complete blood count was performed on Advia 2120 and included red blood cell (RBC, reticulocyte, and platelet counts; hemoglobin; mean corpuscular volume (MCV; mean corpuscular hemoglobin (MCH; reticulocyte haemoglobin content (Ret CHR; RBC distribution width (RDW, mean platelet volume (MPV. No significant variations were observed for MCH and Ret CHR. The RBC, reticulocyte, and hemoglobin values modestly decreased after the run. The MCV significantly increased at the end of running but returned to baseline 3 hours thereafter. The RDW constantly increased, reaching a peak 20 hours after the run. The platelet count and MPV both increased after the run and returned to baseline 3 hours thereafter. These results may have implications for definition of reference ranges and antidoping testing, and may also contribute to explaining the relationship between endurance exercise and mortality, since previous studies reported that RDW and MPV may be significantly associated with cardiovascular disease.

  20. Variation of red blood cell distribution width and mean platelet volume after moderate endurance exercise.

    Science.gov (United States)

    Lippi, Giuseppe; Salvagno, Gian Luca; Danese, Elisa; Tarperi, Cantor; Guidi, Gian Cesare; Schena, Federico

    2014-01-01

    Although physical exercise strongly influences several laboratory parameters, data about the hematological changes after medium distance running are scarce. We studied 31 middle-trained athletes (mean training regimen 217 ± 32 min/week) who performed a 21.1 km, half-marathon run. Blood samples were collected before the run, at the end, and 3 and 20 hours thereafter. The complete blood count was performed on Advia 2120 and included red blood cell (RBC), reticulocyte, and platelet counts; hemoglobin; mean corpuscular volume (MCV); mean corpuscular hemoglobin (MCH); reticulocyte haemoglobin content (Ret CHR); RBC distribution width (RDW), mean platelet volume (MPV). No significant variations were observed for MCH and Ret CHR. The RBC, reticulocyte, and hemoglobin values modestly decreased after the run. The MCV significantly increased at the end of running but returned to baseline 3 hours thereafter. The RDW constantly increased, reaching a peak 20 hours after the run. The platelet count and MPV both increased after the run and returned to baseline 3 hours thereafter. These results may have implications for definition of reference ranges and antidoping testing, and may also contribute to explaining the relationship between endurance exercise and mortality, since previous studies reported that RDW and MPV may be significantly associated with cardiovascular disease. PMID:25197280

  1. Circadian cycle-dependent EEG biomarkers of pathogenicity in adult mice following prenatal exposure to in utero inflammation.

    Science.gov (United States)

    Adler, D A; Ammanuel, S; Lei, J; Dada, T; Borbiev, T; Johnston, M V; Kadam, S D; Burd, I

    2014-09-01

    Intrauterine infection or inflammation in preterm neonates is a known risk for adverse neurological outcomes, including cognitive, motor and behavioral disabilities. Our previous data suggest that there is acute fetal brain inflammation in a mouse model of intrauterine exposure to lipopolysaccharides (LPS). We hypothesized that the in utero inflammation induced by LPS produces long-term electroencephalogram (EEG) biomarkers of neurodegeneration in the exposed mice that could be determined by using continuous quantitative video/EEG/electromyogram (EMG) analyses. A single LPS injection at E17 was performed in pregnant CD1 dams. Control dams were injected with same volumes of saline (LPS n=10, Control n=8). At postnatal age of P90-100, 24-h synchronous video/EEG/EMG recordings were done using a tethered recording system and implanted subdural electrodes. Behavioral state scoring was performed blind to treatment group, on each 10s EEG epoch using synchronous video, EMG and EEG trace signatures to generate individual hypnograms. Automated EEG power spectrums were analyzed for delta and theta-beta power ratios during wake vs. sleep cycles. Both control and LPS hypnograms showed an ultradian wake/sleep cycling. Since rodents are nocturnal animals, control mice showed the expected diurnal variation with significantly longer time spent in wake states during the dark cycle phase. In contrast, the LPS-treated mice lost this circadian rhythm. Sleep microstructure also showed significant alteration in the LPS mice specifically during the dark cycle, caused by significantly longer average non-rapid eye movement (NREM) cycle durations. No significance was found between treatment groups for the delta power data; however, significant activity-dependent changes in theta-beta power ratios seen in controls were absent in the LPS-exposed mice. In conclusion, exposure to in utero inflammation in CD1 mice resulted in significantly altered sleep architecture as adults that were circadian

  2. Variations in insulin responsiveness in rat fat cells are due to metabolic differences rather than insulin binding

    DEFF Research Database (Denmark)

    Hansen, Finn Mølgård; Nilsson, Poul; Sonne, Ole;

    1983-01-01

    Insulin resistance was studied by comparing insulin response and insulin binding in four groups of rats. Glucose metabolism in isolated fat cells from male Wistar rats weighing 340 g was less responsive to a supramaximal dose of insulin than glucose metabolism in fat cells from rats weighing 200 g...... to fat cells. Insulin binding was not correlated to the plasma insulin level which however was reflected in the lipoprotein lipase activity in the adipose tissue. In conclusion, these results indicate that variations in insulin responsiveness in fat cells are due to alterations in cellular metabolism....... Induction of streptozotocin-diabetes in rats weighing 200 g resulted in a marked decrease in the insulin responsiveness of fat cells. Ventromedial hypothalamic lesions of 340 g rats had the opposite effect and restored the insulin responsiveness of fat cells. The responsiveness in the four groups was...

  3. Variations of secretome profiles according to conditioned medium preparation: The example of human mesenchymal stem cell-derived adipocytes.

    Science.gov (United States)

    Clabaut, Aline; Grare, Céline; Léger, Thibaut; Hardouin, Pierre; Broux, Odile

    2015-10-01

    One challenging point in analyzing cellular secretome collected as conditioned medium is cross-contamination by cell culture media components, especially bovine serum proteins. A common approach for serum removal is to wash the cells, an alternative is to grow cells using serum-free conditions. Given that the sample processing may influence the phenotype of cells and thus the secretome, it is important to establish the optimal protocol for each cell type. In this study, we compared two methods for preparing conditioned medium from human adipocytes derived from mesenchymal stem cells. Cells were either washed twice with PBS or cultured the last four days of differentiation in serum-free adipogenic medium. Gene expression of the cells was evaluated by using real-time PCR and 1D LC-MS/MS was used to compare secreted proteins present in the culture supernatants. Surprisingly, results showed significant differences in gene expression patterns of the cells and in protein content of the conditioned media and suggested that PBS washes induced severe modifications of the phenotype of cells and thus changes in protein secretion profiles. These data emphasize the significant variations in protein species related to cell manipulations and underline the importance of procedure optimization prior to any proteomic investigation. PMID:26105977

  4. Genetic Variation in TLR1 is associated with Pam3CSK4-induced effector T cell resistance to regulatory T cell suppression

    OpenAIRE

    Mikacenic, Carmen; Schneider, Anya; Radella, Frank; Buckner, Jane H.; Mark M Wurfel

    2014-01-01

    Toll-like receptors (TLRs) play essential roles in the initiation and modulation of immune responses. TLR1/TLR2 heterodimers recognize tri-acylated bacterial lipopeptides, including the synthetic TLR1/2 lipopeptide, Pam3CSK4. Genetic variation in TLR1 is associated with outcomes in diseases in which regulatory T cells (Treg) play a role, including asthma and allergy. To determine whether genetic polymorphisms in TLR1 are associated with alterations in Treg suppression of effector T cells (Tef...

  5. Observer variation in FDG PET-CT for staging of non-small-cell lung carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Hofman, Michael S. [St Thomas' Hospital, PET Imaging Centre, London (United Kingdom)]|[Southern Health, Nuclear Medicine, Melbourne (Australia); Smeeton, Nigel C. [King' s College London, Division of Health and Social Care Research, London (United Kingdom); Rankin, Sheila C.; Nunan, Tom; O' Doherty, Michael J. [St Thomas' Hospital, PET Imaging Centre, London (United Kingdom)

    2009-02-15

    Error and variation in reporting remains one of the weakest features of clinical imaging despite enormous technological advances in nuclear medicine and radiology. The aim of this study was to evaluate agreement amongst experienced readers in staging non-small-cell lung cancer (NSCLC) with PET-CT. A series of {sup 18}F-FDG PET-CT scans from 100 consecutive patients were reviewed independently by three experienced readers, with two readers reviewing each scan series a second time. Individual mediastinal lymph node stations were assessed as benign/inflammatory, equivocal or malignant, and AJCC N and M stage were also assigned. Kappa ({kappa}) was used to compare ratings from two categories and weighted kappa ({kappa}{sub w}) for three or more categories, and kappa values were interpreted according to the Landis-Koch benchmarks. Both intra- and interobserver agreement for N and M staging were high. For M staging there was almost perfect intra- and interobserver agreement ({kappa} = 0.90-0.93). For N staging, agreement was either almost perfect or substantial (intraobserver {kappa}{sub w} = 0.79, 0.91; interobserver {kappa}{sub w} = 0.75-0.81). Importantly, there was almost perfect agreement for N0/1 vs N2/3 disease ({kappa} = 0.80-0.97). Agreement for inferior and superior mediastinal nodes (stations 1, 2, 3, 7, 8, 9) was either almost perfect or substantial ({kappa}{sub w} = 0.71-0.88), but lower for hilar nodes (10; {kappa}{sub w} = 0.56-0.71). Interreporter variability was greatest for aortopulmonary nodes (5, 6; {kappa}{sub w} = 0.48-0.55). Amongst experienced reporters in a single centre, there was a very high level of agreement for both mediastinal nodal stage and detection of distant metastases with PET-CT. This supports the use of PET-CT as a robust imaging modality for staging NSCLC. (orig.)

  6. Whole-Genome Sequencing Reveals Diverse Models of Structural Variations in Esophageal Squamous Cell Carcinoma.

    Science.gov (United States)

    Cheng, Caixia; Zhou, Yong; Li, Hongyi; Xiong, Teng; Li, Shuaicheng; Bi, Yanghui; Kong, Pengzhou; Wang, Fang; Cui, Heyang; Li, Yaoping; Fang, Xiaodong; Yan, Ting; Li, Yike; Wang, Juan; Yang, Bin; Zhang, Ling; Jia, Zhiwu; Song, Bin; Hu, Xiaoling; Yang, Jie; Qiu, Haile; Zhang, Gehong; Liu, Jing; Xu, Enwei; Shi, Ruyi; Zhang, Yanyan; Liu, Haiyan; He, Chanting; Zhao, Zhenxiang; Qian, Yu; Rong, Ruizhou; Han, Zhiwei; Zhang, Yanlin; Luo, Wen; Wang, Jiaqian; Peng, Shaoliang; Yang, Xukui; Li, Xiangchun; Li, Lin; Fang, Hu; Liu, Xingmin; Ma, Li; Chen, Yunqing; Guo, Shiping; Chen, Xing; Xi, Yanfeng; Li, Guodong; Liang, Jianfang; Yang, Xiaofeng; Guo, Jiansheng; Jia, JunMei; Li, Qingshan; Cheng, Xiaolong; Zhan, Qimin; Cui, Yongping

    2016-02-01

    Comprehensive identification of somatic structural variations (SVs) and understanding their mutational mechanisms in cancer might contribute to understanding biological differences and help to identify new therapeutic targets. Unfortunately, characterization of complex SVs across the whole genome and the mutational mechanisms underlying esophageal squamous cell carcinoma (ESCC) is largely unclear. To define a comprehensive catalog of somatic SVs, affected target genes, and their underlying mechanisms in ESCC, we re-analyzed whole-genome sequencing (WGS) data from 31 ESCCs using Meerkat algorithm to predict somatic SVs and Patchwork to determine copy-number changes. We found deletions and translocations with NHEJ and alt-EJ signature as the dominant SV types, and 16% of deletions were complex deletions. SVs frequently led to disruption of cancer-associated genes (e.g., CDKN2A and NOTCH1) with different mutational mechanisms. Moreover, chromothripsis, kataegis, and breakage-fusion-bridge (BFB) were identified as contributing to locally mis-arranged chromosomes that occurred in 55% of ESCCs. These genomic catastrophes led to amplification of oncogene through chromothripsis-derived double-minute chromosome formation (e.g., FGFR1 and LETM2) or BFB-affected chromosomes (e.g., CCND1, EGFR, ERBB2, MMPs, and MYC), with approximately 30% of ESCCs harboring BFB-derived CCND1 amplification. Furthermore, analyses of copy-number alterations reveal high frequency of whole-genome duplication (WGD) and recurrent focal amplification of CDCA7 that might act as a potential oncogene in ESCC. Our findings reveal molecular defects such as chromothripsis and BFB in malignant transformation of ESCCs and demonstrate diverse models of SVs-derived target genes in ESCCs. These genome-wide SV profiles and their underlying mechanisms provide preventive, diagnostic, and therapeutic implications for ESCCs. PMID:26833333

  7. Somaclonal variation is induced de novo via the tissue culture process: a study quantifying mutated cells in Saintpaulia.

    Directory of Open Access Journals (Sweden)

    Mitsuru Sato

    Full Text Available BACKGROUND: The origin of somaclonal variation has not been questioned previously, i.e., "pre-existing mutations" in explants and "newly induced mutations" arising from the tissue culture process have not been distinguished. This is primarily because there has been no reliable molecular method for estimating or quantifying variation. METHODOLOGY/PRINCIPAL FINDINGS: We adopted a petal-variegated cultivar of Saintpaulia 'Thamires' (Saintpaulia sp. as the model plant. Based on the difference between the pre- and post-transposon excision sequence of the promoter region of flavonoid 3', 5'-hydoroxylase (F3'5'H, we estimated mutated (transposon-excised cell percentages using a quantitative real-time PCR. Mutated cell percentages in leaf laminae used as explants was 4.6 and 2.4% in highly or low variegation flower plants, respectively, although the occurrences of blue color mutants in their regenerants were more than 40%. Preexisting mutated cell percentages in cultured explants were considerably lower than the mutated plant percentage among total regenerants via tissue culture. CONCLUSIONS/SIGNIFICANCE: The estimation of mutated cell percentages became possible using the quantitative real-time PCR. The origins of mutations were successfully distinguished; it was confirmed that somaclonal variations are mainly caused by newly generated mutations arising from tissue culture process.

  8. Variation of radiation sensitivity of Friend Erythroleukemia cells cultured in the presence of the differentiation inducer DMSO

    International Nuclear Information System (INIS)

    Differentiation of Friend erythroleukemia cells (FELC) was induced with 1.5% dimethyl sulfoxide (DMSO) in the culture medium. Cell growth, erythroid differentiation, and radiosensitivity of the proliferative capacity of the cells were measured and compared to a noninduced control culture of identical age. Induced cells first appeared on Day 2 after DMSO addition, and increased to a maximum of 80 to 90% of the cell population on Day 5, whereas in the control culture, induction was less than 2% of the cells. Radiosensitivity of the cells in the induced culture relative to that of cells in the control culture, showed an age-dependent variation. On days 1 and 2 after DMSO addition, the cells in the induced culture were less radiosensitive than those in the control culture. At later times, this relationship was reversed, and between days 3 and 5 the clonable cells in the induced culture were less radiosensitive than those in the control culture. These results suggest that the metabolic events associated with commitment of FELC to differentiate affect their ability to cope with the radiation-induced lesions underlying the loss of division capacity

  9. Variation in assessment of oxidatively damaged DNA in mononuclear blood cells by the comet assay with visual scoring

    DEFF Research Database (Denmark)

    Forchhammer, Lykke; Bräuner, Elvira Vaclavik; Folkmann, Janne Kjaersgaard;

    2008-01-01

    The comet assay is popular for assessments of genotoxicity, but the comparison of results between studies is challenging because of differences in experimental procedures and reports of DNA damage in different units. We investigated the variation of DNA damage in mononuclear blood cells (MNBCs......) measured by the comet assay with focus on the variation related to alkaline unwinding and electrophoresis time, number of cells scored, as well as the putative benefits of transforming the primary end points to common units by the use of reference standards and calibration curves. Eight experienced...... conclusion, our results indicate that inter-investigator difference in scoring is a strong determinant of DNA damage levels measured by the comet assay....

  10. Variational Symplectic Particle-in-cell Simulation of Nonlinear Mode Conversion from Extraordinary waves to Bernstein Waves

    OpenAIRE

    Xiao, Jianyuan; Liu, Jian; Qin, Hong; Yu, Zhi; Xiang, Nong

    2015-01-01

    In this paper, the nonlinear mode conversion of extraordinary waves in nonuniform magnetized plasmas is studied using the variational symplectic particle-in-cell simulation. The accuracy of the nonlinear simulation is guaranteed by the long-term accuracy and conservativeness of the symplectic algorithm. The spectra of the electromagnetic wave, the evolution of the wave reflectivity, the energy deposition profile, and the parameter-dependent properties of radio-frequency waves during the nonli...

  11. Seasonal variations in cell abundance of Noctiluca scintillans in the coastal waters off Chonburi Province, the upper Gulf of Thailand

    OpenAIRE

    Lirdwitayaprasit, Thaithaworn; Meksumpun, Shettapong; Rungsupa, Sompop; Furuya, Ken

    2006-01-01

    Seasonal variations in cell abundance of Noctiluca scintillans was studied from June 2003 to November 2004 in the coastal waters off Chonburi Province, the upper gulf of Thailand. Eight stations from Bangpakong River mouth to Angsila were designed to cover the area where red tides often occurred and were under the influence of Bangpakong River. Numerical abundance was analyzed in relation with some environmental parameters. A total of 9 N. scintillans red tides, 7 Ceratium furca red tides and...

  12. Are we Genomic Mosaics? Variations of the Genome of Somatic Cells can Contribute to Diversify our Phenotypes

    OpenAIRE

    Astolfi, P.A.; Salamini, F.; Sgaramella, V

    2010-01-01

    Theoretical and experimental evidences support the hypothesis that the genomes and the epigenomes may be different in the somatic cells of complex organisms. In the genome, the differences range from single base substitutions to chromosome number; in the epigenome, they entail multiple postsynthetic modifications of the chromatin. Somatic genome variations (SGV) may accumulate during development in response both to genetic programs, which may differ from tissue to tissue, and to environmental...

  13. Functional analyses of coronary artery disease associated variation on chromosome 9p21 in vascular smooth muscle cells

    OpenAIRE

    Motterle, Anna; Pu, Xiangyuan; Wood, Harriet; Xiao, Qingzhong; Gor, Shivani; Liang Ng, Fu; Chan, Kenneth; Cross, Frank; Shohreh, Beski; Poston, Robin N.; Tucker, Arthur T.; Caulfield, Mark J; Ye, Shu

    2012-01-01

    Variation on chromosome 9p21 is associated with risk of coronary artery disease (CAD). This genomic region contains the CDKN2A and CDKN2B genes which encode the cell cycle regulators p16INK4a, p14ARF and p15INK4b and the ANRIL gene which encodes a non-coding RNA. Vascular smooth muscle cell (VSMC) proliferation plays an important role in the pathogenesis of atherosclerosis which causes CAD. We ascertained whether 9p21 genotype had an influence on CDKN2A/CDKN2B/ANRIL expression levels in VSMCs...

  14. Variation of mechanical behavior of β-TCP/collagen two phase composite scaffold with mesenchymal stem cell in vitro.

    Science.gov (United States)

    Arahira, Takaaki; Todo, Mitsugu

    2016-08-01

    The primary aim of this study is to characterize the variational behavior of the compressive mechanical property of bioceramic-based scaffolds using stem cells during the cell culture period. β-Tricalcium phosphate (TCP)/collagen two phase composites and β-TCP scaffolds were fabricated using the polyurethane template technique and a subsequent freeze-drying method. Rat bone-marrow mesenchymal stem cells (rMSCs) were then cultured in these scaffolds for up to 28 days. Compression tests of the scaffolds with rMSCs were periodically conducted. Biological properties, such as the cell number, alkaline phosphatase (ALP) activity, and gene expressions of osteogenesis, were evaluated. The microstructural change due to cell growth and the formation of extracellular matrices was examined using a field-emission scanning electron microscope. The compressive property was then correlated with the biological properties and microstructures to understand the mechanism of the variational behavior of the macroscopic mechanical property. The porous collagen structure in the β-TCP scaffold effectively improved the structural stability of the composite scaffold, whereas the β-TCP scaffold exhibited structural instability with the collapse of the porous structure when immersed in a culture medium. The β-TCP/collagen composite scaffold exhibited higher ALP activity and more active generation of osteoblastic markers than the β-TCP scaffold. PMID:27124803

  15. Business Cycle Dependent Unemployment Insurance

    DEFF Research Database (Denmark)

    Andersen, Torben M.; Svarer, Michael

    The consequences of business cycle contingencies in unemployment insurance systems are considered in a search-matching model allowing for shifts between "good" and "bad" states of nature. We show that not only is there an insurance argument for such contingencies, but there may also be an incentive...

  16. Business cycle dependent unemployment insurance

    OpenAIRE

    Andersen, Torben M.; Svarer, Michael

    2010-01-01

    The consequences of business cycle contingencies in unemployment insurance systems are considered in a search-matching model allowing for shifts between "good" and "bad" states of nature. We show that not only is there an insurance argument for such contingencies, but there may also be an incentive argument. Since benefits may be less distortionary in a recession than a boom, it follows that counter-cyclical benefits reduce average distortions compared to state independent benefits. We show t...

  17. Time related variations in stem cell harvesting of umbilical cord blood

    OpenAIRE

    Gianluigi Mazzoccoli; Giuseppe Miscio; Andrea Fontana; Massimiliano Copetti; Massimo Francavilla; Alberto Bosi; Federico Perfetto; Alice Valoriani; Angelo De Cata; Michele Santodirocco; Angela Totaro; Rosa Rubino; Lazzaro di Mauro; Roberto Tarquini

    2016-01-01

    Umbilical cord blood (UCB) contains hematopoietic stem cells and multipotent mesenchymal cells useful for treatment in malignant/nonmalignant hematologic-immunologic diseases and regenerative medicine. Transplantation outcome is correlated with cord blood volume (CBV), number of total nucleated cells (TNC), CD34+ progenitor cells and colony forming units in UCB donations. Several studies have addressed the role of maternal/neonatal factors associated with the hematopoietic reconstruction pote...

  18. Variation in human cancer cell external phosphatidylserine is regulated by flippase activity and intracellular calcium

    OpenAIRE

    Vallabhapurapu, Subrahmanya D.; Blanco, Víctor M.; Sulaiman, Mahaboob K; Vallabhapurapu, Swarajya Lakshmi; Chu, Zhengtao; Franco, Robert S.; Qi, Xiaoyang

    2015-01-01

    Viable cancer cells expose elevated levels of phosphatidylserine (PS) on the exoplasmic face of the plasma membrane. However, the mechanisms leading to elevated PS exposure in viable cancer cells have not been defined. We previously showed that externalized PS may be used to monitor, target and kill tumor cells. In addition, PS on tumor cells is recognized by macrophages and has implications in antitumor immunity. Therefore, it is important to understand the molecular details of PS exposure o...

  19. Variations in Humanized and Defined Culture Conditions Supporting Derivation of New Human Embryonic Stem Cell Lines

    DEFF Research Database (Denmark)

    Fletcher, Judy M; Ferrier, Patricia M; Gardner, John O;

    2006-01-01

    The evolution of "humanized" (i.e., free of animal sourced reagents) and ultimately chemically defined culture systems for human embryo stem cell (hESC) isolation and culture is of importance to improving their efficacy and safety in research and therapeutic applications. This can be achieved by......ESC derivation, namely the use of animal immune compliment to isolate embryo inner cell mass, and animal sourced serum products and feeder cells to sustain hESC growth and attachment. As a result we report the derivation of six new hESC lines isolated by outgrowth from whole blastocysts on an extracellular...... serum-free medium (SFM) containing only human sourced and recombinant protein. Further, outgrowth of embryonic cells from whole blastocysts in both media could be achieved for up to 1 week without reliance on feeder cells. All variant conditions sustained undifferentiated cell status, a stable karyotype...

  20. NEGATIVE EPISTASIS BETWEEN α+ THALASSAEMIA AND SICKLE CELL TRAIT CAN EXPLAIN INTERPOPULATION VARIATION IN SOUTH ASIA

    OpenAIRE

    Penman, Bridget S.; Habib, Saman; Kanchan, Kanika; Gupta, Sunetra; Read, A.(Department of Physics, University of Oslo, Oslo, Norway)

    2011-01-01

    Recent studies in Kenya and Ghana have shown that individuals who inherit two malaria-protective genetic disorders of haemoglobin—α+ thalassaemia and sickle cell trait—experience a much lower level of malaria protection than those who inherit sickle cell trait alone. We have previously demonstrated that this can limit the frequency of α+ thalassaemia in a population in which sickle cell is present, which may account for the frequency of α+ thalassaemia in sub-Saharan Africa not exceeding 50%....

  1. Genetic Variation in Cell Death Genes and Risk of Non-Hodgkin Lymphoma

    OpenAIRE

    Johanna M. Schuetz; Denise Daley; Jinko Graham; Berry, Brian R.; Gallagher, Richard P.; Connors, Joseph M; Gascoyne, Randy D.; Spinelli, John J.; Angela R Brooks-Wilson

    2012-01-01

    BACKGROUND: Non-Hodgkin lymphomas are a heterogeneous group of solid tumours that constitute the 5(th) highest cause of cancer mortality in the United States and Canada. Poor control of cell death in lymphocytes can lead to autoimmune disease or cancer, making genes involved in programmed cell death of lymphocytes logical candidate genes for lymphoma susceptibility. MATERIALS AND METHODS: We tested for genetic association with NHL and NHL subtypes, of SNPs in lymphocyte cell death genes using...

  2. Rapid cell variation can determine the establishment of a persistent viral infection.

    OpenAIRE

    Martín-Hernández, Ana M.; Carrillo, Elisa C.; Sevilla, Noemí; Domingo, Esteban

    1994-01-01

    Evidence for a mechanism of initiation of viral persistence in which the cell, and not the virus, plays a critical role has been obtained using the important animal pathogen foot-and-mouth disease virus (FMDV). We have developed a virulence assay consisting of quantification of the ability of virus to kill cells and of cells to divide in the presence of virus and to initiate a carrier state. Cells were cured of FMDV at early times following a cytolytic infection of BHK-21 monolayers with FMDV...

  3. Thyroid hormone stimulation in vitro of red blood cell Ca2+-ATPase activity: interspecies variation.

    Science.gov (United States)

    Davis, F B; Kite, J H; Davis, P J; Blas, S D

    1982-01-01

    In vitro susceptibility to thyroid hormone stimulation of membrane-associated Ca2+-ATPase activity has been examined in red blood cells from rat, rabbit, dog, monkey, and man. Monkey and human red cell Ca2+-ATPase activities responded comparably to 10(-10)M T4 or T3. Basal and thyroid hormone-stimulated Ca2+-ATPase activity in rabbit erythrocytes was four-fold higher than in primate red cells. Rat and dog red cell Ca2+-ATPase did not respond to iodothyronines in vitro. PMID:6459228

  4. [CD226 monoclonal antibody induces variation of intracytosolic free calcium level in human umbilical vein endothelial cells].

    Science.gov (United States)

    Chen, Li-Hua; Liu, Xue-Song; Liu, Fei; Jin, Bo-Quan

    2003-06-25

    In order to study the possible mechanism of CD226 monoclonal antibody (mAb)-mediated intracellular message transduction in human umbilical vein endothelial cells (HUVECs), the influence of CD226 mAb and its cross-linking by secondary antibody (II Ab) on the concentration changes in [Ca(2+)](i) in the HUVECs under different conditions were determined by confocal laser scanning microscopy. The main results are as follows. (1) When the culture medium was balanced by Hanks Buffer, [Ca(2+)](i) in HUVECs increased slowly after stimulation by CD226 mAb, whereas [Ca(2+)](i) increase was accompanied by [Ca(2+)](o) decrease after the mAb was cross-linked by goat anti-mouse IgG. Then [Ca(2+)](i) and [Ca(2+)](o) all returned to the normal level. (2) When the culture medium was balanced by D-Hanks buffer, [Ca(2+)](i) in HUVECs showed little variation when the cells were stimulated by CD226 mAb, but [Ca(2+)](i) decreased markedly after cross-linking. (3) When HUVECs were pretreated with EGTA, there was no variation in [Ca(2+)](i) of HUVECs after CD226 mAb stimulation alone or cross-linking of the mAb. Our results suggest that stimulation by CD226 mAb and cross-linking by goat anti-mouse IgG induce the variation of [Ca(2+)](i) in HUVECs under different conditions and the variation of [Ca(2+)](i) in HUVECs may play an important role in many physiological and pathological processes. PMID:12817306

  5. Association of activating KIR copy number variation of NK cells with containment of SIV replication in rhesus monkeys.

    Directory of Open Access Journals (Sweden)

    Ina Hellmann

    2011-12-01

    Full Text Available While the contribution of CD8⁺ cytotoxic T lymphocytes to early containment of HIV-1 spread is well established, a role for NK cells in controlling HIV-1 replication during primary infection has been uncertain. The highly polymorphic family of KIR molecules expressed on NK cells can inhibit or activate these effector cells and might therefore modulate their activity against HIV-1-infected cells. In the present study, we investigated copy number variation in KIR3DH loci encoding the only activating KIR receptor family in rhesus monkeys and its effect on simian immunodeficiency virus (SIV replication during primary infection in rhesus monkeys. We observed an association between copy numbers of KIR3DH genes and control of SIV replication in Mamu-A*01⁻ rhesus monkeys that express restrictive TRIM5 alleles. These findings provide further evidence for an association between NK cells and the early containment of SIV replication, and underscore the potential importance of activating KIRs in stimulating NK cell responses to control SIV spread.

  6. Cell cycle effects for radiosensitivity after heavy ion exposure

    International Nuclear Information System (INIS)

    In order to study the relative contribution of the two major DNA double-strand break (DSB) repair pathways, non-homologous end-joining (NHEJ) and homologous recombinational repair (HRR), to the repair of DSBs and non-DSB clustered DNA damage induced by high linear energy transfer (LET) ionizing radiation through the cell cycle, we exposed wild type (WT), NHEJ-deficient, and HRR-deficient Chinese hamster ovary (CHO) cells synchronized by mitotic shake-off to accelerated heavy ions and X-rays. The cell cycle-dependent variation in survival observed in WT cells after X-irradiation was not observed after exposure to 500 MeV/amu iron ions. Non-homologous end joining (NHEJ) and homologous recombinational repair (HRR)-defective cells showed different patterns of cell cycle-dependent radiosensitivity after X-irradiation compared to WT cells, that were likewise significantly attenuated after iron ion exposures. Higher relative biological effectiveness for several other accelerated heavy ions (C, Ne, Si, Ar) of differing LETs was observed for cells exposed in S phase compared to cells exposed in G1. We also observed that HRR deficiency, unlike NHEJ deficiency, did not affect the progression of irradiated G2 cells into mitosis, thus contributing to increased cell killing observed in G2-phase HRR-deficient cells. The HRR-deficient cells showed significantly increased levels of chromatid-type aberrations that correlated with their cell cycle pattern of survival after both X- and iron ion irradiation. Our results suggest that high LET radiation produces not only complex DSBs but also complex non-DSB clustered lesions that specifically require the HRR-mediated repair of these lesions if encountered during DNA replication. In this year, we focused on Fanconi Anemia DNA repair pathway. Only FancA mutant cells showed hypersensitivity to high LET ionizing radiation among other FancC, FancD1, FancD2, and FancG mutant cells. (author)

  7. Are we Genomic Mosaics? Variations of the Genome of Somatic Cells can Contribute to Diversify our Phenotypes.

    Science.gov (United States)

    Astolfi, P A; Salamini, F; Sgaramella, V

    2010-09-01

    Theoretical and experimental evidences support the hypothesis that the genomes and the epigenomes may be different in the somatic cells of complex organisms. In the genome, the differences range from single base substitutions to chromosome number; in the epigenome, they entail multiple postsynthetic modifications of the chromatin. Somatic genome variations (SGV) may accumulate during development in response both to genetic programs, which may differ from tissue to tissue, and to environmental stimuli, which are often undetected and generally irreproducible. SGV may jeopardize physiological cellular functions, but also create novel coding and regulatory sequences, to be exposed to intraorganismal Darwinian selection. Genomes acknowledged as comparatively poor in genes, such as humans', could thus increase their pristine informational endowment. A better understanding of SGV will contribute to basic issues such as the "nature vs nurture" dualism and the inheritance of acquired characters. On the applied side, they may explain the low yield of cloning via somatic cell nuclear transfer, provide clues to some of the problems associated with transdifferentiation, and interfere with individual DNA analysis. SGV may be unique in the different cells types and in the different developmental stages, and thus explain the several hundred gaps persisting in the human genomes "completed" so far. They may compound the variations associated to our epigenomes and make of each of us an "(epi)genomic" mosaic. An ensuing paradigm is the possibility that a single genome (the ephemeral one assembled at fertilization) has the capacity to generate several different brains in response to different environments. PMID:21358981

  8. Time related variations in stem cell harvesting of umbilical cord blood

    Science.gov (United States)

    Mazzoccoli, Gianluigi; Miscio, Giuseppe; Fontana, Andrea; Copetti, Massimiliano; Francavilla, Massimo; Bosi, Alberto; Perfetto, Federico; Valoriani, Alice; de Cata, Angelo; Santodirocco, Michele; Totaro, Angela; Rubino, Rosa; di Mauro, Lazzaro; Tarquini, Roberto

    2016-02-01

    Umbilical cord blood (UCB) contains hematopoietic stem cells and multipotent mesenchymal cells useful for treatment in malignant/nonmalignant hematologic-immunologic diseases and regenerative medicine. Transplantation outcome is correlated with cord blood volume (CBV), number of total nucleated cells (TNC), CD34+ progenitor cells and colony forming units in UCB donations. Several studies have addressed the role of maternal/neonatal factors associated with the hematopoietic reconstruction potential of UCB, including: gestational age, maternal parity, newborn sex and birth weight, placental weight, labor duration and mode of delivery. Few data exist regarding as to how time influences UCB collection and banking patterns. We retrospectively analyzed 17.936 cord blood donations collected from 1999 to 2011 from Tuscany and Apulia Cord Blood Banks. Results from generalized multivariable linear mixed models showed that CBV, TNC and CD34+ cell were associated with known obstetric and neonatal parameters and showed rhythmic patterns in different time domains and frequency ranges. The present findings confirm that volume, total nucleated cells and stem cells of the UCB donations are hallmarked by rhythmic patterns in different time domains and frequency ranges and suggest that temporal rhythms in addition to known obstetric and neonatal parameters influence CBV, TNC and CD34+ cell content in UBC units.

  9. Dissecting Regional Variations in Stress Fiber Mechanics in Living Cells with Laser Nanosurgery

    Energy Technology Data Exchange (ETDEWEB)

    Tanner, Kandice; Boudreau, Aaron; Bissell, Mina J; Kumar, Sanjay

    2010-03-02

    The ability of a cell to distribute contractile stresses across the extracellular matrix in a spatially heterogeneous fashion underlies many cellular behaviors, including motility and tissue assembly. Here we investigate the biophysical basis of this phenomenon by using femtosecond laser nanosurgery to measure the viscoelastic recoil and cell-shape contributions of contractile stress fibers (SFs) located in specific compartments of living cells. Upon photodisruption and recoil, myosin light chain kinase-dependent SFs located along the cell periphery display much lower effective elasticities and higher plateau retraction distances than Rho-associated kinase-dependent SFs located in the cell center, with severing of peripheral fibers uniquely triggering a dramatic contraction of the entire cell within minutes of fiber irradiation. Image correlation spectroscopy reveals that when one population of SFs is pharmacologically dissipated, actin density flows toward the other population. Furthermore, dissipation of peripheral fibers reduces the elasticity and increases the plateau retraction distance of central fibers, and severing central fibers under these conditions triggers cellular contraction. Together, these findings show that SFs regulated by different myosin activators exhibit different mechanical properties and cell shape contributions. They also suggest that some fibers can absorb components and assume mechanical roles of other fibers to stabilize cell shape.

  10. MR-imaging of the breast at 0.5 Tesla: menstrual-cycle dependency of parenchymal contrast enhancement in healthy volunteers with oral contraceptive use?

    International Nuclear Information System (INIS)

    Introduction: To evaluate changes of contrast medium enhancement of the breast parenchyma due to menstrual cycle in healthy volunteers with oral contraceptive use in MR-imaging of the breast. Material and Methods: 15 healthy volunteers (age: 22 - 36, mean 28,2) without breast disease were examined two times during one menstrual cycle (days 7 - 14 and days 21 - 2). Two volunteers were examined only in the second part of the cycle (days 21 - 2). All volunteers used oral contraceptives for more than 6 month continuously. Examinations were performed with a 0,5 T magnet (dynamic 3D-gradient echo protocol with subtraction postprocessing). We evaluated the number of enhancing foci and the parenchymal contrast medium enhancement during the different phases of the cycle by region of interest. Results: Only a total of two enhancing foci were found in 2 of 17 volunteers. Time/signal intensity diagrams in these both cases were not suspicious (< 80% initial signal increase after of contrast medium injection, no wash-out phenomenon) and sonography of the breast in these two cases was inconspicuous. Contrast medium enhancement of breast parenchyma in cycle days 7 - 14 (mean enhancement: 0.12 - 0.26, minutes 1 - 9 p.i.) was not significantly different (p = 0.2209; Wilcoxon signed rank test) from cycle days 21 - 2 (mean: 0.13 - 0.32). Conclusion: Menstrual cycle dependency of parenchymal contrast medium enhancement seems to be of minor relevance for premenopausal women with use of oral contraceptives. (orig.)

  11. Variation in sensitizing effect of caffeine in human tumour cell lines after γ-irradiation

    International Nuclear Information System (INIS)

    We have investigated whether the protective role of the G2 checkpoint has increasing importance when the p53-dependent G1 checkpoint is inactivated. We have studied the differential effect of caffeine by clonogenic assays and flow cytometry in three human tumour cell lines with different functionality of p53 protein. The radiosensitizing effect of caffeine (2 mM) expressed itself as a significant decrease in surviving fraction at 2 Gy and a significant increase in α-values in RT112 and TE671, both with non-functional p53. However, no radiosensitizing effect was seen in cells with a normal p53 function (MCF-7 BUS). Two millimoles of caffeine also caused important changes in the cell cycle progression after irradiation. MCF-7 BUS showed a G1 arrest after irradiation and an early G2 arrest but those cells that reached the second G2 did not arrest significantly. In contrast, TE671 exhibited radiosensitization by caffeine, no G1 arrest, a G2 arrest in those cells irradiated in G2, no significant accumulation in the second G2 but an overall delay in release from the first cell cycle, which could be abrogated by caffeine. RT112 was similar to TE671 except that the emphasis in a G2 arrest was shifted from the block in cells irradiated in G2 to those irradiated at other cell cycle phases. The data presented confirm that p53 status can be a significant determinant of the efficacy of caffeine as radiosensitizer in these tumour cell lines, and document the importance of the G2 checkpoint in this effect. (author)

  12. Variations of very low-density lipoprotein receptor subtype expression in gastrointestinal adenocarcinoma cells with various differentiations

    Institute of Scientific and Technical Information of China (English)

    Tao Chen; Fan Wu; Feng-Ming Chen; Jun Tian; Shen Qu

    2005-01-01

    AIM: This study is aimed at investigating the expression and possible significances of very low-density lipoprotein receptor (VLDLR) subtypes in gastroenteric adenocarcinoma tissues and cells with various differentiations. METHODS: Thirty-one cases of gastroenteric carcinoma/ adjacent normal tissues were enrolled in the study, which were diagnosed and classified by the clinicopathological diagnosis. The expression of VLDLR subtypes was detected in gastroenteric carcinoma/adjacent normal tissues and three various differentiated human gastric adenocarcinoma cell lines (MKN28, SGC7901 and MKN45) by reverse transcription polymerase chain reaction (RT-PCR) and Western blot analysis.RE,SULTS: Two VLDLR subtypes, namely, type Ⅱ VLDLR and type Ⅰ VLDLR, were found to express changes in gastroenteric carcinoma tissues, their adjacent normal tissue, and gastric adenocarcinoma cell lines as well. Type Ⅱ VLDLR is predominantly expressed in poorly- or moderately-differentiated gastroenteric carcinoma tissues and gastric adenocarcinoma cell lines, whereas type ⅠVLDLR is mainly detected in well-differentiated intestinal carcinoma tissues and gastric adenocarcinoma cells compared with the adjacent normal tissues. CONCLUSION: The results suggested that the variations of the VLDLR subtype expression might be correlated with the progress and differentiation of gastroenteric carcinoma.

  13. Variation of radiation-sensitivity of neural stem and progenitor cell populations within the developing mouse brain

    International Nuclear Information System (INIS)

    We investigated the DNA damage response (DDR) of fetal neural stem and progenitor cells (NSPC), since exposure to ionizing radiation can severely impair the brain development. We compared apoptosis induction in the dorsal tel-encephalon and the lateral ganglionic eminences (LGE) of mouse embryos after an in utero irradiation. We used two thymidine analogs, together with the physical position of nuclei within brain structures, to determine the fate of irradiated NSPC. NSPC did not activate an apparent protein 21(p21)- dependent G1/S checkpoint within the LGE as their counterparts within the dorsal tel-encephalon. However, the levels of radiation induced apoptosis differed between the two tel-encephalic regions, due to the high radiation sensitivity of intermediate progenitors of the LGE. Besides radial glial cells, that function as neural stem cells, were more resistant and were reoriented toward self-renewing within hours following irradiation. The lack of the p21-dependent-cell cycle arrest at the G1/S transition appears to be a general feature of NSPC in the developing brain. However, we found variation of radiation response in function of the types of NSPC. Factors involved in DDR and those involved in the regulation of neurogenesis are intricately linked in determining the cell fate after irradiations. (authors)

  14. Cell morphology variations of Klebsiella pneumoniae induced by acetate stress using biomimetic vesicle assay.

    Science.gov (United States)

    Lu, Shengguo; Han, Yuwang; Duan, Xujia; Luo, Fang; Zhu, Lingyan; Li, Shuang; Huang, He

    2013-10-01

    Supplementation with acetate under low levels was used as a novel approach to control the morphological development of Klebsiella pneumoniae aimed to improve 1,3-propanediol (1,3-PD) production. A full range of morphological types formed from rod shape to oval shape even round shape in response to different concentrations of acetate. The cell growth and 1,3-PD productions in the shake flasks with 0.5 g/L acetate addition were improved by 9.4 and 28.37%, respectively, as compared to the control, while the cell became shorter and began to lose its original shape. The cell membrane penetration by acetate was investigated by the biomimetic vesicles, while higher concentration of acetate led to more moderate colorimetric transitions. Moreover, the percentage composition of unsaturated fatty acid (UFA) was increased as well as the increased concentrations of acetate, whereas higher UFA percentage, higher fluidity of bacterial cell membrane. PMID:23892619

  15. Climatic anomalous patterns associated with the Arctic and Polar cell strength variations

    Science.gov (United States)

    Qian, Weihong; Wu, Kaijun; Leung, Jeremy Cheuk-Hin

    2016-03-01

    The Arctic cell as a reversed and closed loop next to the Polar cell has been recently revealed in the Northern Hemisphere (NH). In this paper, we study the interannual variability of the Arctic and Polar cell strengths during 1979-2012, and their influence on surface air temperature (SAT), precipitation, and sea-ice concentration (SIC) at mid- and high-latitudes of the NH. We show that there is a significant negative correlation between the Arctic and Polar cell strengths. Both the Arctic and Polar cell strengths can well indicate the recurring climatic anomalies of SAT, precipitation, and SIC in their extreme winters. The surface large-scale cold-warm and dry-wet anomalous patterns in these extreme winters are directly linked with the vertical structure of height and temperature anomalies in the troposphere. Results suggest that the past climatic anomalies are better indicated by the strength anomalies of the Polar and Arctic cells than the traditional indices of mid-high latitude pattern such as the Arctic Oscillation and North Atlantic Oscillation. This study illustrates a three-dimensional picture of atmospheric variable anomalies in the troposphere that result in surface climatic anomalies.

  16. Cell cycle-dependent changes in localization of a 210-kDa microtubule-interacting protein in .I.Leishmania./I..

    Czech Academy of Sciences Publication Activity Database

    Libusová, Lenka; Dráberová, Eduarda; Juliano, C.; Viklický, Vladimír; Fiori, P. L.; Cappuccinelli, P.; Dráber, Petr

    2001-01-01

    Roč. 266, č. 2 (2001), s. 270-278. ISSN 0014-4827 R&D Projects: GA ČR GA304/00/0553; GA AV ČR IAA5052004 Keywords : microtubule-associated proteins * Leishmania-antibody Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.096, year: 2001

  17. First and second law performance variations of a coal gasification fuel-cell-based combined cogeneration plant with varying load

    Energy Technology Data Exchange (ETDEWEB)

    Ghosh, S. [Deemed University, Howrah (India). Dept. of Mechanical Engineering; De, S. [Jadavpur University, Calcutta (India). Dept. of Mechanical Engineering

    2004-12-01

    An advanced combined cogeneration plant based on a solid oxide fuel cell (SOFC) stack, fuelled by synthetic gas by coal gasification, upstream of a gas turbine and heat recovery steam generator (HRSG) to generate power as well as process steam downstream of it, has been thermodynamically modelled. While the plant supplies a base load power and process heat, provision of a fuel cell bypass mechanism for the synthetic gas stream offers the flexibility of matching the varying electrical power or the process heat load on the plant. The simulated energetic and exergetic performance of such a plant is presented in this paper and the optimum point of operation is reported. The exergy analysis shows the second law performance variation of significant components of the plant with varying loads. (author)

  18. Global translation variations in host cells upon attack of lytic and sublytic Staphylococcus aureus α-haemolysin.

    Science.gov (United States)

    Clamer, Massimiliano; Tebaldi, Toma; Marchioretto, Marta; Bernabò, Paola; Bertini, Efrem; Guella, Graziano; Dalla Serra, Mauro; Quattrone, Alessandro; Viero, Gabriella

    2015-11-15

    Genome-wide analyses of translation can provide major contributions in our understanding of the complex interplay between virulent factors and host cells. So far, the activation of host translational control mechanisms by bacterial toxins, owing to specific recruitment of mRNAs, RNA-binding proteins (RBPs) and ncRNAs (non-coding RNAs), are far from being understood. In the present study, we characterize for the first time the changes experienced by the translational control system of host cells in response to the well-known Staphylococcus aureus α-haemolysin (AHL) under both sublytic and lytic conditions. By comparing variations occurring in the cellular transcriptome and translatome, we give evidence that global gene expression is primarily rewired at the translational level, with the contribution of the RBP ELAVL1 (HuR) in the sublytic response. These results reveal the importance of translational control during host-pathogen interaction, opening new approaches for AHL-induced diseases. PMID:26371376

  19. Phospholipidomic Profile Variation on THP-1 Cells Exposed to Skin or Respiratory Sensitizers and Respiratory Irritant.

    Science.gov (United States)

    Martins, João D; Maciel, Elisabete A; Silva, Ana; Ferreira, Isabel; Ricardo, Fernando; Domingues, Pedro; Neves, Bruno M; Domingues, Maria Rosário M; Cruz, Maria Teresa

    2016-12-01

    Occupational exposure to low molecular weight reactive chemicals often leads to development of allergic reactions such as allergic contact dermatitis and respiratory allergies. Further insights into the interaction of these chemicals with physiopathological relevant cellular models might provide the foundations for novel non-animal approaches to safety assessment. In this work we used the human THP-1 cell line to determine phospholipidome changes induced by the skin sensitizer 1-fluoro-2,4-dinitrobenzene (DNFB), the respiratory allergen hexamethylene diisocyanate (HDI), and the irritant methyl salicylate (MESA). We detected that these chemicals differently induce lipid peroxidation and modulate THP-1 IL-1β, IL-12B, IL-8, CD86, and HMOX1 transcription. Decreased phosphatidylethanolamine content was detected in cells exposed to MESA, while profound alterations in the relative abundance of cardiolipin species were observed in cells exposed to DNFB. All chemicals tested induced a decrease in the relative abundance of plasmanyl phosphatidylcholine species PC (O-16:0e/18:1) and phosphatidylinositol species PI (34:1), while increasing PI (38:4). An increased abundance of oleic acid was observed in the phospholipids of cells exposed to DNFB while a decreased abundance of palmitic acid was detected in cells treated with MESA or DNFB. We conclude that both specific and common alterations at phospholipidome levels are triggered by the different chemicals, while not allowing a complete distinction between them using a Canonical Analysis of Principal Coordinates (CAP). The common effects observed at phospholipids level with all the chemicals tested might be related to unspecific cell cytotoxic mechanisms that nevertheless may contribute to the elicitation of specific immune responses. J. Cell. Physiol. 231: 2639-2651, 2016. © 2016 Wiley Periodicals, Inc. PMID:26946329

  20. Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways.

    Directory of Open Access Journals (Sweden)

    Martin H Schaefer

    2014-06-01

    Full Text Available Many proteins and signaling pathways are present in most cell types and tissues and yet perform specialized functions. To elucidate mechanisms by which these ubiquitous pathways are modulated, we overlaid information about cross-cell line protein abundance and variability, and evolutionary conservation onto functional pathway components and topological layers in the pathway hierarchy. We found that the input (receptors and the output (transcription factors layers evolve more rapidly than proteins in the intermediary transmission layer. In contrast, protein expression variability decreases from the input to the output layer. We observed that the differences in protein variability between the input and transmission layer can be attributed to both the network position and the tendency of variable proteins to physically interact with constitutively expressed proteins. Differences in protein expression variability and conservation are also accompanied by the tendency of conserved and constitutively expressed proteins to acquire somatic mutations, while germline mutations tend to occur in cell type-specific proteins. Thus, conserved core proteins in the transmission layer could perform a fundamental role in most cell types and are therefore less tolerant to germline mutations. In summary, we propose that the core signal transmission machinery is largely modulated by a variable input layer through physical protein interactions. We hypothesize that the bow-tie organization of cellular signaling on the level of protein abundance variability contributes to the specificity of the signal response in different cell types.

  1. Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways.

    Science.gov (United States)

    Schaefer, Martin H; Yang, Jae-Seong; Serrano, Luis; Kiel, Christina

    2014-06-01

    Many proteins and signaling pathways are present in most cell types and tissues and yet perform specialized functions. To elucidate mechanisms by which these ubiquitous pathways are modulated, we overlaid information about cross-cell line protein abundance and variability, and evolutionary conservation onto functional pathway components and topological layers in the pathway hierarchy. We found that the input (receptors) and the output (transcription factors) layers evolve more rapidly than proteins in the intermediary transmission layer. In contrast, protein expression variability decreases from the input to the output layer. We observed that the differences in protein variability between the input and transmission layer can be attributed to both the network position and the tendency of variable proteins to physically interact with constitutively expressed proteins. Differences in protein expression variability and conservation are also accompanied by the tendency of conserved and constitutively expressed proteins to acquire somatic mutations, while germline mutations tend to occur in cell type-specific proteins. Thus, conserved core proteins in the transmission layer could perform a fundamental role in most cell types and are therefore less tolerant to germline mutations. In summary, we propose that the core signal transmission machinery is largely modulated by a variable input layer through physical protein interactions. We hypothesize that the bow-tie organization of cellular signaling on the level of protein abundance variability contributes to the specificity of the signal response in different cell types. PMID:24922536

  2. Cell cycle effects for radiosensitivity after heavy ion exposure

    International Nuclear Information System (INIS)

    In order to study the relative contribution of the two major DNA double-strand break (DSB) repair pathways, non-homologous end-joining (NHEJ) and homologous recombinational repair (HRR), to the repair of DSBs and non-DSB clustered DNA damage induced by high linear energy transfer (LET) ionizing radiation through the cell cycle, we exposed wild type (WT), NHEJ-deficient, and HRR-deficient Chinese hamster ovary (CHO) cells synchronized by mitotic shake-off to accelerated heavy ions and X-rays. The cell cycle-dependent variation in survival observed in WT cells after X-irradiation was not observed after exposure to 500 MeV/amu iron ions. Non-homologous end joining (NHEJ) and homologous recombinational repair (HRR)-defective cells showed different patterns of cell cycle-dependent radiosensitivity after X-irradiation compared to WT cells, that were likewise significantly attenuated after iron ion exposures. Higher relative biological effectiveness for several other accelerated heavy ions (C, Ne, Si, Ar) of differing LETs was observed for cells exposed in S phase compared to cells exposed in G1. We also observed that HRR deficiency, unlike NHEJ deficiency, did not affect the progression of irradiated G2 cells into mitosis, thus contributing to increased cell killing observed in G2-phase HRR-deficient cells. The HRR-deficient cells showed significantly increased levels of chromatid-type aberrations that correlated with their cell cycle pattern of survival after both X- and iron ion irradiation. Our results suggest that high LET radiation produces not only complex DSBs but also complex non-DSB clustered lesions that specifically require the HRR-mediated repair of these lesions if encountered during DNA replication. (author)

  3. Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data.

    Directory of Open Access Journals (Sweden)

    Anna Gerasimova

    Full Text Available Genome-wide association studies (GWASs identify single nucleotide polymorphisms (SNPs that are enriched in individuals suffering from a given disease. Most disease-associated SNPs fall into non-coding regions, so that it is not straightforward to infer phenotype or function; moreover, many SNPs are in tight genetic linkage, so that a SNP identified as associated with a particular disease may not itself be causal, but rather signify the presence of a linked SNP that is functionally relevant to disease pathogenesis. Here, we present an analysis method that takes advantage of the recent rapid accumulation of epigenomics data to address these problems for some SNPs. Using asthma as a prototypic example; we show that non-coding disease-associated SNPs are enriched in genomic regions that function as regulators of transcription, such as enhancers and promoters. Identifying enhancers based on the presence of the histone modification marks such as H3K4me1 in different cell types, we show that the location of enhancers is highly cell-type specific. We use these findings to predict which SNPs are likely to be directly contributing to disease based on their presence in regulatory regions, and in which cell types their effect is expected to be detectable. Moreover, we can also predict which cell types contribute to a disease based on overlap of the disease-associated SNPs with the locations of enhancers present in a given cell type. Finally, we suggest that it will be possible to re-analyze GWAS studies with much higher power by limiting the SNPs considered to those in coding or regulatory regions of cell types relevant to a given disease.

  4. Mitochondrial Variations in Non-Small Cell Lung Cancer (NSCLC) Survival

    OpenAIRE

    Zhaoxi Wang; Sojung Choi; Jinseon Lee; Yen-Tsung Huang; Feng Chen; Yang Zhao; Xihong Lin; Donna Neuberg; Jhingook Kim; Christiani, David C.

    2015-01-01

    Mutations in the mtDNA genome have long been suspected to play an important role in cancer. Although most cancer cells harbor mtDNA mutations, the question of whether such mutations are associated with clinical prognosis of lung cancer remains unclear. We resequenced the entire mitochondrial genomes of tumor tissue from a population of 250 Korean patients with non-small cell lung cancer (NSCLC). Our analysis revealed that the haplogroup (D/D4) was associated with worse overall survival (OS) o...

  5. Analysis of Pressure Variations in a Low-Pressure Nickel-Hydrogen Battery– Part 2: Cells with Metal Hydride Storage

    Science.gov (United States)

    Purushothaman, B. K.; Wainright, J. S.

    2012-01-01

    A sub-atmospheric pressure nickel hydrogen (Ni-H2) battery with metal hydride for hydrogen storage is developed for implantable neuroprosthetic devices. Pressure variations during charge and discharge of the cell are analyzed at different states of charge and are found to follow the desorption curve of the pressure composition isotherm (PCI) of the metal hydride. The measured pressure agreed well with the calculated theoretical pressure based on the PCI and is used to predict the state of charge of the battery. Hydrogen equilibration with the metal hydride during charge/discharge cycling is fast when the pressure is in the range from 8 to 13 psia and slower in the range from 6 to 8 psia. The time constant for the slower hydrogen equilibration, 1.37h, is similar to the time constant for oxygen recombination and therefore pressure changes due to different mechanisms are difficult to estimate. The self-discharge rate of the cell with metal hydride is two times lower in comparison to the cell with gaseous hydrogen storage alone and is a result of the lower pressure in the cell when the metal hydride is used. PMID:22711974

  6. On temperature variations during 3He Polarization experiments in Pomeranchuk cells

    DEFF Research Database (Denmark)

    Geng, Q.; Rasmussen, Finn Berg

    1984-01-01

    Simple model calculations have been performed in relation to temperature changes in decompression experiments with Pomeranchuk cells, aiming at the production of spin polarized liquid **3He. Comparison with reported experiments indicates that thermal contact with the surroundings is too strong...

  7. Interspecific variation of intracellular localization and postirradiation movement of Ku70-protein in fibroblastic cells

    International Nuclear Information System (INIS)

    Ku (Ku70 and Ku80) Proteins are known as components of DNA-dependent protein kinase (DNA-PK) and play an important role for DNA repair. We previously reported that more than 70% of Ku proteins were located in cytoplasm of rat cells, the Ku proteins moved into nuclei of normal rat cells after X-irradiation, Ku proteins also moved into nuclei after X-irradiation but were not retained in nucleus of radiosensitive LEC rat cells. While reports have been shown about mechanisms on nuclear localization of Ku proteins, how Ku proteins export from nucleus is poorly understood. Here we show that C-terminal region of Ku70 protein is important for its cytoplasmic localization. When transfected into LEC rat cells, exogenous intact Ku70 (1-609) tagged with enhanced green fluorescent protein (EGFP-Ku70) localized mainly in the cytoplasm, whereas C-terminal-deletion mutant of Ku70 (1-593) tagged with EGFP (EGFP-Ku70D) was mainly localized in the nucleus. After X-irradiation, the endogenous intact EGFP-Ku70 once moved into nucleus, but returned into the cytoplasm. On the other hand, EGFP-Ku70D was retained in nucleus for two hours after X-irradiation. These results suggest that C-terminal region of Ku70 is included in the postirradiation nuclear export. Next, we investigated the intracellular localization of Ku70 proteins and the movement after X-irradiation of fibroblastic cells prepared from some mammalian species. Ku70 proteins were localized in nucleus and the postirradiation-extranuclear transport was not observed in human and African green monkey cells. On the other hand, Ku70 proteins were mainly localized in cytoplasm and moved into nucleus in mouse, Chinese hamster, Golden hamster, cotton rat, squirrel, cat and dog cells. These results may show that alternatively Ku70 protein is localized in the cytoplasm or nucleus depends on species and translocation of cytoplasmic Ku70 into nucleus is a response against low dose irradiation in fibroblasts of rodents, cats and dogs

  8. Interspecific variation of intracellular localization and postirradiation movement of Ku70-protein in fibroblastic cells

    Energy Technology Data Exchange (ETDEWEB)

    Endoh, Daiji; Hayashi, Masanobu [Rakuno Gakuen Univ., School of Veterinary Midicine, Ebetsu, Hokkaido (Japan); Okui, Toyo; Kawase, Shiro [Hokkaido Institute of Public Health, Sapporo, Hokkaido (Japan); Kon, Yasushiro [Hokkaido Univ., Graduate School of Veterinary Medicine, Sapporo, Hokkaido (Japan)

    2003-07-01

    Ku (Ku70 and Ku80) Proteins are known as components of DNA-dependent protein kinase (DNA-PK) and play an important role for DNA repair. We previously reported that more than 70% of Ku proteins were located in cytoplasm of rat cells, the Ku proteins moved into nuclei of normal rat cells after X-irradiation, Ku proteins also moved into nuclei after X-irradiation but were not retained in nucleus of radiosensitive LEC rat cells. While reports have been shown about mechanisms on nuclear localization of Ku proteins, how Ku proteins export from nucleus is poorly understood. Here we show that C-terminal region of Ku70 protein is important for its cytoplasmic localization. When transfected into LEC rat cells, exogenous intact Ku70 (1-609) tagged with enhanced green fluorescent protein (EGFP-Ku70) localized mainly in the cytoplasm, whereas C-terminal-deletion mutant of Ku70 (1-593) tagged with EGFP (EGFP-Ku70D) was mainly localized in the nucleus. After X-irradiation, the endogenous intact EGFP-Ku70 once moved into nucleus, but returned into the cytoplasm. On the other hand, EGFP-Ku70D was retained in nucleus for two hours after X-irradiation. These results suggest that C-terminal region of Ku70 is included in the postirradiation nuclear export. Next, we investigated the intracellular localization of Ku70 proteins and the movement after X-irradiation of fibroblastic cells prepared from some mammalian species. Ku70 proteins were localized in nucleus and the postirradiation-extranuclear transport was not observed in human and African green monkey cells. On the other hand, Ku70 proteins were mainly localized in cytoplasm and moved into nucleus in mouse, Chinese hamster, Golden hamster, cotton rat, squirrel, cat and dog cells. These results may show that alternatively Ku70 protein is localized in the cytoplasm or nucleus depends on species and translocation of cytoplasmic Ku70 into nucleus is a response against low dose irradiation in fibroblasts of rodents, cats and dogs

  9. Common altered epigenomic domains in cancer cells: characterization and subtle variations.

    Science.gov (United States)

    Tsai, Yi-Chien; Chiao, Chun-Hui; Chang, Ian Yi-Feng; Chen, Dow-Tien; Liu, Tze-Tze; Hua, Kate; Chang, Chuan-Hsiung; Hsu, Ming-Ta

    2011-01-01

    We have previously identified large megabase-sized hypomethylated zones in the genome of the breast cancer cell line MCF-7 using the TspRI-ExoIII technique. In this report, we used a more convenient high throughput method for mapping the hypomethylated zones in a number of human tumor genomes simultaneously. The method was validated by the bisulfite sequencing of 39 randomly chosen sites in a demethylated domain and by bisulfite genome-wide sequencing of the MCF-7 genome. This showed that the genomes of the various tumor cell lines, as well as some primary tumors, exhibit common hypomethylated domains. Interestingly, these hypomethylated domains are correlated with low CpG density distribution genome-wide, together with the histone H3K27Me3 landscape. Furthermore, they are inversely correlated with the H3K9Ac landscape and gene expression as measured in MCF-7 cells. Treatment with drugs resulted in en-bloc changes to the methylation domains. A close examination of the methylation domains found differences between non-invasive and invasive tumors with respect to tumorigenesis related genes. Taken together these results suggest that the human genome is organized in epigenomic domains that contain various different types of genes and imply that there are cis- and trans-regulators that control these domain-wide epigenetic changes and hence gene expression in the human genome. The hypomethylated domains are located in gene deserts that contain mainly tissue-specific genes and therefore we hypothesize that tumor cells keep these regions demethylated and silenced in order to save energy and resources and allow higher levels of cell proliferation and better survival (a thrifty tumor genome hypothesis). PMID:24212793

  10. A single cell level based method for copy number variation analysis by low coverage massively parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Chunlei Zhang

    Full Text Available Copy number variations (CNVs, a common genomic mutation associated with various diseases, are important in research and clinical applications. Whole genome amplification (WGA and massively parallel sequencing have been applied to single cell CNVs analysis, which provides new insight for the fields of biology and medicine. However, the WGA-induced bias significantly limits sensitivity and specificity for CNVs detection. Addressing these limitations, we developed a practical bioinformatic methodology for CNVs detection at the single cell level using low coverage massively parallel sequencing. This method consists of GC correction for WGA-induced bias removal, binary segmentation algorithm for locating CNVs breakpoints, and dynamic threshold determination for final signals filtering. Afterwards, we evaluated our method with seven test samples using low coverage sequencing (4∼9.5%. Four single-cell samples from peripheral blood, whose karyotypes were confirmed by whole genome sequencing analysis, were acquired. Three other test samples derived from blastocysts whose karyotypes were confirmed by SNP-array analysis were also recruited. The detection results for CNVs of larger than 1 Mb were highly consistent with confirmed results reaching 99.63% sensitivity and 97.71% specificity at base-pair level. Our study demonstrates the potential to overcome WGA-bias and to detect CNVs (>1 Mb at the single cell level through low coverage massively parallel sequencing. It highlights the potential for CNVs research on single cells or limited DNA samples and may prove as a promising tool for research and clinical applications, such as pre-implantation genetic diagnosis/screening, fetal nucleated red blood cells research and cancer heterogeneity analysis.

  11. Local variations of HER2 dimerization in breast cancer cells discovered by correlative fluorescence and liquid electron microscopy.

    Science.gov (United States)

    Peckys, Diana B; Korf, Ulrike; de Jonge, Niels

    2015-07-01

    The formation of HER2 homodimers plays an important role in breast cancer aggressiveness and progression; however, little is known about its localization. We have studied the intra- and intercellular variation of HER2 at the single-molecule level in intact SKBR3 breast cancer cells. Whole cells were visualized in hydrated state with correlative fluorescence microscopy and environmental scanning electron microscopy (ESEM). The locations of individual HER2 receptors were detected using an anti-HER2 affibody in combination with a quantum dot (QD), a fluorescent nanoparticle. Fluorescence microscopy revealed considerable differences of HER2 membrane expression between individual cells and between different membrane regions of the same cell (that is, membrane ruffles and flat areas). Subsequent ESEM of the corresponding cellular regions provided images of individually labeled HER2 receptors. The high spatial resolution of 3 nm and the close proximity between the QD and the receptor allowed quantifying the stoichiometry of HER2 complexes, distinguishing between monomers, dimers, and higher-order clusters. Downstream data analysis based on calculating the pair correlation function from receptor positions showed that cellular regions exhibiting membrane ruffles contained a substantial fraction of HER2 in homodimeric state. Larger-order clusters were also present. Membrane areas with homogeneous membrane topography, on the contrary, displayed HER2 in random distribution. Second, HER2 homodimers appeared to be absent from a small subpopulation of cells exhibiting a flat membrane topography, possibly resting cells. Local differences in homodimer presence may point toward functional differences with possible relevance for studying metastasis and drug response. PMID:26601217

  12. Weibull strength variations between room temperature and high temperature Ni-3YSZ half-cells

    DEFF Research Database (Denmark)

    Curran, Declan; Frandsen, Henrik Lund; Hendriksen, Peter Vang

    2013-01-01

    800°C in a reducing atmosphere. The strength of an as sintered half-cell was also measured at room temperature for comparison. Weibull analysis was performed on large sample sets of 30 for statistical viability. The Weibull strength and elastic modulus of the room temperature tested reduced samples...... show a decrease of approximately 33% and 51% respectively, when compared to the oxidized samples tested at room temperature. When tested at elevated temperatures both Weibull strength and elastic modulus decrease further when compared to the room temperature reduced samples. However these further...... efficiency, increased degradation and/or the complete termination of a functioning stack. This paper investigates the effects of temperature on the mechanical strength of 3% yttria-stabilised zirconia half-cells. Strength was measured using a four-point bend method at room temperature and at 600°C, 700°C and...

  13. A study on the variation of dye-sensitized solar cell parameters under γ irradiation

    International Nuclear Information System (INIS)

    In this paper, we mainly studied the γ irradiation effects and damage mechanism of dye-sensitized solar cells (DSSCs). The DSSCs were irradiated by γ irradiation at room temperature. J-V characteristics of cells showed that DSSC parameters such as short circuit current density (Jsc) and maximum power density (Pmax) decreased significantly after irradiation. The γ irradiation effects on fluorine-doped tin oxide (FTO), dye sensitizer, and anode were studied respectively to investigate the degradation of DSSC after irradiation. The Ultraviolet-visible spectra of FTO showed that the FTO transmittance decreased. The absorption peaks of dye generated a blue-shift. The X-ray diffraction measurement results indicated that the particle size of nano-crystalline TiO2 was changed after γ irradiation. (author)

  14. Strain Variation in Glycosaminoglycan Recognition Influences Cell-Type-Specific Binding by Lyme Disease Spirochetes

    OpenAIRE

    Parveen, Nikhat; Robbins, Douglas; Leong, John M.

    1999-01-01

    Lyme disease, a chronic multisystemic disorder that can affect the skin, heart, joints, and nervous system is caused by Borrelia burgdorferi sensu lato. Lyme disease spirochetes were previously shown to bind glycosaminoglycans (GAGs). In the current study, the GAG-binding properties of eight Lyme disease strains were determined. Binding by two high-passage HB19 derivatives to Vero cells could not be inhibited by enzymatic removal of GAGs or by the addition of exogenous GAG. The other six stra...

  15. Variation in vein density and mesophyll cell architecture in a rice deletion mutant population

    OpenAIRE

    Smillie, I.R.A.; Pyke, K.A.; Murchie, E. H.

    2012-01-01

    There is a need to develop rice plants with improved photosynthetic capacity and efficiency in order to enhance potential grain yield. Alterations in internal leaf morphology may be needed to underpin some of these improvements. One target is the production of a ‘Kranz-like’ anatomy, commonly considered to be required to achieve the desired levels of photosynthesis seen in C4 crops. Kranz anatomy typically has two or three mesophyll cells interspersing adjacent veins. As a first step to deter...

  16. Intratumour variation of biomarker expression by immunohistochemistry in resectable non-small cell lung cancer

    DEFF Research Database (Denmark)

    Jakobsen, Jan Nyrop; Santoni-Rugiu, Eric; Ravn, Jesper;

    2013-01-01

    truly reflect the pattern of biomarker expression. It may also be an important factor in chemo resistance, as tumours with heterogeneous biomarker expression may potentially harbour chemo resistant tumour clones. MATERIALS AND METHODS: Immunohistochemical evaluation of the expression of excision repair...... intratumour heterogeneity in 33-87% of tumours examined. This heterogeneity may influence results in studies investigating the therapeutic impact of predictive biomarkers in non-small cell lung cancer (NSCLC)....

  17. Velocity Variation Assessment of Red Blood Cell Aggregation with Spectral Domain Doppler Optical Coherence Tomography

    OpenAIRE

    Xu, Xiangqun; Yu, Lingfeng; Chen, Zhongping

    2010-01-01

    We propose spectral domain Doppler optical coherence tomography (SD-D-OCT) to qualitatively measure red blood cell aggregation. Variance/standard deviation (SD) of the Doppler frequency spectrum in Doppler variance imaging of flowing blood under shearing conditions was developed as a new aggregation index. In in vitro microchannel-flow experiments, porcine blood at various hematocrits with aggregation characteristics induced by dextran 500 or at the presence of plasma fibrinogen was measured ...

  18. Variation of T cell subset during acute rejection after liver transplantation in rhesus monkeys

    Institute of Scientific and Technical Information of China (English)

    Ran Jiang-hua; Liu Jing; Zhang Xi-bing; Zhang Sheng-ning; Wu Shu-yuan; Li Lai-bang; Li Wang; Li Li

    2014-01-01

    Abstract BACKGROUND: Looking for the early diagnosis of acute rejection indicators after liver transplantation can assess the risk after liver transplantation quickly and effectively, and T lymphocytes play the significant role in acute rejection. OBJECTIVE:To observe the relationship between acute rejection and variation of expression of T cel subset in blood after liver transplantation in rhesus monkey. METHODS: The sixteen liver transplant models in rhesus monkey which were constructed successfuly by the method of “double-cuff and one support tube” were divided into two groups randomly: experiment group (no treated by immunosuppressant in perioperative period) and control group (treated by immunosuppressant in perioperative period). Then the blood specimen and liver tissue respectively were colected at 6, 12, 24 and 72 hours after operation. The levels of alanine transferase, aspartate aminotransferase, and total bilirubin were detected with the fuly automatic biochemical analyser. The levels of CD4+/CD8+were tested by flow cytometry. The liver tissue in rhesus monkey after liver transplantation was detected by hematoxylin-eosin staining. The degree of acute rejection was evaluated by Banff Score System. RESULTS AND CONCLUSION: Acute rejection appeared in the experiment group at 12, 24, and 72 hours after liver transplantation. Levels of alanine transferase, aspartate aminotransferase, and total bilirubin were significantly higher in the experimental group than in the control group at 24 and 72 hours after transplantation (P < 0.05). The expression of CD4+/CD8+of the experiment group and control group began to rise at 6 hours after surgery, but the experiment group increased the most obvious. CD4+/CD8+ expression was significantly greater in the experimental group than in the control group at 24 and 72 hours after transplantation (P < 0.05). Morphological pathology was severer, and Banff score was higher in the experiment group than in the control group at

  19. A self-organized model for cell-differentiation based on variations of molecular decay rates.

    Directory of Open Access Journals (Sweden)

    Rudolf Hanel

    Full Text Available Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN. These networks capture all possible features of cells and are responsible for the immense levels of adaptation characteristic to living systems. At any point in time only small subsets of these networks are active. Any active subset of the GRN leads to the expression of particular sets of molecules (expression modes. The subsets of active networks change over time, leading to the observed complex dynamics of expression patterns. Understanding of these dynamics becomes increasingly important in systems biology and medicine. While the importance of transcription rates and catalytic interactions has been widely recognized in modeling genetic regulatory systems, the understanding of the role of degradation of biochemical agents (mRNA, protein in regulatory dynamics remains limited. Recent experimental data suggests that there exists a functional relation between mRNA and protein decay rates and expression modes. In this paper we propose a model for the dynamics of successions of sequences of active subnetworks of the GRN. The model is able to reproduce key characteristics of molecular dynamics, including homeostasis, multi-stability, periodic dynamics, alternating activity, differentiability, and self-organized critical dynamics. Moreover the model allows to naturally understand the mechanism behind the relation between decay rates and expression modes. The model explains recent experimental observations that decay-rates (or turnovers vary between differentiated tissue-classes at a general systemic level and highlights the role of intracellular decay rate control mechanisms in cell differentiation.

  20. Genetic variation in cell death genes and risk of non-Hodgkin lymphoma.

    Directory of Open Access Journals (Sweden)

    Johanna M Schuetz

    Full Text Available BACKGROUND: Non-Hodgkin lymphomas are a heterogeneous group of solid tumours that constitute the 5(th highest cause of cancer mortality in the United States and Canada. Poor control of cell death in lymphocytes can lead to autoimmune disease or cancer, making genes involved in programmed cell death of lymphocytes logical candidate genes for lymphoma susceptibility. MATERIALS AND METHODS: We tested for genetic association with NHL and NHL subtypes, of SNPs in lymphocyte cell death genes using an established population-based study. 17 candidate genes were chosen based on biological function, with 123 SNPs tested. These included tagSNPs from HapMap and novel SNPs discovered by re-sequencing 47 cases in genes for which SNP representation was judged to be low. The main analysis, which estimated odds ratios by fitting data to an additive logistic regression model, used European ancestry samples that passed quality control measures (569 cases and 547 controls. A two-tiered approach for multiple testing correction was used: correction for number of tests within each gene by permutation-based methodology, followed by correction for the number of genes tested using the false discovery rate. RESULTS: Variant rs928883, near miR-155, showed an association (OR per A-allele: 2.80 [95% CI: 1.63-4.82]; p(F = 0.027 with marginal zone lymphoma that is significant after correction for multiple testing. CONCLUSIONS: This is the first reported association between a germline polymorphism at a miRNA locus and lymphoma.

  1. Bifurcations, chaos, and sensitivity to parameter variations in the Sato cardiac cell model

    Science.gov (United States)

    Otte, Stefan; Berg, Sebastian; Luther, Stefan; Parlitz, Ulrich

    2016-08-01

    The dynamics of a detailed ionic cardiac cell model proposed by Sato et al. (2009) is investigated in terms of periodic and chaotic action potentials, bifurcation scenarios, and coexistence of attractors. Starting from the model's standard parameter values bifurcation diagrams are computed to evaluate the model's robustness with respect to (small) parameter changes. While for some parameters the dynamics turns out to be practically independent from their values, even minor changes of other parameters have a very strong impact and cause qualitative changes due to bifurcations or transitions to coexisting attractors. Implications of this lack of robustness are discussed.

  2. Variations of both bacterial community and extracellular polymers: the inducements of increase of cell hydrophobicity from biofloc to aerobic granule sludge.

    Science.gov (United States)

    Guo, Feng; Zhang, Sheng-Hua; Yu, Xin; Wei, Bo

    2011-06-01

    To investigate the inducements of increase of cell hydrophobicity from aerobic biofloc (ABF) and granular sludge (AGS), in this study, as the first time the hydrophilic and hydrophobic bacterial communities were analyzed independently. Meanwhile, the effect of extracellular polymers (EPS) on the cell hydrophobicity is also studied. Few Bacteroidetes were detected (1.35% in ABF and 3.84% in AGS) in hydrophilic bacteria, whereas they are abundant in the hydrophobic cells (47.8% and 43% for ABF and AGS, respectively). The main species of Bacteroidetes changed from class Sphingobacteria to Flavobacteria in AGS. On the other hand, EPS is directly responsible to cell hydrophobicity. For AGS, cell hydrophobicity was sharply decreased after EPS extraction. Both quantity and property of the extracellular protein are related to hydrophobicity. Our results showed the variation of cell hydrophobicity was resulted from variations of both bacterial population and EPS. PMID:21482465

  3. Variation of Hydroxyapatite Content in Soft Gelatin Affects Mesenchymal Stem Cell Differentiation

    Directory of Open Access Journals (Sweden)

    Fahsai Kantawong

    2016-01-01

    Full Text Available Gelatin is a common material used in tissue engineering and hydroxyapatite (HA has a composition and structure similar to natural bone mineral. HA is also used to increase the adhesion ability of scaffolds. The physical and mechanical properties of gelatin, together with the chemical properties of HA, can affect cell differentiation. The main purpose of this study is to investigate the gene expression of human mesenchymal stem cells (HMSCs upon culturing on gelatin composite with HA. Low amounts of HA were introduced into the gelatin in order to modulate properties of gelatin. Three types of hydrogel were fabricated by glutaraldehyde crosslinking before lyophilization to produce the porous 3D structure: (1 pure gelatin, (2 0.5 mg/ml HA in gelatin, and (3 1 mg/ml HA in gelatin. The fabricated hydrogels were used as scaffolds to cultivate HMSCs for two periods - 24 hours and 3 weeks. The results showed that all types of fabricated hydrogels could be used to cultivate HMSCs. Changes of gene expressions indicated that the HMSCs cultured on the 1 mg/ml HA in gelatin showed neuronal lineage-specific differentiation.

  4. Growth Media Induces Variation in Cell Wall Associated Gene Expression in Arabidopsis thaliana Pollen Tube

    Directory of Open Access Journals (Sweden)

    Mário Luís da Costa

    2013-06-01

    Full Text Available The influence of three different pollen germination media on the transcript profile of Arabidopsis pollen tubes has been assessed by real-time PCR on a selection of cell wall related genes, and by a statistical analysis of microarray Arabidopsis pollen tube data sets. The qPCR assays have shown remarkable differences on the transcript levels of specific genes depending upon the formulation of the germination medium used. With the aid of principal component analysis performed on existing microarray data, a subset of genes has been identified that is more prone to produce diverging transcript levels. A functional classification of those genes showed that the clusters with higher number of members were those for hydrolase activity (based in molecular function and for cell wall (based in cellular component. Taken together, these results may indicate that the nutrient composition of the pollen germination media influences pollen tube metabolism and that caution must be taken when interpreting transcriptomic data of pollen tubes.

  5. Influence of ATM-Mediated DNA Damage Response on Genomic Variation in Human Induced Pluripotent Stem Cells.

    Science.gov (United States)

    Lu, Junjie; Li, Hu; Baccei, Anna; Sasaki, Takayo; Gilbert, David M; Lerou, Paul H

    2016-05-01

    Genome instability is a potential limitation to the research and therapeutic application of induced pluripotent stem cells (iPSCs). Observed genomic variations reflect the combined activities of DNA damage, cellular DNA damage response (DDR), and selection pressure in culture. To understand the contribution of DDR on the distribution of copy number variations (CNVs) in iPSCs, we mapped CNVs of iPSCs with mutations in the central DDR gene ATM onto genome organization landscapes defined by genome-wide replication timing profiles. We show that following reprogramming the early and late replicating genome is differentially affected by CNVs in ATM-deficient iPSCs relative to wild-type iPSCs. Specifically, the early replicating regions had increased CNV losses during retroviral (RV) reprogramming. This differential CNV distribution was not present after later passage or after episomal reprogramming. Comparison of different reprogramming methods in the setting of defective DDR reveals unique vulnerability of early replicating open chromatin to RV vectors. PMID:26935587

  6. Modeling Cu2ZnSnS4 (CZTS) solar cells with kesterite and stannite phase variation

    Science.gov (United States)

    Lund, Elizabeth A.; Scarpulla, Michael A.

    2013-03-01

    Cu2ZnSnS4 (CZTS) may exhibit both kesterite and stannite polymorphs and shows promise as an absorber layer in thin film photovoltaic solar cells to be produced at terawatt scales. This study examines the effects of CZTS polymorphism and inhomogeneous distributions of CZTS polymorphs on device characteristics under scenarios of single phase films, a sinusoidal variation between kesterite and stannite with depth, and single phase films with thin layers of the other polymorph at both interfaces. In general, stannite-only devices are predicted to have higher efficiency than kesterite-only devices and sinusoidal grading results in efficiency between those of the pure phases. However, the device performance is relatively insensitive to the wavelength of the sinusoidal grading and rather is very sensitive to the phase present at the CdS interface. Predicted AM1.5 current-voltage (J-V) curves and descriptive metrics as well as wavelength-resolved quantum efficiencies are reported for all models. Based on these results, we propose control of cation ordering in CZTSSe as a mechanism for device design using bandgap grading and interface engineering without variation of stoichiometry.

  7. Nanoscale surface potential variation correlates with local S/Se ratio in solution-processed CZTSSe solar cells.

    Science.gov (United States)

    Salvador, Michael; Vorpahl, Sarah M; Xin, Hao; Williamson, Wesley; Shao, Guozheng; Karatay, Durmus U; Hillhouse, Hugh W; Ginger, David S

    2014-12-10

    Thin film solar cells made from Cu, Zn, Sn, and S/Se can be processed from solution to yield high-performing kesterite (CZTS or CZTSSe) photovoltaics. We present a microstructural study of solution-deposited CZTSSe films prepared by nanocrystal-based ink approaches using scanning probe microscopy (SPM) and scanning electron microscopy (SEM) coupled with energy dispersive X-ray spectroscopy (EDS). We correlate scanning Kelvin probe microscopy (SKPM) maps of local surface potential with SEM/EDS images of the exact same regions of the film, allowing us to relate observed variations in surface potential to local variations in stoichiometry. Specifically, we find a correlation between surface potential and the S/(S + Se) composition ratio. In particular, we find that regions with high S/(S + Se) ratios are often associated with regions of more negative surface potential and thus higher work function. The change in work function is larger than the expected change in the valence band position with these small changes in sulfur, and thus the data suggest an increase in acceptor-like defects with increasing sulfur. These findings provide new experimental insight into the microscopic relationships between composition, structure, and electronic properties in these promising photovoltaic materials. PMID:25372547

  8. Variational symplectic particle-in-cell simulation of nonlinear mode conversion from extraordinary waves to Bernstein waves

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Jianyuan; Liu, Jian, E-mail: jliuphy@ustc.edu.cn [Department of Modern Physics and School of Nuclear Science and Technology, University of Science and Technology of China, Hefei, Anhui 230026 (China); Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026 (China); Qin, Hong [Department of Modern Physics and School of Nuclear Science and Technology, University of Science and Technology of China, Hefei, Anhui 230026 (China); Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543 (United States); Yu, Zhi; Xiang, Nong [Theory and Simulation Division, Institute of Plasma Physics, Chinese Academy of Sciences, Hefei, Anhui 230031 (China)

    2015-09-15

    In this paper, the nonlinear mode conversion of extraordinary waves in nonuniform magnetized plasmas is studied using the variational symplectic particle-in-cell simulation. The accuracy of the nonlinear simulation is guaranteed by the long-term accuracy and conservativeness of the symplectic algorithm. The spectra of the electromagnetic wave, the evolution of the wave reflectivity, the energy deposition profile, and the parameter-dependent properties of radio-frequency waves during the nonlinear mode conversion are investigated. It is illustrated that nonlinear effects significantly modify the physics of the radio-frequency injection in magnetized plasmas. The evolutions of the radio-frequency wave reflectivity and the energy deposition are observed, as well as the self-interaction of the Bernstein waves and mode excitations. Even for waves with small magnitude, nonlinear effects can also become important after continuous wave injections, which are common in the realistic radio-frequency wave heating and current drive experiments.

  9. Variational symplectic particle-in-cell simulation of nonlinear mode conversion from extraordinary waves to Bernstein waves

    International Nuclear Information System (INIS)

    In this paper, the nonlinear mode conversion of extraordinary waves in nonuniform magnetized plasmas is studied using the variational symplectic particle-in-cell simulation. The accuracy of the nonlinear simulation is guaranteed by the long-term accuracy and conservativeness of the symplectic algorithm. The spectra of the electromagnetic wave, the evolution of the wave reflectivity, the energy deposition profile, and the parameter-dependent properties of radio-frequency waves during the nonlinear mode conversion are investigated. It is illustrated that nonlinear effects significantly modify the physics of the radio-frequency injection in magnetized plasmas. The evolutions of the radio-frequency wave reflectivity and the energy deposition are observed, as well as the self-interaction of the Bernstein waves and mode excitations. Even for waves with small magnitude, nonlinear effects can also become important after continuous wave injections, which are common in the realistic radio-frequency wave heating and current drive experiments

  10. Identification and genetic characterization of maize cell wall variation for improved biorefinery feedstock characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Pauly, Markus [UC Berkeley; Hake, Sarah [USDA Albany

    2013-10-31

    The objectives of this program are to 1) characterize novel maize mutants with altered cell walls for enhanced biorefinery characteristics and 2) find quantitative trait loci (QTLs) related to biorefinery characteristics by taking advantage of the genetic diversity of maize. As a result a novel non-transgenic maize plant (cal1) has been identified, whose stover (leaves and stalk) contain more glucan in their walls leading to a higher saccharification yield, when subjected to a standard enzymatic digestion cocktail. Stacking this trait with altered lignin mutants yielded evene higher saccharification yields. Cal-1 mutants do not show a loss of kernel and or biomass yield when grown in the field . Hence, cal1 biomass provides an excellent feedstock for the biofuel industry.

  11. Variations in elastaselike esterase activities in human leucocytes during cell maturation.

    Science.gov (United States)

    Feinstein, G; Janoff, A

    1976-05-01

    Granules of human peripheral blood leucocytes contain four well-characterized elastase isozymes and one or two slow-moving elastaselike esterases (SE) which have not been as well characterized. SE are capable of hydrolyzing typical elastase synthetic sybstrates such as N-acetyl-dl-alanine-alpha-naphthyl ester (Ac-DL-Ala-1-ONap) and N-t-butyloxycarbonyl-L-alanine-p-nitrophenyl ester (Boc-Ala-ONp), but unlike the highly basic elastase isozymes, SE barely migrate into 13% acrylamide gels during cationic electrophoresis at pH 4.3. Hydrolysis of Ac-DL-Ala-1-ONap by SE requires the presence of Triton in the gel, and hydrolysis of Boc-Ala-ONp by the same enzyme(s) is also enhanced in the presence of the detergent. Triton is not required for these activities, in the case of the elastase isozymes. Diisopropylfluorophosphate (Dip-F) inactivates both SE and the elastase isozymes, whereas Ac-(Ala)2-Pro-AlaCH2Cl (a powerful inactivator of the leucocyte elastase isozymes at 10-4 M concentration) does not inactivate SE at the same concentration. Immunochemical studies revealed antigenic cross-reaction between the rapidly migrating leucocyte elastase isozymes and SE. Two preparations of leucocyte granules from nonleukemic bone marrow cells showed no activity of the rapidly migrating elastase isozymes, but did contain SE activity. SE may be a precursor or zymogen form of the elastase isozymes, present in immature cells and partly retained through later stages of development. PMID:1265076

  12. Hole-transport material variation in fully vacuum deposited perovskite solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Polander, Lauren E.; Pahner, Paul; Schwarze, Martin; Saalfrank, Matthias; Koerner, Christian; Leo, Karl, E-mail: karl.leo@iapp.de [Institut für Angewandte Photophysik, Technische Universität Dresden, 01069 Dresden (Germany)

    2014-08-01

    This work addresses the effect of energy level alignment between the hole-transporting material and the active layer in vacuum deposited, planar-heterojunction CH{sub 3}NH{sub 3}PbI{sub x−3}Cl{sub x} perovskite solar cells. Through a series of hole-transport materials, with conductivity values set using controlled p-doping of the layer, we correlate their ionization potentials with the open-circuit voltage of the device. With ionization potentials beyond 5.3 eV, a substantial decrease in both current density and voltage is observed, which highlights the delicate energetic balance between driving force for hole-extraction and maximizing the photovoltage. In contrast, when an optimal ionization potential match is found, the open-circuit voltage can be maximized, leading to power conversion efficiencies of up to 10.9%. These values are obtained with hole-transport materials that differ from the commonly used Spiro-MeO-TAD and correspond to a 40% performance increase versus this reference.

  13. Proteomic changes resulting from gene copy number variations in cancer cells.

    Directory of Open Access Journals (Sweden)

    Tamar Geiger

    2010-09-01

    Full Text Available Along the transformation process, cells accumulate DNA aberrations, including mutations, translocations, amplifications, and deletions. Despite numerous studies, the overall effects of amplifications and deletions on the end point of gene expression--the level of proteins--is generally unknown. Here we use large-scale and high-resolution proteomics combined with gene copy number analysis to investigate in a global manner to what extent these genomic changes have a proteomic output and therefore the ability to affect cellular transformation. We accurately measure expression levels of 6,735 proteins and directly compare them to the gene copy number. We find that the average effect of these alterations on the protein expression is only a few percent. Nevertheless, by using a novel algorithm, we find the combined impact that many of these regional chromosomal aberrations have at the protein level. We show that proteins encoded by amplified oncogenes are often overexpressed, while adjacent amplified genes, which presumably do not promote growth and survival, are attenuated. Furthermore, regulation of biological processes and molecular complexes is independent of general copy number changes. By connecting the primary genome alteration to their proteomic consequences, this approach helps to interpret the data from large-scale cancer genomics efforts.

  14. Hole-transport material variation in fully vacuum deposited perovskite solar cells

    International Nuclear Information System (INIS)

    This work addresses the effect of energy level alignment between the hole-transporting material and the active layer in vacuum deposited, planar-heterojunction CH3NH3PbIx−3Clx perovskite solar cells. Through a series of hole-transport materials, with conductivity values set using controlled p-doping of the layer, we correlate their ionization potentials with the open-circuit voltage of the device. With ionization potentials beyond 5.3 eV, a substantial decrease in both current density and voltage is observed, which highlights the delicate energetic balance between driving force for hole-extraction and maximizing the photovoltage. In contrast, when an optimal ionization potential match is found, the open-circuit voltage can be maximized, leading to power conversion efficiencies of up to 10.9%. These values are obtained with hole-transport materials that differ from the commonly used Spiro-MeO-TAD and correspond to a 40% performance increase versus this reference

  15. Variation of power generation at different buffer types and conductivities in single chamber microbial fuel cells

    KAUST Repository

    Nam, Joo-Youn

    2010-01-15

    Microbial fuel cells (MFCs) are operated with solutions containing various chemical species required for the growth of electrochemically active microorganisms including nutrients and vitamins, substrates, and chemical buffers. Many different buffers are used in laboratory media, but the effects of these buffers and their inherent electrolyte conductivities have not been examined relative to current generation in MFCs. We investigated the effect of several common buffers (phosphate, MES, HEPES, and PIPES) on power production in single chambered MFCs compared to a non-buffered control. At the same concentrations the buffers produced different solution conductivities which resulted in different ohmic resistances and power densities. Increasing the solution conductivities to the same values using NaCl produced comparable power densities for all buffers. Very large increases in conductivity resulted in a rapid voltage drop at high current densities. Our results suggest that solution conductivity at a specific pH for each buffer is more important in MFC studies than the buffer itself given relatively constant pH conditions. Based on our analysis of internal resistance and a set neutral pH, phosphate and PIPES are the most useful buffers of those examined here because pH was maintained close to the pKa of the buffer, maximizing the ability of the buffer to contribute to increase current generation at high power densities. © 2009 Elsevier B.V. All rights reserved.

  16. Hole-transport material variation in fully vacuum deposited perovskite solar cells

    Directory of Open Access Journals (Sweden)

    Lauren E. Polander

    2014-08-01

    Full Text Available This work addresses the effect of energy level alignment between the hole-transporting material and the active layer in vacuum deposited, planar-heterojunction CH3NH3PbIx−3Clx perovskite solar cells. Through a series of hole-transport materials, with conductivity values set using controlled p-doping of the layer, we correlate their ionization potentials with the open-circuit voltage of the device. With ionization potentials beyond 5.3 eV, a substantial decrease in both current density and voltage is observed, which highlights the delicate energetic balance between driving force for hole-extraction and maximizing the photovoltage. In contrast, when an optimal ionization potential match is found, the open-circuit voltage can be maximized, leading to power conversion efficiencies of up to 10.9%. These values are obtained with hole-transport materials that differ from the commonly used Spiro-MeO-TAD and correspond to a 40% performance increase versus this reference.

  17. Mapping Variation in Cellular and Transcriptional Response to 1,25-Dihydroxyvitamin D3 in Peripheral Blood Mononuclear Cells.

    Science.gov (United States)

    Kariuki, Silvia N; Maranville, Joseph C; Baxter, Shaneen S; Jeong, Choongwon; Nakagome, Shigeki; Hrusch, Cara L; Witonsky, David B; Sperling, Anne I; Di Rienzo, Anna

    2016-01-01

    The active hormonal form of vitamin D, 1,25-dihydroxyvitamin D (1,25D) is an important modulator of the immune system, inhibiting cellular proliferation and regulating transcription of immune response genes. In order to characterize the genetic basis of variation in the immunomodulatory effects of 1,25D, we mapped quantitative traits of 1,25D response at both the cellular and the transcriptional level. We carried out a genome-wide association scan of percent inhibition of cell proliferation (Imax) induced by 1,25D treatment of peripheral blood mononuclear cells from 88 healthy African-American individuals. Two genome-wide significant variants were identified: rs1893662 in a gene desert on chromosome 18 (p = 2.32 x 10-8) and rs6451692 on chromosome 5 (p = 2.55 x 10-8), which may influence the anti-proliferative activity of 1,25D by regulating the expression of nearby genes such as the chemokine gene, CCL28, and the translation initiation gene, PAIP1. We also identified 8 expression quantitative trait loci at a FDRvitamin D receptor binding sites near genes differentially expressed in response to 1,25D, such as FERM Domain Containing 6 (FRMD6), which plays a critical role in regulating both cell proliferation and apoptosis. Combining information from the GWAS of Imax and the response eQTL mapping enabled identification of putative Imax-associated candidate genes such as PAIP1 and the transcriptional repressor gene ZNF649. Overall, the variants identified in this study are strong candidates for immune traits and diseases linked to vitamin D, such as multiple sclerosis. PMID:27454520

  18. Estrous cycle-dependent changes of Fas expression in the bovine corpus luteum: influence of keratin 8/18 intermediate filaments and cytokines

    Directory of Open Access Journals (Sweden)

    Duncan Alice

    2012-10-01

    Full Text Available Abstract Background Fas expression and Fas-induced apoptosis are mechanisms attributed to the selective destruction of cells of the corpus luteum (CL during luteal regression. In certain cell-types, sensitivity to these death-inducing mechanisms is due to the loss or cleavage of keratin-containing intermediate filaments. Specifically, keratin 8/18 (K8/K18 filaments are hypothesized to influence cell death in part by regulating Fas expression at the cell surface. Methods Here, Fas expression on bovine luteal cells was quantified by flow cytometry during the early (Day 5, postovulation and late stages (Days 16–18, postovulation of CL function, and the relationship between Fas expression, K8/K18 filament expression and cytokine-induced cell death in vitro was evaluated. Results Both total and cell surface expression of Fas on luteal cells was greater for early versus late stage bovine CL (89% vs. 44% of cells for total Fas; 65% vs.18% of cells for cell surface Fas; respectively, P0.05, n=4 CL/stage, despite evidence these conditions increased Fas expression on HepG2 cells (P0.05 or stage of CL (P>0.05, n= 4 CL/stage on this outcome. Conclusion In conclusion, we rejected our null hypothesis that the cell surface expression of Fas does not differ between luteal cells of early and late stage CL. The results also did not support the idea that K8/K18 filaments influence the expression of Fas on the surface of bovine luteal cells. Potential downstream effects of these filaments on death signaling, however, remain a possibility. Importantly, the elevated expression of Fas observed on cells of early stage bovine CL compared to late stage bovine CL raises a provocative question concerning the physiological role(s of Fas in the corpus luteum, particularly during early luteal development.

  19. Studies on Single Cell Culture in vitro in Wheat--The variation of grain protein content and its fractions from regenerated plants

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    On the basis of previous studies dealing with the variation of major agronomic and yield characteristics of regenerated plants derived from single cell culture in vitro of common wheat (Triticum aestivum L.Cultivar NE 7742), the grain protein content and its fractions from regenerated plants with stable agronomic characteristics were studied from 1992 to 1995. The results showed that the variation of grain protein content and its fractions in somaclones from single cell culture in vitro were very significant and the range was very wide (11.53~17.70%). Several types of variation were found in the studies, especially the type with higher protein content than that of cultivar NE 7742 (non-culture parent). Among them, -20.69% of lines the grain protein content was significantly higher than that of NE 7742 and combined with high yielding potential. The tendency of variation of the four protein fractions showed that the variation of albumin was not obvious and maintained the same level as NE7742, the content of gliadin increased in some somaclones and decreased in others. However, the percentages both globulin and glutenin tended to increase. The variation of total amount of structural protein and the ratio between globulin and glutenin tended to increase. The variation of total amount of structural protein and the ratio between globulin and albumm was mainly influenced by globulin under the condition of culture in vitro. The variation of total amount of storage protein and the ratio between gliadin and glutenin was mainly affected by glutenin. The results mentioned above demonstrated that the induction and screening of somaclonal variation could be an effective way in wheat improvement in combining high protein content with high yield.

  20. Intracellular coexpression of CXC- and CC– chemokine receptors and their ligands in human melanoma cell lines and dynamic variations after xenotransplantation

    International Nuclear Information System (INIS)

    Chemokines have been implicated in tumor progression and metastasis. In melanoma, chemokine receptors have been implicated in organ selective metastasis by regulating processes such as chemoattraction, adhesion and survival. In this study we have analyzed, using flow cytometry, the systems formed by the chemokine receptors CXCR3, CXCR4, CXCR7, CCR7 and CCR10 and their ligands in thirteen human melanoma cell lines (five established from primary tumors and eight established from metastasis from different tissues). WM-115 and WM-266.4 melanoma cell lines (obtained from a primary and a metastatic melanoma respectively) were xenografted in nude mice and the tumors and cell lines derived from them were also analyzed. Our results show that the melanoma cell lines do not express or express in a low degree the chemokine receptors on their cell surface. However, melanoma cell lines show intracellular expression of all the aforementioned receptors and most of their respective ligands. When analyzing the xenografts and the cell lines obtained from them we found variations in the intracellular expression of chemokines and chemokine receptors that differed between the primary and metastatic cell lines. However, as well as in the original cell lines, minute or no expression of the chemokine receptors was observed at the cell surface. Coexpression of chemokine receptors and their ligands was found in human melanoma cell lines. However, this expression is intracellular and receptors are not found at the cell membrane nor chemokines are secreted to the cell medium. The levels of expressed chemokine receptors and their ligands show dynamic variations after xenotransplantation that differ depending on the origin of the cell line (from primary tumor or from metastasis)

  1. Temporal Variation of the Hemispheric Solar Rotation

    CERN Document Server

    Xie, J -L; Xu, J -C

    2011-01-01

    The daily sunspot numbers of the whole disk as well as the northern and southern hemispheres from January 1, 1945 to December 31, 2010 are used to investigate the temporal variation of the rotational cycle length through the continuous wavelet transformation analysis method. The auto-correlation function analysis of daily hemispheric sunspot numbers shows that the southern hemisphere rotates faster than the northern hemisphere. The results obtained from the wavelet transformation analysis are: there exists no direct relationship between the variation trend of the rotational cycle length and the variation trend of solar activity in the two hemispheres; the rotational cycle length of both hemispheres has no significant period appearing at the 11 years, but has significant period of about 7.6 years. Analysis concerning the solar cycle dependence of the rotational cycle length shows that in the whole disk and the northern hemisphere acceleration seems to appear before the minimum time of solar activity. Furthermo...

  2. Association between genetic variations in tumor necrosis factor receptor genes and survival of patients with T-cell lymphoma

    Institute of Scientific and Technical Information of China (English)

    Kan Zhai; Jiang Chang; Chen Wu; Ning Lu; Li-Ming Huang; Tong-Wen Zhang; Dian-Ke Yu; Wen Tan; Dong-Xin Lin

    2012-01-01

    The prognosis of T-cell lymphoma (TCL) has been shown to be associated with the clinical characteristics of patients.However,there is little knowledge of whether genetic variations also affect the prognosis of TCL.This study investigated the associations between single nucleotide polymorphisms (SNPs) in tumor necrosis factor receptor superfamily (TNFRSF) genes and the survival of patients with TCL.A total of 38tag SNPs in 18 TNFRSF genes were genotyped using Sequenom platform in 150 patients with TCL.Kaplan-Meier survival estimates were plotted and significance was assessed using log-rank tests.Cox proportional hazard models were used to analyze each of these 38 SNPs with adjustment for covariates that might influence patient survival,including sex and international prognostic Index score.Hazard ratios (HRs) and their 95% confidence intervals (Cls) were calculated.Among the 38 SNPs tested,3 were significantly associated with the survival of patients with TCL.These SNPs were located at LTβR (rs3759333C>T) and TNFRSF17 (rs2017662C >T and rs2071336C>T).The 5-year survival rates were significantly different among patients carrying different genotypes and the HRs for death between the different genotypes ranged from 0.45 to 2.46.These findings suggest that the SNPs in TNFRSF genes might be important determinants for the survival of TCL patients.

  3. Effects of variations in electron thermal velocity on the whistler anisotropy instability: Particle-in-cell simulations

    Science.gov (United States)

    Hughes, R. Scott; Wang, Joseph; Decyk, Viktor K.; Gary, S. Peter

    2016-04-01

    This paper investigates how the physics of the whistler anisotropy instability (WAI) is affected by variations in the electron thermal velocity vte, referred to here in terms of the ratio v̂ t e=vt e/c , where c is the speed of light. The WAI is driven by the electron condition RT>1 , where RT=Te ⊥/Te ∥ is the temperature anisotropy ratio and ⊥/∥ signify directions perpendicular/parallel to the background magnetic field B0 . While a typical value of v̂ t e in the solar wind is ˜0.005 , electromagnetic (EM) particle-in-cell (PIC) simulations often use a value near 0.1 in order to maximize the computational time step. In this study, a two-dimensional (2D) Darwin particle-in-cell (DPIC) code, MDPIC2, is used. The time step in the DPIC model is not affected by the choice of v̂ t e , making DPIC suited for this study. A series of simulations are carried out under the condition that the electron βe is held fixed, while v̂ t e is varied over the range 0.1 ≥v̂ t e≥0.025 . The results show that, with βe held fixed, the linear dispersion properties and the nonlinear saturation amplitude and pitch angle scattering rates associated with the WAI are insensitive to the value of v̂ t e . A supplementary investigation is conducted which characterizes how the WAI model is affected at various values of v̂ t e by noise associated with the limited number of particles in a typical PIC simulation. It is found that the evolution of the WAI is more strongly influenced by electrostatic noise as v̂ t e is decreased. The electrostatic noise level is inversely proportional to the number of particles per computational cell ( Nc ); this implies that the number of particles required to remove nonphysical effects from the PIC simulation increases as v̂ t e decreases. It is concluded that PIC simulations of this instability which use an artificially large value of v̂ t e accurately reproduce the response of a cooler plasma as long as a realistic value of βe is used

  4. Determinants of lung fibrosis after chemo radiation for small cell carcinoma of the lung: evidence for inherent interindividual variation

    International Nuclear Information System (INIS)

    Purpose: Clinical observations often reveal discernible individual differences in the severity of lung fibrosis after definitive radiation therapy for lung cancer. Recent experimental studies also suggest that the risk of developing lung fibrosis may be genetically controlled. This study was undertaken to examine the magnitude of individual variation in the incidence and severity of lung fibrosis in a well defined patient population treated by combined chemo radiation for limited small cell lung carcinomas (LSCLC). Materials and Methods: Between 1989 and 1994, 56 patients with LSCLC were enrolled on one of two controlled protocols of combined chemotherapy and concomitant conventional (45 Gy in 25 fractions q.d. over 5 weeks) or accelerated radiotherapy (45 Gy in 30 fractions b.i.d. over 3 weeks). Chemotherapy consisted of cis-platin and etoposide (PE) or PE with ifosfamide and Mesna. Among those patients, 25 patients who had serial computerized tomography (CT) examinations of the chest and were deemed to have unequivocal radiographic complete responses were selected for the study. The severity of lung fibrosis was recorded for each patient on the CT images using an arbitrary scale (0 to 3) at 1 year after treatment. Radiographic fibrosis scores were recorded on 1-3 CT slices in three different dose-areas (20-25 Gy; 30-35 Gy; and 40-45 Gy) that were defined using the corresponding CT slices from the patient's CT plan. Twenty three patients (92%) had at least 2 slices scored; 11 patients had all 3 slices scored. Results: Among all clinical and treatment parameters examined including type of chemotherapy, only total dose and fractionation schedule were identified as significant and independent determinants of lung fibrosis. Radiographic fibrosis scores were higher in high dose areas and in patients treated with the accelerated schedule. Using a fit of the proportional odds (PO) model based on the total dose and fractionation schedule, fibrosis score residuals were

  5. Climatologies of nighttime upper thermospheric winds measured by ground-based Fabry-Perot interferometers during geomagnetically quiet conditions: 1. Local time, latitudinal, seasonal, and solar cycle dependence

    Science.gov (United States)

    Emmert, J. T.; Faivre, M. L.; Hernandez, G.; Jarvis, M. J.; Meriwether, J. W.; Niciejewski, R. J.; Sipler, D. P.; Tepley, C. A.

    2006-12-01

    We analyze ground-based Fabry-Perot interferometer observations of upper thermospheric (˜250 km) horizontal neutral winds derived from Doppler shifts in the 630.0 nm (red line) nightglow. The winds were measured over the following locations: South Pole (90°S), Halley (76°S, 27°W), Arequipa (17°S, 72°W), Arecibo (18°N, 67°W), Millstone Hill (43°N, 72°W), Søndre Strømfjord (67°N, 51°W), and Thule (77°N, 68°W). We derive climatological quiet time (Kp irradiance. Over Millstone Hill and Arecibo, solar EUV has a negative effect on wind magnitudes. As represented by the 10.7 cm radio flux proxy, the solar EUV dependence of the winds at all latitudes is characterized by a saturation or weakening of the effect above moderate values (F10.7 > 150). The seasonal dependence of the winds is generally annual, but there are isolated cases in which a semiannual variation is observed. Within the austral winter, winds measured from the South Pole show a substantial intraseasonal variation only along longitudes directed toward the magnetic pole. IMF effects are described in a companion paper.

  6. Risk stratification of T-cell Acute Lymphoblastic Leukemia patients based on gene expression, mutations and copy number variation.

    Science.gov (United States)

    Mirji, Gauri; Bhat, Jaydeep; Kode, Jyoti; Banavali, Shripad; Sengar, Manju; Khadke, Prashant; Sait, Osama; Chiplunkar, Shubhada

    2016-06-01

    Gene expression, copy number variations (CNV), mutations and survival were studied to delineate TCRγδ+T-cell acute lymphoblastic leukemia (T-ALL) as a distinct subgroup from TCRαβ+T-ALL. Gene Ontology analysis showed that differential regulation of genes involved in pathways for leukemogenesis, apoptosis, cytokine-cytokine receptor interaction and antigen processing/presentation may offer a survival benefit to TCRγδ+T-ALL patients. Genes involved in disease biology and having equal expression in both the subgroups, were further analysed for mutations and CNV using droplet digital PCR. TCRγδ+T-ALL patients exhibited differential level of mutations for NOTCH1 and IKZF3; however BRAF mutations were detected at equal levels in both the subgroups. Although TCRγδ+T-ALL patients with these mutations demonstrated improved disease-free survival (DFS) as compared TCRαβ+T-ALL patients, it was not statistically significant. Patients with homozygous deletion of CDKN2A/CDKN2B showed poor DFS in each subgroup. TCRγδ+T-ALL patients with wild type/heterozygous deletion of CDKN2A/CDKN2B possess significantly better DFS over TCRαβ+T-ALL patients (p=0.017 and 0.045, respectively). Thus, the present study has for the first time demonstrated TCRγδ clonality and CDKN2A/CDKN2B CNV together as potential prognostic markers in management of T-ALL. Further understanding the functional significance of differentially regulated genes in T-ALL patients would aid in designing risk based treatment strategies in subset specific manner. PMID:27070758

  7. Somaclonal Variation Is Induced De Novo via the Tissue Culture Process: A Study Quantifying Mutated Cells in Saintpaulia

    OpenAIRE

    Mitsuru Sato; Munetaka Hosokawa; Motoaki Doi

    2011-01-01

    BACKGROUND: The origin of somaclonal variation has not been questioned previously, i.e., "pre-existing mutations" in explants and "newly induced mutations" arising from the tissue culture process have not been distinguished. This is primarily because there has been no reliable molecular method for estimating or quantifying variation. METHODOLOGY/PRINCIPAL FINDINGS: We adopted a petal-variegated cultivar of Saintpaulia 'Thamires' (Saintpaulia sp.) as the model plant. Based on the difference be...

  8. Significant Impact of Sequence Variations in the Nucleoprotein on CD8 T Cell-Mediated Cross-Protection against Influenza A Virus Infections

    OpenAIRE

    Zhong, Weimin; Dong, Libo; Lu, Xiuhua; Hancock, Kathy; Katz, Jacqueline M.; Sambhara, Suryaprakash; Liu, Feng; Reinherz, Ellis Leonard

    2010-01-01

    Background: Memory CD8 T cells to influenza A viruses are widely detectable in healthy human subjects and broadly cross-reactive for serologically distinct influenza A virus subtypes. However, it is not clear to what extent such pre-existing cellular immunity can provide cross-subtype protection against novel emerging influenza A viruses. Methodology/Principal: Findings We show in the mouse model that naturally occurring sequence variations of the conserved nucleoprotein of the virus signific...

  9. Variations in T Cell Transcription Factor Sequence and Expression Associated with Resistance to the Sheep Nematode Teladorsagia circumcincta.

    Science.gov (United States)

    Wilkie, Hazel; Gossner, Anton; Bishop, Stephen; Hopkins, John

    2016-01-01

    This study used selected lambs that varied in their resistance to the gastrointestinal parasite Teladorsagia circumcincta. Infection over 12 weeks identified susceptible (high adult worm count, AWC; high fecal egg count, FEC; low body weight, BW; low IgA) and resistant sheep (no/low AWC and FEC, high BW and high IgA). Resistance is mediated largely by a Th2 response and IgA and IgE antibodies, and is a heritable characteristic. The polarization of T cells and the development of appropriate immune responses is controlled by the master regulators, T-bet (TBX21), GATA-3 (GATA3), RORγt (RORC2) and RORα (RORA); and several inflammatory diseases of humans and mice are associated with allelic or transcript variants of these transcription factors. This study tested the hypothesis that resistance of sheep to T. circumcincta is associated with variations in the structure, sequence or expression levels of individual master regulator transcripts. We have identified and sequenced one variant of sheep TBX21, two variants of GATA3 and RORC2 and five variants of RORA from lymph node mRNA. Relative RT-qPCR analysis showed that TBX21, GATA3 and RORC2 were not significantly differentially-expressed between the nine most resistant (AWC, 0; FEC, 0) and the nine most susceptible sheep (AWC, mean 6078; FEC, mean 350). Absolute RT-qPCR on all 45 animals identified RORVv5 as being significantly differentially-expressed (p = 0.038) between resistant, intermediate and susceptible groups; RORCv2 was not differentially-expressed (p = 0.77). Spearman's rank analysis showed that RORAv5 transcript copy number was significantly negatively correlated with parameters of susceptibility, AWC and FEC; and was positively correlated with BW. RORCv2 was not correlated with AWC, FEC or BW but was significantly negatively correlated with IgA antibody levels. This study identifies the full length RORA variant (RORAv5) as important in controlling the protective immune response to T. circumcincta infection

  10. Gibberellin-Regulation and Genetic Variations in Leaf Elongation for Tall Fescue in Association with Differential Gene Expression Controlling Cell Expansion.

    Science.gov (United States)

    Xu, Qian; Krishnan, Sanalkumar; Merewitz, Emily; Xu, Jichen; Huang, Bingru

    2016-01-01

    Leaf elongation rate (LER) is an important factor controlling plant growth and productivity. The objective of this study was to determine whether genetic variation in LER for a fast-growing ('K-31'), and a dwarf cultivar ('Bonsai') of tall fescue (Festuca arundinacea) and gibberellic acid (GA) regulation of LER were associated with differential expression of cell-expansion genes. Plants were treated with GA3, trinexapac-ethyl (TE) (GA inhibitor), or water (untreated control) in a hydroponic system. LER of 'K-31' was 63% greater than that of 'Bonsai', which corresponded with 32% higher endogenous GA4 content in leaf and greater cell elongation and production rates under the untreated control condition. Exogenous application of GA3 significantly enhanced LER while TE treatment inhibited leaf elongation due to GA3-stimulation or TE-inhibition of cell elongation and production rate in leaves for both cultivars. Real-time quantitative polymerase chain reaction analysis revealed that three α-expansins, one β-expansin, and three xyloglucan endotransglycosylase (XET) genes were associated with GA-stimulation of leaf elongation, of which, the differential expression of EXPA4 and EXPA7 was related to the genotypic variation in LER of two cultivars. Those differentially-expressed expansin and XET genes could play major roles in genetic variation and GA-regulated leaf elongation in tall fescue. PMID:27457585

  11. Conspicuous variation of the lattice unit cell in the pavonite homologous series and its relation with cation/anion occupational modulations

    International Nuclear Information System (INIS)

    Highlights: ► Strong non-uniform variation of unit cell parameters in the pavonite homologous series. ► Conspicuous unit cell variation due to an underlying sub-lattice with cation/anion occupation. ► A modulated model common to the whole series using the superspace formalism proposed. ► Model successfully applied to the 7P pavonite Ag3(Bi,Pb)7S12. ► The model can be applied in a predictive way to other members of the family. - Abstract: The pavonites is a homologous series of sulfosalts with galena-like modules of variable size. A survey of their unit cells reveals that they are severely constrained by the metrics of an underlying common average sublattice. The unit cell of any compound of the series accommodates with high precision an integer number of approximately equal subcells. This explains a peculiar non-uniform variation of the unit cell parameters within the series and evidences that the interface between the galena-like modules, despite having a very different topology, approximately maintains the subperiodicity of the modules, and must therefore be subject to strong steric restrictions. It also implies that cations and anions occupy the nodes of the observed common underlying average sublattice according to a striking alternate cation/anion occupational modulation. This is the starting point for a description of these materials as modulated structures, which can make a proficient use of the approximate atomic positional non-crystallographic correlations caused by their modular character. Under this approach only four parameters suffice to define a realistic approximate model of any member of the series. A full structural characterization of any of the compounds only requires the determination of additional small/smooth modulations. As an example, the case of the 7P pavonite Ag3Bi6.2Pb0.8S12, is analyzed

  12. Studies on the chromosome variation of mouse tumor cell population by radiation and culture condition in relation to tumorigenicity

    International Nuclear Information System (INIS)

    The effects of radiation and culture conditions on the distribution of chromosome number in mouse Sarcoma 180 Y.S. cells were studied in respect to heterogeneity of their chromosome number and their tumorigenicity; four subpopulations separated by ficoll gradient centrifugation from in vivo cultured tumor cells demonstrated different tumorigenic properties and the hypotetraploid cells were found to be the most tumorigenic. (Author)

  13. KIR2DL4 copy number variation is associated with CD4+ T-cell depletion and function of cytokine-producing NK cell subsets in SIV-infected Mamu-A*01-negative rhesus macaques.

    Science.gov (United States)

    Hellmann, Ina; Letvin, Norman L; Schmitz, Jörn E

    2013-05-01

    Here, we demonstrate that KIR2DL4 copy number variation (CNV) is associated with CD4(+) T-cell decline and functionality of cytokine-producing NK cells during primary simian immunodeficiency virus (SIV) infection in Mamu-A*01(-) Indian-origin rhesus macaques, with higher KIR2DL4 copy numbers being associated with a better preservation of CD4(+) T cells and an increased gamma interferon (IFN-γ) production from stimulated cytokine-producing NK cell subsets during acute SIVmac251 infection. These findings underscore the crucial role of activating killer-cell immunoglobulin-like receptors (KIRs) in NK cell-mediated SIV responses during early SIV infection. PMID:23449795

  14. Celiac disease T-cell epitopes from gamma-gliadins: immunoreactivity depends on the genome of origin, transcript frequency, and flanking protein variation

    Directory of Open Access Journals (Sweden)

    Salentijn Elma MJ

    2012-06-01

    Full Text Available Abstract Background Celiac disease (CD is caused by an uncontrolled immune response to gluten, a heterogeneous mixture of wheat storage proteins. The CD-toxicity of these proteins and their derived peptides is depending on the presence of specific T-cell epitopes (9-mer peptides; CD epitopes that mediate the stimulation of HLA-DQ2/8 restricted T-cells. Next to the thoroughly characterized major T-cell epitopes derived from the α-gliadin fraction of gluten, γ-gliadin peptides are also known to stimulate T-cells of celiac disease patients. To pinpoint CD-toxic γ-gliadins in hexaploid bread wheat, we examined the variation of T-cell epitopes involved in CD in γ-gliadin transcripts of developing bread wheat grains. Results A detailed analysis of the genetic variation present in γ-gliadin transcripts of bread wheat (T. aestivum, allo-hexaploid, carrying the A, B and D genome, together with genomic γ-gliadin sequences from ancestrally related diploid wheat species, enabled the assignment of sequence variants to one of the three genomic γ-gliadin loci, Gli-A1, Gli-B1 or Gli-D1. Almost half of the γ-gliadin transcripts of bread wheat (49% was assigned to locus Gli-D1. Transcripts from each locus differed in CD epitope content and composition. The Gli-D1 transcripts contained the highest frequency of canonical CD epitope cores (on average 10.1 per transcript followed by the Gli-A1 transcripts (8.6 and the Gli-B1 transcripts (5.4. The natural variants of the major CD epitope from γ-gliadins, DQ2-γ-I, showed variation in their capacity to induce in vitro proliferation of a DQ2-γ-I specific and HLA-DQ2 restricted T-cell clone. Conclusions Evaluating the CD epitopes derived from γ-gliadins in their natural context of flanking protein variation, genome specificity and transcript frequency is a significant step towards accurate quantification of the CD toxicity of bread wheat. This approach can be used to predict relative levels of CD toxicity of

  15. Time-Qualified Patterns of Variation of PPARγ, DNMT1, and DNMT3B Expression in Pancreatic Cancer Cell Lines

    Directory of Open Access Journals (Sweden)

    Valerio Pazienza

    2012-01-01

    Full Text Available Carcinogenesis is related to the loss of homeostatic control of cellular processes regulated by transcriptional circuits and epigenetic mechanisms. Among these, the activities of peroxisome proliferator-activated receptors (PPARs and DNA methyltransferases (DNMTs are crucial and intertwined. PPARγ is a key regulator of cell fate, linking nutrient sensing to transcription processes, and its expression oscillates with circadian rhythmicity. Aim of our study was to assess the periodicity of PPARγ and DNMTs in pancreatic cancer (PC. We investigated the time-related patterns of PPARG, DNMT1, and DNMT3B expression monitoring their mRNA levels by qRT-PCR at different time points over a 28-hour span in BxPC-3, CFPAC-1, PANC-1, and MIAPaCa-2 PC cells after synchronization with serum shock. PPARG and DNMT1 expression in PANC-1 cells and PPARG expression in MIAPaCa-2 cells were characterized by a 24 h period oscillation, and a borderline significant rhythm was observed for the PPARG, DNMT1, and DNMT3B expression profiles in the other cell lines. The time-qualified profiles of gene expression showed different shapes and phase relationships in the PC cell lines examined. In conclusion, PPARG and DNMTs expression is characterized by different time-qualified patterns in cell lines derived from human PC, and this heterogeneity could influence cell phenotype and human disease behaviour.

  16. Differential Effects of Variations at Codon 106 on Sprouty2 Functions in Lung Cancer-Derived Cells.

    Science.gov (United States)

    Kral, Rosana; Doriguzzi, Angelina; Mayer, Christoph-Erik; Krenbek, Dagmar; Setinek, Ulrike; Sutterlüty-Fall, Hedwig

    2016-08-01

    Sprouty2 is a modulator of receptor tyrosine kinase-mediated signalling with an important role during lung carcinogenesis. Here, we characterize a Sprouty2 variant harbouring a substitution of proline 106 with serine. Serine substitution fails to influence expression, but accumulation of slower migrating phosphatase-sensitive forms indicates that its presence facilitates phosphorylation. In normal lung cells the serine variant is slightly more potent in inhibiting proliferation and migration. Additionally non-malignant cells expressing the major Sprouty2 variant attach more effective to fibronectin, while the serine variant only weakly stimulates cell adhesion. Mechanistically, the serine variant interferes less effectively with mitogen-activated protein kinase induction in response to serum. Concerning the positive Sprouty2 effect on epidermal growth factor receptor activation the serine variant is more potent. In all lung cancer-derived cell lines proliferation is more effectively inhibited if the Sprouty2 protein harbours the serine. In contrast, an increased interference of the serine Sprouty2 variant is only observed in cells with unaltered K-Ras. In cells harbouring a K-Ras mutation the serine conversion weakens the reduction of migration velocity indicating that dependent on the status of K-Ras the serine influences Sprouty2 functions differently. Accordingly, cell adhesion in cells with unaffected K-Ras is only stimulated by a Sprouty2 protein harbouring proline, while a serine conversion improves the attachment of the cells with constitutive active Ras. In summary our studies demonstrate that substitution of proline by serine at position 106 has biological significance and that the observed effects of this conversion depend on the activation status of endogenous K-Ras. J. Cell. Biochem. 117: 1822-1832, 2016. © 2016 Wiley Periodicals, Inc. PMID:26727965

  17. Microbiological quality and somatic cell count in bulk milk of dromedary camels (Camelus dromedarius): descriptive statistics, correlations, and factors of variation.

    Science.gov (United States)

    Nagy, P; Faye, B; Marko, O; Thomas, S; Wernery, U; Juhasz, J

    2013-09-01

    The objectives of the present study were to monitor the microbiological quality and somatic cell count (SCC) of bulk tank milk at the world's first large-scale camel dairy farm for a 2-yr period, to compare the results of 2 methods for the enumeration of SCC, to evaluate correlation among milk quality indicators, and to determine the effect of specific factors (year, season, stage of lactation, and level of production) on milk quality indicators. The study was conducted from January 2008 to January 2010. Total viable count (TVC), coliform count (CC), California Mastitis Test (CMT) score, and SCC were determined from daily bulk milk samples. Somatic cell count was measured by using a direct microscopic method and with an automatic cell counter. In addition, production parameters [total daily milk production (TDM, kg), number of milking camels (NMC), average milk per camel (AMC, kg)] and stage of lactation (average postpartum days, PPD) were recorded for each test day. A strong correlation (r=0.33) was found between the 2 methods for SCC enumeration; however, values derived using the microscopic method were higher. The geometric means of SCC and TVC were 394×10(3) cells/mL and 5,157 cfu/mL during the observation period, respectively. Somatic cell count was >500×10(3) cells/mL on 14.6% (106/725) and TVC was >10×10(3) cfu/mL on 4.0% (30/742) of the test days. Both milk quality indicators had a distinct seasonal pattern. For log SCC, the mean was lowest in summer and highest in autumn. The seasonal pattern of log TVC was slightly different, with the lowest values being recorded during the spring. The monthly mean TVC pattern showed a clear difference between years. Coliform count was CMT score (r=0.26), and between log TVC and CC in yr 1 (r=0.30). All production parameters and stage of lactation showed strong seasonal variation. Log SCC was negatively correlated with TDM (r=-0.35), AMC (r=-0.37), and NMC (r=-0.15) and positively correlated with PPD (r=0.40). Log TVC

  18. Inter-experiment variation and dependence on culture conditions in assaying the chemosensitivity of human small cell lung cancer cell lines

    DEFF Research Database (Denmark)

    Roed, H; Christensen, I B; Vindeløv, L L; Spang-Thomsen, M; Hansen, H H

    1987-01-01

    Sensitivity of five human small cell lung cancer cell lines to doxorubicin was assessed by a double layer agar technique using two different bottom-layers. Neither of the bottom-layers provided proportionality between numbers of cells plated and numbers of colonies, but they were correlated by a...

  19. Variation of carrier concentration and interface trap density in 8MeV electron irradiated c-Si solar cells

    International Nuclear Information System (INIS)

    The capacitance and conductance measurements were carried out for c-Si solar cells, irradiated with 8 MeV electrons with doses ranging from 5kGy – 100kGy in order to investigate the anomalous degradation of the cells in the radiation harsh environments. Capacitance – Voltage measurements indicate that there is a slight reduction in the carrier concentration upon electron irradiation due to the creation of radiation induced defects. The conductance measurement results reveal that the interface state densities and the trap time constant increases with electron dose due to displacement damages in c-Si solar cells

  20. Epithelial cell renewal in the digestive gland and stomach of mussels, season, age and tidal regime related variations

    OpenAIRE

    Zaldibar, B.; Cancio, I.; Marigómez, I.

    2008-01-01

    The natural variability in cell proliferation activity in the epithelium of the digestive gland and stomach was investigated in mussels, Mytilus galloprovincialis (Lmk), of different age and tidal level at different seasons. After treating mussels with the thymidine analogue bromodeoxyuridine (BrdU) for 6 hours, BrdU immunohistochemistry was performed every 2 hours for the next 36. The relative proportion of BrdU positive cells was quantified as BrdU labelling (‰). ...

  1. Seasonal Variation in Abundance and Species Composition of a Planktonic Diatom Assemblage Including Viable Cells on the Bottom in Matsushima Bay, Northeastern Japan

    Institute of Scientific and Technical Information of China (English)

    ICHINOMIYA Mutsuo; TANIGUCHI Akira

    2003-01-01

    Seasonal variation in abundance and species composition of a planktonic diatom assemblage distributed in the water column and also settled on the bottom was investigated for the shallow coastal water in Matsushima Bay on the Pacific coast of northeastern Japan during the period from October 1999 to September 2000. A spring bloom of diatoms began in April when nutrient concentrations started to increase, indicating the importance of nutrients. Viable cells of Skeletonema costatum and Thalassiosira spp., which were the dominant species in the water column throughout the year, were also always abundant in the bottom sediment. Both populations in the water column and on the bottom fluctuated essentially in parallel.For the planktonic diatoms in shallow coastal waters to maintain their vegetative populations in the water column, it would be advantageous for them to have a seeding population of viable cells on the bottom that are easily resuspended into the upper photic layer.

  2. Variation through the cell cycle in the dose-response of DNA neutral filter elution in X-irradiated synchronous CHO-cells

    International Nuclear Information System (INIS)

    Dose-response curves for DNA neutral (pH 9.6) filter elution were obtained with synchronized CHO cells exposed to X-rays at various phases of cell cycle. The dose response was similar in synchronized and plateau-phase G1 cells, as well as in cells arrested at the G1/S border using aphidicolin; it flattened as cells progressed into S phase and reached a minimum in the middle of this phase. An increase in DNA elution dose response, to values only slightly lower than those obtained with G1 cells, was observed as cells entered G2 phase. Significant alterations in the sedimentation properties of the DNA during S phase were also observed in Ehrlich ascites tumor cells using the neutral sucrose gradient centrifugation technique. A significant proportion of the DNA from S cells irradiated with 10 Gy sedimented at speeds (350S-700S) well above the maximum sedimentation speed expected for free sedimenting DNA molecules (ssub(max) = 350S), indicating the formation of a DNA complex. DNA from G1, G1/S, or G2 + M cells sedimented as expected for free sedimenting molecules. (author)

  3. Variations of circulating endothelial progenitor cells and transforming growth factor-beta-1 (TGF-β1) during thoracic radiotherapy are predictive for radiation pneumonitis

    International Nuclear Information System (INIS)

    The vascular endothelial cells are important targets of radiotherapy, which may be involved in the pathogenesis of radiation pneumonitis (RP). This study investigated the variations of circulating endothelial progenitor cells (EPCs) and transforming growth factor-beta-1 (TGF-β1) during three-dimensional conformal radiation therapy (3D-CRT) in patients with non–small-cell lung cancer (NSCLC) and analyzed the correlation between these variations with the occurrence of RP. From November 2008 to November 2009, eighty-four consecutive patients receiving 3D-CRT for stage III disease were evaluated prospectively. Circulating EPCs and TGF-β1 levels were measured at baseline, every 2 weeks during, and at the end of treatment. RP was evaluated prospectively at 6 weeks after 3D-CRT. Thirty-eight patients (47.5%) experienced score 1 or more of RP. The baseline levels of EPCs and TGF-β1 were analyzed, no difference was found between patients with and without RP during and after 3D-CRT. By serial measurement of TGF-β1 and EPCs levels, we found that the mean levels of EPCs in the whole population remained stable during radiotherapy, but the mean levels of TGF-β1 increased slowly during radiotherapy. TGF-β1 and EPCs levels were all significantly higher at week 2, week 4 and week 6 in patients with RP than that in patients without RP, respectively. During the period of radiation treatment, TGF-β1 levels began to increase in the first 2 weeks and became significantly higher at week 6 (P < 0.01). EPCs levels also began to increase in the first 2 weeks and reached a peak at week 4. Using an ANOVA model for repeated-measures, we found significant associations between the levels of TGF-β1 and EPCs during the course of 3D-CRT and the risk of developing RP (P < 0.01). Most of the dosimetric factors showed a significant association with RP. Early variations of TGF-β1 and EPCs levels during 3D-CRT are significantly associated with the risk of RP. Variations of circulating TGF-β1

  4. Variations in Target Volume Definition for Postoperative Radiotherapy in Stage III Non-Small-Cell Lung Cancer: Analysis of an International Contouring Study

    International Nuclear Information System (INIS)

    Purpose: Postoperative radiotherapy (PORT) in patients with completely resected non-small-cell lung cancer with mediastinal involvement is controversial because of the failure of earlier trials to demonstrate a survival benefit. Improved techniques may reduce toxicity, but the treatment fields used in routine practice have not been well studied. We studied routine target volumes used by international experts and evaluated the impact of a contouring protocol developed for a new prospective study, the Lung Adjuvant Radiotherapy Trial (Lung ART). Methods and Materials: Seventeen thoracic radiation oncologists were invited to contour their routine clinical target volumes (CTV) for 2 representative patients using a validated CD-ROM-based contouring program. Subsequently, the Lung ART study protocol was provided, and both cases were contoured again. Variations in target volumes and their dosimetric impact were analyzed. Results: Routine CTVs were received for each case from 10 clinicians, whereas six provided both routine and protocol CTVs for each case. Routine CTVs varied up to threefold between clinicians, but use of the Lung ART protocol significantly decreased variations. Routine CTVs in a postlobectomy patient resulted in V20 values ranging from 12.7% to 54.0%, and Lung ART protocol CTVs resulted in values of 20.6% to 29.2%. Similar results were seen for other toxicity parameters and in the postpneumectomy patient. With the exception of upper paratracheal nodes, protocol contouring improved coverage of the required nodal stations. Conclusion: Even among experts, significant interclinician variations are observed in PORT fields. Inasmuch as contouring variations can confound the interpretation of PORT results, mandatory quality assurance procedures have been incorporated into the current Lung ART study.

  5. Lethal Sectoring, genomic instability and cell cycle variation of HeLa S3 cells survived after alpha- and X-ray irradiation

    International Nuclear Information System (INIS)

    When cells with infinite growth ability are irradiated by radiation, survived cells occasionally yield cells without colony forming ability after several generations (lethal sectoring). The sectoring is the process to exclude cells with latent lethal damage, which results in the inhibition of cell cycle progression. Further, clonogen still having the infinite growth ability appears during the sectoring process and has genomic instability. The present study was conducted to compare these processes after irradiation of α- and X-ray. A time-lapse motion camera (1 picture/15 min) was used for microscopic recording of HeLa S3-9IV cells within a single scope (about 50 cells). They were irradiated by 0.45 Gy of α-ray (point source of 241Am, fluence rate 1.5 x 106/cm2/min, 0.3 Gy/min, LET=125 keV/μm) or 3 Gy of X-ray (200 kVp, 0.7 Gy/min), of which doses were equivalent to the survival rate of 0.2. The film recording was done for 30 and 150 hr before and after irradiation, respectively, from which the pedigree of individual cells was figured out by selection of surviving clonogen. Analysis of the pedigree of the survived cells revealed that there was an essential difference in the three processes, which was possibly based on the LET difference. (N.I.)

  6. Polymorphic variation in the androgen receptor gene: association with risk of testicular germ cell cancer and metastatic disease

    DEFF Research Database (Denmark)

    Västermark, Åke; Giwercman, Yvonne Lundberg; Hagströmer, Oskar; Rajpert-De Meyts, Ewa; Eberhard, Jakob; Ståhl, Olof; Cedermark, Gabriella Cohn; Rastkhani, Hamideh; Daugaard, Gedske; Arver, Stefan; Giwercman, Aleksander

    2011-01-01

    Increasing incidence of testicular germ cell cancer (TGCC) is most probably related to environment and lifestyle. However, an underlying genetic predisposition may play a role and since sex steroids are assumed to be important for the rise and progression of TGCC, a study of androgen receptor (AR...... endocrine disruptors. From a biological point of view, our findings strengthen the hypothesis of the importance of androgen action in the aetiology and pathogenesis of testicular malignancy. Future studies should focus on the impact of sex hormones on foetal germ cell development and the interaction between...... environmental factors and androgen receptor variants in relation to the risk of testicular malignancy....

  7. Variational MCMC

    OpenAIRE

    De Freitas, Nando; Hojen-Sorensen, Pedro; Jordan, Michael I.; Russell, Stuart

    2013-01-01

    We propose a new class of learning algorithms that combines variational approximation and Markov chain Monte Carlo (MCMC) simulation. Naive algorithms that use the variational approximation as proposal distribution can perform poorly because this approximation tends to underestimate the true variance and other features of the data. We solve this problem by introducing more sophisticated MCMC algorithms. One of these algorithms is a mixture of two MCMC kernels: a random walk Metropolis kernel ...

  8. Conformational variation of surface class II MHC proteins during myeloid dendritic cell differentiation accompanies structural changes in lysosomal MIIC

    Czech Academy of Sciences Publication Activity Database

    Potolicchio, I.; Chitta, S.; Xu, X.; Fonseca, D.; Crisi, G.; Hořejší, Václav; Strominger, J. L.; Stern, L. J.; Raposo, G.; Santambrogio, L.

    2005-01-01

    Roč. 175, č. 8 (2005), s. 4935-4947. ISSN 0022-1767 Institutional research plan: CEZ:AV0Z50520514 Keywords : MHC II * HLA-DR * dendritic cell Subject RIV: EC - Immunology Impact factor: 6.387, year: 2005

  9. Variation of coulombic efficiency versus upper cutoff potential of Li-ion cells tested with aggressive protocols

    Science.gov (United States)

    Xia, Jian; Nie, Mengyun; Ma, Lin; Dahn, J. R.

    2016-02-01

    Three different cycling protocols including "continuous-cycling", "barn-charge" and "cycle-store" were applied with an ultra high precision charger to Li[Ni0.42Mn0.42Co0.16]O2/graphite and/or Li[Ni1/3Mn1/3Co1/3]O2/graphite pouch cells tested using different upper cutoff potentials. The barn-charge and cycle-store protocols were designed so that cells stay at high potential for a larger fraction of their testing time compared to continuous cycling. For cells tested to 4.2, 4.4 or 4.5 V, the greater the fraction of testing time spent at high potential, the lower the coulombic efficiency and the greater the charge endpoint capacity slippage rate, with the effects being more severe at higher potential. These results confirm that Li[Ni0.42Mn0.42Co0.16]O2/graphite and Li[Ni1/3Mn1/3Co1/3]O2/graphite Li-ion cells which are charged and then left at high potential (>4.4 V) for extended periods of time will have much shorter calendar and cycle life compared to those that are continuously cycled as has been recently reported in long-term test results.

  10. Constant phycobilisome size in chromatically adapted cells of the cyanobacterium Tolypothrix tenuis, and variation in Nostoc sp

    Energy Technology Data Exchange (ETDEWEB)

    Ohki, K.; Gantt, E.; Lipschultz, C.A.; Ernst, M.C.

    1985-12-01

    Phycobilisomes of Tolypothrix tenuis, a cyanobacterium capable of complete chromatic adaptation, were studied from cells grown in red and green light, and in darkness. The phycobilisome size remained constant irrespective of the light quality. The hemidiscoidal phycobilisomes had an average diameter of about 52 nanometers and height of about 33 nanometers, by negative staining. The thickness was equivalent to a physocyanin molecule (about 10 nanometers). The molar ratio of allophycocyanin, relative to other phycobiliproteins always remained at about 1:3. Phycobilisomes from red light grown cells and cells grown heterotrophically in darkness were indistinguishable in their pigment composition, polypeptide pattern, and size. Eight polypeptides were resolved in the phycobilin region (17.5 to 23.5 kilodaltons) by isoelectric focusing followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Half of these were invariable, while others were variable in green and red light. It is inferred that phycoerythrin synthesis in green light resulted in a one for one substitution of phycocyanin, thus retaining a constant phycobilisome size. Tolypothrix appears to be one of the best examples of phycobiliprotein regulation with wavelength. By contrast, in Nostoc sp., the decrease in phycoerythrin in red light cells was accompanied by a decrease in phycobilisome size but not a regulated substitution.

  11. Variations in gene and protein expression in canine chondrodystrophic nucleus pulposus cells following long-term three-dimensional culture.

    Directory of Open Access Journals (Sweden)

    Munetaka Iwata

    Full Text Available Intervertebral disc (IVD degeneration greatly affects quality of life. The nucleus pulposus (NP of chondrodystrophic dog breeds (CDBs is similar to the human NP, because the cells disappear with age and are replaced by fibrochondrocyte-like cells. However, because IVD develops as early as within the first year of life, we used canines as a model to investigate in vitro the mechanisms underlying IVD degeneration. Specifically, we evaluated the potential of a three-dimensional (3D culture of healthy NP as an in vitro model system to investigate the mechanisms of IVD degeneration. Agarose hydrogels were populated with healthy NP cells from beagles after performing magnetic resonance imaging, and mRNA expression profiles and pericellular extracellular matrix (ECM protein distribution were determined. After 25 days of 3D culture, there was a tendency for redifferentiation into the native NP phenotype, and mRNA levels of Col2A1, COMP, and CK18 were not significantly different from those of freshly isolated cells. Our findings suggest that long-term 3D culture promoted chondrodystrophic NP redifferentiation through reconstruction of the pericellular microenvironment. Further, lipopolysaccharide (LPS induced expression of TNF-α, MMP3, MMP13, VEGF, and PGES mRNA in the 3D cultures, creating a molecular milieu that mimics that of degenerated NP. These results suggest that this in vitro model represents a reliable and cost-effective tool for evaluating new therapies for disc degeneration.

  12. Genome-wide assessment of the association of rare and common copy number variations to testicular germ cell cancer

    DEFF Research Database (Denmark)

    Edsgard, Stefan Daniel; Dalgaard, Marlene Danner; Weinhold, Nils; Wesolowska, Agata; Rajpert-De Meyts, Ewa; Ottesen, Anne Marie; Juul, Anders; Skakkebæk, Niels Erik; Jensen, Thomas Skøt; Gupta, Ramneek; Leffers, Henrik; Brunak, Søren

    2013-01-01

    Testicular germ cell cancer (TGCC) is one of the most heritable forms of cancer. Previous genome-wide association studies have focused on single nucleotide polymorphisms, largely ignoring the influence of copy number variants (CNVs). Here we present a genome-wide study of CNV on a cohort of 212...

  13. Variations in the villus cell population of intestine in the irradiated Swiss albino mouse with and without herbal treatment

    International Nuclear Information System (INIS)

    Generally, the effects of radiations are hazardous, even in moderate doses. The damage caused by radiation is influenced by the relative radiosensitivity of the tissue. Damage to gastrointestinal tract leads to death of the animals 10 to 15 days after radiation exposure to the lethal dose. When Swiss albino mice were irradiated with 6 and 8 Gy of gamma radiation, it caused cytological, pathological and biochemical changes in the gastrointestinal tract. There was a significant decrease in the total cell population (TCP), whereas pyknotic nuclei (PN) and necrotic cells (NC) showed significant increase after irradiation. Pretreatment with Centella asiatica (CA) resulted in a significantly lesser decrease in TCP, whereas, PN and NC showed significant decrease from respective irradiated controls at each autopsy day. It was observed that CA pretreatment provides protection against radiation induced damage in the intestinal mucosa of Swiss albino mice. (author)

  14. Substantial variation in post-engraftment infection prophylaxis and revaccination practice in autologous stem cell transplant patients.

    Science.gov (United States)

    Lim, H Y; Grigg, A

    2016-03-01

    There is a paucity of evidence supporting the necessity or duration of Pneumocystis jirovecii and antiviral prophylaxis as well as revaccination following autologous stem cell transplant (ASCT). A survey aimed at evaluating these policies was distributed to 34 ASCT centres across Australasia. The 26 survey respondents demonstrated significant heterogeneity in their infection prophylaxis and revaccination strategy post-transplant despite the availability of consensual guidelines. PMID:26968596

  15. Combining multivariate analysis and monosaccharide composition modeling to identify plant cell wall variations by Fourier Transform Near Infrared spectroscopy

    Directory of Open Access Journals (Sweden)

    Smith-Moritz Andreia M

    2011-08-01

    Full Text Available Abstract We outline a high throughput procedure that improves outlier detection in cell wall screens using FT-NIR spectroscopy of plant leaves. The improvement relies on generating a calibration set from a subset of a mutant population by taking advantage of the Mahalanobis distance outlier scheme to construct a monosaccharide range predictive model using PLS regression. This model was then used to identify specific monosaccharide outliers from the mutant population.

  16. Variational analysis

    CERN Document Server

    Rockafellar, R Tyrrell

    1998-01-01

    From its origins in the minimization of integral functionals, the notion of 'variations' has evolved greatly in connection with applications in optimization, equilibrium, and control. It refers not only to constrained movement away from a point, but also to modes of perturbation and approximation that are best describable by 'set convergence', variational convergence of functions and the like. This book develops a unified framework and, in finite dimension, provides a detailed exposition of variational geometry and subdifferential calculus in their current forms beyond classical and convex analysis. Also covered are set-convergence, set-valued mappings, epi-convergence, duality, maximal monotone mappings, second-order subderivatives, measurable selections and normal integrands. The changes in this 3rd printing mainly concern various typographical corrections, and reference omissions that came to light in the previous printings. Many of these reached the authors' notice through their own re-reading, that of th...

  17. Enhancement of synthetic schlieren image resolution using total variation optical flow: application to thermal experiments in a Hele-Shaw cell

    Science.gov (United States)

    Letelier, Juvenal A.; Herrera, Paulo; Mujica, Nicolás; Ortega, Jaime H.

    2016-02-01

    We present an improvement to the standard synthetic schlieren technique to obtain the temperature distribution of a fluid inside of a Hele-Shaw cell. We aim to use the total variation L^1-norm optical flow method to treat experimental images and to obtain quantitative results of the development of thermal convection inside a cell, by detecting the gradients of the optical refractive index. We present a simple algorithm to set the optical flow parameters, which is based on the comparison between the optical flow output and the result obtained by digital PIV using the structural index metric. As an example of the application of the proposed method, we analyze laboratory experiments of thermal convection in porous media using a Hele-Shaw cell. We demonstrate that the application of the proposed method produces important improvements versus digital PIV, for the quantification of the gradients of the refractive index including the detection of small-scale convective structures. In comparison with correlation-based digital methods, we demonstrate the advantages of the proposed method, such as denoising and edge capture. These features allow us to obtain the temperature, for this experimental setting, with better image resolution than other techniques reported in the literature.

  18. Alternative Respiration Induced by Glucose Stimulation and Variation of Adenylate Energy Charge in Glucose-Starved Cells of Green Alga Chlorella Protothecoides

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Effects of inhibitors and glucose on cytochrome and alternative respiration and on adenylate energy charge (AEC) in glucose-starved Chlorella protothecoides were investigated. 1 mmol/L azide (NaN3), which immediately caused an increase of O2 uptake by inhibiting the cytochrome pathway and stimulating alternative respiration, resulted in a decrease of AEC value from 0. 83 to 0. 34 within 3 minutes. When 1 mmol/L salicylhydroxamic acid (SHAM) was added into the cell suspension, there was no apparent variation in AEC. Adding NaN3 and SHAM together into cell suspension to inhibit both cytochrome and alternative pathways showed a same change of AEC as that of adding NaN3 alone. When 2.0 mmol/L of glucose was added to a suspension of glucose-starved cells, the O2 uptake rate was immediately stimulated from 0.81 up to 1.34 [μrnol/L O2 · min-] · (mL PCV)-1]. The respiration stimulated by glucose could be inhibited about 20% by adding 1 mmol/L SHAM. It was found by titration with SHAM in the absence and presence of NaN3 that 53% of O2 uptake went through the cytochrome pathway and 45% of the alternate pathway was operational in enhanced respiration. It implied that induced operation of the alternative respiratory pathway probably resulted from the burst of the electron flux into the electron transport chain by glucose stimulation.

  19. Performance variation from triphenylamine- to carbazole-triphenylamine-rhodaniline-3-acetic acid dyes in dye-sensitized solar cells

    International Nuclear Information System (INIS)

    Highlights: → We synthesized an organic dye of carbazole-rhodaniline-3-acetic acid-triphenylamine. → A dye-sensitized solar cell is fabricated using this dye with efficiency of 4.64%. → Carbazole donor in the dye molecule provides electron in increasing efficiency. → Two rhodaniline-3-acetic acids play a key role in increasing efficiency. → AC impedance proves this dye's effect on enhancing charge transfer in TiO2. - Abstract: Organic dyes have been synthesized which contain an extra-electron donor (carbazole) and electron acceptors (rhodaniline-3-acetic acid) on triphenylamines (TPA). Photophysical, electrochemical, and theoretical computational methods have categorized these compounds. Nanocrystalline TiO2-based dye-sensitized solar cells (DSSCs) are fabricated using these dye molecules as light-harvesting sensitizers. The overall efficiency of sensitized cells has 4.64% relative to a cis-di(thiocyanato)-bis(2,2'-bipyridyl)-4,4'-dicarboxylate ruthenium (II) (N3 dye)-sensitized device (7.83%) fabricated and measured under the same conditions. Carbazole-electron donation in the dye molecules plays a key role in the increased efficiency. Two rhodaniline-3-acetic acid groups appear to help convey the charge transfer from the excited dye molecules to the conduction band of TiO2, leading to a higher efficiency of devices using such a dye. Electrochemical impedance supports this dye's effect on enhancing charge transfer in TiO2 (e-). Computations on this dye compound also indicate the larger charge transfer efficiency in the electronically excited state.

  20. An ECVAG inter-laboratory validation study of the comet assay: inter-laboratory and intra-laboratory variations of DNA strand breaks and FPG-sensitive sites in human mononuclear cells.

    Science.gov (United States)

    Ersson, Clara; Møller, Peter; Forchhammer, Lykke; Loft, Steffen; Azqueta, Amaya; Godschalk, Roger W L; van Schooten, Frederik-Jan; Jones, George D D; Higgins, Jennifer A; Cooke, Marcus S; Mistry, Vilas; Karbaschi, Mahsa; Phillips, David H; Sozeri, Osman; Routledge, Michael N; Nelson-Smith, Kirsty; Riso, Patrizia; Porrini, Marisa; Matullo, Giuseppe; Allione, Alessandra; Stepnik, Maciej; Ferlińska, Magdalena; Teixeira, João Paulo; Costa, Solange; Corcuera, Laura-Ana; López de Cerain, Adela; Laffon, Blanca; Valdiglesias, Vanessa; Collins, Andrew R; Möller, Lennart

    2013-05-01

    The alkaline comet assay is an established, sensitive method extensively used in biomonitoring studies. This method can be modified to measure a range of different types of DNA damage. However, considerable differences in the protocols used by different research groups affect the inter-laboratory comparisons of results. The aim of this study was to assess the inter-laboratory, intra-laboratory, sample and residual (unexplained) variations in DNA strand breaks and formamidopyrimidine DNA glycosylase (FPG)-sensitive sites measured by the comet assay by using a balanced Latin square design. Fourteen participating laboratories used their own comet assay protocols to measure the level of DNA strand breaks and FPG-sensitive sites in coded samples containing peripheral blood mononuclear cells (PBMC) and the level of DNA strand breaks in coded calibration curve samples (cells exposed to different doses of ionising radiation) on three different days of analysis. Eleven laboratories found dose-response relationships in the coded calibration curve samples on two or three days of analysis, whereas three laboratories had technical problems in their assay. In the coded calibration curve samples, the dose of ionising radiation, inter-laboratory variation, intra-laboratory variation and residual variation contributed to 60.9, 19.4, 0.1 and 19.5%, respectively, of the total variation. In the coded PBMC samples, the inter-laboratory variation explained the largest fraction of the overall variation of DNA strand breaks (79.2%) and the residual variation (19.9%) was much larger than the intra-laboratory (0.3%) and inter-subject (0.5%) variation. The same partitioning of the overall variation of FPG-sensitive sites in the PBMC samples indicated that the inter-laboratory variation was the strongest contributor (56.7%), whereas the residual (42.9%), intra-laboratory (0.2%) and inter-subject (0.3%) variations again contributed less to the overall variation. The results suggest that the

  1. Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells

    OpenAIRE

    Yang, Luhan; Grishin, Dennis; Wang, Gang; Aach, John; Zhang, Cheng-Zhong; Chari, Raj; Homsy, Jason; Cai, Xuyu; ZHAO, YUE; Fan, Jian-Bing; Seidman, Christine; Seidman, Jonathan; Pu, William; Church, George

    2014-01-01

    CRISPR/Cas9 has demonstrated a high-efficiency in site-specific gene targeting. However, potential off-target effects of the Cas9 nuclease represent a major safety concern for any therapeutic application. Here, we knock out the Tafazzin gene by CRISPR/Cas9 in human-induced pluripotent stem cells with 54% efficiency. We combine whole-genome sequencing and deep-targeted sequencing to characterise the off-target effects of Cas9 editing. Whole-genome sequencing of Cas9-modified hiPSC clones detec...

  2. Variational principles

    CERN Document Server

    Moiseiwitsch, B L

    2004-01-01

    This graduate-level text's primary objective is to demonstrate the expression of the equations of the various branches of mathematical physics in the succinct and elegant form of variational principles (and thereby illuminate their interrelationship). Its related intentions are to show how variational principles may be employed to determine the discrete eigenvalues for stationary state problems and to illustrate how to find the values of quantities (such as the phase shifts) that arise in the theory of scattering. Chapter-by-chapter treatment consists of analytical dynamics; optics, wave mecha

  3. Gross tumour volume variations in primary non-small-cell lung cancer during the course of treatment with stereotactic body radiation therapy

    International Nuclear Information System (INIS)

    We aim to quantify the variations in the gross tumour volume (GTV) during a course of stereotactic body radiotherapy (SBRT) and determine its impact on dosimetric coverage of the GTV. The GTVs and dose coverage for 14 patients with 16 primary non-small-cell lung tumours treated with SBRT were investigated. Initial GTVs were calculated from treatment planning CT scans. The prescribed doses ranged from 48 to 60 Gy in three to five fractions. Before each treatment, patients underwent a CBCT scan. For each CBCT scan, the GTV and the dose received by the GTV were determined and followed during the course of therapy. There was considerable variation in the measured GTVs during the course of therapy. Increases of up to 63.3% of volume measured by initial CBCT were detected during the first few fractions, after which GTV tended to decrease. Dose coverage (V95) for any given fraction deviated no more than 5% from optimised coverage obtained in the initial treatment plan. In the long term, all patients with follow-up scans demonstrated tumour shrinkage with no radiographic evidence of tumour recurrence. GTV, as evaluated in this study, demonstrates an initial increase in volume followed by a subsequent decrease. This volume change needs to be considered in the design of treatment plans and assignment of treatment margins.

  4. Trade-off between carbon emission and effluent quality of activated sludge processes under seasonal variations of wastewater temperature and mean cell retention time.

    Science.gov (United States)

    Guo, Jingbo; Fu, Xin; Andrés Baquero, G; Sobhani, Reza; Nolasco, Daniel A; Rosso, Diego

    2016-03-15

    Over the seasonal cycles, the mean cell retention time (MCRT) of the activated sludge process is varied to compensate the wastewater temperature variations. The effects of these variations on the carbon footprint (CFP) and effluent quality index (EQI) of a conventional activated sludge (CAS) process and a nitrification/denitrification (NDN) process were quantified. The carbon emission included both biogenic and non-biogenic carbon. Carbon emissions of wasted biosolids management were also addressed. Our results confirmed that the effluent quality indicated by EQI was not necessarily improved by increasing MCRT. Higher MCRT increased the carbon emission and reduced excess sludge production, which decreased the potential for biogas energy recovery. The NDN process was preferable to the CAS process from the perspective of effluent quality. This consideration extended to the whole plant CFP if the N2O emitted during NDN was limited ([N2O]carbon emission per unit effluent quality achieved by NDN process is less than that of the CAS process. By putting forward carbon emission intensity (γ) derived from CFP and EQI, our work provides a quantitative tool for decision makers evaluating process alternatives when there is a trade-off between carbon emission and effluent quality. PMID:26789371

  5. Heterozygous deletion at the RLN1 locus in a family with testicular germ cell cancer identified by integrating copy number variation data with phenome and interactome information

    DEFF Research Database (Denmark)

    Edsgärd, D; Scheel, M; Hansen, N T;

    2011-01-01

    To search for disease-related copy number variations (CNVs) in families with a high frequency of germ cell tumours (GCT), we analysed 16 individuals from four families by array comparative genomic hybridization (aCGH) and applied an integrative systems biology algorithm that prioritizes risk......-associated genes among loci targeted by CNVs. The top-ranked candidate, RLN1, encoding a Relaxin-H1 peptide, although only detected in one of the families, was selected for further investigations. Validation of the CNV at the RLN1 locus was performed as an association study using qPCR with 106 sporadic testicular...... GCT patients and 200 healthy controls. Observed CNV frequencies of 1.9% among cases and 1.5% amongst controls were not significantly different and this was further confirmed by CNV data extracted from a genome-wide analysis of 189 cases and 380 controls, where similar frequencies of 2.2% were observed...

  6. Heterozygous deletion at the RLN1 locus in a family with testicular germ cell cancer identified by integrating copy number variation data with phenome and interactome information

    DEFF Research Database (Denmark)

    Edsgard, Stefan Daniel; Scheel, M.; Hansen, Niclas Tue;

    2011-01-01

    To search for disease‐related copy number variations (CNVs) in families with a high frequency of germ cell tumours (GCT), we analysed 16 individuals from four families by array comparative genomic hybridization (aCGH) and applied an integrative systems biology algorithm that prioritizes risk......‐associated genes among loci targeted by CNVs. The top‐ranked candidate, RLN1, encoding a Relaxin‐H1 peptide, although only detected in one of the families, was selected for further investigations. Validation of the CNV at the RLN1 locus was performed as an association study using qPCR with 106 sporadic testicular...... GCT patients and 200 healthy controls. Observed CNV frequencies of 1.9% among cases and 1.5% amongst controls were not significantly different and this was further confirmed by CNV data extracted from a genome‐wide analysis of 189 cases and 380 controls, where similar frequencies of 2.2% were observed...

  7. The state of cell block variation and satisfaction in the era of molecular diagnostics and personalized medicine

    Directory of Open Access Journals (Sweden)

    John P Crapanzano

    2014-01-01

    Full Text Available Background: In the recent past, algorithms and recommendations to standardize the morphological, immunohistochemical and molecular classification of lung cancers on cytology specimens have been proposed, and several organizations have recommended cell blocks (CBs as the preferred modality for molecular testing. Based on the literature, there are several different techniques available for CB preparation-suggesting that there is no standard. The aim of this study was to conduct a survey of CB preparation techniques utilized in various practice settings and analyze current issues, if any. Materials and Methods: A single E-mail with a link to an electronic survey was distributed to members of the American Society of Cytopathology and other pathologists. Questions pertaining to the participants′ practice setting and CBs-volume, method, quality and satisfaction-were included. Results: Of 95 respondents, 90/95 (94% completed the survey and comprise the study group. Most participants practice in a community hospital/private practice (44% or academic center (41%. On average, 14 CBs (range 0-50; median 10 are prepared by a laboratory daily. Over 10 methods are utilized: Plasma thrombin (33%, HistoGel (27%, Cellient automated cell block system (8% and others (31% respectively. Forty of 90 (44% respondents are either unsatisfied or sometimes satisfied with their CB quality, with low-cellular yield being the leading cause of dissatisfaction. There was no statistical significance between the three most common CB preparation methods and satisfaction with quality. Discussion: Many are dissatisfied with their current method of CB preparation, and there is no consistent method to prepare CBs. In today′s era of personalized medicine with an increasing array of molecular tests being applied to cytological specimens, there is a need for a standardized protocol for CB optimization to enhance cellularity.

  8. Variation in Prescribing Patterns and Therapeutic Drug Monitoring of Intravenous Busulfan in Pediatric Hematopoietic Cell Transplant Recipients

    Science.gov (United States)

    McCune, Jeannine S.; Baker, K. Scott; Blough, David K.; Gamis, Alan; Bemer, Meagan J.; Kelton-Rehkopf, Megan C.; Winter, Laura; Barrett, Jeffrey S.

    2016-01-01

    Personalizing intravenous (IV) busulfan doses in children using therapeutic drug monitoring (TDM) is an integral component of hematopoietic cell transplant. The authors sought to characterize initial dosing and TDM of IV busulfan, along with factors associated with busulfan clearance, in 729 children who underwent busulfan TDM from December 2005 to December 2008. The initial IV busulfan dose in children weighing ≤12 kg ranged 4.8-fold, with only 19% prescribed the package insert dose of 1.1 mg/kg. In those children weighing >12 kg, the initial dose ranged 5.4-fold, and 79% were prescribed the package insert dose. The initial busulfan dose achieved the target exposure in only 24.3% of children. A wide range of busulfan exposures were targeted for children with the same disease (eg, 39 target busulfan exposures for the 264 children diagnosed with acute myeloid leukemia). Considerable heterogeneity exists regarding when TDM is conducted and the number of pharmacokinetic samples obtained. Busulfan clearance varied by age and dosing frequency but not by underlying disease. The authors’ group is currently evaluating how using population pharmacokinetics to optimize initial busulfan dose and TDM (eg, limited sampling schedule in conjunction with maximum a posteriori Bayesian estimation) may affect clinical outcomes in children. PMID:23444282

  9. Epigenetic dynamics across the cell cycle

    DEFF Research Database (Denmark)

    Kheir, Tony Bou; Lund, Anders H.

    2010-01-01

    Progression of the mammalian cell cycle depends on correct timing and co-ordination of a series of events, which are managed by the cellular transcriptional machinery and epigenetic mechanisms governing genome accessibility. Epigenetic chromatin modifications are dynamic across the cell cycle...... a correct inheritance of epigenetic chromatin modifications to daughter cells. In this chapter, we summarize the current knowledge on the dynamics of epigenetic chromatin modifications during progression of the cell cycle....

  10. Copy number variation analysis implicates the cell polarity gene glypican 5 as a human spina bifida candidate gene.

    Science.gov (United States)

    Bassuk, Alexander G; Muthuswamy, Lakshmi B; Boland, Riley; Smith, Tiffany L; Hulstrand, Alissa M; Northrup, Hope; Hakeman, Matthew; Dierdorff, Jason M; Yung, Christina K; Long, Abby; Brouillette, Rachel B; Au, Kit Sing; Gurnett, Christina; Houston, Douglas W; Cornell, Robert A; Manak, J Robert

    2013-03-15

    Neural tube defects (NTDs) are common birth defects of complex etiology. Family and population-based studies have confirmed a genetic component to NTDs. However, despite more than three decades of research, the genes involved in human NTDs remain largely unknown. We tested the hypothesis that rare copy number variants (CNVs), especially de novo germline CNVs, are a significant risk factor for NTDs. We used array-based comparative genomic hybridization (aCGH) to identify rare CNVs in 128 Caucasian and 61 Hispanic patients with non-syndromic lumbar-sacral myelomeningocele. We also performed aCGH analysis on the parents of affected individuals with rare CNVs where parental DNA was available (42 sets). Among the eight de novo CNVs that we identified, three generated copy number changes of entire genes. One large heterozygous deletion removed 27 genes, including PAX3, a known spina bifida-associated gene. A second CNV altered genes (PGPD8, ZC3H6) for which little is known regarding function or expression. A third heterozygous deletion removed GPC5 and part of GPC6, genes encoding glypicans. Glypicans are proteoglycans that modulate the activity of morphogens such as Sonic Hedgehog (SHH) and bone morphogenetic proteins (BMPs), both of which have been implicated in NTDs. Additionally, glypicans function in the planar cell polarity (PCP) pathway, and several PCP genes have been associated with NTDs. Here, we show that GPC5 orthologs are expressed in the neural tube, and that inhibiting their expression in frog and fish embryos results in NTDs. These results implicate GPC5 as a gene required for normal neural tube development. PMID:23223018

  11. Pediatric primary central nervous system germ cell tumors of different prognosis groups show characteristic miRNome traits and chromosome copy number variations

    Directory of Open Access Journals (Sweden)

    Liang Muh-Lii

    2010-02-01

    Full Text Available Abstract Background Intracranial pediatric germ cell tumors (GCTs are rare and heterogeneous neoplasms and vary in histological differentiation, prognosis and clinical behavior. Germinoma and mature teratoma are GCTs that have a good prognosis, while other types of GCTs, termed nongerminomatous malignant germ cell tumors (NGMGCTs, are tumors with an intermediate or poor prognosis. The second group of tumors requires more extensive drug and irradiation treatment regimens. The mechanisms underlying the differences in incidence and prognosis of the various GCT subgroups are unclear. Results We identified a distinct mRNA profile correlating with GCT histological differentiation and prognosis, and also present in this study the first miRNA profile of pediatric primary intracranial GCTs. Most of the differentially expressed miRNAs were downregulated in germinomas, but miR-142-5p and miR-146a were upregulated. Genes responsible for self-renewal (such as POU5F1 (OCT4, NANOG and KLF4 and the immune response were abundant in germinomas, while genes associated with neuron differentiation, Wnt/β-catenin pathway, invasiveness and epithelial-mesenchymal transition (including SNAI2 (SLUG and TWIST2 were abundant in NGMGCTs. Clear transcriptome segregation based on patient survival was observed, with malignant NGMGCTs being closest to embryonic stem cells. Chromosome copy number variations (CNVs at cytobands 4q13.3-4q28.3 and 9p11.2-9q13 correlated with GCT malignancy and clinical risk. Six genes (BANK1, CXCL9, CXCL11, DDIT4L, ELOVL6 and HERC5 within 4q13.3-4q28.3 were more abundant in germinomas. Conclusions Our results integrate molecular profiles with clinical observations and provide insights into the underlying mechanisms causing GCT malignancy. The genes, pathways and microRNAs identified have the potential to be novel therapeutic targets.

  12. In Vivo Zonal Variation and Liver Cell-Type Specific NF-κB Localization after Chronic Adaptation to Ethanol and following Partial Hepatectomy.

    Directory of Open Access Journals (Sweden)

    Harshavardhan Nilakantan

    Full Text Available NF-κB is a major inflammatory response mediator in the liver, playing a key role in the pathogenesis of alcoholic liver injury. We investigated zonal as well as liver cell type-specific distribution of NF-κB activation across the liver acinus following adaptation to chronic ethanol intake and 70% partial hepatectomy (PHx. We employed immunofluorescence staining, digital image analysis and statistical distributional analysis to quantify subcellular localization of NF-κB in hepatocytes and hepatic stellate cells (HSCs. We detected significant spatial heterogeneity of NF-κB expression and cellular localization between cytoplasm and nucleus across liver tissue. Our main aims involved investigating the zonal bias in NF-κB localization and determining to what extent chronic ethanol intake affects this zonal bias with in hepatocytes at baseline and post-PHx. Hepatocytes in the periportal area showed higher NF-κB expression than in the pericentral region in the carbohydrate-fed controls, but not in the ethanol group. However, the distribution of NF-κB nuclear localization in hepatocytes was shifted towards higher levels in pericentral region than in periportal area, across all treatment conditions. Chronic ethanol intake shifted the NF-κB distribution towards higher nuclear fraction in hepatocytes as compared to the pair-fed control group. Ethanol also stimulated higher NF-κB expression in a subpopulation of HSCs. In the control group, PHx elicited a shift towards higher NF-κB nuclear fraction in hepatocytes. However, this distribution remained unchanged in the ethanol group post-PHx. HSCs showed a lower NF-κB expression following PHx in both ethanol and control groups. We conclude that adaptation to chronic ethanol intake attenuates the liver zonal variation in NF-κB expression and limits the PHx-induced NF-κB activation in hepatocytes, but does not alter the NF-κB expression changes in HSCs in response to PHx. Our findings provide new

  13. Evaluating impact of market changes on increasing cell-load variation in dynamic cellular manufacturing systems using a hybrid Tabu search and simulated annealing algorithms

    Directory of Open Access Journals (Sweden)

    Aidin Delgoshaei

    2016-06-01

    Full Text Available In this paper, a new method is proposed for scheduling dynamic cellular manufacturing systems (D-CMS in the presence of uncertain product demands. The aim of this method is to control the process of trading off between in-house manufacturing and outsourcing while product demands are uncertain and can be varied from period to period. To solve the proposed problem, a hybrid Tabu Search and Simulated Annealing are developed to overcome hardness of the proposed model and then results are compared with a Branch and Bound and Simulated Annealing algorithms. A Taguchi method (L_27 orthogonal optimization is used to estimate parameters of the proposed method in order to solve experiments derived from literature. An in-depth analysis is conducted on the results in consideration of various factors. For evaluating the system imbalance in dynamic market demands, a new measuring index is developed. Our findings indicate that the uncertain condition of market demands affects the routing of product parts and may induce machine-load variations that yield to cell-load diversity. The results showed that the proposed hybrid method can provide solutions with better quality.

  14. Temporal variation of hemispheric solar rotation

    Institute of Scientific and Technical Information of China (English)

    Jing-Lan Xie; Xiang-Jun Shi; Jing-Chen Xu

    2012-01-01

    The daily sunspot numbers of the whole disk as well as the northern and southern hemispheres from 1945 January 1 to 2010 December 31 are used to investigate the temporal variation of rotational cycle length through the continuous wavelet transformation analysis method.Auto-correlation function analysis of daily hemispheric sunspot numbers shows that the southern hemisphere rotates faster than the northern hemisphere.The results obtained from the wavelet transformation analysis are that no direct relationship exists between the variation trend of the rotational cycle length and the solar activity in the two hemispheres and that the rotational cycle length of both hemispheres has no significant period appearing at 11 yr,but has a significant period of about 7.6 yr.Analysis concerning the solar cycle dependence of the rotational cycle length shows that acceleration seems to appear before the minimum time of solar activity in the whole disk and the northern hemisphere,respectively.Furthermore,the cross-correlation study indicates that the rotational cycle length of the two hemispheres has different phases,and that the rotational cycle length of the whole disk as well as the northern and southern hemispheres,also has phase shifts with corresponding solar activity.In addition,the temporal variation of the north-south (N- S) asymmetry of the rotational cycle length is also studied.This displays the same variation trend as the N-S asymmetry of solar activity in a solar cycle,as well as in the considered time interval,and has two significant periods of 7.7 and 17.5 yr.Moreover,the rotational cycle length and the N-S asymmetry of solar activity are highly correlated.It is inferred that the northern hemisphere should rotate faster at the beginning of solar cycle 24.

  15. MR-imaging of the breast at 0.5 Tesla: menstrual-cycle dependency of parenchymal contrast enhancement in healthy volunteers with oral contraceptive use?; MR-Mammographie bei 0,5 Tesla: Menstruationszyklusabhaengigkeit der Kontrastmittelanreicherung unter hormoneller Kontrazeption?

    Energy Technology Data Exchange (ETDEWEB)

    Lorenzen, J.; Welger, J.; Krupski, G.; Adam, G. [Klinik und Poliklinik fuer Diagnostische und Interventionelle Radiologie, Universitaetsklinikum Hamburg-Eppendorf (Germany); Lisboa, B.W. [Klinik und Poliklinik fuer Frauenheilkunde und Geburtshilfe, Universitaetsklinikum Hamburg-Eppendorf (Germany)

    2003-04-01

    Introduction: To evaluate changes of contrast medium enhancement of the breast parenchyma due to menstrual cycle in healthy volunteers with oral contraceptive use in MR-imaging of the breast. Material and Methods: 15 healthy volunteers (age: 22 - 36, mean 28,2) without breast disease were examined two times during one menstrual cycle (days 7 - 14 and days 21 - 2). Two volunteers were examined only in the second part of the cycle (days 21 - 2). All volunteers used oral contraceptives for more than 6 month continuously. Examinations were performed with a 0,5 T magnet (dynamic 3D-gradient echo protocol with subtraction postprocessing). We evaluated the number of enhancing foci and the parenchymal contrast medium enhancement during the different phases of the cycle by region of interest. Results: Only a total of two enhancing foci were found in 2 of 17 volunteers. Time/signal intensity diagrams in these both cases were not suspicious (< 80% initial signal increase after of contrast medium injection, no wash-out phenomenon) and sonography of the breast in these two cases was inconspicuous. Contrast medium enhancement of breast parenchyma in cycle days 7 - 14 (mean enhancement: 0.12 - 0.26, minutes 1 - 9 p.i.) was not significantly different (p = 0.2209; Wilcoxon signed rank test) from cycle days 21 - 2 (mean: 0.13 - 0.32). Conclusion: Menstrual cycle dependency of parenchymal contrast medium enhancement seems to be of minor relevance for premenopausal women with use of oral contraceptives. (orig.) [German] Fragestellung: Untersuchung der Kontrastmittelaufnahme des Brustparenchyms in Abhaengigkeit vom Menstruationszyklus bei gesunden Probandinnen unter oraler Kontrazeption. Material und Methode: Bei 15 gesunden Probandinnen ohne Brusterkrankung in der Anamnese wurde eine MR-Mammographie zweimal waehrend eines Menstruationszyklus durchgefuehrt (Zyklustag: 7 - 14 und 21 - 2). Bei zwei weiteren Probandinnen erfolgte die MR-Mammographie nur in der zweiten Zyklushaelfte

  16. Observer variation in contouring gross tumor volume in patients with poorly defined non-small-cell lung tumors on CT: the impact of 18FDG-hybrid PET fusion

    International Nuclear Information System (INIS)

    Purpose: To quantify interobserver variation in gross tumor volume (GTV) localization using CT images for patients with non-small-cell lung carcinoma and poorly defined tumors on CT and to determine whether variability would be reduced if coregistered 2-[18F]fluoro-2-deoxy-d-glucose (FDG)-hybrid positron emission tomography (PET) with CT images were used. Methods and Materials: Prospectively, 30 patients with non-small-cell lung carcinoma had CT and FDG-hybrid PET examinations in radiation treatment position on the same day. Images were coregistered using eight fiducial markers. Guidelines were established for contouring GTVs. Three radiation oncologists performed localization independently. The coefficient of variation was used to assess interobserver variability. Results: The size of the GTV defined showed great variation among observers. The mean ratios of largest to smallest GTV were 2.31 and 1.56 for CT only and for CT/FDG coregistered data, respectively. The addition of PET reduced this ratio in 23 of 30 cases and increased it in 7. The mean coefficient of variation for GTV based on the combined modalities was significantly smaller (p<0.01) than that for CT data only. Conclusions: High observer variability in CT-based definition of the GTV can occur. A more consistent definition of the GTV can often be obtained if coregistered FDG-hybrid PET images are used

  17. A high sensitivity, high throughput, automated single-cell gel electrophoresis ('Comet') DNA damage assay

    International Nuclear Information System (INIS)

    A fully automated microscopy machine vision image capture and analysis system for the collection of data from slides of 'comets' has been developed. The novel image processing algorithms employed in delineating the 'comet head' from the 'comet tail' allow us to determine accurately very low levels of damage. In conjunction with calibrated and automated image capture methods, we are able to eliminate operator subjectivity and analyse large numbers of cells (>2500) in a short time (<1 hour). The image processing algorithm is designed to handle particularly difficult nuclei containing a high degree of structure, due to DNA clumping. We also present techniques used to extend the assay's dynamic range by removing interfering background fluorescence and to define a region of interest. If subtle biological variations are to be quantified (e.g. cell cycle dependant damage), then the use of large cell populations is dictated. Under those circumstances, the use of a fully automated system is particularly advantageous providing that the manner in which data is extracted does not introduce any inadvertent bias. In practice, it is essential that the image processing steps are geared towards the correct recognition of an acceptable cell nucleus, i.e. comet 'head'. We acknowledge the financial support of CRUK, Programme Grant C133/A1812 - SP 2195-01/02 and the US Department of Energy Low Dose Radiation Research Program grant DE-FG07-99ER62878

  18. Genetic variations in multiple myeloma I

    DEFF Research Database (Denmark)

    Vangsted, A.; Klausen, T.W.; Vogel, Ulla Birgitte

    2012-01-01

    variability in a population. The complex interplay between environment and genes for the development of cancer may therefore be influenced by genetic variations. A genetic variation may change the function of the gene, and if the genetic variation is associated with the risk of disease, that particular gene......Few risk factors have been established for the plasma cell disorder multiple myeloma, but some of these like African American ethnicity and a family history of B-cell lymphoproliferative diseases suggest a genetic component for the disease. Genetic variation represents the genetic basis of...

  19. Single nucleotide variation in the TP53 3' untranslated region in diffuse large B-cell lymphoma treated with rituximab-CHOP

    DEFF Research Database (Denmark)

    Li, Yong; Gordon, Michael W; Xu-Monette, Zijun Y;

    2013-01-01

    than patients carrying a wild-type CDS and the reference 3'UTR, yet there is no statistically significance difference in overall survival (OS). In contrast, 3'UTR variation predicted poorer OS for patients with a mutant TP53 CDS. We then sequenced TP53 3'UTR in 247 additional DLBCL patients as a...

  20. Cell cycle and cell signal transduction in marine phytoplankton

    Institute of Scientific and Technical Information of China (English)

    LIU Jingwen; JIAO Nianzhi; CAI Huinong

    2006-01-01

    As unicellular phytoplankton, the growth of a marine phytoplankton population results directly from the completion of a cell cycle, therefore, cell-environment communication is an important way which involves signal transduction pathways to regulate cell cycle progression and contribute to growth, metabolism and primary production and respond to their surrounding environment in marine phytoplankton. Cyclin-CDK and CaM/Ca2+ are essentially key regulators in control of cell cycle and signal transduction pathway, which has important values on both basic research and applied biotechnology. This paper reviews progress made in this research field, which involves the identification and characterization of cyclins and cell signal transduction system, cell cycle control mechanisms in marine phytoplankton cells, cell cycle proteins as a marker of a terminal event to estimate the growth rate of phytoplankton at the species level, cell cycle-dependent toxin production of toxic algae and cell cycle progression regulated by environmental factors.

  1. Variation in drug sensitivity of malignant mesothelioma cell lines with substantial effects of selenite and bortezomib, highlights need for individualized therapy.

    Directory of Open Access Journals (Sweden)

    Adam Szulkin

    Full Text Available BACKGROUND: Malignant mesothelioma cells have an epithelioid or sarcomatoid morphology, both of which may be present in the same tumor. The sarcomatoid phenotype is associated with worse prognosis and heterogeneity of mesothelioma cells may contribute to therapy resistance, which is often seen in mesothelioma. This study aimed to investigate differences in sensitivity between mesothelioma cell lines to anti-cancer drugs. We studied two novel drugs, selenite and bortezomib and compared their effect to four conventional drugs. We also investigated the immunoreactivity of potential predictive markers for drug sensitivity; Pgp, MRP-1, ERCC1, RRM1, TS, xCT and proteasome 20S subunit. MATERIALS AND METHODS: We treated six mesothelioma cell lines with selenite, bortezomib, carboplatin, pemetrexed, doxorubicin or gemcitabine as single agents and in combinations. Viability was measured after 24 and 48 hours. Immunocytochemistry was used to detect predictive markers. RESULTS: As a single agent, selenite was effective on four out of six cell lines, and in combination with bortezomib yielded the greatest response in the studied mesothelioma cell lines. Cells with an epithelioid phenotype were generally more sensitive to the different drugs than the sarcomatoid cells. Extensive S-phase arrest was seen in pemetrexed-sensitive cell lines. MRP-1 predicted sensitivity of cell lines to treatment with carboplatin and xCT predicted pemetrexed effect. CONCLUSIONS: The observed heterogeneity in sensitivity of mesothelioma cell lines with different morphology highlights the need for more individualized therapy, requiring development of methods to predict drug sensitivity of individual tumors. Selenite and bortezomib showed a superior effect compared to conventional drugs, motivating clinical testing of these agents as future treatment regime components for patients with malignant mesothelioma.

  2. Chromosome 1q21 gains confer inferior outcomes in multiple myeloma treated with bortezomib but copy number variation and percentage of plasma cells involved have no additional prognostic value.

    Science.gov (United States)

    An, Gang; Xu, Yan; Shi, Lihui; Shizhen, Zhong; Deng, Shuhui; Xie, Zhenqing; Sui, Weiwei; Zhan, Fenghuang; Qiu, Lugui

    2014-02-01

    Chromosome 1q21 aberrations have not been yet been made part of routine clinical tests and their effect in multiple myeloma is still under investigation. The prognostic value of copy number variation and percentage of plasma cells involved have remained unclear. In the present study, we analyzed the prognostic value of 1q21 in a series of 290 cases of newly diagnosed multiple myeloma treated in a prospective, non-randomized clinical trial (BDH 2008/02). We found that incidence of 1q21 aberration increased at relapse, but its copy numbers and proportion of cells involved did not change. Gains of 1q21 had no impact on survival in patients receiving thalidomide-based treatment but conferred a significantly inferior prognosis in patients under bortezomib-based chemotherapy and was an independent adverse prognostic factor for progression free survival (HR 3.831; 95%CI: 2.125-6.907; Pnumber variation and clone size harboring 1q21 gains carried no additional prognostic value and patients with 1q21 gains did not benefit significantly from regimens incorporating bortezomib. Our results indicate that three copies of 1q21 and 20% of plasma cells with this abnormality were enough to confer bortezomib resistance. Therefore, chromosome 1q21 gains should be considered a high-risk feature in multiple myeloma receiving bortezomib therapy. PMID:24213147

  3. Calculus of variations

    CERN Document Server

    Elsgolc, L E; Stark, M

    1961-01-01

    Calculus of Variations aims to provide an understanding of the basic notions and standard methods of the calculus of variations, including the direct methods of solution of the variational problems. The wide variety of applications of variational methods to different fields of mechanics and technology has made it essential for engineers to learn the fundamentals of the calculus of variations. The book begins with a discussion of the method of variation in problems with fixed boundaries. Subsequent chapters cover variational problems with movable boundaries and some other problems; sufficiency

  4. Diurnal variation of tight junction integrity associates inversely with matrix metalloproteinase expression in Xenopus laevis corneal epithelium: implications for circadian regulation of homeostatic surface cell desquamation.

    Directory of Open Access Journals (Sweden)

    Allan F Wiechmann

    Full Text Available The corneal epithelium provides a protective barrier against pathogen entrance and abrasive forces, largely due to the intercellular junctional complexes between neighboring cells. After a prescribed duration at the corneal surface, tight junctions between squamous surface cells must be disrupted to enable them to desquamate as a component of the tissue homeostatic renewal. We hypothesize that matrix metalloproteinase (MMPs are secreted by corneal epithelial cells and cleave intercellular junctional proteins extracellularly at the epithelial surface. The purpose of this study was to examine the expression of specific MMPs and tight junction proteins during both the light and dark phases of the circadian cycle, and to assess their temporal and spatial relationships in the Xenopus laevis corneal epithelium.Expression of MMP-2, tissue inhibitor of MMP-2 (TIMP-2, membrane type 1-MMP (MT1-MMP and the tight junction proteins occludin and claudin-4 were examined by confocal double-label immunohistochemistry on corneas obtained from Xenopus frogs at different circadian times. Occludin and claudin-4 expression was generally uniformly intact on the surface corneal epithelial cell lateral membranes during the daytime, but was frequently disrupted in small clusters of cells at night. Concomitantly, MMP-2 expression was often elevated in a mosaic pattern at nighttime and associated with clusters of desquamating surface cells. The MMP-2 binding partners, TIMP-2 and MT1-MMP were also localized to surface corneal epithelial cells during both the light and dark phases, with TIMP-2 tending to be elevated during the daytime.MMP-2 protein expression is elevated in a mosaic pattern in surface corneal epithelial cells during the nighttime in Xenopus laevis, and may play a role in homeostatic surface cell desquamation by disrupting intercellular junctional proteins. The sequence of MMP secretion and activation, tight junction protein cleavage, and subsequent surface

  5. Chromosome 1q21 gains confer inferior outcomes in multiple myeloma treated with bortezomib but copy number variation and percentage of plasma cells involved have no additional prognostic value

    OpenAIRE

    An, Gang; Xu, Yan; Shi, Lihui; Shizhen, Zhong; Deng, Shuhui; Xie, Zhenqing; Sui, Weiwei; Zhan, Fenghuang; Qiu, Lugui

    2014-01-01

    Chromosome 1q21 aberrations have not been yet been made part of routine clinical tests and their effect in multiple myeloma is still under investigation. The prognostic value of copy number variation and percentage of plasma cells involved have remained unclear. In the present study, we analyzed the prognostic value of 1q21 in a series of 290 cases of newly diagnosed multiple myeloma treated in a prospective, non-randomized clinical trial (BDH 2008/02). We found that incidence of 1q21 aberrat...

  6. Age and CD161 expression contribute to inter-individual variation in interleukin-23 response in CD8+ memory human T cells.

    Directory of Open Access Journals (Sweden)

    Hui Shen

    Full Text Available The interleukin-23 (IL-23 pathway plays a critical role in the pathogenesis of multiple chronic inflammatory disorders, however, inter-individual variability in IL-23-induced signal transduction in circulating human lymphocytes has not been well-defined. In this study, we observed marked, reproducible inter-individual differences in IL-23 responsiveness (measured by STAT3 phosphorylation in peripheral blood CD8+CD45RO+ memory T and CD3+CD56+ NKT cells. Age, but not gender, was a significant (Pearson's correlation coefficient, r = -0.37, p = 0.001 source of variability observed in CD8+CD45RO+ memory T cells, with IL-23 responsiveness gradually decreasing with increasing age. Relative to cells from individuals demonstrating low responsiveness to IL-23 stimulation, CD8+CD45RO+ memory T cells from individuals demonstrating high responsiveness to IL-23 stimulation showed increased gene expression for IL-23 receptor (IL-23R, RORC (RORγt and CD161 (KLRB1, whereas RORA (RORα and STAT3 expression were equivalent. Similar to CD4+ memory T cells, IL-23 responsiveness is confined to the CD161+ subset in CD8+CD45RO+ memory T cells, suggesting a similar CD161+ precursor as has been reported for CD4+ Th17 cells. We observed a very strong positive correlation between IL-23 responsiveness and the fraction of CD161+, CD8+CD45RO+ memory T cells (r = 0.80, p<0.001. Moreover, the fraction of CD161+, CD8+CD45RO+ memory T cells gradually decreases with aging (r = -0.34, p = 0.05. Our data define the inter-individual differences in IL-23 responsiveness in peripheral blood lymphocytes from the general population. Variable expression of CD161, IL-23R and RORC affects IL-23 responsiveness and contributes to the inter-individual susceptibility to IL-23-mediated defenses and inflammatory processes.

  7. Variation of the symmetrical/asymmetrical ratio in chromatid interchanges during the various phases of the cell cycle of human lymphocytes 'in vitro'

    International Nuclear Information System (INIS)

    Experiments have been performed to verify whether in a human euploid cell system, such as lymphocyte cultures in vitro, there is a differential pattern of induction of chromatid exchanges in the various phases of the cycle. (Auth.)

  8. Parameter variation of the one-diode model of a-Si and a- Si/μc-Si solar cells for modeling light-induced degradation

    International Nuclear Information System (INIS)

    For analyzing the long-term behavior of thin film a-Si/μc-Si photovoltaic modules, it is important to observe the light-induced degradation (LID) in dependence of the temperature for the parameters of the one-diode model for solar cells. According to the IEC 61646 standard, the impact of LID on module parameters of these thin film cells is determined at a constant temperature of 50°C with an irradiation of 1000 W/m2 at open circuit conditions. Previous papers examined the LID of thin film a-Si cells with different temperatures and some others are about a-Si/μc-Si. In these previous papers not all parameters of the one-diode model are examined. We observed the serial resistance (Rs), parallel resistance (Rp), short circuit current (Isc), open circuit voltage (Uoc), the maximum power point (MPP: Umpp, Impp and Pmpp) and the diode factor (n). Since the main reason for the LID of silicon-based thin films is the Staebler Wronski effect in the a-Si part of the cell, the temperature dependence of the healing of defects for all parameters of the one-diode model is also taken into account. We are also measuring modules with different kind of transparent conductive oxides: In a-Si thin film solar cells fluorine-doped tin oxide (FTO) is used and for thin film solar cells of a-Si/μc-Si boron- doped zinc oxide is used. In our work we describe an approach for transferring the parameters of a one-diode model for tandem thin film solar cells into the one-diode model for each part of the solar cell. The measurement of degradation and regeneration at higher temperatures is the necessary base for optimization of the different silicon-based thin films in warm hot climate

  9. Neocarzinostatin-induced Rad51 nuclear focus formation is cell cycle regulated and aberrant in AT cells

    International Nuclear Information System (INIS)

    DNA double-stranded breaks are the most detrimental form of DNA damage and, if not repaired properly, may lead to an accumulation of chromosomal aberrations and eventually tumorigenesis. Proteins of the Rad51/Rad52 epitasis group are crucial for the recombinational repair of DNA double-stranded breaks, whereas the Rad50/NBS1/Mre11 nuclease complex is involved in both the recombinational and the end-joining repair of DNA double-stranded breaks. Herein, we demonstrate that the chemotherapeutic enediyne antibiotic neocarzinostatin induced Rad51, but not NBS1, nuclear focus formation in a cell- cycle-dependent manner. Furthermore, neocarzinostatin-induced Rad51 foci formation revealed a slower kinetic change in AT cells, but not in wild-type or NBS cells. In summary, our results suggest that neocarzinostatin induces Rad51 focus formation through an ATM- and cell-cycle-dependent, but NBS1-independent, pathway

  10. Variations in T-helper 17 and Regulatory T Cells during The Menstrual Cycle in Peripheral Blood of Women with Recurrent Spontaneous Abortion

    Directory of Open Access Journals (Sweden)

    Nasrin Sereshki

    2014-03-01

    Full Text Available Background: Disorders in immune system regulation may result in pregnancy abnormalities such as recurrent spontaneous abortion (RSA. This study aims to determine the ratio of regulatory T (Treg and T helper (Th 17 cells in unexplained RSA (URSA women during proliferative and secretory phases of their menstrual cycles compared to healthy non-pregnant women. Materials and Methods: In this case control study, 25 women with URSA and 35 healthy, non-pregnant women were enrolled. The percentage of Th17 and Treg cells in participants peripheral blood were determined by flow cytometry. Results: The percentage of Th17 cells and their related cytokines in serum (IL-17A were higher in the proliferative and secretory phases of the menstrual cycles of URSA women compared to the control women. However, a lower percentage of Treg cells and their related cytokines in serum, transforming growth factor (TGF β1 and interleukin (IL-10 were detected in the proliferative but not the secretory phase of the URSA group. The ratio of Th17/CD4+ Treg was higher in the URSA group than the control group. We observed an increased ratio of Th17/CD4+ Treg during the proliferative and secretory phases in URSA women. Conclusion: The imbalance between Th17 and Treg cells during the proliferative phase of menstrual cycles in the URSA group may be considered a cause for spontaneous abortion.

  11. Solar Cycle Spectral Irradiance Variation and Stratospheric Ozone

    Science.gov (United States)

    Stolarski, R. S.; Swartz, W. H.; Jackman, C. H.; Fleming, E. L.

    2011-12-01

    Recent measurements from the SIM instrument on the SORCE satellite have been interpreted by Harder et al (Geophys. Res. Lett., 36, L07801, doi:10.1029/2008GL036797, 2009) as implying a different spectral irradiance variation over the solar cycle than that put forward by Lean (Geophys. Res. Lett., 27, 2425-2428, 2000). When we inserted this new wavelength dependent solar cycle variation into our 3D CCM we found a different solar cycle dependence of the ozone concentration as a function of altitude from that we derived using the traditional Lean wavelength dependence. Examination of these results led us to realize that the main issue is the solar cycle variation of radiation at wavelengths less than 240 nm versus the solar cycle variation of radiation at wavelengths between 240 nm and 300 nm. The impact of wavelengths less than 240 nm occurs through photodissociation of O2 leading to the production of ozone. The impact of wavelengths between 240 nm and 300 nm occurs through photodissociation of O3 leading to an increase in O atoms and enhanced ozone destruction. Thus one wavelength region gives an in-phase relationship of ozone with the solar cycle while the other wavelength region gives an out-of-phase relationship of ozone with the solar cycle. We have used the Goddard two-dimensional (2D) photochemistry transport model to examine this relationship in more detail. We calculate the altitude and latitude sensitivity of ozone to changes in the solar UV irradiance as a function of wavelength. These results can be used to construct the ozone response to arbitrary wavelength dependencies of solar UV variation.

  12. On the relationship among the Adriatic–Ionian Bimodal Oscillating System (BiOS, the Eastern Mediterranean salinity variations and the Western Mediterranean thermohaline cell

    Directory of Open Access Journals (Sweden)

    M. Gačić

    2012-07-01

    Full Text Available Previous studies have demonstrated that the salinity in the Levantine depends on the intensity of the Atlantic Water inflow. Moreover, its spreading eastward or northward in the Ionian is determined by the Ionian circulation pattern, i.e. by the Adriatic–Ionian Bimodal Oscillating System mechanism. The aim of this paper is to relate salinity variations in the core of the Levantine Intermediate Water flowing through the Sicily Channel to the salt content in the Levantine and its possible impact on the Western Mediterranean Transition (i.e. the sudden salinity increase in the bottom layer of the Algero-Provençal sub-basin occurring since 2004. From the historical dataset MEDAR/MEDATLAS in the Levantine and Northern Ionian, we present evidence of decadal occurrences of extreme salinities associated with the varying flow pattern of Atlantic Water over the last 60 yr. Furthermore, we show that the salinity variations in the two sub-basins are out of phase. High-salinity events in the Levantine are a pre-conditioning for the potential occurrence of the Eastern Mediterranean Transient (EMT. However, there is no firm evidence of occurrences of EMT-like phenomenon prior to the one in the early 1990s. Cross-correlation between the salinity time series in the Levantine and in the Sicily Channel suggests that the travel time of the salinity signal is between 16 and 18 yr. From the timing of the Western Mediterranean Transition and the salinity maximum in the Levantine Intermediate Water core in the Sicily Channel we also conclude that the time interval needed for the signal propagating from the Levantine to reach the bottom of the Algero-Provençal sub-basin is about 27 yr.

  13. Celiac disease T cell epitopes from gamma-gliadins: immunoreactivity depends on the genome of origin, transcript frequency, and flanking protein variation

    NARCIS (Netherlands)

    Salentijn, E.M.J.; Mitea, D.C.; Goryunova, S.V.; Meer, van der I.M.; Padioleau, I.; Gilissen, L.J.W.J.; Koning, de F.; Smulders, M.J.M.

    2012-01-01

    Background - Celiac disease (CD) is caused by an uncontrolled immune response to gluten, a heterogeneous mixture of wheat storage proteins. The CD-toxicity of these proteins and their derived peptides is depending on the presence of specific T-cell epitopes (9-mer peptides; CD epitopes) that mediate

  14. Non-invasive in-cell determination of free cytosolic [NAD+]/[NADH] ratios using hyperpolarized glucose show large variations in metabolic phenotypes

    DEFF Research Database (Denmark)

    Christensen, Caspar Elo; Karlsson, Magnus; Winther, Jakob R.;

    2014-01-01

    Accumulating evidence suggest that the pyridine nucleotide NAD has far wider biological functions than its classical role in energy metabolism. NAD is used by hundreds of enzymes that catalyse substrate oxidation and as such it plays a key role in various biological processes such as aging, cell...

  15. Impedance Spectroscopic Study of p-i-n Type a-Si Solar Cell by Doping Variation of p-Type Layer

    Directory of Open Access Journals (Sweden)

    Sunhwa Lee

    2012-01-01

    Full Text Available We investigated p-i-n type amorphous silicon (a-Si solar cell where the diborane flow rate of the p-type layer was varied and the solar cell was measured static/dynamic characteristics. The p/i interface of the thin film amorphous silicon solar cells was studied in terms of the coordination number of boron atoms in the p layer. p-type layer and p/i interface properties were obtained from the X-ray photoelectron spectroscopy (XPS and impedance spectroscopy. One of the solar cells shows open circuit voltage (oc=880 mV, short circuit current density (sc=14.21 mA/cm2, fill factor (FF=72.03%, and efficiency (=8.8% while the p-type layer was doped with 0.1%. The impedance spectroscopic measurement showed that the diode ideality factor and built-in potential changed with change in diborane flow rate.

  16. Surfactant protein D, Club cell protein 16, Pulmonary and activation-regulated chemokine, C-reactive protein, and Fibrinogen biomarker variation in chronic obstructive lung disease

    DEFF Research Database (Denmark)

    Johansson, Sofie Lock; Vestbo, J.; Sorensen, G. L.

    2014-01-01

    assessment of patients, prediction of risk, and guidance of treatment. The aim of this review is to provide a comprehensive summary of observations for a selection of recently investigated pulmonary inflammatory biomarkers (Surfactant protein D (SP-D), Club cell protein 16 (CC-16), and Pulmonary and...

  17. Studies of variation in inherent sensitivities to radiation, 5-fluorouracil and methotrexate in a series of human and murine tumor cell lines in vitro

    International Nuclear Information System (INIS)

    Clinical studies have reported reduced response rates to subsequent chemotherapy in certain tumors recurring after radiotherapy. These authors have investigated whether there are any correlations between radiation and drug responses in vitro using a range of murine and human tumor cell lines. They have compared sensitivities to X-irradiation and to 24 hr exposures to two widely used antitumor drugs, methotrexate and 5-fluorouracil. The 4 murine lines selected showed a range of radiation responses with Do values of 0.48-0.76 Gy. Methotrexate sensitivities also exhibited an 800-fold difference which appeared to correlate inversely with radiation response. Sensitivity to 5-FU was less variable in these cells and was unrelated to radiation response. In contrast, in the human lines tested, no correlations were observed between drug sensitivities and radiation response. The six lines tested showed a range of radiation responses with Do values of 0.66-1.59 Gy. Methotrexate sensitivities ranged only over a 150-fold concentration but, contrasting with data from the murine cells, no correlation with radiation response was apparent. Similarly, no correlations between response to 5-fluorouracil and radiation or 5-fluorouracil and methotrexate were noted, which is inconsistent with results using murine cells

  18. Studying Variation in Tunes

    NARCIS (Netherlands)

    Janssen, B.; van Kranenburg, P.

    2014-01-01

    Variation in music can be caused by different phenomena: conscious, creative manipulation of musical ideas; but also unconscious variation during music recall. It is the latter phenomenon that we wish to study: variation which occurs in oral transmission, in which a melody is taught without the help

  19. Interannual Variations of MLS Carbon Monoxide Induced by Solar Cycle

    Science.gov (United States)

    Lee, Jae N.; Wu, Dong L.; Ruzmaikin, Alexander

    2013-01-01

    More than eight years (2004-2012) of carbon monoxide (CO) measurements from the Aura Microwave Limb Sounder (MLS) are analyzed. The mesospheric CO, largely produced by the carbon dioxide (CO2) photolysis in the lower thermosphere, is sensitive to the solar irradiance variability. The long-term variation of observed mesospheric MLS CO concentrations at high latitudes is likely driven by the solar-cycle modulated UV forcing. Despite of different CO abundances in the southern and northern hemispheric winter, the solar-cycle dependence appears to be similar. This solar signal is further carried down to the lower altitudes by the dynamical descent in the winter polar vortex. Aura MLS CO is compared with the Solar Radiation and Climate Experiment (SORCE) total solar irradiance (TSI) and also with the spectral irradiance in the far ultraviolet (FUV) region from the SORCE Solar-Stellar Irradiance Comparison Experiment (SOLSTICE). Significant positive correlation (up to 0.6) is found between CO and FUVTSI in a large part of the upper atmosphere. The distribution of this positive correlation in the mesosphere is consistent with the expectation of CO changes induced by the solar irradiance variations.

  20. Elderly men have low levels of anti-Mullerian hormone and inhibin B, but with high interpersonal variation: a cross-sectional study of the sertoli cell hormones in 615 community-dwelling men.

    Directory of Open Access Journals (Sweden)

    Yih Harng Chong

    Full Text Available The Sertoli cells of the testes secrete anti-Müllerian hormone (Müllerian inhibiting Substance, AMH and inhibin B (InhB. AMH triggers the degeneration of the uterine precursor in male embryos, whereas InhB is part of the gonadal-pituitary axis for the regulation of sperm production in adults. However, both hormones are also putative regulators of homeostasis, and age-related changes in these hormones may therefore be important to the health status of elderly men. The levels of AMH in elderly men are unknown, with limited information being available about age-related changes in InhB. We have therefore used ELISAs to measure Sertoli cell hormone levels in 3 cohorts of community-dwelling men in New Zealand. In total, 615 men were examined, 493 of which were aged 65 or older. Serum AMH and InhB levels inversely correlated with age in men older than 50 years (p<0.001 but not in the younger men. A minority of elderly men had undetectable levels of AMH and InhB. The variation in hormone levels between similarly aged men increased with the age of men. AMH and InhB partially correlated with each other as expected (r = 0.48, p<0.001. However, the ratio of the two Sertoli hormones varied significantly between men, with this variation increasing with age. Elderly men selected for the absence of cardiovascular disease had AMH levels similar to those of young men whereas their InhB levels did not differ from aged-matched controls. These data suggests that Sertoli cell number and function changes with age, but with the extent and nature of the changes varying between men.

  1. Clonal variation of DNA repair in a human glioma cell line This study was supported by the Cancer Research Campaign and the Bob Champion Cancer Trust

    International Nuclear Information System (INIS)

    Clonal heterogeneity in response to ionizing radiation was found for a human glioma cell line, IN859. The authors have investigated the most sensitive clone, the most resistant clone and the parent line for differences in DNA repair fidelity using the method of plasmid reconstitution. Significant differences in repair fidelity were found between the two clones, and between the sensitive clone and the parent line. The resistant clone and the parent lines showed the greater repair fidelity. A comparison of two different restriction enzymes, which cleave the plasmid with blunt or cohesive-ended double-strand breaks, did not reveal differences in repair fidelity. Equal numbers of plasmids were integrated in each cell line, but the sensitive clone showed a higher frequency of misrepair of cleaved plasmid. Misrepair was characterized by partial or complete loss of sequence at the site of plasmid cleavage. It is concluded that the radiosensitive clone exhibits increased misrepair. (author). 15 refs.; 5 figs.; 2 tabs

  2. Age and CD161 Expression Contribute to Inter-Individual Variation in Interleukin-23 Response in CD8+ Memory Human T Cells

    OpenAIRE

    Hui Shen; Wei Zhang; Clara Abraham; Judy H Cho

    2013-01-01

    The interleukin-23 (IL-23) pathway plays a critical role in the pathogenesis of multiple chronic inflammatory disorders, however, inter-individual variability in IL-23-induced signal transduction in circulating human lymphocytes has not been well-defined. In this study, we observed marked, reproducible inter-individual differences in IL-23 responsiveness (measured by STAT3 phosphorylation) in peripheral blood CD8+CD45RO+ memory T and CD3+CD56+ NKT cells. Age, but not gender, was a significant...

  3. Genome-wide immunity studies in the rabbit: transcriptome variations in peripheral blood mononuclear cells after in vitro stimulation by LPS or PMA-Ionomycin

    OpenAIRE

    Jacquier, Vincent; Estellé, Jordi; Schmaltz-Panneau, Barbara; Lecardonnel, Jerôme,; Moroldo, Marco; Lemonnier, Gaetan; Turner-Maier, Jason; Duranthon, Veronique; Oswald, Isabelle; Gidenne, Thierry

    2015-01-01

    BackgroundOur purpose was to obtain genome-wide expression data for the rabbit species on the responses of peripheral blood mononuclear cells (PBMCs) after in vitro stimulation by lipopolysaccharide (LPS) or phorbol myristate acetate (PMA) and ionomycin. This transcriptome profiling was carried out using microarrays enriched with immunity-related genes, and annotated with the most recent data available for the rabbit genome.ResultsThe LPS affected 15 to 20 times fewer genes than PMA-Ionomycin...

  4. Genome-wide immunity studies in the rabbit: transcriptome variations in peripheral blood mononuclear cells after in vitro stimulation by LPS or PMA-Ionomycin

    OpenAIRE

    Jacquier, Vincent; Estellé, Jordi; Schmaltz-Panneau, Barbara; Lecardonnel, Jérôme; Moroldo, Marco; Lemonnier, Gaëtan; Turner-Maier, Jason; Duranthon, Véronique; Oswald, Isabelle P.; Gidenne, Thierry; Rogel-Gaillard, Claire

    2015-01-01

    Background Our purpose was to obtain genome-wide expression data for the rabbit species on the responses of peripheral blood mononuclear cells (PBMCs) after in vitro stimulation by lipopolysaccharide (LPS) or phorbol myristate acetate (PMA) and ionomycin. This transcriptome profiling was carried out using microarrays enriched with immunity-related genes, and annotated with the most recent data available for the rabbit genome. Results The LPS affected 15 to 20 times fewer genes than PMA-Ionomy...

  5. Genetic variation in CD36, HBA, NOS3 and VCAM1 is associated with chronic haemolysis level in sickle cell anaemia: a longitudinal study.

    Science.gov (United States)

    Coelho, Andreia; Dias, Alexandra; Morais, Anabela; Nunes, Baltazar; Ferreira, Emanuel; Picanço, Isabel; Faustino, Paula; Lavinha, João

    2014-03-01

    Chronic haemolysis stands out as one of the hallmarks of sickle cell anaemia, a clinically heterogeneous autosomal recessive monogenic anaemia. However, the genetic architecture of this sub-phenotype is still poorly understood. Here, we report the results of an association study between haemolysis biomarkers (serum LDH, total bilirubin and reticulocyte count) and the inheritance of 41 genetic variants of ten candidate genes in a series of 99 paediatric SS patients (median current age of 9.9 yr) followed up in two general hospitals in Greater Lisboa area (median follow-up per patient of 5.0 yr). Although in a large number of tests a seemingly significant (i.e. P haplotype 7 within VCAM1 gene; (ii) a lower total bilirubin was associated with the 3.7-kb deletion at HBA gene, rs2070744_T allele at NOS3 gene, and haplotype 9 within VCAM1 promoter; and (iii) a diminished reticulocyte count was associated with the 3.7-kb deletion at HBA, whereas an increased count was associated with rs1984112_G allele at CD36 gene. On the whole, our findings suggest a complex genetic architecture for the sickle cell anaemia haemolysis process involving multiple pathways, namely control of vascular cell adhesion, NO synthesis and erythrocyte volume and haemoglobinisation. PMID:24168396

  6. Polarizer reflectivity variations

    International Nuclear Information System (INIS)

    On Shiva the beam energy along the chain is monitored using available reflections and/or transmission through beam steering, splitting, and polarizing optics without the intrusion of any additional glass for diagnostics. On the preamp table the diagnostic signal is obtained from the signal transmitted through turning mirrors. At the input of each chain the signal is obtained from the transmission through one of the mirrors used for the chain input alignment sensor (CHIP). At the chain output the transmission through the final turning mirror is used. These diagnostics have proved stable and reliable. However, one of the prime diagnostic locations is at the output of the beta rod. The energy at this location is measured by collecting small reflections from the last polarizer surface of the beta Pockels cell polarizer package. Unfortunately, calibration of this diagnostic has varied randomly, seldom remaining stable for a week or more. The cause of this fluctuation has been investigated for the past year and'it has been discovered that polarizer reflectivity varies with humidity. This report will deal with the possible causes that were investigated, the evidence that humidity is causing the variation, and the associated mechanism

  7. Effects of clonal variation on growth, metabolism, and productivity in response to trophic factor stimulation: a study of Chinese hamster ovary cells producing a recombinant monoclonal antibody

    OpenAIRE

    Dahodwala, Hussain; Nowey, Mark; Mitina, Tatyana; Sharfstein, Susan T.

    2011-01-01

    The growth, metabolism, and productivity of five Chinese hamster ovary (CHO) clones were explored in response to stimulation with insulin (5 mg/L) and LONG®R3IGF-I (20 μg/L or 100 μg/L). All five clones were derived from the same parental CHO cell line (DG44) and produced the same recombinant monoclonal antibody, with varying specific productivities. There was no uniform response among the clones to stimulation with the different trophic factors. One of the high productivity clones (clone D) ...

  8. Light Harvesting and Charge Recombination in CH3NH3PbI3 Perovskite Solar Cells Studied by Hole Transport Layer Thickness Variation.

    Science.gov (United States)

    Marinova, Nevena; Tress, Wolfgang; Humphry-Baker, Robin; Dar, M Ibrahim; Bojinov, Vladimir; Zakeeruddin, Shaik Mohammed; Nazeeruddin, Mohammad Khaja; Grätzel, Michael

    2015-04-28

    A tailored optimization of perovskite solar cells requires a detailed understanding of the processes limiting the device efficiency. Here, we study the role of the hole transport layer (HTL) spiro-MeOTAD and its thickness in a mesoscopic TiO2-based solar cell architecture. We find that a sufficiently thick (200 nm) HTL not only increases the charge carrier collection efficiency but also the light harvesting efficiency. This is due to an enhanced reflection of a smooth HTL/Au-electrode interface. The rough CH3NH3PbI3 perovskite surface requires an HTL thickness of >400 nm to avoid surface recombination and guarantee a high open-circuit voltage. Analyses of the electroluminescence efficiency and the diode ideality factor show that the open-circuit voltage becomes completely limited by trap-assisted recombination in the perovskite for a thick HTL. Thus, spiro-MeOTAD is a very good HTL choice from the device physics' point of view. The fill factor analyzed by the Suns-Voc method is not transport limited, but trap-recombination limited as well. Consequently, a further optimization of the device has to focus on defects in the polycrystalline perovskite film. PMID:25769194

  9. Long-term variation in the ionosphere and lower thermosphere as seen in the geomagnetic solar quiet daily variation

    Science.gov (United States)

    Shinbori, A.; Koyama, Y.; Hori, T.; Nose, M.; Otsuka, Y.

    2015-12-01

    In order to investigate characteristics of the long-term variation in the ionosphere and lower thermosphere, we analyzed the amplitude of geomagnetic solar quiet (Sq) field daily variation using 1-h geomagnetic field data obtained from 69 geomagnetic stations within the period of 1947-2013. In the present data analysis, we took advantage of the Inter-university Upper atmosphere Global Observation NETwork (IUGONET) products (metadata database and analysis software) for finding and handling the long-term observation data obtained at many observatories. The Sq amplitude observed at these geomagnetic stations showed a clear solar activity dependence and tended to be enhanced during each solar maximum phase. The Sq amplitude was the smallest around the minimum of solar cycle 23/24 in 2008-2009. This significant depression implies that the solar extreme ultraviolet (EUV) radiation responsible for ionization of the upper atmosphere decreased during this solar cycle minimum. In order to examine a global distribution of the long-term trend in the Sq amplitude, we derived the residual Sq amplitude from the deviation from the fitting curve between the solar F10.7 index and Sq amplitude. As a result, a majority of the trends in the residual Sq amplitude showed negative values over a wide region. This tendency was relatively strong in Europe, India, the eastern part of Canada, and New Zealand. Moreover, we estimate the neutral wind in the lower thermosphere from the Sq amplitude and height-integrated ionospheric conductivity in order to know the physical mechanism of the long-term trend in the residual Sq amplitude. As a result, the estimated thermospheric zonal and meridional winds showed a seasonal variation with a period of one year or less, but the solar activity dependence was unclear. This result suggests that the solar cycle dependence of the Sq amplitude may be mainly attributed to the variation of the ionospheric conductivity.

  10. Variation of fundamental constants

    CERN Document Server

    Flambaum, V V

    2006-01-01

    We present a review of recent works devoted to the variation of the fine structure constant alpha, strong interaction and fundamental masses. There are some hints for the variation in quasar absorption spectra, Big Bang nucleosynthesis, and Oklo natural nuclear reactor data. A very promising method to search for the variation of the fundamental constants consists in comparison of different atomic clocks. Huge enhancement of the variation effects happens in transition between accidentally degenerate atomic and molecular energy levels. A new idea is to build a ``nuclear'' clock based on the ultraviolet transition between very low excited state and ground state in Thorium nucleus. This may allow to improve sensitivity to the variation up to 10 orders of magnitude! Huge enhancement of the variation effects is also possible in cold atomic and molecular collisions near Feschbach resonance.

  11. Asynchronous Variational Integrators

    OpenAIRE

    Lew, A.; Marsden, J. E.; Ortiz, M.; West, M

    2003-01-01

    We describe a new class of asynchronous variational integrators (AVI) for nonlinear elastodynamics. The AVIs are distinguished by the following attributes: (i) The algorithms permit the selection of independent time steps in each element, and the local time steps need not bear an integral relation to each other; (ii) the algorithms derive from a spacetime form of a discrete version of Hamilton’s variational principle. As a consequence of this variational structure, the algorith...

  12. Variational multiscale models for charge transport

    OpenAIRE

    Wei, Guo-Wei; Zheng, Qiong; Chen, Zhan; Xia, Kelin

    2012-01-01

    This work presents a few variational multiscale models for charge transport in complex physical, chemical and biological systems and engineering devices, such as fuel cells, solar cells, battery cells, nanofluidics, transistors and ion channels. An essential ingredient of the present models, introduced in an earlier paper (Bulletin of Mathematical Biology, 72, 1562-1622, 2010), is the use of differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic ...

  13. Calculus of variations

    CERN Document Server

    Gelfand, I M

    2000-01-01

    Based on a series of lectures given by I. M. Gelfand at Moscow State University, this book actually goes considerably beyond the material presented in the lectures. The aim is to give a treatment of the elements of the calculus of variations in a form both easily understandable and sufficiently modern. Considerable attention is devoted to physical applications of variational methods, e.g., canonical equations, variational principles of mechanics, and conservation laws.The reader who merely wishes to become familiar with the most basic concepts and methods of the calculus of variations need on

  14. Variação da contagem de células somáticas em vacas leiteiras de acordo com patógenos da mastite Somatic cell counts variation in dairy cows according to mastitis pathogens

    Directory of Open Access Journals (Sweden)

    G.N. Souza

    2009-10-01

    Full Text Available Avaliou-se o efeito de patógenos da mastite sobre a contagem de células somáticas (CCS em leite. Foram coletadas 3.987 amostras de leite de 2.657 animais oriundos de 24 rebanhos leiteiros localizados nos estados do Rio de Janeiro e Minas Gerais. As amostras de leite foram usadas para CCS e identificação de patógenos da mastite. Estatísticas descritivas, teste T para amostras independentes e modelo linear generalizado foram usados para análise dos dados. O modelo linear generalizado identificou os efeitos de rebanho, animal dentro de rebanho, ordem de parto, estação do ano e infecção intramamária causada por Streptococcus agalactiae e Streptococcus spp. que não S. agalactiae como significativos na variação da CCS. O efeito de animal dentro de rebanho foi maior que o efeito de rebanho. S. agalactiae foi o patógeno responsável pelo maior aumento da CCS em vacas e apresentou em média 1.520.000 células/mL. Foi observado efeito específico dos patógenos na variação da CCS.The influence of mastitis pathogens on variation of milk somatic cell count (SCC was evaluated. Three thousand nine hundred eighty-seven milk samples were colected from 2,657 dairy cows in 24 herds located in the states of Minas Gerais and Rio de Janeiro. The milk samples were used to SCC and identification of mastitis pathogens. Descriptive statistics, T test for independent samples, and generalized linear model were used to data analysis. The generalized linear model identified the effects of herd, animal within herd, parity, year season, intramammary infection, and infection caused by Streptococcus agalactiae and Streptococcus spp. except S. agalactiae as significant on SCC variation. The effect of animal within herd was higher than the effect of herd. S. agalactiae was the pathogen responsible for higher SCC increasing and presented the average of 1,520,000 cells/mL. The specific effect on SCC variation was observed in the study.

  15. A Solar Cycle Dependence of Nonlinearity in Magnetospheric Activity

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Jay R; Wing, Simon

    2005-03-08

    The nonlinear dependencies inherent to the historical K(sub)p data stream (1932-2003) are examined using mutual information and cumulant based cost as discriminating statistics. The discriminating statistics are compared with surrogate data streams that are constructed using the corrected amplitude adjustment Fourier transform (CAAFT) method and capture the linear properties of the original K(sub)p data. Differences are regularly seen in the discriminating statistics a few years prior to solar minima, while no differences are apparent at the time of solar maximum. These results suggest that the dynamics of the magnetosphere tend to be more linear at solar maximum than at solar minimum. The strong nonlinear dependencies tend to peak on a timescale around 40-50 hours and are statistically significant up to one week. Because the solar wind driver variables, VB(sub)s and dynamical pressure exhibit a much shorter decorrelation time for nonlinearities, the results seem to indicate that the nonlinearity is related to internal magnetospheric dynamics. Moreover, the timescales for the nonlinearity seem to be on the same order as that for storm/ring current relaxation. We suggest that the strong solar wind driving that occurs around solar maximum dominates the magnetospheric dynamics suppressing the internal magnetospheric nonlinearity. On the other hand, in the descending phase of the solar cycle just prior to solar minimum, when magnetospheric activity is weaker, the dynamics exhibit a significant nonlinear internal magnetospheric response that may be related to increased solar wind speed.

  16. Solar cycle dependence of spatial correlation in the solar wind

    OpenAIRE

    Wicks, R. T.; Chapman, S. C.; Dendy, R. O.

    2007-01-01

    We investigate the spatial correlation properties of the solar wind using simultaneous observations by the ACE and WIND spacecraft. We use mutual information as a nonlinear measure of correlation and compare this to linear correlation. We find that the correlation lengthscales of fluctuations in density and magnetic field magnitude vary strongly with the solar cycle, whereas correlation lengths of fluctuations in B field components do not. We find the correlation length of |B| ~ 120 Re at sol...

  17. Somatic Embryogenesis in Peach Palm Using the Thin Cell Layer Technique: Induction, Morpho-histological Aspects and AFLP Analysis of Somaclonal Variation

    Science.gov (United States)

    Steinmacher, D. A.; Krohn, N. G.; Dantas, A. C. M.; Stefenon, V. M.; Clement, C. R.; Guerra, M. P.

    2007-01-01

    Background and Aims The thin cell layer (TCL) technique is based on the use of very small explants and has allowed enhanced in vitro morphogenesis in several plant species. The present study evaluated the TCL technique as a procedure for somatic embryo production and plantlet regeneration of peach palm. Methods TCL explants from different positions in the shoot apex and leaf sheath of peach palm were cultivated in MS culture medium supplemented with 0–600 µm Picloram in the presence of activated charcoal. The production of primary calli and embryogenic calli was evaluated in these different conditions. Histological and amplified fragment length polymorphism (AFLP) analyses were conducted to study in vitro morphogenetic responses and genetic stability, respectively, of the regenerated plantlets. Key Results Abundant primary callus induction was observed from TCLs of the shoot meristem in culture media supplemented with 150–600 µm Picloram (83–97 %, respectively). The production of embryogenic calli depends on Picloram concentration and explant position. The best response observed was 43 % embryogenic callus production from shoot meristem TCL on 300 µm Picloram. In maturation conditions, 34 ± 4 somatic embryos per embryogenic callus were obtained, and 45·0 ± 3·4 % of these fully developed somatic embryos were converted, resulting in plantlets ready for acclimatization, of which 80 % survived. Histological studies revealed that the first cellular division events occurred in cells adjacent to vascular tissue, resulting in primary calli, whose growth was ensured by a meristematic zone. A multicellular origin of the resulting somatic embryos arising from the meristematic zone is suggested. During maturation, histological analyses revealed bipolarization of the somatic embryos, as well as the development of new somatic embryos. AFLP analyses revealed that 92 % of the regenerated plantlets were true to type. The use of TCL explants considerably improves the

  18. Haloarchaeal myovirus φCh1 harbours a phase variation system for the production of protein variants with distinct cell surface adhesion specificities.

    Science.gov (United States)

    Klein, R; Rössler, N; Iro, M; Scholz, H; Witte, A

    2012-01-01

    The φCh1 myovirus, which infects the haloalkaliphilic archaeon Natrialba magadii, contains an invertible region that comprises the convergent open reading frames (ORFs) 34 and 36, which code for the putative tail fibre proteins gp34 and gp36 respectively. The inversion leads to an exchange of the C-termini of these proteins, thereby creating different types of tail fibres. Gene expression experiments revealed that only ORF34 is transcribed, indicating that φCh1 produces tail fibre proteins exclusively from this particular ORF. Only one of the two types of tail fibres encoded by ORF34 is able to bind to Nab. magadii in vitro. This is reflected by the observation that during the early phases of the infection cycle, the lysogenic strain L11 carries its invertible region exclusively in the orientation that produces that specific type of tail fibre. Obviously, Nab. magadii can only be infected by viruses carrying this particular type of tail fibre. By mutational analysis, the binding domain of gp34 was localized to the C-terminal part of the protein, particularly to a galactose-binding domain. The involvement of galactose residues in cell adhesion was supported by the observation that the addition of α-D-galactose to purified gp34 or whole virions prevented their attachment to Nab. magadii. PMID:22111759

  19. The Variational Fair Autoencoder

    NARCIS (Netherlands)

    C. Louizos; K. Swersky; Y. Li; M. Welling; R. Zemel

    2016-01-01

    We investigate the problem of learning representations that are invariant to certain nuisance or sensitive factors of variation in the data while retaining as much of the remaining information as possible. Our model is based on a variational autoencoding architecture with priors that encourage indep

  20. Clustering in Cell Cycle Dynamics with General Response/Signaling Feedback

    CERN Document Server

    Young, Todd; Buckalew, Richard; Moses, Gregory; Boczko, Erik; 10.1016/j.jtbi.2011.10.002.

    2011-01-01

    Motivated by experimental and theoretical work on autonomous oscillations in yeast, we analyze ordinary differential equations models of large populations of cells with cell-cycle dependent feedback. We assume a particular type of feedback that we call Responsive/Signaling (RS), but do not specify a functional form of the feedback. We study the dynamics and emergent behaviour of solutions, particularly temporal clustering and stability of clustered solutions. We establish the existence of certain periodic clustered solutions as well as "uniform" solutions and add to the evidence that cell-cycle dependent feedback robustly leads to cell-cycle clustering. We highlight the fundamental differences in dynamics between systems with negative and positive feedback. For positive feedback systems the most important mechanism seems to be the stability of individual isolated clusters. On the other hand we find that in negative feedback systems, clusters must interact with each other to reinforce coherence. We conclude fr...

  1. The retinoblastoma-susceptibility gene product becomes phosphorylated in multiple stages during cell cycle entry and progression.

    OpenAIRE

    DeCaprio, J A; Furukawa, Y.; Ajchenbaum, F; Griffin, J D; Livingston, D M

    1992-01-01

    The retinoblastoma-susceptibility gene product (RB) undergoes cell cycle-dependent phosphorylation and dephosphorylation. We characterized RB phosphorylation after mitogenic stimulation of primary human T lymphocytes, initially arrested in the G0 state. RB is phosphorylated in at least three steps when T cells are driven into the cell cycle. The first event occurs during mid G1 phase, the second during S phase, and the third in G2/M. Tryptic phosphopeptide mapping indicates that the different...

  2. Hydrogen Peroxide-Mediated Growth of the Root System Occurs via Auxin Signaling Modification and Variations in the Expression of Cell-Cycle Genes in Rice Seedlings Exposed to Cadmium Stress

    Institute of Scientific and Technical Information of China (English)

    Feng-Yun Zhao; Ming-Ming Han; Shi-Yong Zhang; Kai Wang; Cheng-Ren Zhang; Tao Liu; Wen Liu

    2012-01-01

    The link between root growth,H2O2,auxin signaling,and the cell cycle in cadmium (Cd)-stressed rice (Oryza sativa L.cv.Zhonghua No.11) was analyzed in this study.Exposure to Cd induced a significant accumulation of Cd,but caused a decrease in zinc (Zn) content which resulted from the decreased expression of OsHMA9 and OsZIP.Analysis using a Cd-specific probe showed that Cd was mainly localized in the meristematic zone and vascular tissues.Formation and elongation of the root system were significantly promoted by 3-amino-1,2,4-triazole (AT),but were markedly inhibited by N,N'-dimethylthiourea (DMTU) under Cd stress.The effect of H2O2 on Cd-stressed root growth was further confirmed by examining a gain-of-function rice mutant (carrying catalase1 and glutathione-S-transferase) in the presence or absence of diphenylene iodonium.DR5-GUS staining revealed close associations between H2O2 and the concentration and distribution of auxin.H2O2 affected the expression of key genes,including OsYUCCA,OsPIN,OsARF,and OsIAA,in the auxin signaling pathway in Cd-treated plants.These results suggest that H2O2 functions upstream of the auxin signaling pathway.Furthermore,H2O2 modified the expression of cell-cycle genes in Cd-treated roots.The effects of H2O2 on root system growth are therefore linked to auxin signal modification and to variations in the expression of cell-cycle genes in Cd-stressed rice.A working model for the effects of H2O2 on Cd-stressed root system growth is thus proposed and discussed in this paper.

  3. Ensembl variation resources

    Directory of Open Access Journals (Sweden)

    Marin-Garcia Pablo

    2010-05-01

    Full Text Available Abstract Background The maturing field of genomics is rapidly increasing the number of sequenced genomes and producing more information from those previously sequenced. Much of this additional information is variation data derived from sampling multiple individuals of a given species with the goal of discovering new variants and characterising the population frequencies of the variants that are already known. These data have immense value for many studies, including those designed to understand evolution and connect genotype to phenotype. Maximising the utility of the data requires that it be stored in an accessible manner that facilitates the integration of variation data with other genome resources such as gene annotation and comparative genomics. Description The Ensembl project provides comprehensive and integrated variation resources for a wide variety of chordate genomes. This paper provides a detailed description of the sources of data and the methods for creating the Ensembl variation databases. It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically. It gives a good overview of the variation resources and future plans for expanding the variation data within Ensembl. Conclusions Variation data is an important key to understanding the functional and phenotypic differences between individuals. The development of new sequencing and genotyping technologies is greatly increasing the amount of variation data known for almost all genomes. The Ensembl variation resources are integrated into the Ensembl genome browser and provide a comprehensive way to access this data in the context of a widely used genome bioinformatics system. All Ensembl data is freely available at http://www.ensembl.org and from the public MySQL database server at ensembldb.ensembl.org.

  4. Theory of conjectural variations

    CERN Document Server

    Jean-Marie, Alain

    2004-01-01

    We have witnessed in recent years a revival of Conjectural Variations in Game Theory. This reincarnation of an old idea, using a dynamic point of view, aims at combining the adequacy with facts to the requirements of a firmly grounded theory. This book presents, for the first time, a comprehensive account of conjectural variations equilibria in their static inceptions, featuring new comparative results of equilibria with regard to efficiency. It then describes several advances in Dynamic Game Theory, allowing to understand Conjectural Variations Equilibria as dynamic equilibria. The question o

  5. Integrated single-cell analysis shows Pichia pastoris secretes protein stochastically.

    OpenAIRE

    Love, Kerry Routenberg; Panagiotou, Vasiliki; Jiang, Bo; Stadheim, Terrance A; Love, J. Christopher

    2010-01-01

    The production of heterologous proteins by secretion from cellular hosts is an important determinant for the cost of biotherapeutics. A single-cell analytical method called microengraving was used to examine the heterogeneity in secretion by the methylotrophic yeast Pichia pastoris. We show that constitutive secretion of a human Fc fragment by P. pastoris is not cell-cycle dependent, but rather fluctuates between states of high and low productivity in a stochastic manner.

  6. Quantum variational calculus

    CERN Document Server

    Malinowska, Agnieszka B

    2014-01-01

    This Brief puts together two subjects, quantum and variational calculi by considering variational problems involving Hahn quantum operators. The main advantage of its results is that they are able to deal with nondifferentiable (even discontinuous) functions, which are important in applications. Possible applications in economics are discussed. Economists model time as continuous or discrete. Although individual economic decisions are generally made at discrete time intervals, they may well be less than perfectly synchronized in ways discrete models postulate. On the other hand, the usual assumption that economic activity takes place continuously, is nothing else than a convenient abstraction that in many applications is far from reality. The Hahn quantum calculus helps to bridge the gap between the two families of models: continuous and discrete. Quantum Variational Calculus is self-contained and unified in presentation. It provides an opportunity for an introduction to the quantum calculus of variations fo...

  7. Variational Inequalities with Applications

    CERN Document Server

    Sofonea, Mircea

    2009-01-01

    Motivated by stimulating problems in contact mechanics, emphasizing antiplane frictional contact with linearly elastic and viscoelastic materials, this book focuses on the essentials with respect to the qualitative aspects of several classes of variational inequalities (VIs)

  8. Variational principles in physics

    CERN Document Server

    Basdevant, Jean-Louis

    2007-01-01

    Optimization under constraints is an essential part of everyday life. Indeed, we routinely solve problems by striking a balance between contradictory interests, individual desires and material contingencies. This notion of equilibrium was dear to thinkers of the enlightenment, as illustrated by Montesquieu’s famous formulation: "In all magistracies, the greatness of the power must be compensated by the brevity of the duration." Astonishingly, natural laws are guided by a similar principle. Variational principles have proven to be surprisingly fertile. For example, Fermat used variational methods to demonstrate that light follows the fastest route from one point to another, an idea which came to be known as Fermat’s principle, a cornerstone of geometrical optics. Variational Principles in Physics explains variational principles and charts their use throughout modern physics. The heart of the book is devoted to the analytical mechanics of Lagrange and Hamilton, the basic tools of any physicist. Prof. Basdev...

  9. Generalized quasi variational inequalities

    Energy Technology Data Exchange (ETDEWEB)

    Noor, M.A. [King Saud Univ., Riyadh (Saudi Arabia)

    1996-12-31

    In this paper, we establish the equivalence between the generalized quasi variational inequalities and the generalized implicit Wiener-Hopf equations using essentially the projection technique. This equivalence is used to suggest and analyze a number of new iterative algorithms for solving generalized quasi variational inequalities and the related complementarity problems. The convergence criteria is also considered. The results proved in this paper represent a significant improvement and refinement of the previously known results.

  10. Variational time integrators

    OpenAIRE

    Lew, A.; Marsden, J. E.; Ortiz, M.; West, M

    2004-01-01

    The purpose of this paper is to review and further develop the subject of variational integration algorithms as it applies to mechanical systems of engineering interest. In particular, the conservation properties of both synchronous and asynchronous variational integrators (AVIs) are discussed in detail. We present selected numerical examples which demonstrate the excellent accuracy, conservation and convergence characteristics of AVIs. In these tests, AVIs are found to result in substantial ...

  11. Chromatic variations suppress suprathreshold brightness variations.

    Science.gov (United States)

    Kingdom, Frederick A A; Bell, Jason; Gheorghiu, Elena; Malkoc, Gokhan

    2010-01-01

    Most objects in natural scenes are suprathreshold in both color (chromatic) and luminance contrast. How salient is each dimension? We have developed a novel method employing a stimulus similar to that used by B. C. Regan and J. D. Mollon (1997) who studied the relative saliencies of the two chromatic cardinal directions. Our stimuli consist of left- and right-oblique modulations of color and/or luminance defined within a lattice of circles. In the "separated" condition, the two modulations were presented separately as forced-choice pairs, and the task was to indicate which was more salient. In the "combined" condition, the two orthogonal-in-orientation modulations were added, and the task was to indicate the more salient orientation. The ratio of color to luminance contrast at the PSE was calculated for both conditions. Across color directions, 48% more luminance contrast relative to color contrast was required to achieve a PSE in the "combined" compared to the "separated" condition. A second experiment showed that the PSE difference was due to the luminance being masked by the color, rather than due to superior color grouping. We conclude that suprathreshold brightness variations are masked by suprathreshold color variations. PMID:20884478

  12. Variation in Metaphor Variation in Metaphor

    Directory of Open Access Journals (Sweden)

    Zóltan Kövecses

    2010-05-01

    Full Text Available

    Cognitive linguists have so far paid a great deal of attention to the emarkable universality of many conceptual metaphors. However, their theories fail to account for the equally impressive diversity of metaphorical conceptualization both across and within cultures. The present paper is an attempt to lay down the foundations of a theory of metaphor that is capable of simultaneously accounting for both universality and variation in metaphor.

     

    Cognitive linguists have so far paid a great deal of attention to the emarkable universality of many conceptual metaphors. However, their theories fail to account for the equally impressive diversity of metaphorical conceptualization both across and within cultures. The present paper is an attempt to lay down the foundations of a theory of metaphor that is capable of simultaneously accounting for both universality and variation in metaphor.

  13. Bordetella bronchiseptica phase variation induced by crystal violet.

    OpenAIRE

    Ishikawa, H.; Isayama, Y

    1986-01-01

    A method for effective induction of phase variation in Bordetella bronchiseptica by treatment with crystal violet (CV) is presented. When grown in CV-broth, phase I cells dissociated into three serial phases. Appearance of variant cells was observed simultaneously with the beginning of cell multiplication. The maximum effect of CV was obtained at a concentration of 8 micrograms/ml, when the proportion of variants in the population reached 100%. The main factors which affected phase variation ...

  14. Distinct Regulatory Changes Underlying Differential Expression of TEOSINTE BRANCHED1-CYCLOIDEA-PROLIFERATING CELL FACTOR Genes Associated with Petal Variations in Zygomorphic Flowers of Petrocosmea spp. of the Family Gesneriaceae.

    Science.gov (United States)

    Yang, Xia; Zhao, Xiao-Ge; Li, Chao-Qun; Liu, Jing; Qiu, Zhi-Jing; Dong, Yang; Wang, Yin-Zheng

    2015-11-01

    CYCLOIDEA (CYC)-like genes, belonging to the plant-specific TCP transcription factor family that is named after TEOSINTE BRANCHED1 (TB1) from maize (Zea mays), CYC from Antirrhinum majus, and the PROLIFERATING CELL FACTORS (PCF) from rice (Oryza sativa), have conserved dorsal identity function in patterning floral zygomorphy mainly through specific expression in dorsal petals of a flower. Their expression changes are usually related to morphological diversity of zygomorphic flowers. However, it is still a challenge to elucidate the molecular mechanism underlying their expression differentiation. It is also unknown whether CINCINNATA (CIN)-like TCP genes, locally controlling cell growth and proliferation, are involved in the evolution of floral zygomorphy. To address these questions, we selected two closely related species, i.e. Petrocosmea glabristoma and Petrocosmea sinensis, with distinct petal morphology to conduct expression, hybridization, mutant, and allele-specific expression analyses. The results show that the size change of the dorsal petals between the two species is mainly mediated by the expression differentiation of CYC1C and CYC1D, while the shape variation of all petals is related to the expression change of CIN1. In reciprocal F1 hybrids, the expression of CYC1C, CYC1D, and CIN1 conforms to an additive inheritance mode, consistent with the petal phenotypes of hybrids. Through allele-specific expression analyses, we find that the expression differentiation of these TCP genes is underlain by distinctly different types of regulatory changes. We suggest that highly redundant paralogs with identical expression patterns and interspecific expression differentiation may be controlled by remarkably different regulatory pathways because natural selection may favor different regulatory modifications rather than coding sequence changes of key developmental genes in generating morphological diversity. PMID:26351309

  15. 前列腺癌细胞内冬凌草甲素的浓度动态变化%Intracellular Dynamic Variation of Oridonin in Prostate Cancer Cells

    Institute of Scientific and Technical Information of China (English)

    袁晓勇; 赵永星; 孙倩; 刘丹杏

    2011-01-01

    建立了高效液相色谱法测定人前列腺癌PC-3细胞内的冬凌草甲素.采用C色谱柱,以甲醇-水(53:47)为流动相,检测波长238 nm.细胞内冬凌草甲素在10~300 ng/ml浓度范围内线性关系良好,绝对回收率为77.79%~81.32%,RSD为3.29%~4.09%;日内和日间RSD均小于8%.人前列腺癌PC-3细胞与冬凌草甲素溶液或冬凌草甲素纳米粒孵育后,采用该法测定胞内药物浓度动态变化过程.结果表明,纳米粒可显著提高细胞内冬凌草甲素的聚集并减慢其消除.%An HPLC method was established for the determination of oridonin in human prostate cancer cells (PC-3). A C18 column was used with the mobile phase of methanol-water (53: 47) at the detection wavelength of 238 nm. The calibration curve was linear in the concentration range of 10 - 300 ng/ml. The absolute recoveries were 77.79% - 81.32%, with RSDs of 3.29% - 4.09%. The inter- and intra-day RSDs were less than 8%. PC-3 Cells were treated with oridonin solution or oridonin nanoparticles and the intracellular dynamic variation of oridonin was determined by HPLC. The results showed that oridonin nanoparticles could improve intracellular accumulation of oridonin and decrease elimination of oridonin compared with that of oridonin solution.

  16. Aerotactic Cell Density Variations in Bacterial Turbulence

    Science.gov (United States)

    Fernandez, Vicente; Smriga, Steven; Menolascina, Filippo; Rusconi, Roberto; Stocker, Roman

    2015-11-01

    Concentrated suspensions of motile bacteria such as Bacillus subtilis exhibit group dynamics much larger than the scale of an individual bacterium, visual similar to high Reynolds number turbulence. These suspensions represent a microscale realization of active matter. Individually, B. subtilis are also aerotactic, and will accumulate near oxygen sources. Using a microfluidic device for generating oxygen gradients, we investigate the relationship between individuals' attraction to oxygen and the collective motion resultant from hydrodynamic interactions. We focus on changes in density revealed by a fluorescently labeled sub-population of B. subtilis in the dense suspension. This approach allows us to examine changes in density during the onset of collective motion as well as fully developed bacterial turbulence.

  17. Mediterranean sea level variations.

    Science.gov (United States)

    Vigo, I.; Sánchez Reales, J. M.; García, D.; Chao, B. F.

    2009-04-01

    In this work we report an updated study of the sea level variations for the Mediterranean sea for the period from October 1992 to January 2008. The study addresses two mayor issues: (i)The analysis of the spatial and temporal variability of sea surface height (SSH) from radar altimetry measurements (from TOPEX/Poseidon (T/P) + Jason-1, etc.). We use EOF analysis to explain most of its interannual variation, and how the different basins interact. (ii) The analysis of dynamics and balance of water mass transport for the whole period. We estimate the steric SSH by combining the steric SSH estimated from temperature and salt profiles simulated by the ECCO model with time-variable gravity (TVG) data (from GRACE) for the Mediterranean Sea. The estimated steric SSH together with the SSH obtained from altimetry allow for a more realistic estimation of the water mass variations in the Mediterranean for the whole period.

  18. Variation and Synthetic Speech

    CERN Document Server

    Miller, C; Massey, N; Miller, Corey; Karaali, Orhan; Massey, Noel

    1997-01-01

    We describe the approach to linguistic variation taken by the Motorola speech synthesizer. A pan-dialectal pronunciation dictionary is described, which serves as the training data for a neural network based letter-to-sound converter. Subsequent to dictionary retrieval or letter-to-sound generation, pronunciations are submitted a neural network based postlexical module. The postlexical module has been trained on aligned dictionary pronunciations and hand-labeled narrow phonetic transcriptions. This architecture permits the learning of individual postlexical variation, and can be retrained for each speaker whose voice is being modeled for synthesis. Learning variation in this way can result in greater naturalness for the synthetic speech that is produced by the system.

  19. Essential Variational Poisson Cohomology

    Science.gov (United States)

    De Sole, Alberto; Kac, Victor G.

    2012-08-01

    In our recent paper "The variational Poisson cohomology" (2011) we computed the dimension of the variational Poisson cohomology {{{H}^bullet_K({V})}} for any quasiconstant coefficient ℓ × ℓ matrix differential operator K of order N with invertible leading coefficient, provided that {{{V}}} is a normal algebra of differential functions over a linearly closed differential field. In the present paper we show that, for K skewadjoint, the {{{Z}}} -graded Lie superalgebra {{{H}^bullet_K({V})}} is isomorphic to the finite dimensional Lie superalgebra {{widetilde{H}(Nell,S)}} . We also prove that the subalgebra of "essential" variational Poisson cohomology, consisting of classes vanishing on the Casimirs of K, is zero. This vanishing result has applications to the theory of bi-Hamiltonian structures and their deformations. At the end of the paper we consider also the translation invariant case.

  20. Asynchronous Variational Contact Mechanics

    CERN Document Server

    Vouga, Etienne; Tamstorf, Rasmus; Grinspun, Eitan

    2010-01-01

    An asynchronous, variational method for simulating elastica in complex contact and impact scenarios is developed. Asynchronous Variational Integrators (AVIs) are extended to handle contact forces by associating different time steps to forces instead of to spatial elements. By discretizing a barrier potential by an infinite sum of nested quadratic potentials, these extended AVIs are used to resolve contact while obeying momentum- and energy-conservation laws. A series of two- and three-dimensional examples illustrate the robustness and good energy behavior of the method.

  1. Monitoring concentrations of greenhouse gases based on multi-reflected cell FTIR and variation analysis%反射式FTIR监测温室气体浓度及其变化规律

    Institute of Scientific and Technical Information of China (English)

    冯明春; 焦洋; 刘文清; 高闽光; 徐亮; 程巳阳; 童晶晶; 金岭; 李胜; 魏秀丽; 李相贤

    2011-01-01

    工业革命以来,温室效应引起的全球气候变迁问题越来越受到人们的关注.人类活动相关的主要温室气体是CO2,CH4,N2O和CO,对其浓度进行连续测量,获取浓度随时间的变化规律对大气环境科学具有重要意义.使用多次反射池FTIR系统在浙江地区对这四种气体进行了监测,通过对测量的气体吸收光谱进行光谱定量分析,获取了待测组分的浓度信息,并对其变化规律进行了分析.同时对仪器的性能进行了检测,结果表明,多次反射池FTIR是进行环境气体监测的一种快速有效直接的监测手段.%Since the industrial revolution, global climate change problems caused by greenhouse effect are getting more and more concern. CO2. CH4, N2 0 and CO related to human activities are main greenhouse gases in the atmosphere. It is of important significance for atmospheric environmental science to access greenhouse gases' concentration variation with time. CO2 ,CH4 ,N2O and CO are continuously monitored by using multi-reflected white cell Fourier transform infrared (FTIR) spectrometer at a specific site in Zhejiang. The concentration of components information is obtained by measuring gas atmospheric absorption spectra and concentration variation is also analyzed. In the meantime the performance of instrument is tested and the results show that multi-reflected FTIR of environmental gases monitoring is a fast,direct and effective means of monitoring.

  2. Natural 14C variations

    International Nuclear Information System (INIS)

    This thesis deals with the natural variations in the atmospheric 14C activity, their geophysical origin and their impact on radiocarbon dating. Studies confirm the idea that one is dealing with a mechanism of a certain regularity. The correlation between a 14C variation during the Little Ice Age and the absence of sunspots on the solar surface suggest the sun to be responsible for some kind of modulation of the galactic cosmic ray spectrum. The background of a changing natural 14C level is relevant when studying the antropogenic perturbation of the atmospheric 14C concentration by the addition of CO2 from fossil fuel combustion. The results presented point to a Suess effect over the past 150 years of about 20 per thousand, but also show a local dilution effect. If this local effect is present over large continental parts of the Northern Hemisphere this will put limits to the use of tree ring 14C measurements for testing carbon reservoir models. Finally the influence of 14C variations upon the interpretations of 14C dates for archaeological and geological purposes has been investigated. It is shown that care must be taken especially in the interpretation of highly accurate 14C data of material only covering a few years of growth. One geological example illustrates that 14C variations can easily be interpretated as alternating fast and slow rises of the sea level. (Auth.)

  3. Variational transition state theory

    Energy Technology Data Exchange (ETDEWEB)

    Truhlar, D.G. [Univ. of Minnesota, Minneapolis (United States)

    1993-12-01

    This research program involves the development of variational transition state theory (VTST) and semiclassical tunneling methods for the calculation of gas-phase reaction rates and selected applications. The applications are selected for their fundamental interest and/or their relevance to combustion.

  4. Seasonal Variation in Epidemiology

    Science.gov (United States)

    Marrero, Osvaldo

    2013-01-01

    Seasonality analyses are important in medical research. If the incidence of a disease shows a seasonal pattern, then an environmental factor must be considered in its etiology. We discuss a method for the simultaneous analysis of seasonal variation in multiple groups. The nuts and bolts are explained using simple trigonometry, an elementary…

  5. Bounded variation and around

    CERN Document Server

    Appell, Jürgen; Merentes Díaz, Nelson José

    2013-01-01

    This monographis a self-contained exposition of the definition and properties of functionsof bounded variation and their various generalizations; the analytical properties of nonlinear composition operators in spaces of such functions; applications to Fourier analysis, nonlinear integral equations, and boundary value problems. The book is written for non-specialists. Every chapter closes with a list of exercises and open problems.

  6. Variation and Linguistic Theory.

    Science.gov (United States)

    Bailey, Charles-James N.

    This volume presents principles and models for describing language variation, and introduces a time-based, dynamic framework for linguistic description. The book first summarizes some of the problems of grammatical description encountered from Saussure through the present and then outlines possibilities for new descriptions of language which take…

  7. Diurnal variations of Titan

    Science.gov (United States)

    Cui, J.; Galand, M.; Yelle, R. V.; Vuitton, V.; Wahlund, J.-E.; Lavvas, P. P.; Mueller-Wodarg, I. C. F.; Kasprzak, W. T.; Waite, J. H.

    2009-04-01

    We present our analysis of the diurnal variations of Titan's ionosphere (between 1,000 and 1,400 km) based on a sample of Ion Neutral Mass Spectrometer (INMS) measurements in the Open Source Ion (OSI) mode obtained from 8 close encounters of the Cassini spacecraft with Titan. Though there is an overall ion depletion well beyond the terminator, the ion content on Titan's nightside is still appreciable, with a density plateau of ~700 cm-3 below ~1,300 km. Such a plateau is associated with the combination of distinct diurnal variations of light and heavy ions. Light ions (e.g. CH5+, HCNH+, C2H5+) show strong diurnal variation, with clear bite-outs in their nightside distributions. In contrast, heavy ions (e.g. c-C3H3+, C2H3CNH+, C6H7+) present modest diurnal variation, with significant densities observed on the nightside. We propose that the distinctions between light and heavy ions are associated with their different chemical loss pathways, with the former primarily through "fast" ion-neutral chemistry and the latter through "slow" electron dissociative recombination. The INMS data suggest day-to-night transport as an important source of ions on Titan's nightside, to be distinguished from the conventional scenario of auroral ionization by magnetospheric particles as the only ionizing source on the nightside. This is supported by the strong correlation between the observed night-to-day ion density ratios and the associated ion lifetimes. We construct a time-dependent ion chemistry model to investigate the effects of day-to-night transport on the ionospheric structures of Titan. The predicted diurnal variation has similar general characteristics to those observed, with some apparent discrepancies which could be reconciled by imposing fast horizontal thermal winds in Titan's upper atmosphere.

  8. Dopamine transporters govern diurnal variation in extracellular dopamine tone

    OpenAIRE

    Ferris, Mark J.; España, Rodrigo A.; Locke, Jason L.; Konstantopoulos, Joanne K.; Rose, Jamie H.; Chen, Rong; Jones, Sara R.

    2014-01-01

    The mechanism for diurnal (i.e., light/dark) oscillations in extracellular dopamine tone in mesolimbic and nigrostriatal systems is unknown. This is because, unlike other neurotransmitter systems, variation in dopamine tone does not correlate with variation in dopamine cell firing. The current research pinpoints the dopamine transporter as a critical governor of diurnal variation in both extracellular dopamine tone and the intracellular availability of releasable dopamine. These data describe...

  9. Classifying Measures of Biological Variation

    OpenAIRE

    Gregorius, Hans-Rolf; Gillet, Elizabeth M

    2015-01-01

    Biological variation is commonly measured at two basic levels: variation within individual communities, and the distribution of variation over communities or within a metacommunity. We develop a classification for the measurement of biological variation on both levels: Within communities into the categories of dispersion and diversity, and within metacommunities into the categories of compositional differentiation and partitioning of variation. There are essentially two approaches to characte...

  10. The variational Poisson cohomolgy

    CERN Document Server

    De Sole, Alberto

    2011-01-01

    It is well known that the validity of the so called Lenard-Magri scheme of integrability of a bi-Hamiltonian PDE can be established if one has some precise information on the corresponding 1st variational Poisson cohomology for one of the two Hamiltonian operators. In the first part of the paper we explain how to introduce various cohomology complexes, including Lie superalgebra and Poisson cohomology complexes, and basic and reduced Lie conformal algebra and Poisson vertex algebra cohomology complexes, by making use of the corresponding universal Lie superalebra or Lie conformal superalgebra. The most relevant are certain subcomplexes of the basic and reduced Poisson vertex algebra cohomology complexes, which we identify (non-canonically) with the generalized de Rham complex and the generalized variational complex. In the second part of the paper we compute the cohomology of the generalized de Rham complex, and, via a detailed study of the long exact sequence, we compute the cohomology of the generalized var...

  11. Induction of cell death by chemotherapeutic methylating agents

    International Nuclear Information System (INIS)

    The mechanism of cell death induced by O6 MeG has been investigated and inhibition of homologous recombination as a strategy for sensitization of tumor cells against methylating agents SN1. Dependence of the cell cycle was determined toxic responses triggered by O''6 MeG and evaluated by proliferation assays if apoptotic cells have originated exclusively from the second post-treatment cycle. Dependence of O''6 MeG was found at DSB formation. The activation of the control points of the cell cycle and induction of apoptosis is generated during the second cell cycle. Additionally, a portion of the cells has been determined that triggers apoptosis in subsequent generations in the second cell cycle. Inhibition of homologous recombination has been a reasonable strategy to increase SN1 alkylating agent effectiveness. Evidence has been provided in NHEJ dependent inhibition of DNA-PK that not significantly sensitizes the glioblastoma cells against temozolomide

  12. Automatic Differentiation Variational Inference

    OpenAIRE

    Kucukelbir, Alp; Tran, Dustin; Ranganath, Rajesh; Gelman, Andrew; Blei, David M.

    2016-01-01

    Probabilistic modeling is iterative. A scientist posits a simple model, fits it to her data, refines it according to her analysis, and repeats. However, fitting complex models to large data is a bottleneck in this process. Deriving algorithms for new models can be both mathematically and computationally challenging, which makes it difficult to efficiently cycle through the steps. To this end, we develop automatic differentiation variational inference (ADVI). Using our method, the scientist on...

  13. Planar theory made variational

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, A.D.; Lande, A.; Smith, R.A.

    1985-04-08

    Within the framework of boson parquet-diagram summations in perturbation theory, we show analytically that several simple approximations lead inevitably to the radial distribution function g(r) which would be obtained with the Jastrow hypernetted-chain variational method. This is the first derivation of the Jastrow result from perturbation theory. Without mentioning pair correlation functions, we have a clear interpretation of g(r) and the structure function, S(k), in terms of diagram sums.

  14. Planar theory made variational

    International Nuclear Information System (INIS)

    Within the framework of boson parquet-diagram summations in perturbation theory, we show analytically that several simple approximations lead inevitably to the radial distribution function g(r) which would be obtained with the Jastrow hypernetted-chain variational method. This is the first derivation of the Jastrow result from perturbation theory. Without mentioning pair correlation functions, we have a clear interpretation of g(r) and the structure function, S(k), in terms of diagram sums

  15. Canonical variate regression.

    Science.gov (United States)

    Luo, Chongliang; Liu, Jin; Dey, Dipak K; Chen, Kun

    2016-07-01

    In many fields, multi-view datasets, measuring multiple distinct but interrelated sets of characteristics on the same set of subjects, together with data on certain outcomes or phenotypes, are routinely collected. The objective in such a problem is often two-fold: both to explore the association structures of multiple sets of measurements and to develop a parsimonious model for predicting the future outcomes. We study a unified canonical variate regression framework to tackle the two problems simultaneously. The proposed criterion integrates multiple canonical correlation analysis with predictive modeling, balancing between the association strength of the canonical variates and their joint predictive power on the outcomes. Moreover, the proposed criterion seeks multiple sets of canonical variates simultaneously to enable the examination of their joint effects on the outcomes, and is able to handle multivariate and non-Gaussian outcomes. An efficient algorithm based on variable splitting and Lagrangian multipliers is proposed. Simulation studies show the superior performance of the proposed approach. We demonstrate the effectiveness of the proposed approach in an [Formula: see text] intercross mice study and an alcohol dependence study. PMID:26861909

  16. Variational Asymptotic Micromechanics Modeling of Composite Materials

    OpenAIRE

    Tang, Tian

    2008-01-01

    The issue of accurately determining the effective properties of composite materials has received the attention of numerous researchers in the last few decades and continues to be in the forefront of material research. Micromechanics models have been proven to be very useful tools for design and analysis of composite materials. In the present work, a versatile micromechanics modeling framework, namely, the Variational Asymptotic Method for Unit Cell Homogenization (VAMUCH), has been invented a...

  17. Introduction to global variational geometry

    CERN Document Server

    Krupka, Demeter

    2015-01-01

    The book is devoted to recent research in the global variational theory on smooth manifolds. Its main objective is an extension of the classical variational calculus on Euclidean spaces to (topologically nontrivial) finite-dimensional smooth manifolds; to this purpose the methods of global analysis of differential forms are used. Emphasis is placed on the foundations of the theory of variational functionals on fibered manifolds - relevant geometric structures for variational principles in geometry, physical field theory and higher-order fibered mechanics. The book chapters include: - foundations of jet bundles and analysis of differential forms and vector fields on jet bundles, - the theory of higher-order integral variational functionals for sections of a fibred space, the (global) first variational formula in infinitesimal and integral forms- extremal conditions and the discussion of Noether symmetries and generalizations,- the inverse problems of the calculus of variations of Helmholtz type- variational se...

  18. Harmonically excited orbital variations

    International Nuclear Information System (INIS)

    Rephrasing the equations of motion for orbital maneuvers in terms of Lagrangian generalized coordinates instead of Newtonian rectangular cartesian coordinates can make certain harmonic terms in the orbital angular momentum vector more readily apparent. In this formulation the equations of motion adopt the form of a damped harmonic oscillator when torques are applied to the orbit in a variationally prescribed manner. The frequencies of the oscillator equation are in some ways unexpected but can nonetheless be exploited through resonant forcing functions to achieve large secular variations in the orbital elements. Two cases are discussed using a circular orbit as the control case: (1) large changes in orbital inclination achieved by harmonic excitation rather than one impulsive velocity change, and (2) periodic and secular changes to the longitude of the ascending node using both stable and unstable excitation strategies. The implications of these equations are also discussed for both artificial satellites and natural satellites. For the former, two utilitarian orbits are suggested, each exploiting a form of harmonic excitation. 5 refs

  19. Modeling variation in tumors in vivo

    OpenAIRE

    Stringer, James R.; Larson, Jon S.; Fischer, Jared M; Medvedovic, Mario; Hersh, Megan N; Boivin, Gregory P.; Stringer, Saundra L.

    2005-01-01

    Transgenic mice that allow mutant cells to be visualized in situ were used to study variation in tumors. These mice carry the G11 placental alkaline phosphatase (PLAP) transgene, a mutant allele rendered incapable of producing its enzyme product by a frameshift caused by insertion of a tract of G:C base pairs in a coding region. Spontaneous deletion of one G:C base pair from this tract restores gene function, and cells with PLAP activity can be detected histochemically. To study tumors, the G...

  20. Dynamics of nonholonomic systems from variational principles embedded variation identity

    International Nuclear Information System (INIS)

    Nondeterminacy of dynamics, i.e., the nonholonomic or the vakonomic, fundamental variational principles, e.g., the Lagrange-d'Alembert or Hamiltonian, and variational operators, etc., of nonholonomic mechanical systems can be attributed to the non-uniqueness of ways how to realize nonholonomic constraints. Making use of a variation identity of nonholonomic constraints embedded into the Hamilton's principle with the method of Lagrange undetermined multipliers, three kinds of dynamics for the nonholonomic systems including the vakonomic and nonholonomic ones and a new one are obtained if the variation is respectively reduced to three conditional variations: vakonomic variation, Hoelder's variation and Suslov's variation, defined by the identity. Therefore, different dynamics of nonholonomic systems can be derived from an integral variational principle, utilizing one way of embedding constraints into the principle, with different variations. It is verified that the similar embedding of the identity into the Lagrange-d'Alembert principle gives rise to the nonholonomic dynamics but fails to give the vakonomic one unless the constraints are integrable.

  1. Transient variations of vertical total electron content over some African stations from 2002 to 2012

    Science.gov (United States)

    Shimeis, A.; Amory-Mazaudier, C.; Fleury, R.; Mahrous, A. M.; Hassan, A. F.

    2014-12-01

    This paper presents the vertical total electron content vTEC variations for three African stations, located at mid-low and equatorial latitudes, and operating since more than 10 years. The vTEC of the middle latitude GPS station in Alexandria, Egypt (31.2167°N; 29.9667°E, geographic) is compared to the vTEC of two others GPS stations: the first one in Rabat/Morocco (33.9981°N; 353.1457°E, geographic), and the second in Libreville/Gabon (0.3539°N; 9.6721°E, geographic). Our results discussed the diurnal, seasonal, and solar cycle dependences of vTEC at the local ionospheric conditions, during different phases of solar cycle in the light of the classification of Legrand and Simon. The vTEC over Alexandria exhibits the well-known equinoctial asymmetry which changes with the phases of the solar cycle; the spring vTEC is larger than that of autumn during the maximum, decreasing and minimum phases of solar cycle 23. During the increasing phase of solar cycle 24, it is the contrary. The diurnal variation of the vTEC presents multiple maxima during the equinox from 2005 to 2008 and during the summer solstice from 2006 to 2012. A nighttime vTEC enhancement and winter anomaly are also observed. During the deep solar minimum (2006-2009) the diurnal variation of the vTEC observed over Alexandria is similar to the diurnal variation observed during quiet magnetic period at equatorial latitudes. We observed also that the amplitude of vTEC at Libreville is larger than the amplitude of vTEC observed at Alexandria and Rabat, indeed Libreville is near the southern crest of the Equatorial Ionization anomaly. Finally, the correlation coefficient between vTEC and the sunspot number Rz is high and changes with solar cycle phases.

  2. On the Variational Problems without Having Desired Variational Symmetries

    Directory of Open Access Journals (Sweden)

    Mehdi Nadjafikhah

    2013-01-01

    Full Text Available We will have an attempt to present a method for constructing variational problems without having a desired one-parameter transformation group as a variational symmetry. For this, we use the notation of μ-symmetry which was introduced by Giuseppe Gaeta and Paola Morando in 2004. Moreover, our given method enabled us to solve those constructed variational problems using μ-symmetries.

  3. FROG - Fingerprinting Genomic Variation Ontology.

    Directory of Open Access Journals (Sweden)

    E Abinaya

    Full Text Available Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: "FingeRprinting Ontology of Genomic variations" is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies. FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog.

  4. Cell surface expression level variation between two common Human Leukocyte Antigen alleles, HLA-A2 and HLA-B8, is dependent on the structure of the C terminal part of the alpha 2 and the alpha 3 domains

    DEFF Research Database (Denmark)

    Dellgren, Christoffer; Nehlin, Jan O; Barington, Torben

    2015-01-01

    . Moreover, recent observations suggest that even minor differences in expression levels may influence the course of viral infections and the frequency of complications to stem cell transplantation. We have shown that some human multipotent stem cells have high expression of HLA-A while HLA-B is only weakly......Constitutive cell surface expression of Human Leukocyte Antigen (HLA) class I antigens vary extremely from tissue to tissue and individual antigens may differ widely in expression levels. Down-regulation of class I expression is a known immune evasive mechanism used by cancer cells and viruses...... expressed, and demonstrate here that this is also the case for the human embryonic kidney cell line HEK293T. Using quantitative flow cytometry and quantitative polymerase chain reaction we found expression levels of endogenous HLA-A3 (median 71,204 molecules per cell) 9.2-fold higher than the expression of...

  5. Diurnal variation of mountain waves

    Directory of Open Access Journals (Sweden)

    R. M. Worthington

    2006-11-01

    Full Text Available Mountain waves could be modified as the boundary layer varies between stable and convective. However case studies show mountain waves day and night, and above e.g. convective rolls with precipitation lines over mountains. VHF radar measurements of vertical wind (1990–2006 confirm a seasonal variation of mountain-wave amplitude, yet there is little diurnal variation of amplitude. Mountain-wave azimuth shows possible diurnal variation compared to wind rotation across the boundary layer.

  6. 脓毒症时髓源性抑制细胞亚群及其比值的变化%Variation of subsets of myeloid derived suppressor cells and their ratio in septic mice

    Institute of Scientific and Technical Information of China (English)

    王慧; 赵擎宇; 黄朝峰; 赵梅; 徐小谢

    2016-01-01

    Objective To investigate the dynamic variation of subsets of myeloid derived suppressor cells (MDSC) and their ratio in septic mice, and to discuss their role in the development of sepsis. Methods Male C57BL/6 mice were randomly divided into sepsis model group and sham group according to random number table. Polymicrobial sepsis was induced by using cecal ligation and puncture (CLP), while mice in sham group only underwent laparotomy and laparorrhaphy without CLP. Thirty mice in each group were used to observe living condition, and the 20-day survival rate was compared between the two groups. In addition, subsets of MDSC in peripheral blood, spleen and bone marrow were analyzed with flow cytometry for other 60 mice (12 mice at each time point, as 0, 3, 7, 12 and 20 days). Spleens were harvested at 7 days for weighing, and single cell suspension of spleen tissue was prepared for splenocyte counting. Histopathologic changes in spleen tissue and liver tissue were observed under light microscope after hematoxylin and eosin (HE) stain. Results ① No mice died in sham group within 20 days after the operation. On the other hand, 10 mice in model group died within 20 days, and the difference in survival rate between the two groups was statistically significant (100.0% vs. 66.7%, χ2 = 11.861, P = 0.001). ② The spleens in model group showed obvious enlargement and significantly outweighed as compared with those in sham group (mg: 413.33±41.63 vs. 111.67±17.56, t = 11.564, P = 0.000), and the total count of splenocytes was significantly higher than that in sham group (×109/L: 21.20±2.43 vs. 1.87±0.06, t = 13.578, P = 0.005). ③ Pathological sections with HE staining showed that the liver tissue and spleen tissue remained normal in sham group. In model group, the hepatic tissue showed acute inflammatory reaction, including tissue disruption, capillary congestion, infiltration of neutrophils, marked edema of hepatocytes and focal hepatocellular necrosis. Abnormalities

  7. A Theory of Harmonic Variations

    OpenAIRE

    de Piro, Tristram

    2014-01-01

    We consider a class of "harmonic variations" for nonsingular curves, obtained as asymptotic degenerations along bitangents. On a geometric level, we obtain an attractive relationship between the class and the genus of $C$. The distribution of class points in pairs across nonsingular curves with such variations, further suggests applications to understanding covalent bonding in terms of shared electrons.

  8. Colony Variation in Staphylococcus lugdunensis

    OpenAIRE

    Leung, Michael J.; Nuttall, Nichalas; Pryce, Todd M.; Coombs, Geoffrey W; Pearman, John W.

    1998-01-01

    Staphylococcus lugdunensis is being increasingly reported as a pathogen with an outcome resembling that of S. aureus rather than coagulase-negative staphylococci. Recent local isolates exhibited colonial variation that delayed identification and interpretation of clinical significance. Until now previous descriptions have not emphasized colonial variation as an important identifying characteristic of S. lugdunensis.

  9. Morphogenesis checkpoint kinase Swe1 is the executor of lipolysis-dependent cell-cycle progression.

    Science.gov (United States)

    Chauhan, Neha; Visram, Myriam; Cristobal-Sarramian, Alvaro; Sarkleti, Florian; Kohlwein, Sepp D

    2015-03-10

    Cell growth and division requires the precise duplication of cellular DNA content but also of membranes and organelles. Knowledge about the cell-cycle-dependent regulation of membrane and storage lipid homeostasis is only rudimentary. Previous work from our laboratory has shown that the breakdown of triacylglycerols (TGs) is regulated in a cell-cycle-dependent manner, by activation of the Tgl4 lipase by the major cyclin-dependent kinase Cdc28. The lipases Tgl3 and Tgl4 are required for efficient cell-cycle progression during the G1/S (Gap1/replication phase) transition, at the onset of bud formation, and their absence leads to a cell-cycle delay. We now show that defective lipolysis activates the Swe1 morphogenesis checkpoint kinase that halts cell-cycle progression by phosphorylation of Cdc28 at tyrosine residue 19. Saturated long-chain fatty acids and phytosphingosine supplementation rescue the cell-cycle delay in the Tgl3/Tgl4 lipase-deficient strain, suggesting that Swe1 activity responds to imbalanced sphingolipid metabolism, in the absence of TG degradation. We propose a model by which TG-derived sphingolipids are required to activate the protein phosphatase 2A (PP2A(Cdc55)) to attenuate Swe1 phosphorylation and its inhibitory effect on Cdc28 at the G1/S transition of the cell cycle. PMID:25713391

  10. Controlling variation in the comet assay

    Directory of Open Access Journals (Sweden)

    Andrew Richard Collins

    2014-10-01

    Full Text Available Variability of the comet assay is a serious issue, whether it occurs from experiment to experiment in the same laboratory, or between different laboratories analysing identical samples. Do we have to live with high variability, just because the comet assay is a biological assay rather than analytical chemistry? Numerous attempts have been made to limit variability by standardising the assay protocol, and the critical steps in the assay have been identified; agarose concentration, duration of alkaline incubation, and electrophoresis conditions (time, temperature and voltage gradient are particularly important. Even when these are controlled, variation seems to be inevitable. It is helpful to include in experiments reference standards, i.e. cells with a known amount of specific damage to the DNA. They can be aliquots frozen from a single large batch of cells, either untreated (negative controls or treated with, for example, H2O2 or X-rays to induce strand breaks (positive control for the basic assay, or photosensitiser plus light to oxidise guanine (positive control for Fpg- or OGG1-sensitive sites. Reference standards are especially valuable when performing a series of experiments over a long period - for example, analysing samples of white blood cells from a large human biomonitoring trial - to check that the assay is performing consistently, and to identify anomalous results necessitating a repeat experiment. The reference values of tail intensity can also be used to iron out small variations occurring from day to day. We present examples of the use of reference standards in human trials, both within one laboratory and between different laboratories, and describe procedures that can be used to control variation.

  11. Correlation of the 27-day variation of cosmic rays to the interplanetary magnetic field strength

    Science.gov (United States)

    Sabbah, I.

    2001-08-01

    We analyze cosmic ray data as well as interplanetary magnetic field (IMF) data, to examine the relation and correlation between their 27-day variations during the time interval 1965-1995. The amplitude of the 27day variation of galactic cosmic rays is linearly correlated with: the IMF strength (B), the z-component (Bz) of the IMF vector and the product of the solar wind speed (V) times B (VB). It is well correlated with the heliospheric current sheet tiltangle.Thecross-correlationfunctionofthe27-daycosmic ray variation versus the solar wind speed shows a negative correlation. The solar wind speed leads the cosmic ray variation by 2 years. The 27-day variation of cosmic rays is correlated with the variation in both the xand y-components of the IMF, it lags with 3-5 years. 1. Introduction Galactic cosmic rays are modulated (modified) through their propagation in the heliosphere by the effect of the large scale structure of the interplanetary medium. A wavy structured neutralcurrentsheet(NCS) separatesthe heliosphereintotwo regions of opposite magnetic polarity. During positive magnetic phase, the interplanetary magnetic field (IMF) is directed away from the Sun above the NCS and toward the Sun south of it. During negative magnetic phase the IMF direction is reversed. The angle between the Sun's equatorial plane and the NCS is referred as the tilt angle R, of the neutral sheet. It exhibits a solar activity dependence, R is small near sunspot minimum and large near solar maximum. The 27-day variations of galactic cosmic rays have been related to the changing position of the interplanetary NCS (Swinson and Yasue, 1992; Valdes-Galicia and Dorman, 1997). Here we examine the effect of the interplanetary parameters upon the 27-day variation of galactic cosmic rays during the last three solar cycles. 2. Solar Cycle Dependance We used hourly averaged cosmic ray counts observed with neutron monitors at Deep River (DR) and Huancayo (HU) and muon surface telescope at Nagoya (NA

  12. Variational and quasi-variational inequalities in mechanics

    CERN Document Server

    Kravchuk, Alexander S

    2007-01-01

    The essential aim of the present book is to consider a wide set of problems arising in the mathematical modelling of mechanical systems under unilateral constraints. In these investigations elastic and non-elastic deformations, friction and adhesion phenomena are taken into account. All the necessary mathematical tools are given: local boundary value problem formulations, construction of variational equations and inequalities, and the transition to minimization problems, existence and uniqueness theorems, and variational transformations (Friedrichs and Young-Fenchel-Moreau) to dual and saddle-point search problems. Important new results concern contact problems with friction. The Coulomb friction law and some others are considered, in which relative sliding velocities appear. The corresponding quasi-variational inequality is constructed, as well as the appropriate iterative method for its solution. Outlines of the variational approach to non-stationary and dissipative systems and to the construction of the go...

  13. Statistics, Uncertainty, and Transmitted Variation

    Energy Technology Data Exchange (ETDEWEB)

    Wendelberger, Joanne Roth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2014-11-05

    The field of Statistics provides methods for modeling and understanding data and making decisions in the presence of uncertainty. When examining response functions, variation present in the input variables will be transmitted via the response function to the output variables. This phenomenon can potentially have significant impacts on the uncertainty associated with results from subsequent analysis. This presentation will examine the concept of transmitted variation, its impact on designed experiments, and a method for identifying and estimating sources of transmitted variation in certain settings.

  14. Variational modelling of nonlinear water waves

    Science.gov (United States)

    Kalogirou, Anna; Bokhove, Onno

    2015-11-01

    Mathematical modelling of water waves is demonstrated by investigating variational methods. A potential flow water wave model is derived using variational techniques and extented to include explicit time-dependence, leading to non-autonomous dynamics. As a first example, we consider the problem of a soliton splash in a long wave channel with a contraction at its end, resulting after a sluice gate is removed at a finite time. The removal of the sluice gate is included in the variational principle through a time-dependent gravitational potential. A second example involving non-autonomous dynamics concerns the motion of a free surface in a vertical Hele-Shaw cell. Explicit time-dependence now enters the model through a linear damping term due to the effect of wall friction and a term representing the motion of an artificially driven wave pump. In both cases, the model is solved numerically using a Galerkin FEM and the numerical results are compared to wave structures observed in experiments. The water wave model is also adapted to accommodate nonlinear ship dynamics. The novelty is this case is the coupling between the water wave dynamics, the ship dynamics and water line dynamics on the ship. For simplicity, we consider a simple ship structure consisting of V-shaped cross-sections.

  15. Deuterium content variation of human blood serum

    International Nuclear Information System (INIS)

    We report, for the first time, the variation of deuterium content of blood serum of the patients with cancer disease. The tumorous cell, because of the higher growth speed , is deuterium consuming. The deuterium content of blood serum of cancerous human is diminished by about 5-7 ppm compared with that of the healthy individual. This effect is in accordance with some previous results. The replacement of tap water with deuterium depleted water in a drinking water of tumorous mice diminished the growth rate of tumors and the slight increase in the deuterium concentration stimulates growth because it is more easy for the cells to elevate the intracellular deuterium concentration up to the threshold level. (authors)

  16. The Yeast Cyclin-Dependent Kinase Routes Carbon Fluxes to Fuel Cell Cycle Progression.

    Science.gov (United States)

    Ewald, Jennifer C; Kuehne, Andreas; Zamboni, Nicola; Skotheim, Jan M

    2016-05-19

    Cell division entails a sequence of processes whose specific demands for biosynthetic precursors and energy place dynamic requirements on metabolism. However, little is known about how metabolic fluxes are coordinated with the cell division cycle. Here, we examine budding yeast to show that more than half of all measured metabolites change significantly through the cell division cycle. Cell cycle-dependent changes in central carbon metabolism are controlled by the cyclin-dependent kinase (Cdk1), a major cell cycle regulator, and the metabolic regulator protein kinase A. At the G1/S transition, Cdk1 phosphorylates and activates the enzyme Nth1, which funnels the storage carbohydrate trehalose into central carbon metabolism. Trehalose utilization fuels anabolic processes required to reliably complete cell division. Thus, the cell cycle entrains carbon metabolism to fuel biosynthesis. Because the oscillation of Cdk activity is a conserved feature of the eukaryotic cell cycle, we anticipate its frequent use in dynamically regulating metabolism for efficient proliferation. PMID:27203178

  17. Enforcing temporal control of maternal mRNA translation during oocyte cell-cycle progression

    OpenAIRE

    Arumugam, Karthik; Wang, Yiying; Hardy, Linda L.; MacNicol, Melanie C.; MacNicol, Angus M

    2009-01-01

    Meiotic cell-cycle progression in progesterone-stimulated Xenopus oocytes requires that the translation of pre-existing maternal mRNAs occur in a strict temporal order. Timing of translation is regulated through elements within the mRNA 3′ untranslated region (3′ UTR), which respond to cell cycle-dependant signalling. One element that has been previously implicated in the temporal control of mRNA translation is the cytoplasmic polyadenylation element (CPE). In this study, we show that the CPE...

  18. Representing Term Variation in lemon

    OpenAIRE

    Montiel-Ponsoda, Elena; Aguado de Cea, G.; McCrae, J.

    2011-01-01

    In this contribution our objective is to define term variation, analyze the state of the art, and propose a new classification of term variants according to our representation purposes in lemon, a lexiconontology model to enrich ontologies with linguistic descriptions.

  19. Quality of Variational Trial States

    CERN Document Server

    Lucha, Wolfgang; Lucha, Wolfgang; Schoberl, Franz F.

    1999-01-01

    Besides perturbation theory (which clearly requires the knowledge of the exact unperturbed solution), variational techniques represent the main tool for any investigation of the eigenvalue problem of some semibounded operator H in quantum theory. For a reasonable choice of the employed trial subspace of the domain of H, the lowest eigenvalues of H usually can be located with acceptable precision whereas the trial-subspace vectors corresponding to these eigenvalues approximate, in general, the exact eigenstates of H with much less accuracy. Accordingly, various measures for the accuracy of the approximate eigenstates derived by variational techniques are scrutinized. In particular, the matrix elements of the commutator of the operator H and (suitably chosen) different operators with respect to degenerate approximate eigenstates of H obtained by variational methods are proposed as new criteria for the accuracy of variational eigenstates. These considerations are applied to precisely that Hamiltonian for which t...

  20. Stochastic Annealing for Variational Inference

    OpenAIRE

    Gultekin, San; Zhang, Aonan; Paisley, John

    2015-01-01

    We empirically evaluate a stochastic annealing strategy for Bayesian posterior optimization with variational inference. Variational inference is a deterministic approach to approximate posterior inference in Bayesian models in which a typically non-convex objective function is locally optimized over the parameters of the approximating distribution. We investigate an annealing method for optimizing this objective with the aim of finding a better local optimal solution and compare with determin...

  1. An Overview of Variational Integrators

    OpenAIRE

    Lew, Adrian; Marsden, Jerrold E.; Ortiz, Michael; West, Matthew

    2004-01-01

    The purpose of this paper is to survey some recent advances in variational integrators for both finite dimensional mechanical systems as well as continuum mechanics. These advances include the general development of discrete mechanics, applications to dissipative systems, collisions, spacetime integration algorithms, AVI’s (Asynchronous Variational Integrators), as well as reduction for discrete mechanical systems. To keep the article within the set limits, we will only trea...

  2. Variational Gaussian Process Dynamical Systems

    OpenAIRE

    Damianou, Andreas C.; Titsias, Michalis K.; Lawrence, Neil D.

    2011-01-01

    High dimensional time series are endemic in applications of machine learning such as robotics (sensor data), computational biology (gene expression data), vision (video sequences) and graphics (motion capture data). Practical nonlinear probabilistic approaches to this data are required. In this paper we introduce the variational Gaussian process dynamical system. Our work builds on recent variational approximations for Gaussian process latent variable models to allow for nonlinear dimensional...

  3. Coupled Dark Energy field variation

    OpenAIRE

    García-Zúñiga, Roberto Carlos; Izquierdo, Germán

    2014-01-01

    The variation of the dark energy field is found under the assumption that the dark energy is parametric and interacts with the cold dark matter. Considering that the variation of the field could not exceed the Planck mass, we obtain bounds on the coupling and adiabatic coefficients. Three parameterizations of the adiabatic coefficients are considered and two coupling terms where the energy flows from dark energy to dark matter, or the other way around.

  4. Variational integrators for electric circuits

    International Nuclear Information System (INIS)

    In this contribution, we develop a variational integrator for the simulation of (stochastic and multiscale) electric circuits. When considering the dynamics of an electric circuit, one is faced with three special situations: 1. The system involves external (control) forcing through external (controlled) voltage sources and resistors. 2. The system is constrained via the Kirchhoff current (KCL) and voltage laws (KVL). 3. The Lagrangian is degenerate. Based on a geometric setting, an appropriate variational formulation is presented to model the circuit from which the equations of motion are derived. A time-discrete variational formulation provides an iteration scheme for the simulation of the electric circuit. Dependent on the discretization, the intrinsic degeneracy of the system can be canceled for the discrete variational scheme. In this way, a variational integrator is constructed that gains several advantages compared to standard integration tools for circuits; in particular, a comparison to BDF methods (which are usually the method of choice for the simulation of electric circuits) shows that even for simple LCR circuits, a better energy behavior and frequency spectrum preservation can be observed using the developed variational integrator

  5. Is there much variation in variation? Revisiting statistics of small area variation in health services research

    Directory of Open Access Journals (Sweden)

    Ibáñez Berta

    2009-04-01

    Full Text Available Abstract Background The importance of Small Area Variation Analysis for policy-making contrasts with the scarcity of work on the validity of the statistics used in these studies. Our study aims at 1 determining whether variation in utilization rates between health areas is higher than would be expected by chance, 2 estimating the statistical power of the variation statistics; and 3 evaluating the ability of different statistics to compare the variability among different procedures regardless of their rates. Methods Parametric bootstrap techniques were used to derive the empirical distribution for each statistic under the hypothesis of homogeneity across areas. Non-parametric procedures were used to analyze the empirical distribution for the observed statistics and compare the results in six situations (low/medium/high utilization rates and low/high variability. A small scale simulation study was conducted to assess the capacity of each statistic to discriminate between different scenarios with different degrees of variation. Results Bootstrap techniques proved to be good at quantifying the difference between the null hypothesis and the variation observed in each situation, and to construct reliable tests and confidence intervals for each of the variation statistics analyzed. Although the good performance of Systematic Component of Variation (SCV, Empirical Bayes (EB statistic shows better behaviour under the null hypothesis, it is able to detect variability if present, it is not influenced by the procedure rate and it is best able to discriminate between different degrees of heterogeneity. Conclusion The EB statistics seems to be a good alternative to more conventional statistics used in small-area variation analysis in health service research because of its robustness.

  6. Global variations of zonal mean ozone during stratospheric warming events

    Science.gov (United States)

    Randel, William J.

    1993-01-01

    Eight years of Solar Backscatter Ultraviolet (SBUV) ozone data are examined to study zonal mean variations associated with stratospheric planetary wave (warming) events. These fluctuations are found to be nearly global in extent, with relatively large variations in the tropics, and coherent signatures reaching up to 50 deg in the opposite (summer) hemisphere. These ozone variations are a manifestation of the global circulation cells associated with stratospheric warming events; the ozone responds dynamically in the lower stratosphere to transport, and photochemically in the upper stratosphere to the circulation-induced temperature changes. The observed ozone variations in the tropics are of particular interest because transport is dominated by zonal-mean vertical motions (eddy flux divergences and mean meridional transports are negligible), and hence, substantial simplifications to the governing equations occur. The response of the atmosphere to these impulsive circulation changes provides a situation for robust estimates of the ozone-temperature sensitivity in the upper stratosphere.

  7. Variation within the PPARG gene is associated with residual beta-cell function and glycemic control in children and adolescents during the first year of clinical type 1 diabetes

    DEFF Research Database (Denmark)

    Porksen, S.; Nielsen, L.B.; Mortensen, H.B.;

    2008-01-01

    the PPARG gene in relation to residual beta-cell function and glycemic control in newly diagnosed T1D. Design: Prospective, non-interventional, 12-month follow-up study, conducted in 18 centers in 15 countries. Patients: Two hundred and fifty-seven children and adolescents (aged < 16 yr) with newly...... in the PPARG locus may influence disease progression during the first year after the presentation of T1D Udgivelsesdato: 2008/8...

  8. Avaliação cronológica da variação no volume globular sanguíneo de bovinos leiteiros Cronological evaluation of variation in packed cell volume on dairy cattle

    Directory of Open Access Journals (Sweden)

    Wilmar Sachetin Marçal

    1995-01-01

    Full Text Available Os autores avaliaram a variação no volume globular sangüíneo de 321 bovinos da raça Holandês preta e branca, sadios e criados em granjas leiteiras no Estado de São Paulo. Todos os animais trabalhados na presente pesquisa eram sadios, não reagentes ao vírus da Leucose Bovina, livres de hemoparasitas, brucelose e tuberculose. O volume globular sangüíneo foi efetuado através do método do hematócrito com tubos capilares. Os resultados mostram haver influência da idade sobre o volume globular sangüíneo, com valores médios encontrados de 30,12 ± 2,72%.The packet cell volume was evaluated by the authors in 321 healthy female Holstein cattle raised at Campinas dairy region. São Paulo State. All the animais used in this assay were healthy and free of Leucosis, Tuberculosis, Brucellosis and blood parasites. The packed cell volume has been studied by method of hematocrit with capilary tubos. The results showed an influence of age on packed cell volume with average reference values of 30.12 ± 2.72%.

  9. Variational principle for quasibound states

    International Nuclear Information System (INIS)

    A minimum-variance principle for quasibound states is defined and utilized to investigate the corresponding energy resonances. The variational principle yields simultaneously a resonance energy E and a square-integrable wave function phi, such that minimum variance is obtained for arbitrary variations of a restricted class of square-integrable functions as well as with respect to variations of E. It is further shown that the optimum energy E0 obtained from this method can simultaneously be written as an expectation value of the actual Hamiltonian with respect to phi = phi (E0). The example of the Stark effect in the hydrogen atom is studied. It is shown that the variationally obtained resonance energy coincides with the real part of the complex pole of the m function of Weyl, related to the Green's function of the system under consideration. It is also shown that the corresponding numerical application of the Rayleigh-Ritz variational method only gives meaningful results for field intensities below 0.06 a.u., as compared with the ''exact'' results of Hehenberger, McIntosh, and Brandas

  10. Kernels and ranges in the variational formalism

    International Nuclear Information System (INIS)

    An extension of the concept of variational derivative is introduced which allows one to derive an integral identity in the variational formalism. It is applied to characterize the kernel and range of the variational derivative and the divergence operator. (Auth.)

  11. Variational Lie derivative and cohomology classes

    Science.gov (United States)

    Palese, Marcella; Winterroth, Ekkehart

    2011-07-01

    We relate cohomology defined by a system of local Lagrangian with the cohomology class of the system of local variational Lie derivative, which is in turn a local variational problem; we show that the latter cohomology class is zero, since the variational Lie derivative `trivializes' cohomology classes defined by variational forms. As a consequence, conservation laws associated with symmetries of the second variational derivative of a local variational problem are globally defined.

  12. Solid mechanics a variational approach

    CERN Document Server

    Dym, Clive L

    2013-01-01

    Solid Mechanics: A Variational Approach, Augmented Edition presents a lucid and thoroughly developed approach to solid mechanics for students engaged in the study of elastic structures not seen in other texts currently on the market. This work offers a clear and carefully prepared exposition of variational techniques as they are applied to solid mechanics. Unlike other books in this field, Dym and Shames treat all the necessary theory needed for the study of solid mechanics and include extensive applications. Of particular note is the variational approach used in developing consistent structural theories and in obtaining exact and approximate solutions for many problems.  Based on both semester and year-long courses taught to undergraduate seniors and graduate students, this text is geared for programs in aeronautical, civil, and mechanical engineering, and in engineering science. The authors’ objective is two-fold: first, to introduce the student to the theory of structures (one- and two-dimensional) as ...

  13. Constrained variational calculus: the second variation (part I)

    CERN Document Server

    Massa, Enrico; Pagani, Enrico; Luria, Gianvittorio

    2010-01-01

    This paper is a direct continuation of arXiv:0705.2362 . The Hamiltonian aspects of the theory are further developed. Within the framework provided by the first paper, the problem of minimality for constrained calculus of variations is analyzed among the class of differentiable curves. A necessary and sufficient condition for minimality is proved.

  14. Storm surge variational assimilation model

    Directory of Open Access Journals (Sweden)

    Shi-li HUANG

    2010-06-01

    Full Text Available To eliminate errors caused by uncertainty of parameters and further improve capability of storm surge forecasting, the variational data assimilation method is applied to the storm surge model based on unstructured grid with high spatial resolution. The method can effectively improve the forecasting accuracy of storm surge induced by typhoon through controlling wind drag force coefficient parameter. The model is first theoretically validated with synthetic data. Then, the real storm surge process induced by the TC 0515 typhoon is forecasted by the variational data assimilation model, and results show the feasibility of practical application.

  15. A variational formulation of electrodynamics

    CERN Document Server

    De Nicola, Antonio

    2007-01-01

    We present a variational formulation of electrodynamics using de Rham even and odd differential forms. Our formulation relies on a variational principle more complete than the Hamilton principle and thus leads to field equations with external sources and permits the derivation of the constitutive relations. We interpret a domain in space-time as an odd de Rham 4-current. This permits a treatment of different types of boundary problems in an unified way. In particular we obtain a smooth transition to the infinitesimal version by using a current with a one point support.

  16. Structure variations of carbonizing lignin

    International Nuclear Information System (INIS)

    The studied lignin is a by-product of the process of ethanol production from eucaliptus. It was heat-treated under inert atmosphere conditions at increasing temperatures from 300C up to 2400C. The structural variations were studied by wide-angle X-ray diffraction, small-angle X-ray scattering and infrared absorption spectroscopy. The bulk and 'real' density of the compacted materials have also been determined as functions of the final temperature. These experimental results enabled us to establish a mechanism of structure variation based on the formation of a turbostratic graphite-like and porous structure within the initially amorphous lignin matrix. (Author)

  17. Variation

    OpenAIRE

    2001-01-01

    Veränderung (lat. variatio) einer melodisch oder harmonisch feststehenden Gestalt als epochen- und stilübergreifendes Kompositionsprinzip und im engeren Sinn als eigenständige, an ein (präexistentes) Thema gebundene Form.

  18. Variational approach for quarkonium potentials

    International Nuclear Information System (INIS)

    A variational method based on Coulomb and harmonic oscillator trial functions has been investigated in the context of single and superposition of power potentials which are commonly used for quarkonium systems. Ground state energies being upper bounds are calculated and emerge surprisingly close to their exact values considering the simplicity of the method

  19. Sea level and climate variations

    NARCIS (Netherlands)

    Oerlemans, J.

    1985-01-01

    Review paper, ESA Symposium on Application of Satellite Data to Climate Modelling. Alpbach (Austria) Sea level is an essential component of the climate system, on which many human activities in the coastal zone depend. Climate variations leading to changes in relative sea level are discussed, with

  20. Variational integrators in plasma physics

    International Nuclear Information System (INIS)

    To a large extent, research in plasma physics is concerned with the description and analysis of energy and momentum transfer between different scales and different kinds of waves. In the numerical modelling of such phenomena it appears to be crucial to describe the transfer processes preserving the underlying conservation laws in order to prevent physically spurious solutions. In this work, special numerical methods, so called variational integrators, are developed for several models of plasma physics. Special attention is given to conservation properties like conservation of energy and momentum. By design, variational integrators are applicable to all systems that have a Lagrangian formulation. Usually, equations of motion are derived by Hamilton's action principle and then discretised. In the application of the variational integrator theory, the order of these steps is reversed. At first, the Lagrangian and the accompanying variational principle are discretised, such that discrete equations of motion can be obtained directly by applying the discrete variational principle to the discrete Lagrangian. The advantage of this approach is that the resulting discretisation automatically retains the conservation properties of the continuous system. Following an overview of the geometric formulation of classical mechanics and field theory, which forms the basis of the variational integrator theory, variational integrators are introduced in a framework adapted to problems from plasma physics. The applicability of variational integrators is explored for several important models of plasma physics: particle dynamics (guiding centre dynamics), kinetic theory (the Vlasov-Poisson system) and fluid theory (magnetohydrodynamics). These systems, with the exception of guiding centre dynamics, do not possess a Lagrangian formulation to which the variational integrator methodology is directly applicable. Therefore the theory is extended by linking it to Ibragimov's theory of

  1. Quasi-reflected interface conditions for variational nodal lattice calculations

    International Nuclear Information System (INIS)

    Quasi-reflected interface conditions are formulated to partially decouple periodic lattice effects from the pin-cell to pin-cell flux variation in the finite sub-element form of the variational nodal code VARIANT. With fuel-coolant homogenization eliminated, the interface variables that couple pin-cell sized nodes are divided into low-order and high-order spherical harmonic terms, and reflected interface conditions are applied to the high-order terms. This approach dramatically reduces the dimension of the resulting response matrices and leads to sharply reduced memory and CPU requirements for the solution of the resulting response matrix equations. The method is applied to a two-dimensional OECD/NEA PWR benchmark containing MOX and UO2 fuel assemblies. Results indicate that the quasi-reflected interface conditions result in very little loss of accuracy relative to the corresponding full spherical harmonics expansion. (authors)

  2. Geometric constrained variational calculus. III: The second variation (Part II)

    Science.gov (United States)

    Massa, Enrico; Luria, Gianvittorio; Pagani, Enrico

    2016-03-01

    The problem of minimality for constrained variational calculus is analyzed within the class of piecewise differentiable extremaloids. A fully covariant representation of the second variation of the action functional based on a family of local gauge transformations of the original Lagrangian is proposed. The necessity of pursuing a local adaptation process, rather than the global one described in [1] is seen to depend on the value of certain scalar attributes of the extremaloid, here called the corners’ strengths. On this basis, both the necessary and the sufficient conditions for minimality are worked out. In the discussion, a crucial role is played by an analysis of the prolongability of the Jacobi fields across the corners. Eventually, in the appendix, an alternative approach to the concept of strength of a corner, more closely related to Pontryagin’s maximum principle, is presented.

  3. Variation of Parameters in Differential Equations (A Variation in Making Sense of Variation of Parameters)

    Science.gov (United States)

    Quinn, Terry; Rai, Sanjay

    2012-01-01

    The method of variation of parameters can be found in most undergraduate textbooks on differential equations. The method leads to solutions of the non-homogeneous equation of the form y = u[subscript 1]y[subscript 1] + u[subscript 2]y[subscript 2], a sum of function products using solutions to the homogeneous equation y[subscript 1] and…

  4. Analysis of X-ray induced cell-cycle perturbations in mouse osteosarcoma cells: a two-signal cell-cycle model

    International Nuclear Information System (INIS)

    The effects of X-irradiation on mouse osteosarcoma cells have been studied by time-lapse cinematography and the resulting pedigrees have been analysed statistically. It is shown that the irradiation treatment causes three types of cell kinetic lesions: cell death (disintegration), cell sterilization (failure to divide) and proliferation delay. The first two lesions are the most important with regard to survival of the irradiated cell in a clonal assay. Of these two lesions, sterilization appears to be highly correlated for sister cells, while this is not true for cell disintegration. This indicates that cell survival in a clonal assay may be a function of the ratio of the incidences of these two types of lesions. The X-ray-induced proliferation delay was studied in terms of intermitotic time distributions, mother-daughter correlation and sibling correlation in relation to the current cell-cycle phase at the time of treatment. This analysis shows that the effects of irradiation on these cell-cycle characteristics is highly cell-cycle-dependent. A qualitative model to account for the observations is presented. (author)

  5. Comparing variation across European countries

    DEFF Research Database (Denmark)

    Thygesen, Lau C; Baixauli-Pérez, Cristobal; Librero-López, Julián;

    2015-01-01

    units of analysis in the estimation of systematic variation in three countries. METHODS: Hospital discharges for six conditions (congestive heart failure, short-term complications of diabetes, hip fracture, knee replacement, prostatectomy in prostate cancer and percutaneous coronary intervention......) produced in Denmark, England and Portugal in 2008 and 2009 were allocated to both original geographical units and new ad hoc areas. New areas were built using Ward's minimum variance methods. The impact of the new areas on variability was assessed using Kernel distribution curves and different statistic...... inhabitants vs. 7% in Denmark and 5% in England. Point estimates for Extremal Quotient and Interquartile Interval Ratio were lower in the three countries, particularly in less prevalent conditions. In turn, the Systematic Component of Variation and Empirical Bayes statistic were slightly lower in more...

  6. Variational Integrators for Reduced Magnetohydrodynamics

    CERN Document Server

    Kraus, Michael; Grasso, Daniela

    2015-01-01

    Reduced magnetohydrodynamics is a simplified set of magnetohydrodynamics equations with applications to both fusion and astrophysical plasmas, possessing a noncanonical Hamiltonian structure and consequently a number of conserved functionals. We propose a new discretisation strategy for these equations based on a discrete variational principle applied to a formal Lagrangian. The resulting integrator preserves important quantities like the total energy, magnetic helicity and cross helicity exactly (up to machine precision). As the integrator is free of numerical resistivity, spurious reconnection along current sheets is absent in the ideal case. If effects of electron inertia are added, reconnection of magnetic field lines is allowed, although the resulting model still possesses a noncanonical Hamiltonian structure. After reviewing the conservation laws of the model equations, the adopted variational principle with the related conservation laws are described both at the continuous and discrete level. We verify...

  7. Bernoulli Variational Problem and Beyond

    KAUST Repository

    Lorz, Alexander

    2013-12-17

    The question of \\'cutting the tail\\' of the solution of an elliptic equation arises naturally in several contexts and leads to a singular perturbation problem under the form of a strong cut-off. We consider both the PDE with a drift and the symmetric case where a variational problem can be stated. It is known that, in both cases, the same critical scale arises for the size of the singular perturbation. More interesting is that in both cases another critical parameter (of order one) arises that decides when the limiting behaviour is non-degenerate. We study both theoretically and numerically the values of this critical parameter and, in the symmetric case, ask if the variational solution leads to the same value as for the maximal solution of the PDE. Finally we propose a weak formulation of the limiting Bernoulli problem which incorporates both Dirichlet and Neumann boundary condition. © 2013 Springer-Verlag Berlin Heidelberg.

  8. Diurnal variation of depressive symptoms

    OpenAIRE

    Wirz-Justice, Anna

    2008-01-01

    Diurnal variation of depressive symptoms appears to be part of the core of depression. Yet longitudinal investigation of an individual's pattern regularity, relation to clinical state, and clinical improvement reveals little homogeneity. Morning lows, afternoon slump, evening worsening - all can occur during a single depressive episode. Mood variability, or the propensity to produce mood swings, appears to be the characteristic that most predicts capacity to respond to treatment. Laboratory s...

  9. Regular Variation and Smile Asymptotics

    OpenAIRE

    Benaim, Shalom; Friz, Peter

    2006-01-01

    We consider risk-neutral returns and show how their tail asymptotics translate directly to asymptotics of the implied volatility smile, thereby sharpening Roger Lee's celebrated moment formula. The theory of regular variation provides the ideal mathematical framework to formulate and prove such results. The practical value of our formulae comes from the vast literature on tail asymptotics and our conditions are often seen to be true by simple inspection of known results.

  10. Global Stress Variation over Time

    Science.gov (United States)

    Yi, H.; Lu, Z.; Wen, L.

    2015-12-01

    Understanding how stress changes over time is important as it is related to studies of earthquake triggering and mantle rheology. We calculate stress variation at the Earth's surface on the global scale from 2003 to 2014, resultant from several major physical forces acting on the Earth. The physical forces we considered include the surface loading due to terrestrial water storage (TWS), force associated with post-glacial rebound (PGR) and tidal loading (including solid tide and ocean tide). The stress change associated with TWS is calculated in this way: we infer TWS from monthly gravity field of the Gravity Recovery and Climate Experiment (GRACE), in which gravity variation associated with PGR has been removed; we then estimate stress change at the Earth's surface as the elastic response of the GRACE-inferred TWS change. The stress change associated with PGR is calculated as the rate of viscoelastic stress change responding to ice loading from ICE-5G model. And, tidal stress is calculated as the elastic response of the Earth to the traction forces of the Sun and the Moon (solid tide) and to the loading of ocean tide. The total stress change is the sum of the stress changes associated with these three types of forces. As first result, in the study period from 2003 to 2014, the radial normal stress variation exhibits a prominent decreasing trend in southern Africa and Queen Maud Land of Antarctica, an increasing trend in Alaska of the US (United States), Greenland and Marie Byrd Land of Antarctica, and strong annual cycles in southern Africa and Alaska of the US. We will present the geographical distribution of global stress variation from 2003 to 2014 and discuss its possible implications.

  11. Longitudinal Variations in Jupiter's Winds

    Science.gov (United States)

    Simon-Miller, Amy A.; Gierasch, P. J.; Tierney, G.

    2010-01-01

    Long-term studies of Jupiter's zonal wind field revealed temporal variations on the order of 20 to 40 m/s at many latitudes, greater than the typical data uncertainties of 1 to 10 m/s. No definitive periodicities were evident, however, though some latitudinally-confined signals did appear at periods relevant to the Quasi- Quadrennial Oscillation (Simon-Miller & Gierasch, Icarus, in press). As the QQO appears, from vertical temperature profiles, to propagate downward, it is unclear why a signal is not more obvious, unless other processes dominate over possibly weaker forcing from the QQO. An additional complication is that zonal wind profiles represent an average over some particular set of longitudes for an image pair and most data sets do not offer global wind coverage. Lien avoiding known features, such as the large anticyclonic vortices especially prevalent in the south, there can be distinct variations in longitude. We present results on the full wind field from Voyager and Cassini data, showing apparent longitudinal variations of up to 60 m/s or more. These are particularly obvious near disruptions such as the South Equatorial Disturbance, even when the feature itself is not clearly visible. These two dates represent very different states of the planet for comparison: Voyagers 1 & 2 flew by Jupiter shortly after a global upheaval, while many regions were in a disturbed state, while the Cassini view is typical of a more quiescent period present during much of the 1990s and early 2000s.

  12. WE-G-BRD-06: Variation in Dynamic Positron Emission Tomography Imaging of Tumor Hypoxia in Early Stage Non-Small Cell Lung Cancer Patients Undergoing Stereotactic Body Radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Kelada, O [Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut (United States); Department of Medical Physics in Radiation Oncology, German Cancer Research Center, Heidelberg (Germany); Decker, R; Rockwell, S; Carlson, D [Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut (United States); Zheng, M; Huang, Y; Xia, Y; Gallezot, J; Liu, C; Carson, R [Department of Diagnostic Radiology, Yale University School of Medicine, New Haven, CT (United States); Oelfke, U [Department of Medical Physics in Radiation Oncology, German Cancer Research Center, Heidelberg (Germany)

    2014-06-15

    Purpose: Tumor hypoxia is correlated with treatment failure. To date, there are no published studies investigating hypoxia in non-small cell lung cancer (NSCLC) patients undergoing SBRT. We aim to use 18F-fluoromisonidazole (18F-FMISO) positron emission tomography (PET) imaging to non-invasively quantify the tumor hypoxic volume (HV), to elucidate potential roles of reoxygenation and tumor vascular response at high doses, and to identify an optimal prognostic imaging time-point. Methods: SBRT-eligible patients with NSCLC tumors >1cm were prospectively enrolled in an IRB-approved study. Computed Tomography and dynamic PET images (0–120min, 150–180min, and 210–240min post-injection) were acquired using a Siemens BiographmCT PET/CT scanner. 18F-FMISO PET was performed on a single patient at 3 different time points around a single SBRT delivery of 18 Gy and HVs were compared using a tumor-to-blood ratio (TBR)>1.2 and rate of influx (Ki)>0.0015 (Patlak). Results: Results from our first patient showed substantial temporal changes in HV following SBRT. Using a TBR threshold >1.2 and summed images 210–240min, the HVs were 19%, 31% and 13% of total tumor volume on day 0, 2 (48 hours post-SBRT), and 4 (96 hours post-SBRT). The absolute volume of hypoxia increased by nearly a factor of 2 after 18 Gy and then decreased almost to baseline 96 hours later. Selected imaging timepoints resulted in temporal changes in HV quantification obtained with TBR. Ki, calculated using 4-hour dynamic data, evaluated HVs as 22%, 75% and 21%, respectively. Conclusions: ith the results of only one patient, this novel pilot study highlights the potential benefit of 18F-FMISO PET imaging as results indicate substantial temporal changes in tumor HV post-SBRT. Analysis suggests that TBR is not a robust parameter for accurate HV quantification and heavily influenced by imaging timepoint selection. Kinetic modeling parameters are more sensitive and may aid in future treatment individualization

  13. Cell sensitivity to exogenous agents as a basis of tumor therapy

    International Nuclear Information System (INIS)

    Dose-survival relationship of mammalian cells to exogeous agents, as determined by in vitro and in vivo assays, provides a bases for tumor therapy. The dose-survival response can be altered by several cellular factors: (1) cell cycle dependence of sensitivity, (2) growth phase dependence of sensitivity, (3) repair of sublethal damage, (4) repair of potentially lethal damage, and (5) cell-drug interaction. All of these factors are deeply involved in a therapeutic design for tumors. Repair of potentially lethal damage and cell-drug interaction, and the most recent development in studies of these factors, were mentioned in relation to bleomycin action on mammalian cells. On the basis of these cellular factors the pros and cons of different therapeutic designs for bleomycin were discussed. (auth.)

  14. RCC1-dependent activation of Ran accelerates cell cycle and DNA repair, inhibiting DNA damage-induced cell senescence.

    Science.gov (United States)

    Cekan, Pavol; Hasegawa, Keisuke; Pan, Yu; Tubman, Emily; Odde, David; Chen, Jin-Qiu; Herrmann, Michelle A; Kumar, Sheetal; Kalab, Petr

    2016-04-15

    The coordination of cell cycle progression with the repair of DNA damage supports the genomic integrity of dividing cells. The function of many factors involved in DNA damage response (DDR) and the cell cycle depends on their Ran GTPase-regulated nuclear-cytoplasmic transport (NCT). The loading of Ran with GTP, which is mediated by RCC1, the guanine nucleotide exchange factor for Ran, is critical for NCT activity. However, the role of RCC1 or Ran⋅GTP in promoting cell proliferation or DDR is not clear. We show that RCC1 overexpression in normal cells increased cellular Ran⋅GTP levels and accelerated the cell cycle and DNA damage repair. As a result, normal cells overexpressing RCC1 evaded DNA damage-induced cell cycle arrest and senescence, mimicking colorectal carcinoma cells with high endogenous RCC1 levels. The RCC1-induced inhibition of senescence required Ran and exportin 1 and involved the activation of importin β-dependent nuclear import of 53BP1, a large NCT cargo. Our results indicate that changes in the activity of the Ran⋅GTP-regulated NCT modulate the rate of the cell cycle and the efficiency of DNA repair. Through the essential role of RCC1 in regulation of cellular Ran⋅GTP levels and NCT, RCC1 expression enables the proliferation of cells that sustain DNA damage. PMID:26864624

  15. Diurnal variations of Titan's ionosphere

    Science.gov (United States)

    Cui, J.; Galand, M.; Yelle, R. V.; Vuitton, V.; Wahlund, J.-E.; Lavvas, P. P.; Müller-Wodarg, I. C. F.; Cravens, T. E.; Kasprzak, W. T.; Waite, J. H.

    2009-06-01

    We present our analysis of the diurnal variations of Titan's ionosphere (between 1000 and 1300 km) based on a sample of Ion Neutral Mass Spectrometer (INMS) measurements in the Open Source Ion (OSI) mode obtained from eight close encounters of the Cassini spacecraft with Titan. Although there is an overall ion depletion well beyond the terminator, the ion content on Titan's nightside is still appreciable, with a density plateau of ˜700 cm-3 below ˜1300 km. Such a plateau is a combined result of significant depletion of light ions and modest depletion of heavy ones on Titan's nightside. We propose that the distinctions between the diurnal variations of light and heavy ions are associated with their different chemical loss pathways, with the former primarily through “fast” ion-neutral chemistry and the latter through “slow” electron dissociative recombination. The strong correlation between the observed night-to-day ion density ratios and the associated ion lifetimes suggests a scenario in which the ions created on Titan's dayside may survive well to the nightside. The observed asymmetry between the dawn and dusk ion density profiles also supports such an interpretation. We construct a time-dependent ion chemistry model to investigate the effect of ion survival associated with solid body rotation alone as well as superrotating horizontal winds. For long-lived ions, the predicted diurnal variations have similar general characteristics to those observed. However, for short-lived ions, the model densities on the nightside are significantly lower than the observed values. This implies that electron precipitation from Saturn's magnetosphere may be an additional and important contributor to the densities of the short-lived ions observed on Titan's nightside.

  16. Genetic variation in dieback resistance

    DEFF Research Database (Denmark)

    Lobo, Albin; Hansen, Jon Kehlet; McKinney, Lea Vig;

    2014-01-01

    -eastern Zealand, Denmark, and confirmed the presence of substantial genetic variation in ash dieback susceptibility. The average crown damage increased in the trial from 61% in 2009 to 66% in 2012 and 72% in 2014, while the estimated heritability was 0.42 in both 2009 and 2012 but increased to 0.53 in 2014....... Genetic correlation between assessments was 0.88 between 2009 and 2012 and 0.91 between 2009 and 2014, suggesting fairly good possibilities for early selection of superior genotypes in the presence of high infection levels in the trial. The level of crown damage had strong negative effect on growth and...

  17. Quadratic Variation by Markov Chains

    DEFF Research Database (Denmark)

    Hansen, Peter Reinhard; Horel, Guillaume

    We introduce a novel estimator of the quadratic variation that is based on the the- ory of Markov chains. The estimator is motivated by some general results concerning filtering contaminated semimartingales. Specifically, we show that filtering can in prin- ciple remove the effects of market...... microstructure noise in a general framework where little is assumed about the noise. For the practical implementation, we adopt the dis- crete Markov chain model that is well suited for the analysis of financial high-frequency prices. The Markov chain framework facilitates simple expressions and elegant analyti...

  18. Induced polygenic variation in lentils

    International Nuclear Information System (INIS)

    In a study at the Himachal Pradesh Krishi Vishwa Vidyalay, India microsperma and macrosperma types of lentil seeds were irradiated with 5, 10, 15, 20 and 25 kR of gamma rays to study the nature and magnitude of induced variation in various polygenic traits in both lentil types. Data were recorded for seed yield, biological yield, harvest index, number of pods/plant, 100-seed weight, plant height, time to 50% flowering (days), and time to maturity (days). A sufficient genetic variability was induced for most polygenic traits in both lentil types. However, macrosperma type was found more radio-sensitive

  19. Systematic variations in divergence angle

    CERN Document Server

    Okabe, Takuya

    2012-01-01

    Practical methods for quantitative analysis of radial and angular coordinates of leafy organs of vascular plants are presented and applied to published phyllotactic patterns of various real systems from young leaves on a shoot tip to florets on a flower head. The constancy of divergence angle is borne out with accuracy of less than a degree. It is shown that apparent fluctuations in divergence angle are in large part systematic variations caused by the invalid assumption of a fixed center and/or by secondary deformations, while random fluctuations are of minor importance.

  20. Variational Recurrent Auto-Encoders

    OpenAIRE

    Fabius, Otto; van Amersfoort, Joost R.

    2014-01-01

    In this paper we propose a model that combines the strengths of RNNs and SGVB: the Variational Recurrent Auto-Encoder (VRAE). Such a model can be used for efficient, large scale unsupervised learning on time series data, mapping the time series data to a latent vector representation. The model is generative, such that data can be generated from samples of the latent space. An important contribution of this work is that the model can make use of unlabeled data in order to facilitate supervised...

  1. Variational collocation on finite intervals

    Science.gov (United States)

    Amore, Paolo; Cervantes, Mayra; Fernández, Francisco M.

    2007-10-01

    In this paper, we study a set of functions, defined on an interval of finite width, which are orthogonal and which reduce to the sinc functions when the appropriate limit is taken. We show that these functions can be used within a variational approach to obtain accurate results for a variety of problems. We have applied them to the interpolation of functions on finite domains and to the solution of the Schrödinger equation, and we have compared the performance of the present approach with others.

  2. Gauge Properties Of The Guiding Center Variational Symplectic Integrator

    Energy Technology Data Exchange (ETDEWEB)

    J. Squire, H. Qin and W. Tang

    2012-03-05

    Recently, variational symplectic algorithms have been developed for the long-time simulation of charged particles in magnetic fields1-3. As a direct consequence of their derivation from a discrete variational principle, these algorithms have very good long-time energy conservation, as well as exactly preserving discrete momenta. We present stability results for these algorithms, focusing on understanding how explicit variational integrators can be designed for this type of system. It is found that for explicit algorithms an instability arises because the discrete symplectic structure does not become the continuous structure in the t → 0 limit. We examine how a generalized gauge transformation can be used to put the Lagrangian in the "antisymmetric discretization gauge," in which the discrete symplectic structure has the correct form, thus eliminating the numerical instability. Finally, it is noted that the variational guiding center algorithms are not electromagnetically gauge invariant. By designing a model discrete Lagrangian, we show that the algorithms are approximately gauge invariant as long as A and are relatively smooth. A gauge invariant discrete Lagrangian is very important in a variational particle-in-cell algorithm where it ensures current continuity and preservation of Gauss's law4.

  3. Boundary Variation Diminishing (BVD) reconstruction: a new approach to improve Godunov scheme

    OpenAIRE

    Sun, Ziyao; Inaba, Satoshi; XIAO, FENG

    2016-01-01

    This paper presents a new approach, so-called boundary variation diminishing (BVD), for reconstructions that minimize the discontinuities (jumps) at cell interfaces in Godunov type schemes. It is motivated by the observation that diminishing the jump at the cell boundary might effectively reduce the dissipation in numerical flux. Different from the existing practices which seek high-order polynomials within mesh cells while assuming discontinuities being always at the cell interfaces, we prop...

  4. Cell-cycle-specific interaction of nuclear DNA-binding proteins with a CCAAT sequence from the human thymidine kinase gene

    International Nuclear Information System (INIS)

    Induction of thymidine kinase parallels the onset of DNA synthesis. To investigate the transcriptional regulation of the thymidine kinase gene, the authors have examined whether specific nuclear factors interact in a cell-cycle-dependent manner with sequences upstream of this gene. Two inverted CCAAT boxes near the transcriptional initiation sites were observed to form complexes with nuclear DNA-binding proteins. The nature of the complexes changes dramatically as the cells approach DNA synthesis and correlates well with the previously reported transcriptional increase of the thymidine kinase gene

  5. Dissecting Phenotypic Variation in Pigmentation using Forward and Reverse Genetics

    OpenAIRE

    Hellström, Anders R.

    2010-01-01

    Coat color and patterning phenotypes have been extensively studied as a model for advancing our understanding of the relationship between genetic and phenotypic variation. In this thesis, genes of relevance for pigment cell biology were investigated. The dissertation is divided in two parts. Forward genetics was used in the first part (Paper I and II) to identify the genes controlling the Silver and Sex-linked barring loci in chicken. In the second part, reverse genetics was employed to creat...

  6. Hierarchical Phenotypic and Epigenetic Variation in Cloned Swine1

    OpenAIRE

    Archer, Greg S.; Dindot, Scott; Friend, Ted H.; Walker, Shawn; Zaunbrecher, Gretchen; Lawhorn, Bruce; Piedrahita, Jorge A.

    2003-01-01

    Cloning by somatic cell nuclear transfer can result in the birth of animals with phenotypic and gene expression abnormalities. We compared adult cloned pigs and adult pigs from naturally bred control females using a series of physiological and genetic parameters, including detailed methylation profiles of selected genomic regions. Phenotypic and genetic analyses indicated that there are two classes of traits, one in which the cloned pigs have less variation than controls and another character...

  7. SYSTEM OF GENERALIZED VECTOR VARIATIONAL INEQUALITIES

    Institute of Scientific and Technical Information of China (English)

    Fang Yaping; Huang Nanjing

    2005-01-01

    In this paper, the authors introduce and study system of generalized vector variational inequalities. Under suitable conditions, the existence of solutions for system of generalized vector variational inequalities is presented by Kakutani-Fan-Glicksberg fixed point theorem.

  8. Origins of variation in conducted vasomotor responses

    DEFF Research Database (Denmark)

    Hald, Bjørn Olav; Welsh, Donald G.; Holstein-Rathlou, Niels-Henrik;

    2015-01-01

    variation. Using a computational approach that allows for introduction of structural and electrophysiological heterogeneity, we systematically tested variations in both arteriolar electrophysiology and modes of stimuli. Within the same vessel, our simulations show that conduction efficacy is influenced by...

  9. Protein dynamics in individual human cells: experiment and theory.

    Directory of Open Access Journals (Sweden)

    Ariel Aharon Cohen

    Full Text Available A current challenge in biology is to understand the dynamics of protein circuits in living human cells. Can one define and test equations for the dynamics and variability of a protein over time? Here, we address this experimentally and theoretically, by means of accurate time-resolved measurements of endogenously tagged proteins in individual human cells. As a model system, we choose three stable proteins displaying cell-cycle-dependant dynamics. We find that protein accumulation with time per cell is quadratic for proteins with long mRNA life times and approximately linear for a protein with short mRNA lifetime. Both behaviors correspond to a classical model of transcription and translation. A stochastic model, in which genes slowly switch between ON and OFF states, captures measured cell-cell variability. The data suggests, in accordance with the model, that switching to the gene ON state is exponentially distributed and that the cell-cell distribution of protein levels can be approximated by a Gamma distribution throughout the cell cycle. These results suggest that relatively simple models may describe protein dynamics in individual human cells.

  10. Racial variations in obstetric practice.

    Science.gov (United States)

    Cauchi, M N

    1986-05-01

    This study involves a retrospective analysis of 453 pregnant persons, with the aim of comparing certain disorders of pregnancy as well as infant and placental parameters in various racial groups within the same community. Significant variations were seen in the mean age of the patients, age at first pregnancy, frequency distribution of first pregnancy, infant weight as well as gravida: parity ratio. There was a 3-fold increase in incidence of preeclampsia in the Australian-born population compared to other racial groups. Mild anaemias (haemoglobin less than 11.5 g/dl) were found in up to 61% of the Australian-born population compared to 32% of the other racial groups; however, more significant degrees of anaemia were more commonly found in certain ethnic groups (e.g. Greek 16%, Italian 15%, Australian-born 6%). These studies emphasize that overall incidence studies in a polyglot population can have very limited meaning, and that greater attention must be paid to the actual racial variations within a population. PMID:3464247

  11. On polar daily geomagnetic variation

    Directory of Open Access Journals (Sweden)

    Paola De Michelis

    2015-11-01

    Full Text Available The aim of this work is to investigate the nature of the daily magnetic field perturbations produced by ionospheric and magnetospheric currents at high latitudes. We analyse the hourly means of the X and Y geomagnetic field components recorded by a meridian chain of permanent geomagnetic observatories in the polar region of the Northern Hemisphere during a period of four years (1995-1998 around the solar minimum. We apply a mathematical method, known as natural orthogonal component (NOC, which is capable of characterizing the dominant modes of the geomagnetic field daily variability through a set of empirical orthogonal functions (EOFs. Using the first two modes we reconstruct a two-dimensional equivalent current representation of the ionospheric electric currents, which contribute substantially to the geomagnetic daily variations. The obtained current structures resemble the equivalent current patterns of DP2 and DP1. We characterize these currents by studying their evolution with the geomagnetic activity level and by analysing their dependence on the interplanetary magnetic field. The obtained results support the idea of a coexistence of two main processes during all analysed period although one of them, the directly driven process, represents the dominant component of the geomagnetic daily variation.

  12. Partitioning of genetic variation between regulatory and coding gene segments: the predominance of software variation in genes encoding introvert proteins.

    Science.gov (United States)

    Mitchison, A

    1997-01-01

    In considering genetic variation in eukaryotes, a fundamental distinction can be made between variation in regulatory (software) and coding (hardware) gene segments. For quantitative traits the bulk of variation, particularly that near the population mean, appears to reside in regulatory segments. The main exceptions to this rule concern proteins which handle extrinsic substances, here termed extrovert proteins. The immune system includes an unusually large proportion of this exceptional category, but even so its chief source of variation may well be polymorphism in regulatory gene segments. The main evidence for this view emerges from genome scanning for quantitative trait loci (QTL), which in the case of the immune system points to a major contribution of pro-inflammatory cytokine genes. Further support comes from sequencing of major histocompatibility complex (Mhc) class II promoters, where a high level of polymorphism has been detected. These Mhc promoters appear to act, in part at least, by gating the back-signal from T cells into antigen-presenting cells. Both these forms of polymorphism are likely to be sustained by the need for flexibility in the immune response. Future work on promoter polymorphism is likely to benefit from the input from genome informatics. PMID:9148788

  13. Cytoplasmic genetic variation and extensive cytonuclear interactions influence natural variation in the metabolome

    DEFF Research Database (Denmark)

    Joseph, Bindu; Corwin, Jason A.; Li, Baohua;

    2013-01-01

    affects phenotypic variation. This showed that the cytoplasmic variation had effects similar to, if not larger than, the largest individual nuclear locus. Inclusion of cytoplasmic variation into the genetic model greatly increased the explained phenotypic variation. Cytoplasmic genetic variation was a...... central hub in the epistatic network controlling the plant metabolome. This epistatic influence manifested such that the cytoplasmic background could alter or hide pairwise epistasis between nuclear loci. Thus, cytoplasmic genetic variation plays a central role in controlling natural variation in...... metabolomic networks. This suggests that cytoplasmic genomes must be included in any future analysis of natural variation....

  14. Variations of images to increase their visibility

    OpenAIRE

    Sparavigna, Amelia Carolina

    2012-01-01

    The calculus of variations applied to the image processing requires some numerical models able to perform the variations of images and the extremization of appropriate actions. To produce the variations of images, there are several possibilities based on the brightness maps. Before a numerical model, I propose an experimental approach, based on a tool of Gimp, GNU Image Manipulation Program, in order to visualize how the image variations can be. After the discussion of this tool, which is abl...

  15. Quantum Annealing for Variational Bayes Inference

    OpenAIRE

    Sato, Issei; Kurihara, Kenichi; Tanaka, Shu; Nakagawa, Hiroshi; Miyashita, Seiji

    2014-01-01

    This paper presents studies on a deterministic annealing algorithm based on quantum annealing for variational Bayes (QAVB) inference, which can be seen as an extension of the simulated annealing for variational Bayes (SAVB) inference. QAVB is as easy as SAVB to implement. Experiments revealed QAVB finds a better local optimum than SAVB in terms of the variational free energy in latent Dirichlet allocation (LDA).

  16. Importance of Local Structural Variations on Recrystallization

    DEFF Research Database (Denmark)

    Juul Jensen, Dorte; Lin, Fengxiang; Zhang, Yubin; Zhang, Y.H.

    2013-01-01

    Effects of local variations in the deformation microstructure on subsequent recrystallization are discussed and illustrated by three examples. The three examples consider local variations on different length scales and are: 1. Effects of local variations in the deformation microstructure on the f...

  17. Non-differentiable variational principles

    Science.gov (United States)

    Cresson, Jacky

    2005-07-01

    We develop a calculus of variations for functionals which are defined on a set of non-differentiable curves. We first extend the classical differential calculus in a quantum calculus, which allows us to define a complex operator, called the scale derivative, which is the non-differentiable analogue of the classical derivative. We then define the notion of extremals for our functionals and obtain a characterization in term of a generalized Euler-Lagrange equation. We finally prove that solutions of the Schrödinger equation can be obtained as extremals of a non-differentiable variational principle, leading to an extended Hamilton's principle of least action for quantum mechanics. We compare this approach with the scale relativity theory of Nottale, which assumes a fractal structure of space-time.Résumé (Principes variationnels non différentiable). Nous développons un calcul des variations pour des fonctionnelles définies sur un ensemble de courbes non différentiables. Pour cela, nous étendons le calcul différentiel classique, en calcul appelé calcul quantique, qui nous permet de définir un opérateur à valeur complexes, appelé dérivée d'échelle, qui est l'analogue non différentiable de la dérivée usuelle. On définit alors la notion d'extremale pour ces fonctionnelles pour lesquelles nous obtenons une caractérisation via une équation d'Euler-Lagrange généralisée. On prouve enfin que les solutions de l'équation de Schrödinger peuvent s'obtenir comme solution d'un problème variationnel non différentiable, étendant ainsi le principe de moindre action de Hamilton au cadre de la mécanique quantique. On discute enfin la connexion entre ce travail et la théorie de la relativité d'échelle développée par Nottale, et qui suppose une structure fractale de l'espace-temps.

  18. 岩藻糖在正常人肝细胞、低转移人肝癌细胞和高转移人肝癌细胞表面的含量变化%The variation of fucose on the surfuace of normal hepatocytes,low metastatic hepatocellular carcinoma cells and high metastasis hepatoceHular carcinoma cells

    Institute of Scientific and Technical Information of China (English)

    廖晖; 廖彩仙; 王宇; 龚祖元; 胡育海

    2011-01-01

    目的 比较正常人肝细胞、低转移人肝癌细胞及高转移人肝癌细胞表面岩藻糖的含量差异.方法 利用能与岩藻糖特异性结合的异硫氰酸荧光素标记的荆豆凝集素(FITC-UEA),与正常人肝细胞、低转移人肝癌细胞及高转移人肝癌细胞悬液充分结合.而后用流式细胞仪定量检测细胞表面的荧光强度,据此评定正常人肝细胞、低转移人肝癌细胞和高转移人肝癌细胞表面岩藻糖的含量.结果 正常人肝细胞表面的荧光强度低于低转移人肝癌细胞扣高转移人肝癌细胞(P<0.05),高转移人肝癌细胞表面的荧光强度高于低转移人肝癌细胞(P<0.051.结论 细胞表面的岩藻糖含量变化与细胞癌变及癌变细胞的转移潜能有关.细胞癌变后,细胞表面的岩藻糖含量增加,并且癌变细胞的转移潜能越高,其表面岩藻糖含量也越高.%Objective To compare the differential expression level of fucose on the surface of normal hepa-tocytes, low metastatic hepatocellular carcinoma cells and high metastasis hepatocellular carcinoma cells. Methods The amounts of fucose expressed on normal hepatic cells, low metastatic hepatocellular carcinoma cells and high metastasis hepatocellular carcinoma cells were detected by flow cytometry using fucose-specific fluorescein isothiocyanate-ulex europaeus agglutinin (FITC-UEA) in single cell suspensions. Results The fluorescence intensity detected in hepatocytes was lower than those of low metastatic hepatocellular carcinoma cells and high metastasis hepatocellular carcinoma cells (P<0.05 for both comparisons). Compare with low metastatic hepatocellular carcinoma cells, the fluorescence intensity of high metastasis hepatocellular carcinoma cells was greater (P<0.05). Conclusion The amounts of fucose on cell surface was found to be closely related to the development and metastasis of hepatocellular carcinoma cells. After cell canceration, the fucose content on cell surface

  19. Expression of G protein-coupled receptor 19 in human lung cancer cells is triggered by entry into S phase and supports G2/M cell cycle progression

    International Nuclear Information System (INIS)

    G protein-coupled receptors (GPCRs) represent the largest family of cell surface receptors. However, only a fraction of the more than 800 receptors have been characterized to an extent that their physiological role is reasonably well understood. In fact, current pharmacotherapy only addresses some 60 receptors with a large collection of compounds that represent about 30% of the available drugs. It has long been known that GPCRs are subject to illegitimate expression in cancer cells. Presumably, hijacking the normal physiological functions of GPCRs contributes to all biological capabilities acquired during the multistep development of human cancers. With the goal of linking G protein-coupled receptors to malignant diseases, GPCRs were searched for that revealed high expression levels in small cell lung cancer (SCLC): The mRNA encoding orphan G protein-coupled receptor 19 (GPR19) was found to be frequently overexpressed in tissue samples obtained from patients with SCLC in contrast to samples derived from non-SCLC or normal lung. Several observations indicate that overexpression of Gpr19 confers a specific advantage to human lung cancer-derived cells regarding the transition through the cell cycle. Knockdown of Gpr19 mRNA by RNA interference reduced cell growth of human lung cancer cell lines and led to cell death. Cell cycle progression through G2/M phase was impaired and this was associated with increased protein levels of cyclin B1 and phosphorylated histone H3. Gpr19 exhibited a cell cycle-dependent expression pattern in lung cancer cell lines. When cell cycle distribution profiles of cells released from cell cycle arrest were related to Gpr19 mRNA levels, a peak Gpr19 expression was detected during S phase. The control of Gpr19 expression by E2F transcription factors, which drive gene expression of many genes important for cell cycle progression, was verified by chromatin immunoprecipitation: Antibodies directed against E2F-1 to E2F-4 allowed for the recovery of

  20. Variation of the latissimus dorsi

    Directory of Open Access Journals (Sweden)

    Ishani P Shah

    2014-01-01

    Full Text Available A typical muscle variation of latissimus dorsi - the axillary arch is represented by the muscular or fibromuscular slip detached from the anteroinferior border of the musculus latissimus dorsi passing over the axilla under the axillary fascia crossing the medial side of the brachial plexus to continue as a septum intermusculare mediale brachii distally to the medial epicondyle of humerus. The full extent of the muscle is rarely present. Slips of muscle extend from the latissimus dorsi at the inferior angle of scapula to insert into pectoralis major (Langer, coracobrachilis, biceps or coracoid process forming what is described as a common variant - the muscular axillary arch. We report three cases of variants of latissimus dorsi, one of which has not been reported in the literature before.

  1. Reasoning about Variation: Student Voice

    Directory of Open Access Journals (Sweden)

    Jackie Reid

    2007-10-01

    Full Text Available This paper reports one recent study that was part of a project investigating tertiary students’ understanding of variation. These students completed a questionnaire prior to, and at the end of, an introductory statistics course and this paper focuses on interviews of selected students designed to determine whether more information could have been gathered about the students’ reasoning. Clarification during interviews reinforced researcher interpretation of responses. Prompting assisted students to develop better quality responses but probing was mostly useful for assisting students to re-express reasoning already presented. Cognitive conflict situations proved challenging. The diversity of activities identified by students as assisting the development of their understanding provides a challenge for educators in planning teaching sequences. Both educators and researchers need to listen to students to better understand the development of reasoning.

  2. Equilibrium models and variational inequalities

    CERN Document Server

    Konnov, Igor

    2007-01-01

    The concept of equilibrium plays a central role in various applied sciences, such as physics (especially, mechanics), economics, engineering, transportation, sociology, chemistry, biology and other fields. If one can formulate the equilibrium problem in the form of a mathematical model, solutions of the corresponding problem can be used for forecasting the future behavior of very complex systems and, also, for correcting the the current state of the system under control. This book presents a unifying look on different equilibrium concepts in economics, including several models from related sciences.- Presents a unifying look on different equilibrium concepts and also the present state of investigations in this field- Describes static and dynamic input-output models, Walras, Cassel-Wald, spatial price, auction market, oligopolistic equilibrium models, transportation and migration equilibrium models- Covers the basics of theory and solution methods both for the complementarity and variational inequality probl...

  3. Variational Principle for Planetary Interiors

    CERN Document Server

    Zeng, Li

    2016-01-01

    In the past few years, the number of confirmed planets has grown above 2000. It is clear that they represent a diversity of structures not seen in our own solar system. In addition to very detailed interior modeling, it is valuable to have a simple analytical framework for describing planetary structures. Variational principle is a fundamental principle in physics, entailing that a physical system follows the trajectory which minimizes its action. It is alternative to the differential equation formulation of a physical system. Applying this principle to planetary interior can beautifully summarize the set of differential equations into one, which provides us some insight into the problem. From it, a universal mass-radius relation, an estimate of error propagation from equation of state to mass-radius relation, and a form of virial theorem applicable to planetary interiors are derived.

  4. Variational Approach and Deformed Derivatives

    CERN Document Server

    Weberszpil, José

    2015-01-01

    Recently, we have demonstrated that there exists a possible relationship between q-deformed algebras in two different contexts of Statistical Mechanics, namely, the Tsallis' framework and the Kaniadakis' scenario, with a local form of fractional-derivative operators for fractal media, the so-called Hausdorff derivatives, mapped into a continuous medium with a fractal measure. Here, in this paper, we present an extension of the traditional calculus of variations for systems containing deformed-derivatives embedded into the Lagrangian and the Lagrangian densities for classical and field systems. The results extend the classical Euler-Lagrange equations and the Hamiltonian formalism. The resulting dynamical equations seem to be compatible with those found in the literature, specially with mass-dependent and with nonlinear equations for systems in classical and quantum mechanics. Examples are presented to illustrate applications of the formulation. Also, the conserved Nether current, are worked out.

  5. Some Variations on Maxwell's Equations

    CERN Document Server

    Ascoli, G A; Ascoli, Giorgio A.; Goldin, Gerald A.

    2006-01-01

    In the first sections of this article, we discuss two variations on Maxwell's equations that have been introduced in earlier work---a class of nonlinear Maxwell theories with well-defined Galilean limits (and correspondingly generalized Yang-Mills equations), and a linear modification motivated by the coupling of the electromagnetic potential with a certain nonlinear Schroedinger equation. In the final section, revisiting an old idea of Lorentz, we write Maxwell's equations for a theory in which the electrostatic force of repulsion between like charges differs fundamentally in magnitude from the electrostatic force of attraction between unlike charges. We elaborate on Lorentz' description by means of electric and magnetic field strengths, whose governing equations separate into two fully relativistic Maxwell systems---one describing ordinary electromagnetism, and the other describing a universally attractive or repulsive long-range force. If such a force cannot be ruled out {\\it a priori\\/} by known physical ...

  6. Fisher Algorithm: Variations And Applications

    Directory of Open Access Journals (Sweden)

    Adegoke

    2013-12-01

    Full Text Available This paper examines Fisherface (Linear Discriminant Analysis methods, its different modifications as applied to feature extraction in face recognition. Researchers showed that Fisher algorithm, though it performs better than PCA, Eigenface and some other fundamental methods, computational complexity, enormous hardware resources usage are inhibitors to its implementation. Different versions or adaptations of Fisher algorithm had been developed, and applied to face recognition and validated using some of the available public face databases. If fisher algorithm and its various variations had so marvelously helped in face recognition, application of this effective dimensionality reduction method can be applied to research area of iris recognition system. This will in return enhance performance of biometric systems in its application to computer security and surveillance.

  7. Flux Variation of Cosmic Muons

    CERN Document Server

    Ramesh, Nepal; Martin, Clayton; Bachri, Abdel

    2012-01-01

    In the current paper, we analyzed the variation of cosmic radiation flux with elevation, time of the year and ambient temperature with the help of a portable cosmic muon detector, the construction of which was completed by a team from Southern Arkansas University (SAU) at Lawrence Berkeley National Laboratory (LBNL). Cosmic muons and gamma rays traverse two synchronized scintillators connected to two photomultiplier tubes (PMT) via light guides, and generate electronic pulses which we counted using a Data Acquisition Board (DAQ). Because muons are the product of collisions between high-energy cosmic rays and atmospheric nuclei, and therefore shower onto earth, the scintillators were arranged horizontally for detection. The elevation measurements were recorded at different locations, starting from 60 feet below sea-level at the Underground Radiation Counting Laboratory at Johnson Space Center, TX, to 4200 feet at Mt. Hamilton, CA. Intermediate locations included sea-level Galveston Bay, TX, and Mt. Magazine, A...

  8. Variational approach and deformed derivatives

    Science.gov (United States)

    Weberszpil, J.; Helayël-Neto, J. A.

    2016-05-01

    Recently, we have demonstrated that there exists a possible relationship between q-deformed algebras in two different contexts of Statistical Mechanics, namely, the Tsallis' framework and the Kaniadakis' scenario, with a local form of fractional-derivative operators for fractal media, the so-called Hausdorff derivatives, mapped into a continuous medium with a fractal measure. Here, in this paper, we present an extension of the traditional calculus of variations for systems containing deformed-derivatives embedded into the Lagrangian and the Lagrangian densities for classical and field systems. The results extend the classical Euler-Lagrange equations and the Hamiltonian formalism. The resulting dynamical equations seem to be compatible with those found in the literature, specially with mass-dependent and with nonlinear equations for systems in classical and quantum mechanics. Examples are presented to illustrate applications of the formulation. Also, the conserved ​Noether current is worked out.

  9. Turbidity variations at Hanford since July 1974

    International Nuclear Information System (INIS)

    Spectral turbidity coefficients derived from multiwavelength sunphotometer measurements obtained from July 1974 to December 1976 have been analyzed for seasonal and weekly variations. Weak biannual variations in turbidity are apparent in the data. Day-to-day variations, however, can be much larger than the coefficients for the fitted biannual terms. Consequently, it now appears that observed variations in turbidity at Hanford are related to the synoptic meteorology with a smaller, superimposed seasonality of dust and smoke sources. Turbidity variations are also independent of the day of the week

  10. Some Variational Principles for Coupled Thermoelasticity

    Directory of Open Access Journals (Sweden)

    Francesco Marotti de Sciarra

    2013-01-01

    Full Text Available The nonlinear thermoelasticity of type II proposed by Green and Naghdi is considered. The thermoelastic structural model is formulated in a quasistatic range, and the related thermoelastic variational formulation in the complete set of state variables is recovered. Hence a consistent framework to derive all the variational formulations with different combinations of the state variables is provided, and a family of mixed variational formulations, with different combinations of state variables, is provided starting from the general variational formulation. A uniqueness condition is provided on the basis of a suitable variational formulation.

  11. Variational methods for field theories

    International Nuclear Information System (INIS)

    Four field theory models are studied: Periodic Quantum Electrodynamics (PQED) in (2 + 1) dimensions, free scalar field theory in (1 + 1) dimensions, the Quantum XY model in (1 + 1) dimensions, and the (1 + 1) dimensional Ising model in a transverse magnetic field. The last three parts deal exclusively with variational methods; the PQED part involves mainly the path-integral approach. The PQED calculation results in a better understanding of the connection between electric confinement through monopole screening, and confinement through tunneling between degenerate vacua. This includes a better quantitative agreement for the string tensions in the two approaches. Free field theory is used as a laboratory for a new variational blocking-truncation approximation, in which the high-frequency modes in a block are truncated to wave functions that depend on the slower background modes (Boron-Oppenheimer approximation). This ''adiabatic truncation'' method gives very accurate results for ground-state energy density and correlation functions. Various adiabatic schemes, with one variable kept per site and then two variables per site, are used. For the XY model, several trial wave functions for the ground state are explored, with an emphasis on the periodic Gaussian. A connection is established with the vortex Coulomb gas of the Euclidean path integral approach. The approximations used are taken from the realms of statistical mechanics (mean field approximation, transfer-matrix methods) and of quantum mechanics (iterative blocking schemes). In developing blocking schemes based on continuous variables, problems due to the periodicity of the model were solved. Our results exhibit an order-disorder phase transition. The transfer-matrix method is used to find a good (non-blocking) trial ground state for the Ising model in a transverse magnetic field in (1 + 1) dimensions

  12. Environmental variation, stochastic extinction, and competitive coexistence.

    Science.gov (United States)

    Adler, Peter B; Drake, John M

    2008-11-01

    Understanding how environmental fluctuations affect population persistence is essential for predicting the ecological impacts of expected future increases in climate variability. However, two bodies of theory make opposite predictions about the effect of environmental variation on persistence. Single-species theory, common in conservation biology and population viability analyses, suggests that environmental variation increases the risk of stochastic extinction. By contrast, coexistence theory has shown that environmental variation can buffer inferior competitors against competitive exclusion through a storage effect. We reconcile these two perspectives by showing that in the presence of demographic stochasticity, environmental variation can increase the chance of extinction while simultaneously stabilizing coexistence. Our stochastic simulations of a two-species storage effect model reveal a unimodal relationship between environmental variation and coexistence time, implying maximum coexistence at intermediate levels of environmental variation. The unimodal pattern reflects the fact that the stabilizing influence of the storage effect accumulates rapidly at low levels of environmental variation, whereas the risk of extinction due to the combined effects of environmental variation and demographic stochasticity increases most rapidly at higher levels of variation. Future increases in environmental variation could either increase or decrease an inferior competitor's expected persistence time, depending on the distance between the present level of environmental variation and the optimal level anticipated by this theory. PMID:18817458

  13. Accommodating variation: dialects, idiolects, and speech processing.

    Science.gov (United States)

    Kraljic, Tanya; Brennan, Susan E; Samuel, Arthur G

    2008-04-01

    Listeners are faced with enormous variation in pronunciation, yet they rarely have difficulty understanding speech. Although much research has been devoted to figuring out how listeners deal with variability, virtually none (outside of sociolinguistics) has focused on the source of the variation itself. The current experiments explore whether different kinds of variation lead to different cognitive and behavioral adjustments. Specifically, we compare adjustments to the same acoustic consequence when it is due to context-independent variation (resulting from articulatory properties unique to a speaker) versus context-conditioned variation (resulting from common articulatory properties of speakers who share a dialect). The contrasting results for these two cases show that the source of a particular acoustic-phonetic variation affects how that variation is handled by the perceptual system. We also show that changes in perceptual representations do not necessarily lead to changes in production. PMID:17803986

  14. Fluorescence microscopical studies on chitin distribution in the cell wall of giant cells of Saccharomyces uvarum, grown following X-radiaiton treatment

    International Nuclear Information System (INIS)

    Teast cells are synchronized and modiated with X-rays (1.0 kGy) in the Cr, phase. Their growth behaviour is observed in suspension cultures and the formation of giant cells noted. The chitin structures are selectively stained with the fluorescent dye Calcofluor white. In the unradiated cells the chitin is deposited at the bud constriction site in the form of rings in the mother cell wall, whereas for irradiated cells only one chitin ring of normal appearance is formed between the mother cell and first bud equivalent. Between further bud equivalents an intensification of fluorescence is occasionally noted, however the organisation of the chitin into a regular ring arrangement is disturbed. In giant cells the facility for primary and secondary septa formation is missing and these are essential for successful cell division. By further experiments it was possible to identify the cause of disturbance in the cell cycle of irradiated cells. Giant cells only form one chitin ring because its DNA is replicated one time only. The major cause triggering the actual formation of giant cells must be considered the missing distribution of the once-rephicated DNA. All processes in the cell cycle dependent on this step are therefore stopped and only bud formation which occurs independently continues along its rhytmical path. (orig./MG)

  15. Silica nanoparticles induced metabolic stress through EGR1, CCND, and E2F1 genes in human mesenchymal stem cells.

    Science.gov (United States)

    Periasamy, Vaiyapuri S; Athinarayanan, Jegan; Akbarsha, Mohammad A; Alshatwi, Ali A

    2015-01-01

    The SiO2 synthesized in bulk form, adopting the conventional methods for application in food industry applications, may also contain nano-sized particles. On account of the unique physico-chemical properties, the SiO2 particulates, such as size and shape, cause metabolic toxicity in cells. Poor understanding of the molecular level nanotoxicity resulting from high-volume synthetic SiO2 exposures in humans is a serious issue, since these particles may also contribute to metabolic stress-mediated chronic diseases. In the present study, we examined the structural characteristics of these nano-sized silica particles adopting SEM and dynamic light scattering (DLS) and assessed the alterations in the cell cycle induced by these silica particles in human mesenchymal stem cells (hMSCs) adopting 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) cell viability assay, morphological changes in the cells adopting fluorescent microscopy, cell cycle analysis adopting flow cytometry, and the expression of genes linked to cell cycle (i.e., proliferating cell nuclear antigen (PCNA), early growth response protein (EGR1), E2F transcription factor (E2F1), cyclin D1, cyclin C, and cyclin D3) adopting qPCR. The SEM and DLS studies indicated that the commercial grade SiO2-NPs were in the nano-scale range. Alterations in the cytoplasmic organization, nuclear morphology, cell cycle progression, and expression of genes linked to cell cycle-dependent metabolic stress through EGR1, CCND, and E2F1 genes were the primary indicators of metabolic stress. Overall, the results of this study demonstrate that synthetic SiO2 acutely affects hMSC through cell cycle-dependent oxidative stress gene network. The toxicity mechanisms (both acute and chronic) of food grade silica should be investigated in greater depth with special reference to food safety. PMID:25374141

  16. Biological variation in Trichinella species and genotypes.

    Science.gov (United States)

    Bolas-Fernández, F

    2003-06-01

    At present, the genus Trichinella comprises seven species of which five have encapsulated muscle larvae (T. spiralis, T. nativa, T. britovi, T. nelsoni and T. murrelli) and two do not (T. pseudospiralis and T. papuae) plus three genotypes of non-specific status (T6, T8 and T9). The diagnostic characteristics of these species are based on biological, biochemical and genetic criteria. Of biological significance is variation observed among species and isolates in parameters such as infectivity and immunogenicity. Infectivity of Trichinella species or isolates is determined, among other considerations, by the immune status of the host in response to species- or isolate-specific antigens. Common and particular antigens determine the extent of protective responses against homologous or heterologous challenge. The kinetics of isotype, cytokine and inflammatory responses against T. spiralis infections are isolate-dependent. Trichinella spiralis and T. pseudospiralis induce different dose-dependent T-cell polarizations in the early host response, with T. spiralis initially preferentially promoting Th1-type responses before switching to Th2 and T. pseudospiralis driving Th2-type responses from the outset. PMID:12756064

  17. Muon spectra, expected characteristics of inclined muon monitors by means of generating functions and an analysis of the diurnal variation at Kiruna

    International Nuclear Information System (INIS)

    Successive generations in the nucleon-meson cascade are calculated by means of generating functions. Expected muon spectra at different zenith angles and levels are in excellent agreement with measurements in the 0.2-50 GeV/c momentum range. A functional relation between the absolute value and slope of the primary spectrum and the inelasticity is established. On the average 1.6 intranuclear collisions in an air nucleus are taken into account. The calculated electron and positron content in an unshielded inclined muon telescope is 30%, with 100% detector efficiency. Coupling functions taking into account up to seven generations in the cascade, allowing for the primary composition are calculated. Expected time variations from anisotropies of different angular distributions in inclined meson telescopes at a high latitude station are given. Time characteristics such as expected times of maxima, phase differences and amplitude ratios for the north and south directed telescopes at Kiruna are computed for a variational spectrum of the form Psub(β) cos Λ, where Λ is the angle between the asymptotic direction and the axis of the anisotropy. The reduction in amplitude due to three dimensional cascading is only 0.4(+2.0-0.4)%. A peculiar and persistent phase shift in the Kiruna north directed talescope is interpreted as being due to Forbush decreases and temperature effects. The yearly difference vector of the two telescopes over nearly one solar cycle has been analysed. Based on a variational spectrum with β=0.0 and selected values of the free space amplitude, the phase and upper cut-off Psub(u) of the anisotropy are derived. The variation of Psub(u) with time shows a pronounced solar cycle dependence. (Auth.)

  18. Kinetics of DNA double-strand break repair throughout the cell cycle as assayed by pulsed field gel electrophoresis in CHO cells

    International Nuclear Information System (INIS)

    Repair of DNA double-strand breaks (dsb) was measured in exponentially growing, plateau-phase and synchronized G1, G1/S, early S, mid-S, late S, G2 + M amd mitotic CHO cells. Results suggest that the state of chromatin condensation has only a limited impact on the ability of the cells to rejoin dsb, and indicate that the cell cycle-dependent fluctuations in radiosensitivity cannot be explained by alterations in the rate of rejoining of dsb. Repair half-times of the slow component of dsb rejoining were similar to the half-times of rejoining of chromosome breaks as visualized by the technique of premature chromosome condensation, suggesting a cause-effect relationship between rejoining of this subject of dsb and rejoining of chromosome breaks. (author)

  19. The temporal organization of processes of cell reproduction and its connection with rhythms of radiosensitivity of the body

    Science.gov (United States)

    Druzhinin, Y. P.; Romanov, Y. A.; Vatsek, A.

    1974-01-01

    Radiosensitivity of individual phases of the mitotic cycle was studied in synchronous cell cultures and in several biological objects. It was found that radiosensitivity changed essentially according to phases of the mitotic cycle, depending on the kind of cells, evaluation criteria and the radiation dosage. Tests on partially synchronized HeLa cell populations, according to the criterion of survival, showed them most sensitive during mitosis, as well as in later G sub 1- or early DNA-synthesizing stages. With radiation in doses of 300 rad, the proportion of surviving cells showed a sensitivity directly before DNA synthesis of approximately 4 times higher than the later S-phase and during the major portion of G sub 1- and G sub 2-periods. Sensitivity of cells in mitosis was approximately 3 times higher than in late G sub 1- and early S-phases.

  20. A deep-seated mechanism for cycle-dependent sunspot group tilt angles

    Science.gov (United States)

    Isik, Emre

    2016-07-01

    The cycle-averaged tilt angle of sunspot groups is an important quantity in determining the magnetic flux diffusing across the equator, which is highly correlated with the strength of the next cycle. This quantity has recently been reported to be anti-correlated with the strength of the solar cycle. I suggest that a deep-seated thermodynamic cycle can be responsible for the observed correlation. Motivated by helioseismic indications, I calculate the effect of cooling of the convective overshoot region on the stability and dynamics of thin, unstable flux tubes. I find that only 5-20 K of cooling in the layer can explain the observed range of tilt angle fluctuations among different cycles. This mechanism can play a role in the nonlinear saturation and amplitude fluctuations of the solar dynamo.

  1. Solar cycle dependent characteristics of the equatorial blanketing Es layers and associated irregularities

    Directory of Open Access Journals (Sweden)

    S. Ravindran

    2006-11-01

    Full Text Available The occurrence of blanketing type Es (Esb layers and associated E-region irregularities over the magnetic equatorial location of Trivandrum (8.5° N; 77° E; dip ~0.5° during the summer solstitial months of May, June, July and August has been investigated in detail for the period 1986–2000 to bring out the variabilities in their characteristics with the solar cycle changes. The study has been made using the ionosonde and magnetometer data of Trivandrum from 1986–2000 along with the available data from the 54.95 MHz VHF backscatter radar at Trivandrum for the period 1995–2000. The appearance of blanketing Es layers during these months is observed to be mostly in association with the occurrence of afternoon Counter Electrojet (CEJ events. The physical process leading to the occurrence of a CEJ event is mainly controlled by the nature of the prevailing electro dynamical/neutral dynamical conditions before the event. Hence it is natural that the Esb layer characteristics like the frequency of occurrence, onset time, intensity, nature of gradients in its top and bottom sides etc are also affected by the nature of the background electro dynamical /neutral dynamical processes which in turn are strongly controlled by the solar activity changes. The occurrence of Esb layers during the solstitial months is found to show very strong solar activity dependence with the occurrence frequency being very large during the solar minimum years and very low during solar maximum years. The intensity of the VHF radar backscattered signals from the Esb irregularities is observed to be controlled by the relative roles of the direction and magnitude of the prevailing vertical polarization electric field and the vertical electron density gradient of the prevailing Esb layer depending on the phase of the solar cycle. The gradient of the Esb layer shows a more dominant role in the generation of gradient instabilities during solar minimum periods while it is the electric field that has a more dominant role during solar maximum periods.

  2. Estrous Cycle-Dependent Phasic Changes in the Stoichiometry of Hippocampal Synaptic AMPA Receptors in Rats

    OpenAIRE

    Hirobumi Tada; Mayu Koide; Wakana Ara; Yusuke Shibata; Toshiya Funabashi; Kumiko Suyama; Takahisa Goto; Takuya Takahashi

    2015-01-01

    Cognitive function can be affected by the estrous cycle. However, the effect of the estrous cycle on synaptic functions is poorly understood. Here we show that in female rats, inhibitory-avoidance (IA) task (hippocampus-dependent contextual fear-learning task) drives GluA2-lacking Ca2+-permeable AMPA receptors (CP-AMPARs) into the hippocampal CA3-CA1 synapses during all periods of the estrous cycle except the proestrous period, when estrogen levels are high. In addition, IA task failed to dri...

  3. Estrous Cycle-Dependent Phasic Changes in the Stoichiometry of Hippocampal Synaptic AMPA Receptors in Rats.

    Directory of Open Access Journals (Sweden)

    Hirobumi Tada

    Full Text Available Cognitive function can be affected by the estrous cycle. However, the effect of the estrous cycle on synaptic functions is poorly understood. Here we show that in female rats, inhibitory-avoidance (IA task (hippocampus-dependent contextual fear-learning task drives GluA2-lacking Ca2+-permeable AMPA receptors (CP-AMPARs into the hippocampal CA3-CA1 synapses during all periods of the estrous cycle except the proestrous period, when estrogen levels are high. In addition, IA task failed to drive CP-AMPARs into the CA3-CA1 synapses of ovariectomized rats only when estrogen was present. Thus, changes in the stoichiometry of AMPA receptors during learning depend on estrogen levels. Furthermore, the induction of long-term potentiation (LTP after IA task was prevented during the proestrous period, while intact LTP is still expressed after IA task during other period of the estrous cycle. Consistent with this finding, rats conditioned by IA training failed to acquire hippocampus-dependent Y-maze task during the proestrous period. On the other hand, during other estrous period, rats were able to learn Y-maze task after IA conditioning. These results suggest that high estrogen levels prevent the IA learning-induced delivery of CP-AMPARs into hippocampal CA3-CA1 synapses and limit synaptic plasticity after IA task, thus preventing the acquisition of additional learning.

  4. Estrous Cycle-Dependent Phasic Changes in the Stoichiometry of Hippocampal Synaptic AMPA Receptors in Rats.

    Science.gov (United States)

    Tada, Hirobumi; Koide, Mayu; Ara, Wakana; Shibata, Yusuke; Funabashi, Toshiya; Suyama, Kumiko; Goto, Takahisa; Takahashi, Takuya

    2015-01-01

    Cognitive function can be affected by the estrous cycle. However, the effect of the estrous cycle on synaptic functions is poorly understood. Here we show that in female rats, inhibitory-avoidance (IA) task (hippocampus-dependent contextual fear-learning task) drives GluA2-lacking Ca2+-permeable AMPA receptors (CP-AMPARs) into the hippocampal CA3-CA1 synapses during all periods of the estrous cycle except the proestrous period, when estrogen levels are high. In addition, IA task failed to drive CP-AMPARs into the CA3-CA1 synapses of ovariectomized rats only when estrogen was present. Thus, changes in the stoichiometry of AMPA receptors during learning depend on estrogen levels. Furthermore, the induction of long-term potentiation (LTP) after IA task was prevented during the proestrous period, while intact LTP is still expressed after IA task during other period of the estrous cycle. Consistent with this finding, rats conditioned by IA training failed to acquire hippocampus-dependent Y-maze task during the proestrous period. On the other hand, during other estrous period, rats were able to learn Y-maze task after IA conditioning. These results suggest that high estrogen levels prevent the IA learning-induced delivery of CP-AMPARs into hippocampal CA3-CA1 synapses and limit synaptic plasticity after IA task, thus preventing the acquisition of additional learning. PMID:26121335

  5. The Response of Thermospheric Winds to Geomagnetic Storms and Its Solar Cycle Dependence

    Science.gov (United States)

    Wang, W.; Burns, A. G.; Qian, L.

    2014-12-01

    Thermospheric neutral wind circulation is set up as a result of a number of competing forcing processes. These include the pressure gradient, ion drag, Coriolis, momentum advection and viscosity forces. All of these forces change with varying solar radiation and geomagnetic activity. In this study we employ the thermosphere ionosphere electrodynamics global circulation model (TIEGCM) to elucidate the changes of thermospheric neutral winds with geomagnetic storms when a large amount of energy and momentum is deposited into the thermosphere at high latitudes. We will focus on the low and middle latitudes, where enhanced equatorward and westward winds are seen during the storms. The storm-time westward winds occur at all local times and are sustained well into the storm recovery phase. Diagnostic analysis on TIEGCM simulations suggests that momentum advection, ion drag and pressure gradient are the main drivers of these storm-time wind changes. The TIEGCM has also been run for different solar cycle conditions. Wind changes are smaller during solar maximum at low and middle latitudes. This is the result of higher neutral temperature and pressure gradient at low and middle latitudes in solar maximum, which limits the penetration of wind changes at high latitudes into low and middle latitudes.

  6. Cycle-Dependent Matrix Remodeling Gene Expression Response in Fatigue-Loaded Rat Patellar Tendons

    OpenAIRE

    Hui B. Sun; Andarawis-Puri, Nelly; Li, Yonghui; Fung, David T.; Jonathan Y. Lee; Wang, Vincent M.; Basta-Pljakic, Jelena; Leong, Daniel J.; Sereysky, Jedd B.; Ros, Stephen J.; Klug, Raymond A.; Braman, Jonathan; Schaffler, Mitch B.; Jepsen, Karl J.; Flatow, Evan L.

    2010-01-01

    Expression profiling of selected matrix remodeling genes was conducted to evaluate differences in molecular response to low-cycle (100) and high-cycle (7,200) sub-failure-fatigue loading of patellar tendons. Using our previously developed in vivo patellar tendon model, tendons were loaded for 100 or 7,200 cycles and expression of selected metalloproteinases (MMPs), tissue inhibitors of metalloproteinases (TIMPs), and collagens were quantified by real-time RT-PCR at 1- and 7-day post-loading. ...

  7. How variation between individuals affects species coexistence.

    Science.gov (United States)

    Hart, Simon P; Schreiber, Sebastian J; Levine, Jonathan M

    2016-08-01

    Although the effects of variation between individuals within species are traditionally ignored in studies of species coexistence, the magnitude of intraspecific variation in nature is forcing ecologists to reconsider. Compelling intuitive arguments suggest that individual variation may provide a previously unrecognised route to diversity maintenance by blurring species-level competitive differences or substituting for species-level niche differences. These arguments, which are motivating a large body of empirical work, have rarely been evaluated with quantitative theory. Here we incorporate intraspecific variation into a common model of competition and identify three pathways by which this variation affects coexistence: (1) changes in competitive dynamics because of nonlinear averaging, (2) changes in species' mean interaction strengths because of variation in underlying traits (also via nonlinear averaging) and (3) effects on stochastic demography. As a consequence of the first two mechanisms, we find that intraspecific variation in competitive ability increases the dominance of superior competitors, and intraspecific niche variation reduces species-level niche differentiation, both of which make coexistence more difficult. In addition, individual variation can exacerbate the effects of demographic stochasticity, and this further destabilises coexistence. Our work provides a theoretical foundation for emerging empirical interests in the effects of intraspecific variation on species diversity. PMID:27250037

  8. Successive evaluation of multiple parameters in individual cells: the SEMPIC photometric system.

    Science.gov (United States)

    Dörmer, P; Pachmann, K; Lau, B

    1978-12-28

    An automated microphotometric system has been designed for the successive assessment of a maximum number of parameters from individual cells. The hardware and software elements are described as well as the various photometric functions that can be performed. The aim is to obtain a multiparameter analysis of morphology, cytochemistry, cell surface characteristics, and metabolic activity including cell cycle characteristics for any set of cells selected from a sample. The combination of DNA synthesis rate determination in a really quantitative approach with the analysis of features of nuclear chromatin texture opens up a new field for associating morphology with functional properties. Examples of application are presented to demonstrate the applicability of the system in a heterogeneous cell population of a very limited sample size. For this purpose, human peripheral blood cells grown in diffusion chambers in preirradiated mice were investigated. It is shown that, depending on their functions, different cell types may have quite different nuclear-to-cell area ratios. Further, a crude morphological parameter, such as the degree of basophilia of Giemsa-stained cells, may be associated with the rate of DNA synthesis, thus bearing information on the replicative activity of a cell. Cell surface properties related to the leukemia-associated cALL antigen are investigated in a human-derived cell line and correlated with cell-cycle characteristics. It is concluded that different antigenic sites rather than cell-cycle dependent differences of antigen density account for the outcome of a bimodal distribution. PMID:283066

  9. Single cell enzyme diagnosis on the chip

    DEFF Research Database (Denmark)

    Jensen, Sissel Juul; Harmsen, Charlotte; Nielsen, Mette Juul;

    2013-01-01

    Conventional diagnosis based on ensemble measurements often overlooks the variation among cells. Here, we present a droplet-microfluidics based platform to investigate single cell activities. Adopting a previously developed isothermal rolling circle amplification-based assay, we demonstrate detec...

  10. DNA fork displacement rates in human cells

    International Nuclear Information System (INIS)

    DNA fork displacement rates were measured in 20 human cell lines by a bromodeoxyuridine-313 nm photolysis technique. Cell lines included representatives of normal diploid, Fanconi's anemia, ataxia telangiectasia, xeroderma pigmentosum, trisomy-21 and several transformed lines. The average value for all the cell lines was 0.53 +- 0.08 μm/min. The average value for individual cell lines, however, displayed a 30% variation. Less than 10% of variation in the fork displacement rate appears to be due to the experimental technique; the remainder is probably due to true variation among the cell types and to culture conditions. (Auth.)

  11. Genetic background of phenotypic variation

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    A noteworthy feature of the living world is its bewildering variability. A key issue in several biological disciplines is the achievement of an understanding of the hereditary basis of this variability. Two opposing, but not necessarily irreconcilable conceptions attempt to explain the underlying mechanism. The gene function paradigm postulates that phenotypic variance is generated by the polymorphism in the coding sequences of genes. However, comparisons of a great number of homologous gene and protein sequences have revealed that they predominantly remained functionally conserved even across distantly related phylogenic taxa. Alternatively, the gene regulation paradigm assumes that differences in the cis-regulatory region of genes do account for phenotype variation within species. An extension of this latter concept is that phenotypic variability is generated by the polyrnorphism in the overall gene expression profiles of gene networks.In other words, the activity of a particular gene is a system property determined both by the cis-regulatory sequences of the given genes and by the other genes of a gene network, whose expressions vary among individuals, too. Novel proponents of gene function paradigm claim that functional genetic variance within the coding sequences of regulatory genes is critical for the generation of morphological polymorphism. Note, however, that these developmental genes play direct regulatory roles in the control of gene expression.

  12. Temporal Variations in Jupiter's Atmosphere

    Science.gov (United States)

    Simon-Miller, Amy A.; Chanover, N. J.; Yanamandra-Fisher, P.; Hammel, H. B.; dePater, I.; Noll, K.; Wong, M.; Clarke, J.; Sanchez-Levega, A.; Orton, G. S.; Gonzaga, S.

    2009-01-01

    In recent years, Jupiter has undergone many atmospheric changes from storms turning red to global. cloud upheavals, and most recently, a cornet or asteroid impact. Yet, on top of these seemingly random changes events there are also periodic phenomena, analogous to observed Earth and Saturn atmospheric oscillations. We will present 15 years of Hubble data, from 1994 to 2009, to show how the equatorial tropospheric cloud deck and winds have varied over that time, focusing on the F953N, F41 ON and F255W filters. These filters give leverage on wind speeds plus cloud opacity, cloud height and tropospheric haze thickness, and stratospheric haze, respectively. The wind data consistently show a periodic oscillation near 7-8 S latitude. We will discuss the potential for variations with longitude and cloud height, within the calibration limits of those filters. Finally, we will discuss the role that large atmospheric events, such as the impacts in 1994 and 2009, and the global upheaval of 2007, have on temporal studies, This work was supported by a grant from the NASA Planetary Atmospheres Program. HST observational support was provided by NASA through grants from Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under contract NAS5-26555.

  13. On Quadratic Variation of Martingales

    Indian Academy of Sciences (India)

    Rajeeva L Karandikar; B V Rao

    2014-08-01

    We give a construction of an explicit mapping $$\\Psi: D([0,∞),\\mathbb{R})→ D([0,∞),\\mathbb{R}),$$ where $D([0,∞), \\mathbb{R})$ denotes the class of real valued r.c.l.l. functions on $[0,∞)$ such that for a locally square integrable martingale $(M_t)$ with r.c.l.l. paths, $$\\Psi(M.())=A.()$$ gives the quadratic variation process (written usually as $[M,M]_t$) of $(M_t)$. We also show that this process $(A_t)$ is the unique increasing process $(B_t)$ such that $M_t^2-B_t$ is a local martingale, $B_0=0$ and $$\\mathbb{P}(( B)_t=[( M)_t]^2, 0 < ∞)=1.$$ Apart from elementary properties of martingales, the only result used is the Doob’s maximal inequality. This result can be the starting point of the development of the stochastic integral with respect to r.c.l.l. martingales.

  14. PLURILINGUAL COMPETENCE, STYLES AND VARIATION

    Directory of Open Access Journals (Sweden)

    Jyrki Kalliokoski

    2011-01-01

    Full Text Available The paper explores plurilingual competence in respect to language proficiency, language education and pluri- and multilingualism. The notion of communicative competence was introduced by Hymes (1972 as a reaction to chomskyan view of language as an autonomous system. Hymes’ notion of communicative competence originally included plurilingualism. The concept of communicative competence was quickly adopted to applied linguistics but the idea of a linguistic repertoire consisting of the competencies of linguistic varieties was not imported to SLA or language testing. The Hymesian perspective to plurilingualism as an essential dimension of communicative competence was revived in the Common European Framework (CEFR. However,the practice of applying the CEFR has mostly neglected the dimension on plurilingualism and plurilingual competence. The focus in the use of the CEFR has been on the different areas of language skills within one single language at a time, while the application of plurilingual practices has gained very little attention. The Hymesian notion of communicative competence has lived on in the sociolinguistic research tradition, especially within interactional sociolinguistics. The present paper relates the notion of plurilingual competence to its hymesian origin, to recent trends in plurilingual and pluricultural education, and to the sociolinguistic study of style and linguistic variation in multilingual communities. The article uses Finnish L2 data to show how plurilingual competence is used as an interactional resource.From the perspective of language learning, plurilingual competence enables speakers with different linguistic backgrounds to use their shared linguistic repertoire in order to ensure smooth interaction and achieve mutual understanding.

  15. Synchronous Lagrangian variational principles in General Relativity

    CERN Document Server

    Cremaschini, Claudio

    2016-01-01

    The problem of formulating synchronous variational principles in the context of General Relativity is discussed. Based on the analogy with classical relativistic particle dynamics, the existence of variational principles is pointed out in relativistic classical field theory which are either asynchronous or synchronous. The historical Einstein-Hilbert and Palatini variational formulations are found to belong to the first category. Nevertheless, it is shown that an alternative route exists which permits one to cast these principles in terms of equivalent synchronous Lagrangian variational formulations. The advantage is twofold. First, synchronous approaches allow one to overcome the lack of gauge symmetry of the asynchronous principles. Second, the property of manifest covariance of the theory is also restored at all levels, including the symbolic Euler-Lagrange equations, with the variational Lagrangian density being now identified with a $4-$scalar. As an application, a joint synchronous variational principle...

  16. Procedural facade variations from a single layout

    KAUST Repository

    Bao, Fan

    2013-01-01

    We introduce a framework to generate many variations of a facade design that look similar to a given facade layout. Starting from an input image, the facade is hierarchically segmented and labeled with a collection of manual and automatic tools. The user can then model constraints that should be maintained in any variation of the input facade design. Subsequently, facade variations are generated for different facade sizes, where multiple variations can be produced for a certain size. Computing such new facade variations has many unique challenges, and we propose a new algorithm based on interleaving heuristic search and quadratic programming. In contrast to most previous work, we focus on the generation of new design variations and not on the automatic analysis of the input\\'s structure. Adding a modeling step with the user in the loop ensures that our results routinely are of high quality. © 2013 ACM.

  17. Genetic variation in bovine milk fat composition

    OpenAIRE

    Stoop, W.M.

    2009-01-01

    In her thesis, Stoop shows that there is considerable genetic variation in milk fat composition, which opens opportunities to improve milk fat composition by selective breeding. Short and medium chain fatty acids had high heritabilities, whereas variation due to herd (mainly feed effects) was moderate. Long chain fatty acids had moderate heritabilities, whereas variation due to herd was high. Several genomic regions (QTL) with effect on short and medium chain, long chain, or both types of fat...

  18. DNA fingerprinting and minisatellite variation of swans

    OpenAIRE

    Meng, Anming

    1990-01-01

    Genetic variation in natural populations of four species of swans (Cygnus bewickii, Cygnus olor, Cygnus buccinator and Cygnus cygnus) has been investigated by examining minisatellite loci using human DNA fingerprinting probes pSPT19.6 and pSPT18.15. It has been found that swan minisatellites are highly variable. However, the degree of variation depends on the population structure and species. Bewick's Swans at Slimbridge have the highest degree of minisatellite variation, Whooper Swans at Cae...

  19. Size variation of fossil rodent populations

    OpenAIRE

    Freudenthal, M.; Cuenca Bescos, G.

    1984-01-01

    Pearson's coefficient of variation is in general not applicable in palaeontology, due to the heterogeneity of samples. The heterogeneity may be due to the mixing of two species, mixture of material from various biotopes, or from a relatively large time span. A new coefficient of variation is proposed, based on the range of the sample. This coefficient may be used to estimate the degree of variation of a sample, and to decide whether it is homogeneous. Its application is tested empirically on ...

  20. Measuring human salivary amylase copy number variation

    OpenAIRE

    Dhar, Sugandha

    2010-01-01

    Copy number variations represent large scale genomic alterations varying from 1kb to 3Mb and are proposed as a driving force for genome evolution and variation. One such locus exhibiting copy number variation and genome evolution is salivary amylase, which is responsible for the digestion of starch in the human parotid glands. It was reported that since human salivary amylase gene (AMY1) copy numbers are correlated positively with protein levels, and also due to the correlation of high gene c...

  1. Varying Alpha: New Constraints from Seasonal Variations

    CERN Document Server

    Barrow, John D

    2008-01-01

    We analyze the constraints obtained from new atomic clock data on the possible time variation of the fine structure `constant' and the electron-proton mass ratio and show how they are strengthened when the seasonal variation of Sun's gravitational field at the Earth's surface is taken into account. We compare these bounds with those obtainable from tests of the Weak Equivalence Principle and high-redshift observations of quasar absorption spectra consistent with time variations in the fine structure constant.

  2. Models of Solar Irradiance Variations: Current Status

    Indian Academy of Sciences (India)

    Natalie A. Krivova; Sami K. Solanki

    2008-03-01

    Regular monitoring of solar irradiance has been carried out since 1978 to show that solar total and spectral irradiance varies at different time scales. Whereas variations on time scales of minutes to hours are due to solar oscillations and granulation, variations on longer time scales are driven by the evolution of the solar surface magnetic field. Here the most recent advances in modelling of solar irradiance variations on time scales longer than a day are briefly reviewed.

  3. Variational Inequalities in Critical-State Problems

    OpenAIRE

    Prigozhin, Leonid

    2004-01-01

    Similar evolutionary variational inequalities appear as convenient formulations for continuous quasistationary models for sandpile growth, formation of a network of lakes and rivers, magnetization of type-II superconductors, and elastoplastic deformations. We outline the main steps of such models derivation and try to clarify the origin of this similarity. New dual variational formulations, analogous to mixed variational inequalities in plasticity, are derived for sandpiles and superconductors.

  4. Diurnal Variations in Human Pulmonary Function

    OpenAIRE

    Medarov, Boris I.; Pavlov, Valentin A.; Rossoff, Leonard

    2008-01-01

    Pulmonary function has circadian modulations. Variations in human pulmonary function during the daytime hours (diurnal variations) remain to be well characterized. Discerning these variations will contribute to better understanding the relationship between biorhythms and lung physiology and to improving clinical management of pulmonary diseases. The aim of this study was to determine the magnitude of pulmonary function variability during the usual daytime hours in a population of patients ref...

  5. A Paradigm for Eliciting Story Variation

    OpenAIRE

    Fisseni, Bernhard; Lawrence, Faith

    2013-01-01

    The understanding of story variation, whether motivated by cultural currents or other factors, is important for applications of formal models of narrative such as story generation or story retrieval. We present the first stage of an experiment to elicit natural narrative variation data suitable for evaluation with respect to story similarity, to qualitative and quantitative analysis of story variation, and also for data processing. We also present few prelimary results from the first stage of...

  6. Simplified Variational Principles for Barotropic Magnetohydrodynamics

    OpenAIRE

    Yahalom, Asher; Lynden-Bell, Donald

    2006-01-01

    Variational principles for magnetohydrodynamics were introduced by previous authors both in Lagrangian and Eulerian form. In this paper we introduce simpler Eulerian variational principles from which all the relevant equations of barotropic magnetohydrodynamics can be derived. The variational principle is given in terms of six independent functions for non-stationary barotropic flows and three independent functions for stationary barotropic flows. This is less then the seven variables which a...

  7. Morphometric variation among the Central Indian populations

    OpenAIRE

    Gautam, Rajesh K.; Dipak K. Adak,; Pal, M.; P. Bharati

    2013-01-01

    Data on 8 anthropometric characters of 6663 adult males belonging to 22 caste groups, distributed in 38 districts of Central India were taken for present investigation, to study the morphometric variation. Cephalic index, nasal Index, Generalized Mahalanobis distances and its size and shape components were computed and dendrograms were drawn. Comparison of coefficient of variations shows that there exists variation in nasal breadth, nasal length, weight and hence in nasal index. But no marked...

  8. Statistical interpretations and new findings on Variation in Cancer Risk Among Tissues

    OpenAIRE

    Noble, Robert; Kaltz, Oliver; Hochberg, Michael E.

    2015-01-01

    Tomasetti and Vogelstein (2015a) find that the incidence of a set of cancer types is correlated with the total number of normal stem cell divisions. Here, we separate the effects of standing stem cell number (i.e., organ or tissue size) and per stem cell lifetime replication rate. We show that each has a statistically significant and independent effect on explaining variation in cancer incidence over the 31 cases considered by Tomasetti and Vogelstein. When considering the total number of ste...

  9. Spectrum characteristics of geoelectric field variation

    Institute of Scientific and Technical Information of China (English)

    YE Qing; DU Xue-bin; ZHOU Ke-chang; LI Ning; MA Zhan-hu

    2007-01-01

    The spectrum characteristics of geoelectric diurnal variation and geoelectric storm have been identified by maximum entropy method, based on geoelectric data from seven stations in the Chinese mainland, including Jiayuguan, Changli and Chongming. The study shows that, in geoelectric diurnal variation, the amplitude of the 12 h semidiurnal wave is the largest, followed in turn by the 24~25 h diurnal wave and the 8 h periodic wave; Geoelectric storm usually occurs in a large-scale space, whose spectrum values are higher than those of geoelectric diurnal variation by 2~3 orders of magnitude. A preliminary interpretation is presented for the generative mechanism of predominant waves in geoelectric field variation.

  10. Extensive Variation in Chromatin States Across Humans

    KAUST Repository

    Kasowski, M.

    2013-10-17

    The majority of disease-associated variants lie outside protein-coding regions, suggesting a link between variation in regulatory regions and disease predisposition. We studied differences in chromatin states using five histone modifications, cohesin, and CTCF in lymphoblastoid lines from 19 individuals of diverse ancestry. We found extensive signal variation in regulatory regions, which often switch between active and repressed states across individuals. Enhancer activity is particularly diverse among individuals, whereas gene expression remains relatively stable. Chromatin variability shows genetic inheritance in trios, correlates with genetic variation and population divergence, and is associated with disruptions of transcription factor binding motifs. Overall, our results provide insights into chromatin variation among humans.

  11. Factors influencing variation in dentist service rates.

    Science.gov (United States)

    Grembowski, D; Milgrom, P; Fiset, L

    1990-01-01

    In the previous article, we calculated dentist service rates for 200 general dentists based on a homogeneous, well-educated, upper-middle-class population of patients. Wide variations in the rates were detected. In this analysis, factors influencing variation in the rates were identified. Variation in rates for categories of dental services was explained by practice characteristics, patient exposure to fluoridated water supplies, and non-price competition in the dental market. Rates were greatest in large, busy practices in markets with high fees. Older practices consistently had lower rates across services. As a whole, these variables explained between 5 and 30 percent of the variation in the rates. PMID:2118182

  12. Antimicrobial price variation: Conundrum of medical profession!

    Directory of Open Access Journals (Sweden)

    Rataboli P

    2007-01-01

    Full Text Available Pharmacoeconomics plays a pivotal role in clinical practice. High medicine prices can adversely affect a patient′s finances and compliance. The Indian pharmaceutical industry has become a cornucopia of medicines with wide variation in prices for the same medicine marketed under different brand names. Price list of available antimicrobial brands was procured from a commercial drug directory. Average price of widely prescribed oral antimicrobials was found and price variation between different brands was calculated. The variation in medicine prices was found to be from 95% lower to more than 350% higher than the average price. Implications of price variation in clinical practice are discussed and remedial measures suggested.

  13. Mitochondrial DNA variation analysis in cervical cancer.

    Science.gov (United States)

    Kabekkodu, Shama Prasada; Bhat, Samatha; Mascarenhas, Roshan; Mallya, Sandeep; Bhat, Manoj; Pandey, Deeksha; Kushtagi, Pralhad; Thangaraj, Kumarasamy; Gopinath, P M; Satyamoorthy, Kapaettu

    2014-05-01

    This study was undertaken to investigate the mitochondrial DNA (mtDNA) variation in non-malignant and malignant cervical tissue samples. We have identified 229 and 739 variations non-malignant and malignant tissues respectively distributed over 321 locations in the D-loop (50 in non-malignant and 166 in malignant; 216 variations), coding region (139 in non-malignant and 455 in malignant; 594 variations) tRNA and rRNA genes (39 in non-malignant and 119 in malignant; 158 variations). Besides, 77 novel and 34 various other disease associated variations were identified in non-malignant and malignant samples. A total of 236 tumor specific variations in 201 locations representing 30.1% in D-loop, 59.3% in coding regions and 10.6% in RNA genes were also identified. Our study shows that D loop (in 67 locations) is highly altered followed by ND5 (35 locations) region. Moreover, mtDNA alterations were significantly higher in malignant samples by two tailed Fisher's exact test (P≤0.05) with decreased mtDNA copy numbers. Bioinformatic analysis of 59 non-synonymous changes predicted several variations as damaging leading to decreased stability of the proteins. Taken together, mtDNA is highly altered in cervical cancer and functional studies are needed to be investigated to understand the consequence of these variations in cervical carcinogenesis and their potential application as biomarkers. PMID:23851045

  14. Study on Somaclonal Variation of Spring Wheat

    Institute of Scientific and Technical Information of China (English)

    JIANG Shu-mei; HU Shang-lian; LI Wen-xiong

    2004-01-01

    Somaclonal variation of calli and regenerated plants of spring wheat ware detected by using technique RAPD in the study. Calli at different culture stages and regenerated plants derived from young spikes and immature embryos were used as materials. Molecular variation could be reflected from electrophoresis patternof RAPD fragments at different culture stage in calli, and in regenerated plants derived from different explants, even no phenotype variations were found. Somaclonal variation in calli and in regenerated plants appeared regularly: A higher frequency of variation in hybrids F2 was detected than that of the cultivar that is stable genetically. High variation frequency of RAPD fragments appeared in calli when cultured 75 days. The identical variations of RAPD fragments were observed in calli and in the regenerated plants induced from different genotype or explants. The variation frequency detected is higher in regenerated plants than that of in calli. RAPD could be applied easily and simply to determine variation in level of DNA at each stage cultured in vitro.

  15. Parkinson's disease and mitochondrial gene variations

    DEFF Research Database (Denmark)

    Andalib, Sasan; Vafaee, Manouchehr Seyedi; Gjedde, Albert

    2014-01-01

    Parkinson's disease (PD) is a common disorder of the central nervous system in the elderly. The pathogenesis of PD is a complex process, with genetics as an important contributing factor. This factor may stem from mitochondrial gene variations and mutations as well as from nuclear gene variations...... and mutations. More recently, a particular role of mitochondrial dysfunction has been suggested, arising from mitochondrial DNA variations or acquired mutations in PD pathogenesis. The present review summarizes and weighs the evidence in support of mitochondrial DNA (mtDNA) variations as important...

  16. Duality in optimization and variational inequalities

    CERN Document Server

    Goh, Cj

    2001-01-01

    This comprehensive volume covers a wide range of duality topics ranging from simple ideas in network flows to complex issues in non-convex optimization and multicriteria problems. In addition, it examines duality in the context of variational inequalities and vector variational inequalities, as generalizations to optimization. Duality in Optimization and Variational Inequalities is intended for researchers and practitioners of optimization with the aim of enhancing their understanding of duality. It provides a wider appreciation of optimality conditions in various scenarios and under different assumptions. It will enable the reader to use duality to devise more effective computational methods, and to aid more meaningful interpretation of optimization and variational inequality problems.

  17. Action of caffeine on the survival of x-irradiated cells

    International Nuclear Information System (INIS)

    Post-irradiation treatment of HeLa S3 cells with 1 mM caffeine results in a marked diminution of the surviving fraction as scored by colony formation. The decrease is dose-dependent; the effect of a 24-h post-irradiation treatment of a non-synchronous population with caffeine is to change the terminal slope of the survival curve and its intercept. Do is reduced from 130 to 60 rad; the extrapolation number is increased about twofold. The amount of post-irradiation killing is maximal if cells are exposed to caffeine at a concentration of at least 1 mM for 8 hours; less than 10% of unirradiated cells are killed under these conditions. Dose-response curves were also obtained for synchronous cells at various phases of the cell cycle. Similar results were obtained at all cell ages, but the magnitude of the effect is age-dependent. This age dependence was further explored in experiments in which mitotically collected cells were exposed to 300 or 500 rad doses at 2-hour intervals throughout the cell cycle. Treatment with caffeine for 24 hours after irradiation enhances the killing of cells late in the cycle more than in G1. The sensitivities of two other cell lines, CHO and EMT6, also were examined; both are substantially less sensitive to caffeine. The smaller cell-cycle dependence of CHO cells is qualitatively the same as that of HeLa cells

  18. Exogenous lactate interferes with cell-cycle control in BALB/3T3 mouse fibroblasts

    International Nuclear Information System (INIS)

    Purpose: Previous studies have shown that exogenous lactate may influence proliferation rates, radiation sensitivity, and postirradiation repair capacity of mammalian cells. In the present study, we addressed the question of potential underlying mechanisms and, therefore, examined effects of exogenous lactate on proliferation rates and cell-cycle distribution in immortal but nontumorigenic mammalian cells. Methods and Materials: Cells were grown at 37 deg. C in an incubator with 5% CO2 and 95% air, in a culture medium supplemented or not with lactate at a 10 mM concentration. Daily, we changed the culture medium and counted cells per dish. On selected days, cell-cycle distribution was determined by flow cytometry. Balb/3T3 mouse fibroblasts were used. Results: During the exponential phase of cell proliferation, mean population doubling time was significantly increased from 17.7 to 19.9 h, due to selective prolongation of G2/M. However, in density-inhibited cultures, exogenous lactate stimulated entry into S and proliferation to a significantly higher saturation density. Conclusions: These findings indicate that exogenous lactate interferes with mechanisms of cell-cycle control at two different points in the cell-cycle, depending on cell density and the resulting absence or presence of inhibition of cell proliferation. Interference with cell-cycle control may underlay the modification by exogenous lactate of radiosensitivity and postirradiation repair capacity in mammalian cells

  19. Temporal variations in rainwater methanol

    Science.gov (United States)

    Felix, J. D.; Jones, S. B.; Avery, G. B.; Willey, J. D.; Mead, R. N.; Kieber, R. J.

    2014-10-01

    This work reports the first comprehensive analysis of methanol concentrations in rainwater. Methanol concentrations measured in 49 rain events collected between 28 August 2007 and 10 July 2008 in Wilmington, NC, USA, ranged from below the detection limit of 6 nM to 9.3 μM with a volume-weighted average concentration of 1 ± 0.2 μM. Methanol concentrations in rainwater were up to ~200 times greater than concentrations reported previously in marine waters, indicating wet deposition as a potentially significant source of methanol to marine waters. Assuming that these methanol concentrations are an appropriate proxy for global methanol rainwater concentrations, the global methanol wet deposition sink is estimated as 20 Tg yr-1, which implies that previous methanol budgets underestimate removal by precipitation. Methanol concentrations in rainwater did not correlate significantly with H+, NO3-, and NSS, which suggests that the dominant source of the alcohol to rainwater is not anthropogenic. However, methanol concentrations were strongly correlated with acetaldehyde, which has a primarily biogenic input. The methanol volume-weighted concentration during the summer (2.7 ± 0.9 μM) was ~3 times that of the winter (0.9 ± 0.2 μM), further promoting biogenic emissions as the primary cause of temporal variations of methanol concentrations. Methanol concentrations peaked in rainwater collected during the time period 12 p.m.-6 p.m. Peaking during this period of optimal sunlight implies a possible relationship with photochemical methanol production, but there are also increases in biogenic activity during this time period. Rain events with terrestrial origin had greater concentrations than those of marine origin, demonstrating the significance of the continental source of methanol in rainwater.

  20. Study of 222Rn variations in the soil air

    International Nuclear Information System (INIS)

    A significant source of radon in the indoor atmosphere is represented by 222Rn in the soil air, ie., by the fraction of radon atoms produced by alpha decay of 226Ra in soil grains that escaped into soil pores. In the paper the results are presented of a three year monitoring of radon in soil air, using a 125 ml Lucas type scintillation cell. Radon concentration depth profiles in the soil in various seasons of the year were also measured, and saturated concentration of radon in soil air was found at a depth of about 2 m. Monthly variations in the radon concentration were observed over several months and the possible causes of the variations are discussed. Daily courses of radon concentration were also measured and the results are presented. (A.K.)

  1. Human tumor cell proliferation evaluated using manganese-enhanced MRI.

    Directory of Open Access Journals (Sweden)

    Rod D Braun

    Full Text Available BACKGROUND: Tumor cell proliferation can depend on calcium entry across the cell membrane. As a first step toward the development of a non-invasive test of the extent of tumor cell proliferation in vivo, we tested the hypothesis that tumor cell uptake of a calcium surrogate, Mn(2+ [measured with manganese-enhanced MRI (MEMRI], is linked to proliferation rate in vitro. METHODOLOGY/PRINCIPAL FINDINGS: Proliferation rates were determined in vitro in three different human tumor cell lines: C918 and OCM-1 human uveal melanomas and PC-3 prostate carcinoma. Cells growing at different average proliferation rates were exposed to 1 mM MnCl(2 for one hour and then thoroughly washed. MEMRI R(1 values (longitudinal relaxation rates, which have a positive linear relationship with Mn(2+ concentration, were then determined from cell pellets. Cell cycle distributions were determined using propidium iodide staining and flow cytometry. All three lines showed Mn(2+-induced increases in R(1 compared to cells not exposed to Mn(2+. C918 and PC-3 cells each showed a significant, positive correlation between MEMRI R(1 values and proliferation rate (p≤0.005, while OCM-1 cells showed no significant correlation. Preliminary, general modeling of these positive relationships suggested that pellet R(1 for the PC-3 cells, but not for the C918 cells, could be adequately described by simply accounting for changes in the distribution of the cell cycle-dependent subpopulations in the pellet. CONCLUSIONS/SIGNIFICANCE: These data clearly demonstrate the tumor-cell dependent nature of the relationship between proliferation and calcium influx, and underscore the usefulness of MEMRI as a non-invasive method for investigating this link. MEMRI is applicable to study tumors in vivo, and the present results raise the possibility of evaluating proliferation parameters of some tumor types in vivo using MEMRI.

  2. From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing.

    Science.gov (United States)

    Marinov, Georgi K; Williams, Brian A; McCue, Ken; Schroth, Gary P; Gertz, Jason; Myers, Richard M; Wold, Barbara J

    2014-03-01

    Single-cell RNA-seq mammalian transcriptome studies are at an early stage in uncovering cell-to-cell variation in gene expression, transcript processing and editing, and regulatory module activity. Despite great progress recently, substantial challenges remain, including discriminating biological variation from technical noise. Here we apply the SMART-seq single-cell RNA-seq protocol to study the reference lymphoblastoid cell line GM12878. By using spike-in quantification standards, we estimate the absolute number of RNA molecules per cell for each gene and find significant variation in total mRNA content: between 50,000 and 300,000 transcripts per cell. We directly measure technical stochasticity by a pool/split design and find that there are significant differences in expression between individual cells, over and above technical variation. Specific gene coexpression modules were preferentially expressed in subsets of individual cells, including one enriched for mRNA processing and splicing factors. We assess cell-to-cell variation in alternative splicing and allelic bias and report evidence of significant differences in splice site usage that exceed splice variation in the pool/split comparison. Finally, we show that transcriptomes from small pools of 30-100 cells approach the information content and reproducibility of contemporary RNA-seq from large amounts of input material. Together, our results define an experimental and computational path forward for analyzing gene expression in rare cell types and cell states. PMID:24299736

  3. Heritable epigenetic variation among maize inbreds.

    Directory of Open Access Journals (Sweden)

    Steve R Eichten

    2011-11-01

    Full Text Available Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. There is the potential for pure epigenetic variation that occurs in the absence of any genetic change or for more complex situations that involve both genetic and epigenetic differences. Methylation of cytosine residues provides one mechanism for the inheritance of epigenetic information. A genome-wide profiling of DNA methylation in two different genotypes of Zea mays (ssp. mays, an organism with a complex genome of interspersed genes and repetitive elements, allowed the identification and characterization of examples of natural epigenetic variation. The distribution of DNA methylation was profiled using immunoprecipitation of methylated DNA followed by hybridization to a high-density tiling microarray. The comparison of the DNA methylation levels in the two genotypes, B73 and Mo17, allowed for the identification of approximately 700 differentially methylated regions (DMRs. Several of these DMRs occur in genomic regions that are apparently identical by descent in B73 and Mo17 suggesting that they may be examples of pure epigenetic variation. The methylation levels of the DMRs were further studied in a panel of near-isogenic lines to evaluate the stable inheritance of the methylation levels and to assess the contribution of cis- and trans- acting information to natural epigenetic variation. The majority of DMRs that occur in genomic regions without genetic variation are controlled by cis-acting differences and exhibit relatively stable inheritance. This study provides evidence for naturally occurring epigenetic variation in maize, including examples of pure epigenetic variation that is not conditioned by genetic differences. The epigenetic differences are variable within maize populations and exhibit relatively stable trans-generational inheritance. The detected examples of epigenetic variation, including some without tightly linked genetic

  4. Genetic analysis of the phase variation control of expression of type 1 fimbriae in Escherichia coli.

    OpenAIRE

    Freitag, C S; Abraham, J. M.; Clements, J R; Eisenstein, B. I.

    1985-01-01

    Expression of type 1 fimbriae in Escherichia coli exhibits phase variation, whereby individual cells can alternate between states of organelle expression (Fim+) and nonexpression (Fim-). Strains with a fimD-lac operon fusion, in which lac, rather than fimD, expression is under the control of the fimD promoter, undergo Lac+ in equilibrium Lac- phase variation, instead. After positioning a lambda prophage adjacent to the operon fusion, we were able to isolate specialized lambda phage carrying b...

  5. Numerical analysis of cumulative impact of phytoplankton photoresponses to light variation on carbon assimilation

    OpenAIRE

    Esposito, S.; Botte, V.; Iudicone, D.; Ribera d'Alcala, M.

    2009-01-01

    Abstract Light variation in temporal and spatial domains is a key constraint on the photosynthetic performance of phytoplankton. The most obvious responses are the modification of cell pigment content either to improve photocapture or to mitigate photo-damage. Very few studies have analyzed whether light variation significantly alters carbon assimilation, especially in a fluctuating light environment as in the mixed layer of the ocean. We addressed the question using a modeling app...

  6. STK31 is a cell-cycle regulated protein that contributes to the tumorigenicity of epithelial cancer cells.

    Directory of Open Access Journals (Sweden)

    Pao-Lin Kuo

    Full Text Available Serine/threonine kinase 31 (STK31 is one of the novel cancer/testis antigens for which its biological functions remain largely unclear. Here, we demonstrate that STK31 is overexpressed in many human colorectal cancer cell lines and tissues. STK31 co-localizes with pericentrin in the centrosomal region throughout all phases of the cell cycle. Interestingly, when cells undergo mitosis, STK31 also localizes to the centromeres, central spindle, and midbody. This localization behavior is similar to that of chromosomal passenger proteins, which are known to be the important players of the spindle assembly checkpoint. The expression of STK31 is cell cycle-dependent through the regulation of a putative D-box near its C-terminal region. Ectopically-expressed STK31-GFP increases cell migration and invasive ability without altering the proliferation rate of cancer cells, whereas the knockdown expression of endogenous STK31 by lentivirus-derived shRNA results in microtubule assembly defects that prolong the duration of mitosis and lead to apoptosis. Taken together, our results suggest that the aberrant expression of STK31 contributes to tumorigenicity in somatic cancer cells. STK31 might therefore act as a potential therapeutic target in human somatic cancers.

  7. Anatomy, Medical Education, and Human Ancestral Variation

    Science.gov (United States)

    Strkalj, Goran; Spocter, Muhammad A.; Wilkinson, A. Tracey

    2011-01-01

    It is argued in this article that the human body both in health and disease cannot be fully understood without adequately accounting for the different levels of human variation. The article focuses on variation due to ancestry, arguing that the inclusion of information pertaining to ancestry in human anatomy teaching materials and courses should…

  8. Predicting global variation in infectious disease severity

    DEFF Research Database (Denmark)

    Jensen, Per Moestrup; de Fine Licht, Henrik Hjarvard

    2016-01-01

    Background and objectives: Understanding the underlying causes for the variation in case-fatality-ratios (CFR) is important for assessing the mechanism governing global disparity in the burden of infectious diseases. Variation in CFR is likely to be driven by factors such as population genetics...

  9. Hamiltonian and Variational Linear Distributed Systems

    NARCIS (Netherlands)

    Rapisarda, P.; Trentelman, H.L.

    2002-01-01

    We use the formalism of bilinear- and quadratic differential forms in order to study Hamiltonian and variational linear distributed systems. It was shown that a system described by ordinary linear constant-coefficient differential equations is Hamiltonian if and only if it is variational. In this pa

  10. Item versus System Learning: Explaining Free Variation.

    Science.gov (United States)

    Ellis, Rod

    1999-01-01

    Provides an explanation for the existence of free variation in learner language. Argues that interlanguage is best conceptualized as sets of loose lexical networks that are gradually reorganized into a system or systems. Free variation arises when learners add items to those they have already acquired and before they analyze these items and…

  11. Size variation of fossil rodent populations

    NARCIS (Netherlands)

    Freudenthal, M.; Cuenca Bescos, G.

    1984-01-01

    Pearson's coefficient of variation is in general not applicable in palaeontology, due to the heterogeneity of samples. The heterogeneity may be due to the mixing of two species, mixture of material from various biotopes, or from a relatively large time span. A new coefficient of variation is propose

  12. Size variation in Middle Pleistocene humans.

    Science.gov (United States)

    Arsuaga, J L; Carretero, J M; Lorenzo, C; Gracia, A; Martínez, I; Bermúdez de Castro, J M; Carbonell, E

    1997-08-22

    It has been suggested that European Middle Pleistocene humans, Neandertals, and prehistoric modern humans had a greater sexual dimorphism than modern humans. Analysis of body size variation and cranial capacity variation in the large sample from the Sima de los Huesos site in Spain showed instead that the sexual dimorphism is comparable in Middle Pleistocene and modern populations. PMID:9262474

  13. Varying Constants: Constraints from Seasonal Variations

    CERN Document Server

    Shaw, Douglas J

    2010-01-01

    We analyse the constraints obtained from new atomic clock data on the possible time variation of the fine structure `constant' and the electron-proton mass ratio and show how they are strengthened when the seasonal variation of Sun's gravitational field at the Earth's surface is taken into account.

  14. Stochastic variational approach to minimum uncertainty states

    International Nuclear Information System (INIS)

    We introduce a new variational characterization of Gaussian diffusion processes as minimum uncertainty states. We then define a variational method constrained by kinematics of diffusions and Schroedinger dynamics to seek states of local minimum uncertainty for general non-harmonic potentials. (author)

  15. A Fitting Robot for Variational Analysis

    CERN Document Server

    Cais, A Ó; Mahbub, S; Williams, T

    2008-01-01

    We develop a robot algorithm to maximise the number of distinct states reliably extracted from correlator data using the variational analysis method. The robot explores the variational parameter space and attempts to remove, as far as possible, the human element from the fitting of the subsequent orthogonalised data.

  16. Exploring Duopoly Markets with Conjectural Variations

    Science.gov (United States)

    Julien, Ludovic A.; Musy, Olivier; Saïdi, Aurélien W.

    2014-01-01

    In this article, the authors investigate competitive firm behaviors in a two-firm environment assuming linear cost and demand functions. By introducing conjectural variations, they capture the different market structures as specific configurations of a more general model. Conjectural variations are based on the assumption that each firm believes…

  17. Stochastic Variational Approach to Minimum Uncertainty States

    OpenAIRE

    Illuminati, F.; Viola, L.

    1995-01-01

    We introduce a new variational characterization of Gaussian diffusion processes as minimum uncertainty states. We then define a variational method constrained by kinematics of diffusions and Schr\\"{o}dinger dynamics to seek states of local minimum uncertainty for general non-harmonic potentials.

  18. Stochastic variational approach to minimum uncertainty states

    CERN Document Server

    Illuminati, F; Illuminati, F; Viola, L

    1995-01-01

    We introduce a new variational characterization of Gaussian diffusion processes as minimum uncertainty states. We then define a variational method constrained by kinematics of diffusions and Schr\\"{o}dinger dynamics to seek states of local minimum uncertainty for general non-harmonic potentials.

  19. Stochastic variational approach to minimum uncertainty states

    Energy Technology Data Exchange (ETDEWEB)

    Illuminati, F.; Viola, L. [Dipartimento di Fisica, Padova Univ. (Italy)

    1995-05-21

    We introduce a new variational characterization of Gaussian diffusion processes as minimum uncertainty states. We then define a variational method constrained by kinematics of diffusions and Schroedinger dynamics to seek states of local minimum uncertainty for general non-harmonic potentials. (author)

  20. Variation in animal response to different toxicants

    Science.gov (United States)

    Hilado, C. J.; Cumming, H. J.

    1977-01-01

    The variation in response of different lots of male Swiss albino mice to pyrolysis effluents from surgical cotton and from bisphenol A polycarbonate, and to pure carbon monoxide, is discussed. The variation appeared to be less with the pyrolysis gases from polycarbonate than with pure carbon monoxide.