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Sample records for satb2 polyadenylation signal

  1. Genetics Home Reference: SATB2-associated syndrome

    Science.gov (United States)

    ... reproductive cells (eggs or sperm) or in early embryonic development. Affected individuals have no history of the ... V. Satb2 is a postmitotic determinant for upper-layer neuron specification in the neocortex. Neuron. 2008 Feb ...

  2. SATB2 expression increased anchorage-independent growth and cell migration in human bronchial epithelial cells

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Feng; Jordan, Ashley; Kluz, Thomas [Department of Environmental Medicine, New York University School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987 (United States); Shen, Steven [Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY 10016 (United States); Sun, Hong; Cartularo, Laura A. [Department of Environmental Medicine, New York University School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987 (United States); Costa, Max, E-mail: Max.Costa@nyumc.org [Department of Environmental Medicine, New York University School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987 (United States)

    2016-02-15

    The special AT-rich sequence-binding protein 2 (SATB2) is a protein that binds to the nuclear matrix attachment region of the cell and regulates gene expression by altering chromatin structure. In our previous study, we reported that SATB2 gene expression was induced in human bronchial epithelial BEAS-2B cells transformed by arsenic, chromium, nickel and vanadium. In this study, we show that ectopic expression of SATB2 in the normal human bronchial epithelial cell-line BEAS-2B increased anchorage-independent growth and cell migration, meanwhile, shRNA-mediated knockdown of SATB2 significantly decreased anchorage-independent growth in Ni transformed BEAS-2B cells. RNA sequencing analyses of SATB2 regulated genes revealed the enrichment of those involved in cytoskeleton, cell adhesion and cell-movement pathways. Our evidence supports the hypothesis that SATB2 plays an important role in BEAS-2B cell transformation. - Highlights: • We performed SATB2 overexpression in the BEAS-2B cell line. • We performed SATB2 knockdown in a Ni transformed BEAS-2B cell line. • SATB2 induced anchorage-independent growth and increased cell migration. • SATB2 knockdown significantly decreased anchorage-independent growth. • We identified alterations in gene involved in cytoskeleton, cell adhesion.

  3. SATB2 expression increased anchorage-independent growth and cell migration in human bronchial epithelial cells

    International Nuclear Information System (INIS)

    Wu, Feng; Jordan, Ashley; Kluz, Thomas; Shen, Steven; Sun, Hong; Cartularo, Laura A.; Costa, Max

    2016-01-01

    The special AT-rich sequence-binding protein 2 (SATB2) is a protein that binds to the nuclear matrix attachment region of the cell and regulates gene expression by altering chromatin structure. In our previous study, we reported that SATB2 gene expression was induced in human bronchial epithelial BEAS-2B cells transformed by arsenic, chromium, nickel and vanadium. In this study, we show that ectopic expression of SATB2 in the normal human bronchial epithelial cell-line BEAS-2B increased anchorage-independent growth and cell migration, meanwhile, shRNA-mediated knockdown of SATB2 significantly decreased anchorage-independent growth in Ni transformed BEAS-2B cells. RNA sequencing analyses of SATB2 regulated genes revealed the enrichment of those involved in cytoskeleton, cell adhesion and cell-movement pathways. Our evidence supports the hypothesis that SATB2 plays an important role in BEAS-2B cell transformation. - Highlights: • We performed SATB2 overexpression in the BEAS-2B cell line. • We performed SATB2 knockdown in a Ni transformed BEAS-2B cell line. • SATB2 induced anchorage-independent growth and increased cell migration. • SATB2 knockdown significantly decreased anchorage-independent growth. • We identified alterations in gene involved in cytoskeleton, cell adhesion.

  4. Gain and loss of polyadenylation signals during evolution of green algae

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    Glöckner Gernot

    2007-04-01

    Full Text Available Abstract Background The Viridiplantae (green algae and land plants consist of two monophyletic lineages: the Chlorophyta and the Streptophyta. Most green algae belong to the Chlorophyta, while the Streptophyta include all land plants and a small group of freshwater algae known as Charophyceae. Eukaryotes attach a poly-A tail to the 3' ends of most nuclear-encoded mRNAs. In embryophytes, animals and fungi, the signal for polyadenylation contains an A-rich sequence (often AAUAAA or related sequence 13 to 30 nucleotides upstream from the cleavage site, which is commonly referred to as the near upstream element (NUE. However, it has been reported that the pentanucleotide UGUAA is used as polyadenylation signal for some genes in volvocalean algae. Results We set out to investigate polyadenylation signal differences between streptophytes and chlorophytes that may have emerged shortly after the evolutionary split between Streptophyta and Chlorophyta. We therefore analyzed expressed genes (ESTs from three streptophyte algae, Mesostigma viride, Klebsormidium subtile and Coleochaete scutata, and from two early-branching chlorophytes, Pyramimonas parkeae and Scherffelia dubia. In addition, to extend the database, our analyses included ESTs from six other chlorophytes (Acetabularia acetabulum, Chlamydomonas reinhardtii, Helicosporidium sp. ex Simulium jonesii, Prototheca wickerhamii, Scenedesmus obliquus and Ulva linza and one streptophyte (Closterium peracerosum. Our results indicate that polyadenylation signals in green algae vary widely. The UGUAA motif is confined to late-branching Chlorophyta. Most streptophyte algae do not have an A-rich sequence motif like that in embryophytes, animals and fungi. We observed polyadenylation signals similar to those of Arabidopsis and other land plants only in Mesostigma. Conclusion Polyadenylation signals in green algae show considerable variation. A new NUE (UGUAA was invented in derived chlorophytes and replaced

  5. Gain and loss of polyadenylation signals during evolution of green algae.

    Science.gov (United States)

    Wodniok, Sabina; Simon, Andreas; Glöckner, Gernot; Becker, Burkhard

    2007-04-18

    The Viridiplantae (green algae and land plants) consist of two monophyletic lineages: the Chlorophyta and the Streptophyta. Most green algae belong to the Chlorophyta, while the Streptophyta include all land plants and a small group of freshwater algae known as Charophyceae. Eukaryotes attach a poly-A tail to the 3' ends of most nuclear-encoded mRNAs. In embryophytes, animals and fungi, the signal for polyadenylation contains an A-rich sequence (often AAUAAA or related sequence) 13 to 30 nucleotides upstream from the cleavage site, which is commonly referred to as the near upstream element (NUE). However, it has been reported that the pentanucleotide UGUAA is used as polyadenylation signal for some genes in volvocalean algae. We set out to investigate polyadenylation signal differences between streptophytes and chlorophytes that may have emerged shortly after the evolutionary split between Streptophyta and Chlorophyta. We therefore analyzed expressed genes (ESTs) from three streptophyte algae, Mesostigma viride, Klebsormidium subtile and Coleochaete scutata, and from two early-branching chlorophytes, Pyramimonas parkeae and Scherffelia dubia. In addition, to extend the database, our analyses included ESTs from six other chlorophytes (Acetabularia acetabulum, Chlamydomonas reinhardtii, Helicosporidium sp. ex Simulium jonesii, Prototheca wickerhamii, Scenedesmus obliquus and Ulva linza) and one streptophyte (Closterium peracerosum). Our results indicate that polyadenylation signals in green algae vary widely. The UGUAA motif is confined to late-branching Chlorophyta. Most streptophyte algae do not have an A-rich sequence motif like that in embryophytes, animals and fungi. We observed polyadenylation signals similar to those of Arabidopsis and other land plants only in Mesostigma. Polyadenylation signals in green algae show considerable variation. A new NUE (UGUAA) was invented in derived chlorophytes and replaced not only the A-rich NUE but the complete poly

  6. Gain and loss of polyadenylation signals during evolution of green algae

    OpenAIRE

    Wodniok, Sabina; Simon, Andreas; Glöckner, Gernot; Becker, Burkhard

    2007-01-01

    Abstract Background The Viridiplantae (green algae and land plants) consist of two monophyletic lineages: the Chlorophyta and the Streptophyta. Most green algae belong to the Chlorophyta, while the Streptophyta include all land plants and a small group of freshwater algae known as Charophyceae. Eukaryotes attach a poly-A tail to the 3' ends of most nuclear-encoded mRNAs. In embryophytes, animals and fungi, the signal for polyadenylation contains an A-rich sequence (often AAUAAA or related seq...

  7. Integration of developmental and environmental signals via a polyadenylation factor in Arabidopsis.

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    Man Liu

    Full Text Available The ability to integrate environmental and developmental signals with physiological responses is critical for plant survival. How this integration is done, particularly through posttranscriptional control of gene expression, is poorly understood. Previously, it was found that the 30 kD subunit of Arabidopsis cleavage and polyadenylation specificity factor (AtCPSF30 is a calmodulin-regulated RNA-binding protein. Here we demonstrated that mutant plants (oxt6 deficient in AtCPSF30 possess a novel range of phenotypes--reduced fertility, reduced lateral root formation, and altered sensitivities to oxidative stress and a number of plant hormones (auxin, cytokinin, gibberellic acid, and ACC. While the wild-type AtCPSF30 (C30G was able to restore normal growth and responses, a mutant AtCPSF30 protein incapable of interacting with calmodulin (C30GM could only restore wild-type fertility and responses to oxidative stress and ACC. Thus, the interaction with calmodulin is important for part of AtCPSF30 functions in the plant. Global poly(A site analysis showed that the C30G and C30GM proteins can restore wild-type poly(A site choice to the oxt6 mutant. Genes associated with hormone metabolism and auxin responses are also affected by the oxt6 mutation. Moreover, 19 genes that are linked with calmodulin-dependent CPSF30 functions, were identified through genome-wide expression analysis. These data, in conjunction with previous results from the analysis of the oxt6 mutant, indicate that the polyadenylation factor AtCPSF30 is a regulatory hub where different signaling cues are transduced, presumably via differential mRNA 3' end formation or alternative polyadenylation, into specified phenotypic outcomes. Our results suggest a novel function of a polyadenylation factor in environmental and developmental signal integration.

  8. SATB2 is a Promising Biomarker for Identifying a Colorectal Origin for Liver Metastatic Adenocarcinomas

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    Yi-Jun Zhang

    2018-02-01

    Full Text Available SATB2 (Special AT-rich sequence-binding protein 2 has recently been shown to be a specific biomarker of colorectal cancer (CRC. The aim of this study was to investigate the diagnostic potential of SATB2 as a means of detecting a CRC origin for liver metastases. SATB2 expression was examined in a resection cohort of 101 CRC and 273 non-CRC adenocarcinoma samples using immunohistochemistry (IHC. The diagnostic accuracy of CRC origins of liver metastases based on SATB2 and a three marker panel of SATB2, CK20 and CDX2 was evaluated using an independent cohort of 192 liver biopsies. IHC showed 97 of the 101 (96.0% primary CRC samples were SATB2 positive, compared to only 6 of the 273 (2.1% samples of other cancer types. The sensitivity, specificity and AUC values of SATB2 expression in resection samples were 97%, 97.1% and 0.977, respectively. Meanwhile, for the liver biopsy samples, the sensitivity, specificity and AUC values of a CRC liver metastases was 92.2%, 97.8% and 0.948 for SATB2, 95.1%, 91.0% and 0.959 for CK20, and 100%, 85.4% and 0.976 for CDX2, respectively. Further analysis demonstrated that all three-marker positivity was detected in 92/103 (89.3% CRC and 2/89 (2.2% non-CRC liver metastases sampled by biopsy. Our findings suggest that SATB2, as measured by IHC, could serve as a promising diagnostic biomarker of CRC metastases. Combining evaluation of SATB2 with CK20 and CDX2 to form a three marker panel further improved the detection of metastatic CRCs in liver biopsy tissues.

  9. SATB2 participates in regulation of menadione-induced apoptotic insults to osteoblasts.

    Science.gov (United States)

    Wei, Jyh-Ding; Lin, Yi-Ling; Tsai, Cheng-Hsiu; Shieh, Hui-Shan; Lin, Pei-I; Ho, Wei-Pin; Chen, Ruei-Ming

    2012-07-01

    Special AT-rich sequence binding protein 2 (SATB2), a nuclear matrix attachment region-binding protein, can regulate embryonic development, cell differentiation, and cell survival. Previous studies showed that SATB2 is involved in osteoblast differentiation and skeletal development. In this study, we evaluated the role of SATB2 in oxidative stress-induced apoptotic insults to human osteoblast-like MG63 cells and mouse MC3T3-E1 cells. Exposure of MG63 cells to menadione increased intracellular reactive oxygen species levels in a concentration- and time-dependent manner. Simultaneously, menadione-induced oxidative stress triggered cell shrinkage and decreased cell viability. In addition, treatment of MG63 cells with menadione time-dependently decreased the mitochondrial membrane potential but enhanced caspase-3 activity. As a result, menadione-induced DNA fragmentation and cell apoptosis. As to the mechanism, exposure of MG63 cells to menadione amplified SATB2 messenger (m)RNA and protein expression in a time-dependent manner. Knockdown of translation of SATB2 mRNA using RNA interference led to chromatin disruption and nuclear damage. When MG63 cells and MC3T3-E1 cells were treated with SATB2 small interfering RNA, menadione-induced cell apoptosis was increased. We conclude that menadione causes oxidative stress in human osteoblasts and induces cellular apoptosis via a mitochondrion-caspase protease pathway. In addition, SATB2 may play a crucial role in protecting against oxidative stress-induced osteoblast apoptosis. Copyright © 2012 Orthopaedic Research Society.

  10. Satb2 determines miRNA expression and long-term memory in the adult central nervous system.

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    Jaitner, Clemens; Reddy, Chethan; Abentung, Andreas; Whittle, Nigel; Rieder, Dietmar; Delekate, Andrea; Korte, Martin; Jain, Gaurav; Fischer, Andre; Sananbenesi, Farahnaz; Cera, Isabella; Singewald, Nicolas; Dechant, Georg; Apostolova, Galina

    2016-11-29

    SATB2 is a risk locus for schizophrenia and encodes a DNA-binding protein that regulates higher-order chromatin configuration. In the adult brain Satb2 is almost exclusively expressed in pyramidal neurons of two brain regions important for memory formation, the cerebral cortex and the CA1-hippocampal field. Here we show that Satb2 is required for key hippocampal functions since deletion of Satb2 from the adult mouse forebrain prevents the stabilization of synaptic long-term potentiation and markedly impairs long-term fear and object discrimination memory. At the molecular level, we find that synaptic activity and BDNF up-regulate Satb2, which itself binds to the promoters of coding and non-coding genes. Satb2 controls the hippocampal levels of a large cohort of miRNAs, many of which are implicated in synaptic plasticity and memory formation. Together, our findings demonstrate that Satb2 is critically involved in long-term plasticity processes in the adult forebrain that underlie the consolidation and stabilization of context-linked memory.

  11. Single Nucleotide Polymorphisms Can Create Alternative Polyadenylation Signals and Affect Gene Expression through Loss of MicroRNA-Regulation

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    Thomas, Laurent F.; Sætrom, Pål

    2012-01-01

    Alternative polyadenylation (APA) can for example occur when a protein-coding gene has several polyadenylation (polyA) signals in its last exon, resulting in messenger RNAs (mRNAs) with different 3′ untranslated region (UTR) lengths. Different 3′UTR lengths can give different microRNA (miRNA) regulation such that shortened transcripts have increased expression. The APA process is part of human cells' natural regulatory processes, but APA also seems to play an important role in many human diseases. Although altered APA in disease can have many causes, we reasoned that mutations in DNA elements that are important for the polyA process, such as the polyA signal and the downstream GU-rich region, can be one important mechanism. To test this hypothesis, we identified single nucleotide polymorphisms (SNPs) that can create or disrupt APA signals (APA-SNPs). By using a data-integrative approach, we show that APA-SNPs can affect 3′UTR length, miRNA regulation, and mRNA expression—both between homozygote individuals and within heterozygote individuals. Furthermore, we show that a significant fraction of the alleles that cause APA are strongly and positively linked with alleles found by genome-wide studies to be associated with disease. Our results confirm that APA-SNPs can give altered gene regulation and that APA alleles that give shortened transcripts and increased gene expression can be important hereditary causes for disease. PMID:22915998

  12. The miR-599 promotes non-small cell lung cancer cell invasion via SATB2

    International Nuclear Information System (INIS)

    Tian, Wenjun; Wang, Guanghai; Liu, Yiqing; Huang, Zhenglan; Zhang, Caiqing; Ning, Kang; Yu, Cuixiang; Shen, Yajuan; Wang, Minghui; Li, Yuantang; Wang, Yong; Zhang, Bingchang; Zhao, Yaoran

    2017-01-01

    MicroRNAs (miRNAs) play important roles in the pathogenesis of many types of cancers by negatively regulating gene expression at posttranscriptional level. Here, we identified that miR-599 is up-regulated in non-small cell lung cancer (NSCLC) patients. It promoted NSCLC cell proliferation by negatively regulating SATB2. In NSCLC cell lines, CCK-8 proliferation assay indicated that the cell proliferation is promoted by miR-599 mimics. Transwell assay showed that miR-599 mimics promoted the invasion and migration of NSCLC cells. Luciferase assays confirmed that miR-599 directly binds to the 3'untranslated region of SATB2, and western blotting showed that miR-599 suppresses the expression of SATB2 at the protein level. This study indicates that miR-599 promotes proliferation and invasion of NSCLC cell lines via SATB2. The miR-599 may represent a potential therapeutic target for NSCLC treatment. - Highlights: • miR-599 is up-regulated in NSCLC. • miR-599 promotes the proliferation and invasion of NSCLC cells. • miR-599 inhibitors inhibits the proliferation and invasion of NSCLC cells. • miR-599 targets 3′ UTR of SATB2 in NSCLC cells. • miR-599 inhibits SATB2 in NSCLC cells.

  13. Prediction of non-canonical polyadenylation signals in human genomic sequences based on a novel algorithm using a fuzzy membership function.

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    Kamasawa, Masami; Horiuchi, Jun-Ichi

    2009-05-01

    Computational prediction of polyadenylation signals (PASes) is essential for analysis of alternative polyadenylation that plays crucial roles in gene regulations by generating heterogeneity of 3'-UTR of mRNAs. To date, several algorithms that are mostly based on machine learning methods have been developed to predict PASes. Accuracies of predictions by those algorithms have improved significantly for the last decade. However, they are designed primarily for prediction of the most canonical AAUAAA and its common variant AUUAAA whereas other variants have been ignored in their predictions despite recent studies indicating that non-canonical variants of AAUAAA are more important in the polyadenylation process than commonly recognized. Here we present a new algorithm "PolyF" employing fuzzy logic to confer an advance in computational PAS prediction--enable prediction of the non-canonical variants, and improve the accuracies for the canonical A(A/U)UAAA prediction. PolyF is a simple computational algorithm that is composed of membership functions defining sequence features of downstream sequence element (DSE) and upstream sequence element (USE), together with an inference engine. As a result, PolyF successfully identified the 10 single-nucleotide variants with approximately the same or higher accuracies compared to those for A(A/U)UAAA. PolyF also achieved higher accuracies for A(A/U)UAAA prediction than those by commonly known PAS finder programs, Polyadq and Erpin. Incorporating the USE into the PolyF algorithm was found to enhance prediction accuracies for all the 12 PAS hexamers compared to those using only the DSE, suggesting an important contribution of the USE in the polyadenylation process.

  14. A mammalian conserved element derived from SINE displays enhancer properties recapitulating Satb2 expression in early-born callosal projection neurons.

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    Kensuke Tashiro

    Full Text Available Short interspersed repetitive elements (SINEs are highly repeated sequences that account for a significant proportion of many eukaryotic genomes and are usually considered "junk DNA". However, we previously discovered that many AmnSINE1 loci are evolutionarily conserved across mammalian genomes, suggesting that they may have acquired significant functions involved in controlling mammalian-specific traits. Notably, we identified the AS021 SINE locus, located 390 kbp upstream of Satb2. Using transgenic mice, we showed that this SINE displays specific enhancer activity in the developing cerebral cortex. The transcription factor Satb2 is expressed by cortical neurons extending axons through the corpus callosum and is a determinant of callosal versus subcortical projection. Mouse mutants reveal a crucial function for Sabt2 in corpus callosum formation. In this study, we compared the enhancer activity of the AS021 locus with Satb2 expression during telencephalic development in the mouse. First, we showed that the AS021 enhancer is specifically activated in early-born Satb2(+ neurons. Second, we demonstrated that the activity of the AS021 enhancer recapitulates the expression of Satb2 at later embryonic and postnatal stages in deep-layer but not superficial-layer neurons, suggesting the possibility that the expression of Satb2 in these two subpopulations of cortical neurons is under genetically distinct transcriptional control. Third, we showed that the AS021 enhancer is activated in neurons projecting through the corpus callosum, as described for Satb2(+ neurons. Notably, AS021 drives specific expression in axons crossing through the ventral (TAG1(-/NPY(+ portion of the corpus callosum, confirming that it is active in a subpopulation of callosal neurons. These data suggest that exaptation of the AS021 SINE locus might be involved in enhancement of Satb2 expression, leading to the establishment of interhemispheric communication via the corpus callosum

  15. Small deletions of SATB2 cause some of the clinical features of the 2q33.1 microdeletion syndrome.

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    Jill A Rosenfeld

    Full Text Available Recurrent deletions of 2q32q33 have recently been reported as a new microdeletion syndrome. Clinical features of this syndrome include severe mental retardation, growth retardation, dysmorphic features, thin and sparse hair, feeding difficulties and cleft or high palate. The commonly deleted region contains at least seven genes. Haploinsufficiency of one of these genes, SATB2, a DNA-binding protein that regulates gene expression, has been implicated as causative in the cleft or high palate of individuals with 2q32q33 microdeletion syndrome. In this study we describe three individuals with smaller microdeletions of this region, within 2q33.1. The deletions ranged in size from 173.1 kb to 185.2 kb and spanned part of SATB2. Review of clinical records showed similar clinical features among these individuals, including severe developmental delay and tooth abnormalities. Two of the individuals had behavioral problems. Only one of the subjects presented here had a cleft palate, suggesting reduced penetrance for this feature. Our results suggest that deletion of SATB2 is responsible for several of the clinical features associated with 2q32q33 microdeletion syndrome.

  16. Transplantation of osteoporotic bone marrow stromal cells rejuvenated by the overexpression of SATB2 prevents alveolar bone loss in ovariectomized rats.

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    Xu, Rongyao; Fu, Zongyun; Liu, Xue; Xiao, Tao; Zhang, Ping; Du, Yifei; Yuan, Hua; Cheng, Jie; Jiang, Hongbing

    2016-11-01

    Estrogen-deficient osteoporosis is an aging-related disease with high morbidity that not only significantly increases a woman's risk of fragility fracture but is also associated with tooth and bone loss in the supporting alveolar bone of the jaw. Emerging evidence suggests that the aging of bone marrow stromal cells (BMSCs) contributes to the development of osteoporosis. In this study, we aimed to investigate the role of the special AT-rich sequence-binding protein 2 (SATB2), a stemness and senescence regulator of craniofacial BMSCs, in rat ovariectomy-induced alveolar osteoporosis. We also sought to determine whether transplantation of SATB2-modified BMSCs could ameliorate estrogen deficient alveolar bone loss. Our data revealed that BMSCs from ovariectomy-induced alveolar bone exhibited typical senescence phenotypes such as diminished stemness and osteogenic capacity, increased expression of senescence or osteoclastic markers and enhanced adipogenic potential. These phenotypic changes are a result of SATB2-mediated senescence dysregulation as evidenced by nuclear γH2AX foci formation. Moreover, overexpression of SATB2 significantly alleviated the senescence of osteoporotic BMSCs in vitro. Importantly, transplantation of SATB2-modified BMSCs significantly attenuated ovariectomy-induced alveolar bone loss in vivo. Together, our results revealed that SATB2 is a critical regulator of alveolar BMSC senescence, and its overexpression decreases these senescent changes both in vitro and in vivo. SATB2-modified BMSC delivery could be a viable and promising therapeutic strategy for alveolar bone loss induced by estrogen-deficient osteoporosis. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. RNA regulatory elements and polyadenylation in plants

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    Arthur G. Hunt

    2012-01-01

    Full Text Available Alternative poly(A site choice (also known as alternative polyadenylation, or APA has the potential to affect gene expression in qualitative and quantitative ways. Alternative polyadenylation may affect as many as 82% of all expressed genes in a plant. The consequences of APA include the generation of transcripts with differing 3’-UTRs (and thus differing potential regulatory potential and of transcripts with differing protein-coding potential. Genome-wide studies of possible APA suggest a linkage with pre-mRNA splicing, and indicate a coincidence of and perhaps cooperation between RNA regulatory elements that affect splicing efficiency and the recognition of novel intronic poly(A sites. These studies also raise the possibility of the existence of a novel class of polyadenylation-related cis elements that are distinct from the well-characterized plant polyadenylation signal. Many potential APA events, however, have not been associated with identifiable cis elements. The present state of the field reveals a broad scope of APA, and also numerous opportunities for research into mechanisms that govern both choice and regulation of poly(A sites in plants.

  18. Bacterial/archaeal/organellar polyadenylation

    OpenAIRE

    Mohanty, Bijoy K.; Kushner, Sidney R.

    2010-01-01

    Although the first poly(A) polymerase (PAP) was discovered in Escherichia coli in 1962, the study of polyadenylation in bacteria was largely ignored for the next 30 years. However, with the identification of the structural gene for E. coli PAP I in 1992, it became possible to analyze polyadenylation using both biochemical and genetic approaches. Subsequently, it has been shown that polyadenylation plays a multifunctional role in prokaryotic RNA metabolism. While the bulk of our current unders...

  19. Characterization of Rous sarcoma virus polyadenylation site use in vitro

    International Nuclear Information System (INIS)

    Maciolek, Nicole L.; McNally, Mark T.

    2008-01-01

    Polyadenylation of Rous sarcoma virus (RSV) RNA is inefficient, as approximately 15% of RSV RNAs represent read-through transcripts that use a downstream cellular polyadenylation site (poly(A) site). Read-through transcription has implications for the virus and the host since it is associated with oncogene capture and tumor induction. To explore the basis of inefficient RSV RNA 3'-end formation, we characterized RSV polyadenylation in vitro using HeLa cell nuclear extracts and HEK293 whole cell extracts. RSV polyadenylation substrates composed of the natural 3' end of viral RNA and various lengths of upstream sequence showed little or no polyadenylation, indicating that the RSV poly(A) site is suboptimal. Efficiently used poly(A) sites often have identifiable upstream and downstream elements (USEs and DSEs) in close proximity to the conserved AAUAAA signal. The sequences upstream and downstream of the RSV poly(A) site deviate from those found in efficiently used poly(A) sites, which may explain inefficient RSV polyadenylation. To assess the quality of the RSV USEs and DSEs, the well-characterized SV40 late USEs and/or DSEs were substituted for the RSV elements and vice versa, which showed that the USEs and DSEs from RSV are suboptimal but functional. CstF interacted poorly with the RSV polyadenylation substrate, and the inactivity of the RSV poly(A) site was at least in part due to poor CstF binding since tethering CstF to the RSV substrate activated polyadenylation. Our data are consistent with poor polyadenylation factor binding sites in both the USE and DSE as the basis for inefficient use of the RSV poly(A) site and point to the importance of additional elements within RSV RNA in promoting 3' end formation

  20. The early noncoding region of human papillomavirus type 16 is regulated by cytoplasmic polyadenylation factors

    DEFF Research Database (Denmark)

    Glahder, Jacob-Andreas Harald; Kristiansen, Karen; Durand, Marjorie

    2010-01-01

    All human papillomavirus type 16 (HPV-16) early mRNAs are polyadenylated at the poly(A) signal within the early 3' untranslated region (3'UTR). The 3'end of the early E5 open reading frame and the 3'UTR of HPV-16 is very AU-rich, with five regions similar to cytoplasmic polyadenylation elements (...

  1. Bacterial/archaeal/organellar polyadenylation.

    Science.gov (United States)

    Mohanty, Bijoy K; Kushner, Sidney R

    2011-01-01

    Although the first poly(A) polymerase (PAP) was discovered in Escherichia coli in 1962, the study of polyadenylation in bacteria was largely ignored for the next 30 years. However, with the identification of the structural gene for E. coli PAP I in 1992, it became possible to analyze polyadenylation using both biochemical and genetic approaches. Subsequently, it has been shown that polyadenylation plays a multifunctional role in prokaryotic RNA metabolism. Although the bulk of our current understanding of prokaryotic polyadenylation comes from studies on E. coli, recent limited experiments with Cyanobacteria, organelles, and Archaea have widened our view on the diversity, complexity, and universality of the polyadenylation process. For example, the identification of polynucleotide phosphorylase (PNPase), a reversible phosphorolytic enzyme that is highly conserved in bacteria, as an additional PAP in E. coli caught everyone by surprise. In fact, PNPase has now been shown to be the source of post-transcriptional RNA modifications in a wide range of cells of prokaryotic origin including those that lack a eubacterial PAP homolog. Accordingly, the past few years have witnessed increased interest in the mechanism and role of post-transcriptional modifications in all species of prokaryotic origin. However, the fact that many of the poly(A) tails are very short and unstable as well as the presence of polynucleotide tails has posed significant technical challenges to the scientific community trying to unravel the mystery of polyadenylation in prokaryotes. This review discusses the current state of knowledge regarding polyadenylation and its functions in bacteria, organelles, and Archaea.

  2. Regulatory mechanisms for 3'-end alternative splicing and polyadenylation of the Glial Fibrillary Acidic Protein, GFAP, transcript

    DEFF Research Database (Denmark)

    Blechingberg, Jenny; Lykke-Andersen, Søren; Jensen, Torben Heick

    2007-01-01

    (PTB) protein enhanced both exon 7a polyadenylation and exon 7a splicing. Finally, increasing transcription by the VP16 trans-activator did not affect the frequency of use of the exon 7a polyadenylation signal whereas the exon 7a splicing frequency was decreased. Our data suggest a model...

  3. Polyadenylation of RNA transcribed from mammalian SINEs by RNA polymerase III: Complex requirements for nucleotide sequences.

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    Borodulina, Olga R; Golubchikova, Julia S; Ustyantsev, Ilia G; Kramerov, Dmitri A

    2016-02-01

    It is generally accepted that only transcripts synthesized by RNA polymerase II (e.g., mRNA) were subject to AAUAAA-dependent polyadenylation. However, we previously showed that RNA transcribed by RNA polymerase III (pol III) from mouse B2 SINE could be polyadenylated in an AAUAAA-dependent manner. Many species of mammalian SINEs end with the pol III transcriptional terminator (TTTTT) and contain hexamers AATAAA in their A-rich tail. Such SINEs were united into Class T(+), whereas SINEs lacking the terminator and AATAAA sequences were classified as T(-). Here we studied the structural features of SINE pol III transcripts that are necessary for their polyadenylation. Eight and six SINE families from classes T(+) and T(-), respectively, were analyzed. The replacement of AATAAA with AACAAA in T(+) SINEs abolished the RNA polyadenylation. Interestingly, insertion of the polyadenylation signal (AATAAA) and pol III transcription terminator in T(-) SINEs did not result in polyadenylation. The detailed analysis of three T(+) SINEs (B2, DIP, and VES) revealed areas important for the polyadenylation of their pol III transcripts: the polyadenylation signal and terminator in A-rich tail, β region positioned immediately downstream of the box B of pol III promoter, and τ region located upstream of the tail. In DIP and VES (but not in B2), the τ region is a polypyrimidine motif which is also characteristic of many other T(+) SINEs. Most likely, SINEs of different mammals acquired these structural features independently as a result of parallel evolution. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Polyadenylation state microarray (PASTA) analysis.

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    Beilharz, Traude H; Preiss, Thomas

    2011-01-01

    Nearly all eukaryotic mRNAs terminate in a poly(A) tail that serves important roles in mRNA utilization. In the cytoplasm, the poly(A) tail promotes both mRNA stability and translation, and these functions are frequently regulated through changes in tail length. To identify the scope of poly(A) tail length control in a transcriptome, we developed the polyadenylation state microarray (PASTA) method. It involves the purification of mRNA based on poly(A) tail length using thermal elution from poly(U) sepharose, followed by microarray analysis of the resulting fractions. In this chapter we detail our PASTA approach and describe some methods for bulk and mRNA-specific poly(A) tail length measurements of use to monitor the procedure and independently verify the microarray data.

  5. Alternative Polyadenylation: Methods, Findings, and Impacts

    Directory of Open Access Journals (Sweden)

    Wei Chen

    2017-10-01

    Full Text Available Alternative polyadenylation (APA, a phenomenon that RNA molecules with different 3′ ends originate from distinct polyadenylation sites of a single gene, is emerging as a mechanism widely used to regulate gene expression. In the present review, we first summarized various methods prevalently adopted in APA study, mainly focused on the next-generation sequencing (NGS-based techniques specially designed for APA identification, the related bioinformatics methods, and the strategies for APA study in single cells. Then we summarized the main findings and advances so far based on these methods, including the preferences of alternative polyA (pA site, the biological processes involved, and the corresponding consequences. We especially categorized the APA changes discovered so far and discussed their potential functions under given conditions, along with the possible underlying molecular mechanisms. With more in-depth studies on extensive samples, more signatures and functions of APA will be revealed, and its diverse roles will gradually heave in sight. Keywords: Alternative polyadenylation, Next-generation sequencing, 3′UTR, Alternative splicing, Gene regulation

  6. Alterations in polyadenylation and its implications for endocrine disease

    Directory of Open Access Journals (Sweden)

    Anders eRehfeld

    2013-05-01

    Full Text Available IntroductionPolyadenylation is the process in which the pre-mRNA is cleaved at the poly(A site and a poly(A tail is added - a process necessary for normal mRNA formation. Genes with multiple poly(A sites can undergo alternative polyadenylation, producing distinct mRNA isoforms with different 3’ untranslated regions (3’ UTRs and in some cases different coding regions. Two thirds of all human genes undergo alternative polyadenylation. The efficiency of the polyadenylation process regulates gene expression and alternative polyadenylation plays an important part in post-transcriptional regulation, as the 3’ UTR contains various cis-elements associated with post-transcriptional regulation, such as target sites for microRNAs and RNA-binding proteins.Implications of alterations in polyadenylation for endocrine diseaseAlterations in polyadenylation have been found to be causative of neonatal diabetes and IPEX (immune dysfunction, polyendocrinopathy, enteropathy, X-linked and to be associated with type I and II diabetes, pre-eclampsia, fragile X-associated premature ovarian insufficiency, ectopic Cushing syndrome and many cancer diseases, including several types of endocrine tumor diseases.PerspectivesRecent developments in high-throughput sequencing have made it possible to characterize polyadenylation genome-wide. Antisense elements inhibiting or enhancing specific poly(A site usage can induce desired alterations in polyadenylation, and thus hold the promise of new therapeutic approaches. SummaryThis review gives a detailed description of alterations in polyadenylation in endocrine disease, an overview of the current literature on polyadenylation and summarizes the clinical implications of the current state of research in this field.

  7. Ctip2-, Satb2-, Prox1-, and GAD65-Expressing Neurons in Rat Cultures: Preponderance of Single- and Double-Positive Cells, and Cell Type-Specific Expression of Neuron-Specific Gene Family Members, Nsg-1 (NEEP21) and Nsg-2 (P19).

    Science.gov (United States)

    Digilio, Laura; Yap, Chan Choo; Winckler, Bettina

    2015-01-01

    The brain consists of many distinct neuronal cell types, but which cell types are present in widely used primary cultures of embryonic rodent brain is often not known. We characterized how abundantly four cell type markers (Ctip2, Satb2, Prox1, GAD65) were represented in cultured rat neurons, how easily neurons expressing different markers can be transfected with commonly used plasmids, and whether neuronal-enriched endosomal proteins Nsg-1 (NEEP21) and Nsg-2 (P19) are ubiquitously expressed in all types of cultured neurons. We found that cultured neurons stably maintain cell type identities that are reflective of cell types in vivo. This includes neurons maintaining simultaneous expression of two transcription factors, such as Ctip2+/Satb2+ or Prox1+/Ctip2+ double-positive cells, which have also been described in vivo. Secondly, we established the superior efficiency of CAG promoters for both Lipofectamine-mediated transfection as well as for electroporation. Thirdly, we discovered that Nsg-1 and Nsg-2 were not expressed equally in all neurons: whereas high levels of both Nsg-1 and Nsg-2 were found in Satb2-, Ctip2-, and GAD65-positive neurons, Prox1-positive neurons in hippocampal cultures expressed low levels of both. Our findings thus highlight the importance of identifying neuronal cell types for doing cell biology in cultured neurons: Keeping track of neuronal cell type might uncover effects in assays that might otherwise be masked by the mixture of responsive and non-responsive neurons in the dish.

  8. Alterations in polyadenylation and its implications for endocrine disease

    DEFF Research Database (Denmark)

    Rehfeld, Anders Aagaard; Plass, Mireya; Krogh, Anders

    2013-01-01

    Introduction: Polyadenylation is the process in which the pre-mRNA is cleaved at the poly(A) site and a poly(A) tail is added - a process necessary for normal mRNA formation. Genes with multiple poly(A) sites can undergo alternative polyadenylation (APA), producing distinct mRNA isoforms with dif......Introduction: Polyadenylation is the process in which the pre-mRNA is cleaved at the poly(A) site and a poly(A) tail is added - a process necessary for normal mRNA formation. Genes with multiple poly(A) sites can undergo alternative polyadenylation (APA), producing distinct mRNA isoforms...... with different 3' untranslated regions (3' UTRs) and in some cases different coding regions. Two thirds of all human genes undergo APA. The efficiency of the polyadenylation process regulates gene expression and APA plays an important part in post-transcriptional regulation, as the 3' UTR contains various cis...

  9. Promoter proximal polyadenylation sites reduce transcription activity

    DEFF Research Database (Denmark)

    Andersen, Pia Kjølhede; Lykke-Andersen, Søren; Jensen, Torben Heick

    2012-01-01

    Gene expression relies on the functional communication between mRNA processing and transcription. We previously described the negative impact of a point-mutated splice donor (SD) site on transcription. Here we demonstrate that this mutation activates an upstream cryptic polyadenylation (CpA) site......, which in turn causes reduced transcription. Functional depletion of U1 snRNP in the context of the wild-type SD triggers the same CpA event accompanied by decreased RNA levels. Thus, in accordance with recent findings, U1 snRNP can shield premature pA sites. The negative impact of unshielded pA sites...... on transcription requires promoter proximity, as demonstrated using artificial constructs and supported by a genome-wide data set. Importantly, transcription down-regulation can be recapitulated in a gene context devoid of splice sites by placing a functional bona fide pA site/transcription terminator within ∼500...

  10. Identification of Polyadenylation Sites within Arabidopsis Thaliana

    KAUST Repository

    Kalkatawi, Manal

    2011-09-01

    Machine Learning (ML) is a field of artificial intelligence focused on the design and implementation of algorithms that enable creation of models for clustering, classification, prediction, ranking and similar inference tasks based on information contained in data. Many ML algorithms have been successfully utilized in a variety of applications. The problem addressed in this thesis is from the field of bioinformatics and deals with the recognition of polyadenylation (poly(A)) sites in the genomic sequence of the plant Arabidopsis thaliana. During the RNA processing, a tail consisting of a number of consecutive adenine (A) nucleotides is added to the terminal nucleotide of the 3’- untranslated region (3’UTR) of the primary RNA. The process in which these A nucleotides are added is called polyadenylation. The location in the genomic DNA sequence that corresponds to the start of terminal A nucleotides (i.e. to the end of 3’UTR) is known as a poly(A) site. Recognition of the poly(A) sites in DNA sequence is important for better gene annotation and understanding of gene regulation. In this study, we built an artificial neural network (ANN) for the recognition of poly(A) sites in the Arabidopsis thaliana genome. Our study demonstrates that this model achieves improved accuracy compared to the existing predictive models for this purpose. The key factor contributing to the enhanced predictive performance of our ANN model is a distinguishing set of features used in creation of the model. These features include a number of physico-chemical characteristics of relevance, such as dinucleotide thermodynamic characteristics, electron-ion interaction potential, etc., but also many of the statistical properties of the DNA sequences from the region surrounding poly(A) site, such as nucleotide and polynucleotide properties, common motifs, etc. Our ANN model was compared in performance with several other ML models, as well as with the PAC tool that is specifically developed for

  11. Cell Cycle Regulation by Alternative Polyadenylation of CCND1.

    Science.gov (United States)

    Wang, Qiong; He, Guopei; Hou, Mengmeng; Chen, Liutao; Chen, Shangwu; Xu, Anlong; Fu, Yonggui

    2018-05-01

    Global shortening of 3'UTRs by alternative polyadenylation (APA) has been observed in cancer cells. However, the role of APA in cancer remains unknown. CCND1 is a proto-oncogene that regulates progression through the G1-S phase of the cell cycle; moreover, it has been observed to be switching to proximal APA sites in cancer cells. To investigate the biological function of the APA of CCND1, we edited the weak poly(A) signal (PAS) of the proximal APA site to a canonical PAS using the CRISPR/Cas9 method, which can force the cells to use a proximal APA site. Cell cycle profiling and proliferation assays revealed that the proximal APA sites of CCND1 accelerated the cell cycle and promoted cell proliferation, but UTR-APA and CR-APA act via different molecular mechanisms. These results indicate that PAS editing with CRISPR/Cas9 provides a good method by which to study the biological function of APA.

  12. The STAR protein QKI-7 recruits PAPD4 to regulate post-transcriptional polyadenylation of target mRNAs.

    Science.gov (United States)

    Yamagishi, Ryota; Tsusaka, Takeshi; Mitsunaga, Hiroko; Maehata, Takaharu; Hoshino, Shin-ichi

    2016-04-07

    Emerging evidence has demonstrated that regulating the length of the poly(A) tail on an mRNA is an efficient means of controlling gene expression at the post-transcriptional level. In early development, transcription is silenced and gene expression is primarily regulated by cytoplasmic polyadenylation. In somatic cells, considerable progress has been made toward understanding the mechanisms of negative regulation by deadenylation. However, positive regulation through elongation of the poly(A) tail has not been widely studied due to the difficulty in distinguishing whether any observed increase in length is due to the synthesis of new mRNA, reduced deadenylation or cytoplasmic polyadenylation. Here, we overcame this barrier by developing a method for transcriptional pulse-chase analysis under conditions where deadenylases are suppressed. This strategy was used to show that a member of the Star family of RNA binding proteins, QKI, promotes polyadenylation when tethered to a reporter mRNA. Although multiple RNA binding proteins have been implicated in cytoplasmic polyadenylation during early development, previously only CPEB was known to function in this capacity in somatic cells. Importantly, we show that only the cytoplasmic isoform QKI-7 promotes poly(A) tail extension, and that it does so by recruiting the non-canonical poly(A) polymerase PAPD4 through its unique carboxyl-terminal region. We further show that QKI-7 specifically promotes polyadenylation and translation of three natural target mRNAs (hnRNPA1, p27(kip1)and β-catenin) in a manner that is dependent on the QKI response element. An anti-mitogenic signal that induces cell cycle arrest at G1 phase elicits polyadenylation and translation of p27(kip1)mRNA via QKI and PAPD4. Taken together, our findings provide significant new insight into a general mechanism for positive regulation of gene expression by post-transcriptional polyadenylation in somatic cells. © The Author(s) 2016. Published by Oxford

  13. Pyrogenicity of polyadenylic.polyuridylic acid in rabbits.

    Science.gov (United States)

    Won, S J; Lin, M T

    1991-05-01

    Polyadenylic.polyuridylic acid injected intravenously into rabbits produced a rapid-onset, monophasic fever. Pyrogenic tolerance occurred in rabbits following daily injections of polyadenylic.polyuridylic acid. However, direct injection of the agent into the preoptic anterior hypothalamic region of rabbit's brain produced a markedly different fever. After an intrahypothalamic injection of polyadenylic.polyuridylic acid, fever was delayed in onset and persisted for a longer period. At room temperature, the fever was due to both increased metabolism and cutaneous vasoconstriction. In a colder atmosphere the fever was due solely to increased metabolism, whereas in the heat the fever was due to reduction in cutaneous blood flow and respiratory evaporative heat loss. In addition, the fever induced by intravenous polyadenylic.polyuridylic acid injection was reversed by a cyclooxygenase inhibitor, but not by a protein synthesis inhibitor. Polyadenylic.polyuridylic acid was shown to stimulate PGE2 production from rabbit's hypothalamus in vitro. The results reveal that this agent is a prostaglandin-dependent pyrogen.

  14. Polyadenylation site prediction using PolyA-iEP method.

    Science.gov (United States)

    Kavakiotis, Ioannis; Tzanis, George; Vlahavas, Ioannis

    2014-01-01

    This chapter presents a method called PolyA-iEP that has been developed for the prediction of polyadenylation sites. More precisely, PolyA-iEP is a method that recognizes mRNA 3'ends which contain polyadenylation sites. It is a modular system which consists of two main components. The first exploits the advantages of emerging patterns and the second is a distance-based scoring method. The outputs of the two components are finally combined by a classifier. The final results reach very high scores of sensitivity and specificity.

  15. The role of alternative Polyadenylation in regulation of rhythmic gene expression.

    Science.gov (United States)

    Ptitsyna, Natalia; Boughorbel, Sabri; El Anbari, Mohammed; Ptitsyn, Andrey

    2017-08-04

    Alternative transcription is common in eukaryotic cells and plays important role in regulation of cellular processes. Alternative polyadenylation results from ambiguous PolyA signals in 3' untranslated region (UTR) of a gene. Such alternative transcripts share the same coding part, but differ by a stretch of UTR that may contain important functional sites. The methodoogy of this study is based on mathematical modeling, analytical solution, and subsequent validation by datamining in multiple independent experimental data from previously published studies. In this study we propose a mathematical model that describes the population dynamics of alternatively polyadenylated transcripts in conjunction with rhythmic expression such as transcription oscillation driven by circadian or metabolic oscillators. Analysis of the model shows that alternative transcripts with different turnover rates acquire a phase shift if the transcript decay rate is different. Difference in decay rate is one of the consequences of alternative polyadenylation. Phase shift can reach values equal to half the period of oscillation, which makes alternative transcripts oscillate in abundance in counter-phase to each other. Since counter-phased transcripts share the coding part, the rate of translation becomes constant. We have analyzed a few data sets collected in circadian timeline for the occurrence of transcript behavior that fits the mathematical model. Alternative transcripts with different turnover rate create the effect of rectifier. This "molecular diode" moderates or completely eliminates oscillation of individual transcripts and stabilizes overall protein production rate. In our observation this phenomenon is very common in different tissues in plants, mice, and humans. The occurrence of counter-phased alternative transcripts is also tissue-specific and affects functions of multiple biological pathways. Accounting for this mechanism is important for understanding the natural and engineering

  16. siRNAs targeted to certain polyadenylation sites promote specific, RISC-independent degradation of messenger RNAs.

    Science.gov (United States)

    Vickers, Timothy A; Crooke, Stanley T

    2012-07-01

    While most siRNAs induce sequence-specific target mRNA cleavage and degradation in a process mediated by Ago2/RNA-induced silencing complex (RISC), certain siRNAs have also been demonstrated to direct target RNA reduction through deadenylation and subsequent degradation of target transcripts in a process which involves Ago1/RISC and P-bodies. In the current study, we present data suggesting that a third class of siRNA exist, which are capable of promoting target RNA reduction that is independent of both Ago and RISC. These siRNAs bind the target messenger RNA at the polyA signal and are capable of redirecting a small amount of polyadenylation to downstream polyA sites when present, however, the majority of the activity appears to be due to inhibition of polyadenylation or deadenylation of the transcript, followed by exosomal degradation of the immature mRNA.

  17. The polyadenylation factor subunit CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30: A key factor of programmed cell death and a regulator of immunity in arabidopsis

    KAUST Repository

    Bruggeman, Quentin

    2014-04-04

    Programmed cell death (PCD) is essential for several aspects of plant life, including development and stress responses. Indeed, incompatible plant-pathogen interactions are well known to induce the hypersensitive response, a localized cell death. Mutational analyses have identified several key PCD components, and we recently identified the mips1 mutant of Arabidopsis (Arabidopsis thaliana), which is deficient for the key enzyme catalyzing the limiting step of myoinositol synthesis. One of the most striking features of mips1 is the light-dependent formation of lesions on leaves due to salicylic acid (SA)-dependent PCD, revealing roles for myoinositol or inositol derivatives in the regulation of PCD. Here, we identified a regulator of plant PCD by screening for mutants that display transcriptomic profiles opposing that of the mips1 mutant. Our screen identified the oxt6 mutant, which has been described previously as being tolerant to oxidative stress. In the oxt6 mutant, a transfer DNA is inserted in the CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30 (CPSF30) gene, which encodes a polyadenylation factor subunit homolog. We show that CPSF30 is required for lesion formation in mips1 via SA-dependent signaling, that the prodeath function of CPSF30 is not mediated by changes in the glutathione status, and that CPSF30 activity is required for Pseudomonas syringae resistance. We also show that the oxt6 mutation suppresses cell death in other lesion-mimic mutants, including lesion-simulating disease1, mitogen-activated protein kinase4, constitutive expressor of pathogenesis-related genes5, and catalase2, suggesting that CPSF30 and, thus, the control of messenger RNA 3′ end processing, through the regulation of SA production, is a key component of plant immune responses. © 2014 American Society of Plant Biologists. All rights reserved.

  18. Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression

    OpenAIRE

    Kojima, Shihoko; Sher-Chen, Elaine L.; Green, Carla B.

    2012-01-01

    Green and colleagues perform a global analysis of circadian-controlled poly(A) tails and identify hundreds of mRNAs that display dynamic rhythmic polyadenylation states. They identify three distinct classes of mRNAs with rhythmic poly(A) tails. Interestingly, class III mRNAs are controlled not by transcription, but by rhythmic cytoplasmic polyadenylation, and are regulated by the components of the cytoplasmic polyadenylation machinery, CPEB2 in particular, which are themselves rhythmically ex...

  19. Alternative Polyadenylation Patterns for Novel Gene Discovery and Classification in Cancer

    Directory of Open Access Journals (Sweden)

    Oguzhan Begik

    2017-07-01

    Full Text Available Certain aspects of diagnosis, prognosis, and treatment of cancer patients are still important challenges to be addressed. Therefore, we propose a pipeline to uncover patterns of alternative polyadenylation (APA, a hidden complexity in cancer transcriptomes, to further accelerate efforts to discover novel cancer genes and pathways. Here, we analyzed expression data for 1045 cancer patients and found a significant shift in usage of poly(A signals in common tumor types (breast, colon, lung, prostate, gastric, and ovarian compared to normal tissues. Using machine-learning techniques, we further defined specific subsets of APA events to efficiently classify cancer types. Furthermore, APA patterns were associated with altered protein levels in patients, revealed by antibody-based profiling data, suggesting functional significance. Overall, our study offers a computational approach for use of APA in novel gene discovery and classification in common tumor types, with important implications in basic research, biomarker discovery, and precision medicine approaches.

  20. Dysfunctional transcripts are formed by alternative polyadenylation in OPMD

    OpenAIRE

    Raz, Vered; Dickson, George; ’t Hoen, Peter A.C.

    2017-01-01

    Post-transcription mRNA processing in the 3’-untranslated region (UTR) of transcripts alters mRNA landscape. Alternative polyadenylation (APA) utilization in the 3’-UTR often leads to shorter 3’-UTR affecting mRNA stability, a process that is regulated by PABPN1. In skeletal muscles PABPN1 levels reduce with age and a greater decrease in found in Oculopharyngeal muscular dystrophy (OPMD). OPMD is a late onset autosomal dominant myopathy caused by expansion mutation in PABPN1. In OPMD models a...

  1. Genome-wide dynamics of alternative polyadenylation in rice

    Science.gov (United States)

    Fu, Haihui; Yang, Dewei; Su, Wenyue; Ma, Liuyin; Shen, Yingjia; Ji, Guoli; Ye, Xinfu; Wu, Xiaohui

    2016-01-01

    Alternative polyadenylation (APA), in which a transcript uses one of the poly(A) sites to define its 3′-end, is a common regulatory mechanism in eukaryotic gene expression. However, the potential of APA in determining crop agronomic traits remains elusive. This study systematically tallied poly(A) sites of 14 different rice tissues and developmental stages using the poly(A) tag sequencing (PAT-seq) approach. The results indicate significant involvement of APA in developmental and quantitative trait loci (QTL) gene expression. About 48% of all expressed genes use APA to generate transcriptomic and proteomic diversity. Some genes switch APA sites, allowing differentially expressed genes to use alternate 3′ UTRs. Interestingly, APA in mature pollen is distinct where differential expression levels of a set of poly(A) factors and different distributions of APA sites are found, indicating a unique mRNA 3′-end formation regulation during gametophyte development. Equally interesting, statistical analyses showed that QTL tends to use APA for regulation of gene expression of many agronomic traits, suggesting a potential important role of APA in rice production. These results provide thus far the most comprehensive and high-resolution resource for advanced analysis of APA in crops and shed light on how APA is associated with trait formation in eukaryotes. PMID:27733415

  2. Polyadenylated mRNA from the photosynthetic procaryote Rhodospirillum rubrum

    International Nuclear Information System (INIS)

    Majumdar, P.K.; McFadden, B.A.

    1984-01-01

    Total cellular RNA extracted from Rhodospirillum rubrum cultured in butyrate-containing medium under strict photosynthetic conditions to the stationary phase of growth has been fractionated on an oligodeoxy-thymidylic acid-cellulose column into polyadenylated [poly(A) + ] RNA and poly(A) - RNA fractions. The poly(A) + fraction was 9 to 10% of the total bulk RNA isolated. Analysis of the poly(A) + RNA on a denaturing urea-polyacrylamide gel revealed four sharp bands of RNA distributed in heterodisperse fashion between 16S and 9S. Similar fractionation of the poly(A) - RNA resulted in the separation of 23, 16, and 5S rRNAs and 4S tRNA. Poly(A) + fragments isolated after combined digestion with pancreatic A and T 1 RNases and analysis by denaturing gel electrophoresis demonstrated two major components of 80 and 100 residues. Alkaline hydrolysis of the nuclease-resistant, purified residues showed AMP-rich nucleotides. Through the use of snake venom phosphodiesterase, poly(A) tracts were placed at the 3' end of poly(A) + RNA. Stimulation of [ 3 H]leucine incorporation into hot trichloroacetic acid-precipitable polypeptides in a cell-free system from wheat germ primed by the poly(A) + RNA mixture was found to be 220-fold higher than that for poly(A) - RNAs (on a unit mass basis), a finding which demonstrated that poly(A) + RNAs in R. rubrum are mRNAs. Gel electrophoretic analysis of the translation mixture revealed numerous 3 H-labeled products including a major band (M/sub r/, 52,000). The parent protein was precipitated by antibodies to ribulose bisphosphate carboxylase-oxygenase and comprised 6.5% of the total translation products

  3. Alternative polyadenylation of tumor suppressor genes in small intestinal neuroendocrine tumors

    DEFF Research Database (Denmark)

    Rehfeld, Anders Aagaard; Plass, Mireya; Døssing, Kristina

    2014-01-01

    The tumorigenesis of small intestinal neuroendocrine tumors (SI-NETs) is poorly understood. Recent studies have associated alternative polyadenylation (APA) with proliferation, cell transformation, and cancer. Polyadenylation is the process in which the pre-messenger RNA is cleaved at a polyA site...... and a polyA tail is added. Genes with two or more polyA sites can undergo APA. This produces two or more distinct mRNA isoforms with different 3' untranslated regions. Additionally, APA can also produce mRNAs containing different 3'-terminal coding regions. Therefore, APA alters both the repertoire...... and the expression level of proteins. Here, we used high-throughput sequencing data to map polyA sites and characterize polyadenylation genome-wide in three SI-NETs and a reference sample. In the tumors, 16 genes showed significant changes of APA pattern, which lead to either the 3' truncation of mRNA coding regions...

  4. Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation.

    Directory of Open Access Journals (Sweden)

    Kristel Kaer

    Full Text Available Transcriptional interference has been recently recognized as an unexpectedly complex and mostly negative regulation of genes. Despite a relatively few studies that emerged in recent years, it has been demonstrated that a readthrough transcription derived from one gene can influence the transcription of another overlapping or nested gene. However, the molecular effects resulting from this interaction are largely unknown.Using in silico chromosome walking, we searched for prematurely terminated transcripts bearing signatures of intron retention or exonization of intronic sequence at their 3' ends upstream to human L1 retrotransposons, protein-coding and noncoding nested genes. We demonstrate that transcriptional interference induced by intronic L1s (or other repeated DNAs and nested genes could be characterized by intron retention, forced exonization and cryptic polyadenylation. These molecular effects were revealed from the analysis of endogenous transcripts derived from different cell lines and tissues and confirmed by the expression of three minigenes in cell culture. While intron retention and exonization were comparably observed in introns upstream to L1s, forced exonization was preferentially detected in nested genes. Transcriptional interference induced by L1 or nested genes was dependent on the presence or absence of cryptic splice sites, affected the inclusion or exclusion of the upstream exon and the use of cryptic polyadenylation signals.Our results suggest that transcriptional interference induced by intronic L1s and nested genes could influence the transcription of the large number of genes in normal as well as in tumor tissues. Therefore, this type of interference could have a major impact on the regulation of the host gene expression.

  5. Alternative Polyadenylation of Tumor Suppressor Genes in Small Intestinal Neuroendocrine Tumors

    OpenAIRE

    Rehfeld, Anders; Plass, Mireya; Døssing, Kristina; Knigge, Ulrich; Kjær, Andreas; Krogh, Anders; Friis-Hansen, Lennart

    2014-01-01

    The tumorigenesis of small intestinal neuroendocrine tumors (SI-NETs) is poorly understood. Recent studies have associated alternative polyadenylation (APA) with proliferation, cell transformation, and cancer. Polyadenylation is the process in which the pre-messenger RNA is cleaved at a polyA site and a polyA tail is added. Genes with two or more polyA sites can undergo APA. This produces two or more distinct mRNA isoforms with different 3′ untranslated regions. Additionally, APA can also pro...

  6. The poly(rC)-binding protein αCP2 is a noncanonical factor in X. laevis cytoplasmic polyadenylation

    Science.gov (United States)

    Vishnu, Melanie R.; Sumaroka, Marina; Klein, Peter S.; Liebhaber, Stephen A.

    2011-01-01

    Post-transcriptional control of mRNA stability and translation is central to multiple developmental pathways. This control can be linked to cytoplasmic polyadenylation in certain settings. In maturing Xenopus oocytes, specific mRNAs are targeted for polyadenylation via recruitment of the Cytoplasmic Polyadenylation Element (CPE) binding protein (CPEB) to CPE(s) within the 3′ UTR. Cytoplasmic polyadenylation is also critical to early embryonic events, although corresponding determinants are less defined. Here, we demonstrate that the Xenopus ortholog of the poly(rC) binding protein αCP2 can recruit cytoplasmic poly(A) polymerase activity to mRNAs in Xenopus post-fertilization embryos, and that this recruitment relies on cis sequences recognized by αCP2. We find that the hα-globin 3′ UTR, a validated mammalian αCP2 target, constitutes an effective target for cytoplasmic polyadenylation in Xenopus embryos, but not during Xenopus oocyte maturation. We further demonstrate that the cytoplasmic polyadenylation activity is dependent on the action of the C-rich αCP-binding site in conjunction with the adjacent AAUAAA. Consistent with its ability to target mRNA for poly(A) addition, we find that XαCP2 associates with core components of the Xenopus cytoplasmic polyadenylation complex, including the cytoplasmic poly(A) polymerase XGLD2. Furthermore, we observe that the C-rich αCP-binding site can robustly enhance the activity of a weak canonical oocyte maturation CPE in early embryos, possibly via a direct interaction between XαCP2 and CPEB1. These studies establish XαCP2 as a novel cytoplasmic polyadenylation trans factor, indicate that C-rich sequences can function as noncanonical cytoplasmic polyadenylation elements, and expand our understanding of the complexities underlying cytoplasmic polyadenylation in specific developmental settings. PMID:21444632

  7. Gene expression profiling of non-polyadenylated RNA-seq across species

    Directory of Open Access Journals (Sweden)

    Xiao-Ou Zhang

    2014-12-01

    Full Text Available Transcriptomes are dynamic and unique, with each cell type/tissue, developmental stage and species expressing a different repertoire of RNA transcripts. Most mRNAs and well-characterized long noncoding RNAs are shaped with a 5′ cap and 3′ poly(A tail, thus conventional transcriptome analyses typically start with the enrichment of poly(A+ RNAs by oligo(dT selection, followed by deep sequencing approaches. However, accumulated lines of evidence suggest that many RNA transcripts are processed by alternative mechanisms without 3′ poly(A tails and, therefore, fail to be enriched by oligo(dT purification and are absent following deep sequencing analyses. We have described an enrichment strategy to purify non-polyadenylated (poly(A−/ribo− RNAs from human total RNAs by removal of both poly(A+ RNA transcripts and ribosomal RNAs, which led to the identification of many novel RNA transcripts with non-canonical 3′ ends in human. Here, we describe the application of non-polyadenylated RNA-sequencing in rhesus monkey and mouse cell lines/tissue, and further profile the transcription of non-polyadenylated RNAs across species, providing new resources for non-polyadenylated RNA identification and comparison across species.

  8. Alternative polyadenylation and miR-34 family members regulate tau expression

    DEFF Research Database (Denmark)

    Dickson, John R; Kruse, Carla; Montagna, Daniel R

    2013-01-01

    . Tau expresses two 3'-UTR isoforms, long and short, as a result of alternative polyadenylation. Using luciferase reporter constructs, we found that expression from these isoforms is differentially controlled in human neuroblastoma cell lines M17D and SH-SY5Y. Several microRNAs were computationally...

  9. Useful Bicistronic Reporter System for Studying Poly(A Site-Defining cis Elements and Regulation of Alternative Polyadenylation

    Directory of Open Access Journals (Sweden)

    Zhongyuan Deng

    2018-01-01

    Full Text Available The link between polyadenylation (pA and various biological, behavioral, and pathological events of eukaryotes underlines the need to develop in vivo polyadenylation assay methods for characterization of the cis-acting elements, trans-acting factors and environmental stimuli that affect polyadenylation efficiency and/or relative usage of two alternative polyadenylation (APA sites. The current protein-based CAT or luciferase reporter systems can measure the polyadenylation efficiency of a single pA site or candidate cis element but not the choice of two APA sites. To address this issue, we developed a set of four new bicistronic reporter vectors that harbor either two luciferase or fluorescence protein open reading frames connected with one Internal Ribosome Entry Site (IRES. Transfection of single or dual insertion constructs of these vectors into mammalian cells demonstrated that they could be utilized not only to quantify the strength of a single candidate pA site or cis element, but also to accurately measure the relative usage of two APA sites at both the mRNA (qRT-PCR and protein levels. This represents the first reporter system that can study polyadenylation efficiency of a single pA site or element and regulation of two APA sites at both the mRNA and protein levels.

  10. Deciphering the Mechanism of Alternative Cleavage and Polyadenylation in Mantle Cell Lymphoma (MCL)

    Science.gov (United States)

    2015-12-01

    event. The discovery that transformed and rapidly proliferating cells use alternative cleavage and polyadenylation ( APA ) to shorten the 3´UTR of their... APA . However, the mechanism that APA is still unknown. The goal of this project is to identify the mechanism of cyclin D1 APA regulation in cancer...for APA in MCL. In addition, by using RNA Seq. CFIm25 has been identified as an important global regulator of shortening of cyclin D1 mRNA and other

  11. VAAPA: a web platform for visualization and analysis of alternative polyadenylation.

    Science.gov (United States)

    Guan, Jinting; Fu, Jingyi; Wu, Mingcheng; Chen, Longteng; Ji, Guoli; Quinn Li, Qingshun; Wu, Xiaohui

    2015-02-01

    Polyadenylation [poly(A)] is an essential process during the maturation of most mRNAs in eukaryotes. Alternative polyadenylation (APA) as an important layer of gene expression regulation has been increasingly recognized in various species. Here, a web platform for visualization and analysis of alternative polyadenylation (VAAPA) was developed. This platform can visualize the distribution of poly(A) sites and poly(A) clusters of a gene or a section of a chromosome. It can also highlight genes with switched APA sites among different conditions. VAAPA is an easy-to-use web-based tool that provides functions of poly(A) site query, data uploading, downloading, and APA sites visualization. It was designed in a multi-tier architecture and developed based on Smart GWT (Google Web Toolkit) using Java as the development language. VAAPA will be a valuable addition to the community for the comprehensive study of APA, not only by making the high quality poly(A) site data more accessible, but also by providing users with numerous valuable functions for poly(A) site analysis and visualization. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling

    Directory of Open Access Journals (Sweden)

    Mo Min

    2008-05-01

    Full Text Available Abstract Background The polyadenylation of mRNA is one of the critical processing steps during expression of almost all eukaryotic genes. It is tightly integrated with transcription, particularly its termination, as well as other RNA processing events, i.e. capping and splicing. The poly(A tail protects the mRNA from unregulated degradation, and it is required for nuclear export and translation initiation. In recent years, it has been demonstrated that the polyadenylation process is also involved in the regulation of gene expression. The polyadenylation process requires two components, the cis-elements on the mRNA and a group of protein factors that recognize the cis-elements and produce the poly(A tail. Here we report a comprehensive pairwise protein-protein interaction mapping and gene expression profiling of the mRNA polyadenylation protein machinery in Arabidopsis. Results By protein sequence homology search using human and yeast polyadenylation factors, we identified 28 proteins that may be components of Arabidopsis polyadenylation machinery. To elucidate the protein network and their functions, we first tested their protein-protein interaction profiles. Out of 320 pair-wise protein-protein interaction assays done using the yeast two-hybrid system, 56 (~17% showed positive interactions. 15 of these interactions were further tested, and all were confirmed by co-immunoprecipitation and/or in vitro co-purification. These interactions organize into three distinct hubs involving the Arabidopsis polyadenylation factors. These hubs are centered around AtCPSF100, AtCLPS, and AtFIPS. The first two are similar to complexes seen in mammals, while the third one stands out as unique to plants. When comparing the gene expression profiles extracted from publicly available microarray datasets, some of the polyadenylation related genes showed tissue-specific expression, suggestive of potential different polyadenylation complex configurations. Conclusion An

  13. Alternative polyadenylation of tumor suppressor genes in small intestinal neuroendocrine tumors.

    Science.gov (United States)

    Rehfeld, Anders; Plass, Mireya; Døssing, Kristina; Knigge, Ulrich; Kjær, Andreas; Krogh, Anders; Friis-Hansen, Lennart

    2014-01-01

    The tumorigenesis of small intestinal neuroendocrine tumors (SI-NETs) is poorly understood. Recent studies have associated alternative polyadenylation (APA) with proliferation, cell transformation, and cancer. Polyadenylation is the process in which the pre-messenger RNA is cleaved at a polyA site and a polyA tail is added. Genes with two or more polyA sites can undergo APA. This produces two or more distinct mRNA isoforms with different 3' untranslated regions. Additionally, APA can also produce mRNAs containing different 3'-terminal coding regions. Therefore, APA alters both the repertoire and the expression level of proteins. Here, we used high-throughput sequencing data to map polyA sites and characterize polyadenylation genome-wide in three SI-NETs and a reference sample. In the tumors, 16 genes showed significant changes of APA pattern, which lead to either the 3' truncation of mRNA coding regions or 3' untranslated regions. Among these, 11 genes had been previously associated with cancer, with 4 genes being known tumor suppressors: DCC, PDZD2, MAGI1, and DACT2. We validated the APA in three out of three cases with quantitative real-time-PCR. Our findings suggest that changes of APA pattern in these 16 genes could be involved in the tumorigenesis of SI-NETs. Furthermore, they also point to APA as a new target for both diagnostic and treatment of SI-NETs. The identified genes with APA specific to the SI-NETs could be further tested as diagnostic markers and drug targets for disease prevention and treatment.

  14. A germline variant in the TP53 polyadenylation signal confers cancer susceptibility

    DEFF Research Database (Denmark)

    Stacey, Simon N; Sulem, Patrick; Jonasdottir, Aslaug

    2011-01-01

    To identify new risk variants for cutaneous basal cell carcinoma, we performed a genome-wide association study of 16 million SNPs identified through whole-genome sequencing of 457 Icelanders. We imputed genotypes for 41,675 Illumina SNP chip-typed Icelanders and their relatives. In the discovery...

  15. Alternative Polyadenylation and Nonsense-Mediated Decay Coordinately Regulate the Human HFE mRNA Levels

    Science.gov (United States)

    Martins, Rute; Proença, Daniela; Silva, Bruno; Barbosa, Cristina; Silva, Ana Luísa; Faustino, Paula; Romão, Luísa

    2012-01-01

    Nonsense-mediated decay (NMD) is an mRNA surveillance pathway that selectively recognizes and degrades defective mRNAs carrying premature translation-termination codons. However, several studies have shown that NMD also targets physiological transcripts that encode full-length proteins, modulating their expression. Indeed, some features of physiological mRNAs can render them NMD-sensitive. Human HFE is a MHC class I protein mainly expressed in the liver that, when mutated, can cause hereditary hemochromatosis, a common genetic disorder of iron metabolism. The HFE gene structure comprises seven exons; although the sixth exon is 1056 base pairs (bp) long, only the first 41 bp encode for amino acids. Thus, the remaining downstream 1015 bp sequence corresponds to the HFE 3′ untranslated region (UTR), along with exon seven. Therefore, this 3′ UTR encompasses an exon/exon junction, a feature that can make the corresponding physiological transcript NMD-sensitive. Here, we demonstrate that in UPF1-depleted or in cycloheximide-treated HeLa and HepG2 cells the HFE transcripts are clearly upregulated, meaning that the physiological HFE mRNA is in fact an NMD-target. This role of NMD in controlling the HFE expression levels was further confirmed in HeLa cells transiently expressing the HFE human gene. Besides, we show, by 3′-RACE analysis in several human tissues that HFE mRNA expression results from alternative cleavage and polyadenylation at four different sites – two were previously described and two are novel polyadenylation sites: one located at exon six, which confers NMD-resistance to the corresponding transcripts, and another located at exon seven. In addition, we show that the amount of HFE mRNA isoforms resulting from cleavage and polyadenylation at exon seven, although present in both cell lines, is higher in HepG2 cells. These results reveal that NMD and alternative polyadenylation may act coordinately to control HFE mRNA levels, possibly varying its

  16. Subcellular RNA profiling links splicing and nuclear DICER1 to alternative cleavage and polyadenylation.

    Science.gov (United States)

    Neve, Jonathan; Burger, Kaspar; Li, Wencheng; Hoque, Mainul; Patel, Radhika; Tian, Bin; Gullerova, Monika; Furger, Andre

    2016-01-01

    Alternative cleavage and polyadenylation (APA) plays a crucial role in the regulation of gene expression across eukaryotes. Although APA is extensively studied, its regulation within cellular compartments and its physiological impact remains largely enigmatic. Here, we used a rigorous subcellular fractionation approach to compare APA profiles of cytoplasmic and nuclear RNA fractions from human cell lines. This approach allowed us to extract APA isoforms that are subjected to differential regulation and provided us with a platform to interrogate the molecular regulatory pathways that shape APA profiles in different subcellular locations. Here, we show that APA isoforms with shorter 3' UTRs tend to be overrepresented in the cytoplasm and appear to be cell-type-specific events. Nuclear retention of longer APA isoforms occurs and is partly a result of incomplete splicing contributing to the observed cytoplasmic bias of transcripts with shorter 3' UTRs. We demonstrate that the endoribonuclease III, DICER1, contributes to the establishment of subcellular APA profiles not only by expected cytoplasmic miRNA-mediated destabilization of APA mRNA isoforms, but also by affecting polyadenylation site choice. © 2016 Neve et al.; Published by Cold Spring Harbor Laboratory Press.

  17. Microarray Meta-Analysis of RNA-Binding Protein Functions in Alternative Polyadenylation

    Science.gov (United States)

    Hu, Wenchao; Liu, Yuting; Yan, Jun

    2014-01-01

    Alternative polyadenylation (APA) is a post-transcriptional mechanism to generate diverse mRNA transcripts with different 3′UTRs from the same gene. In this study, we systematically searched for the APA events with differential expression in public mouse microarray data. Hundreds of genes with over-represented differential APA events and the corresponding experiments were identified. We further revealed that global APA differential expression occurred prevalently in tissues such as brain comparing to peripheral tissues, and biological processes such as development, differentiation and immune responses. Interestingly, we also observed widespread differential APA events in RNA-binding protein (RBP) genes such as Rbm3, Eif4e2 and Elavl1. Given the fact that RBPs are considered as the main regulators of differential APA expression, we constructed a co-expression network between APAs and RBPs using the microarray data. Further incorporation of CLIP-seq data of selected RBPs showed that Nova2 represses and Mbnl1 promotes the polyadenylation of closest poly(A) sites respectively. Altogether, our study is the first microarray meta-analysis in a mammal on the regulation of APA by RBPs that integrated massive mRNA expression data under a wide-range of biological conditions. Finally, we present our results as a comprehensive resource in an online website for the research community. PMID:24622240

  18. Involvement of hGLD-2 in cytoplasmic polyadenylation of human p53 mRNA

    DEFF Research Database (Denmark)

    Glahder, Jacob-Andreas Harald; Norrild, Bodil

    2011-01-01

    Cytoplasmic polyadenylation is a post-transcriptional mechanism regulating mRNA stability and translation. The human p53 3'-untranslated region (3'-UTR) contains two regions similar to cytoplasmic polyadenylation elements (CPEs) just upstream of the poly(A) hexanucleotide. Evaluation of the p53 CPE......-like elements was performed by luciferase reporter assays, qPCR, and poly(A) assays. Herein, we report the down regulation of a luciferase reporter fused to the p53 3'-UTR, when human CPE-binding protein 1 (hCPEB1) is overexpressed. This inhibition is partially rescued when hCPEB1fused to hGLD-2 [a human...... cytoplasmic poly(A) polymerase] is overexpressed instead. The stability of a luciferase mRNA containing the p53 3'-UTR downstream, is decreased when hCPEB1 is overexpressed as seen by qPCR. Expression of hGLD-2 restores the mRNA stability. This is due to elongation of the poly(A) tail as seen by a PCR...

  19. Polyadenylated Sequencing Primers Enable Complete Readability of PCR Amplicons Analyzed by Dideoxynucleotide Sequencing

    Directory of Open Access Journals (Sweden)

    Martin Beránek

    2012-01-01

    Full Text Available Dideoxynucleotide DNA sequencing is one of the principal procedures in molecular biology. Loss of an initial part of nucleotides behind the 3' end of the sequencing primer limits the readability of sequenced amplicons. We present a method which extends the readability by using sequencing primers modified by polyadenylated tails attached to their 5' ends. Performing a polymerase chain reaction, we amplified eight amplicons of six human genes (AMELX, APOE, HFE, MBL2, SERPINA1 and TGFB1 ranging from 106 bp to 680 bp. Polyadenylation of the sequencing primers minimized the loss of bases in all amplicons. Complete sequences of shorter products (AMELX 106 bp, SERPINA1 121 bp, HFE 208 bp, APOE 244 bp, MBL2 317 bp were obtained. In addition, in the case of TGFB1 products (366 bp, 432 bp, and 680 bp, respectively, the lengths of sequencing readings were significantly longer if adenylated primers were used. Thus, single strand dideoxynucleotide sequencing with adenylated primers enables complete or near complete readability of short PCR amplicons.

  20. Role of Alternative Polyadenylation during Adipogenic Differentiation: An In Silico Approach

    Science.gov (United States)

    Spangenberg, Lucía; Correa, Alejandro; Dallagiovanna, Bruno; Naya, Hugo

    2013-01-01

    Post-transcriptional regulation of stem cell differentiation is far from being completely understood. Changes in protein levels are not fully correlated with corresponding changes in mRNAs; the observed differences might be partially explained by post-transcriptional regulation mechanisms, such as alternative polyadenylation. This would involve changes in protein binding, transcript usage, miRNAs and other non-coding RNAs. In the present work we analyzed the distribution of alternative transcripts during adipogenic differentiation and the potential role of miRNAs in post-transcriptional regulation. Our in silico analysis suggests a modest, consistent, bias in 3′UTR lengths during differentiation enabling a fine-tuned transcript regulation via small non-coding RNAs. Including these effects in the analyses partially accounts for the observed discrepancies in relative abundance of protein and mRNA. PMID:24143171

  1. The synthesis of polyadenylated messenger RNA in herpes simplex type I virus infected BHK cells.

    Science.gov (United States)

    Harris, T J; Wildy, P

    1975-09-01

    The pattern of polyadenylated messenger RNA (mRNA) synthesis in BHK cell monolayers, infected under defined conditions with herpes simplex type I virus has been investigated by polyacrylamide gel electrophoresis or pulse-labelled RNA isolated by oligo dT-cellulose chromatography. Two classes of mRNA molecules were synthesized in infected cells; these were not detected in uninfected cells. The rate of synthesis of the larger, 18 to 30S RNA class reached a maximum soon after injection and then declined, whereas the rate of synthesis of the 7 to 11 S RNA class did not reach a maximum until much later and did not decline. In the presence of cytosine arabinoside, the rate of mRNA synthesis in infected cells was reduced but the electrophoretic pattern remained the same.

  2. Paxillin and embryonic PolyAdenylation Binding Protein (ePABP) engage to regulate androgen-dependent Xenopus laevis oocyte maturation - A model of kinase-dependent regulation of protein expression.

    Science.gov (United States)

    Miedlich, Susanne U; Taya, Manisha; Young, Melissa Rasar; Hammes, Stephen R

    2017-06-15

    Steroid-triggered Xenopus laevis oocyte maturation is an elegant physiologic model of nongenomic steroid signaling, as it proceeds completely independent of transcription. We previously demonstrated that androgens are the main physiologic stimulator of oocyte maturation in Xenopus oocytes, and that the adaptor protein paxillin plays a crucial role in mediating this process through a positive feedback loop in which paxillin first enhances Mos protein translation, ensued by Erk2 activation and Erk-dependent phosphorylation of paxillin on serine residues. Phosphoserine-paxillin then further augments Mos protein translation and downstream Erk2 activation, resulting in meiotic progression. We hypothesized that paxillin enhances Mos translation by interacting with embryonic PolyAdenylation Binding Protein (ePABP) on polyadenylated Mos mRNA. Knockdown of ePABP phenocopied paxillin knockdown, with reduced Mos protein expression, Erk2 and Cdk1 activation, as well as oocyte maturation. In both Xenopus oocytes and mammalian cells (HEK-293), paxillin and ePABP constitutively interacted. Testosterone (Xenopus) or EGF (HEK-293) augmented ePABP-paxillin binding, as well as ePABP binding to Mos mRNA (Xenopus), in an Erk-dependent fashion. Thus, ePABP and paxillin work together in an Erk-dependent fashion to enhance Mos protein translation and promote oocyte maturation. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Molecular Regulation of Alternative Polyadenylation (APA) within the Drosophila Nervous System.

    Science.gov (United States)

    Vallejos Baier, Raul; Picao-Osorio, Joao; Alonso, Claudio R

    2017-10-27

    Alternative polyadenylation (APA) is a widespread gene regulatory mechanism that generates mRNAs with different 3'-ends, allowing them to interact with different sets of RNA regulators such as microRNAs and RNA-binding proteins. Recent studies have shown that during development, neural tissues produce mRNAs with particularly long 3'UTRs, suggesting that such extensions might be important for neural development and function. Despite this, the mechanisms underlying neural APA are not well understood. Here, we investigate this problem within the Drosophila nervous system, focusing on the roles played by general cleavage and polyadenylation factors (CPA factors). In particular, we examine the model that modulations in CPA factor concentration may affect APA during development. For this, we first analyse the expression of the Drosophila orthologues of all mammalian CPA factors and note that their expression decreases during embryogenesis. In contrast to this global developmental decrease in CPA factor expression, we see that cleavage factor I (CFI) expression is actually elevated in the late embryonic central nervous system, suggesting that CFI might play a special role in neural tissues. To test this, we use the UAS/Gal4 system to deplete CFI proteins from neural tissue and observe that in this condition, multiple genes switch their APA patterns, demonstrating a role of CFI in APA control during Drosophila neural development. Furthermore, analysis of genes with 3'UTR extensions of different length leads us to suggest a novel relation between 3'UTR length and sensitivity to CPA factor expression. Our work thus contributes to the understanding of the mechanisms of APA control within the developing central nervous system. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. The STAR protein QKI-7 recruits PAPD4 to regulate post-transcriptional polyadenylation of target mRNAs

    OpenAIRE

    Yamagishi, Ryota; Tsusaka, Takeshi; Mitsunaga, Hiroko; Maehata, Takaharu; Hoshino, Shin-ichi

    2016-01-01

    Emerging evidence has demonstrated that regulating the length of the poly(A) tail on an mRNA is an efficient means of controlling gene expression at the post-transcriptional level. In early development, transcription is silenced and gene expression is primarily regulated by cytoplasmic polyadenylation. In somatic cells, considerable progress has been made toward understanding the mechanisms of negative regulation by deadenylation. However, positive regulation through elongation of the poly(A)...

  5. Putative alternative polyadenylation (APA) events in the early interaction of Salmonella enterica Typhimurium and human host cells.

    Science.gov (United States)

    Afonso-Grunz, Fabian

    2015-12-01

    The immune response of epithelial cells upon infection is mediated by changing activity levels of a variety of proteins along with changes in mRNA, and also ncRNA abundance. Alternative polyadenylation (APA) represents a mechanism that diversifies gene expression similar to alternative splicing. T-cell activation, neuronal activity, development and several human diseases including viral infections involve APA, but at present it remains unclear if this mechanism is also implicated in the response to bacterial infections. Our recently published study of interacting Salmonella enterica Typhimurium and human host cells includes genome-wide expression profiles of human epithelial cells prior and subsequent to infection with the invasive pathogen. The generated dataset (GEO accession number: GSE61730) covers several points of time post infection, and one of these interaction stages was additionally profiled with MACE-based dual 3'Seq, which allows for identification of polyadenylation (PA) sites. The present study features the polyadenylation landscape in early interacting cells based on this data, and provides a comparison of the identified PA sites with those of a corresponding 3P-Seq dataset of non-interacting cells. Differential PA site usage of FTL , PRDX1 and VAPA results in transcription of mRNA isoforms with distinct sets of miRNA and protein binding sites that influence processing, localization, stability, and translation of the respective mRNA. APA of these candidate genes consequently harbors the potential to modulate the host cell response to bacterial infection.

  6. Putative alternative polyadenylation (APA events in the early interaction of Salmonella enterica Typhimurium and human host cells

    Directory of Open Access Journals (Sweden)

    Fabian Afonso-Grunz

    2015-12-01

    Full Text Available The immune response of epithelial cells upon infection is mediated by changing activity levels of a variety of proteins along with changes in mRNA, and also ncRNA abundance. Alternative polyadenylation (APA represents a mechanism that diversifies gene expression similar to alternative splicing. T-cell activation, neuronal activity, development and several human diseases including viral infections involve APA, but at present it remains unclear if this mechanism is also implicated in the response to bacterial infections. Our recently published study of interacting Salmonella enterica Typhimurium and human host cells includes genome-wide expression profiles of human epithelial cells prior and subsequent to infection with the invasive pathogen. The generated dataset (GEO accession number: GSE61730 covers several points of time post infection, and one of these interaction stages was additionally profiled with MACE-based dual 3'Seq, which allows for identification of polyadenylation (PA sites. The present study features the polyadenylation landscape in early interacting cells based on this data, and provides a comparison of the identified PA sites with those of a corresponding 3P-Seq dataset of non-interacting cells. Differential PA site usage of FTL, PRDX1 and VAPA results in transcription of mRNA isoforms with distinct sets of miRNA and protein binding sites that influence processing, localization, stability, and translation of the respective mRNA. APA of these candidate genes consequently harbors the potential to modulate the host cell response to bacterial infection.

  7. Extreme heterogeneity of polyadenylation sites in mRNAs encoding chloroplast RNA-binding proteins in Nicotiana plumbaginifolia.

    Science.gov (United States)

    Klahre, U; Hemmings-Mieszczak, M; Filipowicz, W

    1995-06-01

    We have previously characterized nuclear cDNA clones encoding two RNA binding proteins, CP-RBP30 and CP-RBP-31, which are targeted to chloroplasts in Nicotiana plumbaginifolia. In this report we describe the analysis of the 3'-untranslated regions (3'-UTRs) in 22 CP-RBP30 and 8 CP-RBP31 clones which reveals that mRNAs encoding both proteins have a very complex polyadenylation pattern. Fourteen distinct poly(A) sites were identified among CP-RBP30 clones and four sites among the CP-RBP31 clones. The authenticity of the sites was confirmed by RNase A/T1 mapping of N. plumbaginifolia RNA. CP-RBP30 provides an extreme example of the heterogeneity known to be a feature of mRNA polyadenylation in higher plants. Using PCR we have demonstrated that CP-RBP genes in N. plumbaginifolia and N. sylvestris, in addition to the previously described introns interrupting the coding region, contain an intron located in the 3' non-coding part of the gene. In the case of the CP-RBP31, we have identified one polyadenylation event occurring in this intron.

  8. Modified Polyadenylation-Based RT-qPCR Increases Selectivity of Amplification of 3′-MicroRNA Isoforms

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    Charlotte Nejad

    2018-01-01

    Full Text Available MicroRNA (miRNA detection by reverse transcription (RT quantitative real-time PCR (RT-qPCR is the most popular method currently used to measure miRNA expression. Although the majority of miRNA families are constituted of several 3′-end length variants (“isomiRs”, little attention has been paid to their differential detection by RT-qPCR. However, recent evidence indicates that 3′-end miRNA isoforms can exhibit 3′-length specific regulatory functions, underlining the need to develop strategies to differentiate 3′-isomiRs by RT-qPCR approaches. We demonstrate here that polyadenylation-based RT-qPCR strategies targeted to 20–21 nt isoforms amplify entire miRNA families, but that primers targeted to >22 nt isoforms were specific to >21 nt isoforms. Based on this observation, we developed a simple method to increase selectivity of polyadenylation-based RT-qPCR assays toward shorter isoforms, and demonstrate its capacity to help distinguish short RNAs from longer ones, using synthetic RNAs and biological samples with altered isomiR stoichiometry. Our approach can be adapted to many polyadenylation-based RT-qPCR technologies already exiting, providing a convenient way to distinguish long and short 3′-isomiRs.

  9. RNA polyadenylation sites on the genomes of microorganisms, animals, and plants.

    Directory of Open Access Journals (Sweden)

    Xiu-Qing Li

    Full Text Available Pre-messenger RNA (mRNA 3'-end cleavage and subsequent polyadenylation strongly regulate gene expression. In comparison with the upstream or downstream motifs, relatively little is known about the feature differences of polyadenylation [poly(A] sites among major kingdoms. We suspect that the precise poly(A sites are very selective, and we therefore mapped mRNA poly(A sites on complete and nearly complete genomes using mRNA sequences available in the National Center for Biotechnology Information (NCBI Nucleotide database. In this paper, we describe the mRNA nucleotide [i.e., the poly(A tail attachment position] that is directly in attachment with the poly(A tail and the pre-mRNA nucleotide [i.e., the poly(A tail starting position] that corresponds to the first adenosine of the poly(A tail in the 29 most-mapped species (2 fungi, 2 protists, 18 animals, and 7 plants. The most representative pre-mRNA dinucleotides covering these two positions were UA, CA, and GA in 17, 10, and 2 of the species, respectively. The pre-mRNA nucleotide at the poly(A tail starting position was typically an adenosine [i.e., A-type poly(A sites], sometimes a uridine, and occasionally a cytidine or guanosine. The order was U>C>G at the attachment position but A>>U>C≥G at the starting position. However, in comparison with the mRNA nucleotide composition (base composition, the poly(A tail attachment position selected C over U in plants and both C and G over U in animals, in both A-type and non-A-type poly(A sites. Animals, dicot plants, and monocot plants had clear differences in C/G ratios at the poly(A tail attachment position of the non-A-type poly(A sites. This study of poly(A site evolution indicated that the two positions within poly(A sites had distinct nucleotide compositions and were different among kingdoms.

  10. LPS injection reprograms the expression and the 3' UTR of a CAP gene by alternative polyadenylation and the formation of a GAIT element in Ciona intestinalis.

    Science.gov (United States)

    Vizzini, Aiti; Bonura, Angela; Longo, Valeria; Sanfratello, Maria Antonietta; Parrinello, Daniela; Cammarata, Matteo; Colombo, Paolo

    2016-09-01

    The diversification of cellular functions is one of the major characteristics of multicellular organisms which allow cells to modulate their gene expression, leading to the formation of transcripts and proteins with different functions and concentrations in response to different stimuli. CAP genes represent a widespread family of proteins belonging to the cysteine-rich secretory protein, antigen 5 and pathogenesis-related 1 superfamily which, it has been proposed, play key roles in the infection process and the modulation of immune responses in host animals. The ascidian Ciona intestinalis represents a group of proto-chordates with an exclusively innate immune system that has been widely studied in the field of comparative and developmental immunology. Using this biological system, we describe the identification of a novel APA mechanism by which an intronic polyadenylation signal is activated by LPS injection, leading to the formation of a shorter CAP mRNA capable of expressing the first CAP exon plus 19 amino acid residues whose sequence is contained within the first intron of the annotated gene. Furthermore, such an APA event causes the expression of a translational controlling cis-acting GAIT element which is not present in the previously isolated CAP isoform and identified in the 3'-UTR of other immune-related genes, suggesting an intriguing scenario in which both transcriptional and post-transcriptional control mechanisms are involved in the activation of the CAP gene during inflammatory response in C. intestinalis. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Evaluation of Two Statistical Methods Provides Insights into the Complex Patterns of Alternative Polyadenylation Site Switching

    Science.gov (United States)

    Li, Jie; Li, Rui; You, Leiming; Xu, Anlong; Fu, Yonggui; Huang, Shengfeng

    2015-01-01

    Switching between different alternative polyadenylation (APA) sites plays an important role in the fine tuning of gene expression. New technologies for the execution of 3’-end enriched RNA-seq allow genome-wide detection of the genes that exhibit significant APA site switching between different samples. Here, we show that the independence test gives better results than the linear trend test in detecting APA site-switching events. Further examination suggests that the discrepancy between these two statistical methods arises from complex APA site-switching events that cannot be represented by a simple change of average 3’-UTR length. In theory, the linear trend test is only effective in detecting these simple changes. We classify the switching events into four switching patterns: two simple patterns (3’-UTR shortening and lengthening) and two complex patterns. By comparing the results of the two statistical methods, we show that complex patterns account for 1/4 of all observed switching events that happen between normal and cancerous human breast cell lines. Because simple and complex switching patterns may convey different biological meanings, they merit separate study. We therefore propose to combine both the independence test and the linear trend test in practice. First, the independence test should be used to detect APA site switching; second, the linear trend test should be invoked to identify simple switching events; and third, those complex switching events that pass independence testing but fail linear trend testing can be identified. PMID:25875641

  12. Fip1 regulates mRNA alternative polyadenylation to promote stem cell self-renewal

    Science.gov (United States)

    Lackford, Brad; Yao, Chengguo; Charles, Georgette M; Weng, Lingjie; Zheng, Xiaofeng; Choi, Eun-A; Xie, Xiaohui; Wan, Ji; Xing, Yi; Freudenberg, Johannes M; Yang, Pengyi; Jothi, Raja; Hu, Guang; Shi, Yongsheng

    2014-01-01

    mRNA alternative polyadenylation (APA) plays a critical role in post-transcriptional gene control and is highly regulated during development and disease. However, the regulatory mechanisms and functional consequences of APA remain poorly understood. Here, we show that an mRNA 3′ processing factor, Fip1, is essential for embryonic stem cell (ESC) self-renewal and somatic cell reprogramming. Fip1 promotes stem cell maintenance, in part, by activating the ESC-specific APA profiles to ensure the optimal expression of a specific set of genes, including critical self-renewal factors. Fip1 expression and the Fip1-dependent APA program change during ESC differentiation and are restored to an ESC-like state during somatic reprogramming. Mechanistically, we provide evidence that the specificity of Fip1-mediated APA regulation depends on multiple factors, including Fip1-RNA interactions and the distance between APA sites. Together, our data highlight the role for post-transcriptional control in stem cell self-renewal, provide mechanistic insight on APA regulation in development, and establish an important function for APA in cell fate specification. PMID:24596251

  13. Regulators of alternative polyadenylation operate at the transition from mitosis to meiosis.

    Science.gov (United States)

    Shan, Lingjuan; Wu, Chan; Chen, Di; Hou, Lei; Li, Xin; Wang, Lixia; Chu, Xiao; Hou, Yifeng; Wang, Zhaohui

    2017-02-20

    In the sexually reproductive organisms, gametes are produced by meiosis following a limited mitotic amplification. However, the intrinsic program switching cells from mitotic to meiotic cycle is unclear. Alternative polyadenylation (APA) is a highly conserved means of gene regulation and is achieved by the RNA 3'-processing machinery to generate diverse 3'UTR profiles. In Drosophila spermatogenesis, we observed distinct profiles of transcriptome-wide 3'UTR between mitotic and meiotic cells. In mutant germ cells stuck in mitosis, 3'UTRs of hundreds of genes were consistently shifted. Remarkably, altering the levels of multiple 3'-processing factors disrupted germline's progression to meiosis, indicative of APA's active role in this transition. An RNA-binding protein (RBP) Tut could directly bind 3'UTRs of 3'-processing factors whose expressions were repressed in the presence of Tut-containing complex. Further, we demonstrated that this RBP complex could execute the repression post-transcriptionally by recruiting CCR4/Twin of deadenylation complex. Thus, we propose that an RBP complex regulates the dynamic APA profile to promote the mitosis-to-meiosis transition. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  14. The Cstf2t Polyadenylation Gene Plays a Sex-Specific Role in Learning Behaviors in Mice.

    Directory of Open Access Journals (Sweden)

    Jaryse C Harris

    Full Text Available Polyadenylation is an essential mechanism for the processing of mRNA 3' ends. CstF-64 (the 64,000 Mr subunit of the cleavage stimulation factor; gene symbol Cstf2 is an RNA-binding protein that regulates mRNA polyadenylation site usage. We discovered a paralogous form of CstF-64 called τCstF-64 (Cstf2t. The Cstf2t gene is conserved in all eutherian mammals including mice and humans, but the τCstF-64 protein is expressed only in a subset of mammalian tissues, mostly testis and brain. Male mice that lack Cstf2t (Cstf2t-/- mice experience disruption of spermatogenesis and are infertile, although female fertility is unaffected. However, a role for τCstF-64 in the brain has not yet been determined. Given the importance of RNA polyadenylation and splicing in neuronal gene expression, we chose to test the hypothesis that τCstF-64 is important for brain function. Male and female 185-day old wild type and Cstf2t-/- mice were examined for motor function, general activity, learning, and memory using rotarod, open field activity, 8-arm radial arm maze, and Morris water maze tasks. Male wild type and Cstf2t-/- mice did not show differences in learning and memory. However, female Cstf2t-/- mice showed significantly better retention of learned maze tasks than did female wild type mice. These results suggest that τCstf-64 is important in memory function in female mice. Interestingly, male Cstf2t-/- mice displayed less thigmotactic behavior than did wild type mice, suggesting that Cstf2t may play a role in anxiety in males. Taken together, our studies highlight the importance of mRNA processing in cognition and behavior as well as their established functions in reproduction.

  15. In Vivo Visualizing the IFN-β Response Required for Tumor Growth Control in a Therapeutic Model of Polyadenylic-Polyuridylic Acid Administration.

    Science.gov (United States)

    Nocera, David Andrés; Roselli, Emiliano; Araya, Paula; Nuñez, Nicolás Gonzalo; Lienenklaus, Stefan; Jablonska, Jadwiga; Weiss, Siegfried; Gatti, Gerardo; Brinkmann, Melanie M; Kröger, Andrea; Morón, Gabriel; Maccioni, Mariana

    2016-03-15

    The crucial role that endogenously produced IFN-β plays in eliciting an immune response against cancer has recently started to be elucidated. Endogenous IFN-β has an important role in immune surveillance and control of tumor development. Accordingly, the role of TLR agonists as cancer therapeutic agents is being revisited via the strategy of intra/peritumoral injection with the idea of stimulating the production of endogenous type I IFN inside the tumor. Polyadenylic-polyuridylic acid (poly A:U) is a dsRNA mimetic explored empirically in cancer immunotherapy a long time ago with little knowledge regarding its mechanisms of action. In this work, we have in vivo visualized the IFN-β required for the antitumor immune response elicited in a therapeutic model of poly A:U administration. In this study, we have identified the role of host type I IFNs, cell populations that are sources of IFN-β in the tumor microenvironment, and other host requirements for tumor control in this model. One single peritumoral dose of poly A:U was sufficient to induce IFN-β, readily visualized in vivo. IFN-β production relied mainly on the activation of the transcription factor IFN regulatory factor 3 and the molecule UNC93B1, indicating that TLR3 is required for recognizing poly A:U. CD11c(+) cells were an important, but not the only source of IFN-β. Host type I IFN signaling was absolutely required for the reduced tumor growth, prolonged mice survival, and the strong antitumor-specific immune response elicited upon poly A:U administration. These findings add new perspectives to the use of IFN-β-inducing compounds in tumor therapy. Copyright © 2016 by The American Association of Immunologists, Inc.

  16. LPS challenge regulates gene expression and tissue localization of a Ciona intestinalis gene through an alternative polyadenylation mechanism.

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    Aiti Vizzini

    Full Text Available A subtractive hybridization strategy for the identification of differentially expressed genes was performed between LPS-challenged and naive Ciona intestinalis. This strategy allowed the characterization of two transcripts (Ci8short and Ci8long generated by the use of two Alternative Polyadenylation sites. The Ci8long transcript contains a protein domain with relevant homology to several components of the Receptor Transporting Protein (RTP family not present in the Ci8short mRNA. By means of Real Time PCR and Northern Blot, the Ci8short and Ci8long transcripts showed a different pattern of gene expression with the Ci8short mRNA being strongly activated after LPS injection in the pharynx. In situ hybridization analysis demonstrated that the activation of the APA site also influenced the tissue localization of the Ci8short transcript. This analysis showed that the Ci8long mRNA was expressed in hemocytes meanwhile the Ci8short mRNA was highly transcribed also in vessel endothelial cells and in the epithelium of pharynx. These findings demonstrated that regulation of gene expression based on different polyadenylation sites is an ancestral powerful strategy influencing both the level of expression and tissue distribution of alternative transcripts.

  17. Dynamic Analyses of Alternative Polyadenylation from RNA-Seq Reveal 3′-UTR Landscape Across 7 Tumor Types

    Science.gov (United States)

    Xia, Zheng; Donehower, Lawrence A; Cooper, Thomas A.; Neilson, Joel R.; Wheeler, David A.; Wagner, Eric J.; Li, Wei

    2015-01-01

    Alternative polyadenylation (APA) is a pervasive mechanism in the regulation of most human genes, and its implication in diseases including cancer is only beginning to be appreciated. Since conventional APA profiling has not been widely adopted, global cancer APA studies are very limited. Here we develop a novel bioinformatics algorithm (DaPars) for the de novo identification of dynamic APAs from standard RNA-seq. When applied to 358 TCGA Pan-Cancer tumor/normal pairs across 7 tumor types, DaPars reveals 1,346 genes with recurrent and tumor-specific APAs. Most APA genes (91%) have shorter 3′ UTRs in tumors that can avoid miRNA-mediated repression, including glutaminase (GLS), a key metabolic enzyme for tumor proliferation. Interestingly, selected APA events add strong prognostic power beyond common clinical and molecular variables, suggesting their potential as novel prognostic biomarkers. Finally, our results implicate CstF64, an essential polyadenylation factor, as a master regulator of 3′ UTR shortening across multiple tumor types. PMID:25409906

  18. The rotaviral NSP3 protein stimulates translation of polyadenylated target mRNAs independently of its RNA-binding domain

    International Nuclear Information System (INIS)

    Keryer-Bibens, Cecile; Legagneux, Vincent; Namanda-Vanderbeken, Allen; Cosson, Bertrand; Paillard, Luc; Poncet, Didier; Osborne, H. Beverley

    2009-01-01

    The non-structural protein 3 (NSP3) of rotaviruses is an RNA-binding protein that specifically recognises a 4 nucleotide sequence at the 3' extremity of the non-polyadenylated viral mRNAs. NSP3 also has a high affinity for eIF4G. These two functions are clearly delimited in separate domains the structures of which have been determined. They are joined by a central domain implicated in the dimerisation of the full length protein. The bridging function of NSP3 between the 3' end of the viral mRNA and eIF4G has been proposed to enhance the synthesis of viral proteins. However, this role has been questioned as knock-down of NSP3 did not impair viral protein synthesis. We show here using a MS2/MS2-CP tethering assay that a C-terminal fragment of NSP3 containing the eIF4G binding domain and the dimerisation domain can increase the expression of a protein encoded by a target reporter mRNA in HEK 293 cells. The amount of reporter mRNA in the cells is not significantly affected by the presence of the NSP3 derived fusion protein showing that the enhanced protein expression is due to increased translation. These results show that NSP3 can act as a translational enhancer even on a polyadenylated mRNA that should be a substrate for PABP1.

  19. Enterovirus 71 3C protease cleaves a novel target CstF-64 and inhibits cellular polyadenylation.

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    Kuo-Feng Weng

    2009-09-01

    Full Text Available Identification of novel cellular proteins as substrates to viral proteases would provide a new insight into the mechanism of cell-virus interplay. Eight nuclear proteins as potential targets for enterovirus 71 (EV71 3C protease (3C(pro cleavages were identified by 2D electrophoresis and MALDI-TOF analysis. Of these proteins, CstF-64, which is a critical factor for 3' pre-mRNA processing in a cell nucleus, was selected for further study. A time-course study to monitor the expression levels of CstF-64 in EV71-infected cells also revealed that the reduction of CstF-64 during virus infection was correlated with the production of viral 3C(pro. CstF-64 was cleaved in vitro by 3C(pro but neither by mutant 3C(pro (in which the catalytic site was inactivated nor by another EV71 protease 2A(pro. Serial mutagenesis was performed in CstF-64, revealing that the 3C(pro cleavage sites are located at position 251 in the N-terminal P/G-rich domain and at multiple positions close to the C-terminus of CstF-64 (around position 500. An accumulation of unprocessed pre-mRNA and the depression of mature mRNA were observed in EV71-infected cells. An in vitro assay revealed the inhibition of the 3'-end pre-mRNA processing and polyadenylation in 3C(pro-treated nuclear extract, and this impairment was rescued by adding purified recombinant CstF-64 protein. In summing up the above results, we suggest that 3C(pro cleavage inactivates CstF-64 and impairs the host cell polyadenylation in vitro, as well as in virus-infected cells. This finding is, to our knowledge, the first to demonstrate that a picornavirus protein affects the polyadenylation of host mRNA.

  20. Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster.

    Science.gov (United States)

    Liu, Xiaochuan; Freitas, Jaime; Zheng, Dinghai; Oliveira, Marta S; Hoque, Mainul; Martins, Torcato; Henriques, Telmo; Tian, Bin; Moreira, Alexandra

    2017-12-01

    Alternative polyadenylation (APA) is a mechanism that generates multiple mRNA isoforms with different 3'UTRs and/or coding sequences from a single gene. Here, using 3' region extraction and deep sequencing (3'READS), we have systematically mapped cleavage and polyadenylation sites (PASs) in Drosophila melanogaster , expanding the total repertoire of PASs previously identified for the species, especially those located in A-rich genomic sequences. Cis -element analysis revealed distinct sequence motifs around fly PASs when compared to mammalian ones, including the greater enrichment of upstream UAUA elements and the less prominent presence of downstream UGUG elements. We found that over 75% of mRNA genes in Drosophila melanogaster undergo APA. The head tissue tends to use distal PASs when compared to the body, leading to preferential expression of APA isoforms with long 3'UTRs as well as with distal terminal exons. The distance between the APA sites and intron location of PAS are important parameters for APA difference between body and head, suggesting distinct PAS selection contexts. APA analysis of the RpII215 C4 mutant strain, which harbors a mutant RNA polymerase II (RNAPII) with a slower elongation rate, revealed that a 50% decrease in transcriptional elongation rate leads to a mild trend of more usage of proximal, weaker PASs, both in 3'UTRs and in introns, consistent with the "first come, first served" model of APA regulation. However, this trend was not observed in the head, suggesting a different regulatory context in neuronal cells. Together, our data expand the PAS collection for Drosophila melanogaster and reveal a tissue-specific effect of APA regulation by RNAPII elongation rate. © 2017 Liu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  1. Translation of a nonpolyadenylated viral RNA is enhanced by binding of viral coat protein or polyadenylation of the RNA.

    Science.gov (United States)

    Neeleman, L; Olsthoorn, R C; Linthorst, H J; Bol, J F

    2001-12-04

    On entering a host cell, positive-strand RNA virus genomes have to serve as messenger for the translation of viral proteins. Efficient translation of cellular messengers requires interactions between initiation factors bound to the 5'-cap structure and the poly(A) binding protein bound to the 3'-poly(A) tail. Initiation of infection with the tripartite RNA genomes of alfalfa mosaic virus (AMV) and viruses from the genus Ilarvirus requires binding of a few molecules of coat protein (CP) to the 3' end of the nonpolyadenylated viral RNAs. Moreover, infection with the genomic RNAs can be initiated by addition of the subgenomic messenger for CP, RNA 4. We report here that extension of the AMV RNAs with a poly(A) tail of 40 to 80 A-residues permitted initiation of infection independently of CP or RNA 4 in the inoculum. Specifically, polyadenylation of RNA 1 relieved an apparent bottleneck in the translation of the viral RNAs. Translation of RNA 4 in plant protoplasts was autocatalytically stimulated by its encoded CP. Mutations that interfered with CP binding to the 3' end of viral RNAs reduced translation of RNA 4 to undetectable levels. Possibly, CP of AMV and ilarviruses stimulates translation of viral RNAs by acting as a functional analogue of poly(A) binding protein or other cellular proteins.

  2. Nuclear relocalization of polyadenylate binding protein during rift valley fever virus infection involves expression of the NSs gene.

    Science.gov (United States)

    Copeland, Anna Maria; Altamura, Louis A; Van Deusen, Nicole M; Schmaljohn, Connie S

    2013-11-01

    Rift Valley fever virus (RVFV), an ambisense member of the family Bunyaviridae, genus Phlebovirus, is the causative agent of Rift Valley fever, an important zoonotic infection in Africa and the Middle East. Phlebovirus proteins are translated from virally transcribed mRNAs that, like host mRNA, are capped but, unlike host mRNAs, are not polyadenylated. Here, we investigated the role of PABP1 during RVFV infection of HeLa cells. Immunofluorescence studies of infected cells demonstrated a gross relocalization of PABP1 to the nucleus late in infection. Immunofluorescence microscopy studies of nuclear proteins revealed costaining between PABP1 and markers of nuclear speckles. PABP1 relocalization was sharply decreased in cells infected with a strain of RVFV lacking the gene encoding the RVFV nonstructural protein S (NSs). To determine whether PABP1 was required for RVFV infection, we measured the production of nucleocapsid protein (N) in cells transfected with small interfering RNAs (siRNAs) targeting PABP1. We found that the overall percentage of RVFV N-positive cells was not changed by siRNA treatment, indicating that PABP1 was not required for RVFV infection. However, when we analyzed populations of cells producing high versus low levels of PABP1, we found that the percentage of RVFV N-positive cells was decreased in cell populations producing physiologic levels of PABP1 and increased in cells with reduced levels of PABP1. Together, these results suggest that production of the NSs protein during RVFV infection leads to sequestration of PABP1 in the nuclear speckles, creating a state within the cell that favors viral protein production.

  3. Transcript Lifetime Is Balanced between Stabilizing Stem-Loop Structures and Degradation-Promoting Polyadenylation in Plant Mitochondria

    Science.gov (United States)

    Kuhn, Josef; Tengler, Ulrike; Binder, Stefan

    2001-01-01

    To determine the influence of posttranscriptional modifications on 3′ end processing and RNA stability in plant mitochondria, pea atp9 and Oenothera atp1 transcripts were investigated for the presence and function of 3′ nonencoded nucleotides. A 3′ rapid amplification of cDNA ends approach initiated at oligo(dT)-adapter primers finds the expected poly(A) tails predominantly attached within the second stem or downstream of the double stem-loop structures at sites of previously mapped 3′ ends. Functional studies in a pea mitochondrial in vitro processing system reveal a rapid removal of the poly(A) tails up to termini at the stem-loop structure but little if any influence on further degradation of the RNA. In contrast 3′ poly(A) tracts at RNAs without such stem-loop structures significantly promote total degradation in vitro. To determine the in vivo identity of 3′ nonencoded nucleotides more accurately, pea atp9 transcripts were analyzed by a direct anchor primer ligation-reverse transcriptase PCR approach. This analysis identified maximally 3-nucleotide-long nonencoded extensions most frequently of adenosines combined with cytidines. Processing assays with substrates containing homopolymer stretches of different lengths showed that 10 or more adenosines accelerate RNA processivity, while 3 adenosines have no impact on RNA life span. Thus polyadenylation can generally stimulate the decay of RNAs, but processivity of degradation is almost annihilated by the stabilizing effect of the stem-loop structures. These antagonistic actions thus result in the efficient formation of 3′ processed and stable transcripts. PMID:11154261

  4. The stress-induced heat shock protein 70.3 expression is regulated by a dual-component mechanism involving alternative polyadenylation and HuR.

    Science.gov (United States)

    Kraynik, Stephen M; Gabanic, Andrew; Anthony, Sarah R; Kelley, Melissa; Paulding, Waltke R; Roessler, Anne; McGuinness, Michael; Tranter, Michael

    2015-06-01

    Heat shock protein 70.3 (Hsp70.3) expression increases in response to cellular stress and plays a cytoprotective role. We have previously shown that Hsp70.3 expression is controlled through coordinated post-transcriptional regulation by miRNAs and alternative polyadenylation (APA), and APA-mediated shortening of the Hsp70.3 3'-UTR facilitates increased protein expression. A stress-induced increase in Hsp70.3 mRNA and protein expression is accompanied by alternative polyadenylation (APA)-mediated truncation of the 3'UTR of the Hsp70.3 mRNA transcript. However, the role that APA plays in stress-induced expression of Hsp70.3 remains unclear. Our results show that APA-mediated truncation of the Hsp70.3 3'UTR increases protein expression through enhanced polyribosome loading. Additionally, we demonstrate that the RNA binding protein HuR, which has been previously shown to play a role in mediating APA, is necessary for heat shock mediated increase in Hsp70.3 mRNA and protein. However, it is somewhat surprising to note that HuR does not play a role in APA of the Hsp70.3 mRNA, and these two regulatory events appear to be mutually exclusive regulators of Hsp70.3 expression. These results not only provide important insight to the regulation of stress response genes following heat shock, but also contribute an enhanced understanding of how alternative polyadenylation contributes to gene regulation. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. A Defective mRNA Cleavage and Polyadenylation Complex Facilitates Expansions of Transcribed (GAAn Repeats Associated with Friedreich’s Ataxia

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    Ryan J. McGinty

    2017-09-01

    Full Text Available Expansions of microsatellite repeats are responsible for numerous hereditary diseases in humans, including myotonic dystrophy and Friedreich’s ataxia. Whereas the length of an expandable repeat is the main factor determining disease inheritance, recent data point to genomic trans modifiers that can impact the likelihood of expansions and disease progression. Detection of these modifiers may lead to understanding and treating repeat expansion diseases. Here, we describe a method for the rapid, genome-wide identification of trans modifiers for repeat expansion in a yeast experimental system. Using this method, we found that missense mutations in the endoribonuclease subunit (Ysh1 of the mRNA cleavage and polyadenylation complex dramatically increase the rate of (GAAn repeat expansions but only when they are actively transcribed. These expansions correlate with slower transcription elongation caused by the ysh1 mutation. These results reveal an interplay between RNA processing and repeat-mediated genome instability, confirming the validity of our approach.

  6. Interaction of nitroaromatic radiosensitizers with irradiated polyadenylic acid as measured by an indirect immunochemical assay with specificity for the 8,5'-cycloadenosine moiety

    Energy Technology Data Exchange (ETDEWEB)

    Fuciarelli, A F; Mele, F G; Raleigh, J A

    1987-04-01

    The relative reactivity of a series of nitroaromatic radiosensitizers toward the C(5') radical intermediate leading to 8,5'-cycloadenosine formation in deoxygenated solutions of irradiated polyadenylic acid (poly A) was assessed using standard competition kinetic analysis. Formation of 8,5'-cycloadenosine was assayed by an indirect, competitive, enzyme-linked immunosorbent assay (ELISA) described in an earlier report. In the absence of oxygen, the nitroaromatics inhibit 8,5'-cyclonucleoside formation in a way which generally increases with radiosensitizer electron affinity. Although hydroxyl radical scavenging by the nitroaromatics may account for a relatively small decrease in 8,5'cyclonucleoside formation, the data suggest that oxidation of the C(5') radical intermediate is the more plausible explanation for the decreased yield of the 8,5'-cyclonucleoside with increasing nitroaromatic electron affinity.

  7. Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A Polymerases in Arabidopsis thaliana.

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    Christian Kappel

    2015-08-01

    Full Text Available The poly(A tail at 3' ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A polymerases, PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.

  8. Systematic Profiling of Poly(A)+ Transcripts Modulated by Core 3’ End Processing and Splicing Factors Reveals Regulatory Rules of Alternative Cleavage and Polyadenylation

    Science.gov (United States)

    Li, Wencheng; You, Bei; Hoque, Mainul; Zheng, Dinghai; Luo, Wenting; Ji, Zhe; Park, Ji Yeon; Gunderson, Samuel I.; Kalsotra, Auinash; Manley, James L.; Tian, Bin

    2015-01-01

    Alternative cleavage and polyadenylation (APA) results in mRNA isoforms containing different 3’ untranslated regions (3’UTRs) and/or coding sequences. How core cleavage/polyadenylation (C/P) factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3’UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A) sites (pAs), CFI-25/68, PABPN1 and PABPC1 promote usage of distal pAs. Strong cis element biases were found for pAs regulated by CFI-25/68 or Fip1, and the distance between pAs plays an important role in APA regulation. In addition, intronic pAs are substantially regulated by splicing factors, with U1 mostly inhibiting C/P events in introns near the 5’ end of gene and U2 suppressing those in introns with features for efficient splicing. Furthermore, PABPN1 inhibits expression of transcripts with pAs near the transcription start site (TSS), a property possibly related to its role in RNA degradation. Finally, we found that groups of APA events regulated by C/P factors are also modulated in cell differentiation and development with distinct trends. Together, our results support an APA code where an APA event in a given cellular context is regulated by a number of parameters, including relative location to the TSS, splicing context, distance between competing pAs, surrounding cis elements and concentrations of core C/P factors. PMID:25906188

  9. Systematic profiling of poly(A+ transcripts modulated by core 3' end processing and splicing factors reveals regulatory rules of alternative cleavage and polyadenylation.

    Directory of Open Access Journals (Sweden)

    Wencheng Li

    2015-04-01

    Full Text Available Alternative cleavage and polyadenylation (APA results in mRNA isoforms containing different 3' untranslated regions (3'UTRs and/or coding sequences. How core cleavage/polyadenylation (C/P factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3'UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A sites (pAs, CFI-25/68, PABPN1 and PABPC1 promote usage of distal pAs. Strong cis element biases were found for pAs regulated by CFI-25/68 or Fip1, and the distance between pAs plays an important role in APA regulation. In addition, intronic pAs are substantially regulated by splicing factors, with U1 mostly inhibiting C/P events in introns near the 5' end of gene and U2 suppressing those in introns with features for efficient splicing. Furthermore, PABPN1 inhibits expression of transcripts with pAs near the transcription start site (TSS, a property possibly related to its role in RNA degradation. Finally, we found that groups of APA events regulated by C/P factors are also modulated in cell differentiation and development with distinct trends. Together, our results support an APA code where an APA event in a given cellular context is regulated by a number of parameters, including relative location to the TSS, splicing context, distance between competing pAs, surrounding cis elements and concentrations of core C/P factors.

  10. Capturing the Alternative Cleavage and Polyadenylation Sites of 14 NAC Genes in Populus Using a Combination of 3′-RACE and High-Throughput Sequencing

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    Haoran Wang

    2018-03-01

    Full Text Available Detection of complex splice sites (SSs and polyadenylation sites (PASs of eukaryotic genes is essential for the elucidation of gene regulatory mechanisms. Transcriptome-wide studies using high-throughput sequencing (HTS have revealed prevalent alternative splicing (AS and alternative polyadenylation (APA in plants. However, small-scale and high-depth HTS aimed at detecting genes or gene families are very few and limited. We explored a convenient and flexible method for profiling SSs and PASs, which combines rapid amplification of 3′-cDNA ends (3′-RACE and HTS. Fourteen NAC (NAM, ATAF1/2, CUC2 transcription factor genes of Populus trichocarpa were analyzed by 3′-RACE-seq. Based on experimental reproducibility, boundary sequence analysis and reverse transcription PCR (RT-PCR verification, only canonical SSs were considered to be authentic. Based on stringent criteria, candidate PASs without any internal priming features were chosen as authentic PASs and assumed to be PAS-rich markers. Thirty-four novel canonical SSs, six intronic/internal exons and thirty 3′-UTR PAS-rich markers were revealed by 3′-RACE-seq. Using 3′-RACE and real-time PCR, we confirmed that three APA transcripts ending in/around PAS-rich markers were differentially regulated in response to plant hormones. Our results indicate that 3′-RACE-seq is a robust and cost-effective method to discover SSs and label active regions subjected to APA for genes or gene families. The method is suitable for small-scale AS and APA research in the initial stage.

  11. FIP1 Plays an Important Role in Nitrate Signaling and Regulates CIPK8 and CIPK23 Expression in Arabidopsis

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    Chao Wang

    2018-05-01

    Full Text Available Unraveling the molecular mechanisms of nitrate regulation and deciphering the underlying genetic network is vital for elucidating nitrate uptake and utilization in plants. Such knowledge could lead to the improvement of nitrogen-use efficiency in agriculture. Here, we report that the FIP1 gene (factor interacting with poly(A polymerase 1 plays an important role in nitrate signaling in Arabidopsis thaliana. FIP1 encodes a putative core component of the polyadenylation factor complex. We found that FIP1 interacts with the cleavage and polyadenylation specificity factor 30-L (CPSF30-L, which is also an essential player in nitrate signaling. The induction of nitrate-responsive genes following nitrate treatment was inhibited in the fip1 mutant. The nitrate content was also reduced in fip1 seedlings due to their decreased nitrate uptake activity. Furthermore, the nitrate content was higher in the roots but lower in the roots of fip1, which may result from the downregulation of NRT1.8 and the upregulation of the nitrate assimilation genes. In addition, qPCR analyses revealed that FIP1 negatively regulated the expression of CIPK8 and CIPK23, two protein kinases involved in nitrate signaling. In the fip1 mutant, the increased expression of CIPK23 may affect nitrate uptake, resulting in its lower nitrate content. Genetic and molecular evidence suggests that FIP1 and CPSF30-L function in the same nitrate-signaling pathway, with FIP1 mediating signaling through its interaction with CPSF30-L and its regulation of CIPK8 and CIPK23. Analysis of the 3′-UTR of NRT1.1 showed that the pattern of polyadenylation sites was altered in the fip1 mutant. These findings add a novel component to the nitrate regulation network and enhance our understanding of the underlying mechanisms for nitrate signaling.

  12. Changes in Cellular mRNA Stability, Splicing, and Polyadenylation through HuR Protein Sequestration by a Cytoplasmic RNA Virus

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    Michael D. Barnhart

    2013-11-01

    Full Text Available The impact of RNA viruses on the posttranscriptional regulation of cellular gene expression is unclear. Sindbis virus causes a dramatic relocalization of the cellular HuR protein from the nucleus to the cytoplasm in infected cells. This is to the result of the expression of large amounts of viral RNAs that contain high-affinity HuR binding sites in their 3′ UTRs effectively serving as a sponge for the HuR protein. Sequestration of HuR by Sindbis virus is associated with destabilization of cellular mRNAs that normally bind HuR and rely on it to regulate their expression. Furthermore, significant changes can be observed in nuclear alternative polyadenylation and splicing events on cellular pre-mRNAs as a result of sequestration of HuR protein by the 3′ UTR of transcripts of this cytoplasmic RNA virus. These studies suggest a molecular mechanism of virus-host interaction that probably has a significant impact on virus replication, cytopathology, and pathogenesis.

  13. The BARD1 C-Terminal Domain Structure and Interactions with Polyadenylation Factor CstF-50

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    Edwards, Ross A.; Lee, Megan S.; Tsutakawa, Susan E.; Williams, R. Scott; Tainer, John A.; Glover, J. N. Mark

    2009-07-13

    The BARD1 N-terminal RING domain binds BRCA1 while the BARD1 C-terminal ankyrin and tandem BRCT repeat domains bind CstF-50 to modulate mRNA processing and RNAP II stability in response to DNA damage. Here we characterize the BARD1 structural biochemistry responsible for CstF- 50 binding. The crystal structure of the BARD1 BRCT domain uncovers a degenerate phosphopeptide binding pocket lacking the key arginine required for phosphopeptide interactions in other BRCT proteins.Small angle X-ray scattering together with limited proteolysis results indicates that ankyrin and BRCT domains are linked by a flexible tether and do not adopt a fixed orientation relative to one another. Protein pull-down experiments utilizing a series of purified BARD1 deletion mutants indicate that interactions between the CstF-50 WD-40 domain and BARD1 involve the ankyrin-BRCT linker but do not require ankyrin or BRCT domains. The structural plasticity imparted by the ANK-BRCT linker helps to explain the regulated assembly of different protein BARD1 complexes with distinct functions in DNA damage signaling including BARD1-dependent induction of apoptosis plus p53 stabilization and interactions. BARD1 architecture and plasticity imparted by the ANK-BRCT linker are suitable to allow the BARD1 C-terminus to act as a hub with multiple binding sites to integrate diverse DNA damage signals directly to RNA polymerase.

  14. A universal protocol to generate consensus level genome sequences for foot-and-mouth disease virus and other positive-sense polyadenylated RNA viruses using the Illumina MiSeq.

    Science.gov (United States)

    Logan, Grace; Freimanis, Graham L; King, David J; Valdazo-González, Begoña; Bachanek-Bankowska, Katarzyna; Sanderson, Nicholas D; Knowles, Nick J; King, Donald P; Cottam, Eleanor M

    2014-09-30

    Next-Generation Sequencing (NGS) is revolutionizing molecular epidemiology by providing new approaches to undertake whole genome sequencing (WGS) in diagnostic settings for a variety of human and veterinary pathogens. Previous sequencing protocols have been subject to biases such as those encountered during PCR amplification and cell culture, or are restricted by the need for large quantities of starting material. We describe here a simple and robust methodology for the generation of whole genome sequences on the Illumina MiSeq. This protocol is specific for foot-and-mouth disease virus (FMDV) or other polyadenylated RNA viruses and circumvents both the use of PCR and the requirement for large amounts of initial template. The protocol was successfully validated using five FMDV positive clinical samples from the 2001 epidemic in the United Kingdom, as well as a panel of representative viruses from all seven serotypes. In addition, this protocol was successfully used to recover 94% of an FMDV genome that had previously been identified as cell culture negative. Genome sequences from three other non-FMDV polyadenylated RNA viruses (EMCV, ERAV, VESV) were also obtained with minor protocol amendments. We calculated that a minimum coverage depth of 22 reads was required to produce an accurate consensus sequence for FMDV O. This was achieved in 5 FMDV/O/UKG isolates and the type O FMDV from the serotype panel with the exception of the 5' genomic termini and area immediately flanking the poly(C) region. We have developed a universal WGS method for FMDV and other polyadenylated RNA viruses. This method works successfully from a limited quantity of starting material and eliminates the requirement for genome-specific PCR amplification. This protocol has the potential to generate consensus-level sequences within a routine high-throughput diagnostic environment.

  15. Nuclear Phosphatidylinositol-Phosphate Type I Kinase α-Coupled Star-PAP Polyadenylation Regulates Cell Invasion.

    Science.gov (United States)

    A P, Sudheesh; Laishram, Rakesh S

    2018-03-01

    Star-PAP, a nuclear phosphatidylinositol (PI) signal-regulated poly(A) polymerase (PAP), couples with type I PI phosphate kinase α (PIPKIα) and controls gene expression. We show that Star-PAP and PIPKIα together regulate 3'-end processing and expression of pre-mRNAs encoding key anti-invasive factors ( KISS1R , CDH1 , NME1 , CDH13 , FEZ1 , and WIF1 ) in breast cancer. Consistently, the endogenous Star-PAP level is negatively correlated with the cellular invasiveness of breast cancer cells. While silencing Star-PAP or PIPKIα increases cellular invasiveness in low-invasiveness MCF7 cells, Star-PAP overexpression decreases invasiveness in highly invasive MDA-MB-231 cells in a cellular Star-PAP level-dependent manner. However, expression of the PIPKIα-noninteracting Star-PAP mutant or the phosphodeficient Star-PAP (S6A mutant) has no effect on cellular invasiveness. These results strongly indicate that PIPKIα interaction and Star-PAP S6 phosphorylation are required for Star-PAP-mediated regulation of cancer cell invasion and give specificity to target anti-invasive gene expression. Our study establishes Star-PAP-PIPKIα-mediated 3'-end processing as a key anti-invasive mechanism in breast cancer. Copyright © 2018 A.P. and Laishram.

  16. Signal Words

    Science.gov (United States)

    SIGNAL WORDS TOPIC FACT SHEET NPIC fact sheets are designed to answer questions that are commonly asked by the ... making decisions about pesticide use. What are Signal Words? Signal words are found on pesticide product labels, ...

  17. Mutation in cpsf6/CFIm68 (Cleavage and Polyadenylation Specificity Factor Subunit 6 causes short 3'UTRs and disturbs gene expression in developing embryos, as revealed by an analysis of primordial germ cell migration using the medaka mutant naruto.

    Directory of Open Access Journals (Sweden)

    Takao Sasado

    Full Text Available Our previous studies analyzing medaka mutants defective in primordial germ cell (PGC migration identified cxcr4b and cxcr7, which are both receptors of the chemokine sdf1/cxcl12, as key regulators of PGC migration. Among PGC migration mutants, naruto (nar is unique in that the mutant phenotype includes gross morphological abnormalities of embryos, suggesting that the mutation affects a broader range of processes. A fine genetic linkage mapping and genome sequencing showed the nar gene encodes Cleavage and Polyadenylation Specificity Factor subunit 6 (CPSF6/CFIm68. CPSF6 is a component of the Cleavage Factor Im complex (CFIm which plays a key role in pre-mRNA 3'-cleavage and polyadenylation. 3'RACE of sdf1a/b and cxcr7 transcripts in the mutant embryos indicated shorter 3'UTRs with poly A additions occurring at more upstream positions than wild-type embryos, suggesting CPSF6 functions to prevent premature 3'UTR cleavage. In addition, expression of the coding region sequences of sdf1a/b in nar mutants was more anteriorly extended in somites than wild-type embryos, accounting for the abnormally extended distribution of PGCs in nar mutants. An expected consequence of shortening 3'UTR is the escape from the degradation mechanism mediated by microRNAs interacting with distal 3'UTR sequence. The abnormal expression pattern of sdf1a coding sequence may be at least partially accounted for by this mechanism. Given the pleiotropic effects of nar mutation, further analysis using the nar mutant will reveal processes in which CPSF6 plays essential regulatory roles in poly A site selection and involvement of 3'UTRs in posttranscriptional gene regulation in various genes in vivo.

  18. Mutation in cpsf6/CFIm68 (Cleavage and Polyadenylation Specificity Factor Subunit 6) causes short 3'UTRs and disturbs gene expression in developing embryos, as revealed by an analysis of primordial germ cell migration using the medaka mutant naruto.

    Science.gov (United States)

    Sasado, Takao; Kondoh, Hisato; Furutani-Seiki, Makoto; Naruse, Kiyoshi

    2017-01-01

    Our previous studies analyzing medaka mutants defective in primordial germ cell (PGC) migration identified cxcr4b and cxcr7, which are both receptors of the chemokine sdf1/cxcl12, as key regulators of PGC migration. Among PGC migration mutants, naruto (nar) is unique in that the mutant phenotype includes gross morphological abnormalities of embryos, suggesting that the mutation affects a broader range of processes. A fine genetic linkage mapping and genome sequencing showed the nar gene encodes Cleavage and Polyadenylation Specificity Factor subunit 6 (CPSF6/CFIm68). CPSF6 is a component of the Cleavage Factor Im complex (CFIm) which plays a key role in pre-mRNA 3'-cleavage and polyadenylation. 3'RACE of sdf1a/b and cxcr7 transcripts in the mutant embryos indicated shorter 3'UTRs with poly A additions occurring at more upstream positions than wild-type embryos, suggesting CPSF6 functions to prevent premature 3'UTR cleavage. In addition, expression of the coding region sequences of sdf1a/b in nar mutants was more anteriorly extended in somites than wild-type embryos, accounting for the abnormally extended distribution of PGCs in nar mutants. An expected consequence of shortening 3'UTR is the escape from the degradation mechanism mediated by microRNAs interacting with distal 3'UTR sequence. The abnormal expression pattern of sdf1a coding sequence may be at least partially accounted for by this mechanism. Given the pleiotropic effects of nar mutation, further analysis using the nar mutant will reveal processes in which CPSF6 plays essential regulatory roles in poly A site selection and involvement of 3'UTRs in posttranscriptional gene regulation in various genes in vivo.

  19. ATP signals

    DEFF Research Database (Denmark)

    Novak, Ivana

    2016-01-01

    The Department of Biology at the University of Copenhagen explains the function of ATP signalling in the pancreas......The Department of Biology at the University of Copenhagen explains the function of ATP signalling in the pancreas...

  20. Signaling aggression.

    Science.gov (United States)

    van Staaden, Moira J; Searcy, William A; Hanlon, Roger T

    2011-01-01

    From psychological and sociological standpoints, aggression is regarded as intentional behavior aimed at inflicting pain and manifested by hostility and attacking behaviors. In contrast, biologists define aggression as behavior associated with attack or escalation toward attack, omitting any stipulation about intentions and goals. Certain animal signals are strongly associated with escalation toward attack and have the same function as physical attack in intimidating opponents and winning contests, and ethologists therefore consider them an integral part of aggressive behavior. Aggressive signals have been molded by evolution to make them ever more effective in mediating interactions between the contestants. Early theoretical analyses of aggressive signaling suggested that signals could never be honest about fighting ability or aggressive intentions because weak individuals would exaggerate such signals whenever they were effective in influencing the behavior of opponents. More recent game theory models, however, demonstrate that given the right costs and constraints, aggressive signals are both reliable about strength and intentions and effective in influencing contest outcomes. Here, we review the role of signaling in lieu of physical violence, considering threat displays from an ethological perspective as an adaptive outcome of evolutionary selection pressures. Fighting prowess is conveyed by performance signals whose production is constrained by physical ability and thus limited to just some individuals, whereas aggressive intent is encoded in strategic signals that all signalers are able to produce. We illustrate recent advances in the study of aggressive signaling with case studies of charismatic taxa that employ a range of sensory modalities, viz. visual and chemical signaling in cephalopod behavior, and indicators of aggressive intent in the territorial calls of songbirds. Copyright © 2011 Elsevier Inc. All rights reserved.

  1. Crosstalk between Wnt Signaling and RNA Processing in Colorectal Cancer

    Directory of Open Access Journals (Sweden)

    Michael Bordonaro

    2013-01-01

    Full Text Available RNA processing involves a variety of processes affecting gene expression, including the removal of introns through RNA splicing, as well as 3' end processing (cleavage and polyadenylation. Alternative RNA processing is fundamentally important for gene regulation, and aberrant processing is associated with the initiation and progression of cancer. Deregulated Wnt signaling, which is the initiating event in the development of most cases of human colorectal cancer (CRC, has been linked to modified RNA processing, which may contribute to Wnt-mediated colonic carcinogenesis. Crosstalk between Wnt signaling and alternative RNA splicing with relevance to CRC includes effects on the expression of Rac1b, an alternatively spliced gene associated with tumorigenesis, which exhibits alternative RNA splicing that is influenced by Wnt activity. In addition, Tcf4, a crucial component of Wnt signaling, also exhibits alternative splicing, which is likely involved in colonic tumorigenesis. Modulation of 3' end formation, including of the Wnt target gene COX-2, also can influence the neoplastic process, with implications for CRC. While many human genes are dependent on introns and splicing for normal levels of gene expression, naturally intronless genes exist with a unique metabolism that allows for intron-independent gene expression. Effects of Wnt activity on the RNA metabolism of the intronless Wnt-target gene c-jun is a likely contributor to cancer development. Further, butyrate, a breakdown product of dietary fiber and a histone deacetylase inhibitor, upregulates Wnt activity in CRC cells, and also modulates RNA processing; therefore, the interplay between Wnt activity, the modulation of this activity by butyrate, and differential RNA metabolism in colonic cells can significantly influence tumorigenesis. Determining the role played by altered RNA processing in Wnt-mediated neoplasia may lead to novel interventions aimed at restoring normal RNA metabolism for

  2. Crosstalk between Wnt Signaling and RNA Processing in Colorectal Cancer.

    Science.gov (United States)

    Bordonaro, Michael

    2013-01-01

    RNA processing involves a variety of processes affecting gene expression, including the removal of introns through RNA splicing, as well as 3' end processing (cleavage and polyadenylation). Alternative RNA processing is fundamentally important for gene regulation, and aberrant processing is associated with the initiation and progression of cancer. Deregulated Wnt signaling, which is the initiating event in the development of most cases of human colorectal cancer (CRC), has been linked to modified RNA processing, which may contribute to Wnt-mediated colonic carcinogenesis. Crosstalk between Wnt signaling and alternative RNA splicing with relevance to CRC includes effects on the expression of Rac1b, an alternatively spliced gene associated with tumorigenesis, which exhibits alternative RNA splicing that is influenced by Wnt activity. In addition, Tcf4, a crucial component of Wnt signaling, also exhibits alternative splicing, which is likely involved in colonic tumorigenesis. Modulation of 3' end formation, including of the Wnt target gene COX-2, also can influence the neoplastic process, with implications for CRC. While many human genes are dependent on introns and splicing for normal levels of gene expression, naturally intronless genes exist with a unique metabolism that allows for intron-independent gene expression. Effects of Wnt activity on the RNA metabolism of the intronless Wnt-target gene c-jun is a likely contributor to cancer development. Further, butyrate, a breakdown product of dietary fiber and a histone deacetylase inhibitor, upregulates Wnt activity in CRC cells, and also modulates RNA processing; therefore, the interplay between Wnt activity, the modulation of this activity by butyrate, and differential RNA metabolism in colonic cells can significantly influence tumorigenesis. Determining the role played by altered RNA processing in Wnt-mediated neoplasia may lead to novel interventions aimed at restoring normal RNA metabolism for therapeutic benefit

  3. Signal detection

    International Nuclear Information System (INIS)

    Tholomier, M.

    1985-01-01

    In a scanning electron microscope, whatever is the measured signal, the same set is found: incident beam, sample, signal detection, signal amplification. The resulting signal is used to control the spot luminosity with the observer cathodoscope. This is synchronized with the beam scanning on the sample; on the cathodoscope, the image in secondary electrons, backscattered electrons,... of the sample surface is reconstituted. The best compromise must be found between a register time low enough to remove eventual variations (under the incident beam) of the nature of the observed phenomenon, and a good spatial resolution of the image and a signal-to-noise ratio high enough. The noise is one of the basic limitations of the scanning electron microscope performance. The whose measurement line must be optimized to reduce it [fr

  4. Omni-PolyA: a method and tool for accurate recognition of Poly(A) signals in human genomic DNA

    KAUST Repository

    Magana-Mora, Arturo

    2017-08-15

    BackgroundPolyadenylation is a critical stage of RNA processing during the formation of mature mRNA, and is present in most of the known eukaryote protein-coding transcripts and many long non-coding RNAs. The correct identification of poly(A) signals (PAS) not only helps to elucidate the 3′-end genomic boundaries of a transcribed DNA region and gene regulatory mechanisms but also gives insight into the multiple transcript isoforms resulting from alternative PAS. Although progress has been made in the in-silico prediction of genomic signals, the recognition of PAS in DNA genomic sequences remains a challenge.ResultsIn this study, we analyzed human genomic DNA sequences for the 12 most common PAS variants. Our analysis has identified a set of features that helps in the recognition of true PAS, which may be involved in the regulation of the polyadenylation process. The proposed features, in combination with a recognition model, resulted in a novel method and tool, Omni-PolyA. Omni-PolyA combines several machine learning techniques such as different classifiers in a tree-like decision structure and genetic algorithms for deriving a robust classification model. We performed a comparison between results obtained by state-of-the-art methods, deep neural networks, and Omni-PolyA. Results show that Omni-PolyA significantly reduced the average classification error rate by 35.37% in the prediction of the 12 considered PAS variants relative to the state-of-the-art results.ConclusionsThe results of our study demonstrate that Omni-PolyA is currently the most accurate model for the prediction of PAS in human and can serve as a useful complement to other PAS recognition methods. Omni-PolyA is publicly available as an online tool accessible at www.cbrc.kaust.edu.sa/omnipolya/.

  5. Comparative analysis of the full genome sequence of European bat lyssavirus type 1 and type 2 with other lyssaviruses and evidence for a conserved transcription termination and polyadenylation motif in the G-L 3' non-translated region.

    Science.gov (United States)

    Marston, D A; McElhinney, L M; Johnson, N; Müller, T; Conzelmann, K K; Tordo, N; Fooks, A R

    2007-04-01

    We report the first full-length genomic sequences for European bat lyssavirus type-1 (EBLV-1) and type-2 (EBLV-2). The EBLV-1 genomic sequence was derived from a virus isolated from a serotine bat in Hamburg, Germany, in 1968 and the EBLV-2 sequence was derived from a virus isolate from a human case of rabies that occurred in Scotland in 2002. A long-distance PCR strategy was used to amplify the open reading frames (ORFs), followed by standard and modified RACE (rapid amplification of cDNA ends) techniques to amplify the 3' and 5' ends. The lengths of each complete viral genome for EBLV-1 and EBLV-2 were 11 966 and 11 930 base pairs, respectively, and follow the standard rhabdovirus genome organization of five viral proteins. Comparison with other lyssavirus sequences demonstrates variation in degrees of homology, with the genomic termini showing a high degree of complementarity. The nucleoprotein was the most conserved, both intra- and intergenotypically, followed by the polymerase (L), matrix and glyco- proteins, with the phosphoprotein being the most variable. In addition, we have shown that the two EBLVs utilize a conserved transcription termination and polyadenylation (TTP) motif, approximately 50 nt upstream of the L gene start codon. All available lyssavirus sequences to date, with the exception of Pasteur virus (PV) and PV-derived isolates, use the second TTP site. This observation may explain differences in pathogenicity between lyssavirus strains, dependent on the length of the untranslated region, which might affect transcriptional activity and RNA stability.

  6. Signal Processing

    International Nuclear Information System (INIS)

    Anon.

    1992-01-01

    Signal processing techniques, extensively used nowadays to maximize the performance of audio and video equipment, have been a key part in the design of hardware and software for high energy physics detectors since pioneering applications in the UA1 experiment at CERN in 1979

  7. The fission yeast RNA binding protein Mmi1 regulates meiotic genes by controlling intron specific splicing and polyadenylation coupled RNA turnover.

    Directory of Open Access Journals (Sweden)

    Huei-Mei Chen

    Full Text Available The polyA tails of mRNAs are monitored by the exosome as a quality control mechanism. We find that fission yeast, Schizosaccharomyces pombe, adopts this RNA quality control mechanism to regulate a group of 30 or more meiotic genes at the level of both splicing and RNA turnover. In vegetative cells the RNA binding protein Mmi1 binds to the primary transcripts of these genes. We find the novel motif U(U/C/GAAAC highly over-represented in targets of Mmi1. Mmi1 can specifically regulate the splicing of particular introns in a transcript: it inhibits the splicing of introns that are in the vicinity of putative Mmi1 binding sites, while allowing the splicing of other introns that are far from such sites. In addition, binding of Mmi1, particularly near the 3' end, alters 3' processing to promote extremely long polyA tails of up to a kilobase. The hyperadenylated transcripts are then targeted for degradation by the nuclear exonuclease Rrp6. The nuclear polyA binding protein Pab2 assists this hyperadenylation-mediated RNA decay. Rrp6 also targets other hyperadenylated transcripts, which become hyperadenylated in an unknown, but Mmi1-independent way. Thus, hyperadenylation may be a general signal for RNA degradation. In addition, binding of Mmi1 can affect the efficiency of 3' cleavage. Inactivation of Mmi1 in meiosis allows meiotic expression, through splicing and RNA stabilization, of at least 29 target genes, which are apparently constitutively transcribed.

  8. Integrin Signalling

    OpenAIRE

    Schelfaut, Roselien

    2005-01-01

    Integrins are receptors presented on most cells. By binding ligand they can generate signalling pathways inside the cell. Those pathways are a linkage to proteins in the cytosol. It is known that tumor cells can survive and proliferate in the absence of a solid support while normal cells need to be bound to ligand. To understand why tumour cells act that way, we first have to know how ligand-binding to integrins affect the cell. This research field includes studies on activation of proteins b...

  9. In silico Analysis of 3′-End-Processing Signals in Aspergillus oryzae Using Expressed Sequence Tags and Genomic Sequencing Data

    Science.gov (United States)

    Tanaka, Mizuki; Sakai, Yoshifumi; Yamada, Osamu; Shintani, Takahiro; Gomi, Katsuya

    2011-01-01

    To investigate 3′-end-processing signals in Aspergillus oryzae, we created a nucleotide sequence data set of the 3′-untranslated region (3′ UTR) plus 100 nucleotides (nt) sequence downstream of the poly(A) site using A. oryzae expressed sequence tags and genomic sequencing data. This data set comprised 1065 sequences derived from 1042 unique genes. The average 3′ UTR length in A. oryzae was 241 nt, which is greater than that in yeast but similar to that in plants. The 3′ UTR and 100 nt sequence downstream of the poly(A) site is notably U-rich, while the region located 15–30 nt upstream of the poly(A) site is markedly A-rich. The most frequently found hexanucleotide in this A-rich region is AAUGAA, although this sequence accounts for only 6% of all transcripts. These data suggested that A. oryzae has no highly conserved sequence element equivalent to AAUAAA, a mammalian polyadenylation signal. We identified that putative 3′-end-processing signals in A. oryzae, while less well conserved than those in mammals, comprised four sequence elements: the furthest upstream U-rich element, A-rich sequence, cleavage site, and downstream U-rich element flanking the cleavage site. Although these putative 3′-end-processing signals are similar to those in yeast and plants, some notable differences exist between them. PMID:21586533

  10. Basic digital signal processing

    CERN Document Server

    Lockhart, Gordon B

    1985-01-01

    Basic Digital Signal Processing describes the principles of digital signal processing and experiments with BASIC programs involving the fast Fourier theorem (FFT). The book reviews the fundamentals of the BASIC program, continuous and discrete time signals including analog signals, Fourier analysis, discrete Fourier transform, signal energy, power. The text also explains digital signal processing involving digital filters, linear time-variant systems, discrete time unit impulse, discrete-time convolution, and the alternative structure for second order infinite impulse response (IIR) sections.

  11. Retroactive signaling in short signaling pathways.

    Directory of Open Access Journals (Sweden)

    Jacques-Alexandre Sepulchre

    Full Text Available In biochemical signaling pathways without explicit feedback connections, the core signal transduction is usually described as a one-way communication, going from upstream to downstream in a feedforward chain or network of covalent modification cycles. In this paper we explore the possibility of a new type of signaling called retroactive signaling, offered by the recently demonstrated property of retroactivity in signaling cascades. The possibility of retroactive signaling is analysed in the simplest case of the stationary states of a bicyclic cascade of signaling cycles. In this case, we work out the conditions for which variables of the upstream cycle are affected by a change of the total amount of protein in the downstream cycle, or by a variation of the phosphatase deactivating the same protein. Particularly, we predict the characteristic ranges of the downstream protein, or of the downstream phosphatase, for which a retroactive effect can be observed on the upstream cycle variables. Next, we extend the possibility of retroactive signaling in short but nonlinear signaling pathways involving a few covalent modification cycles.

  12. Signal sciences workshop proceedings

    Energy Technology Data Exchange (ETDEWEB)

    Candy, J.V.

    1997-05-01

    This meeting is aimed primarily at signal processing and controls. The technical program for the 1997 Workshop includes a variety of efforts in the Signal Sciences with applications in the Microtechnology Area a new program at LLNL and a future area of application for both Signal/Image Sciences. Special sessions organized by various individuals in Seismic and Optical Signal Processing as well as Micro-Impulse Radar Processing highlight the program, while the speakers at the Signal Processing Applications session discuss various applications of signal processing/control to real world problems. For the more theoretical, a session on Signal Processing Algorithms was organized as well as for the more pragmatic, featuring a session on Real-Time Signal Processing.

  13. Signal sciences workshop. Proceedings

    International Nuclear Information System (INIS)

    Candy, J.V.

    1997-01-01

    This meeting is aimed primarily at signal processing and controls. The technical program for the 1997 Workshop includes a variety of efforts in the Signal Sciences with applications in the Microtechnology Area a new program at LLNL and a future area of application for both Signal/Image Sciences. Special sessions organized by various individuals in Seismic and Optical Signal Processing as well as Micro-Impulse Radar Processing highlight the program, while the speakers at the Signal Processing Applications session discuss various applications of signal processing/control to real world problems. For the more theoretical, a session on Signal Processing Algorithms was organized as well as for the more pragmatic, featuring a session on Real-Time Signal Processing

  14. ECG signal processing

    NARCIS (Netherlands)

    2009-01-01

    A system extracts an ECG signal from a composite signal (308) representing an electric measurement of a living subject. Identification means (304) identify a plurality of temporal segments (309) of the composite signal corresponding to a plurality of predetermined segments (202,204,206) of an ECG

  15. Optimal Signal Quality Index for Photoplethysmogram Signals

    Directory of Open Access Journals (Sweden)

    Mohamed Elgendi

    2016-09-01

    Full Text Available A photoplethysmogram (PPG is a noninvasive circulatory signal related to the pulsatile volume of blood in tissue and is typically collected by pulse oximeters. PPG signals collected via mobile devices are prone to artifacts that negatively impact measurement accuracy, which can lead to a significant number of misleading diagnoses. Given the rapidly increased use of mobile devices to collect PPG signals, developing an optimal signal quality index (SQI is essential to classify the signal quality from these devices. Eight SQIs were developed and tested based on: perfusion, kurtosis, skewness, relative power, non-stationarity, zero crossing, entropy, and the matching of systolic wave detectors. Two independent annotators annotated all PPG data (106 recordings, 60 s each and a third expert conducted the adjudication of differences. The independent annotators labeled each PPG signal with one of the following labels: excellent, acceptable or unfit for diagnosis. All indices were compared using Mahalanobis distance, linear discriminant analysis, quadratic discriminant analysis, and support vector machine with leave-one-out cross-validation. The skewness index outperformed the other seven indices in differentiating between excellent PPG and acceptable, acceptable combined with unfit, and unfit recordings, with overall F 1 scores of 86.0%, 87.2%, and 79.1%, respectively.

  16. Optimal Signal Quality Index for Photoplethysmogram Signals.

    Science.gov (United States)

    Elgendi, Mohamed

    2016-09-22

    A photoplethysmogram (PPG) is a noninvasive circulatory signal related to the pulsatile volume of blood in tissue and is typically collected by pulse oximeters. PPG signals collected via mobile devices are prone to artifacts that negatively impact measurement accuracy, which can lead to a significant number of misleading diagnoses. Given the rapidly increased use of mobile devices to collect PPG signals, developing an optimal signal quality index (SQI) is essential to classify the signal quality from these devices. Eight SQIs were developed and tested based on: perfusion, kurtosis, skewness, relative power, non-stationarity, zero crossing, entropy, and the matching of systolic wave detectors. Two independent annotators annotated all PPG data (106 recordings, 60 s each) and a third expert conducted the adjudication of differences. The independent annotators labeled each PPG signal with one of the following labels: excellent, acceptable or unfit for diagnosis. All indices were compared using Mahalanobis distance, linear discriminant analysis, quadratic discriminant analysis, and support vector machine with leave-one-out cross-validation. The skewness index outperformed the other seven indices in differentiating between excellent PPG and acceptable, acceptable combined with unfit, and unfit recordings, with overall F 1 scores of 86.0%, 87.2%, and 79.1%, respectively.

  17. Second-hand signals

    DEFF Research Database (Denmark)

    Bergenholtz, Carsten

    2014-01-01

    Studies of signaling theory have traditionally focused on the dyadic link between the sender and receiver of the signal. Within a science‐based perspective this framing has led scholars to investigate how patents and publications of firms function as signals. I explore another important type...... used by various agents in their search for and assessment of products and firms. I conclude by arguing how this second‐hand nature of signals goes beyond a simple dyadic focus on senders and receivers of signals, and thus elucidates the more complex interrelations of the various types of agents...

  18. Identification of transcriptional signals in Encephalitozoon cuniculi widespread among Microsporidia phylum: support for accurate structural genome annotation

    Directory of Open Access Journals (Sweden)

    Wincker Patrick

    2009-12-01

    Full Text Available Abstract Background Microsporidia are obligate intracellular eukaryotic parasites with genomes ranging in size from 2.3 Mbp to more than 20 Mbp. The extremely small (2.9 Mbp and highly compact (~1 gene/kb genome of the human parasite Encephalitozoon cuniculi has been fully sequenced. The aim of this study was to characterize noncoding motifs that could be involved in regulation of gene expression in E. cuniculi and to show whether these motifs are conserved among the phylum Microsporidia. Results To identify such signals, 5' and 3'RACE-PCR experiments were performed on different E. cuniculi mRNAs. This analysis confirmed that transcription overrun occurs in E. cuniculi and may result from stochastic recognition of the AAUAAA polyadenylation signal. Such experiments also showed highly reduced 5'UTR's (E. cuniculi genes presented a CCC-like motif immediately upstream from the coding start. To characterize other signals involved in differential transcriptional regulation, we then focused our attention on the gene family coding for ribosomal proteins. An AAATTT-like signal was identified upstream from the CCC-like motif. In rare cases the cytosine triplet was shown to be substituted by a GGG-like motif. Comparative genomic studies confirmed that these different signals are also located upstream from genes encoding ribosomal proteins in other microsporidian species including Antonospora locustae, Enterocytozoon bieneusi, Anncaliia algerae (syn. Brachiola algerae and Nosema ceranae. Based on these results a systematic analysis of the ~2000 E. cuniculi coding DNA sequences was then performed and brings to highlight that 364 translation initiation codons (18.29% of total CDSs had been badly predicted. Conclusion We identified various signals involved in the maturation of E. cuniculi mRNAs. Presence of such signals, in phylogenetically distant microsporidian species, suggests that a common regulatory mechanism exists among the microsporidia. Furthermore

  19. Method of signal analysis

    International Nuclear Information System (INIS)

    Berthomier, Charles

    1975-01-01

    A method capable of handling the amplitude and the frequency time laws of a certain kind of geophysical signals is described here. This method is based upon the analytical signal idea of Gabor and Ville, which is constructed either in the time domain by adding an imaginary part to the real signal (in-quadrature signal), or in the frequency domain by suppressing negative frequency components. The instantaneous frequency of the initial signal is then defined as the time derivative of the phase of the analytical signal, and his amplitude, or envelope, as the modulus of this complex signal. The method is applied to three types of magnetospheric signals: chorus, whistlers and pearls. The results obtained by analog and numerical calculations are compared to results obtained by classical systems using filters, i.e. based upon a different definition of the concept of frequency. The precision with which the frequency-time laws are determined leads then to the examination of the principle of the method and to a definition of instantaneous power density spectrum attached to the signal, and to the first consequences of this definition. In this way, a two-dimensional representation of the signal is introduced which is less deformed by the analysis system properties than the usual representation, and which moreover has the advantage of being obtainable practically in real time [fr

  20. Measurand transient signal suppressor

    Science.gov (United States)

    Bozeman, Richard J., Jr. (Inventor)

    1994-01-01

    A transient signal suppressor for use in a controls system which is adapted to respond to a change in a physical parameter whenever it crosses a predetermined threshold value in a selected direction of increasing or decreasing values with respect to the threshold value and is sustained for a selected discrete time interval is presented. The suppressor includes a sensor transducer for sensing the physical parameter and generating an electrical input signal whenever the sensed physical parameter crosses the threshold level in the selected direction. A manually operated switch is provided for adapting the suppressor to produce an output drive signal whenever the physical parameter crosses the threshold value in the selected direction of increasing or decreasing values. A time delay circuit is selectively adjustable for suppressing the transducer input signal for a preselected one of a plurality of available discrete suppression time and producing an output signal only if the input signal is sustained for a time greater than the selected suppression time. An electronic gate is coupled to receive the transducer input signal and the timer output signal and produce an output drive signal for energizing a control relay whenever the transducer input is a non-transient signal which is sustained beyond the selected time interval.

  1. Wnt signaling in cancer

    Science.gov (United States)

    Zhan, T; Rindtorff, N; Boutros, M

    2017-01-01

    Wnt signaling is one of the key cascades regulating development and stemness, and has also been tightly associated with cancer. The role of Wnt signaling in carcinogenesis has most prominently been described for colorectal cancer, but aberrant Wnt signaling is observed in many more cancer entities. Here, we review current insights into novel components of Wnt pathways and describe their impact on cancer development. Furthermore, we highlight expanding functions of Wnt signaling for both solid and liquid tumors. We also describe current findings how Wnt signaling affects maintenance of cancer stem cells, metastasis and immune control. Finally, we provide an overview of current strategies to antagonize Wnt signaling in cancer and challenges that are associated with such approaches. PMID:27617575

  2. Cooperative ethylene receptor signaling

    OpenAIRE

    Liu, Qian; Wen, Chi-Kuang

    2012-01-01

    The gaseous plant hormone ethylene is perceived by a family of five ethylene receptor members in the dicotyledonous model plant Arabidopsis. Genetic and biochemical studies suggest that the ethylene response is suppressed by ethylene receptor complexes, but the biochemical nature of the receptor signal is unknown. Without appropriate biochemical measures to trace the ethylene receptor signal and quantify the signal strength, the biological significance of the modulation of ethylene responses ...

  3. Traffic signal synchronization.

    Science.gov (United States)

    Huang, Ding-wei; Huang, Wei-neng

    2003-05-01

    The benefits of traffic signal synchronization are examined within the cellular automata approach. The microsimulations of traffic flow are obtained with different settings of signal period T and time delay delta. Both numerical results and analytical approximations are presented. For undersaturated traffic, the green-light wave solutions can be realized. For saturated traffic, the correlation among the traffic signals has no effect on the throughput. For oversaturated traffic, the benefits of synchronization are manifest only when stochastic noise is suppressed.

  4. Digital signal processing the Tevatron BPM signals

    International Nuclear Information System (INIS)

    Cancelo, G.; James, E.; Wolbers, S.

    2005-01-01

    The Beam Position Monitor (TeV BPM) readout system at Fermilab's Tevatron has been updated and is currently being commissioned. The new BPMs use new analog and digital hardware to achieve better beam position measurement resolution. The new system reads signals from both ends of the existing directional stripline pickups to provide simultaneous proton and antiproton measurements. The signals provided by the two ends of the BPM pickups are processed by analog band-pass filters and sampled by 14-bit ADCs at 74.3MHz. A crucial part of this work has been the design of digital filters that process the signal. This paper describes the digital processing and estimation techniques used to optimize the beam position measurement. The BPM electronics must operate in narrow-band and wide-band modes to enable measurements of closed-orbit and turn-by-turn positions. The filtering and timing conditions of the signals are tuned accordingly for the operational modes. The analysis and the optimized result for each mode are presented

  5. Nichtkontinuierliche (zeitdiskrete) Signale

    Science.gov (United States)

    Plaßmann, Wilfried

    Zeitdiskrete Signale werden häufig aus zeitkontinuierlichen Signalen durch Abtastung erzeugt. Dass beide Signale gleichwertig sind, zeigt das Abtasttheorem (Kap. 116) von Shannon, sofern die Bedingung nach (116.2), f_{ab}≈(2{,}2 {\\ldots} 4)\\cdot fg) eingehalten wird. Digitale Signale haben Vorteile: Einfache Speicherung, Weiterverarbeitung in Rechnern, wenig störanfällige Übertragung. Für die Bearbeitung dieser Signale dienen die im Kapitel dargestellten Hilfsmittel: Diskrete Fouriertransformation; Schnelle Fouriertransformation; z-Transformation: Darstellung, Sätze zur z-Transformation, Korrespondenzen zu Zeitfunktionen, Beispiele.

  6. Biomedical signals and systems

    CERN Document Server

    Tranquillo, Joseph V

    2013-01-01

    Biomedical Signals and Systems is meant to accompany a one-semester undergraduate signals and systems course. It may also serve as a quick-start for graduate students or faculty interested in how signals and systems techniques can be applied to living systems. The biological nature of the examples allows for systems thinking to be applied to electrical, mechanical, fluid, chemical, thermal and even optical systems. Each chapter focuses on a topic from classic signals and systems theory: System block diagrams, mathematical models, transforms, stability, feedback, system response, control, time

  7. Radiation signal processing system

    International Nuclear Information System (INIS)

    Bennett, M.; Knoll, G.; Strange, D.

    1980-01-01

    An improved signal processing system for radiation imaging apparatus comprises: a radiation transducer producing transducer signals proportional to apparent spatial coordinates of detected radiation events; means for storing true spatial coordinates corresponding to a plurality of predetermined apparent spatial coordinates relative to selected detected radiation events said means for storing responsive to said transducer signal and producing an output signal representative of said true spatial coordinates; and means for interpolating the true spatial coordinates of the detected radiation events located intermediate the stored true spatial coordinates, said means for interpolating communicating with said means for storing

  8. Digital signal processing

    CERN Document Server

    O'Shea, Peter; Hussain, Zahir M

    2011-01-01

    In three parts, this book contributes to the advancement of engineering education and that serves as a general reference on digital signal processing. Part I presents the basics of analog and digital signals and systems in the time and frequency domain. It covers the core topics: convolution, transforms, filters, and random signal analysis. It also treats important applications including signal detection in noise, radar range estimation for airborne targets, binary communication systems, channel estimation, banking and financial applications, and audio effects production. Part II considers sel

  9. Drought Signaling in Plants

    Indian Academy of Sciences (India)

    depending upon the source and nature of signaling: (i) hormone signal, (ii) .... plants to regulate the rate of transpiration through minor structural .... cell has to keep spending energy (in the form of A TP) to maintain a .... enzymes and proteins in the regulation of cellular metabolism can be determined by either inactivating.

  10. Ubiquitination in apoptosis signaling

    NARCIS (Netherlands)

    van de Kooij, L.W.

    2014-01-01

    The work described in this thesis focuses on ubiquitination and protein degradation, with an emphasis on how these processes regulate apoptosis signaling. More specifically, our aims were: 1. To increase the understanding of ubiquitin-mediated regulation of apoptosis signaling. 2. To identify the E3

  11. Multiresolution signal decomposition schemes

    NARCIS (Netherlands)

    J. Goutsias (John); H.J.A.M. Heijmans (Henk)

    1998-01-01

    textabstract[PNA-R9810] Interest in multiresolution techniques for signal processing and analysis is increasing steadily. An important instance of such a technique is the so-called pyramid decomposition scheme. This report proposes a general axiomatic pyramid decomposition scheme for signal analysis

  12. SignalR blueprints

    CERN Document Server

    Ingebrigtsen, Einar

    2015-01-01

    This book is designed for software developers, primarily those with knowledge of C#, .NET, and JavaScript. Good knowledge and understanding of SignalR is assumed to allow efficient programming of core elements and applications in SignalR.

  13. Optimal fault signal estimation

    NARCIS (Netherlands)

    Stoorvogel, Antonie Arij; Niemann, H.H.; Saberi, A.; Sannuti, P.

    2002-01-01

    We consider here both fault identification and fault signal estimation. Regarding fault identification, we seek either exact or almost fault identification. On the other hand, regarding fault signal estimation, we seek either $H_2$ optimal, $H_2$ suboptimal or Hinfinity suboptimal estimation. By

  14. Signal sampling circuit

    NARCIS (Netherlands)

    Louwsma, S.M.; Vertregt, Maarten

    2011-01-01

    A sampling circuit for sampling a signal is disclosed. The sampling circuit comprises a plurality of sampling channels adapted to sample the signal in time-multiplexed fashion, each sampling channel comprising a respective track-and-hold circuit connected to a respective analogue to digital

  15. Signal sampling circuit

    NARCIS (Netherlands)

    Louwsma, S.M.; Vertregt, Maarten

    2010-01-01

    A sampling circuit for sampling a signal is disclosed. The sampling circuit comprises a plurality of sampling channels adapted to sample the signal in time-multiplexed fashion, each sampling channel comprising a respective track-and-hold circuit connected to a respective analogue to digital

  16. Bioelectric Signal Measuring System

    Science.gov (United States)

    Guadarrama-Santana, A.; Pólo-Parada, L.; García-Valenzuela, A.

    2015-01-01

    We describe a low noise measuring system based on interdigitated electrodes for sensing bioelectrical signals. The system registers differential voltage measurements in order of microvolts. The base noise during measurements was in nanovolts and thus, the sensing signals presented a very good signal to noise ratio. An excitation voltage of 1Vrms with 10 KHz frequency was applied to an interdigitated capacitive sensor without a material under test and to a mirror device simultaneously. The output signals of both devices was then subtracted in order to obtain an initial reference value near cero volts and reduce parasitic capacitances due to the electronics, wiring and system hardware as well. The response of the measuring system was characterized by monitoring temporal bioelectrical signals in real time of biological materials such as embryo chicken heart cells and bovine suprarenal gland cells.

  17. Acoustic Signals and Systems

    DEFF Research Database (Denmark)

    2008-01-01

    The Handbook of Signal Processing in Acoustics will compile the techniques and applications of signal processing as they are used in the many varied areas of Acoustics. The Handbook will emphasize the interdisciplinary nature of signal processing in acoustics. Each Section of the Handbook...... will present topics on signal processing which are important in a specific area of acoustics. These will be of interest to specialists in these areas because they will be presented from their technical perspective, rather than a generic engineering approach to signal processing. Non-specialists, or specialists...... from different areas, will find the self-contained chapters accessible and will be interested in the similarities and differences between the approaches and techniques used in different areas of acoustics....

  18. Molecular and Cellular Signaling

    CERN Document Server

    Beckerman, Martin

    2005-01-01

    A small number of signaling pathways, no more than a dozen or so, form a control layer that is responsible for all signaling in and between cells of the human body. The signaling proteins belonging to the control layer determine what kinds of cells are made during development and how they function during adult life. Malfunctions in the proteins belonging to the control layer are responsible for a host of human diseases ranging from neurological disorders to cancers. Most drugs target components in the control layer, and difficulties in drug design are intimately related to the architecture of the control layer. Molecular and Cellular Signaling provides an introduction to molecular and cellular signaling in biological systems with an emphasis on the underlying physical principles. The text is aimed at upper-level undergraduates, graduate students and individuals in medicine and pharmacology interested in broadening their understanding of how cells regulate and coordinate their core activities and how diseases ...

  19. Adaptive signal processor

    Energy Technology Data Exchange (ETDEWEB)

    Walz, H.V.

    1980-07-01

    An experimental, general purpose adaptive signal processor system has been developed, utilizing a quantized (clipped) version of the Widrow-Hoff least-mean-square adaptive algorithm developed by Moschner. The system accommodates 64 adaptive weight channels with 8-bit resolution for each weight. Internal weight update arithmetic is performed with 16-bit resolution, and the system error signal is measured with 12-bit resolution. An adapt cycle of adjusting all 64 weight channels is accomplished in 8 ..mu..sec. Hardware of the signal processor utilizes primarily Schottky-TTL type integrated circuits. A prototype system with 24 weight channels has been constructed and tested. This report presents details of the system design and describes basic experiments performed with the prototype signal processor. Finally some system configurations and applications for this adaptive signal processor are discussed.

  20. Adaptive signal processor

    International Nuclear Information System (INIS)

    Walz, H.V.

    1980-07-01

    An experimental, general purpose adaptive signal processor system has been developed, utilizing a quantized (clipped) version of the Widrow-Hoff least-mean-square adaptive algorithm developed by Moschner. The system accommodates 64 adaptive weight channels with 8-bit resolution for each weight. Internal weight update arithmetic is performed with 16-bit resolution, and the system error signal is measured with 12-bit resolution. An adapt cycle of adjusting all 64 weight channels is accomplished in 8 μsec. Hardware of the signal processor utilizes primarily Schottky-TTL type integrated circuits. A prototype system with 24 weight channels has been constructed and tested. This report presents details of the system design and describes basic experiments performed with the prototype signal processor. Finally some system configurations and applications for this adaptive signal processor are discussed

  1. Zinc Signals and Immunity.

    Science.gov (United States)

    Maywald, Martina; Wessels, Inga; Rink, Lothar

    2017-10-24

    Zinc homeostasis is crucial for an adequate function of the immune system. Zinc deficiency as well as zinc excess result in severe disturbances in immune cell numbers and activities, which can result in increased susceptibility to infections and development of especially inflammatory diseases. This review focuses on the role of zinc in regulating intracellular signaling pathways in innate as well as adaptive immune cells. Main underlying molecular mechanisms and targets affected by altered zinc homeostasis, including kinases, caspases, phosphatases, and phosphodiesterases, will be highlighted in this article. In addition, the interplay of zinc homeostasis and the redox metabolism in affecting intracellular signaling will be emphasized. Key signaling pathways will be described in detail for the different cell types of the immune system. In this, effects of fast zinc flux, taking place within a few seconds to minutes will be distinguish from slower types of zinc signals, also designated as "zinc waves", and late homeostatic zinc signals regarding prolonged changes in intracellular zinc.

  2. Orexin/Hypocretin Signaling.

    Science.gov (United States)

    Kukkonen, Jyrki P

    Orexin/hypocretin peptide (orexin-A and orexin-B) signaling is believed to take place via the two G-protein-coupled receptors (GPCRs), named OX 1 and OX 2 orexin receptors, as described in the previous chapters. Signaling of orexin peptides has been investigated in diverse endogenously orexin receptor-expressing cells - mainly neurons but also other types of cells - and in recombinant cells expressing the receptors in a heterologous manner. Findings in the different systems are partially convergent but also indicate cellular background-specific signaling. The general picture suggests an inherently high degree of diversity in orexin receptor signaling.In the current chapter, I present orexin signaling on the cellular and molecular levels. Discussion of the connection to (potential) physiological orexin responses is only brief since these are in focus of other chapters in this book. The same goes for the post-synaptic signaling mechanisms, which are dealt with in Burdakov: Postsynaptic actions of orexin. The current chapter is organized according to the tissue type, starting from the central nervous system. Finally, receptor signaling pathways are discussed across tissues, cell types, and even species.

  3. Signal flow analysis

    CERN Document Server

    Abrahams, J R; Hiller, N

    1965-01-01

    Signal Flow Analysis provides information pertinent to the fundamental aspects of signal flow analysis. This book discusses the basic theory of signal flow graphs and shows their relation to the usual algebraic equations.Organized into seven chapters, this book begins with an overview of properties of a flow graph. This text then demonstrates how flow graphs can be applied to a wide range of electrical circuits that do not involve amplification. Other chapters deal with the parameters as well as circuit applications of transistors. This book discusses as well the variety of circuits using ther

  4. Genetic Algorithms for Optimization of Machine-learning Models and their Applications in Bioinformatics

    KAUST Repository

    Magana-Mora, Arturo

    2017-01-01

    Finally, the third challenge is the accurate prediction of polyadenylation signals in human genomic DNA. To achieve this, we analyzed genomic DNA sequences for the 12 most frequent polyadenylation signal variants and proposed a new set of features that may contribute to the understanding of the polyadenylation process. We derived Omni-PolyA, a model, and tool based on OmniGA for the prediction of the polyadenylation signals. Results show that Omni-PolyA significantly reduced the average classification error rate compared to the state-of-the-art results.

  5. Underwater Acoustic Signal Processing

    National Research Council Canada - National Science Library

    Culver, Richard L; Sibul, Leon H; Bradley, David L

    2007-01-01

    .... The research is directed toward passive sonar detection and classification, continuous wave (CW) and broadband signals, shallow water operation, both platform-mounted and distributed systems, and frequencies below 1 kHz...

  6. Signals and systems

    CERN Document Server

    Rao, K Deergha

    2018-01-01

    This textbook covers the fundamental theories of signals and systems analysis, while incorporating recent developments from integrated circuits technology into its examples. Starting with basic definitions in signal theory, the text explains the properties of continuous-time and discrete-time systems and their representation by differential equations and state space. From those tools, explanations for the processes of Fourier analysis, the Laplace transform, and the z-Transform provide new ways of experimenting with different kinds of time systems. The text also covers the separate classes of analog filters and their uses in signal processing applications. Intended for undergraduate electrical engineering students, chapter sections include exercise for review and practice for the systems concepts of each chapter. Along with exercises, the text includes MATLAB-based examples to allow readers to experiment with signals and systems code on their own. An online repository of the MATLAB code from this textbook can...

  7. Topological signal processing

    CERN Document Server

    Robinson, Michael

    2014-01-01

    Signal processing is the discipline of extracting information from collections of measurements. To be effective, the measurements must be organized and then filtered, detected, or transformed to expose the desired information.  Distortions caused by uncertainty, noise, and clutter degrade the performance of practical signal processing systems. In aggressively uncertain situations, the full truth about an underlying signal cannot be known.  This book develops the theory and practice of signal processing systems for these situations that extract useful, qualitative information using the mathematics of topology -- the study of spaces under continuous transformations.  Since the collection of continuous transformations is large and varied, tools which are topologically-motivated are automatically insensitive to substantial distortion. The target audience comprises practitioners as well as researchers, but the book may also be beneficial for graduate students.

  8. Acoustic MIMO signal processing

    CERN Document Server

    Huang, Yiteng; Chen, Jingdong

    2006-01-01

    A timely and important book addressing a variety of acoustic signal processing problems under multiple-input multiple-output (MIMO) scenarios. It uniquely investigates these problems within a unified framework offering a novel and penetrating analysis.

  9. Ultrahigh bandwidth signal processing

    DEFF Research Database (Denmark)

    Oxenløwe, Leif Katsuo

    2016-01-01

    Optical time lenses have proven to be very versatile for advanced optical signal processing. Based on a controlled interplay between dispersion and phase-modulation by e.g. four-wave mixing, the processing is phase-preserving, an hence useful for all types of data signals including coherent multi......-level modulation founats. This has enabled processing of phase-modulated spectrally efficient data signals, such as orthogonal frequency division multiplexed (OFDM) signa In that case, a spectral telescope system was used, using two time lenses with different focal lengths (chirp rates), yielding a spectral...... regeneratio These operations require a broad bandwidth nonlinear platform, and novel photonic integrated nonlinear platform like aluminum gallium arsenide nano-waveguides used for 1.28 Tbaud optical signal processing will be described....

  10. Traffic Signal Cycle Lengths

    Data.gov (United States)

    Town of Chapel Hill, North Carolina — Traffic signal location list for the town of Chapel Hill. This data set includes light cycle information as well as as intersection information.The Town of Chapel...

  11. Foundations of signal processing

    CERN Document Server

    Vetterli, Martin; Goyal, Vivek K

    2014-01-01

    This comprehensive and engaging textbook introduces the basic principles and techniques of signal processing, from the fundamental ideas of signals and systems theory to real-world applications. Students are introduced to the powerful foundations of modern signal processing, including the basic geometry of Hilbert space, the mathematics of Fourier transforms, and essentials of sampling, interpolation, approximation and compression. The authors discuss real-world issues and hurdles to using these tools, and ways of adapting them to overcome problems of finiteness and localisation, the limitations of uncertainty and computational costs. Standard engineering notation is used throughout, making mathematical examples easy for students to follow, understand and apply. It includes over 150 homework problems and over 180 worked examples, specifically designed to test and expand students' understanding of the fundamentals of signal processing, and is accompanied by extensive online materials designed to aid learning, ...

  12. Source of seismic signals

    Energy Technology Data Exchange (ETDEWEB)

    Frankovskii, B.A.; Khor' yakov, K.A.

    1980-08-30

    Patented is a source of seismic signals consisting of a shock generator with a basic low-voltage and auxillary high-voltage stator coils, a capacitive transformer and control switches. To increase the amplitude of signal excitation a condensor battery and auxillary commutator are introduced into the device, which are connected in parallel and serially into the circuit of the main low-voltage stator coil.

  13. Redox signaling in plants.

    Science.gov (United States)

    Foyer, Christine H; Noctor, Graham

    2013-06-01

    Our aim is to deliver an authoritative and challenging perspective of current concepts in plant redox signaling, focusing particularly on the complex interface between the redox and hormone-signaling pathways that allow precise control of plant growth and defense in response to metabolic triggers and environmental constraints and cues. Plants produce significant amounts of singlet oxygen and other reactive oxygen species (ROS) as a result of photosynthetic electron transport and metabolism. Such pathways contribute to the compartment-specific redox-regulated signaling systems in plant cells that convey information to the nucleus to regulate gene expression. Like the chloroplasts and mitochondria, the apoplast-cell wall compartment makes a significant contribution to the redox signaling network, but unlike these organelles, the apoplast has a low antioxidant-buffering capacity. The respective roles of ROS, low-molecular antioxidants, redox-active proteins, and antioxidant enzymes are considered in relation to the functions of plant hormones such as salicylic acid, jasmonic acid, and auxin, in the composite control of plant growth and defense. Regulation of redox gradients between key compartments in plant cells such as those across the plasma membrane facilitates flexible and multiple faceted opportunities for redox signaling that spans the intracellular and extracellular environments. In conclusion, plants are recognized as masters of the art of redox regulation that use oxidants and antioxidants as flexible integrators of signals from metabolism and the environment.

  14. Transient-Switch-Signal Suppressor

    Science.gov (United States)

    Bozeman, Richard J., Jr.

    1995-01-01

    Circuit delays transmission of switch-opening or switch-closing signal until after preset suppression time. Used to prevent transmission of undesired momentary switch signal. Basic mode of operation simple. Beginning of switch signal initiates timing sequence. If switch signal persists after preset suppression time, circuit transmits switch signal to external circuitry. If switch signal no longer present after suppression time, switch signal deemed transient, and circuit does not pass signal on to external circuitry, as though no transient switch signal. Suppression time preset at value large enough to allow for damping of underlying pressure wave or other mechanical transient.

  15. Digital Signal Processing applied to Physical Signals

    CERN Document Server

    Alberto, Diego; Musa, L

    2011-01-01

    It is well known that many of the scientific and technological discoveries of the XXI century will depend on the capability of processing and understanding a huge quantity of data. With the advent of the digital era, a fully digital and automated treatment can be designed and performed. From data mining to data compression, from signal elaboration to noise reduction, a processing is essential to manage and enhance features of interest after every data acquisition (DAQ) session. In the near future, science will go towards interdisciplinary research. In this work there will be given an example of the application of signal processing to different fields of Physics from nuclear particle detectors to biomedical examinations. In Chapter 1 a brief description of the collaborations that allowed this thesis is given, together with a list of the publications co-produced by the author in these three years. The most important notations, definitions and acronyms used in the work are also provided. In Chapter 2, the last r...

  16. Cellular signalling properties in microcircuits

    DEFF Research Database (Denmark)

    Toledo-Rodriguez, Maria; El Manira, Abdeljabbar; Wallén, Peter

    2005-01-01

    Molecules and cells are the signalling elements in microcircuits. Recent studies have uncovered bewildering diversity in postsynaptic signalling properties in all areas of the vertebrate nervous system. Major effort is now being invested in establishing the specialized signalling properties...

  17. VLSI signal processing technology

    CERN Document Server

    Swartzlander, Earl

    1994-01-01

    This book is the first in a set of forthcoming books focussed on state-of-the-art development in the VLSI Signal Processing area. It is a response to the tremendous research activities taking place in that field. These activities have been driven by two factors: the dramatic increase in demand for high speed signal processing, especially in consumer elec­ tronics, and the evolving microelectronic technologies. The available technology has always been one of the main factors in determining al­ gorithms, architectures, and design strategies to be followed. With every new technology, signal processing systems go through many changes in concepts, design methods, and implementation. The goal of this book is to introduce the reader to the main features of VLSI Signal Processing and the ongoing developments in this area. The focus of this book is on: • Current developments in Digital Signal Processing (DSP) pro­ cessors and architectures - several examples and case studies of existing DSP chips are discussed in...

  18. Signal integrity characterization techniques

    CERN Document Server

    Bogatin, Eric

    2009-01-01

    "Signal Integrity Characterization Techniques" addresses the gap between traditional digital and microwave curricula all while focusing on a practical and intuitive understanding of signal integrity effects within the data transmission channel. High-speed interconnects such as connectors, PCBs, cables, IC packages, and backplanes are critical elements of differential channels that must be designed using today's most powerful analysis and characterization tools.Both measurements and simulation must be done on the device under test, and both activities must yield data that correlates with each other. Most of this book focuses on real-world applications of signal integrity measurements - from backplane for design challenges to error correction techniques to jitter measurement technologies. The authors' approach wisely addresses some of these new high-speed technologies, and it also provides valuable insight into its future direction and will teach the reader valuable lessons on the industry.

  19. Quantum signaling game

    International Nuclear Information System (INIS)

    Frackiewicz, Piotr

    2014-01-01

    We present a quantum approach to a signaling game; a special kind of extensive game of incomplete information. Our model is based on quantum schemes for games in strategic form where players perform unitary operators on their own qubits of some fixed initial state and the payoff function is given by a measurement on the resulting final state. We show that the quantum game induced by our scheme coincides with a signaling game as a special case and outputs nonclassical results in general. As an example, we consider a quantum extension of the signaling game in which the chance move is a three-parameter unitary operator whereas the players' actions are equivalent to classical ones. In this case, we study the game in terms of Nash equilibria and refine the pure Nash equilibria adapting to the quantum game the notion of a weak perfect Bayesian equilibrium. (paper)

  20. PKD signaling and pancreatitis

    Science.gov (United States)

    Yuan, Jingzhen; Pandol, Stephen J.

    2016-01-01

    Background Acute pancreatitis is a serious medical disorder with no current therapies directed to the molecular pathogenesis of the disorder. Inflammation, inappropriate intracellular activation of digestive enzymes, and parenchymal acinar cell death by necrosis are the critical pathophysiologic processes of acute pancreatitis. Thus, it is necessary to elucidate the key molecular signals that mediate these pathobiologic processes and develop new therapeutic strategies to attenuate the appropriate signaling pathways in order to improve outcomes for this disease. A novel serine/threonine protein kinase D (PKD) family has emerged as key participants in signal transduction, and this family is increasingly being implicated in the regulation of multiple cellular functions and diseases. Methods This review summarizes recent findings of our group and others regarding the signaling pathway and the biological roles of the PKD family in pancreatic acinar cells. In particular, we highlight our studies of the functions of PKD in several key pathobiologic processes associated with acute pancreatitis in experimental models. Results Our findings reveal that PKD signaling is required for NF-κB activation/inflammation, intracellular zymogen activation, and acinar cell necrosis in rodent experimental pancreatitis. Novel small-molecule PKD inhibitors attenuate the severity of pancreatitis in both in vitro and in vivo experimental models. Further, this review emphasizes our latest advances in the therapeutic application of PKD inhibitors to experimental pancreatitis after the initiation of pancreatitis. Conclusions These novel findings suggest that PKD signaling is a necessary modulator in key initiating pathobiologic processes of pancreatitis, and that it constitutes a novel therapeutic target for treatments of this disorder. PMID:26879861

  1. Signal processing in microdosimetry

    International Nuclear Information System (INIS)

    Arbel, A.

    1984-01-01

    Signals occurring in microdosimetric measurements cover a dynamic range of 100 dB at a counting rate which normally stays below 10 4 but could increase significantly in case of an accident. The need for high resolution at low energies, non-linear signal processing to accommodate the specified dynamic range, easy calibration and thermal stability are conflicting requirements which pose formidable design problems. These problems are reviewed, and a practical approach to their solution is given employing a single processing channel. (author)

  2. Understanding signal integrity

    CERN Document Server

    Thierauf, Stephen C

    2010-01-01

    This unique book provides you with practical guidance on understanding and interpreting signal integrity (SI) performance to help you with your challenging circuit board design projects. You find high-level discussions of important SI concepts presented in a clear and easily accessible format, including question and answer sections and bulleted lists.This valuable resource features rules of thumb and simple equations to help you make estimates of critical signal integrity parameters without using circuit simulators of CAD (computer-aided design). The book is supported with over 120 illustratio

  3. Electronic signal conditioning

    CERN Document Server

    NEWBY, BRUCE

    1994-01-01

    At technician level, brief references to signal conditioning crop up in a fragmented way in various textbooks, but there has been no single textbook, until now!More advanced texts do exist but they are more mathematical and presuppose a higher level of understanding of electronics and statistics. Electronic Signal Conditioning is designed for HNC/D students and City & Guilds Electronics Servicing 2240 Parts 2 & 3. It will also be useful for BTEC National, Advanced GNVQ, A-level electronics and introductory courses at degree level.

  4. TOR signalling in plants.

    Science.gov (United States)

    Rexin, Daniel; Meyer, Christian; Robaglia, Christophe; Veit, Bruce

    2015-08-15

    Although the eukaryotic TOR (target of rapamycin) kinase signalling pathway has emerged as a key player for integrating nutrient-, energy- and stress-related cues with growth and metabolic outputs, relatively little is known of how this ancient regulatory mechanism has been adapted in higher plants. Drawing comparisons with the substantial knowledge base around TOR kinase signalling in fungal and animal systems, functional aspects of this pathway in plants are reviewed. Both conserved and divergent elements are discussed in relation to unique aspects associated with an autotrophic mode of nutrition and adaptive strategies for multicellular development exhibited by plants. © 2015 Authors; published by Portland Press Limited.

  5. Genomic signal processing

    CERN Document Server

    Shmulevich, Ilya

    2007-01-01

    Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

  6. Television picture signal processing

    NARCIS (Netherlands)

    1998-01-01

    Field or frame memories are often used in television receivers for video signal processing functions, such as noise reduction and/or flicker reduction. Television receivers also have graphic features such as teletext, menu-driven control systems, multilingual subtitling, an electronic TV-Guide, etc.

  7. Signals: Applying Academic Analytics

    Science.gov (United States)

    Arnold, Kimberly E.

    2010-01-01

    Academic analytics helps address the public's desire for institutional accountability with regard to student success, given the widespread concern over the cost of higher education and the difficult economic and budgetary conditions prevailing worldwide. Purdue University's Signals project applies the principles of analytics widely used in…

  8. Communication Signals in Lizards.

    Science.gov (United States)

    Carpenter, Charles C.

    1983-01-01

    Discusses mechanisms and functional intent of visual communication signals in iguanid/agamid lizards. Demonstrated that lizards communicate with each other by using pushups and head nods and that each species does this in its own way, conveying different types of information. (JN)

  9. Modeling binaural signal detection

    NARCIS (Netherlands)

    Breebaart, D.J.

    2001-01-01

    With the advent of multimedia technology and powerful signal processing systems, audio processing and reproduction has gained renewed interest. Examples of products that have been developed are audio coding algorithms to efficiently store and transmit music and speech, or audio reproduction systems

  10. Quantum cloning and signaling

    International Nuclear Information System (INIS)

    Simon, C.; Weihs, G.; Zeilinger, A.

    1999-01-01

    We discuss the close connections between cloning of quantum states and superluminal signaling. We present an optimal universal cloning machine based on stimulated emission recently proposed by the authors. As an instructive example, we show how a scheme for superluminal communication based on this cloning machine fails. (Authors)

  11. "Utilizing" signal detection theory.

    Science.gov (United States)

    Lynn, Spencer K; Barrett, Lisa Feldman

    2014-09-01

    What do inferring what a person is thinking or feeling, judging a defendant's guilt, and navigating a dimly lit room have in common? They involve perceptual uncertainty (e.g., a scowling face might indicate anger or concentration, for which different responses are appropriate) and behavioral risk (e.g., a cost to making the wrong response). Signal detection theory describes these types of decisions. In this tutorial, we show how incorporating the economic concept of utility allows signal detection theory to serve as a model of optimal decision making, going beyond its common use as an analytic method. This utility approach to signal detection theory clarifies otherwise enigmatic influences of perceptual uncertainty on measures of decision-making performance (accuracy and optimality) and on behavior (an inverse relationship between bias magnitude and sensitivity optimizes utility). A "utilized" signal detection theory offers the possibility of expanding the phenomena that can be understood within a decision-making framework. © The Author(s) 2014.

  12. Critical nodes in signalling pathways

    DEFF Research Database (Denmark)

    Taniguchi, Cullen M; Emanuelli, Brice; Kahn, C Ronald

    2006-01-01

    Physiologically important cell-signalling networks are complex, and contain several points of regulation, signal divergence and crosstalk with other signalling cascades. Here, we use the concept of 'critical nodes' to define the important junctions in these pathways and illustrate their unique role...... using insulin signalling as a model system....

  13. Sinusoidal Representation of Acoustic Signals

    Science.gov (United States)

    Honda, Masaaki

    Sinusoidal representation of acoustic signals has been an important tool in speech and music processing like signal analysis, synthesis and time scale or pitch modifications. It can be applicable to arbitrary signals, which is an important advantage over other signal representations like physical modeling of acoustic signals. In sinusoidal representation, acoustic signals are composed as sums of sinusoid (sine wave) with different amplitudes, frequencies and phases, which is based on the timedependent short-time Fourier transform (STFT). This article describes the principles of acoustic signal analysis/synthesis based on a sinusoid representation with focus on sine waves with rapidly varying frequency.

  14. The newest digital signal processing

    International Nuclear Information System (INIS)

    Lee, Chae Uk

    2002-08-01

    This book deal with the newest digital signal processing, which contains introduction on conception of digital signal processing, constitution and purpose, signal and system such as signal, continuos signal, discrete signal and discrete system, I/O expression on impress response, convolution, mutual connection of system and frequency character,z transform of definition, range, application of z transform and relationship with laplace transform, Discrete fourier, Fast fourier transform on IDFT algorithm and FFT application, foundation of digital filter of notion, expression, types, frequency characteristic of digital filter and design order of filter, Design order of filter, Design of FIR digital filter, Design of IIR digital filter, Adaptive signal processing, Audio signal processing, video signal processing and application of digital signal processing.

  15. Variable reflectivity signal mirrors and signal response measurements

    International Nuclear Information System (INIS)

    Vine, Glenn de; Shaddock, Daniel A; McClelland, David E

    2002-01-01

    Future gravitational wave detectors will include some form of signal mirror in order to alter the signal response of the device. We introduce interferometer configurations which utilize a variable reflectivity signal mirror allowing a tunable peak frequency and variable signal bandwidth. A detector configured with a Fabry-Perot cavity as the signal mirror is compared theoretically with one using a Michelson interferometer for a signal mirror. A system for the measurement of the interferometer signal responses is introduced. This technique is applied to a power-recycled Michelson interferometer with resonant sideband extraction. We present broadband measurements of the benchtop prototype's signal response for a range of signal cavity detunings. This technique is also applicable to most other gravitational wave detector configurations

  16. Variable reflectivity signal mirrors and signal response measurements

    CERN Document Server

    Vine, G D; McClelland, D E

    2002-01-01

    Future gravitational wave detectors will include some form of signal mirror in order to alter the signal response of the device. We introduce interferometer configurations which utilize a variable reflectivity signal mirror allowing a tunable peak frequency and variable signal bandwidth. A detector configured with a Fabry-Perot cavity as the signal mirror is compared theoretically with one using a Michelson interferometer for a signal mirror. A system for the measurement of the interferometer signal responses is introduced. This technique is applied to a power-recycled Michelson interferometer with resonant sideband extraction. We present broadband measurements of the benchtop prototype's signal response for a range of signal cavity detunings. This technique is also applicable to most other gravitational wave detector configurations.

  17. Lymphocyte signaling: beyond knockouts.

    Science.gov (United States)

    Saveliev, Alexander; Tybulewicz, Victor L J

    2009-04-01

    The analysis of lymphocyte signaling was greatly enhanced by the advent of gene targeting, which allows the selective inactivation of a single gene. Although this gene 'knockout' approach is often informative, in many cases, the phenotype resulting from gene ablation might not provide a complete picture of the function of the corresponding protein. If a protein has multiple functions within a single or several signaling pathways, or stabilizes other proteins in a complex, the phenotypic consequences of a gene knockout may manifest as a combination of several different perturbations. In these cases, gene targeting to 'knock in' subtle point mutations might provide more accurate insight into protein function. However, to be informative, such mutations must be carefully based on structural and biophysical data.

  18. Sphingosine signaling and atherogenesis

    DEFF Research Database (Denmark)

    Xu, Cang-bao; Hansen-Schwartz, Jacob; Edvinsson, Lars

    2004-01-01

    Sphingosine-1-phosphate (S1P) has diverse biological functions acting inside cells as a second messenger to regulate cell proliferation and survival, and extracellularly, as a ligand for a group of G protein-coupled receptors (GPCRs) named the endothelial differentiation gene (EDG) family. Five...... closely related GPCRs of EDG family (EDG1, EDG3, EDG5, EDG6, and EDG8) have recently been identified as high-affinity S1P receptors. These receptors are coupled via Gi, Gq, G12/13, and Rho. The signaling pathways are linked to vascular cell migration, proliferation, apoptosis, intracellular Ca2......+ mobilization, and expression of adhesion molecules. The formation of an atherosclerotic lesion occurs through activation of cellular events that include monocyte adhesion to the endothelium and vascular smooth muscle cell (VSMC) migration and proliferation. Thus, S1P signaling may play an important role...

  19. NMR signal transducer

    International Nuclear Information System (INIS)

    Kucheryaev, A.G.; Oliferchuk, N.L.

    1975-01-01

    A signal transducer of nuclear magnetic resonance for simultaneously measuring frequency and intensitivity of two various isotope signals, which are in one specimen is described. The transducer represents radiofrequency circuit with two resonance frequences, which is common for two autodyne generators. To decrease measuring time and to increase recording diagram stability the radiofrequency circuit has LC netork, in the inductivity of which investigated specimen is located; a circuit variable capacity is connected in parallel with one of the autodyne generators. Besides the radiofrequency circuit has an inductance coil in series with a standard specimen inside as well as a variable capacitor connected in parallel with the second autodyne generator. An amplitude of oscillation of each resonance frequency is controlled and adjusted separately. The transducer described can be used for the measurement of a nuclei concentration, isotope concentration and for the spin determination

  20. Biomedical signal analysis

    CERN Document Server

    Rangayyan, Rangaraj M

    2015-01-01

    The book will help assist a reader in the development of techniques for analysis of biomedical signals and computer aided diagnoses with a pedagogical examination of basic and advanced topics accompanied by over 350 figures and illustrations. Wide range of filtering techniques presented to address various applications. 800 mathematical expressions and equations. Practical questions, problems and laboratory exercises. Includes fractals and chaos theory with biomedical applications.

  1. Calcium signaling in liver.

    Science.gov (United States)

    Gaspers, Lawrence D; Thomas, Andrew P

    2005-01-01

    In hepatocytes, hormones linked to the formation of the second messenger inositol 1,4,5-trisphosphate (InsP3) evoke transient increases or spikes in cytosolic free calcium ([Ca2+]i), that increase in frequency with the agonist concentration. These oscillatory Ca2+ signals are thought to transmit the information encoded in the extracellular stimulus to down-stream Ca2+-sensitive metabolic processes. We have utilized both confocal and wide field fluorescence microscopy techniques to study the InsP3-dependent signaling pathway at the cellular and subcellular levels in the intact perfused liver. Typically InsP3-dependent [Ca2+]i spikes manifest as Ca2+ waves that propagate throughout the entire cytoplasm and nucleus, and in the intact liver these [Ca2+]i increases are conveyed through gap junctions to encompass entire lobular units. The translobular movement of Ca2+ provides a means to coordinate the function of metabolic zones of the lobule and thus, liver function. In this article, we describe the characteristics of agonist-evoked [Ca2+]i signals in the liver and discuss possible mechanisms to explain the propagation of intercellular Ca2+ waves in the intact organ.

  2. Biomedical signal and image processing

    CERN Document Server

    Najarian, Kayvan

    2012-01-01

    INTRODUCTION TO DIGITAL SIGNAL AND IMAGE PROCESSINGSignals and Biomedical Signal ProcessingIntroduction and OverviewWhat is a ""Signal""?Analog, Discrete, and Digital SignalsProcessing and Transformation of SignalsSignal Processing for Feature ExtractionSome Characteristics of Digital ImagesSummaryProblemsFourier TransformIntroduction and OverviewOne-Dimensional Continuous Fourier TransformSampling and NYQUIST RateOne-Dimensional Discrete Fourier TransformTwo-Dimensional Discrete Fourier TransformFilter DesignSummaryProblemsImage Filtering, Enhancement, and RestorationIntroduction and Overview

  3. Signal multiplexing scheme for LINAC

    International Nuclear Information System (INIS)

    Sujo, C.I.; Mohan, Shyam; Joshi, Gopal; Singh, S.K.; Karande, Jitendra

    2004-01-01

    For the proper operation of the LINAC some signals, RF (radio frequency) as well as LF (low frequency) have to be available at the Master Control Station (MCS). These signals are needed to control, calibrate and characterize the RF fields in the resonators. This can be achieved by proper multiplexing of various signals locally and then routing the selected signals to the MCS. A multiplexing scheme has been designed and implemented, which will allow the signals from the selected cavity to the MCS. High isolation between channels and low insertion loss for a given signal are important issues while selecting the multiplexing scheme. (author)

  4. Pathophysiology of Glucocorticoid Signaling.

    Science.gov (United States)

    Vitellius, Géraldine; Trabado, Séverine; Bouligand, Jérôme; Delemer, Brigitte; Lombès, Marc

    2018-06-01

    Glucocorticoids (GC), such as cortisol or dexamethasone, control various physiological functions, notably those involved in development, metabolism, inflammatory processes and stress, and exert most of their effects upon binding to the glucocorticoid receptor (GR, encoded by NR3C1 gene). GC signaling follows several consecutive steps leading to target gene transactivation, including ligand binding, nuclear translocation of ligand-activated GR complexes, DNA binding, coactivator interaction and recruitment of functional transcriptional machinery. Any step may be impaired and may account for altered GC signaling. Partial or generalized glucocorticoid resistance syndrome may result in a reduced level of functional GR, a decreased hormone affinity and binding, a defect in nuclear GR translocation, a decrease or lack of DNA binding and/or post-transcriptional GR modifications. To date, 26 loss-of-function NR3C1 mutations have been reported in the context of hypertension, hirsutism, adrenal hyperplasia or metabolic disorders. These clinical signs are generally associated with biological features including hypercortisolism without negative regulatory feedback loop on the hypothalamic-pituitary-adrenal axis. Patients had often low plasma aldosterone and renin levels despite hypertension. Only one GR gain-of-function mutation has been described associating Cushing's syndrome phenotype with normal urinary-free cortisol. Some GR polymorphisms (ER22/23EK, GR-9β) have been linked to glucocorticoid resistance and a healthier metabolic profile whereas some others seemed to be associated with GC hypersensitivity (N363S, BclI), increasing cardiovascular risk (diabetes type 2, visceral obesity). This review focuses on the earlier findings on the pathophysiology of GR signaling and presents criteria facilitating identification of novel NR3C1 mutations in selected patients. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

  5. Purinergic Signalling: Therapeutic Developments

    Directory of Open Access Journals (Sweden)

    Geoffrey Burnstock

    2017-09-01

    Full Text Available Purinergic signalling, i.e., the role of nucleotides as extracellular signalling molecules, was proposed in 1972. However, this concept was not well accepted until the early 1990’s when receptor subtypes for purines and pyrimidines were cloned and characterised, which includes four subtypes of the P1 (adenosine receptor, seven subtypes of P2X ion channel receptors and 8 subtypes of the P2Y G protein-coupled receptor. Early studies were largely concerned with the physiology, pharmacology and biochemistry of purinergic signalling. More recently, the focus has been on the pathophysiology and therapeutic potential. There was early recognition of the use of P1 receptor agonists for the treatment of supraventricular tachycardia and A2A receptor antagonists are promising for the treatment of Parkinson’s disease. Clopidogrel, a P2Y12 antagonist, is widely used for the treatment of thrombosis and stroke, blocking P2Y12 receptor-mediated platelet aggregation. Diquafosol, a long acting P2Y2 receptor agonist, is being used for the treatment of dry eye. P2X3 receptor antagonists have been developed that are orally bioavailable and stable in vivo and are currently in clinical trials for the treatment of chronic cough, bladder incontinence, visceral pain and hypertension. Antagonists to P2X7 receptors are being investigated for the treatment of inflammatory disorders, including neurodegenerative diseases. Other investigations are in progress for the use of purinergic agents for the treatment of osteoporosis, myocardial infarction, irritable bowel syndrome, epilepsy, atherosclerosis, depression, autism, diabetes, and cancer.

  6. Phonocardiography Signal Processing

    CERN Document Server

    Abbas, Abbas K

    2009-01-01

    The auscultation method is an important diagnostic indicator for hemodynamic anomalies. Heart sound classification and analysis play an important role in the auscultative diagnosis. The term phonocardiography refers to the tracing technique of heart sounds and the recording of cardiac acoustics vibration by means of a microphone-transducer. Therefore, understanding the nature and source of this signal is important to give us a tendency for developing a competent tool for further analysis and processing, in order to enhance and optimize cardiac clinical diagnostic approach. This book gives the

  7. Nichtperiodische zeitkontinuierliche Signale

    Science.gov (United States)

    Plaßmann, Wilfried

    Nichtperiodische Signale haben eine große Bedeutung für die Nachrichten- und Datenübertragung, weil Information nur in nichtdeterministischen Signalen enthalten ist (Teil "Nachrichtentechnik", Abschn. 92.4.1). Aber auch für die Energie- und Regelungstechnik sind sie von Interesse, weil sie entweder Ein- und Ausschaltvorgänge erfassen oder den Übergang von einem momentan stationären Zustand in einen neuen darstellen (Kurzschluss im Energieversorgungsnetz, Auftreten einer Störgröße im Regelsystem). Die Fourier- und die Laplacetransformation können bei nichtperiodischen zeitkontinuierlichen Signalen eingesetzt werden.

  8. Generation of earthquake signals

    International Nuclear Information System (INIS)

    Kjell, G.

    1994-01-01

    Seismic verification can be performed either as a full scale test on a shaker table or as numerical calculations. In both cases it is necessary to have an earthquake acceleration time history. This report describes generation of such time histories by filtering white noise. Analogue and digital filtering methods are compared. Different methods of predicting the response spectrum of a white noise signal filtered by a band-pass filter are discussed. Prediction of both the average response level and the statistical variation around this level are considered. Examples with both the IEEE 301 standard response spectrum and a ground spectrum suggested for Swedish nuclear power stations are included in the report

  9. Multiscale Signal Analysis and Modeling

    CERN Document Server

    Zayed, Ahmed

    2013-01-01

    Multiscale Signal Analysis and Modeling presents recent advances in multiscale analysis and modeling using wavelets and other systems. This book also presents applications in digital signal processing using sampling theory and techniques from various function spaces, filter design, feature extraction and classification, signal and image representation/transmission, coding, nonparametric statistical signal processing, and statistical learning theory. This book also: Discusses recently developed signal modeling techniques, such as the multiscale method for complex time series modeling, multiscale positive density estimations, Bayesian Shrinkage Strategies, and algorithms for data adaptive statistics Introduces new sampling algorithms for multidimensional signal processing Provides comprehensive coverage of wavelets with presentations on waveform design and modeling, wavelet analysis of ECG signals and wavelet filters Reviews features extraction and classification algorithms for multiscale signal and image proce...

  10. A Serpentine Way to Signaling

    Indian Academy of Sciences (India)

    IAS Admin

    the cell. The receptor transfers the signal to intracellular proteins ... and molecular mechanisms of GPCR signaling and how this discovery impacts ..... stabilize GPCR–G-protein interaction and resolve dynamics of ... elucidation stages. Kobilka.

  11. Biological signals classification and analysis

    CERN Document Server

    Kiasaleh, Kamran

    2015-01-01

    This authored monograph presents key aspects of signal processing analysis in the biomedical arena. Unlike wireless communication systems, biological entities produce signals with underlying nonlinear, chaotic nature that elude classification using the standard signal processing techniques, which have been developed over the past several decades for dealing primarily with standard communication systems. This book separates what is random from that which appears to be random, and yet is truly deterministic with random appearance. At its core, this work gives the reader a perspective on biomedical signals and the means to classify and process such signals. In particular, a review of random processes along with means to assess the behavior of random signals is also provided. The book also includes a general discussion of biological signals in order to demonstrate the inefficacy of the well-known techniques to correctly extract meaningful information from such signals. Finally, a thorough discussion of recently ...

  12. Two-dimensional signal analysis

    CERN Document Server

    Garello, René

    2010-01-01

    This title sets out to show that 2-D signal analysis has its own role to play alongside signal processing and image processing.Concentrating its coverage on those 2-D signals coming from physical sensors (such as radars and sonars), the discussion explores a 2-D spectral approach but develops the modeling of 2-D signals and proposes several data-oriented analysis techniques for dealing with them. Coverage is also given to potential future developments in this area.

  13. Wireless data signal transmission system

    DEFF Research Database (Denmark)

    2014-01-01

    The present invention relates to a method for providing a radio frequency signal for transmission, a system for providing a radio frequency signal for transmission and a method for wireless data transmission between a transmitter and a receiver.......The present invention relates to a method for providing a radio frequency signal for transmission, a system for providing a radio frequency signal for transmission and a method for wireless data transmission between a transmitter and a receiver....

  14. Astrocytes in endocannabinoid signalling.

    Science.gov (United States)

    Navarrete, Marta; Díez, Adolfo; Araque, Alfonso

    2014-10-19

    Astrocytes are emerging as integral functional components of synapses, responding to synaptically released neurotransmitters and regulating synaptic transmission and plasticity. Thus, they functionally interact with neurons establishing tripartite synapses: a functional concept that refers to the existence of communication between astrocytes and neurons and its crucial role in synaptic function. Here, we discuss recent evidence showing that astrocytes are involved in the endocannabinoid (ECB) system, responding to exogenous cannabinoids as well as ECBs through activation of type 1 cannabinoid receptors, which increase intracellular calcium and stimulate the release of glutamate that modulates synaptic transmission and plasticity. We also discuss the consequences of ECB signalling in tripartite synapses on the astrocyte-mediated regulation of synaptic function, which reveal novel properties of synaptic regulation by ECBs, such as the spatially controlled dual effect on synaptic strength and the lateral potentiation of synaptic efficacy. Finally, we discuss the potential implications of ECB signalling for astrocytes in brain pathology and animal behaviour. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  15. Salicylic acid signaling inhibits apoplastic reactive oxygen species signaling.

    Science.gov (United States)

    Xu, Enjun; Brosché, Mikael

    2014-06-04

    Reactive oxygen species (ROS) are used by plants as signaling molecules during stress and development. Given the amount of possible challenges a plant face from their environment, plants need to activate and prioritize between potentially conflicting defense signaling pathways. Until recently, most studies on signal interactions have focused on phytohormone interaction, such as the antagonistic relationship between salicylic acid (SA)-jasmonic acid and cytokinin-auxin. In this study, we report an antagonistic interaction between SA signaling and apoplastic ROS signaling. Treatment with ozone (O3) leads to a ROS burst in the apoplast and induces extensive changes in gene expression and elevation of defense hormones. However, Arabidopsis thaliana dnd1 (defense no death1) exhibited an attenuated response to O3. In addition, the dnd1 mutant displayed constitutive expression of defense genes and spontaneous cell death. To determine the exact process which blocks the apoplastic ROS signaling, double and triple mutants involved in various signaling pathway were generated in dnd1 background. Simultaneous elimination of SA-dependent and SA-independent signaling components from dnd1 restored its responsiveness to O3. Conversely, pre-treatment of plants with SA or using mutants that constitutively activate SA signaling led to an attenuation of changes in gene expression elicited by O3. Based upon these findings, we conclude that plants are able to prioritize the response between ROS and SA via an antagonistic action of SA and SA signaling on apoplastic ROS signaling.

  16. Signals and systems for dummies

    CERN Document Server

    Wickert, Mark

    2013-01-01

    Getting mixed signals in your signals and systems course? The concepts covered in a typical signals and systems course are often considered by engineering students to be some of the most difficult to master. Thankfully, Signals & Systems For Dummies is your intuitive guide to this tricky course, walking you step-by-step through some of the more complex theories and mathematical formulas in a way that is easy to understand. From Laplace Transforms to Fourier Analyses, Signals & Systems For Dummies explains in plain English the difficult concepts that can trip you up

  17. Detection of signals in noise

    CERN Document Server

    Whalen, Anthony D; Declaris, Nicholas

    1971-01-01

    Detection of Signals in Noise serves as an introduction to the principles and applications of the statistical theory of signal detection. The book discusses probability and random processes; narrowband signals, their complex representation, and their properties described with the aid of the Hilbert transform; and Gaussian-derived processes. The text also describes the application of hypothesis testing for the detection of signals and the fundamentals required for statistical detection of signals in noise. Problem exercises, references, and a supplementary bibliography are included after each c

  18. Multimodal signal variation in space and time : how important is matching a signal with its signaler?

    OpenAIRE

    Taylor, Ryan C.; Klein, Barrett; Stein, Joey; Ryan, Michael J.

    2011-01-01

    Multimodal signals (acoustic+visual) are known to be used by many anuran amphibians during courtship displays. The relative degree to which each signal component influences female mate choice, however, remains poorly understood. In this study we used a robotic frog with an inflating vocal sac and acoustic playbacks to document responses of female túngara frogs to unimodal signal components (acoustic and visual). We then tested female responses to a synchronous multimodal signal. Finally, we t...

  19. Purinergic signalling and diabetes

    DEFF Research Database (Denmark)

    Burnstock, Geoffrey; Novak, Ivana

    2013-01-01

    , and common and divergent roles of receptors for nucleotides and nucleosides in different organ systems will be given. This integrated picture will aid our understanding of the challenges of the potential and currently used drugs targeted to specific organ/cells or disorders associated with diabetes.......The pancreas is an organ with a central role in nutrient breakdown, nutrient sensing and release of hormones regulating whole body nutrient homeostasis. In diabetes mellitus, the balance is broken-cells can be starving in the midst of plenty. There are indications that the incidence of diabetes...... type 1 and 2, and possibly pancreatogenic diabetes, is rising globally. Events leading to insulin secretion and action are complex, but there is emerging evidence that intracellular nucleotides and nucleotides are not only important as intracellular energy molecules but also as extracellular signalling...

  20. Machine intelligence and signal processing

    CERN Document Server

    Vatsa, Mayank; Majumdar, Angshul; Kumar, Ajay

    2016-01-01

    This book comprises chapters on key problems in machine learning and signal processing arenas. The contents of the book are a result of a 2014 Workshop on Machine Intelligence and Signal Processing held at the Indraprastha Institute of Information Technology. Traditionally, signal processing and machine learning were considered to be separate areas of research. However in recent times the two communities are getting closer. In a very abstract fashion, signal processing is the study of operator design. The contributions of signal processing had been to device operators for restoration, compression, etc. Applied Mathematicians were more interested in operator analysis. Nowadays signal processing research is gravitating towards operator learning – instead of designing operators based on heuristics (for example wavelets), the trend is to learn these operators (for example dictionary learning). And thus, the gap between signal processing and machine learning is fast converging. The 2014 Workshop on Machine Intel...

  1. Wavelet analysis for nonstationary signals

    International Nuclear Information System (INIS)

    Penha, Rosani Maria Libardi da

    1999-01-01

    Mechanical vibration signals play an important role in anomalies identification resulting of equipment malfunctioning. Traditionally, Fourier spectral analysis is used where the signals are assumed to be stationary. However, occasional transient impulses and start-up process are examples of nonstationary signals that can be found in mechanical vibrations. These signals can provide important information about the equipment condition, as early fault detection. The Fourier analysis can not adequately be applied to nonstationary signals because the results provide data about the frequency composition averaged over the duration of the signal. In this work, two methods for nonstationary signal analysis are used: Short Time Fourier Transform (STFT) and wavelet transform. The STFT is a method of adapting Fourier spectral analysis for nonstationary application to time-frequency domain. To have a unique resolution throughout the entire time-frequency domain is its main limitation. The wavelet transform is a new analysis technique suitable to nonstationary signals, which handles the STFT drawbacks, providing multi-resolution frequency analysis and time localization in a unique time-scale graphic. The multiple frequency resolutions are obtained by scaling (dilatation/compression) the wavelet function. A comparison of the conventional Fourier transform, STFT and wavelet transform is made applying these techniques to: simulated signals, arrangement rotor rig vibration signal and rotate machine vibration signal Hanning window was used to STFT analysis. Daubechies and harmonic wavelets were used to continuos, discrete and multi-resolution wavelet analysis. The results show the Fourier analysis was not able to detect changes in the signal frequencies or discontinuities. The STFT analysis detected the changes in the signal frequencies, but with time-frequency resolution problems. The wavelet continuos and discrete transform demonstrated to be a high efficient tool to detect

  2. Seismic signals hard clipping overcoming

    Science.gov (United States)

    Olszowa, Paula; Sokolowski, Jakub

    2018-01-01

    In signal processing the clipping is understand as the phenomenon of limiting the signal beyond certain threshold. It is often related to overloading of a sensor. Two particular types of clipping are being recognized: soft and hard. Beyond the limiting value soft clipping reduces the signal real gain while the hard clipping stiffly sets the signal values at the limit. In both cases certain amount of signal information is lost. Obviously if one possess the model which describes the considered signal and the threshold value (which might be slightly more difficult to obtain in the soft clipping case), the attempt of restoring the signal can be made. Commonly it is assumed that the seismic signals take form of an impulse response of some specific system. This may lead to belief that the sine wave may be the most appropriate to fit in the clipping period. However, this should be tested. In this paper the possibility of overcoming the hard clipping in seismic signals originating from a geoseismic station belonging to an underground mine is considered. A set of raw signals will be hard-clipped manually and then couple different functions will be fitted and compared in terms of least squares. The results will be then analysed.

  3. Pleiotrophin Signaling Through PTNR in Breast Cancer

    National Research Council Canada - National Science Library

    Powers, Ciaron

    2001-01-01

    ... of intracellular signaling cascades. The pleiotrophin signaling pathway is known to be important in angiogenesis and breast cancer growth, but the exact mechanisms of pleiotrophin signaling remain undefined...

  4. Digitally programmable signal generator

    International Nuclear Information System (INIS)

    Priatko, G.J.; Kaskey, J.A.

    1988-01-01

    A digitally programmable signal generator (DPSG) includes a first memory from which data is written into a second memory formed of n banks. Each bank includes four memories and a multiplexer, the banks being read once during each time frame, the read-out bits being multiplexed and fed out serially in synchronism with a plurality of clock pulses occuring during a time frame. The resulting serial bit streams may be fed in parallel to a digital-to-analog converter. The DPSG can be used in applications such as Atomic Vapor Laser Isotope Separation (AVLIS) to create an optimal match between the process laser's spectral profile and that of the vaporized material, optical telecommunications, non-optical telecommunication in the microwave and radio spectrum, radar, electronic countermeasures, high speed computer interconnects, local area networks, high definition video transport and the multiplexing of large quantities of slow digital memory into high speed data streams. This invention extends the operation of DPSGs into the GHz range. (author)

  5. Volcanic signals in oceans

    KAUST Repository

    Stenchikov, Georgiy L.

    2009-08-22

    Sulfate aerosols resulting from strong volcanic explosions last for 2–3 years in the lower stratosphere. Therefore it was traditionally believed that volcanic impacts produce mainly short-term, transient climate perturbations. However, the ocean integrates volcanic radiative cooling and responds over a wide range of time scales. The associated processes, especially ocean heat uptake, play a key role in ongoing climate change. However, they are not well constrained by observations, and attempts to simulate them in current climate models used for climate predictions yield a range of uncertainty. Volcanic impacts on the ocean provide an independent means of assessing these processes. This study focuses on quantification of the seasonal to multidecadal time scale response of the ocean to explosive volcanism. It employs the coupled climate model CM2.1, developed recently at the National Oceanic and Atmospheric Administration\\'s Geophysical Fluid Dynamics Laboratory, to simulate the response to the 1991 Pinatubo and the 1815 Tambora eruptions, which were the largest in the 20th and 19th centuries, respectively. The simulated climate perturbations compare well with available observations for the Pinatubo period. The stronger Tambora forcing produces responses with higher signal-to-noise ratio. Volcanic cooling tends to strengthen the Atlantic meridional overturning circulation. Sea ice extent appears to be sensitive to volcanic forcing, especially during the warm season. Because of the extremely long relaxation time of ocean subsurface temperature and sea level, the perturbations caused by the Tambora eruption could have lasted well into the 20th century.

  6. Multimodal signalling in estrildid finches

    DEFF Research Database (Denmark)

    Gomes, A. C. R.; Funghi, C.; Soma, M.

    2017-01-01

    Sexual traits (e.g. visual ornaments, acoustic signals, courtship behaviour) are often displayed together as multimodal signals. Some hypotheses predict joint evolution of different sexual signals (e.g. to increase the efficiency of communication) or that different signals trade off with each other...... (e.g. due to limited resources). Alternatively, multiple signals may evolve independently for different functions, or to communicate different information (multiple message hypothesis). We evaluated these hypotheses with a comparative study in the family Estrildidae, one of the largest songbird...... compromise, but generally courtship dance also evolved independently from other signals. Instead of correlated evolution, we found that song, dance and colour are each related to different socio-ecological traits. Song complexity evolved together with ecological generalism, song performance with investment...

  7. Fundamentals of statistical signal processing

    CERN Document Server

    Kay, Steven M

    1993-01-01

    A unified presentation of parameter estimation for those involved in the design and implementation of statistical signal processing algorithms. Covers important approaches to obtaining an optimal estimator and analyzing its performance; and includes numerous examples as well as applications to real- world problems. MARKETS: For practicing engineers and scientists who design and analyze signal processing systems, i.e., to extract information from noisy signals — radar engineer, sonar engineer, geophysicist, oceanographer, biomedical engineer, communications engineer, economist, statistician, physicist, etc.

  8. Semi-classical signal analysis

    KAUST Repository

    Laleg-Kirati, Taous-Meriem

    2012-09-30

    This study introduces a new signal analysis method, based on a semi-classical approach. The main idea in this method is to interpret a pulse-shaped signal as a potential of a Schrödinger operator and then to use the discrete spectrum of this operator for the analysis of the signal. We present some numerical examples and the first results obtained with this method on the analysis of arterial blood pressure waveforms. © 2012 Springer-Verlag London Limited.

  9. Signal generation in gas detectors

    International Nuclear Information System (INIS)

    Stillman, A.

    1993-01-01

    This tutorial describes the generation of electrical signals in gas detectors. Ionization of the gas by the passage of charged particles generates these signals. Starting with the Bethe-Bloch equation, the treatment is a general introduction to the production of ion-pairs in gas devices. I continue with the characterization of the ionization as an electrical signal, and calculate the signal current in a simple example. Another example demonstrates the effect of space charge on the design of a detector. The AGS Booster ionization profile monitor is a model for this calculation

  10. Paracrine signaling in a bacterium.

    Science.gov (United States)

    López, Daniel; Vlamakis, Hera; Losick, Richard; Kolter, Roberto

    2009-07-15

    Cellular differentiation is triggered by extracellular signals that cause target cells to adopt a particular fate. Differentiation in bacteria typically involves autocrine signaling in which all cells in the population produce and respond to the same signal. Here we present evidence for paracrine signaling in bacterial populations-some cells produce a signal to which only certain target cells respond. Biofilm formation in Bacillus involves two centrally important signaling molecules, ComX and surfactin. ComX triggers the production of surfactin. In turn, surfactin causes a subpopulation of cells to produce an extracellular matrix. Cells that produced surfactin were themselves unable to respond to it. Likewise, once surfactin-responsive cells commenced matrix production, they no longer responded to ComX and could not become surfactin producers. Insensitivity to ComX was the consequence of the extracellular matrix as mutant cells unable to make matrix responded to both ComX and surfactin. Our results demonstrate that extracellular signaling was unidirectional, with one subpopulation producing a signal and a different subpopulation responding to it. Paracrine signaling in a bacterial population ensures the maintenance, over generations, of particular cell types even in the presence of molecules that would otherwise cause those cells to differentiate into other cell types.

  11. The Evolution of Covert Signaling.

    Science.gov (United States)

    Smaldino, Paul E; Flamson, Thomas J; McElreath, Richard

    2018-03-20

    Human sociality depends upon the benefits of mutual aid and extensive communication. However, diverse norms and preferences complicate mutual aid, and ambiguity in meaning hinders communication. Here we demonstrate that these two problems can work together to enhance cooperation through the strategic use of deliberately ambiguous signals: covert signaling. Covert signaling is the transmission of information that is accurately received by its intended audience but obscured when perceived by others. Such signals may allow coordination and enhanced cooperation while also avoiding the alienation or hostile reactions of individuals with different preferences. Although the empirical literature has identified potential mechanisms of covert signaling, such as encryption in humor, there is to date no formal theory of its dynamics. We introduce a novel mathematical model to assess when a covert signaling strategy will evolve, as well as how receiver attitudes coevolve with covert signals. Covert signaling plausibly serves an important function in facilitating within-group cooperative assortment by allowing individuals to pair up with similar group members when possible and to get along with dissimilar ones when necessary. This mechanism has broad implications for theories of signaling and cooperation, humor, social identity, political psychology, and the evolution of human cultural complexity.

  12. Signal anomaly detection and characterization

    International Nuclear Information System (INIS)

    Morgenstern, V.M.; Upadhyaya, B.R.; Gloeckler, O.

    1988-08-01

    As part of a comprehensive signal validation system, we have developed a signal anomaly detector, without specifically establishing the cause of the anomaly. A signal recorded from process instrumentation is said to have an anomaly, if during steady-state operation, the deviation in the level of the signal, its root-mean-square (RMS) value, or its statistical distribution changes by a preset value. This deviation could be an unacceptable increase or a decrease in the quantity being monitored. An anomaly in a signal may be characterized by wideband or single-frequency noise, bias error, pulse-type error, nonsymmetric behavior, or a change in the signal bandwidth. Various signatures can be easily computed from data samples and compared against specified threshold values. We want to point out that in real processes, pulses can appear with different time widths, and at different rates of change of the signal. Thus, in characterizing an anomaly as a pulse-type, the fastest pulse width is constrained by the signal sampling interval. For example, if a signal is sampled at 100 Hz, we will not be able to detect pulses occurring at kHz rates. Discussion with utility and Combustion Engineering personnel indicated that it is not practical to detect pulses having a narrow time width. 9 refs., 11 figs., 8 tabs

  13. Thermal resonance in signal transmission

    International Nuclear Information System (INIS)

    Reigada, Ramon; Sarmiento, Antonio; Lindenberg, Katja

    2001-01-01

    We use temperature tuning to control signal propagation in simple one-dimensional arrays of masses connected by hard anharmonic springs and with no local potentials. In our numerical model a sustained signal is applied at one site of a chain immersed in a thermal environment and the signal-to-noise ratio is measured at each oscillator. We show that raising the temperature can lead to enhanced signal propagation along the chain, resulting in thermal resonance effects akin to the resonance observed in arrays of bistable systems

  14. Thermal resonance in signal transmission

    Energy Technology Data Exchange (ETDEWEB)

    Reigada, Ramon; Sarmiento, Antonio; Lindenberg, Katja

    2001-06-01

    We use temperature tuning to control signal propagation in simple one-dimensional arrays of masses connected by hard anharmonic springs and with no local potentials. In our numerical model a sustained signal is applied at one site of a chain immersed in a thermal environment and the signal-to-noise ratio is measured at each oscillator. We show that raising the temperature can lead to enhanced signal propagation along the chain, resulting in thermal resonance effects akin to the resonance observed in arrays of bistable systems.

  15. Smoke Signal or Smoke Screen?

    DEFF Research Database (Denmark)

    Vergne, Jean-Philippe; Wernicke, Georg; Brenner, Steffen

    This paper explains the amount of disapproval faced by firms that overpay their CEO by integrating signaling and categorization theories. We argue that, in contexts characterized by intense scrutiny, ambivalent signals sent by firms suspend categorization by stakeholders, leading to further disap...

  16. Signals and systems with MATLAB

    CERN Document Server

    Yang, Won Young; Song, Ik H; Cho, Yong S

    2009-01-01

    Covers some of the theoretical foundations and mathematical derivations that can be used in higher-level related subjects such as signal processing, communication, and control, minimizing the mathematical difficulty and computational burden. This book illustrates the usage of MATLAB and Simulink for signal and system analysis and design.

  17. Signaling equilibria in sensorimotor interactions.

    Science.gov (United States)

    Leibfried, Felix; Grau-Moya, Jordi; Braun, Daniel A

    2015-08-01

    Although complex forms of communication like human language are often assumed to have evolved out of more simple forms of sensorimotor signaling, less attention has been devoted to investigate the latter. Here, we study communicative sensorimotor behavior of humans in a two-person joint motor task where each player controls one dimension of a planar motion. We designed this joint task as a game where one player (the sender) possesses private information about a hidden target the other player (the receiver) wants to know about, and where the sender's actions are costly signals that influence the receiver's control strategy. We developed a game-theoretic model within the framework of signaling games to investigate whether subjects' behavior could be adequately described by the corresponding equilibrium solutions. The model predicts both separating and pooling equilibria, in which signaling does and does not occur respectively. We observed both kinds of equilibria in subjects and found that, in line with model predictions, the propensity of signaling decreased with increasing signaling costs and decreasing uncertainty on the part of the receiver. Our study demonstrates that signaling games, which have previously been applied to economic decision-making and animal communication, provide a framework for human signaling behavior arising during sensorimotor interactions in continuous and dynamic environments. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Noisy signaling: theory and experiment

    NARCIS (Netherlands)

    de Haan, T.; Offerman, T.; Sloof, R.

    2011-01-01

    We introduce noise in the signaling technology of an otherwise standard wasteful signaling model (Spence, 1973). We theoretically derive the properties of the equilibria under different levels of noise and we experimentally test how behavior changes with noise. We obtain three main insights. First,

  19. Signals in Communication Engineering History

    Science.gov (United States)

    Consonni, Denise; Silva, Magno T. M.

    2010-01-01

    This paper is a study of various electric signals, which have been employed throughout the history of communication engineering in its two main landmarks: the telegraph and the telephone. The signals are presented in their time and frequency domain representations. The historical order has been followed in the presentation: wired systems, spark…

  20. Non-Smad signaling pathways.

    Science.gov (United States)

    Mu, Yabing; Gudey, Shyam Kumar; Landström, Maréne

    2012-01-01

    Transforming growth factor-beta (TGFβ) is a key regulator of cell fate during embryogenesis and has also emerged as a potent driver of the epithelial-mesenchymal transition during tumor progression. TGFβ signals are transduced by transmembrane type I and type II serine/threonine kinase receptors (TβRI and TβRII, respectively). The activated TβR complex phosphorylates Smad2 and Smad3, converting them into transcriptional regulators that complex with Smad4. TGFβ also uses non-Smad signaling pathways such as the p38 and Jun N-terminal kinase (JNK) mitogen-activated protein kinase (MAPK) pathways to convey its signals. Ubiquitin ligase tumor necrosis factor (TNF)-receptor-associated factor 6 (TRAF6) and TGFβ-associated kinase 1 (TAK1) have recently been shown to be crucial for the activation of the p38 and JNK MAPK pathways. Other TGFβ-induced non-Smad signaling pathways include the phosphoinositide 3-kinase-Akt-mTOR pathway, the small GTPases Rho, Rac, and Cdc42, and the Ras-Erk-MAPK pathway. Signals induced by TGFβ are tightly regulated and specified by post-translational modifications of the signaling components, since they dictate the subcellular localization, activity, and duration of the signal. In this review, we discuss recent findings in the field of TGFβ-induced responses by non-Smad signaling pathways.

  1. Signal analysis of ventricular fibrillation

    NARCIS (Netherlands)

    Herbschleb, J.N.; Heethaar, R.M.; Tweel, L.H. van der; Zimmerman, A.N.E.; Meijler, F.L.

    Signal analysis of electro(cardio)grams during ventricular fibrillation (VF) in dogs and human patients indicates more organization and regularity than the official WHO definition suggests. The majority of the signal is characterized by a power spectrum with narrow, equidistant peaks. In a further

  2. Semi-classical signal analysis

    KAUST Repository

    Laleg-Kirati, Taous-Meriem; Cré peau, Emmanuelle; Sorine, Michel

    2012-01-01

    This study introduces a new signal analysis method, based on a semi-classical approach. The main idea in this method is to interpret a pulse-shaped signal as a potential of a Schrödinger operator and then to use the discrete spectrum

  3. Signaling a Change of Heart

    DEFF Research Database (Denmark)

    Schumacher, Gijs

    2011-01-01

    introduced welfare state retrenchment measures. Social Democrats can win votes and join coalitions by shifting rightwards. In contrast, they can pursue policy objectives by shifting leftwards. To communicate these shifts, in other words, ‘changes of heart’, parties send signals to voters and other parties...... after having signalled ‘a change of heart’....

  4. Intracellular signal modulation by nanomaterials.

    Science.gov (United States)

    Hussain, Salik; Garantziotis, Stavros; Rodrigues-Lima, Fernando; Dupret, Jean-Marie; Baeza-Squiban, Armelle; Boland, Sonja

    2014-01-01

    A thorough understanding of the interactions of nanomaterials with biological systems and the resulting activation of signal transduction pathways is essential for the development of safe and consumer friendly nanotechnology. Here we present an overview of signaling pathways induced by nanomaterial exposures and describe the possible correlation of their physicochemical characteristics with biological outcomes. In addition to the hierarchical oxidative stress model and a review of the intrinsic and cell-mediated mechanisms of reactive oxygen species (ROS) generating capacities of nanomaterials, we also discuss other oxidative stress dependent and independent cellular signaling pathways. Induction of the inflammasome, calcium signaling, and endoplasmic reticulum stress are reviewed. Furthermore, the uptake mechanisms can be of crucial importance for the cytotoxicity of nanomaterials and membrane-dependent signaling pathways have also been shown to be responsible for cellular effects of nanomaterials. Epigenetic regulation by nanomaterials, effects of nanoparticle-protein interactions on cell signaling pathways, and the induction of various cell death modalities by nanomaterials are described. We describe the common trigger mechanisms shared by various nanomaterials to induce cell death pathways and describe the interplay of different modalities in orchestrating the final outcome after nanomaterial exposures. A better understanding of signal modulations induced by nanomaterials is not only essential for the synthesis and design of safer nanomaterials but will also help to discover potential nanomedical applications of these materials. Several biomedical applications based on the different signaling pathways induced by nanomaterials are already proposed and will certainly gain a great deal of attraction in the near future.

  5. Algebraic Methods to Design Signals

    Science.gov (United States)

    2015-08-27

    to date on designing signals using algebraic and combinatorial methods. Mathematical tools from algebraic number theory, representation theory and... combinatorial objects in designing signals for communication purposes. Sequences and arrays with desirable autocorrelation properties have many...multiple access methods in mobile radio communication systems. We continue our mathematical framework based on group algebras, character theory

  6. Hippo signalling directs intestinal fate

    DEFF Research Database (Denmark)

    le Bouteiller, Marie Catherine M; Jensen, Kim Bak

    2015-01-01

    Hippo signalling has been associated with many important tissue functions including the regulation of organ size. In the intestinal epithelium differing functions have been proposed for the effectors of Hippo signalling, YAP and TAZ1. These are now shown to have a dual role in the intestinal...

  7. Signal processing for radiation detectors

    CERN Document Server

    Nakhostin, Mohammad

    2018-01-01

    This book provides a clear understanding of the principles of signal processing of radiation detectors. It puts great emphasis on the characteristics of pulses from various types of detectors and offers a full overview on the basic concepts required to understand detector signal processing systems and pulse processing techniques. Signal Processing for Radiation Detectors covers all of the important aspects of signal processing, including energy spectroscopy, timing measurements, position-sensing, pulse-shape discrimination, and radiation intensity measurement. The book encompasses a wide range of applications so that readers from different disciplines can benefit from all of the information. In addition, this resource: * Describes both analog and digital techniques of signal processing * Presents a complete compilation of digital pulse processing algorithms * Extrapolates content from more than 700 references covering classic papers as well as those of today * Demonstrates concepts with more than 340 origin...

  8. Aberrant Signaling Pathways in Glioma

    International Nuclear Information System (INIS)

    Nakada, Mitsutoshi; Kita, Daisuke; Watanabe, Takuya; Hayashi, Yutaka; Teng, Lei; Pyko, Ilya V.; Hamada, Jun-Ichiro

    2011-01-01

    Glioblastoma multiforme (GBM), a WHO grade IV malignant glioma, is the most common and lethal primary brain tumor in adults; few treatments are available. Median survival rates range from 12–15 months. The biological characteristics of this tumor are exemplified by prominent proliferation, active invasiveness, and rich angiogenesis. This is mainly due to highly deregulated signaling pathways in the tumor. Studies of these signaling pathways have greatly increased our understanding of the biology and clinical behavior of GBM. An integrated view of signal transduction will provide a more useful approach in designing novel therapies for this devastating disease. In this review, we summarize the current understanding of GBM signaling pathways with a focus on potential molecular targets for anti-signaling molecular therapies

  9. Quorum Quenching Revisited—From Signal Decays to Signalling Confusion

    Directory of Open Access Journals (Sweden)

    Kok-Gan Chan

    2012-04-01

    Full Text Available In a polymicrobial community, while some bacteria are communicating with neighboring cells (quorum sensing, others are interrupting the communication (quorum quenching, thus creating a constant arms race between intercellular communication. In the past decade, numerous quorum quenching enzymes have been found and initially thought to inactivate the signalling molecules. Though this is widely accepted, the actual roles of these quorum quenching enzymes are now being uncovered. Recent evidence extends the role of quorum quenching to detoxification or metabolism of signalling molecules as food and energy source; this includes “signalling confusion”, a term coined in this paper to refer to the phenomenon of non-destructive modification of signalling molecules. While quorum quenching has been explored as a novel anti-infective therapy targeting, quorum sensing evidence begins to show the development of resistance against quorum quenching.

  10. Alternatives to Pyrotechnic Distress Signals; Additional Signal Evaluation

    Science.gov (United States)

    2017-06-01

    device performance standard that addresses Coast Guard project sponsor and stakeholders needs. 17. Key Words Visual Distress Signal Device (VDSD...devices. The report discussed the concept of “effective intensity,” as used by the International Association of Marine Aids to Navigation and Lighthouse...efficacy of Cyan as a signal color. In order to move forward, the RDC project team met with CG-ENG-4 and other Coast Guard stakeholders (Offices of

  11. Fast digitizing and digital signal processing of detector signals

    International Nuclear Information System (INIS)

    Hannaske, Roland

    2008-01-01

    A fast-digitizer data acquisition system recently installed at the neutron time-of-flight experiment nELBE, which is located at the superconducting electron accelerator ELBE of Forschungszentrum Dresden-Rossendorf, is tested with two different detector types. Preamplifier signals from a high-purity germanium detector are digitized, stored and finally processed. For a precise determination of the energy of the detected radiation, the moving-window deconvolution algorithm is used to compensate the ballistic deficit and different shaping algorithms are applied. The energy resolution is determined in an experiment with γ-rays from a 22 Na source and is compared to the energy resolution achieved with analogously processed signals. On the other hand, signals from the photomultipliers of barium fluoride and plastic scintillation detectors are digitized. These signals have risetimes of a few nanoseconds only. The moment of interaction of the radiation with the detector is determined by methods of digital signal processing. Therefore, different timing algorithms are implemented and tested with data from an experiment at nELBE. The time resolutions achieved with these algorithms are compared to each other as well as to reference values coming from analog signal processing. In addition to these experiments, some properties of the digitizing hardware are measured and a program for the analysis of stored, digitized data is developed. The analysis of the signals shows that the energy resolution achieved with the 10-bit digitizer system used here is not competitive to a 14-bit peak-sensing ADC, although the ballistic deficit can be fully corrected. However, digital methods give better result in sub-ns timing than analog signal processing. (orig.)

  12. Advanced optical signal processing of broadband parallel data signals

    DEFF Research Database (Denmark)

    Oxenløwe, Leif Katsuo; Hu, Hao; Kjøller, Niels-Kristian

    2016-01-01

    Optical signal processing may aid in reducing the number of active components in communication systems with many parallel channels, by e.g. using telescopic time lens arrangements to perform format conversion and allow for WDM regeneration.......Optical signal processing may aid in reducing the number of active components in communication systems with many parallel channels, by e.g. using telescopic time lens arrangements to perform format conversion and allow for WDM regeneration....

  13. ESR signals of irradiated insects

    International Nuclear Information System (INIS)

    Ukai, Mitsuko; Kameya, Hiromi; Imamura, Taro; Miyanoshita, Akihiro; Todoriki, Setsuko; Shimoyama, Yuhei

    2009-01-01

    Analysis of irradiated insects using Electron Spin Resonance (ESR) spectroscopy was reported. The insects were maize weevil, red flour beetle, Indian meal moth and cigarette beetle that are hazardous to crops. The ESR spectra were consisted of a singlet at g=2 and a sextet centered at the similar g-value. The singlet signal is due to an organic free radical. The sextet signal is attributable to the hyperfine interactions from Mn 2+ ions. Upon irradiation, new signals were not detected. The relaxation times, T 1 and T 2 , showed no variations before and after irradiation. (author)

  14. Statistical theory of signal detection

    CERN Document Server

    Helstrom, Carl Wilhelm; Costrell, L; Kandiah, K

    1968-01-01

    Statistical Theory of Signal Detection, Second Edition provides an elementary introduction to the theory of statistical testing of hypotheses that is related to the detection of signals in radar and communications technology. This book presents a comprehensive survey of digital communication systems. Organized into 11 chapters, this edition begins with an overview of the theory of signal detection and the typical detection problem. This text then examines the goals of the detection system, which are defined through an analogy with the testing of statistical hypotheses. Other chapters consider

  15. Subjective Evaluation of Audiovisual Signals

    Directory of Open Access Journals (Sweden)

    F. Fikejz

    2010-01-01

    Full Text Available This paper deals with subjective evaluation of audiovisual signals, with emphasis on the interaction between acoustic and visual quality. The subjective test is realized by a simple rating method. The audiovisual signal used in this test is a combination of images compressed by JPEG compression codec and sound samples compressed by MPEG-1 Layer III. Images and sounds have various contents. It simulates a real situation when the subject listens to compressed music and watches compressed pictures without the access to original, i.e. uncompressed signals.

  16. On Generalized Fractional Differentiator Signals

    Directory of Open Access Journals (Sweden)

    Hamid A. Jalab

    2013-01-01

    Full Text Available By employing the generalized fractional differential operator, we introduce a system of fractional order derivative for a uniformly sampled polynomial signal. The calculation of the bring in signal depends on the additive combination of the weighted bring-in of N cascaded digital differentiators. The weights are imposed in a closed formula containing the Stirling numbers of the first kind. The approach taken in this work is to consider that signal function in terms of Newton series. The convergence of the system to a fractional time differentiator is discussed.

  17. Ultrasound imaging using coded signals

    DEFF Research Database (Denmark)

    Misaridis, Athanasios

    Modulated (or coded) excitation signals can potentially improve the quality and increase the frame rate in medical ultrasound scanners. The aim of this dissertation is to investigate systematically the applicability of modulated signals in medical ultrasound imaging and to suggest appropriate...... methods for coded imaging, with the goal of making better anatomic and flow images and three-dimensional images. On the first stage, it investigates techniques for doing high-resolution coded imaging with improved signal-to-noise ratio compared to conventional imaging. Subsequently it investigates how...... coded excitation can be used for increasing the frame rate. The work includes both simulated results using Field II, and experimental results based on measurements on phantoms as well as clinical images. Initially a mathematical foundation of signal modulation is given. Pulse compression based...

  18. Digital storage of repeated signals

    International Nuclear Information System (INIS)

    Prozorov, S.P.

    1984-01-01

    An independent digital storage system designed for repeated signal discrimination from background noises is described. The signal averaging is performed off-line in the real time mode by means of multiple selection of the investigated signal and integration in each point. Digital values are added in a simple summator and the result is recorded the storage device with the volume of 1024X20 bit from where it can be output on an oscillograph, a plotter or transmitted to a compUter for subsequent processing. The described storage is reliable and simple device on one base of which the systems for the nuclear magnetic resonapce signal acquisition in different experiments are developed

  19. Zufällige Signale

    Science.gov (United States)

    Plaßmann, Wilfried

    Die hier betrachteten Signale werden auch als stochastische Signale bezeichnet. Sie sind zufällig, d. h. ihr Augenblickswert ist nicht vorhersagbar. Abb. 118.1 zeigt eine Unterteilung nach den Signaleigenschaften. Über die nichtstationären Signale lässt sich keinerlei Aussage machen, und sie werden hier deshalb auch nicht weiter betrachtet. Für die stationären Signale gilt, dass ihr Momentanwert zwar auch nicht vorhergesagt werden kann, dass sie aber trotzdem gewisse auswertbare Eigenschaften besitzen, die allerdings statistischer Art sind und deshalb nur mit den Gesetzen der Wahrscheinlichkeitstheorie erfasst werden können. Zwar sind - theoretisch - für die Anwendung der Wahrscheinlichkeitstheorie unendlich viele Probenwerte zu nehmen, in der Praxis hat sich aber gezeigt, dass man auch mit einer endlichen Anzahl dem gesuchten Wert schon ausreichend nahe kommen kann.

  20. Signal Incongruence and its Consequences

    DEFF Research Database (Denmark)

    Vergne, Jean-Philippe; Wernicke, Maria Stokholm; Brenner, Steffen

    2018-01-01

    theory on signal incongruence, we find that firms engaged in philanthropy receive more media disapproval when they overcompensate their CEO, but they are also more likely to decrease CEO overcompensation as a response. Our study contributes to the signaling literature by theorizing about signal......We draw on the signaling and infomediary literatures to examine how media evaluations of CEO overcompensation (a negative cue associated with selfishness and greed) are affected by the presence of corporate philanthropy (a positive cue associated with altruism and generosity). In line with our...... incongruence, and to infomediary and corporate governance research by showing that media disapproval can lead to lower executive compensation. We also reconcile two conflicting views on firm prosocial behavior by showing that, in the presence of incongruent cues, philanthropy can simultaneously enhance...

  1. Mathematical Modelling Plant Signalling Networks

    KAUST Repository

    Muraro, D.; Byrne, H.M.; King, J.R.; Bennett, M.J.

    2013-01-01

    methods for modelling gene and signalling networks and their application in plants. We then describe specific models of hormonal perception and cross-talk in plants. This mathematical analysis of sub-cellular molecular mechanisms paves the way for more

  2. Signal transforms in dynamic measurements

    CERN Document Server

    Layer, Edward

    2015-01-01

    This book is devoted to the analysis of measurement signals which requires specific mathematical operations like Convolution, Deconvolution, Laplace, Fourier, Hilbert, Wavelet or Z transform which are all presented in the present book. The different problems refer to the modulation of signals, filtration of disturbance as well as to the orthogonal signals and their use in digital form for the measurement of current, voltage, power and frequency are also widely discussed. All the topics covered in this book are presented in detail and illustrated by means of examples in MathCad and LabVIEW. This book provides a useful source for researchers, scientists and engineers who in their daily work are required to deal with problems of measurement and signal processing and can also be helpful to undergraduate students of electrical engineering.    

  3. Dopamine signaling: target in glioblastoma

    Czech Academy of Sciences Publication Activity Database

    Bartek, Jiří; Hodný, Zdeněk

    2014-01-01

    Roč. 5, č. 5 (2014), 1116-1117 ISSN 1949-2553 Institutional support: RVO:68378050 Keywords : Dopamine signaling * glioblastoma * MAPK Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 6.359, year: 2014

  4. Pedestrian Friendly Traffic Signal Control.

    Science.gov (United States)

    2016-01-01

    This project continues research aimed at real-time detection and use of pedestrian : traffic flow information to enhance adaptive traffic signal control in urban areas : where pedestrian traffic is substantial and must be given appropriate attention ...

  5. Nuclear Receptor Signaling Atlas (NURSA)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Nuclear Receptor Signaling Atlas (NURSA) is designed to foster the development of a comprehensive understanding of the structure, function, and role in disease...

  6. Intercellular signalling in Stigmatella aurantiaca.

    Science.gov (United States)

    Plaga, W; Ulrich, S H

    1999-12-01

    The myxobacterium Stigmatella aurantiaca is a prokaryotic model used to study intercellular signalling and the genetic determination of morphogenesis. Signalling factors and genes required for the generation of the elaborate multicellular fruiting body are to be identified. Recently, the structure of stigmolone, which is the pheromone necessary for fruiting body formation, was elucidated, and genes involved in development were characterised. Progress has also been made in the genetic accessibility of S. aurantiaca.

  7. Neurotransmitter signaling in white matter.

    Science.gov (United States)

    Butt, Arthur M; Fern, Robert F; Matute, Carlos

    2014-11-01

    White matter (WM) tracts are bundles of myelinated axons that provide for rapid communication throughout the CNS and integration in grey matter (GM). The main cells in myelinated tracts are oligodendrocytes and astrocytes, with small populations of microglia and oligodendrocyte precursor cells. The prominence of neurotransmitter signaling in WM, which largely exclude neuronal cell bodies, indicates it must have physiological functions other than neuron-to-neuron communication. A surprising aspect is the diversity of neurotransmitter signaling in WM, with evidence for glutamatergic, purinergic (ATP and adenosine), GABAergic, glycinergic, adrenergic, cholinergic, dopaminergic and serotonergic signaling, acting via a wide range of ionotropic and metabotropic receptors. Both axons and glia are potential sources of neurotransmitters and may express the respective receptors. The physiological functions of neurotransmitter signaling in WM are subject to debate, but glutamate and ATP-mediated signaling have been shown to evoke Ca(2+) signals in glia and modulate axonal conduction. Experimental findings support a model of neurotransmitters being released from axons during action potential propagation acting on glial receptors to regulate the homeostatic functions of astrocytes and myelination by oligodendrocytes. Astrocytes also release neurotransmitters, which act on axonal receptors to strengthen action potential propagation, maintaining signaling along potentially long axon tracts. The co-existence of multiple neurotransmitters in WM tracts suggests they may have diverse functions that are important for information processing. Furthermore, the neurotransmitter signaling phenomena described in WM most likely apply to myelinated axons of the cerebral cortex and GM areas, where they are doubtless important for higher cognitive function. © 2014 Wiley Periodicals, Inc.

  8. Sentiment analysis for PTSD signals

    CERN Document Server

    Kagan, Vadim; Sapounas, Demetrios

    2013-01-01

    This book describes a computational framework for real-time detection of psychological signals related to Post-Traumatic Stress Disorder (PTSD) in online text-based posts, including blogs and web forums. Further, it explores how emerging computational techniques such as sentiment mining can be used in real-time to identify posts that contain PTSD-related signals, flag those posts, and bring them to the attention of psychologists, thus providing an automated flag and referral capability.

  9. Aberrant Wnt Signaling in Leukemia

    Directory of Open Access Journals (Sweden)

    Frank J. T. Staal

    2016-08-01

    Full Text Available The Wnt signaling pathway is essential in the development and homeostasis of blood and immune cells, but its exact role is still controversial and is the subject of intense research. The malignant counterpart of normal hematopoietic cells, leukemic (stem cells, have hijacked the Wnt pathway for their self-renewal and proliferation. Here we review the multiple ways dysregulated Wnt signaling can contribute to leukemogenesis, both cell autonomously as well as by changes in the microenvironment.

  10. Wnt signaling in limb organogenesis

    OpenAIRE

    Geetha-Loganathan, Poongodi; Nimmagadda, Suresh; Scaal, Martin

    2008-01-01

    Secreted signaling molecules of the Wnt family have been found to play a central role in controlling embryonic development of a wide range of taxa from Hydra to humans. The most extensively studied Wnt signaling pathway is the canonical Wnt pathway, which controls gene expression by stabilizing β-catenin, and regulates a multitude of developmental processes. More recently, noncanonical Wnt pathways, which are β-catenin-independent, have been found to be important developmental regulators. Und...

  11. Handbook of signal processing systems

    CERN Document Server

    Deprettere, Ed; Leupers, Rainer; Takala, Jarmo

    2013-01-01

    Handbook of Signal Processing Systems is organized in three parts. The first part motivates representative applications that drive and apply state-of-the art methods for design and implementation of signal processing systems; the second part discusses architectures for implementing these applications; the third part focuses on compilers and simulation tools, describes models of computation and their associated design tools and methodologies. This handbook is an essential tool for professionals in many fields and researchers of all levels.

  12. Hedgehog Signaling in Endochondral Ossification

    Directory of Open Access Journals (Sweden)

    Shinsuke Ohba

    2016-06-01

    Full Text Available Hedgehog (Hh signaling plays crucial roles in the patterning and morphogenesis of various organs within the bodies of vertebrates and insects. Endochondral ossification is one of the notable developmental events in which Hh signaling acts as a master regulator. Among three Hh proteins in mammals, Indian hedgehog (Ihh is known to work as a major Hh input that induces biological impact of Hh signaling on the endochondral ossification. Ihh is expressed in prehypertrophic and hypertrophic chondrocytes of developing endochondral bones. Genetic studies so far have demonstrated that the Ihh-mediated activation of Hh signaling synchronizes chondrogenesis and osteogenesis during endochondral ossification by regulating the following processes: (1 chondrocyte differentiation; (2 chondrocyte proliferation; and (3 specification of bone-forming osteoblasts. Ihh not only forms a negative feedback loop with parathyroid hormone-related protein (PTHrP to maintain the growth plate length, but also directly promotes chondrocyte propagation. Ihh input is required for the specification of progenitors into osteoblast precursors. The combinatorial approaches of genome-wide analyses and mouse genetics will facilitate understanding of the regulatory mechanisms underlying the roles of Hh signaling in endochondral ossification, providing genome-level evidence of the potential of Hh signaling for the treatment of skeletal disorders.

  13. Hedgehog Signaling in Endochondral Ossification

    Science.gov (United States)

    Ohba, Shinsuke

    2016-01-01

    Hedgehog (Hh) signaling plays crucial roles in the patterning and morphogenesis of various organs within the bodies of vertebrates and insects. Endochondral ossification is one of the notable developmental events in which Hh signaling acts as a master regulator. Among three Hh proteins in mammals, Indian hedgehog (Ihh) is known to work as a major Hh input that induces biological impact of Hh signaling on the endochondral ossification. Ihh is expressed in prehypertrophic and hypertrophic chondrocytes of developing endochondral bones. Genetic studies so far have demonstrated that the Ihh-mediated activation of Hh signaling synchronizes chondrogenesis and osteogenesis during endochondral ossification by regulating the following processes: (1) chondrocyte differentiation; (2) chondrocyte proliferation; and (3) specification of bone-forming osteoblasts. Ihh not only forms a negative feedback loop with parathyroid hormone-related protein (PTHrP) to maintain the growth plate length, but also directly promotes chondrocyte propagation. Ihh input is required for the specification of progenitors into osteoblast precursors. The combinatorial approaches of genome-wide analyses and mouse genetics will facilitate understanding of the regulatory mechanisms underlying the roles of Hh signaling in endochondral ossification, providing genome-level evidence of the potential of Hh signaling for the treatment of skeletal disorders. PMID:29615586

  14. Metabolites in vertebrate Hedgehog signaling.

    Science.gov (United States)

    Roberg-Larsen, Hanne; Strand, Martin Frank; Krauss, Stefan; Wilson, Steven Ray

    2014-04-11

    The Hedgehog (HH) signaling pathway is critical in embryonic development, stem cell biology, tissue homeostasis, chemoattraction and synapse formation. Irregular HH signaling is associated with a number of disease conditions including congenital disorders and cancer. In particular, deregulation of HH signaling has been linked to skin, brain, lung, colon and pancreatic cancers. Key mediators of the HH signaling pathway are the 12-pass membrane protein Patched (PTC), the 7-pass membrane protein Smoothened (SMO) and the GLI transcription factors. PTC shares homology with the RND family of small-molecule transporters and it has been proposed that it interferes with SMO through metabolites. Although a conclusive picture is lacking, substantial efforts are made to identify and understand natural metabolites/sterols, including cholesterol, vitamin D3, oxysterols and glucocorticoides, that may be affected by, or influence the HH signaling cascade at the level of PTC and SMO. In this review we will elaborate the role of metabolites in HH signaling with a focus on oxysterols, and discuss advancements in modern analytical approaches in the field. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Bystander signaling via oxidative metabolism.

    Science.gov (United States)

    Sawal, Humaira Aziz; Asghar, Kashif; Bureik, Matthias; Jalal, Nasir

    2017-01-01

    The radiation-induced bystander effect (RIBE) is the initiation of biological end points in cells (bystander cells) that are not directly traversed by an incident-radiation track, but are in close proximity to cells that are receiving the radiation. RIBE has been indicted of causing DNA damage via oxidative stress, besides causing direct damage, inducing tumorigenesis, producing micronuclei, and causing apoptosis. RIBE is regulated by signaling proteins that are either endogenous or secreted by cells as a means of communication between cells, and can activate intracellular or intercellular oxidative metabolism that can further trigger signaling pathways of inflammation. Bystander signals can pass through gap junctions in attached cell lines, while the suspended cell lines transmit these signals via hormones and soluble proteins. This review provides the background information on how reactive oxygen species (ROS) act as bystander signals. Although ROS have a very short half-life and have a nanometer-scale sphere of influence, the wide variety of ROS produced via various sources can exert a cumulative effect, not only in forming DNA adducts but also setting up signaling pathways of inflammation, apoptosis, cell-cycle arrest, aging, and even tumorigenesis. This review outlines the sources of the bystander effect linked to ROS in a cell, and provides methods of investigation for researchers who would like to pursue this field of science.

  16. Insulin Signaling and Heart Failure

    Science.gov (United States)

    Riehle, Christian; Abel, E. Dale

    2016-01-01

    Heart failure is associated with generalized insulin resistance. Moreover, insulin resistant states such as type 2 diabetes and obesity increases the risk of heart failure even after adjusting for traditional risk factors. Insulin resistance or type 2 diabetes alters the systemic and neurohumoral milieu leading to changes in metabolism and signaling pathways in the heart that may contribute to myocardial dysfunction. In addition, changes in insulin signaling within cardiomyocytes develop in the failing heart. The changes range from activation of proximal insulin signaling pathways that may contribute to adverse left ventricular remodeling and mitochondrial dysfunction to repression of distal elements of insulin signaling pathways such as forkhead (FOXO) transcriptional signaling or glucose transport which may also impair cardiac metabolism, structure and function. This article will review the complexities of insulin signaling within the myocardium and ways in which these pathways are altered in heart failure or in conditions associated with generalized insulin resistance. The implications of these changes for therapeutic approaches to treating or preventing heart failure will be discussed. PMID:27034277

  17. SignalPlant: an open signal processing software platform.

    Science.gov (United States)

    Plesinger, F; Jurco, J; Halamek, J; Jurak, P

    2016-07-01

    The growing technical standard of acquisition systems allows the acquisition of large records, often reaching gigabytes or more in size as is the case with whole-day electroencephalograph (EEG) recordings, for example. Although current 64-bit software for signal processing is able to process (e.g. filter, analyze, etc) such data, visual inspection and labeling will probably suffer from rather long latency during the rendering of large portions of recorded signals. For this reason, we have developed SignalPlant-a stand-alone application for signal inspection, labeling and processing. The main motivation was to supply investigators with a tool allowing fast and interactive work with large multichannel records produced by EEG, electrocardiograph and similar devices. The rendering latency was compared with EEGLAB and proves significantly faster when displaying an image from a large number of samples (e.g. 163-times faster for 75  ×  10(6) samples). The presented SignalPlant software is available free and does not depend on any other computation software. Furthermore, it can be extended with plugins by third parties ensuring its adaptability to future research tasks and new data formats.

  18. Bystander signaling via oxidative metabolism

    Directory of Open Access Journals (Sweden)

    Sawal HA

    2017-08-01

    Full Text Available Humaira Aziz Sawal,1 Kashif Asghar,2 Matthias Bureik,3 Nasir Jalal4 1Healthcare Biotechnology Department, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, 2Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan; 3Health Science Platform, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China; 4Health Science Platform, Department of Molecular and Cellular Pharmacology, Tianjin University, Tianjin, China Abstract: The radiation-induced bystander effect (RIBE is the initiation of biological end points in cells (bystander cells that are not directly traversed by an incident-radiation track, but are in close proximity to cells that are receiving the radiation. RIBE has been indicted of causing DNA damage via oxidative stress, besides causing direct damage, inducing tumorigenesis, producing micronuclei, and causing apoptosis. RIBE is regulated by signaling proteins that are either endogenous or secreted by cells as a means of communication between cells, and can activate intracellular or intercellular oxidative metabolism that can further trigger signaling pathways of inflammation. Bystander signals can pass through gap junctions in attached cell lines, while the suspended cell lines transmit these signals via hormones and soluble proteins. This review provides the background information on how reactive oxygen species (ROS act as bystander signals. Although ROS have a very short half-life and have a nanometer-scale sphere of influence, the wide variety of ROS produced via various sources can exert a cumulative effect, not only in forming DNA adducts but also setting up signaling pathways of inflammation, apoptosis, cell-cycle arrest, aging, and even tumorigenesis. This review outlines the sources of the bystander effect linked to ROS in a cell, and provides methods of investigation for researchers who would like to

  19. Liquid Argon TPC Signal Formation, Signal Processing and Hit Reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Baller, Bruce [Fermilab

    2017-03-11

    This document describes the early stage of the reconstruction chain that was developed for the ArgoNeuT and MicroBooNE experiments at Fermilab. These experiments study accelerator neutrino interactions that occur in a Liquid Argon Time Projection Chamber. Reconstructing the properties of particles produced in these interactions requires knowledge of the micro-physics processes that affect the creation and transport of ionization electrons to the readout system. A wire signal deconvolution technique was developed to convert wire signals to a standard form for hit reconstruction, to remove artifacts in the electronics chain and to remove coherent noise.

  20. Overlay Spectrum Sharing using Improper Gaussian Signaling

    KAUST Repository

    Amin, Osama; Abediseid, Walid; Alouini, Mohamed-Slim

    2016-01-01

    in overlay cognitive radio system, where the secondary transmitter broadcasts a mixture of two different signals. The first signal is selected from the PGS scheme to match the primary message transmission. On the other hand, the second signal is chosen

  1. 300 Area signal cable study

    International Nuclear Information System (INIS)

    Whattam, J.W.

    1994-01-01

    This report was prepared to discuss the alternatives available for removing the 300 Area overhead signal cable system. This system, installed in 1969, has been used for various monitoring and communication signaling needs throughout the 300 Area. Over the years this cabling system has deteriorated, has been continually reconfigured, and has been poorly documented to the point of nonreliability. The first step was to look at the systems utilizing the overhead signal cable that are still required for operation. Of the ten systems that once operated via the signal cable, only five are still required; the civil defense evacuation alarms, the public address (PA) system, the criticality alarms, the Pacific Northwest Laboratory Facilities Management Control System (FMCS), and the 384 annunciator panel. Of these five, the criticality alarms and the FMCS have been dealt with under other proposals. Therefore, this study focused on the alternatives available for the remaining three systems (evacuation alarms, PA system, and 384 panel) plus the accountability aid phones. Once the systems to be discussed were determined, then three alternatives for providing the signaling pathway were examined for each system: (1) re-wire using underground communication ducts, (2) use the Integrated Voice/Data Telecommunications System (IVDTS) already installed and operated by US West, and (3) use radio control. Each alternative was developed with an estimated cost, advantages, and disadvantages. Finally, a recommendation was provided for the best alternative for each system

  2. Calcium Signaling in Taste Cells

    Science.gov (United States)

    Medler, Kathryn F.

    2014-01-01

    The sense of taste is a common ability shared by all organisms and is used to detect nutrients as well as potentially harmful compounds. Thus taste is critical to survival. Despite its importance, surprisingly little is known about the mechanisms generating and regulating responses to taste stimuli. All taste responses depend on calcium signals to generate appropriate responses which are relayed to the brain. Some taste cells have conventional synapses and rely on calcium influx through voltage-gated calcium channels. Other taste cells lack these synapses and depend on calcium release to formulate an output signal through a hemichannel. Beyond establishing these characteristics, few studies have focused on understanding how these calcium signals are formed. We identified multiple calcium clearance mechanisms that regulate calcium levels in taste cells as well as a calcium influx that contributes to maintaining appropriate calcium homeostasis in these cells. Multiple factors regulate the evoked taste signals with varying roles in different cell populations. Clearly, calcium signaling is a dynamic process in taste cells and is more complex than has previously been appreciated. PMID:25450977

  3. Biomedical signal and image processing.

    Science.gov (United States)

    Cerutti, Sergio; Baselli, Giuseppe; Bianchi, Anna; Caiani, Enrico; Contini, Davide; Cubeddu, Rinaldo; Dercole, Fabio; Rienzo, Luca; Liberati, Diego; Mainardi, Luca; Ravazzani, Paolo; Rinaldi, Sergio; Signorini, Maria; Torricelli, Alessandro

    2011-01-01

    Generally, physiological modeling and biomedical signal processing constitute two important paradigms of biomedical engineering (BME): their fundamental concepts are taught starting from undergraduate studies and are more completely dealt with in the last years of graduate curricula, as well as in Ph.D. courses. Traditionally, these two cultural aspects were separated, with the first one more oriented to physiological issues and how to model them and the second one more dedicated to the development of processing tools or algorithms to enhance useful information from clinical data. A practical consequence was that those who did models did not do signal processing and vice versa. However, in recent years,the need for closer integration between signal processing and modeling of the relevant biological systems emerged very clearly [1], [2]. This is not only true for training purposes(i.e., to properly prepare the new professional members of BME) but also for the development of newly conceived research projects in which the integration between biomedical signal and image processing (BSIP) and modeling plays a crucial role. Just to give simple examples, topics such as brain–computer machine or interfaces,neuroengineering, nonlinear dynamical analysis of the cardiovascular (CV) system,integration of sensory-motor characteristics aimed at the building of advanced prostheses and rehabilitation tools, and wearable devices for vital sign monitoring and others do require an intelligent fusion of modeling and signal processing competences that are certainly peculiar of our discipline of BME.

  4. Signal analysis for failure detection

    International Nuclear Information System (INIS)

    Parpaglione, M.C.; Perez, L.V.; Rubio, D.A.; Czibener, D.; D'Attellis, C.E.; Brudny, P.I.; Ruzzante, J.E.

    1994-01-01

    Several methods for analysis of acoustic emission signals are presented. They are mainly oriented to detection of changes in noisy signals and characterization of higher amplitude discrete pulses or bursts. The aim was to relate changes and events with failure, crack or wear in materials, being the final goal to obtain automatic means of detecting such changes and/or events. Performance evaluation was made using both simulated and laboratory test signals. The methods being presented are the following: 1. Application of the Hopfield Neural Network (NN) model for classifying faults in pipes and detecting wear of a bearing. 2. Application of the Kohonnen and Back Propagation Neural Network model for the same problem. 3. Application of Kalman filtering to determine time occurrence of bursts. 4. Application of a bank of Kalman filters (KF) for failure detection in pipes. 5. Study of amplitude distribution of signals for detecting changes in their shape. 6. Application of the entropy distance to measure differences between signals. (author). 10 refs, 11 figs

  5. Neurotrophin signaling and visceral hypersensitivity.

    Science.gov (United States)

    Qiao, Li-Ya

    2014-06-01

    Neurotrophin family are traditionally recognized for their nerve growth promoting function and are recently identified as crucial factors in regulating neuronal activity in the central and peripheral nervous systems. The family members including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and neurotrophin-3 (NT-3) are reported to have distinct roles in the development and maintenance of sensory phenotypes in normal states and in the modulation of sensory activity in disease. This paper highlights receptor tyrosine kinase (Trk) -mediated signal transduction by which neurotrophins regulate neuronal activity in the visceral sensory reflex pathways with emphasis on the distinct roles of NGF and BDNF signaling in physiologic and pathophysiological processes. Viscero-visceral cross-organ sensitization exists widely in human diseases. The role of neurotrophins in mediating neural cross talk and interaction in primary afferent neurons in the dorsal root ganglia (DRG) and neurotrophin signal transduction in the context of cross-organ sensitization are also discussed.

  6. Cytokinin signaling during root development.

    Science.gov (United States)

    Bishopp, Anthony; Help, Hanna; Helariutta, Ykä

    2009-01-01

    The cytokinin class of phytohormones regulates division and differentiation of plant cells. They are perceived and signaled by a phosphorelay mechanism similar to those observed in prokaryotes. Research into the components of phosphorelay had previously been marred by genetic redundancy. However, recent studies have addressed this with the creation of high-order mutants. In addition, several new elements regulating cytokinin signaling have been identified. This has uncovered many roles in diverse developmental and physiological processes. In this review, we look at these processes specifically in the context of root development. We focus on the formation and maintenance of the root apical meristem, primary and secondary vascular development, lateral root emergence and development, and root nodulation. We believe that the root is an ideal organ with which to investigate cytokinin signaling in a wider context.

  7. Neural networks in signal processing

    International Nuclear Information System (INIS)

    Govil, R.

    2000-01-01

    Nuclear Engineering has matured during the last decade. In research and design, control, supervision, maintenance and production, mathematical models and theories are used extensively. In all such applications signal processing is embedded in the process. Artificial Neural Networks (ANN), because of their nonlinear, adaptive nature are well suited to such applications where the classical assumptions of linearity and second order Gaussian noise statistics cannot be made. ANN's can be treated as nonparametric techniques, which can model an underlying process from example data. They can also adopt their model parameters to statistical change with time. Algorithms in the framework of Neural Networks in Signal processing have found new applications potentials in the field of Nuclear Engineering. This paper reviews the fundamentals of Neural Networks in signal processing and their applications in tasks such as recognition/identification and control. The topics covered include dynamic modeling, model based ANN's, statistical learning, eigen structure based processing and generalization structures. (orig.)

  8. Wavelets and multiscale signal processing

    CERN Document Server

    Cohen, Albert

    1995-01-01

    Since their appearance in mid-1980s, wavelets and, more generally, multiscale methods have become powerful tools in mathematical analysis and in applications to numerical analysis and signal processing. This book is based on "Ondelettes et Traitement Numerique du Signal" by Albert Cohen. It has been translated from French by Robert D. Ryan and extensively updated by both Cohen and Ryan. It studies the existing relations between filter banks and wavelet decompositions and shows how these relations can be exploited in the context of digital signal processing. Throughout, the book concentrates on the fundamentals. It begins with a chapter on the concept of multiresolution analysis, which contains complete proofs of the basic results. The description of filter banks that are related to wavelet bases is elaborated in both the orthogonal case (Chapter 2), and in the biorthogonal case (Chapter 4). The regularity of wavelets, how this is related to the properties of the filters and the importance of regularity for t...

  9. Ocean circulation generated magnetic signals

    DEFF Research Database (Denmark)

    Manoj, C.; Kuvshinov, A.; Maus, S.

    2006-01-01

    Conducting ocean water, as it flows through the Earth's magnetic field, generates secondary electric and magnetic fields. An assessment of the ocean-generated magnetic fields and their detectability may be of importance for geomagnetism and oceanography. Motivated by the clear identification...... of ocean tidal signatures in the CHAMP magnetic field data we estimate the ocean magnetic signals of steady flow using a global 3-D EM numerical solution. The required velocity data are from the ECCO ocean circulation experiment and alternatively from the OCCAM model for higher resolution. We assume...... of the magnetic field, as compared to the ECCO simulation. Besides the expected signatures of the global circulation patterns, we find significant seasonal variability of ocean magnetic signals in the Indian and Western Pacific Oceans. Compared to seasonal variation, interannual variations produce weaker signals....

  10. Chansporter complexes in cell signaling.

    Science.gov (United States)

    Abbott, Geoffrey W

    2017-09-01

    Ion channels facilitate diffusion of ions across cell membranes for such diverse purposes as neuronal signaling, muscular contraction, and fluid homeostasis. Solute transporters often utilize ionic gradients to move aqueous solutes up their concentration gradient, also fulfilling a wide variety of tasks. Recently, an increasing number of ion channel-transporter ('chansporter') complexes have been discovered. Chansporter complex formation may overcome what could otherwise be considerable spatial barriers to rapid signal integration and feedback between channels and transporters, the ions and other substrates they transport, and environmental factors to which they must respond. Here, current knowledge in this field is summarized, covering both heterologous expression structure/function findings and potential mechanisms by which chansporter complexes fulfill contrasting roles in cell signaling in vivo. © 2017 Federation of European Biochemical Societies.

  11. The Dynamics of Costly Signaling

    Directory of Open Access Journals (Sweden)

    Elliott O. Wagner

    2013-04-01

    Full Text Available Costly signaling is a mechanism through which the honesty of signals can be secured in equilibrium, even in interactions where communicators have conflicting interests. This paper explores the dynamics of one such signaling game: Spence’s model of education. It is found that separating equilibria are unlikely to emerge under either the replicator or best response dynamics, but that partially communicative mixed equilibria are quite important dynamically. These mixtures are Lyapunov stable in the replicator dynamic and asymptotically stable in the best response dynamic. Moreover, they have large basins of attraction, in fact larger than those of either pooling or separating equilibria. This suggests that these mixtures may play significant, and underappreciated, roles in the explanation of the emergence and stability of information transfer.

  12. Signals, systems, transforms, and digital signal processing with Matlab

    CERN Document Server

    Corinthios, Michael

    2009-01-01

    Continuous-Time and Discrete-Time Signals and SystemsIntroductionContinuous-Time SignalsPeriodic FunctionsUnit Step FunctionGraphical Representation of FunctionsEven and Odd Parts of a FunctionDirac-Delta ImpulseBasic Properties of the Dirac-Delta ImpulseOther Important Properties of the ImpulseContinuous-Time SystemsCausality, StabilityExamples of Electrical Continuous-Time SystemsMechanical SystemsTransfer Function and Frequency ResponseConvolution and CorrelationA Right-Sided and a Left-Sided FunctionConvolution with an Impulse and Its DerivativesAdditional Convolution PropertiesCorrelation FunctionProperties of the Correlation FunctionGraphical InterpretationCorrelation of Periodic FunctionsAverage, Energy and Power of Continuous-Time SignalsDiscrete-Time SignalsPeriodicityDifference EquationsEven/Odd DecompositionAverage Value, Energy and Power SequencesCausality, StabilityProblemsAnswers to Selected ProblemsFourier Series ExpansionTrigonometric Fourier SeriesExponential Fourier SeriesExponential versus ...

  13. Signal transduction by growth factor receptors: signaling in an instant

    DEFF Research Database (Denmark)

    Dengjel, Joern; Akimov, Vyacheslav; Blagoev, Blagoy

    2007-01-01

    Phosphorylation-based signaling events happening within the first minute of receptor stimulation have so far only been analyzed by classical cell biological approaches like live-cell microscopy. The development of a quench flow system with a time resolution of one second coupled to a read...

  14. Conversion of interlaced image signals into progressive scanned image signals.

    NARCIS (Netherlands)

    2008-01-01

    In a method of de-interlacing video data (F), at least three different de-interlacing algorithms (VTF, MED1, CM3) are applied on the video data (F) to obtain at least three de-interlaced signals (DIO-1, DIO-2, DIO-3), no majority of de-interlacing algorithms copying a single spatio-temporally

  15. Signals of Opportunity Navigation Using Wi-Fi Signals

    Science.gov (United States)

    2011-03-24

    Multiplexed Signals of Opportunity. Master’s Thesis, Air Force Institute of Technology, 2007. 33. Wiles, Charles. “Introducing the Gears Geolocation ... API for All Laptop WiFi Users”, October 2008. URL http://googlecode.blogspot.com. 88 REPORT DOCUMENTATION PAGE Form ApprovedOMB No. 0704–0188 The public

  16. Chaotic signals in digital communications

    CERN Document Server

    Eisencraft, Marcio; Suyama, Ricardo

    2013-01-01

    Chaotic Signals in Digital Communications combines fundamental background knowledge with state-of-the-art methods for using chaotic signals and systems in digital communications. The book builds a bridge between theoretical works and practical implementation to help researchers attain consistent performance in realistic environments. It shows the possible shortcomings of the chaos-based communication systems proposed in the literature, particularly when they are subjected to non-ideal conditions. It also presents a toolbox of techniques for researchers working to actually implement such system

  17. Digital signal processing for NDT

    International Nuclear Information System (INIS)

    Georgel, B.

    1994-01-01

    NDT begins to adapt and use the most recent developments of digital signal and image processing. We briefly sum up the main characteristics of NDT situations (particularly noise and inverse problem formulation) and comment on techniques already used or just emerging (SAFT, split spectrum, adaptive learning network, noise reference filtering, stochastic models, neural networks). This survey is focused on ultrasonics, eddy currents and X-ray radiography. The final objective of end users (availability of automatic diagnosis systems) cannot be achieved only by signal processing algorithms. A close cooperation with other techniques such as artificial intelligence has therefore to be implemented. (author). 20 refs

  18. Subgraph detection using graph signals

    KAUST Repository

    Chepuri, Sundeep Prabhakar

    2017-03-06

    In this paper we develop statistical detection theory for graph signals. In particular, given two graphs, namely, a background graph that represents an usual activity and an alternative graph that represents some unusual activity, we are interested in answering the following question: To which of the two graphs does the observed graph signal fit the best? To begin with, we assume both the graphs are known, and derive an optimal Neyman-Pearson detector. Next, we derive a suboptimal detector for the case when the alternative graph is not known. The developed theory is illustrated with numerical experiments.

  19. Signal processing for cognitive radios

    CERN Document Server

    Jayaweera, Sudharman K

    2014-01-01

    This book covers power electronics, in depth, by presenting the basic principles and application details, and it can be used both as a textbook and reference book.  Introduces the specific type of CR that has gained the most research attention in recent years: the CR for Dynamic Spectrum Access (DSA). Provides signal processing solutions to each task by relating the tasks to materials covered in Part II. Specialized chapters then discuss specific signal processing algorithms required for DSA and DSS cognitive radios  

  20. PSpice for digital signal processing

    CERN Document Server

    Tobin, Paul

    2007-01-01

    PSpice for Digital Signal Processing is the last in a series of five books using Cadence Orcad PSpice version 10.5 and introduces a very novel approach to learning digital signal processing (DSP). DSP is traditionally taught using Matlab/Simulink software but has some inherent weaknesses for students particularly at the introductory level. The 'plug in variables and play' nature of these software packages can lure the student into thinking they possess an understanding they don't actually have because these systems produce results quicklywithout revealing what is going on. However, it must be

  1. Signal recovery in imaging photoplethysmography

    International Nuclear Information System (INIS)

    Holton, Benjamin D; Mannapperuma, Kavan; Lesniewski, Peter J; Thomas, John C

    2013-01-01

    Imaging photoplethysmography is an emerging technique for the extraction of biometric information from people using video recordings. The focus is on extracting the cardiac heart rate of the subject by analysing the luminance of the colour video signal and identifying periodic components. Advanced signal processing is needed to recover the information required. In this paper, independent component analysis (ICA), principal component analysis, auto- and cross-correlation are investigated and compared with respect to their effectiveness in extracting the relevant information from video recordings. Results obtained are compared with those recorded by a modern commercial finger pulse oximeter. It is found that ICA produces the most consistent results. (paper)

  2. Queen signaling in social wasps

    DEFF Research Database (Denmark)

    van Zweden, Jelle Stijn; Bonckaert, Wim; Wenseleers, Tom

    2014-01-01

    Social Hymenoptera are characterized by a reproductive division of labor, whereby queens perform most of the reproduction and workers help to raise her offspring. A long-lasting debate is whether queens maintain this reproductive dominance by manipulating their daughter workers into remaining...... sterile (queen control), or if instead queens honestly signal their fertility and workers reproduce according to their own evolutionary incentives (queen signaling). Here, we test these competing hypotheses using data from Vespine wasps. We show that in natural colonies of the Saxon wasp, Dolichovespula...

  3. Subgraph detection using graph signals

    KAUST Repository

    Chepuri, Sundeep Prabhakar; Leus, Geert

    2017-01-01

    In this paper we develop statistical detection theory for graph signals. In particular, given two graphs, namely, a background graph that represents an usual activity and an alternative graph that represents some unusual activity, we are interested in answering the following question: To which of the two graphs does the observed graph signal fit the best? To begin with, we assume both the graphs are known, and derive an optimal Neyman-Pearson detector. Next, we derive a suboptimal detector for the case when the alternative graph is not known. The developed theory is illustrated with numerical experiments.

  4. Signal recovery in imaging photoplethysmography.

    Science.gov (United States)

    Holton, Benjamin D; Mannapperuma, Kavan; Lesniewski, Peter J; Thomas, John C

    2013-11-01

    Imaging photoplethysmography is an emerging technique for the extraction of biometric information from people using video recordings. The focus is on extracting the cardiac heart rate of the subject by analysing the luminance of the colour video signal and identifying periodic components. Advanced signal processing is needed to recover the information required. In this paper, independent component analysis (ICA), principal component analysis, auto- and cross-correlation are investigated and compared with respect to their effectiveness in extracting the relevant information from video recordings. Results obtained are compared with those recorded by a modern commercial finger pulse oximeter. It is found that ICA produces the most consistent results.

  5. DMPD: Signal integration between IFNgamma and TLR signalling pathways in macrophages. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 16920490 Signal integration between IFNgamma and TLR signalling pathways in macroph...tml) (.csml) Show Signal integration between IFNgamma and TLR signalling pathways in macrophages. PubmedID 16920490 Title Signal inte...gration between IFNgamma and TLR signalling pathways in

  6. Maternal health Indicators Signal Optimism

    African Journals Online (AJOL)

    user

    Maternal health Indicators Signal Optimism. Abraham Haileamlak, MD, Professor of Pediatrics and Child Health. Maternal health is a major health priority for international agencies and the Ethiopian. Government. Many low income countries including. Ethiopia, made substantial improvements in maternal health achieving ...

  7. Cholinergic signalling in gut immunity

    NARCIS (Netherlands)

    Dhawan, Shobhit; Cailotto, Cathy; Harthoorn, Lucien F.; de Jonge, Wouter J.

    2012-01-01

    The gut immune system shares many signalling molecules and receptors with the autonomic nervous system. A good example is the vagal neurotransmitter acetylcholine (ACh), for which many immune cell types express cholinergic receptors (AChR). In the last decade the vagal nerve has emerged as an

  8. Multipactor theory for multicarrier signals

    International Nuclear Information System (INIS)

    Anza, S.; Vicente, C.; Gil, J.; Mattes, M.; Raboso, D.; Boria, V. E.; Gimeno, B.

    2011-01-01

    This work presents a new theory of multipactor under multicarrier signals for parallel-plate geometries, assuming a homogeneous electric field and one-dimensional electron motion. It is the generalization of the nonstationary multipactor theory for single-carrier signals [S. Anza et al.,Phys. Plasmas 17, 062110 (2010)]. It is valid for multicarrier signals with an arbitrary number of carriers with different amplitude, arbitrary frequency, and phase conditions and for any material coating. This new theory is able to model the real dynamics of the electrons during the multipactor discharge for both single and double surface interactions. Among other parameters of the discharge, it calculates the evolution in time of the charge growth, electron absorption, and creation rates as well as the instantaneous secondary emission yield and order. An extensive set of numerical tests with particle-in-cell software has been carried out in order to validate the theory under many different conditions. This theoretical development constitutes the first multipactor theory which completely characterizes the multipactor discharge for arbitrary multicarrier signals, setting the first step for further investigations in the field.

  9. Eliminating ambiguity in digital signals

    Science.gov (United States)

    Weber, W. J., III

    1979-01-01

    Multiamplitude minimum shift keying (mamsk) transmission system, method of differential encoding overcomes problem of ambiguity associated with advanced digital-transmission techniques with little or no penalty in transmission rate, error rate, or system complexity. Principle of method states, if signal points are properly encoded and decoded, bits are detected correctly, regardless of phase ambiguities.

  10. Mathematical Modelling Plant Signalling Networks

    KAUST Repository

    Muraro, D.

    2013-01-01

    During the last two decades, molecular genetic studies and the completion of the sequencing of the Arabidopsis thaliana genome have increased knowledge of hormonal regulation in plants. These signal transduction pathways act in concert through gene regulatory and signalling networks whose main components have begun to be elucidated. Our understanding of the resulting cellular processes is hindered by the complex, and sometimes counter-intuitive, dynamics of the networks, which may be interconnected through feedback controls and cross-regulation. Mathematical modelling provides a valuable tool to investigate such dynamics and to perform in silico experiments that may not be easily carried out in a laboratory. In this article, we firstly review general methods for modelling gene and signalling networks and their application in plants. We then describe specific models of hormonal perception and cross-talk in plants. This mathematical analysis of sub-cellular molecular mechanisms paves the way for more comprehensive modelling studies of hormonal transport and signalling in a multi-scale setting. © EDP Sciences, 2013.

  11. [Automated processing of electrophysiologic signals].

    Science.gov (United States)

    Korenevskiĭ, N A; Gubanov, V V

    1995-01-01

    The paper outlines a diagram of a multichannel analyzer of electrophysiological signals while are significantly non-stationary (such as those of electroencephalograms, myograms, etc.), by using a method based on the ranging procedure by the change-over points which may be the points of infection, impaired locality, minima, maxima, discontinuity, etc.

  12. Biophysical Aspects of Transmembrane Signaling

    CERN Document Server

    Damjanovich, Sandor

    2005-01-01

    Transmembrane signaling is one of the most significant cell biological events in the life and death of cells in general and lymphocytes in particular. Until recently biochemists and biophysicists were not accustomed to thinking of these processes from the side of a high number of complex biochemical events and an equally high number of physical changes at molecular and cellular levels at the same time. Both types of researchers were convinced that their findings are the most decisive, having higher importance than the findings of the other scientist population. Both casts were wrong. Life, even at cellular level, has a number of interacting physical and biochemical mechanisms, which finally build up the creation of an "excited" cell that will respond to particular signals from the outer or inner world. This book handles both aspects of the signalling events, and in some cases tries to unify our concepts and help understand the signals that govern the life and death of our cells. Not only the understanding, bu...

  13. EUROmediCAT signal detection

    DEFF Research Database (Denmark)

    Given, Joanne E; Loane, Maria; Luteijn, Johannes Michiel

    2016-01-01

    AIMS: To evaluate congenital anomaly (CA)-medication exposure associations produced by the new EUROmediCAT signal detection system and determine which require further investigation. METHODS: Data from 15 EUROCAT registries (1995-2011) with medication exposures at the chemical substance (5th level...

  14. Syndecans, signaling, and cell adhesion

    DEFF Research Database (Denmark)

    Couchman, J R; Woods, A

    1996-01-01

    structures within the heparan sulfate chains, leaving the roles of chondroitin sulfate chains and extracellular portion of the core proteins to be elucidated. Evidence that syndecans are a class of receptor involved in cell adhesion is mounting, and their small cytoplasmic domains may link...... transmembrane signaling from matrix to cytoskeleton, as proposed for other classes of adhesion receptors....

  15. Tyrosine Phosphorylation in Brassinosteroid Signaling

    Science.gov (United States)

    Brassinosteroids (BRs) regulate plant growth and development through a complex signal transduction pathway involving BRASSINOSTEROID INSENSITIVE 1 (BRI1), which is the BR receptor, and its co-receptor BRI1-ASSOCIATED KINASE 1 (BAK1). Both proteins are classified as Ser/Thr protein kinases. Recently,...

  16. VEGF Signaling in Neurological Disorders

    Directory of Open Access Journals (Sweden)

    Joon W. Shim

    2018-01-01

    Full Text Available Vascular endothelial growth factor (VEGF is a potent growth factor playing diverse roles in vasculogenesis and angiogenesis. In the brain, VEGF mediates angiogenesis, neural migration and neuroprotection. As a permeability factor, excessive VEGF disrupts intracellular barriers, increases leakage of the choroid plexus endothelia, evokes edema, and activates the inflammatory pathway. Recently, we discovered that a heparin binding epidermal growth factor like growth factor (HB-EGF—a class of EGF receptor (EGFR family ligands—contributes to the development of hydrocephalus with subarachnoid hemorrhage through activation of VEGF signaling. The objective of this review is to entail a recent update on causes of death due to neurological disorders involving cerebrovascular and age-related neurological conditions and to understand the mechanism by which angiogenesis-dependent pathological events can be treated with VEGF antagonisms. The Global Burden of Disease study indicates that cancer and cardiovascular disease including ischemic and hemorrhagic stroke are two leading causes of death worldwide. The literature suggests that VEGF signaling in ischemic brains highlights the importance of concentration, timing, and alternate route of modulating VEGF signaling pathway. Molecular targets distinguishing two distinct pathways of VEGF signaling may provide novel therapies for the treatment of neurological disorders and for maintaining lower mortality due to these conditions.

  17. Robust power detector for wideband signals among many single tone signals

    Science.gov (United States)

    Musgrove, Cameron H.; Thompson, Douglas

    2018-03-06

    Various technologies for isolating a signal of interest from signals received contemporaneously by an antenna are described herein. A time period for which a signal of interest is present in a second signal can be identified based upon ratios of values of the second signal to the mean value of the second signal. When the ratio of the value of the second signal at a particular time to the mean of the second signal exceeds a threshold value, the signal of interest is considered to be present in the second signal.

  18. Predicting Secretory Proteins with SignalP

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2017-01-01

    SignalP is the currently most widely used program for prediction of signal peptides from amino acid sequences. Proteins with signal peptides are targeted to the secretory pathway, but are not necessarily secreted. After a brief introduction to the biology of signal peptides and the history...

  19. Measuring displacement signal with an accelerometer

    International Nuclear Information System (INIS)

    Han, Sang Bo

    2010-01-01

    An effective and simple way to reconstruct displacement signal from a measured acceleration signal is proposed in this paper. To reconstruct displacement signal by means of double-integrating the time domain acceleration signal, the Nyquist frequency of the digital sampling of the acceleration signal should be much higher than the highest frequency component of the signal. On the other hand, to reconstruct displacement signal by taking the inverse Fourier transform, the magnitude of the significant frequency components of the Fourier transform of the acceleration signal should be greater than the 6 dB increment line along the frequency axis. With a predetermined resolution in time and frequency domain, determined by the sampling rate to measure and record the original signal, reconstructing high-frequency signals in the time domain and reconstructing low-frequency signals in the frequency domain will produce biased errors. Furthermore, because of the DC components inevitably included in the sampling process, low-frequency components of the signals are overestimated when displacement signals are reconstructed from the Fourier transform of the acceleration signal. The proposed method utilizes curve-fitting around the significant frequency components of the Fourier transform of the acceleration signal before it is inverse-Fourier transformed. Curve-fitting around the dominant frequency components provides much better results than simply ignoring the insignificant frequency components of the signal

  20. Liquid argon TPC signal formation, signal processing and reconstruction techniques

    Science.gov (United States)

    Baller, B.

    2017-07-01

    This document describes a reconstruction chain that was developed for the ArgoNeuT and MicroBooNE experiments at Fermilab. These experiments study accelerator neutrino interactions that occur in a Liquid Argon Time Projection Chamber. Reconstructing the properties of particles produced in these interactions benefits from the knowledge of the micro-physics processes that affect the creation and transport of ionization electrons to the readout system. A wire signal deconvolution technique was developed to convert wire signals to a standard form for hit reconstruction, to remove artifacts in the electronics chain and to remove coherent noise. A unique clustering algorithm reconstructs line-like trajectories and vertices in two dimensions which are then matched to create of 3D objects. These techniques and algorithms are available to all experiments that use the LArSoft suite of software.

  1. The Fog signaling pathway: Insights into signaling in morphogenesis

    Science.gov (United States)

    Manning, Alyssa J.; Rogers, Stephen L.

    2014-01-01

    Epithelia form the building blocks of many tissue and organ types. Epithelial cells often form a contiguous 2-dimensional sheet that is held together by strong adhesions. The mechanical properties conferred by these adhesions allow the cells to undergo dramatic three-dimensional morphogenetic movements while maintaining cell–cell contacts during embryogenesis and post-embryonic development. The Drosophila Folded gastrulation pathway triggers epithelial cell shape changes that drive gastrulation and tissue folding and is one of the most extensively studied examples of epithelial morphogenesis. This pathway has yielded key insights into the signaling mechanisms and cellular machinery involved in epithelial remodeling. In this review, we discuss principles of morphogenesis and signaling that have been discovered through genetic and cell biological examination of this pathway. We also consider various regulatory mechanisms and the system's relevance to mammalian development. We propose future directions that will continue to broaden our knowledge of morphogenesis across taxa. PMID:25127992

  2. Experiment and practice on signal processing

    International Nuclear Information System (INIS)

    2002-11-01

    The contents of this book contains basic practice of CEM Tool, discrete time signal and experiment and practice of system, experiment and practice of discrete time signal sampling, practice of frequency analysis, experiment of digital filter design, application of digital signal processing, project related voice, basic principle of signal processing, the technique of basic image signal processing, biology astronomy and Robot soccer with apply of image signal processing technique, control video signal and project related image. It also has an introduction of CEM Linker I. O in the end.

  3. Experiment and practice on signal processing

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2002-11-15

    The contents of this book contains basic practice of CEM Tool, discrete time signal and experiment and practice of system, experiment and practice of discrete time signal sampling, practice of frequency analysis, experiment of digital filter design, application of digital signal processing, project related voice, basic principle of signal processing, the technique of basic image signal processing, biology astronomy and Robot soccer with apply of image signal processing technique, control video signal and project related image. It also has an introduction of CEM Linker I. O in the end.

  4. Flanking signal and mature peptide residues influence signal peptide cleavage

    Directory of Open Access Journals (Sweden)

    Ranganathan Shoba

    2008-12-01

    Full Text Available Abstract Background Signal peptides (SPs mediate the targeting of secretory precursor proteins to the correct subcellular compartments in prokaryotes and eukaryotes. Identifying these transient peptides is crucial to the medical, food and beverage and biotechnology industries yet our understanding of these peptides remains limited. This paper examines the most common type of signal peptides cleavable by the endoprotease signal peptidase I (SPase I, and the residues flanking the cleavage sites of three groups of signal peptide sequences, namely (i eukaryotes (Euk (ii Gram-positive (Gram+ bacteria, and (iii Gram-negative (Gram- bacteria. Results In this study, 2352 secretory peptide sequences from a variety of organisms with amino-terminal SPs are extracted from the manually curated SPdb database for analysis based on physicochemical properties such as pI, aliphatic index, GRAVY score, hydrophobicity, net charge and position-specific residue preferences. Our findings show that the three groups share several similarities in general, but they display distinctive features upon examination in terms of their amino acid compositions and frequencies, and various physico-chemical properties. Thus, analysis or prediction of their sequences should be separated and treated as distinct groups. Conclusion We conclude that the peptide segment recognized by SPase I extends to the start of the mature protein to a limited extent, upon our survey of the amino acid residues surrounding the cleavage processing site. These flanking residues possibly influence the cleavage processing and contribute to non-canonical cleavage sites. Our findings are applicable in defining more accurate prediction tools for recognition and identification of cleavage site of SPs.

  5. SignalPlant: an open signal processing software platform

    Czech Academy of Sciences Publication Activity Database

    Plešinger, Filip; Jurčo, Juraj; Halámek, Josef; Jurák, Pavel

    2016-01-01

    Roč. 37, č. 7 (2016), N38-N48 ISSN 0967-3334 R&D Projects: GA ČR GAP103/11/0933; GA MŠk(CZ) LO1212; GA ČR GAP102/12/2034 Institutional support: RVO:68081731 Keywords : data visualization * software * signal processing * ECG * EEG Subject RIV: FS - Medical Facilities ; Equipment Impact factor: 2.058, year: 2016

  6. Signal-to-Signal Ratio Independent Speaker Identification for Co-channel Speech Signals

    DEFF Research Database (Denmark)

    Saeidi, Rahim; Mowlaee, Pejman; Kinnunen, Tomi

    2010-01-01

    In this paper, we consider speaker identification for the co-channel scenario in which speech mixture from speakers is recorded by one microphone only. The goal is to identify both of the speakers from their mixed signal. High recognition accuracies have already been reported when an accurately...

  7. Signal processing for smart cards

    Science.gov (United States)

    Quisquater, Jean-Jacques; Samyde, David

    2003-06-01

    In 1998, Paul Kocher showed that when a smart card computes cryptographic algorithms, for signatures or encryption, its consumption or its radiations leak information. The keys or the secrets hidden in the card can then be recovered using a differential measurement based on the intercorrelation function. A lot of silicon manufacturers use desynchronization countermeasures to defeat power analysis. In this article we detail a new resynchronization technic. This method can be used to facilitate the use of a neural network to do the code recognition. It becomes possible to reverse engineer a software code automatically. Using data and clock separation methods, we show how to optimize the synchronization using signal processing. Then we compare these methods with watermarking methods for 1D and 2D signal. The very last watermarking detection improvements can be applied to signal processing for smart cards with very few modifications. Bayesian processing is one of the best ways to do Differential Power Analysis, and it is possible to extract a PIN code from a smart card in very few samples. So this article shows the need to continue to set up effective countermeasures for cryptographic processors. Although the idea to use advanced signal processing operators has been commonly known for a long time, no publication explains that results can be obtained. The main idea of differential measurement is to use the cross-correlation of two random variables and to repeat consumption measurements on the processor to be analyzed. We use two processors clocked at the same external frequency and computing the same data. The applications of our design are numerous. Two measurements provide the inputs of a central operator. With the most accurate operator we can improve the signal noise ratio, re-synchronize the acquisition clock with the internal one, or remove jitter. The analysis based on consumption or electromagnetic measurements can be improved using our structure. At first sight

  8. ROS signalling - specificity is required

    DEFF Research Database (Denmark)

    Møller, Ian M; Sweetlove, Lee J

    2010-01-01

    Reactive oxygen species (ROS) production increases in plants under stress. ROS can damage cellular components, but they can also act in signal transduction to help the cell counteract the oxidative damage in the stressed compartment. H2O2 might induce a general stress response, but it does not have...... the required specificity to selectively regulate nuclear genes required for dealing with localized stress, e.g. in chloroplasts or mitochondria. Here we argue that peptides deriving from proteolytic breakdown of oxidatively damaged proteins have the requisite specificity to act as secondary ROS messengers...... and regulate source-specific genes and in this way contribute to retrograde ROS signalling during oxidative stress. Likewise, unmodified peptides deriving from the breakdown of redundant proteins could help coordinate organellar and nuclear gene expression...

  9. Cellular semiotics and signal transduction

    DEFF Research Database (Denmark)

    Bruni, Luis Emilio

    2007-01-01

    Semiosis, the processes of production, communication and interpretation of signs - coding and de-coding - takes place within and between organisms. The term "endosemiosis" refers to the processes of interpretation and sign transmission inside an organism (as opposed to "exosemiosis", which refers...... to the processes of sign interpretation and transmission between organisms of the same or different species). In Biosemiotics it is customary to recognise the cell as the most elementary integration unit for semiosis. Therefore intra and intercellular communication constitute the departure point for the study...... considering semiotic logic in order to construct our understanding of living phenomena. Given the central integrating role of signal transduction in physiological and ecological studies, this chapter outlines its semiotic implications. The multi-modality and modularity of signal molecules and relative...

  10. Ambient temperature signalling in plants.

    Science.gov (United States)

    Wigge, Philip A

    2013-10-01

    Plants are exposed to daily and seasonal fluctuations in temperature. Within the 'ambient' temperature range (about 12-27°C for Arabidopsis) temperature differences have large effects on plant growth and development, disease resistance pathways and the circadian clock without activating temperature stress pathways. It is this developmental sensing and response to non-stressful temperatures that will be covered in this review. Recent advances have revealed key players in mediating temperature signals. The bHLH transcription factor PHYTOCHROME INTERACTING FACTOR4 (PIF4) has been shown to be a hub for multiple responses to warmer temperature in Arabidopsis, including flowering and hypocotyl elongation. Changes in chromatin state are involved in transmitting temperature signals to the transcriptome. Determining the precise mechanisms of temperature perception represents an exciting goal for the field. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Multimedia signal coding and transmission

    CERN Document Server

    Ohm, Jens-Rainer

    2015-01-01

    This textbook covers the theoretical background of one- and multidimensional signal processing, statistical analysis and modelling, coding and information theory with regard to the principles and design of image, video and audio compression systems. The theoretical concepts are augmented by practical examples of algorithms for multimedia signal coding technology, and related transmission aspects. On this basis, principles behind multimedia coding standards, including most recent developments like High Efficiency Video Coding, can be well understood. Furthermore, potential advances in future development are pointed out. Numerous figures and examples help to illustrate the concepts covered. The book was developed on the basis of a graduate-level university course, and most chapters are supplemented by exercises. The book is also a self-contained introduction both for researchers and developers of multimedia compression systems in industry.

  12. Acoustic Localization with Infrasonic Signals

    Science.gov (United States)

    Threatt, Arnesha; Elbing, Brian

    2015-11-01

    Numerous geophysical and anthropogenic events emit infrasonic frequencies (<20 Hz), including volcanoes, hurricanes, wind turbines and tornadoes. These sounds, which cannot be heard by the human ear, can be detected from large distances (in excess of 100 miles) due to low frequency acoustic signals having a very low decay rate in the atmosphere. Thus infrasound could be used for long-range, passive monitoring and detection of these events. An array of microphones separated by known distances can be used to locate a given source, which is known as acoustic localization. However, acoustic localization with infrasound is particularly challenging due to contamination from other signals, sensitivity to wind noise and producing a trusted source for system development. The objective of the current work is to create an infrasonic source using a propane torch wand or a subwoofer and locate the source using multiple infrasonic microphones. This presentation will present preliminary results from various microphone configurations used to locate the source.

  13. The IRS-1 signaling system.

    Science.gov (United States)

    Myers, M G; Sun, X J; White, M F

    1994-07-01

    Insulin-receptor substrate 1 (IRS-1) is a principal substrate of the receptor tyrosine kinase for insulin and insulin-like growth factor 1, and a substrate for a tyrosine kinase activated by interleukin 4. IRS-1 undergoes multisite tyrosine phosphorylation and mediates downstream signals by 'docking' various proteins that contain Src homology 2 domains. IRS-1 appears to be a unique molecule; however, 4PS, a protein found mainly in hemopoietic cells, may represent another member of this family.

  14. Cell signalling and phospholipid metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Boss, W.F.

    1990-01-01

    These studies explored whether phosphoinositide (PI) has a role in plants analogous to its role in animal cells. Although no parallel activity of PI in signal transduction was found in plant cells, activity of inositol phospholipid kinase was found to be modulated by light and by cell wall degrading enzymes. These studies indicate a major role for inositol phospholipids in plant growth and development as membrane effectors but not as a source of second messengers.

  15. Signals of new gauge bosons

    International Nuclear Information System (INIS)

    Djouadi, A.; Leike, A.; Riemann, T.; Schaile, D.; Verzegnassi, C.

    1991-12-01

    We analyze signals of additional neutral gauge bosons originating from E 6 and Left-Right models, at a future e + e - collider with 500 GeV c.m. energy. Radiative corrections as well as the experimental situation are taken into account. We show that masses considerably higher than the total energy can be probed, and that a discrimination between theoretical models is possible. (orig.)

  16. Signal and image multiresolution analysis

    CERN Document Server

    Ouahabi, Abdelialil

    2012-01-01

    Multiresolution analysis using the wavelet transform has received considerable attention in recent years by researchers in various fields. It is a powerful tool for efficiently representing signals and images at multiple levels of detail with many inherent advantages, including compression, level-of-detail display, progressive transmission, level-of-detail editing, filtering, modeling, fractals and multifractals, etc.This book aims to provide a simple formalization and new clarity on multiresolution analysis, rendering accessible obscure techniques, and merging, unifying or completing

  17. Job market signals and signs

    OpenAIRE

    Streb, Jorge M.

    2006-01-01

    What happens to job market signaling under two-dimensional asymmetric information? With 2 types of productivity and noise, the equilibrium remains separating if an extended single-crossing condition is satisfied. If not, there are partially pooling equilibria where only extreme types can be distinguished, and supplementary information is needed. On-the-job interaction gives employers private information on productivity, which employment relationships may reveal to the market. While sticky wag...

  18. Cytoskeleton in mast cell signaling

    Czech Academy of Sciences Publication Activity Database

    Dráber, Pavel; Sulimenko, Vadym; Dráberová, Eduarda

    2012-01-01

    Roč. 3, May (2012), s. 130 ISSN 1664-3224 R&D Projects: GA ČR GAP302/10/1701; GA ČR GPP302/11/P709; GA ČR GAP302/12/1673 Grant - others:ECST(XE) Action BM1007 Institutional research plan: CEZ:AV0Z50520514 Keywords : cytoskeleton * mast cell activation * signal transduction Subject RIV: EB - Genetics ; Molecular Biology

  19. Detection of signals in noise

    CERN Document Server

    McDonough, Robert N

    1995-01-01

    The Second Edition is an updated revision to the authors highly successful and widely used introduction to the principles and application of the statistical theory of signal detection. This book emphasizes those theories that have been found to be particularly useful in practice including principles applied to detection problems encountered in digital communications, radar, and sonar.Detection processing based upon the fast Fourier transform

  20. Intracellular calcium homeostasis and signaling.

    Science.gov (United States)

    Brini, Marisa; Calì, Tito; Ottolini, Denis; Carafoli, Ernesto

    2013-01-01

    Ca(2+) is a universal carrier of biological information: it controls cell life from its origin at fertilization to its end in the process of programmed cell death. Ca(2+) is a conventional diffusible second messenger released inside cells by the interaction of first messengers with plasma membrane receptors. However, it can also penetrate directly into cells to deliver information without the intermediation of first or second messengers. Even more distinctively, Ca(2+) can act as a first messenger, by interacting with a plasma membrane receptor to set in motion intracellular signaling pathways that involve Ca(2+) itself. Perhaps the most distinctive property of the Ca(2+) signal is its ambivalence: while essential to the correct functioning of cells, Ca(2+) becomes an agent that mediates cell distress, or even (toxic) cell death, if its concentration and movements inside cells are not carefully tuned. Ca(2+) is controlled by reversible complexation to specific proteins, which could be pure Ca(2+) buffers, or which, in addition to buffering Ca(2+), also decode its signal to pass it on to targets. The most important actors in the buffering of cell Ca(2+) are proteins that transport it across the plasma membrane and the membrane of the organelles: some have high Ca(2+) affinity and low transport capacity (e.g., Ca(2+) pumps), others have opposite properties (e.g., the Ca(2+) uptake system of mitochondria). Between the initial event of fertilization, and the terminal event of programmed cell death, the Ca(2+) signal regulates the most important activities of the cell, from the expression of genes, to heart and muscle contraction and other motility processes, to diverse metabolic pathways involved in the generation of cell fuels.

  1. Dynamics in atomic signaling games

    KAUST Repository

    Fox, Michael J.

    2015-04-08

    We study an atomic signaling game under stochastic evolutionary dynamics. There are a finite number of players who repeatedly update from a finite number of available languages/signaling strategies. Players imitate the most fit agents with high probability or mutate with low probability. We analyze the long-run distribution of states and show that, for sufficiently small mutation probability, its support is limited to efficient communication systems. We find that this behavior is insensitive to the particular choice of evolutionary dynamic, a property that is due to the game having a potential structure with a potential function corresponding to average fitness. Consequently, the model supports conclusions similar to those found in the literature on language competition. That is, we show that efficient languages eventually predominate the society while reproducing the empirical phenomenon of linguistic drift. The emergence of efficiency in the atomic case can be contrasted with results for non-atomic signaling games that establish the non-negligible possibility of convergence, under replicator dynamics, to states of unbounded efficiency loss.

  2. Calcium Signals from the Vacuole

    Directory of Open Access Journals (Sweden)

    Gerald Schönknecht

    2013-10-01

    Full Text Available The vacuole is by far the largest intracellular Ca2+ store in most plant cells. Here, the current knowledge about the molecular mechanisms of vacuolar Ca2+ release and Ca2+ uptake is summarized, and how different vacuolar Ca2+ channels and Ca2+ pumps may contribute to Ca2+ signaling in plant cells is discussed. To provide a phylogenetic perspective, the distribution of potential vacuolar Ca2+ transporters is compared for different clades of photosynthetic eukaryotes. There are several candidates for vacuolar Ca2+ channels that could elicit cytosolic [Ca2+] transients. Typical second messengers, such as InsP3 and cADPR, seem to trigger vacuolar Ca2+ release, but the molecular mechanism of this Ca2+ release still awaits elucidation. Some vacuolar Ca2+ channels have been identified on a molecular level, the voltage-dependent SV/TPC1 channel, and recently two cyclic-nucleotide-gated cation channels. However, their function in Ca2+ signaling still has to be demonstrated. Ca2+ pumps in addition to establishing long-term Ca2+ homeostasis can shape cytosolic [Ca2+] transients by limiting their amplitude and duration, and may thus affect Ca2+ signaling.

  3. Bile Acid Metabolism and Signaling

    Science.gov (United States)

    Chiang, John Y. L.

    2015-01-01

    Bile acids are important physiological agents for intestinal nutrient absorption and biliary secretion of lipids, toxic metabolites, and xenobiotics. Bile acids also are signaling molecules and metabolic regulators that activate nuclear receptors and G protein-coupled receptor (GPCR) signaling to regulate hepatic lipid, glucose, and energy homeostasis and maintain metabolic homeostasis. Conversion of cholesterol to bile acids is critical for maintaining cholesterol homeostasis and preventing accumulation of cholesterol, triglycerides, and toxic metabolites, and injury in the liver and other organs. Enterohepatic circulation of bile acids from the liver to intestine and back to the liver plays a central role in nutrient absorption and distribution, and metabolic regulation and homeostasis. This physiological process is regulated by a complex membrane transport system in the liver and intestine regulated by nuclear receptors. Toxic bile acids may cause inflammation, apoptosis, and cell death. On the other hand, bile acid-activated nuclear and GPCR signaling protects against inflammation in liver, intestine, and macrophages. Disorders in bile acid metabolism cause cholestatic liver diseases, dyslipidemia, fatty liver diseases, cardiovascular diseases, and diabetes. Bile acids, bile acid derivatives, and bile acid sequestrants are therapeutic agents for treating chronic liver diseases, obesity, and diabetes in humans. PMID:23897684

  4. Diabetes: Models, Signals and control

    Science.gov (United States)

    Cobelli, C.

    2010-07-01

    Diabetes and its complications impose significant economic consequences on individuals, families, health systems, and countries. The control of diabetes is an interdisciplinary endeavor, which includes significant components of modeling, signal processing and control. Models: first, I will discuss the minimal (coarse) models which describe the key components of the system functionality and are capable of measuring crucial processes of glucose metabolism and insulin control in health and diabetes; then, the maximal (fine-grain) models which include comprehensively all available knowledge about system functionality and are capable to simulate the glucose-insulin system in diabetes, thus making it possible to create simulation scenarios whereby cost effective experiments can be conducted in silico to assess the efficacy of various treatment strategies - in particular I will focus on the first in silico simulation model accepted by FDA as a substitute to animal trials in the quest for optimal diabetes control. Signals: I will review metabolic monitoring, with a particular emphasis on the new continuous glucose sensors, on the crucial role of models to enhance the interpretation of their time-series signals, and on the opportunities that they present for automation of diabetes control. Control: I will review control strategies that have been successfully employed in vivo or in silico, presenting a promise for the development of a future artificial pancreas and, in particular, I will discuss a modular architecture for building closed-loop control systems, including insulin delivery and patient safety supervision layers.

  5. Dynamics in atomic signaling games

    KAUST Repository

    Fox, Michael J.; Touri, Behrouz; Shamma, Jeff S.

    2015-01-01

    We study an atomic signaling game under stochastic evolutionary dynamics. There are a finite number of players who repeatedly update from a finite number of available languages/signaling strategies. Players imitate the most fit agents with high probability or mutate with low probability. We analyze the long-run distribution of states and show that, for sufficiently small mutation probability, its support is limited to efficient communication systems. We find that this behavior is insensitive to the particular choice of evolutionary dynamic, a property that is due to the game having a potential structure with a potential function corresponding to average fitness. Consequently, the model supports conclusions similar to those found in the literature on language competition. That is, we show that efficient languages eventually predominate the society while reproducing the empirical phenomenon of linguistic drift. The emergence of efficiency in the atomic case can be contrasted with results for non-atomic signaling games that establish the non-negligible possibility of convergence, under replicator dynamics, to states of unbounded efficiency loss.

  6. Signalling crosstalk in plants: emerging issues.

    Science.gov (United States)

    Taylor, Jane E; McAinsh, Martin R

    2004-01-01

    The Oxford English Dictionary defines crosstalk as 'unwanted transfer of signals between communication channels'. How does this definition relate to the way in which we view the organization and function of signalling pathways? Recent advances in the field of plant signalling have challenged the traditional view of a signalling transduction cascade as isolated linear pathways. Instead the picture emerging of the mechanisms by which plants transduce environmental signals is of the interaction between transduction chains. The manner in which these interactions occur (and indeed whether the transfer of these signals is 'unwanted' or beneficial) is currently the topic of intense research.

  7. Advanced digital signal processing and noise reduction

    CERN Document Server

    Vaseghi, Saeed V

    2008-01-01

    Digital signal processing plays a central role in the development of modern communication and information processing systems. The theory and application of signal processing is concerned with the identification, modelling and utilisation of patterns and structures in a signal process. The observation signals are often distorted, incomplete and noisy and therefore noise reduction, the removal of channel distortion, and replacement of lost samples are important parts of a signal processing system. The fourth edition of Advanced Digital Signal Processing and Noise Reduction updates an

  8. Problems of the Synthesis of Radar Signals,

    Science.gov (United States)

    1981-05-14

    recorded, finding out approximation/approach to certain signal x(t) , logical to ascribe a(w.) the phase spc -ctrum cf signal xft). the diffsrences...of the given cne). e will r~ spc -.ively d-stirguish se- cf Ch, signals of fixed Fericd cf rims X. frcm the sst cf Ch. signals of drbitrary duration X...XeXP~j IjM+a .t * An error in asymptotic soluticr can be ccnsidered now, being congruent/ squating found ChM signal z.,g(t) with ganerating signal

  9. Detection of Noise in Composite Step Signal Pattern by Visualizing Signal Waveforms

    Directory of Open Access Journals (Sweden)

    Chaman Verma

    2018-03-01

    Full Text Available The Step Composite Signals is the combination of vital informative signals that are compressed and coded to produce a predefined test image on a display device. It carries the desired sequence of information from source to destination. This information may be transmitted as digital signal, video information or data signal required as an input for the destination module. For testing of display panels, Composite Test Signals are the most important attribute of test signal transmission system. In the current research paper we present an approach for the noise detection in Composite Step Signal by analysing Composite Step Signal waveforms. The analysis of the signal waveforms reveals that the noise affected components of the signal and subsequently noise reduction process is initiated which targets noisy signal component only. Thus the quality of signal is not compromised during noise reduction process.

  10. EUROmediCAT signal detection

    DEFF Research Database (Denmark)

    Luteijn, Johannes Michiel; Morris, Joan K; Garne, Ester

    2016-01-01

    AIMS: Information about medication safety in pregnancy is inadequate. We aimed to develop a signal detection methodology to routinely identify unusual associations between medications and congenital anomalies using data collected by 15 European congenital anomaly registries. METHODS: EUROmedi...... for 40 385 medication anomaly combinations in the data. Simes multiple testing procedure with a 50% false discovery rate (FDR) identified associations least likely to be due to chance and those associations with more than two cases with the exposure and the anomaly were selected for further investigation...

  11. Small signal microwave amplifier design

    CERN Document Server

    Grosch, Theodore

    2000-01-01

    This book explains techniques and examples for designing stable amplifiers for high-frequency applications in which the signal is small and the amplifier circuit is linear. An in-depth discussion of linear network theory provides the foundation needed to develop actual designs. Examples throughout the book will show you how to apply the knowledge gained in each chapter leading to the complex design of low noise amplifiers. Many exercises at the end of each chapter will help students to practice their skills. The solutions to these design problems are available in an accompanying solutions book

  12. Fixed-point signal processing

    CERN Document Server

    Padgett, Wayne T

    2009-01-01

    This book is intended to fill the gap between the ""ideal precision"" digital signal processing (DSP) that is widely taught, and the limited precision implementation skills that are commonly required in fixed-point processors and field programmable gate arrays (FPGAs). These skills are often neglected at the university level, particularly for undergraduates. We have attempted to create a resource both for a DSP elective course and for the practicing engineer with a need to understand fixed-point implementation. Although we assume a background in DSP, Chapter 2 contains a review of basic theory

  13. Low power digital signal processing

    DEFF Research Database (Denmark)

    Paker, Ozgun

    2003-01-01

    hardwired ASICs and more than 6 21 times lower than current state of the art low-power DSP processors. An orthogonal but practical contribution of this thesis is the test bench implementation. A PCI-based FPGA board has been used to equip a standard desktop PC with tester facilities. The test bench proved...... to be a viable alternative to conventional expensive test equipment. Finally, the work presented in this thesis has been published at several IEEE workshops and conferences, and in the Journal of VLSI Signal Processing....

  14. New shaper of scintillation signals

    International Nuclear Information System (INIS)

    Brovchenko, V.G.

    2001-01-01

    Summation of the exponential shape pulse (abrupt front, exponential fall-off) with the pulse, proportional to its integral (the integration time constant is equal to the exponent fall-off constant), results in the pulse, the apex whereof is horizontal (parallel to the base line). Such a pulse is suitable for registration through standard analog-to-digital converters of the consecutive binary approximation, The described scheme is accomplished for verification of the basic principle of the shaper action. The parameters of the scheme are approximated to those ones, necessary for processing scintillation signals NaI(Tl) [ru

  15. Small Signal Loudspeaker Impedance Emulator

    DEFF Research Database (Denmark)

    Iversen, Niels Elkjær; Knott, Arnold

    2014-01-01

    Specifying the performance of audio amplifiers is typically done by playing sine waves into a pure ohmic load. However real loudspeaker impedances are not purely ohmic but characterized by the mechanical resonance between the mass of the diaphragm and the compliance of its suspension which vary...... from driver to driver. Therefore, a loudspeaker emulator capable of adjusting its impedance to that of a given driver is desired for measurement purposes. This paper proposes a loudspeaker emulator circuit for small signals. Simulations and experimental results are compared and show that it is possible...... to emulate the loudspeaker impedance with an electric circuit and that its resonance frequency can be changed by tuning two resistors....

  16. Biomedical signals, imaging, and informatics

    CERN Document Server

    Bronzino, Joseph D

    2014-01-01

    Known as the bible of biomedical engineering, The Biomedical Engineering Handbook, Fourth Edition, sets the standard against which all other references of this nature are measured. As such, it has served as a major resource for both skilled professionals and novices to biomedical engineering.Biomedical Signals, Imaging, and Informatics, the third volume of the handbook, presents material from respected scientists with diverse backgrounds in biosignal processing, medical imaging, infrared imaging, and medical informatics.More than three dozen specific topics are examined, including biomedical s

  17. Cognitive Algorithms for Signal Processing

    Science.gov (United States)

    2011-03-18

    Analysis of Millennial Spiritual Issues,” Zygon, Journal of Science and Religion , 43(4), 797-821, 2008. [46] R. Linnehan, C. Mutz, L.I. Perlovsky, B...dimensions of X and Y : (a) true ‘smile’ and ‘frown’ patterns are shown without clutter; (b) actual image available for recognition (signal is below...clutter in 2 dimensions of X(n) = (X, Y ), is given by l(X(n)|m = clutter) = 1/ (X •  Y ), X = (Xmax-Xmin),  Y = (Ymax-Ymin); (6) 13 Minimal

  18. Expert AE signal arrival detection

    Czech Academy of Sciences Publication Activity Database

    Chlada, Milan; Převorovský, Zdeněk

    2011-01-01

    Roč. 6, 3/4 (2011), s. 191-205 ISSN 1741-8410. [NDT in PROGRESS /4./. Praha, 05.11.2007-07.11.2007] R&D Projects: GA MPO(CZ) FR-TI1/274; GA ČR GA101/07/1518 Institutional research plan: CEZ:AV0Z20760514 Keywords : acoustic emission * signal arrival detection Subject RIV: BI - Acoustics http://www.inderscience.com/search/index.php?mainAction=search& action =record&rec_id=43215&prevQuery=&ps=10&m=or

  19. Signaling and the Education Premium

    OpenAIRE

    Gregory Kurtzon

    2004-01-01

    A large portion of the rise in the education premium can be explained by a signaling theory of education which predicts that in the future, increases in the education level of the workforce will actually cause the education premium to rise, simply because different workers are being labeled as “highly educated†. This prediction is supported by past behavior of the high school education premium. It runs counter to the view that increases in the relative supply of high education workers wil...

  20. Surface Weather, Signal Service and Weather Bureau

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Surface Weather, Signal Service and Weather Bureau (SWSSWB) Records primarily created by the United States Army Signal Service from 1819 until the paid and voluntary...

  1. Ghost signals in Allison emittance scanners

    International Nuclear Information System (INIS)

    Stockli, Martin P.; Leitner, M.; Moehs, D.P.; Keller, R.; Welton, R.F.

    2004-01-01

    For over 20 years, Allison scanners have been used to measure emittances of low-energy ion beams. We show that scanning large trajectory angles produces ghost signals caused by the sampled beamlet impacting on an electric deflection plate. The ghost signal strength is proportional to the amount of beam entering the scanner. Depending on the ions, and their velocity, the ghost signals can have the opposite or the same polarity as the main beam signals. The ghost signals cause significant errors in the emittance estimates because they appear at large trajectory angles. These ghost signals often go undetected because they partly overlap with the real signals, are mostly below the 1% level, and often hide in the noise. A simple deflection plate modification is shown to reduce the ghost signal strength by over 99%

  2. Detection of Transient Signals in Doppler Spectra

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Signal processing is used to detect transient signals in the presence of noise. Two embodiments are disclosed. In both embodiments, the time series from a remote...

  3. Sonic Hedgehog Signaling Promotes Tumor Growth

    National Research Council Canada - National Science Library

    Bushman, Wade

    2007-01-01

    ... of the DOD New Investigator award indicate that Shh signaling promotes tumor growth. This proposal addresses the hypothesis that Sonic hedgehog signaling promotes tumor growth by activating stromal cell gene expression...

  4. Induced disease resistance signaling in plants

    NARCIS (Netherlands)

    Verhagen, B.W.M.; Loon, L.C. van; Pieterse, C.M.J.

    2006-01-01

    To protect themselves from disease, plants have evolved sophisticated inducible defense mechanisms in which the signal molecules salicylic acid, jasmonic acid and ethylene often play crucial roles. Elucidation of signaling pathways controlling induced disease resistance is a major objective in

  5. Ghost Signals In Allison Emittance Scanners

    International Nuclear Information System (INIS)

    Stockli, Martin P.; Leitner, M.; Keller, R.; Moehs, D.P.; Welton, R. F.

    2005-01-01

    For over 20 years, Allison scanners have been used to measure emittances of low-energy ion beams. We show that scanning large trajectory angles produces ghost signals caused by the sampled beamlet impacting on an electric deflection plate. The ghost signal strength is proportional to the amount of beam entering the scanner. Depending on the ions, and their velocity, the ghost signals can have the opposite or the same polarity as the main beam signals. The ghost signals cause significant errors in the emittance estimates because they appear at large trajectory angles. These ghost signals often go undetected because they partly overlap with the real signals, are mostly below the 1% level, and often hide in the noise. A simple deflection plate modification is shown to reduce the ghost signal strength by over 99%

  6. Blind Signal Classification via Spare Coding

    Science.gov (United States)

    2016-04-10

    Blind Signal Classification via Sparse Coding Youngjune Gwon MIT Lincoln Laboratory gyj@ll.mit.edu Siamak Dastangoo MIT Lincoln Laboratory sia...achieve blind signal classification with no prior knowledge about signals (e.g., MCS, pulse shaping) in an arbitrary RF channel. Since modulated RF...classification method. Our results indicate that we can separate different classes of digitally modulated signals from blind sampling with 70.3% recall and 24.6

  7. Purinergic signalling in epithelial ion transport

    DEFF Research Database (Denmark)

    Novak, Ivana

    2011-01-01

    , including ion transport. In this review, I will first introduce the main components of the extracellular ATP signalling, which have become known as the purinergic signalling system. With more than 50 components or processes, just at cell membranes, it ranks as one of the most versatile signalling systems......-regulators of secretion. On an organ level, both receptor types can exert physiological functions and together with other partners in the purinergic signalling, integrated models for epithelial secretion and absorption are emerging....

  8. Signals of lepton number violation

    CERN Document Server

    Panella, O; Srivastava, Y N

    1999-01-01

    The production of like-sign-dileptons (LSD), in the high energy lepton number violating ( Delta L=+2) reaction, pp to 2jets+l/sup +/l /sup +/, (l=e, mu , tau ), of interest for the experiments to be performed at the forthcoming Large Hadron Collider (LHC), is reported, taking up a composite model scenario in which the exchanged virtual composite neutrino is assumed to be a Majorana particle. Numerical estimates of the corresponding signal cross-section that implement kinematical cuts needed to suppress the standard model background, are presented which show that in some regions of the parameter space the total number of LSD events is well above the background. Assuming non-observation of the LSD signal it is found that LHC would exclude a composite Majorana neutrino up to 700 GeV (if one requires 10 events for discovery). The sensitivity of LHC experiments to the parameter space is then compared to that of the next generation of neutrinoless double beta decay ( beta beta /sub 0 nu /) experiment, GENIUS, and i...

  9. Redox signaling in acute pancreatitis

    Science.gov (United States)

    Pérez, Salvador; Pereda, Javier; Sabater, Luis; Sastre, Juan

    2015-01-01

    Acute pancreatitis is an inflammatory process of the pancreatic gland that eventually may lead to a severe systemic inflammatory response. A key event in pancreatic damage is the intracellular activation of NF-κB and zymogens, involving also calcium, cathepsins, pH disorders, autophagy, and cell death, particularly necrosis. This review focuses on the new role of redox signaling in acute pancreatitis. Oxidative stress and redox status are involved in the onset of acute pancreatitis and also in the development of the systemic inflammatory response, being glutathione depletion, xanthine oxidase activation, and thiol oxidation in proteins critical features of the disease in the pancreas. On the other hand, the release of extracellular hemoglobin into the circulation from the ascitic fluid in severe necrotizing pancreatitis enhances lipid peroxidation in plasma and the inflammatory infiltrate into the lung and up-regulates the HIF–VEGF pathway, contributing to the systemic inflammatory response. Therefore, redox signaling and oxidative stress contribute to the local and systemic inflammatory response during acute pancreatitis. PMID:25778551

  10. Redox signaling in acute pancreatitis

    Directory of Open Access Journals (Sweden)

    Salvador Pérez

    2015-08-01

    Full Text Available Acute pancreatitis is an inflammatory process of the pancreatic gland that eventually may lead to a severe systemic inflammatory response. A key event in pancreatic damage is the intracellular activation of NF-κB and zymogens, involving also calcium, cathepsins, pH disorders, autophagy, and cell death, particularly necrosis. This review focuses on the new role of redox signaling in acute pancreatitis. Oxidative stress and redox status are involved in the onset of acute pancreatitis and also in the development of the systemic inflammatory response, being glutathione depletion, xanthine oxidase activation, and thiol oxidation in proteins critical features of the disease in the pancreas. On the other hand, the release of extracellular hemoglobin into the circulation from the ascitic fluid in severe necrotizing pancreatitis enhances lipid peroxidation in plasma and the inflammatory infiltrate into the lung and up-regulates the HIF–VEGF pathway, contributing to the systemic inflammatory response. Therefore, redox signaling and oxidative stress contribute to the local and systemic inflammatory response during acute pancreatitis.

  11. Prostaglandin Receptor Signaling in Disease

    Directory of Open Access Journals (Sweden)

    Toshiyuki Matsuoka

    2007-01-01

    Full Text Available Prostanoids, consisting of the prostaglandins (PGs and the thromboxanes (TXs, are a group of lipid mediators formed in response to various stimuli. They include PGD2, PGE2, PGF2α, PGI2, and TXA2. They are released outside of the cells immediately after synthesis, and exert their actions by binding to a G-protein coupled rhodopsin-type receptor on the surface of target cells. There are eight types of the prostanoid receptors conserved in mammals from mouse to human. They are the PGD receptor (DP, four subtypes of the PGE receptor (EP1, EP2, EP3, and EP4, the PGF receptor (FP, PGI receptor (IP, and TXA receptor (TP. Recently, mice deficient in each of these prostanoid receptors were generated and subjected to various experimental models of disease. These studies have revealed the roles of PG receptor signaling in various pathological conditions, and suggest that selective manipulation of the prostanoid receptors may be beneficial in treatment of the pathological conditions. Here we review these recent findings of roles of prostanoid receptor signaling and their therapeutic implications.

  12. Simulation of Silicon Photomultiplier Signals

    Science.gov (United States)

    Seifert, Stefan; van Dam, Herman T.; Huizenga, Jan; Vinke, Ruud; Dendooven, Peter; Lohner, Herbert; Schaart, Dennis R.

    2009-12-01

    In a silicon photomultiplier (SiPM), also referred to as multi-pixel photon counter (MPPC), many Geiger-mode avalanche photodiodes (GM-APDs) are connected in parallel so as to combine the photon counting capabilities of each of these so-called microcells into a proportional light sensor. The discharge of a single microcell is relatively well understood and electronic models exist to simulate this process. In this paper we introduce an extended model that is able to simulate the simultaneous discharge of multiple cells. This model is used to predict the SiPM signal in response to fast light pulses as a function of the number of fired cells, taking into account the influence of the input impedance of the SiPM preamplifier. The model predicts that the electronic signal is not proportional to the number of fired cells if the preamplifier input impedance is not zero. This effect becomes more important for SiPMs with lower parasitic capacitance (which otherwise is a favorable property). The model is validated by comparing its predictions to experimental data obtained with two different SiPMs (Hamamatsu S10362-11-25u and Hamamatsu S10362-33-25c) illuminated with ps laser pulses. The experimental results are in good agreement with the model predictions.

  13. Extracellular nucleotide signaling in plants

    Energy Technology Data Exchange (ETDEWEB)

    Stacey, Gary [Univ. of Missouri, Columbia, MO (United States)

    2016-09-08

    Over the life of this funded project, our research group identified and characterized two key receptor proteins in plants; one mediating the innate immunity response to chitin and the other elucidating the key receptor for extracellular ATP. In the case of chitin recognition, we recently described the quaternary structure of this receptor, shedding light on how the receptor functions. Perhaps more importantly, we demonstrated that all plants have the ability to recognize both chitin oligomers and lipochitooligosacchardes, fundamentally changing how the community views the evolution of these systems and strategies that might be used, for example, to extend symbiotic nitrogen fixation to non-legumes. Our discovery of DORN1 opens a new chapter in plant physiology documenting conclusively that eATP is an important extracellular signal in plants, as it is in animals. At this point, we cannot predict just how far reaching this discovery may prove to be but we are convinced that eATP signaling is fundamental to plant growth and development and, hence, we believe that the future will be very exciting for the study of DORN1 and its overall function in plants.

  14. Cytoskeleton in Mast Cell Signaling

    Science.gov (United States)

    Dráber, Pavel; Sulimenko, Vadym; Dráberová, Eduarda

    2012-01-01

    Mast cell activation mediated by the high affinity receptor for IgE (FcεRI) is a key event in allergic response and inflammation. Other receptors on mast cells, as c-Kit for stem cell factor and G protein-coupled receptors (GPCRs) synergistically enhance the FcεRI-mediated release of inflammatory mediators. Activation of various signaling pathways in mast cells results in changes in cell morphology, adhesion to substrate, exocytosis, and migration. Reorganization of cytoskeleton is pivotal in all these processes. Cytoskeletal proteins also play an important role in initial stages of FcεRI and other surface receptors induced triggering. Highly dynamic microtubules formed by αβ-tubulin dimers as well as microfilaments build up from polymerized actin are affected in activated cells by kinases/phosphatases, Rho GTPases and changes in concentration of cytosolic Ca2+. Also important are nucleation proteins; the γ-tubulin complexes in case of microtubules or Arp 2/3 complex with its nucleation promoting factors and formins in case of microfilaments. The dynamic nature of microtubules and microfilaments in activated cells depends on many associated/regulatory proteins. Changes in rigidity of activated mast cells reflect changes in intermediate filaments build up from vimentin. This review offers a critical appraisal of current knowledge on the role of cytoskeleton in mast cells signaling. PMID:22654883

  15. TOR Signaling and Nutrient Sensing.

    Science.gov (United States)

    Dobrenel, Thomas; Caldana, Camila; Hanson, Johannes; Robaglia, Christophe; Vincentz, Michel; Veit, Bruce; Meyer, Christian

    2016-04-29

    All living organisms rely on nutrients to sustain cell metabolism and energy production, which in turn need to be adjusted based on available resources. The evolutionarily conserved target of rapamycin (TOR) protein kinase is a central regulatory hub that connects environmental information about the quantity and quality of nutrients to developmental and metabolic processes in order to maintain cellular homeostasis. TOR is activated by both nitrogen and carbon metabolites and promotes energy-consuming processes such as cell division, mRNA translation, and anabolism in times of abundance while repressing nutrient remobilization through autophagy. In animals and yeasts, TOR acts antagonistically to the starvation-induced AMP-activated kinase (AMPK)/sucrose nonfermenting 1 (Snf1) kinase, called Snf1-related kinase 1 (SnRK1) in plants. This review summarizes the immense knowledge on the relationship between TOR signaling and nutrients in nonphotosynthetic organisms and presents recent findings in plants that illuminate the crucial role of this pathway in conveying nutrient-derived signals and regulating many aspects of metabolism and growth.

  16. Calcium signaling in smooth muscle.

    Science.gov (United States)

    Hill-Eubanks, David C; Werner, Matthias E; Heppner, Thomas J; Nelson, Mark T

    2011-09-01

    Changes in intracellular Ca(2+) are central to the function of smooth muscle, which lines the walls of all hollow organs. These changes take a variety of forms, from sustained, cell-wide increases to temporally varying, localized changes. The nature of the Ca(2+) signal is a reflection of the source of Ca(2+) (extracellular or intracellular) and the molecular entity responsible for generating it. Depending on the specific channel involved and the detection technology employed, extracellular Ca(2+) entry may be detected optically as graded elevations in intracellular Ca(2+), junctional Ca(2+) transients, Ca(2+) flashes, or Ca(2+) sparklets, whereas release of Ca(2+) from intracellular stores may manifest as Ca(2+) sparks, Ca(2+) puffs, or Ca(2+) waves. These diverse Ca(2+) signals collectively regulate a variety of functions. Some functions, such as contractility, are unique to smooth muscle; others are common to other excitable cells (e.g., modulation of membrane potential) and nonexcitable cells (e.g., regulation of gene expression).

  17. Temporal expectation weights visual signals over auditory signals.

    Science.gov (United States)

    Menceloglu, Melisa; Grabowecky, Marcia; Suzuki, Satoru

    2017-04-01

    Temporal expectation is a process by which people use temporally structured sensory information to explicitly or implicitly predict the onset and/or the duration of future events. Because timing plays a critical role in crossmodal interactions, we investigated how temporal expectation influenced auditory-visual interaction, using an auditory-visual crossmodal congruity effect as a measure of crossmodal interaction. For auditory identification, an incongruent visual stimulus produced stronger interference when the crossmodal stimulus was presented with an expected rather than an unexpected timing. In contrast, for visual identification, an incongruent auditory stimulus produced weaker interference when the crossmodal stimulus was presented with an expected rather than an unexpected timing. The fact that temporal expectation made visual distractors more potent and visual targets less susceptible to auditory interference suggests that temporal expectation increases the perceptual weight of visual signals.

  18. Evaluation of blind signal separation methods

    NARCIS (Netherlands)

    Schobben, D.W.E.; Torkkola, K.; Smaragdis, P.

    1999-01-01

    Recently many new Blind Signal Separation BSS algorithms have been introduced Authors evaluate the performance of their algorithms in various ways Among these are speech recognition rates plots of separated signals plots of cascaded mixingunmixing impulse responses and signal to noise ratios Clearly

  19. Audibility of modulation noise in stationary signals

    NARCIS (Netherlands)

    Neelen, J.J.M.

    1970-01-01

    Recordings of an acoustic signal on magnetic tape often show noise, which may be divided into two main classes: additive noise and multiplicative noise. A characteristic of the latter is that it is weak with weak signals and strong with strong signals. This modulation noise has been subjected to a

  20. Radar signal analysis and processing using Matlab

    CERN Document Server

    Mahafza, Bassem R

    2008-01-01

    Offering radar-related software for the analysis and design of radar waveform and signal processing, this book provides comprehensive coverage of radar signals and signal processing techniques and algorithms. It contains numerous graphical plots, common radar-related functions, table format outputs, and end-of-chapter problems. The complete set of MATLAB[registered] functions and routines are available for download online.

  1. Signal processing for boiling noise detection

    International Nuclear Information System (INIS)

    Ledwidge, T.J.; Black, J.L.

    1989-01-01

    The present paper deals with investigations of acoustic signals from a boiling experiment performed on the KNS I loop at KfK Karlsruhe. Signals have been analysed in frequency as well as in time domain. Signal characteristics successfully used to detect the boiling process have been found in time domain. (author). 6 refs, figs

  2. 33 CFR 118.130 - Fog signals.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Fog signals. 118.130 Section 118... LIGHTING AND OTHER SIGNALS § 118.130 Fog signals. On waterways where visibility is frequently reduced due to fog or other causes, the District Commander may require or authorize the installation of one or...

  3. 30 CFR 56.14219 - Brakeman signals.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Brakeman signals. 56.14219 Section 56.14219... Safety Practices and Operational Procedures § 56.14219 Brakeman signals. When a train is under the direction of a brakeman and the train operator cannot clearly recognize the brakeman's signals, the train...

  4. 30 CFR 57.14219 - Brakeman signals.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Brakeman signals. 57.14219 Section 57.14219... Equipment Safety Practices and Operational Procedures § 57.14219 Brakeman signals. When a train is under the direction of a brakeman and the train operator cannot clearly recognize the brakeman's signals, the train...

  5. 40 CFR 156.64 - Signal word.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 23 2010-07-01 2010-07-01 false Signal word. 156.64 Section 156.64... REQUIREMENTS FOR PESTICIDES AND DEVICES Human Hazard and Precautionary Statements § 156.64 Signal word. (a... signal word, reflecting the highest Toxicity Category (Category I is the highest toxicity category) to...

  6. Next Steps in Signaling (NSIS): Framework

    NARCIS (Netherlands)

    Hancock, R.; Loughney, J.; van den Bosch, S.; Hancock, R.; Karagiannis, Georgios; Loughney, J.; van den Bosch, S.

    The Next Steps in Signaling (NSIS) working group is considering protocols for signaling information about a data flow along its path in the network. The NSIS suite of protocols is envisioned to support various signaling applications that need to install and/or manipulate such state in the network.

  7. 49 CFR 236.806 - Signal, home.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Signal, home. 236.806 Section 236.806 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... Signal, home. A roadway signal at the entrance to a route or block to govern trains in entering and using...

  8. 49 CFR 236.804 - Signal, block.

    Science.gov (United States)

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Signal, block. 236.804 Section 236.804 Transportation Other Regulations Relating to Transportation (Continued) FEDERAL RAILROAD ADMINISTRATION... Signal, block. A roadway signal operated either automatically or manually at the entrance to a block. ...

  9. Programmable delay circuit for sparker signal analysis

    Digital Repository Service at National Institute of Oceanography (India)

    Pathak, D.

    The sparker echo signal had been recorded along with the EPC recorder trigger on audio cassettes in a dual channel analog recorder. The sparker signal in the analog form had to be digitised for further signal processing techniques to be performed...

  10. Adaptive Evolution of Signaling Partners

    Science.gov (United States)

    Urano, Daisuke; Dong, Taoran; Bennetzen, Jeffrey L.; Jones, Alan M.

    2015-01-01

    Proteins that interact coevolve their structures. When mutation disrupts the interaction, compensation by the partner occurs to restore interaction otherwise counterselection occurs. We show in this study how a destabilizing mutation in one protein is compensated by a stabilizing mutation in its protein partner and their coevolving path. The pathway in this case and likely a general principle of coevolution is that the compensatory change must tolerate both the original and derived structures with equivalence in function and activity. Evolution of the structure of signaling elements in a network is constrained by specific protein pair interactions, by requisite conformational changes, and by catalytic activity. The heterotrimeric G protein-coupled signaling is a paragon of this protein interaction/function complexity and our deep understanding of this pathway in diverse organisms lends itself to evolutionary study. Regulators of G protein Signaling (RGS) proteins accelerate the intrinsic GTP hydrolysis rate of the Gα subunit of the heterotrimeric G protein complex. An important RGS-contact site is a hydroxyl-bearing residue on the switch I region of Gα subunits in animals and most plants, such as Arabidopsis. The exception is the grasses (e.g., rice, maize, sugarcane, millets); these plants have Gα subunits that replaced the critical hydroxyl-bearing threonine with a destabilizing asparagine shown to disrupt interaction between Arabidopsis RGS protein (AtRGS1) and the grass Gα subunit. With one known exception (Setaria italica), grasses do not encode RGS genes. One parsimonious deduction is that the RGS gene was lost in the ancestor to the grasses and then recently acquired horizontally in the lineage S. italica from a nongrass monocot. Like all investigated grasses, S. italica has the Gα subunit with the destabilizing asparagine residue in the protein interface but, unlike other known grass genomes, still encodes an expressed RGS gene, SiRGS1. SiRGS1

  11. A signal theoretic introduction to random processes

    CERN Document Server

    Howard, Roy M

    2015-01-01

    A fresh introduction to random processes utilizing signal theory By incorporating a signal theory basis, A Signal Theoretic Introduction to Random Processes presents a unique introduction to random processes with an emphasis on the important random phenomena encountered in the electronic and communications engineering field. The strong mathematical and signal theory basis provides clarity and precision in the statement of results. The book also features:  A coherent account of the mathematical fundamentals and signal theory that underpin the presented material Unique, in-depth coverage of

  12. Signal trend identification with fuzzy methods

    International Nuclear Information System (INIS)

    Reifman, J.; Tsoukalas, L. H.; Wang, X.; Wei, T. Y. C.

    1999-01-01

    A fuzzy-logic-based methodology for on-line signal trend identification is introduced. Although signal trend identification is complicated by the presence of noise, fuzzy logic can help capture important features of on-line signals and classify incoming power plant signals into increasing, decreasing and steady-state trend categories. In order to verify the methodology, a code named PROTREN is developed and tested using plant data. The results indicate that the code is capable of detecting transients accurately, identifying trends reliably, and not misinterpreting a steady-state signal as a transient one

  13. Multidimensional signaling via wavelet packets

    Science.gov (United States)

    Lindsey, Alan R.

    1995-04-01

    This work presents a generalized signaling strategy for orthogonally multiplexed communication. Wavelet packet modulation (WPM) employs the basis functions from an arbitrary pruning of a full dyadic tree structured filter bank as orthogonal pulse shapes for conventional QAM symbols. The multi-scale modulation (MSM) and M-band wavelet modulation (MWM) schemes which have been recently introduced are handled as special cases, with the added benefit of an entire library of potentially superior sets of basis functions. The figures of merit are derived and it is shown that the power spectral density is equivalent to that for QAM (in fact, QAM is another special case) and hence directly applicable in existing systems employing this standard modulation. Two key advantages of this method are increased flexibility in time-frequency partitioning and an efficient all-digital filter bank implementation, making the WPM scheme more robust to a larger set of interferences (both temporal and sinusoidal) and computationally attractive as well.

  14. Generator of combined logical signals

    International Nuclear Information System (INIS)

    Laviron, Andre; Berard, Claude.

    1982-01-01

    The invention concerns a generator of combined logical signals to form combinations of two outputs at logical level 1 and N-2 outputs at logical level 0, among N generator outputs. This generator is characterized in that it includes a set of N means for storing combinations. Means enable the N storage means to be loaded with the logical levels corresponding to a pre-set starting combination, to control the operations for shifting the contents of the storage means and to control, by transfer facilities, the transfers of contents between these storage means. Controls enable the storage means to be actuated in order to obtain combinations of logical levels 1 and 0. The generation of combinations can be stopped after another pre-set combination. Application is for testing of safety circuits for nuclear power stations [fr

  15. Digital signal processing using MATLAB

    CERN Document Server

    Schilling, Robert L

    2016-01-01

    Focus on the development, implementation, and application of modern DSP techniques with DIGITAL SIGNAL PROCESSING USING MATLAB(R), 3E. Written in an engaging, informal style, this edition immediately captures your attention and encourages you to explore each critical topic. Every chapter starts with a motivational section that highlights practical examples and challenges that you can solve using techniques covered in the chapter. Each chapter concludes with a detailed case study example, a chapter summary with learning outcomes, and practical homework problems cross-referenced to specific chapter sections for your convenience. DSP Companion software accompanies each book to enable further investigation. The DSP Companion software operates with MATLAB(R) and provides intriguing demonstrations as well as interactive explorations of analysis and design concepts.

  16. Engagement Assessment Using EEG Signals

    Science.gov (United States)

    Li, Feng; Li, Jiang; McKenzie, Frederic; Zhang, Guangfan; Wang, Wei; Pepe, Aaron; Xu, Roger; Schnell, Thomas; Anderson, Nick; Heitkamp, Dean

    2012-01-01

    In this paper, we present methods to analyze and improve an EEG-based engagement assessment approach, consisting of data preprocessing, feature extraction and engagement state classification. During data preprocessing, spikes, baseline drift and saturation caused by recording devices in EEG signals are identified and eliminated, and a wavelet based method is utilized to remove ocular and muscular artifacts in the EEG recordings. In feature extraction, power spectrum densities with 1 Hz bin are calculated as features, and these features are analyzed using the Fisher score and the one way ANOVA method. In the classification step, a committee classifier is trained based on the extracted features to assess engagement status. Finally, experiment results showed that there exist significant differences in the extracted features among different subjects, and we have implemented a feature normalization procedure to mitigate the differences and significantly improved the engagement assessment performance.

  17. Signal propagation along the axon.

    Science.gov (United States)

    Rama, Sylvain; Zbili, Mickaël; Debanne, Dominique

    2018-03-08

    Axons link distant brain regions and are usually considered as simple transmission cables in which reliable propagation occurs once an action potential has been generated. Safe propagation of action potentials relies on specific ion channel expression at strategic points of the axon such as nodes of Ranvier or axonal branch points. However, while action potentials are generally considered as the quantum of neuronal information, their signaling is not entirely digital. In fact, both their shape and their conduction speed have been shown to be modulated by activity, leading to regulations of synaptic latency and synaptic strength. We report here newly identified mechanisms of (1) safe spike propagation along the axon, (2) compartmentalization of action potential shape in the axon, (3) analog modulation of spike-evoked synaptic transmission and (4) alteration in conduction time after persistent regulation of axon morphology in central neurons. We discuss the contribution of these regulations in information processing. Copyright © 2018 Elsevier Ltd. All rights reserved.

  18. TAM receptor signaling in development.

    Science.gov (United States)

    Burstyn-Cohen, Tal

    2017-01-01

    TYRO3, AXL and MERTK comprise the TAM family of receptor protein tyrosine kinases. Activated by their ligands, protein S (PROS1) and growth-arrest-specific 6 (GAS6), they mediate numerous cellular functions throughout development and adulthood. Expressed by a myriad of cell types and tissues, they have been implicated in homeostatic regulation of the immune, nervous, vascular, bone and reproductive systems. The loss-of-function of TAM signaling in adult tissues culminates in the destruction of tissue homeostasis and diseased states, while TAM gain-of-function in various tumors promotes cancer phenotypes. Combinatorial ligand-receptor interactions may elicit different molecular and cellular responses. Many of the TAM regulatory functions are essentially developmental, taking place both during embryogenesis and postnatally. This review highlights current knowledge on the role of TAM receptors and their ligands during these developmental processes in the immune, nervous, vascular and reproductive systems.

  19. Fundamentals of adaptive signal processing

    CERN Document Server

    Uncini, Aurelio

    2015-01-01

    This book is an accessible guide to adaptive signal processing methods that equips the reader with advanced theoretical and practical tools for the study and development of circuit structures and provides robust algorithms relevant to a wide variety of application scenarios. Examples include multimodal and multimedia communications, the biological and biomedical fields, economic models, environmental sciences, acoustics, telecommunications, remote sensing, monitoring, and, in general, the modeling and prediction of complex physical phenomena. The reader will learn not only how to design and implement the algorithms but also how to evaluate their performance for specific applications utilizing the tools provided. While using a simple mathematical language, the employed approach is very rigorous. The text will be of value both for research purposes and for courses of study.

  20. Molecular basis for mitochondrial signaling

    CERN Document Server

    2017-01-01

    This book covers recent advances in the study of structure, function, and regulation of metabolite, protein and ion translocating channels, and transporters in mitochondria. A wide array of cutting-edge methods are covered, ranging from electrophysiology and cell biology to bioinformatics, as well as structural, systems, and computational biology. At last, the molecular identity of two important channels in the mitochondrial inner membrane, the mitochondrial calcium uniporter and the mitochondrial permeability transition pore have been established. After years of work on the physiology and structure of VDAC channels in the mitochondrial outer membrane, there have been multiple discoveries on VDAC permeation and regulation by cytosolic proteins. Recent breakthroughs in structural studies of the mitochondrial cholesterol translocator reveal a set of novel unexpected features and provide essential clues for defining therapeutic strategies. Molecular Basis for Mitochondrial Signaling covers these and many more re...

  1. Canonical Wnt signaling in diabetic retinopathy.

    Science.gov (United States)

    Chen, Qian; Ma, Jian-Xing

    2017-10-01

    Diabetic retinopathy (DR) is a common eye complication of diabetes, and the pathogenic mechanism of DR is still under investigation. The canonical Wnt signaling pathway is an evolutionarily conserved pathway that plays fundamental roles in embryogenesis and adult tissue homeostasis. Wnt signaling regulates expression of multiple genes that control retinal development and eye organogenesis, and dysregulated Wnt signaling plays pathophysiological roles in many ocular diseases, including DR. This review highlights recent progress in studies of Wnt signaling in DR. We discuss Wnt signaling regulation in the retina and dysregulation of Wnt signaling associated with ocular diseases with an emphasis on DR. We also discuss the therapeutic potential of modulating Wnt signaling in DR. Continued studies in this field will advance our current understanding on DR and contribute to the development of new treatments. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Signalling chains with probe and adjust learning

    Science.gov (United States)

    Gosti, Giorgio

    2018-04-01

    Many models explain the evolution of signalling in repeated stage games on social networks, differently in this study each signalling game evolves a communication strategy to transmit information across the network. Specifically, I formalise signalling chain games as a generalisation of Lewis' signalling games, where a number of players are placed on a chain network and play a signalling game in which they have to propagate information across the network. I show that probe and adjust learning allows the system to develop communication conventions, but it may temporarily perturb the system out of conventions. Through simulations, I evaluate how long the system takes to evolve a signalling convention and the amount of time it stays in it. This discussion presents a mechanism in which simple players can evolve signalling across a social network without necessarily understanding the entire system.

  3. Phantom phone signals: An investigation into the prevalence and predictors of imagined cell phone signals

    NARCIS (Netherlands)

    Tanis, M.A.; Beukeboom, C.J.; Hartmann, T.; Vermeulen, I.E.

    2015-01-01

    This paper aims to elucidate the peculiar phenomenon of imagined cell phone signals, or Phantom Phone Signals (PPS), which is defined as an individual's perception of a phone signal, indicating an incoming call, message, or social media notification, when in fact no such signal was transmitted. A

  4. Updating signal typing in voice: addition of type 4 signals.

    Science.gov (United States)

    Sprecher, Alicia; Olszewski, Aleksandra; Jiang, Jack J; Zhang, Yu

    2010-06-01

    The addition of a fourth type of voice to Titze's voice classification scheme is proposed. This fourth voice type is characterized by primarily stochastic noise behavior and is therefore unsuitable for both perturbation and correlation dimension analysis. Forty voice samples were classified into the proposed four types using narrowband spectrograms. Acoustic, perceptual, and correlation dimension analyses were completed for all voice samples. Perturbation measures tended to increase with voice type. Based on reliability cutoffs, the type 1 and type 2 voices were considered suitable for perturbation analysis. Measures of unreliability were higher for type 3 and 4 voices. Correlation dimension analyses increased significantly with signal type as indicated by a one-way analysis of variance. Notably, correlation dimension analysis could not quantify the type 4 voices. The proposed fourth voice type represents a subset of voices dominated by noise behavior. Current measures capable of evaluating type 4 voices provide only qualitative data (spectrograms, perceptual analysis, and an infinite correlation dimension). Type 4 voices are highly complex and the development of objective measures capable of analyzing these voices remains a topic of future investigation.

  5. Mitochondrial Energy and Redox Signaling in Plants

    Science.gov (United States)

    Schwarzländer, Markus

    2013-01-01

    Abstract Significance: For a plant to grow and develop, energy and appropriate building blocks are a fundamental requirement. Mitochondrial respiration is a vital source for both. The delicate redox processes that make up respiration are affected by the plant's changing environment. Therefore, mitochondrial regulation is critically important to maintain cellular homeostasis. This involves sensing signals from changes in mitochondrial physiology, transducing this information, and mounting tailored responses, by either adjusting mitochondrial and cellular functions directly or reprogramming gene expression. Recent Advances: Retrograde (RTG) signaling, by which mitochondrial signals control nuclear gene expression, has been a field of very active research in recent years. Nevertheless, no mitochondrial RTG-signaling pathway is yet understood in plants. This review summarizes recent advances toward elucidating redox processes and other bioenergetic factors as a part of RTG signaling of plant mitochondria. Critical Issues: Novel insights into mitochondrial physiology and redox-regulation provide a framework of upstream signaling. On the other end, downstream responses to modified mitochondrial function have become available, including transcriptomic data and mitochondrial phenotypes, revealing processes in the plant that are under mitochondrial control. Future Directions: Drawing parallels to chloroplast signaling and mitochondrial signaling in animal systems allows to bridge gaps in the current understanding and to deduce promising directions for future research. It is proposed that targeted usage of new technical approaches, such as quantitative in vivo imaging, will provide novel leverage to the dissection of plant mitochondrial signaling. Antioxid. Redox Signal. 18, 2122–2144. PMID:23234467

  6. Decoding resistant hypertension signalling pathways.

    Science.gov (United States)

    Parreira, Ricardo Cambraia; Lacerda, Leandro Heleno Guimarães; Vasconcellos, Rebecca; Lima, Swiany Silveira; Santos, Anderson Kenedy; Fontana, Vanessa; Sandrim, Valéria Cristina; Resende, Rodrigo Ribeiro

    2017-12-01

    Resistant hypertension (RH) is a clinical condition in which the hypertensive patient has become resistant to drug therapy and is often associated with increased cardiovascular morbidity and mortality. Several signalling pathways have been studied and related to the development and progression of RH: modulation of sympathetic activity by leptin and aldosterone, primary aldosteronism, arterial stiffness, endothelial dysfunction and variations in the renin-angiotensin-aldosterone system (RAAS). miRNAs comprise a family of small non-coding RNAs that participate in the regulation of gene expression at post-transcriptional level. miRNAs are involved in the development of both cardiovascular damage and hypertension. Little is known of the molecular mechanisms that lead to development and progression of this condition. This review aims to cover the potential roles of miRNAs in the mechanisms associated with the development and consequences of RH, and explore the current state of the art of diagnostic and therapeutic tools based on miRNA approaches. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  7. Tyrosine phosphorylation in signal transduction

    International Nuclear Information System (INIS)

    Roberts, T.M.; Kaplan, D.; Morgan, W.; Keller, T.; Mamon, H.; Piwnica-Worms, H.; Druker, B.; Whitman, M.; Morrison, D.; Cohen, B.; Schaffhausen, B.; Cantley, L.; Rapp, U.

    1988-01-01

    Recent work has focused on the elucidation of the mechanisms by which membrane-bound tyrosine kinases transmit signals within the cell. To examine the role of tyrosine phosphorylation the authors have employed the following strategy. First, they have utilized antibodies to phosphotyrosine (anti-P.Tyr) to identify candidate substrates of various tyrosine kinases, such as pp60 c-src , the CSF- receptor, or the platelet-derived growth factor (PDGF) receptor. Second, they have attempted to characterize the biochemical properties of the putative substrates and to determine in what manner these properties are modified by phosphorylation on tyrosine residues. In this endeavor, they are recapitulating the classic biochemical analysis used to study the effect of kinases on metabolism. The final portion of our work consists of using modern molecular biological strategies to clone the genes or cDNAs for the substrates and overproduce the relevant proteins for studies in vitro in defined systems. This paper describes the first and second aspects of this strategy, the identification and characterization of novel substrate molecules

  8. Advances in thermographic signal reconstruction

    Science.gov (United States)

    Shepard, Steven M.; Frendberg Beemer, Maria

    2015-05-01

    Since its introduction in 2001, the Thermographic Signal Reconstruction (TSR) method has emerged as one of the most widely used methods for enhancement and analysis of thermographic sequences, with applications extending beyond industrial NDT into biomedical research, art restoration and botany. The basic TSR process, in which a noise reduced replica of each pixel time history is created, yields improvement over unprocessed image data that is sufficient for many applications. However, examination of the resulting logarithmic time derivatives of each TSR pixel replica provides significant insight into the physical mechanisms underlying the active thermography process. The deterministic and invariant properties of the derivatives have enabled the successful implementation of automated defect recognition and measurement systems. Unlike most approaches to analysis of thermography data, TSR does not depend on flawbackground contrast, so that it can also be applied to characterization and measurement of thermal properties of flaw-free samples. We present a summary of recent advances in TSR, a review of the underlying theory and examples of its implementation.

  9. Interception of LPI radar signals

    Science.gov (United States)

    Lee, Jim P.

    1991-11-01

    Most current radars are designed to transmit short duration pulses with relatively high peak power. These radars can be detected easily by the use of relatively modest EW intercept receivers. Three radar functions (search, anti-ship missile (ASM) seeker, and navigation) are examined to evaluate the effectiveness of potential low probability of intercept (LPI) techniques, such as waveform coding, antenna profile control, and power management that a radar may employ against current Electronic Warfare (EW) receivers. The general conclusion is that it is possible to design a LPI radar which is effective against current intercept EW receivers. LPI operation is most easily achieved at close ranges and against a target with a large radar cross section. The general system sensitivity requirement for the detection of current and projected LPI radars is found to be on the order of -100 dBmi which cannot be met by current EW receivers. Finally, three potential LPI receiver architectures, using channelized, superhet, and acousto-optic receivers with narrow RF and video bandwidths are discussed. They have shown some potential in terms of providing the sensitivity and capability in an environment where both conventional and LPI signals are present.

  10. Signals for supersymmetry at HERA

    International Nuclear Information System (INIS)

    Dreiner, H.; Morawitz, P.

    1994-07-01

    We consider the baryon parity signals at HERA for the case of the MSSM production mechanisms and the decays via the lepton number violating couplings L i Q anti D. We can probe very small Yukawa couplings λ'> or ∼3.10 -6 , limited only by the decay length of the LSP. We assume the LSP to be the lightest neutralino and study its decays in detail. We present the matrix element squared for the tree-level decay amplitude of a generally mixed neutralino explicitly. We find that the branching fraction to charged leptons strongly depends on the SUSY parameters and can differ significantly from the naively expected 50%. The SUSY mass reaches of the studied processes in the ZEUS detector at HERA were found to be: (m(e, anti ν)+m( anti q)) ≤ 170 GeV, 195 GeV and 205 GeV for the L t Q anti D, L μ Q anti D and L e Q anti D couplings respectively. These are well above existing limits on R-parity violating (R p ) SUSY from previous experiments. We conclude that HERA offers a very promising discovery potential for R p SUSY. (orig.)

  11. Digital signal processing with kernel methods

    CERN Document Server

    Rojo-Alvarez, José Luis; Muñoz-Marí, Jordi; Camps-Valls, Gustavo

    2018-01-01

    A realistic and comprehensive review of joint approaches to machine learning and signal processing algorithms, with application to communications, multimedia, and biomedical engineering systems Digital Signal Processing with Kernel Methods reviews the milestones in the mixing of classical digital signal processing models and advanced kernel machines statistical learning tools. It explains the fundamental concepts from both fields of machine learning and signal processing so that readers can quickly get up to speed in order to begin developing the concepts and application software in their own research. Digital Signal Processing with Kernel Methods provides a comprehensive overview of kernel methods in signal processing, without restriction to any application field. It also offers example applications and detailed benchmarking experiments with real and synthetic datasets throughout. Readers can find further worked examples with Matlab source code on a website developed by the authors. * Presents the necess...

  12. Roles of STATs signaling in cardiovascular diseases.

    Science.gov (United States)

    Kishore, Raj; Verma, Suresh K

    2012-04-01

    In cardiac and many other systems, chronic stress activates avfamily of structurally and functionally conserved receptors and their downstream signaling molecules that entail tyrosine, serine or threonine phosphorylation to transfer the messages to the genetic machinery. However, the activation of the Janus kinases (JAKs) and their downstream signal transducer and activator of transcription (STATs) proteins is both characteristic of and unique to cytokine and growth factor signaling which plays a central role in heart physiology. Dysregulation of JAK-STAT signaling is associated with various cardiovascular diseases. The molecular signaling and specificity of the JAK-STAT pathway are modulated at many levels by distinct regulatory proteins. Here, we review recent studies on the regulation of the STAT signaling pathway that will enhance our ability to design rational therapeutic strategies for stress-induced heart failure.

  13. Acoustic signal recovery by thermal demodulation

    Science.gov (United States)

    Boullosa, R. R.; Santillán, Arturo O.

    2006-10-01

    One operating mode of recently developed thermoacoustic transducers is as an audio speaker that uses an input superimposed on a direct current; as a result, the audio signal occurs at the same frequency as the input signal. To extend the potential applications of these kinds of sources, the authors propose an alternative driving mode in which a simple thermoacoustic device, consisting of a metal film over a substrate and a heat sink, is excited with a high frequency sinusoid that is amplitude modulated by a lower frequency signal. They show that the modulating signal is recovered in the radiated waves due to a mechanism that is inherent to this type of thermoacoustic process. If the frequency of the carrier is higher than 30kHz and any modulating signal (the one of interest) is in the audio frequency range, only this signal will be heard. Thus, the thermoacoustic device operates as an audio-band, self-demodulating speaker.

  14. Signal Processing and Neural Network Simulator

    Science.gov (United States)

    Tebbe, Dennis L.; Billhartz, Thomas J.; Doner, John R.; Kraft, Timothy T.

    1995-04-01

    The signal processing and neural network simulator (SPANNS) is a digital signal processing simulator with the capability to invoke neural networks into signal processing chains. This is a generic tool which will greatly facilitate the design and simulation of systems with embedded neural networks. The SPANNS is based on the Signal Processing WorkSystemTM (SPWTM), a commercial-off-the-shelf signal processing simulator. SPW provides a block diagram approach to constructing signal processing simulations. Neural network paradigms implemented in the SPANNS include Backpropagation, Kohonen Feature Map, Outstar, Fully Recurrent, Adaptive Resonance Theory 1, 2, & 3, and Brain State in a Box. The SPANNS was developed by integrating SAIC's Industrial Strength Neural Networks (ISNN) Software into SPW.

  15. Selection-Mutation Dynamics of Signaling Games

    Directory of Open Access Journals (Sweden)

    Josef Hofbauer

    2015-01-01

    Full Text Available We study the structure of the rest points of signaling games and their dynamic behavior under selection-mutation dynamics by taking the case of three signals as our canonical example. Many rest points of the replicator dynamics of signaling games are not isolated and, therefore, not robust under perturbations. However, some of them attract open sets of initial conditions. We prove the existence of certain rest points of the selection-mutation dynamics close to Nash equilibria of the signaling game and show that all but the perturbed rest points close to strict Nash equilibria are dynamically unstable. This is an important result for the evolution of signaling behavior, since it shows that the second-order forces that are governed by mutation can increase the chances of successful signaling.

  16. Long-distance signalling in plant defence.

    Science.gov (United States)

    Heil, Martin; Ton, Jurriaan

    2008-06-01

    Plants use inducible defence mechanisms to fend off harmful organisms. Resistance that is induced in response to local attack is often expressed systemically, that is, in organs that are not yet damaged. In the search for translocated defence signals, biochemical studies follow the physical movement of putative signals, and grafting experiments use mutants that are impaired in the production or perception of these signals. Long-distance signals can directly activate defence or can prime for the stronger and faster induction of defence. Historically, research has focused on the vascular transport of signalling metabolites, but volatiles can play a crucial role as well. We compare the advantages and constraints of vascular and airborne signals for the plant, and discuss how they can act in synergy to achieve optimised resistance in distal plant parts.

  17. Modified BTC Algorithm for Audio Signal Coding

    Directory of Open Access Journals (Sweden)

    TOMIC, S.

    2016-11-01

    Full Text Available This paper describes modification of a well-known image coding algorithm, named Block Truncation Coding (BTC and its application in audio signal coding. BTC algorithm was originally designed for black and white image coding. Since black and white images and audio signals have different statistical characteristics, the application of this image coding algorithm to audio signal presents a novelty and a challenge. Several implementation modifications are described in this paper, while the original idea of the algorithm is preserved. The main modifications are performed in the area of signal quantization, by designing more adequate quantizers for audio signal processing. The result is a novel audio coding algorithm, whose performance is presented and analyzed in this research. The performance analysis indicates that this novel algorithm can be successfully applied in audio signal coding.

  18. Automatic modulation recognition of communication signals

    CERN Document Server

    Azzouz, Elsayed Elsayed

    1996-01-01

    Automatic modulation recognition is a rapidly evolving area of signal analysis. In recent years, interest from the academic and military research institutes has focused around the research and development of modulation recognition algorithms. Any communication intelligence (COMINT) system comprises three main blocks: receiver front-end, modulation recogniser and output stage. Considerable work has been done in the area of receiver front-ends. The work at the output stage is concerned with information extraction, recording and exploitation and begins with signal demodulation, that requires accurate knowledge about the signal modulation type. There are, however, two main reasons for knowing the current modulation type of a signal; to preserve the signal information content and to decide upon the suitable counter action, such as jamming. Automatic Modulation Recognition of Communications Signals describes in depth this modulation recognition process. Drawing on several years of research, the authors provide a cr...

  19. Signal and image processing in medical applications

    CERN Document Server

    Kumar, Amit; Rahim, B Abdul; Kumar, D Sravan

    2016-01-01

    This book highlights recent findings on and analyses conducted on signals and images in the area of medicine. The experimental investigations involve a variety of signals and images and their methodologies range from very basic to sophisticated methods. The book explains how signal and image processing methods can be used to detect and forecast abnormalities in an easy-to-follow manner, offering a valuable resource for researchers, engineers, physicians and bioinformatics researchers alike.

  20. Calcium and Nuclear Signaling in Prostate Cancer

    OpenAIRE

    Ivan V. Maly; Wilma A. Hofmann

    2018-01-01

    Recently, there have been a number of developments in the fields of calcium and nuclear signaling that point to new avenues for a more effective diagnosis and treatment of prostate cancer. An example is the discovery of new classes of molecules involved in calcium-regulated nuclear import and nuclear calcium signaling, from the G protein-coupled receptor (GPCR) and myosin families. This review surveys the new state of the calcium and nuclear signaling fields with the aim of identifying the un...

  1. Photoacoustic signal amplification through plasmonic nanoparticle aggregation

    OpenAIRE

    Bayer, Carolyn L.; Nam, Seung Yun; Chen, Yun-Sheng; Emelianov, Stanislav Y.

    2013-01-01

    Photoacoustic imaging, using targeted plasmonic metallic nanoparticles, is a promising noninvasive molecular imaging method. Analysis of the photoacoustic signal generated by plasmonic metallic nanoparticles is complex because of the dependence upon physical properties of both the nanoparticle and the surrounding environment. We studied the effect of the aggregation of gold nanoparticles on the photoacoustic signal amplitude. We found that the photoacoustic signal from aggregated silica-coate...

  2. High Frequency Components Recovery in Music Signals

    Directory of Open Access Journals (Sweden)

    V. Sebesta

    1999-04-01

    Full Text Available A new technique is presented which improves the subjective quality of band-limited music by recovery of high frequency components. Sequences of harmonics are found in the band-limited signal and these sequences are expanded to the high frequency band to estimate the lost part of spectrum. High frequency signal is generated to match this estimation and is added to the band-limited signal.

  3. Pseudo random signal processing theory and application

    CERN Document Server

    Zepernick, Hans-Jurgen

    2013-01-01

    In recent years, pseudo random signal processing has proven to be a critical enabler of modern communication, information, security and measurement systems. The signal's pseudo random, noise-like properties make it vitally important as a tool for protecting against interference, alleviating multipath propagation and allowing the potential of sharing bandwidth with other users. Taking a practical approach to the topic, this text provides a comprehensive and systematic guide to understanding and using pseudo random signals. Covering theoretical principles, design methodologies and applications

  4. Interactive Teaching of Adaptive Signal Processing

    OpenAIRE

    Stewart, R W; Harteneck, M; Weiss, S

    2000-01-01

    Over the last 30 years adaptive digital signal processing has progressed from being a strictly graduate level advanced class in signal processing theory to a topic that is part of the core curriculum for many undergraduate signal processing classes. The key reason is the continued advance of communications technology, with its need for echo control and equalisation, and the widespread use of adaptive filters in audio, biomedical, and control applications. In this paper we will review the basi...

  5. The Signalling Role of Promotion in Japan

    OpenAIRE

    Okamura, Kazuaki

    2011-01-01

    Under asymmetric information conditions regarding worker productivity between current and prospective employers, a worker's promotion signals his/her productivity. In this Paper, we tested the signalling role of promotion, using Japanese micro-level data. We found that among lower-level positions, promotion seems to signal a worker's ability, and both the business cycle and foreign-capital ratio of his/her company significantly strengthen this effects. These results suggest that external labo...

  6. The genetic algorithm for a signal enhancement

    International Nuclear Information System (INIS)

    Karimova, L.; Kuadykov, E.; Makarenko, N.

    2004-01-01

    The paper is devoted to the problem of time series enhancement, which is based on the analysis of local regularity. The model construction using this analysis does not require any a priori assumption on the structure of the noise and the functional relationship between original signal and noise. The signal itself may be nowhere differentiable with rapidly varying local regularity, what is overcome with the help of the new technique of increasing the local Hoelder regularity of the signal under research. A new signal with prescribed regularity is constructed using the genetic algorithm. This approach is applied to enhancement of time series in the paleoclimatology, solar physics, dendrochronology, meteorology and hydrology

  7. The genetic algorithm for a signal enhancement

    Energy Technology Data Exchange (ETDEWEB)

    Karimova, L. [Laboratory of Computer Modelling, Institute of Mathematics, Pushkin Street 125, 480100 Almaty (Kazakhstan)]. E-mail: karimova@math.kz; Kuadykov, E. [Laboratory of Computer Modelling, Institute of Mathematics, Pushkin Street 125, 480100 Almaty (Kazakhstan); Makarenko, N. [Laboratory of Computer Modelling, Institute of Mathematics, Pushkin Street 125, 480100 Almaty (Kazakhstan)

    2004-11-21

    The paper is devoted to the problem of time series enhancement, which is based on the analysis of local regularity. The model construction using this analysis does not require any a priori assumption on the structure of the noise and the functional relationship between original signal and noise. The signal itself may be nowhere differentiable with rapidly varying local regularity, what is overcome with the help of the new technique of increasing the local Hoelder regularity of the signal under research. A new signal with prescribed regularity is constructed using the genetic algorithm. This approach is applied to enhancement of time series in the paleoclimatology, solar physics, dendrochronology, meteorology and hydrology.

  8. Cross-talk in abscisic acid signaling

    Science.gov (United States)

    Fedoroff, Nina V.

    2002-01-01

    "Cross-talk" in hormone signaling reflects an organism's ability to integrate different inputs and respond appropriately, a crucial function at the heart of signaling network operation. Abscisic acid (ABA) is a plant hormone involved in bud and seed dormancy, growth regulation, leaf senescence and abscission, stomatal opening, and a variety of plant stress responses. This review summarizes what is known about ABA signaling in the control of stomatal opening and seed dormancy and provides an overview of emerging knowledge about connections between ABA, ethylene, sugar, and auxin synthesis and signaling.

  9. On-line signal trend identification

    International Nuclear Information System (INIS)

    Tambouratzis, T.; Antonopoulos-Domis, M.

    2004-01-01

    An artificial neural network, based on the self-organizing map, is proposed for on-line signal trend identification. Trends are categorized at each incoming signal as steady-state, increasing and decreasing, while they are further classified according to characteristics such signal shape and rate of change. Tests with model-generated signals illustrate the ability of the self-organizing map to accurately and reliably perform on-line trend identification in terms of both detection and classification. The proposed methodology has been found robust to the presence of white noise

  10. Signals and systems primer with Matlab

    CERN Document Server

    Poularikas, Alexander D

    2006-01-01

    Signals and Systems Primer with MATLAB® equally emphasizes the fundamentals of both analog and digital signals and systems. To ensure insight into the basic concepts and methods, the text presents a variety of examples that illustrate a wide range of applications, from microelectromechanical to worldwide communication systems. It also provides MATLAB functions and procedures for practice and verification of these concepts.Taking a pedagogical approach, the author builds a solid foundation in signal processing as well as analog and digital systems. The book first introduces orthogonal signals,

  11. Multivariate Analysis for the Processing of Signals

    Directory of Open Access Journals (Sweden)

    Beattie J.R.

    2014-01-01

    Full Text Available Real-world experiments are becoming increasingly more complex, needing techniques capable of tracking this complexity. Signal based measurements are often used to capture this complexity, where a signal is a record of a sample’s response to a parameter (e.g. time, displacement, voltage, wavelength that is varied over a range of values. In signals the responses at each value of the varied parameter are related to each other, depending on the composition or state sample being measured. Since signals contain multiple information points, they have rich information content but are generally complex to comprehend. Multivariate Analysis (MA has profoundly transformed their analysis by allowing gross simplification of the tangled web of variation. In addition MA has also provided the advantage of being much more robust to the influence of noise than univariate methods of analysis. In recent years, there has been a growing awareness that the nature of the multivariate methods allows exploitation of its benefits for purposes other than data analysis, such as pre-processing of signals with the aim of eliminating irrelevant variations prior to analysis of the signal of interest. It has been shown that exploiting multivariate data reduction in an appropriate way can allow high fidelity denoising (removal of irreproducible non-signals, consistent and reproducible noise-insensitive correction of baseline distortions (removal of reproducible non-signals, accurate elimination of interfering signals (removal of reproducible but unwanted signals and the standardisation of signal amplitude fluctuations. At present, the field is relatively small but the possibilities for much wider application are considerable. Where signal properties are suitable for MA (such as the signal being stationary along the x-axis, these signal based corrections have the potential to be highly reproducible, and highly adaptable and are applicable in situations where the data is noisy or

  12. Mitochondrial signaling in health and disease

    National Research Council Canada - National Science Library

    Orrenius, Sten; Packer, Lester; Cadenas, Enrique

    2012-01-01

    .... The text covers themes essential for the maintenance of mitochondrial activity, including electron transport and energy production, mitochondrial biogenesis and dynamics, mitochondrial signaling...

  13. Digital signal processing an experimental approach

    CERN Document Server

    Engelberg, Shlomo

    2008-01-01

    Digital Signal Processing is a mathematically rigorous but accessible treatment of digital signal processing that intertwines basic theoretical techniques with hands-on laboratory instruction. Divided into three parts, the book covers various aspects of the digital signal processing (DSP) ""problem."" It begins with the analysis of discrete-time signals and explains sampling and the use of the discrete and fast Fourier transforms. The second part of the book???covering digital to analog and analog to digital conversion???provides a practical interlude in the mathematical content before Part II

  14. Signalling and obfuscation for congestion control

    Science.gov (United States)

    Mareček, Jakub; Shorten, Robert; Yu, Jia Yuan

    2015-10-01

    We aim to reduce the social cost of congestion in many smart city applications. In our model of congestion, agents interact over limited resources after receiving signals from a central agent that observes the state of congestion in real time. Under natural models of agent populations, we develop new signalling schemes and show that by introducing a non-trivial amount of uncertainty in the signals, we reduce the social cost of congestion, i.e., improve social welfare. The signalling schemes are efficient in terms of both communication and computation, and are consistent with past observations of the congestion. Moreover, the resulting population dynamics converge under reasonable assumptions.

  15. Advanced Methods of Biomedical Signal Processing

    CERN Document Server

    Cerutti, Sergio

    2011-01-01

    This book grew out of the IEEE-EMBS Summer Schools on Biomedical Signal Processing, which have been held annually since 2002 to provide the participants state-of-the-art knowledge on emerging areas in biomedical engineering. Prominent experts in the areas of biomedical signal processing, biomedical data treatment, medicine, signal processing, system biology, and applied physiology introduce novel techniques and algorithms as well as their clinical or physiological applications. The book provides an overview of a compelling group of advanced biomedical signal processing techniques, such as mult

  16. Radar signal processing and its applications

    CERN Document Server

    Hummel, Robert; Stoica, Petre; Zelnio, Edmund

    2003-01-01

    Radar Signal Processing and Its Applications brings together in one place important contributions and up-to-date research results in this fast-moving area. In twelve selected chapters, it describes the latest advances in architectures, design methods, and applications of radar signal processing. The contributors to this work were selected from the leading researchers and practitioners in the field. This work, originally published as Volume 14, Numbers 1-3 of the journal, Multidimensional Systems and Signal Processing, will be valuable to anyone working or researching in the field of radar signal processing. It serves as an excellent reference, providing insight into some of the most challenging issues being examined today.

  17. Computing angle of arrival of radio signals

    Science.gov (United States)

    Borchardt, John J.; Steele, David K.

    2017-11-07

    Various technologies pertaining to computing angle of arrival of radio signals are described. A system that is configured for computing the angle of arrival of a radio signal includes a cylindrical sheath wrapped around a cylindrical object, where the cylindrical sheath acts as a ground plane. The system further includes a plurality of antennas that are positioned about an exterior surface of the cylindrical sheath, and receivers respectively coupled to the antennas. The receivers output measurements pertaining to the radio signal. A processing circuit receives the measurements and computes the angle of arrival of the radio signal based upon the measurements.

  18. Plant monitoring and signal validation at HFIR

    International Nuclear Information System (INIS)

    Mullens, J.A.

    1991-01-01

    This paper describes a monitoring system for the Oak Ridge National Laboratory's (ORNL'S) High Flux Isotope Reactor (HFIR). HFIR is an 85 MW pressurized water reactor designed to produce isotopes and intense neutron beams. The monitoring system is described with respect to plant signals and computer system; monitoring overview; data acquisition, logging and network distribution; signal validation; status displays; reactor condition monitoring; reactor operator aids. Future work will include the addition of more plant signals, more signal validation and diagnostic capabilities, improved status display, integration of the system with the RELAP plant simulation and graphical interface, improved operator aids, and an alarm filtering system. 8 refs., 7 figs. (MB)

  19. Ultrafast Nonlinear Signal Processing in Silicon Waveguides

    DEFF Research Database (Denmark)

    Oxenløwe, Leif Katsuo; Mulvad, Hans Christian Hansen; Hu, Hao

    2012-01-01

    We describe recent demonstrations of exploiting highly nonlinear silicon waveguides for ultrafast optical signal processing. We describe wavelength conversion and serial-to-parallel conversion of 640 Gbit/s data signals and 1.28 Tbit/s demultiplexing and all-optical sampling.......We describe recent demonstrations of exploiting highly nonlinear silicon waveguides for ultrafast optical signal processing. We describe wavelength conversion and serial-to-parallel conversion of 640 Gbit/s data signals and 1.28 Tbit/s demultiplexing and all-optical sampling....

  20. Estimation of neural energy in microelectrode signals

    Science.gov (United States)

    Gaumond, R. P.; Clement, R.; Silva, R.; Sander, D.

    2004-09-01

    We considered the problem of determining the neural contribution to the signal recorded by an intracortical electrode. We developed a linear least-squares approach to determine the energy fraction of a signal attributable to an arbitrary number of autocorrelation-defined signals buried in noise. Application of the method requires estimation of autocorrelation functions Rap(tgr) characterizing the action potential (AP) waveforms and Rn(tgr) characterizing background noise. This method was applied to the analysis of chronically implanted microelectrode signals from motor cortex of rat. We found that neural (AP) energy consisted of a large-signal component which grows linearly with the number of threshold-detected neural events and a small-signal component unrelated to the count of threshold-detected AP signals. The addition of pseudorandom noise to electrode signals demonstrated the algorithm's effectiveness for a wide range of noise-to-signal energy ratios (0.08 to 39). We suggest, therefore, that the method could be of use in providing a measure of neural response in situations where clearly identified spike waveforms cannot be isolated, or in providing an additional 'background' measure of microelectrode neural activity to supplement the traditional AP spike count.

  1. Transcription factor and bone marrow stromal cells in osseointegration of dental implants

    Directory of Open Access Journals (Sweden)

    SG Yan

    2018-05-01

    Full Text Available Titanium implants are widely used in dental clinics and orthopaedic surgery. However, bone formation surrounding the implant is relatively slow after inserting the implant. The current study assessed the effects of bone marrow stromal cells (BMSCs with forced expression of special AT-rich sequence-binding protein 2 (SATB2 on the osseointegration of titanium implants. To determine whether SATB2 overexpression in BMSCs can enhance the osseointegration of implants, BMSCs were infected with the retrovirus encoding Satb2 (pBABE-Satb2 and were locally applied to bone defects before implanting the titanium implants in the mouse femur. Seven and twenty-one days after implantation, the femora were isolated for immunohistochemical (IHC staining, haematoxylin eosin (H&E staining, real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR, and micro-computed tomography (μCT analysis. IHC staining analysis revealed that SATB2-overexpressing BMSCs were intensely distributed in the bone tissue surrounding the implant. Histological analysis showed that SATB2-overexpressing BMSCs significantly enhanced new bone formation and bone-to-implant contact 3 weeks after implantation. Real-time qRT-PCR results showed that the local delivery of SATB2-overexpressing BMSCs enhanced expression levels of potent osteogenic transcription factors and bone matrix proteins in the implantation sites. μCT analysis demonstrated that SATB2-overexpressing BMSCs significantly increased the density of the newly formed bone surrounding the implant 3 weeks post-operatively. These results conclude that local delivery of SATB2-overexpressing BMSCs significantly accelerates osseointegration of titanium implants. These results provide support for future pharmacological and clinical applications of SATB2, which accelerates bone regeneration around titanium implants.

  2. Corticosteroid signaling in frog metamorphosis.

    Science.gov (United States)

    Kulkarni, Saurabh S; Buchholz, Daniel R

    2014-07-01

    Stress in fetal and larval life can impact later health and fitness in humans and wildlife. Long-term effects of early life stress are mediated by altered stress physiology induced during the process of relaying environmental effects on development. Amphibian metamorphosis has been an important model system to study the role of hormones in development in an environmental context. Thyroid hormone (TH) is necessary and sufficient to initiate the dramatic morphological and physiological changes of metamorphosis, but TH alone is insufficient to complete metamorphosis. Other hormones, importantly corticosteroid hormones (CSs), influence the timing and nature of post-embryonic development. Stressors or treatments with CSs delay or accelerate metamorphic change, depending on the developmental stage of treatment. Also, TH and CSs have synergistic, antagonistic, and independent effects on gene regulation. Importantly, the identity of the endogenous corticosteroid hormone or receptor underlying any gene induction or remodeling event has not been determined. Levels of both CSs, corticosterone and aldosterone, peak at metamorphic climax, and the corticosteroid receptors, glucocorticoid and mineralocorticoid receptors, have wide expression distribution among tadpole tissues. Conclusive experiments to identify the endogenous players have been elusive due to difficulties in experimental control of corticosteroid production and signaling. Current data are consistent with the hypothesis that the two CSs and their receptors serve largely overlapping functions in regulating metamorphosis and synergy with TH. Knowledge of the endogenous players is critical to understanding the basic mechanisms and significance of corticosteroid action in regulating post-embryonic development in environmental contexts. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Phase synchronization of instrumental music signals

    Science.gov (United States)

    Mukherjee, Sayan; Palit, Sanjay Kumar; Banerjee, Santo; Ariffin, M. R. K.; Bhattacharya, D. K.

    2014-06-01

    Signal analysis is one of the finest scientific techniques in communication theory. Some quantitative and qualitative measures describe the pattern of a music signal, vary from one to another. Same musical recital, when played by different instrumentalists, generates different types of music patterns. The reason behind various patterns is the psycho-acoustic measures - Dynamics, Timber, Tonality and Rhythm, varies in each time. However, the psycho-acoustic study of the music signals does not reveal any idea about the similarity between the signals. For such cases, study of synchronization of long-term nonlinear dynamics may provide effective results. In this context, phase synchronization (PS) is one of the measures to show synchronization between two non-identical signals. In fact, it is very critical to investigate any other kind of synchronization for experimental condition, because those are completely non identical signals. Also, there exists equivalence between the phases and the distances of the diagonal line in Recurrence plot (RP) of the signals, which is quantifiable by the recurrence quantification measure τ-recurrence rate. This paper considers two nonlinear music signals based on same raga played by two eminent sitar instrumentalists as two non-identical sources. The psycho-acoustic study shows how the Dynamics, Timber, Tonality and Rhythm vary for the two music signals. Then, long term analysis in the form of phase space reconstruction is performed, which reveals the chaotic phase spaces for both the signals. From the RP of both the phase spaces, τ-recurrence rate is calculated. Finally by the correlation of normalized tau-recurrence rate of their 3D phase spaces and the PS of the two music signals has been established. The numerical results well support the analysis.

  4. Calcium signalling silencing in atrial fibrillation.

    Science.gov (United States)

    Greiser, Maura

    2017-06-15

    Subcellular calcium signalling silencing is a novel and distinct cellular and molecular adaptive response to rapid cardiac activation. Calcium signalling silencing develops during short-term sustained rapid atrial activation as seen clinically during paroxysmal atrial fibrillation (AF). It is the first 'anti-arrhythmic' adaptive response in the setting of AF and appears to counteract the maladaptive changes that lead to intracellular Ca 2+ signalling instability and Ca 2+ -based arrhythmogenicity. Calcium signalling silencing results in a failed propagation of the [Ca 2+ ] i signal to the myocyte centre both in patients with AF and in a rabbit model. This adaptive mechanism leads to a substantial reduction in the expression levels of calcium release channels (ryanodine receptors, RyR2) in the sarcoplasmic reticulum, and the frequency of Ca 2+ sparks and arrhythmogenic Ca 2+ waves remains low. Less Ca 2+ release per [Ca 2+ ] i transient, increased fast Ca 2+ buffering strength, shortened action potentials and reduced L-type Ca 2+ current contribute to a substantial reduction of intracellular [Na + ]. These features of Ca 2+ signalling silencing are distinct and in contrast to the changes attributed to Ca 2+ -based arrhythmogenicity. Some features of Ca 2+ signalling silencing prevail in human AF suggesting that the Ca 2+ signalling 'phenotype' in AF is a sum of Ca 2+ stabilizing (Ca 2+ signalling silencing) and Ca 2+ destabilizing (arrhythmogenic unstable Ca 2+ signalling) factors. Calcium signalling silencing is a part of the mechanisms that contribute to the natural progression of AF and may limit the role of Ca 2+ -based arrhythmogenicity after the onset of AF. © 2017 The Authors. The Journal of Physiology © 2017 The Physiological Society.

  5. The Hippo signaling functions through the Notch signaling to regulate intrahepatic bile duct development in mammals

    Science.gov (United States)

    Wu, Nan; Nguyen, Quy; Wan, Ying; Zhou, Tiaohao; Venter, Julie; Frampton, Gabriel A; DeMorrow, Sharon; Pan, Duojia; Meng, Fanyin; Glaser, Shannon; Alpini, Gianfranco; Bai, Haibo

    2018-01-01

    The Hippo signaling pathway and the Notch signaling pathway are evolutionary conserved signaling cascades that have important roles in embryonic development of many organs. In murine liver, disruption of either pathway impairs intrahepatic bile duct development. Recent studies suggested that the Notch signaling receptor Notch2 is a direct transcriptional target of the Hippo signaling pathway effector YAP, and the Notch signaling is a major mediator of the Hippo signaling in maintaining biliary cell characteristics in adult mice. However, it remains to be determined whether the Hippo signaling pathway functions through the Notch signaling in intrahepatic bile duct development. We found that loss of the Hippo signaling pathway tumor suppressor Nf2 resulted in increased expression levels of the Notch signaling pathway receptor Notch2 in cholangiocytes but not in hepatocytes. When knocking down Notch2 on the background of Nf2 deficiency in mouse livers, the excessive bile duct development induced by Nf2 deficiency was suppressed by heterozygous and homozygous deletion of Notch2 in a dose-dependent manner. These results implicated that Notch signaling is one of the downstream effectors of the Hippo signaling pathway in regulating intrahepatic bile duct development. PMID:28581486

  6. Process Dissociation and Mixture Signal Detection Theory

    Science.gov (United States)

    DeCarlo, Lawrence T.

    2008-01-01

    The process dissociation procedure was developed in an attempt to separate different processes involved in memory tasks. The procedure naturally lends itself to a formulation within a class of mixture signal detection models. The dual process model is shown to be a special case. The mixture signal detection model is applied to data from a widely…

  7. Power Spectrum Estimation of Randomly Sampled Signals

    DEFF Research Database (Denmark)

    Velte, Clara M.; Buchhave, Preben; K. George, William

    2014-01-01

    proportional to velocity magnitude that consist of well-defined frequency content, which makes bias easy to spot. The idea is that if the algorithms are not able to produce correct statistics from this simple signal, then they will certainly not be able to function well for a more complex measured LDA signal...

  8. Atmospheric signals produced by cavity rebound

    International Nuclear Information System (INIS)

    Jones, E.M.; App, F.N.; Whitaker, R.W.

    1993-01-01

    An analysis of the atmospheric acoustic signals produced by a class of low-yield tests conducted just below the base of the alluvial cover in Yucca Flat of the Nevada Test Site (NTS), has revealed a clear manifestation of an elastic, cavity rebound signal. We use modeling as the basis for understanding the observed phenomena

  9. Intestinal Hedgehog signaling in tumors and inflammation

    NARCIS (Netherlands)

    Büller, N.V.J.A.

    2015-01-01

    In this thesis we investigated the role of Hedgehog signaling in tumors and inflammation. By using an inducible Indian Hedgehog (Ihh) knockout mouse we show that Ihh signals via the mesenchyme to the proliferating cells in the crypt to attenuate proliferation. Despite its anti-proliferative role in

  10. Prediction of twin-arginine signal peptides

    DEFF Research Database (Denmark)

    Bendtsen, Jannick Dyrløv; Nielsen, Henrik; Widdick, D.

    2005-01-01

    expressions, whereas hydrophobicity discrimination of Tat- and Sec- signal peptides is carried out by an artificial neural network. A potential cleavage site of the predicted Tat signal peptide is also reported. The TatP prediction server is available as a public web server at http://www.cbs.dtu.dk/services/TatP/....

  11. Cloning and superluminal signaling£

    Indian Academy of Sciences (India)

    Cloning; cloning fidelity; superluminal signaling; state discrimination. PACS No. 03.65.Bz. 1. .... The possibility of superluminal signaling in quantum mechanics stems from the concept .... quantum mechanics and relativity [13]. .... [13] A Shimony, in Foundations of quantum mechanics in the light of new technology edited by.

  12. Wnt Signaling in Kidney Development and Disease.

    Science.gov (United States)

    Wang, Yongping; Zhou, Chengji J; Liu, Youhua

    2018-01-01

    Wnt signal cascade is an evolutionarily conserved, developmental pathway that regulates embryogenesis, injury repair, and pathogenesis of human diseases. It is well established that Wnt ligands transmit their signal via canonical, β-catenin-dependent and noncanonical, β-catenin-independent mechanisms. Mounting evidence has revealed that Wnt signaling plays a key role in controlling early nephrogenesis and is implicated in the development of various kidney disorders. Dysregulations of Wnt expression cause a variety of developmental abnormalities and human diseases, such as congenital anomalies of the kidney and urinary tract, cystic kidney, and renal carcinoma. Multiple Wnt ligands, their receptors, and transcriptional targets are upregulated during nephron formation, which is crucial for mediating the reciprocal interaction between primordial tissues of ureteric bud and metanephric mesenchyme. Renal cysts are also associated with disrupted Wnt signaling. In addition, Wnt components are important players in renal tumorigenesis. Activation of Wnt/β-catenin is instrumental for tubular repair and regeneration after acute kidney injury. However, sustained activation of this signal cascade is linked to chronic kidney diseases and renal fibrosis in patients and experimental animal models. Mechanistically, Wnt signaling controls a diverse array of biologic processes, such as cell cycle progression, cell polarity and migration, cilia biology, and activation of renin-angiotensin system. In this chapter, we have reviewed recent findings that implicate Wnt signaling in kidney development and diseases. Targeting this signaling may hold promise for future treatment of kidney disorders in patients. Copyright © 2018 Elsevier Inc. All rights reserved.

  13. Motion sensing using WLAN signal fluctuations

    NARCIS (Netherlands)

    Kavitha Muthukrishnan, K.; Lijding, M.E.M.; Meratnia, Nirvana; Havinga, Paul J.M.

    2006-01-01

    The ability to infer the motion of the user has previously been possible only with the usage of additional hardware. In this paper we show how motion sensing can be obtained just by observing the WLAN radio’s signal strength and its fluctuations. For the first time, we have analyzed the signal

  14. Net analyte signal based statistical quality control

    NARCIS (Netherlands)

    Skibsted, E.T.S.; Boelens, H.F.M.; Westerhuis, J.A.; Smilde, A.K.; Broad, N.W.; Rees, D.R.; Witte, D.T.

    2005-01-01

    Net analyte signal statistical quality control (NAS-SQC) is a new methodology to perform multivariate product quality monitoring based on the net analyte signal approach. The main advantage of NAS-SQC is that the systematic variation in the product due to the analyte (or property) of interest is

  15. Demystifying communication signal lost for network redundancy ...

    African Journals Online (AJOL)

    These studies report on the communication signal lost factors that were analyzed and supported by evidences on coverage analysis activities for Automatic Meter Reading (AMR) systems. We have categorized the influential signal lost factors into four core elements that were concluded based on our field measurement ...

  16. Spectral integration in binaural signal detection

    NARCIS (Netherlands)

    Breebaart, D.J.; Par, van de S.L.J.D.E.; Kohlrausch, A.G.

    1997-01-01

    For both monaural and binaural masking, the spectral content of the masker and of the signal to be detected are important stimulus properties influencing the detection process. It is generally accepted that the auditory system separates the incoming signals in several frequency bands. It is not

  17. Electrical Signaling, Photosynthesis and Systemic Acquired Acclimation

    Directory of Open Access Journals (Sweden)

    Magdalena Szechyńska-Hebda

    2017-09-01

    Full Text Available Electrical signaling in higher plants is required for the appropriate intracellular and intercellular communication, stress responses, growth and development. In this review, we have focus on recent findings regarding the electrical signaling, as a major regulator of the systemic acquired acclimation (SAA and the systemic acquired resistance (SAR. The electric signaling on its own cannot confer the required specificity of information to trigger SAA and SAR, therefore, we have also discussed a number of other mechanisms and signaling systems that can operate in combination with electric signaling. We have emphasized the interrelation between ionic mechanism of electrical activity and regulation of photosynthesis, which is intrinsic to a proper induction of SAA and SAR. In a special way, we have summarized the role of non-photochemical quenching and its regulator PsbS. Further, redox status of the cell, calcium and hydraulic waves, hormonal circuits and stomatal aperture regulation have been considered as components of the signaling. Finally, a model of light-dependent mechanisms of electrical signaling propagation has been presented together with the systemic regulation of light-responsive genes encoding both, ion channels and proteins involved in regulation of their activity. Due to space limitations, we have not addressed many other important aspects of hormonal and ROS signaling, which were presented in a number of recent excellent reviews.

  18. Thyroid hormone signaling in the hypothalamus

    NARCIS (Netherlands)

    Alkemade, Anneke; Visser, Theo J.; Fliers, Eric

    2008-01-01

    PURPOSE OF REVIEW: Proper thyroid hormone signaling is essential for brain development and adult brain function. Signaling can be disrupted at many levels due to altered thyroid hormone secretion, conversion or thyroid hormone receptor binding. RECENT FINDINGS: Mutated genes involved in thyroid

  19. Signal-regulated systems and networks

    CSIR Research Space (South Africa)

    Van Zyl, TL

    2010-07-01

    Full Text Available The article presents the use of signal regulatory networks (SRNs), a biologically inspired model based on gene regulatory networks. SRNs are a way of understanding a class of self-organizing IT systems, signal-regulated systems (SRSs). This article...

  20. A Study on Setting of Traffic Signal

    OpenAIRE

    本多, 義明

    1981-01-01

    In this paper,effect of traffic signal setting are Studied according to regional characteristics. Firstly, regional and accident characteristics are analized by factor analysis. Secondly,88 regions in Aichi Prefecture are clustered into six clusters. Finally,effect of traffic signal setting is discussed.

  1. Type I signal peptidases of Bacillus subtilis

    NARCIS (Netherlands)

    Tjalsma, Harold; Bolhuis, Albert; Bron, Sierd; Jongbloed, Jan; Meijer, Wilfried J.J.; Noback, Michiel; van Roosmalen, Maarten; Venema, Gerhardus; van Dijl, Jan Maarten; Hopsu Havu, VK; Jarvinen, M; Kirschke, H

    1997-01-01

    Bacillus subtilis contains at least three chromosomally-encoded type I signal peptidases (SPases; SipS, SipT, and SipU), which remove signal peptides from secretory proteins. In addition, certain B. subtilis (natto) strains contain plasmid-encoded type I SPases (SipP). The known type I SPases from

  2. Jamming Signal Reduction in Spread Spectrum Systems.

    Science.gov (United States)

    1979-04-26

    the addition of an appropriate equalizer netowrk . The original signal and the estimate of the jamming signal are matched and added by a resistor...ADDRESS(SI different from Controllln~ OWce) IS. SECURITY CLASS. (of this report) Unclassified IS.. OECLASSIFICATION /DOWNGRAD IHO SCHEDULE $6. DISTRIB

  3. Wnt Signaling in Cancer Stem Cell Biology

    NARCIS (Netherlands)

    de Sousa E Melo, Felipe; Vermeulen, Louis

    2016-01-01

    Aberrant regulation of Wnt signaling is a common theme seen across many tumor types. Decades of research have unraveled the epigenetic and genetic alterations that result in elevated Wnt pathway activity. More recently, it has become apparent that Wnt signaling levels identify stem-like tumor cells

  4. Multi-Modal Intelligent Traffic Signal Systems Signal Plans for Roadside Equipment

    Data.gov (United States)

    Department of Transportation — Data were collected during the Multi-Modal Intelligent Transportation Signal Systems (MMITSS) study. MMITSS is a next-generation traffic signal system that seeks to...

  5. Spectral Correlation of Multicarrier Modulated Signals and Its Application for Signal Detection

    Directory of Open Access Journals (Sweden)

    Zhang Haijian

    2010-01-01

    Full Text Available Spectral correlation theory for cyclostationary time-series signals has been studied for decades. Explicit formulas of spectral correlation function for various types of analog-modulated and digital-modulated signals are already derived. In this paper, we investigate and exploit the cyclostationarity characteristics for two kinds of multicarrier modulated (MCM signals: conventional OFDM and filter bank based multicarrier (FBMC signals. The spectral correlation characterization of MCM signal can be described by a special linear periodic time-variant (LPTV system. Using this LPTV description, we have derived the explicit theoretical formulas of nonconjugate and conjugate cyclic autocorrelation function (CAF and spectral correlation function (SCF for OFDM and FBMC signals. According to theoretical spectral analysis, Cyclostationary Signatures (CS are artificially embedded into MCM signal and a low-complexity signature detector is, therefore, presented for detecting MCM signal. Theoretical analysis and simulation results demonstrate the efficiency and robustness of this CS detector compared to traditionary energy detector.

  6. Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe

    KAUST Repository

    Schlackow, M.

    2013-10-23

    Polyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation signals was missing in fission yeast, even though it is an important model organism. We demonstrate that the canonical AATAAA motif is the most frequent and functional polyadenylation signal in Schizosaccharomyces pombe. Using analysis of RNA-Seq data sets from cells grown under various physiological conditions, we identify 3\\' UTRs for nearly 90% of the yeast genes. Heterogeneity of cleavage sites is common, as is alternative polyadenylation within and between conditions. We validated the computationally identified sequence elements likely to promote polyadenylation by functional assays, including qRT-PCR and 3\\'RACE analysis. The biological importance of the AATAAA motif is underlined by functional analysis of the genes containing it. Furthermore, it has been shown that convergent genes require trans elements, like cohesin for efficient transcription termination. Here we show that convergent genes lacking cohesin (on chromosome 2) are generally associated with longer overlapping mRNA transcripts. Our bioinformatic and experimental genome-wide results are summarized and can be accessed and customized in a user-friendly database Pomb(A).

  7. Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe

    KAUST Repository

    Schlackow, M.; Marguerat, S.; Proudfoot, N. J.; Bahler, J.; Erban, R.; Gullerova, M.

    2013-01-01

    Polyadenylation of pre-mRNAs, a critical step in eukaryotic gene expression, is mediated by cis elements collectively called the polyadenylation signal. Genome-wide analysis of such polyadenylation signals was missing in fission yeast, even though it is an important model organism. We demonstrate that the canonical AATAAA motif is the most frequent and functional polyadenylation signal in Schizosaccharomyces pombe. Using analysis of RNA-Seq data sets from cells grown under various physiological conditions, we identify 3' UTRs for nearly 90% of the yeast genes. Heterogeneity of cleavage sites is common, as is alternative polyadenylation within and between conditions. We validated the computationally identified sequence elements likely to promote polyadenylation by functional assays, including qRT-PCR and 3'RACE analysis. The biological importance of the AATAAA motif is underlined by functional analysis of the genes containing it. Furthermore, it has been shown that convergent genes require trans elements, like cohesin for efficient transcription termination. Here we show that convergent genes lacking cohesin (on chromosome 2) are generally associated with longer overlapping mRNA transcripts. Our bioinformatic and experimental genome-wide results are summarized and can be accessed and customized in a user-friendly database Pomb(A).

  8. The polyadenylation factor subunit CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30: A key factor of programmed cell death and a regulator of immunity in arabidopsis

    KAUST Repository

    Bruggeman, Quentin; Garmier, Marie; De Bont, Linda; Soubigou-Taconnat, Ludivine; Mazubert, Christelle; Benhamed, Moussa; Raynaud, Cé cile; Bergounioux, Catherine; Delarue, Marianne

    2014-01-01

    striking features of mips1 is the light-dependent formation of lesions on leaves due to salicylic acid (SA)-dependent PCD, revealing roles for myoinositol or inositol derivatives in the regulation of PCD. Here, we identified a regulator of plant PCD

  9. Handbook of Signal Processing in Acoustics

    CERN Document Server

    Havelock, David; Vorländer, Michael

    2009-01-01

    The Handbook of Signal Processing in Acoustics presents signal processing as it is practiced in the field of acoustics. The Handbook is organized by areas of acoustics, with recognized leaders coordinating the self-contained chapters of each section. It brings together a wide range of perspectives from over 100 authors to reveal the interdisciplinary nature of signal processing in acoustics. Success in acoustic applications often requires juggling both the acoustic and the signal processing parameters of the problem. This handbook brings the key issues from both into perspective and is complementary to other reference material on the two subjects. It is a unique resource for experts and practitioners alike to find new ideas and techniques within the diversity of signal processing in acoustics.

  10. Modularized Smad-regulated TGFβ signaling pathway.

    Science.gov (United States)

    Li, Yongfeng; Wang, Minli; Carra, Claudio; Cucinotta, Francis A

    2012-12-01

    The transforming Growth Factor β (TGFβ) signaling pathway is a prominent regulatory signaling pathway controlling various important cellular processes. TGFβ signaling can be induced by several factors including ionizing radiation. The pathway is regulated in a negative feedback loop through promoting the nuclear import of the regulatory Smads and a subsequent expression of inhibitory Smad7, that forms ubiquitin ligase with Smurf2, targeting active TGFβ receptors for degradation. In this work, we proposed a mathematical model to study the Smad-regulated TGFβ signaling pathway. By modularization, we are able to analyze mathematically each component subsystem and recover the nonlinear dynamics of the entire network system. Meanwhile the excitability, a common feature observed in the biological systems, in the TGFβ signaling pathway is discussed and supported as well by numerical simulation, indicating the robustness of the model. Published by Elsevier Inc.

  11. Seizure detection algorithms based on EMG signals

    DEFF Research Database (Denmark)

    Conradsen, Isa

    Background: the currently used non-invasive seizure detection methods are not reliable. Muscle fibers are directly connected to the nerves, whereby electric signals are generated during activity. Therefore, an alarm system on electromyography (EMG) signals is a theoretical possibility. Objective...... on the amplitude of the signal. The other algorithm was based on information of the signal in the frequency domain, and it focused on synchronisation of the electrical activity in a single muscle during the seizure. Results: The amplitude-based algorithm reliably detected seizures in 2 of the patients, while...... the frequency-based algorithm was efficient for detecting the seizures in the third patient. Conclusion: Our results suggest that EMG signals could be used to develop an automatic seizuredetection system. However, different patients might require different types of algorithms /approaches....

  12. Signal classification for acoustic neutrino detection

    International Nuclear Information System (INIS)

    Neff, M.; Anton, G.; Enzenhöfer, A.; Graf, K.; Hößl, J.; Katz, U.; Lahmann, R.; Richardt, C.

    2012-01-01

    This article focuses on signal classification for deep-sea acoustic neutrino detection. In the deep sea, the background of transient signals is very diverse. Approaches like matched filtering are not sufficient to distinguish between neutrino-like signals and other transient signals with similar signature, which are forming the acoustic background for neutrino detection in the deep-sea environment. A classification system based on machine learning algorithms is analysed with the goal to find a robust and effective way to perform this task. For a well-trained model, a testing error on the level of 1% is achieved for strong classifiers like Random Forest and Boosting Trees using the extracted features of the signal as input and utilising dense clusters of sensors instead of single sensors.

  13. Electronic devices for analog signal processing

    CERN Document Server

    Rybin, Yu K

    2012-01-01

    Electronic Devices for Analog Signal Processing is intended for engineers and post graduates and considers electronic devices applied to process analog signals in instrument making, automation, measurements, and other branches of technology. They perform various transformations of electrical signals: scaling, integration, logarithming, etc. The need in their deeper study is caused, on the one hand, by the extension of the forms of the input signal and increasing accuracy and performance of such devices, and on the other hand, new devices constantly emerge and are already widely used in practice, but no information about them are written in books on electronics. The basic approach of presenting the material in Electronic Devices for Analog Signal Processing can be formulated as follows: the study with help from self-education. While divided into seven chapters, each chapter contains theoretical material, examples of practical problems, questions and tests. The most difficult questions are marked by a diamon...

  14. Ras signaling in aging and metabolic regulation.

    Science.gov (United States)

    Slack, Cathy

    2017-12-07

    Aberrant signal transduction downstream of the Ras GTPase has a well-established role in tumorigenesis. Mutations that result in hyperactivation of Ras are responsible for a third of all human cancers. Hence, small molecule inhibitors of the Ras signal transduction cascade have been under intense focus as potential cancer treatments. In both invertebrate and mammalian models, emerging evidence has also implicated components of the Ras signaling pathway in aging and metabolic regulation. Here, I review the current evidence for Ras signaling in these newly discovered roles highlighting the interactions between the Ras pathway and other longevity assurance mechanisms. Defining the role of Ras signaling in maintaining age-related health may have important implications for the development of interventions that could not only increase lifespan but also delay the onset and/or progression of age-related functional decline.

  15. ROS and ROS-Mediated Cellular Signaling

    Directory of Open Access Journals (Sweden)

    Jixiang Zhang

    2016-01-01

    Full Text Available It has long been recognized that an increase of reactive oxygen species (ROS can modify the cell-signaling proteins and have functional consequences, which successively mediate pathological processes such as atherosclerosis, diabetes, unchecked growth, neurodegeneration, inflammation, and aging. While numerous articles have demonstrated the impacts of ROS on various signaling pathways and clarify the mechanism of action of cell-signaling proteins, their influence on the level of intracellular ROS, and their complex interactions among multiple ROS associated signaling pathways, the systemic summary is necessary. In this review paper, we particularly focus on the pattern of the generation and homeostasis of intracellular ROS, the mechanisms and targets of ROS impacting on cell-signaling proteins (NF-κB, MAPKs, Keap1-Nrf2-ARE, and PI3K-Akt, ion channels and transporters (Ca2+ and mPTP, and modifying protein kinase and Ubiquitination/Proteasome System.

  16. Distributed traffic signal control using fuzzy logic

    Science.gov (United States)

    Chiu, Stephen

    1992-01-01

    We present a distributed approach to traffic signal control, where the signal timing parameters at a given intersection are adjusted as functions of the local traffic condition and of the signal timing parameters at adjacent intersections. Thus, the signal timing parameters evolve dynamically using only local information to improve traffic flow. This distributed approach provides for a fault-tolerant, highly responsive traffic management system. The signal timing at an intersection is defined by three parameters: cycle time, phase split, and offset. We use fuzzy decision rules to adjust these three parameters based only on local information. The amount of change in the timing parameters during each cycle is limited to a small fraction of the current parameters to ensure smooth transition. We show the effectiveness of this method through simulation of the traffic flow in a network of controlled intersections.

  17. Mathematical properties of a semi-classical signal analysis method: Noisy signal case

    KAUST Repository

    Liu, Dayan

    2012-08-01

    Recently, a new signal analysis method based on a semi-classical approach has been proposed [1]. The main idea in this method is to interpret a signal as a potential of a Schrodinger operator and then to use the discrete spectrum of this operator to analyze the signal. In this paper, we are interested in a mathematical analysis of this method in discrete case considering noisy signals. © 2012 IEEE.

  18. Mathematical properties of a semi-classical signal analysis method: Noisy signal case

    KAUST Repository

    Liu, Dayan; Laleg-Kirati, Taous-Meriem

    2012-01-01

    Recently, a new signal analysis method based on a semi-classical approach has been proposed [1]. The main idea in this method is to interpret a signal as a potential of a Schrodinger operator and then to use the discrete spectrum of this operator to analyze the signal. In this paper, we are interested in a mathematical analysis of this method in discrete case considering noisy signals. © 2012 IEEE.

  19. Social knowledge and signals in primates.

    Science.gov (United States)

    Bergman, Thore J; Sheehan, Michael J

    2013-07-01

    Primates are notable for having a rich and detailed understanding of their social environment and there has been great interest in the evolution and function of social knowledge in primates. Indeed, primates have been shown to have impressive understandings of not only other group members but also the complex relationships among them. To be useful, however, social knowledge requires memories from previous encounters and observations about individual traits that are stable. Here, we argue that social systems or traits that make social knowledge more costly or less accurate will favor signals that either supplement or replace social knowledge. Thus, the relationship between signals and social knowledge can be complementary or antagonistic depending on the type of signal. Our goal in this review is to elucidate the relationships between signals and social knowledge in primates. We categorize signals into three types, each with different relationships to social knowledge. (1) Identity signals directly facilitate social knowledge, (2) current-state signals supplement information gained through social knowledge, and (3) badges of status replace social knowledge. Primates rely extensively on identity information, but it remains to be determined to what extent this is based on receiver perception of individual variation or senders using identity signals. Primates frequently utilize current-state signals including signals of intent to augment their interactions with familiar individuals. Badges of status are rare in primates, and the cases where they are used point to a functional and evolutionary trade-off between badges of status and social knowledge. However, the nature of this relationship needs further exploration. © 2012 Wiley Periodicals, Inc.

  20. The Hedgehog Signal Induced Modulation of Bone Morphogenetic Protein Signaling: An Essential Signaling Relay for Urinary Tract Morphogenesis

    Science.gov (United States)

    Nakagata, Naomi; Miyagawa, Shinichi; Suzuki, Kentaro; Kitazawa, Sohei; Yamada, Gen

    2012-01-01

    Background Congenital diseases of the urinary tract are frequently observed in infants. Such diseases present a number of developmental anomalies such as hydroureter and hydronephrosis. Although some genetically-modified mouse models of growth factor signaling genes reproduce urinary phenotypes, the pathogenic mechanisms remain obscure. Previous studies suggest that a portion of the cells in the external genitalia and bladder are derived from peri-cloacal mesenchymal cells that receive Hedgehog (Hh) signaling in the early developmental stages. We hypothesized that defects in such progenitor cells, which give rise to urinary tract tissues, may be a cause of such diseases. Methodology/Principal Findings To elucidate the pathogenic mechanisms of upper urinary tract malformations, we analyzed a series of Sonic hedgehog (Shh) deficient mice. Shh−/− displayed hydroureter and hydronephrosis phenotypes and reduced expression of several developmental markers. In addition, we suggested that Shh modulation at an early embryonic stage is responsible for such phenotypes by analyzing the Shh conditional mutants. Tissue contribution assays of Hh-responsive cells revealed that peri-cloacal mesenchymal cells, which received Hh signal secreted from cloacal epithelium, could contribute to the ureteral mesenchyme. Gain- and loss-of-functional mutants for Hh signaling revealed a correlation between Hh signaling and Bone morphogenetic protein (Bmp) signaling. Finally, a conditional ablation of Bmp receptor type IA (BmprIA) gene was examined in Hh-responsive cell lineages. This system thus made it possible to analyze the primary functions of the growth factor signaling relay. The defective Hh-to-Bmp signaling relay resulted in severe urinary tract phenotypes with a decrease in the number of Hh-responsive cells. Conclusions/Significance This study identified the essential embryonic stages for the pathogenesis of urinary tract phenotypes. These results suggested that Hh

  1. Signals in Science - On the Importance of Signaling in Gaining Attention in Science

    NARCIS (Netherlands)

    H.P. van Dalen (Hendrik); K. Henkens

    2004-01-01

    textabstractWhich signals are important in gaining attention in science? For a group of 1,371 scientific articles published in 17 demography journals in the years 1990-1992 we track their influence and discern which signals are important in receiving citations. Three types of signals are examined:

  2. Silicon Photonics for Signal Processing of Tbit/s Serial Data Signals

    DEFF Research Database (Denmark)

    Oxenløwe, Leif Katsuo; Ji, Hua; Galili, Michael

    2012-01-01

    In this paper, we describe our recent work on signal processing of terabit per second optical serial data signals using pure silicon waveguides. We employ nonlinear optical signal processing in nanoengineered silicon waveguides to perform demultiplexing and optical waveform sampling of 1.28-Tbit/...

  3. UV cross-linking of polypeptides associated with 3'-terminal exons

    International Nuclear Information System (INIS)

    Stolow, D.T.; Berget, S.M.

    1990-01-01

    Association of nuclear proteins with chimeric vertebrate precursor RNAs containing both polyadenylation signals and an intron was examined by UV cross-linking. One major difference in cross-linking pattern was observed between this chimeric precursor RNA and precursors containing only polyadenylation or splicing signals. The heterogeneous nuclear ribonucleoprotein (hnRNP) polypeptide C cross-linked strongly to sequences downstream of the A addition site in polyadenylation precursor RNA containing only the polyadenylation signal from the simian virus 40 (SV40) late transcription unit. In contrast, the hnRNP C polypeptide cross-linked to chimeric RNA containing the same SV40 late poly(A) cassette very poorly, at a level less than 5% of that observed with the precursor RNA containing just the poly(A) site. Observation that cross-linking of the hnRNP C polypeptide to elements within the SV40 late poly(A) site was altered by the presence of an upstream intron suggests differences in the way nuclear factors associate with poly(A) sites in the presence and absence of an upstream intron. Cross-linking of C polypeptide to chimeric RNA increased with RNAs mutated for splicing or polyadenylation consensus sequences and under reaction conditions (high magnesium) that inhibited polyadenylation. Furthermore, cross-linking of hnRNP C polypeptide to precursors containing just the SV40 late poly(A) site was eliminated in the presence of competing poly(U); polyadenylation, however, was unaffected. Correlation of loss of activity with high levels of hnRNP C polypeptide cross-linking raises questions about the specificity of the interaction between the hnRNP C polypeptide and polyadenylation precursor RNAs in vitro

  4. All-optical signal processing of OTDM and OFDM signals based on time-domain Optical Fourier Transformation

    DEFF Research Database (Denmark)

    Clausen, Anders; Guan, Pengyu; Mulvad, Hans Christian Hansen

    2014-01-01

    All-optical time-domain Optical Fourier Transformation utilised for signal processing of ultra-high-speed OTDM signals and OFDM signals will be presented.......All-optical time-domain Optical Fourier Transformation utilised for signal processing of ultra-high-speed OTDM signals and OFDM signals will be presented....

  5. Calibration of Galileo signals for time metrology.

    Science.gov (United States)

    Defraigne, Pascale; Aerts, Wim; Cerretto, Giancarlo; Cantoni, Elena; Sleewaegen, Jean-Marie

    2014-12-01

    Using global navigation satellite system (GNSS) signals for accurate timing and time transfer requires the knowledge of all electric delays of the signals inside the receiving system. GNSS stations dedicated to timing or time transfer are classically calibrated only for Global Positioning System (GPS) signals. This paper proposes a procedure to determine the hardware delays of a GNSS receiving station for Galileo signals, once the delays of the GPS signals are known. This approach makes use of the broadcast satellite inter-signal biases, and is based on the ionospheric delay measured from dual-frequency combinations of GPS and Galileo signals. The uncertainty on the so-determined hardware delays is estimated to 3.7 ns for each isolated code in the L5 frequency band, and 4.2 ns for the ionosphere-free combination of E1 with a code of the L5 frequency band. For the calibration of a time transfer link between two stations, another approach can be used, based on the difference between the common-view time transfer results obtained with calibrated GPS data and with uncalibrated Galileo data. It is shown that the results obtained with this approach or with the ionospheric method are equivalent.

  6. GEFs: Dual regulation of Rac1 signaling.

    Science.gov (United States)

    Marei, Hadir; Malliri, Angeliki

    2017-04-03

    GEFs play a critical role in regulating Rac1 signaling. They serve as signaling nodes converting upstream signals into downstream Rac1-driven cellular responses. Through associating with membrane-bound Rac1, GEFs facilitate the exchange of GDP for GTP, thereby activating Rac1. As a result, Rac1 undergoes conformational changes that mediate its interaction with downstream effectors, linking Rac1 to a multitude of physiological and pathological processes. Interestingly, there are at least 20 GEFs involved in Rac1 activation, suggesting a more complex role of GEFs in regulating Rac1 signaling apart from promoting the exchange of GDP for GTP. Indeed, accumulating evidence implicates GEFs in directing the specificity of Rac1-driven signaling cascades, although the underlying mechanisms were poorly defined. Recently, through conducting a comparative study, we highlighted the role of 2 Rac-specific GEFs, Tiam1 and P-Rex1, in dictating the biological outcome downstream of Rac1. Importantly, further proteomic analysis uncovered a GEF activity-independent function for both GEFs in modulating the Rac1 interactome, which results in the stimulation of GEF-specific signaling cascades. Here, we provide an overview of our recent findings and discuss the role of GEFs as master regulators of Rac1 signaling with a particular focus on GEF-mediated modulation of cell migration following Rac1 activation.

  7. The function of endocytosis in Wnt signaling.

    Science.gov (United States)

    Brunt, Lucy; Scholpp, Steffen

    2018-03-01

    Wnt growth factors regulate one of the most important signaling networks during development, tissue homeostasis and disease. Despite the biological importance of Wnt signaling, the mechanism of endocytosis during this process is ill described. Wnt molecules can act as paracrine signals, which are secreted from the producing cells and transported through neighboring tissue to activate signaling in target cells. Endocytosis of the ligand is important at several stages of action: One central function of endocytic trafficking in the Wnt pathway occurs in the source cell. Furthermore, the β-catenin-dependent Wnt ligands require endocytosis for signal activation and to regulate gene transcription in the responding cells. Alternatively, Wnt/β-catenin-independent signaling regulates endocytosis of cell adherence plaques to control cell migration. In this comparative review, we elucidate these three fundamental interconnected functions, which together regulate cellular fate and cellular behavior. Based on established hypotheses and recent findings, we develop a revised picture for the complex function of endocytosis in the Wnt signaling network.

  8. Attending to weak signals: the leader's challenge.

    Science.gov (United States)

    Kerfoot, Karlene

    2005-12-01

    Halverson and Isham (2003) quote sources that report the accidental death rate of simply being in a hospital is " ... four hundred times more likely than your risk of death from traveling by train, forty times higher than driving a car, and twenty times higher than flying in a commercial aircraft" (p. 13). High-reliability organizations such as nuclear power plants and aircraft carriers have been pioneers in the business of recognizing weak signals. Weike and Sutcliffe (2001) note that high-reliability organizations distinguish themselves from others because of their mindfulness which enables them to see the significance of weak signals and to give strong interventions to weak signals. To act mindfully, these organizations have an underlying mental model of continually updating, anticipating, and focusing the possibility of failure using the intelligence that weak signals provides. Much of what happens is unexpected in health care. However, with a culture that is continually looking for weak signals, and intervenes and rescues when these signals are detected, the unexpected happens less often. This is the epitome of how leaders can build a culture of safety that focuses on recognizing the weak signals to manage the unforeseen.

  9. MP3 compression of Doppler ultrasound signals.

    Science.gov (United States)

    Poepping, Tamie L; Gill, Jeremy; Fenster, Aaron; Holdsworth, David W

    2003-01-01

    The effect of lossy, MP3 compression on spectral parameters derived from Doppler ultrasound (US) signals was investigated. Compression was tested on signals acquired from two sources: 1. phase quadrature and 2. stereo audio directional output. A total of 11, 10-s acquisitions of Doppler US signal were collected from each source at three sites in a flow phantom. Doppler signals were digitized at 44.1 kHz and compressed using four grades of MP3 compression (in kilobits per second, kbps; compression ratios in brackets): 1400 kbps (uncompressed), 128 kbps (11:1), 64 kbps (22:1) and 32 kbps (44:1). Doppler spectra were characterized by peak velocity, mean velocity, spectral width, integrated power and ratio of spectral power between negative and positive velocities. The results suggest that MP3 compression on digital Doppler US signals is feasible at 128 kbps, with a resulting 11:1 compression ratio, without compromising clinically relevant information. Higher compression ratios led to significant differences for both signal sources when compared with the uncompressed signals. Copyright 2003 World Federation for Ultrasound in Medicine & Biology

  10. Acoustic signal analysis in the creeping discharge

    International Nuclear Information System (INIS)

    Nakamiya, T; Sonoda, Y; Tsuda, R; Ebihara, K; Ikegami, T

    2008-01-01

    We have previously succeeded in measuring the acoustic signal due to the dielectric barrier discharge and discriminating the dominant frequency components of the acoustic signal. The dominant frequency components appear over 20kHz of acoustic signal by the dielectric barrier discharge. Recently surface discharge control technology has been focused from practical applications such as ozonizer, NO X reactors, light source or display. The fundamental experiments are carried to examine the creeping discharge using the acoustic signal. When the high voltage (6kV, f = 10kHz) is applied to the electrode, the discharge current flows and the acoustic sound is generated. The current, voltage waveforms of creeping discharge and the sound signal detected by the condenser microphone are stored in the digital memory scope. In this scheme, Continuous Wavelet Transform (CWT) is applied to discriminate the acoustic sound of the micro discharge and the dominant frequency components are studied. CWT results of sound signal show the frequency spectrum of wideband up to 100kHz. In addition, the energy distributions of acoustic signal are examined by CWT

  11. Macroevolution of perfume signalling in orchid bees.

    Science.gov (United States)

    Weber, Marjorie G; Mitko, Lukasz; Eltz, Thomas; Ramírez, Santiago R

    2016-11-01

    Theory predicts that both stabilising selection and diversifying selection jointly contribute to the evolution of sexual signalling traits by (1) maintaining the integrity of communication signals within species and (2) promoting the diversification of traits among lineages. However, for many important signalling traits, little is known about whether these dynamics translate into predictable macroevolutionary signatures. Here, we test for macroevolutionary patterns consistent with sexual signalling theory in the perfume signals of neotropical orchid bees, a group well studied for their chemical sexual communication. Our results revealed both high species-specificity and elevated rates of evolution in perfume signals compared to nonsignalling traits. Perfume complexity was correlated with the number of congeners in a species' range, suggesting that perfume evolution may be tied to the remarkably high number of orchid bee species coexisting together in some neotropical communities. Finally, sister-pair comparisons were consistent with both rapid divergence at speciation and character displacement upon secondary contact. Together, our results provide new insight into the macroevolution of sexual signalling in insects. © 2016 The Authors. Ecology Letters published by CNRS and John Wiley & Sons Ltd.

  12. Signals and systems laboratory with Matlab

    CERN Document Server

    Palamides, Alex

    2010-01-01

    Introduction to MATLAB®Working EnvironmentGetting StartedMemory ManagementVectorsMatricesPlotting with MATLABComplex NumbersM-FilesInput-Output CommandsFile ManagementLogical-Relational OperatorsControl FlowSymbolic VariablesPolynomials(Pseudo)Random NumbersSignalsCategorization by the Variable TypeBasic Continuous-Time SignalsDiscrete-Time SignalsProperties of SignalsTransformations of the Time Variable for Continuous-Time SignalsTransformations of the Time Variable for Discrete-Time SignalsSystemsSystems ClassificationProperties of SystemsTime Domain System AnalysisImpulse ResponseContinuous Time Convolution Convolution PropertiesInterconnections of SystemsStabilityDiscrete-Time ConvolutionSystems Described by Difference EquationsFiltersStability Criterion for Discrete-Time SystemsSystems Described by Differential EquationsStep Response of a SystemFourier SeriesOrthogonality of Complex Exponential SignalsComplex Exponential Fourier SeriesTrigonometric Fourier SeriesFourier Series in the Cosine with Phase F...

  13. Magnetoencephalography signals are influenced by skull defects.

    Science.gov (United States)

    Lau, S; Flemming, L; Haueisen, J

    2014-08-01

    Magnetoencephalography (MEG) signals had previously been hypothesized to have negligible sensitivity to skull defects. The objective is to experimentally investigate the influence of conducting skull defects on MEG and EEG signals. A miniaturized electric dipole was implanted in vivo into rabbit brains. Simultaneous recording using 64-channel EEG and 16-channel MEG was conducted, first above the intact skull and then above a skull defect. Skull defects were filled with agar gels, which had been formulated to have tissue-like homogeneous conductivities. The dipole was moved beneath the skull defects, and measurements were taken at regularly spaced points. The EEG signal amplitude increased 2-10 times, whereas the MEG signal amplitude reduced by as much as 20%. The EEG signal amplitude deviated more when the source was under the edge of the defect, whereas the MEG signal amplitude deviated more when the source was central under the defect. The change in MEG field-map topography (relative difference measure, RDM(∗)=0.15) was geometrically related to the skull defect edge. MEG and EEG signals can be substantially affected by skull defects. MEG source modeling requires realistic volume conductor head models that incorporate skull defects. Copyright © 2013 International Federation of Clinical Neurophysiology. Published by Elsevier Ireland Ltd. All rights reserved.

  14. Signal Quality Evaluation of Emerging EEG Devices

    Directory of Open Access Journals (Sweden)

    Thea Radüntz

    2018-02-01

    Full Text Available Electroencephalogram (EEG registration as a direct measure of brain activity has unique potentials. It is one of the most reliable and predicative indicators when studying human cognition, evaluating a subject's health condition, or monitoring their mental state. Unfortunately, standard signal acquisition procedures limit the usability of EEG devices and narrow their application outside the lab. Emerging sensor technology allows gel-free EEG registration and wireless signal transmission. Thus, it enables quick and easy application of EEG devices by users themselves. Although a main requirement for the interpretation of an EEG is good signal quality, there is a lack of research on this topic in relation to new devices. In our work, we compared the signal quality of six very different EEG devices. On six consecutive days, 24 subjects wore each device for 60 min and completed tasks and games on the computer. The registered signals were evaluated in the time and frequency domains. In the time domain, we examined the percentage of artifact-contaminated EEG segments and the signal-to-noise ratios. In the frequency domain, we focused on the band power variation in relation to task demands. The results indicated that the signal quality of a mobile, gel-based EEG system could not be surpassed by that of a gel-free system. However, some of the mobile dry-electrode devices offered signals that were almost comparable and were very promising. This study provided a differentiated view of the signal quality of emerging mobile and gel-free EEG recording technology and allowed an assessment of the functionality of the new devices. Hence, it provided a crucial prerequisite for their general application, while simultaneously supporting their further development.

  15. Poisson pre-processing of nonstationary photonic signals: Signals with equality between mean and variance.

    Science.gov (United States)

    Poplová, Michaela; Sovka, Pavel; Cifra, Michal

    2017-01-01

    Photonic signals are broadly exploited in communication and sensing and they typically exhibit Poisson-like statistics. In a common scenario where the intensity of the photonic signals is low and one needs to remove a nonstationary trend of the signals for any further analysis, one faces an obstacle: due to the dependence between the mean and variance typical for a Poisson-like process, information about the trend remains in the variance even after the trend has been subtracted, possibly yielding artifactual results in further analyses. Commonly available detrending or normalizing methods cannot cope with this issue. To alleviate this issue we developed a suitable pre-processing method for the signals that originate from a Poisson-like process. In this paper, a Poisson pre-processing method for nonstationary time series with Poisson distribution is developed and tested on computer-generated model data and experimental data of chemiluminescence from human neutrophils and mung seeds. The presented method transforms a nonstationary Poisson signal into a stationary signal with a Poisson distribution while preserving the type of photocount distribution and phase-space structure of the signal. The importance of the suggested pre-processing method is shown in Fano factor and Hurst exponent analysis of both computer-generated model signals and experimental photonic signals. It is demonstrated that our pre-processing method is superior to standard detrending-based methods whenever further signal analysis is sensitive to variance of the signal.

  16. Deregulation of Interferon Signaling in Malignant Cells

    Directory of Open Access Journals (Sweden)

    Leonidas C. Platanias

    2010-02-01

    Full Text Available Interferons (IFNs are a family of cytokines with potent antiproliferative, antiviral, and immunomodulatory properties. Much has been learned about IFNs and IFN-activated signaling cascades over the last 50 years. Due to their potent antitumor effects in vitro and in vivo, recombinant IFNs have been used extensively over the years, alone or in combination with other drugs, for the treatment of various malignancies. This review summarizes the current knowledge on IFN signaling components and pathways that are deregulated in human malignancies. The relevance of deregulation of IFN signaling pathways in defective innate immune surveillance and tumorigenesis are discussed.

  17. MASCOTTE: analytical model of eddy current signals

    International Nuclear Information System (INIS)

    Delsarte, G.; Levy, R.

    1992-01-01

    Tube examination is a major application of the eddy current technique in the nuclear and petrochemical industries. Such examination configurations being specially adapted to analytical modes, a physical model is developed on portable computers. It includes simple approximations made possible by the effective conditions of the examinations. The eddy current signal is described by an analytical formulation that takes into account the tube dimensions, the sensor conception, the physical characteristics of the defect and the examination parameters. Moreover, the model makes it possible to associate real signals and simulated signals

  18. Analog and mixed-signal electronics

    CERN Document Server

    Stephan, Karl

    2015-01-01

    A practical guide to analog and mixed-signal electronics, with an emphasis on design problems and applications This book provides an in-depth coverage of essential analog and mixed-signal topics such as power amplifiers, active filters, noise and dynamic range, analog-to-digital and digital-to-analog conversion techniques, phase-locked loops, and switching power supplies. Readers will learn the basics of linear systems, types of nonlinearities and their effects, op-amp circuits, the high-gain analog filter-amplifier, and signal generation. The author uses system design examples to motivate

  19. An Implantable CMOS Amplifier for Nerve Signals

    DEFF Research Database (Denmark)

    Nielsen, Jannik Hammel; Lehmann, Torsten

    2003-01-01

    In this paper, a low noise high gain CMOS amplifier for minute nerve signals is presented. The amplifier is constructed in a fully differential topology to maximize noise rejection. By using a mixture of weak- and strong inversion transistors, optimal noise suppression in the amplifier is achieved....... A continuous-time current-steering offset-compensation technique is utilized in order to minimize the noise contribution and to minimize dynamic impact on the amplifier input nodes. The method for signal recovery from noisy nerve signals is presented. A prototype amplifier is realized in a standard digital 0...

  20. Advances in heuristic signal processing and applications

    CERN Document Server

    Chatterjee, Amitava; Siarry, Patrick

    2013-01-01

    There have been significant developments in the design and application of algorithms for both one-dimensional signal processing and multidimensional signal processing, namely image and video processing, with the recent focus changing from a step-by-step procedure of designing the algorithm first and following up with in-depth analysis and performance improvement to instead applying heuristic-based methods to solve signal-processing problems. In this book the contributing authors demonstrate both general-purpose algorithms and those aimed at solving specialized application problems, with a spec

  1. The LISA zero-signal solution

    International Nuclear Information System (INIS)

    Tinto, Massimo; Larson, Shane L

    2005-01-01

    We derive a time-delay interferometric (TDI) combination that has zero-response to a gravitational wave signal. This combination, which we have called the zero-signal solution, is a two-parameter family of linear combinations of the generators of the TDI space that has null gravitational wave response when its two parameters coincide with the values of the angles of the source location in the sky. Remarkably, the zero-signal solution does not rely on any assumptions about the gravitational waveform, and in fact it works for waveforms of any kind

  2. Signal Enhancement with Variable Span Linear Filters

    DEFF Research Database (Denmark)

    Benesty, Jacob; Christensen, Mads Græsbøll; Jensen, Jesper Rindom

    . Variable span filters combine the ideas of optimal linear filters with those of subspace methods, as they involve the joint diagonalization of the correlation matrices of the desired signal and the noise. The book shows how some well-known filter designs, e.g. the minimum distortion, maximum signal...... the time and STFT domains, and, lastly, in time-domain binaural enhancement. In these contexts, the properties of these filters are analyzed in terms of their noise reduction capabilities and desired signal distortion, and the analyses are validated and further explored in simulations....

  3. Discrete-Time Biomedical Signal Encryption

    Directory of Open Access Journals (Sweden)

    Victor Grigoraş

    2017-12-01

    Full Text Available Chaotic modulation is a strong method of improving communication security. Analog and discrete chaotic systems are presented in actual literature. Due to the expansion of digital communication, discrete-time systems become more efficient and closer to actual technology. The present contribution offers an in-depth analysis of the effects chaos encryption produce on 1D and 2D biomedical signals. The performed simulations show that modulating signals are precisely recovered by the synchronizing receiver if discrete systems are digitally implemented and the coefficients precisely correspond. Channel noise is also applied and its effects on biomedical signal demodulation are highlighted.

  4. Microwave signal processing with photorefractive dynamic holography

    Science.gov (United States)

    Fotheringham, Edeline B.

    Have you ever found yourself listening to the music playing from the closest stereo rather than to the bromidic (uninspiring) person speaking to you? Your ears receive information from two sources but your brain listens to only one. What if your cell phone could distinguish among signals sharing the same bandwidth too? There would be no "full" channels to stop you from placing or receiving a call. This thesis presents a nonlinear optical circuit capable of distinguishing uncorrelated signals that have overlapping temporal bandwidths. This so called autotuning filter is the size of a U.S. quarter dollar and requires less than 3 mW of optical power to operate. It is basically an oscillator in which the losses are compensated with dynamic holographic gain. The combination of two photorefractive crystals in the resonator governs the filter's winner-take-all dynamics through signal-competition for gain. This physical circuit extracts what is mathematically referred to as the largest principal component of its spatio-temporal input space. The circuit's practicality is demonstrated by its incorporation in an RF-photonic system. An unknown mixture of unknown microwave signals, received by an antenna array, constitutes the input to the system. The output electronically returns one of the original microwave signals. The front-end of the system down converts the 10 GHz microwave signals and amplifies them before the signals phase modulate optical beams. The optical carrier is suppressed from these beams so that it may not be considered as a signal itself to the autotuning filter. The suppression is achieved with two-beam coupling in a single photorefractive crystal. The filter extracts the more intense of the signals present on the carrier-suppressed input beams. The detection of the extracted signal restores the microwave signal to an electronic form. The system, without the receiving antenna array, is packaged in a 13 x 18 x 6″ briefcase. Its power consumption equals that

  5. OPTIMAL CORRELATION ESTIMATORS FOR QUANTIZED SIGNALS

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, M. D.; Chou, H. H.; Gwinn, C. R., E-mail: michaeltdh@physics.ucsb.edu, E-mail: cgwinn@physics.ucsb.edu [Department of Physics, University of California, Santa Barbara, CA 93106 (United States)

    2013-03-10

    Using a maximum-likelihood criterion, we derive optimal correlation strategies for signals with and without digitization. We assume that the signals are drawn from zero-mean Gaussian distributions, as is expected in radio-astronomical applications, and we present correlation estimators both with and without a priori knowledge of the signal variances. We demonstrate that traditional estimators of correlation, which rely on averaging products, exhibit large and paradoxical noise when the correlation is strong. However, we also show that these estimators are fully optimal in the limit of vanishing correlation. We calculate the bias and noise in each of these estimators and discuss their suitability for implementation in modern digital correlators.

  6. Reconstruction of periodic signals using neural networks

    Directory of Open Access Journals (Sweden)

    José Danilo Rairán Antolines

    2014-01-01

    Full Text Available In this paper, we reconstruct a periodic signal by using two neural networks. The first network is trained to approximate the period of a signal, and the second network estimates the corresponding coefficients of the signal's Fourier expansion. The reconstruction strategy consists in minimizing the mean-square error via backpro-pagation algorithms over a single neuron with a sine transfer function. Additionally, this paper presents mathematical proof about the quality of the approximation as well as a first modification of the algorithm, which requires less data to reach the same estimation; thus making the algorithm suitable for real-time implementations.

  7. Signal processing in noise waveform radar

    CERN Document Server

    Kulpa, Krzysztof

    2013-01-01

    This book is devoted to the emerging technology of noise waveform radar and its signal processing aspects. It is a new kind of radar, which use noise-like waveform to illuminate the target. The book includes an introduction to basic radar theory, starting from classical pulse radar, signal compression, and wave radar. The book then discusses the properties, difficulties and potential of noise radar systems, primarily for low-power and short-range civil applications. The contribution of modern signal processing techniques to making noise radar practical are emphasized, and application examples

  8. Neutrino signals from dark matter decay

    Energy Technology Data Exchange (ETDEWEB)

    Covi, Laura; Grefe, Michael [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Ibarra, Alejandro; Tran, David [Technische Univ. Muenchen, Garching (Germany). Physik-Department T30d

    2009-12-15

    We investigate different neutrino signals from the decay of dark matter particles to determine the prospects for their detection, and more specifically if any spectral signature can be disentangled from the background in present and future neutrino observatories. If detected, such a signal could bring an independent confirmation of the dark matter interpretation of the dramatic rise in the positron fraction above 10 GeV recently observed by the PAMELA satellite experiment and offer the possibility of distinguishing between astrophysical sources and dark matter decay or annihilation. In combination with other signals, it may also be possible to distinguish among different dark matter decay channels. (orig.)

  9. Neutrino signals from dark matter decay

    International Nuclear Information System (INIS)

    Covi, Laura; Grefe, Michael; Ibarra, Alejandro; Tran, David

    2009-12-01

    We investigate different neutrino signals from the decay of dark matter particles to determine the prospects for their detection, and more specifically if any spectral signature can be disentangled from the background in present and future neutrino observatories. If detected, such a signal could bring an independent confirmation of the dark matter interpretation of the dramatic rise in the positron fraction above 10 GeV recently observed by the PAMELA satellite experiment and offer the possibility of distinguishing between astrophysical sources and dark matter decay or annihilation. In combination with other signals, it may also be possible to distinguish among different dark matter decay channels. (orig.)

  10. Endocannabinoid signaling in reward and addiction

    Science.gov (United States)

    Parsons, Loren H.; Hurd, Yasmin L.

    2015-01-01

    Brain endocannabinoid signaling influences the motivation for natural rewards (such as palatable food, sexual activity and social interaction) and modulates the rewarding effects of addictive drugs. Pathological forms of natural and drug-induced reward are associated with dysregulated endocannabinoid signaling that may derive from pre-existing genetic factors or from prolonged drug exposure. Impaired endocannabinoid signaling contributes to dysregulated synaptic plasticity, increased stress responsivity, negative emotional states, and craving that propel addiction. Understanding the contributions of endocannabinoid disruptions to behavioral and physiological traits provides insight into the endocannabinoid influence on addiction vulnerability. PMID:26373473

  11. OPTIMAL CORRELATION ESTIMATORS FOR QUANTIZED SIGNALS

    International Nuclear Information System (INIS)

    Johnson, M. D.; Chou, H. H.; Gwinn, C. R.

    2013-01-01

    Using a maximum-likelihood criterion, we derive optimal correlation strategies for signals with and without digitization. We assume that the signals are drawn from zero-mean Gaussian distributions, as is expected in radio-astronomical applications, and we present correlation estimators both with and without a priori knowledge of the signal variances. We demonstrate that traditional estimators of correlation, which rely on averaging products, exhibit large and paradoxical noise when the correlation is strong. However, we also show that these estimators are fully optimal in the limit of vanishing correlation. We calculate the bias and noise in each of these estimators and discuss their suitability for implementation in modern digital correlators.

  12. Signal processing for liquid ionization calorimeters

    International Nuclear Information System (INIS)

    Cleland, W.E.; Stern, E.G.

    1992-01-01

    We present the results of a study of the effects of thermal and pileup noise in liquid ionization calorimeters operating in a high luminosity calorimeters operating in a high luminosity environment. The method of optimal filtering of multiply-sampled signals which may be used to improve the timing and amplitude resolution of calorimeter signals is described, and its implications for signal shaping functions are examined. The dependence of the time and amplitude resolution on the relative strength of the pileup and thermal noise, which varies with such parameters as luminosity, rapidity and calorimeter cell size, is examined

  13. Microphone detected ionacoustic signal from metals

    International Nuclear Information System (INIS)

    Dioszeghy, T.; Szoekefalvi-Nagy, Z.; Biro, T.

    1986-12-01

    An experimental system for studying the radiation-induced acoustic signal generated by a modulated 2 MeV He + ion beam in metals is described. For detection, a closed cell on the rear side of the copper or aluminium sample, a half-inch condenser microphone, and a lock-in amplifier were employed. The signal was found to be proportional to beam current and particle energy, and inversely proportional to cell length. A decrease of the signal magnitude and an increase of the phase delay with increasing modulation frequency and sample thickness were also observed. (author)

  14. Na, K-ATPase as signaling transducer

    OpenAIRE

    Li, Juan

    2007-01-01

    It is now generally agreed that Na,K-ATPase (NKA), in addition to its role in the maintenance of Na+ and K+ gradients across the cell membrane, is a signal transducer. Our group has identified a novel signaling pathway where NKA interact with IP3R to form a signaling microdomain. Ouabain, a specific ligand of NKA, activates this pathway, triggers slow Ca2+ oscillations and activates NF-κB. In current study, the molecular mechanisms and some important downstream effects of NK...

  15. Knee joint vibroarthrographic signal processing and analysis

    CERN Document Server

    Wu, Yunfeng

    2015-01-01

    This book presents the cutting-edge technologies of knee joint vibroarthrographic signal analysis for the screening and detection of knee joint injuries. It describes a number of effective computer-aided methods for analysis of the nonlinear and nonstationary biomedical signals generated by complex physiological mechanics. This book also introduces several popular machine learning and pattern recognition algorithms for biomedical signal classifications. The book is well-suited for all researchers looking to better understand knee joint biomechanics and the advanced technology for vibration arthrometry. Dr. Yunfeng Wu is an Associate Professor at the School of Information Science and Technology, Xiamen University, Xiamen, Fujian, China.

  16. Wnt Signalling in Gastrointestinal Epithelial Stem Cells

    Directory of Open Access Journals (Sweden)

    Dustin J. Flanagan

    2018-03-01

    Full Text Available Wnt signalling regulates several cellular functions including proliferation, differentiation, apoptosis and migration, and is critical for embryonic development. Stem cells are defined by their ability for self-renewal and the ability to be able to give rise to differentiated progeny. Consequently, they are essential for the homeostasis of many organs including the gastrointestinal tract. This review will describe the huge advances in our understanding of how stem cell functions in the gastrointestinal tract are regulated by Wnt signalling, including how deregulated Wnt signalling can hijack these functions to transform cells and lead to cancer.

  17. Fast storage of nuclear quadrupole resonance signals

    International Nuclear Information System (INIS)

    Anferov, V.P.; Molchanov, S.V.; Levchun, O.D.

    1988-01-01

    Fast multichannel storage of nuclear quadrupole resonance (NQR) signals is described. Analog-to-digital converter, arithmetic-logical unit, internal memory device (IMD) selection-storage unit and control unit are the storage main units. The storage is based on 43 microcircuits and provides for record and storage of NQR-signals at the contributed operation with Mera-60 microcomputer. Time of analog-to-digital conversion and signal recording into IMD is ∼ 1 mks. Capacity of analog-to-digital converter constitutes 8-10 bits. IMD capacity is 4 K bitsx16. Number of storage channels is 4

  18. Detection test of wireless network signal strength and GPS positioning signal in underground pipeline

    Science.gov (United States)

    Li, Li; Zhang, Yunwei; Chen, Ling

    2018-03-01

    In order to solve the problem of selecting positioning technology for inspection robot in underground pipeline environment, the wireless network signal strength and GPS positioning signal testing are carried out in the actual underground pipeline environment. Firstly, the strength variation of the 3G wireless network signal and Wi-Fi wireless signal provided by China Telecom and China Unicom ground base stations are tested, and the attenuation law of these wireless signals along the pipeline is analyzed quantitatively and described. Then, the receiving data of the GPS satellite signal in the pipeline are tested, and the attenuation of GPS satellite signal under underground pipeline is analyzed. The testing results may be reference for other related research which need to consider positioning in pipeline.

  19. Dynamic decomposition of spatiotemporal neural signals.

    Directory of Open Access Journals (Sweden)

    Luca Ambrogioni

    2017-05-01

    Full Text Available Neural signals are characterized by rich temporal and spatiotemporal dynamics that reflect the organization of cortical networks. Theoretical research has shown how neural networks can operate at different dynamic ranges that correspond to specific types of information processing. Here we present a data analysis framework that uses a linearized model of these dynamic states in order to decompose the measured neural signal into a series of components that capture both rhythmic and non-rhythmic neural activity. The method is based on stochastic differential equations and Gaussian process regression. Through computer simulations and analysis of magnetoencephalographic data, we demonstrate the efficacy of the method in identifying meaningful modulations of oscillatory signals corrupted by structured temporal and spatiotemporal noise. These results suggest that the method is particularly suitable for the analysis and interpretation of complex temporal and spatiotemporal neural signals.

  20. Transit signal priority with connected vehicle technology.

    Science.gov (United States)

    2014-01-01

    A new TSP logic was proposed, taking advantage of the resources provided by Connected Vehicle (CV) : technology, including two-way communication between the bus and the traffic signal controller, accurate bus : location detection and prediction, and ...