Fourth Graders' Heuristic Problem-Solving Behavior.

ERIC Educational Resources Information Center

Lee, Kil S.

1982-01-01

Eight boys and eight girls from a rural elementary school participated in the investigation. Specific heuristics were adopted from Polya; and the students selected represented two substages of Piaget's concrete operational stage. Five hypotheses were generated, based on observed results and the study's theoretical rationale. (MP)

Human La binds mRNAs through contacts to the poly(A) tail.

PubMed

Vinayak, Jyotsna; Marrella, Stefano A; Hussain, Rawaa H; Rozenfeld, Leonid; Solomon, Karine; Bayfield, Mark A

2018-05-04

In addition to a role in the processing of nascent RNA polymerase III transcripts, La proteins are also associated with promoting cap-independent translation from the internal ribosome entry sites of numerous cellular and viral coding RNAs. La binding to RNA polymerase III transcripts via their common UUU-3'OH motif is well characterized, but the mechanism of La binding to coding RNAs is poorly understood. Using electromobility shift assays and cross-linking immunoprecipitation, we show that in addition to a sequence specific UUU-3'OH binding mode, human La exhibits a sequence specific and length dependent poly(A) binding mode. We demonstrate that this poly(A) binding mode uses the canonical nucleic acid interaction winged helix face of the eponymous La motif, previously shown to be vacant during uridylate binding. We also show that cytoplasmic, but not nuclear La, engages poly(A) RNA in human cells, that La entry into polysomes utilizes the poly(A) binding mode, and that La promotion of translation from the cyclin D1 internal ribosome entry site occurs in competition with cytoplasmic poly(A) binding protein (PABP). Our data are consistent with human La functioning in translation through contacts to the poly(A) tail.

Education and Thinking: The Role of Knowledge

DTIC Science & Technology

1983-06-21

failing to construct a representation of the problem. Through carefully designed problem " exercises , the program elicits procedures for reasoning and...guiding spirits. Polya -. .,• . . .. ~ -, • ° -. -- , ",r , • , , . . .. • . . , . .-r. Page9 9 recommends that explicit attention be paid to heuristic...reflects, according to Carey, a reorganization of knowledge brought about by school learning and world knowledge: for 4- to 7-year olds, biological

PlantAPA: A Portal for Visualization and Analysis of Alternative Polyadenylation in Plants

PubMed Central

Wu, Xiaohui; Zhang, Yumin; Li, Qingshun Q.

2016-01-01

Alternative polyadenylation (APA) is an important layer of gene regulation that produces mRNAs that have different 3′ ends and/or encode diverse protein isoforms. Up to 70% of annotated genes in plants undergo APA. Increasing numbers of poly(A) sites collected in various plant species demand new methods and tools to access and mine these data. We have created an open-access web service called PlantAPA (http://bmi.xmu.edu.cn/plantapa) to visualize and analyze genome-wide poly(A) sites in plants. PlantAPA provides various interactive and dynamic graphics and seamlessly integrates a genome browser that can profile heterogeneous cleavage sites and quantify expression patterns of poly(A) sites across different conditions. Particularly, through PlantAPA, users can analyze poly(A) sites in extended 3′ UTR regions, intergenic regions, and ambiguous regions owing to alternative transcription or RNA processing. In addition, it also provides tools for analyzing poly(A) site selections, 3′ UTR lengthening or shortening, non-canonical APA site switching, and differential gene expression between conditions, making it more powerful for the study of APA-mediated gene expression regulation. More importantly, PlantAPA offers a bioinformatics pipeline that allows users to upload their own short reads or ESTs for poly(A) site extraction, enabling users to further explore poly(A) site selection using stored PlantAPA poly(A) sites together with their own poly(A) site datasets. To date, PlantAPA hosts the largest database of APA sites in plants, including Oryza sativa, Arabidopsis thaliana, Medicago truncatula, and Chlamydomonas reinhardtii. As a user-friendly web service, PlantAPA will be a valuable addition to the community of biologists studying APA mechanisms and gene expression regulation in plants. PMID:27446120

Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features.

PubMed

Di, Chao; Yuan, Jiapei; Wu, Yue; Li, Jingrui; Lin, Huixin; Hu, Long; Zhang, Ting; Qi, Yijun; Gerstein, Mark B; Guo, Yan; Lu, Zhi John

2014-12-01

Recently, in addition to poly(A)+ long non-coding RNAs (lncRNAs), many lncRNAs without poly(A) tails, have been characterized in mammals. However, the non-polyA lncRNAs and their conserved motifs, especially those associated with environmental stresses, have not been fully investigated in plant genomes. We performed poly(A)- RNA-seq for seedlings of Arabidopsis thaliana under four stress conditions, and predicted lncRNA transcripts. We classified the lncRNAs into three confidence levels according to their expression patterns, epigenetic signatures and RNA secondary structures. Then, we further classified the lncRNAs to poly(A)+ and poly(A)- transcripts. Compared with poly(A)+ lncRNAs and coding genes, we found that poly(A)- lncRNAs tend to have shorter transcripts and lower expression levels, and they show significant expression specificity in response to stresses. In addition, their differential expression is significantly enriched in drought condition and depleted in heat condition. Overall, we identified 245 poly(A)+ and 58 poly(A)- lncRNAs that are differentially expressed under various stress stimuli. The differential expression was validated by qRT-PCR, and the signaling pathways involved were supported by specific binding of transcription factors (TFs), phytochrome-interacting factor 4 (PIF4) and PIF5. Moreover, we found many conserved sequence and structural motifs of lncRNAs from different functional groups (e.g. a UUC motif responding to salt and a AU-rich stem-loop responding to cold), indicated that the conserved elements might be responsible for the stress-responsive functions of lncRNAs. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

Polyadenylation state microarray (PASTA) analysis.

PubMed

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.

Behavior of adsorbed Poly-A onto sodium montmorillonite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Palomino-Aquino, Nayeli; Negrón-Mendoza, Alicia, E-mail: negron@nucleares.unam.mx

2015-07-23

The adsorption of Poly-A (a polynucleotide consisting of adenine, ribose and a phosphate group), onto a clay mineral, was studied to investigate the extent of adsorption, the site of binding, and the capacity of the clay to protect Poly-A, while it is adsorbed onto the clay, from external sources of energy. The results showed that Poly-A presented a high percentage of adsorption at the edges of the clay and that the survival of the polynucleotide was superior to irradiating the polymer in the absence of the clay.

Human La binds mRNAs through contacts to the poly(A) tail

PubMed Central

Vinayak, Jyotsna; Marrella, Stefano A; Hussain, Rawaa H; Rozenfeld, Leonid; Solomon, Karine; Bayfield, Mark A

2018-01-01

Abstract In addition to a role in the processing of nascent RNA polymerase III transcripts, La proteins are also associated with promoting cap-independent translation from the internal ribosome entry sites of numerous cellular and viral coding RNAs. La binding to RNA polymerase III transcripts via their common UUU-3’OH motif is well characterized, but the mechanism of La binding to coding RNAs is poorly understood. Using electromobility shift assays and cross-linking immunoprecipitation, we show that in addition to a sequence specific UUU-3’OH binding mode, human La exhibits a sequence specific and length dependent poly(A) binding mode. We demonstrate that this poly(A) binding mode uses the canonical nucleic acid interaction winged helix face of the eponymous La motif, previously shown to be vacant during uridylate binding. We also show that cytoplasmic, but not nuclear La, engages poly(A) RNA in human cells, that La entry into polysomes utilizes the poly(A) binding mode, and that La promotion of translation from the cyclin D1 internal ribosome entry site occurs in competition with cytoplasmic poly(A) binding protein (PABP). Our data are consistent with human La functioning in translation through contacts to the poly(A) tail. PMID:29447394

Problem-Solving Test: Expression Cloning of the Erythropoietin Receptor

ERIC Educational Resources Information Center

Szeberenyi, Jozsef

2008-01-01

Terms to be familiar with before you start to solve the test: cytokines, cytokine receptors, cDNA library, cDNA synthesis, poly(A)[superscript +] RNA, primer, template, reverse transcriptase, restriction endonucleases, cohesive ends, expression vector, promoter, Shine-Dalgarno sequence, poly(A) signal, DNA helicase, DNA ligase, topoisomerases,…

The poly(A) tail length of casein mRNA in the lactating mammary gland changes depending upon the accumulation and removal of milk.

PubMed Central

Kuraishi, T; Sun, Y; Aoki, F; Imakawa, K; Sakai, S

2000-01-01

The length of casein mRNA from the lactating mouse mammary gland, as assessed on Northern blots, is shorter after weaning, but is elongated following the removal of milk. In order to investigate this phenomenon, the molecular structures of beta- and gamma-casein mRNAs were analysed. The coding and non-coding regions of the two forms were the same length, but the long form of casein mRNA had a longer poly(A) tail than the short form (P<0.05). In order to examine the stability of casein mRNA under identical conditions, casein mRNAs with the long and short poly(A) tails were incubated in the rabbit reticulocyte lysate (RRL) cell-free translation system. Casein mRNA with the long poly(A) tail had a longer half-life than that with the short tail (P<0.05). The beta- and gamma-casein mRNAs were first degraded into 0.92 and 0.81 kb fragments respectively. With undegraded mRNA, the poly(A) tail shortening by exoribonuclease was not observed until the end of the incubation. Northern blot analysis showed that casein mRNA with the long poly(A) tail was protected efficiently from endoribonucleases. We conclude that the length of the poly(A) tail of casein mRNA in the lactating mammary gland changes depending upon the accumulation and removal of the gland's milk, and we show that the longer poly(A) tail potentially protects the mRNA from degradation by endoribonucleases. PMID:10749689

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

PubMed

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.

Poly(A) RNA a new component of Cajal bodies.

PubMed

Kołowerzo, Agnieszka; Smoliński, Dariusz Jan; Bednarska, Elzbieta

2009-07-01

In European larch microsporocytes, spherical structures 0.5 to 6 microm in diameter are present in which poly(A) RNA accumulates. There were one to several bodies per cell and they were often present in the vicinity of the nucleolus. No nascent transcripts were observed within them. Splicing factors of the SR family, including protein SC35, which participates in bringing the 3' and 5' sites closer in the splicing reaction, were also not observed. The absence of the above-mentioned elements within bodies containing poly(A) RNA disqualifies them as sites of synthesis and preliminary stages of primary transcript maturation. However, they contained abundant elements of the splicing machinery commonly occurring in Cajal bodies, i.e., Sm proteins or small nuclear RNA (snRNA). The molecular composition as well as the characteristic ultrastructure of bodies containing poly(A) RNA proves that these were Cajal bodies. This is the first report of such poly(A) RNA localization.

Poly(A)-tag deep sequencing data processing to extract poly(A) sites.

PubMed

Wu, Xiaohui; Ji, Guoli; Li, Qingshun Quinn

2015-01-01

Polyadenylation [poly(A)] is an essential posttranscriptional processing step in the maturation of eukaryotic mRNA. The advent of next-generation sequencing (NGS) technology has offered feasible means to generate large-scale data and new opportunities for intensive study of polyadenylation, particularly deep sequencing of the transcriptome targeting the junction of 3'-UTR and the poly(A) tail of the transcript. To take advantage of this unprecedented amount of data, we present an automated workflow to identify polyadenylation sites by integrating NGS data cleaning, processing, mapping, normalizing, and clustering. In this pipeline, a series of Perl scripts are seamlessly integrated to iteratively map the single- or paired-end sequences to the reference genome. After mapping, the poly(A) tags (PATs) at the same genome coordinate are grouped into one cleavage site, and the internal priming artifacts removed. Then the ambiguous region is introduced to parse the genome annotation for cleavage site clustering. Finally, cleavage sites within a close range of 24 nucleotides and from different samples can be clustered into poly(A) clusters. This procedure could be used to identify thousands of reliable poly(A) clusters from millions of NGS sequences in different tissues or treatments.

Leisure Activities for the Development of Creative Intelligence in Mathematical Problem Solving

ERIC Educational Resources Information Center

Castro, Angélica Mercedes Tumbaco; Guerra, Galo Ernestro Cabanilla; Brito, Christian Antonio Pavón; Chávez, Tannia Gabriela Acosta

2018-01-01

The present work studies the influence of leisure activities on the creative intelligence of the students. An experimental pre- and post-test design was carried out with individuals selected in a sampling process. The design identifies the ease of students to place themselves in possible contexts and solve them mathematically through Polya's…

Activation of HIV-1 pre-mRNA 3' processing in vitro requires both an upstream element and TAR.

PubMed Central

Gilmartin, G M; Fleming, E S; Oetjen, J

1992-01-01

The architecture of the human immunodeficiency virus type 1 (HIV-1) genome presents an intriguing dilemma for the 3' processing of viral transcripts--to disregard a canonical 'core' poly(A) site processing signal present at the 5' end of the transcript and yet to utilize efficiently an identical signal that resides at the 3' end of the message. The choice of processing sites in HIV-1 appears to be influenced by two factors: (i) proximity to the cap site, and (ii) sequences upstream of the core poly(A) site. We now demonstrate that an in vivo-defined upstream element that resides within the U3 region, 76 nucleotides upstream of the AAUAAA hexamer, acts specifically to enhance 3' processing at the HIV-1 core poly(A) site in vitro. We furthermore show that efficient in vitro 3' processing requires the RNA stem-loop structure of TAR, which serves to juxtapose spatially the upstream element and the core poly(A) site. An analysis of the stability of 3' processing complexes formed at the HIV-1 poly(A) site in vitro suggests that the upstream element may function by increasing processing complex stability at the core poly(A) site. Images PMID:1425577

Characterization of Rous sarcoma virus polyadenylation site use in vitro

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maciolek, Nicole L.; McNally, Mark T.

2008-05-10

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 RSVmore » 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.« less

A nonradioactive assay for poly(a)-specific ribonuclease activity by methylene blue colorimetry.

PubMed

Cheng, Yuan; Liu, Wei-Feng; Yan, Yong-Bin; Zhou, Hai-Meng

2006-01-01

A simple nonradioactive assay, which was based on the specific shift of the absorbance maximum of methylene blue induced by its intercalation into poly(A) molecules, was developed for poly(A)-specific ribonuclease (PARN). A good linear relationship was found between the absorbance at 662 nm and the poly(A) concentration. The assay conditions, including the concentration of methylene blue, the incubation temperature and time, and the poly(A) concentration were evaluated and optimized.

APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals

PubMed Central

You, Leiming; Wu, Jiexin; Feng, Yuchao; Fu, Yonggui; Guo, Yanan; Long, Liyuan; Zhang, Hui; Luan, Yijie; Tian, Peng; Chen, Liangfu; Huang, Guangrui; Huang, Shengfeng; Li, Yuxin; Li, Jie; Chen, Chengyong; Zhang, Yaqing; Chen, Shangwu; Xu, Anlong

2015-01-01

Increasing amounts of genes have been shown to utilize alternative polyadenylation (APA) 3′-processing sites depending on the cell and tissue type and/or physiological and pathological conditions at the time of processing, and the construction of genome-wide database regarding APA is urgently needed for better understanding poly(A) site selection and APA-directed gene expression regulation for a given biology. Here we present a web-accessible database, named APASdb (http://mosas.sysu.edu.cn/utr), which can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3′-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites, much better than the previous databases using conventional methods. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads, making our database more useful. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3′-untranslated regions (3′-UTRs). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish. PMID:25378337

TSAPA: identification of tissue-specific alternative polyadenylation sites in plants.

PubMed

Ji, Guoli; Chen, Moliang; Ye, Wenbin; Zhu, Sheng; Ye, Congting; Su, Yaru; Peng, Haonan; Wu, Xiaohui

2018-06-15

Alternative polyadenylation (APA) is now emerging as a widespread mechanism modulated tissue-specifically, which highlights the need to define tissue-specific poly(A) sites for profiling APA dynamics across tissues. We have developed an R package called TSAPA based on the machine learning model for identifying tissue-specific poly(A) sites in plants. A feature space including more than 200 features was assembled to specifically characterize poly(A) sites in plants. The classification model in TSAPA can be customized by selecting desirable features or classifiers. TSAPA is also capable of predicting tissue-specific poly(A) sites in unannotated intergenic regions. TSAPA will be a valuable addition to the community for studying dynamics of APA in plants. https://github.com/BMILAB/TSAPA. Supplementary data are available at Bioinformatics online.

Interaction of phenazinium dyes with double-stranded poly(A): Spectroscopy and isothermal titration calorimetry studies

NASA Astrophysics Data System (ADS)

Khan, Asma Yasmeen; Saha, Baishakhi; Kumar, Gopinatha Suresh

2014-10-01

A comprehensive study on the binding of phenazinium dyes viz. janus green B, indoine blue, safranine O and phenosafranine with double stranded poly(A) using various spectroscopic and calorimetric techniques is presented. A higher binding of janus green B and indoine blue over safranine O and phenosafranine to poly(A) was observed from all experiments. Intercalative mode of binding of the dyes was inferred from fluorescence polarization anisotropy, iodide quenching and viscosity experiments. Circular dichroism study revealed significant perturbation of the secondary structure of poly(A) on binding of these dyes. Results from isothermal titration calorimetry experiments suggested that the binding was predominantly entropy driven with a minor contribution of enthalpy to the standard molar Gibbs energy. The results presented here may open new opportunities in the application of these dyes as RNA targeted therapeutic agents.

A pause site for RNA polymerase II is associated with termination of transcription.

PubMed Central

Enriquez-Harris, P; Levitt, N; Briggs, D; Proudfoot, N J

1991-01-01

Termination of transcription by RNA polymerase II has been postulated to involve a pausing process. We have identified such a pause signal, 350 bp into the 3' flanking region of the human alpha 2 globin gene at a position where termination is thought to occur. We show that this pause signal enhances the utilization of an upstream poly(A) site which is otherwise out-competed by a stronger downstream poly(A) site. We also demonstrate that the pause site rescues a poly(A) site that is inactive due to its location within an intron. Using nuclear run-on analysis we show that elongating RNA polymerase II molecules accumulate over this pause signal. Furthermore we show that when the pause site is positioned immediately downstream of a strong poly(A) signal, significant levels of transcription termination take place. Images PMID:2050120

Influence of nucleotide modifications at the C2’ position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA

PubMed Central

Copp, William; Denisov, Alexey Y.; Xie, Jingwei; Noronha, Anne M.; Liczner, Christopher; Safaee, Nozhat

2017-01-01

Abstract Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2′-deoxyribose, 2′-O-methyl-ribose, 2′-deoxy-2′-fluoro-ribose, arabinose and 2′-deoxy-2′-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2’ modifications gave a variety of effects. Arabinose and 2′-deoxy-2′-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2′-O-methyl and 2′-deoxy-2′-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability. PMID:28973475

Influence of nucleotide modifications at the C2' position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA.

PubMed

Copp, William; Denisov, Alexey Y; Xie, Jingwei; Noronha, Anne M; Liczner, Christopher; Safaee, Nozhat; Wilds, Christopher J; Gehring, Kalle

2017-09-29

Polyadenylate (poly(A)) has the ability to form a parallel duplex with Hoogsteen adenine:adenine base pairs at low pH or in the presence of ammonium ions. In order to evaluate the potential of this structural motif for nucleic acid-based nanodevices, we characterized the effects on duplex stability of substitutions of the ribose sugar with 2'-deoxyribose, 2'-O-methyl-ribose, 2'-deoxy-2'-fluoro-ribose, arabinose and 2'-deoxy-2'-fluoro-arabinose. Deoxyribose substitutions destabilized the poly(A) duplex both at low pH and in the presence of ammonium ions: no duplex formation could be detected with poly(A) DNA oligomers. Other sugar C2' modifications gave a variety of effects. Arabinose and 2'-deoxy-2'-fluoro-arabinose nucleotides strongly destabilized poly(A) duplex formation. In contrast, 2'-O-methyl and 2'-deoxy-2'-fluoro-ribo modifications were stabilizing either at pH 4 or in the presence of ammonium ions. The differential effect suggests they could be used to design molecules selectively responsive to pH or ammonium ions. To understand the destabilization by deoxyribose, we determined the structures of poly(A) duplexes with a single DNA residue by nuclear magnetic resonance spectroscopy and X-ray crystallography. The structures revealed minor structural perturbations suggesting that the combination of sugar pucker propensity, hydrogen bonding, pKa shifts and changes in hydration determine duplex stability. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Histone-poly(A) hybrid molecules as tools to block nuclear pores.

PubMed

Cremer, G; Wojtech, E; Kalbas, M; Agutter, P S; Prochnow, D

1995-04-01

Histone-poly(A) hybrid molecules were used for transport experiments with resealed nuclear envelopes and after attachment of a cleavable cross-linker (SASD) to identify nuclear proteins. In contrast to histones, the hybrid molecules cannot be accumulated in resealed nuclear envelopes, and in contrast to poly(A), the export of hybrids from preloaded nuclear envelopes is completely impaired. The experiments strongly confirm the existence of poly(A) as an export signal in mRNA which counteracts the nuclear location signals (NLS) in histones. The contradicting transport signals in the hybrid molecules impair translocation through the nuclear pore complex. The failure to accumulate hybrid molecules into resealed nuclear envelopes results from the covalent attachment of polyadenylic acid to histones in a strict 1:1 molar ratio. This was demonstrated in control transport experiments where radiolabeled histones were simply mixed with nonlabeled poly(A) or radiolabeled poly(A) mixed with nonlabeled histones. In comparison, control uptake experiments with histones covalently linked to a single UMP-mononucleotide are strongly enhanced. Such controls exclude the conceivable possibility of a simple masking of the nuclear location signal in the histones by the covalent attached poly(A) moiety. Photoreactive histone-poly(A) hybrid analogs serve to identify nuclear envelope proteins--presumably in the nuclear pore--with molecular weights of 110, 80, and 71.4 kDa.

Fluorescence in-situ hybridization method reveals that carboxyl-terminal fragments of transactive response DNA-binding protein-43 truncated at the amino acid residue 218 reduce poly(A)+ RNA expression.

PubMed

Higashi, Shinji; Watanabe, Ryohei; Arai, Tetsuaki

2018-07-04

Transactive response (TAR) DNA-binding protein 43 (TDP-43) has emerged as an important contributor to amyotrophic lateral sclerosis and frontotemporal lobar degeneration. To understand the association of TDP-43 with complex RNA processing in disease pathogenesis, we performed fluorescence in-situ hybridization using HeLa cells transfected with a series of deleted TDP-43 constructs and investigated the effect of truncation of TDP-43 on the expression of poly(A) RNA. Endogenous and overexpressed full-length TDP-43 localized to the perichromatin region and interchromatin space adjacent to poly(A) RNA. Deleted variants of TDP-43 containing RNA recognition motif 1 and truncating N-terminal region induced cytoplasmic inclusions in which poly(A) RNA was recruited. Carboxyl-terminal TDP-43 truncated at residue 202 or 218 was distributed in the cytoplasm as punctate structures. Carboxyl-terminal TDP-43 truncated at residue 218, but not at 202, significantly decreased poly(A) RNA expression by ∼24% compared with the level in control cells. Our results suggest that the disturbance of RNA metabolism induced by pathogenic fragments plays central roles in the pathogenesis of amyotrophic lateral sclerosis and frontotemporal lobar degeneration.

A deadenylase assay by size-exclusion chromatography.

PubMed

He, Guang-Jun; Yan, Yong-Bin

2012-01-01

The shortening of the 3'-end poly(A) tail, also called deadenylation, is crucial to the regulation of mRNA processing, transportation, translation and degradation. The deadenylation process is achieved by deadenylases, which specifically catalyze the removal of the poly(A) tail at the 3'-end of eukaryotic mRNAs and release 5'-AMP as the product. To achieve their physiological functions, all deadenylases have numerous binding partners that may regulate their catalytic properties or recruit them into various protein complexes. To study the effects of various partners, it is important to develop new deadenylase assay that can be applied either in vivo or in vitro. In this research, we developed the deadenylase assay by the size-exclusion chromatography (SEC) method. The SEC analysis indicated that the poly(A) or oligo(A) substrate and the product AMP could be successfully separated and quantified. The enzymatic parameters of deadenylase could be obtained by quantifying the AMP generation. When using the commercial poly(A) as the substrate, a biphasic catalytic process was observed, which might correlate to the two distinct states of poly(A) in the commercial samples. Different lots of commercial poly(A) had dissimilar size distributions and were dissimilar in response to the degradation of deadenylase. The deadenylation pattern, processive or distributive, could also be investigated using the SEC assay by monitoring the status of the substrate and the generation kinetics of AMP and A2. The SEC assay was applicable to both simple samples using the purified enzyme and complex enzyme reaction conditions such as using protein mixtures or crude cell extracts as samples. The influence of solutes with absorption at 254 nm could be successfully eliminated by constructing the different SEC profiles.

Improving mathematical problem solving skills through visual media

NASA Astrophysics Data System (ADS)

Widodo, S. A.; Darhim; Ikhwanudin, T.

2018-01-01

The purpose of this article was to find out the enhancement of students’ mathematical problem solving by using visual learning media. The ability to solve mathematical problems is the ability possessed by students to solve problems encountered, one of the problem-solving model of Polya. This preliminary study was not to make a model, but it only took a conceptual approach by comparing the various literature of problem-solving skills by linking visual learning media. The results of the study indicated that the use of learning media had not been appropriated so that the ability to solve mathematical problems was not optimal. The inappropriateness of media use was due to the instructional media that was not adapted to the characteristics of the learners. Suggestions that can be given is the need to develop visual media to increase the ability to solve problems.

Human mRNA polyadenylate binding protein: evolutionary conservation of a nucleic acid binding motif.

PubMed Central

Grange, T; de Sa, C M; Oddos, J; Pictet, R

1987-01-01

We have isolated a full length cDNA (cDNA) coding for the human poly(A) binding protein. The cDNA derived 73 kd basic translation product has the same Mr, isoelectric point and peptidic map as the poly(A) binding protein. DNA sequence analysis reveals a 70,244 dalton protein. The N terminal part, highly homologous to the yeast poly(A) binding protein, is sufficient for poly(A) binding activity. This domain consists of a four-fold repeated unit of approximately 80 amino acids present in other nucleic acid binding proteins. In the C terminal part there is, as in the yeast protein, a sequence of approximately 150 amino acids, rich in proline, alanine and glutamine which together account for 48% of the residues. A 2,9 kb mRNA corresponding to this cDNA has been detected in several vertebrate cell types and in Drosophila melanogaster at every developmental stage including oogenesis. Images PMID:2885805

Semantics of Procedures: A Cognitive Basis for Maintenance Training Competency

DTIC Science & Technology

1988-04-01

provided by presenting these multiple, interacting views. These 0 conclusions are similar to the views of George Polya , who proposed the use of... exercises . It is also clear that at least some understanding of machine structure and function is required to interpret much of the information in the...check of the problem lists provides the names of all the usual subpects. This accessibility permits the technician to modify the sequence according to

Naval Research Logistics Quarterly. Volume 27, Number 2.

DTIC Science & Technology

1980-06-01

research area in recent years. Van Zyl [11] provided the first major study on single-product perishable inventories, but the field only began to...Journal of Applied Mathematics 30, 483-500 (1976). [III Van Zyl, G.J.J., "Inventory Control for Perishable Commodities," Unpublished Ph.D. dissertation...Hollatz and B. Bank, "Theorie der Linearen Parametrischen Optimierung," Akademie-Verlag, Berlin (1974). [4] Polya, G. and G. Szego, "Problems and

Distinct solvent- and temperature-dependent packing arrangements of anti-parallel β-sheet polyalanines studied with solid-state 13C NMR and MD simulation.

PubMed

Kametani, Shunsuke; Tasei, Yugo; Nishimura, Akio; Asakura, Tetsuo

2017-08-09

Polyalanine (polyA) sequences are well known as the simplest sequence that naturally forms anti-parallel β-sheets and constitute a key element in the structure of spider and wild silkworm silk fibers. We have carried out a systematic analysis of the packing of anti-parallel β-sheets for (Ala) n , n = 5, 6, 7 and 12, using primarily 13 C solid-state NMR and MD simulation. HFIP and TFA are frequently used as the dope solvents for recombinant silks, and polyA was solidified from both HFIP and TFA solutions by drying. An analysis of Ala Cβ peaks in the 13 C CP/MAS NMR spectra indicated that polyA from HFIP was mainly rectangular but polyA from TFA was mainly staggered. The transition from the rectangular to the staggered arrangement in (Ala) 6 was observed for the first time from the change in the Ala Cβ peak through heat treatment at 200 °C for 4 h. The removal of the bound water was confirmed by thermal analysis. This transition could be reproduced by MD simulation of (Ala) 6 molecules at 200 °C after removal of the bound water molecules. In this way, the origin of the stability of the different packing arrangements of polyA was clarified.

Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion.

PubMed

Zhao, Shanrong; Zhang, Ying; Gamini, Ramya; Zhang, Baohong; von Schack, David

2018-03-19

To allow efficient transcript/gene detection, highly abundant ribosomal RNAs (rRNA) are generally removed from total RNA either by positive polyA+ selection or by rRNA depletion (negative selection) before sequencing. Comparisons between the two methods have been carried out by various groups, but the assessments have relied largely on non-clinical samples. In this study, we evaluated these two RNA sequencing approaches using human blood and colon tissue samples. Our analyses showed that rRNA depletion captured more unique transcriptome features, whereas polyA+ selection outperformed rRNA depletion with higher exonic coverage and better accuracy of gene quantification. For blood- and colon-derived RNAs, we found that 220% and 50% more reads, respectively, would have to be sequenced to achieve the same level of exonic coverage in the rRNA depletion method compared with the polyA+ selection method. Therefore, in most cases we strongly recommend polyA+ selection over rRNA depletion for gene quantification in clinical RNA sequencing. Our evaluation revealed that a small number of lncRNAs and small RNAs made up a large fraction of the reads in the rRNA depletion RNA sequencing data. Thus, we recommend that these RNAs are specifically depleted to improve the sequencing depth of the remaining RNAs.

APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data.

PubMed

Ye, Congting; Long, Yuqi; Ji, Guoli; Li, Qingshun Quinn; Wu, Xiaohui

2018-06-01

Alternative polyadenylation (APA) has been increasingly recognized as a crucial mechanism that contributes to transcriptome diversity and gene expression regulation. As RNA-seq has become a routine protocol for transcriptome analysis, it is of great interest to leverage such unprecedented collection of RNA-seq data by new computational methods to extract and quantify APA dynamics in these transcriptomes. However, research progress in this area has been relatively limited. Conventional methods rely on either transcript assembly to determine transcript 3' ends or annotated poly(A) sites. Moreover, they can neither identify more than two poly(A) sites in a gene nor detect dynamic APA site usage considering more than two poly(A) sites. We developed an approach called APAtrap based on the mean squared error model to identify and quantify APA sites from RNA-seq data. APAtrap is capable of identifying novel 3' UTRs and 3' UTR extensions, which contributes to locating potential poly(A) sites in previously overlooked regions and improving genome annotations. APAtrap also aims to tally all potential poly(A) sites and detect genes with differential APA site usages between conditions. Extensive comparisons of APAtrap with two other latest methods, ChangePoint and DaPars, using various RNA-seq datasets from simulation studies, human and Arabidopsis demonstrate the efficacy and flexibility of APAtrap for any organisms with an annotated genome. Freely available for download at https://apatrap.sourceforge.io. liqq@xmu.edu.cn or xhuister@xmu.edu.cn. Supplementary data are available at Bioinformatics online.

Tissue-specific autoregulation of Drosophila suppressor of forked by alternative poly(A) site utilization leads to accumulation of the suppressor of forked protein in mitotically active cells.

PubMed Central

Juge, F; Audibert, A; Benoit, B; Simonelig, M

2000-01-01

The Suppressor of forked protein is the Drosophila homolog of the 77K subunit of human cleavage stimulation factor, a complex required for the first step of the mRNA 3'-end-processing reaction. We have shown previously that wild-type su(f) function is required for the accumulation of a truncated su(f) transcript polyadenylated in intron 4 of the gene. This led us to propose a model in which the Su(f) protein would negatively regulate its own accumulation by stimulating 3'-end formation of this truncated su(f) RNA. In this article, we demonstrate this model and show that su(f) autoregulation is tissue specific. The Su(f) protein accumulates at a high level in dividing tissues, but not in nondividing tissues. We show that this distribution of the Su(f) protein results from stimulation by Su(f) of the tissue-specific utilization of the su(f) intronic poly(A) site, leading to the accumulation of the truncated su(f) transcript in nondividing tissues. Utilization of this intronic poly(A) site is affected in a su(f) mutant and restored in the mutant with a transgene encoding wild-type Su(f) protein. These data provide an in vivo example of cell-type-specific regulation of a protein level by poly(A) site choice, and confirm the role of Su(f) in regulation of poly(A) site utilization. PMID:11105753

Evidence for a Complex Class of Nonadenylated mRNA in Drosophila

PubMed Central

Zimmerman, J. Lynn; Fouts, David L.; Manning, Jerry E.

1980-01-01

The amount, by mass, of poly(A+) mRNA present in the polyribosomes of third-instar larvae of Drosophila melanogaster, and the relative contribution of the poly(A+) mRNA to the sequence complexity of total polysomal RNA, has been determined. Selective removal of poly(A+) mRNA from total polysomal RNA by use of either oligo-dT-cellulose, or poly(U)-sepharose affinity chromatography, revealed that only 0.15% of the mass of the polysomal RNA was present as poly(A+) mRNA. The present study shows that this RNA hybridized at saturation with 3.3% of the single-copy DNA in the Drosophila genome. After correction for asymmetric transcription and reactability of the DNA, 7.4% of the single-copy DNA in the Drosophila genome is represented in larval poly(A+) mRNA. This corresponds to 6.73 x 106 nucleotides of mRNA coding sequences, or approximately 5,384 diverse RNA sequences of average size 1,250 nucleotides. However, total polysomal RNA hybridizes at saturation to 10.9% of the single-copy DNA sequences. After correcting this value for asymmetric transcription and tracer DNA reactability, 24% of the single-copy DNA in Drosophila is represented in total polysomal RNA. This corresponds to 2.18 x 107 nucleotides of RNA coding sequences or 17,440 diverse RNA molecules of size 1,250 nucleotides. This value is 3.2 times greater than that observed for poly(A+) mRNA, and indicates that ≃69% of the polysomal RNA sequence complexity is contributed by nonadenylated RNA. Furthermore, if the number of different structural genes represented in total polysomal RNA is ≃1.7 x 104, then the number of genes expressed in third-instar larvae exceeds the number of chromomeres in Drosophila by about a factor of three. This numerology indicates that the number of chromomeres observed in polytene chromosomes does not reflect the number of structural gene sequences in the Drosophila genome. PMID:6777246

Mathematics in the Making: Mapping Verbal Discourse in Polya's "Let Us Teach Guessing" Lesson

ERIC Educational Resources Information Center

Truxaw, Mary P.; DeFranco, Thomas C.

2007-01-01

This paper describes a detailed analysis of verbal discourse within an exemplary mathematics lesson--that is, George Polya teaching in the Mathematics Association of America [MAA] video classic, "Let Us Teach Guessing" (1966). The results of the analysis reveal an inductive model of teaching that represents recursive cycles rather than linear…

An Improved Estimation Using Polya-Gamma Augmentation for Bayesian Structural Equation Models with Dichotomous Variables

ERIC Educational Resources Information Center

Kim, Seohyun; Lu, Zhenqiu; Cohen, Allan S.

2018-01-01

Bayesian algorithms have been used successfully in the social and behavioral sciences to analyze dichotomous data particularly with complex structural equation models. In this study, we investigate the use of the Polya-Gamma data augmentation method with Gibbs sampling to improve estimation of structural equation models with dichotomous variables.…

Poly(A) tail length regulates PABPC1 expression to tune translation in the heart.

PubMed

Chorghade, Sandip; Seimetz, Joseph; Emmons, Russell; Yang, Jing; Bresson, Stefan M; Lisio, Michael De; Parise, Gianni; Conrad, Nicholas K; Kalsotra, Auinash

2017-06-27

The rate of protein synthesis in the adult heart is one of the lowest in mammalian tissues, but it increases substantially in response to stress and hypertrophic stimuli through largely obscure mechanisms. Here, we demonstrate that regulated expression of cytosolic poly(A)-binding protein 1 (PABPC1) modulates protein synthetic capacity of the mammalian heart. We uncover a poly(A) tail-based regulatory mechanism that dynamically controls PABPC1 protein synthesis in cardiomyocytes and thereby titrates cellular translation in response to developmental and hypertrophic cues. Our findings identify PABPC1 as a direct regulator of cardiac hypertrophy and define a new paradigm of gene regulation in the heart, where controlled changes in poly(A) tail length influence mRNA translation.

PolyaPeak: Detecting Transcription Factor Binding Sites from ChIP-seq Using Peak Shape Information

PubMed Central

Wu, Hao; Ji, Hongkai

2014-01-01

ChIP-seq is a powerful technology for detecting genomic regions where a protein of interest interacts with DNA. ChIP-seq data for mapping transcription factor binding sites (TFBSs) have a characteristic pattern: around each binding site, sequence reads aligned to the forward and reverse strands of the reference genome form two separate peaks shifted away from each other, and the true binding site is located in between these two peaks. While it has been shown previously that the accuracy and resolution of binding site detection can be improved by modeling the pattern, efficient methods are unavailable to fully utilize that information in TFBS detection procedure. We present PolyaPeak, a new method to improve TFBS detection by incorporating the peak shape information. PolyaPeak describes peak shapes using a flexible Pólya model. The shapes are automatically learnt from the data using Minorization-Maximization (MM) algorithm, then integrated with the read count information via a hierarchical model to distinguish true binding sites from background noises. Extensive real data analyses show that PolyaPeak is capable of robustly improving TFBS detection compared with existing methods. An R package is freely available. PMID:24608116

Poly(A) code analyses reveal key determinants for tissue-specific mRNA alternative polyadenylation

PubMed Central

Weng, Lingjie; Li, Yi; Xie, Xiaohui; Shi, Yongsheng

2016-01-01

mRNA alternative polyadenylation (APA) is a critical mechanism for post-transcriptional gene regulation and is often regulated in a tissue- and/or developmental stage-specific manner. An ultimate goal for the APA field has been to be able to computationally predict APA profiles under different physiological or pathological conditions. As a first step toward this goal, we have assembled a poly(A) code for predicting tissue-specific poly(A) sites (PASs). Based on a compendium of over 600 features that have known or potential roles in PAS selection, we have generated and refined a machine-learning algorithm using multiple high-throughput sequencing-based data sets of tissue-specific and constitutive PASs. This code can predict tissue-specific PASs with >85% accuracy. Importantly, by analyzing the prediction performance based on different RNA features, we found that PAS context, including the distance between alternative PASs and the relative position of a PAS within the gene, is a key feature for determining the susceptibility of a PAS to tissue-specific regulation. Our poly(A) code provides a useful tool for not only predicting tissue-specific APA regulation, but also for studying its underlying molecular mechanisms. PMID:27095026

Changes in Gene Expression during Tomato Fruit Ripening 1

PubMed Central

Biggs, M. Scott; Harriman, Robert W.; Handa, Avtar K.

1986-01-01

Total proteins from pericarp tissue of different chronological ages from normally ripening tomato (Lycopersicon esculentum Mill. cv Rutgers) fruits and from fruits of the isogenic ripening-impaired mutants rin, nor, and Nr were extracted and separated by sodium dodecylsulfate-polyacrylamide gel electrophoresis. Analysis of the stained bands revealed increases in 5 polypeptides (94, 44, 34, 20, and 12 kilodaltons), decreases in 12 polypeptides (106, 98, 88, 76, 64, 52, 48, 45, 36, 28, 25, and 15 kilodaltons), and fluctuations in 5 polypeptides (85, 60, 26, 21, and 16 kilodaltons) as normal ripening proceeded. Several polypeptides present in ripening normal pericarp exhibited very low or undetectable levels in developing mutant pericarp. Total RNAs extracted from various stages of Rutgers pericarp and from 60 to 65 days old rin, nor, and Nr pericarp were fractionated into poly(A)+ and poly(A)− RNAs. Peak levels of total RNA, poly(A)+ RNA, and poly(A)+ RNA as percent of total RNA occurred between the mature green to breaker stages of normal pericarp. In vitro translation of poly(A)+ RNAs from normal pericarp in rabbit reticulocyte lysates revealed increases in mRNAs for 9 polypeptides (116, 89, 70, 42, 38, 33, 31, 29, and 26 kilodaltons), decreases in mRNAs for 2 polypeptides (41 and 35 kilodaltons), and fluctuations in mRNAs for 5 polypeptides (156, 53, 39, 30, and 14 kilodaltons) during normal ripening. Analysis of two-dimensional separation of in vitro translated polypeptides from poly(A)+ RNAs isolated from different developmental stages revealed even more extensive changes in mRNA populations during ripening. In addition, a polygalacturonase precursor (54 kilodaltons) was immunoprecipitated from breaker, turning, red ripe, and 65 days old Nr in vitro translation products. Images Fig. 1 Fig. 3 Fig. 5 Fig. 6 Fig. 7 PMID:16664828

Genome-wide dynamics of alternative polyadenylation in rice

PubMed Central

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

Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase.

PubMed

Kaufmann, Isabelle; Martin, Georges; Friedlein, Arno; Langen, Hanno; Keller, Walter

2004-02-11

In mammals, polyadenylation of mRNA precursors (pre-mRNAs) by poly(A) polymerase (PAP) depends on cleavage and polyadenylation specificity factor (CPSF). CPSF is a multisubunit complex that binds to the canonical AAUAAA hexamer and to U-rich upstream sequence elements on the pre-mRNA, thereby stimulating the otherwise weakly active and nonspecific polymerase to elongate efficiently RNAs containing a poly(A) signal. Based on sequence similarity to the Saccharomyces cerevisiae polyadenylation factor Fip1p, we have identified human Fip1 (hFip1) and found that the protein is an integral subunit of CPSF. hFip1 interacts with PAP and has an arginine-rich RNA-binding motif that preferentially binds to U-rich sequence elements on the pre-mRNA. Recombinant hFip1 is sufficient to stimulate the in vitro polyadenylation activity of PAP in a U-rich element-dependent manner. hFip1, CPSF160 and PAP form a ternary complex in vitro, suggesting that hFip1 and CPSF160 act together in poly(A) site recognition and in cooperative recruitment of PAP to the RNA. These results show that hFip1 significantly contributes to CPSF-mediated stimulation of PAP activity.

Human Fip1 is a subunit of CPSF that binds to U-rich RNA elements and stimulates poly(A) polymerase

PubMed Central

Kaufmann, Isabelle; Martin, Georges; Friedlein, Arno; Langen, Hanno; Keller, Walter

2004-01-01

In mammals, polyadenylation of mRNA precursors (pre-mRNAs) by poly(A) polymerase (PAP) depends on cleavage and polyadenylation specificity factor (CPSF). CPSF is a multisubunit complex that binds to the canonical AAUAAA hexamer and to U-rich upstream sequence elements on the pre-mRNA, thereby stimulating the otherwise weakly active and nonspecific polymerase to elongate efficiently RNAs containing a poly(A) signal. Based on sequence similarity to the Saccharomyces cerevisiae polyadenylation factor Fip1p, we have identified human Fip1 (hFip1) and found that the protein is an integral subunit of CPSF. hFip1 interacts with PAP and has an arginine-rich RNA-binding motif that preferentially binds to U-rich sequence elements on the pre-mRNA. Recombinant hFip1 is sufficient to stimulate the in vitro polyadenylation activity of PAP in a U-rich element-dependent manner. hFip1, CPSF160 and PAP form a ternary complex in vitro, suggesting that hFip1 and CPSF160 act together in poly(A) site recognition and in cooperative recruitment of PAP to the RNA. These results show that hFip1 significantly contributes to CPSF-mediated stimulation of PAP activity. PMID:14749727

Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation

PubMed Central

Zhang, Yong; Gu, Lianfeng; Hou, Yifeng; Wang, Lulu; Deng, Xian; Hang, Runlai; Chen, Dong; Zhang, Xiansheng; Zhang, Yi; Liu, Chunyan; Cao, Xiaofeng

2015-01-01

Alternative polyadenylation (APA) is a widespread mechanism for gene regulation and has been implicated in flowering, but the molecular basis governing the choice of a specific poly(A) site during the vegetative-to-reproductive growth transition remains unclear. Here we characterize HLP1, an hnRNP A/B protein as a novel regulator for pre-mRNA 3′-end processing in Arabidopsis. Genetic analysis reveals that HLP1 suppresses Flowering Locus C (FLC), a key repressor of flowering in Arabidopsis. Genome-wide mapping of HLP1-RNA interactions indicates that HLP1 binds preferentially to A-rich and U-rich elements around cleavage and polyadenylation sites, implicating its role in 3′-end formation. We show HLP1 is significantly enriched at transcripts involved in RNA metabolism and flowering. Comprehensive profiling of the poly(A) site usage reveals that HLP1 mutations cause thousands of poly(A) site shifts. A distal-to-proximal poly(A) site shift in the flowering regulator FCA, a direct target of HLP1, leads to upregulation of FLC and delayed flowering. Our results elucidate that HLP1 is a novel factor involved in 3′-end processing and controls reproductive timing via targeting APA. PMID:26099751

Two Drosophila chorion genes terminate transcription in discrete regions near their poly(A) sites.

PubMed Central

Osheim, Y N; Miller, O L; Beyer, A L

1986-01-01

We have examined transcription termination of two closely linked Drosophila melanogaster chorion genes, s36-1 and s38-1, using the electron microscope. Our method is unusual and is independent of in vitro nuclear run-on transcription. By measuring transcription unit lengths in chromatin spreads, we can localize efficient termination sites to a region of approximately 210 bp for s36-1 and approximately 365 bp for s38-1. The center of this region is approximately 105 nucleotides downstream of the poly(A) site for the s36-1 gene, and approximately 400 nucleotides downstream for the s38-1 gene. Thus, these two Drosophila chorion genes terminate more closely to their poly(A) addition sites and in a shorter region than many other polyadenylated genes examined to date. Images Fig. 1. Fig. 2. PMID:3104029

tRNA nuclear export in saccharomyces cerevisiae: in situ hybridization analysis.

PubMed

Sarkar, S; Hopper, A K

1998-11-01

To understand the factors specifically affecting tRNA nuclear export, we adapted in situ hybridization procedures to locate endogenous levels of individual tRNA families in wild-type and mutant yeast cells. Our studies of tRNAs encoded by genes lacking introns show that nucleoporin Nup116p affects both poly(A) RNA and tRNA export, whereas Nup159p affects only poly(A) RNA export. Los1p is similar to exportin-t, which facilitates vertebrate tRNA export. A los1 deletion mutation affects tRNA but not poly(A) RNA export. The data support the notion that Los1p and exportin-t are functional homologues. Because LOS1 is nonessential, tRNA export in vertebrate and yeast cells likely involves factors in addition to exportin-t. Mutation of RNA1, which encodes RanGAP, causes nuclear accumulation of tRNAs and poly(A) RNA. Many yeast mutants, including those with the rna1-1 mutation, affect both pre-tRNA splicing and RNA export. Our studies of the location of intron-containing pre-tRNAs in the rna1-1 mutant rule out the possibility that this results from tRNA export occurring before splicing. Our results also argue against inappropriate subnuclear compartmentalization causing defects in pre-tRNA splicing. Rather, the data support "feedback" of nucleus/cytosol exchange to the pre-tRNA splicing machinery.

tRNA Nuclear Export in Saccharomyces cerevisiae: In Situ Hybridization Analysis

PubMed Central

Sarkar, Srimonti; Hopper, Anita K.

1998-01-01

To understand the factors specifically affecting tRNA nuclear export, we adapted in situ hybridization procedures to locate endogenous levels of individual tRNA families in wild-type and mutant yeast cells. Our studies of tRNAs encoded by genes lacking introns show that nucleoporin Nup116p affects both poly(A) RNA and tRNA export, whereas Nup159p affects only poly(A) RNA export. Los1p is similar to exportin-t, which facilitates vertebrate tRNA export. A los1 deletion mutation affects tRNA but not poly(A) RNA export. The data support the notion that Los1p and exportin-t are functional homologues. Because LOS1 is nonessential, tRNA export in vertebrate and yeast cells likely involves factors in addition to exportin-t. Mutation of RNA1, which encodes RanGAP, causes nuclear accumulation of tRNAs and poly(A) RNA. Many yeast mutants, including those with the rna1-1 mutation, affect both pre-tRNA splicing and RNA export. Our studies of the location of intron-containing pre-tRNAs in the rna1-1 mutant rule out the possibility that this results from tRNA export occurring before splicing. Our results also argue against inappropriate subnuclear compartmentalization causing defects in pre-tRNA splicing. Rather, the data support “feedback” of nucleus/cytosol exchange to the pre-tRNA splicing machinery. PMID:9802895

Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures1[w

PubMed Central

Loke, Johnny C.; Stahlberg, Eric A.; Strenski, David G.; Haas, Brian J.; Wood, Paul Chris; Li, Qingshun Quinn

2005-01-01

Using a novel program, SignalSleuth, and a database containing authenticated polyadenylation [poly(A)] sites, we analyzed the composition of mRNA poly(A) signals in Arabidopsis (Arabidopsis thaliana), and reevaluated previously described cis-elements within the 3′-untranslated (UTR) regions, including near upstream elements and far upstream elements. As predicted, there are absences of high-consensus signal patterns. The AAUAAA signal topped the near upstream elements patterns and was found within the predicted location to only approximately 10% of 3′-UTRs. More importantly, we identified a new set, named cleavage elements, of poly(A) signals flanking both sides of the cleavage site. These cis-elements were not previously revealed by conventional mutagenesis and are contemplated as a cluster of signals for cleavage site recognition. Moreover, a single-nucleotide profile scan on the 3′-UTR regions unveiled a distinct arrangement of alternate stretches of U and A nucleotides, which led to a prediction of the formation of secondary structures. Using an RNA secondary structure prediction program, mFold, we identified three main types of secondary structures on the sequences analyzed. Surprisingly, these observed secondary structures were all interrupted in previously constructed mutations in these regions. These results will enable us to revise the current model of plant poly(A) signals and to develop tools to predict 3′-ends for gene annotation. PMID:15965016

αCP Poly(C) Binding Proteins Act as Global Regulators of Alternative Polyadenylation

PubMed Central

Ji, Xinjun; Wan, Ji; Vishnu, Melanie

2013-01-01

We have previously demonstrated that the KH-domain protein αCP binds to a 3′ untranslated region (3′UTR) C-rich motif of the nascent human alpha-globin (hα-globin) transcript and enhances the efficiency of 3′ processing. Here we assess the genome-wide impact of αCP RNA-protein (RNP) complexes on 3′ processing with a specific focus on its role in alternative polyadenylation (APA) site utilization. The major isoforms of αCP were acutely depleted from a human hematopoietic cell line, and the impact on mRNA representation and poly(A) site utilization was determined by direct RNA sequencing (DRS). Bioinformatic analysis revealed 357 significant alterations in poly(A) site utilization that could be specifically linked to the αCP depletion. These APA events correlated strongly with the presence of C-rich sequences in close proximity to the impacted poly(A) addition sites. The most significant linkage was the presence of a C-rich motif within a window 30 to 40 bases 5′ to poly(A) signals (AAUAAA) that were repressed upon αCP depletion. This linkage is consistent with a general role for αCPs as enhancers of 3′ processing. These findings predict a role for αCPs in posttranscriptional control pathways that can alter the coding potential and/or levels of expression of subsets of mRNAs in the mammalian transcriptome. PMID:23629627

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

PubMed

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

2007-01-01

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

Spectroscopic study of a DNA brush synthesized in situ by surface initiated enzymatic polymerization.

PubMed

Khan, M Nuruzzaman; Tjong, Vinalia; Chilkoti, Ashutosh; Zharnikov, Michael

2013-08-29

We used a combination of synchrotron-based X-ray photoelectron spectroscopy (XPS) and angle-resolved near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to study the chemical integrity, purity, and possible internal alignment of single-strand (ss) adenine deoxynucleotide (poly(A)) DNA brushes. The brushes were synthesized by surface-initiated enzymatic polymerization (SIEP) on a 25-mer of adenine self-assembled monolayer (SAM) on gold (A25-SH), wherein the terminal 3'-OH of the A25-SH serve as the initiation sites for SIEP of poly(A). XPS and NEXAFS spectra of poly(A) brushes were found to be almost identical to those of A25-SH initiator, with no unambiguous traces of contamination. Apart from the well-defined chemical integrity and contamination-free character, the brushes were found to have a high degree of orientational order, with an upright orientation of individual strands, despite their large thickness up to ~55 nm, that corresponds to a chain length of at least several hundred nucleotides for individual ssDNA molecules. The orientational order exhibited by these poly(A) DNA brushes, mediated presumably by base stacking, was found to be independent of the brush thickness as long as the packing density was high enough. The well-defined character and orientational ordering of the ssDNA brushes make them a potentially promising system for different applications.

Analysis of problem solving on project based learning with resource based learning approach computer-aided program

NASA Astrophysics Data System (ADS)

Kuncoro, K. S.; Junaedi, I.; Dwijanto

2018-03-01

This study aimed to reveal the effectiveness of Project Based Learning with Resource Based Learning approach computer-aided program and analyzed problem-solving abilities in terms of problem-solving steps based on Polya stages. The research method used was mixed method with sequential explanatory design. The subject of this research was the students of math semester 4. The results showed that the S-TPS (Strong Top Problem Solving) and W-TPS (Weak Top Problem Solving) had good problem-solving abilities in each problem-solving indicator. The problem-solving ability of S-MPS (Strong Middle Problem Solving) and (Weak Middle Problem Solving) in each indicator was good. The subject of S-BPS (Strong Bottom Problem Solving) had a difficulty in solving the problem with computer program, less precise in writing the final conclusion and could not reflect the problem-solving process using Polya’s step. While the Subject of W-BPS (Weak Bottom Problem Solving) had not been able to meet almost all the indicators of problem-solving. The subject of W-BPS could not precisely made the initial table of completion so that the completion phase with Polya’s step was constrained.

Endoplasmic reticulum stress in vasopressin neurons of familial diabetes insipidus model mice: aggregate formation and mRNA poly(A) tail shortening.

PubMed

Arima, Hiroshi; Morishita, Yoshiaki; Hagiwara, Daisuke; Hayashi, Masayuki; Oiso, Yutaka

2014-01-01

The immunoglobulin heavy chain binding protein (BiP) is an endoplasmic reticulum (ER) chaperone, which binds to newly synthesized secretory and transmembrane proteins to facilitate protein folding. BiP mRNA is expressed in the arginine vasopressin (AVP) neurons in the supraoptic nucleus of wild-type mice even in basal conditions, and the expression levels increase in response to dehydration. These data suggest that AVP neurons are subjected to ER stress. Familial neurohypophysial diabetes insipidus (FNDI) is caused by mutations in the gene locus of AVP. The mutant proteins could accumulate in the ER and possibly increase ER stress in the AVP neurons. We bred mice possessing a mutation causing FNDI, which manifested progressive polyuria, as do the patients with FNDI. Electron microscopic analyses demonstrated that aggregates accumulated in the ER of AVP neurons in FNDI mice. Despite polyuria, which could potentially induce dehydration, AVP mRNA expression was decreased in the supraoptic nucleus, and the AVP mRNA poly(A) tail length was shortened in FNDI mice compared with wild-type mice. Incubation of hypothalamic explants of wild-type mice with ER stressors caused shortening of the poly(A) tail length of AVP mRNA, accompanied by decreases in the expression. These data revealed a mechanism by which ER stress decreases poly(A) tail length of AVP mRNA, and this reduces the load of unfolded proteins that form the aggregates in ER of the AVP neurons in FNDI mice.

The 5'-poly(A) leader of poxvirus mRNA confers a translational advantage that can be achieved in cells with impaired cap-dependent translation

PubMed Central

Dhungel, Pragyesh; Cao, Shuai

2017-01-01

The poly(A) leader at the 5’-untranslated region (5’-UTR) is an unusually striking feature of all poxvirus mRNAs transcribed after viral DNA replication (post-replicative mRNAs). These poly(A) leaders are non-templated and of heterogeneous lengths; and their function during poxvirus infection remains a long-standing question. Here, we discovered that a 5’-poly(A) leader conferred a selective translational advantage to mRNA in poxvirus-infected cells. A constitutive and uninterrupted 5’-poly(A) leader with 12 residues was optimal. Because the most frequent lengths of the 5’-poly(A) leaders are 8–12 residues, the result suggests that the poly(A) leader has been evolutionarily optimized to boost poxvirus protein production. A 5’-poly(A) leader also could increase protein production in the bacteriophage T7 promoter-based expression system of vaccinia virus, the prototypic member of poxviruses. Interestingly, although vaccinia virus post-replicative mRNAs do have 5’- methylated guanosine caps and can use cap-dependent translation, in vaccinia virus-infected cells, mRNA with a 5’-poly(A) leader could also be efficiently translated in cells with impaired cap-dependent translation. However, the translation was not mediated through an internal ribosome entry site (IRES). These results point to a fundamental mechanism poxvirus uses to efficiently translate its post-replicative mRNAs. PMID:28854224

Pre-service mathematics teachers’ ability in solving well-structured problem

NASA Astrophysics Data System (ADS)

Paradesa, R.

2018-01-01

This study aimed to describe the mathematical problem-solving ability of undergraduate students of mathematics education in solving the well-structured problem. The type of this study was qualitative descriptive. The subjects in this study were 100 undergraduate students of Mathematics Education at one of the private universities in Palembang city. The data in this study was collected through two test items with essay form. The results of this study showed that, from the first problem, only 8% students can solve it, but do not check back again to validate the process. Based on a scoring rubric that follows Polya strategy, their answer satisfied 2 4 2 0 patterns. But, from the second problem, 45% students satisfied it. This is because the second problem imitated from the example that was given in learning process. The average score of undergraduate students mathematical problem-solving ability in solving well-structured problems showed 56.00 with standard deviation was 13.22. It means that, from 0 - 100 scale, undergraduate students mathematical problem-solving ability can be categorized low. From this result, the conclusion was undergraduate students of mathematics education in Palembang still have a problem in solving mathematics well-structured problem.

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

PubMed

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.

Alternative Polyadenylation of Tumor Suppressor Genes in Small Intestinal Neuroendocrine Tumors

PubMed Central

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. PMID:24782827

E2F mediates enhanced alternative polyadenylation in proliferation.

PubMed

Elkon, Ran; Drost, Jarno; van Haaften, Gijs; Jenal, Mathias; Schrier, Mariette; Oude Vrielink, Joachim A F; Agami, Reuven

2012-07-02

The majority of mammalian genes contain multiple poly(A) sites in their 3' UTRs. Alternative cleavage and polyadenylation are emerging as an important layer of gene regulation as they generate transcript isoforms that differ in their 3' UTRs, thereby modulating genes' response to 3' UTR-mediated regulation. Enhanced cleavage at 3' UTR proximal poly(A) sites resulting in global 3' UTR shortening was recently linked to proliferation and cancer. However, mechanisms that regulate this enhanced alternative polyadenylation are unknown. Here, we explored, on a transcriptome-wide scale, alternative polyadenylation events associated with cellular proliferation and neoplastic transformation. We applied a deep-sequencing technique for identification and quantification of poly(A) sites to two human cellular models, each examined under proliferative, arrested and transformed states. In both cell systems we observed global 3' UTR shortening associated with proliferation, a link that was markedly stronger than the association with transformation. Furthermore, we found that proliferation is also associated with enhanced cleavage at intronic poly(A) sites. Last, we found that the expression level of the set of genes that encode for 3'-end processing proteins is globally elevated in proliferation, and that E2F transcription factors contribute to this regulation. Our results comprehensively identify alternative polyadenylation events associated with cellular proliferation and transformation, and demonstrate that the enhanced alternative polyadenylation in proliferative conditions results not only in global 3' UTR shortening but also in enhanced premature cleavage in introns. Our results also indicate that E2F-mediated co-transcriptional regulation of 3'-end processing genes is one of the mechanisms that links enhanced alternative polyadenylation to proliferation.

3' rapid amplification of cDNA ends (RACE) walking for rapid structural analysis of large transcripts.

PubMed

Ozawa, Tatsuhiko; Kondo, Masato; Isobe, Masaharu

2004-01-01

The 3' rapid amplification of cDNA ends (3' RACE) is widely used to isolate the cDNA of unknown 3' flanking sequences. However, the conventional 3' RACE often fails to amplify cDNA from a large transcript if there is a long distance between the 5' gene-specific primer and poly(A) stretch, since the conventional 3' RACE utilizes 3' oligo-dT-containing primer complementary to the poly(A) tail of mRNA at the first strand cDNA synthesis. To overcome this problem, we have developed an improved 3' RACE method suitable for the isolation of cDNA derived from very large transcripts. By using the oligonucleotide-containing random 9mer together with the GC-rich sequence for the suppression PCR technology at the first strand of cDNA synthesis, we have been able to amplify the cDNA from a very large transcript, such as the microtubule-actin crosslinking factor 1 (MACF1) gene, which codes a transcript of 20 kb in size. When there is no splicing variant, our highly specific amplification allows us to perform the direct sequencing of 3' RACE products without requiring cloning in bacterial hosts. Thus, this stepwise 3' RACE walking will help rapid characterization of the 3' structure of a gene, even when it encodes a very large transcript.

Inhibition of Poly(A)-binding protein with a synthetic RNA mimic reduces pain sensitization in mice.

PubMed

Barragán-Iglesias, Paulino; Lou, Tzu-Fang; Bhat, Vandita D; Megat, Salim; Burton, Michael D; Price, Theodore J; Campbell, Zachary T

2018-01-02

Nociceptors rely on cap-dependent translation to rapidly induce protein synthesis in response to pro-inflammatory signals. Comparatively little is known regarding the role of the regulatory factors bound to the 3' end of mRNA in nociceptor sensitization. Poly(A)-binding protein (PABP) stimulates translation initiation by bridging the Poly(A) tail to the eukaryotic initiation factor 4F complex associated with the mRNA cap. Here, we use unbiased assessment of PABP binding specificity to generate a chemically modified RNA-based competitive inhibitor of PABP. The resulting RNA mimic, which we designated as the Poly(A) SPOT-ON, is more stable than unmodified RNA and binds PABP with high affinity and selectivity in vitro. We show that injection of the Poly(A) SPOT-ON at the site of an injury can attenuate behavioral response to pain. Collectively, these results suggest that PABP is integral for nociceptive plasticity. The general strategy described here provides a broad new source of mechanism-based inhibitors for RNA-binding proteins and is applicable for in vivo studies.

Regression analysis using dependent Polya trees.

PubMed

Schörgendorfer, Angela; Branscum, Adam J

2013-11-30

Many commonly used models for linear regression analysis force overly simplistic shape and scale constraints on the residual structure of data. We propose a semiparametric Bayesian model for regression analysis that produces data-driven inference by using a new type of dependent Polya tree prior to model arbitrary residual distributions that are allowed to evolve across increasing levels of an ordinal covariate (e.g., time, in repeated measurement studies). By modeling residual distributions at consecutive covariate levels or time points using separate, but dependent Polya tree priors, distributional information is pooled while allowing for broad pliability to accommodate many types of changing residual distributions. We can use the proposed dependent residual structure in a wide range of regression settings, including fixed-effects and mixed-effects linear and nonlinear models for cross-sectional, prospective, and repeated measurement data. A simulation study illustrates the flexibility of our novel semiparametric regression model to accurately capture evolving residual distributions. In an application to immune development data on immunoglobulin G antibodies in children, our new model outperforms several contemporary semiparametric regression models based on a predictive model selection criterion. Copyright © 2013 John Wiley & Sons, Ltd.

Sign changes in sums of the Liouville function

NASA Astrophysics Data System (ADS)

Borwein, Peter; Ferguson, Ron; Mossinghoff, Michael J.

2008-09-01

The Liouville function λ(n) is the completely multiplicative function whose value is -1 at each prime. We develop some algorithms for computing the sum T(n)Dsum_{kD1}^n λ(k)/k , and use these methods to determine the smallest positive integer n where T(n)<0 . This answers a question originating in some work of Turan, who linked the behavior of T(n) to questions about the Riemann zeta function. We also study the problem of evaluating Polya's sum L(n)Dsum_{kD1}^nλ(k) , and we determine some new local extrema for this function, including some new positive values.

Investigation and Implementation of Matrix Permanent Algorithms for Identity Resolution

DTIC Science & Technology

2014-12-01

calculation of the permanent of a matrix whose dimension is a function of target count [21]. However, the optimal approach for computing the permanent is...presently unclear. The primary objective of this project was to determine the optimal computing strategy(-ies) for the matrix permanent in tactical and...solving various combinatorial problems (see [16] for details and appli- cations to a wide variety of problems) and thus can be applied to compute a

Novel mechanism of conjoined gene formation in the human genome.

PubMed

Kim, Ryong Nam; Kim, Aeri; Choi, Sang-Haeng; Kim, Dae-Soo; Nam, Seong-Hyeuk; Kim, Dae-Won; Kim, Dong-Wook; Kang, Aram; Kim, Min-Young; Park, Kun-Hyang; Yoon, Byoung-Ha; Lee, Kang Seon; Park, Hong-Seog

2012-03-01

Recently, conjoined genes (CGs) have emerged as important genetic factors necessary for understanding the human genome. However, their formation mechanism and precise structures have remained mysterious. Based on a detailed structural analysis of 57 human CG transcript variants (CGTVs, discovered in this study) and all (833) known CGs in the human genome, we discovered that the poly(A) signal site from the upstream parent gene region is completely removed via the skipping or truncation of the final exon; consequently, CG transcription is terminated at the poly(A) signal site of the downstream parent gene. This result led us to propose a novel mechanism of CG formation: the complete removal of the poly(A) signal site from the upstream parent gene is a prerequisite for the CG transcriptional machinery to continue transcribing uninterrupted into the intergenic region and downstream parent gene. The removal of the poly(A) signal sequence from the upstream gene region appears to be caused by a deletion or truncation mutation in the human genome rather than post-transcriptional trans-splicing events. With respect to the characteristics of CG sequence structures, we found that intergenic regions are hot spots for novel exon creation during CGTV formation and that exons farther from the intergenic regions are more highly conserved in the CGTVs. Interestingly, many novel exons newly created within the intergenic and intragenic regions originated from transposable element sequences. Additionally, the CGTVs showed tumor tissue-biased expression. In conclusion, our study provides novel insights into the CG formation mechanism and expands the present concepts of the genetic structural landscape, gene regulation, and gene formation mechanisms in the human genome.

E2F mediates enhanced alternative polyadenylation in proliferation

PubMed Central

2012-01-01

Background The majority of mammalian genes contain multiple poly(A) sites in their 3' UTRs. Alternative cleavage and polyadenylation are emerging as an important layer of gene regulation as they generate transcript isoforms that differ in their 3' UTRs, thereby modulating genes' response to 3' UTR-mediated regulation. Enhanced cleavage at 3' UTR proximal poly(A) sites resulting in global 3' UTR shortening was recently linked to proliferation and cancer. However, mechanisms that regulate this enhanced alternative polyadenylation are unknown. Results Here, we explored, on a transcriptome-wide scale, alternative polyadenylation events associated with cellular proliferation and neoplastic transformation. We applied a deep-sequencing technique for identification and quantification of poly(A) sites to two human cellular models, each examined under proliferative, arrested and transformed states. In both cell systems we observed global 3' UTR shortening associated with proliferation, a link that was markedly stronger than the association with transformation. Furthermore, we found that proliferation is also associated with enhanced cleavage at intronic poly(A) sites. Last, we found that the expression level of the set of genes that encode for 3'-end processing proteins is globally elevated in proliferation, and that E2F transcription factors contribute to this regulation. Conclusions Our results comprehensively identify alternative polyadenylation events associated with cellular proliferation and transformation, and demonstrate that the enhanced alternative polyadenylation in proliferative conditions results not only in global 3' UTR shortening but also in enhanced premature cleavage in introns. Our results also indicate that E2F-mediated co-transcriptional regulation of 3'-end processing genes is one of the mechanisms that links enhanced alternative polyadenylation to proliferation. PMID:22747694

Maintaining a permanent plot data base for growth and yield research: Solutions to some recurring problems

Treesearch

John C. Byrne

1993-01-01

Methods for solving some recurring problems of maintaining a permanent plot data base for growth and yield reseuch are described. These methods include documenting data from diverse sampling designs, changing sampling designs, changing field procedures, and coordinating activities in the plots with the land management agency. Managing a permanent plot data base (...

UV-VIS extinction spectra of gold particle coated by oligonucleotide shell

NASA Astrophysics Data System (ADS)

Bogatyrev, Vladimir A.; Vrublevsky, Stanislav A.; Trachuk, Lyubov A.; Khlebtsov, Nikolai G.

2005-06-01

We describe synthesis process of an oligonucleotide-functionalized colloidal gold marker CG-l5-T28, its optical properties and interaction with poly(A) in solution and on a solid-phase substrate. The marker is a complex of 15 nm diameter colloidal gold nanoparticles with covalently attached 5'-thiolated 28-base oligothymidine macromolecules. A positive hybridization reaction of the marker with poly(A) is observed by solid-phase analysis on hanging a spot color (from red to blue ) or on appearance of a red dye in dot-blot test as compared to control experiments with poly(U) target. The principles of spectrophotometric monitoring all stages of the marker preparation and application of spectrophotometry to detection of the polynucleotide hybridization in vitro are described. Experimental data were compared with theoretical calculations based on Mie theory for 2-layer model of gold core in polymeric shell with imaginary part of refractive index that typical for the real absorption spectra of NA. To explain the aggregation of CG-15-T28 caused by interaction with poly(A) in solution, we suggest a new model differing from a standard model of cross-linker binding.

Binding of Phenazinium Dye Safranin T to Polyriboadenylic Acid: Spectroscopic and Thermodynamic Study

PubMed Central

Roy, Snigdha; Das, Suman

2014-01-01

Here, we report results from experiments designed to explore the association of the phenazinium dye safranin T (ST, 3,7-diamino-2,8-dimethyl-5-phenylphenazinium chloride) with single and double stranded form of polyriboadenylic acid (hereafter poly-A) using several spectroscopic techniques. We demonstrate that the dye binds to single stranded polyriboadenylic acid (hereafter ss poly-A) with high affinity while it does not interact at all with the double stranded (ds) form of the polynucleotide. Fluorescence and absorption spectral studies reveal the molecular aspects of binding of ST to single stranded form of the polynucleotide. This observation is also supported by the circular dichroism study. Thermodynamic data obtained from temperature dependence of binding constant reveals that association is driven by negative enthalpy change and opposed by negative entropy change. Ferrocyanide quenching studies have shown intercalative binding of ST to ss poly-A. Experiments on viscosity measurements confirm the binding mode of the dye to be intercalative. The effect of [Na+] ion concentration on the binding process suggests the role of electrostatic forces in the complexation. Present studies reveal the utility of the dye in probing nucleic acid structure. PMID:24498422

Binding of phenazinium dye safranin T to polyriboadenylic acid: spectroscopic and thermodynamic study.

PubMed

Pradhan, Ankur Bikash; Haque, Lucy; Roy, Snigdha; Das, Suman

2014-01-01

Here, we report results from experiments designed to explore the association of the phenazinium dye safranin T (ST, 3,7-diamino-2,8-dimethyl-5-phenylphenazinium chloride) with single and double stranded form of polyriboadenylic acid (hereafter poly-A) using several spectroscopic techniques. We demonstrate that the dye binds to single stranded polyriboadenylic acid (hereafter ss poly-A) with high affinity while it does not interact at all with the double stranded (ds) form of the polynucleotide. Fluorescence and absorption spectral studies reveal the molecular aspects of binding of ST to single stranded form of the polynucleotide. This observation is also supported by the circular dichroism study. Thermodynamic data obtained from temperature dependence of binding constant reveals that association is driven by negative enthalpy change and opposed by negative entropy change. Ferrocyanide quenching studies have shown intercalative binding of ST to ss poly-A. Experiments on viscosity measurements confirm the binding mode of the dye to be intercalative. The effect of [Na⁺] ion concentration on the binding process suggests the role of electrostatic forces in the complexation. Present studies reveal the utility of the dye in probing nucleic acid structure.

PAPERCLIP identifies microRNA targets and a role of CstF64/64tau in promoting non-canonical poly(A) site usage

PubMed Central

Hwang, Hun-Way; Park, Christopher Y.; Goodarzi, Hani; Fak, John J.; Mele, Aldo; Moore, Michael J.; Saito, Yuhki; Darnell, Robert B.

2016-01-01

Accurate and precise annotation of the 3′ untranslated regions (3′ UTRs) is critical in understanding how mRNAs are regulated by microRNAs (miRNAs) and RNA-binding proteins (RBPs). Here we describe a method, PAPERCLIP (Poly(A) binding Protein-mediated mRNA 3′ End Retrieval by CrossLinking ImmunoPrecipitation), which shows high specificity for the mRNA 3′ ends and compares favorably to existing 3′ end mapping methods. PAPERCLIP uncovers a previously unrecognized role of CstF64/64tau in promoting the usage of a selected group of non-canonical poly(A) sites, the majority of them containing a downstream GUKKU motif. Furthermore, in mouse brain, PAPERCLIP discovers extended 3′ UTR sequences harboring functional miRNA binding sites and reveals developmentally regulated APA shifts including one in Atp2b2 that is evolutionarily conserved in human and results in a gain of a functional binding site of miR-137. PAPERCLIP provides a powerful tool to decipher post-transcriptional regulation of mRNAs through APA in vivo. PMID:27050522

Poly(A) polymerase contains multiple functional domains.

PubMed Central

Raabe, T; Murthy, K G; Manley, J L

1994-01-01

Poly(A) polymerase (PAP) contains regions of similarity with several known protein domains. Through site-directed mutagenesis, we provide evidence that PAP contains a functional ribonucleoprotein-type RNA binding domain (RBD) that is responsible for primer binding, making it the only known polymerase to contain such a domain. The RBD is adjacent to, and probably overlaps with, an apparent catalytic region responsible for polymerization. Despite the presence of sequence similarities, this catalytic domain appears to be distinct from the conserved polymerase module found in a large number of RNA-dependent polymerases. PAP contains two nuclear localization signals (NLSs) in its C terminus, each by itself similar to the consensus bipartite NLS found in many nuclear proteins. Mutagenesis experiments indicate that both signals, which are separated by nearly 140 residues, play important roles in directing PAP exclusively to the nucleus. Surprisingly, basic amino acids in the N-terminal-most NLS are also essential for AAUAAA-dependent polyadenylation but not for nonspecific poly(A) synthesis, suggesting that this region of PAP is involved in interactions both with nuclear targeting proteins and with nuclear polyadenylation factors. The serine/threonine-rich C terminus is multiply phosphorylated, including at sites affected by mutations in either NLS. Images PMID:8164653

Rrp6p controls mRNA polyA tail length and its decoration with polyA binding proteins

PubMed Central

Schmid, Manfred; Poulsen, Mathias Bach; Olszewski, Pawel; Pelechano, Vicent; Saguez, Cyril; Gupta, Ishaan; Steinmetz, Lars M.; Moore, Claire; Jensen, Torben Heick

2012-01-01

PolyA (pA) tail binding proteins (PABPs) control mRNA polyadenylation, stability and translation. In a purified system, S. cerevisiae PABPs, Pab1p and Nab2p, are individually sufficient to provide normal pA tail length. However, it is unknown how this occurs in more complex environments. Here we find that the nuclear exosome subunit Rrp6p counteracts the in vitro and in vivo extension of mature pA tails by the non-canonical pA polymerase Trf4p. Moreover, PABP loading onto nascent pA tails is controlled by Rrp6p; while Pab1p is the major PABP, Nab2p only associates in the absence of Rrp6p. This is because Rrp6p can interact with Nab2p and displace it from pA tails, potentially leading to RNA turnover as evidenced for certain pre-mRNAs. We suggest that a nuclear mRNP surveillance step involves targeting of Rrp6p by Nab2p-bound pA-tailed RNPs and that pre-mRNA abundance is regulated at this level. PMID:22683267

Some Biochemical Properties of an Acido-Thermophilic Archae-Bacterium Sulfolobus Acidocaldarius

NASA Astrophysics Data System (ADS)

Oshima, Tairo; Ohba, Masayuki; Wagaki, Takayoshi

1984-12-01

To elucidate the phylogenic status of archaebacteria, some basic cellular components of an acido-thermophilic archaebacterium,Sulfolobus acidocaldarius, were studied. Poly(A) containing RNA was present in the cells, and performed the role of mRNA in a cell-free extract of reticulocyte or the archaebacteria. Poly(A) containing RNA was also found in other archaebacterial cells. The absence of cap structure was suggested in these RNAs. The cell-free protein synthesis using the archaebacterial extract was inhibited by anisomycin, a specific inhibitor for eukaryotic ribosomes. Two unique membrane-bound ATPases were detected. Based on resistance to H+-ATPase inhibitors, these enzymes seemed not to be F0F1-ATPase.

Association between work-related health problems and job insecurity in permanent and temporary employees

PubMed Central

2013-01-01

Objectives This research was conducted with an aim of determining the correlation between job insecurity and an employee’s work-related health problems among permanent and temporary workers. Methods Using the data from the First Korean Working Conditions Survey conducted in 2006, a total of 7,071 workers, excluding employers and the self-employed, were analyzed. Work-related health problems were categorized as backache, headache, abdominal pain, muscular pain, stress, fatigue, insomnia, anxiety or depression. Each problem was then analyzed for its relationship to job insecurity through logistic regression analysis. Results Among the 7,071 workers, 5,294 (74.9%) were permanent workers and 1,777 (25.1%) were temporary workers. For the permanent workers, presence of high or moderate job insecurity appeared more closely linked to backache, headache, abdominal pain, muscular pain, stress, fatigue, insomnia, anxiety, and depression compared to absence of job insecurity. However, for the temporary workers, only depression appeared to be associated with the presence of high job insecurity. Conclusion The study showed that the presence of job insecurity is correlated with work-related health problems. The deleterious effects of job insecurity appeared to be stronger in permanent than temporary workers. Additional research should investigate ways to effectively reduce job insecurity. PMID:24472497

Changes in RNA polymerase II progression influence somatic hypermutation of Ig-related genes by AID

PubMed Central

Kodgire, Prashant; Mukkawar, Priyanka; Ratnam, Sarayu; Martin, Terence E.

2013-01-01

Somatic hypermutation (SHM) of Ig genes is initiated by the activation-induced cytidine deaminase (AID), and requires target gene transcription. We previously proposed that AID may associate with the RNA polymerase II (Pol). Here, to determine aspects of the transcription process required for SHM, we knocked-in a transcription terminator into an Ig gene variable region in DT40 chicken B cell line. We found that the human β-globin terminator was an efficient inhibitor of downstream transcription in these cells. The terminator reduced mutations downstream of the poly(A) signal, suggesting that the process of transcription is essential for efficient SHM and that AID has better access to its target when Pol is in the elongating rather than terminating mode. Mutations upstream of the poly(A) site were almost doubled in the active terminator clones compared with an inactivated terminator, and this region showed more single-stranded DNA, indicating that Pol pausing assists SHM. Moreover, the nontranscribed DNA strand was the preferred SHM target upstream of the active terminator. Pol pausing during poly(A) site recognition may facilitate persistence of negative supercoils, exposing the coding single strand and possibly allowing the nascent RNA intermittent reannealing with the template strand, for prolonged access of AID. PMID:23752228

Replacement of the yeast TRP4 3' untranslated region by a hammerhead ribozyme results in a stable and efficiently exported mRNA that lacks a poly(A) tail.

PubMed Central

Düvel, Katrin; Valerius, Oliver; Mangus, David A; Jacobson, Allan; Braus, Gerhard H

2002-01-01

The mRNA poly(A) tail serves different purposes, including the facilitation of nuclear export, mRNA stabilization, efficient translation, and, finally, specific degradation. The posttranscriptional addition of a poly(A) tail depends on sequence motifs in the 3' untranslated region (3' UTR) of the mRNA and a complex trans-acting protein machinery. In this study, we have replaced the 3' UTR of the yeast TRP4 gene with sequences encoding a hammerhead ribozyme that efficiently cleaves itself in vivo. Expression of the TRP4-ribozyme allele resulted in the accumulation of a nonpolyadenylated mRNA. Cells expressing the TRP4-ribozyme mRNA showed a reduced growth rate due to a reduction in Trp4p enzyme activity. The reduction in enzyme activity was not caused by inefficient mRNA export from the nucleus or mRNA destabilization. Rather, analyses of mRNA association with polyribosomes indicate that translation of the ribozyme-containing mRNA is impaired. This translational defect allows sufficient synthesis of Trp4p to support growth of trp4 cells, but is, nevertheless, of such magnitude as to activate the general control network of amino acid biosynthesis. PMID:12003493

Tales around the clock: Poly(A) tails in circadian gene expression.

PubMed

Beta, Rafailia A A; Balatsos, Nikolaos A A

2018-06-17

Circadian rhythms are ubiquitous time-keeping processes in eukaryotes with a period of ~24 hr. Light is perhaps the main environmental cue (zeitgeber) that affects several aspects of physiology and behaviour, such as sleep/wake cycles, orientation of birds and bees, and leaf movements in plants. Temperature can serve as the main zeitgeber in the absence of light cycles, even though it does not lead to rhythmicity through the same mechanism as light. Additional cues include feeding patterns, humidity, and social rhythms. At the molecular level, a master oscillator orchestrates circadian rhythms and organizes molecular clocks located in most cells. The generation of the 24 hr molecular clock is based on transcriptional regulation, as it drives intrinsic rhythmic changes based on interlocked transcription/translation feedback loops that synchronize expression of genes. Thus, processes and factors that determine rhythmic gene expression are important to understand circadian rhythms. Among these, the poly(A) tails of RNAs play key roles in their stability, translational efficiency and degradation. In this article, we summarize current knowledge and discuss perspectives on the role and significance of poly(A) tails and associating factors in the context of the circadian clock. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability RNA Processing > 3' End Processing. © 2018 Wiley Periodicals, Inc.

Analysis of RNA Processing Reactions Using Cell Free Systems: 3' End Cleavage of Pre-mRNA Substrates in vitro

PubMed Central

Jablonski, Joseph; Clementz, Mark; Ryan, Kevin; Valente, Susana T.

2014-01-01

The 3’ end of mammalian mRNAs is not formed by abrupt termination of transcription by RNA polymerase II (RNPII). Instead, RNPII synthesizes precursor mRNA beyond the end of mature RNAs, and an active process of endonuclease activity is required at a specific site. Cleavage of the precursor RNA normally occurs 10-30 nt downstream from the consensus polyA site (AAUAAA) after the CA dinucleotides. Proteins from the cleavage complex, a multifactorial protein complex of approximately 800 kDa, accomplish this specific nuclease activity. Specific RNA sequences upstream and downstream of the polyA site control the recruitment of the cleavage complex. Immediately after cleavage, pre-mRNAs are polyadenylated by the polyA polymerase (PAP) to produce mature stable RNA messages. Processing of the 3’ end of an RNA transcript may be studied using cellular nuclear extracts with specific radiolabeled RNA substrates. In sum, a long 32P-labeled uncleaved precursor RNA is incubated with nuclear extracts in vitro, and cleavage is assessed by gel electrophoresis and autoradiography. When proper cleavage occurs, a shorter 5’ cleaved product is detected and quantified. Here, we describe the cleavage assay in detail using, as an example, the 3’ end processing of HIV-1 mRNAs. PMID:24835792

Isolation and characterization of cDNA clones for carrot extensin and a proline-rich 33-kDa protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, J.; Varner, J.E.

1985-07-01

Extensins are hydroxyproline-rich glycoproteins associated with most dicotyledonous plant cell walls. To isolate cDNA clones encoding extensin, the authors started by isolating poly(A) RNA from carrot root tissue, and then translating the RNA in vitro, in the presence of tritiated leucine or proline. A 33-kDa peptide was identified in the translation products as a putative extensin precursor. From a cDNA library constructed with poly(A) RNA from wounded carrots, one cDNA clone (pDC5) was identified that specifically hybridized to poly(A) RNA encoding this 33-kDa peptide. They isolated three cDNA clones (pDC11, pDC12, and pDC16) from another cDNA library using pCD5 asmore » a probe. DNA sequence data, RNA hybridization analysis, and hybrid released in vitro translation indicate that the cDNA clones pDC11 encodes extensin and that cDNA clones pDC12 and pDC16 encode the 33-kDa peptide, which as yet has an unknown identity and function. The assumption that the 33-kDa peptide was an extensin precursor was invalid. RNA hybridization analysis showed that RNA encoded by both clone types is accumulated upon wounding.« less

Structural Features of a Picornavirus Polymerase Involved in the Polyadenylation of Viral RNA

PubMed Central

Kempf, Brian J.; Kelly, Michelle M.; Springer, Courtney L.; Peersen, Olve B.

2013-01-01

Picornaviruses have 3′ polyadenylated RNA genomes, but the mechanisms by which these genomes are polyadenylated during viral replication remain obscure. Based on prior studies, we proposed a model wherein the poliovirus RNA-dependent RNA polymerase (3Dpol) uses a reiterative transcription mechanism while replicating the poly(A) and poly(U) portions of viral RNA templates. To further test this model, we examined whether mutations in 3Dpol influenced the polyadenylation of virion RNA. We identified nine alanine substitution mutations in 3Dpol that resulted in shorter or longer 3′ poly(A) tails in virion RNA. These mutations could disrupt structural features of 3Dpol required for the recruitment of a cellular poly(A) polymerase; however, the structural orientation of these residues suggests a direct role of 3Dpol in the polyadenylation of RNA genomes. Reaction mixtures containing purified 3Dpol and a template RNA with a defined poly(U) sequence provided data consistent with a template-dependent reiterative transcription mechanism for polyadenylation. The phylogenetically conserved structural features of 3Dpol involved in the polyadenylation of virion RNA include a thumb domain alpha helix that is positioned in the minor groove of the double-stranded RNA product and lysine and arginine residues that interact with the phosphates of both the RNA template and product strands. PMID:23468507

Regions of conservation and divergence in the 3' untranslated sequences of genomic RNA from Ross River virus isolates.

PubMed

Faragher, S G; Dalgarno, L

1986-07-20

The 3' untranslated (UT) sequences of the genomic RNAs of five geographic variants of the alphavirus Ross River virus (RRV) were determined and compared with the 3' UT sequence of RRV T48, the prototype strain. Part of the 3' UT region of Getah virus, a close serological relative of RRV, was also sequenced. The RRV 3' UT region varies markedly in length between variants. Large deletions or insertions, sequence rearrangements and single nucleotide substitutions are observed. A sequence tract of 49 to 58 nucleotides, which is repeated as four blocks in the RRV T48 3' UT region, occurs only once in the 3' UT region of one RRV strain (NB5092), indicating that the existence of repeat sequence blocks is not essential for RRV replication. However, the precise sequence of the 3' proximal copy of the repeat block and its position relative to the poly(A) tail were identical in all RRV isolates examined, suggesting that it has an important role in RRV replication. Nucleotide substitutions between RRV variants are distributed non-randomly along the length of the 3' UT region. The sequence of 120 to 130 nucleotides adjacent to the poly(A) tail is strongly conserved. Getah virus RNA contains three repeat sequence blocks in the 3' UT region. These are similar in sequence to those in RRV RNA but differ in their arrangement. Homology between the RRV and Getah 3' UT sequences is greatest in the 3' proximal repeat sequence block that shows three differences in 49 nucleotides. The 3' proximal repeat in Getah RNA occurs at the same position, relative to the poly(A) tail, as in all RRV variants. The RRV and Getah virus 3' UT sequences show extensive homology in the region between the 3' proximal repeat and the poly(A) tail but, apart from the repeat blocks themselves, they show no significant homology elsewhere.

Novel mouse models of oculopharyngeal muscular dystrophy (OPMD) reveal early onset mitochondrial defects and suggest loss of PABPN1 may contribute to pathology.

PubMed

Vest, Katherine E; Phillips, Brittany L; Banerjee, Ayan; Apponi, Luciano H; Dammer, Eric B; Xu, Weiting; Zheng, Dinghai; Yu, Julia; Tian, Bin; Pavlath, Grace K; Corbett, Anita H

2017-09-01

Oculopharyngeal muscular dystrophy (OPMD) is a late onset disease caused by polyalanine expansion in the poly(A) binding protein nuclear 1 (PABPN1). Several mouse models have been generated to study OPMD; however, most of these models have employed transgenic overexpression of alanine-expanded PABPN1. These models do not recapitulate the OPMD patient genotype and PABPN1 overexpression could confound molecular phenotypes. We have developed a knock-in mouse model of OPMD (Pabpn1+/A17) that contains one alanine-expanded Pabpn1 allele under the control of the native promoter and one wild-type Pabpn1 allele. This mouse is the closest available genocopy of OPMD patients. We show that Pabpn1+/A17 mice have a mild myopathic phenotype in adult and aged animals. We examined early molecular and biochemical phenotypes associated with expressing native levels of A17-PABPN1 and detected shorter poly(A) tails, modest changes in poly(A) signal (PAS) usage, and evidence of mitochondrial damage in these mice. Recent studies have suggested that a loss of PABPN1 function could contribute to muscle pathology in OPMD. To investigate a loss of function model of pathology, we generated a heterozygous Pabpn1 knock-out mouse model (Pabpn1+/Δ). Like the Pabpn1+/A17 mice, Pabpn1+/Δ mice have mild histologic defects, shorter poly(A) tails, and evidence of mitochondrial damage. However, the phenotypes detected in Pabpn1+/Δ mice only partially overlap with those detected in Pabpn1+/A17 mice. These results suggest that loss of PABPN1 function could contribute to but may not completely explain the pathology detected in Pabpn1+/A17 mice. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Budding yeast telomerase RNA transcription termination is dictated by the Nrd1/Nab3 non-coding RNA termination pathway

PubMed Central

Noël, Jean-François; Larose, Stéphanie; Abou Elela, Sherif; Wellinger, Raymund J.

2012-01-01

The RNA component of budding yeast telomerase (Tlc1) occurs in two forms, a non-polyadenylated form found in functional telomerase and a rare polyadenylated version with unknown function. Previous work suggested that the functional Tlc1 polyA− RNA is processed from the polyA+ form, but the mechanisms regulating its transcription termination and 3′-end formation remained unclear. Here we examined transcription termination of Tlc1 RNA in the sequences 3′ of the TLC1 gene and relate it to telomere maintenance. Strikingly, disruption of all probable or cryptic polyadenylation signals near the 3′-end blocked the accumulation of the previously reported polyA+ RNA without affecting the level, function or specific 3′ nucleotide of the mature polyA− form. A genetic approach analysing TLC1 3′-end sequences revealed that transcription terminates upstream of the polyadenylation sites. Furthermore, the results also demonstrate that the function of this Tlc1 terminator depends on the Nrd1/Nab3 transcription termination pathway. The data thus show that transcription termination of the budding yeast telomerase RNA occurs as that of snRNAs and Tlc1 functions in telomere maintenance are not strictly dependent on a polyadenylated precursor, even if the polyA+ form can serve as intermediate in a redundant termination/maturation pathway. PMID:22379137

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq

PubMed Central

Shepard, Peter J.; Choi, Eun-A; Lu, Jente; Flanagan, Lisa A.; Hertel, Klemens J.; Shi, Yongsheng

2011-01-01

Alternative polyadenylation (APA) of mRNAs has emerged as an important mechanism for post-transcriptional gene regulation in higher eukaryotes. Although microarrays have recently been used to characterize APA globally, they have a number of serious limitations that prevents comprehensive and highly quantitative analysis. To better characterize APA and its regulation, we have developed a deep sequencing-based method called Poly(A) Site Sequencing (PAS-Seq) for quantitatively profiling RNA polyadenylation at the transcriptome level. PAS-Seq not only accurately and comprehensively identifies poly(A) junctions in mRNAs and noncoding RNAs, but also provides quantitative information on the relative abundance of polyadenylated RNAs. PAS-Seq analyses of human and mouse transcriptomes showed that 40%–50% of all expressed genes produce alternatively polyadenylated mRNAs. Furthermore, our study detected evolutionarily conserved polyadenylation of histone mRNAs and revealed novel features of mitochondrial RNA polyadenylation. Finally, PAS-Seq analyses of mouse embryonic stem (ES) cells, neural stem/progenitor (NSP) cells, and neurons not only identified more poly(A) sites than what was found in the entire mouse EST database, but also detected significant changes in the global APA profile that lead to lengthening of 3′ untranslated regions (UTR) in many mRNAs during stem cell differentiation. Together, our PAS-Seq analyses revealed a complex landscape of RNA polyadenylation in mammalian cells and the dynamic regulation of APA during stem cell differentiation. PMID:21343387

Distinct regulation of alternative polyadenylation and gene expression by nuclear poly(A) polymerases

PubMed Central

Li, Wencheng; Laishram, Rakesh S.; Hoque, Mainul; Ji, Zhe

2017-01-01

Abstract Polyadenylation of nascent RNA by poly(A) polymerase (PAP) is important for 3′ end maturation of almost all eukaryotic mRNAs. Most mammalian genes harbor multiple polyadenylation sites (PASs), leading to expression of alternative polyadenylation (APA) isoforms with distinct functions. How poly(A) polymerases may regulate PAS usage and hence gene expression is poorly understood. Here, we show that the nuclear canonical (PAPα and PAPγ) and non-canonical (Star-PAP) PAPs play diverse roles in PAS selection and gene expression. Deficiencies in the PAPs resulted in perturbations of gene expression, with Star-PAP impacting lowly expressed mRNAs and long-noncoding RNAs to the greatest extent. Importantly, different PASs of a gene are distinctly regulated by different PAPs, leading to widespread relative expression changes of APA isoforms. The location and surrounding sequence motifs of a PAS appear to differentiate its regulation by the PAPs. We show Star-PAP-specific PAS usage regulates the expression of the eukaryotic translation initiation factor EIF4A1, the tumor suppressor gene PTEN and the long non-coding RNA NEAT1. The Star-PAP-mediated APA of PTEN is essential for DNA damage-induced increase of PTEN protein levels. Together, our results reveal a PAS-guided and PAP-mediated paradigm for gene expression in response to cellular signaling cues. PMID:28911096

Biallelic insertion of a transcriptional terminator via the CRISPR/Cas9 system efficiently silences expression of protein-coding and non-coding RNA genes.

PubMed

Liu, Yangyang; Han, Xiao; Yuan, Junting; Geng, Tuoyu; Chen, Shihao; Hu, Xuming; Cui, Isabelle H; Cui, Hengmi

2017-04-07

The type II bacterial CRISPR/Cas9 system is a simple, convenient, and powerful tool for targeted gene editing. Here, we describe a CRISPR/Cas9-based approach for inserting a poly(A) transcriptional terminator into both alleles of a targeted gene to silence protein-coding and non-protein-coding genes, which often play key roles in gene regulation but are difficult to silence via insertion or deletion of short DNA fragments. The integration of 225 bp of bovine growth hormone poly(A) signals into either the first intron or the first exon or behind the promoter of target genes caused efficient termination of expression of PPP1R12C , NSUN2 (protein-coding genes), and MALAT1 (non-protein-coding gene). Both NeoR and PuroR were used as markers in the selection of clonal cell lines with biallelic integration of a poly(A) signal. Genotyping analysis indicated that the cell lines displayed the desired biallelic silencing after a brief selection period. These combined results indicate that this CRISPR/Cas9-based approach offers an easy, convenient, and efficient novel technique for gene silencing in cell lines, especially for those in which gene integration is difficult because of a low efficiency of homology-directed repair. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Research and simulation of the decoupling transformation in AC motor vector control

NASA Astrophysics Data System (ADS)

He, Jiaojiao; Zhao, Zhongjie; Liu, Ken; Zhang, Yongping; Yao, Tuozhong

2018-04-01

Permanent magnet synchronous motor (PMSM) is a nonlinear, strong coupling, multivariable complex object, and transformation decoupling can solve the coupling problem of permanent magnet synchronous motor. This paper gives a permanent magnet synchronous motor (PMSM) mathematical model, introduces the permanent magnet synchronous motor vector control coordinate transformation in the process of modal matrix inductance matrix transform through the matrix related knowledge of different coordinates of diagonalization, which makes the coupling between the independent, realize the control of motor current and excitation the torque current coupling separation, and derived the coordinate transformation matrix, the thought to solve the coupling problem of AC motor. Finally, in the Matlab/Simulink environment, through the establishment and combination between the PMSM ontology, coordinate conversion module, built the simulation model of permanent magnet synchronous motor vector control, introduces the model of each part, and analyzed the simulation results.

Specific Tandem 3'UTR Patterns and Gene Expression Profiles in Mouse Thy1+ Germline Stem Cells

PubMed Central

Lin, Zhuoheng; Feng, Xuyang; Jiang, Xue; Songyang, Zhou; Huang, Junjiu

2015-01-01

A recently developed strategy of sequencing alternative polyadenylation (APA) sites (SAPAS) with second-generation sequencing technology can be used to explore complete genome-wide patterns of tandem APA sites and global gene expression profiles. spermatogonial stem cells (SSCs) maintain long-term reproductive abilities in male mammals. The detailed mechanisms by which SSCs self-renew and generate mature spermatozoa are not clear. To understand the specific alternative polyadenylation pattern and global gene expression profile of male germline stem cells (GSCs, mainly referred to SSCs here), we isolated and purified mouse Thy1+ cells from testis by magnetic-activated cell sorting (MACS) and then used the SAPAS method for analysis, using pluripotent embryonic stem cells (ESCs) and differentiated mouse embryonic fibroblast cells (MEFs) as controls. As a result, we obtained 99,944 poly(A) sites, approximately 40% of which were newly detected in our experiments. These poly(A) sites originated from three mouse cell types and covered 17,499 genes, including 831 long non-coding RNA (lncRNA) genes. We observed that GSCs tend to have shorter 3'UTR lengths while MEFs tend towards longer 3'UTR lengths. We also identified 1337 genes that were highly expressed in GSCs, and these genes were highly consistent with the functional characteristics of GSCs. Our detailed bioinformatics analysis identified APA site-switching events at 3'UTRs and many new specifically expressed genes in GSCs, which we experimentally confirmed. Furthermore, qRT-PCR was performed to validate several events of the 334 genes with distal-to-proximal poly(A) switch in GSCs. Consistently APA reporter assay confirmed the total 3'UTR shortening in GSCs compared to MEFs. We also analyzed the cis elements around the proximal poly(A) site preferentially used in GSCs and found C-rich elements may contribute to this regulation. Overall, our results identified the expression level and polyadenylation site profiles and these data provide new insights into the processes potentially involved in the GSC life cycle and spermatogenesis. PMID:26713853

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

PubMed Central

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

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

PubMed Central

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

Effect of Environmental Education Based on Transformational Learning Theory on Perceptions towards Environmental Problems and Permanency of Learning

ERIC Educational Resources Information Center

Uyanik, Gökhan

2016-01-01

The aim of the study is to determine effect of environmental education based on transformational learning theory on primary school teacher candidates' perceptions towards environmental problems and permanency of learning. Pretest-posttest quasi-experimental design have been used in this study. The study group consists of 66 teacher candidates who…

[Assessment of the prevalence and perception of skin problems in patients with permanent stoma].

PubMed

Piccinellil, Margherita; Brazzale, Roberta; Saracco, Carla

2009-01-01

The incidence of peristomal skin in ostomy patients ranges from 25 to 35%. In a recent paper it was reported that patients may not be aware of the skin problem. To describe the prevalence and characteristics of skin disorders in ostomy patients and to assess their perception of the skin problem. Consecutive patients attending the stoma care clinic of Varese Hospital and with a permanent stoma (>1 year) were asked if they had any skin problem subsequently visited by the stoma care nurse. The skin problems were classified with two different scales (Mosè le tavole and SACS). Of 48 patients, 35 (73%) declared no skin problems but overall 27 patients had a skin disorder (11/13 of those aware of having a problem and 16/35 of those not aware). Patients that self cared for their stoma did not report any problem although 27/31 had some skin disorder. No patient reported to have a skin erosion although 13 were detected by the stoma care nurse. Although "expert" patients may not be aware of their skin problems. Attention should be paid not only to patients with recent stomas but also to those with permanent stoma, that may need further educational support.

mRNA interactome capture in mammalian cells.

PubMed

Kastelic, Nicolai; Landthaler, Markus

2017-08-15

Throughout their entire life cycle, mRNAs are associated with RNA-binding proteins (RBPs), forming ribonucleoprotein (RNP) complexes with highly dynamic compositions. Their interplay is one key to control gene regulatory mechanisms from mRNA synthesis to decay. To assay the global scope of RNA-protein interactions, we and others have published a method combining crosslinking with highly stringent oligo(dT) affinity purification to enrich proteins associated with polyadenylated RNA (poly(A)+ RNA). Identification of the poly(A)+ RNA-bound proteome (also: mRNA interactome capture) has by now been applied to a diversity of cell lines and model organisms, uncovering comprehensive repertoires of RBPs and hundreds of novel RBP candidates. In addition to determining the RBP catalog in a given biological system, mRNA interactome capture allows the examination of changes in protein-mRNA interactions in response to internal and external stimuli, altered cellular programs and disease. Copyright © 2017. Published by Elsevier Inc.

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

PubMed

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.

PABP is not essential for microRNA-mediated translational repression and deadenylation in vitro

PubMed Central

Fukaya, Takashi; Tomari, Yukihide

2011-01-01

MicroRNAs silence their complementary target genes via formation of the RNA-induced silencing complex (RISC) that contains an Argonaute (Ago) protein at its core. It was previously proposed that GW182, an Ago-associating protein, directly binds to poly(A)-binding protein (PABP) and interferes with its function, leading to silencing of the target mRNAs. Here we show that Drosophila Ago1-RISC induces silencing via two independent pathways: shortening of the poly(A) tail and pure repression of translation. Our data suggest that although PABP generally modulates poly(A) length and translation efficiency, neither PABP function nor GW182–PABP interaction is a prerequisite for these two silencing pathways. Instead, we propose that each of the multiple functional domains within GW182 has a potential for silencing, and yet they need to act together in the context of full-length GW182 to exert maximal silencing. PMID:22117217

Quantum Matching Theory (with new complexity-theoretic, combinatorial and topical insights on the nature of the quantum entanglement)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gurvits, L.

2002-01-01

Classical matching theory can be defined in terms of matrices with nonnegative entries. The notion of Positive operator, central in Quantum Theory, is a natural generalization of matrices with non-negative entries. Based on this point of view, we introduce a definition of perfect Quantum (operator) matching. We show that the new notion inherits many 'classical' properties, but not all of them. This new notion goes somewhere beyound matroids. For separable bipartite quantum states this new notion coinsides with the full rank property of the intersection of two corresponding geometric matroids. In the classical situation, permanents are naturally associated with perfectsmore » matchings. We introduce an analog of permanents for positive operators, called Quantum Permanent and show how this generalization of the permanent is related to the Quantum Entanglement. Besides many other things, Quantum Permanents provide new rational inequalities necessary for the separability of bipartite quantum states. Using Quantum Permanents, we give deterministic poly-time algorithm to solve Hidden Matroids Intersection Problem and indicate some 'classical' complexity difficulties associated with the Quantum Entanglement. Finally, we prove that the weak membership problem for the convex set of separable bipartite density matrices is NP-HARD.« less

[Greetings from Sherlock Holmes].

PubMed

Horn, B

1991-10-29

Just at a time, when practical education and post-graduate training is really a permanent problem, it is necessary to pay attention again and again to the rare problems, which also appear in the doctor's office. They are by far not only "rare and useless": The recognition by the physician may be vital for the patient. Four examples from daily practice illustrate the significance of rarities in the physician's office as a permanent challenge.

Promoter-Terminator Gene Loops Affect Alternative 3'-End Processing in Yeast.

PubMed

Lamas-Maceiras, Mónica; Singh, Badri Nath; Hampsey, Michael; Freire-Picos, María A

2016-04-22

Many eukaryotic genes undergo alternative 3'-end poly(A)-site selection producing transcript isoforms with 3'-UTRs of different lengths and post-transcriptional fates. Gene loops are dynamic structures that juxtapose the 3'-ends of genes with their promoters. Several functions have been attributed to looping, including memory of recent transcriptional activity and polarity of transcription initiation. In this study, we investigated the relationship between gene loops and alternative poly(A)-site. Using the KlCYC1 gene of the yeast Kluyveromyces lactis, which includes a single promoter and two poly(A) sites separated by 394 nucleotides, we demonstrate in two yeast species the formation of alternative gene loops (L1 and L2) that juxtapose the KlCYC1 promoter with either proximal or distal 3'-end processing sites, resulting in the synthesis of short and long forms of KlCYC1 mRNA. Furthermore, synthesis of short and long mRNAs and formation of the L1 and L2 loops are growth phase-dependent. Chromatin immunoprecipitation experiments revealed that the Ssu72 RNA polymerase II carboxyl-terminal domain phosphatase, a critical determinant of looping, peaks in early log phase at the proximal poly(A) site, but as growth phase advances, it extends to the distal site. These results define a cause-and-effect relationship between gene loops and alternative poly(A) site selection that responds to different physiological signals manifested by RNA polymerase II carboxyl-terminal domain phosphorylation status. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

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

PubMed Central

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

Poly(adenylic acid) complementary DNA real-time polymerase chain reaction in pancreatic ductal juice in patients undergoing pancreaticoduodenectomy.

PubMed

Oliveira-Cunha, Melissa; Byers, Richard J; Siriwardena, Ajith K

2010-03-01

There is a need to develop methods of early diagnosis for pancreatic cancer. Pancreatic juice is easily collected by endoscopic retrograde cholangiopancreatography and may facilitate diagnosis using molecular markers. The aim of this work was to explore the feasibility of measurement of gene expression in RNA isolated from ductal juice. Intraoperative sampling of pancreatic juice was undertaken in 27 patients undergoing pancreaticoduodenectomy for suspected tumor. Total RNA was extracted and used as template for poly(adenylic acid) (poly[A]) polymerase chain reaction (PCR) to generate a globally amplified complementary DNA pool representative of all expressed messenger RNAs. Real-time PCR was performed for trefoil factor 2 (TFF2), carboxypeptidase B1 (CPB1), and kallikrein-related peptidase 3 (KLK3) in a subset of samples; all samples were normalized for 3 reference genes (glyceraldehyde-3-phosphate dehydrogenase [GAPDH], PSMB6, and beta-2-microglobulin [B2M]). The median volume of the pancreatic juice obtained was 1245 microL (range, 50-5000 microL). The RNA integrity number ranged from 1.9 to 10. Reverse transcriptase PCR was positive for pancreas-specific genes (TFF2 and CPB1) and negative for prostatic-specific antigen in all samples. These results demonstrate that RNA analysis of pancreatic juice is feasible using a combination of poly(A) PCR and real-time PCR. In addition, the poly(A) complementary DNA generated can be probed for multiple genes and is indefinitely renewable, thereby representing a molecular block of importance for future research.

Number-Theory in Nuclear-Physics in Number-Theory: Non-Primality Factorization As Fission VS. Primality As Fusion; Composites' Islands of INstability: Feshbach-Resonances?

NASA Astrophysics Data System (ADS)

Siegel, Edward

2011-10-01

Numbers: primality/indivisibility/non-factorization versus compositeness/divisibility /factor-ization, often in tandem but not always, provocatively close analogy to nuclear-physics: (2 + 1)=(fusion)=3; (3+1)=(fission)=4[=2 × 2]; (4+1)=(fusion)=5; (5 +1)=(fission)=6[=2 × 3]; (6 + 1)=(fusion)=7; (7+1)=(fission)=8[= 2 × 4 = 2 × 2 × 2]; (8 + 1) =(non: fission nor fusion)= 9[=3 × 3]; then ONLY composites' Islands of fusion-INstability: 8, 9, 10; then 14, 15, 16,... Could inter-digit Feshbach-resonances exist??? Applications to: quantum-information/computing non-Shore factorization, millennium-problem Riemann-hypotheses proof as Goodkin BEC intersection with graph-theory ``short-cut'' method: Rayleigh(1870)-Polya(1922)-``Anderson'' (1958)-localization, Goldbach-conjecture, financial auditing/accounting as quantum-statistical-physics;... abound!!!

Number-Theory in Nuclear-Physics in Number-Theory: Non-Primality Factorization As Fission VS. Primality As Fusion; Composites' Islands of INstability: Feshbach-Resonances?

NASA Astrophysics Data System (ADS)

Siegel, Edward

2011-04-01

Numbers: primality/indivisibility/non-factorization versus compositeness/divisibility /factor-ization, often in tandem but not always, provocatively close analogy to nuclear-physics: (2 + 1)=(fusion)=3; (3+1)=(fission)=4[=2 x 2]; (4+1)=(fusion)=5; (5+1)=(fission)=6[=2 x 3]; (6 + 1)=(fusion)=7; (7+1)=(fission)=8[= 2 x 4 = 2 x 2 x 2]; (8 + 1) =(non: fission nor fusion)= 9[=3 x 3]; then ONLY composites' Islands of fusion-INstability: 8, 9, 10; then 14, 15, 16,... Could inter-digit Feshbach-resonances exist??? Applications to: quantum-information and computing non-Shore factorization, millennium-problem Riemann-hypotheses physics-proof as numbers/digits Goodkin Bose-Einstein Condensation intersection with graph-theory ``short-cut'' method: Rayleigh(1870)-Polya(1922)-``Anderson'' (1958)-localization, Goldbach-conjecture, financial auditing/accounting as quantum-statistical-physics;... abound!!!

Topology optimization for design of segmented permanent magnet arrays with ferromagnetic materials

NASA Astrophysics Data System (ADS)

Lee, Jaewook; Yoon, Minho; Nomura, Tsuyoshi; Dede, Ercan M.

2018-03-01

This paper presents multi-material topology optimization for the co-design of permanent magnet segments and iron material. Specifically, a co-design methodology is proposed to find an optimal border of permanent magnet segments, a pattern of magnetization directions, and an iron shape. A material interpolation scheme is proposed for material property representation among air, permanent magnet, and iron materials. In this scheme, the permanent magnet strength and permeability are controlled by density design variables, and permanent magnet magnetization directions are controlled by angle design variables. In addition, a scheme to penalize intermediate magnetization direction is proposed to achieve segmented permanent magnet arrays with discrete magnetization directions. In this scheme, permanent magnet strength is controlled depending on magnetization direction, and consequently the final permanent magnet design converges into permanent magnet segments having target discrete directions. To validate the effectiveness of the proposed approach, three design examples are provided. The examples include the design of a dipole Halbach cylinder, magnetic system with arbitrarily-shaped cavity, and multi-objective problem resembling a magnetic refrigeration device.

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

PubMed Central

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

A comprehensive analysis of 3′ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation

PubMed Central

Gruber, Andreas J.; Schmidt, Ralf; Gruber, Andreas R.; Martin, Georges; Ghosh, Souvik; Belmadani, Manuel; Keller, Walter

2016-01-01

Alternative polyadenylation (APA) is a general mechanism of transcript diversification in mammals, which has been recently linked to proliferative states and cancer. Different 3′ untranslated region (3′ UTR) isoforms interact with different RNA-binding proteins (RBPs), which modify the stability, translation, and subcellular localization of the corresponding transcripts. Although the heterogeneity of pre-mRNA 3′ end processing has been established with high-throughput approaches, the mechanisms that underlie systematic changes in 3′ UTR lengths remain to be characterized. Through a uniform analysis of a large number of 3′ end sequencing data sets, we have uncovered 18 signals, six of which are novel, whose positioning with respect to pre-mRNA cleavage sites indicates a role in pre-mRNA 3′ end processing in both mouse and human. With 3′ end sequencing we have demonstrated that the heterogeneous ribonucleoprotein C (HNRNPC), which binds the poly(U) motif whose frequency also peaks in the vicinity of polyadenylation (poly(A)) sites, has a genome-wide effect on poly(A) site usage. HNRNPC-regulated 3′ UTRs are enriched in ELAV-like RBP 1 (ELAVL1) binding sites and include those of the CD47 gene, which participate in the recently discovered mechanism of 3′ UTR–dependent protein localization (UDPL). Our study thus establishes an up-to-date, high-confidence catalog of 3′ end processing sites and poly(A) signals, and it uncovers an important role of HNRNPC in regulating 3′ end processing. It further suggests that U-rich elements mediate interactions with multiple RBPs that regulate different stages in a transcript's life cycle. PMID:27382025

ARX polyalanine expansions are highly implicated in familial cases of mental retardation with infantile epilepsy and/or hand dystonia.

PubMed

Cossée, Mireille; Faivre, Laurence; Philippe, Christophe; Hichri, Heifa; de Saint-Martin, Anne; Laugel, Vincent; Bahi-Buisson, Nadia; Lemaitre, Jean-François; Leheup, Bruno; Delobel, Bruno; Demeer, Bénédicte; Poirier, Karine; Biancalana, Valérie; Pinoit, Jean-Michel; Julia, Sophie; Chelly, Jamel; Devys, Didier; Mandel, Jean-Louis

2011-01-01

Mutations in the ARX gene cause both nonsyndromic and several forms of syndromic mental retardation (MR). Two polyalanine (polyA) expansions of ARX are recurrent mutations. The most common one, the c.428_451dup, is associated with a wide spectrum of phenotypes, ranging from the most severe West syndrome to Partington syndrome (MR and hand dystonia), and even nonsyndromic X-linked mental retardation (NS-XLMR). Studies of patients not selected for specific clinical signs showed that the c.428_451dup is relatively frequent in families harboring X-linked MR (7.5%), but less common in familial cases compatible with X-linked NR (1%), and very rare in sporadic cases (0.1%). The c.333_334ins(GCG)7 expansion is less frequent and mainly associated with West syndrome. We screened for both ARX polyA expansions in 98 unrelated patients selected for the presence of NR associated with different types of epilepsy and/or with hand dystonia. We also studied two families with an initial diagnosis of NS-XLMR, one of which was identified as showing linkage to the ARX locus. The c.428_451dup was identified in three patients and the c.333_334ins(GCG)7 in one; all of the patients were from families with two affected brothers. We also found the c.428_451dup in the family linked to ARX, and clinical re-evaluation showed subtle, previously undetected signs. Our study illustrates that ARX polyA expansions are primarily associated with syndromic MR and shows a higher yield (18% in our cohort) when these mutations are screened in familial cases of MR with epilepsy and/or dystonia. Copyright © 2010 Wiley-Liss, Inc.

Gene activity during germination of spores of the fern, Onoclea sensibilis: RNA and protein synthesis and the role of stored mRNA

NASA Technical Reports Server (NTRS)

Raghavan, V.

1991-01-01

Pattern of 3H-uridine incorporation into RNA of spores of Onoclea sensibilis imbibed in complete darkness (non-germinating conditions) and induced to germinate in red light was followed by oligo-dT cellulose chromatography, gel electrophoresis coupled with fluorography and autoradiography. In dark-imbibed spores, RNA synthesis was initiated about 24 h after sowing, with most of the label accumulating in the high mol. wt. poly(A) -RNA fraction. There was no incorporation of the label into poly(A) +RNA until 48 h after sowing. In contrast, photo-induced spores began to synthesize all fractions of RNA within 12 h after sowing and by 24 h, incorporation of 3H-uridine into RNA of irradiated spores was nearly 70-fold higher than that into dark-imbibed spores. Protein synthesis, as monitored by 3H-arginine incorporation into the acid-insoluble fraction and by autoradiography, was initiated in spores within 1-2 h after sowing under both conditions. Autoradiographic experiments also showed that onset of protein synthesis in the cytoplasm of the germinating spore is independent of the transport of newly synthesized nuclear RNA. One-dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis of 35S-methionine-labelled proteins revealed a good correspondence between proteins synthesized in a cell-free translation system directed by poly(A) +RNA of dormant spores and those synthesized in vivo by dark-imbibed and photo-induced spores. These results indicate that stored mRNAs of O. sensibilis spores are functionally competent and provide templates for the synthesis of proteins during dark-imbibition and germination.

Complete nucleotide sequence and genome structure of a Japanese isolate of hibiscus latent Fort Pierce virus, a unique tobamovirus that contains an internal poly(A) region in its 3' end.

PubMed

Yoshida, Tetsuya; Kitazawa, Yugo; Komatsu, Ken; Neriya, Yutaro; Ishikawa, Kazuya; Fujita, Naoko; Hashimoto, Masayoshi; Maejima, Kensaku; Yamaji, Yasuyuki; Namba, Shigetou

2014-11-01

In this study, we detected a Japanese isolate of hibiscus latent Fort Pierce virus (HLFPV-J), a member of the genus Tobamovirus, in a hibiscus plant in Japan and determined the complete sequence and organization of its genome. HLFPV-J has four open reading frames (ORFs), each of which shares more than 98 % nucleotide sequence identity with those of other HLFPV isolates. Moreover, HLFPV-J contains a unique internal poly(A) region of variable length, ranging from 44 to 78 nucleotides, in its 3'-untranslated region (UTR), as is the case with hibiscus latent Singapore virus (HLSV), another hibiscus-infecting tobamovirus. The length of the HLFPV-J genome was 6431 nucleotides, including the shortest internal poly(A) region. The sequence identities of ORFs 1, 2, 3 and 4 of HLFPV-J to other tobamoviruses were 46.6-68.7, 49.9-70.8, 31.0-70.8 and 39.4-70.1 %, respectively, at the nucleotide level and 39.8-75.0, 43.6-77.8, 19.2-70.4 and 31.2-74.2 %, respectively, at the amino acid level. The 5'- and 3'-UTRs of HLFPV-J showed 24.3-58.6 and 13.0-79.8 % identity, respectively, to other tobamoviruses. In particular, when compared to other tobamoviruses, each ORF and UTR of HLFPV-J showed the highest sequence identity to those of HLSV. Phylogenetic analysis showed that HLFPV-J, other HLFPV isolates and HLSV constitute a malvaceous-plant-infecting tobamovirus cluster. These results indicate that the genomic structure of HLFPV-J has unique features similar to those of HLSV. To our knowledge, this is the first report of the complete genome sequence of HLFPV.

Modified nucleoside dependent Watson-Crick and wobble codon binding by tRNALysUUU species.

PubMed

Yarian, C; Marszalek, M; Sochacka, E; Malkiewicz, A; Guenther, R; Miskiewicz, A; Agris, P F

2000-11-07

Nucleoside modifications are important to the structure of all tRNAs and are critical to the function of some tRNA species. The transcript of human tRNA(Lys3)(UUU) with a UUU anticodon, and the corresponding anticodon stem and loop domain (ASL(Lys3)(UUU)), are unable to bind to poly-A programmed ribosomes. To determine if specific anticodon domain modified nucleosides of tRNA(Lys) species would restore ribosomal binding and also affect thermal stability, we chemically synthesized ASL(Lys) heptadecamers and site-specifically incorporated the anticodon domain modified nucleosides pseudouridine (Psi(39)), 5-methylaminomethyluridine (mnm(5)U(34)) and N6-threonylcarbamoyl-adenosine (t(6)A(37)). Incorporation of t(6)A(37) and mnm(5)U(34) contributed structure to the anticodon loop, apparent by increases in DeltaS, and significantly enhanced the ability of ASL(Lys3)(UUU) to bind poly-A programmed ribosomes. Neither ASL(Lys3)(UUU)-t(6)A(37) nor ASL(Lys3)(UUU)-mnm(5)U(34) bound AAG programmed ribosomes. Only the presence of both t(6)A(37) and mnm(5)U(34) enabled ASL(Lys3)(UUU) to bind AAG programmed ribosomes, as well as increased its affinity for poly-A programmed ribosomes to the level of native Escherichia coli tRNA(Lys). The completely unmodified anticodon stem and loop of human tRNA(Lys1,2)(CUU) with a wobble position-34 C bound AAG, but did not wobble to AAA, even when the ASL was modified with t(6)A(37). The data suggest that tRNA(Lys)(UUU) species require anticodon domain modifications in the loop to impart an ordered structure to the anticodon for ribosomal binding to AAA and require a combination of modified nucleosides to bind AAG.

Nonsense mutations in the alcohol dehydrogenase gene of Drosophila melanogaster correlate with an abnormal 3' end processing of the corresponding pre-mRNA.

PubMed Central

Brogna, S

1999-01-01

From bacteria to mammals, mutations that generate premature termination codons have been shown to result in the reduction in the abundance of the corresponding mRNA. In mammalian cells, more often than not, the reduction happens while the RNA is still associated with the nucleus. Here, it is reported that mutations in the alcohol dehydrogenase gene (Adh) of Drosophila melanogaster that generate premature termination codons lead to reduced levels of cytoplasmic and nuclear mRNA. Unexpectedly, it has been found that the poly(A) tails of Adh mRNAs and pre-mRNAs that carry a premature termination codon are longer than in the wild-type transcript. The more 5' terminal the mutation is, the longer is the poly(A) tail of the transcript. These findings suggest that the integrity of the coding region may be required for accurate mRNA 3' end processing. PMID:10199572

The length of an internal poly(A) tract of hibiscus latent Singapore virus is crucial for its replication.

PubMed

Niu, Shengniao; Cao, Shishu; Huang, Li-Jing; Tan, Kelvin Chee-Leong; Wong, Sek-Man

2015-01-01

Hibiscus latent Singapore virus (HLSV) mutants were constructed to study roles of its internal poly(A) tract (IPAT) in viral replication and coat protein (CP) expression. Shortening of the IPAT resulted in reduced HLSV RNA accumulation and its minimal length required for HLSV CP expression in plants was 24 nt. Disruption of a putative long range RNA-RNA interacting structure between 5' and 3' untranslated regions of HLSV-22A and -24A resulted in reduced viral RNA and undetectable CP accumulation in inoculated leaves. Replacement of the IPAT in HLSV with an upstream pseudoknot domain (UPD) of Tobacco mosaic virus (TMV) or insertion of the UPD to the immediate downstream of a 24 nt IPAT in HLSV resulted in drastically reduced viral RNA replication. Plants infected with a TMV mutant by replacement of the UPD with 43 nt IPAT exhibited milder mosaic symptoms without necrosis. We have proposed a model for HLSV replication. Copyright © 2014 Elsevier Inc. All rights reserved.

Polynucleotide: adenosine glycosidase activity of saporin-L1: effect on DNA, RNA and poly(A).

PubMed Central

Barbieri, L; Valbonesi, P; Gorini, P; Pession, A; Stirpe, F

1996-01-01

The ribosome-inactivating proteins (RIPs) are a family of plant enzymes for which a unique activity has been determined: rRNA N-glycosidase, which removes adenine at a specific universally conserved position (A4324 in the case of rat ribosomes). Here we report that saporin-L1, a RIP from the leaves of Saponaria officinalis, recognizes other substrates, including RNAs from different sources, DNA and poly(A). Saporin-L1 depurinated DNA extensively and released adenine from all adenine-containing polynucleotides tested. Adenine was the only base released from DNA or artificial polynucleotides. The characteristics of the reactions catalysed by saporin-L1 have been determined: optimal pH and temperature, ionic requirements, and the kinetic parameters Km and kcat. The reaction proceeded without cofactors, at low ionic strength, in the absence of Mg2+ and K+. Saporin-L1 had no activity towards various adenine-containing non-polynucleotide compounds (cytokinins, cofactors, nucleotides). This plant protein may now be classified as a polynucleotide: adenosine glycosidase. PMID:8912688

Purification and Properties of Bacteriophage T4-Induced RNA Ligase*

PubMed Central

Silber, Robert; Malathi, V. G.; Hurwitz, Jerard

1972-01-01

An enzyme, purified 300-fold from Escherichia coli infected with bacteriophage T4, catalyzes the conversion of 5′-termini of polyribonucleotides to internal phosphodiester bonds. The reaction requires ATP and Mg++. For every 5′-32P terminus rendered resistant to alkaline phosphatase, an equal amount of AMP and PPi are formed. Various polyribonucleotides are substrates in the reaction; to date, the best substrate is [5′-32P]polyriboadenylate. With the latter substrate, no evidence of intermolecular reaction was obtained. However, the 5′-32P termini of poly(A) rendered resistant to alkaline phosphatase are also resistant to attack by RNase II, polynucleotide phosphorylase, and low concentrations of venom phosphodiesterase. Since the product formed with poly(A) lacks 3′-hydroxyl ends, as measured with these exonucleases, the enzyme appears to convert linear molecules of polyriboadenylate to a circular form by the intramolecular covalent linkage of the 5′-phosphate end to the 3′-hydroxyl terminus. Images PMID:4342972

Statistics of concentrations due to single air pollution sources to be applied in numerical modelling of pollutant dispersion

NASA Astrophysics Data System (ADS)

Tumanov, Sergiu

A test of goodness of fit based on rank statistics was applied to prove the applicability of the Eggenberger-Polya discrete probability law to hourly SO 2-concentrations measured in the vicinity of single sources. With this end in view, the pollutant concentration was considered an integral quantity which may be accepted if one properly chooses the unit of measurement (in this case μg m -3) and if account is taken of the limited accuracy of measurements. The results of the test being satisfactory, even in the range of upper quantiles, the Eggenberger-Polya law was used in association with numerical modelling to estimate statistical parameters, e.g. quantiles, cumulative probabilities of threshold concentrations to be exceeded, and so on, in the grid points of a network covering the area of interest. This only needs accurate estimations of means and variances of the concentration series which can readily be obtained through routine air pollution dispersion modelling.

High-Level Radioactive Waste: Safe Storage and Ultimate Disposal.

ERIC Educational Resources Information Center

Dukert, Joseph M.

Described are problems and techniques for safe disposal of radioactive waste. Degrees of radioactivity, temporary storage, and long-term permanent storage are discussed. Included are diagrams of estimated waste volumes to the year 2000 and of an artist's conception of a permanent underground disposal facility. (SL)

Student Achievement: Improving Our Focus.

ERIC Educational Resources Information Center

Hawkins, Amber

An efficient way to help students achieve academically is to maximize the consistent attendance of permanent teachers in the classroom. Students nationwide are spending increased amounts of time with instructors other than their permanent teachers. A large contributor to the problem of teacher absenteeism is mandatory leave for professional…

Treatment of ectopic eruption of maxillary permanent first molars.

PubMed

Taloumis, L J; Allinder, J R

1993-01-01

A review of treatment of the ectopic maxillary permanent first molar is presented; prevalence and possible etiologies of the condition are explained. A step-by-step procedure for correctly diagnosing and treating the problem is suggested. A case is described in which diagnosis and treatment followed the principles outlined.

Alfalfa virus S, a new species in the family Alphaflexiviridae

USDA-ARS?s Scientific Manuscript database

A new species of the family Alphaflexiviridae provisionally named alfalfa virus S (AVS) was discovered in alfalfa samples originating from Sudan. A complete nucleotide sequence of the viral genome consisting of 8,349 nucleotides excluding the 3’ poly(A) tail was determined by high throughput sequenc...

Imre Lakatos's Use of Dialogue.

ERIC Educational Resources Information Center

Greig, Judith Maxwell

This paper uses a book, "Proofs and Refutations: The Logic of Mathematical Discovery," as an example of Lakatos's use of dialogue. The book was originally adapted from his dissertation and influenced by Polya and Popper. His discussion of the Euler conjecture is summarized. Three purposes for choosing the dialogue form for the book were…

Cross-sectional study of object permanence in domestic puppies (Canis familiaris).

PubMed

Gagnon, S; Doré, F Y

1994-09-01

Visual accommodation and object permanence tests were administered to 70 puppies (Canis familiaris), aged 4 weeks to 9 months. The results showed that understanding of visible displacement problems emerged at the 5th weeks and developed rapidly until the 8th week. Although the search behaviors of older puppies were more flexible, no further significant development was observed between 8 weeks and 9 months. The results on invisible displacement tests suggest that understanding of invisible displacement problems appears around the 1st year in dogs' development.

Deep brain stimulation

MedlinePlus

... the skull Problems with speech, memory, muscle weakness, balance, vision, coordination, and other functions, which may be short-term or permanent Seizures Stroke Risks of general anesthesia are: Reactions to medicines Problems breathing

Lithium toxicity

MedlinePlus

... diagnose at first. This delay can lead to long-term problems. If dialysis is done quickly, the person may feel much better. But symptoms such as memory and mood problems may be permanent. Acute on ...

What Can Quantum Optics Say about Computational Complexity Theory?

NASA Astrophysics Data System (ADS)

Rahimi-Keshari, Saleh; Lund, Austin P.; Ralph, Timothy C.

2015-02-01

Considering the problem of sampling from the output photon-counting probability distribution of a linear-optical network for input Gaussian states, we obtain results that are of interest from both quantum theory and the computational complexity theory point of view. We derive a general formula for calculating the output probabilities, and by considering input thermal states, we show that the output probabilities are proportional to permanents of positive-semidefinite Hermitian matrices. It is believed that approximating permanents of complex matrices in general is a #P-hard problem. However, we show that these permanents can be approximated with an algorithm in the BPPNP complexity class, as there exists an efficient classical algorithm for sampling from the output probability distribution. We further consider input squeezed-vacuum states and discuss the complexity of sampling from the probability distribution at the output.

Autistic children and the object permanence task.

PubMed

Adrien, J L; Tanguay, P; Barthélémy, C; Martineaú, J; Perrot, A; Hameury, L; Sauvage, D

1993-01-01

Many mentally retarded autistic children can understand the concept of object permanence, but, in comparison to developmental-age matched normal children, the behavioral strategies they employ in carrying out the Casati-Lezine Object Permanence Test are deficient and lead to failure. These deficiencies appear unrelated to interference of stereotypic or other bizarre behavior in task performance. Similar problem-solving deficiencies can be found in mentally retarded children who are not autistic, suggesting that the deficiencies themselves are less related to the social-communication deficits of autistic children, but more to the general problem-solving difficulties found in children with a lower developmental quotient. Nevertheless, the qualitative analysis of results shows a tendency in autistic children, despite their better developmental level, to use less coordinated and regular sequences to solve the task than normal or mentally retarded children.

The Population Problem as Economic Disarticulation.

ERIC Educational Resources Information Center

Yapa, Lakshman S.

1985-01-01

Overpopulation exists when people lack the basic means of subsistence, or when there is massive and permanent unemployment. Population problems of developing countries are examined, and causes of high rates of fertility are discussed. The utilization of productive resources in solving population problems is also examined. (RM)

How Spherical Are the Archimedean Solids and Their Duals?

ERIC Educational Resources Information Center

Aravind, P. K.

2011-01-01

The Isoperimetric Quotient, or IQ, introduced by G. Polya, characterizes the degree of sphericity of a convex solid. This paper obtains closed form expressions for the surface area and volume of any Archimedean polyhedron in terms of the integers specifying the type and number of regular polygons occurring around each vertex. Similar results are…

Complete nucleotide sequence and genome organization of a novel allexivirus from alfalfa (Medicago sativa)

USDA-ARS?s Scientific Manuscript database

A new species of the family Alphaflexiviridae provisionally named Alfalfa virus S (AVS) was diagnosed in alfalfa samples originating from Sudan. A complete nucleotide sequence of the viral genome consisting of 8,349 nucleotides excluding the 3’ poly(A) tail was determined by Illumina NGS technology ...

Statistical properties of alternative national forest inventory area estimators

Treesearch

Francis Roesch; John Coulston; Andrew D. Hill

2012-01-01

The statistical properties of potential estimators of forest area for the USDA Forest Service's Forest Inventory and Analysis (FIA) program are presented and discussed. The current FIA area estimator is compared and contrasted with a weighted mean estimator and an estimator based on the Polya posterior, in the presence of nonresponse. Estimator optimality is...

Complete genome sequence of a novel potyvirus, Callistephus mottle virus identified in Callistephus chinensis

USDA-ARS?s Scientific Manuscript database

The complete genomic sequence of a novel putative member of the genus Potyvirus was detected from Callistephus chinensis (china aster) in South Korea. The genomic RNA consists of 9,859 nucleotides excluding the 3’ poly(A) tail. The Callistephus virus genome, which contains the typical open reading f...

Simple methods for the 3' biotinylation of RNA.

PubMed

Moritz, Bodo; Wahle, Elmar

2014-03-01

Biotinylation of RNA allows its tight coupling to streptavidin and is thus useful for many types of experiments, e.g., pull-downs. Here we describe three simple techniques for biotinylating the 3' ends of RNA molecules generated by chemical or enzymatic synthesis. First, extension with either the Schizosaccharomyces pombe noncanonical poly(A) polymerase Cid1 or Escherichia coli poly(A) polymerase and N6-biotin-ATP is simple, efficient, and generally applicable independently of the 3'-end sequences of the RNA molecule to be labeled. However, depending on the enzyme and the reaction conditions, several or many biotinylated nucleotides are incorporated. Second, conditions are reported under which splint-dependent ligation by T4 DNA ligase can be used to join biotinylated and, presumably, other chemically modified DNA oligonucleotides to RNA 3' ends even if these are heterogeneous as is typical for products of enzymatic synthesis. Third, we describe the use of 29 DNA polymerase for a template-directed fill-in reaction that uses biotin-dUTP and, thanks to the enzyme's proofreading activity, can cope with more extended 3' heterogeneities.

Star-PAP, a poly(A) polymerase, functions as a tumor suppressor in an orthotopic human breast cancer model.

PubMed

Yu, C; Gong, Y; Zhou, H; Wang, M; Kong, L; Liu, J; An, T; Zhu, H; Li, Y

2017-02-02

Star-PAP is a noncanonical poly(A) polymerase and required for the expression of a select set of mRNAs. However, the pathological role of Star-PAP in cancer largely remains unknown. In this study, we observed decreased expression of Star-PAP in breast cancer cell lines and tissues. Ectopic Star-PAP expression inhibited proliferation as well as colony-forming ability of breast cancer cells. In breast cancer patients, high levels of Star-PAP correlated with an improved prognosis. Moreover, by regulating the expression of BIK (BCL2-interacting killer), Star-PAP induced apoptosis of breast cancer cells through the mitochondrial pathway. The growth of breast cancer xenografts in NOD/SCID mice was also inhibited by the doxycycline-induced Star-PAP overexpression. Furthermore, Star-PAP sensitized breast cancer cells to chemotherapy drugs both in vitro and in vivo. In mammary epithelial cells, Star-PAP knockdown partially transformed these cells and induced them to undergo epithelial-mesenchymal transition (EMT). These findings suggested that Star-PAP possesses tumor-suppressing activity and can be a valuable target for developing new cancer therapeutic strategies.

Lineage-specific roles of the cytoplasmic polyadenylation factor CPEB4 in the regulation of melanoma drivers

PubMed Central

Pérez-Guijarro, Eva; Karras, Panagiotis; Cifdaloz, Metehan; Martínez-Herranz, Raúl; Cañón, Estela; Graña, Osvaldo; Horcajada-Reales, Celia; Alonso-Curbelo, Direna; Calvo, Tonantzin G.; Gómez-López, Gonzalo; Bellora, Nicolas; Riveiro-Falkenbach, Erica; Ortiz-Romero, Pablo L.; Rodríguez-Peralto, José L.; Maestre, Lorena; Roncador, Giovanna; de Agustín Asensio, Juan C.; Goding, Colin R.; Eyras, Eduardo; Megías, Diego; Méndez, Raúl; Soengas, María S.

2016-01-01

Nuclear 3'-end-polyadenylation is essential for the transport, stability and translation of virtually all eukaryotic mRNAs. Poly(A) tail extension can also occur in the cytoplasm, but the transcripts involved are incompletely understood, particularly in cancer. Here we identify a lineage-specific requirement of the cytoplasmic polyadenylation binding protein 4 (CPEB4) in malignant melanoma. CPEB4 is upregulated early in melanoma progression, as defined by computational and histological analyses. Melanoma cells are distinct from other tumour cell types in their dependency on CPEB4, not only to prevent mitotic aberrations, but to progress through G1/S cell cycle checkpoints. RNA immunoprecipitation, sequencing of bound transcripts and poly(A) length tests link the melanoma-specific functions of CPEB4 to signalling hubs specifically enriched in this disease. Essential in these CPEB4-controlled networks are the melanoma drivers MITF and RAB7A, a feature validated in clinical biopsies. These results provide new mechanistic links between cytoplasmic polyadenylation and lineage specification in melanoma. PMID:27857118

Search behavior in various breeds of adult dogs (Canis familiaris): object permanence and olfactory cues.

PubMed

Gagnon, S; Doré, F Y

1992-03-01

Human analog tests of object permanence were administered to various breeds of adult dogs (Canis familiaris). Experiment 1 showed that the performance of terriers, sporting, and working dogs did not differ. Dogs succeeded in solving invisible displacement problems, but performance was lower than in visible displacement tests. Familiarity with the task had some influence because invisible displacement tests were more successful if they were preceded by visible displacement tests. In Experiment 2, odor cues from the target object and the hiding screens were available or were masked. Results confirmed that success was lower in invisible than in visible displacement tests and that these problems were solved on the basis of representation of visual information rather than on the basis of olfactory cues or of local rule learning. Dogs are compared with other species that display Stage 6 object permanence.

Systematic Review of Kinship Care Effects on Safety, Permanency, and Well-Being Outcomes

ERIC Educational Resources Information Center

Winokur, Marc A.; Holtan, Amy; Batchelder, Keri E.

2018-01-01

Objective: Children in out-of-home placements typically display more educational, behavioral, and psychological problems than do their peers. This systematic review evaluated the effect of kinship care placement compared to foster care placement on the safety, permanency, and well-being of children removed from the home for maltreatment. Methods:…

Expanding the Adoption on Private Lands : Blowing-and-Drifting Snow Control Treatments and the Cost Effectiveness of Permanent versus Non-Permanent Treatment Options

DOT National Transportation Integrated Search

2017-11-01

Previous research that estimated the costs and benefits of snow-fences for MnDOT in terms of a reduction in the costs of mitigating blowing-and-drifting snow problem areas (MN/RC 2012-03) demonstrated the ability of snow-fences to significantly lower...

Existence as a Psychological Problem: Object Permanence in Adults and Preschool Children.

ERIC Educational Resources Information Center

Subbotskii, E. V.

1991-01-01

Examines perceptions of adults compared with preschool children in assuming object permanence or discontinuity of existence when an object is removed from their immediate perceptual field. Results showed that a belief in the possibility of the discontinuity of material objects is not unique to the minds of preschool children but can also be…

Prevalence of enamel defects in primary and permanent teeth in a group of schoolchildren from Granada (Spain).

PubMed

Robles, Maria-Jesús; Ruiz, Matilde; Bravo-Perez, Manuel; González, Encarnación; Peñalver, Maria-Angustias

2013-03-01

The purpose of this study was to determine and compare the prevalence and presentations of developmental defects of the enamel (DDE) in the primary and permanent dentitions of a group of healthy schoolchildren residing in Granada (Spain). A total of 1,414 healthy schoolchildren were examined using modified DDE criteria for recording enamel defects. The prevalence of DDE of any type was 40.2% in primary dentition and 52% in permanent dentition (p<0.033). Of the 31,820 primary and permanent teeth examined in the study, 699 (4.1%) primary and 1,232 (8.3%) permanent teeth had some form of DDE. Diffuse opacity was the most common type of DDE observed in primary teeth, and demarcated opacity in the permanent teeth. Enamel hypoplasia was the least prevalent defect in both dentition types. The study population showed a high prevalence of DDE in primary as well as in permanent dentition, reflecting the current increasing trend of this condition, which should be considered as a significant public health problem.

Optimization of Streptomyces bacteriophage phi C31 integrase system to prevent post integrative gene silencing in pulmonary type II cells.

PubMed

Aneja, Manish Kumar; Geiger, Johannes; Imker, Rabea; Uzgun, Senta; Kormann, Michael; Hasenpusch, Guenther; Maucksch, Christof; Rudolph, Carsten

2009-12-31

phi C31 integrase has emerged as a potent tool for achieving long-term gene expression in different tissues. The present study aimed at optimizing elements of phi C31 integrase system for alveolar type II cells. Luciferase and beta-galactosidase activities were measured at different time points post transfection. 5-Aza-2'deoxycytidine (AZA) and trichostatin A (TSA) were used to inhibit DNA methyltransferase and histone deacetylase complex (HDAC) respectively. In A549 cells, expression of the integrase using a CMV promoter resulted in highest integrase activity, whereas in MLE12 cells, both CAG and CMV promoter were equally effective. Effect of polyA site was observed only in A549 cells, where replacement of SV40 polyA by bovine growth hormone (BGH) polyA site resulted in an enhancement of integrase activity. Addition of a C-terminal SV40 nuclear localization signal (NLS) did not result in any significant increase in integrase activity. Long-term expression studies with AZA and TSA, provided evidence for post-integrative gene silencing. In MLE12 cells, both DNA methylases and HDACs played a significant role in silencing, whereas in A549 cells, it could be attributed majorly to HDAC activity. Donor plasmids comprising cellular promoters ubiquitin B (UBB), ubiquitin C (UCC) and elongation factor 1 alpha (EF1 alpha) in an improved backbone prevented post-integrative gene silencing. In contrast to A549 and MLE12 cells, no silencing could be observed in human bronchial epithelial cells, BEAS-2B. Donor plasmid coding for murine erythropoietin under the EF1 alpha promoter when combined with phi C31 integrase resulted in higher long-term erythropoietin expression and subsequently higher hematocrit levels in mice after intravenous delivery to the lungs. These results provide evidence for cell specific post integrative gene silencing with C31 integrase and demonstrate the pivotal role of donor plasmid in long-term expression attained with this system.

The Oncogenic Fusion Proteins SET-Nup214 and Sequestosome-1 (SQSTM1)-Nup214 Form Dynamic Nuclear Bodies and Differentially Affect Nuclear Protein and Poly(A)+ RNA Export.

PubMed

Port, Sarah A; Mendes, Adélia; Valkova, Christina; Spillner, Christiane; Fahrenkrog, Birthe; Kaether, Christoph; Kehlenbach, Ralph H

2016-10-28

Genetic rearrangements are a hallmark of several forms of leukemia and can lead to oncogenic fusion proteins. One example of an affected chromosomal region is the gene coding for Nup214, a nucleoporin that localizes to the cytoplasmic side of the nuclear pore complex (NPC). We investigated two such fusion proteins, SET-Nup214 and SQSTM1 (sequestosome)-Nup214, both containing C-terminal portions of Nup214. SET-Nup214 nuclear bodies containing the nuclear export receptor CRM1 were observed in the leukemia cell lines LOUCY and MEGAL. Overexpression of SET-Nup214 in HeLa cells leads to the formation of similar nuclear bodies that recruit CRM1, export cargo proteins, and certain nucleoporins and concomitantly affect nuclear protein and poly(A) + RNA export. SQSTM1-Nup214, although mostly cytoplasmic, also forms nuclear bodies and inhibits nuclear protein but not poly(A) + RNA export. The interaction of the fusion proteins with CRM1 is RanGTP-dependent, as shown in co-immunoprecipitation experiments and binding assays. Further analysis revealed that the Nup214 parts mediate the inhibition of nuclear export, whereas the SET or SQSTM1 part determines the localization of the fusion protein and therefore the extent of the effect. SET-Nup214 nuclear bodies are highly mobile structures, which are in equilibrium with the nucleoplasm in interphase and disassemble during mitosis or upon treatment of cells with the CRM1-inhibitor leptomycin B. Strikingly, we found that nucleoporins can be released from nuclear bodies and reintegrated into existing NPC. Our results point to nuclear bodies as a means of preventing the formation of potentially insoluble and harmful protein aggregates that also may serve as storage compartments for nuclear transport factors. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

The Oncogenic Fusion Proteins SET-Nup214 and Sequestosome-1 (SQSTM1)-Nup214 Form Dynamic Nuclear Bodies and Differentially Affect Nuclear Protein and Poly(A)+ RNA Export*

PubMed Central

Port, Sarah A.; Mendes, Adélia; Valkova, Christina; Spillner, Christiane; Fahrenkrog, Birthe; Kaether, Christoph; Kehlenbach, Ralph H.

2016-01-01

Genetic rearrangements are a hallmark of several forms of leukemia and can lead to oncogenic fusion proteins. One example of an affected chromosomal region is the gene coding for Nup214, a nucleoporin that localizes to the cytoplasmic side of the nuclear pore complex (NPC). We investigated two such fusion proteins, SET-Nup214 and SQSTM1 (sequestosome)-Nup214, both containing C-terminal portions of Nup214. SET-Nup214 nuclear bodies containing the nuclear export receptor CRM1 were observed in the leukemia cell lines LOUCY and MEGAL. Overexpression of SET-Nup214 in HeLa cells leads to the formation of similar nuclear bodies that recruit CRM1, export cargo proteins, and certain nucleoporins and concomitantly affect nuclear protein and poly(A)+ RNA export. SQSTM1-Nup214, although mostly cytoplasmic, also forms nuclear bodies and inhibits nuclear protein but not poly(A)+ RNA export. The interaction of the fusion proteins with CRM1 is RanGTP-dependent, as shown in co-immunoprecipitation experiments and binding assays. Further analysis revealed that the Nup214 parts mediate the inhibition of nuclear export, whereas the SET or SQSTM1 part determines the localization of the fusion protein and therefore the extent of the effect. SET-Nup214 nuclear bodies are highly mobile structures, which are in equilibrium with the nucleoplasm in interphase and disassemble during mitosis or upon treatment of cells with the CRM1-inhibitor leptomycin B. Strikingly, we found that nucleoporins can be released from nuclear bodies and reintegrated into existing NPC. Our results point to nuclear bodies as a means of preventing the formation of potentially insoluble and harmful protein aggregates that also may serve as storage compartments for nuclear transport factors. PMID:27613868

Design of heavy duty mixes.

DOT National Transportation Integrated Search

1991-01-01

Permanent deformation of asphalt concrete, which is frequently manifested by excessive pavement rutting, has become a problem in much of the United States. Virginia began to experience rutting problems on highways with heavy traffic in the early 1980...

Elaborately designed diblock nanoprobes for simultaneous multicolor detection of microRNAs

NASA Astrophysics Data System (ADS)

Wang, Chenguang; Zhang, Huan; Zeng, Dongdong; Sun, Wenliang; Zhang, Honglu; Aldalbahi, Ali; Wang, Yunsheng; San, Lili; Fan, Chunhai; Zuo, Xiaolei; Mi, Xianqiang

2015-09-01

Simultaneous detection of multiple biomarkers has important prospects in the biomedical field. In this work, we demonstrated a novel strategy for the detection of multiple microRNAs (miRNAs) based on gold nanoparticles (Au NPs) and polyadenine (polyA) mediated nanoscale molecular beacon (MB) probes (denoted p-nanoMBs). Novel fluorescent labeled p-nanoMBs bearing consecutive adenines were designed, of which polyA served as an effective anchoring block binding to the surface of Au NPs, and the appended hairpin block formed an upright conformation that favored the hybridization with targets. Using the co-assembling method and the improved hybridization conformation of the hairpin probes, we achieved high selectivity for specifically distinguishing DNA targets from single-base mismatched DNA targets. We also realized multicolor detection of three different synthetic miRNAs in a wide dynamic range from 0.01 nM to 200 nM with a detection limit of 10 pM. What's more, we even detected miRNAs in a simulated serum environment, which indicated that our method could be used in complex media. Compared with the traditional method, our strategy provides a promising alternative method for the qualitative and quantitative detection of miRNAs.Simultaneous detection of multiple biomarkers has important prospects in the biomedical field. In this work, we demonstrated a novel strategy for the detection of multiple microRNAs (miRNAs) based on gold nanoparticles (Au NPs) and polyadenine (polyA) mediated nanoscale molecular beacon (MB) probes (denoted p-nanoMBs). Novel fluorescent labeled p-nanoMBs bearing consecutive adenines were designed, of which polyA served as an effective anchoring block binding to the surface of Au NPs, and the appended hairpin block formed an upright conformation that favored the hybridization with targets. Using the co-assembling method and the improved hybridization conformation of the hairpin probes, we achieved high selectivity for specifically distinguishing DNA targets from single-base mismatched DNA targets. We also realized multicolor detection of three different synthetic miRNAs in a wide dynamic range from 0.01 nM to 200 nM with a detection limit of 10 pM. What's more, we even detected miRNAs in a simulated serum environment, which indicated that our method could be used in complex media. Compared with the traditional method, our strategy provides a promising alternative method for the qualitative and quantitative detection of miRNAs. Electronic supplementary information (ESI) available: Sequences for oligonucleotides used for this work, dynamic light scattering (DLS) measurements, fluorescent signal intensity with different ratios between p-MBs and A5 oligonucleotides, quantification of the fluorescent p-MB, and UV-Vis spectra for naked AuNPs and the p-nanoMB. See DOI: 10.1039/c5nr04618a

Standards on the permanence of recording materials

NASA Astrophysics Data System (ADS)

Adelstein, Peter Z.

1996-02-01

The permanence of recording materials is dependent upon many factors, and these differ for photographic materials, magnetic tape and optical disks. Photographic permanence is affected by the (1) stability of the material, (2) the photographic processing and (3) the storage conditions. American National Standards on the material and the processing have been published for different types of film and standard test methods have been established for color film. The third feature of photographic permanence is the storage requirements and these have been established for photographic film, prints and plates. Standardization on the permanence of electronic recording materials is more complicated. As with photographic materials, stability is dependent upon (1) the material itself and (2) the storage environment. In addition, retention of the necessary (3) hardware and (4) software is also a prerequisite. American National Standards activity in these areas has been underway for the past six years. A test method for the material which determines the life expectancy of CD-ROMs has been standardized. The problems of determining the expected life of magnetic tape have been more formidable but the critical physical properties have been determined. A specification for the storage environment of magnetic tape has been finalized and one on the storage of optical disks is being worked on. Critical but unsolved problems are the obsolescence of both the hardware and the software necessary to read digital images.

Standards on the permanence of recording materials

NASA Astrophysics Data System (ADS)

Adelstein, Peter Z.

1996-01-01

The permanence of recording materials is dependent upon many factors, and these differ for photographic materials, magnetic tape and optical disks. Photographic permanence is affected by the (1) stability of the material, (2) the photographic processing, and (3) the storage conditions. American National Standards on the material and the processing have been published for different types of film and standard test methods have been established for color film. The third feature of photographic permanence is the storage requirements and these have been established for photographic film, prints, and plates. Standardization on the permanence of electronic recording materials is more complicated. As with photographic materials, stability is dependent upon (1) the material itself and (2) the storage environment. In addition, retention of the necessary (3) hardware and (4) software is also a prerequisite. American National Standards activity in these areas has been underway for the past six years. A test method for the material which determines the life expectancy of CD-ROMs has been standardized. The problems of determining the expected life of magnetic tape have been more formidable but the critical physical properties have been determined. A specification for the storage environment of magnetic tapes has been finalized and one on the storage of optical disks is being worked on. Critical but unsolved problems are the obsolescence of both the hardware and the software necessary to read digital images.

Unstable child welfare permanent placements and early adolescent physical and mental health: The roles of adverse childhood experiences and post-traumatic stress.

PubMed

Villodas, Miguel T; Cromer, Kelly D; Moses, Jacqueline O; Litrownik, Alan J; Newton, Rae R; Davis, Inger P

2016-12-01

Although researchers have found that child welfare placement disruptions are associated with elevated youth physical and mental health problems, the mechanisms that explain this association have not been previously studied. The present study built on a previous investigation of the physical and behavioral consequences of long-term permanent placement patterns among youth who participated in the Longitudinal Studies of Child Abuse and Neglect (LONGSCAN). The current investigation (n=251) aimed to (a) report the early adolescent living situations of youth with different long-term placement patterns, and (b) to delineate the roles of adverse childhood experiences (ACEs) and post-traumatic stress (PTS) reactions in the association between unstable long-term placement patterns and physical and mental health problems during the transition to adolescence. Information about youth's living situations, ACEs, and physical and mental health was gathered prospectively from child protective services records and biannual caregiver and youth interviews when youth were 4-14 years old. The majority of youth remained with the same caregiver during early adolescence, but youth with chronically unstable permanent placement patterns continued to experience instability. Path analyses revealed that ACEs mediated the association between unstable placement patterns and elevated mental, but not physical, health problems during late childhood. Additionally, late childhood PTS mediated the association between unstable placement patterns and subsequent escalations in physical and mental health problems during the transition to adolescence. Findings highlight the importance of long-term permanency planning for youth who enter the child welfare system and emphasize the importance of trauma-focused assessment and intervention for these youth. Copyright © 2016 Elsevier Ltd. All rights reserved.

Permanent magnet design for magnetic heat pumps using total cost minimization

NASA Astrophysics Data System (ADS)

Teyber, R.; Trevizoli, P. V.; Christiaanse, T. V.; Govindappa, P.; Niknia, I.; Rowe, A.

2017-11-01

The active magnetic regenerator (AMR) is an attractive technology for efficient heat pumps and cooling systems. The costs associated with a permanent magnet for near room temperature applications are a central issue which must be solved for broad market implementation. To address this problem, we present a permanent magnet topology optimization to minimize the total cost of cooling using a thermoeconomic cost-rate balance coupled with an AMR model. A genetic algorithm identifies cost-minimizing magnet topologies. For a fixed temperature span of 15 K and 4.2 kg of gadolinium, the optimal magnet configuration provides 3.3 kW of cooling power with a second law efficiency (ηII) of 0.33 using 16.3 kg of permanent magnet material.

Application of permanents of square matrices for DNA identification in multiple-fatality cases

PubMed Central

2013-01-01

Background DNA profiling is essential for individual identification. In forensic medicine, the likelihood ratio (LR) is commonly used to identify individuals. The LR is calculated by comparing two hypotheses for the sample DNA: that the sample DNA is identical or related to a reference DNA, and that it is randomly sampled from a population. For multiple-fatality cases, however, identification should be considered as an assignment problem, and a particular sample and reference pair should therefore be compared with other possibilities conditional on the entire dataset. Results We developed a new method to compute the probability via permanents of square matrices of nonnegative entries. As the exact permanent is known as a #P-complete problem, we applied the Huber–Law algorithm to approximate the permanents. We performed a computer simulation to evaluate the performance of our method via receiver operating characteristic curve analysis compared with LR under the assumption of a closed incident. Differences between the two methods were well demonstrated when references provided neither obligate alleles nor impossible alleles. The new method exhibited higher sensitivity (0.188 vs. 0.055) at a threshold value of 0.999, at which specificity was 1, and it exhibited higher area under a receiver operating characteristic curve (0.990 vs. 0.959, P = 9.6E-15). Conclusions Our method therefore offers a solution for a computationally intensive assignment problem and may be a viable alternative to LR-based identification for closed-incident multiple-fatality cases. PMID:23962363

Hermite-Birkhoff interpolation in the nth roots of unity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cavaretta, A.S. Jr.; Sharma, A.; Varga, R.S.

1980-06-01

Consider, as nodes for polynomial interpolation, the nth roots of unity. For a sufficiently smooth function f(z), we require a polynomial p(z) to interpolate f and certain of its derivatives at each node. It is shown that the so-called Polya conditions, which are necessary for unique interpolation, are in this setting also sufficient.

Accelerated development of object permanence in Down's syndrome infants.

PubMed

Pasnak, C F; Pasnak, R

1987-01-01

Six infants with Down's syndrome, aged 3-19 months, were taught to solve object permanence problems. The instruction took place in the infants' homes and in a child development centre, and was conducted both by parents and by a child psychologist. Object permanence tasks ranging over stages 3-6 of the sensorimotor period of intelligence were utilized in the intervention, which lasted for up to 8 months. The infants were able to progress rather rapidly on these tasks. When the instruction was terminated most had mastered multiple visible displacements, which index the fifth stage of sensorimotor intelligence.

Reasons for and patterns relating to the extraction of permanent teeth in a subset of the Saudi population.

PubMed

Alesia, Khalil; Khalil, Hesham S

2013-01-01

The purpose of this study was to investigate the reasons for and patterns of extraction of permanent teeth in a subset of the Saudi population. During a 3-month period, dentists were asked to record, using a specially designed survey form, the reasons for every extraction of a permanent tooth. The reasons for tooth extraction were assigned to different causes, ie, dental caries, periodontal disease, eruption problems, trauma, orthodontics, failed root canal treatment, and others. The data requested for each extraction were: patient age, gender, nationality, and type of tooth removed and the reason for its extraction. The highest percentage of extractions was observed in young females aged 10-30 years. Presence of caries was observed to be the main reason for extraction (50.2%) followed by orthodontic problems (18.2%), eruption problems (17.5%), and periodontal problems (8.2%). The most frequently extracted posterior teeth were the third mandibular molar (19.4%), the third maxillary molar (16.4%), the first maxillary premolar (13.2%), and the first mandibular molar (10.9%). Dental caries was found to be the most common reason for extraction of teeth. Molar teeth were found to be the most frequently extracted, with an increased number of extracted first premolars as a result of orthodontic treatment. The highest percentage of extractions was observed in young females aged 10-30 years.

Dental treatment needs of permanent first molars in mashhad schoolchildren.

PubMed

Ebrahimi, Masoumeh; Ajami, Behjat-Al-Molook; Sarraf Shirazi, Ali Reza; Afzal Aghaee, Monavar; Rashidi, Somayeh

2010-01-01

In spite of their enormous importance, permanent first molars might be affected by caries in children in developing countries. The aim of this study was to evaluate the treatment needs of first permanent molars in a group of schoolchildren in Mashhad. This cross-sectional descriptive study was carried out on 700, 7-9 year-old students in primary schools in Mashhad. The schools were randomly selected from each district. Treatment needs and DMFT of first perma-nent molars were calculated. Data was analyzed using ANOVA, Chi-Square and t-test. A total of 95.3% of the children required dental treatment. Fissure sealant application and filling were the treat-ments most required in all age groups. The mean DMFT of first permanent molars was 1.31±1.4. It was significantly higher in girls than boys (P=0.040). Great treatment needs and caries prevalence in permanent first molars in Mashhad schoolchildren show that dental caries is still a serious problem in the children of our society; therefore, education of parents and teachers is necessary for promoting children's oral health.

Draft Genome Sequence of a Picorna-Like Virus Associated with Gill Tissue in Clinically Normal Brook Trout, Salvelinus fontinalis.

PubMed

Iwanowicz, Luke R; Iwanowicz, Deborah D; Adams, Cynthia R; Galbraith, Heather; Aunins, Aaron; Cornman, Robert S

2017-10-12

Here, we report a draft genome sequence of a picorna-like virus associated with brook trout, Salvelinus fontinalis , gill tissue. The draft genome comprises 8,681 nucleotides, excluding the poly(A) tract, and contains two open reading frames. It is most similar to picorna-like viruses that infect invertebrates.

Draft genome sequence of a picorna-like virus associated with gill tissue in clinically normal brook trout, Salvelinus fontinalis

USGS Publications Warehouse

Iwanowicz, Luke R.; Iwanowicz, Deborah; Adams, Cynthia; Galbraith, Heather S.; Aunins, Aaron W.; Cornman, Robert S.

2017-01-01

Here, we report a draft genome sequence of a picorna-like virus associated with brook trout, Salvelinus fontinalis, gill tissue. The draft genome comprises 8,681 nucleotides, excluding the poly(A) tract, and contains two open reading frames. It is most similar to picorna-like viruses that infect invertebrates.

Star-PAP, a poly(A) polymerase, functions as a tumor suppressor in an orthotopic human breast cancer model

PubMed Central

Yu, C; Gong, Y; Zhou, H; Wang, M; Kong, L; Liu, J; An, T; Zhu, H; Li, Y

2017-01-01

Star-PAP is a noncanonical poly(A) polymerase and required for the expression of a select set of mRNAs. However, the pathological role of Star-PAP in cancer largely remains unknown. In this study, we observed decreased expression of Star-PAP in breast cancer cell lines and tissues. Ectopic Star-PAP expression inhibited proliferation as well as colony-forming ability of breast cancer cells. In breast cancer patients, high levels of Star-PAP correlated with an improved prognosis. Moreover, by regulating the expression of BIK (BCL2-interacting killer), Star-PAP induced apoptosis of breast cancer cells through the mitochondrial pathway. The growth of breast cancer xenografts in NOD/SCID mice was also inhibited by the doxycycline-induced Star-PAP overexpression. Furthermore, Star-PAP sensitized breast cancer cells to chemotherapy drugs both in vitro and in vivo. In mammary epithelial cells, Star-PAP knockdown partially transformed these cells and induced them to undergo epithelial–mesenchymal transition (EMT). These findings suggested that Star-PAP possesses tumor-suppressing activity and can be a valuable target for developing new cancer therapeutic strategies. PMID:28151486

Vector modifications to eliminate transposase expression following piggyBac-mediated transgenesis

PubMed Central

Chakraborty, Syandan; Ji, HaYeun; Chen, Jack; Gersbach, Charles A.; Leong, Kam W.

2014-01-01

Transgene insertion plays an important role in gene therapy and in biological studies. Transposon-based systems that integrate transgenes by transposase-catalyzed “cut-and-paste” mechanism have emerged as an attractive system for transgenesis. Hyperactive piggyBac transposon is particularly promising due to its ability to integrate large transgenes with high efficiency. However, prolonged expression of transposase can become a potential source of genotoxic effects due to uncontrolled transposition of the integrated transgene from one chromosomal locus to another. In this study we propose a vector design to decrease post-transposition expression of transposase and to eliminate the cells that have residual transposase expression. We design a single plasmid construct that combines the transposase and the transpositioning transgene element to share a single polyA sequence for termination. Consequently, the separation of the transposase element from the polyA sequence after transposition leads to its deactivation. We also co-express Herpes Simplex Virus thymidine kinase (HSV-tk) with the transposase. Therefore, cells having residual transposase expression can be eliminated by the administration of ganciclovir. We demonstrate the utility of this combination transposon system by integrating and expressing a model therapeutic gene, human coagulation Factor IX, in HEK293T cells. PMID:25492703

The Geographic Distribution of Human Y Chromosome Variation

PubMed Central

Hammer, M. F.; Spurdle, A. B.; Karafet, T.; Bonner, M. R.; Wood, E. T.; Novelletto, A.; Malaspina, P.; Mitchell, R. J.; Horai, S.; Jenkins, T.; Zegura, S. L.

1997-01-01

We examined variation on the nonrecombining portion of the human Y chromosome to investigate human evolution during the last 200,000 years. The Y-specific polymorphic sites included the Y Alu insertional polymorphism or ``YAP'' element (DYS287), the poly(A) tail associated with the YAP element, three point mutations in close association with the YAP insertion site, an A-G polymorphic transition (DYS271), and a tetranucleotide microsatellite (DYS19). Global variation at the five bi-allelic sites (DYS271, DYS287, and the three point mutations) gave rise to five ``YAP haplotypes'' in 60 populations from Africa, Europe, Asia, Australasia, and the New World (n = 1500). Combining the multi-allelic variation at the microsatellite loci (poly(A) tail and DYS19) with the YAP haplotypes resulted in a total of 27 ``combination haplotypes''. All five of the YAP haplotypes and 21 of the 27 combination haplotypes were found in African populations, which had greater haplotype diversity than did populations from other geographical locations. Only subsets of the five YAP haplotypes were found outside of Africa. Patterns of observed variation were compatible with a variety of hypotheses, including multiple human migrations and range expansions. PMID:9055088

[Study of fusion of bacteriophage f2 double-stranded RNA, poly(A).poly(U), and poly(G).poly(C) in the presence of tetraethylammonium bromide].

PubMed

Permogorov, V I; Tiaglov, B V; Minaev, V E

1980-01-01

The data on the dependence of the melting curve parameters of double-stranded RNA (replicative form of RNA of f2 bacteriophage) poly(A) times poly(U) and poly(G) times poly(C) on the concentration of (C2H5)4NBr were obtained. The RNA melting range width is shown to pass through the minimum value T =2.1+/-0.1degrees at the point of inversion of relative stability of GC and AU pairs that corresponds to 4.0+/-0.1 M concentration of (C2H5)4NBr. Using the melting temperatures of poly(A) times poly(U) and poly(G) times poly(C) the rependence of Tgc-Tau parameter on (C2H5)4NBr concentration was shown. It was concluded from these data that the effect of the double-stranded RNA stacking heterogeneity was negligible in the 0-3 M range of (C2H5)4NBr concentration. Melting curves of RNA were obtained at various values of Tgc-Tau parameter. It was shown that the profile of fine structure of melting curves depends on the value of Tgc-Tau parameter.

The Apc5 Subunit of the Anaphase-Promoting Complex/Cyclosome Interacts with Poly(A) Binding Protein and Represses Internal Ribosome Entry Site-Mediated Translation

PubMed Central

Koloteva-Levine, Nadejda; Pinchasi, Dalia; Pereman, Idan; Zur, Amit; Brandeis, Michael; Elroy-Stein, Orna

2004-01-01

The anaphase-promoting complex/cyclosome (APC/C) is a multisubunit ubiquitin ligase that mediates the proteolysis of cell cycle proteins in mitosis and G1. We used a yeast three-hybrid screen to identify proteins that interact with the internal ribosome entry site (IRES) of platelet-derived growth factor 2 mRNA. Surprisingly, this screen identified Apc5, although it does not harbor a classical RNA binding domain. We found that Apc5 binds the poly(A) binding protein (PABP), which directly binds the IRES element. PABP was found to enhance IRES-mediated translation, whereas Apc5 overexpression counteracted this effect. In addition to its association with the APC/C complex, Apc5 binds much heavier complexes and cosediments with the ribosomal fraction. In contrast to Apc3, which is associated only with the APC/C and remains intact during differentiation, Apc5 is degraded upon megakaryocytic differentiation in correlation with IRES activation. Expression of Apc5 in differentiated cells abolished IRES activation. This is the first report implying an additional role for an APC/C subunit, apart from its being part of the APC/C complex. PMID:15082755

Targeted gene deletion of miRNAs in mice by TALEN system.

PubMed

Takada, Shuji; Sato, Tempei; Ito, Yoshiaki; Yamashita, Satoshi; Kato, Tomoko; Kawasumi, Miyuri; Kanai-Azuma, Masami; Igarashi, Arisa; Kato, Tomomi; Tamano, Moe; Asahara, Hiroshi

2013-01-01

Mice are among the most valuable model animal species with an enormous amount of heritage in genetic modification studies. However, targeting genes in mice is sometimes difficult, especially for small genes, such as microRNAs (miRNAs) and targeting genes in repeat sequences. Here we optimized the application of TALEN system for mice and successfully obtained gene targeting technique in mice for intergenic region and series of microRNAs. Microinjection of synthesized RNA of TALEN targeting each gene in one cell stage of embryo was carried out and injected oocytes were transferred into pseudopregnant ICR female mice, producing a high success rate of the targeted deletion of miRNA genes. In our condition, TALEN RNA without poly(A) tail worked better than that of with poly(A) tail. This mutated allele in miRNA was transmitted to the next generation, suggesting the successful germ line transmission of this targeting method. Consistent with our notion of miRNAs maturation mechanism, in homozygous mutant mice of miR-10a, the non- mutated strand of miRNAs expression was completely diminished. This method will lead us to expand and accelerate our genetic research using mice in a high throughput way.

The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs

PubMed Central

Garzia, Aitor; Jafarnejad, Seyed Mehdi; Meyer, Cindy; Chapat, Clément; Gogakos, Tasos; Morozov, Pavel; Amiri, Mehdi; Shapiro, Maayan; Molina, Henrik; Tuschl, Thomas; Sonenberg, Nahum

2017-01-01

Cryptic polyadenylation within coding sequences (CDS) triggers ribosome-associated quality control (RQC), followed by degradation of the aberrant mRNA and polypeptide, ribosome disassembly and recycling. Although ribosomal subunit dissociation and nascent peptide degradation are well-understood, the molecular sensors of aberrant mRNAs and their mechanism of action remain unknown. We studied the Zinc Finger Protein 598 (ZNF598) using PAR-CLIP and revealed that it cross-links to tRNAs, mRNAs and rRNAs, thereby placing the protein on translating ribosomes. Cross-linked reads originating from AAA-decoding tRNALys(UUU) were 10-fold enriched over its cellular abundance, and poly-lysine encoded by poly(AAA) induced RQC in a ZNF598-dependent manner. Encounter with translated polyA segments by ZNF598 triggered ubiquitination of several ribosomal proteins, requiring the E2 ubiquitin ligase UBE2D3 to initiate RQC. Considering that human CDS are devoid of >4 consecutive AAA codons, sensing of prematurely placed polyA tails by a specialized RNA-binding protein is a novel nucleic-acid-based surveillance mechanism of RQC. PMID:28685749

The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs.

PubMed

Garzia, Aitor; Jafarnejad, Seyed Mehdi; Meyer, Cindy; Chapat, Clément; Gogakos, Tasos; Morozov, Pavel; Amiri, Mehdi; Shapiro, Maayan; Molina, Henrik; Tuschl, Thomas; Sonenberg, Nahum

2017-07-07

Cryptic polyadenylation within coding sequences (CDS) triggers ribosome-associated quality control (RQC), followed by degradation of the aberrant mRNA and polypeptide, ribosome disassembly and recycling. Although ribosomal subunit dissociation and nascent peptide degradation are well-understood, the molecular sensors of aberrant mRNAs and their mechanism of action remain unknown. We studied the Zinc Finger Protein 598 (ZNF598) using PAR-CLIP and revealed that it cross-links to tRNAs, mRNAs and rRNAs, thereby placing the protein on translating ribosomes. Cross-linked reads originating from AAA-decoding tRNA Lys (UUU) were 10-fold enriched over its cellular abundance, and poly-lysine encoded by poly(AAA) induced RQC in a ZNF598-dependent manner. Encounter with translated polyA segments by ZNF598 triggered ubiquitination of several ribosomal proteins, requiring the E2 ubiquitin ligase UBE2D3 to initiate RQC. Considering that human CDS are devoid of >4 consecutive AAA codons, sensing of prematurely placed polyA tails by a specialized RNA-binding protein is a novel nucleic-acid-based surveillance mechanism of RQC.

Pressure sores–a constant problem for plegic patients and a permanent challenge for plastic surgery

PubMed Central

Marinescu, S; Florescu, IP; Jecan, C

2010-01-01

Pressure sores–a constant problem for plegic patients and a permanent challenge for plastic surgery Pressure sores can be defined as lesions caused by unrelieved pressure resulting in damage of the underlying tissue. They represent a common problem in the pathology of plegic patients and, plastic surgery has a significant role in their treatment. Pressure sores occur over bony prominences and so, they are most commonly seen at the sacrum and trochanters in paralyzed patients and at ischium for the patients who sit in a wheelchair for a long time. For these patients, surgical treatment is very important because on one hand, it stops the loss of nutrients and proteins at the site of the pressure sore, and on the other hand, it permits the initiation of neuromuscular recuperation treatment much faster. PMID:20968200

JPRS Report. Soviet Union: Political Affairs.

DTIC Science & Technology

1990-07-10

following three essential features: voluntary member- ship; self -management; and a permanent nature. All NATIONAL PARTY AND STATE AFFAIRS JPRS-UPA-90-040...voluntary, self -managed, permanently functioning association of citizens organized on a not- for-profit basis. This wording, which takes in the basic...problems which had long been present in the depths of society, including a most serious one—national self -preservation. As soon as the possibility of

[Permanent education in health: a review].

PubMed

Miccas, Fernanda Luppino; Batista, Sylvia Helena Souza da Silva

2014-02-01

To undertake a meta-synthesis of the literature on the main concepts and practices related to permanent education in health. A bibliographical search was conducted for original articles in the PubMed, Web of Science, LILACS, IBECS and SciELO databases, using the following search terms: "public health professional education", "permanent education", "continuing education", "permanent education health". Of the 590 articles identified, after applying inclusion and exclusion criteria, 48 were selected for further analysis, grouped according to the criteria of key elements, and then underwent meta-synthesis. The 48 original publications were classified according to four thematic units of key elements: 1) concepts, 2) strategies and difficulties, 3) public policies and 4) educational institutions. Three main conceptions of permanent education in health were found: problem-focused and team work, directly related to continuing education and education that takes place throughout life. The main strategies for executing permanent education in health are discussion, maintaining an open space for permanent education , and permanent education clusters. The most limiting factor is mainly related to directly or indirect management. Another highlight is the requirement for implementation and maintenance of public policies, and the availability of financial and human resources. The educational institutions need to combine education and service aiming to form critical-reflexive graduates. The coordination between health and education is based as much on the actions of health services as on management and educational institutions. Thus, it becomes a challenge to implement the teaching-learning processes that are supported by critical-reflexive actions. It is necessary to carry out proposals for permanent education in health involving the participation of health professionals, teachers and educational institutions. To undertake a meta-synthesis of the literature on the main concepts and practices related to permanent education in health. A bibliographical search was conducted for original articles in the PubMed, Web of Science, LILACS, IBECS and SciELO databases, using the following search terms: "public health professional education", "permanent education", "continuing education", "permanent education health". Of the 590 articles identified, after applying inclusion and exclusion criteria, 48 were selected for further analysis, grouped according to the criteria of key elements, and then underwent meta-synthesis. The 48 original publications were classified according to four thematic units of key elements: 1) concepts, 2) strategies and difficulties, 3) public policies and 4) educational institutions. Three main conceptions of permanent education in health were found: problem-focused and team work, directly related to continuing education and education that takes place throughout life. The main strategies for executing permanent education in health are discussion, maintaining an open space for permanent education, and permanent education clusters. The most limiting factor is mainly related to directly or indirect management. Another highlight is the requirement for implementation and maintenance of public policies, and the availability of financial and human resources. The educational institutions need to combine education and service aiming to form critical-reflexive graduates. The coordination between health and education is based as much on the actions of health services as on management and educational institutions. Thus, it becomes a challenge to implement the teaching-learning processes that are supported by critical-reflexive actions. It is necessary to carry out proposals for permanent education in health involving the participation of health professionals, teachers and educational institutions.

Dynamic loading and stress life analysis of permanent space station modules

NASA Astrophysics Data System (ADS)

Anisimov, A. V.; Krokhin, I. A.; Likhoded, A. I.; Malinin, A. A.; Panichkin, N. G.; Sidorov, V. V.; Titov, V. A.

2016-11-01

Some methodological approaches to solving several key problems of dynamic loading and structural strength analysis of Permanent Space Station (PSS)modules developed on the basis of the working experience of Soviet and Russian PSS and the International Space station (ISS) are presented. The solutions of the direct and semi-inverse problems of PSS structure dynamics are mathematically stated. Special attention is paid to the use of the results of ground structural strength tests of space station modules and the data on the actual flight actions on the station and its dynamic responses in the orbital operation regime. The procedure of determining the dynamics and operation life parameters of elements of the PSS modules is described.

Intelligent design of permanent magnet synchronous motor based on CBR

NASA Astrophysics Data System (ADS)

Li, Cong; Fan, Beibei

2018-05-01

Aiming at many problems in the design process of Permanent magnet synchronous motor (PMSM), such as the complexity of design process, the over reliance on designers' experience and the lack of accumulation and inheritance of design knowledge, a design method of PMSM Based on CBR is proposed in order to solve those problems. In this paper, case-based reasoning (CBR) methods of cases similarity calculation is proposed for reasoning suitable initial scheme. This method could help designers, by referencing previous design cases, to make a conceptual PMSM solution quickly. The case retain process gives the system self-enrich function which will improve the design ability of the system with the continuous use of the system.

Draft Genome Sequence of a Picorna-Like Virus Associated with Gill Tissue in Clinically Normal Brook Trout, Salvelinus fontinalis

PubMed Central

2017-01-01

ABSTRACT Here, we report a draft genome sequence of a picorna-like virus associated with brook trout, Salvelinus fontinalis, gill tissue. The draft genome comprises 8,681 nucleotides, excluding the poly(A) tract, and contains two open reading frames. It is most similar to picorna-like viruses that infect invertebrates. PMID:29025930

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

PubMed

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(A) signal in all chlorophytes investigated except Scherffelia (only NUE replaced) and Pyramimonas (UGUAA completely missing). The UGUAA element is completely absent from streptophytes. However, the structure of the poly(A) signal was often modified in streptophyte algae. In most species investigated, an A-rich NUE is missing; instead, these species seem to rely mainly on U-rich elements.

Permanent Quadriplegia Following Replacement of Voice Prosthesis.

PubMed

Ozturk, Kayhan; Erdur, Omer; Kibar, Ertugrul

2016-11-01

The authors presented a patient with quadriplegia caused by cervical spine abscess following voice prosthesis replacement. The authors present the first reported permanent quadriplegia patient caused by voice prosthesis replacement. The authors wanted to emphasize that life-threatening complications may be faced during the replacement of voice prosthesis. Care should be taken during the replacement of voice prosthesis and if some problems have been faced during the procedure patients must be followed closely.

Quality of life in rectal cancer patients with permanent colostomy in Xi'an.

PubMed

Yang, Xiuxiu; Li, Qin; Zhao, Haihong; Li, Junhua; Duan, Jiaobo; Wang, Dandan; Fang, Ningning; Zhu, Ping; Fu, Jufang

2014-03-01

To observe the quality of life (QOL) in rectal cancer patients with permanent colostomy in different periods after operation. A 1-,3-,6-month prospective study of QOL in 51 rectal cancer patients with permanent colostomy and 50 without permanent colostomy was assessed using European Organization for Research and Treatment of Cancer (EORTC) QOL-30 and CR38 questionnaires. The variation of QOL in different periods was "v" type. In the 1st postoperative month, these patients had the lowest quality of life scores, accompanied significantly varied functions and severe symptoms. Almost of all indexes of these patients had improved consistently in the postoperative period. The scores of global QOL even better than pre-operative level at 6th months post-operation, but the social function, body image, chemotherapy side effects and financial difficulties had not restored to the baseline level. Patients without permanent colostomy had a better score in most of categories of QOL-30 and CR38. The 1st postoperative month was crucial for patients' recovery, in which we should pay great attention to these problems which relate to the recovery of rectal cancer patients with permanent colostomy.

Riemann-Hypothesis Millennium-Problem(MP) Physics Proof via CATEGORY-SEMANTICS(C-S)/F=C Aristotle SQUARE-of-OPPOSITION(SoO) DEduction-LOGIC DichotomY

NASA Astrophysics Data System (ADS)

Baez, J.; Lapidaryus, M.; Siegel, Edward Carl-Ludwig

2011-03-01

Riemann-hypothesis physics-proof combines: Siegel-Antonoff-Smith[AMS Joint Mtg.(2002)-Abs.973-03-126] digits on-average statistics HIll[Am. J. Math 123, 3, 887(1996)] logarithm-function's (1,0)-fixed-point base=units=scale-invariance proven Newcomb[Am. J. Math. 4, 39(1881)]-Weyl[Goett. Nachr.(1914); Math. Ann. 7, 313(1916)]-Benford[Proc. Am. Phil. Soc. 78, 4, 51(1938)]-law [Kac, Math. of Stat.-Reasoning(1955); Raimi, Sci. Am. 221, 109(1969)] algebraic-inversion to ONLY Bose-Einstein quantum-statistics(BEQS) with digit d = 0 gapFUL Bose-Einstein Condensation(BEC) insight that digits are quanta are bosons were always digits, via Siegel-Baez category-semantics tabular list-format matrix truth-table analytics in Plato-Aristotle classic "square-of-opposition" : FUZZYICS=CATEGORYICS/Category-Semantics, with Goodkind Bose-Einstein condensation(BEC) ABOVE ground-state with/and Rayleigh(cut-limit of "short-cut method";1870)-Polya(1922)-"Anderson"(1958) localization [Doyle and Snell, Random-Walks and Electrical-Networks, MAA(1981)-p.99-100!!!].

Study on the application of permanent magnet synchronous motors in underground belt conveyors

NASA Astrophysics Data System (ADS)

Ma, S. H.

2017-12-01

This paper analyzes and compares the advantages and disadvantages of several kinds of drive devices of belt conveyors from the angle of energy saving, and summarizes the application advantages and using problems of permanent magnet motor variable frequency drive system in belt conveyors. An example is given to demonstrate the energy saving effect of this system compared with other driving methods. This paper points out the application prospect of permanent magnet motor variable frequency drive system on belt conveyors and other large mining machines in coal mine. This paper is aimed to provide the design direction for the designer and the choice basis for the user on belt conveyor.

Family income, maternal psychological distress and child socio-emotional behaviour: Longitudinal findings from the UK Millennium Cohort Study.

PubMed

Noonan, Katharine; Burns, Richéal; Violato, Mara

2018-04-01

The association between low family income and socio-emotional behaviour problems in early childhood has been well-documented, and maternal psychological distress is highlighted as central in mediating this relationship. However, whether this relationship holds for older children, and the precise mechanisms by which income may influence child behaviour is unclear. This study investigated the relationship between family income and child socio-emotional behaviour at 11 years of age, and examined the mediating role of maternal psychological distress over time using the UK Millennium Cohort Study. The primary outcome was parent-reported behavioural problems, as captured by the Total Difficulties Score (TDS), derived from the Strengths and Difficulties Questionnaire (SDQ). Secondary outcomes were the emotional, peer-related, conduct, and hyperactivity/inattention problems subscales of the SDQ; and teacher-reported TDS. Permanent family income was the primary exposure variable; frequency of poverty up to age 11 years was the secondary exposure variable. Maternal psychological distress was operationalised to reflect the trajectory from child birth to age 11. Multivariable logistic regression models were used to estimate the effect of permanent family income on child behaviour at age 11, controlling for maternal psychological distress and other relevant covariates. Results showed a statistically significant protective effect of increased permanent family income on the likelihood of behavioural problems at age 11. This finding was consistent for all SDQ subscales apart from emotional problems, and was strongest for teacher-reported behavioural problems. Maternal distress was an important mediator in the income-child behaviour relationship for parent-reported, but not teacher-reported, behavioural problems. The results of this study strengthen empirical evidence that the child behaviour-income gradient is maintained in older childhood. Mother's psychological distress, particularly longstanding or recurrent, appears to contribute to this relationship. These findings may validate calls for psychosocial and financial supports for families affected by parental mental health issues.

Impact of childhood and adulthood psychological health on labour force participation and exit in later life.

PubMed

Clark, C; Smuk, M; Lain, D; Stansfeld, S A; Carr, E; Head, J; Vickerstaff, S

2017-07-01

Adulthood psychological health predicts labour force activity but few studies have examined childhood psychological health. We hypothesized that childhood psychological ill-health would be associated with labour force exit at 55 years. Data were from the 55-year follow-up of the National Child Development Study (n = 9137). Labour force participation and exit (unemployment, retirement, permanent sickness, homemaking/other) were self-reported at 55 years. Internalizing and externalizing problems in childhood (7, 11 and 16 years) and malaise in adulthood (23, 33, 42, 50 years) were assessed. Education, social class, periods of unemployment, partnership separations, number of children, and homemaking activity were measured throughout adulthood. Childhood internalizing and externalizing problems were associated with unemployment, permanent sickness and homemaking/other at 55 years, after adjustment for adulthood psychological health and education: one or two reports of internalizing was associated with increased risk for unemployment [relative risk (RR) 1.59, 95% confidence interval (CI) 1.12-2.25; RR 2.37, 95% CI 1.48-3.79] and permanent sickness (RR 1.32, 95% CI 1.00-1.74; RR, 1.48, 95% CI 1.00-2.17); three reports of externalizing was associated with increased risk for unemployment (RR 2.26, 95% CI 1.01-5.04), permanent sickness (RR 2.63, 95% CI 1.46-4.73) and homemaking/other (RR 1.95, 95% CI 1.00-3.78). Psychological ill-health across the lifecourse, including during childhood, reduces the likelihood of working in older age. Support for those with mental health problems at different life stages and for those with limited connections to the labour market, including homemakers, is an essential dimension of attempts to extend working lives.

[Permanent essential defacement--remarks on the possibilities of verification of the accepted criteria in medico-legal certification in criminal and civil law proceedings].

PubMed

Chowaniec, Czesław; Nowak, Agnieszka; Jabłoński, Christian; Neniczka, Stanisława

2007-01-01

Despite the fact that some criteria of medico-legal certification in criminal and civil proceedings have been established, there are still some topics which are controversial and thus require modification. This is also true of the notion of "permanent essential defacement". In the opinion of the authors, changes in social conventions that are occurring nowadays, as well as a highly diversified, subjective perception of esthetic values indicate the need for discussing a possible modification of the presently obligatory criteria. Apart from the assessment of posttraumatic changes, an important problem is posed by defining the notion of "a part of the body customarily open to the view ". Additionally, the authors bring up for discussion the issue of experts taking into consideration the age and sex of the victims while assessing damages. A separate problem lies in difficulties in assessing the degree of detriment to health because of defacement due to the fact that official tables for evaluating permanent or long-term detriment to health do not include relevant information.

Permanency and the Foster Care System.

PubMed

Lockwood, Katie K; Friedman, Susan; Christian, Cindy W

2015-10-01

Each year over 20,000 youth age out of the child welfare system without reaching a permanent placement in a family. Certain children, such as those spending extended time in foster care, with a diagnosed disability, or adolescents, are at the highest risk for aging out. As young adults, this population is at and increased risk of incarceration; food, housing, and income insecurity; unemployment; educational deficits; receipt of public assistance; and mental health disorders. We reviewed the literature on foster care legislation, permanency, outcomes, and interventions. The outcomes of children who age out of the child welfare system are poor. Interventions to increase permanency include training programs for youth and foster parents, age extension for foster care and insurance coverage, an adoption tax credit, and specialized services and programs that support youth preparing for their transition to adulthood. Future ideas include expanding mentoring, educational support, mental health services, and post-permanency services to foster stability in foster care placements and encourage permanency planning. Children in the child welfare system are at a high risk for physical, mental, and emotional health problems that can lead to placement instability and create barriers to achieving permanency. Failure to reach the permanency of a family leads to poor outcomes, which have negative effects on the individual and society. Supporting youth in foster care throughout transitions may mediate the negative outcomes that have historically followed placement in out-of-home care. Copyright © 2015 Mosby, Inc. All rights reserved.

Permanent right ventricular pacing through an anomalous left superior vena cava.

PubMed Central

Amikam, S; Lemer, J; Riss, E

1977-01-01

A persistent left superior vena cava can complicate the implantation of a transvenous pacemaker. In a patient who required a permanent pacemaker, this venous anomaly was discovered during the insertion of the electrode but it did not prevent long-term right ventricular pacing. This was achieved after the electrode had been manipulated through the coronary sinus and right atrium. A plan of management is proposed for dealing with this unexpected problem. Images PMID:601745

Plausible Reasoning in Tactical Planning.

DTIC Science & Technology

1987-04-01

different contexts and tasks that give rise to mappings, and the set of issues and different resolutions to these issues that have been proposed in the...humans use in reasoning about the wo~ ld ( Polya , 1958; Collins, 1978a). Our work attempts to formalize the plausible inferences that frequently occur in...are interconnected by traces. Each hierarchy represents knowledge about a class of concepts arranged in a tree structure according to some viewpoint

Sage Gene Expression Profiles Characterizing Cure

DTIC Science & Technology

2006-10-01

including suggestions for reducing this burden to Department of Defense, Washington Headquarters Services , Directorate for Information Operations and...all of which have concluded that the effect is largely consistent among high quality studies. If their breast cancer surgery is done in the luteal...at different phases of the estrous cycle. 2. prepare RNA from tumors using dynel poly-A beads 3. prepare double-stranded cDNA 4. check quality of

In vitro labeling strategies for in cellulo fluorescence microscopy of single ribonucleoprotein machines.

PubMed

Custer, Thomas C; Walter, Nils G

2017-07-01

RNA plays a fundamental, ubiquitous role as either substrate or functional component of many large cellular complexes-"molecular machines"-used to maintain and control the readout of genetic information, a functional landscape that we are only beginning to understand. The cellular mechanisms for the spatiotemporal organization of the plethora of RNAs involved in gene expression are particularly poorly understood. Intracellular single-molecule fluorescence microscopy provides a powerful emerging tool for probing the pertinent mechanistic parameters that govern cellular RNA functions, including those of protein coding messenger RNAs (mRNAs). Progress has been hampered, however, by the scarcity of efficient high-yield methods to fluorescently label RNA molecules without the need to drastically increase their molecular weight through artificial appendages that may result in altered behavior. Herein, we employ T7 RNA polymerase to body label an RNA with a cyanine dye, as well as yeast poly(A) polymerase to strategically place multiple 2'-azido-modifications for subsequent fluorophore labeling either between the body and tail or randomly throughout the tail. Using a combination of biochemical and single-molecule fluorescence microscopy approaches, we demonstrate that both yeast poly(A) polymerase labeling strategies result in fully functional mRNA, whereas protein coding is severely diminished in the case of body labeling. © 2016 The Protein Society.

Characterization and chromosomal mapping of the human TFG gene involved in thyroid carcinoma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mencinger, M.; Panagopoulos, I.; Andreasson, P.

1997-05-01

Homology searches in the Expressed Sequence Tag Database were performed using SPYGQ-rich regions as query sequences to find genes encoding protein regions similar to the N-terminal parts of the sarcoma-associated EWS and FUS proteins. Clone 22911 (T74973), encoding a SPYGQ-rich region in its 5{prime} end, and several other clones that overlapped 22911 were selected. The combined data made it possible to assemble a full-length cDNA sequence. This cDNA sequence is 1677 bp, containing an initiation codon ATG, an open reading frame of 400 amino acids, a poly(A) signal, and a poly(A) tail. We found 100% identity between the 5{prime} partmore » of the consensus sequence and the 598-bp-long sequence named TFG. The TFG sequence is fused to the 3{prime} end of NTRK1, generating the TRK-T3 fusion transcript found in papillary thyroid carcinoma. The cDNA therefore represents the full-length transcript of the TFG gene. TFG was localized to 3q11-q12 by fluorescence in situ hybridization. The 3{prime} and the 5{prime} ends of the TFG cDNA probe hybridized to a 2.2-kb band on Northern blot filters in all tissues examined. 28 refs., 5 figs., 1 tab.« less

RNA binding and replication by the poliovirus RNA polymerase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oberste, M.S.

1988-01-01

RNA binding and RNA synthesis by the poliovirus RNA-dependent RNA polymerase were studied in vitro using purified polymerase. Templates for binding and RNA synthesis studies were natural RNAs, homopolymeric RNAs, or subgenomic poliovirus-specific RNAs synthesized in vitro from cDNA clones using SP6 or T7 RNA polymerases. The binding of the purified polymerase to poliovirion and other RNAs was studied using a protein-RNA nitrocellulose filter binding assay. A cellular poly(A)-binding protein was found in the viral polymerase preparations, but was easily separated from the polymerase by chromatography on poly(A) Sepharose. The binding of purified polymerase to {sup 32}P-labeled ribohomopolymeric RNAs wasmore » examined, and the order of binding observed was poly(G) >>> poly(U) > poly(C) > poly(A). The K{sub a} for polymerase binding to poliovirion RNA and to a full-length negative strand transcript was about 1 {times} 10{sup 9} M{sup {minus}1}. The polymerase binds to a subgenomic RNAs which contain the 3{prime} end of the genome with a K{sub a} similar to that for virion RNA, but binds less well to 18S rRNA, globin mRNA, and subgenomic RNAs which lack portions of the 3{prime} noncoding region.« less

Dye-induced aggregation of single stranded RNA: a mechanistic approach.

PubMed

Biver, Tarita; Ciatto, Carlo; Secco, Fernando; Venturini, Marcella

2006-08-15

The binding of proflavine (D) to single stranded poly(A) (P) was investigated at pH 7.0 and 25 degrees C using T-jump, stopped-flow and spectrophotometric methods. Equilibrium measurements show that an external complex PD(I) and an internal complex PD(II) form upon reaction between P and D and that their concentrations depend on the polymer/dye concentration ratio (C(P)/C(D)). For C(P)/C(D)<2.5, cooperative formation of stacks external to polymer strands prevails (PD(I)). Equilibria and T-jump experiments, performed at I=0.1M and analyzed according to the Schwarz theory for cooperative binding, provide the values of site size (g=1), equilibrium constant for the nucleation step (K( *)=(1.4+/-0.6)x10(3)M(-1)), equilibrium constant for the growth step (K=(1.2+/-0.6)x10(5)M(-1)), cooperativity parameter (q=85) and rate constants for the growth step (k(r)=1.2x10(7)M(-1)s(-1), k(d)=1.1 x 10(2)s(-1)). Stopped-flow experiments, performed at low ionic strength (I=0.01 M), indicate that aggregation of stacked poly(A) strands do occur provided that C(P)/C(D)<2.5.

3′ UTR lengthening as a novel mechanism in regulating cellular senescence

PubMed Central

Chen, Meng; Lyu, Guoliang; Han, Miao; Nie, Hongbo; Shen, Ting; Chen, Wei; Niu, Yichi; Song, Yifan; Li, Xueping; Li, Huan; Chen, Xinyu; Wang, Ziyue; Xia, Zheng; Li, Wei; Tian, Xiao-Li; Ding, Chen; Gu, Jun; Zheng, Yufang; Liu, Xinhua; Hu, Jinfeng; Wei, Gang; Tao, Wei

2018-01-01

Cellular senescence has been viewed as a tumor suppression mechanism and also as a contributor to individual aging. Widespread shortening of 3′ untranslated regions (3′ UTRs) in messenger RNAs (mRNAs) by alternative polyadenylation (APA) has recently been discovered in cancer cells. However, the role of APA in the process of cellular senescence remains elusive. Here, we found that hundreds of genes in senescent cells tended to use distal poly(A) (pA) sites, leading to a global lengthening of 3′ UTRs and reduced gene expression. Genes that harbor longer 3′ UTRs in senescent cells were enriched in senescence-related pathways. Rras2, a member of the Ras superfamily that participates in multiple signal transduction pathways, preferred longer 3′ UTR usage and exhibited decreased expression in senescent cells. Depletion of Rras2 promoted senescence, while rescue of Rras2 reversed senescence-associated phenotypes. Mechanistically, splicing factor TRA2B bound to a core “AGAA” motif located in the alternative 3′ UTR of Rras2, thereby reducing the RRAS2 protein level and causing senescence. Both proximal and distal poly(A) signals showed strong sequence conservation, highlighting the vital role of APA regulation during evolution. Our results revealed APA as a novel mechanism in regulating cellular senescence. PMID:29440281

Structural basis of UGUA recognition by the Nudix protein CFIm25 and implications for a regulatory role in mRNA 3′ processing

PubMed Central

Yang, Qin; Gilmartin, Gregory M.; Doublié, Sylvie

2010-01-01

Human Cleavage Factor Im (CFIm) is an essential component of the pre-mRNA 3′ processing complex that functions in the regulation of poly(A) site selection through the recognition of UGUA sequences upstream of the poly(A) site. Although the highly conserved 25 kDa subunit (CFIm25) of the CFIm complex possesses a characteristic α/β/α Nudix fold, CFIm25 has no detectable hydrolase activity. Here we report the crystal structures of the human CFIm25 homodimer in complex with UGUAAA and UUGUAU RNA sequences. CFIm25 is the first Nudix protein to be reported to bind RNA in a sequence-specific manner. The UGUA sequence contributes to binding specificity through an intramolecular G:A Watson–Crick/sugar-edge base interaction, an unusual pairing previously found to be involved in the binding specificity of the SAM-III riboswitch. The structures, together with mutational data, suggest a novel mechanism for the simultaneous sequence-specific recognition of two UGUA elements within the pre-mRNA. Furthermore, the mutually exclusive binding of RNA and the signaling molecule Ap4A (diadenosine tetraphosphate) by CFIm25 suggests a potential role for small molecules in the regulation of mRNA 3′ processing. PMID:20479262

Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing.

PubMed

Yang, Qin; Gilmartin, Gregory M; Doublié, Sylvie

2010-06-01

Human Cleavage Factor Im (CFI(m)) is an essential component of the pre-mRNA 3' processing complex that functions in the regulation of poly(A) site selection through the recognition of UGUA sequences upstream of the poly(A) site. Although the highly conserved 25 kDa subunit (CFI(m)25) of the CFI(m) complex possesses a characteristic alpha/beta/alpha Nudix fold, CFI(m)25 has no detectable hydrolase activity. Here we report the crystal structures of the human CFI(m)25 homodimer in complex with UGUAAA and UUGUAU RNA sequences. CFI(m)25 is the first Nudix protein to be reported to bind RNA in a sequence-specific manner. The UGUA sequence contributes to binding specificity through an intramolecular G:A Watson-Crick/sugar-edge base interaction, an unusual pairing previously found to be involved in the binding specificity of the SAM-III riboswitch. The structures, together with mutational data, suggest a novel mechanism for the simultaneous sequence-specific recognition of two UGUA elements within the pre-mRNA. Furthermore, the mutually exclusive binding of RNA and the signaling molecule Ap(4)A (diadenosine tetraphosphate) by CFI(m)25 suggests a potential role for small molecules in the regulation of mRNA 3' processing.

Musashi Protein-directed Translational Activation of Target mRNAs Is Mediated by the Poly(A) Polymerase, Germ Line Development Defective-2*

PubMed Central

Cragle, Chad; MacNicol, Angus M.

2014-01-01

The mRNA-binding protein, Musashi, has been shown to regulate translation of select mRNAs and to control cellular identity in both stem cells and cancer cells. Within the mammalian cells, Musashi has traditionally been characterized as a repressor of translation. However, we have demonstrated that Musashi is an activator of translation in progesterone-stimulated oocytes of the frog Xenopus laevis, and recent evidence has revealed Musashi's capability to function as an activator of translation in mammalian systems. The molecular mechanism by which Musashi directs activation of target mRNAs has not been elucidated. Here, we report a specific association of Musashi with the noncanonical poly(A) polymerase germ line development defective-2 (GLD2) and map the association domain to 31 amino acids within the C-terminal domain of Musashi. We show that loss of GLD2 interaction through deletion of the binding domain or treatment with antisense oligonucleotides compromises Musashi function. Additionally, we demonstrate that overexpression of both Musashi and GLD2 significantly enhances Musashi function. Finally, we report a similar co-association also occurs between murine Musashi and GLD2 orthologs, suggesting that coupling of Musashi to the polyadenylation apparatus is a conserved mechanism to promote target mRNA translation. PMID:24644291

CPSF30 at the Interface of Alternative Polyadenylation and Cellular Signaling in Plants

PubMed Central

Chakrabarti, Manohar; Hunt, Arthur G.

2015-01-01

Post-transcriptional processing, involving cleavage of precursor messenger RNA (pre mRNA), and further incorporation of poly(A) tail to the 3' end is a key step in the expression of genetic information. Alternative polyadenylation (APA) serves as an important check point for the regulation of gene expression. Recent studies have shown widespread prevalence of APA in diverse systems. A considerable amount of research has been done in characterizing different subunits of so-called Cleavage and Polyadenylation Specificity Factor (CPSF). In plants, CPSF30, an ortholog of the 30 kD subunit of mammalian CPSF is a key polyadenylation factor. CPSF30 in the model plant Arabidopsis thaliana was reported to possess unique biochemical properties. It was also demonstrated that poly(A) site choice in a vast majority of genes in Arabidopsis are CPSF30 dependent, suggesting a pivotal role of this gene in APA and subsequent regulation of gene expression. There are also indications of this gene being involved in oxidative stress and defense responses and in cellular signaling, suggesting a role of CPSF30 in connecting physiological processes and APA. This review will summarize the biochemical features of CPSF30, its role in regulating APA, and possible links with cellular signaling and stress response modules. PMID:26061761

[Polyadenylated RNA and mRNA export factors in extrachromosomal nuclear domains of vitellogenic oocytes of the insect Tenebrio molitor].

PubMed

Bogoliubov, D S; Kiselev, A M; Shabel'nikov, S V; Parfenov, V N

2012-01-01

The nucleus ofvitellogenic oocytes of the yellow mealworm, Tenebrio molitor, contains a karyosphere that consists of the condensed chromatin embedded in an extrachromosomal fibrogranular material. Numerous nuclear bodies located freely in the nucleoplasm are also observed. Amongst these bodies, counterparts of nuclear speckles (= interchromatin granule clusters, IGCs) can be identified by the presence of the marker protein SC35. Microinjections of fluorescently tagged methyloligoribonucleotide probes 2'-O-Me(U)22, complementary to poly(A) tails of RNAs, revealed poly(A)+ RNA in the vast majority of IGCs. We found that all T. molitor oocyte IGCs contain heterogeneous ribonucleoprotein (hnRNP) core protein Al that localizes to IGCs in an RNA-dependent manner. The extrachromosomal material of the karyosphere and a part of nucleoplasmic IGCs also contain the adapter protein Aly that is known to provide a link between pre-mRNA splicing and mRNA export. The essential mRNA export factor/receptor NXF1 was observed to colocalize with Aly. In nucleoplasmic IGCs, NXF1 was found to localize in an RNA-dependent manner whereas it is RNA-independently located in the extrachromosomal material of the karyosphere. We believe our data suggest on a role of the nucleoplasmic IGCs in mRNA biogenesis and retention in a road to nuclear export.

The Multidimensional Structure of University Absenteeism: An Exploratory Study

ERIC Educational Resources Information Center

López-Bonilla, Jesús Manuel; López-Bonilla, Luis Miguel

2015-01-01

Absenteeism has been a common and very extended problem in university spheres for several years. This problem has become a permanent feature in academic studies in general, yet it has received scarce empirical research attention. This work is focused on the analysis of the factors that determine university absenteeism. It evaluates a series of…

lnvasive pests ('biological pollutants') and US forests: whose problem, who pays?

Treesearch

W.E. Wallner

1996-01-01

Invasive pests, or 'biological pollutants' are among the most serious threats to biological diversity in the forest ecosystems of the USA. Additionally, they can disrupt forest management practices and cause enormous financial losses. In the USA, as elsewhere, the receiving country inherits the problem and, along with its citizenry, bears the permanent...

Language Abilities of Secondary Age Pupils at Risk of School Exclusion: A Preliminary Report

ERIC Educational Resources Information Center

Clegg, Judy; Stackhouse, Joy; Finch, Katy; Murphy, Claire; Nicholls, Shelley

2009-01-01

In the UK, exclusions from school because of behaviour problems usually occur when other alternatives have proved unsuccessful. There is some evidence to suggest that behaviour problems and resulting school exclusions are associated with language impairment. In older children who are permanently excluded, expressive rather than receptive language…

Malnutrition

MedlinePlus

... permanent, even though you survive. Poverty, natural disasters, political problems, and war can all contribute to malnutrition ... verify that A.D.A.M. follows rigorous standards of quality and accountability. A.D.A.M. ...

Permanent education in health: a review

PubMed Central

Miccas, Fernanda Luppino; Batista, Sylvia Helena Souza da Silva

2014-01-01

OBJECTIVE To undertake a meta-synthesis of the literature on the main concepts and practices related to permanent education in health. METHODS A bibliographical search was conducted for original articles in the PubMed, Web of Science, LILACS, IBECS and SciELO databases, using the following search terms: “public health professional education”, “permanent education”, “continuing education”, “permanent education health”. Of the 590 articles identified, after applying inclusion and exclusion criteria, 48 were selected for further analysis, grouped according to the criteria of key elements, and then underwent meta-synthesis. RESULTS The 48 original publications were classified according to four thematic units of key elements: 1) concepts, 2) strategies and difficulties, 3) public policies and 4) educational institutions. Three main conceptions of permanent education in health were found: problem-focused and team work, directly related to continuing education and education that takes place throughout life. The main strategies for executing permanent education in health are discussion, maintaining an open space for permanent education, and permanent education clusters. The most limiting factor is mainly related to directly or indirect management. Another highlight is the requirement for implementation and maintenance of public policies, and the availability of financial and human resources. The educational institutions need to combine education and service aiming to form critical-reflexive graduates. CONCLUSIONS The coordination between health and education is based as much on the actions of health services as on management and educational institutions. Thus, it becomes a challenge to implement the teaching-learning processes that are supported by critical-reflexive actions. It is necessary to carry out proposals for permanent education in health involving the participation of health professionals, teachers and educational institutions. PMID:24789649

Do permanent night workers show circadian adjustment? A review based on the endogenous melatonin rhythm.

PubMed

Folkard, Simon

2008-04-01

"Permanent" or "fixed" night shifts have been argued to offer a potential benefit over rotating shift systems in that they may serve to maximize circadian adjustment and hence minimize the various health and safety problems associated with night work. For this reason, some authors have argued in favor of permanent shift systems, but their arguments assume at least a substantial, if not complete, adjustment of the circadian clock. They have emphasized the finding that the day sleeps taken between successive night shifts by permanent night workers are rather longer than those of either slowly or rapidly rotating shift workers, but this could simply reflect increased pressure for sleep. The present paper reviews the literature on the adjustment to permanent night work of the circadian rhythm in the secretion of melatonin, which is generally considered to be the best known indicator of the state of the endogenous circadian body clock. Studies of workers in "abnormal" environments, such as oil rigs and remote mining operations, were excluded, as the nature of these unique settings might serve to assist adjustment. The results of the six studies included indicate that only a very small minority (<3%) of permanent night workers evidence "complete"adjustment of their endogenous melatonin rhythm to night work, less than one in four permanent night workers evidence sufficiently "substantial" adjustment to derive any benefit from it, there is no difference between studies conducted in normal or dim lighting, and there is no evidence of gender difference in the adjustment to permanent night work. It is concluded that in normal environments, permanent night-shift systems are unlikely to result in sufficient circadian adjustment in most individuals to benefit health and safety.

Diabetes insipidus

MedlinePlus

... may be caused by: Certain drugs, such as lithium Genetic problems High level of calcium in the ... years of use of some medicines, such as lithium, nephrogenic DI can be permanent. Hereditary nephrogenic DI ...

The Heuristic of George Polya and Its Relation to Artificial Intelligence

DTIC Science & Technology

1981-07-01

entitled Mathematical methods in physical science -- odd, in not being the standard freshman fare of physics, chemistry , western civilization and...the questions teachers should use. The first I I Having used a linguistic variation lo convey a matter of substance, a comment on etymology is in...Intelligence to Chemistry : The DEN ORAL project. New York- McGraw-Hill 1980. McDermott, J. Learning to use analogies. Proceedings of the International Joint

Symposium on Chemical Applications of Topology and Graph Theory, April 18-22, 1983.

DTIC Science & Technology

1983-04-01

illustrated by application to the Lotka - Volterra oscillator. ELECTRICAL NETWORK REPRESENTATION OF n-DIMENSIONAL CHEMICAL MANIFOLDS L. Peusner P.O. Box 380...like molecules and others; the original formulas by Cayley were extended by Polya in a general enumeration theorem, simplified by Otter, and also studied...Gutman, leading to a joint paper which generalized it, using line graphs. Finally, electroneqativity consider- ations tell the strength of a chemical

Emerging Technologies for Real-Time Continuous Monitoring of Wellbore Integrity

NASA Astrophysics Data System (ADS)

Freifeld, B. M.

2017-12-01

Assessment of a well's integrity has traditionally been carried out through periodic wireline logging, often performed only when an operational problem was noted at the surface. There are several emerging technologies that can be installed permanently as part of the well completion and offer the ability to monitor operations while providing continuous indicators to evaluate the structural health of a well. Permanent behind casing instrumentation, such as pressure and temperature gauges can monitor for behind casing leakage. Similarly, fiber-optic distributed temperature and acoustic sensing provide additional information for assessing unwanted movement of fluid, which is indicative of problems either inside or outside of casing. Furthermore, these technologies offer the benefit of providing real-time continuous streams of information that serve as leading-indicators of wellbore problems to allow for early intervention. Additional research is still needed to develop best practices for the installation and operation of these technologies, as they increase cost and add additional risks that must be managed.

Transition from Nondestructive Testing (NDT) to Structural Health Monitoring (SHM): potential and challenges (presentation video)

NASA Astrophysics Data System (ADS)

Cawley, Peter

2014-03-01

There is a gradual shift in emphasis from periodic inspection with detachable transducers (NDT) to permanently installed monitoring systems giving information about the structural integrity at pre-programmed intervals or on demand (SHM). The drivers of this change are discussed, together with the requirements of successful SHM systems. Particular issues are that NDT often involves scanning and this is not possible with typical SHM configurations; it therefore becomes important to cover a significant area of structure from each transducer position. Guided waves provide a possible solution to this problem and permanently installed guided wave pipe inspection systems are now available. The sensitivity obtained with a permanently installed system is significantly better than that in a one-off test as baseline subtraction can be employed. However, this is far from trivial as it is necessary to compensate for benign changes such as temperature. The guided wave technique does not provide accurate remaining thickness information and is best complemented by point measurements at selected locations. Another issue is that the SHM transducers must survive in operational conditions, which is particularly difficult at high temperatures. Recent work at Imperial College and associated spin-out companies on solutions to these problems is discussed.

Object permanence in lemurs.

PubMed

Deppe, Anja M; Wright, Patricia C; Szelistowski, William A

2009-03-01

Object permanence, the ability to mentally represent objects that have disappeared from view, should be advantageous to animals in their interaction with the natural world. The objective of this study was to examine whether lemurs possess object permanence. Thirteen adult subjects representing four species of diurnal lemur (Eulemur fulvus rufus, Eulemur mongoz, Lemur catta and Hapalemur griseus) were presented with seven standard Piagetian visible and invisible object displacement tests, plus one single visible test where the subject had to wait predetermined times before allowed to search, and two invisible tests where each hiding place was made visually unique. In all visible tests lemurs were able to find an object that had been in clear view before being hidden. However, when lemurs were not allowed to search for up to 25-s, performance declined with increasing time-delay. Subjects did not outperform chance on any invisible displacements regardless of whether hiding places were visually uniform or unique, therefore the upper limit of object permanence observed was Stage 5b. Lemur species in this study eat stationary foods and are not subject to stalking predators, thus Stage 5 object permanence is probably sufficient to solve most problems encountered in the wild.

Management of Chronic Hyperplastic Pulpitis in Mandibular Molars of Middle Aged Adults- A Multidisciplinary Approach

PubMed Central

Lingeswaran, Somiya; Ari, Geetha; Thyagarajan, Ramakrishnan; Logaranjani, Anitha

2016-01-01

The molar tooth of children and young adults is a common site for chronic hyperplastic pulpitis (pulp polyp). It rarely occurs in middle aged adults. This condition is usually characterized by extensive involvement of the pulp, dictating the extraction of involved tooth. Extraction of permanent molars can lead to transient or permanent malocclusion, aesthetic, phonetic and functional problems. Here we report a case of pulp polyp in mandibular first molar of a 33-year-old woman that grew into the carious cavity. The aim of this case report is to describe the diagnosis of a chronic hyperplastic pulpitis involving the permanent molar as well as to describe its management in order to preserve them as a functional unit of the dentition. PMID:26894192

Management of Chronic Hyperplastic Pulpitis in Mandibular Molars of Middle Aged Adults- A Multidisciplinary Approach.

PubMed

Anilkumar, Kanakamedala; Lingeswaran, Somiya; Ari, Geetha; Thyagarajan, Ramakrishnan; Logaranjani, Anitha

2016-01-01

The molar tooth of children and young adults is a common site for chronic hyperplastic pulpitis (pulp polyp). It rarely occurs in middle aged adults. This condition is usually characterized by extensive involvement of the pulp, dictating the extraction of involved tooth. Extraction of permanent molars can lead to transient or permanent malocclusion, aesthetic, phonetic and functional problems. Here we report a case of pulp polyp in mandibular first molar of a 33-year-old woman that grew into the carious cavity. The aim of this case report is to describe the diagnosis of a chronic hyperplastic pulpitis involving the permanent molar as well as to describe its management in order to preserve them as a functional unit of the dentition.

Persistence and extinction for a class of stochastic SIS epidemic models with nonlinear incidence rate

NASA Astrophysics Data System (ADS)

Teng, Zhidong; Wang, Lei

2016-06-01

In this paper, a class of stochastic SIS epidemic models with nonlinear incidence rate is investigated. It is shown that the extinction and persistence of the disease in probability are determined by a threshold value R˜0. That is, if R˜0 < 1 and an additional condition holds then disease dies out, and if R˜0 > 1 then disease is weak permanent with probability one. To obtain the permanence in the mean of the disease, a new quantity R̂0 is introduced, and it is proved that if R̂0 > 1 the disease is permanent in the mean with probability one. Furthermore, the numerical simulations are presented to illustrate some open problems given in Remarks 1-3 and 5 of this paper.

[Innovations in continuing/permanent education methods for the intensive care nurses].

PubMed

Vázquez Guillamet, B; Guillamet Lloveras, A; Martínez Estalella, G; Pérez Ramírez, F

2014-01-01

Intensive care nursing is carried out in a dynamic environment characterized by the continuous incorporation of new technologies, approaches to care and a request for safety, participation and transparency by the public. Continuing/permanent intensive care nursing training in the acquisition of new competencies is key in this setting. In order to achieve this goal, simulation and problem based learning should be incorporated as essential methodologies to teach these skills. At the same time research should be done on which attitudes, competences, and knowledge are necessary to increase their intellectual knowledge. The core characteristics of ICU and its nursing should allow a deep change in their approach to continuing/permanent nursing education. Copyright © 2013 Elsevier España, S.L. y SEEIUC. All rights reserved.

An Improved Fungal Mounting Technique for Nomarski Microscopy.

ERIC Educational Resources Information Center

Fairclough, Andrew; And Others

1985-01-01

Conventional sellotape techniques for fungal mounting produce interference patterns when using Normarsky microscopy. A technique is described which overcomes this problem and produces a permanent mount with a completely clear background. (Author/JN)

Approximation-Based Discrete-Time Adaptive Position Tracking Control for Interior Permanent Magnet Synchronous Motors.

PubMed

Yu, Jinpeng; Shi, Peng; Yu, Haisheng; Chen, Bing; Lin, Chong

2015-07-01

This paper considers the problem of discrete-time adaptive position tracking control for a interior permanent magnet synchronous motor (IPMSM) based on fuzzy-approximation. Fuzzy logic systems are used to approximate the nonlinearities of the discrete-time IPMSM drive system which is derived by direct discretization using Euler method, and a discrete-time fuzzy position tracking controller is designed via backstepping approach. In contrast to existing results, the advantage of the scheme is that the number of the adjustable parameters is reduced to two only and the problem of coupling nonlinearity can be overcome. It is shown that the proposed discrete-time fuzzy controller can guarantee the tracking error converges to a small neighborhood of the origin and all the signals are bounded. Simulation results illustrate the effectiveness and the potentials of the theoretic results obtained.

Guided eruption of palatally impacted canines through combined use of 3-dimensional computerized tomography scans and the easy cuspid device.

PubMed

Caprioglio, Alberto; Siani, Lea; Caprioglio, Claudia

2007-01-01

The permanent maxillary canine has a high incidence of impaction. In the clinical treatment of impaction, the first problem is diagnosis and localization. The new diagnostic 3-dimensional systems shown in this article provide valid support in understanding anatomic connections and planning the movements needed for orthodontic correction. Thus, the clinician can reduce the incidence of iatrogenic damage of adjacent structures. This article reviews several biomedical systems for guided eruption of palatally impacted canines and discusses a new device for guided eruption of the surgically disimpacted tooth. This device, called Easy Cuspid, is designed to reduce recognized problems with reaction forces through a simple method. A clinical case of bilateral impaction of the permanent maxillary canines shows the application of the diagnostic method and the biomechanical system, Easy Cuspid.

Design of high-perveance confined-flow guns for periodic-permanent-magnet-focused tubes

NASA Technical Reports Server (NTRS)

Stankiewicz, N.

1979-01-01

An approach to the design of high perveance, low compression guns is described in which confinement is used to stabilize the beam for subsequent periodic-permanent-magnet focusing. The computed results for two cases are presented. A magnetic boundary value problem was solved for the scalar potential from which the axial magnetic field was computed. A solution was found by iterating between Poisson's equation and the electron trajectory calculations. Magnetic field values were varied in magnitude until a laminar beam with minimum scalloping was produced.

Comparison of conventional and novel quadrupole drift tube magnets inspired by Klaus Halbach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feinberg, B.

1995-02-01

Quadrupole drift tube magnets for a heavy-ion linac provide a demanding application of magnet technology. A comparison is made of three different solutions to the problem of providing an adjustable high-field-strength quadrupole magnet in a small volume. A conventional tape-wound electromagnet quadrupole magnet (conventional) is compared with an adjustable permanent-magnet/iron quadrupole magnet (hybrid) and a laced permanent-magnet/iron/electromagnet (laced). Data is presented from magnets constructed for the SuperHILAC heavy-ion linear accelerator, and conclusions are drawn for various applications.

Genome-Wide Association Study of a Validated Case Definition of Gulf War Illness in a Population-Representative Sample

DTIC Science & Technology

2013-09-01

sequence dataset. All procedures were performed by personnel in the IIMT UT Southwestern Genomics and Microarray Core using standard protocols. More... sequencing run, samples were demultiplexed using standard algorithms in the Genomics and Microarray Core and processed into individual sample Illumina single... Sequencing (RNA-Seq), using Illumina’s multiplexing mRNA-Seq to generate full sequence libraries from the poly-A tailed RNA to a read depth of 30

RNA-Mediated Gene Duplication and Retroposons: Retrogenes, LINEs, SINEs, and Sequence Specificity

PubMed Central

2013-01-01

A substantial number of “retrogenes” that are derived from the mRNA of various intron-containing genes have been reported. A class of mammalian retroposons, long interspersed element-1 (LINE1, L1), has been shown to be involved in the reverse transcription of retrogenes (or processed pseudogenes) and non-autonomous short interspersed elements (SINEs). The 3′-end sequences of various SINEs originated from a corresponding LINE. As the 3′-untranslated regions of several LINEs are essential for retroposition, these LINEs presumably require “stringent” recognition of the 3′-end sequence of the RNA template. However, the 3′-ends of mammalian L1s do not exhibit any similarity to SINEs, except for the presence of 3′-poly(A) repeats. Since the 3′-poly(A) repeats of L1 and Alu SINE are critical for their retroposition, L1 probably recognizes the poly(A) repeats, thereby mobilizing not only Alu SINE but also cytosolic mRNA. Many flowering plants only harbor L1-clade LINEs and a significant number of SINEs with poly(A) repeats, but no homology to the LINEs. Moreover, processed pseudogenes have also been found in flowering plants. I propose that the ancestral L1-clade LINE in the common ancestor of green plants may have recognized a specific RNA template, with stringent recognition then becoming relaxed during the course of plant evolution. PMID:23984183

The human myelin oligodendrocyte glycoprotein (MOG) gene: Complete nucleotide sequence and structural characterization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paule Roth, M.; Malfroy, L.; Offer, C.

1995-07-20

Human myelin oligodendrocyte glycoprotein (MOG), a myelin component of the central nervous system, is a candidate target antigen for autoimmune-mediated demyelination. We have isolated and sequenced part of a cosmid clone that contains the entire human MOG gene. The primary nuclear transcript, extending from the putative start of transcription to the site of poly(A) addition, is 15,561 nucleotides in length. The human MOG gene contains 8 exons, separated by 7 introns; canonical intron/exon boundary sites are observed at each junction. The introns vary in size from 242 to 6484 bp and contain numerous repetitive DNA elements, including 14 Alu sequencesmore » within 3 introns. Another Alu element is located in the 3{prime}-untranslated region of the gene. Alu sequences were classified with respect to subfamily assignment. Seven hundred sixty-three nucleotides 5{prime} of the transcription start and 1214 nucleotides 3{prime} of the poly(A) addition sites were also sequenced. The 5{prime}-flanking region revealed the presence of several consensus sequences that could be relevant in the transcription of the MOG gene, in particular binding sites in common with other myelin gene promoters. Two polymorphic intragenic dinucleotide (CA){sub n} and tetranucleotide (TAAA){sub n} repeats were identified and may provide genetic marker tools for association and linkage studies. 50 refs., 3 figs., 3 tabs.« less

Stimulation of translation by human Unr requires cold shock domains 2 and 4, and correlates with poly(A) binding protein interaction.

PubMed

Ray, Swagat; Anderson, Emma C

2016-03-03

The RNA binding protein Unr, which contains five cold shock domains, has several specific roles in post-transcriptional control of gene expression. It can act as an activator or inhibitor of translation initiation, promote mRNA turnover, or stabilise mRNA. Its role depends on the mRNA and other proteins to which it binds, which includes cytoplasmic poly(A) binding protein 1 (PABP1). Since PABP1 binds to all polyadenylated mRNAs, and is involved in translation initiation by interaction with eukaryotic translation initiation factor 4G (eIF4G), we investigated whether Unr has a general role in translational control. We found that Unr strongly stimulates translation in vitro, and mutation of cold shock domains 2 or 4 inhibited its translation activity. The ability of Unr and its mutants to stimulate translation correlated with its ability to bind RNA, and to interact with PABP1. We found that Unr stimulated the binding of PABP1 to mRNA, and that Unr was required for the stable interaction of PABP1 and eIF4G in cells. siRNA-mediated knockdown of Unr reduced the overall level of cellular translation in cells, as well as that of cap-dependent and IRES-dependent reporters. These data describe a novel role for Unr in regulating cellular gene expression.

Cloning and characterization of a type 3 iodothyronine deiodinase (D3) in the liver of the chondrichtyan Chiloscyllium punctatum.

PubMed

Martínez, Lidia Mayorga; Orozco, Aurea; Villalobos, Patricia; Valverde-R, Carlos

2008-05-01

Thyroid hormone bioactivity is finely regulated at the cellular level by the peripheral iodothyronine deiodinases (D). The study of thyroid function in fish has been restricted mainly to teleosts, whereas the study and characterization of Ds have been overlooked in chondrichthyes. Here we report the cloning and operational characterization of both the native and the recombinant hepatic type 3 iodothyronine deiodinase in the tropical shark Chiloscyllium punctatum. Native and recombinant sD3 show identical catalytic activities: a strong preference for T3-inner-ring deiodination, a requirement for a high concentration of DTT, a sequential reaction mechanism, and resistance to PTU inhibition. The cloned cDNA contains 1298 nucleotides [excluding the poly(A) tail] and encodes a predicted protein of 259 amino acids. The triplet TGA coding for selenocysteine (Sec) is at position 123. The consensus selenocysteine insertion sequence (SECIS) was identified 228 bp upstream of the poly(A) tail and corresponds to form 2. The deduced amino acid sequence was 77% and 72% identical to other D3 cDNAs in fishes and other vertebrates, respectively. As in the case of other piscivore teleost species, shark expresses hepatic D3 through adulthood. This characteristic may be associated with the alimentary strategy in which the protection from an exogenous overload of thyroid hormones could be of physiological importance for thyroidal homeostasis.

Control of storage-protein synthesis during seed development in pea (Pisum sativum L.).

PubMed Central

Gatehouse, J A; Evans, I M; Bown, D; Croy, R R; Boulter, D

1982-01-01

The tissue-specific syntheses of seed storage proteins in the cotyledons of developing pea (Pisum sativum L.) seeds have been demonstrated by estimates of their qualitative and quantitative accumulation by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis and rocket immunoelectrophoresis respectively. Vicilin-fraction proteins initially accumulated faster than legumin, but whereas legumin was accumulated throughout development, different components of the vicilin fraction had their predominant periods of synthesis at different stages of development. The translation products in vitro of polysomes isolated from cotyledons at different stages of development reflected the synthesis in vivo of storage-protein polypeptides at corresponding times. The levels of storage-protein mRNA species during development were estimated by 'Northern' hybridization using cloned complementary-DNA probes. This technique showed that the levels of legumin and vicilin (47000-Mr precursors) mRNA species increased and decreased in agreement with estimated rates of synthesis of the respective polypeptides. The relative amounts of these messages, estimated by kinetic hybridization were also consistent. Legumin mRNA was present in leaf poly(A)+ RNA at less than one-thousandth of the level in cotyledon poly(A)+ (polyadenylated) RNA, demonstrating tissue-specific expression. Evidence is presented that storage-protein mRNA species are relatively long-lived, and it is suggested that storage-protein synthesis is regulated primarily at the transcriptional level. Images Fig. 2. Fig. 3. PMID:6897609

Expression of small cytoplasmic transcripts of the rat identifier element in vivo and in cultured cells.

PubMed Central

McKinnon, R D; Danielson, P; Brow, M A; Bloom, F E; Sutcliffe, J G

1987-01-01

We examined the level of expression of small RNA transcripts hybridizing to a rodent repetitive DNA element, the identifier (ID) sequence, in a variety of cell types in vivo and in cultured mammalian cells. A 160-nucleotide (160n) cytoplasmic poly(A)+ RNA (BC1) appeared in late embryonic and early postnatal rat brain development, was enriched in the cerebral cortex, and appeared to be restricted to neural tissue and the anterior pituitary gland. A 110n RNA (BC2) was specifically enriched in brain, especially the postnatal cortex, but was detectable at low levels in peripheral tissues. A third, related 75n poly(A)- RNA (T3) was found in rat brain and at lower levels in peripheral tissues but was very abundant in the testes. The BC RNAs were found in a variety of rat cell lines, and their level of expression was dependent upon cell culture conditions. A rat ID probe detected BC-like RNAs in mouse brain but not liver and detected a 200n RNA in monkey brain but not liver at lower hybridization stringencies. These RNAs were expressed by mouse and primate cell lines. Thus, tissue-specific expression of small ID-sequence-related transcripts is conserved among mammals, but the tight regulation found in vivo is lost by cells in culture. Images PMID:2439903

Highly abundant and stage-specific mRNAs in the obligate pathogen Bremia lactucae.

PubMed

Judelson, H S; Michelmore, R W

1990-01-01

Germinating spores of the obligate pathogen Bremia lactucae (lettuce downy mildew) contain several unusually abundant species of mRNA. Thirty-nine cDNA clones corresponding to prevalent transcripts were isolated from a library synthesized using poly(A)+ RNA from germinating spores; these clones represented only five distinct classes. Each corresponding mRNA accounted for from 0.4 to 9 percent by mass of poly(A)+ RNA from germinating spores and together represented greater than 20 percent of the mRNA. The expression of the corresponding genes, and a gene encoding Hsp70, was analyzed in spores during germination and during growth in planta. The Hsp70 mRNA and mRNA from one abundant cDNA clone (ham34) were expressed constitutively. Two clones (ham9 and ham12) hybridized only to mRNA from spores and germinating spores. Two clones (ham37 and ham27) showed hybridization specific to germinating spores. Quantification of the number of genes homologous to each cDNA clone indicated that four clones corresponded to one or two copies per haploid genome, and one hybridized to an approximately 11-member family of genes. A sequence of the gene corresponding to ham34 was obtained to investigate its function and to identify sequences conferring high levels of gene expression for use in constructing vectors for the transformation of B. lactucae.

Efficient combination of a 3D Quasi-Newton inversion algorithm and a vector dual-primal finite element tearing and interconnecting method

NASA Astrophysics Data System (ADS)

Voznyuk, I.; Litman, A.; Tortel, H.

2015-08-01

A Quasi-Newton method for reconstructing the constitutive parameters of three-dimensional (3D) penetrable scatterers from scattered field measurements is presented. This method is adapted for handling large-scale electromagnetic problems while keeping the memory requirement and the time flexibility as low as possible. The forward scattering problem is solved by applying the finite-element tearing and interconnecting full-dual-primal (FETI-FDP2) method which shares the same spirit as the domain decomposition methods for finite element methods. The idea is to split the computational domain into smaller non-overlapping sub-domains in order to simultaneously solve local sub-problems. Various strategies are proposed in order to efficiently couple the inversion algorithm with the FETI-FDP2 method: a separation into permanent and non-permanent subdomains is performed, iterative solvers are favorized for resolving the interface problem and a marching-on-in-anything initial guess selection further accelerates the process. The computational burden is also reduced by applying the adjoint state vector methodology. Finally, the inversion algorithm is confronted to measurements extracted from the 3D Fresnel database.

Solving Large-Scale Inverse Magnetostatic Problems using the Adjoint Method

PubMed Central

Bruckner, Florian; Abert, Claas; Wautischer, Gregor; Huber, Christian; Vogler, Christoph; Hinze, Michael; Suess, Dieter

2017-01-01

An efficient algorithm for the reconstruction of the magnetization state within magnetic components is presented. The occurring inverse magnetostatic problem is solved by means of an adjoint approach, based on the Fredkin-Koehler method for the solution of the forward problem. Due to the use of hybrid FEM-BEM coupling combined with matrix compression techniques the resulting algorithm is well suited for large-scale problems. Furthermore the reconstruction of the magnetization state within a permanent magnet as well as an optimal design application are demonstrated. PMID:28098851

Calculus Problem Solving Behavior of Mathematic Education Students

NASA Astrophysics Data System (ADS)

Rizal, M.; Mansyur, J.

2017-04-01

The purpose of this study is to obtain a description of the problem-solving behaviour of mathematics education students. The attainment of the purpose consisted of several stages: (1) to gain the subject from the mathematic education of first semester students, each of them who has a high, medium, and low competence of mathematic case. (2) To give two mathematical problems with different characteristics. The first problem (M1), the statement does not lead to a resolution. The second problem (M2), a statement leads to problem-solving. (3) To explore the behaviour of problem-solving based on the step of Polya (Rizal, 2011) by way of thinking aloud and in-depth interviews. The obtained data are analysed as suggested by Miles and Huberman (1994) but at first, time triangulation is done or data’s credibility by providing equivalent problem contexts and at different times. The results show that the behavioral problem solvers (mathematic education students) who are capable of high mathematic competency (ST). In understanding M1, ST is more likely to pay attention to an image first, read the texts piecemeal and repeatedly, then as a whole and more focus to the sentences that contain equations, numbers or symbols. As a result, not all information can be received well. When understanding the M2, ST can link the information from a problem that is stored in the working memory to the information on the long-term memory. ST makes planning to the solution of M1 and M2 by using a formula based on similar experiences which have been ever received before. Another case when implementing the troubleshooting plans, ST complete the M1 according to the plan, but not all can be resolved correctly. In contrast to the implementation of the solving plan of M2, ST can solve the problem according to plan quickly and correctly. According to the solving result of M1 and M2, ST conducts by reading the job based on an algorithm and reasonability. Furthermore, when SS and SR understand the problem of M1 and M2 similar to the ST’s, but both of the problem solvers read the questions with not complete so that they cannot pay attention to the questions of the problems. SS and SR create and execute M2 plan same as ST, but for M1, SS and SR cannot do it, but only active on reading the statement of the problem. On the checking of the M2 task, SS and SR retrace the task according to the used formula.

PolyA Single Strand DNA Translocation Through an Alpha-Hemolysin Pore Stem

NASA Technical Reports Server (NTRS)

OKeeffe, James; Cozmuta, Ioana; Stolc, Viktor

2003-01-01

A new model for the polymer-pore interaction energy is introduced, based on an atomic-scale description of coulombic polymer-pore interaction. The enhanced drift velocity, experimentally observed for short polymers, is successfully accounted for, using this interaction energy model. For R/R(sub 0)>4 (R(sub 0)=7 angstroms) the translocation velocity approaches the free space drift velocity v(sub 0). This motivates the need to appropriately derivatize artificial nanopores, where R>R(sub 0).

Aerospace Medicine and Biology. A Continuing Bibliography with Indexes

DTIC Science & Technology

1987-12-01

GLYCERALDEHYDE AS A SOURCE OF SIMULATION ABOUT THE ORIGIN OF LIFE ENERGY AND MONOMERS FOR PREBIOTIC CONDENSATION URSULA NIESERT (Freiburg, Universitaet, Freiburg...primitive prebiotic replication system. The adsorption of Poly-C, Poly-U, Poly-A, Poly-G, and 5’-AMP, 5’-GMP, 5’-CMP and 5’-UMP onto gypsum was studied. It...Cambridge University Press. 1986. 378 p. For individual titles see A87-49035 to A87-49049. Topics discussed include prebiotic systems and evolutionary

Bradley Fighting Vehicle Gunnery: An Analysis of Engagement Strategies for the M242 25-mm Automatic Gun

DTIC Science & Technology

1993-03-01

source for this estimate of eight rounds per BMP target. According to analyst Donna Quirido, AMSAA does not provide or support any such estimate (30...engagement or in the case of. the Bradley, stabilization inaccuracies. According to Helgert: These errors give rise to aim-wander, a term that derives from...the same area. (6:14_5) The resulting approximation to the truncated normal integral has a maximum relative error of 0.0075. Using Polya -Williams, an

The Activity-Based Approach to Achieving Theoretical and Practical Consensus in Pedagogy of N. F. Talyzina

ERIC Educational Resources Information Center

Chapaev, Nikolay K.; Akimova, Olga B.; Selivanov, Andrey V.; Shaforostova, Tatiana V.

2016-01-01

The relevance of the problem under study is based on the necessity to solve the permanent problem of the unity of theory and practice in the content of students' cognitive activity in the modern conditions. The purpose of the article is to analyze and to generalize the main concepts of pedagogy by N.F. Talyzina for implementation of the…

Planetary Data Workshop, Part 1

NASA Technical Reports Server (NTRS)

1984-01-01

The community of planetary scientists addresses two general problems regarding planetary science data: (1) important data sets are being permanently lost; and (2) utilization is constrainted by difficulties in locating and accessing science data and supporting information necessary for its use. A means to correct the problems, provide science and functional requirements for a systematic and phased approach, and suggest technologies and standards appropriate to the solution were explored.

Influence of the geometry on magnetic interactions in a retina fixator based on a magnetoactive elastomer seal

NASA Astrophysics Data System (ADS)

Nadzharyan, T. A.; Makarova, L. A.; Kazimirova, E. G.; Perov, N. S.; Kramarenko, E. Yu

2018-03-01

We study the effects the geometric configuration has on magnetic interactions between a magnetoactive elastomer (MAE) sample and various systems of permanent magnets for problems with both flat and curved geometry. MAEs consist of a silicone polymer matrix and iron filler microparticles embedded in it. Permanent magnets are cylindrical neodymium magnets arranged in a line on a flat or curved solid surfaces. We use computer simulations, namely the finite element method, in order to study the interaction force and magnetic pressure in a system with an MAE sample and permanent magnets. The model is based on classical Maxwell magnetostatics and two factors taking into account field dependence of MAE’s magnetic properties and inhomogeneities caused by local demagnetization. We calculate magnetic pressure dependences on various geometric parameters of the system, namely, the diameter and the height of permanent magnets, the distance between the magnets and dimensions of MAE samples. This research aims to create a set of guidelines for choosing the geometric configuration of a retina fixator based on MAE seals to be used in eye surgery for retinal detachment treatment.

Modeling of non-ideal hard permanent magnets with an affine-linear model, illustrated for a bar and a horseshoe magnet

NASA Astrophysics Data System (ADS)

Glane, Sebastian; Reich, Felix A.; Müller, Wolfgang H.

2017-11-01

This study is dedicated to continuum-scale material modeling of isotropic permanent magnets. An affine-linear extension to the commonly used ideal hard model for permanent magnets is proposed, motivated, and detailed. In order to demonstrate the differences between these models, bar and horseshoe magnets are considered. The structure of the boundary value problem for the magnetic field and related solution techniques are discussed. For the ideal model, closed-form analytical solutions were obtained for both geometries. Magnetic fields of the boundary value problems for both models and differently shaped magnets were computed numerically by using the boundary element method. The results show that the character of the magnetic field is strongly influenced by the model that is used. Furthermore, it can be observed that the shape of an affine-linear magnet influences the near-field significantly. Qualitative comparisons with experiments suggest that both the ideal and the affine-linear models are relevant in practice, depending on the magnetic material employed. Mathematically speaking, the ideal magnetic model is a special case of the affine-linear one. Therefore, in applications where knowledge of the near-field is important, the affine-linear model can yield more accurate results—depending on the magnetic material.

Hair cosmetics.

PubMed

O'Donoghue, M N

1987-07-01

Porosity, elasticity, and texture influence the hair's ability to be changed. The types of color--temporary, gradual, natural, semipermanent, and permanent--depend upon the size of the "coloring" molecule to determine whether they penetrate the cortex (permanent) or precipitate on the cuticle. Different types of hair--thick or coarse, fine or thin--have varying affinity for different products and coloring/waving methods. Damaged hair is treated differently from hair with healthy, less porous shafts. Because so many people have color-treated hair today, dermatologists should be aware of all the latest changes and improvements, in order to assist patients with damaged or congenitally deformed hair. Acid-based permanents are becoming the most commonly used. Daily care with shampooing and conditioning has attained its most sophisticated level with the use of anionic and cationic surfactants in all hair-care products. It is also important for the dermatologist to be aware of what help is available for his or her patients. Cosmetic companies are eager to help any patient with severe problems with texture, dullness, over-fine or congenitally defective hair. The physician should send the patient with a severe problem directly to the nearest company headquarters or major city office to have a hair analysis, and receive suggestions from the experts of that company. For patients with moderate to mild problems, the dermatologist should be able to recommend three or four good salons in the local area with which he or she is familiar. Our main goal as physicians is to take care of the entire patient and to enable him or her to have a good self-image.

Effort-reward imbalance and its association with health among permanent and fixed-term workers

PubMed Central

2010-01-01

Background In the past decade, the changing labor market seems to have rejected the traditional standards employment and has begun to support a variety of non-standard forms of work in their place. The purpose of our study was to compare the degree of job stress, sources of job stress, and association of high job stress with health among permanent and fixed-term workers. Methods Our study subjects were 709 male workers aged 30 to 49 years in a suburb of Tokyo, Japan. In 2008, we conducted a cross-sectional study to compare job stress using an effort-reward imbalance (ERI) model questionnaire. Lifestyles, subjective symptoms, and body mass index were also observed from the 2008 health check-up data. Results The rate of job stress of the high-risk group measured by ERI questionnaire was not different between permanent and fixed-term workers. However, the content of the ERI components differed. Permanent workers were distressed more by effort, overwork, or job demand, while fixed-term workers were distressed more by their job insecurity. Moreover, higher ERI was associated with existence of subjective symptoms (OR = 2.07, 95% CI: 1.42-3.03) and obesity (OR = 2.84, 95% CI:1.78-4.53) in fixed-term workers while this tendency was not found in permanent workers. Conclusions Our study showed that workers with different employment types, permanent and fixed-term, have dissimilar sources of job stress even though their degree of job stress seems to be the same. High ERI was associated with existing subjective symptoms and obesity in fixed-term workers. Therefore, understanding different sources of job stress and their association with health among permanent and fixed-term workers should be considered to prevent further health problems. PMID:21054838

Performance improvement: one model to reduce length of stay.

PubMed

Chisari, E; Mele, J A

1994-01-01

Dedicated quality professionals are tired of quick fixes, Band-Aids, and other first-aid strategies that offer only temporary relief of nagging problems rather than a long-term cure. Implementing strategies that can produce permanent solutions to crucial problems is a challenge confronted by organizations striving for continuous performance improvement. One vehicle, driven by data and customer requirements, that can help to solve problems and sustain success over time is the storyboard. This article illustrates the use of the storyboard as the framework for reducing length of stay--one of the most important problems facing healthcare organizations today.

Permanence induced by life-cycle resonances: the periodical cicada problem.

PubMed

Kon, Ryusuke

2012-01-01

Periodical cicadas are known for their unusually long life cycle for insects and their prime periodicity of either 13 or 17 years. One of the explanations for the prime periodicity is that the prime periods are selected to prevent cicadas from resonating with predators with submultiple periods. This paper considers this hypothesis by investigating a population model for periodical predator and prey. The study shows that if the periods of the two periodical species are not coprime, then the predator cannot resist the invasion of the prey. On the other hand, if the periods are coprime, then the predator can resist the invasion of the prey. It is also shown that if the periods are not coprime, then the life-cycle resonance can induce a permanent system, in which no cohorts are missing in both populations. On the other hand, if the periods are coprime, then the system cannot be permanent.

RNA Modulates the Interaction between Influenza A Virus NS1 and Human PABP1.

PubMed

Arias-Mireles, Bryan H; de Rozieres, Cyrus M; Ly, Kevin; Joseph, Simpson

2018-05-25

Nonstructural protein 1 (NS1) is a multifunctional protein involved in preventing host-interferon response in influenza A virus (IAV). Previous studies have indicated that NS1 also stimulates the translation of viral mRNA by binding to conserved sequences in the viral 5'-UTR. Additionally, NS1 binds to poly(A) binding protein 1 (PABP1) and eukaryotic initiation factor 4G (eIF4G). The interaction of NS1 with the viral 5'-UTR, PABP1, and eIF4G has been suggested to specifically enhance the translation of viral mRNAs. In contrast, we report that NS1 does not directly bind to sequences in the viral 5'-UTR, indicating that NS1 is not responsible for providing the specificity to stimulate viral mRNA translation. We also monitored the interaction of NS1 with PABP1 using a new, quantitative FRET assay. Our data show that NS1 binds to PABP1 with high affinity; however, the binding of double-stranded RNA (dsRNA) to NS1 weakens the binding of NS1 to PABP1. Correspondingly, the binding of PABP1 to NS1 weakens the binding of NS1 to double-stranded RNA (dsRNA). In contrast, the affinity of PABP1 for binding to poly(A) RNA is not significantly changed by NS1. We propose that the modulation of NS1·PABP1 interaction by dsRNA may be important for the viral cycle.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ogami, Koichi; Cho, Rihe; Hoshino, Shin-ichi, E-mail: hoshino@phar.nagoya-cu.ac.jp

Highlights: ► So far, only an enzymatically inactive isoform of PAPD7 was reported. ► The novel isoform: PAPD7 l shows robust nucleotidyl transferase activity. ► The newly identified amino terminal region is required for the activity. ► PAPD7 l localizes to the nucleoplasm. ► The N terminal region identified is also required for the nuclear localization. - Abstract: Non-canonical poly(A) polymerases (ncPAPs) catalyze the addition of poly(A) tail to the 3′ end of RNA to play pivotal roles in the regulation of gene expression and also in quality control. Here we identified a novel isoform of the 7th member ofmore » ncPAPs: PAPD7 (PAPD7 l), which contains 230 extra amino acids at the amino terminus of the previously identified PAPD7 (PAPD7 s). In sharp contrast to the inactive PAPD7 s, PAPD7 l showed robust nucleotidyl transferase activity when tethered to an RNA. A region required for the activity was localized to 187–219 aa, and this region was also required for the nuclear retention of PAPD7 l. Western blot analysis revealed that 94 kDa band (corresponding to PAPD7 l) but not 62 kDa band (corresponding to PAPD7 s) detected by PAPD7 antibody was specifically depleted by treatment with PAPD7 siRNA in both HeLa and U2OS cells. These results suggest that PAPD7 l is the major and active isoform of PAPD7 expressed in cells.« less

Human SUV3 helicase regulates growth rate of the HeLa cells and can localize in the nucleoli.

PubMed

Szewczyk, Maciej; Fedoryszak-Kuśka, Natalia; Tkaczuk, Katarzyna; Dobrucki, Jurek; Waligórska, Agnieszka; Stępień, Piotr P

2017-01-01

The human SUV3 helicase (SUV3, hSUV3, SUPV3L1) is a DNA/RNA unwinding enzyme belonging to the class of DexH-box helicases. It localizes predominantly in the mitochondria, where it forms an RNA-degrading complex called mitochondrial degradosome with exonuclease PNP (polynucleotide phosphorylase). Association of this complex with the polyA polymerase can modulate mitochondrial polyA tails. Silencing of the SUV3 gene was shown to inhibit the cell cycle and to induce apoptosis in human cell lines. However, since small amounts of the SUV3 helicase were found in the cell nuclei, it was not clear whether the observed phenotypes of SUV3 depletion were of mitochondrial or nuclear origin. In order to answer this question we have designed gene constructs able to inhibit the SUV3 activity exclusively in the cell nuclei. The results indicate that the observed growth rate impairment upon SUV3 depletion is due to its nuclear function(s). Unexpectedly, overexpression of the nuclear-targeted wild-type copies of the SUV3 gene resulted in a higher growth rate. In addition, we demonstrate that the SUV3 helicase can be found in the HeLa cell nucleoli, but it is not detectable in the DNA-repair foci. Our results indicate that the nucleolar-associated human SUV3 protein is an important factor in regulation of the cell cycle.

Aberrant termination of reproduction-related TMEM30C transcripts in the hominoids.

PubMed

Osada, Naoki; Hashimoto, Katsuyuki; Hirai, Momoki; Kusuda, Jun

2007-05-01

Finding genetic novelties that may contribute to human-specific physiology and diseases is a key issue of current biomedical studies. TMEM30C is a gene containing two transmembrane (TM) domains and homologous to the yeast CDC50 family, which is related to polarized cell division. It is conserved among mammals along with two other paralogs, TMEM30A and TMEM30B. We found that TMEM30C is expressed specifically in the testis of mammals, in contrast to the relatively wide expression distributions of the other paralogs. While macaques expressed two alternative splicing isoforms which include one or two TM domains, humans and chimpanzees predominantly expressed truncated transcripts because of the mutations in the splicing and/or poly(A) signal sites. The major transcript in humans harbored non-stop ORF (open reading frame) while the chimpanzee counterpart encoded a protein with one TM domain. The difference was due to the 1-bp indel upstream of the poly(A) signal site. In addition, both the hominoids expressed minor transcripts encoding short proteins with one TM domain. Phylogenetic analysis has showed the acceleration of amino acid substitution after the human and chimpanzee divergence, which may have been caused by a recent relaxation in functional constraints or positive selection on TMEM30C. Elucidating the precise reproductive function of TMEM30C in mammals will be important to the foundation of divergence in higher primates at a molecular level.

The Novel Poly(A) Polymerase Star-PAP is a Signal-Regulated Switch at the 3′-end of mRNAs

PubMed Central

Li, Weimin; Laishram, Rakesh S.; Anderson, Richard A.

2013-01-01

The mRNA 3′-untranslated region (3′-UTR) modulates message stability, transport, intracellular location and translation. We have discovered a novel nuclear poly(A) polymerase termed Star-PAP (nuclear speckle targeted PIPKIα regulated-poly(A) polymerase) that couples with the transcriptional machinery and is regulated by the phosphoinositide lipid messenger phosphatidylinositol-4,5-bisphosphate (PI4,5P2), the central lipid in phosphoinositide signaling. PI4,5P2 is generated primarily by type I phosphatidylinositol phosphate kinases (PIPKI). Phosphoinositides are present in the nucleus including at nuclear speckles compartments separate from known membrane structures. PIPKs regulate cellular functions by interacting with PI4,5P2 effectors where PIPKs generate PI4,5P2 that then modulates the activity of the associated effectors. Nuclear PIPKIα interacts with and regulates Star-PAP, and PI4,5P2 specifically activates Star-PAP in a gene- and signaling-dependent manner. Importantly, other select signaling molecules integrated into the Star-PAP complex seem to regulate Star-PAP activities and processivities toward RNA substrates, and unique sequence elements around the Star-PAP binding sites within the 3′-UTR of target genes contribute to Star-PAP specificity for processing. Therefore, Star-PAP and its regulatory molecules form a signaling nexus at the 3′-end of target mRNAs to control the expression of select group of genes including the ones involved in stress responses. PMID:23306079

Structure of an Rrp6-RNA exosome complex bound to poly(A) RNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wasmuth, Elizabeth V.; Januszyk, Kurt; Lima, Christopher D.

The eukaryotic RNA exosome processes and degrades RNA by directing substrates to the distributive or processive 3' to 5' exoribonuclease activities of Rrp6 or Rrp44, respectively. The non-catalytic nine-subunit exosome core (Exo9) features a prominent central channel. Although RNA can pass through the channel to engage Rrp44, it is not clear how RNA is directed to Rrp6 or whether Rrp6 uses the central channel. Here we report a 3.3 Å crystal structure of a ten-subunit RNA exosome complex from Saccharomyces cerevisiae composed of the Exo9 core and Rrp6 bound to single-stranded poly(A) RNA. The Rrp6 catalytic domain rests on topmore » of the Exo9 S1/KH ring above the central channel, the RNA 3' end is anchored in the Rrp6 active site, and the remaining RNA traverses the S1/KH ring in an opposite orientation to that observed in a structure of a Rrp44-containing exosome complex. Solution studies with human and yeast RNA exosome complexes suggest that the RNA path to Rrp6 is conserved and dependent on the integrity of the S1/KH ring. Although path selection to Rrp6 or Rrp44 is stochastic in vitro, the fate of a particular RNA may be determined in vivo by the manner in which cofactors present RNA to the RNA exosome.« less

hnRNP L controls HPV16 RNA polyadenylation and splicing in an Akt kinase-dependent manner

PubMed Central

Kajitani, Naoko; Glahder, Jacob; Wu, Chengjun; Yu, Haoran; Nilsson, Kersti

2017-01-01

Abstract Inhibition of the Akt kinase activates HPV16 late gene expression by reducing HPV16 early polyadenylation and by activating HPV16 late L1 mRNA splicing. We identified ‘hot spots’ for RNA binding proteins at the early polyA signal and at splice sites on HPV16 late mRNAs. We observed that hnRNP L was associated with sequences at all HPV16 late splice sites and at the early polyA signal. Akt kinase inhibition resulted in hnRNP L dephosphorylation and reduced association of hnRNP L with HPV16 mRNAs. This was accompanied by an increased binding of U2AF65 and Sam68 to HPV16 mRNAs. Furthermore, siRNA knock-down of hnRNP L or Akt induced HPV16 gene expression. Treatment of HPV16 immortalized keratinocytes with Akt kinase inhibitor reduced hnRNP L binding to HPV16 mRNAs and induced HPV16 L1 mRNA production. Finally, deletion of the hnRNP L binding sites in HPV16 subgenomic expression plasmids resulted in activation of HPV16 late gene expression. In conclusion, the Akt kinase inhibits HPV16 late gene expression at the level of RNA processing by controlling the RNA-binding protein hnRNP L. We speculate that Akt kinase activity upholds an intracellular milieu that favours HPV16 early gene expression and suppresses HPV16 late gene expression. PMID:28934469

Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo (Phyllostachys edulis).

PubMed

Wang, Taotao; Wang, Huiyuan; Cai, Dawei; Gao, Yubang; Zhang, Hangxiao; Wang, Yongsheng; Lin, Chentao; Ma, Liuyin; Gu, Lianfeng

2017-08-01

Moso bamboo (Phyllostachys edulis) represents one of the fastest-spreading plants in the world, due in part to its well-developed rhizome system. However, the post-transcriptional mechanism for the development of the rhizome system in bamboo has not been comprehensively studied. We therefore used a combination of single-molecule long-read sequencing technology and polyadenylation site sequencing (PAS-seq) to re-annotate the bamboo genome, and identify genome-wide alternative splicing (AS) and alternative polyadenylation (APA) in the rhizome system. In total, 145 522 mapped full-length non-chimeric (FLNC) reads were analyzed, resulting in the correction of 2241 mis-annotated genes and the identification of 8091 previously unannotated loci. Notably, more than 42 280 distinct splicing isoforms were derived from 128 667 intron-containing full-length FLNC reads, including a large number of AS events associated with rhizome systems. In addition, we characterized 25 069 polyadenylation sites from 11 450 genes, 6311 of which have APA sites. Further analysis of intronic polyadenylation revealed that LTR/Gypsy and LTR/Copia were two major transposable elements within the intronic polyadenylation region. Furthermore, this study provided a quantitative atlas of poly(A) usage. Several hundred differential poly(A) sites in the rhizome-root system were identified. Taken together, these results suggest that post-transcriptional regulation may potentially have a vital role in the underground rhizome-root system. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Parallel Optimization of Polynomials for Large-scale Problems in Stability and Control

NASA Astrophysics Data System (ADS)

Kamyar, Reza

In this thesis, we focus on some of the NP-hard problems in control theory. Thanks to the converse Lyapunov theory, these problems can often be modeled as optimization over polynomials. To avoid the problem of intractability, we establish a trade off between accuracy and complexity. In particular, we develop a sequence of tractable optimization problems --- in the form of Linear Programs (LPs) and/or Semi-Definite Programs (SDPs) --- whose solutions converge to the exact solution of the NP-hard problem. However, the computational and memory complexity of these LPs and SDPs grow exponentially with the progress of the sequence - meaning that improving the accuracy of the solutions requires solving SDPs with tens of thousands of decision variables and constraints. Setting up and solving such problems is a significant challenge. The existing optimization algorithms and software are only designed to use desktop computers or small cluster computers --- machines which do not have sufficient memory for solving such large SDPs. Moreover, the speed-up of these algorithms does not scale beyond dozens of processors. This in fact is the reason we seek parallel algorithms for setting-up and solving large SDPs on large cluster- and/or super-computers. We propose parallel algorithms for stability analysis of two classes of systems: 1) Linear systems with a large number of uncertain parameters; 2) Nonlinear systems defined by polynomial vector fields. First, we develop a distributed parallel algorithm which applies Polya's and/or Handelman's theorems to some variants of parameter-dependent Lyapunov inequalities with parameters defined over the standard simplex. The result is a sequence of SDPs which possess a block-diagonal structure. We then develop a parallel SDP solver which exploits this structure in order to map the computation, memory and communication to a distributed parallel environment. Numerical tests on a supercomputer demonstrate the ability of the algorithm to efficiently utilize hundreds and potentially thousands of processors, and analyze systems with 100+ dimensional state-space. Furthermore, we extend our algorithms to analyze robust stability over more complicated geometries such as hypercubes and arbitrary convex polytopes. Our algorithms can be readily extended to address a wide variety of problems in control such as Hinfinity synthesis for systems with parametric uncertainty and computing control Lyapunov functions.

How Many Pupils Are Being Excluded?

ERIC Educational Resources Information Center

Stirling, Margaret

1992-01-01

This article examines the problem of British children permanently excluded from school, especially those excluded "unofficially" usually for behavioral difficulties. The article presents evidence of the incidence of unofficial exclusions, schools' options for dealing with exclusions, possible consequences of exclusions, and possible…

Kicking the Silver Habit: Confessions of a Former Addict.

ERIC Educational Resources Information Center

Spaulding, Carl M.

1978-01-01

Reviews and compares three types of microfilm--silver halide, diazo, and vesicular. Storage and handing requirements for permanent collections are discussed, and some suggestions are offered to solve problems caused by the proliferation of nonsilver films in libraries. (MBR)

Generation of RNA in abiotic conditions.

NASA Astrophysics Data System (ADS)

di Mauro, Ernesto

Generation of RNA in abiotic conditions. Ernesto Di Mauro Dipartimento di Genetica Bi-ologia Molecolare, Universit` "Sapienza" Roma, Italy. a At least four conditions must be satisfied for the spontaneous generation of (pre)-genetic poly-mers: 1) availability of precursors that are activated enough to spontaneously polymerize. Preliminary studies showed that (a) nucleic bases and acyclonucleosides can be synthesized from formamide H2NCOH by simply heating with prebiotically available mineral catalysts [last reviewed in (1)], and that b) nucleic bases can be phosphorylated in every possible posi-tion [2'; 3'; 5'; cyclic 2',3'; cyclic 3',5' (2)]. The higher stability of the cyclic forms allows their accumulation. 2) A polymerization mechanism. A reaction showing the formation of RNA polymers starting from prebiotically plausible precursors (3',5' cyclic GMP and 3', 5'cyclic AMP) was recently reported (3). Polymerization in these conditions is thermodynamically up-hill and an equilibrium is attained that limits the maximum length of the polymer produced to about 40 nucleotides for polyG and 100 nucleotides for polyA. 3) Ligation of the synthesized oligomers. If this type of reaction could occur according to a terminal-joining mechanism and could generate canonical 3',5' phosphodiester bonds, exponential growth would be obtained of the generated oligomers. This type of reaction has been reported (4) , limited to homogeneous polyA sequences and leading to the production of polyA dimers and tetramers. What is still missing are: 4) mechanisms that provide the proof of principle for the generation of sequence complexity. We will show evidence for two mechanisms providing this proof of principle for simple complementary sequences. Namely: abiotic sequence complementary-driven terminal ligation and sequence-complementary terminal growth. In conclusion: all the steps leading to the generation of RNA in abiotic conditions are satisfied. (1) R Saladino, C Crestini, F. Ciciriello, S. Pino, G. Costanzo, E. Di Mauro. From formamide to RNA: the roles of formamide and water in the evolution of chemical information. Research In Microbiology, Special Issue on The Origin of life and Microbiology (2009) 160:441-448. (2) Costanzo, G., Saladino, R., Crestini, C., Ciciriello, F., and Di Mauro, E. Nucleoside phos-phorylation by phosphate minerals. J. Biol. Chem. (2007) 282: 16729-16735. (3) Samanta Pino, Fabiana Ciciriello, Giovanna Costanzo and E. Di Mauro, Nonenzymatic RNA Ligation in Water J. Biol. Chem. (2008), 283: 36494-36503 (4) Costanzo, G., Pino, S., Ciciriello, F., and Di Mauro, E. Generation of long RNA chains in water. J Biol Chem. (2009) 284:33206-33216.

OpenSees

Science.gov Websites

, through soil-structure interaction, to structural response. New computer simulation tools are necessary to of structures and soils to investigate challenging problems in soil-structure-foundation interaction including foundations and soils is used to study the effects of soil liquefaction and permanent

An Online Observer for Minimization of Pulsating Torque in SMPM Motors

PubMed Central

Roșca, Lucian

2016-01-01

A persistent problem of surface mounted permanent magnet (SMPM) motors is the non-uniformity of the developed torque. Either the motor design or the motor control needs to be improved in order to minimize the periodic disturbances. This paper proposes a new control technique for reducing periodic disturbances in permanent magnet (PM) electro-mechanical actuators, by advancing a new observer/estimator paradigm. A recursive estimation algorithm is implemented for online control. The compensating signal is identified and added as feedback to the control signal of the servo motor. Compensation is evaluated for different values of the input signal, to show robustness of the proposed method. PMID:27089182

Overview of NORM and activities by a NORM licensed permanent decontamination and waste processing facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mirro, G.A.

1997-02-01

This paper presents an overview of issues related to handling NORM materials, and provides a description of a facility designed for the processing of NORM contaminated equipment. With regard to handling NORM materials the author discusses sources of NORM, problems, regulations and disposal options, potential hazards, safety equipment, and issues related to personnel protection. For the facility, the author discusses: description of the permanent facility; the operations of the facility; the license it has for handling specific radioactive material; operating and safety procedures; decontamination facilities on site; NORM waste processing capabilities; and offsite NORM services which are available.

Predictive control of a chaotic permanent magnet synchronous generator in a wind turbine system

NASA Astrophysics Data System (ADS)

Manal, Messadi; Adel, Mellit; Karim, Kemih; Malek, Ghanes

2015-01-01

This paper investigates how to address the chaos problem in a permanent magnet synchronous generator (PMSG) in a wind turbine system. Predictive control approach is proposed to suppress chaotic behavior and make operating stable; the advantage of this method is that it can only be applied to one state of the wind turbine system. The use of the genetic algorithms to estimate the optimal parameter values of the wind turbine leads to maximization of the power generation. Moreover, some simulation results are included to visualize the effectiveness and robustness of the proposed method. Project supported by the CMEP-TASSILI Project (Grant No. 14MDU920).

Trading permanent and temporary carbon emissions credits

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marland, Gregg; Marland, Eric

2009-08-01

In this issue of Climatic Change, Van Kooten (2009) addresses an issue that has bedeviled negotiators since the drafting stage of the Kyoto Protocol. If we accept that increasing withdrawals of carbon dioxide from the atmpshere has the same net impact on the climate system as reducing emissions of carbon dioxide to the atmosphere, how do we design a system that allows trading of one for the other? As van Kooten expresses the challenge: 'The problem is that emissions reduction and carbon sequestration, while opposite sides of the same coin in some sense, are not directly comparable, thereby inhibiting theirmore » trade in carbon markets.' He explains: 'The difficulty centers on the length of time that mitigation strategies without CO{sub 2} from entering the atmosphere - the duration problem.' While reducing emissions of CO{sub 2} represents an essentially permanent benefit for the atmosphere, capturing CO{sub 2} that has been produced (whether capture is from the atmosphere or directly from, for example, the exhaust from power plants) there is the challenge of storing the carbon adn the risk that it will yet escape to the atmosphere. Permanent benefit to the atmosphere is often not assured for carbon sequestration activities. This is especially true if the carbon is taken up and stored in the biosphere - e.g. in forest trees or agricultural soils.« less

Supportive Communication to Facilitate Chinese Patients' Adaptation to a Permanent Colostomy: A Qualitative Case Study Approach.

PubMed

Tao, Hui; Songwathana, Praneed; Isaramalai, Sang-Arun; Wang, Qingxi

2016-01-01

This study, which is a part of action research, aims to explore how supportive communication can impact individuals' adaptation to a permanent colostomy in a Chinese cultural context. Two Chinese rectal cancer patients with complexity and difficulty in living with a permanent colostomy were selected using a qualitative case study approach. The researcher (H.T.) interacted with the participants along their journey from the preoperative period until the third postoperative month after discharge via face-to-face or telephone interviews. Content analysis was applied. Supportive communication was characterized by "communication as a supportive tool," which consisted of 4 elements: respect, description, empathy, and empowerment. The nursing strategies included (1) developing a collaborative relationship with patients and families; (2) understanding patients' concerns and problems; (3) discussing potential solutions; (4) encouraging patients to take action; (5) bringing out emotional expression; (6) normalizing negative emotions; and (7) protecting hope. The findings of this study informed that supportive communication is a valuable tool for nurses to provide informational and emotional support to Chinese patients in order to enhance their adaptation to living with a permanent colostomy. Developing an operational manual to enhance supportive communication for patients with colostomy is suggested.

Generalized concurrence in boson sampling.

PubMed

Chin, Seungbeom; Huh, Joonsuk

2018-04-17

A fundamental question in linear optical quantum computing is to understand the origin of the quantum supremacy in the physical system. It is found that the multimode linear optical transition amplitudes are calculated through the permanents of transition operator matrices, which is a hard problem for classical simulations (boson sampling problem). We can understand this problem by considering a quantum measure that directly determines the runtime for computing the transition amplitudes. In this paper, we suggest a quantum measure named "Fock state concurrence sum" C S , which is the summation over all the members of "the generalized Fock state concurrence" (a measure analogous to the generalized concurrences of entanglement and coherence). By introducing generalized algorithms for computing the transition amplitudes of the Fock state boson sampling with an arbitrary number of photons per mode, we show that the minimal classical runtime for all the known algorithms directly depends on C S . Therefore, we can state that the Fock state concurrence sum C S behaves as a collective measure that controls the computational complexity of Fock state BS. We expect that our observation on the role of the Fock state concurrence in the generalized algorithm for permanents would provide a unified viewpoint to interpret the quantum computing power of linear optics.

Functional Analysis of Chk2-Kiaa0170 Interaction

DTIC Science & Technology

2006-09-01

terminal repeat; NEO, neomycin resistance gene; pA, poly-A; PGK, phosphoglycerate kinase-1; BTK , Bru- ton’s tyrosine kinase; SA and SD, splice acceptor...Briefly, MEFs were lysed in buffer I (50 mM HEPES [pH 7.5], 150 mM NaCl, 1 mM EDTA, 0.05% NP40, and protease and phosphatase inhibitors ) for 5 min on...0.5% DOC, 0.1% SDS, and protease and phosphatase inhibitors ) on ice for 20 min. The extracts were centrifuged at 14,000 rpm for 20 min at 4ºC. The

Detection of a divergent variant of grapevine virus F by next-generation sequencing.

PubMed

Molenaar, Nicholas; Burger, Johan T; Maree, Hans J

2015-08-01

The complete genome sequence of a South African isolate of grapevine virus F (GVF) is presented. It was first detected by metagenomic next-generation sequencing of field samples and validated through direct Sanger sequencing. The genome sequence of GVF isolate V5 consists of 7539 nucleotides and contains a poly(A) tail. It has a typical vitivirus genome arrangement that comprises five open reading frames (ORFs), which share only 88.96 % nucleotide sequence identity with the existing complete GVF genome sequence (JX105428).

Novel dicistrovirus from bat guano.

PubMed

Reuter, Gábor; Pankovics, Péter; Gyöngyi, Zoltán; Delwart, Eric; Boros, Akos

2014-12-01

A novel dicistrovirus (strain NB-1/2011/HUN, KJ802403) genome was detected from guano collected from an insectivorous bat (species Pipistrellus pipistrellus) in Hungary, using viral metagenomics. The complete genome of NB-1 is 9136 nt in length, excluding the poly(A) tail. NB-1 has a genome organization typical of a dicistrovirus with multiple 3B(VPg) and a cripavirus-like intergenic region (IGR)-IRES. NB-1 shares only 41 % average amino acid sequence identity with capsid proteins of Himetobi P virus, indicating a potential novel species in the genus Cripavirus, family Dicistroviridae.

CONTROL OF CHELATOR-BASED UPSETS IN SURFACE FINISHING SHOP WASTE WATER TREATMENT SYSTEMS

EPA Science Inventory

Actual surface finishing shop examples are used to illustrate the use of process chemistry understanding and analyses to identify immediate, interim and permanent response options for industrial waste water treatment plant (IWTP) upset problems caused by chelating agents. There i...

Sensorless control for permanent magnet synchronous motor using a neural network based adaptive estimator

NASA Astrophysics Data System (ADS)

Kwon, Chung-Jin; Kim, Sung-Joong; Han, Woo-Young; Min, Won-Kyoung

2005-12-01

The rotor position and speed estimation of permanent-magnet synchronous motor(PMSM) was dealt with. By measuring the phase voltages and currents of the PMSM drive, two diagonally recurrent neural network(DRNN) based observers, a neural current observer and a neural velocity observer were developed. DRNN which has self-feedback of the hidden neurons ensures that the outputs of DRNN contain the whole past information of the system even if the inputs of DRNN are only the present states and inputs of the system. Thus the structure of DRNN may be simpler than that of feedforward and fully recurrent neural networks. If the backpropagation method was used for the training of the DRNN the problem of slow convergence arise. In order to reduce this problem, recursive prediction error(RPE) based learning method for the DRNN was presented. The simulation results show that the proposed approach gives a good estimation of rotor speed and position, and RPE based training has requires a shorter computation time compared to backpropagation based training.

Number-Theory in Nuclear-Physics in Number-Theory: Non-Primality Factorization As Fission VS. Primality As Fusion; Composites' Islands of INstability: Feshbach-Resonances?

NASA Astrophysics Data System (ADS)

Smith, A.; Siegel, Edward Carl-Ludwig

2011-03-01

Numbers: primality/indivisibility/non-factorization versus compositeness/divisibility/ factorization, often in tandem but not always, provocatively close analogy to nuclear-physics: (2 + 1)=(fusion)=3; (3+1)=(fission)=4[=2 x 2]; (4+1)=(fusion)=5; (5 +1)=(fission)=6[=2 x 3]; (6 + 1)=(fusion)=7; (7+1)=(fission)=8[= 2 x 4 = 2 x 2 x 2]; (8 + 1) =(non: fission nor fusion)= 9[=3 x 3]; then ONLY composites' Islands of fusion-INstability: 8, 9, 10; then 14, 15, 16, ... Could inter-digit Feshbach-resonances exist??? Possible applications to: quantum-information/ computing non-Shore factorization, millennium-problem Riemann-hypotheses proof as Goodkin BEC intersection with graph-theory "short-cut" method: Rayleigh(1870)-Polya(1922)-"Anderson"(1958)-localization, Goldbach-conjecture, financial auditing/accounting as quantum-statistical-physics; ...abound!!! Watkins [www.secamlocal.ex.ac.uk/people/staff/mrwatkin/] "Number-Theory in Physics" many interconnections: "pure"-maths number-theory to physics including Siegel [AMS Joint Mtg.(2002)-Abs.# 973-60-124] inversion of statistics on-average digits' Newcomb(1881)-Weyl(14-16)-Benford(38)-law to reveal both the quantum and BEQS (digits = bosons = digits:"spinEless-boZos"). 1881 1885 1901 1905 1925 < 1927, altering quantum-theory history!!!

Complexes of mismatched and complementary DNA with minor groove binders. Structures at nucleotide resolution via an improved hydroxyl radical cleavage methodology

PubMed Central

Bialonska, Dobroslawa; Song, Kenneth; Bolton, Philip H.

2011-01-01

Tumor cell lines can replicate faster than normal cells and many also have defective DNA repair pathways. This has lead to the investigation of the inhibition of DNA repair proteins as a means of therapeutic intervention. An alternative approach is to hide or mask damaged DNA from the repair systems. We have developed a protocol to investigate the structures of the complexes of damaged DNA with drug like molecules. Nucleotide resolution structural information can be obtained using an improved hydroxyl radical cleavage protocol. The use of a dTn tail increases the length of the smallest fragments of interest and allows efficient co-precipitation of the fragments with poly(A). The use of a fluorescent label, on the 5′ end of the dTn tail, in conjunction with modified cleavage reaction conditions, avoids the lifetime and other problems with 32P labeling. The structures of duplex DNAs containing AC and CC mismatches in the presence and absence of minor groove binders have been investigated as have those of the fully complementary DNA. The results indicate that the structural perturbations of the mismatches are localized, are sequence dependent and that the presence of a mismatch can alter the binding of drug like molecules. PMID:21893212

Site partitioning for distributed redundant disk arrays

NASA Technical Reports Server (NTRS)

Mourad, Antoine N.; Fuchs, W. K.; Saab, Daniel G.

1992-01-01

Distributed redundant disk arrays can be used in a distributed computing system or database system to provide recovery in the presence of temporary and permanent failures of single sites. In this paper, we look at the problem of partitioning the sites into redundant arrays in such way that the communication costs for maintaining the parity information are minimized. We show that the partitioning problem is NP-complete and we propose two heuristic algorithms for finding approximate solutions.

Comparison of fundamental and simulative test methods for evaluating permanent deformation of hot mix asphalt

DOT National Transportation Integrated Search

2002-10-01

Rutting has long been a problem in hot mix asphalt (HMA) pavement. Through the years, researchers have used different kinds of fundamental and simulative test methods to estimate the rutting performance of HMA. It has been recognized that most fundam...

Malnutrition, Learning, and Behavior.

ERIC Educational Resources Information Center

Read, Merrill S.; Felson, David

The problems of those children who are chronically malnourished, the cultural environment of malnutrition, and the extent to which children are temporarily or permanently handicapped in learning because of malnutrition are discussed in this booklet. It also describes hunger and its effects on child development. The topics addressed are: definition…

The Object Permanence Fallacy.

ERIC Educational Resources Information Center

Greenberg, Daniel E.

1996-01-01

Developmentalists have overlooked the problem of the real impermanence of things. Though the metaphor of impermanence is central to Piagetian and neo-nativist accounts of representation, the development of the understanding of impermanence is unstudied. This article proposes that the development of the concept of impermanence is distinct from the…

The Vietnam Conflict: "America's Best Documented War?"

ERIC Educational Resources Information Center

Shaughnessy, C. A.

1991-01-01

Discusses problems with military documentation during the Vietnam War. Reports poor record keeping practices, destruction of permanent files, and mislabeled and missing records. Describes the National Archives' Vietnam project that organized and preserved the remaining military records. Concludes that the Vietnam War was better documented than the…

Research on the effect of the external magnetic field in the joule balance at NIM

NASA Astrophysics Data System (ADS)

Xu, Jinxin; You, Qiang; Li, Zhengkun; Bai, Yang; Lu, Yunfeng; Zhang, Zhonghua; He, Qing

2018-06-01

The first determination of the Planck constant with the second generation of the joule balance, NIM-2, was completed in 2017 with an uncertainty of 2.4  ×  10‑7. Due to the movement of the magnet during the measurement process, the effect of the external field is a critical problem in NIM-2. At present, the electromagnet system is used in NIM-2. By taking the average of the results with positive and negative exciting currents, the uncertainty from the external field is reduced to 1.7  ×  10‑7, which is still the largest source in the uncertainty budget as all the other items are less than 1  ×  10‑7. In the near future, a permanent magnet system will be applied in NIM-2 and the main field cannot be reversed. Although the coupling of the external magnetic field in the permanent magnet system is about 40 times less than that in the electromagnet system, further reduction of this effect is still required in the permanent magnet system. In this paper, the effect of the external field is analyzed in both an electromagnet system and a permanent magnet system based on simulations and experiments. Then, the methods of magnetic shielding and compensation coils are proposed and simulated in the permanent magnet system. The results show that it may be possible to reduce the uncertainty of the external field to less than 2  ×  10‑8 in the permanent magnet system by employing the two methods.

Taking a Glance at Anterior Crossbite in Children: Case Series

PubMed Central

Ceyhan, Derya; Akdik, Canan

2017-01-01

Anterior crossbite is a malocclusion that takes place for various reasons, leads to major problems and may be fixed using various methods. This study aimed to provide an update regarding the methods used for anterior crossbite treatment presenting treatments of the removable active acrylic appliance with bite plane. Clinical examination of aged 9–15, seven healthy children who visited our clinic due to crowding and esthetic displeasure in anterior teeth indicated that one or more permanent maxillar incisor teeth were positioned behind of permanent mandibular incisor teeth. After clinical-radiographical examinations, removable active acrylic appliances with bite plane were decided to apply. Patients with adapted-activated appliances were called to follow-ups once a week. Treatments continued 4–6 weeks in mixed dentition, 7–8 weeks in permanent dentition. In choosing the method, advantages-disadvantages, indications-contraindications of methods should be discussed. Correct indication and suitable motivation are important for the success of anterior crossbite treatment. PMID:29326528

Finite element analysis of gradient z-coil induced eddy currents in a permanent MRI magnet.

PubMed

Li, Xia; Xia, Ling; Chen, Wufan; Liu, Feng; Crozier, Stuart; Xie, Dexin

2011-01-01

In permanent magnetic resonance imaging (MRI) systems, pulsed gradient fields induce strong eddy currents in the conducting structures of the magnet body. The gradient field for image encoding is perturbed by these eddy currents leading to MR image distortions. This paper presents a comprehensive finite element (FE) analysis of the eddy current generation in the magnet conductors. In the proposed FE model, the hysteretic characteristics of ferromagnetic materials are considered and a scalar Preisach hysteresis model is employed. The developed FE model was applied to study gradient z-coil induced eddy currents in a 0.5 T permanent MRI device. The simulation results demonstrate that the approach could be effectively used to investigate eddy current problems involving ferromagnetic materials. With the knowledge gained from this eddy current model, our next step is to design a passive magnet structure and active gradient coils to reduce the eddy current effects. Copyright © 2010 Elsevier Inc. All rights reserved.

Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing

PubMed Central

Shen, Yingjia; Venu, R.C.; Nobuta, Kan; Wu, Xiaohui; Notibala, Varun; Demirci, Caghan; Meyers, Blake C.; Wang, Guo-Liang; Ji, Guoli; Li, Qingshun Q.

2011-01-01

Polyadenylation sites mark the ends of mRNA transcripts. Alternative polyadenylation (APA) may alter sequence elements and/or the coding capacity of transcripts, a mechanism that has been demonstrated to regulate gene expression and transcriptome diversity. To study the role of APA in transcriptome dynamics, we analyzed a large-scale data set of RNA “tags” that signify poly(A) sites and expression levels of mRNA. These tags were derived from a wide range of tissues and developmental stages that were mutated or exposed to environmental treatments, and generated using digital gene expression (DGE)–based protocols of the massively parallel signature sequencing (MPSS-DGE) and the Illumina sequencing-by-synthesis (SBS-DGE) sequencing platforms. The data offer a global view of APA and how it contributes to transcriptome dynamics. Upon analysis of these data, we found that ∼60% of Arabidopsis genes have multiple poly(A) sites. Likewise, ∼47% and 82% of rice genes use APA, supported by MPSS-DGE and SBS-DGE tags, respectively. In both species, ∼49%–66% of APA events were mapped upstream of annotated stop codons. Interestingly, 10% of the transcriptomes are made up of APA transcripts that are differentially distributed among developmental stages and in tissues responding to environmental stresses, providing an additional level of transcriptome dynamics. Examples of pollen-specific APA switching and salicylic acid treatment-specific APA clearly demonstrated such dynamics. The significance of these APAs is more evident in the 3034 genes that have conserved APA events between rice and Arabidopsis. PMID:21813626

CKI isoforms α and ε regulate Star–PAP target messages by controlling Star–PAP poly(A) polymerase activity and phosphoinositide stimulation

PubMed Central

Laishram, Rakesh S.; Barlow, Christy A.; Anderson, Richard A.

2011-01-01

Star–PAP is a non-canonical, nuclear poly(A) polymerase (PAP) that is regulated by the lipid signaling molecule phosphatidylinositol 4,5 bisphosphate (PI4,5P2), and is required for the expression of a select set of mRNAs. It was previously reported that a PI4,5P2 sensitive CKI isoform, CKIα associates with and phosphorylates Star–PAP in its catalytic domain. Here, we show that the oxidative stress-induced by tBHQ treatment stimulates the CKI mediated phosphorylation of Star–PAP, which is critical for both its polyadenylation activity and stimulation by PI4,5P2. CKI activity was required for the expression and efficient 3′-end processing of its target mRNAs in vivo as well as the polyadenylation activity of Star–PAP in vitro. Specific CKI activity inhibitors (IC261 and CKI7) block in vivo Star–PAP activity, but the knockdown of CKIα did not equivalently inhibit the expression of Star–PAP targets. We show that in addition to CKIα, Star–PAP associates with another CKI isoform, CKIε in the Star–PAP complex that phosphorylates Star–PAP and complements the loss of CKIα. Knockdown of both CKI isoforms (α and ε) resulted in the loss of expression and the 3′-end processing of Star–PAP targets similar to the CKI activity inhibitors. Our results demonstrate that CKI isoforms α and ε modulate Star–PAP activity and regulates Star–PAP target messages. PMID:21729869

The developmental transcriptome of the mosquito Aedes aegypti, an invasive species and major arbovirus vector.

PubMed

Akbari, Omar S; Antoshechkin, Igor; Amrhein, Henry; Williams, Brian; Diloreto, Race; Sandler, Jeremy; Hay, Bruce A

2013-09-04

Mosquitoes are vectors of a number of important human and animal diseases. The development of novel vector control strategies requires a thorough understanding of mosquito biology. To facilitate this, we used RNA-seq to identify novel genes and provide the first high-resolution view of the transcriptome throughout development and in response to blood feeding in a mosquito vector of human disease, Aedes aegypti, the primary vector for Dengue and yellow fever. We characterized mRNA expression at 34 distinct time points throughout Aedes development, including adult somatic and germline tissues, by using polyA+ RNA-seq. We identify a total of 14,238 novel new transcribed regions corresponding to 12,597 new loci, as well as many novel transcript isoforms of previously annotated genes. Altogether these results increase the annotated fraction of the transcribed genome into long polyA+ RNAs by more than twofold. We also identified a number of patterns of shared gene expression, as well as genes and/or exons expressed sex-specifically or sex-differentially. Expression profiles of small RNAs in ovaries, early embryos, testes, and adult male and female somatic tissues also were determined, resulting in the identification of 38 new Aedes-specific miRNAs, and ~291,000 small RNA new transcribed regions, many of which are likely to be endogenous small-interfering RNAs and Piwi-interacting RNAs. Genes of potential interest for transgene-based vector control strategies also are highlighted. Our data have been incorporated into a user-friendly genome browser located at www.Aedes.caltech.edu, with relevant links to Vectorbase (www.vectorbase.org).

Enzymes Involved in Post-transcriptional RNA Metabolism in Gram-negative bacteria

PubMed Central

Mohanty, Bijoy K.

2018-01-01

Gene expression in Gram-negative bacteria is regulated at many levels, including transcription initiation, RNA processing, RNA/RNA interactions, mRNA decay, and translational controls involving enzymes that alter translational efficiency. In this chapter we discuss the various enzymes that control transcription, translation and RNA stability through RNA processing and degradation. RNA processing is essential to generate functional RNAs, while degradation helps control the steady-state level of each individual transcript. For example, all the pre-tRNAs are transcribed with extra nucleotides at both their 5′ and 3′ termini, which are subsequently processed to produce mature tRNAs that can be aminoacylated. Similarly, rRNAs that are transcribed as part of a 30S polycistronic transcript, are matured to individual 16S, 23S and 5S rRNAs. Decay of mRNAs plays a key role in gene regulation through controlling the steady-state level of each transcript, which is essential for maintaining appropriate protein levels. In addition, degradation of both translated and non-translated RNAs recycles nucleotides to facilitate new RNA synthesis. To carry out all these reactions Gram-negative bacteria employ a large number of endonucleases, exonucleases, RNA helicases, and poly(A) polymerase as well as proteins that regulate the catalytic activity of particular ribonucleases. Under certain stress conditions an additional group of specialized endonucleases facilitate the cell’s ability to adapt and survive. Many of the enzymes, such as RNase E, RNase III, polynucleotide phosphorylase, RNase R, and poly(A) polymerase I participate in multiple RNA processing and decay pathways. PMID:29676246

[Interaction of trivaline with single-stranded polyribonucleotides].

PubMed

Strel'tsov, S A; Lysov, Iu P; Semenov, T E; Vengerov, Iu Iu; Khorlin, A A; Surovaia, A N; Gurskiĭ, G V

1991-01-01

Binding of tripeptide H-Val3-(NH)2-Dns (TVP) to polyribonucleotides was studied by fluorescence methods, circular and flow linear dichroism, equilibrium dialysis and electron microscopy. It was found that TVP binds to poly(U) in monomer, dimer and tetramer forms with binding constants of about 10(3), 40, 18.10(4) M, respectively. The cooperativity parameter for peptide dimer binding is 2000. The peptide forms tetramer complexes with poly(A), poly(C), poly(G) also. The formation of a complex between the peptide tetramer and nucleic acid is accompanied by a significant increase in the fluorescence intensity. The cooperative binding of TVP dimers to poly(U), poly(A), poly(C) is accompanied by a dramatic decrease in the flexibility of polynucleotide chains. However, it has a small effect (if any) on the flexibility of the poly(G) chain. The observed similarity of thermodynamic, optical and hydrodynamic++ properties of TVP complexes with single-stranded and double-stranded nucleic acids may reflect a similarity in the geometries of peptide complexes with nucleic acids. Electron microscopy studies show that peptide binding to poly(U) and dsDNA leads to compactization of the nucleic acids caused by interaction between the peptide tetramers bound to a nucleic acid. At the first stage of the compactization process the well-organized rod-like particles are formed, each consisting of one or more single-stranded polynucleotide fibers. Increasing the peptide concentration stimulates a side-by-side association and folding of the rods with the formation of macromolecular "leech-like" structures with the thickness of 20-50 nm.

Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq.

PubMed

Macaulay, Iain C; Teng, Mabel J; Haerty, Wilfried; Kumar, Parveen; Ponting, Chris P; Voet, Thierry

2016-11-01

Parallel sequencing of a single cell's genome and transcriptome provides a powerful tool for dissecting genetic variation and its relationship with gene expression. Here we present a detailed protocol for G&T-seq, a method for separation and parallel sequencing of genomic DNA and full-length polyA(+) mRNA from single cells. We provide step-by-step instructions for the isolation and lysis of single cells; the physical separation of polyA(+) mRNA from genomic DNA using a modified oligo-dT bead capture and the respective whole-transcriptome and whole-genome amplifications; and library preparation and sequence analyses of these amplification products. The method allows the detection of thousands of transcripts in parallel with the genetic variants captured by the DNA-seq data from the same single cell. G&T-seq differs from other currently available methods for parallel DNA and RNA sequencing from single cells, as it involves physical separation of the DNA and RNA and does not require bespoke microfluidics platforms. The process can be implemented manually or through automation. When performed manually, paired genome and transcriptome sequencing libraries from eight single cells can be produced in ∼3 d by researchers experienced in molecular laboratory work. For users with experience in the programming and operation of liquid-handling robots, paired DNA and RNA libraries from 96 single cells can be produced in the same time frame. Sequence analysis and integration of single-cell G&T-seq DNA and RNA data requires a high level of bioinformatics expertise and familiarity with a wide range of informatics tools.

Supernumerary Teeth in Primary Dentition and Early Intervention: A Series of Case Reports

PubMed Central

Bahadure, Rakesh N.; Thosar, Nilima; Jain, Eesha S.; Kharabe, Vidhi; Gaikwad, Rahul

2012-01-01

Supernumerary teeth are considered as one of the most significant dental anomalies during the primary and early mixed dentition stages. They are of great concern to the dentists and parents because of the eruption, occlusal, and esthetic problems they can cause. Supernumerary teeth occur more frequently in the permanent dentition but rarely in primary dentition. Mesiodens is the most common type of supernumerary teeth but rarely seen in lower arch. Early recognition and diagnosis of supernumerary teeth is important to prevent further complications in permanent dentition. Four cases of supernumerary teeth with mesiodens in upper and lower arch in primary dentition and their management have been discussed. PMID:22888456

A novel safety device with metal counter meshing gears discriminator directly driven by axial flux permanent magnet micromotors based on MEMS technology

NASA Astrophysics Data System (ADS)

Zhang, Weiping; Chen, Wenyuan; Zhao, Xiaolin; Li, Shengyong; Jiang, Yong

2005-08-01

In a novel safety device based on MEMS technology for high consequence systems, the discriminator consists of two groups of metal counter meshing gears and two pawl/ratchet wheel mechanisms. Each group of counter meshing gears is onepiece and driven directly by an axial flux permanent magnet micromotor respectively. The energy-coupling element is an optical shutter with two collimators and a coupler wheel. The safety device's probability is less than 1/106. It is fabricated by combination of an LiGA-like process and precision mechanical engineering. The device has simple structure, few dynamic problems, high strength and strong reliability.

[Recognizing and preventing disturbances in eruption].

PubMed

van der Linden, F P G M

2014-04-01

Disturbances in eruption and related problems are quite common in permanent dentition but rare in deciduous dentition. For the timely recognition of disturbances in eruption, knowledge of the normal development of dentition is essential. Disturbances in eruption comprise disturbances in which eruption does not occur at all, in which it is delayed or incomplete, or in which the normal direction of eruption is influenced. If identified early enough, many undesirable dental conditions can be avoided or their seriousness can be limited. A possible impacting of permanent cuspids, for example, can be avoided by extracting the deciduous cuspids at the right moment; in cases of a large overjet or the threat of a cover-bite, lip interference can be prevented.

Escape From Deja Vu: On Strengthening Teacher Education.

ERIC Educational Resources Information Center

Mertens, Sally K.; Yarger, Sam J.

1982-01-01

Efforts to reform teacher education are traced, and the need for a prestigious, permanent national body to bring educational constituencies together is proposed. Such an organization could work on national education problems, set certification standards, and do long-range planning on difficulties such as fluctuations in teacher supply and demand.…

78 FR 49735 - Intent To Prepare a Draft Environmental Impact Statement for Dam Safety Study, Lake Lewisville...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-15

... determine appropriate permanent methods for correcting potential problems, interim risk reduction measures... Environmental Impact Statement for Dam Safety Study, Lake Lewisville Dam, Elm Fork Trinity River, Denton County... primary purposes of the project are flood risk management, [[Page 49736

Pernicious anemia

MedlinePlus

... They are also more likely to develop gastric cancer and gastric carcinoid tumors. Brain and nervous system problems may continue or be permanent if treatment is delayed. A woman with a low B12 level may have a false positive Pap ... MD, Hematology/Oncology, Florida Cancer Specialists & Research Institute, Wellington, FL. Review provided by ...

Exact solution for spin precession in the radiationless relativistic Kepler problem

NASA Astrophysics Data System (ADS)

Mane, S. R.

2014-11-01

There is interest in circulating beams of polarized particles in all-electric storage rings to search for nonzero permanent electric dipole moments of subatomic particles. To this end, it is helpful to derive exact analytical solutions of the spin precession in idealized models, both for pedagogical reasons and to serve as benchmark tests for analysis and design of experiments. This paper derives exact solutions for the spin precession in the relativistic Kepler problem. Some counterintuitive properties of the solutions are pointed out.

Dental enamel defects in German medieval and early-modern-age populations.

PubMed

Lang, J; Birkenbeil, S; Bock, S; Heinrich-Weltzien, R; Kromeyer-Hauschild, K

2016-11-01

Aim of this study was to investigate the frequency and type of developmental defects of enamel (DDE) in a medieval and an early-modern-age population from Thuringia, Germany. Sixty-six skeletons subdivided into 31 single burials (12 th /13 th c.) and 35 individuals buried in groups (15 th /16 th c.) were examined. DDE were classified on 1,246 teeth according to the DDE index. Molar-incisor-hypomineralisation (MIH), a special type of DDE, was recorded according to the European Academy of Paediatric Dentistry (EAPD) criteria. DDE was found in 89.4% of the individuals (single burials 90.3% and group burials 88.6%). Hypoplastic pits were the most frequent defect in primary teeth and linear enamel hypoplasia (LEH) in permanent teeth. 13 individuals (24.1%) showed at least one hypomineralised permanent tooth, 12.2% had MIH on at least one first permanent molar and 10.0% in permanent incisors. Second primary molars were affected in 8.0% of the children and juveniles. No individual suffered from affected molars and incisors in combination. Endogenous factors like nutritional deficiencies and health problems in early childhood could have been aetiological reasons of DDE and MIH. The frequency of DDE and MIH might have been masked by extended carious lesions, dental wear and ante-mortem tooth loss.

Object permanence in the food-storing coal tit (Periparus ater) and the non-storing great tit (Parus major): Is the mental representation required?

PubMed

Marhounová, Lucie; Frynta, Daniel; Fuchs, Roman; Landová, Eva

2017-05-01

Object permanence is a cognitive ability that enables animals to mentally represent the continuous existence of temporarily hidden objects. Generally, it develops gradually through six qualitative stages, the evolution of which may be connected with some specific ecological and behavioral factors. In birds, the advanced object permanence skills were reported in several storing species of the Corvidae family. In order to test the association between food-storing and achieved performance within the stages, we compared food-storing coal tits (Periparus ater) and nonstoring great tits (Parus major) using an adapted version of Uzgiris & Hunt's Scale 1 tasks. The coal tits significantly outperformed the great tits in searching for completely hidden objects. Most of the great tits could not solve the task when the object disappeared completely. However, the upper limit for both species is likely to be Stage 4. The coal tits could solve problems with simply hidden objects, but they used alternative strategies rather than mental representation when searching for completely hidden objects, especially if choosing between two locations. Our results also suggest that neophobia did not affect the overall performance in the object permanence tasks. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Uprighting Bilateral Impacted Mandibular Permanent Second Molars with the Brass Wire Technique: A Case Report.

PubMed

Perdigão, João Paulo Veloso; Lustosa, Romulo Maciel; Tolentino, Elen de Souza; Iwaki Filho, Liogi; Iwaki, Lilian Cristina Vessoni

2016-01-01

Revalence of impaction of mandibular permanent second molars is between 0.06 and 2.3 percent. In order to reduce treatment time and complications associated with tooth impaction, intervention should take place once the problem is detected. The usual treatment options consists of surgical exposure, luxation of the impacted tooth, extraction of adjacent third molar, orthodontic treatment, and uprighting with brass wires or mini-screws. The present paper reports a case of bilateral impaction of mandibular permanent second molars ' (MM2s) treated with extraction of the mandibular third molars (MM3s) and surgical-orthodontic uprighting with the brass wire technique. The MM3s were removed, and the impacted MM2s were surgically exposed. Brass wire was placed apicaly to the mesial of the MM2 from the lingual tissue out toward the buccal. The lingual end of the wire was bent over the area of contact and twisted with the buccal end Monthly wire tightening gradually moved the MM2s distally and towards the occlusal plane. Uprighting was achieved in 4-5 months, with discrete pain caused by activation of the wire. This technique proved to be a simple, low-cost, and quick treatment option for uprighting impacted mandibular permanent second molars.

Stability of Black-and-White Photographic Images, with Special Reference to Microfilm.

ERIC Educational Resources Information Center

Reilly, James M.; And Others

1988-01-01

Reviews the history of silver image (black-and-white photographic image) stability, and discusses the redox blemish problem and solutions. A study conducted during 1987-88 by the Image Permanence Institute of the benefits of selenium treatment of microfilm to improve its image stability is then summarized. (21 references) (MES)

Ambiguous Spaces for Troubled Youth: Home, Therapeutic Institution or School?

ERIC Educational Resources Information Center

Severinsson, Susanne; Nord, Catharina; Reimers, Eva

2015-01-01

In Sweden and elsewhere, students permanently excluded from school are removed from their local environment, and sometimes their parental home, and moved to a rural residential care home. Thus "home" and "school" are clearly considered places where problems exist, but it is the young people themselves who are scrutinised and…

Undernutrition and the Developing Brain: The Relevance of Animal Models to the Human Problem

ERIC Educational Resources Information Center

Dobbing, John

1972-01-01

Discusses evidence for a permanent, measurable effect of early restriction on the physical growth of the brain, arguing that undernutrition has been considered for too long in adult terms as a series of deficiency diseases whose main consequences can be reversed on restoration of the deficient component. (Author/JM)

Evaluating the Effects of Comprehensive Substance Abuse Intervention on Successful Reunification

ERIC Educational Resources Information Center

Brook, Jody; McDonald, Thomas P.

2007-01-01

Objective: This study examines permanency outcomes of families with children in foster care who participated in a comprehensive service-delivery program designed to assist families and communities in dealing with alcohol and other drug (AOD) problems. Method: Survival analysis is used to measure the impact of program participation on family…

The Effects of Differential Criteria on the Assessment of Cognitive-Linguistic Relationships.

ERIC Educational Resources Information Center

Smolak, Linda; Levine, Michael P.

1984-01-01

Studies 40 children ages 1 to 3 with respect to stage 6 object permanence, representational language, and symbolic play. Examines methodological problems in investigations of Piaget's model of cognitive-linguistic relationships related to the definition of these variables and associated with the use of correlations for data analysis. (Author/CB)

Stories of Renewal: Community Building and the Future of Urban America.

ERIC Educational Resources Information Center

Walsh, Joan

Community building is an approach to urban poverty that rejects a programmatic approach in favor of efforts that catalyze personal relationships and social networks to improve community life. Community building analyzes urban poverty as a web of interwoven problems that can lock families out of opportunity permanently. Community building…

Magnetic bearings for inertial energy storage

NASA Technical Reports Server (NTRS)

Rodriguez, G. Ernest; Eakin, Vickie

1987-01-01

Advanced flywheels utilizing high strength fibers must operate at high rotational speeds and as such must operate in vacuum to reduce windage losses. The utilization of magnetic bearings in the flywheels overcome lubrication and seal problems, resulting in an energy storage system offering potential improvements over conventional electrochemical energy storage. Magnetic bearings evolved in the 1950s from the simple application of permanent magnets positioned to exert repulsive forces to the present where permanent magnets and electromagnets have been combined to provide axial and radial suspension. Further development of magnetic suspension has led to the design of a shaftless flywheel system for aerospace application. Despite the lack of proof of concept, integrated magnetic suspension in inertial storage systems can provide significant performance improvements to warrant development and tests.

Adaptive fuzzy dynamic surface control for the chaotic permanent magnet synchronous motor using Nussbaum gain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, Shaohua

This paper is concerned with the problem of adaptive fuzzy dynamic surface control (DSC) for the permanent magnet synchronous motor (PMSM) system with chaotic behavior, disturbance and unknown control gain and parameters. Nussbaum gain is adopted to cope with the situation that the control gain is unknown. And the unknown items can be estimated by fuzzy logic system. The proposed controller guarantees that all the signals in the closed-loop system are bounded and the system output eventually converges to a small neighborhood of the desired reference signal. Finally, the numerical simulations indicate that the proposed scheme can suppress the chaosmore » of PMSM and show the effectiveness and robustness of the proposed method.« less

YUCCA MOUNTAIN PROJECT - A BRIEFING --

DOE Office of Scientific and Technical Information (OSTI.GOV)

NA

2003-08-05

This report has the following articles: Nuclear waste--a long-term national problem; Spent nuclear fuel; High-level radioactive waste; Radioactivity and the environment; Current storage methods; Disposal options; U.S. policy on nuclear waste; The focus on Yucca Mountain; The purpose and scope of the Yucca Mountain Project; The approach for permanently disposing of waste; The scientific studies at Yucca Mountain; The proposed design for a repository at Yucca Mountain; Natural and engineered barriers would work together to isolate waste; Meticulous science and technology to protect people and the environment; Licensing a repository; Transporting waste to a permanent repository; The Environmental Impact Statementmore » for a repository; Current status of the Yucca Mountain Project; and Further information available on the Internet.« less

Design of permanent magnet synchronous motor speed loop controller based on sliding mode control algorithm

NASA Astrophysics Data System (ADS)

Qiang, Jiang; Meng-wei, Liao; Ming-jie, Luo

2018-03-01

Abstract.The control performance of Permanent Magnet Synchronous Motor will be affected by the fluctuation or changes of mechanical parameters when PMSM is applied as driving motor in actual electric vehicle,and external disturbance would influence control robustness.To improve control dynamic quality and robustness of PMSM speed control system, a new second order integral sliding mode control algorithm is introduced into PMSM vector control.The simulation results show that, compared with the traditional PID control,the modified control scheme optimized has better control precision and dynamic response ability and perform better with a stronger robustness facing external disturbance,it can effectively solve the traditional sliding mode variable structure control chattering problems as well.

Adaptive fuzzy dynamic surface control for the chaotic permanent magnet synchronous motor using Nussbaum gain.

PubMed

Luo, Shaohua

2014-09-01

This paper is concerned with the problem of adaptive fuzzy dynamic surface control (DSC) for the permanent magnet synchronous motor (PMSM) system with chaotic behavior, disturbance and unknown control gain and parameters. Nussbaum gain is adopted to cope with the situation that the control gain is unknown. And the unknown items can be estimated by fuzzy logic system. The proposed controller guarantees that all the signals in the closed-loop system are bounded and the system output eventually converges to a small neighborhood of the desired reference signal. Finally, the numerical simulations indicate that the proposed scheme can suppress the chaos of PMSM and show the effectiveness and robustness of the proposed method.

Neural network-based adaptive dynamic surface control for permanent magnet synchronous motors.

PubMed

Yu, Jinpeng; Shi, Peng; Dong, Wenjie; Chen, Bing; Lin, Chong

2015-03-01

This brief considers the problem of neural networks (NNs)-based adaptive dynamic surface control (DSC) for permanent magnet synchronous motors (PMSMs) with parameter uncertainties and load torque disturbance. First, NNs are used to approximate the unknown and nonlinear functions of PMSM drive system and a novel adaptive DSC is constructed to avoid the explosion of complexity in the backstepping design. Next, under the proposed adaptive neural DSC, the number of adaptive parameters required is reduced to only one, and the designed neural controllers structure is much simpler than some existing results in literature, which can guarantee that the tracking error converges to a small neighborhood of the origin. Then, simulations are given to illustrate the effectiveness and potential of the new design technique.

Influenza A Virus Host Shutoff Disables Antiviral Stress-Induced Translation Arrest

PubMed Central

Khaperskyy, Denys A.; Emara, Mohamed M.; Johnston, Benjamin P.; Anderson, Paul; Hatchette, Todd F.; McCormick, Craig

2014-01-01

Influenza A virus (IAV) polymerase complexes function in the nucleus of infected cells, generating mRNAs that bear 5′ caps and poly(A) tails, and which are exported to the cytoplasm and translated by host machinery. Host antiviral defences include mechanisms that detect the stress of virus infection and arrest cap-dependent mRNA translation, which normally results in the formation of cytoplasmic aggregates of translationally stalled mRNA-protein complexes known as stress granules (SGs). It remains unclear how IAV ensures preferential translation of viral gene products while evading stress-induced translation arrest. Here, we demonstrate that at early stages of infection both viral and host mRNAs are sensitive to drug-induced translation arrest and SG formation. By contrast, at later stages of infection, IAV becomes partially resistant to stress-induced translation arrest, thereby maintaining ongoing translation of viral gene products. To this end, the virus deploys multiple proteins that block stress-induced SG formation: 1) non-structural protein 1 (NS1) inactivates the antiviral double-stranded RNA (dsRNA)-activated kinase PKR, thereby preventing eIF2α phosphorylation and SG formation; 2) nucleoprotein (NP) inhibits SG formation without affecting eIF2α phosphorylation; 3) host-shutoff protein polymerase-acidic protein-X (PA-X) strongly inhibits SG formation concomitant with dramatic depletion of cytoplasmic poly(A) RNA and nuclear accumulation of poly(A)-binding protein. Recombinant viruses with disrupted PA-X host shutoff function fail to effectively inhibit stress-induced SG formation. The existence of three distinct mechanisms of IAV-mediated SG blockade reveals the magnitude of the threat of stress-induced translation arrest during viral replication. PMID:25010204

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

PubMed Central

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

Characterization of mRNA-Cytoskeleton Interactions In Situ Using FMTRIP and Proximity Ligation

PubMed Central

Jung, Jeenah; Lifland, Aaron W.; Alonas, Eric J.; Zurla, Chiara; Santangelo, Philip J.

2013-01-01

Many studies have demonstrated an association between the cytoskeleton and mRNA, as well as the asymmetric distribution of mRNA granules within the cell in response to various signaling events. It is likely that the extensive cytoskeletal network directs mRNA transport and localization, with different cytoskeletal elements having their own specific roles. In order to understand the spatiotemporal changes in the interactions between the mRNA and the cytoskeleton as a response to a stimulus, a technique that can visualize and quantify these changes across a population of cells while capturing cell-to-cell variations is required. Here, we demonstrate a method for imaging and quantifying mRNA-cytoskeleton interactions on a per cell basis with single-interaction sensitivity. Using a proximity ligation assay with flag-tagged multiply-labeled tetravalent RNA imaging probes (FMTRIP), we quantified interactions between mRNAs and β-tubulin, vimentin, or filamentous actin (F-actin) for two different mRNAs, poly(A) + and β-actin mRNA, in two different cell types, A549 cells and human dermal fibroblasts (HDF). We found that the mRNAs interacted predominantly with F-actin (>50% in HDF, >20% in A549 cells), compared to β-tubulin (<5%) and vimentin (11-13%). This likely reflects differences in mRNA management by the two cell types. We then quantified changes in these interactions in response to two perturbations, F-actin depolymerization and arsenite-induced oxidative stress, both of which alter either the cytoskeleton itself and mRNA localization. Both perturbations led to a decrease in poly(A) + mRNA interactions with F-actin and an increase in the interactions with microtubules, in a time dependent manner. PMID:24040294

Mass spectrometric identification of proteins that interact through specific domains of the poly(A) binding protein

PubMed Central

Zhang, Chongxu; Nielsen, Maria E. O.; Chiang, Yueh-Chin; Kierkegaard, Morten; Wang, Xin; Lee, Darren J.; Andersen, Jens S.; Yao, Gang

2013-01-01

Poly(A) binding protein (PAB1) is involved in a number of RNA metabolic functions in eukaryotic cells and correspondingly is suggested to associate with a number of proteins. We have used mass spectrometric analysis to identify 55 non-ribosomal proteins that specifically interact with PAB1 from Saccharomyces cerevisiae. Because many of these factors may associate only indirectly with PAB1 by being components of the PAB1-mRNP structure, we additionally conducted mass spectrometric analyses on seven metabolically defined PAB1 deletion derivatives to delimit the interactions between these proteins and PAB1. These latter analyses identified 13 proteins whose associations with PAB1 were reduced by deleting one or another of PAB1’s defined domains. Included in this list of 13 proteins were the translation initiation factors eIF4G1 and eIF4G2, translation termination factor eRF3, and PBP2, all of whose previously known direct interactions with specific PAB1 domains were either confirmed, delimited, or extended. The remaining nine proteins that interacted through a specific PAB1 domain were CBF5, SLF1, UPF1, CBC1, SSD1, NOP77, yGR250c, NAB6, and GBP2. In further study, UPF1, involved in nonsense-mediated decay, was confirmed to interact with PAB1 through the RRM1 domain. We additionally established that while the RRM1 domain of PAB1 was required for UPF1-induced acceleration of deadenylation during nonsense-mediated decay, it was not required for the more critical step of acceleration of mRNA decapping. These results begin to identify the proteins most likely to interact with PAB1 and the domains of PAB1 through which these contacts are made. PMID:22836166

Mass spectrometric identification of proteins that interact through specific domains of the poly(A) binding protein.

PubMed

Richardson, Roy; Denis, Clyde L; Zhang, Chongxu; Nielsen, Maria E O; Chiang, Yueh-Chin; Kierkegaard, Morten; Wang, Xin; Lee, Darren J; Andersen, Jens S; Yao, Gang

2012-09-01

Poly(A) binding protein (PAB1) is involved in a number of RNA metabolic functions in eukaryotic cells and correspondingly is suggested to associate with a number of proteins. We have used mass spectrometric analysis to identify 55 non-ribosomal proteins that specifically interact with PAB1 from Saccharomyces cerevisiae. Because many of these factors may associate only indirectly with PAB1 by being components of the PAB1-mRNP structure, we additionally conducted mass spectrometric analyses on seven metabolically defined PAB1 deletion derivatives to delimit the interactions between these proteins and PAB1. These latter analyses identified 13 proteins whose associations with PAB1 were reduced by deleting one or another of PAB1's defined domains. Included in this list of 13 proteins were the translation initiation factors eIF4G1 and eIF4G2, translation termination factor eRF3, and PBP2, all of whose previously known direct interactions with specific PAB1 domains were either confirmed, delimited, or extended. The remaining nine proteins that interacted through a specific PAB1 domain were CBF5, SLF1, UPF1, CBC1, SSD1, NOP77, yGR250c, NAB6, and GBP2. In further study, UPF1, involved in nonsense-mediated decay, was confirmed to interact with PAB1 through the RRM1 domain. We additionally established that while the RRM1 domain of PAB1 was required for UPF1-induced acceleration of deadenylation during nonsense-mediated decay, it was not required for the more critical step of acceleration of mRNA decapping. These results begin to identify the proteins most likely to interact with PAB1 and the domains of PAB1 through which these contacts are made.

The CCR4-NOT complex mediates deadenylation and degradation of stem cell mRNAs and promotes planarian stem cell differentiation.

PubMed

Solana, Jordi; Gamberi, Chiara; Mihaylova, Yuliana; Grosswendt, Stefanie; Chen, Chen; Lasko, Paul; Rajewsky, Nikolaus; Aboobaker, A Aziz

2013-01-01

Post-transcriptional regulatory mechanisms are of fundamental importance to form robust genetic networks, but their roles in stem cell pluripotency remain poorly understood. Here, we use freshwater planarians as a model system to investigate this and uncover a role for CCR4-NOT mediated deadenylation of mRNAs in stem cell differentiation. Planarian adult stem cells, the so-called neoblasts, drive the almost unlimited regenerative capabilities of planarians and allow their ongoing homeostatic tissue turnover. While many genes have been demonstrated to be required for these processes, currently almost no mechanistic insight is available into their regulation. We show that knockdown of planarian Not1, the CCR4-NOT deadenylating complex scaffolding subunit, abrogates regeneration and normal homeostasis. This abrogation is primarily due to severe impairment of their differentiation potential. We describe a stem cell specific increase in the mRNA levels of key neoblast genes after Smed-not1 knock down, consistent with a role of the CCR4-NOT complex in degradation of neoblast mRNAs upon the onset of differentiation. We also observe a stem cell specific increase in the frequency of longer poly(A) tails in these same mRNAs, showing that stem cells after Smed-not1 knock down fail to differentiate as they accumulate populations of transcripts with longer poly(A) tails. As other transcripts are unaffected our data hint at a targeted regulation of these key stem cell mRNAs by post-transcriptional regulators such as RNA-binding proteins or microRNAs. Together, our results show that the CCR4-NOT complex is crucial for stem cell differentiation and controls stem cell-specific degradation of mRNAs, thus providing clear mechanistic insight into this aspect of neoblast biology.

The CCR4-NOT Complex Mediates Deadenylation and Degradation of Stem Cell mRNAs and Promotes Planarian Stem Cell Differentiation

PubMed Central

Solana, Jordi; Gamberi, Chiara; Mihaylova, Yuliana; Grosswendt, Stefanie; Chen, Chen; Lasko, Paul; Rajewsky, Nikolaus; Aboobaker, A. Aziz

2013-01-01

Post-transcriptional regulatory mechanisms are of fundamental importance to form robust genetic networks, but their roles in stem cell pluripotency remain poorly understood. Here, we use freshwater planarians as a model system to investigate this and uncover a role for CCR4-NOT mediated deadenylation of mRNAs in stem cell differentiation. Planarian adult stem cells, the so-called neoblasts, drive the almost unlimited regenerative capabilities of planarians and allow their ongoing homeostatic tissue turnover. While many genes have been demonstrated to be required for these processes, currently almost no mechanistic insight is available into their regulation. We show that knockdown of planarian Not1, the CCR4-NOT deadenylating complex scaffolding subunit, abrogates regeneration and normal homeostasis. This abrogation is primarily due to severe impairment of their differentiation potential. We describe a stem cell specific increase in the mRNA levels of key neoblast genes after Smed-not1 knock down, consistent with a role of the CCR4-NOT complex in degradation of neoblast mRNAs upon the onset of differentiation. We also observe a stem cell specific increase in the frequency of longer poly(A) tails in these same mRNAs, showing that stem cells after Smed-not1 knock down fail to differentiate as they accumulate populations of transcripts with longer poly(A) tails. As other transcripts are unaffected our data hint at a targeted regulation of these key stem cell mRNAs by post-transcriptional regulators such as RNA-binding proteins or microRNAs. Together, our results show that the CCR4-NOT complex is crucial for stem cell differentiation and controls stem cell-specific degradation of mRNAs, thus providing clear mechanistic insight into this aspect of neoblast biology. PMID:24367277

Genome Modification Leads to Phenotype Reversal in Human Myotonic Dystrophy type 1 iPS-cell Derived Neural Stem Cells

PubMed Central

Xia, Guangbin; Gao, Yuanzheng; Jin, Shouguang; Subramony, SH.; Terada, Naohiro; Ranum, Laura P.W.; Swanson, Maurice S.; Ashizawa, Tetsuo

2015-01-01

Objective Myotonic dystrophy type 1 (DM1) is caused by expanded CTG repeats in the 3'-untranslated region (3’ UTR) of the DMPK gene. Correcting the mutation in DM1 stem cells would be an important step towards autologous stem cell therapy. The objective of this study is to demonstrate in vitro genome editing to prevent production of toxic mutant transcripts and reverse phenotypes in DM1 stem cells. Methods Genome editing was performed in DM1 neural stem cells (NSCs) derived from human DM1 iPS cells. An editing cassette containing SV40/bGH polyA signals was integrated upstream of the CTG repeats by TALEN-mediated homologous recombination (HR). The expression of mutant CUG repeats transcript was monitored by nuclear RNA foci, the molecular hallmarks of DM1, using RNA fluorescence in situ hybridization (RNA-FISH). Alternative splicing of microtubule-associated protein tau (MAPT) and muscleblind-like (MBNL) proteins were analyzed to further monitor the phenotype reversal after genome modification. Results The cassette was successfully inserted into DMPK intron 9 and this genomic modification led to complete disappearance of nuclear RNA foci. MAPT and MBNL 1, 2 aberrant splicing in DM1 NSCs was reversed to normal pattern in genome-modified NSCs. Interpretation Genome modification by integration of exogenous polyA signals upstream of the DMPK CTG repeat expansion prevents the production of toxic RNA and leads to phenotype reversal in human DM1 iPS-cells derived stem cells. Our data provide proof-of-principle evidence that genome modification may be used to generate genetically modified progenitor cells as a first step toward autologous cell transfer therapy for DM1. PMID:25702800

Complex alternative splicing of acetylcholinesterase transcripts in Torpedo electric organ; primary structure of the precursor of the glycolipid-anchored dimeric form.

PubMed Central

Sikorav, J L; Duval, N; Anselmet, A; Bon, S; Krejci, E; Legay, C; Osterlund, M; Reimund, B; Massoulié, J

1988-01-01

In this paper, we show the existence of alternative splicing in the 3' region of the coding sequence of Torpedo acetylcholinesterase (AChE). We describe two cDNA structures which both diverge from the previously described coding sequence of the catalytic subunit of asymmetric (A) forms (Schumacher et al., 1986; Sikorav et al., 1987). They both contain a coding sequence followed by a non-coding sequence and a poly(A) stretch. Both of these structures were shown to exist in poly(A)+ RNAs, by S1 mapping experiments. The divergent region encoded by the first sequence corresponds to the precursor of the globular dimeric form (G2a), since it contains the expected C-terminal amino acids, Ala-Cys. These amino acids are followed by a 29 amino acid extension which contains a hydrophobic segment and must be replaced by a glycolipid in the mature protein. Analyses of intact G2a AChE showed that the common domain of the protein contains intersubunit disulphide bonds. The divergent region of the second type of cDNA consists of an adjacent genomic sequence, which is removed as an intron in A and Ga mRNAs, but may encode a distinct, less abundant catalytic subunit. The structures of the cDNA clones indicate that they are derived from minor mRNAs, shorter than the three major transcripts which have been described previously (14.5, 10.5 and 5.5 kb). Oligonucleotide probes specific for the asymmetric and globular terminal regions hybridize with the three major transcripts, indicating that their size is determined by 3'-untranslated regions which are not related to the differential splicing leading to A and Ga forms. Images PMID:3181125

Long-read sequencing of nascent RNA reveals coupling among RNA processing events.

PubMed

Herzel, Lydia; Straube, Korinna; Neugebauer, Karla M

2018-06-14

Pre-mRNA splicing is accomplished by the spliceosome, a megadalton complex that assembles de novo on each intron. Because spliceosome assembly and catalysis occur cotranscriptionally, we hypothesized that introns are removed in the order of their transcription in genomes dominated by constitutive splicing. Remarkably little is known about splicing order and the regulatory potential of nascent transcript remodeling by splicing, due to the limitations of existing methods that focus on analysis of mature splicing products (mRNAs) rather than substrates and intermediates. Here, we overcome this obstacle through long-read RNA sequencing of nascent, multi-intron transcripts in the fission yeast Schizosaccharomyces pombe Most multi-intron transcripts were fully spliced, consistent with rapid cotranscriptional splicing. However, an unexpectedly high proportion of transcripts were either fully spliced or fully unspliced, suggesting that splicing of any given intron is dependent on the splicing status of other introns in the transcript. Supporting this, mild inhibition of splicing by a temperature-sensitive mutation in prp2 , the homolog of vertebrate U2AF65, increased the frequency of fully unspliced transcripts. Importantly, fully unspliced transcripts displayed transcriptional read-through at the polyA site and were degraded cotranscriptionally by the nuclear exosome. Finally, we show that cellular mRNA levels were reduced in genes with a high number of unspliced nascent transcripts during caffeine treatment, showing regulatory significance of cotranscriptional splicing. Therefore, overall splicing of individual nascent transcripts, 3' end formation, and mRNA half-life depend on the splicing status of neighboring introns, suggesting crosstalk among spliceosomes and the polyA cleavage machinery during transcription elongation. © 2018 Herzel et al.; Published by Cold Spring Harbor Laboratory Press.

The dopamine precursor L-dihydroxyphenylalanine is transported by the amino acid transporters rBAT and LAT2 in renal cortex.

PubMed

Quiñones, Henry; Collazo, Roberto; Moe, Orson W

2004-07-01

The intrarenal autocrine-paracrine dopamine (DA) system is critical for Na(+) homeostasis. l-Dihydroxyphenylalanine (l-DOPA) uptake from the glomerular filtrate and plasma provides the substrate for DA generation by the renal proximal tubule. The transporter(s) responsible for proximal tubule l-DOPA uptake has not been characterized. Renal cortical poly-A(+) RNA injected into Xenopus laevis oocytes induced l-DOPA uptake in a time- and dose-dependent fashion with biphasic K(m)s in the millimolar and micromolar range and independent of inward Na(+), K(+), or H(+) gradients, suggesting the presence of low- and high-affinity l-DOPA carriers. Complementary RNA from two amino acid transporters yielded l-DOPA uptake significantly above water-injected controls the rBAT/b(0,+)AT dimer (rBAT) and the LAT2/4F2 dimer (LAT2). In contradistinction to renal cortical poly-A(+), l-DOPA kinetics of rBAT and LAT2 showed classic Michaelis-Menton kinetics with K(m)s in the micromolar and millimolar range, respectively. Sequence-specific antisense oligonucleotides to rBAT or LAT2 (AS) caused inhibition of rBAT and LAT2 cRNA-induced l-DOPA transport and cortical poly-A(+)-induced arginine and phenylalanine transport. However, the same ASs only partially blocked poly-A(+)-induced l-DOPA transport. In cultured kidney cells, silencing inhibitory RNA (siRNA) to rBAT significantly inhibited l-DOPA uptake. We conclude that rBAT and LAT2 can mediate apical and basolateral l-DOPA uptake into the proximal tubule, respectively. Additional l-DOPA transport mechanisms exist in the renal cortex that remain to be identified.

CCR4-NOT deadenylates mRNA associated with RNA-induced silencing complexes in human cells.

PubMed

Piao, Xianghua; Zhang, Xue; Wu, Ligang; Belasco, Joel G

2010-03-01

MicroRNAs (miRNAs) repress gene expression posttranscriptionally by inhibiting translation and by expediting deadenylation so as to trigger rapid mRNA decay. Their regulatory influence is mediated by the protein components of the RNA-induced silencing complex (RISC), which deliver miRNAs and siRNAs to their mRNA targets. Here, we present evidence that CCR4-NOT is the deadenylase that removes poly(A) from messages destabilized by miRNAs in human cells. Overproducing a mutationally inactivated form of either of the catalytic subunits of this deadenylase (CCR4 or CAF1/POP2) significantly impedes the deadenylation and decay of mRNA targeted by a partially complementary miRNA. The same deadenylase initiates the degradation of "off-target" mRNAs that are bound by an imperfectly complementary siRNA introduced by transfection. The greater inhibitory effect of inactive CAF1 or POP2 (versus inactive CCR4) suggests a predominant role for this catalytic subunit of CCR4-NOT in miRNA- or small interfering RNA (siRNA)-mediated deadenylation. These effects of mi/siRNAs and CCR4-NOT can be fully reproduced by directly tethering RISC to mRNA without the guidance of a small RNA, indicating that the ability of RISC to accelerate deadenylation is independent of RNA base pairing. Despite its importance for mi/siRNA-mediated deadenylation, CCR4-NOT appears not to associate significantly with RISC, as judged by the failure of CAF1 and POP2 to coimmunoprecipitate detectably with either the Ago or TNRC6 subunit of RISC, a finding at odds with deadenylase recruitment as the mechanism by which RISC accelerates poly(A) removal.

Comparative Life Cycle Transcriptomics Revises Leishmania mexicana Genome Annotation and Links a Chromosome Duplication with Parasitism of Vertebrates

PubMed Central

Fiebig, Michael; Kelly, Steven; Gluenz, Eva

2015-01-01

Leishmania spp. are protozoan parasites that have two principal life cycle stages: the motile promastigote forms that live in the alimentary tract of the sandfly and the amastigote forms, which are adapted to survive and replicate in the harsh conditions of the phagolysosome of mammalian macrophages. Here, we used Illumina sequencing of poly-A selected RNA to characterise and compare the transcriptomes of L. mexicana promastigotes, axenic amastigotes and intracellular amastigotes. These data allowed the production of the first transcriptome evidence-based annotation of gene models for this species, including genome-wide mapping of trans-splice sites and poly-A addition sites. The revised genome annotation encompassed 9,169 protein-coding genes including 936 novel genes as well as modifications to previously existing gene models. Comparative analysis of gene expression across promastigote and amastigote forms revealed that 3,832 genes are differentially expressed between promastigotes and intracellular amastigotes. A large proportion of genes that were downregulated during differentiation to amastigotes were associated with the function of the motile flagellum. In contrast, those genes that were upregulated included cell surface proteins, transporters, peptidases and many uncharacterized genes, including 293 of the 936 novel genes. Genome-wide distribution analysis of the differentially expressed genes revealed that the tetraploid chromosome 30 is highly enriched for genes that were upregulated in amastigotes, providing the first evidence of a link between this whole chromosome duplication event and adaptation to the vertebrate host in this group. Peptide evidence for 42 proteins encoded by novel transcripts supports the idea of an as yet uncharacterised set of small proteins in Leishmania spp. with possible implications for host-pathogen interactions. PMID:26452044

Determining miRNA Expression Levels in Degraded RNA Samples Using Real-Time RT-qPCR and Microarray Technologies

PubMed Central

Tighe, S.; Holbrook, J.; Nadella, V.; Carmical, R.; Sol-Church, K.; Yueng, A.T.; Chittur, S.

2011-01-01

The Nucleic Acid Research Group (NARG) has previously conducted studies evaluating the impact of RNA integrity and priming strategies on cDNA synthesis and real-time RT-qPCR. The results of last year's field study as it relates to degraded RNA will be presented. In continuation of the RNA integrity theme, this year's study was designed to evaluate the impact of RNA integrity on the analysis of miRNA expression using real-time RT-qPCR. Target section was based on data obtained by the Microarray Research Group (MARG) and other published data from next gen sequencing. These 9 miRNAs represent three groups of miRNA that are expressed at low, medium or high levels in the First Choice human brain reference RNA sample. Two popular RT priming strategies tested in this study include the Megaplex miRNA TaqMan assay (ABI) and the RT2 miRNA qPCR assay (Qiagen/SA Biosciences). The basis for the ABI assay design is a target-specific stem-loop structure and reverse-transcription primer, while the Qiagen design combines poly(A) tailing and a universal reverse transcription in one cDNA synthesis reaction. For this study, the human brain reference RNA was subject to controlled degradation using RNase A to RIN (RNA Integrity Number) values of 7 (good), 4 (moderately degraded), and 2 (severely degraded).These templates were then used to assess both RT methods. In addition to this real-time RT-qPCR data, the same RNA templates were further analyzed using universal poly(A) tailing and hybridization to Affymetrix miRNA GeneChips. This talk will provide insights into RT priming strategies for miRNA and contrast the qPCR results obtained using different technologies.

Remodeling of the pioneer translation initiation complex involves translation and the karyopherin importin β

PubMed Central

Sato, Hanae; Maquat, Lynne E.

2009-01-01

Mammalian mRNAs lose and acquire proteins throughout their life span while undergoing processing, transport, translation, and decay. How translation affects messenger RNA (mRNA)–protein interactions is largely unknown. The pioneer round of translation uses newly synthesized mRNA that is bound by cap-binding protein 80 (CBP80)–CBP20 (also known as the cap-binding complex [CBC]) at the cap, poly(A)-binding protein N1 (PABPN1) and PABPC1 at the poly(A) tail, and, provided biogenesis involves pre-mRNA splicing, exon junction complexes (EJCs) at exon–exon junctions. Subsequent rounds of translation engage mRNA that is bound by eukaryotic translation initiation factor 4E (eIF4E) at the cap and PABPC1 at the poly(A) tail, but that lacks detectable EJCs and PABPN1. Using the level of intracellular iron to regulate the translation of specific mRNAs, we show that translation promotes not only removal of EJC constituents, including the eIF4AIII anchor, but also replacement of PABPN1 by PABPC1. Remarkably, translation does not affect replacement of CBC by eIF4E. Instead, replacement of CBC by eIF4E is promoted by importin β (IMPβ): Inhibiting the binding of IMPβ to the complex of CBC–IMPα at an mRNA cap using the IMPα IBB (IMPβ-binding) domain or a RAN variant increases the amount of CBC-bound mRNA and decreases the amount of eIF4E-bound mRNA. Our studies uncover a previously unappreciated role for IMPβ and a novel paradigm for how newly synthesized messenger ribonucleoproteins (mRNPs) are matured. PMID:19884259

Characteristics and significance of intergenic polyadenylated RNA transcription in Arabidopsis.

PubMed

Moghe, Gaurav D; Lehti-Shiu, Melissa D; Seddon, Alex E; Yin, Shan; Chen, Yani; Juntawong, Piyada; Brandizzi, Federica; Bailey-Serres, Julia; Shiu, Shin-Han

2013-01-01

The Arabidopsis (Arabidopsis thaliana) genome is the most well-annotated plant genome. However, transcriptome sequencing in Arabidopsis continues to suggest the presence of polyadenylated (polyA) transcripts originating from presumed intergenic regions. It is not clear whether these transcripts represent novel noncoding or protein-coding genes. To understand the nature of intergenic polyA transcription, we first assessed its abundance using multiple messenger RNA sequencing data sets. We found 6,545 intergenic transcribed fragments (ITFs) occupying 3.6% of Arabidopsis intergenic space. In contrast to transcribed fragments that map to protein-coding and RNA genes, most ITFs are significantly shorter, are expressed at significantly lower levels, and tend to be more data set specific. A surprisingly large number of ITFs (32.1%) may be protein coding based on evidence of translation. However, our results indicate that these "translated" ITFs tend to be close to and are likely associated with known genes. To investigate if ITFs are under selection and are functional, we assessed ITF conservation through cross-species as well as within-species comparisons. Our analysis reveals that 237 ITFs, including 49 with translation evidence, are under strong selective constraint and relatively distant from annotated features. These ITFs are likely parts of novel genes. However, the selective pressure imposed on most ITFs is similar to that of randomly selected, untranscribed intergenic sequences. Our findings indicate that despite the prevalence of ITFs, apart from the possibility of genomic contamination, many may be background or noisy transcripts derived from "junk" DNA, whose production may be inherent to the process of transcription and which, on rare occasions, may act as catalysts for the creation of novel genes.

The specificity and flexibility of l1 reverse transcription priming at imperfect T-tracts.

PubMed

Monot, Clément; Kuciak, Monika; Viollet, Sébastien; Mir, Ashfaq Ali; Gabus, Caroline; Darlix, Jean-Luc; Cristofari, Gaël

2013-05-01

L1 retrotransposons have a prominent role in reshaping mammalian genomes. To replicate, the L1 ribonucleoprotein particle (RNP) first uses its endonuclease (EN) to nick the genomic DNA. The newly generated DNA end is subsequently used as a primer to initiate reverse transcription within the L1 RNA poly(A) tail, a process known as target-primed reverse transcription (TPRT). Prior studies demonstrated that most L1 insertions occur into sequences related to the L1 EN consensus sequence (degenerate 5'-TTTT/A-3' sites) and frequently preceded by imperfect T-tracts. However, it is currently unclear whether--and to which degree--the liberated 3'-hydroxyl extremity on the genomic DNA needs to be accessible and complementary to the poly(A) tail of the L1 RNA for efficient priming of reverse transcription. Here, we employed a direct assay for the initiation of L1 reverse transcription to define the molecular rules that guide this process. First, efficient priming is detected with as few as 4 matching nucleotides at the primer 3' end. Second, L1 RNP can tolerate terminal mismatches if they are compensated within the 10 last bases of the primer by an increased number of matching nucleotides. All terminal mismatches are not equally detrimental to DNA extension, a C being extended at higher levels than an A or a G. Third, efficient priming in the context of duplex DNA requires a 3' overhang. This suggests the possible existence of additional DNA processing steps, which generate a single-stranded 3' end to allow L1 reverse transcription. Based on these data we propose that the specificity of L1 reverse transcription initiation contributes, together with the specificity of the initial EN cleavage, to the distribution of new L1 insertions within the human genome.

Dental Aspect of Distal Tubular Renal Acidosis with Genu Valgum Secondary to Rickets: A Case Report

PubMed Central

Bahadure, Rakesh N.; Thosar, Nilima; Kriplani, Ritika; Baliga, Sudhindra; Fulzele, Punit

2012-01-01

Distal renal tubular acidosis is a disease that occurs when the kidneys do not remove acid properly into the urine, leaving the blood too acidic (called acidosis). Distal renal tubular acidosis (type I RTA) is caused by a defect in the kidney tubes that causes acid to build up in the bloodstream. It ultimately results rickets which include chronic skeletal pain, in skeletal deformities, skeletal fractures. Rickets is among the most frequent childhood diseases in many developing countries. Dental problems in rickets include delayed eruption of permanent teeth, premature fall of deciduous teeth, defects in structure of teeth, enamel defects in permanent teeth (hypoplastic), pulp defects, intraglobular dentine, and caries tooth. Herewith, reported a case of distal tubular renal acidosis with genu valgum secondary to rickets, with pain and extraoral swelling associated with right and left mandibular 1st permanent molars. Teeth were infected with pulp without being involved with caries. Radiographically cracks in enamel and dentin were observed. Pulp revascularization with 46 and root canal treatment was done for 36 with followup of 1 year. PMID:22567455

Do frequent exposures to threats and violence at work affect later workforce participation?

PubMed

Biering, Karin; Andersen, Lars Peter Sønderbo; Hogh, Annie; Andersen, Johan Hviid

2018-05-01

Threats and violence at work are common problems in the human service sector. It can result in physical and psychological health symptoms. The aim of this study was to examine the association between exposure to threats and violence and workforce participation in four human service sectors. 5170 employees answered questionnaires about threats and violence in 2010 and were followed in a register for public transfer incomes for 3.5 years to identify episodes of sick leave, general workforce participation, and permanent health-related benefits. We found associations between exposures to threats and violence at work and workforce participation, though only a few specific types of threats and violence were associated on their own. Self-rated severity of both threatening and violent episodes was associated with overall low workforce participation, new sick leave episodes, and permanent health-related benefits. However, the latter was not statistically significant. The same pattern seems to be present in the relation between the total amount of exposure to threats and violence (threats score and violence score), respectively, and overall low workforce participation and new sick leave episodes. The threats score was also related to permanent health-related benefits. Exposure to threats and violence is associated with temporary and permanent health-related benefits as well as with low workforce participation in general, although some of the associations were not statistically significant.

Locum tenens consultant doctors in a rural general hospital - an essential part of the medical workforce or an expensive stopgap?

PubMed

Sim, Andrew Jw

2011-01-01

Maintaining hospital consultant staffing levels often requires the employment of locum tenens to meet service needs. This is particularly so in hospitals where core clinical services are run by a small number of permanently appointed consultants. The problems associated with locum employment are underestimated and little attention has been directed towards addressing the issue in the rural general hospitals of Scotland. This study looked at the permanent and short- and long-term locum consultant usage over an 8 year period in one Scottish rural general hospital, the Western Isles Hospital in Stornoway. Data were extracted from the Human Resources Department of NHS Western Isles' list of locum consultants for most weeks from the beginning of January 2002 to the end of December 2009. The Western Isles Hospital in Stornoway has an establishment of 17 permanent consultants. During the 8 year study period 239 different consultants were employed, 20 held substantive permanent positions, 31 were long-term locums (employed >3 months) and 188 were short-term locums. The short-term locums worked for 535 different locum episodes. The pattern of usage varied according to service configuration. Study data revealed the alarming scope of the locum tenens issue, which will increase unless action is taken. For sustainable medical services to continue in the rural general hospitals of Scotland, staffing models must minimise the need to employ locum consultants.

Complexes of mismatched and complementary DNA with minor groove binders. Structures at nucleotide resolution via an improved hydroxyl radical cleavage methodology.

PubMed

Bialonska, Dobroslawa; Song, Kenneth; Bolton, Philip H

2011-11-27

Tumor cell lines can replicate faster than normal cells and many also have defective DNA repair pathways. This has lead to the investigation of the inhibition of DNA repair proteins as a means of therapeutic intervention. An alternative approach is to hide or mask damaged DNA from the repair systems. We have developed a protocol to investigate the structures of the complexes of damaged DNA with drug like molecules. Nucleotide resolution structural information can be obtained using an improved hydroxyl radical cleavage protocol. The use of a dT(n) tail increases the length of the smallest fragments of interest and allows efficient co-precipitation of the fragments with poly(A). The use of a fluorescent label, on the 5' end of the dT(n) tail, in conjunction with modified cleavage reaction conditions, avoids the lifetime and other problems with (32)P labeling. The structures of duplex DNAs containing AC and CC mismatches in the presence and absence of minor groove binders have been investigated as have those of the fully complementary DNA. The results indicate that the structural perturbations of the mismatches are localized, are sequence dependent and that the presence of a mismatch can alter the binding of drug like molecules. Copyright © 2011 Elsevier B.V. All rights reserved.

Sleep and autonomic nervous system changes - enhanced cardiac sympathetic modulations during sleep in permanent night shift nurses.

PubMed

Chung, Min-Huey; Kuo, Terry B J; Hsu, Nanly; Chu, Hsin; Chou, Kuei-Ru; Yang, Cheryl C H

2009-05-01

Disturbed sleep is the most common problem among the many health-related effects of shift work, with shift workers clearly having higher rates of cardiac disorders. However, the possible mechanism underlying the related health effects of shift work has yet to be examined. Consequently, this study aimed to explore the influence of long-term night shift work on the sleep patterns of nurses and their cardiac autonomic nervous system during sleep. Our sample comprised ten permanent night shift and ten regular morning shift nurses. Nurses slept in their dormitory where they were allowed to sleep and wake spontaneously. All sleep parameters were digitized using an ambulatory polysomnographic recorder. Using sleep patterns and heart rate variability, the day- and nighttime sleep of permanent night shift nurses were compared with the nighttime sleep of regular morning shift nurses. Compared with the nighttime sleep of regular morning shift nurses, the pattern of daytime sleep of permanent night shift nurses showed significantly lower sleep onset latency. Permanent night shift nurses' daytime sleep also had greater proportions of Stage 3 and 4 (deep sleep), and arousal index than recorded during their nighttime sleep. Both the low frequency and low to high frequency ratio of the nighttime sleep of night shift nurses were significantly higher during periods of non-rapid eye movement (NREM) sleep than the nighttime sleep of morning shift workers. In addition, the electroencephalography delta-power of the nighttime sleep of night shift nurses was significantly lower during the first NREM episode sleep than those of both the daytime sleep of night shift workers and the nighttime sleep of morning shift nurses. Permanent night shift nurses have higher sympathetic activity during nighttime sleep than regular morning shift nurses. Night shift working may have effects on the sleeping patterns of nurses in the long run, inducing higher cardiac sympathetic regulation.

RCT of a Mentoring and Skills Group Program: Placement and Permanency Outcomes for Foster Youth

PubMed Central

Culhane, Sara E.; Garrido, Edward; Knudtson, Michael D.

2012-01-01

OBJECTIVE: To examine the impact of a mentoring and skills group intervention for preadolescent children in foster care on placement stability and permanence at 1-year postintervention. METHODS: A randomized controlled trial was conducted with 9- to 11-year-old children who were maltreated and placed in foster care (n = 54 control; n = 56 intervention). State child welfare records provided information on number of placement changes, placement in residential treatment, and case closure (ie, permanency). Rates of adoption and reunification were also examined. Analysis was by intention to treat. RESULTS: After controlling for baseline functioning and preintervention placement history, intervention youth were 71% less likely to be placed in residential treatment (odds ratio [OR] = 0.29, 95% confidence interval [CI] 0.09–0.98). There were no significant treatment differences in predicting placement changes or permanency for the total sample. Among a subsample of children living in nonrelative foster care at baseline, intervention youth had 44% fewer placement changes (incidence ratio = 0.56, 95% CI 0.34–0.93), were 82% less likely to be placed in a residential treatment center (OR = 0.18, 95% CI 0.03–0.96), and were 5 times more likely to have attained permanency at 1 year postintervention (OR = 5.14, 95% CI 1.55–17.07). More intervention youth had reunified 1-year postintervention [χ2(1, N = 78) = 3.99; P < .05], and the pattern of findings suggested that intervention youth had higher rates of adoption. A significant interaction [χ2(1, N = 110) = 5.43; P = .02] demonstrated that the intervention attenuated the impact of baseline behavior problems on placement changes. CONCLUSIONS: The findings suggest that participation in a 9-month mentoring and skills group intervention leads to greater placement stability and permanence, especially for children in nonrelative foster care. PMID:22689870

Singular Optimal Controls of Rocket Motion (Survey)

NASA Astrophysics Data System (ADS)

Kiforenko, B. N.

2017-05-01

Survey of modern state and discussion of problems of the perfection of methods of investigation of variational problems with a focus on mechanics of space flight are presented. The main attention is paid to the enhancement of the methods of solving of variational problems of rocket motion in the gravitational fields, including rocket motion in the atmosphere. These problems are directly connected with the permanently actual problem of the practical astronautics to increase the payload that is orbited by the carrier rockets in the circumplanetary orbits. An analysis of modern approaches to solving the problems of control of rockets and spacecraft motion on the trajectories with singular arcs that are optimal for the motion of the variable mass body in the medium with resistance is given. The presented results for some maneuvers can serve as an information source for decision making on designing promising rocket and space technology

Dental Decay in Southern Illinois Migrant and Seasonal Farmworkers: An Analysis of Clinical Data

ERIC Educational Resources Information Center

Lukes, Sherri M.; Simon, Bret

2005-01-01

Context: Migrant and seasonal farmworkers are a population at risk for oral health problems. Data on the oral health conditions of migrant and seasonal farmworkers? permanent teeth are particularly lacking. Purpose: To document the relative rates of treated and untreated dental decay in a sample of southern Illinois migrant and seasonal…

Our Children are Waiting for Adoptive Homes: A Review of New York State Adoption Services.

ERIC Educational Resources Information Center

Pisani, Joseph R.

The history and current problems of adoption services provided by the state of New York are discussed. First, statutory reforms since the creation in 1968 of the nation's first statewide adoption subsidy program are reviewed and adoption services aimed at providing permanent homes for children in foster care are described. Subsequently, the…

How Can "Weightless" Astronauts Be Weighed?

ERIC Educational Resources Information Center

Carnicer, Jesus; Reyes, Francisco; Guisasola, Jenaro

2012-01-01

In introductory physics courses, within the context of studying Newton's laws, it is common to consider the problem of a body's "weight" when it is in free fall. The solution shows that the "weight" is zero and this leads to a discussion of the concept of weight. There are permanent free-fall situations such as astronauts in a spacecraft orbiting…

Preserving ancient artifacts for the next millennia

Treesearch

Samuel L. Zelinka

2014-01-01

When wood is kept dry, it can remain intact for millennia, as evidenced by numerous artifacts from ancient Egypt (1). However, when wood interacts with water, numerous problems arise that can cause the wood to become permanently damaged or destroyed completely. Wood exhibits swelling on moisture uptake and shrinkage on drying, and these cyclical moisture changes lead...

What Is an Ideal Critical Thinker Expected to Conclude about Anthropogenic Global Warming?

ERIC Educational Resources Information Center

Guzzo, Guilherme Brambatti; Dall'Alba, Gabriel

2017-01-01

Critical thinking involves the ability to properly assess statements and actions, and it also requires a permanent disposition to appropriately use cognitive skills in the evaluation of any claim. In the present paper, we discuss the characteristics of an ideal critical thinker, and apply them to a contemporary problem, namely anthropogenic global…

The Culture Integration in The Context of National Art Schools--Prioritized Direction of Development of the Modern Humanities

ERIC Educational Resources Information Center

Melekhova, Ksenia Alexandrovna; Lichman, Yelena Yurievna

2016-01-01

The modern picture of the world is experiencing a permanent transformation, adapting to the influence of various globalization factors, the dominance of information technology, dynamic development of a material environment, etc. In these circumstances, the society faces a problem of a technocratic knowledge domination without attention to…

Dental Decay in Southern Illinois Migrant and Seasonal Farmworkers: An Analysis of Clinical Data

ERIC Educational Resources Information Center

Lukes, Sherri M.; Simon, Bret

2005-01-01

Context: Migrant and seasonal farmworkers are a population at risk for oral health problems. Data on the oral health conditions of migrant and seasonal farmworkers' permanent teeth are particularly lacking. Purpose: To document the relative rates of treated and untreated dental decay in a sample of southern Illinois migrant and seasonal…

Natural durability of tropical and native woods against termite damage by Reticulitermes flavipes (Kollar)

Treesearch

Rachel A. Arango; Frederick Green; Kristina Hintz; Patricia K. Lebow; Regis B. Miller

2006-01-01

Environmental pressure has resulted in voluntary removal of chromated copper arsenate (CCA) from wood preservatives in residential applications in the United States. A new generation of copper organic preservatives was formulated as replacements, but these preservatives may not provide a permanent solution to all related problems. Some of these issues include concern...

Automatic Promotion and Student Dropout: Evidence from Uganda, Using Propensity Score in Difference in Differences Model

ERIC Educational Resources Information Center

Okurut, Jeje Moses

2018-01-01

The impact of automatic promotion practice on students dropping out of Uganda's primary education was assessed using propensity score in difference in differences analysis technique. The analysis strategy was instrumental in addressing the selection bias problem, as well as biases arising from common trends over time, and permanent latent…

Child and Adolescent Traumatic Brain Injury: Academic, Behavioural, and Social Consequences in the Classroom

ERIC Educational Resources Information Center

Jantz, Paul B.; Coulter, Gail A.

2007-01-01

More than five million children suffer from brain injuries each year. While the majority of these children are treated and released without permanent consequences, many children return to the classroom with lasting effects. Symptoms of brain injury can be misconstrued as common behaviour or academic problems. Therefore, teachers need to recognize…

Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes I: Finite element solutions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu Benzhuo; Holst, Michael J.; Center for Theoretical Biological Physics, University of California San Diego, La Jolla, CA 92093

2010-09-20

In this paper we developed accurate finite element methods for solving 3-D Poisson-Nernst-Planck (PNP) equations with singular permanent charges for simulating electrodiffusion in solvated biomolecular systems. The electrostatic Poisson equation was defined in the biomolecules and in the solvent, while the Nernst-Planck equation was defined only in the solvent. We applied a stable regularization scheme to remove the singular component of the electrostatic potential induced by the permanent charges inside biomolecules, and formulated regular, well-posed PNP equations. An inexact-Newton method was used to solve the coupled nonlinear elliptic equations for the steady problems; while an Adams-Bashforth-Crank-Nicolson method was devised formore » time integration for the unsteady electrodiffusion. We numerically investigated the conditioning of the stiffness matrices for the finite element approximations of the two formulations of the Nernst-Planck equation, and theoretically proved that the transformed formulation is always associated with an ill-conditioned stiffness matrix. We also studied the electroneutrality of the solution and its relation with the boundary conditions on the molecular surface, and concluded that a large net charge concentration is always present near the molecular surface due to the presence of multiple species of charged particles in the solution. The numerical methods are shown to be accurate and stable by various test problems, and are applicable to real large-scale biophysical electrodiffusion problems.« less

Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions

PubMed Central

Lu, Benzhuo; Holst, Michael J.; McCammon, J. Andrew; Zhou, Y. C.

2010-01-01

In this paper we developed accurate finite element methods for solving 3-D Poisson-Nernst-Planck (PNP) equations with singular permanent charges for electrodiffusion in solvated biomolecular systems. The electrostatic Poisson equation was defined in the biomolecules and in the solvent, while the Nernst-Planck equation was defined only in the solvent. We applied a stable regularization scheme to remove the singular component of the electrostatic potential induced by the permanent charges inside biomolecules, and formulated regular, well-posed PNP equations. An inexact-Newton method was used to solve the coupled nonlinear elliptic equations for the steady problems; while an Adams-Bashforth-Crank-Nicolson method was devised for time integration for the unsteady electrodiffusion. We numerically investigated the conditioning of the stiffness matrices for the finite element approximations of the two formulations of the Nernst-Planck equation, and theoretically proved that the transformed formulation is always associated with an ill-conditioned stiffness matrix. We also studied the electroneutrality of the solution and its relation with the boundary conditions on the molecular surface, and concluded that a large net charge concentration is always present near the molecular surface due to the presence of multiple species of charged particles in the solution. The numerical methods are shown to be accurate and stable by various test problems, and are applicable to real large-scale biophysical electrodiffusion problems. PMID:21709855

Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions.

PubMed

Lu, Benzhuo; Holst, Michael J; McCammon, J Andrew; Zhou, Y C

2010-09-20

In this paper we developed accurate finite element methods for solving 3-D Poisson-Nernst-Planck (PNP) equations with singular permanent charges for electrodiffusion in solvated biomolecular systems. The electrostatic Poisson equation was defined in the biomolecules and in the solvent, while the Nernst-Planck equation was defined only in the solvent. We applied a stable regularization scheme to remove the singular component of the electrostatic potential induced by the permanent charges inside biomolecules, and formulated regular, well-posed PNP equations. An inexact-Newton method was used to solve the coupled nonlinear elliptic equations for the steady problems; while an Adams-Bashforth-Crank-Nicolson method was devised for time integration for the unsteady electrodiffusion. We numerically investigated the conditioning of the stiffness matrices for the finite element approximations of the two formulations of the Nernst-Planck equation, and theoretically proved that the transformed formulation is always associated with an ill-conditioned stiffness matrix. We also studied the electroneutrality of the solution and its relation with the boundary conditions on the molecular surface, and concluded that a large net charge concentration is always present near the molecular surface due to the presence of multiple species of charged particles in the solution. The numerical methods are shown to be accurate and stable by various test problems, and are applicable to real large-scale biophysical electrodiffusion problems.

Characterization of short interspersed elements (SINEs) in a red alga, Porphyra yezoensis.

PubMed

Zhang, Wenbo; Lin, Xiaofei; Peddigari, Suresh; Takechi, Katsuaki; Takano, Hiroyoshi; Takio, Susumu

2007-02-01

Short interspersed element (SINE)-like sequences referred to as PySN1 and PySN2 were identified in a red alga, Porphyra yezoensis. Both elements contained an internal promoter with motifs (A box and B box) recognized by RNA polymerase III, and target site duplications at both ends. Genomic Southern blot analysis revealed that both elements were widely and abundantly distributed on the genome. 3' and 5' RACE suggested that PySN1 was expressed as a chimera transcript with flanking SINE-unrelated sequences and possessed the poly-A tail at the same position near the 3' end of PySN1.

AT-rich sequence elements promote nascent transcript cleavage leading to RNA polymerase II termination

PubMed Central

White, Eleanor; Kamieniarz-Gdula, Kinga; Dye, Michael J.; Proudfoot, Nick J.

2013-01-01

RNA Polymerase II (Pol II) termination is dependent on RNA processing signals as well as specific terminator elements located downstream of the poly(A) site. One of the two major terminator classes described so far is the Co-Transcriptional Cleavage (CoTC) element. We show that homopolymer A/T tracts within the human β-globin CoTC-mediated terminator element play a critical role in Pol II termination. These short A/T tracts, dispersed within seemingly random sequences, are strong terminator elements, and bioinformatics analysis confirms the presence of such sequences in 70% of the putative terminator regions (PTRs) genome-wide. PMID:23258704

Expression of eukaryotic polypeptides in chloroplasts

DOEpatents

Mayfield, Stephen P.

2013-06-04

The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

Plasmodium falciparum spliceosomal RNAs: 3' and 5' end processing.

PubMed

Eliana, Calvo; Javier, Escobar; Moisés, Wasserman

2011-02-01

The major spliceosomal small nuclear ribonucleoproteins (snRNPs) consist of snRNA (U1, U2, U4 or U5) and several proteins which can be unique or common to each snRNP particle. The common proteins are known as Sm proteins; they are crucial for RNP assembly and nuclear import of spliceosomal RNPs. This paper reports detecting the interaction between Plasmodium falciparum snRNAs and Sm proteins, and the usual 5' trimethylated caps on the snRNAs, by immunoprecipitation with specific antibodies. Furthermore, an unusual poly(A) tail was detected on these non-coding RNAs. 2010 Elsevier B.V. All rights reserved.

Evaluation of the Permanence of Land Use Change Induced by Payments for Environmental Services in Quindío, Colombia.

PubMed

Pagiola, Stefano; Honey-Rosés, Jordi; Freire-González, Jaume

2016-01-01

The effectiveness of conservation interventions such as Payments for Environmental Services (PES) is often evaluated--if it is evaluated at all--only at the completion of the intervention. Since gains achieved by the intervention may be lost after it ends, even apparently successful interventions may not result in long-term conservation benefits, a problem known as that of permanence. This paper uses a unique dataset to examine the permanence of land use change induced by a short-term, asset-building PES program implemented in Quindío, Colombia, between 2003 and 2008. This the first PES program to have a control group for comparison. Under this program, PES had been found to have a positive and highly significant impact on land use. To assess the long-term permanence of these changes, both PES recipients and control households were re-surveyed in 2011, four years after the last payment was made. We find that the land use changes that had been induced by PES were broadly sustained in intervening years, with minor differences across specific practices and sub-groups of participants, indicating that these changes were in fact permanent. The patterns of change in the period after the PES program was completed also help better understand the reasons for the program's success. These results suggest that, at least in the case of productive land uses such as silvopastoral practices under conditions such as those at the study site, asset-building PES programs can be effective at encouraging land owners to adopt environmentally-beneficial land management practices and that the benefits will persist after payments cease.

Socio-medical situation for long-term survivors of Hodgkin's disease: a survey of 459 patients treated at one institution.

PubMed

Abrahamsen, A F; Loge, J H; Hannisdal, E; Holte, H; Kvaløy, S

1998-11-01

We present the socio-medical situation for 459 adult disease-free long-term survivors of Hodgkin's disease (HD) 3-23 years after first line curative treatment. In 1994, 557 patients were sent a self-report questionnaire relating to their social status and 459 patients (82%) replied. Educational or professional plans were changed due to HD in 142 patients (32%). After 6, 12 and 18 months from start of treatment, 52, 82 and 95% of the patients, respectively, had returned to their job or education. The sum of full-time and part-time employment was in men 78% at diagnosis and 85% at follow-up, and in women 57% at diagnosis and 64% at follow-up. Only 2% of men and 3% of women did not have a job at follow-up in 1994. At diagnosis 2% of the patients were permanently disabled versus 19% at follow-up in 1994. Age > 40 years at diagnosis, increased the total score of psychological distress and fatigue and long-term disablement after first line treatment were predictors for permanent disablement. Transient or permanent sexual problems were reported in 16% and 13%, respectively. MVPP (mustine, vinblastine, procarbazine and prednisone) or LVPP (chlorambucil, vinblastine, procarbazine and prednisone) chemotherapy was responsible for most cases of early menopause in women older than 30 years, and of infertility in both men and women. In summary, most long-term HD survivors had adapted well to their socio-medical situation except a high number of permanently disabled patients. By focusing more on factors predisposing for permanent disablement and early treatment for these, more patients may be helped to return to their job.

Low permanent pacemaker rates following Lotus device implantation for transcatheter aortic valve replacement due to modified implantation protocol.

PubMed

Krackhardt, Florian; Kherad, Behrouz; Krisper, Maximilian; Pieske, Burkert; Laule, Michael; Tschöpe, Carsten

2017-01-01

Conduction disturbances requiring permanent pacemaker implantation following transcatheter aortic valve replacement (TAVR) are a common problem. Pacemaker implantation rates after TAVR appear to be higher compared to conventional aortic valve replacement. The aim of this study was to analyze whether a high annulus implantation conveys the benefit of a decreased rate of permanent pacemaker implantation while being safe and successful according to Valve Academic Research Consortium 2 (VARC2)-criteria. A total of 23 patients with symptomatic severe aortic valve stenosis, an aortic annulus of 19-27 mm and at high risk for surgery were treated with the Lotus valve. In all patients the valve was implanted in a high annulus position via femoral access. The primary device performance endpoint was VARC2-defined device success after 30 days and the primary safety endpoint was the need for permanent pacemaker implantation. The mean age was 73.23 ± 7.65 years, 46% were female, 38% were New York Heart Association class III/IV at baseline. Thirty-day follow-up data were available for all patients. The VARC2-defined device success rate after 30 days was 22/23 (96%). 2/21 (10%) patients required a newly implanted pacemaker due to 3rd degree atrioventricular block. 25% of the patients developed a new left bundle branch block after valvuloplasty or device implantation. 21 of the 23 patients (96%) had no other signs of conduction disturbances after 30 days. The approach of the modified implantation technique of Lotus TAVR device was safe and effective. The incidence of need for a permanent pacemaker following TAVR could be significantly reduced due to adopted implantation protocol.

Conversion of a Temporary Tent with Steel Frame into a Permanent Warehouse

NASA Astrophysics Data System (ADS)

Georgescu, Mircea; Ungureanu, Viorel; Grecea, Daniel; Petran, Ioan

2017-10-01

The paper is dealing with the problem of a functional conversion (involving both architectural and structural issues) applied to the case of an industrial building. As well known, temporary tents, designed according to the European Code EN13782, represent a remarkable stake on the building market and a fast and practical solution for some situations. It is exactly the case approached by the paper, where the investor has initially decided to erect on his platform a provisional shelter for agricultural machines and subsequent staff, built of a light steel structure covered by PVC roofing and cladding. This temporary tent has been acquired from a specialized supplier in form of a series product. After using the tent for a number of years, the investor has decided to convert the existing structure from architectural and structural point of view by switching to a permanent structure designed accordingly. Important changes were thus imposed both to the architectural part (technological flows, openings, facades) and especially to the structural part where this switch imposed a re-design to the codes of permanent structures (especially as far as climatic loadings are concerned). The required architectural change implied the building of a 70 cm high concrete plinth and replacing the PVC membrane temporary roofing and cladding by permanent 60 mm thick PUR sandwich panels. Together with a new system of openings this has led to renewed facades of the buildings. As for the structural change, the required conversion has imposed a thorough checking of the existing steel structure (very slender and typical to a tent) in view of transforming it into a permanent structure. The consolidation measures of the existing galvanized steel structure are described, together with the measures applied at infrastructure level in order to implement the required conversion.

Vertical and lateral forces when a permanent magnet above a superconductor traverses in arbitrary directions

NASA Astrophysics Data System (ADS)

Yang, Yong

2008-12-01

In an actual levitation system composed of high temperature superconductors (HTSs) and permanent magnets (PMs), the levitating bodies may traverse in arbitrary directions. Many previous researchers assumed that the levitating bodies moved in a vertical direction or a lateral direction in order to simplify the problem. In this paper, the vertical and lateral forces acting on the PM are calculated by the modified frozen-image method when a PM above an HTS traverses in arbitrary directions. In order to study the effects of the movement directions on the vertical and lateral forces, comparisons of the forces that act on a PM traversing in a tilted direction with those that act on a PM traversing in a vertical direction or a lateral direction have been presented.

The Status of the Career Teacher: Its Effect upon the Teacher Dropout Problem.

ERIC Educational Resources Information Center

Bush, Robert N.

As the education of pupils may be better in a school staffed with permanent career teachers rather than with itinerant teachers, every attempt should be made to increase the status of teaching and consequently the likelihood of attracting and retaining better teachers. Several steps could be taken to raise teaching to the level of other…

Acetylcholine Esterase Activity and Behavioral Response in Hypoxia Induced Neonatal Rats: Effect of Glucose, Oxygen and Epinephrine Supplementation

ERIC Educational Resources Information Center

Chathu, Finla; Krishnakumar, Amee; Paulose, Cheramadathikudyil S.

2008-01-01

Brain damage due to an episode of hypoxia remains a major problem in infants causing deficit in motor and sensory function. Hypoxia leads to neuronal functional failure, cerebral palsy and neuro-developmental delay with characteristic biochemical and molecular alterations resulting in permanent or transitory neurological sequelae or even death.…

A NEW LOOK AT SPECIAL PROBLEMS, PROJECT BEACON--A PROJECT ADDRESSED TO THE NEEDS OF THE SOCIALLY DISADVANTAGED.

ERIC Educational Resources Information Center

FISHMAN, JOSHUA

A GREAT NUMBER OF AMERICAN CHILDREN ARE GROWING UP IN SOCIALLY DEPRIVED SURROUNDINGS. THESE DEPRIVATIONS ARE REFLECTED IN LOWER EDUCATIONAL ACHIEVEMENT. TEACHERS SHOULD HAVE SPECIAL PREPARATION IN ORDER TO LESSEN THIS WASTE OF EDUCATIONAL POTENTIAL. PROJECT BEACON IS AN EFFORT TO INTRODUCE WITHIN THE PUBLIC SCHOOL SYSTEM A PERMANENT CORPS OF…

Plant Closings. Limited Advance Notice and Assistance Provided Dislocated Workers. Report to Congressional Committees.

ERIC Educational Resources Information Center

General Accounting Office, Washington, DC. Div. of Human Resources.

This is the final report in a series issued to assist Congress in assessing the problems of worker dislocation and employer practices related to advance notice and assistance provided to workers. A national survey of 2,600 business establishments was conducted to determine: (1) the extent of business closures and permanent layoffs between January…

[Realization of an adaptive method of simulating the process of temperature change of a cadaver on a microcomputer].

PubMed

Shved, E F; Novikov, P I; Vlasov, A Iu

1989-01-01

Programme based on mathematical model of the process of dead body temperature changing was developed for estimation of postmortem interval. Automatic retrieval of problem solution was performed on programmable microcalculators of "Electronica MK-61" type using adaptive approach. Diagnostical accuracy in case of dead body being preserved in permanent cooling conditions is +/- 3%.

African American Males in Foster Care and the Risk of Delinquency: The Value of Social Bonds and Permanence

ERIC Educational Resources Information Center

Ryan, Joseph P.; Testa, Mark F.; Zhai, Fuhua

2008-01-01

Juvenile delinquency remains a significant problem for child welfare systems throughout the United States. Victims of child abuse and neglect are more likely relative to children in the general population to engage in delinquency (Ryan & Testa, 2005; Widom, 1989). Although the magnitude of this relationship is not fully understood (Zingraff,…

Population Mobility in the People's Republic of China. Papers of the East-West Population Institute, No. 95.

ERIC Educational Resources Information Center

Goldstein, Sidney; Goldstein, Alice

In attempts to forestall problems inherent in too-rapid urbanization, China has instituted a migration policy designed to strictly control changes in permanent residence from rural areas or small urban places to larger cities and to encourage the development of small cities and towns. The policy is enforced through the household registration…

A Review of New Labour's Policy on School Exclusion: The Political Challenge of School Disaffection in England

ERIC Educational Resources Information Center

Reed, Jodie

2003-01-01

Shortly after coming to power, Tony Blair's New Labour government expressed its strong commitment to tackling the problem of school expulsion. The Treasury's 1998 Spending Review included the bold target to achieve "a reduction by one third in... exclusions (from 12,500 to 8,400 permanent exclusions a year) by 2002". This article gives…

Improvement of microwave feeding on a large bore ECRIS with permanent magnets by using coaxial semi-dipole antenna

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kurisu, Yosuke; Sakamoto, Naoki; Kiriyama, Ryutaro

2012-11-06

We are constructing a tandem type electron cyclotron resonance (ECR) ion source (ECRIS). The first stage of this ECRIS has a large-bore with cylindrically comb-shaped permanent magnets. 2.45GHz and 11-13GHz microwaves can be supplied individually and simultaneously to the plasma chamber. For 2.45GHz, a coaxial semi-dipole antenna is used to feed the microwaves. In previous experiments, there were two problems encountered when running the 2.45GHz microwaves. High incident power was necessary to keep ECR discharge at low operating pressure because of high reflected microwave power. The surface of a support insulator between the inner and the outer electrodes of coaxialmore » semi-dipole antenna was easily metalized by sputtering of the metal wall inside the chamber. The purpose of this study was to solve these problems. Performing several simulation experiments supports the hypothesis that the position of the support insulator is significant for microwave power efficiency. The end result was the ability to sustain ECR discharges at extremely low incident microwave power, several tens of watts, by optimized matching of the position and shape of the insulator.« less

Double talon cusps on supernumerary tooth fused to maxillary central incisor: Review of literature and report of case

PubMed Central

2014-01-01

Human tooth development is a continuous process begin at the sixth weeks in utero and extends to about sixth months after birth for the primary dentition and from sixteenth week in utero to late adolescence for permanent dentition. There is no other organ of the human body which takes so long to attain its ultimate morphology as dentition. Several physiologic growth processes participate in the progressive development of the teeth including: initiation, proliferation, histodifferentiation, morphodifferentiation, apposition, calcification, and eruption. Aberrations in different stages of tooth development can result in unique manifestations both in primary and permanent dentitions. The fact that premaxilla is the predilection site for the occurrence of supernumerary teeth, talon cusp, dens invaginatus, and geminated teeth may suggest that the embryological development of premaxilla differ from other sites of the jaws. The dental abnormalities presented in this review are of great concern to dentist and parents because they create clinical, pathological and esthetic problems. Dental practitioner should be aware of the clinical sign, associated problems and treatment options for a given case. Key words:Double talon cusps, fusion, supernumerary, case report. PMID:25593664

Environmental refugees: a growing phenomenon of the 21st century.

PubMed Central

Myers, Norman

2002-01-01

There is a new phenomenon in the global arena: environmental refugees. These are people who can no longer gain a secure livelihood in their homelands because of drought, soil erosion, desertification, deforestation and other environmental problems, together with the associated problems of population pressures and profound poverty. In their desperation, these people feel they have no alternative but to seek sanctuary elsewhere, however hazardous the attempt. Not all of them have fled their countries, many being internally displaced. But all have abandoned their homelands on a semi-permanent if not permanent basis, with little hope of a foreseeable return. In 1995, environmental refugees totalled at least 25 million people, compared with 27 million traditional refugees (people fleeing political oppression, religious persecution and ethnic troubles). The total number of environmental refugees could well double by the year 2010, and increase steadily for a good while thereafter as growing numbers of impoverished people press ever harder on overloaded environments. When global warming takes hold, there could be as many as 200 million people overtaken by sea-level rise and coastal flooding, by disruptions of monsoon systems and other rainfall regimes, and by droughts of unprecedented severity and duration. PMID:12028796

Dermatosis associated with menopause

PubMed Central

Nair, Pragya A.

2014-01-01

Menopause is defined as permanent irreversible cessation of menses brought by decline in ovarian follicular activity. Hormonal alteration results in various physical, psychological, and sexual changes in menopausal women. Associated dermatological problems can be classified as physiological changes, age-related changes, changes due to estrogen deficiency and due to hormone replacement therapy. Dermatosis seen due to estrogen deficiency includes Atrophic Vulvovaginitis, Vulvar Lichen Sclerosus, Dyaesthetic Vulvodynia, Hirsutism, Alopecia, Menopausal Flushing, Keratoderma Climactericum, Vulvovaginal Candidiasis. Dermatologists and gynecologists need to be familiar with the problems of menopausal women, as with increase in life expectancy, women passing through this phase is rising. PMID:25540566

Satellite capture as a restricted 2 + 2 body problem

NASA Astrophysics Data System (ADS)

Kanaan, Wafaa; Farrelly, David; Lanchares, Víctor

2018-04-01

A restricted 2 + 2 body problem is proposed as a possible mechanism to explain the capture of small bodies by a planet. In particular, we consider two primaries revolving in a circular mutual orbit and two small bodies of equal mass, neither of which affects the motion of the primaries. If the small bodies are temporarily captured in the Hill sphere of the smaller primary, they may get close enough to each other to exchange energy in such a way that one of them becomes permanently captured. Numerical simulations show that capture is possible for both prograde and retrograde orbits.

Recent progress in developing durable and permanent impeller pump.

PubMed

Qian, K X; Zeng, P; Ru, W M; Yuan, H Y

2002-04-01

Since 1980s, the author's impeller pump has successively achieved the device implantability, blood compatibility and flow pulsatility. In order to realize a performance durability, the author has concentrated in past years on solving the bearing problems of the impeller pump. Recent progress has been obtained in developing durable and permanent impeller blood pumps. At first, a durable impeller pump with rolling bearing and purge system has been developed, in which the wear-less rollers made of super-high-molecular weight polythene make the pump to work for years without mechanical wear; and the purge system enables the bearing to work in saline and heparin, and no thrombus therefore could be formed. Secondly, a durable centrifugal pump with rolling bearing and axially reciprocating impeller has been developed, the axial reciprocation of rotating impeller makes the fresh blood in and out of the bearing and to wash the rollers once a circle; in such way, no thrombus could be formed and no fluid infusion is necessary, which may bring inconvenience and discomfort to the receptors. Finally, a permanent maglev impeller pump has been developed, its rotor is suspended and floating in the blood under the action of permanent magnetic force and nonmagnetic forces, without need for position measurement and feed-back control. In conclusion, an implantable, pulsatile, and blood compatible impeller pump with durability may have more extensive applications than ever before and could replace the donor heart for transplantation in the future.

Female pattern alopecia: current perspectives

PubMed Central

Levy, Lauren L; Emer, Jason J

2013-01-01

Hair loss is a commonly encountered problem in clinical practice, with men presenting with a distinctive pattern involving hairline recession and vertex balding (Norwood-Hamilton classification) and women exhibiting diffuse hair thinning over the crown (increased part width) and sparing of the frontal hairline (Ludwig classification). Female pattern hair loss has a strikingly overwhelming psychological effect; thus, successful treatments are necessary. Difficulty lies in successful treatment interventions, as only two medications – minoxidil and finasteride – are approved for the treatment of androgenetic alopecia, and these medications offer mediocre results, lack of a permanent cure, and potential complications. Hair transplantation is the only current successful permanent option, and it requires surgical procedures. Several other medical options, such as antiandrogens (eg, spironolactone, oral contraceptives, cyproterone, flutamide, dutasteride), prostaglandin analogs (eg, bimatoprost, latanoprost), and ketoconazole are reported to be beneficial. Laser and light therapies have also become popular despite the lack of a profound benefit. Management of expectations is crucial, and the aim of therapy, given the current therapeutic options, is to slow or stop disease progression with contentment despite patient expectations of permanent hair regrowth. This article reviews current perspectives on therapeutic options for female pattern hair loss. PMID:24039457

Cerebral infarction caused by traumatic carotid artery dissection.

PubMed

Bayır, Ayşegül; Aydoğdu Kıreşi, Demet; Söylemez, Ali; Demirci, Osman

2012-07-01

Traumatic carotid artery dissection, if not diagnosed and treated early, is a serious problem with permanent neurological deficit and a high mortality rate of up to 40%. We present a case with delayed diagnosis of traumatic carotid artery dissection in a 21-year-old female. While there were no ischemic infarct findings on the admission cerebral computerized tomography (CT), such findings were observed on two cerebral CTs taken because of the left hemiplegia noticed seven days later when the patient regained consciousness. The patient was referred to our emergency service, and definitive diagnosis was achieved with arterial Doppler ultrasonography, cerebral magnetic resonance imaging (MRI), diffusion MRI, and MR angiography. We did not consider invasive treatment since the neurological damage was permanent and dissection grade was IV according to angiography findings. The case was discharged within a week and physiotherapy was advised. Despite the advances in diagnostic methods, diagnosis of traumatic carotid artery dissection is still missed or delayed, as in the case presented here. Early diagnosis can ameliorate permanent neurological damage or even prevent it. However, the vital factors for early diagnosis are the obtained anamnesis leading to appropriate radiological examinations, detailed physical examination and high clinical suspicion.

[Improved radiation protection for medical personnel in angiography and interventional radiology using permanent shielding devices in accordance with section 21 of the Radiography Regulation].

PubMed

Eder, H

1995-03-01

Presently examiners using angiographic methods are not accustomed to measure the exposition of parts of the body. This results in a considerable undervaluation of the really received doses (in terms of effective dose). Only a consequent application of dosimetry in parts of the body--demanded by section 35 of the German X-Ray Regulation and also by the corresponding guide-line--demonstrates the real problems i.e. oversteppings of dose limits. The use of practicable installations for permanent shielding will lead to an improvement of the situation and result in a significant decrease of the received doses and--at the same time--a minor physical burden of the examinator. Dosimetry of radiation was performed at the position of the examiner both with and without the application of permanent shielding (acrylic glass (PMMA) containing lead plus shielding of the lower part of the body). It could be demonstrated that a decrease of the received dose can be reached by a rate of 2.5 to 5 concerning the trunk and of 50 concerning the skull, upper arm and hands.

The association between prune belly syndrome and dental anomalies: a case report.

PubMed

Basso, Maria Daniela; Favretto, Carla Oliveira; Cunha, Robson Frederico

2012-12-18

Prune belly syndrome is a rare condition produced by an early mesodermal defect that causes abdominal abnormalities. However, the literature indicates that disturbances related to ectodermal development may also be present. This is the first case report in the literature to suggest that dental abnormalities are part of the broad spectrum of clinical features of prune belly syndrome. Because the syndrome causes many serious medical problems, early diagnosis of abnormalities involving the primary and permanent dentitions are encouraged. The authors report the clinical case of a 4-year-old Caucasian boy with prune belly syndrome. In addition to the triad of abdominal muscle deficiency, abnormalities of the gastrointestinal and urinary tracts, and cryptorchidism, a geminated mandibular right central incisor, agenesis of a mandibular permanent left incisor, and congenitally missing primary teeth (namely, the mandibular right and left lateral incisors) were noted. This original case report about prune belly syndrome highlights the possibility that dental abnormalities are a part of the broad spectrum of clinical features of the syndrome. Therefore, an accurate intra-oral clinical examination and radiographic evaluation are required for patients with this syndrome in order to provide an early diagnosis of abnormalities involving the primary and permanent dentitions.

Prevalence of traumatic dental injuries to permanent incisors among 12-year-old school children in Davangere, South India.

PubMed

Ravishankar, Telgi Lingesh; Kumar, Mohapatra Ashok; Ramesh, Nagrajappa; Chaitra, Telgi Ravishankar

2010-01-01

To assess the prevalence and factors associated with traumatic injuries to permanent incisors of 12-year-old school children in Davangere, India. In total, 1020 12-year-old school children were selected. Two trained and calibrated clinicians examined the children in the school environment using the World Health Organization Classification of Tooth Fracture (1978). Examination was also done for lip coverage and maxillary overjet using the Community Periodontal Index probe. Children were then interviewed using a structured questionnaire for demographic data and history of the injury. The overall prevalence rate of traumatic dental injuries (TDI) to permanent incisor teeth was 15.1%. The prevalence of TDI was higher in boys compared to girls. The major cause of TDI was falling followed by collision. The maxillary incisors were commonly injured, involving mainly enamel fracture. Children with excessive overjet and inadequate lip coverage were more likely to have injuries. TDI could be a serious dental public health problem among children. Thus, there is an urgent need to collect local data on dental injuries in order to obtain a more comprehensive picture of dental health.

[Management of financial resources of permanent education in health: challenge of the in-service learning integration committees].

PubMed

Ferraz, Fabiane; Backes, Vânia Marli Schubert; Mercado-Martinez, Francisco Javier; Feuerwerker, Laura Camargo Macruz; Lino, Mônica Motta

2013-06-01

Despite adhering to the dynamics established in the Management Pact, the use of financial resources of Permanent Education in Health (PEH) still features as a problem in Brazil. This study analyzes how the management of these financial resources by two Permanent In-Service Learning Integration Committees (ICLS) evolves in the State of Santa Catarina, Brazil. It involves a qualitative, participatory research study adapted from Paulo Freire's Thematic Research conducted with 56 members from two ICLS between May and December 2009. After setting up the research groups, the members participated in the stages of theme generation surveys, encoding, decoding, and critical exposition of the reality. Participant observation and dialogue were the main data collection techniques. The results indicate that the two ICLS are not dissimilar in terms of issues of management of resources destined for policy, with bureaucracy, the indefinition of forms of financial management and delays that permeate regional structures responsible for resource management being the main factors detected. The participants considered the elaboration of PEH actions in the management of financial resources at state level to be the main opportunities for change.

Dynamics of magnetic particles in cylindrical Halbach array: implications for magnetic cell separation and drug targeting.

PubMed

Babinec, Peter; Krafcík, Andrej; Babincová, Melánia; Rosenecker, Joseph

2010-08-01

Magnetic nanoparticles for therapy and diagnosis are at the leading edge of the rapidly developing field of bionanotechnology. In this study, we have theoretically studied motion of magnetic nano- as well as micro-particles in the field of cylindrical Halbach array of permanent magnets. Magnetic flux density was modeled as magnetostatic problem by finite element method and particle motion was described using system of ordinary differential equations--Newton law. Computations were done for nanoparticles Nanomag-D with radius 65 nm, which are often used in magnetic drug targeting, as well as microparticles DynaBeads-M280 with radius 1.4 microm, which can be used for magnetic separation. Analyzing snapshots of trajectories of hundred magnetite particles of each size in the water as well as in the air, we have found that optimally designed magnetic circuits of permanent magnets in quadrupolar Halbach array have substantially shorter capture time than simple blocks of permanent magnets commonly used in experiments, therefore, such a Halbach array may be useful as a potential source of magnetic field for magnetic separation and targeting of magnetic nanoparticles as well as microparticles for delivery of drugs, genes, and cells in various biomedical applications.

Permanent magnet assembly producing a strong tilted homogeneous magnetic field: towards magic angle field spinning NMR and MRI.

PubMed

Sakellariou, Dimitris; Hugon, Cédric; Guiga, Angelo; Aubert, Guy; Cazaux, Sandrine; Hardy, Philippe

2010-12-01

We introduce a cylindrical permanent magnet design that generates a homogeneous and strong magnetic field having an arbitrary inclination with respect to the axis of the cylinder. The analytical theory of 3 D magnetostatics has been applied to this problem, and a hybrid magnet structure has been designed. This structure contains two magnets producing a longitudinal and transverse component for the magnetic field, whose amplitudes and homogeneities can be fully controlled by design. A simple prototype has been constructed using inexpensive small cube magnets, and its magnetic field has been mapped using Hall and NMR probe sensors. This magnet can, in principle, be used for magic angle field spinning NMR and MRI experiments allowing for metabolic chemical shift profiling in small living animals. Copyright © 2010 John Wiley & Sons, Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bachman, Daniel; Chen, Zhijiang; Wang, Christopher

Phase errors caused by fabrication variations in silicon photonic integrated circuits are an important problem, which negatively impacts device yield and performance. This study reports our recent progress in the development of a method for permanent, postfabrication phase error correction of silicon photonic circuits based on femtosecond laser irradiation. Using beam shaping technique, we achieve a 14-fold enhancement in the phase tuning resolution of the method with a Gaussian-shaped beam compared to a top-hat beam. The large improvement in the tuning resolution makes the femtosecond laser method potentially useful for very fine phase trimming of silicon photonic circuits. Finally, wemore » also show that femtosecond laser pulses can directly modify silicon photonic devices through a SiO 2 cladding layer, making it the only permanent post-fabrication method that can tune silicon photonic circuits protected by an oxide cladding.« less

The Effect of Early Confirmation of Hearing Loss on the Behaviour in Middle Childhood of Children with Bilateral Hearing Impairment

ERIC Educational Resources Information Center

Stevenson, Jim; McCann, Donna C.; Law, Catherine M.; Mullee, Mark; Petrou, Stavros; Worsfold, Sarah; Yuen, Ho M.; Kennedy, Colin R.

2011-01-01

Aim: To determine if the benefit of early confirmation of permanent childhood hearing impairment (PCHI) on children's receptive language development is associated with fewer behavioural problems. Method: Follow-up of a total population cohort of 120 children with PCHI of moderate or greater severity (greater than or equal to 40 decibels relative…

Preliminary survey of markets and prices of forest products in the Del-Mar-Va Peninsula

Treesearch

George E. Doverspike

1949-01-01

This preliminary survey was designed to explore the present methods of marketing farm products and the problems involved in collecting price information about primary forest products. No attempt was made to initiate a permanent price-reporting service, since that was beyond the scope of the survey. However, certain price information was obtained; it is shown in table 2...

The American Farmworker Community. Prepared for the Migrant Head Start Resource Center's Health/Disability/Social Service/Parent Involvement Institute (San Antonio, Texas, January 5-10, 1992).

ERIC Educational Resources Information Center

Velarde, Servando Jose

The social, cultural and economic issues of America's migrant farmworkers are producing an ever widening gap between the farmworker community and mainstream society. Comprehensive and coordinated efforts by public and private sectors are needed to stabilize the farm labor force and to permanently resolve the migrant farmworkers problems. The…

The Collision of the Adoption and Safe Families Act and Substance Abuse: Research-Based Education and Training Priorities for Child Welfare Professionals

ERIC Educational Resources Information Center

Schroeder, Julie; Lemieux, Catherine; Pogue, Rene

2008-01-01

A large body of descriptive literature demonstrates the problem of substance abuse in child welfare. The 1997 Adoption and Safe Families Act (ASFA) established time frames that make children's need for permanency the overriding priority in families involved with the child welfare system. Child welfare workers often lack proper knowledge and skill…

Unlocking hidden genomic sequence

PubMed Central

Keith, Jonathan M.; Cochran, Duncan A. E.; Lala, Gita H.; Adams, Peter; Bryant, Darryn; Mitchelson, Keith R.

2004-01-01

Despite the success of conventional Sanger sequencing, significant regions of many genomes still present major obstacles to sequencing. Here we propose a novel approach with the potential to alleviate a wide range of sequencing difficulties. The technique involves extracting target DNA sequence from variants generated by introduction of random mutations. The introduction of mutations does not destroy original sequence information, but distributes it amongst multiple variants. Some of these variants lack problematic features of the target and are more amenable to conventional sequencing. The technique has been successfully demonstrated with mutation levels up to an average 18% base substitution and has been used to read previously intractable poly(A), AT-rich and GC-rich motifs. PMID:14973330

Mechanisms and consequences of alternative polyadenylation

PubMed Central

Di Giammartino, Dafne Campigli; Nishida, Kensei; Manley, James L.

2011-01-01

Summary Alternative polyadenylation (APA) is emerging as a widespread mechanism used to control gene expression. Like alternative splicing, usage of alternative poly(A) sites allows a single gene to encode multiple mRNA transcripts. In some cases, this changes the mRNA coding potential; in other cases, the code remains unchanged but the 3’UTR length is altered, influencing the fate of mRNAs in several ways, for example, by altering the availability of RNA binding protein sites and microRNA binding sites. The mechansims governing both global and gene-specific APA are only starting to be deciphered. Here we review what is known about these mechanisms and the functional consequences of alternative polyadenlyation. PMID:21925375

Complete genome sequence of keunjorong mosaic virus, a potyvirus from Cynanchum wilfordii.

PubMed

Nam, Moon; Lee, Joo-Hee; Choi, Hong Soo; Lim, Hyoun-Sub; Moon, Jae Sun; Lee, Su-Heon

2013-08-01

We have determined the complete genome sequence of keunjorong mosaic virus (KjMV). The KjMV genome is composed of 9,611 nucleotides, excluding the 3'-terminal poly(A) tail. It contains two open reading frames (ORFs), with the large one encoding a polyprotein of 3,070 amino acids and the small overlapping ORF encoding a PIPO protein of 81 amino acids. The KjMV genome shared the highest nucleotide sequence identity (57.5  %) with pepper mottle virus and freesia mosaic virus, two members of the genus Potyvirus. Based on the phylogenetic relatedness to known potyviruses, KjMV appears to be a member of a new species in the genus Potyvirus.

The use of carrier RNA to enhance DNA extraction from microfluidic-based silica monoliths.

PubMed

Shaw, Kirsty J; Thain, Lauren; Docker, Peter T; Dyer, Charlotte E; Greenman, John; Greenway, Gillian M; Haswell, Stephen J

2009-10-12

DNA extraction was carried out on silica-based monoliths within a microfluidic device. Solid-phase DNA extraction methodology was applied in which the DNA binds to silica in the presence of a chaotropic salt, such as guanidine hydrochloride, and is eluted in a low ionic strength solution, such as water. The addition of poly-A carrier RNA to the chaotropic salt solution resulted in a marked increase in the effective amount of DNA that could be recovered (25ng) compared to the absence of RNA (5ng) using the silica-based monolith. These findings confirm that techniques utilising nucleic acid carrier molecules can enhance DNA extraction methodologies in microfluidic applications.

RNA binding protein and binding site useful for expression of recombinant molecules

DOEpatents

Mayfield, Stephen P.

2006-10-17

The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

RNA binding protein and binding site useful for expression of recombinant molecules

DOEpatents

Mayfield, Stephen

2000-01-01

The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

Riemann-Hypothesis Millennium-Problem(MP) Physics Proof via CATEGORY-SEMANTICS(C-S)/F =C Aristotle SQUARE-of-OPPOSITION(SoO) DEduction-LOGIC DichotomY

NASA Astrophysics Data System (ADS)

Baez, Joao-Joan; Lapidaryus, Michelle; Siegel, Edward Carl-Ludwig

2013-03-01

Riemann-hypothesis physics-proof combines: Siegel-Antono®-Smith[AMS Joint Mtg.(2002)- Abs.973-03-126] digits on-average statistics HIll[Am. J. Math 123, 3, 887(1996)] logarithm-function's (1,0)- xed-point base =units =scale-invariance proven Newcomb [Am. J. Math. 4, 39(1881)]-Weyl[Goett. Nachr.(1914); Math. Ann.7, 313(1916)]-Benford[Proc. Am. Phil. Soc. 78, 4, 51(1938)]-law [Kac,Math. of Stat.-Reasoning(1955); Raimi, Sci. Am. 221, 109(1969)] algebraic-inversion to ONLY Bose-Einstein quantum-statistics(BEQS) with digit d = 0 gapFUL Bose-Einstein Condensation(BEC) insight that digits are quanta are bosons because bosons are and always were quanta are and always were digits, via Siegel-Baez category-semantics tabular list-format matrix truth-table analytics in Plato-Aristotle classic ''square-of-opposition'' : FUZZYICS =CATEGORYICS/Category-Semantics, with Goodkind Bose-Einstein Condensation (BEC) ABOVE ground-state with/and Rayleigh(cut-limit of ''short-cut method''1870)-Polya(1922)-''Anderson''(1958) localization [Doyle and Snell,Random-Walks and Electrical-Networks, MAA(1981)-p.99-100!!!] in Brillouin[Wave-Propagation in Periodic-Structures(1946) Dover(1922)]-Hubbard-Beeby[J.Phys.C(1967)] Siegel[J.Nonxline-Sol.40,453(1980)] generalized-disorder collective-boson negative-dispersion mode-softening universality-principle(G...P) first use of the ``square-of-opposition'' in physics since Plato and Aristote!!!

Full genome analysis of swine genotype 3 hepatitis E virus isolated from eastern China.

PubMed

Shuai, Jiang-Bing; Li, Lu-Huan; Li, Ai-Yun; He, Yong-Qiang; Zhang, Xiao-Feng

2017-06-01

Hepatitis E is believed to occur in both endemic and sporadic forms in developing countries, which causes a major public health problem in Asia and Africa (Meng, 2010; Wang et al., 2016a). Recent studies have documented that the disease is also endemic in many industrialized countries (Wenzel et al., 2011). The causative agent, hepatitis E virus (HEV), belonging to the genus Orthohepevirus, is a non-enveloped RNA virus with a single-stranded, positive-sense genome of approximately 7.2 kb (Smith et al., 2014). The genome consists of a short 5' un-translated region (UTR), three open reading frames (ORFs), and a 3' UTR containing a poly(A) tail (Meng, 2011). Four recognized major genotypes of HEV are identified: genotype 1 (Asian and African strains), genotype 2 (a Mexican strain), genotype 3 (primarily from America and Europe, and some Asian countries), and genotype 4 (mainly Asian strains) (Smith et al., 2016). Previous study revealed that HEV genotype 4 is the dominant zoonotic HEV genotype in China (Wang et al., 2016a). However, infections with HEV 3 have been found more commonly in recent years in China (Liu et al., 2012; Zhang et al., 2013). To date, only one full genome of Chinese swine genotype 3 HEV strain from Shanghai has been documented (Si et al., 2009). We report here the first full genome sequence of a genotype 3 swine HEV strain from Zhejiang, China.

No Solutions: Resisting Certainty in Water Supply Management

NASA Astrophysics Data System (ADS)

Cockerill, K.; Armstrong, M.; Richter, J.; Okie, J. G.

2017-12-01

Although most scholars and water managers implicitly understand that managing water resources is an ongoing need, both popular and academic literature routinely use the words `solution' and `solve' in discussing water management concerns. The word `solution' reflects a quest for certainty, stability, permanence. A focus on `solving' creates a simplistic expectation that some person or institution is responsible for implementing a solution and that once `solved' the issue no longer requires attention. The reality, however, is water management is a wicked problem, meaning it is amorphous, involves multiple definitions, is embedded in complex systems, and hence is intractable. By definition, wicked problems defy solution. Our interdisciplinary project integrates research from across a broad spectrum of biological, physical, and social sciences. We find that framing a problem in terms of `solving' affects how people think, feel, behave toward the problem. Further, our work suggests that the prevalence of solution- based language has simultaneously generated expectations that science / scientists can predict and control biophysical systems and that science is not to be trusted because it has failed to deliver on previous promises to permanently `solve' events like floods or droughts. Hydrologic systems, are, of course highly uncertain. Hence, reiterating a simplistic insistence on `solving' water management concerns may result in decreased public attention to or support for more complex policy discussions that could provide long-term management strategies. Using the language of `solutions' with expectations of certainty sets hydrologic researchers and water managers up to fail. Managing water is a social responsibility and it will require consistent attention in the future, just as it has throughout human history. Scientists have a key role to play in explaining how various hydrologic systems function, but they should not be expected to `solve' pressing water management needs. Rather, reconsidering the language used to frame water management concerns can help us recognize our own culpability in creating water problems and our responsibility in continuously managing this most essential resource.

The Difficult Stoma: Challenges and Strategies

PubMed Central

Strong, Scott A.

2016-01-01

The problems that a patient experiences after the creation of a temporary or permanent stoma can result from many factors, but a carefully constructed stoma located in an ideal location is typically associated with appropriate function and an acceptable quality of life. The construction of the stoma can be confounded by many concomitant conditions that increase the distance that the bowel must traverse or shorten the bowel's capacity to reach. Stomas can be further troubled by a variety of problems that potentially arise early in the recovery period or months later. Surgeons must be familiar with these obstacles and complications to avoid their occurrence and minimize their impact. PMID:27247541

Addressing homelessness among people with mental illnesses: a model of long-term philanthropic effectiveness.

PubMed

Brousseau, Ruth Tebbets

2009-01-01

Foundations are often criticized for their short attention spans and inability to continue funding the toughest social problems. Homelessness among people with mental illnesses is considered among the most intractable of social issues. This paper explores the role of permanent supportive housing in reducing homelessness among the mentally ill; the role of the Corporation for Supportive Housing in developing, authenticating, and disseminating its model; and its long-term funding relationship with the Conrad N. Hilton Foundation, which has facilitated this trajectory. The paper tells the story of how long-term funding, strategically used, is making inroads into this serious mental health problem.

Site Partitioning for Redundant Arrays of Distributed Disks

NASA Technical Reports Server (NTRS)

Mourad, Antoine N.; Fuchs, W. Kent; Saab, Daniel G.

1996-01-01

Redundant arrays of distributed disks (RADD) can be used in a distributed computing system or database system to provide recovery in the presence of disk crashes and temporary and permanent failures of single sites. In this paper, we look at the problem of partitioning the sites of a distributed storage system into redundant arrays in such a way that the communication costs for maintaining the parity information are minimized. We show that the partitioning problem is NP-hard. We then propose and evaluate several heuristic algorithms for finding approximate solutions. Simulation results show that significant reduction in remote parity update costs can be achieved by optimizing the site partitioning scheme.

Colostomy irrigation: an important issue for Muslim individuals.

PubMed

Karadag, Ayise; Baykara, Zehra Göçmen

2009-01-01

Colostomy irrigation (CI) is a bowel management method in individuals with permanent colostomy, as an alternative to pouch use, which may provide continence. CI helps the individuals with an artificial stoma to adjust to the stoma and may increase their quality of life (QOL). An uncontrolled intestinal gas discharge invalidates ablution, and noisy gas discharge and smell prevents congregational prayers, which cause problems to Muslims with stomas. Therefore, CI may be an appropriate solution for this patient group. Using the example of one affected individual we discuss how the praying problem can be resolved with teaching to self-perform CI and emphasize the beneficial effects on QOL.

Combustion and fires in low gravity

NASA Technical Reports Server (NTRS)

Friedman, Robert

1994-01-01

Fire safety always receives priority attention in NASA mission designs and operations, with emphasis on fire prevention and material acceptance standards. Recently, interest in spacecraft fire-safety research and development has increased because improved understanding of the significant differences between low-gravity and normal-gravity combustion suggests that present fire-safety techniques may be inadequate or, at best, non-optimal; and the complex and permanent orbital operations in Space Station Freedom demand a higher level of safety standards and practices. This presentation outlines current practices and problems in fire prevention and detection for spacecraft, specifically the Space Station Freedom's fire protection. Also addressed are current practices and problems in fire extinguishment for spacecraft.

Comparative analysis of techniques for evaluating the effectiveness of aircraft computing systems

NASA Technical Reports Server (NTRS)

Hitt, E. F.; Bridgman, M. S.; Robinson, A. C.

1981-01-01

Performability analysis is a technique developed for evaluating the effectiveness of fault-tolerant computing systems in multiphase missions. Performability was evaluated for its accuracy, practical usefulness, and relative cost. The evaluation was performed by applying performability and the fault tree method to a set of sample problems ranging from simple to moderately complex. The problems involved as many as five outcomes, two to five mission phases, permanent faults, and some functional dependencies. Transient faults and software errors were not considered. A different analyst was responsible for each technique. Significantly more time and effort were required to learn performability analysis than the fault tree method. Performability is inherently as accurate as fault tree analysis. For the sample problems, fault trees were more practical and less time consuming to apply, while performability required less ingenuity and was more checkable. Performability offers some advantages for evaluating very complex problems.

Successful Management of Infected Facial Filler with Brucella.

PubMed

Alshaer, Zahra; Alsaadi, Yazeed; Mrad, Mohamed Amir

2018-06-11

The widespread desire to maintain youth and beauty with minimally invasive procedures made the use of soft tissue fillers an attractive option to correct numerous aesthetic problems. However, many complications have emerged recently especially with the use of non-FDA-approved permanent materials. In this case report, we are demonstrating the effective management of a patient with Brucella isolated from a facial abscess at the site of prior permanent filler injection done 17 years ago. A 56-year-old woman presented complaining of painful swelling of the right cheek after a failed trial of filler evacuation and intralesional corticosteroid injection. The patient was interviewed carefully, and physical examination was performed, followed by culture and imaging. The patient had a facial abscess that was complicated by parotid infiltration by Brucella. Eventually she was managed successfully by anti-Brucella antibiotics for 6 months with no further complaints. A review of causative organisms in the literature along with recommendations for management is discussed. Permanent fillers have shown many complications that can occur even years after injection. Therefore, physicians should be careful when using permanent fillers and should restrict their use to certain situations. Moreover, rare infections must be kept in mind and careful history, including travel history and animal contact, needs to be considered particularly in the unusual scenarios. This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

National Transonic Facility model and model support vibration problems

NASA Technical Reports Server (NTRS)

Young, Clarence P., Jr.; Popernack, Thomas G., Jr.; Gloss, Blair B.

1990-01-01

Vibrations of models and model support system were encountered during testing in the National Transonic Facility. Model support system yaw plane vibrations have resulted in model strain gage balance design load limits being reached. These high levels of vibrations resulted in limited aerodynamic testing for several wind tunnel models. The yaw vibration problem was the subject of an intensive experimental and analytical investigation which identified the primary source of the yaw excitation and resulted in attenuation of the yaw oscillations to acceptable levels. This paper presents the principal results of analyses and experimental investigation of the yaw plane vibration problems. Also, an overview of plans for development and installation of a permanent model system dynamic and aeroelastic response measurement and monitoring system for the National Transonic Facility is presented.

Spontaneous and engineered deletions in the 3' noncoding region of tick-borne encephalitis virus: construction of highly attenuated mutants of a flavivirus.

PubMed

Mandl, C W; Holzmann, H; Meixner, T; Rauscher, S; Stadler, P F; Allison, S L; Heinz, F X

1998-03-01

The flavivirus genome is a positive-strand RNA molecule containing a single long open reading frame flanked by noncoding regions (NCR) that mediate crucial processes of the viral life cycle. The 3' NCR of tick-borne encephalitis (TBE) virus can be divided into a variable region that is highly heterogeneous in length among strains of TBE virus and in certain cases includes an internal poly(A) tract and a 3'-terminal conserved core element that is believed to fold as a whole into a well-defined secondary structure. We have now investigated the genetic stability of the TBE virus 3' NCR and its influence on viral growth properties and virulence. We observed spontaneous deletions in the variable region during growth of TBE virus in cell culture and in mice. These deletions varied in size and location but always included the internal poly(A) element of the TBE virus 3' NCR and never extended into the conserved 3'-terminal core element. Subsequently, we constructed specific deletion mutants by using infectious cDNA clones with the entire variable region and increasing segments of the core element removed. A virus mutant lacking the entire variable region was indistinguishable from wild-type virus with respect to cell culture growth properties and virulence in the mouse model. In contrast, even small extensions of the deletion into the core element led to significant biological effects. Deletions extending to nucleotides 10826, 10847, and 10870 caused distinct attenuation in mice without measurable reduction of cell culture growth properties, which, however, were significantly restricted when the deletion was extended to nucleotide 10919. An even larger deletion (to nucleotide 10994) abolished viral viability. In spite of their high degree of attenuation, these mutants efficiently induced protective immune responses even at low inoculation doses. Thus, 3'-NCR deletions represent a useful technique for achieving stable attenuation of flaviviruses that can be included in the rational design of novel flavivirus live vaccines.

Comprehensive annotation of Glossina pallidipes salivary gland hypertrophy virus from Ethiopian tsetse flies: a proteogenomics approach

PubMed Central

Kariithi, Henry M.; Cousserans, François; Parker, Nicolas J.; İnce, İkbal Agah; Scully, Erin D.; Boeren, Sjef; Geib, Scott M.; Mekonnen, Solomon; Vlak, Just M.; Parker, Andrew G.; Vreysen, Marc J. B.; Bergoin, Max

2016-01-01

Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; family Hytrosaviridae) can establish asymptomatic and symptomatic infection in its tsetse fly host. Here, we present a comprehensive annotation of the genome of an Ethiopian GpSGHV isolate (GpSGHV-Eth) compared with the reference Ugandan GpSGHV isolate (GpSGHV-Uga; GenBank accession number EF568108). GpSGHV-Eth has higher salivary gland hypertrophy syndrome prevalence than GpSGHV-Uga. We show that the GpSGHV-Eth genome has 190 291 nt, a low G+C content (27.9 %) and encodes 174 putative ORFs. Using proteogenomic and transcriptome mapping, 141 and 86 ORFs were mapped by transcripts and peptides, respectively. Furthermore, of the 174 ORFs, 132 had putative transcriptional signals [TATA-like box and poly(A) signals]. Sixty ORFs had both TATA-like box promoter and poly(A) signals, and mapped by both transcripts and peptides, implying that these ORFs encode functional proteins. Of the 60 ORFs, 10 ORFs are homologues to baculovirus and nudivirus core genes, including three per os infectivity factors and four RNA polymerase subunits (LEF4, 5, 8 and 9). Whereas GpSGHV-Eth and GpSGHV-Uga are 98.1 % similar at the nucleotide level, 37 ORFs in the GpSGHV-Eth genome had nucleotide insertions (n = 17) and deletions (n = 20) compared with their homologues in GpSGHV-Uga. Furthermore, compared with the GpSGHV-Uga genome, 11 and 24 GpSGHV ORFs were deleted and novel, respectively. Further, 13 GpSGHV-Eth ORFs were non-canonical; they had either CTG or TTG start codons instead of ATG. Taken together, these data suggest that GpSGHV-Eth and GpSGHV-Uga represent two different lineages of the same virus. Genetic differences combined with host and environmental factors possibly explain the differential GpSGHV pathogenesis observed in different G. pallidipes colonies. PMID:26801744

Enhanced expression of rat hepatic CYP2B1/2B2 and 2E1 by pyridine: differential induction kinetics and molecular basis of expression.

PubMed

Kim, H; Putt, D; Reddy, S; Hollenberg, P F; Novak, R F

1993-11-01

Expression of the cytochrome P450 (CYP) 2B subfamily in rat and rabbit hepatic tissues after pyridine (PY) treatment has been examined, and the molecular basis for enhanced 2B1/2B2 expression has been determined. P450 expression was monitored using metabolic activity, sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblot analyses, and the identity of the proteins was confirmed through N-terminus microsequence analysis. PY caused a dose-dependent elevation of hepatic CYP2B1/B2B levels in rats, which ranged from 4- to 22-fold over the dosing regimen of 100 to 400 mg PY/kg/day, for 3 days, respectively. PY at low dose failed to induce CYP2B in rabbit hepatic tissue, suggesting a species-dependent response in 2B expression. Anti-2B1 IgG addition to PY-induced microsomes inhibited benzphetamine N-demethylase activity by only approximately 15%, in sharp contrast to the approximately 73% inhibition observed for phenobarbital-induced microsomes, suggesting the induction of other form(s) of P450 having benzphetamine N-demethylase activity. Northern blot analysis revealed that PY treatment increased 2B1 and 2B2 poly(A)+ RNA levels approximately 69- and approximately 34-fold, respectively, whereas the 2E1 poly(A)+ RNA levels failed to increase. The results of this study show that PY induces CYP2B1/2B2 and that induction is species-dependent and kinetically distinguishable from 2E1 induction. Moreover, 2B1/2B2 induction occurs as a result of elevated mRNA levels associated with either transcriptional activation or mRNA stabilization, and it differs from the mechanism of hepatic 2E1 induction by PY.

Efficient Cleavage of Ribosome-Associated Poly(A)-Binding Protein by Enterovirus 3C Protease

PubMed Central

Kuyumcu-Martinez, N. Muge; Joachims, Michelle; Lloyd, Richard E.

2002-01-01

Poliovirus (PV) causes a rapid and drastic inhibition of host cell cap-dependent protein synthesis during infection while preferentially allowing cap-independent translation of its own genomic RNA via an internal ribosome entry site element. Inhibition of cap-dependent translation is partly mediated by cleavage of an essential translation initiation factor, eIF4GI, during PV infection. In addition to cleavage of eIF4GI, cleavage of eIF4GII and poly(A)-binding protein (PABP) has been recently proposed to contribute to complete host translation shutoff; however, the relative importance of eIF4GII and PABP cleavage has not been determined. At times when cap-dependent translation is first blocked during infection, only 25 to 35% of the total cellular PABP is cleaved; therefore, we hypothesized that the pool of PABP associated with polysomes may be preferentially targeted by viral proteases. We have investigated what cleavage products of PABP are produced in vivo and the substrate determinants for cleavage of PABP by 2A protease (2Apro) or 3C protease (3Cpro). Our results show that PABP in ribosome-enriched fractions is preferentially cleaved in vitro and in vivo compared to PABP in other fractions. Furthermore, we have identified four N-terminal PABP cleavage products produced during PV infection and have shown that viral 3C protease generates three of the four cleavage products. Also, 3Cpro is more efficient in cleaving PABP in ribosome-enriched fractions than 2Apro in vitro. In addition, binding of PABP to poly(A) RNA stimulates 3Cpro-mediated cleavage and inhibits 2Apro-mediated cleavage. These results suggest that 3Cpro plays a major role in processing PABP during virus infection and that the interaction of PABP with translation initiation factors, ribosomes, or poly(A) RNA may promote its cleavage by viral 2A and 3C proteases. PMID:11836384

HuR binding to cytoplasmic mRNA is perturbed by heat shock

PubMed Central

Gallouzi, Imed-Eddine; Brennan, Christopher M.; Stenberg, Myrna G.; Swanson, Maurice S.; Eversole, Ashley; Maizels, Nancy; Steitz, Joan A.

2000-01-01

AU-rich elements (AREs) located in the 3′ untranslated region target the mRNAs encoding many protooncoproteins, cytokines, and lymphokines for rapid degradation. HuR, a ubiquitously expressed member of the embryonic lethal abnormal vision (ELAV) family of RNA-binding proteins, binds ARE sequences and selectively stabilizes ARE-containing reporter mRNAs when overexpressed in transiently transfected cells. HuR appears predominantly nucleoplasmic but has been shown to shuttle between the nucleus and cytoplasm via a novel shuttling sequence HNS. We report generation of a mouse monoclonal antibody 3A2 that both immunoblots and immunoprecipitates HuR protein; it recognizes an epitope located in the first of HuR's three RNA recognition motifs. This antibody was used to probe HuR interactions with mRNA before and after heat shock, a condition that has been reported to stabilize ARE-containing mRNAs. At 37°C, approximately one-third of the cytoplasmic HuR appears polysome associated, and in vivo UV crosslinking reveals that HuR interactions with poly(A)+ RNA are predominantly cytoplasmic rather than nuclear. This comprises evidence that HuR directly interacts with mRNA in vivo. After heat shock, 12–15% of HuR accumulates in discrete foci in the cytoplasm, but surprisingly the majority of HuR crosslinks instead to nuclear poly(A)+ RNA, whose levels are dramatically increased in the stressed cells. This behavior of HuR differs from that of another ARE-binding protein, hnRNP D, which has been implicated as an effector of mRNA decay rather than mRNA stabilization and of the general pre-RNA-binding protein hnRNP A1. We interpret these differences to mean that the temporal association of HuR with ARE-containing mRNAs is different from that of these other two proteins. PMID:10737787

Nucleotide sequence and genetic organization of barley stripe mosaic virus RNA gamma.

PubMed

Gustafson, G; Hunter, B; Hanau, R; Armour, S L; Jackson, A O

1987-06-01

The complete nucleotide sequences of RNA gamma from the Type and ND18 strains of barley stripe mosaic virus (BSMV) have been determined. The sequences are 3164 (Type) and 2791 (ND18) nucleotides in length. Both sequences contain a 5'-noncoding region (87 or 88 nucleotides) which is followed by a long open reading frame (ORF1). A 42-nucleotide intercistronic region separates ORF1 from a second, shorter open reading frame (ORF2) located near the 3'-end of the RNA. There is a high degree of homology between the Type and ND18 strains in the nucleotide sequence of ORF1. However, the Type strain contains a 366 nucleotide direct tandem repeat within ORF1 which is absent in the ND18 strain. Consequently, the predicted translation product of Type RNA gamma ORF1 (mol wt 87,312) is significantly larger than that of ND18 RNA gamma ORF1 (mol wt 74,011). The amino acid sequence of the ORF1 polypeptide contains homologies with putative RNA polymerases from other RNA viruses, suggesting that this protein may function in replication of the BSMV genome. The nucleotide sequence of RNA gamma ORF2 is nearly identical in the Type and ND18 strains. ORF2 codes for a polypeptide with a predicted molecular weight of 17,209 (Type) or 17,074 (ND18) which is known to be translated from a subgenomic (sg) RNA. The initiation point of this sgRNA has been mapped to a location 27 nucleotides upstream of the ORF2 initiation codon in the intercistronic region between ORF1 and ORF2. The sgRNA is not coterminal with the 3'-end of the genomic RNA, but instead contains heterogeneous poly(A) termini up to 150 nucleotides long (J. Stanley, R. Hanau, and A. O. Jackson, 1984, Virology 139, 375-383). In the genomic RNA gamma, ORF2 is followed by a short poly(A) tract and a 238-nucleotide tRNA-like structure.

The Specificity and Flexibility of L1 Reverse Transcription Priming at Imperfect T-Tracts

PubMed Central

Viollet, Sébastien; Mir, Ashfaq Ali; Gabus, Caroline; Darlix, Jean-Luc; Cristofari, Gaël

2013-01-01

L1 retrotransposons have a prominent role in reshaping mammalian genomes. To replicate, the L1 ribonucleoprotein particle (RNP) first uses its endonuclease (EN) to nick the genomic DNA. The newly generated DNA end is subsequently used as a primer to initiate reverse transcription within the L1 RNA poly(A) tail, a process known as target-primed reverse transcription (TPRT). Prior studies demonstrated that most L1 insertions occur into sequences related to the L1 EN consensus sequence (degenerate 5′-TTTT/A-3′ sites) and frequently preceded by imperfect T-tracts. However, it is currently unclear whether—and to which degree—the liberated 3′-hydroxyl extremity on the genomic DNA needs to be accessible and complementary to the poly(A) tail of the L1 RNA for efficient priming of reverse transcription. Here, we employed a direct assay for the initiation of L1 reverse transcription to define the molecular rules that guide this process. First, efficient priming is detected with as few as 4 matching nucleotides at the primer 3′ end. Second, L1 RNP can tolerate terminal mismatches if they are compensated within the 10 last bases of the primer by an increased number of matching nucleotides. All terminal mismatches are not equally detrimental to DNA extension, a C being extended at higher levels than an A or a G. Third, efficient priming in the context of duplex DNA requires a 3′ overhang. This suggests the possible existence of additional DNA processing steps, which generate a single-stranded 3′ end to allow L1 reverse transcription. Based on these data we propose that the specificity of L1 reverse transcription initiation contributes, together with the specificity of the initial EN cleavage, to the distribution of new L1 insertions within the human genome. PMID:23675310

2′-O Methylation of Internal Adenosine by Flavivirus NS5 Methyltransferase

PubMed Central

Dong, Hongping; Chang, David C.; Hua, Maggie Ho Chia; Lim, Siew Pheng; Chionh, Yok Hian; Hia, Fabian; Lee, Yie Hou; Kukkaro, Petra; Lok, Shee-Mei; Dedon, Peter C.; Shi, Pei-Yong

2012-01-01

RNA modification plays an important role in modulating host-pathogen interaction. Flavivirus NS5 protein encodes N-7 and 2′-O methyltransferase activities that are required for the formation of 5′ type I cap (m7GpppAm) of viral RNA genome. Here we reported, for the first time, that flavivirus NS5 has a novel internal RNA methylation activity. Recombinant NS5 proteins of West Nile virus and Dengue virus (serotype 4; DENV-4) specifically methylates polyA, but not polyG, polyC, or polyU, indicating that the methylation occurs at adenosine residue. RNAs with internal adenosines substituted with 2′-O-methyladenosines are not active substrates for internal methylation, whereas RNAs with adenosines substituted with N6-methyladenosines can be efficiently methylated, suggesting that the internal methylation occurs at the 2′-OH position of adenosine. Mass spectroscopic analysis further demonstrated that the internal methylation product is 2′-O-methyladenosine. Importantly, genomic RNA purified from DENV virion contains 2′-O-methyladenosine. The 2′-O methylation of internal adenosine does not require specific RNA sequence since recombinant methyltransferase of DENV-4 can efficiently methylate RNAs spanning different regions of viral genome, host ribosomal RNAs, and polyA. Structure-based mutagenesis results indicate that K61-D146-K181-E217 tetrad of DENV-4 methyltransferase forms the active site of internal methylation activity; in addition, distinct residues within the methyl donor (S-adenosyl-L-methionine) pocket, GTP pocket, and RNA-binding site are critical for the internal methylation activity. Functional analysis using flavivirus replicon and genome-length RNAs showed that internal methylation attenuated viral RNA translation and replication. Polymerase assay revealed that internal 2′-O-methyladenosine reduces the efficiency of RNA elongation. Collectively, our results demonstrate that flavivirus NS5 performs 2′-O methylation of internal adenosine of viral RNA in vivo and host ribosomal RNAs in vitro. PMID:22496660

The Sines industrial complex monitoring programme: A preliminary report.

PubMed

Jones, M P; Catarino, F M; Sérgio, C; Bento-Pereira, F

1981-06-01

It is anticipated that the establishment of the industrial complex at Sines, Alentejo, Portugal, will have some impact on the environment. Details of the methods used in the monitoring programme are provided. Records of the epiphytic lichen vegetation in permanent quadrats have been made and changes shown in selected sites over a three year period are discussed. Material has been collected for analysis for heavy metals and the results discussed. There is considerable variation in replicates and in interspecies values. The problem of age and bio-accumulation is mentioned. Scanning electron microscopy has shown the accumulation of particulates, as yet unidentified, the quantity varying with increase in age and surface texture. A broadly based study of the local epiphytic flora is being carried out to record the present day diversity. There appears, as yet, to be no detectable influence of the industrial complex on the epiphytic flora of the permanent quadrats.

Effect of pole number and slot number on performance of dual rotor permanent magnet wind power generator using ferrite magnets

NASA Astrophysics Data System (ADS)

Xu, Peifeng; Shi, Kai; Sun, Yuxin; Zhua, Huangqiu

2017-05-01

Dual rotor permanent magnet (DRPM) wind power generator using ferrite magnets has the advantages of low cost, high efficiency, and high torque density. How to further improve the performance and reduce the cost of the machine by proper choice of pole number and slot number is an important problem to be solved when performing preliminarily design a DRPM wind generator. This paper presents a comprehensive performance comparison of a DRPM wind generator using ferrite magnets with different slot and pole number combinations. The main winding factors are calculated by means of the star of slots. Under the same machine volume and ferrite consumption, the flux linkage, back-electromotive force (EMF), cogging torque, output torque, torque pulsation, and losses are investigated and compared using finite element analysis (FEA). The results show that the slot and pole number combinations have an important impact on the generator properties.

Calculating the Magnetic Anisotropy of Rare-Earth-Transition-Metal Ferrimagnets

NASA Astrophysics Data System (ADS)

Patrick, Christopher E.; Kumar, Santosh; Balakrishnan, Geetha; Edwards, Rachel S.; Lees, Martin R.; Petit, Leon; Staunton, Julie B.

2018-03-01

Magnetocrystalline anisotropy, the microscopic origin of permanent magnetism, is often explained in terms of ferromagnets. However, the best performing permanent magnets based on rare earths and transition metals (RE-TM) are in fact ferrimagnets, consisting of a number of magnetic sublattices. Here we show how a naive calculation of the magnetocrystalline anisotropy of the classic RE-TM ferrimagnet GdCo5 gives numbers that are too large at 0 K and exhibit the wrong temperature dependence. We solve this problem by introducing a first-principles approach to calculate temperature-dependent magnetization versus field (FPMVB) curves, mirroring the experiments actually used to determine the anisotropy. We pair our calculations with measurements on a recently grown single crystal of GdCo5 , and find excellent agreement. The FPMVB approach demonstrates a new level of sophistication in the use of first-principles calculations to understand RE-TM magnets.

Electric Propulsion Laboratory Vacuum Chamber

NASA Image and Video Library

1964-06-21

Engineer Paul Reader and his colleagues take environmental measurements during testing of a 20-inch diameter ion engine in a vacuum tank at the Electric Propulsion Laboratory (EPL). Researchers at the Lewis Research Center were investigating the use of a permanent-magnet circuit to create the magnetic field required power electron bombardment ion engines. Typical ion engines use a solenoid coil to create this magnetic field. It was thought that the substitution of a permanent magnet would create a comparable magnetic field with a lower weight. Testing of the magnet system in the EPL vacuum tanks revealed no significant operational problems. Reader found the weight of the two systems was similar, but that the thruster’s efficiency increased with the magnet. The EPL contained a series of large vacuum tanks that could be used to simulate conditions in space. Large vacuum pumps reduced the internal air pressure, and a refrigeration system created the cryogenic temperatures found in space.

Postfabrication Phase Error Correction of Silicon Photonic Circuits by Single Femtosecond Laser Pulses

DOE PAGES

Bachman, Daniel; Chen, Zhijiang; Wang, Christopher; ...

2016-11-29

Phase errors caused by fabrication variations in silicon photonic integrated circuits are an important problem, which negatively impacts device yield and performance. This study reports our recent progress in the development of a method for permanent, postfabrication phase error correction of silicon photonic circuits based on femtosecond laser irradiation. Using beam shaping technique, we achieve a 14-fold enhancement in the phase tuning resolution of the method with a Gaussian-shaped beam compared to a top-hat beam. The large improvement in the tuning resolution makes the femtosecond laser method potentially useful for very fine phase trimming of silicon photonic circuits. Finally, wemore » also show that femtosecond laser pulses can directly modify silicon photonic devices through a SiO 2 cladding layer, making it the only permanent post-fabrication method that can tune silicon photonic circuits protected by an oxide cladding.« less

[Chronological assessment of the preventive measures taken in the field of road traffic accidents in France. Methodological problems and results. (author's transl)].

PubMed

Hatton, F; Bouvier, M H; Maujol, L

1981-01-01

Corresponding to a non-experimental approach and based upon the study of indices obtained from permanent statistics, this assessment presents methodological difficulties linked both: to the choice of permanant indicators and to the interpretation of their variations in a situation of observation. The results permit us to appraise the consequences of the global policy of prevention in the field of road traffic accidents in France during many consecutive years: - the decrease of mortality and morbidity demographic indices; - the strengthening of the regressive tendency of the risk indices linked to road traffic (number of dead and wounded in relation to the "km" covered, to the consumption of motor-fuel...). The agreement of the evolutive tendencies of these indicators lets us think that the campaign against traffic accidents has had the desired effects even if they are still incomplete.

A polyvalent harmonic coil testing method for small-aperture magnets

NASA Astrophysics Data System (ADS)

Arpaia, Pasquale; Buzio, Marco; Golluccio, Giancarlo; Walckiers, Louis

2012-08-01

A method to characterize permanent and fast-pulsed iron-dominated magnets with small apertures is presented. The harmonic coil measurement technique is enhanced specifically for small-aperture magnets by (1) in situ calibration, for facing search-coil production inaccuracy, (2) rotating the magnet around its axis, for correcting systematic effects, and (3) measuring magnetic fluxes by stationary coils at different angular positions for measuring fast pulsed magnets. This method allows a quadrupole magnet for particle accelerators to be characterized completely, by assessing multipole field components, magnetic axis position, and field direction. In this paper, initially the metrological problems arising from testing small-aperture magnets are highlighted. Then, the basic ideas of the proposed method and the architecture of the corresponding measurement system are illustrated. Finally, experimental validation results are shown for small-aperture permanent and fast-ramped quadrupole magnets for the new linear accelerator Linac4 at CERN (European Organization for Nuclear Research).

Research on the Filtering Algorithm in Speed and Position Detection of Maglev Trains

PubMed Central

Dai, Chunhui; Long, Zhiqiang; Xie, Yunde; Xue, Song

2011-01-01

This paper introduces in brief the traction system of a permanent magnet electrodynamic suspension (EDS) train. The synchronous traction mode based on long stators and track cable is described. A speed and position detection system is recommended. It is installed on board and is used as the feedback end. Restricted by the maglev train’s structure, the permanent magnet electrodynamic suspension (EDS) train uses the non-contact method to detect its position. Because of the shake and the track joints, the position signal sent by the position sensor is always aberrant and noisy. To solve this problem, a linear discrete track-differentiator filtering algorithm is proposed. The filtering characters of the track-differentiator (TD) and track-differentiator group are analyzed. The four series of TD are used in the signal processing unit. The result shows that the track-differentiator could have a good effect and make the traction system run normally. PMID:22164012

Research on the filtering algorithm in speed and position detection of maglev trains.

PubMed

Dai, Chunhui; Long, Zhiqiang; Xie, Yunde; Xue, Song

2011-01-01

This paper introduces in brief the traction system of a permanent magnet electrodynamic suspension (EDS) train. The synchronous traction mode based on long stators and track cable is described. A speed and position detection system is recommended. It is installed on board and is used as the feedback end. Restricted by the maglev train's structure, the permanent magnet electrodynamic suspension (EDS) train uses the non-contact method to detect its position. Because of the shake and the track joints, the position signal sent by the position sensor is always aberrant and noisy. To solve this problem, a linear discrete track-differentiator filtering algorithm is proposed. The filtering characters of the track-differentiator (TD) and track-differentiator group are analyzed. The four series of TD are used in the signal processing unit. The result shows that the track-differentiator could have a good effect and make the traction system run normally.

Dental treatment considerations for a pediatric patient with incontinentia pigmenti (Bloch-Sulzberger syndrome)

PubMed Central

Chen, Amy Yi-Ling; Chen, Kevin

2017-01-01

Incontinentia pigmenti (IP) is a uncommon gene disorder, heritage with X-linked dominant mode. IP patients have a characteristic dentition varying from marked hypodontia to delayed eruption and conical crowns on both dentitions. A 5½-year-old girl, whose mother and younger sister were also diagnosed with IP, has the whirling-like pigmented skin lesion over her trunk and four extremities. Four primary teeth and multiple permanent tooth germs were found to be congenital missing. Dental considerations of further treatment were discussed with her parents including the preservation of primary molars, possible interim prosthesis in mixed or permanent dentition, full mouth rehabilitation with orthodontic and prosthodontic combined treatment, and implant therapy in adulthood. Early and longitudinal involvement of pediatric dentist to deal with the dental complications of IP can not only solve the esthetic problem and oral function but also maintain the oral health of children with IP to adulthood. PMID:28729805

Calculating the Magnetic Anisotropy of Rare-Earth-Transition-Metal Ferrimagnets.

PubMed

Patrick, Christopher E; Kumar, Santosh; Balakrishnan, Geetha; Edwards, Rachel S; Lees, Martin R; Petit, Leon; Staunton, Julie B

2018-03-02

Magnetocrystalline anisotropy, the microscopic origin of permanent magnetism, is often explained in terms of ferromagnets. However, the best performing permanent magnets based on rare earths and transition metals (RE-TM) are in fact ferrimagnets, consisting of a number of magnetic sublattices. Here we show how a naive calculation of the magnetocrystalline anisotropy of the classic RE-TM ferrimagnet GdCo_{5} gives numbers that are too large at 0 K and exhibit the wrong temperature dependence. We solve this problem by introducing a first-principles approach to calculate temperature-dependent magnetization versus field (FPMVB) curves, mirroring the experiments actually used to determine the anisotropy. We pair our calculations with measurements on a recently grown single crystal of GdCo_{5}, and find excellent agreement. The FPMVB approach demonstrates a new level of sophistication in the use of first-principles calculations to understand RE-TM magnets.

[Computer-assisted education in problem-solving in neurology; a randomized educational study].

PubMed

Weverling, G J; Stam, J; ten Cate, T J; van Crevel, H

1996-02-24

To determine the effect of computer-based medical teaching (CBMT) as a supplementary method to teach clinical problem-solving during the clerkship in neurology. Randomized controlled blinded study. Academic Medical Centre, Amsterdam, the Netherlands. 103 Students were assigned at random to a group with access to CBMT and a control group. CBMT consisted of 20 computer-simulated patients with neurological diseases, and was permanently available during five weeks to students in the CBMT group. The ability to recognize and solve neurological problems was assessed with two free-response tests, scored by two blinded observers. The CBMT students scored significantly better on the test related to the CBMT cases (mean score 7.5 on a zero to 10 point scale; control group 6.2; p < 0.001). There was no significant difference on the control test not related to the problems practised with CBMT. CBMT can be an effective method for teaching clinical problem-solving, when used as a supplementary teaching facility during a clinical clerkship. The increased ability to solve problems learned by CBMT had no demonstrable effect on the performance with other neurological problems.

Baseline results from the Lichen Community Indicator Program in the Pacific Northwest: Air quality patterns and evidence of a nitrogen pollution problem

Treesearch

Sarah Jovan

2009-01-01

Why Are Epiphytic Lichen Communities Important? Lichens are one of the bioindicators used by the Forest Inventory and Analysis (FIA) Program to monitor forest health. To obtain data for use in its Lichen Community Indicator Program, FIA samples a regular network of permanent field plots to determine the composition of epiphytic, i.e., tree dwelling, lichen communities...

Archeological Investigations in Cochiti Reservoir, New Mexico. Volume 1. A Survey of Regional Variability.

DTIC Science & Technology

1977-06-01

Abstract (Umit =0 worfs) A total of 325 archeological sites were documented during surveys of Cochiti Reservoir. Detailed summaries of environmental...ted sites within a regional context. during the course of this project. This and continuing re- search problems wer selected which focused upon search...for sites newly documented during survey. Survey of the permanent pool was conducted by Richard C.. Chapman, supervisory archeologist James

The association between prune belly syndrome and dental anomalies: a case report

PubMed Central

2012-01-01

Background Prune belly syndrome is a rare condition produced by an early mesodermal defect that causes abdominal abnormalities. However, the literature indicates that disturbances related to ectodermal development may also be present. This is the first case report in the literature to suggest that dental abnormalities are part of the broad spectrum of clinical features of prune belly syndrome. Because the syndrome causes many serious medical problems, early diagnosis of abnormalities involving the primary and permanent dentitions are encouraged. Case presentation The authors report the clinical case of a 4-year-old Caucasian boy with prune belly syndrome. In addition to the triad of abdominal muscle deficiency, abnormalities of the gastrointestinal and urinary tracts, and cryptorchidism, a geminated mandibular right central incisor, agenesis of a mandibular permanent left incisor, and congenitally missing primary teeth (namely, the mandibular right and left lateral incisors) were noted. Conclusion This original case report about prune belly syndrome highlights the possibility that dental abnormalities are a part of the broad spectrum of clinical features of the syndrome. Therefore, an accurate intra-oral clinical examination and radiographic evaluation are required for patients with this syndrome in order to provide an early diagnosis of abnormalities involving the primary and permanent dentitions. PMID:23249412

Solvent-Induced Shift of Spectral Lines in Polar–Polarizable Solvents

DOE PAGES

Matyushov, Dmitry V.; Newton, Marshall D.

2017-03-09

Solvent-induced shift of optical transition lines is traditionally described by the Lippert- McRae equation given in terms of the Onsager theory for dipole solvation. It splits the overall shift into the equilibrium solvation by induced dipoles and the reaction field by the permanent dipoles in equilibrium with the chromophore in the ground state. Here we have reconsidered this classical problem from the perspective of microscopic solvation theories. A microscopic solvation functional is derived and continuum solvation is consistently introduced by taking the limit of zero wavevector in the reciprocal-space solvation susceptibility functions. We show that the phenomenological expression for themore » reaction field of permanent dipoles in the Lippert-McRae equation is not consistent with the microscopic theory. The main deficiency of the Lippert- McRae equation equation is the use of additivity of the response by permanent and induced dipoles of the liquid. An alternative closed-form equation for the spectral shift is derived. Its continuum limit allows a new, non-additive functionality for the solvent-induced shift in terms of the high-frequency and static dielectric constants. Finally, the main qualitative outcome of the theory is a significantly weaker dependence of the spectral shift on the polarizability of the solvent than predicted by the Lippert-McRae formula.« less

Solvent-Induced Shift of Spectral Lines in Polar-Polarizable Solvents.

PubMed

Matyushov, Dmitry V; Newton, Marshall D

2017-03-23

Solvent-induced shift of optical transition lines is traditionally described by the Lippert-McRae equation given in terms of the Onsager theory for dipole solvation. It splits the overall shift into the equilibrium solvation by induced dipoles and the reaction field by the permanent dipoles in equilibrium with the chromophore in the ground state. We have reconsidered this classical problem from the perspective of microscopic solvation theories. A microscopic solvation functional is derived, and continuum solvation is consistently introduced by taking the limit of zero wavevector in the reciprocal-space solvation susceptibility functions. We show that the phenomenological expression for the reaction field of permanent dipoles in the Lippert-McRae equation is not consistent with the microscopic theory. The main deficiency of the Lippert-McRae equation is the use of additivity of the response by permanent and induced dipoles of the liquid. An alternative closed-form equation for the spectral shift is derived. Its continuum limit allows a new, nonadditive functionality for the solvent-induced shift in terms of the high-frequency and static dielectric constants. The main qualitative outcome of the theory is a significantly weaker dependence of the spectral shift on the polarizability of the solvent than predicted by the Lippert-McRae formula.

Dental caries prevalence in the permanent teeth in Greek schoolchildren related to age, sex, urbanization and social status.

PubMed

Megas, B F; Athanassouli, T N

1989-06-01

An epidemiological study of caries experience in permanent teeth of 1739 schoolchildren aged 6-17 years was conducted in Epirus, a northwestern region of Greece. Dental caries was found to be prevalent in the population examined and to increase with age. The mean DMFT values at the ages of 6, 12 and 17 years were 0.53 +/- 1.13, 4.93 +/- 4.04 and 8.88 +/- 6.19 respectively, while the average DMFT value for the total population examined was 4.96 +/- 4.83. The percentages of the children with caries-free permanent dentitions were 80 per cent at the age of 6 years, 24 per cent at 12 years and 7 per cent at 17 years. The total percentage of caries-free children was 20 per cent. Girls were found to have a higher caries prevalence than boys in all age groups. Small differences in the caries prevalence were found between rural and urban children population. Children of lower socioeconomic levels exhibited slightly higher caries prevalence than children of higher levels. The results of this baseline study indicate that dental caries is a major problem in this region of Greece and therefore an active and effective programme of dental care is necessary for the child population.

Lingual eruption of mandibular permanent incisors: a space correlated phenomenon?

PubMed

Aminabadi, Naser Asl; Farahani, Ramin Mostofi Zadeh; Sohrabi, Aydin; Pouralibaba, Firuz

2009-01-01

The aim of the present study was to investigate the prevalence and distribution according to various arch length conditions of lingually erupted mandibular permanent incisors and the effect of space condition on this phenomenon with long-term follow-up of these teeth. A total of 105 children aged 5-7.5 years with one or more permanent mandibular incisors erupting lingual to the corresponding primary incisors were included in the study. A space analysis was performed. The subjects were divided into six groups according to various space conditions. The subjects were followed for 2 years. In this study the prevalence of lingual eruption was 18.4%. Eighty-three point seven percent of the subjects had either equivalent space, mild space excess, or a space deficiency (not more than 3 mm). No relationship was found between groups and clinical outcomes (P>.05). Follow up of the main three groups (according to the space analysis results) revealed in the adequate space group 75% of the children lost their primary incisors without any intervention. Similar outcomes occurred in 85.7% and 57.14% of cases in the mild space excess and space deficiency groups, respectively. Considering the three main groups combined, equivalent space, mild space excess, and mild space deficiency, 70.45% of children lost their primary incisors without any intervention and 14.8% needed primary incisor extraction (17.4%, 14.3%, and 10.7% in each group, respectively). There was no predisposition toward a space deficiency or excess found in these subjects so the wait-and-see policy versus early extraction can be considered for lingually erupting permanent mandibular incisors. Lingual eruption of mandibular incisors is a common clinical problem in the early mixed dentition period that is a source of discomfort for parents of patients with this condition. The present study provides a unique insight into the prevalence of the problem as well as the clinical decisions such as favoring retention of primary incisors as long as possible, the extraction of these primary teeth, placement of lower lingual holding arches, or referral for comprehensive orthodontic treatment. These types of data should not be regarded as standards but as illustrative of several key factors that are still not well-understood or which are still ignored.

Rational choice of peritoneal dialysis catheter.

PubMed

Dell'Aquila, Roberto; Chiaramonte, Stefano; Rodighiero, Maria Pia; Spanó, Emilia; Di Loreto, Pierluigi; Kohn, Catalina Ocampo; Cruz, Dinna; Polanco, Natalia; Kuang, Dingwei; Corradi, Valentina; De Cal, Massimo; Ronco, Claudio

2007-06-01

The peritoneal catheter should be a permanent and safe access to the peritoneal cavity. Catheter-related problems are often the cause of permanent transfer to hemodialysis (HD) in up to 20% of peritoneal dialysis (PD) patients; in some cases, these problems require a temporary period on HD. Advances in connectology have reduced the incidence of peritonitis, and so catheter-related complications during PD have become a major concern. In the last few years, novel techniques have emerged in the field of PD: new dialysis solutions, better connectology, and cyclers for automated PD. However, extracorporeal dialysis has continued to improve in terms of methods and patient survival, but PD has failed to do so. The main reason is that peritoneal access has remained problematical. The peritoneal catheter is the major obstacle to wide-spread use of PD. Overcoming catheter-related problems means giving a real chance to development of the peritoneal technique. Catheters should be as efficient, safe, and acceptable as possible. Since its introduction in the mid-1960s, the Tenckhoff catheter has not become obsolete: dozens of new models have been proposed, but none has significantly reduced the pre-dominance of the first catheter. No convincing prospective data demonstrate the superiority of any peritoneal catheter, and so it seems that factors other than choice of catheter are what affect survival and complication rates. Efforts to improve peritoneal catheter survival and complication rates should probably focus on factors other than the choice of catheter. The present article provides an overview of the characteristics of the best-known peritoneal catheters.

Cell-type specific features of circular RNA expression.

PubMed

Salzman, Julia; Chen, Raymond E; Olsen, Mari N; Wang, Peter L; Brown, Patrick O

2013-01-01

Thousands of loci in the human and mouse genomes give rise to circular RNA transcripts; at many of these loci, the predominant RNA isoform is a circle. Using an improved computational approach for circular RNA identification, we found widespread circular RNA expression in Drosophila melanogaster and estimate that in humans, circular RNA may account for 1% as many molecules as poly(A) RNA. Analysis of data from the ENCODE consortium revealed that the repertoire of genes expressing circular RNA, the ratio of circular to linear transcripts for each gene, and even the pattern of splice isoforms of circular RNAs from each gene were cell-type specific. These results suggest that biogenesis of circular RNA is an integral, conserved, and regulated feature of the gene expression program.

Nucleotide sequence of Hungarian grapevine chrome mosaic nepovirus RNA1.

PubMed Central

Le Gall, O; Candresse, T; Brault, V; Dunez, J

1989-01-01

The nucleotide sequence of the RNA1 of hungarian grapevine chrome mosaic virus, a nepovirus very closely related to tomato black ring virus, has been determined from cDNA clones. It is 7212 nucleotides in length excluding the 3' terminal poly(A) tail and contains a large open reading frame extending from nucleotides 216 to 6971. The presumably encoded polyprotein is 2252 amino acids in length with a molecular weight of 250 kDa. The primary structure of the polyprotein was compared with that of other viral polyproteins, revealing the same general genetic organization as that of other picorna-like viruses (comoviruses, potyviruses and picornaviruses), except that an additional protein is suspected to occupy the N-terminus of the polyprotein. PMID:2798128

Skin problems in ostomy patients: a case-control study of risk factors.

PubMed

Nybaek, Hanne; Bang Knudsen, Dorte; Nørgaard Laursen, Troels; Karlsmark, Tonny; Jemec, Gregor B E

2009-01-01

Skin complications are frequent in ostomy patients and a number of risk factors have been suggested. The data on risk factors have, however, been documented mainly in single-centre studies and the actual importance of the suggested risk factors should therefore be verified in a group of ostomy patients broadly selected from the gene-ral population. All patients with permanent ostomies living in Roskilde County, Denmark, were invited to participate in the study. A total of 338 responded and 199 agreed to participate. Forty-five percent of all patients presented a skin problem. Less than half (43%) of patients with a skin problem were aware of the skin problems, and less than 1 in 5 (16%) had sought treatment for their skin problem. Ileostomies, ostomies with leakage and ostomies in patients with body mass index >30 were associated with skin problems. In conclusion, ileostomy, leakage and obesity predisposed patients to peristomal skin problems. Other suggested risk factors appear to be weak or insignificant. Patients under-report the presence of peristomal skin problems and therefore it is suggested that they need to be assessed by a professional on a routine basis in order to avoid or better manage peristomal skin complications.

Restraint systems for the prevention of injury to children in automobile accidents.

PubMed Central

Scherz, R G

1976-01-01

Highway accidents are the leading cause of child deaths in the United States from the ages of 1-14 years-6,122 such deaths occurred in 1973. In most instances deaths and permanent injuries occurred with the child as a passenger in an automobile. One approach toward alleviating this problem is the restraint of children in automobiles to reduce the likelihood of injury in a crash. PMID:1275118

Russia and the Caspian Sea: Projecting Power or Competing for Influence?

DTIC Science & Technology

2014-08-01

and illegal poaching of sturgeon is a serious problem for the littoral states. Poaching and uncontrolled fishing have had a dramatic impact on the...zone of privileged interest” and the impact on its relations with states in what is considered to be its “near abroad.” DOUGLAS C. LOVELACE...Mediterranean Seas and brought significant economic and security benefits. Pipelines have a permanency and an impact on political relations that

Implementation of Siemens USS protocol into LabVIEW.

PubMed

Hosek, P; Diblik, M

2011-10-01

This article gives basic overview of the USS protocol as a communication interface to drive Siemens frequency inverters. It presents our implementation of this protocol into LabVIEW, as there was permanent demand from the community of the users to have native LabVIEW implementation of the USS protocol. It also states encountered problems and their solutions. Copyright © 2011 Society for Laboratory Automation and Screening. Published by Elsevier Inc. All rights reserved.

[Problems of occupational rehabilitation in the shipbuilding industry. II. Rehabilitation in a group of ship welders].

PubMed

Sygit, M; Wecławik, Z

1987-01-01

The causes of rehabilitation of welders employed in the Maritime Shipyard in Szczecin have been analysed for the period 1979-1984. The main causes were found to be diseases of the musculo-osseous system (18.9%) and respiratory tract (14.8%). Temporary rehabilitation covered 67.3% of welders (2/3 for respiratory tract diseases), whereas permanent rehabilitation--23.5% (2/3 for musculo-osseous diseases).

Child Pornography and Pedophillia. Report Made by the Permanent Subcommittee on Investigations of the Committee on Governmental Affairs. United States Senate, Ninety-Ninth Congress, Second Session.

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. Senate Committee on Governmental Affairs.

This document contains an extensive overview of the topics of child pornography and pedophilia. Pedophilia is defined for this report as a condition in which an adult's primary sexual attraction is to prepubescent children roughly between the ages of 6 and 12. The introduction discusses the recent history of public awareness of the problem,…

Towards Water Sensitive City: Lesson Learned From Bogor Flood Hazard in 2017

NASA Astrophysics Data System (ADS)

Ramdhan, Muhammad; Arifin, Hadi Susilo; Suharnoto, Yuli; Tarigan, Suria Darma

2018-02-01

Bogor known as rain city and it's located at an altitude range of 190-330 meters above sea level. In February 2017 Bogor experienced a series of natural disasters related to heavy rainfall that fell during that time. The hazard in the form of flash floods that cause casualties was shocked, due to the location of Bogor city that located in the foothills with a fairly steep slope. There is a problem with the drainage system in the city of Bogor. Australia Indonesia Center in cooperation with Bogor city government held a focus group discussion to seek a permanent solution for the problems and so that similar incidents do not occur in the future.

Physiology-based face recognition in the thermal infrared spectrum.

PubMed

Buddharaju, Pradeep; Pavlidis, Ioannis T; Tsiamyrtzis, Panagiotis; Bazakos, Mike

2007-04-01

The current dominant approaches to face recognition rely on facial characteristics that are on or over the skin. Some of these characteristics have low permanency can be altered, and their phenomenology varies significantly with environmental factors (e.g., lighting). Many methodologies have been developed to address these problems to various degrees. However, the current framework of face recognition research has a potential weakness due to its very nature. We present a novel framework for face recognition based on physiological information. The motivation behind this effort is to capitalize on the permanency of innate characteristics that are under the skin. To establish feasibility, we propose a specific methodology to capture facial physiological patterns using the bioheat information contained in thermal imagery. First, the algorithm delineates the human face from the background using the Bayesian framework. Then, it localizes the superficial blood vessel network using image morphology. The extracted vascular network produces contour shapes that are characteristic to each individual. The branching points of the skeletonized vascular network are referred to as Thermal Minutia Points (TMPs) and constitute the feature database. To render the method robust to facial pose variations, we collect for each subject to be stored in the database five different pose images (center, midleft profile, left profile, midright profile, and right profile). During the classification stage, the algorithm first estimates the pose of the test image. Then, it matches the local and global TMP structures extracted from the test image with those of the corresponding pose images in the database. We have conducted experiments on a multipose database of thermal facial images collected in our laboratory, as well as on the time-gap database of the University of Notre Dame. The good experimental results show that the proposed methodology has merit, especially with respect to the problem of low permanence over time. More importantly, the results demonstrate the feasibility of the physiological framework in face recognition and open the way for further methodological and experimental research in the area.

Demonstration of variable speed permanent magnet generator at small, low-head hydro site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown Kinloch, David

Small hydro developers face a limited set of bad choices when choosing a generator for a small low-head hydro site. Direct drive synchronous generators are expensive and technically complex to install. Simpler induction generators are higher speed, requiring a speed increaser, which results in inefficiencies and maintenance problems. In addition, both induction and synchronous generators turn at a fixed speed, causing the turbine to run off its peak efficiency curve whenever the available head is different than the designed optimum head.The solution to these problems is the variable speed Permanent Magnet Generators (PMG). At the Weisenberger Mill in Midway, KY,more » a variable speed Permanent Magnet Generator has been installed and demonstrated. This new PMG system replaced an existing induction generator that had a HTD belt drive speed increaser system. Data was taken from the old generator before it was removed and compared to data collected after the PMG system was installed. The new variable speed PMG system is calculated to produce over 96% more energy than the old induction generator system during an average year. This significant increase was primarily due to the PMG generator operating at the correct speed at the maximum head, and the ability for the PMG generator to reduce its speed to lower optimum speeds as the stream flow increased and the net head decreased.This demonstration showed the importance of being able to adjust the speed of fixed blade turbines. All fixed blade turbines with varying net heads could achieve higher efficiencies if the speed can be matched to the optimum speed as the head changes. In addition, this demonstration showed that there are many potential efficiencies that could be realized with variable speed technology at hydro sites where mismatched turbine and generator speeds result in lower power output, even at maximum head. Funding for this project came from the US Dept. of Energy, through Award Number DE-EE0005429.« less

Sexual Function and Health-Related Quality of Life in Long-Term Rectal Cancer Survivors

PubMed Central

Sun, Virginia; Grant, Marcia; Wendel, Christopher S.; McMullen, Carmit K.; Bulkley, Joanna E.; Herrinton, Lisa J.; Hornbrook, Mark C.; Krouse, Robert S.

2016-01-01

Introduction Sexual dysfunction is a treatment sequela in rectal cancer (RC) survivors. Differences in health-related quality of life (HRQOL) may occur based on ostomy status (permanent ostomy versus anastomosis). Aim To describe alterations in sexual function and HRQOL based on ostomy status in long-term (≥ 5 years) RC survivors. Methods RC survivors with an ostomy (N=181) or anastomosis (N=394) were surveyed using validated HRQOL and functional status tools. We compared sexuality outcomes between the ostomy and anastomosis group, and reported differences adjusted for clinical and demographic characteristics. Qualitative data from one open-ended question on survivors’ greatest challenges since their surgery were analyzed to explore sexuality, symptoms, and relationships. Main Outcome Measures Whether sexually active, satisfaction with sexual activity, and select sexual dysfunction items from the Modified City of Hope Quality of Life-Ostomy (mCOH-QOL-O). Results Survivors with a permanent ostomy were more likely to have been sexually inactive after surgery if it occurred before year 2000, and experience dissatisfaction with appearance, interference with personal relationships and intimacy, and lower overall HRQOL. Female RC survivors with an ostomy were more likely to have problems with vaginal strictures and vaginal pain after surgery that persisted at the time of survey (5+ years later). Radiation treatment, tumor stage, soilage of garments in bed, and higher Charlson-Deyo co-morbidity scores were negatively associated with outcomes. Six qualitative themes emerged: loss of and decreased sexual activity; psychological issues with sexual activity, physical issues with sexual activity; partner rejection; ostomy interference with sexual activity; and positive experiences with sexuality. Conclusions Sexual dysfunction is a common long-term sequela of RC treatment, with more problems observed in survivors with a permanent ostomy. This warrants widespread implementation of targeted interventions to manage sexual dysfunction and improve HRQOL for these survivors. PMID:27318020

Sexual Function and Health-Related Quality of Life in Long-Term Rectal Cancer Survivors.

PubMed

Sun, Virginia; Grant, Marcia; Wendel, Christopher S; McMullen, Carmit K; Bulkley, Joanna E; Herrinton, Lisa J; Hornbrook, Mark C; Krouse, Robert S

2016-07-01

Sexual dysfunction is a treatment sequela in survivors of rectal cancer (RC). Differences in health-related quality of life (HRQOL) can occur based on ostomy status (permanent ostomy vs anastomosis). To describe alterations in sexual function and HRQOL based on ostomy status in long-term (≥5 years) survivors of RC. Survivors of RC with an ostomy (n = 181) or anastomosis (n = 394) were surveyed using validated HRQOL and functional status tools. We compared sexuality outcomes between the ostomy and anastomosis groups and reported differences adjusted for clinical and demographic characteristics. Qualitative data from one open-ended question on survivors' greatest challenges since their surgery were analyzed to explore sexuality, symptoms, and relationships. Whether sexually active, satisfaction with sexual activity, and select sexual dysfunction items from the Modified City of Hope Quality of Life-Colorectal. Survivors with a permanent ostomy were more likely to have been sexually inactive after surgery if it occurred before 2000 and experience dissatisfaction with appearance, interference with personal relationships and intimacy, and lower overall HRQOL. Female survivors of RC with an ostomy were more likely to have problems with vaginal strictures and vaginal pain after surgery that persisted at the time of the survey (≥5 years later). Radiation treatment, tumor stage, soilage of garments in bed, and higher Charlson-Deyo comorbidity scores were negatively associated with outcomes. Six qualitative themes emerged: loss of and decreased sexual activity, psychological issues with sexual activity, physical issues with sexual activity, partner rejection, ostomy interference with sexual activity, and positive experiences with sexuality. Sexual dysfunction is a common long-term sequela of RC treatment, with more problems observed in survivors with a permanent ostomy. This warrants widespread implementation of targeted interventions to manage sexual dysfunction and improve HRQOL for these survivors. Copyright © 2016 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

Models And Experiments Of Laminar Diffusion Flames In Non-Uniform Magnetic Fields

NASA Technical Reports Server (NTRS)

Baker, J.; Varagani, R.; Saito, K.

2003-01-01

Non-uniform magnetic fields affect laminar diffusion flames as a result of the paramagnetic and diamagnetic properties of the products and reactants. Paramagnetism is the weak attraction to a magnetic field a material exhibits as a result of permanent magnetic dipole moments in the atoms of the material. Diamagnetism is the weak repulsion to a magnetic field exhibited by a material due to the lack of permanent magnetic dipole moments in the atoms of a material. The forces associated with paramagnetic and diamagnetism are several orders of magnitude less than the forces associated with the more familiar ferromagnetism. A typical example of a paramagnetic gas is oxygen while hydrocarbon fuels and products of combustion are almost always diamagnetic. The fact that magnets can affect flame behavior has been recognized for more than one hundred years. Early speculation was that such behavior was due to the magnetic interaction with the ionized gases associated with a flame. Using a scaling analysis, it was later shown that for laminar diffusion flames the magnetic field/ionized gas interaction was insignificant to the paramagnetic and diamagnetic influences. In this effort, the focus has been on examining laminar diffusion slot flames in the presence of non-uniform upward decreasing magnetic fields produced using permanent magnets. The principal reason for choosing slot flames was mathematical models of such flames show an explicit dependence on gravitational body forces, in the buoyancy-controlled regime, and an applied magnetic field would also impose a body force. In addition, the behavior of such flames was more easily visualized while maintaining the symmetry of the two-dimensional problem whereas it would have been impossible to obtain a symmetric magnetic field around a circular flame and still visually record the flame height and shape along the burner axis. The motivation for choosing permanent magnets to produce the magnetic fields was the assumption that space-related technologies based on the knowledge gained during this investigation would more likely involve permanent magnets as opposed to electromagnets. While no analysis has been done here to quantify the impact that an electric field, associated with an electromagnetic, would have relative to the paramagnetic and diamagnetic interactions, by using permanent magnets this potential effect was completely eliminated and thus paramagnetic and diamagnetic effects were isolated.

Outcome in adolescence of brachial plexus birth palsy

PubMed Central

Hulleberg, Gunn; Elvrum, Ann-Kristin G; Brandal, Merethe; Vik, Torstein

2014-01-01

Background and purpose — The frequency and severity of a permanent lesion after brachial plexus birth palsy (BPBP) and its impact on activities of daily living are not well documented. We therefore investigated the outcome of BPBP in adolescents, regarding arm function and consequences for activity and participation. Participants and methods — Of 30,574 babies born at St. Olavs University Hospital in 1991–2000, 91 had BPBP (prevalence 3 per 1,000), and 69 of these individuals were examined at a median age of 14 (10–20) years. The examination included the modified Mallet classification, range of motion, shoulder rotation and grip strength, Assisting Hand Assessment, and Canadian Occupational Performance Measure. Of the 22 subjects who were not examined, 3 could not be traced and 19 reported having no problems in the affected arm. Results — At follow-up, 17 adolescents had a permanent lesion (i.e. individual Mallet subscore below 4) with a median Mallet total score of 15 (9–19), while 52 had good or normal shoulder function (median Mallet total score 25 (23–25)). All participants with a permanent lesion had reduced active shoulder rotation (≤ 15°), 16 had elbow extension deficit, and 10 had subnormal grip strength. External rotation was considerably weaker in the affected shoulder. In addition, they had ineffective use of the affected arm in bimanual activities. Even so, all except 1 were independent in activities of daily living, although 15 experienced minor difficulties. Interpretation — Every fourth to fifth child with BPBP had a permanent lesion as an adolescent. External rotation was the most impaired movement. Despite ineffective use of the affected arm in bimanual activities, all of the participants except one were independent in activities of daily living. PMID:25238434

Outcome in adolescence of brachial plexus birth palsy. 69 individuals re-examined after 10–20 years.

PubMed

Hulleberg, Gunn; Elvrum, Ann-Kristin G; Brandal, Merethe; Vik, Torstein

2014-12-01

The frequency and severity of a permanent lesion after brachial plexus birth palsy (BPBP) and its impact on activities of daily living are not well documented. We therefore investigated the outcome of BPBP in adolescents, regarding arm function and consequences for activity and participation. Of 30,574 babies born at St. Olavs University Hospital in 1991-2000, 91 had BPBP (prevalence 3 per 1,000), and 69 of these individuals were examined at a median age of 14 (10-20) years. The examination included the modified Mallet classification, range of motion, shoulder rotation and grip strength, Assisting Hand Assessment, and Canadian Occupational Performance Measure. Of the 22 subjects who were not examined, 3 could not be traced and 19 reported having no problems in the affected arm. At follow-up, 17 adolescents had a permanent lesion (i.e. individual Mallet subscore below 4) with a median Mallet total score of 15 (9-19), while 52 had good or normal shoulder function (median Mallet total score 25 (23-25)). All participants with a permanent lesion had reduced active shoulder rotation (≤15°), 16 had elbow extension deficit, and 10 had subnormal grip strength. External rotation was considerably weaker in the affected shoulder. In addition, they had ineffective use of the affected arm in bimanual activities. Even so, all except 1 were independent in activities of daily living, although 15 experienced minor difficulties. Every fourth to fifth child with BPBP had a permanent lesion as an adolescent. External rotation was the most impaired movement. Despite ineffective use of the affected arm in bimanual activities, all of the participants except one were independent in activities of daily living.

Abuses in Federal Student Grant Programs. Hearings before the Permanent Subcommittee on Investigations of the Committee on Governmental Affairs, United States Senate, One Hundred Third Congress, First Session (October 27-28, 1993).

ERIC Educational Resources Information Center

Congress of the U.S., Washington, DC. Senate Committee on Governmental Affairs.

It appears that many of the problems plaguing the Federal Student Aid Programs are also undermining the Pell Grant program, not so much from dishonesty on the part of students, but by dishonesty on the part of schools. This document presents testimony and prepared statements concerning the allegations of fraud, abuse, and mismanagement in the…

Transforming the U.S. Immigration System After 9/11: The Impact of Organizational Change and Collaboration in the Context of Homeland Security

DTIC Science & Technology

2008-12-01

disqualifying criminal conviction from an application to become a Lawful Permanent Resident of the U.S.10 10...developing Collaborative Capacity Builders (CCBs) is another method to sustain and continue to build an effective USCIS and ICE network into the 21st...Weber and Anne M. Khademian, “Wicked Problems, Knowledge Challenges, and Collaborative Capacity Builders in Network Settings,” Public Administration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rubin, R.L.; Doku, H.C.

In recent years, therapeutic radiology has been used extensively in the management of head and neck malignancies. An increasing number of the population who have been exposed to such therapy are being seen by the dentist for dental treatment. It is recognized that radiation therapy may cause temporary and permanent alterations in tissue. A discussion of the various therapeutic modalities and their side effects on the oral tissues has been presented to aid the dental practitioner in understanding the problems and care of such patients. (auth)

A Feasibility Randomised Controlled Trial of the New Orleans Intervention for Infant Mental Health: A Study Protocol

PubMed Central

Fitzpatrick, Bridie; Watson, Nicholas; Cotmore, Richard; Wilson, Philip; Donaldson, Julia; Boyd, Kathleen; Zeanah, Charles; Norrie, John; Messow, Martina; Turner, Fiona; Irving, Susan

2013-01-01

Child maltreatment is associated with life-long social, physical, and mental health problems. Intervening early to provide maltreated children with safe, nurturing care can improve outcomes. The need for prompt decisions about permanent placement (i.e., regarding adoption or return home) is internationally recognised. However, a recent Glasgow audit showed that many maltreated children “revolve” between birth families and foster carers. This paper describes the protocol of the first exploratory randomised controlled trial of a mental health intervention aimed at improving placement permanency decisions for maltreated children. This trial compares an infant's mental health intervention with the new enhanced service as usual for maltreated children entering care in Glasgow. As both are new services, the trial is being conducted from a position of equipoise. The outcome assessment covers various fields of a child's neurodevelopment to identify problems in any ESSENCE domain. The feasibility, reliability, and developmental appropriateness of all outcome measures are examined. Additionally, the potential for linkage with routinely collected data on health and social care and, in the future, education is explored. The results will inform a definitive randomised controlled trial that could potentially lead to long lasting benefits for the Scottish population and which may be applicable to other areas of the world. This trial is registered with ClinicalTrials.gov (NC01485510). PMID:24023537

Are students prone to depression and suicidal thoughts? Assessment of the risk of depression in university students from rural and urban areas.

PubMed

Mojs, Ewa; Warchoł-Biedermann, Katarzyna; Głowacka, Maria Danuta; Strzelecki, Wojciech; Ziemska, Beata; Marcinkowski, Jerzy T

2012-01-01

Depressive disorders in adolescents and young adults may have serious developmental and functional consequences, such as academic failure or persistent psychosocial problems. University students are affected by specific agents which may play a role in the onset of depression. The problem of student depression is particularly important in Poland because of a recent increase in student numbers, therefore, the aim of the presented study was to evaluate the prevalence of the risk of depression and suicidal thoughts among university students in Poznan, Poland, and to analyze the role of gender, current living arrangements, background (rural/small town or urban permanent place of residence), and reported financial status. 1,065 respondent students, mean age 21.1 years, 72% of whom were females, anonymously answered a questionnaire on the risk of depression (Kutcher's KADS) and a demographics survey. The obtained data were then analyzed statistically with the SPSS programme. 6.1 subjects were at risk of depression while 1.6 % of them had suicidal thoughts. Among analyzed determinants, perceived financial status and student's background (permanent place of residence) were found to have a statistically significant influence on the risk of depression. Students with rural/small town background and/or lower rather than good reported financial status are more likely to become depressed.

Dental caries is common in Finnish children infected with Helicobacter pylori.

PubMed

Kolho, K L; Hölttä, P; Alaluusua, S; Lindahl, H; Savilahti, E; Rautelin, H

2001-01-01

Childhood factors such as low socioeconomic status are risk factors for Helicobacter pylori infection and Streptococcus mutans-related dental caries. We examined whether H. pylori infection and dental caries are present today in the same group of children examined previously. We reviewed the public dental health service files of 21 H. pylori-positive children (upper gastrointestinal endoscopy at a median age of 13.5 y) and 27 H. pylori-negative children (endoscopy at a median age of 12.5 y) examined during 1995-98 at the Helsinki University Central Hospital, Finland. All H. pylori-positive children had experienced dental caries in their primary or permanent teeth or in both whereas among H. pylori-negative children the respective proportion was 70% (p < 0.01). At the age of 7 y, 18% (3/17) of the H. pylori-positive children had experienced caries in permanent teeth as compared to 0% among H. pylori-negative children (0/24; p < 0.05). At the age of 12 y, H. pylori-positive children had more decayed, missing or filled permanent teeth than H. pylori-negative children (80% vs. 38%; p < 0.05). Although a causal relationship between H. pylori and dental caries is unlikely, it is possible that H. pylori-infected children have an increased risk of other health problems, such as dental caries, for which proper treatment is needed.

Radioactive waste storage issues

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kunz, Daniel E.

1994-08-15

In the United States we generate greater than 500 million tons of toxic waste per year which pose a threat to human health and the environment. Some of the most toxic of these wastes are those that are radioactively contaminated. This thesis explores the need for permanent disposal facilities to isolate radioactive waste materials that are being stored temporarily, and therefore potentially unsafely, at generating facilities. Because of current controversies involving the interstate transfer of toxic waste, more states are restricting the flow of wastes into - their borders with the resultant outcome of requiring the management (storage and disposal)more » of wastes generated solely within a state`s boundary to remain there. The purpose of this project is to study nuclear waste storage issues and public perceptions of this important matter. Temporary storage at generating facilities is a cause for safety concerns and underscores, the need for the opening of permanent disposal sites. Political controversies and public concern are forcing states to look within their own borders to find solutions to this difficult problem. Permanent disposal or retrievable storage for radioactive waste may become a necessity in the near future in Colorado. Suitable areas that could support - a nuclear storage/disposal site need to be explored to make certain the health, safety and environment of our citizens now, and that of future generations, will be protected.« less

Stewardship of very large digital data archives

NASA Technical Reports Server (NTRS)

Savage, Patric

1991-01-01

An archive is a permanent store. There are relatively few very large digital data archives in existence. Most business records are expired within five or ten years. Many kinds of business records that do have long lives are embedded in data bases that are continually updated and re-issued cyclically. Also, a great deal of permanent business records are actually archived as microfilm, fiche, or optical disk images - their digital version being an operational convenience rather than an archive. The problems forseen in stewarding the very large digital data archives that will accumulate during the mission of the Earth Observing System (EOS) are addressed. It focuses on the function of shepherding archived digital data into an endless future. Stewardship entails storing and protecting the archive and providing meaningful service to the community of users. The steward will (1) provide against loss due to physical phenomena; (2) assure that data is not lost due to storage technology obsolescence; and (3) maintain data in a current formatting methodology.

Development of a Double Glass Mounting Method Using Formaldehyde Alcohol Azocarmine Lactophenol (FAAL) and its Evaluation for Permanent Mounting of Small Nematodes.

PubMed

Zahabiun, Farzaneh; Sadjjadi, Seyed Mahmoud; Esfandiari, Farideh

2015-01-01

Permanent slide preparation of nematodes especially small ones is time consuming, difficult and they become scarious margins. Regarding this problem, a modified double glass mounting method was developed and compared with classic method. A total of 209 nematode samples from human and animal origin were fixed and stained with Formaldehyde Alcohol Azocarmine Lactophenol (FAAL) followed by double glass mounting and classic dehydration method using Canada balsam as their mounting media. The slides were evaluated in different dates and times, more than four years. Different photos were made with different magnification during the evaluation time. The double glass mounting method was stable during this time and comparable with classic method. There were no changes in morphologic structures of nematodes using double glass mounting method with well-defined and clear differentiation between different organs of nematodes in this method. Using this method is cost effective and fast for mounting of small nematodes comparing to classic method.

Development of a Double Glass Mounting Method Using Formaldehyde Alcohol Azocarmine Lactophenol (FAAL) and its Evaluation for Permanent Mounting of Small Nematodes

PubMed Central

ZAHABIUN, Farzaneh; SADJJADI, Seyed Mahmoud; ESFANDIARI, Farideh

2015-01-01

Background: Permanent slide preparation of nematodes especially small ones is time consuming, difficult and they become scarious margins. Regarding this problem, a modified double glass mounting method was developed and compared with classic method. Methods: A total of 209 nematode samples from human and animal origin were fixed and stained with Formaldehyde Alcohol Azocarmine Lactophenol (FAAL) followed by double glass mounting and classic dehydration method using Canada balsam as their mounting media. The slides were evaluated in different dates and times, more than four years. Different photos were made with different magnification during the evaluation time. Results: The double glass mounting method was stable during this time and comparable with classic method. There were no changes in morphologic structures of nematodes using double glass mounting method with well-defined and clear differentiation between different organs of nematodes in this method. Conclusion: Using this method is cost effective and fast for mounting of small nematodes comparing to classic method. PMID:26811729

Application of textured YBCO bulks with artificial holes for superconducting magnetic bearing

NASA Astrophysics Data System (ADS)

Dias, D. H. N.; Sotelo, G. G.; Moysés, L. A.; Telles, L. G. T.; Bernstein, P.; Kenfaui, D.; Aburas, M.; Chaud, X.; Noudem, J. G.

2015-07-01

The levitation force between a superconductor and a permanent magnet has been investigated for the development of superconducting magnetic bearings (SMBs). Depending on the proposed application, the SMBs can be arranged with two kinds of symmetries: rotational or linear. The SMBs present passive operation, low level of noise and no friction, but they need a cooling system for their operation. Nowadays the cooling problem may be easily solved by the use of a commercial cryocooler. The levitation force of SMBs is directly related to the quality of the superconductor material (which depends on its critical current density) and the permanent magnet arrangement. Also, research about the YBa2Cu3Ox (Y123) bulk materials has shown that artificial holes enhance the superconducting properties, in particular the magnetic trapped field. In this context, this work proposes the investigation of the levitation force of a bulk Y123 sample with multiple holes and the comparison of its performances with those of conventional plain Y123 superconductors.

Palliative sedation until death: an approach from Kant's ethics of virtue.

PubMed

Hasselaar, Jeroen G J

2008-01-01

This paper is concerned with the moral justification for palliative sedation until death. Palliative sedation involves the intentional lowering of consciousness for the relief of untreatable symptoms. The paper focuses on the moral problems surrounding the intentional lowering of consciousness until death itself, rather than possible adjacent life-shortening effects. Starting from a Kantian perspective on virtue, it is shown that continuous deep sedation until death (CDS) does not conflict with the perfect duty of moral self-preservation because CDS does not destroy capacities for agency. In addition, it is argued that CDS can frustrate the imperfect duty of self-cultivation by reducing consciousness permanently. Nevertheless, there are cases where CDS is morally acceptable, namely, cases where the agent has already permanently lost the possibility for free action in advance of sedation--for example, due to excruciating and ongoing pain. Because the latter can be difficult to diagnose properly, safeguards may be needed in order to prevent the application of CDS for the wrong reasons.

Isolated Power Generation System Using Permanent Magnet Synchronous Generator with Improved Power Quality

NASA Astrophysics Data System (ADS)

Arya, Sabha Raj; Patel, Ashish; Giri, Ashutosh

2018-06-01

This paper deals wind energy based power generation system using Permanent Magnet Synchronous Generator (PMSG). It is controlled using advanced enhanced phase-lock loop for power quality features using distribution static compensator to eliminate the harmonics and to provide KVAR compensation as well as load balancing. It also manages rated potential at the point of common interface under linear and non-linear loads. In order to have better efficiency and reliable operation of PMSG driven by wind turbine, it is necessary to analyze the governing equation of wind based turbine and PMSG under fixed and variable wind speed. For handling power quality problems, power electronics based shunt connected custom power device is used in three wire system. The simulations in MATLAB/Simulink environment have been carried out in order to demonstrate this model and control approach used for the power quality enhancement. The performance results show the adequate performance of PMSG based power generation system and control algorithm.

Surgical management of impacted incisors in associate with supernumerary teeth: a combine case report of spontaneous eruption and orthodontic extrusion.

PubMed

Das, D; Misra, J

2012-01-01

Maxillary permanent incisors impaction is not a frequent case in dental practice, but its treatment is challenging because of its importance to facial esthetics. Supernumerary teeth are the main cause of impaction of upper incisors. Supernumerary teeth when present can cause both esthetic and pathologic problems. Early detection of such teeth is most important if complications are to be avoided. In this reported case, the orthopantamogram of a 9-year-old boy revealed two impacted supernumerary teeth in the maxillary anterior region, which was interfering with the eruption of the permanent central incisors. The impacted supernumerary teeth were surgically removed, 11 was repositioned in the arch as it was situated very high in the arch, close to the nasal floor. Twenty-one erupted spontaneously but orthodontic force was applied over 11 to bring it into the occlusion and alignment was achieved with 0.014 mm NiTi wire.

Isolated Power Generation System Using Permanent Magnet Synchronous Generator with Improved Power Quality

NASA Astrophysics Data System (ADS)

Arya, Sabha Raj; Patel, Ashish; Giri, Ashutosh

2018-03-01

This paper deals wind energy based power generation system using Permanent Magnet Synchronous Generator (PMSG). It is controlled using advanced enhanced phase-lock loop for power quality features using distribution static compensator to eliminate the harmonics and to provide KVAR compensation as well as load balancing. It also manages rated potential at the point of common interface under linear and non-linear loads. In order to have better efficiency and reliable operation of PMSG driven by wind turbine, it is necessary to analyze the governing equation of wind based turbine and PMSG under fixed and variable wind speed. For handling power quality problems, power electronics based shunt connected custom power device is used in three wire system. The simulations in MATLAB/Simulink environment have been carried out in order to demonstrate this model and control approach used for the power quality enhancement. The performance results show the adequate performance of PMSG based power generation system and control algorithm.

Change of occurance of type 1 and type 2 decompression sickness of divers treated at the Croatian Naval Medical Institute in the period from 1967 to 2000.

PubMed

Andrić, Dejan; Petri, Nadan M; Stipancević, Hrvoje; Petri, Lena Vranjković; Kovacević, Hasan

2003-01-01

A significant change of occurrence (p=0.0343) of type 1 and type 2 decompression sickness (DCS) of divers in Croatia was observed in the period from 1991 to 2002 (type 1: n=26, 37.68% and type 2: n=43, 62.32%) compared with the period from 1967 to 1990 (type 1: n=93, 52.84% and type 2: n=83, 47.16%). The change was attributed to the extensive usage of diving computers and artificial gas mixtures which enable extended bottom times and deeper dives, thus putting divers at an increased decompression risk. The importance of the results of this report is in the fact that permanent neurological deficit occurs only after type 2 DCS. Injured divers with permanent loss after type 2 DCS are not fit for diving and require a long term medical care, thus becoming a significant public health problem.

Rehabilitation outcomes of children with cerebral palsy.

PubMed

Yalcinkaya, Ebru Yilmaz; Caglar, Nil Sayıner; Tugcu, Betul; Tonbaklar, Aysegul

2014-02-01

[Purpose] To evaluate the results of Bobath-based rehabilitation performed at a pediatric cerebral palsy (CP) inpatient clinic. [Subjects and Methods] The study subjects were 28 children with CP who were inpatients at a pediatric service. Inclusion criteria were: being an inpatient of our hospital aged 2-12 with a diagnosis of CP; having one permanent primary caregiver; and the caregiver having no medical or psychotic problems. All of the patients received Bobath treatment for 1 hour per day, 5 days a week. The locomotor system, neurologic and orthopedic examination, Gross Motor Function Measure (GMFM) of the patients, and Short Form-36 (SF-36) of permanent caregivers were evaluated at the time of admission to hospital, discharge from hospital, and at 1 and 3 months after discharge. [Results] Post-admission scores of GMFM at discharge, and 1 and 3 months later showed significant increase. Social function and emotional role subscores of SF-36 had increased significantly at discharge. [Conclusion] Bobath treatment is promising and randomized controlled further studies are needed for rehabilitation technics.

Rehabilitation Outcomes of Children with Cerebral Palsy

PubMed Central

Yalcinkaya, Ebru Yilmaz; Caglar, Nil Sayıner; Tugcu, Betul; Tonbaklar, Aysegul

2014-01-01

[Purpose] To evaluate the results of Bobath-based rehabilitation performed at a pediatric cerebral palsy (CP) inpatient clinic. [Subjects and Methods] The study subjects were 28 children with CP who were inpatients at a pediatric service. Inclusion criteria were: being an inpatient of our hospital aged 2–12 with a diagnosis of CP; having one permanent primary caregiver; and the caregiver having no medical or psychotic problems. All of the patients received Bobath treatment for 1 hour per day, 5 days a week. The locomotor system, neurologic and orthopedic examination, Gross Motor Function Measure (GMFM) of the patients, and Short Form-36 (SF-36) of permanent caregivers were evaluated at the time of admission to hospital, discharge from hospital, and at 1 and 3 months after discharge. [Results] Post-admission scores of GMFM at discharge, and 1 and 3 months later showed significant increase. Social function and emotional role subscores of SF-36 had increased significantly at discharge. [Conclusion] Bobath treatment is promising and randomized controlled further studies are needed for rehabilitation technics. PMID:24648650

Use of Permanent Magnets in Electromagnetic Facilities for the Treatment of Aluminum Alloys

NASA Astrophysics Data System (ADS)

Beinerts, Toms; Bojarevičs, Andris; Bucenieks, Imants; Gelfgat, Yuri; Kaldre, Imants

2016-06-01

The possibility of applying the electromagnetic induction pump with permanent magnets for the transportation and stirring of aluminum melts in metallurgical furnaces is investigated. The electromagnetic and hydraulic characteristics of the pump have been investigated theoretically and experimentally with regard to its position in the furnace. The results of the experiments performed with a model in a eutectic InGaSn melt are in good agreement with the calculation data. Extrapolation of the experimental results on the physical characteristics of aluminum melts allows recommending such pumps for contactless control of motion and heat/mass transfer in aluminum melts in different technological processes. A high temperature and the aggressive properties of aluminum alloys make it complicated to use different mechanical devices to solve technological problems, such as liquid metal transportation, dosing, stirring, etc. In this case, any device units or elements moving in or contacting with the melt suffer from corrosion polluting the melt. Therefore, of more importance and topicality are contactless electromagnetic methods for processing of molten metals.

Transponders as permanent identification markers for domestic ferrets, black-footed ferrets, and other wildlife

USGS Publications Warehouse

Fagerstone, Kathleen A.; Johns, Brad E.

1987-01-01

A 0.05-g transponder implanted subcutaneously was tested to see if it provided a reliable identification method. In laboratory tests 20 domestic ferrets (Mustela putorius furo) received transponders and were monitored for a minimum of 6 months. None showed signs of inflammation, and necropsies conducted at the end of the study showed no scar tissue or transponder migration. Seven of 23 transponders failed during the test because of leakage through the plastic case, and a glass case is now being manufactured that does not have the leakage problem. During mark-recapture studies in September and October 1985, transponders were implanted in 20 black-footed ferrets (M. nigripes), 11 of which were subsequently recaptured and 9 of which were brought into captivity; none showed signs of inflammation. Transponders provide a reliable new method for identifying hard-to-mark wildlife with a unique, permanent number than can be read with the animal in-hand or by remote equipment.

The control of measles in tropical Africa: a review of past and present efforts.

PubMed

Ofosu-Amaah, S

1983-01-01

Measles in tropical Africa is endemic and cyclical, with a high incidence that usually peaks during the dry seasons. Measles may be a contributing factor in 10% of all deaths among African children. Several problems have hindered measles immunization programs in Africa; these include difficulties in maintaining the cold chain, poor epidemiologic surveillance, and the logistical problems involved in reaching a population that is 80% rural. The United States Agency for International Development and the World Health Organization both have programs that are helping to increase immunization coverage and to solve the problems just mentioned. Many countries have begun to train their own personnel to administer immunization programs. However, because of limited staff and equipment, a high birth rate, and an uncertain social situation, no firm predictions can be made concerning the permanent control of measles in tropical Africa.

User satisfaction with realtime teleneurology.

PubMed

Craig, J; Russell, C; Patterson, V; Wootton, R

1999-01-01

User satisfaction (i.e. that of patients, medical staff at a remote hospital and medical staff at a neurological centre) with realtime teleneurology consultations was studied prospectively. Twenty-five patients with neurological problems admitted to a hospital without permanent neurological cover were assessed from a neurological centre by specialist neurologists using realtime video-links transmitting at 384 kbit/s. All users reported high levels of satisfaction with the technical aspects of the consultations. Patients, almost universally, reported confidence in teleneurology as a means of dealing with their presenting complaints. Similarly, medical staff at either site felt confident in managing patients using teleneurology and almost always felt that a telephone consultation would not have achieved as good an outcome. No major organizational problems were identified. These findings suggest overall user satisfaction with realtime teleneurology for managing patients with neurological problems admitted to hospitals that do not have resident neurologists.

Genomic big data hitting the storage bottleneck.

PubMed

Papageorgiou, Louis; Eleni, Picasi; Raftopoulou, Sofia; Mantaiou, Meropi; Megalooikonomou, Vasileios; Vlachakis, Dimitrios

2018-01-01

During the last decades, there is a vast data explosion in bioinformatics. Big data centres are trying to face this data crisis, reaching high storage capacity levels. Although several scientific giants examine how to handle the enormous pile of information in their cupboards, the problem remains unsolved. On a daily basis, there is a massive quantity of permanent loss of extensive information due to infrastructure and storage space problems. The motivation for sequencing has fallen behind. Sometimes, the time that is spent to solve storage space problems is longer than the one dedicated to collect and analyse data. To bring sequencing to the foreground, scientists have to slide over such obstacles and find alternative ways to approach the issue of data volume. Scientific community experiences the data crisis era, where, out of the box solutions may ease the typical research workflow, until technological development meets the needs of Bioinformatics.

Probabilistic sharing solves the problem of costly punishment

NASA Astrophysics Data System (ADS)

Chen, Xiaojie; Szolnoki, Attila; Perc, Matjaž

2014-08-01

Cooperators that refuse to participate in sanctioning defectors create the second-order free-rider problem. Such cooperators will not be punished because they contribute to the public good, but they also eschew the costs associated with punishing defectors. Altruistic punishers—those that cooperate and punish—are at a disadvantage, and it is puzzling how such behaviour has evolved. We show that sharing the responsibility to sanction defectors rather than relying on certain individuals to do so permanently can solve the problem of costly punishment. Inspired by the fact that humans have strong but also emotional tendencies for fair play, we consider probabilistic sanctioning as the simplest way of distributing the duty. In well-mixed populations the public goods game is transformed into a coordination game with full cooperation and defection as the two stable equilibria, while in structured populations pattern formation supports additional counterintuitive solutions that are reminiscent of Parrondo's paradox.

Cell-Type Specific Features of Circular RNA Expression

PubMed Central

Salzman, Julia; Chen, Raymond E.; Olsen, Mari N.; Wang, Peter L.; Brown, Patrick O.

2013-01-01

Thousands of loci in the human and mouse genomes give rise to circular RNA transcripts; at many of these loci, the predominant RNA isoform is a circle. Using an improved computational approach for circular RNA identification, we found widespread circular RNA expression in Drosophila melanogaster and estimate that in humans, circular RNA may account for 1% as many molecules as poly(A) RNA. Analysis of data from the ENCODE consortium revealed that the repertoire of genes expressing circular RNA, the ratio of circular to linear transcripts for each gene, and even the pattern of splice isoforms of circular RNAs from each gene were cell-type specific. These results suggest that biogenesis of circular RNA is an integral, conserved, and regulated feature of the gene expression program. PMID:24039610

Aminoacyl transfer from an adenylate anhydride to polyribonucleotides

NASA Technical Reports Server (NTRS)

Weber, A. L.; Lacey, J. C., Jr.

1975-01-01

Imidazole catalysis of phenylalanyl transfer from phenylalanine adenylate to hydroxyl groups of homopolyribonucleotides is studied as a possible chemical model of biochemical aminoacylation of transfer RNA (tRNA). The effect of pH on imidazole-catalyzed transfer of phenylalanyl residues to poly(U) and poly(A) double helix strands, the number of peptide linkages and their lability to base and neutral hydroxylamine, and the nature of adenylate condensation products are investigated. The chemical model entertained exhibits a constraint by not acylating the hydroxyl groups of polyribonucleotides in a double helix. The constraint is consistent with selective biochemical aminoacylation at the tRNA terminus. Interest in imidazole as a model of histidine residue in protoenzymes participating in prebiotic aminoacyl transfer to polyribonucleotides, and in rendering the tRNA a more efficient adaptor, is indicated.

Proteins bound to polyribosomal mRNA of the embryonic axis of kidney bean seeds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pushkarev, V.M.; Galkin, A.P.

The protein composition of polyribosome-bound mRNAs from the embryonic axis of germinating kidney bean seeds, isolated by an improved procedure including treatment with EDTA, low concentrations of RNase T/sub 1/, and centrifugation in a linear 15-40% sucrose concentration gradient, was investigated. Electrophoretic analysis of the proteins of purified fragments of mRNP obtained by the method described showed the presence of two to three major polypeptides (molecular weights 50, 38, 32 kilodaltons) and a number of minor ones. It was established that one of the major proteins is associated with the poly(A) sequences of mRNA (50 kilodaltons). The similarity of themore » protein compositions of polyribosomal mRNAs of kidney bean embryos and other objects studied is discussed.« less

Complete mitochondrial genome of Chocolate Pansy, Junonia iphita (Lepidoptera: Nymphalidae: Nymphalinae).

PubMed

Vanlalruati, Catherine; Mandal, Surajit De; Gurusubramanian, Guruswami; Senthil Kumar, Nachimuthu

2016-07-01

The complete mitochondrial genome of Junonia iphita was determined to be 15,433 bp in length, including 37 typical mitochondrial genes and an AT-rich region. All the protein coding genes (PCGs) are initiated by typical ATN codons, except cox1 gene that is by CGA codon. Eight genes use complete termination codon (TAA), whereas the cox1, cox2 and nad5 genes end with single T; nad4 and nad1 ends with stop codon TA. All the tRNA show secondary cloverleaf structures except trnS1 (AGN). The A + T rich region is 546 bp in length containing ATAGA motif followed by a 18 bp poly-T stretch, two microsatellite-like (TA)9 elements and 8 bp poly-A stretch immediately upstream of trnM gene.

Xenopus laevis ribosomal protein genes: isolation of recombinant cDNA clones and study of the genomic organization.

PubMed Central

Bozzoni, I; Beccari, E; Luo, Z X; Amaldi, F

1981-01-01

Poly-A+ mRNA from Xenopus laevis oocytes, partially enriched for r-protein coding capacity has been used as starting material for preparing a cDNA bank in plasmid pBR322. The clones containing sequences specific for r-proteins have been selected by translation of the complementary mRNAs. Clones for six different r-proteins have been identified and utilized as probes for studying their genomic organization. Two gene copies per haploid genome were found for r-proteins L1, L14, S19, and four-five for protein S1, S8 and L32. Moreover a population polymorphism has been observed for the genomic regions containing sequences for r-protein S1, S8 and L14. Images PMID:6112733

Investigation of Heat Transfer at the Mold/Metal Interface in Permanent Mold Casting of Light Alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Robert D. Pehlke; John T. Berry

2005-12-16

Accurate modeling of the metal casting process prior to creating a mold design demands reliable knowledge of the interfacial heat transfer coefficient at the mold metal interface as a function of both time and location. The phenomena concerned with the gap forming between the mold and the solidifying metal are complex but need to be understood before any modeling is attempted. The presence of mold coatings further complicates the situation. A commercial casting was chosen and studied in a gravity permanent mold casting process. The metal/mold interfacial heat transfer coefficient (IHTC) was the focus of the research. A simple, directmore » method has been used to evaluate the IHTC. Both the simulation and experiments have shown that a reasonably good estimate of the heat transfer coefficient could be made in the case studied. It has been found that there is a good agreement between experiments and simulations in the temperature profiles during the solidification process, given that the primary mechanism of heat transfer across the gap in permanent mold casting of light alloys is by conduction across the gap. The procedure utilized to determine the interfacial heat transfer coefficient can be applied to other casting processes. A recently completed project involving The University of Michigan and Mississippi State University, together with several industrial partners, which was supported by the USDOE through the Cast Metals Coalition, examined a number of cases of thermal contact. In an investigation which gave special consideration to the techniques of measurement, several mold coatings were employed and results presented as a function of time. Realistic conditions of coating thickness and type together with an appropriate combination of mold preheat and metal pouring temperature were strictly maintained throughout the investigation. Temperature sensors, in particular thermocouples, play an important part in validating the predictions of solidification models. Cooling curve information, as well as temperature gradient history both in the solidifying metal and within the mold are invariably required to be validated. This validation depends upon the response of the sensor concerned, but also on its own effect upon the thermal environment. A joint university/industry team has completed an investigation of the invasive effects of thermocouples upon temperature history in permanent molds determining the degree of uncertainty associated with placement and indicating how the time-temperature history may be recovered. In addition to its relevance to the all important study of thermal contact of the casting with metallic molds, the observations also impact the determination of heat flux and interfacial heat transfer coefficients. In these respects the study represents the first of its kind that has tackled the problem in depth for permanent mold castings. An important ramification of this investigation has been the errors likely to be encountered in mold temperature measurement with thin section aluminum castings, especially with respect to the plans for thermocouple placement. A comparison between the degree of uncertainty experienced in sand molds compared with that found in permanent molds reveals that the associated problems have a lesser impact. These conclusions and the related recommendations have been disseminated to industry and the technical community through project reports and publications.« less

Torsion Tests of Stiffened Circular Cylinders

NASA Technical Reports Server (NTRS)

Moore, R L; Wescoat, C

1944-01-01

The design of curved sheet panels to resist shear involves a consideration of several factors: the buckling resistance of the sheet, the stress at which buckling becomes permanent, and the strength which may be developed beyond the buckling limit by tension-field action. Although some experimental as well as theoretical work has been done on the buckling and tension-field phases of this problem, neither of these types of action appears to be very well understood. The problem is of sufficient importance from the standpoint of aircraft design, it is believed, to warrant further experimental investigation. This report presents the results of the first series of torsion tests of stiffened circular cylinders to be completed in connection with this study at Aluminum Research Laboratories. (author)

Object permanence in domestic dogs (Canis lupus familiaris) and gray wolves (Canis lupus).

PubMed

Fiset, Sylvain; Plourde, Vickie

2013-05-01

Recent evidence suggests that phylogenetic constraints exerted on dogs by the process of domestication have altered the ability of dogs to represent the physical world and the displacement of objects. In this study, invisible (Experiment 1) and visible (Experiment 2) displacement problems were administered to determine whether domestic dogs' and gray wolves' cognitive capacities to infer the position of a hidden object differ. The results revealed that adult dogs and wolves performed similarly in searching for disappearing objects: Both species succeeded the visible displacement tasks but failed the invisible displacement problems. We conclude that physical cognition for finding hidden objects in domestic dogs and gray wolves is alike and unrelated to the process of domestication.

The black cloud over the Sunshine State: health disparities in south Florida.

PubMed

Dyer, Janyce G

2003-01-01

Florida, the "Sunshine State", is paradise for international tourists and has been adopted as seasonal or permanent home by many wealthy individuals and celebrities. However, Florida is not paradise for the growing number of residents who suffer from poverty, health problems, and a lack of access to health care and social services. The purpose of this paper is to present data on health care problems and disparities throughout the state of Florida and in select south Florida counties. Flaskerud and Winslow (1998) have provided a framework which can be used to analyze disparities in resource availability, relative risk, and health status indicators and suggests areas in which nursing and other health professionals can ethically intervene through research, practice, and political action.

The Golden bypass landslide, Golden, Colorado

USGS Publications Warehouse

Highland, L.M.; Brown, W. M.

1993-01-01

Slope instability along a new highway bypass in Golden, Colorado, became a major concern in 1993. Rains and snowmelt accelerated movement of a landslide that had begun to develop before the bypass was opened to traffic in July of 1991. The downslope movement of earth materials increased significantly in 1993. During the first few months of the year, the landslide pushed onto the west shoulder of the road and crumpled the pavement beneath the south-bound lane. As we prepare this article (September, 1993), the slide continues to encroach onto the highway, posing a persistent problem despite repeated efforts to slow or stop its movement. As this article will show, permanent solutions to landslide problems of this kind are difficult to obtain. 

Pressure sores--a constant problem for plegic patients and a permanent challenge for plastic surgery.

PubMed

Giuglea, Carmen; Marinescu, Sllviu; Florescu, Ioan Petre; Jecan, Crenguta

2010-01-01

Pressure sores can be defined as lesions caused by unrelieved pressure resulting in damage of the underlying tissue. They represent a common problem in the pathology of plegic patients and, plastic surgery has a significant role in their treatment. Pressure sores occur over bony prominences and so, they are most commonly seen at the sacrum and trochanters in paralyzed patients and at ischium for the patients who sit in a wheelchair for a long time. For these patients, surgical treatment is very important because on one hand, it stops the loss of nutrients and proteins at the site of the pressure sore, and on the other hand, it permits the initiation of neuromuscular recuperation treatment much faster.

Health issues of Afghan refugees in California.

PubMed Central

Lipson, J G; Omidian, P A

1992-01-01

Since the 1979 Soviet invasion of Afghanistan, more than 6 million Afghan refugees have become the world's largest refugee population. Although refugees in Pakistan and Iran are now beginning to repatriate, continuing political turmoil in Afghanistan and children's acculturation and educational opportunities will keep many Afghans in the United States permanently. Although there are no accurate statistics, local resettlement agencies and Afghan community leaders estimate that there are 10,000 to 35,000 Afghans in northern California. They suffer from a variety of problems common to refugees: language, economic and occupational problems, and substantial challenges in psychological, family, social, and cultural adjustment to the United States. Although many Afghans are doing well, many others have depression, psychosomatic symptoms, and posttraumatic stress disorder. PMID:1413768

Archaeological Survey and Site Testing in Sloughing Easement Areas along the Sac River Downstream from Stockton Dam, Missouri.

DTIC Science & Technology

1986-01-01

Inventories from Sites Outside of the Easement 288 28. Summary of Artifact Frequencies by Functional Category 290 29. Proportions of General Tool...farming community to that of a resort town, with its week-end and holiday crowds of skiers , fishermen, and sightseers. Also but on a more permanent...the Sac River drainage and adjacent drainages has identified a number of specific problems and gaps In our knowledge of the prehistory of the region

Stability of controlled inverted pendulum under permanent horizontal perturbations of the supporting point

NASA Astrophysics Data System (ADS)

Aleksandrov, V. V.; Reyes-Romero, M.; Sidorenko, G. Yu.; Temoltzi-Auila, R.

2010-04-01

We consider the problem of choosing a test perturbation of a movable foundation of a single-link inverted pendulum so as to test a vestibular prosthesis prototype located at the top of this pendulum in an extreme situation. The obtained results permit concluding that the information transmitted from otolithic organs of the human vestibular system to muscles of the locomotor apparatus is very important and improves the quality of stabilization of the human vertical posture preventing the possible fall.

Stability Analysis of Finite Difference Approximations to Hyperbolic Systems,and Problems in Applied and Computational Matrix and Operator Theory

DTIC Science & Technology

1990-12-07

Fundaqao Calouste Gulbenkian, Instituto Gulbenkian de Ci~ncia, Centro de C6lculo Cientifico , Coimbra, 1973. 28, Dirac, P. A. M., Spinors in Hilbert Space...Office of Scientific Research grants 1965 Mathematical Association of America Editorial Prize for the article entitled: "Linear Transformations on...matrices" 1966 L.R. Ford Memorial Prize awarded by the Mathematical Association of America for the article , "Permanents" 1989 Outstanding Computer

Reconnaissance Report. Sedimentation Problem, Quincy Bay, Illinois

DTIC Science & Technology

1987-09-01

are shown on figure 7 of the Fish and Wildife Service’s Planning Aid Report. Area D5 is primarily an agricultural site located within the Indian Grave...and that the placement of dredged material will be permanent. 20 Disposal Site 1 (designated D5 in the Fish and Wildife Service’s Planning Aid Report...provide a more than adequate depth for recreational craft. The U.S. Fish and Wildife Service, in their Planning Aid Report (appendix B), also has

[Secretion of growth hormone in hyperthyroidism].

PubMed

Hervás, F; Morreale de Escobar, G; Escobar Del Rey, F; Pozuelo, V

1976-01-01

The authors studied growth hormone (GH) secretion in a group of adult controls and another group of hyperthyroid patients after stimulation with intravenous insulin-induced (0,1 IU/kg) hypoglycemia, aiming to clear out the problem of discrepancies in literature concerning GH secretion in hyperthyroidism. They concluded that in this syndrome, GH levels are significantly higher than those of controls. The GH releasing response is normal, though it could be expected to be decreased due to decreased pituitary GH contents as a result of permanent somatotrophic cell stimulation.

Human Adaptation Along the Columbia River 4700 - 1600 BP. A Report of Test Excavation at River Mile 590, North Central Washington.

DTIC Science & Technology

1984-01-01

represent a high energy investment in shelter . Pithouses, thus represent, in our view, semi-permanent base-camp use of a site. Mussel shell and FCR... Cordillera to beyond Yellowstone Park (Wadding ton and Wright 1974; Mehringer et al. 1977). A cold-adapted form of Artemisia (sagebrush) dominated... sheltered sites, away from the cold, drying winds and root-damaging effects of permafrost (Mack et al. 1976). Birches and (i) There are problems with

Pollution Permanent Monitoring PANEL--2013 Annual Report

NASA Astrophysics Data System (ADS)

Everett, Lorne G.

2014-07-01

The following sections are included: * POLLUTION PANEL ACTIVITIES 2013 * NATIONAL ACADEMY OF SCIENCES 2013 * MTBE NEW HAMPSHIRE LITIGATION--APRIL 12, 2013 * ALTERNATIVES FOR MANAGING THE NATION's COMPLEX CONTAMINATED GROUNDWATER SITES--NATIONAL ACADEMY OF SCIENCES, 2013 * HUMAN HEALTH EFFECTS OF TRICHLOROETHYLENE: KEY FINDINGS AND SCIENTIFIC ISSUES. MARCH 1, 2013 REVIEWS * BAROMETRIC PRESSURE DRIVES SOIL-GAS CONCENTRATIONS * WATER RESOURCES--TERRORISM TARGETS * WITH A LITTLE INGENUITY THE PROBLEM IS NOT INSOLUBLE * HIGH RISE BUILDINGS * TERRORIST MATERIAL MAY DESTROY WATER TRANSMISSION INFRASTRUCTURE * WATER THREAT CONCLUSIONS * MULTINATIONAL REPOSITORIES

Tracking problem for electromechanical system under influence of external perturbations

NASA Astrophysics Data System (ADS)

Kochetkov, Sergey A.; Krasnova, Svetlana A.; Utkin, Victor A.

2017-01-01

For electromechanical objects the new control algorithms (vortex algprithms) are developed on the base of discontinuous functions. The distinctive feature of these algorithms is providing of asymptotical convergence of the output variables to zero under influence of unknown bounded disturbances of prescribed class. The advantages of proposed approach is demonstrated for direct current motor with permanent excitation. It is shown that inner variables of the system converge to unknown bounded disturbances and guarantee asymptotical convergence of output variables to zero.

Finite element modelling of non-linear magnetic circuits using Cosmic NASTRAN

NASA Technical Reports Server (NTRS)

Sheerer, T. J.

1986-01-01

The general purpose Finite Element Program COSMIC NASTRAN currently has the ability to model magnetic circuits with constant permeablilities. An approach was developed which, through small modifications to the program, allows modelling of non-linear magnetic devices including soft magnetic materials, permanent magnets and coils. Use of the NASTRAN code resulted in output which can be used for subsequent mechanical analysis using a variation of the same computer model. Test problems were found to produce theoretically verifiable results.

Impulse Noise and Neurosensory Hearing Loss—Relationship to Small Arms Fire

PubMed Central

Keim, Robert J.

1970-01-01

The problems of noise are not limited to the simple annoyance of an individual. Noise can produce a permanent hearing handicap. Many everyday activities and hobbies are associated with hazardous exposure to noise. The hunter and the sport shooter are potential subjects of severe and unresolvable hearing loss. Noise-induced hearing loss develops insidiously. The means of prevention are far more simple than is correction of the loss. Wearing ear protectors, plugs or earmuffs, is advisable during exposure to hazardous noise. PMID:5460217

The EUROSEISTEST Experimental Test Site in Greece

NASA Astrophysics Data System (ADS)

Pitilakis, K.; Manos, G.; Raptakis, D.; Anastasiadis, A.; Makra, K.; Manakou, M.

2009-04-01

The European experimental site EUROSEISTEST has been established since 1993 in the epicentral area of the June 20th 1978 earthquake (40.8˚ N, 23.2˚ E, Ms 6.5, Imax VIII+ MSK, Papazachos et al., 1979), located in the active tectonic Mygdonian basin, 30km NNE from Thessaloniki, Greece. Euroseistest has been funded by the European Commission - Directorate General for Research and Development under the framework of consecutive EC research projects (EuroseisTest, EuroseisMod and Eurroseisrisk). It is specially designed and dedicated to conduct experimental and theoretical studies on site effects, soil and site characterization and soil-foundation-structure interaction phenomena. The geological, geophysical and geotechnical conditions of the Euroseistest valley (Mygdonian graben) is very well constrained through numerous in situ campaigns and laboratory tests. The permanent accelerometric network comprises 21 digital 3D stations, including vertical arrays down to 200m (schist bedrock), covering a surface of about 100 sq Km. The site is also covered by a permanent seismological network. A number of high quality recordings, from temporary and permanent arrays, gave the possibility to perform advanced experimental and theoretical studies on site effects (e.g. Raptakis et al., 1998; Pitilakis et al., 1999; Raptakis et al., 2000; Chávez-García et al., 2000; Makra, 2000; Makra et al., 2001 & 2005). The main advantage of Euroseistest is the detailed knowledge of the 3D geological-geotechnical structure of the basin (Manakou, 2007) and its dense permanent accelerometric network. For this reason the site has been recently selected by CEA to validate and check the advanced numerical codes to be used in Cadarache ITER project. Besides the study of site effects, Euroseistest offers interesting possibilities to study SSI problems through two model structures (scaled 1:3). A 6-storey building and a bridge pier, which have been constructed and instrumented in the centre of the valley, close to the main vertical array. Euroseistest experimental site provides a rigorous high quality database comprising geological, geotechnical, geophysical and seismological data, as well as a valuable set of experimental facilities to study both experimentally and theoretically complex site effects and soil-foundation structure problems. Numerous publications have been already released (see in the web page). It is foreseen to strengthen in the near future the possibility to provide wide access to European and international scientific community to perform joint studies, to validate their models and to improve or develop new ones.

Analysis of embryonic development in the unsequenced axolotl: waves of transcriptomic upheaval and stability

PubMed Central

Jiang, Peng; Nelson, Jeffrey D.; Leng, Ning; Collins, Michael; Swanson, Scott; Dewey, Colin N.; Thomson, James A.; Stewart, Ron

2016-01-01

The axolotl (Ambystoma mexicanum) has long been the subject of biological research, primarily owing to its outstanding regenerative capabilities. However, the gene expression programs governing its embryonic development are particularly underexplored, especially when compared to other amphibian model species. Therefore, we performed whole transcriptome polyA+ RNA sequencing experiments on 17 stages of embryonic development. As the axolotl genome is unsequenced and its gene annotation is incomplete, we built de novo transcriptome assemblies for each stage and garnered functional annotation by comparing expressed contigs with known genes in other organisms. In evaluating the number of differentially expressed genes over time, we identify three waves of substantial transcriptome upheaval each followed by a period of relative transcriptome stability. The first wave of upheaval is between the one and two cell stage. We show that the number of differentially expressed genes per unit time is higher between the one and two cell stage than it is across the mid-blastula transition (MBT), the period of zygotic genome activation. We use total RNA sequencing to demonstrate that the vast majority of genes with increasing polyA+ signal between the one and two cell stage result from polyadenylation rather than de novo transcription. The first stable phase begins after the two cell stage and continues until the mid-blastula transition, corresponding with the pre-MBT phase of transcriptional quiescence in amphibian development. Following this is a peak of differential gene expression corresponding with the activation of the zygotic genome and a phase of transcriptomic stability from stages 9 to 11. We observe a third wave of transcriptomic change between stages 11 and 14, followed by a final stable period. The last two stable phases have not been documented in amphibians previously and correspond to times of major morphogenic change in the axolotl embryo: gastrulation and neurulation. These results yield new insights into global gene expression during early stages of amphibian embryogenesis and will help to further develop the axolotl as a model species for developmental and regenerative biology. PMID:27475628

Unit-length line-1 transcripts in human teratocarcinoma cells.

PubMed Central

Skowronski, J; Fanning, T G; Singer, M F

1988-01-01

We have characterized the approximately 6.5-kilobase cytoplasmic poly(A)+ Line-1 (L1) RNA present in a human teratocarcinoma cell line, NTera2D1, by primer extension and by analysis of cloned cDNAs. The bulk of the RNA begins (5' end) at the residue previously identified as the 5' terminus of the longest known primate genomic L1 elements, presumed to represent "unit" length. Several of the cDNA clones are close to 6 kilobase pairs, that is, close to full length. The partial sequences of 18 cDNA clones and full sequence of one (5,975 base pairs) indicate that many different genomic L1 elements contribute transcripts to the 6.5-kilobase cytoplasmic poly(A)+ RNA in NTera2D1 cells because no 2 of the 19 cDNAs analyzed had identical sequences. The transcribed elements appear to represent a subset of the total genomic L1s, a subset that has a characteristic consensus sequence in the 3' noncoding region and a high degree of sequence conservation throughout. Two open reading frames (ORFs) of 1,122 (ORF1) and 3,852 (ORF2) bases, flanked by about 800 and 200 bases of sequence at the 5' and 3' ends, respectively, can be identified in the cDNAs. Both ORFs are in the same frame, and they are separated by 33 bases bracketed by two conserved in-frame stop codons. ORF 2 is interrupted by at least one randomly positioned stop codon in the majority of the cDNAs. The data support proposals suggesting that the human L1 family includes one or more functional genes as well as an extraordinarily large number of pseudogenes whose ORFs are broken by stop codons. The cDNA structures suggest that both genes and pseudogenes are transcribed. At least one of the cDNAs (cD11), which was sequenced in its entirety, could, in principle, represent an mRNA for production of the ORF1 polypeptide. The similarity of mammalian L1s to several recently described invertebrate movable elements defines a new widely distributed class of elements which we term class II retrotransposons. Images PMID:2454389

A label-free and enzyme-free system for operating various logic devices using poly(thymine)-templated CuNPs and SYBR Green I as signal transducers

NASA Astrophysics Data System (ADS)

Wu, Changtong; Zhou, Chunyang; Wang, Erkang; Dong, Shaojun

2016-07-01

For the first time by integrating fluorescent polyT-templated CuNPs and SYBR Green I, a basic INHIBIT gate and four advanced logic circuits (2-to-1 encoder, 4-to-2 encoder, 1-to-2 decoder and 1-to-2 demultiplexer) have been conceptually realized under label-free and enzyme-free conditions. Taking advantage of the selective formation of CuNPs on ss-DNA, the implementation of these advanced logic devices were achieved without any usage of dye quenching groups or other nanomaterials like graphene oxide or AuNPs since polyA strands not only worked as an input but also acted as effective inhibitors towards polyT templates, meeting the aim of developing bio-computing with cost-effective and operationally simple methods. In short, polyT-templated CuNPs, as promising fluorescent signal reporters, are successfully applied to fabricate advanced logic devices, which may present a potential path for future development of molecular computations.For the first time by integrating fluorescent polyT-templated CuNPs and SYBR Green I, a basic INHIBIT gate and four advanced logic circuits (2-to-1 encoder, 4-to-2 encoder, 1-to-2 decoder and 1-to-2 demultiplexer) have been conceptually realized under label-free and enzyme-free conditions. Taking advantage of the selective formation of CuNPs on ss-DNA, the implementation of these advanced logic devices were achieved without any usage of dye quenching groups or other nanomaterials like graphene oxide or AuNPs since polyA strands not only worked as an input but also acted as effective inhibitors towards polyT templates, meeting the aim of developing bio-computing with cost-effective and operationally simple methods. In short, polyT-templated CuNPs, as promising fluorescent signal reporters, are successfully applied to fabricate advanced logic devices, which may present a potential path for future development of molecular computations. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr04069a

The Rhinovirus Subviral A-Particle Exposes 3′-Terminal Sequences of Its Genomic RNA

PubMed Central

Harutyunyan, Shushan; Kowalski, Heinrich

2014-01-01

ABSTRACT Enteroviruses, which represent a large genus within the family Picornaviridae, undergo important conformational modifications during infection of the host cell. Once internalized by receptor-mediated endocytosis, receptor binding and/or the acidic endosomal environment triggers the native virion to expand and convert into the subviral (altered) A-particle. The A-particle is lacking the internal capsid protein VP4 and exposes N-terminal amphipathic sequences of VP1, allowing for its direct interaction with a lipid bilayer. The genomic single-stranded (+)RNA then exits through a hole close to a 2-fold axis of icosahedral symmetry and passes through a pore in the endosomal membrane into the cytosol, leaving behind the empty shell. We demonstrate that in vitro acidification of a prototype of the minor receptor group of common cold viruses, human rhinovirus A2 (HRV-A2), also results in egress of the poly(A) tail of the RNA from the A-particle, along with adjacent nucleotides totaling ∼700 bases. However, even after hours of incubation at pH 5.2, 5′-proximal sequences remain inside the capsid. In contrast, the entire RNA genome is released within minutes of exposure to the acidic endosomal environment in vivo. This finding suggests that the exposed 3′-poly(A) tail facilitates the positioning of the RNA exit site onto the putative channel in the lipid bilayer, thereby preventing the egress of viral RNA into the endosomal lumen, where it may be degraded. IMPORTANCE For host cell infection, a virus transfers its genome from within the protective capsid into the cytosol; this requires modifications of the viral shell. In common cold viruses, exit of the RNA genome is prepared by the acidic environment in endosomes converting the native virion into the subviral A-particle. We demonstrate that acidification in vitro results in RNA exit starting from the 3′-terminal poly(A). However, the process halts as soon as about 700 bases have left the viral shell. Conversely, inside the cell, RNA egress completes in about 2 min. This suggests the existence of cellular uncoating facilitators. PMID:24672023