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Sample records for a-rich upstream sequence

  1. A Partial Least Squares Based Procedure for Upstream Sequence Classification in Prokaryotes.

    PubMed

    Mehmood, Tahir; Bohlin, Jon; Snipen, Lars

    2015-01-01

    The upstream region of coding genes is important for several reasons, for instance locating transcription factor, binding sites, and start site initiation in genomic DNA. Motivated by a recently conducted study, where multivariate approach was successfully applied to coding sequence modeling, we have introduced a partial least squares (PLS) based procedure for the classification of true upstream prokaryotic sequence from background upstream sequence. The upstream sequences of conserved coding genes over genomes were considered in analysis, where conserved coding genes were found by using pan-genomics concept for each considered prokaryotic species. PLS uses position specific scoring matrix (PSSM) to study the characteristics of upstream region. Results obtained by PLS based method were compared with Gini importance of random forest (RF) and support vector machine (SVM), which is much used method for sequence classification. The upstream sequence classification performance was evaluated by using cross validation, and suggested approach identifies prokaryotic upstream region significantly better to RF (p-value < 0.01) and SVM (p-value < 0.01). Further, the proposed method also produced results that concurred with known biological characteristics of the upstream region.

  2. Simian virus 40 major late promoter: an upstream DNA sequence required for efficient in vitro transcription.

    PubMed Central

    Brady, J; Radonovich, M; Thoren, M; Das, G; Salzman, N P

    1984-01-01

    We have previously identified an 11-base DNA sequence, 5'-G-G-T-A-C-C-T-A-A-C-C-3' (simian virus 40 [SV40] map position 294 to 304), which is important in the control of SV40 late RNA expression in vitro and in vivo (Brady et al., Cell 31:625-633, 1982). We report here the identification of another domain of the SV40 late promoter. A series of mutants with deletions extending from SV40 map position 0 to 300 was prepared by nuclease BAL 31 treatment. The cloned templates were then analyzed for efficiency and accuracy of late SV40 RNA expression in the Manley in vitro transcription system. Our studies showed that, in addition to the promoter domain near map position 300, there are essential DNA sequences between nucleotide positions 74 and 95 that are required for efficient expression of late SV40 RNA. Included in this SV40 DNA sequence were two of the six GGGCGG SV40 repeat sequences and an 11-nucleotide segment which showed strong homology with the upstream sequences required for the efficient in vitro and in vivo expression of the histone H2A gene. This upstream promoter sequence supported transcription with the same efficiency even when it was moved 72 nucleotides closer to the major late cap site. In vitro promoter competition analysis demonstrated that the upstream promoter sequence, independent of the 294 to 304 promoter element, is capable of binding polymerase-transcription factors required for SV40 late gene transcription. Finally, we show that DNA sequences which control the specificity of RNA initiation at nucleotide 325 lie downstream of map position 294. Images PMID:6321950

  3. Ebola virus RNA editing depends on the primary editing site sequence and an upstream secondary structure.

    PubMed

    Mehedi, Masfique; Hoenen, Thomas; Robertson, Shelly; Ricklefs, Stacy; Dolan, Michael A; Taylor, Travis; Falzarano, Darryl; Ebihara, Hideki; Porcella, Stephen F; Feldmann, Heinz

    2013-01-01

    Ebolavirus (EBOV), the causative agent of a severe hemorrhagic fever and a biosafety level 4 pathogen, increases its genome coding capacity by producing multiple transcripts encoding for structural and nonstructural glycoproteins from a single gene. This is achieved through RNA editing, during which non-template adenosine residues are incorporated into the EBOV mRNAs at an editing site encoding for 7 adenosine residues. However, the mechanism of EBOV RNA editing is currently not understood. In this study, we report for the first time that minigenomes containing the glycoprotein gene editing site can undergo RNA editing, thereby eliminating the requirement for a biosafety level 4 laboratory to study EBOV RNA editing. Using a newly developed dual-reporter minigenome, we have characterized the mechanism of EBOV RNA editing, and have identified cis-acting sequences that are required for editing, located between 9 nt upstream and 9 nt downstream of the editing site. Moreover, we show that a secondary structure in the upstream cis-acting sequence plays an important role in RNA editing. EBOV RNA editing is glycoprotein gene-specific, as a stretch encoding for 7 adenosine residues located in the viral polymerase gene did not serve as an editing site, most likely due to an absence of the necessary cis-acting sequences. Finally, the EBOV protein VP30 was identified as a trans-acting factor for RNA editing, constituting a novel function for this protein. Overall, our results provide novel insights into the RNA editing mechanism of EBOV, further understanding of which might result in novel intervention strategies against this viral pathogen.

  4. Rearrangement of Upstream Sequences of the hTERT Gene During Cellular Immortalization

    PubMed Central

    Zhao, Yuanjun; Wang, Shuwen; Popova, Evgenya Y.; Grigoryev, Sergei A.; Zhu, Jiyue

    2010-01-01

    Telomerase expression, resulting from transcriptional activation of the hTERT gene, allows cells to acquire indefinite proliferative potential during cellular immortalization and tumorigenesis. However, mechanisms of hTERT gene activation in many immortal cell lines and cancer cells are poorly understood. Here, we report our studies on hTERT activation using genetically related pairs of telomerase-negative (Tel−) and -positive (Tel+) fibroblast lines. First, whereas transiently transfected plasmid reporters did not recapitulate the endogenous hTERT promoter, the promoter in chromosomally integrated bacterial artificial chromosome (BAC) reporters was activated in a subset of Tel+ cells, indicating that activation of the hTERT promoter required native chromatin context and/or distal regulatory elements. Second, the hTERT gene, located near the telomere of chromosome 5p, was translocated in all three Tel+ cell lines but not in their parental pre-crisis cells and Tel− immortal siblings. The breakage points were mapped to regions upstream of the hTERT promoter, indicating that the hTERT gene was the target of these chromosomal rearrangements. In two Tel+ cell lines, translocation of the endogenous hTERT gene appeared to be the major mechanism of its activation as the activity of hTERT promoter in many chromosomally integrated BAC reporters, with intact upstream and downstream neighboring loci, remained relatively low. Therefore, our results suggest that rearrangement of upstream sequences is an important new mechanism of hTERT promoter activation during cellular immortalization. The chromosomal rearrangements likely occurred during cellular crisis and facilitated by telomere dysfunction. Such translocations allowed the hTERT promoter to escape from the native condensed chromatin environment. PMID:19672873

  5. DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants

    PubMed Central

    Barta, Endre; Sebestyén, Endre; Pálfy, Tamás B.; Tóth, Gábor; Ortutay, Csaba P.; Patthy, László

    2005-01-01

    DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters. Release 1.0 of DoOP contains 21 061 chordate clusters from 284 different species and 7548 plant clusters from 269 different species. The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions. Users can search DoOP with either sequence or text (annotation) to find promoter clusters of various genes. In addition to the sequence data, the positions of the conserved sequence blocks derived from multiple alignments, the positions of repetitive elements and the positions of transcription start sites known from the Eukaryotic Promoter Database (EPD) can be viewed graphically. PMID:15608291

  6. DoOP: Databases of Orthologous Promoters, collections of clusters of orthologous upstream sequences from chordates and plants.

    PubMed

    Barta, Endre; Sebestyén, Endre; Pálfy, Tamás B; Tóth, Gábor; Ortutay, Csaba P; Patthy, László

    2005-01-01

    DoOP (http://doop.abc.hu/) is a database of eukaryotic promoter sequences (upstream regions) aiming to facilitate the recognition of regulatory sites conserved between species. The annotated first exons of human and Arabidopsis thaliana genes were used as queries in BLAST searches to collect the most closely related orthologous first exon sequences from Chordata and Viridiplantae species. Up to 3000 bp DNA segments upstream from these first exons constitute the clusters in the chordate and plant sections of the Database of Orthologous Promoters. Release 1.0 of DoOP contains 21,061 chordate clusters from 284 different species and 7548 plant clusters from 269 different species. The database can be used to find and retrieve promoter sequences of a given gene from various species and it is also suitable to see the most trivial conserved sequence blocks in the orthologous upstream regions. Users can search DoOP with either sequence or text (annotation) to find promoter clusters of various genes. In addition to the sequence data, the positions of the conserved sequence blocks derived from multiple alignments, the positions of repetitive elements and the positions of transcription start sites known from the Eukaryotic Promoter Database (EPD) can be viewed graphically.

  7. Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae

    SciTech Connect

    Buchman, A.R.; Kimmerly, W.J.; Rine, J.

    1988-01-01

    Two DNA-binding factors from Saccharomyces cerevisiae have been characterized, GRFI (general regulatory factor I) and ABFI (ARS-binding factor I), that recognize specific sequences within diverse genetic elements. GRFI bound to sequences at the negative regulatory elements (silencers) of the silent mating type loci HML E and HMR E and to the upstream activating sequence (UAS) required for transcription of the MAT ..cap alpha.. genes. A putative conserved UAS located at genes involved in translation (RPG box) was also recognized by GRFI. In addition, GRFI bound with high affinity to sequences within the (C/sub 1-3/A)-repeat region at yeast telomeres. Binding sitesmore » for GRFI with the highest affinity appeared to be of the form 5'-(A/G)(A/C)ACCCAN NCA(T/C)(T/C)-3', where N is any nucleotide. ABFI-binding sites were located next to autonomously replicating sequences (ARSs) at controlling elements of the silent mating type loci HMR E, HMR I, and HML I and were associated with ARS1, ARS2, and the 2..mu..m plasmid ARS. Two tandem ABFI binding sites were found between the HIS3 and DED1 genes, several kilobase pairs from any ARS, indicating that ABFI-binding sites are not restricted to ARSs. The sequences recognized by AFBI showed partial dyad-symmetry and appeared to be variations of the consensus 5'-TATCATTNNNNACGA-3'. GRFI and ABFI were both abundant DNA-binding factors and did not appear to be encoded by the SIR genes, whose product are required for repression of the silent mating type loci. Together, these results indicate that both GRFI and ABFI play multiple roles within the cell.« less

  8. Identification of novel craniofacial regulatory domains located far upstream of SOX9 and disrupted in Pierre Robin sequence

    PubMed Central

    Gordon, Christopher T.; Attanasio, Catia; Bhatia, Shipra; Benko, Sabina; Ansari, Morad; Tan, Tiong Y.; Munnich, Arnold; Pennacchio, Len A.; Abadie, Véronique; Temple, I. Karen; Goldenberg, Alice; van Heyningen, Veronica; Amiel, Jeanne; FitzPatrick, David; Kleinjan, Dirk A.; Visel, Axel; Lyonnet, Stanislas

    2015-01-01

    Mutations in the coding sequence of SOX9 cause campomelic dysplasia (CD), a disorder of skeletal development associated with 46,XY disorders of sex development (DSDs). Translocations, deletions and duplications within a ~2 Mb region upstream of SOX9 can recapitulate the CD-DSD phenotype fully or partially, suggesting the existence of an unusually large cis-regulatory control region. Pierre Robin sequence (PRS) is a craniofacial disorder that is frequently an endophenotype of CD and a locus for isolated PRS at ~1.2-1.5 Mb upstream of SOX9 has been previously reported. The craniofacial regulatory potential within this locus, and within the greater genomic domain surrounding SOX9, remains poorly defined. We report two novel deletions upstream of SOX9 in families with PRS, allowing refinement of the regions harbouring candidate craniofacial regulatory elements. In parallel, ChIP-Seq for p300 binding sites in mouse craniofacial tissue led to the identification of several novel craniofacial enhancers at the SOX9 locus, which were validated in transgenic reporter mice and zebrafish. Notably, some of the functionally validated elements fall within the PRS deletions. These studies suggest that multiple non-coding elements contribute to the craniofacial regulation of SOX9 expression, and that their disruption results in PRS. PMID:24934569

  9. Sequence Elements Upstream of the Core Promoter Are Necessary for Full Transcription of the Capsule Gene Operon in Streptococcus pneumoniae Strain D39

    PubMed Central

    Wen, Zhensong; Sertil, Odeniel; Cheng, Yongxin; Zhang, Shanshan; Liu, Xue; Wang, Wen-Ching

    2015-01-01

    Streptococcus pneumoniae is a major bacterial pathogen in humans. Its polysaccharide capsule is a key virulence factor that promotes bacterial evasion of human phagocytic killing. While S. pneumoniae produces at least 94 antigenically different types of capsule, the genes for biosynthesis of almost all capsular types are arranged in the same locus. The transcription of the capsular polysaccharide (cps) locus is not well understood. This study determined the transcriptional features of the cps locus in the type 2 virulent strain D39. The initial analysis revealed that the cps genes are cotranscribed from a major transcription start site at the −25 nucleotide (G) upstream of cps2A, the first gene in the locus. Using unmarked chromosomal truncations and a luciferase-based transcriptional reporter, we showed that the full transcription of the cps genes not only depends on the core promoter immediately upstream of cps2A, but also requires additional elements upstream of the core promoter, particularly a 59-bp sequence immediately upstream of the core promoter. Unmarked deletions of these promoter elements in the D39 genome also led to significant reduction in CPS production and virulence in mice. Lastly, common cps gene (cps2ABCD) mutants did not show significant abnormality in cps transcription, although they produced significantly less CPS, indicating that the CpsABCD proteins are involved in the encapsulation of S. pneumoniae in a posttranscriptional manner. This study has yielded important information on the transcriptional characteristics of the cps locus in S. pneumoniae. PMID:25733517

  10. B-Bolivia, an Allele of the Maize b1 Gene with Variable Expression, Contains a High Copy Retrotransposon-Related Sequence Immediately Upstream1

    PubMed Central

    Selinger, David A.; Chandler, Vicki L.

    2001-01-01

    The maize (Zea mays) b1 gene encodes a transcription factor that regulates the anthocyanin pigment pathway. Of the b1 alleles with distinct tissue-specific expression, B-Peru and B-Bolivia are the only alleles that confer seed pigmentation. B-Bolivia produces variable and weaker seed expression but darker, more regular plant expression relative to B-Peru. Our experiments demonstrated that B-Bolivia is not expressed in the seed when transmitted through the male. When transmitted through the female the proportion of kernels pigmented and the intensity of pigment varied. Molecular characterization of B-Bolivia demonstrated that it shares the first 530 bp of the upstream region with B-Peru, a region sufficient for seed expression. Immediately upstream of 530 bp, B-Bolivia is completely divergent from B-Peru. These sequences share sequence similarity to retrotransposons. Transient expression assays of various promoter constructs identified a 33-bp region in B-Bolivia that can account for the reduced aleurone pigment amounts (40%) observed with B-Bolivia relative to B-Peru. Transgenic plants carrying the B-Bolivia promoter proximal region produced pigmented seeds. Similar to native B-Bolivia, some transgene loci are variably expressed in seeds. In contrast to native B-Bolivia, the transgene loci are expressed in seeds when transmitted through both the male and female. Some transgenic lines produced pigment in vegetative tissues, but the tissue-specificity was different from B-Bolivia, suggesting the introduced sequences do not contain the B-Bolivia plant-specific regulatory sequences. We hypothesize that the chromatin context of the B-Bolivia allele controls its epigenetic seed expression properties, which could be influenced by the adjacent highly repeated retrotransposon sequence. PMID:11244116

  11. Sequence Requirements of the 5-Enolpyruvylshikimate-3-phosphate Synthase 5[prime]-Upstream Region for Tissue-Specific Expression in Flowers and Seedlings.

    PubMed Central

    Benfey, PN; Takatsuji, H; Ren, L; Shah, DM; Chua, NH

    1990-01-01

    We have analyzed expression from deletion derivatives of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) 5[prime]-upstream region in transgenic petunia flowers and seedlings. In seedlings, expression was strongest in root cortex cells and in trichomes. High-level expression in petals and in seedling roots was conferred by large (>500 base-pair) stretches of sequence, but was lost when smaller fragments were analyzed individually. This apparent requirement for extensive sequence suggests that combinations of cis-elements that are widely separated control tissue-specific expression from the EPSPS promoter. We have also used the high-level, petal-specific expression of the EPSPS promoter to change petal color in two mutant petunia lines. PMID:12354968

  12. A SHORT SEQUENCE IMMEDIATELY UPSTREAM OF THE INTERNAL REPEAT ELEMENTS IS CRITICAL FOR KSHV LANA MEDIATED DNA REPLICATION AND IMPACTS EPISOME PERSISTENCE

    PubMed Central

    León Vázquez, Erika De; Juillard, Franceline; Rosner, Bernard; Kaye, Kenneth M.

    2013-01-01

    Kaposi’s sarcoma-associated herpesvirus LANA (1162 residues) mediates episomal persistence of viral genomes during latency. LANA mediates viral DNA replication and segregates episomes to daughter nuclei. A 59 residue deletion immediately upstream of the internal repeat elements rendered LANA highly deficient for DNA replication and modestly deficient for the ability to segregate episomes, while smaller deletions did not. The 59 amino acid deletion reduced LANA episome persistence by ~14-fold, while sequentially smaller deletions resulted in ~3-fold, or no deficiency. Three distinct LANA regions reorganized heterochromatin, one of which contains the deleted sequence, but the deletion did not abolish LANA’s ability to alter chromatin. Therefore, this work identifies a short internal LANA sequence that is critical for DNA replication, has modest effects on episome segregation, and substantially impacts episome persistence; this region may exert its effects through an interacting host cell protein(s). PMID:24314665

  13. A sequence upstream of canonical PDZ-binding motif within CFTR COOH-terminus enhances NHERF1 interaction

    PubMed Central

    Sharma, Neeraj; LaRusch, Jessica; Sosnay, Patrick R.; Gottschalk, Laura B.; Lopez, Andrea P.; Pellicore, Matthew J.; Evans, Taylor; Davis, Emily; Atalar, Melis; Na, Chan-Hyun; Rosson, Gedge D.; Belchis, Deborah; Milewski, Michal; Pandey, Akhilesh

    2016-01-01

    The development of cystic fibrosis transmembrane conductance regulator (CFTR) targeted therapy for cystic fibrosis has generated interest in maximizing membrane residence of mutant forms of CFTR by manipulating interactions with scaffold proteins, such as sodium/hydrogen exchange regulatory factor-1 (NHERF1). In this study, we explored whether COOH-terminal sequences in CFTR beyond the PDZ-binding motif influence its interaction with NHERF1. NHERF1 displayed minimal self-association in blot overlays (NHERF1, Kd = 1,382 ± 61.1 nM) at concentrations well above physiological levels, estimated at 240 nM from RNA-sequencing and 260 nM by liquid chromatography tandem mass spectrometry in sweat gland, a key site of CFTR function in vivo. However, NHERF1 oligomerized at considerably lower concentrations (10 nM) in the presence of the last 111 amino acids of CFTR (20 nM) in blot overlays and cross-linking assays and in coimmunoprecipitations using differently tagged versions of NHERF1. Deletion and alanine mutagenesis revealed that a six-amino acid sequence 1417EENKVR1422 and the terminal 1478TRL1480 (PDZ-binding motif) in the COOH-terminus were essential for the enhanced oligomerization of NHERF1. Full-length CFTR stably expressed in Madin-Darby canine kidney epithelial cells fostered NHERF1 oligomerization that was substantially reduced (∼5-fold) on alanine substitution of EEN, KVR, or EENKVR residues or deletion of the TRL motif. Confocal fluorescent microscopy revealed that the EENKVR and TRL sequences contribute to preferential localization of CFTR to the apical membrane. Together, these results indicate that COOH-terminal sequences mediate enhanced NHERF1 interaction and facilitate the localization of CFTR, a property that could be manipulated to stabilize mutant forms of CFTR at the apical surface to maximize the effect of CFTR-targeted therapeutics. PMID:27793802

  14. A sequence upstream of canonical PDZ-binding motif within CFTR COOH-terminus enhances NHERF1 interaction.

    PubMed

    Sharma, Neeraj; LaRusch, Jessica; Sosnay, Patrick R; Gottschalk, Laura B; Lopez, Andrea P; Pellicore, Matthew J; Evans, Taylor; Davis, Emily; Atalar, Melis; Na, Chan-Hyun; Rosson, Gedge D; Belchis, Deborah; Milewski, Michal; Pandey, Akhilesh; Cutting, Garry R

    2016-12-01

    The development of cystic fibrosis transmembrane conductance regulator (CFTR) targeted therapy for cystic fibrosis has generated interest in maximizing membrane residence of mutant forms of CFTR by manipulating interactions with scaffold proteins, such as sodium/hydrogen exchange regulatory factor-1 (NHERF1). In this study, we explored whether COOH-terminal sequences in CFTR beyond the PDZ-binding motif influence its interaction with NHERF1. NHERF1 displayed minimal self-association in blot overlays (NHERF1, K d = 1,382 ± 61.1 nM) at concentrations well above physiological levels, estimated at 240 nM from RNA-sequencing and 260 nM by liquid chromatography tandem mass spectrometry in sweat gland, a key site of CFTR function in vivo. However, NHERF1 oligomerized at considerably lower concentrations (10 nM) in the presence of the last 111 amino acids of CFTR (20 nM) in blot overlays and cross-linking assays and in coimmunoprecipitations using differently tagged versions of NHERF1. Deletion and alanine mutagenesis revealed that a six-amino acid sequence 1417 EENKVR 1422 and the terminal 1478 TRL 1480 (PDZ-binding motif) in the COOH-terminus were essential for the enhanced oligomerization of NHERF1. Full-length CFTR stably expressed in Madin-Darby canine kidney epithelial cells fostered NHERF1 oligomerization that was substantially reduced (∼5-fold) on alanine substitution of EEN, KVR, or EENKVR residues or deletion of the TRL motif. Confocal fluorescent microscopy revealed that the EENKVR and TRL sequences contribute to preferential localization of CFTR to the apical membrane. Together, these results indicate that COOH-terminal sequences mediate enhanced NHERF1 interaction and facilitate the localization of CFTR, a property that could be manipulated to stabilize mutant forms of CFTR at the apical surface to maximize the effect of CFTR-targeted therapeutics. Copyright © 2016 the American Physiological Society.

  15. Deletions involving long-range conserved nongenic sequences upstream and downstream of FOXL2 as a novel disease-causing mechanism in blepharophimosis syndrome.

    PubMed

    Beysen, D; Raes, J; Leroy, B P; Lucassen, A; Yates, J R W; Clayton-Smith, J; Ilyina, H; Brooks, S Sklower; Christin-Maitre, S; Fellous, M; Fryns, J P; Kim, J R; Lapunzina, P; Lemyre, E; Meire, F; Messiaen, L M; Oley, C; Splitt, M; Thomson, J; Van de Peer, Y; Veitia, R A; De Paepe, A; De Baere, E

    2005-08-01

    The expression of a gene requires not only a normal coding sequence but also intact regulatory regions, which can be located at large distances from the target genes, as demonstrated for an increasing number of developmental genes. In previous mutation studies of the role of FOXL2 in blepharophimosis syndrome (BPES), we identified intragenic mutations in 70% of our patients. Three translocation breakpoints upstream of FOXL2 in patients with BPES suggested a position effect. Here, we identified novel microdeletions outside of FOXL2 in cases of sporadic and familial BPES. Specifically, four rearrangements, with an overlap of 126 kb, are located 230 kb upstream of FOXL2, telomeric to the reported translocation breakpoints. Moreover, the shortest region of deletion overlap (SRO) contains several conserved nongenic sequences (CNGs) harboring putative transcription-factor binding sites and representing potential long-range cis-regulatory elements. Interestingly, the human region orthologous to the 12-kb sequence deleted in the polled intersex syndrome in goat, which is an animal model for BPES, is contained in this SRO, providing evidence of human-goat conservation of FOXL2 expression and of the mutational mechanism. Surprisingly, in a fifth family with BPES, one rearrangement was found downstream of FOXL2. In addition, we report nine novel rearrangements encompassing FOXL2 that range from partial gene deletions to submicroscopic deletions. Overall, genomic rearrangements encompassing or outside of FOXL2 account for 16% of all molecular defects found in our families with BPES. In summary, this is the first report of extragenic deletions in BPES, providing further evidence of potential long-range cis-regulatory elements regulating FOXL2 expression. It contributes to the enlarging group of developmental diseases caused by defective distant regulation of gene expression. Finally, we demonstrate that CNGs are candidate regions for genomic rearrangements in developmental

  16. Deletions Involving Long-Range Conserved Nongenic Sequences Upstream and Downstream of FOXL2 as a Novel Disease-Causing Mechanism in Blepharophimosis Syndrome

    PubMed Central

    Beysen, D.; Raes, J.; Leroy, B. P.; Lucassen, A.; Yates, J. R. W.; Clayton-Smith, J.; Ilyina, H.; Brooks, S. Sklower; Christin-Maitre, S.; Fellous, M.; Fryns, J. P.; Kim, J. R.; Lapunzina, P.; Lemyre, E.; Meire, F.; Messiaen, L. M.; Oley, C.; Splitt, M.; Thomson, J.; Peer, Y. Van de; Veitia, R. A.; De Paepe, A.; De Baere, E.

    2005-01-01

    The expression of a gene requires not only a normal coding sequence but also intact regulatory regions, which can be located at large distances from the target genes, as demonstrated for an increasing number of developmental genes. In previous mutation studies of the role of FOXL2 in blepharophimosis syndrome (BPES), we identified intragenic mutations in 70% of our patients. Three translocation breakpoints upstream of FOXL2 in patients with BPES suggested a position effect. Here, we identified novel microdeletions outside of FOXL2 in cases of sporadic and familial BPES. Specifically, four rearrangements, with an overlap of 126 kb, are located 230 kb upstream of FOXL2, telomeric to the reported translocation breakpoints. Moreover, the shortest region of deletion overlap (SRO) contains several conserved nongenic sequences (CNGs) harboring putative transcription-factor binding sites and representing potential long-range cis-regulatory elements. Interestingly, the human region orthologous to the 12-kb sequence deleted in the polled intersex syndrome in goat, which is an animal model for BPES, is contained in this SRO, providing evidence of human-goat conservation of FOXL2 expression and of the mutational mechanism. Surprisingly, in a fifth family with BPES, one rearrangement was found downstream of FOXL2. In addition, we report nine novel rearrangements encompassing FOXL2 that range from partial gene deletions to submicroscopic deletions. Overall, genomic rearrangements encompassing or outside of FOXL2 account for 16% of all molecular defects found in our families with BPES. In summary, this is the first report of extragenic deletions in BPES, providing further evidence of potential long-range cis-regulatory elements regulating FOXL2 expression. It contributes to the enlarging group of developmental diseases caused by defective distant regulation of gene expression. Finally, we demonstrate that CNGs are candidate regions for genomic rearrangements in developmental

  17. Translation of the mRNA of the maize transcriptional activator Opaque-2 is inhibited by upstream open reading frames present in the leader sequence.

    PubMed Central

    Lohmer, S; Maddaloni, M; Motto, M; Salamini, F; Thompson, R D

    1993-01-01

    The protein encoded by the Opaque-2 (O2) gene is a transcription factor, translated from an mRNA that possesses an unusually long 5' leader sequence containing three upstream open reading frames (uORFs). The efficiency of translation of O2 mRNA has been tested in vivo by a transient assay in which the level of activation of the b32 promoter, a natural target of O2 protein, is measured. We show that uORF-less O2 alleles possess a higher transactivation value than the wild-type allele and that the reduction in transactivation due to the uORFs is a cis-dominant effect. The data presented indicate that both uORF1 and uORF2 are involved in the reducing effect and suggest that both are likely to be translated. PMID:8439744

  18. Investigations of Escherichia coli promoter sequences with artificial neural networks: New signals discovered upstream of the transcriptional startpoint

    SciTech Connect

    Pedersen, A.G.; Engelbrecht, J.

    1995-12-31

    In this paper we present a novel method for using the learning ability of a neural network as a measure of information in local regions of input data. Using the method to analyze Escherichia coli promoters, we discover all previously described signals, and furthermore find new signals that are regularly spaced along the promoter region. The spacing of all signals correspond to the helical periodicity of DNA, meaning that the signals are all present on the same face of the DNA helix in the promoter region. This is consistent with a model where the RNA polymerase contacts the promoter onmore » one side of the DNA, and suggests that the regions important for promoter recognition may include more positions on the DNA than usually assumed. We furthermore analyze the E.coli promoters by calculating the Kullback Leibler distance, and by constructing sequence logos.« less

  19. An upstream sequence modulates phenazine production at the level of transcription and translation in the biological control strain Pseudomonas chlororaphis 30-84

    PubMed Central

    Wang, Dongping; Ries, Tessa R.; Pierson, Leland S.; Pierson, Elizabeth A.

    2018-01-01

    Phenazines are bacterial secondary metabolites and play important roles in the antagonistic activity of the biological control strain P. chlororaphis 30–84 against take-all disease of wheat. The expression of the P. chlororaphis 30–84 phenazine biosynthetic operon (phzXYFABCD) is dependent on the PhzR/PhzI quorum sensing system located immediately upstream of the biosynthetic operon as well as other regulatory systems including Gac/Rsm. Bioinformatic analysis of the sequence between the divergently oriented phzR and phzX promoters identified features within the 5’-untranslated region (5’-UTR) of phzX that are conserved only among 2OHPCA producing Pseudomonas. The conserved sequence features are potentially capable of producing secondary structures that negatively modulate one or both promoters. Transcriptional and translational fusion assays revealed that deletion of 90-bp of sequence at the 5’-UTR of phzX led to up to 4-fold greater expression of the reporters with the deletion compared to the controls, which indicated this sequence negatively modulates phenazine gene expression both transcriptionally and translationally. This 90-bp sequence was deleted from the P. chlororaphis 30–84 chromosome, resulting in 30-84Enh, which produces significantly more phenazine than the wild-type while retaining quorum sensing control. The transcriptional expression of phzR/phzI and amount of AHL signal produced by 30-84Enh also were significantly greater than for the wild-type, suggesting this 90-bp sequence also negatively affects expression of the quorum sensing genes. In addition, deletion of the 90-bp partially relieved RsmE-mediated translational repression, indicating a role for Gac/RsmE interaction. Compared to the wild-type, enhanced phenazine production by 30-84Enh resulted in improvement in fungal inhibition, biofilm formation, extracellular DNA release and suppression of take-all disease of wheat in soil without negative consequences on growth or

  20. Regulatory interactions between the human HOXB1, HOXB2, and HOXB3 proteins and the upstream sequence of the Otx2 gene in embryonal carcinoma cells.

    PubMed

    Guazzi, S; Pintonello, M L; Viganò, A; Boncinelli, E

    1998-05-01

    Vertebrate Hox and Otx genes encode homeodomain-containing transcription factors thought to transduce positional information along the body axis in the segmental portion of the trunk and in the rostral brain, respectively. Moreover, Hox and Otx2 genes show a complementary spatial regulation during embryogenesis. In this report, we show that a 1821-base pair (bp) upstream DNA fragment of the Otx2 gene is positively regulated by co-transfection with expression vectors for the human HOXB1, HOXB2, and HOXB3 proteins in an embryonal carcinoma cell line (NT2/D1) and that a shorter fragment of only 534 bp is able to drive this regulation. We also identified the HOXB1, HOXB2, and HOXB3 DNA-binding region on the 534-bp Otx2 genomic fragment using nuclear extracts from Hox-transfected COS cells and 12.5 days postcoitum mouse embryos or HOXB3 homeodomain-containing bacterial extracts. HOXB1, HOXB3, and nuclear extracts from 12.5 days postcoitum mouse embryos bind to a sequence containing two palindromic TAATTA sites, which bear four copies of the ATTA core sequence, a common feature of most HOM-C/HOX binding sites. HOXB2 protected an adjacent site containing a direct repeat of an ACTT sequence, quite divergent from the ATTA consensus. The region bound by the three homeoproteins is strikingly conserved through evolution and necessary (at least for HOXB1 and HOXB3) to mediate the up-regulation of the Otx2 transcription. Taken together, our data support the hypothesis that anteriorly expressed Hox genes might play a role in the refinement of the Otx2 early expression boundaries in vivo.

  1. The yeast DNA ligase gene CDC9 is controlled by six orientation specific upstream activating sequences that respond to cellular proliferation but which alone cannot mediate cell cycle regulation.

    PubMed Central

    White, J H; Johnson, A L; Lowndes, N F; Johnston, L H

    1991-01-01

    By fusing the CDC9 structural gene to the PGK upstream sequences and the CDC9 upstream to lacZ, we showed that the cell cycle expression of CDC9 is largely due to transcriptional regulation. To investigate the role of six ATGATT upstream repeats in CDC9 regulation, synthetic copies of the sequence were attached to a heterologous gene. The repeats stimulated transcription strongly and additively, but, unlike conventional yeast UAS elements, only when present in one orientation. Transcription driven by the repeats declines in cells held at START of the cell cycle or in stationary phase, as occurs with CDC9. However, the repeats by themselves cannot impart cell cycle regulation to a heterologous gene. CDC9 may therefore be controlled by an activating system operating through the repeats that is sensitive to cellular proliferation and a separate mechanism that governs the periodic expression in the cell cycle. Images PMID:1901644

  2. COUP-TF (chicken ovalbumin upstream promoter transcription factor)-interacting protein 1 (CTIP1) is a sequence-specific DNA binding protein.

    PubMed Central

    Avram, Dorina; Fields, Andrew; Senawong, Thanaset; Topark-Ngarm, Acharawan; Leid, Mark

    2002-01-01

    Chicken ovalbumin upstream promoter transcription factor (COUP-TF)-interacting proteins 1 and 2 [CTIP1/Evi9/B cell leukaemia (Bcl) l1a and CTIP2/Bcl11b respectively] are highly related C(2)H(2) zinc finger proteins that are abundantly expressed in brain and the immune system, and are associated with immune system malignancies. A selection procedure was employed to isolate high-affinity DNA binding sites for CTIP1. The core binding site on DNA identified in these studies, 5'-GGCCGG-3' (upper strand), is highly related to the canonical GC box and was bound by a CTIP1 oligomeric complex(es) in vitro. Furthermore, both CTIP1 and CTIP2 repressed transcription of a reporter gene harbouring a multimerized CTIP binding site, and this repression was neither reversed by trichostatin A (an inhibitor of known class I and II histone deacetylases) nor stimulated by co-transfection of a COUP-TF family member. These results demonstrate that CTIP1 is a sequence-specific DNA binding protein and a bona fide transcriptional repressor that is capable of functioning independently of COUP-TF family members. These findings may be relevant to the physiological and/or pathological action(s) of CTIPs in cells that do not express COUP-TF family members, such as cells of the haematopoietic and immune systems. PMID:12196208

  3. Classification of G-protein coupled receptors based on a rich generation of convolutional neural network, N-gram transformation and multiple sequence alignments.

    PubMed

    Li, Man; Ling, Cheng; Xu, Qi; Gao, Jingyang

    2018-02-01

    Sequence classification is crucial in predicting the function of newly discovered sequences. In recent years, the prediction of the incremental large-scale and diversity of sequences has heavily relied on the involvement of machine-learning algorithms. To improve prediction accuracy, these algorithms must confront the key challenge of extracting valuable features. In this work, we propose a feature-enhanced protein classification approach, considering the rich generation of multiple sequence alignment algorithms, N-gram probabilistic language model and the deep learning technique. The essence behind the proposed method is that if each group of sequences can be represented by one feature sequence, composed of homologous sites, there should be less loss when the sequence is rebuilt, when a more relevant sequence is added to the group. On the basis of this consideration, the prediction becomes whether a query sequence belonging to a group of sequences can be transferred to calculate the probability that the new feature sequence evolves from the original one. The proposed work focuses on the hierarchical classification of G-protein Coupled Receptors (GPCRs), which begins by extracting the feature sequences from the multiple sequence alignment results of the GPCRs sub-subfamilies. The N-gram model is then applied to construct the input vectors. Finally, these vectors are imported into a convolutional neural network to make a prediction. The experimental results elucidate that the proposed method provides significant performance improvements. The classification error rate of the proposed method is reduced by at least 4.67% (family level I) and 5.75% (family Level II), in comparison with the current state-of-the-art methods. The implementation program of the proposed work is freely available at: https://github.com/alanFchina/CNN .

  4. Identification of a factor in HeLa cells specific for an upstream transcriptional control sequence of an EIA-inducible adenovirus promoter and its relative abundance in infected and uninfected cells.

    PubMed Central

    SivaRaman, L; Subramanian, S; Thimmappaya, B

    1986-01-01

    Utilizing the gel electrophoresis/DNA binding assay, a factor specific for the upstream transcriptional control sequence of the EIA-inducible adenovirus EIIA-early promoter has been detected in HeLa cell nuclear extract. Analysis of linker-scanning mutants of the promoter by DNA binding assays and methylation-interference experiments show that the factor binds to the 17-nucleotide sequence 5' TGGAGATGACGTAGTTT 3' located between positions -66 and -82 upstream from the cap site. This sequence has been shown to be essential for transcription of this promoter. The EIIA-early-promoter specific factor was found to be present at comparable levels in uninfected HeLa cells and in cells infected with either wild-type adenovirus or the EIA-deletion mutant dl312 under conditions in which the EIA proteins are induced to high levels [7 or 20 hr after infection in the presence of arabinonucleoside (cytosine arabinoside)]. Based on the quantitation in DNA binding assays, it appears that the mechanism of EIA-activated transcription of the EIIA-early promoter does not involve a net change in the amounts of this factor. Images PMID:2942943

  5. Molecular cloning and analysis of Schizosaccharomyces pombe Reb1p: sequence-specific recognition of two sites in the far upstream rDNA intergenic spacer.

    PubMed Central

    Zhao, A; Guo, A; Liu, Z; Pape, L

    1997-01-01

    The coding sequences for a Schizosaccharomyces pombe sequence-specific DNA binding protein, Reb1p, have been cloned. The predicted S. pombe Reb1p is 24-29% identical to mouse TTF-1 (transcription termination factor-1) and Saccharomyces cerevisiae REB1 protein, both of which direct termination of RNA polymerase I catalyzed transcripts. The S.pombe Reb1 cDNA encodes a predicted polypeptide of 504 amino acids with a predicted molecular weight of 58.4 kDa. The S. pombe Reb1p is unusual in that the bipartite DNA binding motif identified originally in S.cerevisiae and Klyveromyces lactis REB1 proteins is uninterrupted and thus S.pombe Reb1p may contain the smallest natural REB1 homologous DNA binding domain. Its genomic coding sequences were shown to be interrupted by two introns. A recombinant histidine-tagged Reb1 protein bearing the rDNA binding domain has two homologous, sequence-specific binding sites in the S. pomber DNA intergenic spacer, located between 289 and 480 nt downstream of the end of the approximately 25S rRNA coding sequences. Each binding site is 13-14 bp downstream of two of the three proposed in vivo termination sites. The core of this 17 bp site, AGGTAAGGGTAATGCAC, is specifically protected by Reb1p in footprinting analysis. PMID:9016645

  6. Sequence and transcriptional analysis of the barley ctDNA region upstream of psbD-psbC encoding trnK(UUU), rps16, trnQ(UUG), psbK, psbI, and trnS(GCU).

    PubMed

    Berends Sexton, T; Jones, J T; Mullet, J E

    1990-05-01

    A 6.25 kbp barley plastid DNA region located between psbA and psbD-psbC were sequenced and RNAs produced from this DNA were analyzed. TrnK(UUU), rps16 and trnQ(UUG) were located upstream of psbA. These genes were transcribed from the same DNA strand as psbA and multiple RNAs hybridized to them. TrnK and rsp16 contained introns; a 504 amino acid open reading frame (ORF504) was located within the trnK intron. Between trnQ and psbD-psbC was a 2.24 kbp region encoding psbK, psbI and trnS(GCU). PsbK and psbI are encoded on the same DNA strand as psbD-psbC whereas trnS(GCU) is transcribed from the opposite strand. Two large RNAs accumulate in barley etioplasts which contain psbK, psbI, anti-sense trnS(GCU) and psbD-psbC sequences. Other RNAs encode psbK and psbI only, or psbK only. The divergent trnS(GCU) located upstream of psbD-psbC and a second divergent trnS(UGA) located downstream of psbD-psbC were both expressed. Furthermore, RNA complementary to psbK and psbI mRNA was detected, suggesting that transcription from divergent overlapping transcription units may modulate expression from this DNA region.

  7. Upstream health law.

    PubMed

    Sage, William M; McIlhattan, Kelley

    2014-01-01

    For the first time, entrepreneurs are aggressively developing new technologies and business models designed to improve individual and population health, not just to deliver specialized medical care. Consumers of these goods and services are not yet "patients"; they are simply people. As this sector of the health care industry expands, it is likely to require new forms of legal governance, which we term "upstream health law." © 2014 American Society of Law, Medicine & Ethics, Inc.

  8. pH-Modulated Watson-Crick duplex-quadruplex equilibria of guanine-rich and cytosine-rich DNA sequences 140 base pairs upstream of the c-kit transcription initiation site.

    PubMed

    Bucek, Pavel; Jaumot, Joaquim; Aviñó, Anna; Eritja, Ramon; Gargallo, Raimundo

    2009-11-23

    Guanine-rich regions of DNA are sequences capable of forming G-quadruplex structures. The formation of a G-quadruplex structure in a region 140 base pairs (bp) upstream of the c-kit transcription initiation site was recently proposed (Fernando et al., Biochemistry, 2006, 45, 7854). In the present study, the acid-base equilibria and the thermally induced unfolding of the structures formed by a guanine-rich region and by its complementary cytosine-rich strand in c-kit were studied by means of circular dichroism and molecular absorption spectroscopies. In addition, competition between the Watson-Crick duplex and the isolated structures was studied as a function of pH value and temperature. Multivariate data analysis methods based on both hard and soft modeling were used to allow accurate quantification of the various acid-base species present in the mixtures. Results showed that the G-quadruplex and i-motif coexist with the Watson-Crick duplex over the pH range from 3.0 to 6.5, approximately, under the experimental conditions tested in this study. At pH 7.0, the duplex is practically the only species present.

  9. Corticosteroids: way upstream

    PubMed Central

    2010-01-01

    Studies into the mechanisms of corticosteroid action continue to be a rich bed of research, spanning the fields of neuroscience and endocrinology through to immunology and metabolism. However, the vast literature generated, in particular with respect to corticosteroid actions in the brain, tends to be contentious, with some aspects suffering from loose definitions, poorly-defined models, and appropriate dissection kits. Here, rather than presenting a comprehensive review of the subject, we aim to present a critique of key concepts that have emerged over the years so as to stimulate new thoughts in the field by identifying apparent shortcomings. This article will draw on experience and knowledge derived from studies of the neural actions of other steroid hormones, in particular estrogens, not only because there are many parallels but also because 'learning from differences' can be a fruitful approach. The core purpose of this review is to consider the mechanisms through which corticosteroids might act rapidly to alter neural signaling. PMID:20180948

  10. 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

  11. Draft genome sequence of a KPC-2-producing Klebsiella pneumoniae ST340 carrying blaCTX-M-15 and blaCTX-M-59 genes: a rich genome of mobile genetic elements and genes encoding antibiotic resistance.

    PubMed

    Casella, Tiago; de Morais, Andressa Batista Zequini; de Paula Barcelos, Diego Diniz; Tolentino, Fernanda Modesto; Cerdeira, Louise Teixeira; Bueno, Maria Fernanda Campagnari; Francisco, Gabriela Rodrigues; de Andrade, Leonardo Neves; da Costa Darini, Ana Lucia; de Oliveira Garcia, Doroti; Lincopan, Nilton; Nogueira, Mara Corrêa Lelles

    2018-06-01

    Klebsiella pneumoniae is considered an opportunistic pathogen and an important agent of nosocomial and community infections. It presents the ability to capture and harbour several antimicrobial resistance genes and, in this context, the extensive use of carbapenems to treat serious infections has been responsible for the selection of several resistance genes. This study reports the draft genome sequence of a KPC-2-producing K. pneumoniae strain (Kp10) simultaneously harbouring bla CTX-M-15 and bla CTX-M-59 genes isolated from urine culture of a patient with Parkinson's disease. Classical microbiological methods were applied to isolate and identify the strain, and PCR and sequencing were used to identify and characterise the genes and the genetic environment. Whole-genome sequencing (WGS) was performed using a Nextera XT DNA library and a NextSeq platform. WGS analysis revealed the presence of 5915 coding genes, 46 RNA-encoding genes and 255 pseudogenes. Kp10 belonged to sequence type 340 (ST340) of clonal complex 258 (CC258) and carried 20 transferable genes associated with antimicrobial resistance, comprising seven drug classes. Although the simultaneous presence of different bla CTX-M genes in the same strain is rarely reported, the bla KPC-2 , bla CTX-M-15 and bla CTX-M-59 genes were not associated with the same genetic mobile structure in Kp10. These results confirm the capacity of K. pneumoniae to harbour several antimicrobial resistance genes. Thus, this draft genome could help in future epidemiological studies regarding the dissemination of clinically relevant resistance genes. Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

  12. Upstream waves in Saturn's foreshock

    NASA Technical Reports Server (NTRS)

    Bavassano Cattaneo, M. B.; Cattaneo, P.; Moreno, G.; Lepping, R. P.

    1991-01-01

    An analysis based on plasma and magnetic-field data obtained from Voyager 1 during its Saturn encounter is reported. The plasma data provided every 96 sec and magnetic-field data averaged over 48 sec are utilized. The evidence of upstream waves at Saturn are detected. The waves have a period, in the spacecraft frame, of about 550 sec and a relative amplitude larger than 0.3, are left- and right-hand elliptically polarized, and propagate at about 30 deg with respect to the average magnetic field. The appearance of the waves is correlated with the spacecraft being magnetically connected to the bow shock.

  13. Evolution of Advection Upstream Splitting Method Schemes

    NASA Technical Reports Server (NTRS)

    Liou, Meng-Sing

    2010-01-01

    This paper focuses on the evolution of advection upstream splitting method(AUSM) schemes. The main ingredients that have led to the development of modern computational fluid dynamics (CFD) methods have been reviewed, thus the ideas behind AUSM. First and foremost is the concept of upwinding. Second, the use of Riemann problem in constructing the numerical flux in the finite-volume setting. Third, the necessity of including all physical processes, as characterised by the linear (convection) and nonlinear (acoustic) fields. Fourth, the realisation of separating the flux into convection and pressure fluxes. The rest of this review briefly outlines the technical evolution of AUSM and more details can be found in the cited references. Keywords: Computational fluid dynamics methods, hyperbolic systems, advection upstream splitting method, conservation laws, upwinding, CFD

  14. Upstream Design and 1D-CAE

    NASA Astrophysics Data System (ADS)

    Sawada, Hiroyuki

    Recently, engineering design environment of Japan is changing variously. Manufacturing companies are being challenged to design and bring out products that meet the diverse demands of customers and are competitive against those produced by rising countries(1). In order to keep and strengthen the competitiveness of Japanese companies, it is necessary to create new added values as well as conventional ones. It is well known that design at the early stages has a great influence on the final design solution. Therefore, design support tools for the upstream design is necessary for creating new added values. We have established a research society for 1D-CAE (1 Dimensional Computer Aided Engineering)(2), which is a general term for idea, methodology and tools applicable for the upstream design support, and discuss the concept and definition of 1D-CAE. This paper reports our discussion about 1D-CAE.

  15. Upstream and Downstream Influence in STBLI Instability

    NASA Astrophysics Data System (ADS)

    Martin, Pino; Priebe, Stephan; Helm, Clara

    2016-11-01

    Priebe and Martín (JFM, 2012) show that the low-frequency unsteadiness in shockwave and turbulent boundary layer interactions (STBLI) is governed by an inviscid instability. Priebe, Tu, Martín and Rowley (JFM, 2016) show that the instability is an inviscid centrifugal one, i.e Görtlerlike vortices. Previous works had given differing conclusions as to whether the low-frequency unsteadiness in STBLI is caused by an upstream or downstream mechanism. In this paper, we reconcile these opposite views and show that upstream and downstream correlations co-exist in the context of the nature of Görtler vortices. We find that the instability is similar to that in separated subsonic and laminar flows. Since the turbulence is modulated but passive to the global mode, the turbulent separated flows are amenable to linear global analysis. As such, the characteristic length and time scales, and the receptivity of the global mode might be determined, and low-order models that represent the low-frequency dynamics in STBLI might be developed. The centrifugal instability persists even under hypersonic conditions. This work is funded by the AFOSR Grant Number AF9550-15-1-0284 with Dr. Ivett Leyva.

  16. Upstream Optioneering: Optimising Higher Activity Waste Management

    SciTech Connect

    McTeer, Jennifer; Morris, Jenny; Wickham, Stephen

    2013-07-01

    The Upstream Optioneering project was created by the Nuclear Decommissioning Authority (NDA) Radioactive Waste Management Directorate (RWMD) to support the development and implementation of opportunities to optimise the management of UK higher activity waste, spent fuel and other materials that may be disposed of in a geological disposal facility. The project works in an integrative manner with the NDA, RWMD and waste producers, and was split into three phases: - In Phase 1 waste management opportunities were identified and collated from across the NDA estate. - In Phase 2, opportunities collated during Phase 1, were further consolidated, analysed and prioritisedmore » to develop a three year work programme. Prioritisation ensured that resources were deployed appropriately and opportunities can be realised before the potential benefit diminishes. - Phase 3, which began in April 2012, comprises a three year work programme to address the prioritised opportunities. Work varies from direct implementation of opportunities to scoping studies that may pave the way for more detailed subsequent work by Site Licence Companies. The work programme is flexible and, subject to change control, varies depending on the needs of project sponsors (RWMD, NDA Strategy and NDA Delivery). This paper provides an overview of the Upstream Optioneering project (focusing particularly on Phases 2 and 3), summarises work carried out to date within the three year work programme, and provides some examples of the main findings concerning specific opportunities from Year One of the Phase 3 work programme. (authors)« less

  17. Upstream/downstream: Issues in environmental ethics

    SciTech Connect

    Scherer, D.

    1991-01-01

    Upstream/Downstream reminds us that there are four issues that are more or less distinctive to environmental ethics. First, and most distinctively, environmental issues involve the standing of nonhuman living things and systems. Thus, environmental politics is only partly a clash among the interest of the parties involved; it often involves actions on behalf of the existence rights of nonhuman life forms. Second, environmental ethics concern the intergenerational distribution of benefits more explicitly than do most other ethical issues, which brings out serious weaknesses in legal frameworks that rely on claims for damages. Third, the complexity and indirectness of many environmentalmore » impacts introduces a high degree of uncertainty and thus technical as well as ethical issues of prudent behavior. Specifically, where science may not fully reveal environmental risks, should development proceed; should analysis proceed if it is known to have a Pollyanna bias Fourth, insofar as environmental damage is typically done to common property, and thus its regulation is generally a matter for governmental regulation, the obligations of private actors to make sacrifices beyond what government requires is at issue - an issue that one would expect to be taken up at length in the other volumes.« less

  18. Developmental Origins, Epigenetics, and Equity: Moving Upstream.

    PubMed

    Wallack, Lawrence; Thornburg, Kent

    2016-05-01

    The Developmental Origins of Health and Disease and the related science of epigenetics redefines the meaning of what constitutes upstream approaches to significant social and public health problems. An increasingly frequent concept being expressed is "When it comes to your health, your zip code may be more important than your genetic code". Epigenetics explains how the environment-our zip code-literally gets under our skin, creates biological changes that increase our vulnerability for disease, and even children's prospects for social success, over their life course and into future generations. This science requires us to rethink where disease comes from and the best way to promote health. It identifies the most fundamental social equity issue in our society: that initial social and biological disadvantage, established even prior to birth, and linked to the social experience of prior generations, is made worse by adverse environments throughout the life course. But at the same time, it provides hope because it tells us that a concerted focus on using public policy to improve our social, physical, and economic environments can ultimately change our biology and the trajectory of health and social success into future generations.

  19. 3. Credit JTL Long distance view looking upstream towards New ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. Credit JTL Long distance view looking upstream towards New Hampshire; commercial structures in foreground. - Bellows Falls Arch Bridge, Spanning Connecticut River, North Walpole, Cheshire County, NH

  20. A partnership in upstream HSE technology transfer

    SciTech Connect

    Olszewski, R.E. Wahjosoedibjo, A.S.; Hunley, M.; Peargin, J.C.

    1996-11-01

    The oil and gas industry was for nearly two decades the dominant force in the Indonesian economy and the single largest contributor to the nation`s development. Because of the success of Indonesia`s long-term development and diversification program, this once-dominant sector today occupies a more equal but still vital position in a better-balanced economy. The Indonesian government understands the danger to the environment posed by rapid industrial expansion and has enacted laws and regulations to ensure the sustainable development of its resources while protecting its rain forest environment. In 1992, the government oil company approached Chevron and Texaco for assistance inmore » training its Health, Safety, and Environment (HSE) professionals. The upstream environment, health and safety training program was developed to transfer HSE knowledge and technology to PERTAMINA, PT Caltex Pacific Indonesia, a C&T affiliate, and indirectly, to the entire Indonesian oil and gas industry and government ministries. The four companies have demonstrated the effectiveness of a partnership approach in developing and carrying out HSE training. During 1994 and 1995, four groups, each consisting of about twenty representatives from PERTAMINA, the Directorate of Oil and Gas (MIGAS), the Indonesian Environmental Impact Management Agency (BAPEDAL), CPI, and Chevron and Texaco worldwide subsidiaries, traveled to the United States for an intensive four-month program of study in HSE best practices and technology conducted by Chevron and Texaco experts. This paper describes the development and realization of The PERTAMINA/CPI Health, Safety and Environment Training Program, outlines subjects covered and explains the methodology used to ensure the effective transfer of HSE knowledge and technology. The paper also offers an evaluation of the sessions and presents the plans developed by participant-teams for follow up on their return to Indonesia.« less

  1. Analysis of alterative cleavage and polyadenylation by 3′ region extraction and deep sequencing

    PubMed Central

    Hoque, Mainul; Ji, Zhe; Zheng, Dinghai; Luo, Wenting; Li, Wencheng; You, Bei; Park, Ji Yeon; Yehia, Ghassan; Tian, Bin

    2012-01-01

    Alternative cleavage and polyadenylation (APA) leads to mRNA isoforms with different coding sequences (CDS) and/or 3′ untranslated regions (3′UTRs). Using 3′ Region Extraction And Deep Sequencing (3′READS), a method which addresses the internal priming and oligo(A) tail issues that commonly plague polyA site (pA) identification, we comprehensively mapped pAs in the mouse genome, thoroughly annotating 3′ ends of genes and revealing over five thousand pAs (~8% of total) flanked by A-rich sequences, which have hitherto been overlooked. About 79% of mRNA genes and 66% of long non-coding RNA (lncRNA) genes have APA; but these two gene types have distinct usage patterns for pAs in introns and upstream exons. Promoter-distal pAs become relatively more abundant during embryonic development and cell differentiation, a trend affecting pAs in both 3′-most exons and upstream regions. Upregulated isoforms generally have stronger pAs, suggesting global modulation of the 3′ end processing activity in development and differentiation. PMID:23241633

  2. Increased upstream ionization due to formation of a double layer.

    PubMed

    Thakur, S Chakraborty; Harvey, Z; Biloiu, I A; Hansen, A; Hardin, R A; Przybysz, W S; Scime, E E

    2009-01-23

    We report observations that confirm a theoretical prediction that formation of a current-free double layer in a plasma expanding into a chamber of larger diameter is accompanied by an increase in ionization upstream of the double layer. The theoretical model argues that the increased ionization is needed to balance the difference in diffusive losses upstream and downstream of the expansion region. In our expanding helicon source experiments, we find that the upstream plasma density increases sharply at the same antenna frequency at which the double layer appears.

  3. Short interspersed elements (SINEs) from insectivores. Two classes of mammalian SINEs distinguished by A-rich tail structure.

    PubMed

    Borodulina, O R; Kramerov, D A

    2001-10-01

    Four tRNA-related SINE families were isolated from the genome of the shrew Sorex araneus (SOR element), mole Mogera robusta (TAL element), and hedgehog Mesechinus dauuricus (ERI-1 and ERI-2 elements). Each of these SINEs families is specific for a single Insectivora family: SOR, for Soricidae (shrews); TAL, for Talpidae (moles and desmans); ERI-1 and ERI-2, for Erinaceidae (hedgehogs). There is a long polypyrimidine region (TC-motif) in TAL, ERI-1, and ERI-2 elements located immediately upstream of an A-rich tail with polyadenylation signals (AATAAA) and an RNA polymerase III terminator (T(4-6)) or TCT(3-4)). Ten out of 14 analyzed mammalian tRNA-related SINE families have an A-rich tail similar to that of TAL, ERI-1, and ERI-2 elements. These elements were assigned to class T+. The other four SINEs including SOR element have no polyadenylation signal and transcription terminator in their A-rich tail and were assigned to class T-. Class T+ SINEs occur only in mammals, and most of them have a long polypyrimidine region. Possible models of retroposition of class T+ and T- SINEs are discussed.

  4. 29. VIEW OF TWIN FALLS MAIN CANAL BRIDGE FROM UPSTREAM ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    29. VIEW OF TWIN FALLS MAIN CANAL BRIDGE FROM UPSTREAM LOOKING DOWNSTREAM. - Milner Dam & Main Canal: Twin Falls Canal Company, On Snake River, 11 miles West of city of Burley, Idaho, Twin Falls, Twin Falls County, ID

  5. UPSTREAM LOCK GATE DETAIL AND DOG HOUSE. NOTE ARM AND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    UPSTREAM LOCK GATE DETAIL AND DOG HOUSE. NOTE ARM AND GEARING FOR CONTROLLING LOCK GATE. LOOKING WEST SOUTHWEST. - Illinois Waterway, Brandon Road Lock and Dam , 1100 Brandon Road, Joliet, Will County, IL

  6. DOG HOUSE AT UPSTREAM LOCK GATE. ALSO SEEN AT LEFT ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    DOG HOUSE AT UPSTREAM LOCK GATE. ALSO SEEN AT LEFT IN PHOTO NO. IL-164-A-23. - Illinois Waterway, La Grange Lock and Dam, 3/4 mile south of Country 795N at Illinois River, Versailles, Brown County, IL

  7. 2. OVERALL VIEW OF LOWWATER DAM, LOOKING UPSTREAM. CHAIN OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. OVERALL VIEW OF LOW-WATER DAM, LOOKING UPSTREAM. CHAIN OF ROCKS BRIDGE AND ST. LOUIS WATER DEPARTMENT INTAKE IN BACKGROUND, LOOKING NORTHWEST - Upper Mississippi River 9-Foot Channel Project, Lock & Dam 27, Granite City, Madison County, IL

  8. 9. Upstream view showing diversion flume at lower left and ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. Upstream view showing diversion flume at lower left and mixing plant at left center. Photographer unknown, June 9, 1924. Source: Salt River Project. - Mormon Flat Dam, On Salt River, Eastern Maricopa County, east of Phoenix, Phoenix, Maricopa County, AZ

  9. 9. View to northeast. Oblique view of upstream side of ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. View to northeast. Oblique view of upstream side of bridge from approximately deck level. (90mm lens) - South Fork Trinity River Bridge, State Highway 299 spanning South Fork Trinity River, Salyer, Trinity County, CA

  10. STEEL ERECTION. View of upstream side of bridge, looking north ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    STEEL ERECTION. View of upstream side of bridge, looking north from the old suspension bridge at unjoined cantilever arms - South Fork Trinity River Bridge, State Highway 299 spanning South Fork Trinity River, Salyer, Trinity County, CA

  11. 4. View to westsouthwest. Oblique view of upstream side of ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. View to west-southwest. Oblique view of upstream side of bridge from approximately deck level. (90mm lens) - South Fork Trinity River Bridge, State Highway 299 spanning South Fork Trinity River, Salyer, Trinity County, CA

  12. 4. VIEW SHOWING UPSTREAM FACE OF DAM, LOOKING NORTHEAST ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. VIEW SHOWING UPSTREAM FACE OF DAM, LOOKING NORTHEAST - High Mountain Dams in Upalco Unit, Kidney Lake Dam, Ashley National Forest, 4.7 miles North of Miners Gulch Campground, Mountain Home, Duchesne County, UT

  13. 3. OVERALL VIEW OF DAM, SHOWING UPSTREAM FACE, LOOKING EAST ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. OVERALL VIEW OF DAM, SHOWING UPSTREAM FACE, LOOKING EAST - High Mountain Dams in Upalco Unit, Kidney Lake Dam, Ashley National Forest, 4.7 miles North of Miners Gulch Campground, Mountain Home, Duchesne County, UT

  14. 1. Rockwork approximately 6 of a mile upstream from Keystone ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. Rockwork approximately 6 of a mile upstream from Keystone Bridge. View looking south from a distance of 50 feet. - Denver & Rio Grande Rockwork, East of South Platte, Waterton, Jefferson County, CO

  15. 18. VIEW OF SETTLING BASIN FROM UPSTREAM TRESTLE, SHOWING BULKHEAD ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    18. VIEW OF SETTLING BASIN FROM UPSTREAM TRESTLE, SHOWING BULKHEAD ON RIGHT AND SAND BANK ON LEFT, LOOKING NORTHWEST - Electron Hydroelectric Project, Along Puyallup River, Electron, Pierce County, WA

  16. 65. VIEW LOOKING UPSTREAM FROM FLUME SUBSTRUCTURE, SHOWING COLUMBIA IMPROVEMENT ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    65. VIEW LOOKING UPSTREAM FROM FLUME SUBSTRUCTURE, SHOWING COLUMBIA IMPROVEMENT COMPANY'S NEISSON CREEK SAWMILL. Print No. 177, November 1903 - Electron Hydroelectric Project, Along Puyallup River, Electron, Pierce County, WA

  17. Unit 5, upstream toward incline bridge Johnstown Local Flood ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Unit 5, upstream toward incline bridge - Johnstown Local Flood Protection Project, Beginning on Conemaugh River approx 3.8 miles downstream from confluence of Little Conemaugh & Stony Creek Rivers at Johnstown, Johnstown, Cambria County, PA

  18. Unit 4, upstream from Johns Street Bridge Johnstown Local ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Unit 4, upstream from Johns Street Bridge - Johnstown Local Flood Protection Project, Beginning on Conemaugh River approx 3.8 miles downstream from confluence of Little Conemaugh & Stony Creek Rivers at Johnstown, Johnstown, Cambria County, PA

  19. Unit 6, upstream from Hickory Street Bridge Johnstown Local ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Unit 6, upstream from Hickory Street Bridge - Johnstown Local Flood Protection Project, Beginning on Conemaugh River approx 3.8 miles downstream from confluence of Little Conemaugh & Stony Creek Rivers at Johnstown, Johnstown, Cambria County, PA

  20. Unit 3, upstream from footbridge Johnstown Local Flood Protection ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Unit 3, upstream from footbridge - Johnstown Local Flood Protection Project, Beginning on Conemaugh River approx 3.8 miles downstream from confluence of Little Conemaugh & Stony Creek Rivers at Johnstown, Johnstown, Cambria County, PA

  1. 41. Upstream end of emergency spillway excavation. Photographer unknown, 1929. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    41. Upstream end of emergency spillway excavation. Photographer unknown, 1929. Source: Arizona Department of Water Resources (ADWR). - Waddell Dam, On Agua Fria River, 35 miles northwest of Phoenix, Phoenix, Maricopa County, AZ

  2. 3. AN IMAGE LOOKING SOUTH, TOWARD THE UPSTREAM SIDE OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. AN IMAGE LOOKING SOUTH, TOWARD THE UPSTREAM SIDE OF THE CENTRAL PIER AND SHOWING THE SOUTHEAST ABUTMENT AND ERODED STARLING. - Cement Plant Road Bridge, Spanning Leatherwood Creek on County Road 50 South, Bedford, Lawrence County, IN

  3. 5. A VIEW LOOKING WEST, TOWARD THE UPSTREAM SIDE OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. A VIEW LOOKING WEST, TOWARD THE UPSTREAM SIDE OF THE PIER, SHOWING THE DETERIORATED SHEARWATER EDGE, THE NORTHEAST ABUTMENT AND WING WALL. - Cement Plant Road Bridge, Spanning Leatherwood Creek on County Road 50 South, Bedford, Lawrence County, IN

  4. 1. Credit JTL General view looking upstream and towards New ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. Credit JTL General view looking upstream and towards New Hampshire, unidentified 'crazy man' perched on top of arch. - Bellows Falls Arch Bridge, Spanning Connecticut River, North Walpole, Cheshire County, NH

  5. 7. VIEW WEST ALONG THE UPSTREAM SLOPE OF THE EMBANKMENT, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    7. VIEW WEST ALONG THE UPSTREAM SLOPE OF THE EMBANKMENT, SHOWING ROCK PAVING IN PROGRESS.... Volume XIX, No. 7, June 24, 1940. - Prado Dam, Embankment, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

  6. 22. UPSTREAM VIEW OF THE OUTLET CONTROL STRUCTURE AND THE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    22. UPSTREAM VIEW OF THE OUTLET CONTROL STRUCTURE AND THE PIER FOR THE SERVICE BRIDGE.... Volume XVIII, No. 12, January 29, 1940. - Prado Dam, Outlet Works, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

  7. 10. UPSTREAM EXTENSION TO 60' INFILTRATION PIPE: MISCELLANEOUS METAL DETAILS. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    10. UPSTREAM EXTENSION TO 60' INFILTRATION PIPE: MISCELLANEOUS METAL DETAILS. Sheet A-22, November, 1940. File no. SA 342/31. - Prado Dam, Embankment, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

  8. 26. UPSTREAM VIEW OF DISCHARGE END OF OUTLET STRUCTURE.... Volume ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    26. UPSTREAM VIEW OF DISCHARGE END OF OUTLET STRUCTURE.... Volume XVI, No. 17, September 29, 1939. - Prado Dam, Outlet Works, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

  9. 24. UPSTREAM VIEW OF A PORTION OF THE CLOSED CONDUIT ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    24. UPSTREAM VIEW OF A PORTION OF THE CLOSED CONDUIT SECTION OF OUTLET WORKS.... Volume XVI, No. 15, August 16, 1939. - Prado Dam, Outlet Works, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

  10. 16. VIEW EASTERLY ALONG THE UPSTREAM SIDE OF THE OGEE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    16. VIEW EASTERLY ALONG THE UPSTREAM SIDE OF THE OGEE SECTION OF THE SPILLWAY.... Volume XVIII, No. 13, January 29, 1940. - Prado Dam, Spillway, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

  11. 1. View from the northwest of the bridge's northwest (upstream) ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. View from the northwest of the bridge's northwest (upstream) elevation - Big Cottonwood River Bridge No. 246, Spanning Big Cottonwood River at Cottonwood Street (City Road No. 165), New Ulm, Brown County, MN

  12. 2. View from the north of the bridge's northwest (upstream) ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. View from the north of the bridge's northwest (upstream) elevation - Big Cottonwood River Bridge No. 246, Spanning Big Cottonwood River at Cottonwood Street (City Road No. 165), New Ulm, Brown County, MN

  13. 7. DETAIL CENTRAL PIER (SKEWBACK) WITH BREAKWATER, UPSTREAM (EAST) SIDE. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    7. DETAIL CENTRAL PIER (SKEWBACK) WITH BREAKWATER, UPSTREAM (EAST) SIDE. NOTE FRACTURES ALONG BARREL ARCH EXTRADOS. - Roaring Creek Bridge, State Road 2005 spanning Roaring Creek in Locust Township, Slabtown, Columbia County, PA

  14. 47. VIEW OF UPSTREAM GUIDEWALL, SHOWING LIGHT STANDARD, LOOKING NORTH ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    47. VIEW OF UPSTREAM GUIDEWALL, SHOWING LIGHT STANDARD, LOOKING NORTH - Upper Mississippi River 9-Foot Channel, Lock & Dam No. 8, On Mississippi River near Houston County, MN, Genoa, Vernon County, WI

  15. 3. General view of upstream face, looking northwest. Spillway is ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. General view of upstream face, looking northwest. Spillway is at the far end of the dam. The Antelope Valley is visible in center background. - Little Rock Creek Dam, Little Rock Creek, Littlerock, Los Angeles County, CA

  16. 7. Detail view of reinforced concrete archrings comprising dam's upstream ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    7. Detail view of reinforced concrete arch-rings comprising dam's upstream face. Impressions of the wooden formwork used in construction are visible in the concrete. - Little Rock Creek Dam, Little Rock Creek, Littlerock, Los Angeles County, CA

  17. 2. STONE ARCH BRIDGE. TIMBERS ON THE UPSTREAM FACE OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. STONE ARCH BRIDGE. TIMBERS ON THE UPSTREAM FACE OF THE PIER PROTECTED THE STONEWORK FROM DAMAGE FROM ICE FLOWS, BARGES, ETC. - Lockport Historic District, Stone Arch Bridge, Spanning Des Plaines River at Ninth Street, Lockport, Will County, IL

  18. 23. VIEW LOOKING UPSTREAM FROM WEST BANK OF HEADRACE SHOWING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    23. VIEW LOOKING UPSTREAM FROM WEST BANK OF HEAD-RACE SHOWING RECONSTRUCTED MAIN AND DIVERSION DAMS; HEAD-RACE IS JUST OUT OF PICTURE AT LEFT. - Forge Creek Dam-John Cable Mill, Townsend, Blount County, TN

  19. Barriers impede upstream spawning migration of flathead chub

    USGS Publications Warehouse

    Walters, David M.; Zuellig, Robert E.; Crockett, Harry J.; Bruce, James F.; Lukacs, Paul M.; Fitzpatrick, Ryan M.

    2014-01-01

    Many native cyprinids are declining throughout the North American Great Plains. Some of these species require long reaches of contiguous, flowing riverine habitat for drifting eggs or larvae to develop, and their declining populations have been attributed to habitat fragmentation or barriers (e.g., dams, dewatered channels, and reservoirs) that restrict fish movement. Upstream dispersal is also needed to maintain populations of species with passively drifting eggs or larvae, and prior researchers have suggested that these fishes migrate upstream to spawn. To test this hypothesis, we conducted a mark–recapture study of Flathead Chub Platygobio gracilis within a 91-km reach of continuous riverine habitat in Fountain Creek, Colorado. We measured CPUE, spawning readiness (percent of Flathead Chub expressing milt), and fish movement relative to a channel-spanning dam. Multiple lines of evidence indicate that Flathead Chub migrate upstream to spawn during summer. The CPUE was much higher at the base of the dam than at downstream sites; the seasonal increases in CPUE at the dam closely tracked seasonal increases in spawning readiness, and marked fish moved upstream as far as 33 km during the spawning run. The upstream migration was effectively blocked by the dam. The CPUE of Flathead Chub was much lower upstream of the OHDD than at downstream sites, and <0.2% of fish marked at the dam were recaptured upstream. This study provides the first direct evidence of spawning migration for Flathead Chub and supports the general hypothesis that barriers limit adult dispersal of these and other plains fishes.

  20. 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

  1. Clustering in large networks does not promote upstream reciprocity.

    PubMed

    Masuda, Naoki

    2011-01-01

    Upstream reciprocity (also called generalized reciprocity) is a putative mechanism for cooperation in social dilemma situations with which players help others when they are helped by somebody else. It is a type of indirect reciprocity. Although upstream reciprocity is often observed in experiments, most theories suggest that it is operative only when players form short cycles such as triangles, implying a small population size, or when it is combined with other mechanisms that promote cooperation on their own. An expectation is that real social networks, which are known to be full of triangles and other short cycles, may accommodate upstream reciprocity. In this study, I extend the upstream reciprocity game proposed for a directed cycle by Boyd and Richerson to the case of general networks. The model is not evolutionary and concerns the conditions under which the unanimity of cooperative players is a Nash equilibrium. I show that an abundance of triangles or other short cycles in a network does little to promote upstream reciprocity. Cooperation is less likely for a larger population size even if triangles are abundant in the network. In addition, in contrast to the results for evolutionary social dilemma games on networks, scale-free networks lead to less cooperation than networks with a homogeneous degree distribution.

  2. Participation costs can suppress the evolution of upstream reciprocity.

    PubMed

    Peña, Jorge; Pestelacci, Enea; Berchtold, André; Tomassini, Marco

    2011-03-21

    Indirect reciprocity, one of the many mechanisms proposed to explain the evolution of cooperation, is the idea that altruistic actions can be rewarded by third parties. Upstream or generalized reciprocity is one type of indirect reciprocity in which individuals help someone if they have been helped by somebody else in the past. Although empirically found to be at work in humans, the evolution of upstream reciprocity is difficult to explain from a theoretical point of view. A recent model of upstream reciprocity, first proposed by Nowak and Roch (2007) and further analyzed by Iwagami and Masuda (2010), shows that while upstream reciprocity alone does not lead to the evolution of cooperation, it can act in tandem with mechanisms such as network reciprocity and increase the total level of cooperativity in the population. We argue, however, that Nowak and Roch's model systematically leads to non-uniform interaction rates, where more cooperative individuals take part in more games than less cooperative ones. As a result, the critical benefit-to-cost ratios derived under this model in previous studies are not invariant with respect to the addition of participation costs. We show that accounting for these costs can hinder and even suppress the evolution of upstream reciprocity, both for populations with non-random encounters and graph-structured populations. Copyright © 2011 Elsevier Ltd. All rights reserved.

  3. Clustering in Large Networks Does Not Promote Upstream Reciprocity

    PubMed Central

    Masuda, Naoki

    2011-01-01

    Upstream reciprocity (also called generalized reciprocity) is a putative mechanism for cooperation in social dilemma situations with which players help others when they are helped by somebody else. It is a type of indirect reciprocity. Although upstream reciprocity is often observed in experiments, most theories suggest that it is operative only when players form short cycles such as triangles, implying a small population size, or when it is combined with other mechanisms that promote cooperation on their own. An expectation is that real social networks, which are known to be full of triangles and other short cycles, may accommodate upstream reciprocity. In this study, I extend the upstream reciprocity game proposed for a directed cycle by Boyd and Richerson to the case of general networks. The model is not evolutionary and concerns the conditions under which the unanimity of cooperative players is a Nash equilibrium. I show that an abundance of triangles or other short cycles in a network does little to promote upstream reciprocity. Cooperation is less likely for a larger population size even if triangles are abundant in the network. In addition, in contrast to the results for evolutionary social dilemma games on networks, scale-free networks lead to less cooperation than networks with a homogeneous degree distribution. PMID:21998641

  4. Valuating Indonesian upstream oil management scenario through system dynamics modelling

    NASA Astrophysics Data System (ADS)

    Ketut Gunarta, I.; Putri, F. A.

    2018-04-01

    Under the existing regulation in Constitution Number 22 Year 2001 (UU No 22 Tahun 2001), Production Sharing Contract (PSC) continues to be the scenario in conducting oil and gas upstream mining activities as the previous regulation (UU No. 8 Tahun 1971). Because of the high costs and risks in upstream mining activities, the contractors are dominated by foreign companies, meanwhile National Oil Company (NOC) doesn’t act much. The domination of foreign contractor companies also warned Indonesia in several issues addressing to energy independence and energy security. Therefore, to achieve the goals of energy which is independence and security, there need to be a revision in upstream oil activities regulating scenario. The scenarios will be comparing the current scenario, which is PSC, with the “full concession” scenario for National Oil Company (NOC) in managing oil upstream mining activities. Both scenario will be modelled using System Dynamics methodology and assessed furthermore using financial valuation method of income approach. Under the 2 scenarios, the author will compare which scenario is better for upstream oil management in reaching the goals mentioned before and more profitable in financial aspect. From the simulation, it is gathered that concession scenario offers better option than PSC in reaching energy independence and energy security.

  5. The giant mottled eel, Anguilla marmorata, uses blue-shifted rod photoreceptors during upstream migration.

    PubMed

    Wang, Feng-Yu; Fu, Wen-Chun; Wang, I-Li; Yan, Hong Young; Wang, Tzi-Yuan

    2014-01-01

    Catadromous fishes migrate between ocean and freshwater during particular phases of their life cycle. The dramatic environmental changes shape their physiological features, e.g. visual sensitivity, olfactory ability, and salinity tolerance. Anguilla marmorata, a catadromous eel, migrates upstream on dark nights, following the lunar cycle. Such behavior may be correlated with ontogenetic changes in sensory systems. Therefore, this study was designed to identify changes in spectral sensitivity and opsin gene expression of A. marmorata during upstream migration. Microspectrophotometry analysis revealed that the tropical eel possesses a duplex retina with rod and cone photoreceptors. The λmax of rod cells are 493, 489, and 489 nm in glass, yellow, and wild eels, while those of cone cells are 508, and 517 nm in yellow, and wild eels, respectively. Unlike European and American eels, Asian eels exhibited a blue-shifted pattern of rod photoreceptors during upstream migration. Quantitative gene expression analyses of four cloned opsin genes (Rh1f, Rh1d, Rh2, and SWS2) revealed that Rh1f expression is dominant at all three stages, while Rh1d is expressed only in older yellow eel. Furthermore, sequence comparison and protein modeling studies implied that a blue shift in Rh1d opsin may be induced by two known (N83, S292) and four putative (S124, V189, V286, I290) tuning sites adjacent to the retinal binding sites. Finally, expression of blue-shifted Rh1d opsin resulted in a spectral shift in rod photoreceptors. Our observations indicate that the giant mottled eel is color-blind, and its blue-shifted scotopic vision may influence its upstream migration behavior and habitat choice.

  6. Human Resource Local Content in Ghana's Upstream Petroleum Industry

    NASA Astrophysics Data System (ADS)

    Benin, Papa

    Enactment of Ghana's Petroleum (Local Content and Local Participation) Regulations, 2013 (L.I. 2204) was intended to regulate the percentage of local products, personnel, financing, and goods and services rendered within Ghana's upstream petroleum industry value chain. Five years after the inception of Ghana's upstream oil and gas industry, a gap is evident between the requirements of L.I. 2204 and professional practice. Drawing on Lewin's change theory, a cross-sectional study was conducted to examine the extent of differences between the prevailing human resource local content and the requirements of L.I. 2204 in Ghana's upstream petroleum industry. The extent to which training acquired by indigenous Ghanaians seeking jobs in Ghana's oil fields affects the prevalent local content in its upstream petroleum industry was also examined. Survey data were collected from 97 management, technical, and other staff in 2 multinational petroleum companies whose oil and gas development plans have been approved by the Petroleum Commission of Ghana. To answer the research questions and test their hypotheses, one-way ANOVA was performed with staff category (management, technical, and other) as the independent variable and prevalent local content as the dependent variable. Results indicated that prevailing local content in Ghana's upstream petroleum industry meets the requirements of L.I. 2204. Further, training acquired by indigenous Ghanaians seeking jobs in Ghana's oil fields affects the prevalent local content in its offshore petroleum industry. Findings may encourage leaders within multinational oil companies and the Petroleum Commission of Ghana to organize educational seminars that equip indigenous Ghanaians with specialized skills for working in Ghana's upstream petroleum industry.

  7. Transition duct with divided upstream and downstream portions

    SciTech Connect

    McMahan, Kevin Weston; LeBegue, Jeffrey Scott; Maldonado, Jaime Javier

    2015-07-14

    Turbine systems are provided. In one embodiment, a turbine system includes a transition duct comprising an inlet, an outlet, and a duct passage extending between the inlet and the outlet and defining a longitudinal axis, a radial axis, and a tangential axis. The outlet of the transition duct is offset from the inlet along the longitudinal axis and the tangential axis. The duct passage includes an upstream portion extending from the inlet and a downstream portion extending from the outlet. The turbine system further includes a rib extending from an outer surface of the duct passage, the rib dividing themore » upstream portion and the downstream portion.« less

  8. The Gaia mission a rich resource for outreach activities

    NASA Astrophysics Data System (ADS)

    O'Flaherty, K. S.; Douglas, J.; Prusti, T.

    2008-07-01

    Space science missions, and astronomy missions in particular, capture the public imagination at all levels. ESA's Gaia mission is no exception to this. In addition to its key scientific goal of providing new insight into the origin, formation, and evolution of the Milky Way, Gaia also touches on many other scientific topics of broad appeal, for example, solar system objects, stars (including rare and exotic ones), dark matter, gravitational light bending. The mission naturally provides a rich resource for outreach possibilities whether it be to the general public, or to specific interest groups, such as scientists from other fields or educators. We present some examples of possible outreach activities for Gaia.

  9. 9. Detail, typical bearing, upstream side of west end of ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. Detail, typical bearing, upstream side of west end of Bridge Number 301.85, view to east, 210mm lens with electronic flash fill. - Southern Pacific Railroad Shasta Route, Bridge No. 301.85, Milepost 301.85, Pollard Flat, Shasta County, CA

  10. Aeroacoustic catastrophes: upstream cusp beaming in Lilley's equation.

    PubMed

    Stone, J T; Self, R H; Howls, C J

    2017-05-01

    The downstream propagation of high-frequency acoustic waves from a point source in a subsonic jet obeying Lilley's equation is well known to be organized around the so-called 'cone of silence', a fold catastrophe across which the amplitude may be modelled uniformly using Airy functions. Here we show that acoustic waves not only unexpectedly propagate upstream, but also are organized at constant distance from the point source around a cusp catastrophe with amplitude modelled locally by the Pearcey function. Furthermore, the cone of silence is revealed to be a cross-section of a swallowtail catastrophe. One consequence of these discoveries is that the peak acoustic field upstream is not only structurally stable but also at a similar level to the known downstream field. The fine structure of the upstream cusp is blurred out by distributions of symmetric acoustic sources, but peak upstream acoustic beaming persists when asymmetries are introduced, from either arrays of discrete point sources or perturbed continuum ring source distributions. These results may pose interesting questions for future novel jet-aircraft engine designs where asymmetric source distributions arise.

  11. 18. View of Tombigbee River Bridge facing east showing upstream ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    18. View of Tombigbee River Bridge facing east showing upstream side of bridge opposite broken railing located on the downstream side. Fallen power pole and telephone cable is shown in the center of the photograph. - Tombigbee River Bridge, Spanning Tombigbee River at State Highway 182, Columbus, Lowndes County, MS

  12. 14. VIEW SHOWING UPSTREAM FACE OF HORSE MESA. TRACK FROM ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    14. VIEW SHOWING UPSTREAM FACE OF HORSE MESA. TRACK FROM AGGREGATE BARGES TO MIXING PLANT IS AT LOWER LEFT, RIGHT SPILLWAY CHUTE IS TAKING FORM AT UPPER RIGHT April 29, 1927 - Horse Mesa Dam, Salt River, 65 miles East of Phoenix, Phoenix, Maricopa County, AZ

  13. 18. View to southwest. Detail, bearing shoe, upstream side of ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    18. View to southwest. Detail, bearing shoe, upstream side of east pier. Copy negative made from 35mm color transparency made with with 135mm lens by John Snyder, due to lack of sufficiently long lens for 4x5 camera. - South Fork Trinity River Bridge, State Highway 299 spanning South Fork Trinity River, Salyer, Trinity County, CA

  14. 6. UPSTREAM VIEW OF THE SPILLWAY OF THE POST FALLS ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. UPSTREAM VIEW OF THE SPILLWAY OF THE POST FALLS POWERHOUSE, WITH A PARTIAL VIEW OF THE MODERN TRANSFORMER IN THE FOREGROUND, AND THE OLD SWITCHING BUILDING IN THE LEFT BACKGROUND, LOOKING SOUTHEAST. - Washington Water Power Company Post Falls Power Plant, Middle Channel Powerhouse & Dam, West of intersection of Spokane & Fourth Streets, Post Falls, Kootenai County, ID

  15. 5. UPSTREAM VIEW OF THE TRASH RAKES, GATES AND GATELIFTING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. UPSTREAM VIEW OF THE TRASH RAKES, GATES AND GATE-LIFTING MECHANISMS FOR THE POST FALLS DAM AND POWERHOUSE, LOOKING NORTHWEST. - Washington Water Power Company Post Falls Power Plant, Middle Channel Powerhouse & Dam, West of intersection of Spokane & Fourth Streets, Post Falls, Kootenai County, ID

  16. 32. AERIAL VIEW OF TIETON DAM, UPSTREAM FACE OF DAM ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    32. AERIAL VIEW OF TIETON DAM, UPSTREAM FACE OF DAM (Trashrack-structure for outlet at lower left in reservoir, spillway at upper left. Reservoir nearly empty due to drought.) - Tieton Dam, South & East of State Highway 12, Naches, Yakima County, WA

  17. 10. VIEW UPSTREAM OF PIPELINE SECTION AT JUNCTION OF HUME ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    10. VIEW UPSTREAM OF PIPELINE SECTION AT JUNCTION OF HUME CEMENT PIPE AND CAST-IRON (460'). NOTE CYLINDRICAL COLLAR OF CEMENT SECTIONS AND BELL JUNCTIONS OF IRON PIPE. - Kalaupapa Water Supply System, Waikolu Valley to Kalaupapa Settlement, Island of Molokai, Kalaupapa, Kalawao County, HI

  18. 25. TWIN FALLS MAIN CANAL HEADWORKS FROM UPSTREAM LOOKING TOWARD ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    25. TWIN FALLS MAIN CANAL HEADWORKS FROM UPSTREAM LOOKING TOWARD THE WEST (DAM-TENDER RICHARD CARL ADJUSTING THE GATES TO ALLOW 3400 CFS THROUGH). - Milner Dam & Main Canal: Twin Falls Canal Company, On Snake River, 11 miles West of city of Burley, Idaho, Twin Falls, Twin Falls County, ID

  19. 9. UPSTREAM EXTENSION TO 60' INFILTRATION PIPE: REINFORCEMENT DETAILS OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. UPSTREAM EXTENSION TO 60' INFILTRATION PIPE: REINFORCEMENT DETAILS OF VALVE CONTROL STRUCTURE. Sheet A-20, July, 1939. File no. SA 342/29. - Prado Dam, Embankment, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

  20. 25. UPSTREAM VIEW OF LOWER END OF OUTLET STRUCTURE SHOWING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    25. UPSTREAM VIEW OF LOWER END OF OUTLET STRUCTURE SHOWING FORMS IN PLACE FOR GRAVITY WALL SECTIONS.... Volume XVI, No. 16, August 16, 1939. - Prado Dam, Outlet Works, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

  1. View of Stehr Lake from FS 502 looking upstream (northeast). ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View of Stehr Lake from FS 502 looking upstream (northeast). Vehicle at right center is parked on earthen Upper Stehr Lake Dam. - Childs-Irving Hydroelectric Project, Childs System, Stehr Lake & Dams, Forest Service Road 708/502, Camp Verde, Yavapai County, AZ

  2. VIEW OF UPSTREAM (EAST) SIDES OF UPPER (EAST) END OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    VIEW OF UPSTREAM (EAST) SIDES OF UPPER (EAST) END OF LOCK, SOUTHEAST AND NORTHEAST CONTROL HOUSES, LOCK UNDER REPAIR, BUILDING NOS. 51, 52 AND SOUTHWEST CONTROL HOUSE IN BACKGROUND, VIEW TOWARDS WEST-NORTHWEST - Ortona Lock, Lock No. 2, Machinery and Control Houses, Caloosahatchee River, Cross-State Canal, Okeechobee Intracoastal Waterway, Ortona, Glades County, FL

  3. 23. VIEW LOOKING UPSTREAM AND TOWARD LEFT ABUTMENT OF DAM. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    23. VIEW LOOKING UPSTREAM AND TOWARD LEFT ABUTMENT OF DAM. NOTE FORMS FOR LEFT GRAVITY ABUTMENT AT UPPER RIGHT CORNER OF PICTURE. ARCHES 3, 4, 5, AND 7 COMPLETED TO ELEVATION 1795. 5 OR 7.5 FEET BELOW TOP OF PARAPET WALL. November 29, 1938 - Bartlett Dam, Verde River, Phoenix, Maricopa County, AZ

  4. 4. AERATOR AT 525', CONSTRUCTED 19371938, VIEW FROM UPSTREAM (TRASH ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. AERATOR AT 525', CONSTRUCTED 1937-1938, VIEW FROM UPSTREAM (TRASH SCREEN REMOVED FOR CLARITY), WATER FROM INTAKE FLOWS THROUGH FLUME, THEN DAMS, AND SPILLS OVER STEPS TO MIX WITH OXYGEN, THUS REDUCING ACIDITY LEVELS. ACID INDUCES FASTER CORROSION OF PIPES AND SPOILS TASTE. - Kalaupapa Water Supply System, Waikolu Valley to Kalaupapa Settlement, Island of Molokai, Kalaupapa, Kalawao County, HI

  5. On-line soft sensing in upstream bioprocessing.

    PubMed

    Randek, Judit; Mandenius, Carl-Fredrik

    2018-02-01

    This review provides an overview and a critical discussion of novel possibilities of applying soft sensors for on-line monitoring and control of industrial bioprocesses. Focus is on bio-product formation in the upstream process but also the integration with other parts of the process is addressed. The term soft sensor is used for the combination of analytical hardware data (from sensors, analytical devices, instruments and actuators) with mathematical models that create new real-time information about the process. In particular, the review assesses these possibilities from an industrial perspective, including sensor performance, information value and production economy. The capabilities of existing analytical on-line techniques are scrutinized in view of their usefulness in soft sensor setups and in relation to typical needs in bioprocessing in general. The review concludes with specific recommendations for further development of soft sensors for the monitoring and control of upstream bioprocessing.

  6. Torque fluctuations caused by upstream mean flow and turbulence

    NASA Astrophysics Data System (ADS)

    Farr, T. D.; Hancock, P. E.

    2014-12-01

    A series of studies are in progress investigating the effects of turbine-array-wake interactions for a range of atmospheric boundary layer states by means of the EnFlo meteorological wind tunnel. The small, three-blade model wind turbines drive 4-quadrant motor-generators. Only a single turbine in neutral flow is considered here. The motor-generator current can be measured with adequate sensitivity by means of a current sensor allowing the mean and fluctuating torque to be inferred. Spectra of torque fluctuations and streamwise velocity fluctuations ahead of the rotor, between 0.1 and 2 diameters, show that only the large-scale turbulent motions contribute significantly to the torque fluctuations. Time-lagged cross-correlation between upstream velocity and torque fluctuations are largest over the inner part of the blade. They also show the turbulence to be frozen in behaviour over the 2 diameters upstream of the turbine.

  7. 8. SEDIMENTATION CHAMBER, VIEW UPSTREAM (PLANK COVER REMOVED FOR CLARITY). ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. SEDIMENTATION CHAMBER, VIEW UPSTREAM (PLANK COVER REMOVED FOR CLARITY). BOX FLUME DROPS SLIGHTLY INTO CHAMBER ON LEFT SIDE. CHAMBER IS A SERIES OF BAFFLES DESIGNED TO SLOW THE FLOW OF WATER. FLOW IS REDUCED TO ALLOW PARTICULATES TO SETTLE TO THE BOTTOM. TWO SCREENS (NOT SHOWN) FILTER LARGER DEBRIS. - Kalaupapa Water Supply System, Waikolu Valley to Kalaupapa Settlement, Island of Molokai, Kalaupapa, Kalawao County, HI

  8. Short wavelength ion waves upstream of the earth's bow shock

    NASA Technical Reports Server (NTRS)

    Fuselier, S. A.; Gurnett, D. A.

    1984-01-01

    The identification and explanation of short wavelength antenna interference effects observed in spacecraft plasma wave data have provided an important new method of determining limits on the wavelength, direction of propagation, and Doppler shift of short wavelength electrostatic waves. Using the ISEE-1 wideband electric field data, antenna interference effects have been identified in the ion waves upstream of the earth's bow shock. This identification implies that wavelengths of the upstream ion waves are shorter than the antenna length. The interference effects also provide new measurements of the direction of propagation of the ion waves. The new measurements show that the wave vectors of the ion waves are not parallel to the interplanetary magnetic field (IMF) as previously reported. The direction of propagation does not appear to be controlled by the IMF. In addition, analysis of the Doppler shift of the short wavelength ion waves has provided a measurement of the dispersion relation. The upper limit of the rest frame frequency was found to be on the order of the ion plasma frequency. At this frequency, the wavelength is on the order of a few times the Debye length. The results of this study now provide strong evidence that the ion waves in the upstream region are Doppler-shifted ion acoustic waves. Previously announced in STAR as N83-36328

  9. DENSITY FLUCTUATIONS UPSTREAM AND DOWNSTREAM OF INTERPLANETARY SHOCKS

    SciTech Connect

    Pitňa, A.; Šafránková, J.; Němeček, Z.

    2016-03-01

    Interplanetary (IP) shocks as typical large-scale disturbances arising from processes such as stream–stream interactions or Interplanetary Coronal Mass Ejection (ICME) launching play a significant role in the energy redistribution, dissipation, particle heating, acceleration, etc. They can change the properties of the turbulent cascade on shorter scales. We focus on changes of the level and spectral properties of ion flux fluctuations upstream and downstream of fast forward oblique shocks. Although the fluctuation level increases by an order of magnitude across the shock, the spectral slope in the magnetohydrodynamic range is conserved. The frequency spectra upstream of IP shocks are the same as those inmore » the solar wind (if not spoiled by foreshock waves). The spectral slopes downstream are roughly proportional to the corresponding slopes upstream, suggesting that the properties of the turbulent cascade are conserved across the shock; thus, the shock does not destroy the shape of the spectrum as turbulence passes through it. Frequency spectra downstream of IP shocks often exhibit “an exponential decay” in the ion kinetic range that was earlier reported at electron scales in the solar wind or at ion scales in the interstellar medium. We suggest that the exponential shape of ion flux spectra in this range is caused by stronger damping of the fluctuations in the downstream region.« less

  10. Catalytic Ignition and Upstream Reaction Propagation in Monolith Reactors

    NASA Technical Reports Server (NTRS)

    Struk, Peter M.; Dietrich, Daniel L.; Miller, Fletcher J.; T'ien, James S.

    2007-01-01

    Using numerical simulations, this work demonstrates a concept called back-end ignition for lighting-off and pre-heating a catalytic monolith in a power generation system. In this concept, a downstream heat source (e.g. a flame) or resistive heating in the downstream portion of the monolith initiates a localized catalytic reaction which subsequently propagates upstream and heats the entire monolith. The simulations used a transient numerical model of a single catalytic channel which characterizes the behavior of the entire monolith. The model treats both the gas and solid phases and includes detailed homogeneous and heterogeneous reactions. An important parameter in the model for back-end ignition is upstream heat conduction along the solid. The simulations used both dry and wet CO chemistry as a model fuel for the proof-of-concept calculations; the presence of water vapor can trigger homogenous reactions, provided that gas-phase temperatures are adequately high and there is sufficient fuel remaining after surface reactions. With sufficiently high inlet equivalence ratio, back-end ignition occurs using the thermophysical properties of both a ceramic and metal monolith (coated with platinum in both cases), with the heat-up times significantly faster for the metal monolith. For lower equivalence ratios, back-end ignition occurs without upstream propagation. Once light-off and propagation occur, the inlet equivalence ratio could be reduced significantly while still maintaining an ignited monolith as demonstrated by calculations using complete monolith heating.

  11. Upstream paths for Hippo signaling in Drosophila organ development.

    PubMed

    Choi, Kwang-Wook

    2018-03-01

    Organ growth is fundamental to animal development. One of major mechanisms for growth control is mediated by the conserved Hippo signaling pathway initially identified in Drosophila. The core of this pathway in Drosophila consists of a cascade of protein kinases Hippo and Warts that negatively regulate transcriptional coactivator Yorkie (Yki). Activation of Yki promotes cell survival and proliferation to induce organ growth. A key issue in Hippo signaling is to understand how core kinase cascade is activated. Activation of Hippo kinase cascade is regulated in the upstream by at least two transmembrane proteins Crumbs and Fat that act in parallel. These membrane proteins interact with additional factors such as FERM-domain proteins Expanded and Merlin to modulate subcellular localization and function of the Hippo kinase cascade. Hippo signaling is also influenced by cytoskeletal networks and cell tension in epithelia of developing organs. These upstream events in the regulation of Hippo signaling are only partially understood. This review focuses on our current understanding of some upstream processes involved in Hippo signaling in developing Drosophila organs. [BMB Reports 2018; 51(3): 134-142].

  12. Interaction of upstream flow distortions with high Mach number cascades

    NASA Technical Reports Server (NTRS)

    Englert, G. W.

    1981-01-01

    Features of the interaction of flow distortions, such as gusts and wakes with blade rows of advance type fans and compressors having high tip Mach numbers are modeled. A typical disturbance was assumed to have harmonic time dependence and was described, at a far upstream location, in three orthogonal spatial coordinates by a double Fourier series. It was convected at supersonic relative to a linear cascade described as an unrolled annulus. Conditions were selected so that the component of this velocity parallel to the axis of the turbomachine was subsonic, permitting interaction between blades through the upstream as well as downstream flow media. A strong, nearly normal shock was considered in the blade passages which was allowed curvature and displacement. The flows before and after the shock were linearized relative to uniform mean velocities in their respective regions. Solution of the descriptive equations was by adaption of the Wiener-Hopf technique, enabling a determination of distortion patterns through and downstream of the cascade as well as pressure distributions on the blade and surfaces. Details of interaction of the disturbance with the in-passage shock were discussed. Infuences of amplitude, wave length, and phase of the disturbance on lifts and moments of cascade configurations are presented. Numerical results are clarified by reference to an especially orderly pattern of upstream vertical motion in relation to the cascade parameters.

  13. Functional analysis of the upstream regulatory region of chicken miR-17-92 cluster.

    PubMed

    Cheng, Min; Zhang, Wen-jian; Xing, Tian-yu; Yan, Xiao-hong; Li, Yu-mao; Li, Hui; Wang, Ning

    2016-08-01

    miR-17-92 cluster plays important roles in cell proliferation, differentiation, apoptosis, animal development and tumorigenesis. The transcriptional regulation of miR-17-92 cluster has been extensively studied in mammals, but not in birds. To date, avian miR-17-92 cluster genomic structure has not been fully determined. The promoter location and sequence of miR-17-92 cluster have not been determined, due to the existence of a genomic gap sequence upstream of miR-17-92 cluster in all the birds whose genomes have been sequenced. In this study, genome walking was used to close the genomic gap upstream of chicken miR-17-92 cluster. In addition, bioinformatics analysis, reporter gene assay and truncation mutagenesis were used to investigate functional role of the genomic gap sequence. Genome walking analysis showed that the gap region was 1704 bp long, and its GC content was 80.11%. Bioinformatics analysis showed that in the gap region, there was a 200 bp conserved sequence among the tested 10 species (Gallus gallus, Homo sapiens, Pan troglodytes, Bos taurus, Sus scrofa, Rattus norvegicus, Mus musculus, Possum, Danio rerio, Rana nigromaculata), which is core promoter region of mammalian miR-17-92 host gene (MIR17HG). Promoter luciferase reporter gene vector of the gap region was constructed and reporter assay was performed. The result showed that the promoter activity of pGL3-cMIR17HG (-4228/-2506) was 417 times than that of negative control (empty pGL3 basic vector), suggesting that chicken miR-17-92 cluster promoter exists in the gap region. To further gain insight into the promoter structure, two different truncations for the cloned gap sequence were generated by PCR. One had a truncation of 448 bp at the 5'-end and the other had a truncation of 894 bp at the 3'-end. Further reporter analysis showed that compared with the promoter activity of pGL3-cMIR17HG (-4228/-2506), the reporter activities of the 5'-end truncation and the 3'-end truncation were reduced by 19

  14. Transcription of the Streptococcus pyogenes Hyaluronic Acid Capsule Biosynthesis Operon Is Regulated by Previously Unknown Upstream Elements

    PubMed Central

    Falaleeva, Marina; Zurek, Oliwia W.; Watkins, Robert L.; Reed, Robert W.; Ali, Hadeel; Sumby, Paul; Voyich, Jovanka M.

    2014-01-01

    The important human pathogen Streptococcus pyogenes (group A Streptococcus [GAS]) produces a hyaluronic acid (HA) capsule that plays critical roles in immune evasion. Previous studies showed that the hasABC operon encoding the capsule biosynthesis enzymes is under the control of a single promoter, P1, which is negatively regulated by the two-component regulatory system CovR/S. In this work, we characterize the sequence upstream of P1 and identify a novel regulatory region controlling transcription of the capsule biosynthesis operon in the M1 serotype strain MGAS2221. This region consists of a promoter, P2, which initiates transcription of a novel small RNA, HasS, an intrinsic transcriptional terminator that inefficiently terminates HasS, permitting read-through transcription of hasABC, and a putative promoter which lies upstream of P2. Electrophoretic mobility shift assays, quantitative reverse transcription-PCR, and transcriptional reporter data identified CovR as a negative regulator of P2. We found that the P1 and P2 promoters are completely repressed by CovR, and capsule expression is regulated by the putative promoter upstream of P2. Deletion of hasS or of the terminator eliminates CovR-binding sequences, relieving repression and increasing read-through, hasA transcription, and capsule production. Sequence analysis of 44 GAS genomes revealed a high level of polymorphism in the HasS sequence region. Most of the HasS variations were located in the terminator sequences, suggesting that this region is under strong selective pressure. We discovered that the terminator deletion mutant is highly resistant to neutrophil-mediated killing and is significantly more virulent in a mouse model of GAS invasive disease than the wild-type strain. Together, these results are consistent with the naturally occurring mutations in this region modulating GAS virulence. PMID:25287924

  15. A RICH detector for hadron identification at Jlab

    SciTech Connect

    Mammoliti, Francesco; Cisbani, Evaristo; Cusanno, Francesco

    2011-08-01

    The “standard” Hall A apparatus at Jefferson Lab (TOF and aerogel threshold Cherenkov detectors) does not provide complete identification for proton, kaon and pion. To this aim, a proximity focusing C6F14/CsI RICH (Ring Image Cherenkov) detector has been designed, built, tested and operated to separate kaons from pions with a pion contamination of a few percent up to 2.4 GeV/c. Two quite different experimental investigations have benefitted of the RICH identification: on one side, the high-resolution hypernuclear spectroscopy series of experiments on carbon, beryllium and oxygen, devoted to the study of the lambda-nucleon potential. On the other side, the measurementsmore » of the single spin asymmetries of pion and kaon on a transversely polarized 3He target are of utmost interest in understanding QCD dynamics in the nucleon. We present the technical features of such a RICH detector and comment on the presently achieved performance in hadron identification.« less

  16. The conserved upstream region of lscB/C determines expression of different levansucrase genes in plant pathogen Pseudomonas syringae

    PubMed Central

    2014-01-01

    Background Pseudomonas syringae pv. glycinea PG4180 is an opportunistic plant pathogen which causes bacterial blight of soybean plants. It produces the exopolysaccharide levan by the enzyme levansucrase. Levansucrase has three gene copies in PG4180, two of which, lscB and lscC, are expressed while the third, lscA, is cryptic. Previously, nucleotide sequence alignments of lscB/C variants in various P. syringae showed that a ~450-bp phage-associated promoter element (PAPE) including the first 48 nucleotides of the ORF is absent in lscA. Results Herein, we tested whether this upstream region is responsible for the expression of lscB/C and lscA. Initially, the transcriptional start site for lscB/C was determined. A fusion of the PAPE with the ORF of lscA (lscB UpN A) was generated and introduced to a levan-negative mutant of PG4180. Additionally, fusions comprising of the non-coding part of the upstream region of lscB with lscA (lscB Up A) or the upstream region of lscA with lscB (lscA Up B) were generated. Transformants harboring the lscB UpN A or the lscB Up A fusion, respectively, showed levan formation while the transformant carrying lscA Up B did not. qRT-PCR and Western blot analyses showed that lscB UpN A had an expression similar to lscB while lscB Up A had a lower expression. Accuracy of protein fusions was confirmed by MALDI-TOF peptide fingerprinting. Conclusions Our data suggested that the upstream sequence of lscB is essential for expression of levansucrase while the N-terminus of LscB mediates an enhanced expression. In contrast, the upstream region of lscA does not lead to expression of lscB. We propose that lscA might be an ancestral levansucrase variant upstream of which the PAPE got inserted by potentially phage-mediated transposition events leading to expression of levansucrase in P. syringae. PMID:24670199

  17. Defective distal regulatory element at the 5' upstream of rat prolactin gene of steroid-nonresponsive GH-subclone.

    PubMed

    Kumar, V; Wong, D T; Pasion, S G; Biswas, D K

    1987-12-08

    The prolactin-nonproducing (PRL-) GH cell strains (rat pituitary tumor cells in culture). GH12C1 and F1BGH12C1, do not respond to steroid hormones estradiol or hydrocortisone (HC). However, the stimulatory effect of estradiol and the inhibitory effect of hydrocortisone on prolactin synthesis can be demonstrated in the prolactin-producing GH cell strain, GH4C1. In this investigation we have examined the 5' end flanking region of rat prolactin (rat PRL) gene of steroid-responsive, GH4C1 cells to identify the positive and negative regulatory elements and to verify the status of these elements in steroid-nonresponsive F1BGH12C1 cells. Results presented in this report demonstrate that the basel level expression of the co-transferred Neo gene (neomycin phosphoribosyl transferase) is modulated by the distal upstream regulatory elements of rat PRL gene in response to steroid hormones. The expression of adjacent Neo gene is inhibited by dexamethasone and is stimulated by estradiol in transfectants carrying distal regulatory elements (SRE) of steroid-responsive cells. These responses are not observed in transfectants with the rat PRL upstream sequences derived from steroid-nonresponsive cells. The basal level expression of the host cell alpha-2 tubulin gene is not affected by dexamethasone. We report here the identification of the distal steroid regulatory element (SRE) located between 3.8 and 7.8 kb upstream of the transcription initiation site of rat PRL gene. Both the positive and the negative effects of steroid hormones can be identified within this upstream sequence. This distal SRE appears to be nonfunctional in steroid-nonresponsive cells. Though the proximal SRE is functional, the defect in the distal SRE makes the GH substrain nonresponsive to steroid hormones. These results suggest that both the proximal and the distal SREs are essential for the mediation of action of steroid hormones in GH cells.

  18. Increased risk of oesophageal adenocarcinoma among upstream petroleum workers

    PubMed Central

    Kirkeleit, Jorunn; Riise, Trond; Bjørge, Tone; Moen, Bente E; Bråtveit, Magne; Christiani, David C

    2013-01-01

    Objectives To investigate cancer risk, particularly oesophageal cancer, among male upstream petroleum workers offshore potentially exposed to various carcinogenic agents. Methods Using the Norwegian Registry of Employers and Employees, 24 765 male offshore workers registered from 1981 to 2003 was compared with 283 002 male referents from the general working population matched by age and community of residence. The historical cohort was linked to the Cancer Registry of Norway and the Norwegian Cause of Death Registry. Results Male offshore workers had excess risk of oesophageal cancer (RR 2.6, 95% CI 1.4 to 4.8) compared with the reference population. Only the adenocarcinoma type had a significantly increased risk (RR 2.7, 95% CI 1.0 to 7.0), mainly because of an increased risk among upstream operators (RR 4.3, 95% CI 1.3 to 14.5). Upstream operators did not have significant excess of respiratory system or colon cancer or mortality from any other lifestyle-related diseases investigated. Conclusion We found a fourfold excess risk of oesophageal adenocarcinoma among male workers assumed to have had the most extensive contact with crude oil. Due to the small number of cases, and a lack of detailed data on occupational exposure and lifestyle factors associated with oesophageal adenocarcinoma, the results must be interpreted with caution. Nevertheless, given the low risk of lifestyle-related cancers and causes of death in this working group, the results add to the observations in other low-powered studies on oesophageal cancer, further suggesting that factors related to the petroleum stream or carcinogenic agents used in the production process might be associated with risk of oesophageal adenocarcinoma. PMID:19858535

  19. 2. View of Potomac River at Great Falls looking upstream ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. View of Potomac River at Great Falls looking upstream from Observation Tower. The majestic character of this wild and untrammeled spot is vividly shown. Scanty flow is evidenced by light colored normal water line markings on rock formation. Washington Agueduct Dam is shown in upper portion. Maryland on right and Virginia on left. Natives quoted as saying the water was as low or lower than during the drought conditions of 1930. Mr. Horyduzak, Photographer, 1943. - Potowmack Company: Great Falls Canal & Locks, Great Falls, Fairfax County, VA

  20. Intron Definition Is Required for Excision of the Minute Virus of Mice Small Intron and Definition of the Upstream Exon

    PubMed Central

    Haut, Donald D.; Pintel, D. J.

    1998-01-01

    Alternative splicing of pre-mRNAs plays a critical role in maximizing the coding capacity of the small parvovirus genome. The small-intron region of minute virus of mice (MVM) pre-mRNAs undergoes an unusual pattern of overlapping alternative splicing—using two donors (D1 and D2) and two acceptors (A1 and A2) within a region of 120 nucleotides—that determines the steady-state ratios of the various viral mRNAs. In this report, we show that the determinants that govern excision of the small intron are complex and are also required for efficient definition of the upstream exon. For the MVM small intron in its natural context, the two donors appear to compete for the splicing machinery: the position of D1 favors its usage, while the primary sequence of D2 must be more like the consensus sequence than is D1 to be used efficiently. We have genetically defined the branch points that are used for generation of the major and minor spliced forms and show that recognition of components of the small-intron acceptors is likely to be the dominant determinant in alternative small-intron excision. We have also identified a G-rich intronic enhancer sequence within the small intron that is essential for splicing of the minor form (D2 to A2) but not the major form (D1 to A1) of MVM mRNAs and is required for efficient definition of the upstream NS2-specific exon. In its natural context, the small intron appears to be excised by a mechanism consistent with intron definition. When the MVM small intron is expanded, various parameters of its excision are altered, indicating that critical cis-acting signals are context dependent. Relative use of the donors and acceptors is altered, and the upstream NS2-specific exon is no longer efficiently defined. The fact that definition of the upstream NS2-specific exon can be achieved by the MVM small intron in its natural context, but not when it is expanded, suggests that the multiple determinants that govern definition and excision of the small

  1. Moving further upstream: from toxics reduction to the precautionary principle.

    PubMed

    Mayer, Brian; Brown, Phil; Linder, Meadow

    2002-01-01

    Early policies to reduce the amount of toxic waste in the environment focused on cleaning up downstream sources of pollution, such as toxic disposal sites. Public attention in the 1980s encouraged both industry and government to develop an alternative to this command-and-control approach. This article describes the emergence of that alternative-pollution prevention-and its application in Massachusetts through the 1989 Toxics Use Reduction Act. Pollution prevention focuses on the sources of pollution, both metaphorically and physically, more upstream than its predecessors. The success of the Toxics Use Reduction Act in Massachusetts helped create an opportunity where an alternative pollution prevention paradigm could develop. That paradigm, the precautionary principle, is popular among environment activists because it focuses further upstream than pollution prevention by calling attention to the role the social construction of risk plays in decisions regarding the use of hazardous substances. The authors examine the evolution of the precautionary principle through an investigation of three major pathways in its development and expansion. The article concludes with a discussion of the increased potential for protecting public health and the environment afforded by this new perspective.

  2. The effects of upstream plasma properties on Titan's ionosphere

    NASA Astrophysics Data System (ADS)

    Ledvina, S. A.; Brecht, S. H.

    2016-12-01

    Cassini observations have found that the plasma and magnetic field conditions upstream of Titan are far more complex than they were thought to be after the Voyager encounter. Rymer et al., (2009) used the Cassini Plasma Spectrometer (CAPS) electron observations to classify the plasma conditions along Titan's orbit into 5 types (Plasma Sheet, Lobe, Mixed, Magnetosheath and Misc.). Nemeth et al., (2011) found that the CAPS ion observations could also be separated into the same plasma regions as defined by Rymer et al. Additionally the T-96 encounter found Titan in the solar wind adding a sixth classification. Understanding the effects of the variable upstream plasma conditions on Titan's plasma interaction and the evolution of Titan's ionosphere/atmosphere is one of the main objectives of the Cassini mission. To compliment the mission we perform hybrid simulations of Titan's plasma interaction to examine how the properties of the incident plasma (composition, density, temperature etc…) affect Titan's ionosphere. We examine how much ionospheric plasma is lost from Titan as well as the amount of mass and energy deposited into Titan's atmosphere.

  3. Influence of upstream solar wind on thermospheric flows at Jupiter

    NASA Astrophysics Data System (ADS)

    Yates, J. N.; Achilleos, N.; Guio, P.

    2012-02-01

    The coupling of Jupiter's magnetosphere and ionosphere plays a vital role in creating its auroral emissions. The strength of these emissions is dependent on the difference in speed of the rotational flows within Jupiter's high-latitude thermosphere and the planet's magnetodisc. Using an azimuthally symmetric global circulation model, we have simulated how upstream solar wind conditions affect the energy and direction of atmospheric flows. In order to simulate the effect of a varying dynamic pressure in the upstream solar wind, we calculated three magnetic field profiles representing compressed, averaged and expanded ‘middle’ magnetospheres. These profiles were then used to solve for the angular velocity of plasma in the magnetosphere. This angular velocity determines the strength of currents flowing between the ionosphere and magnetosphere. We examine the influence of variability in this current system upon the global winds and energy inputs within the Jovian thermosphere. We find that the power dissipated by Joule heating and ion drag increases by ∼190% and ∼185% from our compressed to expanded model respectively. We investigated the effect of exterior boundary conditions on our models and found that by reducing the radial current at the outer edge of the magnetodisc, we also limit the thermosphere's ability to transmit angular momentum to this region.

  4. EMMPRIN, an upstream regulator of MMPs, in CNS biology.

    PubMed

    Kaushik, Deepak Kumar; Hahn, Jennifer Nancy; Yong, V Wee

    2015-01-01

    Matrix metalloproteinases (MMPs) are engaged in pathologies associated with infections, tumors, autoimmune disorders and neurological dysfunctions. With the identification of an upstream regulator of MMPs, EMMPRIN (Extracellular matrix metalloproteinase inducer, CD147), it is relevant to address if EMMPRIN plays a role in the pathology of central nervous system (CNS) diseases. This would enable the possibility of a more upstream and effective therapeutic target. Indeed, conditions including gliomas, Alzheimer's disease (AD), multiple sclerosis (MS), and other insults such as hypoxia/ischemia show elevated levels of EMMPRIN which correlate with MMP production. In contrast, given EMMPRIN's role in CNS homeostasis with respect to regulation of monocarboxylate transporters (MCTs) and interactions with adhesion molecules including integrins, we need to consider that EMMPRIN may also serve important regulatory or protective functions. This review summarizes the current understanding of EMMPRIN's involvement in CNS homeostasis, its possible roles in escalating or reducing neural injury, and the mechanisms of EMMPRIN including and apart from MMP induction. Copyright © 2015 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

  5. Computational sciences in the upstream oil and gas industry

    PubMed Central

    Halsey, Thomas C.

    2016-01-01

    The predominant technical challenge of the upstream oil and gas industry has always been the fundamental uncertainty of the subsurface from which it produces hydrocarbon fluids. The subsurface can be detected remotely by, for example, seismic waves, or it can be penetrated and studied in the extremely limited vicinity of wells. Inevitably, a great deal of uncertainty remains. Computational sciences have been a key avenue to reduce and manage this uncertainty. In this review, we discuss at a relatively non-technical level the current state of three applications of computational sciences in the industry. The first of these is seismic imaging, which is currently being revolutionized by the emergence of full wavefield inversion, enabled by algorithmic advances and petascale computing. The second is reservoir simulation, also being advanced through the use of modern highly parallel computing architectures. Finally, we comment on the role of data analytics in the upstream industry. This article is part of the themed issue ‘Energy and the subsurface’. PMID:27597785

  6. Absence of mutation at the 5'-upstream promoter region of the TPM4 gene from cardiac mutant axolotl (Ambystoma mexicanum).

    PubMed

    Denz, Christopher R; Zhang, Chi; Jia, Pingping; Du, Jianfeng; Huang, Xupei; Dube, Syamalima; Thomas, Anish; Poiesz, Bernard J; Dube, Dipak K

    2011-09-01

    Tropomyosins are a family of actin-binding proteins that show cell-specific diversity by a combination of multiple genes and alternative RNA splicing. Of the 4 different tropomyosin genes, TPM4 plays a pivotal role in myofibrillogenesis as well as cardiac contractility in amphibians. In this study, we amplified and sequenced the upstream regulatory region of the TPM4 gene from both normal and mutant axolotl hearts. To identify the cis-elements that are essential for the expression of the TPM4, we created various deletion mutants of the TPM4 promoter DNA, inserted the deleted segments into PGL3 vector, and performed promoter-reporter assay using luciferase as the reporter gene. Comparison of sequences of the promoter region of the TPM4 gene from normal and mutant axolotl revealed no mutations in the promoter sequence of the mutant TPM4 gene. CArG box elements that are generally involved in controlling the expression of several other muscle-specific gene promoters were not found in the upstream regulatory region of the TPM4 gene. In deletion experiments, loss of activity of the reporter gene was noted upon deletion which was then restored upon further deletion suggesting the presence of both positive and negative cis-elements in the upstream regulatory region of the TPM4 gene. We believe that this is the first axolotl promoter that has ever been cloned and studied with clear evidence that it functions in mammalian cell lines. Although striated muscle-specific cis-acting elements are absent from the promoter region of TPM4 gene, our results suggest the presence of positive and negative cis-elements in the promoter region, which in conjunction with positive and negative trans-elements may be involved in regulating the expression of TPM4 gene in a tissue-specific manner.

  7. Thinking Upstream: A 25-Year Retrospective and Conceptual Model Aimed at Reducing Health Inequities.

    PubMed

    Butterfield, Patricia G

    Thinking upstream was first introduced into the nursing vernacular in 1990 with the goal of advancing broad and context-rich perspectives of health. Initially invoked as conceptual framing language, upstream precepts were subsequently adopted and adapted by a generation of thoughtful nursing scholars. Their work reduced health inequities by redirecting actions further up etiologic pathways and by emphasizing economic, political, and environmental health determinants. US health care reform has fostered a much broader adoption of upstream language in policy documents. This article includes a semantic exploration of thinking upstream and a new model, the Butterfield Upstream Model for Population Health (BUMP Health).

  8. Hormone-induced modifications of the chromatin structure surrounding upstream regulatory regions conserved between the mouse and rabbit whey acidic protein genes.

    PubMed Central

    Millot, Benjamin; Montoliu, Lluís; Fontaine, Marie-Louise; Mata, Teresa; Devinoy, Eve

    2003-01-01

    The upstream regulatory regions of the mouse and rabbit whey acidic protein (WAP) genes have been used extensively to target the efficient expression of foreign genes into the mammary gland of transgenic animals. Therefore both regions have been studied to elucidate fully the mechanisms controlling WAP gene expression. Three DNase I-hypersensitive sites (HSS0, HSS1 and HSS2) have been described upstream of the rabbit WAP gene in the lactating mammary gland and correspond to important regulatory regions. These sites are surrounded by variable chromatin structures during mammary-gland development. In the present study, we describe the upstream sequence of the mouse WAP gene. Analysis of genomic sequences shows that the mouse WAP gene is situated between two widely expressed genes (Cpr2 and Ramp3). We show that the hypersensitive sites found upstream of the rabbit WAP gene are also detected in the mouse WAP gene. Further, they encompass functional signal transducer and activator of transcription 5-binding sites, as has been observed in the rabbit. A new hypersensitive site (HSS3), not specific to the mammary gland, was mapped 8 kb upstream of the rabbit WAP gene. Unlike the three HSSs described above, HSS3 is also detected in the liver, but similar to HSS1, it does not depend on lactogenic hormone treatments during cell culture. The region surrounding HSS3 encompasses a potential matrix attachment region, which is also conserved upstream of the mouse WAP gene and contains a functional transcription factor Ets-1 (E26 transformation-specific-1)-binding site. Finally, we demonstrate for the first time that variations in the chromatin structure are dependent on prolactin alone. PMID:12580766

  9. Shape and shear guide sperm cells spiraling upstream

    NASA Astrophysics Data System (ADS)

    Kantsler, Vasily; Dunkel, Jorn; Goldstein, Raymond E.

    2014-11-01

    A major puzzle in biology is how mammalian sperm determine and maintain the correct swimming direction during the various phases of the sexual reproduction process. Currently debated mechanisms for sperm long range travel vary from peristaltic pumping to temperature sensing (thermotaxis) and direct response to fluid flow (rheotaxis), but little is known quantitatively about their relative importance. Here, we report the first quantitative experimental study of mammalian sperm rheotaxis. Using microfluidic devices, we investigate systematically the swimming behavior of human and bull sperm over a wide range of physiologically relevant shear rates and viscosities. Our measurements show that the interplay of fluid shear, steric surface-interactions and chirality of the flagellar beat leads to a stable upstream spiraling motion of sperm cells, thus providing a generic and robust rectification mechanism to support mammalian fertilization. To rationalize these findings, we identify a minimal mathematical model that is capable of describing quantitatively the experimental observations.

  10. 5. Looking west upstream, towards the location of the erstwhile ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. Looking west upstream, towards the location of the erstwhile intake flume into canal from the upper reaches of the Potomac River above the Great Falls, on the old Potowmack Canal built by George Washington. The plan contemplated canal navigation around the Great Falls of the Potomac River, located on the Virginia side of the Potomac, about 15 miles above Washington, D.C. The Company was organized in 1785, and by 1802, this and three or four smaller canals were substantially completed and raft-like boats began operation with materials from the west to the city of Georgetown. 'Although the canals and locks of the Potomac Canal were considered a great engineering accomplishment, the improvements to the river channel were inadequate. Disappointment ... - Potowmack Company: Great Falls Canal & Locks, Great Falls, Fairfax County, VA

  11. Interaction of Energetic Particles with Discontinuities Upstream of Strong Shocks

    NASA Astrophysics Data System (ADS)

    Malkov, Mikhail; Diamond, Patrick

    2008-11-01

    Acceleration of particles in strong astrophysical shocks is known to be accompanied and promoted by a number of instabilities which are driven by the particles themselves. One of them is an acoustic (also known as Drury's) instability driven by the pressure gradient of accelerated particles upstream. The generated sound waves naturally steepen into shocks thus forming a shocktrain. Similar magnetoacoustic or Alfven type structures may be driven by pick-up ions, for example. We consider the solutions of kinetic equation for accelerated particles within the shocktrain. The accelerated particles are assumed to be coupled to the flow by an intensive pitch-angle scattering on the self-generated Alfven waves. The implications for acceleration and confinement of cosmic rays in this shock environment will be discussed.

  12. The Effect of Upstream Vane Wakes on Annular Diffuser Flows

    NASA Astrophysics Data System (ADS)

    Cherry, Erica; Padilla, Angelina; Elkins, Christopher; Eaton, John

    2008-11-01

    Experiments were performed to determine the sensitivity to inlet conditions of the flow in two annular diffusers. One of the diffusers was a conservative design typical of a diffuser directly upstream of the combustor in a jet engine. The other had the same length and inlet shape as the first diffuser but a larger area ratio and was meant to operate on the verge of separation. Each diffuser was connected to two different inlets, one containing a fully-developed channel flow, the other containing wakes from a row of airfoils. Three-component velocity measurements were taken on the flow in each inlet/diffuser combination using Magnetic Resonance Velocimetry. Results will be presented on the 3D velocity fields in the two diffusers and the effect of the airfoil wakes on separation and secondary flows.

  13. From worker health to citizen health: moving upstream.

    PubMed

    Sepulveda, Martin-Jose

    2013-12-01

    New rapid growth economies, urbanization, health systems crises, and "big data" are causing fundamental changes in social structures and systems, including health. These forces for change have significant consequences for occupational and environmental medicine and will challenge the specialty to think beyond workers and workplaces as the principal locus of innovation for health and performance. These trends are placing great emphasis on upstream strategies for addressing the complex systems dynamics of the social determinants of health. The need to engage systems in communities for healthier workforces is a shift in orientation from worker and workplace centric to citizen and community centric. This change for occupational and environmental medicine requires extending systems approaches in the workplace to communities that are systems of systems and that require different skills, data, tools, and partnerships.

  14. From Worker Health To Citizen Health: Moving Upstream

    PubMed Central

    Sepulveda, Martin-Jose

    2014-01-01

    New rapid growth economies, urbanization, health systems crises and “big data” are causing fundamental changes in social structures and systems including health. These forces for change have significant consequences for occupational and environmental medicine and will challenge the specialty to think beyond workers and workplaces as the principal locus of innovation for health and performance. These trends are placing great emphasis on upstream strategies for addressing the complex systems dynamics of the social determinants of health. The need to engage systems in communities for healthier workforces is a shift in orientation from worker and workplace centric to citizen and community centric. This change for occupational and environmental medicine requires extending systems approaches in the workplace to communities which are systems of systems and which require different skills, data, tools and partnerships. PMID:24284749

  15. Observed and Simulated Eddy Diffusivity Upstream of the Drake Passage

    NASA Astrophysics Data System (ADS)

    Tulloch, R.; Ferrari, R. M.; Marshall, J.

    2012-12-01

    Estimates of eddy diffusivity in the Southern Ocean are poorly constrained due to lack of observations. We compare the first direct estimate of isopycnal eddy diffusivity upstream of the Drake Passage (from Ledwell et al. 2011) with a numerical simulation. The estimate is computed from a point tracer release as part of the Diapycnal and Isopycnal Mixing Experiment in the Southern Ocean (DIMES). We find that the observational diffusivity estimate of about 500m^2/s at 1500m depth is close to that computed in a data-constrained, 1/20th of a degree simulation of the Drake Passage region. This tracer estimate also agrees with Lagrangian float calculations in the model. The role of mean flow suppression of eddy diffusivity at shallower depths will also be discussed.

  16. Continuous Manufacturing of Recombinant Therapeutic Proteins: Upstream and Downstream Technologies.

    PubMed

    Patil, Rohan; Walther, Jason

    2017-03-07

    Continuous biomanufacturing of recombinant therapeutic proteins offers several potential advantages over conventional batch processing, including reduced cost of goods, more flexible and responsive manufacturing facilities, and improved and consistent product quality. Although continuous approaches to various upstream and downstream unit operations have been considered and studied for decades, in recent years interest and application have accelerated. Researchers have achieved increasingly higher levels of process intensification, and have also begun to integrate different continuous unit operations into larger, holistically continuous processes. This review first discusses approaches for continuous cell culture, with a focus on perfusion-enabling cell separation technologies including gravitational, centrifugal, and acoustic settling, as well as filtration-based techniques. We follow with a review of various continuous downstream unit operations, covering categories such as clarification, chromatography, formulation, and viral inactivation and filtration. The review ends by summarizing case studies of integrated and continuous processing as reported in the literature.

  17. Explosion Clad for Upstream Oil and Gas Equipment

    NASA Astrophysics Data System (ADS)

    Banker, John G.; Massarello, Jack; Pauly, Stephane

    2011-01-01

    Today's upstream oil and gas facilities frequently involve the combination of high pressures, high temperatures, and highly corrosive environments, requiring equipment that is thick wall, corrosion resistant, and cost effective. When significant concentrations of CO2 and/or H2S and/or chlorides are present, corrosion resistant alloys (CRA) can become the material of choice for separator equipment, piping, related components, and line pipe. They can provide reliable resistance to both corrosion and hydrogen embrittlement. For these applications, the more commonly used CRA's are 316L, 317L and duplex stainless steels, alloy 825 and alloy 625, dependent upon the application and the severity of the environment. Titanium is also an exceptional choice from the technical perspective, but is less commonly used except for heat exchangers. Explosion clad offers significant savings by providing a relatively thin corrosion resistant alloy on the surface metallurgically bonded to a thick, lower cost, steel substrate for the pressure containment. Developed and industrialized in the 1960's the explosion cladding technology can be used for cladding the more commonly used nickel based and stainless steel CRA's as well as titanium. It has many years of proven experience as a reliable and highly robust clad manufacturing process. The unique cold welding characteristics of explosion cladding reduce problems of alloy sensitization and dissimilar metal incompatibility. Explosion clad materials have been used extensively in both upstream and downstream oil, gas and petrochemical facilities for well over 40 years. The explosion clad equipment has demonstrated excellent resistance to corrosion, embrittlement and disbonding. Factors critical to insure reliable clad manufacture and equipment design and fabrication are addressed.

  18. Corporation-induced Diseases, Upstream Epidemiologic Surveillance, and Urban Health

    PubMed Central

    2008-01-01

    Corporation-induced diseases are defined as diseases of consumers, workers, or community residents who have been exposed to disease agents contained in corporate products. To study the epidemiology and to guide expanded surveillance of these diseases, a new analytical framework is proposed. This framework is based on the agent–host–environment model and the upstream multilevel epidemiologic approach and posits an epidemiologic cascade starting with government-sanctioned corporate profit making and ending in a social cost, i.e., harm to population health. Each of the framework’s levels addresses a specific level of analysis, including government, corporations, corporate conduits, the environment of the host, and the host. The explained variable at one level is also the explanatory variable at the next lower level. In this way, a causal chain can be followed along the epidemiologic cascade from the site of societal power down to the host. The framework thus describes the pathways by which corporate decisions filter down to disease production in the host and identifies opportunities for epidemiologic surveillance. Since the environment of city dwellers is strongly shaped by corporations that are far upstream and several levels away, the framework has relevance for the study of urban health. Corporations that influence the health of urban populations include developers and financial corporations that determine growth or decay of urban neighborhoods, as well as companies that use strategies based on neighborhood characteristics to sell products that harm consumer health. Epidemiological inquiry and surveillance are necessary at all levels to provide the knowledge needed for action to protect the health of the population. To achieve optimal inquiry and surveillance at the uppermost levels, epidemiologists will have to work with political scientists and other social scientists and to utilize novel sources of information. PMID:18437580

  19. Upstream Disaster Management to Support People Experiencing Homelessness.

    PubMed

    Sundareswaran, Madura; Ghazzawi, Andrea; O'Sullivan, Tracey L

    2015-08-18

    The unique context of day-to-day living for people who are chronically homeless or living with housing insecurity puts them at high risk during community disasters. The impacts of extreme events, such as flooding, storms, riots, and other sources of community disruption, underscore the importance of preparedness efforts and fostering community resilience. This study is part of larger initiative focused on enhancing resilience and preparedness among high risk populations. The purpose of this study was to explore critical issues and strategies to promote resilience and disaster preparedness among people who are homeless in Canada. A sample of interviews (n=21) from key informants across Canada was analyzed to explore existing programs and supports for homeless populations. The data was selected from a larger sample of (n=43) interviews focused on programs and supports for people who are at heightened risk for negative impacts during disasters. Qualitative content analysis was used to extract emergent themes and develop a model of multi-level collaboration to support disaster resilience among people who are homeless. The results indicate there is a need for more upstream continuity planning, collaboration and communication between the emergency management sector and community service organizations that support people who are homeless. Prioritization and investment in the social determinants of health and community supports is necessary to promote resilience among this high-risk population. The findings from this study highlight the importance of acknowledging community support organizations as assets in disaster preparedness. Day-to-day resilience is an ongoing theme for people who are chronically homeless or living with housing insecurity. Upstream investment to build adaptive capacity and collaborate with community organizations is an important strategy to enhance community resilience.

  20. Specific Increase of Protein Levels by Enhancing Translation Using Antisense Oligonucleotides Targeting Upstream Open Frames.

    PubMed

    Liang, Xue-Hai; Shen, Wen; Crooke, Stanley T

    2017-01-01

    A number of diseases are caused by low levels of key proteins; therefore, increasing the amount of specific proteins in human bodies is of therapeutic interest. Protein expression is downregulated by some structural or sequence elements present in the 5' UTR of mRNAs, such as upstream open reading frames (uORF). Translation initiation from uORF(s) reduces translation from the downstream primary ORF encoding the main protein product in the same mRNA, leading to a less efficient protein expression. Therefore, it is possible to use antisense oligonucleotides (ASOs) to specifically inhibit translation of the uORF by base-pairing with the uAUG region of the mRNA, redirecting translation machinery to initiate from the primary AUG site. Here we review the recent findings that translation of specific mRNAs can be enhanced using ASOs targeting uORF regions. Appropriately designed and optimized ASOs are highly specific, and they act in a sequence- and position-dependent manner, with very minor off-target effects. Protein levels can be increased using this approach in different types of human and mouse cells, and, importantly, also in mice. Since uORFs are present in around half of human mRNAs, the uORF-targeting ASOs may thus have valuable potential as research tools and as therapeutics to increase the levels of proteins for a variety of genes.

  1. The Bastille Day Magnetic Clouds and Upstream Shocks: Near Earth Interplanetary Observations

    NASA Technical Reports Server (NTRS)

    Lepping, R. P.; Berdichevsky, D. B.; Burlaga, L. F.; Lazarus, A. J.; Kasper, J.; Desch, M. D.; Wu, C.-C.; Reames, D. V.; Singer, H. J.; Singer, H. J.; hide

    2001-01-01

    The energetic charged particle, interplanetary magnetic field, and plasma characteristics of the 'Bastille Day' shock and ejecta/magnetic cloud events at 1 AU occurring over the days 14-16 July 2000 are described. Profiles of MeV (WIND/LEMT) energetic ions help to organize the overall sequence of events from the solar source to 1 AU. Stressed are analyses of an outstanding magnetic cloud (MC2) starting late on 15 July and its upstream shock about 4 hours earlier in WIND magnetic field and plasma data. Also analyzed is a less certain, but likely, magnetic cloud (MC1) occurring early on 15 July; this was separated from MC2 by its upstream shock and many heliospheric current sheet (HCS) crossings. Other HCS crossings occurred throughout the 3-day period. Overall this dramatic series of interplanetary events caused a large multi-phase magnetic storm with min Dst lower than -300 nT. The very fast solar wind speed (greater than or equal to 1100 km/s) in and around the front of MC2 (for near average densities) was responsible for a very high solar wind ram pressure driving in the front of the magnetosphere to geocentric distances estimated to be as low as approx. 5 R(sub E), much lower than the geosynchronous orbit radius. This was consistent with magnetic field observations from two GOES satellites which indicated they were in the magnetosheath for extended times. A static force free field model is used to fit the two magnetic cloud profiles providing estimates of the clouds' physical and geometrical properties. MC2 was much larger than MCI, but their axes were nearly antiparallel, and their magnetic fields had the same left-handed helicity. MC2's axis and its upstream shock normal were very close to being perpendicular to each other, as might be expected if the cloud were driving the shock at the time of observation. The estimated axial magnetic flux carried by MC2 was 52 x 10(exp 20) Mx, which is about 5 times the typical magnetic flux estimated for other magnetic

  2. Robust Translation of the Nucleoid Protein Fis Requires a Remote Upstream AU Element and Is Enhanced by RNA Secondary Structure

    PubMed Central

    Nafissi, Maryam; Chau, Jeannette; Xu, Jimin

    2012-01-01

    Synthesis of the Fis nucleoid protein rapidly increases in response to nutrient upshifts, and Fis is one of the most abundant DNA binding proteins in Escherichia coli under nutrient-rich growth conditions. Previous work has shown that control of Fis synthesis occurs at transcription initiation of the dusB-fis operon. We show here that while translation of the dihydrouridine synthase gene dusB is low, unusual mechanisms operate to enable robust translation of fis. At least two RNA sequence elements located within the dusB coding region are responsible for high fis translation. The most important is an AU element centered 35 nucleotides (nt) upstream of the fis AUG, which may function as a binding site for ribosomal protein S1. In addition, a 44-nt segment located upstream of the AU element and predicted to form a stem-loop secondary structure plays a prominent role in enhancing fis translation. On the other hand, mutations close to the AUG, including over a potential Shine-Dalgarno sequence, have little effect on Fis protein levels. The AU element and stem-loop regions are phylogenetically conserved within dusB-fis operons of representative enteric bacteria. PMID:22389479

  3. Upstream oversight assessment for agrifood nanotechnology: a case studies approach.

    PubMed

    Kuzma, Jennifer; Romanchek, James; Kokotovich, Adam

    2008-08-01

    Although nanotechnology is broadly receiving attention in public and academic circles, oversight issues associated with applications for agriculture and food remain largely unexplored. Agrifood nanotechnology is at a critical stage in which informed analysis can help shape funding priorities, risk assessment, and oversight activities. This analysis is designed to help society and policymakers anticipate and prepare for challenges posed by complicated, convergent applications of agrifood nanotechnology. The goal is to identify data, risk assessment, regulatory policy, and engagement needs for overseeing these products so they can be addressed prior to market entry. Our approach, termed upstream oversight assessment (UOA), has potential as a key element of anticipatory governance. It relies on distinct case studies of proposed applications of agrifood nanotechnology to highlight areas that need study and attention. As a tool for preparation, UOA anticipates the types and features of emerging applications; their endpoints of use in society; the extent to which users, workers, ecosystems, or consumers will be exposed; the nature of the material and its safety; whether and where the technologies might fit into current regulatory system(s); the strengths and weaknesses of the system(s) in light of these novel applications; and the possible social concerns related to oversight for them.

  4. Modulation of a methane Bunsen flame by upstream perturbations

    NASA Astrophysics Data System (ADS)

    de Souza, T. Cardoso; Bastiaans, R. J. M.; De Goey, L. P. H.; Geurts, B. J.

    2017-04-01

    In this paper the effects of an upstream spatially periodic modulation acting on a turbulent Bunsen flame are investigated using direct numerical simulations of the Navier-Stokes equations coupled with the flamelet generated manifold (FGM) method to parameterise the chemistry. The premixed Bunsen flame is spatially agitated with a set of coherent large-scale structures of specific wave-number, K. The response of the premixed flame to the external modulation is characterised in terms of time-averaged properties, e.g. the average flame height ⟨H⟩ and the flame surface wrinkling ⟨W⟩. Results show that the flame response is notably selective to the size of the length scales used for agitation. For example, both flame quantities ⟨H⟩ and ⟨W⟩ present an optimal response, in comparison with an unmodulated flame, when the modulation scale is set to relatively low wave-numbers, 4π/L ≲ K ≲ 6π/L, where L is a characteristic scale. At the agitation scales where the optimal response is observed, the average flame height, ⟨H⟩, takes a clearly defined minimal value while the surface wrinkling, ⟨W⟩, presents an increase by more than a factor of 2 in comparison with the unmodulated reference case. Combined, these two response quantities indicate that there is an optimal scale for flame agitation and intensification of combustion rates in turbulent Bunsen flames.

  5. What's Upstream? GIS's critical role in developing nutrient ...

    EPA Pesticide Factsheets

    Eutrophication due to excess levels of nitrogen and phosphorus can seriously impair ecological function in estuaries. Protective criteria for nutrients are difficult to establish because the source can vary spatially and seasonally, originate either from the watershed or the ocean, and be natural or anthropogenic. GIS tools and processes can help in developing nutrient criteria by establishing reference conditions representative of natural background nutrient levels. Along the Oregon Coast in the Pacific Northwest, the primary source of nutrients in the wet season (November-April) is generally riverine. We delineated and extracted explicit spatial data from watersheds upstream of riverine water quality monitoring stations for parametric comparison to recorded nutrient levels. The SPARROW model (Wise and Johnson, 2011) was used to estimate relative contributions of nutrient sources at each station. Both raster and vector spatial data were used and include land use / land cover, demography, geology, terrain, precipitation and forest type. The relationships of nutrients to spatial data were then explored as an approach to establishing the reference expectation. The abstract introduces Geographic Information Systems (GIS) tools and processes employed for research conducted under the Safe and Sustainable Water Resources (SSWR) Task 2.3A, entitled “Nutrient Management for Sustainability of Aquatic Ecosystems.” One of the goals of the EPA Office of Water is to

  6. Rating Curve Estimation from Local Levels and Upstream Discharges

    NASA Astrophysics Data System (ADS)

    Franchini, M.; Mascellani, G.

    2003-04-01

    Current technology allows for low cost and easy level measurements while the discharge measurements are still difficult and expensive. Thus, these are rarely performed and usually not in flood conditions because of lack of safety and difficulty in activating the measurement team in due time. As a consequence, long series of levels are frequently available without the corresponding discharge values. However, for the purpose of planning, management of water resources and real time flood forecasting, discharge is needed and it is therefore essential to convert local levels into discharge values by using the appropriate rating curve. Over this last decade, several methods have been proposed to relate local levels at a site of interest to data recorded at a river section located upstream where a rating curve is available. Some of these methods are based on a routing approach which uses the Muskingum model structure in different ways; others are based on the entropy concepts. Lately, fuzzy logic has been applied more and more frequently in the framework of hydraulic and hydrologic problems and this has prompted to the authors to use it for synthesising the rating curves. A comparison between all these strategies is performed, highlighting the difficulties and advantages of each of them, with reference to a long reach of the Po river in Italy, where several hydrometers and the relevant rating curves are available, thus allowing for both a parameterization and validation of the different strategies.

  7. Rheotaxis facilitates upstream navigation of mammalian sperm cells

    PubMed Central

    Kantsler, Vasily; Dunkel, Jörn; Blayney, Martyn; Goldstein, Raymond E

    2014-01-01

    A major puzzle in biology is how mammalian sperm maintain the correct swimming direction during various phases of the sexual reproduction process. Whilst chemotaxis may dominate near the ovum, it is unclear which cues guide spermatozoa on their long journey towards the egg. Hypothesized mechanisms range from peristaltic pumping to temperature sensing and response to fluid flow variations (rheotaxis), but little is known quantitatively about them. We report the first quantitative study of mammalian sperm rheotaxis, using microfluidic devices to investigate systematically swimming of human and bull sperm over a range of physiologically relevant shear rates and viscosities. Our measurements show that the interplay of fluid shear, steric surface-interactions, and chirality of the flagellar beat leads to stable upstream spiralling motion of sperm cells, thus providing a generic and robust rectification mechanism to support mammalian fertilisation. A minimal mathematical model is presented that accounts quantitatively for the experimental observations. DOI: http://dx.doi.org/10.7554/eLife.02403.001 PMID:24867640

  8. Large amplitude MHD waves upstream of the Jovian bow shock

    NASA Technical Reports Server (NTRS)

    Goldstein, M. L.; Smith, C. W.; Matthaeus, W. H.

    1983-01-01

    Observations of large amplitude magnetohydrodynamics (MHD) waves upstream of Jupiter's bow shock are analyzed. The waves are found to be right circularly polarized in the solar wind frame which suggests that they are propagating in the fast magnetosonic mode. A complete spectral and minimum variance eigenvalue analysis of the data was performed. The power spectrum of the magnetic fluctuations contains several peaks. The fluctuations at 2.3 mHz have a direction of minimum variance along the direction of the average magnetic field. The direction of minimum variance of these fluctuations lies at approximately 40 deg. to the magnetic field and is parallel to the radial direction. We argue that these fluctuations are waves excited by protons reflected off the Jovian bow shock. The inferred speed of the reflected protons is about two times the solar wind speed in the plasma rest frame. A linear instability analysis is presented which suggests an explanation for many of the observed features of the observations.

  9. Rapid acceleration of protons upstream of earthward propagating dipolarization fronts

    PubMed Central

    Ukhorskiy, AY; Sitnov, MI; Merkin, VG; Artemyev, AV

    2013-01-01

    [1] Transport and acceleration of ions in the magnetotail largely occurs in the form of discrete impulsive events associated with a steep increase of the tail magnetic field normal to the neutral plane (Bz), which are referred to as dipolarization fronts. The goal of this paper is to investigate how protons initially located upstream of earthward moving fronts are accelerated at their encounter. According to our analytical analysis and simplified two-dimensional test-particle simulations of equatorially mirroring particles, there are two regimes of proton acceleration: trapping and quasi-trapping, which are realized depending on whether the front is preceded by a negative depletion in Bz. We then use three-dimensional test-particle simulations to investigate how these acceleration processes operate in a realistic magnetotail geometry. For this purpose we construct an analytical model of the front which is superimposed onto the ambient field of the magnetotail. According to our numerical simulations, both trapping and quasi-trapping can produce rapid acceleration of protons by more than an order of magnitude. In the case of trapping, the acceleration levels depend on the amount of time particles stay in phase with the front which is controlled by the magnetic field curvature ahead of the front and the front width. Quasi-trapping does not cause particle scattering out of the equatorial plane. Energization levels in this case are limited by the number of encounters particles have with the front before they get magnetized behind it. PMID:26167430

  10. Resistance to MEK inhibitors: should we co-target upstream?

    PubMed

    Poulikakos, Poulikos I; Solit, David B

    2011-03-29

    Aberrant activation of the ERK pathway is common in human tumors. This pathway consists of a three-tiered kinase module [comprising the kinases RAF, mitogen-activated protein kinase (MAPK) kinase (MEK), and extracellular signal-regulated kinase (ERK)] that functions as a negative feedback amplifier to confer robustness and stabilization of pathway output. Because this pathway is frequently dysregulated in human cancers, intense efforts are under way to develop selective inhibitors of the ERK pathway as anticancer drugs. Although promising results have been reported in early trials for inhibitors of RAF or MEK, resistance invariably occurs. Amplification of the upstream oncogenic driver of ERK signaling has been identified as a mechanism for MEK inhibitor resistance in cells with mutant BRAF or KRAS. Increased abundance of the oncogenic driver (either KRAS or BRAF in the appropriate cellular context) in response to prolonged drug treatment results in increased flux through the ERK pathway and restoration of ERK activity above the threshold required for cell growth. For patients with BRAF mutant tumors, the results suggest that the addition of a RAF inhibitor to a MEK inhibitor may delay or overcome drug resistance. The data thus provide a mechanistic basis for ongoing trials testing concurrent treatment with RAF and MEK inhibitors.

  11. "Upstream Thinking": the catchment management approach of a water provider

    NASA Astrophysics Data System (ADS)

    Grand-Clement, E.; Ross, M.; Smith, D.; Anderson, K.; Luscombe, D.; Le Feuvre, N.; Brazier, R. E.

    2012-04-01

    Human activities have large impacts on water quality and provision. Water companies throughout the UK are faced with the consequences of poor land management and need to find appropriate solutions to decreasing water quality. This is particularly true in the South West of England, where 93% of the drinking water is sourced from rivers and reservoirs: large areas of drained peatlands (i.e. Exmoor and Dartmoor National Parks) are responsible for a significant input of dissolved organic carbon (DOC) discolouring the water, whilst poorly managed farming activities can lead to diffuse pollution. Alongside the direct environmental implications, poor water quality is partly increasing water treatment costs and will drive significant future investment in additional water treatment, with further repercussions on customers. This highlights the need for water companies throughout the UK, and further afield, to be more involved in catchment management. "Upstream Thinking" is South West Water's (SWW) approach to catchment management, where working with stakeholders to improve water quality upstream aims to avoid increasingly costly solutions downstream. This approach has led the company to invest in two major areas of work: (1) The Farmland programme where problematic farm management practices and potential solutions are identified, typically 40% of the required investment is then offered in exchange for a legal undertaking to maintain the new farm assets in good condition for 25 years; (2) The Mires programme which involves heavy investment in peatland restoration through the blocking of open ditches in order to improve water storage and quality in the long term. From these two projects, it has been clear that stakeholder involvement of groups such as local farmers, the Westcountry Rivers Trust, the Exmoor National Park Authority, the Environment Agency, Natural England and the Exmoor Society is essential, first because it draws in catchment improvement expertise which is not

  12. Geological nominations at UNESCO World Heritage, an upstream struggle

    NASA Astrophysics Data System (ADS)

    Olive-Garcia, Cécile; van Wyk de Vries, Benjamin

    2017-04-01

    Using my 10 years experience in setting up and defending a UNESCO world Heritage Geological nomination, this presentation aims to give a personal insight into this international process and the differential use of science, subjective perception (aesthetic and 'naturality'), and politics. At this point in the process, new protocols have been tested in order to improve the dialogue, accountability and transparency between the different stake-holders. These are, the State parties, the IUCN, the scientific community, and UNESCO itself. Our proposal is the Chaîne des Puys-Limagne fault ensemble, which combines tectonic, geomorphological evolution and volcanology. The project's essence is a conjunction of inseparable geological features and processes, set in the context of plate tectonics. This very unicit yof diverse forms and processes creates the value of the site. However, it is just this that has caused a problem, as the advisory body has a categorical approach of nominations that separates items to assess them in an unconnected manner.From the start we proposed a combined approach, where a property is seen in its entirety, and the constituent elements seen as interlinked elements reflecting the joint underlying phenomena. At this point, our project has received the first ever open review by an independent technical mission (jointly set up by IUCN, UNESCO and the State party). The subsequent report was broadly supportive of the project's approach and of the value of the ensemble of features. The UNESCO committee in 2016, re-referred the nomination, acknowledging the potential Outstanding Universal Value of the site and requesting the parties to continue the upstream process (e.g. collaborative work), notably on the recommendations and conclusions of the Independent Technical mission report. Meetings are continuing, and I shall provide you with the hot-off-the-press news as this ground breaking nomination progresses.

  13. Oxytocin Intranasal Administration Affects Neural Networks Upstream of GNRH Neurons.

    PubMed

    Salehi, Mohammad Saied; Khazali, Homayoun; Mahmoudi, Fariba; Janahmadi, Mahyar

    2017-08-01

    The last decade has witnessed a surge in studies on the clinical applications of intranasal oxytocin as a method of enhancing social interaction. However, the molecular and cellular mechanisms underlying its function are not completely understood. Since oxytocin is involved in the regulation of hypothalamic-pituitary-gonadal axis by affecting the gonadotropin-releasing hormone (GNRH) system, the present study addressed whether intranasal application of oxytocin has a role in affecting GNRH expression in the male rat hypothalamus. In addition, we assessed expression of two excitatory (kisspeptin and neurokinin B) and two inhibitory (dynorphin and RFamide-related peptide-3) neuropeptides upstream of GNRH neurons as a possible route to relay oxytocin information. Here, adult male rats received 20, 40, or 80 μg oxytocin intranasally once a day for 10 consecutive days, and then, the posterior (PH) and anterior hypothalamus (AH) dissected for evaluation of target genes. Using qRT-PCR, we found that oxytocin treatment increased Gnrh mRNA levels in both the PH and AH. In addition, oxytocin at its highest dose increased kisspeptin expression in the AH by around 400%, whereas treatments, dose dependently decreased kisspeptin mRNA in the PH. The expression of neurokinin B was increased from the basal levels following the intervention. Furthermore, although intranasal-applied oxytocin decreased hypothalamic RFamide-related peptide-3 mRNA level, the dynorphin mRNA was not affected. These observations are consistent with the hypothesis that applications of intranasal oxytocin can affect the GNRH system.

  14. Catalytic Ignition and Upstream Reaction Propagation in a Platinum Tube

    NASA Technical Reports Server (NTRS)

    Struk, P. M.; Dietrich, D. L.; Mellish, B. P.; Miller, F. J.; T'ien, J. S.

    2007-01-01

    A challenge for catalytic combustion in monolithic reactors at elevated temperatures is the start-up or "light-off" from a cold initial condition. In this work, we demonstrate a concept called "back-end catalytic ignition that potentially can be utilized in the light-off of catalytic monoliths. An external downstream flame or Joule heating raises the temperature of a small portion of the catalyst near the outlet initiating a localized catalytic reaction that propagates upstream heating the entire channel. This work uses a transient numerical model to demonstrate "back-end" ignition within a single channel which can characterize the overall performance of a monolith. The paper presents comparisons to an experiment using a single non-adiabatic channel but the concept can be extended to the adiabatic monolith case. In the model, the time scales associated with solid heat-up are typically several orders of magnitude larger than the gas-phase and chemical kinetic time-scales. Therefore, the model assumes a quasi-steady gas-phase with respect to a transient solid. The gas phase is one-dimensional. Appropriate correlations, however, account for heat and mass transfer in a direction perpendicular to the flow. The thermally-thin solid includes axial conduction. The gas phase, however, does not include axial conduction due to the high Peclet number flows. The model includes both detailed gas-phase and catalytic surface reactions. The experiment utilizes a pure platinum circular channel oriented horizontally though which a CO/O2 mixture (equivalence ratios ranging from 0.6 to 0.9) flows at 2 m/s.

  15. Innovation and performance: The case of the upstream petroleum sector

    NASA Astrophysics Data System (ADS)

    Persaud, A. C. Jai

    This thesis investigates innovation in the upstream crude oil and natural gas sector, a strategic part of the Canadian economy and a vital industry for North American energy trade and security. Significant interest exists in understanding innovation in this sector from a private and public policy perspective. Interest in the sector has intensified recently due to concerns about world oil supply, Canada's oil sands development, and the potential that Canada may become an "energy superpower." The study examines the factors that drive companies involved in exploration, development, and production in the upstream petroleum sector to innovate and the impact of their innovation activities through major technologies on their performance. The thesis focuses on process innovation, which involves the adoption of new or significantly improved production processes, and is distinct from product innovation, which is based on the development and commercialization of a product with improved product characteristics to deliver new services to the consumer. The thesis provides a comprehensive review of the literature and develops an investigative model framework to examine the drivers of innovation and the impact of innovation on performance in the upstream petroleum sector. The research employs a survey questionnaire that was developed to obtain data and information, which was missing in the literature or not publicly available to test key relationships of innovation and performance indicators. In addition to the survey questionnaire, a number of knowledgeable experts in the industry were also interviewed. A total of 68 respondents completed the survey questionnaire, accounting for 40 percent of the firms in the industry. This percentage goes up to over 50 percent when account is taken of extremely small firms who could not fill out the survey. Further, the 68 respondents account for most of the industry revenues, production, and employment. The respondents include most of the key

  16. Analysis of key thresholds leading to upstream dependencies in global transboundary water bodies

    NASA Astrophysics Data System (ADS)

    Munia, Hafsa Ahmed; Guillaume, Joseph; Kummu, Matti; Mirumachi, Naho; Wada, Yoshihide

    2017-04-01

    Transboundary water bodies supply 60% of global fresh water flow and are home to about 1/3 of the world's population; creating hydrological, social and economic interdependencies between countries. Trade-offs between water users are delimited by certain thresholds, that, when crossed, result in changes in system behavior, often related to undesirable impacts. A wide variety of thresholds are potentially related to water availability and scarcity. Scarcity can occur because of the country's own water use, and that is potentially intensified by upstream water use. In general, increased water scarcity escalates the reliance on shared water resources, which increases interdependencies between riparian states. In this paper the upstream dependencies of global transboundary river basins are examined at the scale of sub-basin areas. We aim to assess how upstream water withdrawals cause changes in the scarcity categories, such that crossing thresholds is interpreted in terms of downstream dependency on upstream water availability. The thresholds are defined for different types of water availability on which a sub-basin relies: - reliable local runoff (available even in a dry year), - less reliable local water (available in the wet year), - reliable dry year inflows from possible upstream area, and - less reliable wet year inflows from upstream. Possible upstream withdrawals reduce available water downstream, influencing the latter two water availabilities. Upstream dependencies have then been categorized by comparing a sub-basin's scarcity category across different water availability types. When population (or water consumption) grows, the sub-basin satisfies its needs using less reliable water. Thus, the factors affecting the type of water availability being used are different not only for each type of dependency category, but also possibly for every sub- basin. Our results show that, in the case of stress (impacts from high use of water), in 104 (12%) sub- basins out of

  17. An Upstream Open Reading Frame Is Essential for Feedback Regulation of Ascorbate Biosynthesis in Arabidopsis

    PubMed Central

    Laing, William A.; Martínez-Sánchez, Marcela; Wright, Michele A.; Bulley, Sean M.; Brewster, Di; Dare, Andrew P.; Rassam, Maysoon; Wang, Daisy; Storey, Roy; Macknight, Richard C.; Hellens, Roger P.

    2015-01-01

    Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms. PMID:25724639

  18. An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in Arabidopsis.

    PubMed

    Laing, William A; Martínez-Sánchez, Marcela; Wright, Michele A; Bulley, Sean M; Brewster, Di; Dare, Andrew P; Rassam, Maysoon; Wang, Daisy; Storey, Roy; Macknight, Richard C; Hellens, Roger P

    2015-03-01

    Ascorbate (vitamin C) is an essential antioxidant and enzyme cofactor in both plants and animals. Ascorbate concentration is tightly regulated in plants, partly to respond to stress. Here, we demonstrate that ascorbate concentrations are determined via the posttranscriptional repression of GDP-l-galactose phosphorylase (GGP), a major control enzyme in the ascorbate biosynthesis pathway. This regulation requires a cis-acting upstream open reading frame (uORF) that represses the translation of the downstream GGP open reading frame under high ascorbate concentration. Disruption of this uORF stops the ascorbate feedback regulation of translation and results in increased ascorbate concentrations in leaves. The uORF is predicted to initiate at a noncanonical codon (ACG rather than AUG) and encode a 60- to 65-residue peptide. Analysis of ribosome protection data from Arabidopsis thaliana showed colocation of high levels of ribosomes with both the uORF and the main coding sequence of GGP. Together, our data indicate that the noncanonical uORF is translated and encodes a peptide that functions in the ascorbate inhibition of translation. This posttranslational regulation of ascorbate is likely an ancient mechanism of control as the uORF is conserved in GGP genes from mosses to angiosperms. © 2015 American Society of Plant Biologists. All rights reserved.

  19. Cloning and functional analysis of 5'-upstream region of the Pokemon gene.

    PubMed

    Yang, Yutao; Zhou, Xiaowei; Zhu, Xudong; Zhang, Chuanfu; Yang, Zhixin; Xu, Long; Huang, Peitang

    2008-04-01

    Pokemon, the POK erythroid myeloid ontogenic factor, not only regulates the expression of many genes, but also plays an important role in cell tumorigenesis. To investigate the molecular mechanism regulating expression of the Pokemon gene in humans, its 5'-upstream region was cloned and analyzed. Transient analysis revealed that the Pokemon promoter is constitutive. Deletion analysis and a DNA decoy assay indicated that the NEG-U and NEG-D elements were involved in negative regulation of the Pokemon promoter, whereas the POS-D element was mainly responsible for its strong activity. Electrophoretic mobility shift assays suggested that the NEG-U, NEG-D and POS-D elements were specifically bound by the nuclear extract from A549 cells in vitro. Mutation analysis demonstrated that cooperation of the NEG-U and NEG-D elements led to negative regulation of the Pokemon promoter. Moreover, the NEG-U and NEG-D elements needed to be an appropriate distance apart in the Pokemon promoter in order to cooperate. Taken together, our results elucidate the mechanism underlying the regulation of Pokemon gene transcription, and also define a novel regulatory sequence that may be used to decrease expression of the Pokemon gene in cancer gene therapy.

  20. Internal Associations of the Acidic Region of Upstream Binding Factor Control Its Nucleolar Localization.

    PubMed

    Ueshima, Shuhei; Nagata, Kyosuke; Okuwaki, Mitsuru

    2017-11-15

    Upstream binding factor (UBF) is a member of the high-mobility group (HMG) box protein family, characterized by multiple HMG boxes and a C-terminal acidic region (AR). UBF is an essential transcription factor for rRNA genes and mediates the formation of transcriptionally active chromatin in the nucleolus. However, it remains unknown how UBF is specifically localized to the nucleolus. Here, we examined the molecular mechanisms that localize UBF to the nucleolus. We found that the first HMG box (HMG box 1), the linker region (LR), and the AR cooperatively regulate the nucleolar localization of UBF1. We demonstrated that the AR intramolecularly associates with and attenuates the DNA binding activity of HMG boxes and confers the structured DNA preference to HMG box 1. In contrast, the LR was found to serve as a nuclear localization signal and compete with HMG boxes to bind the AR, permitting nucleolar localization of UBF1. The LR sequence binds DNA and assists the stable chromatin binding of UBF. We also showed that the phosphorylation status of the AR does not clearly affect the localization of UBF1. Our results strongly suggest that associations of the AR with HMG boxes and the LR regulate UBF nucleolar localization. Copyright © 2017 American Society for Microbiology.

  1. Flow Instabilities in Feather Seals due to Upstream Harmonic Pressure Fluctuations

    NASA Technical Reports Server (NTRS)

    Deng, D.; Braun, M. J.; Henricks, Robert C.

    2008-01-01

    Feather seals (also called slot seals) typically found in turbine stators limit leakage from the platform into the core cavities and from the shroud to the case. They are of various geometric shapes, yet all are contoured to fit the aerodynamic shape of the stator and placed as close as thermomechanically reasonable the powerstream flow passage. Oscillations engendered in the compressor or combustor alter the steady leakage characteristics of these sealing elements and in some instances generate flow instabilities downstream of the seal interface. In this study, a generic feather seal geometry was studied numerically by imposing an upstream harmonic pressure disturbance on the simulated stator-blade gap. The flow and thermal characteristics were determined; it was found that for high pressure drops, large fluctuations in flows in the downstream blade-stator gap can occur. These leakages and pulsations in themselves are not all that significant, yet if coupled with cavity parameters, they could set up resonance events. Computationally generated time-dependent flow fields are captured in sequence video streaming.

  2. Energetic-ion acceleration and transport in the upstream region of Jupiter: Voyager 1 and 2

    NASA Technical Reports Server (NTRS)

    Baker, D. N.; Zwickl, R. D.; Carbary, J. F.; Krimigis, S. M.; Lepping, R. P.

    1982-01-01

    Long-lived upstream energetic ion events at Jupiter appear to be very similar in nearly all respects to upstream ion events at Earth. A notable difference between the two planetary systems is the enhanced heavy ion compositional signature reported for the Jovian events. This compositional feature has suggested that ions escaping from the Jovian magnetosphere play an important role in forming upstream ion populations at Jupiter. In contrast, models of energetic upstream ions at Earth emphasize in situ acceleration of reflected solar wind ions within the upstream region itself. Using Voyager 1 and 2 energetic ( approximately 30 keV) ion measurements near the magnetopause, in the magnetosheath, and immediately upstream of the bow shock, the compositional patterns are examined together with typical energy spectra in each of these regions. A model involving upstream Fermi acceleration early in events and emphasizing energetic particle escape in the prenoon part of the Jovian magnetosphere late in events is presented to explain many of the features in the upstream region of Jupiter.

  3. Floods, Habitat Hydraulics and Upstream Migration of Neritina virginea (Gastropoda: Neritidae) in Northeastern Puerto Rico.

    Treesearch

    JUAN F. BLANCO; FREDERICK N. SCATENA

    2005-01-01

    Massive upstream migrations of neritid snails (Neritidae: Gastropoda) occur in tropical and subtropical streams worldwide, but their seasonality and proximate causes are unknown. We monitored massive upstream migrations of Neritina virginea for 99 weeks, and conducted a detailed study of snail density, size, and hydraulic descriptors in lower Río Mameyes, northeastern...

  4. Upstream proton cyclotron waves at Venus near solar maximum

    NASA Astrophysics Data System (ADS)

    Delva, M.; Bertucci, C.; Volwerk, M.; Lundin, R.; Mazelle, C.; Romanelli, N.

    2015-01-01

    magnetometer data of Venus Express are analyzed for the occurrence of waves at the proton cyclotron frequency in the spacecraft frame in the upstream region of Venus, for conditions of rising solar activity. The data of two Venus years up to the time of highest sunspot number so far (1 Mar 2011 to 31 May 2012) are studied to reveal the properties of the waves and the interplanetary magnetic field (IMF) conditions under which they are observed. In general, waves generated by newborn protons from exospheric hydrogen are observed under quasi- (anti)parallel conditions of the IMF and the solar wind velocity, as is expected from theoretical models. The present study near solar maximum finds significantly more waves than a previous study for solar minimum, with an asymmetry in the wave occurrence, i.e., mainly under antiparallel conditions. The plasma data from the Analyzer of Space Plasmas and Energetic Atoms instrument aboard Venus Express enable analysis of the background solar wind conditions. The prevalence of waves for IMF in direction toward the Sun is related to the stronger southward tilt of the heliospheric current sheet for the rising phase of Solar Cycle 24, i.e., the "bashful ballerina" is responsible for asymmetric background solar wind conditions. The increase of the number of wave occurrences may be explained by a significant increase in the relative density of planetary protons with respect to the solar wind background. An exceptionally low solar wind proton density is observed during the rising phase of Solar Cycle 24. At the same time, higher EUV increases the ionization in the Venus exosphere, resulting in higher supply of energy from a higher number of newborn protons to the wave. We conclude that in addition to quasi- (anti)parallel conditions of the IMF and the solar wind velocity direction, the higher relative density of Venus exospheric protons with respect to the background solar wind proton density is the key parameter for the higher number of

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

    PubMed

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

    2016-02-01

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

  6. Familial 46,XY sex reversal without campomelic dysplasia caused by a deletion upstream of the SOX9 gene

    PubMed Central

    Layman, Lawrence C.; Ullmann, Reinhard; Shen, Yiping; Ha, Kyungsoo; Rehman, Khurram; Looney, Stephen; McDonough, Paul G.; Kim, Hyung-Goo; Carr, Bruce R.

    2014-01-01

    Background 46,XY sex reversal is a rare disorder and familial cases are even more rare. The purpose of the present study was to determine the molecular basis for a family with three affected siblings who had 46,XY sex reversal. Methods DNA was extracted from three females with 46,XY sex reversal, two normal sisters, and both unaffected parents. All protein coding exons of the SRY and NR5A1 genes were subjected to PCR-based DNA sequencing. In addition, array comparative genomic hybridization was performed on DNA from all seven family members. A deletion was confirmed using quantitative polymerase chain reaction. Expression of SOX9 gene was quantified using reverse transcriptase polymerase chain reaction. Results A 349kb heterozygous deletion located 353kb upstream of the SOX9 gene on the long arm of chromosome 17 was discovered in the father and three affected siblings, but not in the mother. The expression of SOX9 was significantly decreased in the affected siblings. Two of three affected sisters had gonadoblastomas. Conclusion This is the first report of 46,XY sex reversal in three siblings who have a paternally inherited deletion upstream of SOX9 associated with reduced SOX9 mRNA expression. PMID:24907458

  7. Functional analysis of the EspR binding sites upstream of espR in Mycobacterium tuberculosis.

    PubMed

    Cao, Guangxiang; Howard, Susan T; Zhang, Peipei; Hou, Guihua; Pang, Xiuhua

    2013-11-01

    The ESX-1 secretion system exports substrate proteins into host cells and is crucial for the pathogenesis of Mycobacterium tuberculosis. EspR is one of the characterized transcriptional regulators that modulates the ESX-1 system by binding the conserved EspR binding sites in the promoter of espA, the encoding gene of EspA, which is also a substrate protein of the ESX-1 system and is required for the ESX-1 activity. EspR is autoregulatory and conserved EspR binding sites are present upstream of espR. In this study, we showed that these EspR sites had varying affinities for EspR, with site B being the strongest one. Point mutations of the DNA sequence at site B abolished binding of EspR to oligonucleotides containing site B alone or with other sites, further suggesting that site B is a major binding site for EspR. Complementation studies showed that constructs containing espR, and the upstream intergenic region fully restored espR expression in a ΔespR mutant strain. Although recombinant strains with mutations at more than one EspR site showed minimal differences in espR expression, reduced expression of other EspR target genes was observed, suggesting that slight changes in EspR levels can have downstream regulatory effects. These findings contribute to our understanding of the regulation of the ESX-1 system.

  8. The 'upstream wake' of swimming and flying animals and its correlation with propulsive efficiency.

    PubMed

    Peng, Jifeng; Dabiri, John O

    2008-08-01

    The interaction between swimming and flying animals and their fluid environments generates downstream wake structures such as vortices. In most studies, the upstream flow in front of the animal is neglected. In this study, we demonstrate the existence of upstream fluid structures even though the upstream flow is quiescent or possesses a uniform incoming velocity. Using a computational model, the flow generated by a swimmer (an oscillating flexible plate) is simulated and a new fluid mechanical analysis is applied to the flow to identify the upstream fluid structures. These upstream structures show the exact portion of fluid that is going to interact with the swimmer. A mass flow rate is then defined based on the upstream structures, and a metric for propulsive efficiency is established using the mass flow rate and the kinematics of the swimmer. We propose that the unsteady mass flow rate defined by the upstream fluid structures can be used as a metric to measure and objectively compare the efficiency of locomotion in water and air.

  9. Upstream regulatory elements are necessary and sufficient for transcription of a U6 RNA gene by RNA polymerase III.

    PubMed Central

    Das, G; Henning, D; Wright, D; Reddy, R

    1988-01-01

    Whereas the genes coding for trimethyl guanosine-capped snRNAs are transcribed by RNA polymerase II, the U6 RNA genes are transcribed by RNA polymerase III. In this study, we have analyzed the cis-regulatory elements involved in the transcription of a mouse U6 snRNA gene in vitro and in frog oocytes. Transcriptional analysis of mutant U6 gene constructs showed that, unlike most known cases of polymerase III transcription, intragenic sequences except the initiation nucleotide are dispensable for efficient and accurate transcription of U6 gene in vitro. Transcription of 5' deletion mutants in vitro and in frog oocytes showed that the upstream region, within 79 bp from the initiation nucleotide, contains elements necessary for U6 gene transcription. Transcription studies were carried out in frog oocytes with U6 genes containing 5' distal sequence; these studies revealed that the distal element acts as an orientation-dependent enhancer when present upstream to the gene, while it is orientation-independent but distance-dependent enhancer when placed down-stream to the U6 gene. Analysis of 3' deletion mutants showed that the transcription termination of U6 RNA is dependent on a T cluster present on the 3' end of the gene, thus providing further support to other lines of evidence that U6 genes are transcribed by RNA polymerase III. These observations suggest the involvement of a composite of components of RNA polymerase II and III transcription machineries in the transcription of U6 genes by RNA polymerase III. Images PMID:3366121

  10. The Upstream and Downstream impact of Milankovitch cycles in continental nonmarine sedimentary records

    NASA Astrophysics Data System (ADS)

    Valero, Luis; Garcés, Miguel; Huerta, Pedro; Cabrera, Lluís

    2016-04-01

    Discerning the effects of climate in the stratigraphic record is crucial for the comprehension of past climate changes. The signature of climate in sedimentary sequences is often assessed by the identification of Milankovitch cycles, as they can be recognized due to their (quasi) periodic behaviour. The integration of diverse stratigraphic disciplines is required in order to understand the different processes involved in the expression of the orbital cycles in the sedimentary records. New advances in Stratigraphy disclose the different variables that affect the sedimentation along the sediment routing systems. These variables can be summarized as the relationship between accommodation and sediment supply (AS/SS), because they account for the shifts of the total mass balance of a basin. Based in these indicators we propose a synthetic model for the understanding of the expression of climate in continental basins. Sedimentation in internally drained lake basins is particularly sensitive to net precipitation/evaporation variations. Rapid base level oscillations modify the AS/SS ratio sufficiently as to mask possible sediment flux variations associated to the changing discharge. On the other hand, basins lacking a central lacustrine system do not experience climatically-driven accommodation changes, and thus are more sensitive to archive sediment pulses. Small basins lacking carbonate facies are the ideal candidates to archive the impact of orbital forcing in the landscapes, as their small-scale sediment transfer systems are unable to buffer the upstream signal. Sedimentation models that include the relationship between accommodation and sediment supply, the effects of density and type of vegetation, and its coupled response with climate are needed to enhance their reliability.

  11. Regulation of translation by upstream translation initiation codons of surfactant protein A1 splice variants

    PubMed Central

    Tsotakos, Nikolaos; Silveyra, Patricia; Lin, Zhenwu; Thomas, Neal; Vaid, Mudit

    2014-01-01

    Surfactant protein A (SP-A), a molecule with roles in lung innate immunity and surfactant-related functions, is encoded by two genes in humans: SFTPA1 (SP-A1) and SFTPA2 (SP-A2). The mRNAs from these genes differ in their 5′-untranslated regions (5′-UTR) due to differential splicing. The 5′-UTR variant ACD′ is exclusively found in transcripts of SP-A1, but not in those of SP-A2. Its unique exon C contains two upstream AUG codons (uAUGs) that may affect SP-A1 translation efficiency. The first uAUG (u1) is in frame with the primary start codon (p), but the second one (u2) is not. The purpose of this study was to assess the impact of uAUGs on SP-A1 expression. We employed RT-qPCR to determine the presence of exon C-containing SP-A1 transcripts in human RNA samples. We also used in vitro techniques including mutagenesis, reporter assays, and toeprinting analysis, as well as in silico analyses to determine the role of uAUGs. Exon C-containing mRNA is present in most human lung tissue samples and its expression can, under certain conditions, be regulated by factors such as dexamethasone or endotoxin. Mutating uAUGs resulted in increased luciferase activity. The mature protein size was not affected by the uAUGs, as shown by a combination of toeprint and in silico analysis for Kozak sequence, secondary structure, and signal peptide and in vitro translation in the presence of microsomes. In conclusion, alternative splicing may introduce uAUGs in SP-A1 transcripts, which in turn negatively affect SP-A1 translation, possibly affecting SP-A1/SP-A2 ratio, with potential for clinical implication. PMID:25326576

  12. Adaptive upstream optical power adjustment depending on required power budget in PON access

    NASA Astrophysics Data System (ADS)

    Yeh, C. H.; Chow, C. W.; Liu, Y. L.

    2012-11-01

    According to the present passive optical network (PON) standard, the fiber transmission lengths are from 500 m to 20 km between the optical line terminal (OLT) and different optical network units (ONUs). It will result in difference power losses (ΔPloss) from 4 to 5 dB. Hence, we propose to adjust adaptively the output optical power of the upstream laser diode (LD) depending on the different fiber lengths. With the different fiber transmission lengths, we can properly adjust the bias current and modulation index of upstream LD for energy-saving. We characterize and analyze experimentally the relationship of output optical power and modulation amplitude Vamp under different fiber transmissions in PON access. Moreover, due to the adaptive power control of upstream signal, the optical upstream equalization also can be retrieved with power variation of 1.1 dB in this experiment.

  13. 8. UPSTREAM EXTENSION TO 60' INFILTRATION PIPE. Sheet A19, November, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. UPSTREAM EXTENSION TO 60' INFILTRATION PIPE. Sheet A-19, November, 1940. File no. SA 342/13. - Prado Dam, Embankment, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

  14. Measurement of Emissions from Produced Water Ponds: Upstream Oil and Gas Study #1; Final Report

    EPA Science Inventory

    Significant uncertainty exists regarding air pollutant emissions from upstream oil and gas production operations. Oil and gas operations present unique and challenging emission testing issues due to the large variety and quantity of potential emissions sources. This report summ...

  15. Energetic particle diffusion coefficients upstream of quasi-parallel interplanetary shocks

    NASA Technical Reports Server (NTRS)

    Tan, L. C.; Mason, G. M.; Gloeckler, G.; Ipavich, F. M.

    1989-01-01

    The properties of about 30 to 130-keV/e protons and alpha particles upstream of six quasi-parallel interplanetary shocks that passed by the ISEE 3 spacecraft during 1978-1979 were analyzed, and the values for the upstream energegic particle diffusion coefficient, kappa, in these six events were deduced for a number of energies and upstream positions. These observations were compared with predictions of Lee's (1983) theory of shock acceleration. It was found that the observations verified the prediction of the A/Q dependence (where A and Q are the particle atomic mass and ionization state, respectively) of kappa for alpha and proton particles upstream of the quasi-parallel shocks.

  16. Evidence for specularly reflected ions upstream from the quasi-parallel bow shock

    NASA Technical Reports Server (NTRS)

    Gosling, J. T.; Thomsen, M. F.; Bame, S. J.; Feldman, W. C.; Paschmann, G.; Sckopke, N.

    1982-01-01

    Ion velocity distributions in the form of bunches of gyrating particles traveling along helical paths have been observed moving sunward immediately upstream from quasi-parallel parts of the earth's bow shock using Los Alamos/Garching instruments on ISEE-1 and -2. These distributions have characteristics which indicate that they are produced by the nearly specular reflection at the shock of a portion of the incident solar wind ions. In particular, the guiding center motion and the gyrospeeds of the gyrating ions are quantitatively consistent with simple geometrical considerations for specular reflection. These considerations reveal that specularly reflected ions can escape upstream when the angle between the upstream magnetic field and the local shock normal is less than 45 deg but not when the angle is greater than 45 deg. These upstream gyrating ions are an important signature of one of the processes by which solar wind streaming energy is dissipated into other forms of energy at the shock.

  17. Optical signal suppression by a cascaded SOA/RSOA for wavelength reusing reflective PON upstream transmission.

    PubMed

    Jung, Sang Min; Mun, Kyoung Hak; Kang, Soo Min; Han, Sang Kook

    2017-09-18

    An optical signal suppression technique based on a cascaded SOA and RSOA is proposed for the reflective passive optical networks (PONs) with wavelength division multiplexing (WDM). By suppressing the downstream signal of the optical carrier, the proposed reflective PON effectively reuses the downstream optical carrier for upstream signal transmission. As an experimental demonstration, we show that the proposed optical signal suppression technique is effective in terms of the signal bandwidth and bit-error-rate (BER) performance of the remodulated upstream transmission.

  18. 6. Oblique view of upstream side of Bridge Number 310.58, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    6. Oblique view of upstream side of Bridge Number 310.58, 135mm lens. Note ashlar stone masonry abutment built in 1886, Tunnel 15 at left. Heavy vegetation cover, steep banks, and lack of streamside footing precluded full elevation views of the upstream and downstream sides of this bridge. - Southern Pacific Railroad Shasta Route, Bridge No. 310.58, Milepost 310.58, Sims, Shasta County, CA

  19. Investigation of flow turning phenomenon - Effect of upstream and downstream propagation

    NASA Astrophysics Data System (ADS)

    Baum, Joseph D.

    1988-01-01

    Upstream acoustic-wave propagation in flow injected laterally through the boundary layer of a tube (simulating the flow in a solid-rocket motor) is investigated analytically. A noniterative linearized-block implicit scheme is used to solve the time-dependent compressible Navier-Stokes equations, and the results are presented in extensive graphs and characterized. Acoustic streaming interaction is shown to be significantly greater for upstream than for downstream propagation.

  20. Upstream energetic ions under radial IMF - A critical test of the Fermi model

    NASA Technical Reports Server (NTRS)

    Sarris, E. T.; Krimigis, S. M.

    1988-01-01

    Eight years of interplanetary magnetic field (IMF) and energetic particle observations obtained by the IMP-8 spacecraft upstream from the bow shock have been surveyed, and 63 cases when the upstream IMF remained radial for extended periods of time (greater than 1 hour) have been accumulated. Of these, two cases have been selected during which measurable fluxes of ambient solar or corotating energetic particle events were absent. These conditions provide an excellent test to the theories of the origin of upstream energetic ions. It is shown that there are extended periods with radial IMF when no upstream energetic ions were detected. It is further shown that energetic ions in the range E of between 50 keV and 1 MeV, inclusive, are not continuously present but appear in bursts of intensities varying by more than an order of magnitude under persistently radial IMF. These measurements contradict a fundamental prediction of the Fermi mechanism for the origin of the upstream energetic ions, namely that such ions should always be present on radial IMF lines. The observations are consistent with the hypothesis that energetic (greater than about 50 keV) ions leak out from, and appear in the upstream medium sporadically, following the onset of magnetic activity within the magnetosphere.

  1. Upstream capacity upgrade in TDM-PON using RSOA based tunable fiber ring laser.

    PubMed

    Yi, Lilin; Li, Zhengxuan; Dong, Yi; Xiao, Shilin; Chen, Jian; Hu, Weisheng

    2012-04-23

    An upstream multi-wavelength shared (UMWS) time division multiplexing passive optical network (TDM-PON) is presented by using a reflective semiconductor amplifier (RSOA) and tunable optical filter (TOF) based directly modulated fiber ring laser as upstream laser source. The stable laser operation is easily achieved no matter what the bandwidth and shape of the TOF is and it can be directly modulated when the RSOA is driven at its saturation region. In this UMWS TDM-PON system, an individual wavelength can be assigned to the user who has a high bandwidth demand by tuning the central wavelength of the TOF in its upgraded optical network unit (ONU), while others maintain their traditional ONU structure and share the bandwidth via time slots, which greatly and dynamically upgrades the upstream capacity. We experimentally demonstrated the bidirectional transmission of downstream data at 10-Gb/s and upstream data at 1.25-Gb/s per wavelength over 25-km single mode fiber (SMF) with almost no power penalty at both ends. A stable performance is observed for the upstream wavelength tuned from 1530 nm to 1595 nm. Moreover, due to the high extinction ratio (ER) of the upstream signal, the burst-mode transmitting is successfully presented and a better time-division multiplexing performance can be obtained by turning off the unused lasers thanks to the rapid formation of the laser in the fiber ring. © 2012 Optical Society of America

  2. A Rich Assessment Task as a Window into Students' Multiplicative Reasoning

    ERIC Educational Resources Information Center

    Downton, Ann; Wright, Vince

    2016-01-01

    This study explored the potential of a rich assessment task to reveal students' multiplicative thinking in respect to a hypothetical learning trajectory. Thirty pairs of students in grades 5 and 6 attempted the task. Twenty-two pairs applied multiplicative structure to find the number of items in arrays. However counting and computational errors…

  3. A Case Study on Using Prediction Markets as a Rich Environment for Active Learning

    ERIC Educational Resources Information Center

    Buckley, Patrick; Garvey, John; McGrath, Fergal

    2011-01-01

    In this paper, prediction markets are presented as an innovative pedagogical tool which can be used to create a Rich Environment for Active Learning (REAL). Prediction markets are designed to make forecasts about specific future events by using a market mechanism to aggregate the information held by a large group of traders about that event into a…

  4. Identification of a second flagellin gene and functional characterization of a sigma70-like promoter upstream of a Leptospira borgpetersenii flaB gene.

    PubMed

    Lin, Min; Dan, Hanhong; Li, Yijing

    2004-02-01

    Leptospira borgpetersenii, one of the causative agents of leptospirosis in both animals and humans, is a bacterial pathogen with characteristic motility that is mediated by the rotation of two periplasmic flagella (PF). The flaB gene coding for a core polypeptide subunit of PF was previously characterized by sequence analysis of its open reading frame (ORF) (M. Lin, J Biochem Mol Biol Biophys 2:181-187, 1999). The present study was undertaken to isolate and clone the uncharacterized sequence upstream of the flaB gene by using a PCR-based genome walking procedure. This has resulted in a 1470-bp genomic DNA sequence in which an 846-bp ORF coding for a 281-amino acid polypeptide (31.3 kDa) is identified 455 bp upstream from the flaB start codon. The encoded protein exhibits 72% amino acid identity to the deduced FlaB protein sequence of L. borgpetersenii and a high degree of sequence homology to the FlaB proteins of other spirochaetes. This has demonstrated for the first time that a second flaB gene homolog is present in a Leptospira species. The newly identified gene is designated flaB1, and the previously cloned flaB renamed flaB2. Within the intergenic sequence between flaB1 and flaB2, a potential stem-loop structure (12-bp inverted repeats) was identified 25 bp downstream of the flaB1 stop codon; this could serve as a transcription terminator for the flaB1 mRNA. Three E. coli-like promoter regions (I, II, and III) for binding Esigma(70), a regulatory sequence uncommonly found in flagellar genes, were predicted upstream of the flaB2 ORF. Only promoter region II contains a promoter that is functional in E. coli, as revealed at phenotypic and transcriptional levels by its capability of directing the expression of the chloramphenicol acetyltransferase (CAT) gene in the promoter probe vector pKK232-8. These observations may suggest that flaB1 and flaB2 are transcribed separately and do not form a transcriptional operon controlled by a single promoter.

  5. Water Stress in Global Transboundary River Basins: Significance of Upstream Water Use on Downstream Stress

    NASA Technical Reports Server (NTRS)

    Munia, H.; Guillaume, J. H. A.; Mirumachi, N.; Porkka,M.; Wada, Yoshihide; Kummu, M.

    2016-01-01

    Growing population and water demand have increased pressure on water resources in various parts of the globe, including many transboundary river basins. While the impacts of upstream water use on downstream water availability have been analyzed in many of these international river basins, this has not been systematically done at the global scale using coherent and comparable datasets. In this study, we aim to assess the change in downstream water stress due to upstream water use in the world's transboundary river basins. Water stress was first calculated considering only local water use of each sub-basin based on country-basin mesh, then compared with the situation when upstream water use was subtracted from downstream water availability. Wefound that water stress was generally already high when considering only local water use, affecting 0.95-1.44 billion people or 33%-51% of the population in transboundary river basins. After accounting for upstream water use, stress level increased by at least 1 percentage-point for 30-65 sub-basins, affecting 0.29-1.13 billion people. Altogether 288 out of 298 middle-stream and downstream sub-basin areas experienced some change in stress level. Further, we assessed whether there is a link between increased water stress due to upstream water use and the number of conflictive and cooperative events in the transboundary river basins, as captured by two prominent databases. No direct relationship was found. This supports the argument that conflicts and cooperation events originate from a combination of different drivers, among which upstream-induced water stress may play a role. Our findings contribute to better understanding of upstream-downstream dynamics in water stress to help address water allocation problems.

  6. A rare case of 46, XX SRY-negative male with approximately 74-kb duplication in a region upstream of SOX9.

    PubMed

    Xiao, Bing; Ji, Xing; Xing, Ya; Chen, Ying-Wei; Tao, Jiong

    2013-12-01

    The 46, XX male disorder of sex development (DSD) is a rare genetic condition. Here, we report the case of a 46, XX SRY-negative male with complete masculinization. The coding region and exon/intron boundaries of the DAX1, SOX9 and RSPO1 genes were sequenced, and no mutations were detected. Using whole genome array analysis and real-time PCR, we identified a approximately 74-kb duplication in a region approximately 510-584 kb upstream of SOX9 (chr17:69,533,305-69,606,825, hg19). Combined with the results of previous studies, the minimum critical region associated with gonadal development is a 67-kb region located 584-517 kb upstream of SOX9. The amplification of this region might lead to SOX9 overexpression, causing female-to-male sex reversal. Gonadal-specific enhancers in the region upstream of SOX9 may activate the SOX9 expression through long-range regulation, thus triggering testicular differentiation. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  7. The glnAntrBC operon of Herbaspirillum seropedicae is transcribed by two oppositely regulated promoters upstream of glnA.

    PubMed

    Schwab, Stefan; Souza, Emanuel M; Yates, Marshall G; Persuhn, Darlene C; Steffens, M Berenice R; Chubatsu, Leda S; Pedrosa, Fábio O; Rigo, Liu U

    2007-01-01

    Herbaspirillum seropedicae is an endophytic bacterium that fixes nitrogen under microaerophilic conditions. The putative promoter sequences glnAp1 (sigma70-dependent) and glnAp2 (sigma54), and two NtrC-binding sites were identified upstream from the glnA, ntrB and ntrC genes of this microorganism. To study their transcriptional regulation, we used lacZ fusions to the H. seropedicae glnA gene, and the glnA-ntrB and ntrB-ntrC intergenic regions. Expression of glnA was up-regulated under low ammonium, but no transcription activity was detected from the intergenic regions under any condition tested, suggesting that glnA, ntrB and ntrC are co-transcribed from the promoters upstream of glnA. Ammonium regulation was lost in the ntrC mutant strain. A point mutation was introduced in the conserved -25/-24 dinucleotide (GG-->TT) of the putative sigma54-dependent promoter (glnAp2). Contrary to the wild-type promoter, glnA expression with the mutant glnAp2 promoter was repressed in the wild-type strain under low ammonium levels, but this repression was abolished in an ntrC background. Together our results indicate that the H. seropedicae glnAntrBC operon is regulated from two functional promoters upstream from glnA, which are oppositely regulated by the NtrC protein.

  8. Dna Sequencing

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  9. Utility of an appropriate reporter assay: Heliotrine interferes with GAL4/upstream activation sequence-driven reporter gene systems.

    PubMed

    Luckert, Claudia; Hessel, Stefanie; Lampen, Alfonso; Braeuning, Albert

    2015-10-15

    Reporter gene assays are widely used for the assessment of transcription factor activation following xenobiotic exposure of cells. A critical issue with such assays is the possibility of interference of test compounds with the test system, for example, by direct inhibition of the reporter enzyme. Here we show that the pyrrolizidine alkaloid heliotrine interferes with reporter signals derived from GAL4-based nuclear receptor transactivation assays by a mechanism independent of luciferase enzyme inhibition. These data highlight the necessity to conduct proper control experiments in order to avoid perturbation of reporter assays by test chemicals. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Upstream dispersal of an invasive crayfish aided by a fish passage facility

    USGS Publications Warehouse

    Welsh, Stuart A.; Loughman, Zachary J.

    2015-01-01

    Fish passage facilities for reservoir dams have been used to restore habitat connectivity within riverine networks by allowing upstream passage for native species. These facilities may also support the spread of invasive species, an unintended consequence and potential downside of upstream passage structures. We documented dam passage of the invasive virile crayfish, Orconectes virilis (Hagen, 1870), at fish ladders designed for upstream passage of American eels, Anguilla rostrata (Lesueur, 1817), in the Shenandoah River drainage, USA. Ladder use and upstream passage of 11 virile crayfish occurred from 2007–2014 during periods of low river discharge (<30 m3s–1) and within a wide range of water temperatures from 9.0–28.6 °C. Virile crayfish that used the eel ladders were large adults with a mean carapace length and width of 48.0 mm and 24.1 mm, respectively. Our data demonstrated the use of species-specific fish ladders by a non-target non-native species, which has conservation and management implications for the spread of aquatic invasive species and upstream passage facilities. Specifically, managers should consider implementing long-term monitoring of fish passage facilities with emphasis on detection of invasive species, as well as methods to reduce or eliminate passage of invasive species. 

  11. Unmasking Upstream Gene Expression Regulators with miRNA-corrected mRNA Data

    PubMed Central

    Bollmann, Stephanie; Bu, Dengpan; Wang, Jiaqi; Bionaz, Massimo

    2015-01-01

    Expressed micro-RNA (miRNA) affects messenger RNA (mRNA) abundance, hindering the accuracy of upstream regulator analysis. Our objective was to provide an algorithm to correct such bias. Large mRNA and miRNA analyses were performed on RNA extracted from bovine liver and mammary tissue. Using four levels of target scores from TargetScan (all miRNA:mRNA target gene pairs or only the top 25%, 50%, or 75%). Using four levels of target scores from TargetScan (all miRNA:mRNA target gene pairs or only the top 25%, 50%, or 75%) and four levels of the magnitude of miRNA effect (ME) on mRNA expression (30%, 50%, 75%, and 83% mRNA reduction), we generated 17 different datasets (including the original dataset). For each dataset, we performed upstream regulator analysis using two bioinformatics tools. We detected an increased effect on the upstream regulator analysis with larger miRNA:mRNA pair bins and higher ME. The miRNA correction allowed identification of several upstream regulators not present in the analysis of the original dataset. Thus, the proposed algorithm improved the prediction of upstream regulators. PMID:27279737

  12. Moving Upstream in U.S. Hospital Care Toward Investments in Population Health.

    PubMed

    Begun, James W; Potthoff, Sandra

    The root causes for most health outcomes are often collectively referred to as the social determinants of health. Hospitals and health systems now must decide how much to "move upstream," or invest in programs that directly affect the social determinants of health. Moving upstream in healthcare delivery requires an acceptance of responsibility for the health of populations. We examine responses of 950 nonfederal, general hospitals in the United States to the 2015 American Hospital Association Population Health Survey to identify characteristics that distinguish those hospitals that are most aligned with population health and most engaged in addressing social determinants of health. Those "upstream" hospitals are significantly more likely to be large, not-for-profit, metropolitan, teaching-affiliated, and members of systems. Internally, the more upstream hospitals are more likely to organize their population health activities with strong executive-level involvement, full-time-equivalent support, and coordination at the system level.The characteristics differentiating hospitals strongly involved in population health and upstream activity are not unlike those characteristics associated with diffusion of many innovations in hospitals. These hospitals may be the early adopters in a diffusion process that will eventually include most hospitals or, at least, most not-for-profit hospitals. Alternatively, the population health and social determinants movements could be transient or could be limited to a small portion of hospitals such as those identified here, with distinctive patient populations, missions, and resources.

  13. The muscle creatine kinase gene is regulated by multiple upstream elements, including a muscle-specific enhancer

    SciTech Connect

    Jaynes, J.B.; Johnson, J.E.; Buskin, J.N.

    1988-01-01

    Muscle creatine kinase (MCK) is induced to high levels during skeletal muscle differentiation. The authors examined the upstream regulatory elements of the mouse MCK gene which specify its activation during myogenesis in culture. Fusion genes containing up to 3,300 nucleotides (nt) of MCK 5' flanking DNA in various positions and orientations relative to the bacterial chloramphenicol acetyltransferase (CAT) structural gene were transfected into cultured cells. Transient expression of CAT was compared between proliferating and differentiated MM14 mouse myoblasts and with nonmyogenic mouse L cells. The major effector of high-level expression was found to have the properties of a transcriptional enhancer.more » This element, located between 1,050 and 1,256 nt upstream of the transcription start site, was also found to have a major influence on the tissue and differentiation specificity of MCK expression; it activated either the MCK promoter or heterologous promoters only in differentiated muscle cells. Comparisons of viral and cellular enhancer sequences with the MCK enhancer revealed some similarities to essential regions of the simian virus 40 enhancer as well as to a region of the immunoglobulin heavy-chain enhancer, which has been implicated in tissue-specific protein binding. Even in the absence of the enhancer, low-level expression from a 776-nt MCK promoter retained differentiation specificity. In addition to positive regulatory elements, our data provide some evidence for negative regulatory elements with activity in myoblasts. These may contribute to the cell type and differentiation specificity of MCK expression.« less

  14. Measurement of turbulent flow upstream and downstream of a circular pipe bend

    SciTech Connect

    Sakakibara, Jun; Machida, Nobuteru

    2012-04-15

    We measured velocity distribution in cross sections of a fully developed turbulent pipe flow upstream and downstream of a 90 degree sign bend by synchronizing two sets of a particle image velocimetry (PIV) system. Unsteady undulation of Dean vortices formed downstream from the bend was characterized by the azimuthal position of the stagnation point found on the inner and outer sides of the bend. Linear stochastic estimation was applied to capture the upstream flow field conditioned by the azimuthal location of the stagnation point downstream from the bend. When the inner-side stagnation point stayed below (above) the symmetry plane, themore » conditional streamwise velocity upstream from the bend exhibited high-speed streaks extended in a quasi-streamwise direction on the outer side of the curvature above (below) the symmetry plane.« less

  15. An experimental and numerical study of wave motion and upstream influence in a stratified fluid

    NASA Technical Reports Server (NTRS)

    Hurdis, D. A.

    1974-01-01

    A system consisting of two superimposed layers of liquid of different densities, with a thin transition layer at the interface, provides a good laboratory model of an ocean thermocline or of an atmospheric inversion layer. This research was to gain knowledge about the propagation of disturbances within these two geophysical systems. The technique used was to observe the propagation of internal waves and of upstream influence within the density-gradient region between the two layers of liquid. The disturbances created by the motion of a vertical flat plate, which was moved longitudinally through this region, were examined both experimentally and numerically. An upstream influence, which resulted from a balance of inertial and gravitational forces, was observed, and it was possible to predict the behavior of this influence with the numerical model. The prediction included a description of the propagation of the upstream influence to steadily increasing distances from the flat plate and the shapes and magnitudes of the velocity profiles.

  16. Upstream-advancing waves generated by a current over a sinusoidal bed

    NASA Astrophysics Data System (ADS)

    Kyotoh, Harumichi; Fukushima, Masaki

    1997-07-01

    Upstream-advancing waves are observed in open channel flows over a fixed sinusoidal bed with large amplitude, when the Froude number is less than the resonant value, at which stream velocity is equal to the celerity of the wave with wavelength equal to that of the bottom surface. Their wavelength is about 3-6 times as long as the bottom wavelength and the celerity is close to that obtained from potential flow theory. Therefore, the wavelength of upstream-advancing waves is determined by linear stability analyses assuming that they are induced by the Benjamin-Feir-type instability of steady flow. Here, two formulas for the wavelength with different scaling are introduced and compared with experiment. In addition, the mechanisms of upstream-advancing waves are investigated qualitatively using the forced Schrödinger equation.

  17. PUTATIVE GENE PROMOTER SEQUENCES IN THE CHLORELLA VIRUSES

    PubMed Central

    Fitzgerald, Lisa A.; Boucher, Philip T.; Yanai-Balser, Giane; Suhre, Karsten; Graves, Michael V.; Van Etten, James L.

    2008-01-01

    Three short (7 to 9 nucleotides) highly conserved nucleotide sequences were identified in the putative promoter regions (150 bp upstream and 50 bp downstream of the ATG translation start site) of three members of the genus Chlorovirus, family Phycodnaviridae. Most of these sequences occurred in similar locations within the defined promoter regions. The sequence and location of the motifs were often conserved among homologous ORFs within the Chlorovirus family. One of these conserved sequences (AATGACA) is predominately associated with genes expressed early in virus replication. PMID:18768195

  18. Effect of a curved duct upstream on performance of small centrifugal compressors for automobile turbochargers

    NASA Astrophysics Data System (ADS)

    Kikuchi, Shigeta; Yamasaki, Nobuhiko; Yamagata, Akihiro

    2013-02-01

    Since the automobile turbochargers are installed in an engine compartment with limited space, the ducts upstream of the turbocharger compressor may be curved in a complex manner. In the present paper, the effect of a curved duct upstream on performance of small centrifugal compressors for automobile turbochargers is discussed. The computational fluid dynamics (CFD) analysis of a turbocharger compressor validated for the compressor model with the straight pipe applied to the compressor with the curved pipe are executed, and the deterioration of the performance for the curved pipe is confirmed. It is also found that the deterioration of compressor performance is caused by the interaction of the secondary flow and the impeller.

  19. Method and system for control of upstream flowfields of vehicle in supersonic or hypersonic atmospheric flight

    NASA Technical Reports Server (NTRS)

    Daso, Endwell O. (Inventor); Pritchett, II, Victor E. (Inventor); Wang, Ten-See (Inventor); Farr, Rebecca Ann (Inventor)

    2012-01-01

    The upstream flowfield of a vehicle traveling in supersonic or hypersonic atmospheric flight is actively controlled using attribute(s) experienced by the vehicle. Sensed attribute(s) include pressure along the vehicle's outer mold line, temperature along the vehicle's outer mold line, heat flux along the vehicle's outer mold line, and/or local acceleration response of the vehicle. A non-heated, non-plasma-producing gas is injected into an upstream flowfield of the vehicle from at least one surface location along the vehicle's outer mold line. The pressure of the gas so-injected is adjusted based on the attribute(s) so-sensed.

  20. Upstream-advancing waves generated by three-dimensional moving disturbances

    NASA Astrophysics Data System (ADS)

    Lee, Seung-Joon; Grimshaw, Roger H. J.

    1990-02-01

    The wave field resulting from a surface pressure or a bottom topography in a horizontally unbounded domain is studied. Upstream-advancing waves successively generated by various forcing disturbances moving with near-resonant speeds are found by numerically solving a forced Kadomtsev-Petviashvili (fKP) equation, which shows in its simplest form the interplay of a basic linear wave operator, longitudinal and transverse dispersion, nonlinearity, and forcing. Curved solitary waves are found as a slowly varying similarity solution of the Kadomtsev-Petviashvili (KP) equation, and are favorably compared with the upstream-advancing waves numerically obtained.

  1. Upstream ionization instability associated with a current-free double layer.

    PubMed

    Aanesland, A; Charles, C; Lieberman, M A; Boswell, R W

    2006-08-18

    A low frequency instability has been observed using various electrostatic probes in a low-pressure expanding helicon plasma. The instability is associated with the presence of a current-free double layer (DL). The frequency of the instability increases linearly with the potential drop of the DL, and simultaneous measurements show their coexistence. A theory for an upstream ionization instability has been developed, which shows that electrons accelerated through the DL increase the ionization upstream and are responsible for the observed instability. The theory is in good agreement with the experimental results.

  2. Differential expression of upstream stimulatory factor (USF) 2 variants in eutopic endometria from women with endometriosis: estradiol regulation.

    PubMed

    Castro, Jazmin; Araya, Germán; Inostroza, Pamela; Hidalgo, Paulina; González-Ramos, Reinaldo; Sovino, Hugo; Boric, M Angélica; Fuentes, Ariel; Johnson, M Cecilia

    2015-10-09

    Endometriosis, pro-inflammatory and invasive benign disease estrogen dependent, abnormally express in endometria the enzyme P450Arom, positively regulated by steroid factor-1 (SF-1). Our objective was to study the nuclear protein contents of upstream stimulating factor 2 (USF2a and USF2b), a positive regulator of SF-1, throughout the menstrual cycle in eutopic endometria from women with and without (control) endometriosis and the involvement of nuclear estrogen receptors (ER) and G-coupled protein estrogen receptor (GPER)-1. Upstream stimulating factor 2 protein contents were higher in mid (USF2b) and late (USF2a and USF2b) secretory phase in eutopic endometria from endometriosis than control (p < 0.05). In isolated control epithelial cells incubated with E2 and PGE2, to resemble the endometriosis condition, the data showed: (a) significant increase of USF2a and USF2b nuclear protein contents when treated with E2, PPT (specific agonist for ERα) or G1 (specific agonist for GPER1); (b) no increase in USF2 binding to SF-1 E-Box/DNA consensus sequence in E2-treated cells; (c) USF2 variants protein contents were not modified by PGE2; (d) SF-1 nuclear protein content was significantly higher than basal when treated with PGE2, E2 or G1, stimulation unaffected by ICI (nuclear ER antagonist); and (e) increased (p < 0.05) cytosolic protein contents of P450Arom when treated with PGE2, E2, PPT or G1 compared to basal, effect that was additive with E2 + PGE2 together. Nevertheless, in endometriosis cells, the high USF2, SF-1 and P450Arom protein contents in basal condition were unmodified. These data strongly suggest that USF2 variants and P450Arom are regulated by E2 through ERα and GPER1, whereas SF-1 through GPER1, visualized by the response of the cells obtained from control endometria, being unaffected the endogenously stimulated cells from endometriosis origin. The lack of E2 stimulation on USF2/SF-1 E-Box/DNA-sequence binding and the absence of PGE2 effect on USF

  3. Induction of surfactin production in Bacillus subtilis by gsp, a gene located upstream of the gramicidin S operon in Bacillus brevis.

    PubMed Central

    Borchert, S; Stachelhaus, T; Marahiel, M A

    1994-01-01

    The deduced amino acid sequence of the gsp gene, located upstream of the 5' end of the gramicidin S operon (grs operon) in Bacillus brevis, showed a high degree of similarity to the sfp gene product, which is located downstream of the srfA operon in B. subtilis. The gsp gene complemented in trans a defect in the sfp gene (sfpO) and promoted production of the lipopeptide antibiotic surfactin. The functional homology of Gsp and Sfp and the sequence similarity of these two proteins to EntD suggest that the three proteins represent a new class of proteins involved in peptide secretion, in support of a hypothesis published previously (T. H. Grossman, M. Tuckman, S. Ellestad, and M. S. Osburne, J. Bacteriol. 175:6203-6211, 1993). Images PMID:7512553

  4. Implications of Upstream Flow Availability for Watershed Surface Water Supply Across the Conterminous United States

    Treesearch

    Kai Duan; Ge Sun; Peter V. Caldwell; Steven G. McNulty; Yang Zhang

    2018-01-01

    Although it is well established that the availability of upstream flow (AUF) affects downstream water supply, its significance has not been rigorously categorized and quantified at fine resolutions. This study aims to fill this gap by providing a nationwide inventory of AUF and local water resource, and assessing their roles in securing water supply across the 2,099 8-...

  5. Trends in U.S. Oil and Natural Gas Upstream Costs

    EIA Publications

    2016-01-01

    Average 2015 well drilling and completion costs in five onshore areas decline 25% and 30% below their level in 2012 The U.S. Energy Information Administration (EIA) commissioned IHS Global Inc. (IHS) to perform a study of upstream drilling and production costs. The IHS report assesses capital and operating costs associated with drilling, completing, and operating wells and facilities.

  6. Sodium Pick-Up Ion Observations in the Solar Wind Upstream of Mercury

    NASA Astrophysics Data System (ADS)

    Jasinski, J. M.; Raines, J. M.; Slavin, J. A.; Regoli, L. R.; Murphy, N.

    2018-05-01

    We present the first observations of sodium pick-up ions upstream of Mercury’s magnetosphere. From these observations we infer properties of Mercury’s sodium exosphere and implications for the solar wind interaction with Mercury’s magnetosphere.

  7. INDIRECT UPSTREAM EFFECTS OF DAMS: CONSEQUENCES OF MIGRATORY CONSUMER EXTIRPATION IN PUERTO RICO

    Treesearch

    EFFIE A. GREATHOUSE; CATHERINE M. PRINGLE; WILLIAM H. MCDOWELL; JEFF G. HOLMQUIST

    2006-01-01

    Large dams degrade the integrity of a wide variety of ecosystems, yet direct downstream effects of dams have received the most attention from ecosystem managers and researchers. We investigated indirect upstream effects of dams resulting from decimation of migratory freshwater shrimp and fish populations in Puerto Rico, USA, in both high- and low-gradient streams. In...

  8. Enhancer elements upstream of the SHOX gene are active in the developing limb.

    PubMed

    Durand, Claudia; Bangs, Fiona; Signolet, Jason; Decker, Eva; Tickle, Cheryll; Rappold, Gudrun

    2010-05-01

    Léri-Weill Dyschondrosteosis (LWD) is a dominant skeletal disorder characterized by short stature and distinct bone anomalies. SHOX gene mutations and deletions of regulatory elements downstream of SHOX resulting in haploinsufficiency have been found in patients with LWD. SHOX encodes a homeodomain transcription factor and is known to be expressed in the developing limb. We have now analyzed the regulatory significance of the region upstream of the SHOX gene. By comparative genomic analyses, we identified several conserved non-coding elements, which subsequently were tested in an in ovo enhancer assay in both chicken limb bud and cornea, where SHOX is also expressed. In this assay, we found three enhancers to be active in the developing chicken limb, but none were functional in the developing cornea. A screening of 60 LWD patients with an intact SHOX coding and downstream region did not yield any deletion of the upstream enhancer region. Thus, we speculate that SHOX upstream deletions occur at a lower frequency because of the structural organization of this genomic region and/or that SHOX upstream deletions may cause a phenotype that differs from the one observed in LWD.

  9. Enhancer elements upstream of the SHOX gene are active in the developing limb

    PubMed Central

    Durand, Claudia; Bangs, Fiona; Signolet, Jason; Decker, Eva; Tickle, Cheryll; Rappold, Gudrun

    2010-01-01

    Léri-Weill Dyschondrosteosis (LWD) is a dominant skeletal disorder characterized by short stature and distinct bone anomalies. SHOX gene mutations and deletions of regulatory elements downstream of SHOX resulting in haploinsufficiency have been found in patients with LWD. SHOX encodes a homeodomain transcription factor and is known to be expressed in the developing limb. We have now analyzed the regulatory significance of the region upstream of the SHOX gene. By comparative genomic analyses, we identified several conserved non-coding elements, which subsequently were tested in an in ovo enhancer assay in both chicken limb bud and cornea, where SHOX is also expressed. In this assay, we found three enhancers to be active in the developing chicken limb, but none were functional in the developing cornea. A screening of 60 LWD patients with an intact SHOX coding and downstream region did not yield any deletion of the upstream enhancer region. Thus, we speculate that SHOX upstream deletions occur at a lower frequency because of the structural organization of this genomic region and/or that SHOX upstream deletions may cause a phenotype that differs from the one observed in LWD. PMID:19997128

  10. Upstream structural management measures for an urban area flooding in Turkey

    NASA Astrophysics Data System (ADS)

    Akyurek, Z.; Bozoğlu, B.; Sürer, S.; Mumcu, H.

    2015-06-01

    In recent years, flooding has become an increasing concern across many parts of the world of both the general public and their governments. The climate change inducing more intense rainfall events occurring in short period of time lead flooding in rural and urban areas. In this study the flood modelling in an urbanized area, namely Samsun-Terme in Blacksea region of Turkey is performed. MIKE21 with flexible grid is used in 2-dimensional shallow water flow modelling. 1 × 1000-1 scaled maps with the buildings for the urbanized area and 1 × 5000-1 scaled maps for the rural parts are used to obtain DTM needed in the flood modelling. The bathymetry of the river is obtained from additional surveys. The main river passing through the urbanized area has a capacity of 500 m3 s-1 according to the design discharge obtained by simple ungauged discharge estimation depending on catchment area only. The upstream structural base precautions against flooding are modelled. The effect of four main upstream catchments on the flooding in the downstream urban area are modelled as different scenarios. It is observed that if the flow from the upstream catchments can be retarded through a detention pond constructed in one of the upstream catchments, estimated Q100 flood can be conveyed by the river without overtopping from the river channel. The operation of the upstream detention ponds and the scenarios to convey Q500 without causing flooding are also presented. Structural management measures to address changes in flood characteristics in water management planning are discussed.

  11. Numerical Investigation of Dual-Mode Scramjet Combustor with Large Upstream Interaction

    NASA Technical Reports Server (NTRS)

    Mohieldin, T. O.; Tiwari, S. N.; Reubush, David E. (Technical Monitor)

    2004-01-01

    Dual-mode scramjet combustor configuration with significant upstream interaction is investigated numerically, The possibility of scaling the domain to accelerate the convergence and reduce the computational time is explored. The supersonic combustor configuration was selected to provide an understanding of key features of upstream interaction and to identify physical and numerical issues relating to modeling of dual-mode configurations. The numerical analysis was performed with vitiated air at freestream Math number of 2.5 using hydrogen as the sonic injectant. Results are presented for two-dimensional models and a three-dimensional jet-to-jet symmetric geometry. Comparisons are made with experimental results. Two-dimensional and three-dimensional results show substantial oblique shock train reaching upstream of the fuel injectors. Flow characteristics slow numerical convergence, while the upstream interaction slowly increases with further iterations. As the flow field develops, the symmetric assumption breaks down. A large separation zone develops and extends further upstream of the step. This asymmetric flow structure is not seen in the experimental data. Results obtained using a sub-scale domain (both two-dimensional and three-dimensional) qualitatively recover the flow physics obtained from full-scale simulations. All results show that numerical modeling using a scaled geometry provides good agreement with full-scale numerical results and experimental results for this configuration. This study supports the argument that numerical scaling is useful in simulating dual-mode scramjet combustor flowfields and could provide an excellent convergence acceleration technique for dual-mode simulations.

  12. The immediate upstream region of the 5′-UTR from the AUG start codon has a pronounced effect on the translational efficiency in Arabidopsis thaliana

    PubMed Central

    Kim, Younghyun; Lee, Goeun; Jeon, Eunhyun; Sohn, Eun ju; Lee, Yongjik; Kang, Hyangju; Lee, Dong wook; Kim, Dae Heon; Hwang, Inhwan

    2014-01-01

    The nucleotide sequence around the translational initiation site is an important cis-acting element for post-transcriptional regulation. However, it has not been fully understood how the sequence context at the 5′-untranslated region (5′-UTR) affects the translational efficiency of individual mRNAs. In this study, we provide evidence that the 5′-UTRs of Arabidopsis genes showing a great difference in the nucleotide sequence vary greatly in translational efficiency with more than a 200-fold difference. Of the four types of nucleotides, the A residue was the most favourable nucleotide from positions −1 to −21 of the 5′-UTRs in Arabidopsis genes. In particular, the A residue in the 5′-UTR from positions −1 to −5 was required for a high-level translational efficiency. In contrast, the T residue in the 5′-UTR from positions −1 to −5 was the least favourable nucleotide in translational efficiency. Furthermore, the effect of the sequence context in the −1 to −21 region of the 5′-UTR was conserved in different plant species. Based on these observations, we propose that the sequence context immediately upstream of the AUG initiation codon plays a crucial role in determining the translational efficiency of plant genes. PMID:24084084

  13. MSLICE Sequencing

    NASA Technical Reports Server (NTRS)

    Crockett, Thomas M.; Joswig, Joseph C.; Shams, Khawaja S.; Norris, Jeffrey S.; Morris, John R.

    2011-01-01

    MSLICE Sequencing is a graphical tool for writing sequences and integrating them into RML files, as well as for producing SCMF files for uplink. When operated in a testbed environment, it also supports uplinking these SCMF files to the testbed via Chill. This software features a free-form textural sequence editor featuring syntax coloring, automatic content assistance (including command and argument completion proposals), complete with types, value ranges, unites, and descriptions from the command dictionary that appear as they are typed. The sequence editor also has a "field mode" that allows tabbing between arguments and displays type/range/units/description for each argument as it is edited. Color-coded error and warning annotations on problematic tokens are included, as well as indications of problems that are not visible in the current scroll range. "Quick Fix" suggestions are made for resolving problems, and all the features afforded by modern source editors are also included such as copy/cut/paste, undo/redo, and a sophisticated find-and-replace system optionally using regular expressions. The software offers a full XML editor for RML files, which features syntax coloring, content assistance and problem annotations as above. There is a form-based, "detail view" that allows structured editing of command arguments and sequence parameters when preferred. The "project view" shows the user s "workspace" as a tree of "resources" (projects, folders, and files) that can subsequently be opened in editors by double-clicking. Files can be added, deleted, dragged-dropped/copied-pasted between folders or projects, and these operations are undoable and redoable. A "problems view" contains a tabular list of all problems in the current workspace. Double-clicking on any row in the table opens an editor for the appropriate sequence, scrolling to the specific line with the problem, and highlighting the problematic characters. From there, one can invoke "quick fix" as described

  14. Insertion Sequences

    PubMed Central

    Mahillon, Jacques; Chandler, Michael

    1998-01-01

    Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available. PMID:9729608

  15. The cytochrome oxidase subunit I and subunit III genes in Oenothera mitochondria are transcribed from identical promoter sequences

    PubMed Central

    Hiesel, Rudolf; Schobel, Werner; Schuster, Wolfgang; Brennicke, Axel

    1987-01-01

    Two loci encoding subunit III of the cytochrome oxidase (COX) in Oenothera mitochondria have been identified from a cDNA library of mitochondrial transcripts. A 657-bp sequence block upstream from the open reading frame is also present in the two copies of the COX subunit I gene and is presumably involved in homologous sequence rearrangement. The proximal points of sequence rearrangements are located 3 bp upstream from the COX I and 1139 bp upstream from the COX III initiation codons. The 5'-termini of both COX I and COX III mRNAs have been mapped in this common sequence confining the promoter region for the Oenothera mitochondrial COX I and COX III genes to the homologous sequence block. ImagesFig. 5. PMID:15981332

  16. Arabidopsis intragenomic conserved noncoding sequence

    PubMed Central

    Thomas, Brian C.; Rapaka, Lakshmi; Lyons, Eric; Pedersen, Brent; Freeling, Michael

    2007-01-01

    After the most recent tetraploidy in the Arabidopsis lineage, most gene pairs lost one, but not both, of their duplicates. We manually inspected the 3,179 retained gene pairs and their surrounding gene space still present in the genome using a custom-made viewer application. The display of these pairs allowed us to define intragenic conserved noncoding sequences (CNSs), identify exon annotation errors, and discover potentially new genes. Using a strict algorithm to sort high-scoring pair sequences from the bl2seq data, we created a database of 14,944 intragenomic Arabidopsis CNSs. The mean CNS length is 31 bp, ranging from 15 to 285 bp. There are ≈1.7 CNSs associated with a typical gene, and Arabidopsis CNSs are found in all areas around exons, most frequently in the 5′ upstream region. Gene ontology classifications related to transcription, regulation, or “response to …” external or endogenous stimuli, especially hormones, tend to be significantly overrepresented among genes containing a large number of CNSs, whereas protein localization, transport, and metabolism are common among genes with no CNSs. There is a 1.5% overlap between these CNSs and the 218,982 putative RNAs in the Arabidopsis Small RNA Project database, allowing for two mismatches. These CNSs provide a unique set of noncoding sequences enriched for function. CNS function is implied by evolutionary conservation and independently supported because CNS-richness predicts regulatory gene ontology categories. PMID:17301222

  17. Eco-Design of River Fishways for Upstream Passage: Application for Hanfeng Dam, Pengxi River, China

    SciTech Connect

    Johnson, Gary E.; Rainey, William S.

    2012-05-20

    This paper provides a scientific approach to eco-design of river fishways to allow upstream movement of fish past new and existing dams in China. This eco-design approach integrates principles of fish ecology/behavior and engineering, a scientific field also known as bio-engineering or eco-hydraulics. We define a fishway as a structure or mechanism to convey fish upstream past a dam. Man-made or natural stream beds can be part of the fishway mechanism. Fish include bony and non-bony fishes, and upstream passage is the concern here, not downstream passage. The problem is dams block access to upstream habitat used for spawning, rearing,more » and refuge, i.e., dams decrease habitat connectivity. A solution to alleviate this problem is to design fishways, preferably while the dam is being designed, but if necessary, as retrofits afterward to provide a route that fish can and will use to pass safely upstream without undue delay. Our eco-design approach for fishways involves eight steps: 1) identify the primary species of importance; 2) understand basic ecology and behavior of these fish; 3) characterize the environmental conditions where passage is or will be blocked; 4 identify fishway alternatives and select a preferred alternative; 5) establish eco-design criteria for the fishway, either from management agencies or, if necessary, developed specifically for the given site; 6) where needed, identify and perform research required to resolve critical uncertainties and finalize the eco-design criteria; 7) apply the eco-design criteria and site-specific considerations to design the fishway, involving peer-review by local stakeholders in the process; 8) build the fishway, monitor its effectiveness, and apply the lessons learned. Example fishways are described showing a range of eco-designs depending on the dam site and fish species of concern. We apply the eco-design principles to recommend an approach and next steps for a fishway to pass fish upstream at Hanfeng Dam, an

  18. Regulation of CYBB Gene Expression in Human Phagocytes by a Distant Upstream NF-κB Binding Site.

    PubMed

    Frazão, Josias B; Thain, Alison; Zhu, Zhiqing; Luengo, Marcos; Condino-Neto, Antonio; Newburger, Peter E

    2015-09-01

    The human CYBB gene encodes the gp91-phox component of the phagocyte oxidase enzyme complex, which is responsible for generating superoxide and other downstream reactive oxygen species essential to microbial killing. In the present study, we have identified by sequence analysis a putative NF-κB binding site in a DNase I hypersensitive site, termed HS-II, located in the distant 5' flanking region of the CYBB gene. Electrophoretic mobility assays showed binding of the sequence element by recombinant NF-κB protein p50 and by proteins in nuclear extract from the HL-60 myeloid leukemia cell line corresponding to p50 and to p50/p65 heterodimers. Chromatin immunoprecipitation demonstrated NF-κB binding to the site in intact HL-60 cells. Chromosome conformation capture (3C) assays demonstrated physical interaction between the NF-κB binding site and the CYBB promoter region. Inhibition of NF-κB activity by salicylate reduced CYBB expression in peripheral blood neutrophils and differentiated U937 monocytic leukemia cells. U937 cells transfected with a mutant inhibitor of κB "super-repressor" showed markedly diminished CYBB expression. Luciferase reporter analysis of the NF-κB site linked to the CYBB 5' flanking promoter region revealed enhanced expression, augmented by treatment with interferon-γ. These studies indicate a role for this distant, 15 kb upstream, binding site in NF-κB regulation of the CYBB gene, an essential component of phagocyte-mediated host defense. © 2015 Wiley Periodicals, Inc.

  19. Identification of the first PAR1 deletion encompassing upstream SHOX enhancers in a family with idiopathic short stature.

    PubMed

    Benito-Sanz, Sara; Aza-Carmona, Miriam; Rodríguez-Estevez, Amaya; Rica-Etxebarria, Ixaso; Gracia, Ricardo; Campos-Barros, Angel; Heath, Karen E

    2012-01-01

    Short stature homeobox-containing gene, MIM 312865 (SHOX) is located within the pseudoautosomal region 1 (PAR1) of the sex chromosomes. Mutations in SHOX or its downstream transcriptional regulatory elements represent the underlying molecular defect in ~60% of Léri-Weill dyschondrosteosis (LWD) and ~5-15% of idiopathic short stature (ISS) patients. Recently, three novel enhancer elements have been identified upstream of SHOX but to date, no PAR1 deletions upstream of SHOX have been observed that only encompass these enhancers in LWD or ISS patients. We set out to search for genetic alterations of the upstream SHOX regulatory elements in 63 LWD and 100 ISS patients with no known alteration in SHOX or the downstream enhancer regions using a specifically designed MLPA assay, which covers the PAR1 upstream of SHOX. An upstream SHOX deletion was identified in an ISS proband and her affected father. The deletion was confirmed and delimited by array-CGH, to extend ~286 kb. The deletion included two of the upstream SHOX enhancers without affecting SHOX. The 13.3-year-old proband had proportionate short stature with normal GH and IGF-I levels. In conclusion, we have identified the first PAR1 deletion encompassing only the upstream SHOX transcription regulatory elements in a family with ISS. The loss of these elements may result in SHOX haploinsufficiency because of decreased SHOX transcription. Therefore, this upstream region should be included in the routine analysis of PAR1 in patients with LWD, LMD and ISS.

  20. Upstream energetic ions and electrons - Bow shock-associated or magnetospheric origin

    NASA Technical Reports Server (NTRS)

    Scholer, M.; Hovestadt, D.; Ipavich, F. M.; Gloeckler, G.

    1981-01-01

    An analysis is made of 35 proton bursts observed with the Max-Planck-Institut/University of Maryland sensor system on ISEE 3 far upstream of the earth's bow shock. These upstream bursts are found to fall into two distinctive groups. The first is accompanied by energetic electrons (more than about 75 keV), and the proton spectrum extends up to energies greater than about 300 keV and higher and bends over toward lower energies (less than about 30 keV). The second group, which is unaccompanied by energetic electron bursts, exhibits spectra which can be represented extremely well by exponentials in energy with a mean e-folding energy of approximately 15 keV. The first group is thought to be of a magnetospheric origin, and the second to be bow-shock associated.

  1. Antibiotic Resistance in Aeromonas Upstream and Downstream of a Water Resource Recovery Facility

    PubMed Central

    Henderson, Samantha K.; Askew, Maegan L.; Risenhoover, Hollie G.; McAndrews, Chrystle R.; Kennedy, S. Dawn; Paine, C. Sue

    2014-01-01

    Aeromonas strains isolated from sediments upstream and downstream of a water resource recovery facility (WRRF) over a two-year time period were tested for susceptibility to thirteen antibiotics. Incidence of resistance to antibiotics, antibiotic resistance phenotypes, and diversity (based on resistance phenotypes) were compared in the two populations. At the beginning of the study, the upstream and downstream Aeromonas populations were different for incidence of antibiotic resistance (p < 0.01), resistance phenotypes (p < 0.005), and diversity. However, these differences declined over time and were not significant at the end of the study. These results (1) indicate that antibiotic resistance in Aeromonas in stream sediments fluctuates considerably over time and (2) suggest that WRRF effluent does not, when examined over the long term, affect antibiotic resistance in Aeromonas in downstream sediment. PMID:25327024

  2. Upstream electron oscillations and ion overshoot at an interplanetary shock wave

    NASA Technical Reports Server (NTRS)

    Potter, D. W.; Parks, G. K.

    1983-01-01

    During the passage of a large interplanetary shock on Oct. 13, 1981, the ISEE-1 and -2 spacecraft were in the solar wind outside of the upstream region of the bow shock. The high time resolution data of the University of California particle instruments allow pinpointing the expected electron spike as occurring just before the magnetic ramp. In addition, two features that occur at this shock have not been observed before: electron oscillations associated with low frequency waves upstream of the shock and sharp 'overshoot' (about 1 sec) in the ion fluxes that occur right after the magnetic ramp. This interplanetary shock exhibits many of the same characteristics that are observed at the earth's bow shock.

  3. Manipulation of upstream rotor leading edge vortex and its effects on counter rotating propeller noise

    NASA Technical Reports Server (NTRS)

    Squires, Becky

    1993-01-01

    The leading edge vortex of a counter rotating propeller (CRP) model was altered by using shrouds and by turning the upstream rotors to a forward sweep configuration. Performance, flow, and acoustic data were used to determine the effect of vortex impingement on the noise signature of the CRP system. Forward sweep was found to eliminate the leading edge vortex of the upstream blades. Removal of the vortex had little effect on the tone noise at the forward and rear blade passing frequencies (BPF's) but significantly altered both the sound pressure level and directivity of the interaction tone which occurs at the sum of the two BPF's. A separate manipulation of the leading edge vortex performed by installing shrouds of various inlet length on the CRP verified that diverting the vortex path increases the noise level of the interaction tone. An unexpected link has been established between the interaction tone and the leading edge vortex-blade interaction phenomenon.

  4. Essential roles of caspases and their upstream regulators in rotenone-induced apoptosis

    SciTech Connect

    Lee Jihjong; Huang, M.-S.; Yang, I-C.

    2008-06-20

    In the present study, we examined whether caspases and their upstream regulators are involved in rotenone-induced cytotoxicity. Rotenone significantly inhibited the proliferation of oral cancer cell lines in a dose-dependent manner compared to normal oral mucosal fibroblasts. Flow cytometric analysis of DNA content showed that rotenone treatment induced apoptosis following G2/M arrest. Western blotting showed activation of both the caspase-8 and caspase-9 pathways, which differed from previous studies conducted in other cell types. Furthermore, p53 protein and its downstream pro-apoptotic target, Bax, were induced in SAS cells after treatment with rotenone. Rotenone-induced apoptosis was inhibited by antioxidants (glutathione, N-acetylcysteine, andmore » tiron). In conclusion, our results demonstrate significant involvement of caspases and their upstream regulators in rotenone-induced cytotoxicity.« less

  5. Shock Characteristics Measured Upstream of Both a Forward-Swept and an Aft-Swept Fan

    NASA Technical Reports Server (NTRS)

    Podboy, Gary G.; Krupar, Martin J.; Sutliff, Daniel L.; Horvath, Csaba

    2007-01-01

    Three different types of diagnostic data-blade surface flow visualization, shroud unsteady pressure, and laser Doppler velocimeter (LDV)--were obtained on two fans, one forward-swept and one aft-swept, in order to learn more about the shocks which propagate upstream of these rotors when they are operated at transonic tip speeds. Flow visualization data are presented for the forward-swept fan operating at 13831 rpm(sub c), and for the aft-swept fan operating at 12500 and 13831 rpm(sub c) (corresponding to tip rotational Mach numbers of 1.07 and 1.19, respectively). The flow visualization data identify where the shocks occur on the suction side of the rotor blades. These data show that at the takeoff speed, 13831 rpm(sub c), the shocks occurring in the tip region of the forward-swept fan are further downstream in the blade passage than with the aft-swept fan. Shroud unsteady pressure measurements were acquired using a linear array of 15 equally-spaced pressure transducers extending from two tip axial chords upstream to 0.8 tip axial chords downstream of the static position of the tip leading edge of each rotor. Such data are presented for each fan operating at one subsonic and five transonic tip speeds. The unsteady pressure data show relatively strong detached shocks propagating upstream of the aft-swept rotor at the three lowest transonic tip speeds, and weak, oblique pressure disturbances attached to the tip of the aft-swept fan at the two highest transonic tip speeds. The unsteady pressure measurements made with the forward-swept fan do not show strong shocks propagating upstream of that rotor at any of the tested speeds. A comparison of the forward-swept and aft-swept shroud unsteady pressure measurements indicates that at any given transonic speed the pressure disturbance just upstream of the tip of the forward-swept fan is much weaker than that of the aft-swept fan. The LDV data suggest that at 12500 and 13831 rpm(sub c), the forward-swept fan swallowed the

  6. Upstream waves and particles /Tutorial Lecture/. [from shocks in interplanetary space

    NASA Technical Reports Server (NTRS)

    Russell, C. T.; Hoppe, M. M.

    1983-01-01

    The plasma waves, MHD waves, energetic electrons and ions associated with the proximity of the region upstream from terrestrial, planetary and interplanetary shocks are discussed in view of observations and current theories concerning their origin. These waves cannot be separated from the study of shock structure. Since the shocks are supersonic, they continually overtake any ULF waves created in the plasma in front of the shock. The upstream particles and waves are also of intrinsic interest because they provide a plasma laboratory for the study of wave-particle interactions in a plasma which, at least at the earth, is accessible to sophisticated probing. Insight may be gained into interstellar medium cosmic ray acceleration through the study of these phenomena.

  7. Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians.

    PubMed

    Marsh, Adam G; Hoadley, Kenneth D; Warner, Mark E

    2016-01-01

    Coral reefs are under assault from stressors including global warming, ocean acidification, and urbanization. Knowing how these factors impact the future fate of reefs requires delineating stress responses across ecological, organismal and cellular scales. Recent advances in coral reef biology have integrated molecular processes with ecological fitness and have identified putative suites of temperature acclimation genes in a Scleractinian coral Acropora hyacinthus. We wondered what unique characteristics of these genes determined their coordinate expression in response to temperature acclimation, and whether or not other corals and cnidarians would likewise possess these features. Here, we focus on cytosine methylation as an epigenetic DNA modification that is responsive to environmental stressors. We identify common conserved patterns of cytosine-guanosine dinucleotide (CpG) motif frequencies in upstream promoter domains of different functional gene groups in two cnidarian genomes: a coral (Acropora digitifera) and an anemone (Nematostella vectensis). Our analyses show that CpG motif frequencies are prominent in the promoter domains of functional genes associated with environmental adaptation, particularly those identified in A. hyacinthus. Densities of CpG sites in upstream promoter domains near the transcriptional start site (TSS) are 1.38x higher than genomic background levels upstream of -2000 bp from the TSS. The increase in CpG usage suggests selection to allow for DNA methylation events to occur more frequently within 1 kb of the TSS. In addition, observed shifts in CpG densities among functional groups of genes suggests a potential role for epigenetic DNA methylation within promoter domains to impact functional gene expression responses in A. digitifera and N. vectensis. Identifying promoter epigenetic sequence motifs among genes within specific functional groups establishes an approach to describe integrated cellular responses to environmental stress in

  8. MESSENGER Magnetic Field Observations of Upstream Ultra-Low Frequency Waves at Mercury

    NASA Technical Reports Server (NTRS)

    Le, G.; Chi, P. J.; Boardsen, S.; Blanco-Cano, X.; Anderosn, B. J.; Korth, H.

    2012-01-01

    The region upstream from a planetary bow shock is a natural plasma laboratory containing a variety of wave particle phenomena. The study of foreshocks other than the Earth's is important for extending our understanding of collisionless shocks and foreshock physics since the bow shock strength varies with heliocentric distance from the Sun, and the sizes of the bow shocks are different at different planets. The Mercury's bow shock is unique in our solar system as it is produced by low Mach number solar wind blowing over a small magnetized body with a predominately radial interplanetary magnetic field. Previous observations of Mercury upstream ultra-low frequency (ULF) waves came exclusively from two Mercury flybys of Mariner 10. The MESSENGER orbiter data enable us to study of upstream waves in the Mercury's foreshock in depth. This paper reports an overview of upstream ULF waves in the Mercury's foreshock using high-time resolution magnetic field data, 20 samples per second, from the MESSENGER spacecraft. The most common foreshock waves have frequencies near 2 Hz, with properties similar to the I-Hz waves in the Earth's foreshock. They are present in both the flyby data and in every orbit of the orbital data we have surveyed. The most common wave phenomenon in the Earth's foreshock is the large-amplitude 30-s waves, but similar waves at Mercury have frequencies at near 0.1 Hz and occur only sporadically with short durations (a few wave cycles). Superposed on the "30-s" waves, there are spectral peaks at near 0.6 Hz, not reported previously in Mariner 10 data. We will discuss wave properties and their occurrence characteristics in this paper.

  9. Upstream migration of Pacific lampreys in the John Day River, Oregon: Behavior, timing, and habitat use

    USGS Publications Warehouse

    Robinson, T. Craig; Bayer, J.M.

    2005-01-01

    Adult Pacific lamprey migration and habitat preferences for over-winter holding and spawning, and larval rearing in tributaries to the Columbia River are not well understood. The John Day River is one such tributary where larval and adult stages of this species have been documented, and its free-flowing character provided the opportunity to study migration of Pacific lampreys unimpeded by passage constraints. Forty-two adult Pacific lampreys were captured in the John Day River near its mouth during their upstream migration. Pacific lampreys were surgically implanted with radio transmitters and released onsite, and tracked by fixed-site, aerial, and terrestrial telemetry methods for nearly one year. Adults moved upstream exclusively at night, with a mean rate of 11.1 ?? 6.3 km/day. They halted upstream migration by September, and held a single position for approximately six months in the lateral margins of riffles and glides, using boulders for cover. More than half of Pacific lampreys resumed migration in March before ending movement in early May. Pacific lampreys that resumed migration in spring completed a median of 87% of their upstream migration before over-winter holding. Upon completing migration. Pacific lampreys briefly held position before beginning downstream movement at the end of May. Though not directly observed, halting migration and movement downstream were likely the result of spawning and death. Gains in adult Pacific lamprey passage through the Columbia River hydrosystem and tributaries may be made by improvements that would expedite migration during spring and summer and increase the quantity and variety of cover and refuge opportunities. ?? 2005 by the Northwest Scientific Association. All rights reserved.

  10. Diel periodicity and chronology of upstream migration in yellow-phase American eels (Anguilla rostrata)

    USGS Publications Warehouse

    Aldinger, Joni L.; Welsh, Stuart A.

    2017-01-01

    Yellow-phase American eel (Anguilla rostrata) upstream migration is temporally punctuated, yet migration chronology within diel time periods is not well-understood. This study examined diel periodicity, chronology, and total length (TL) of six multi-day, high-count (285–1,868 eels) passage events of upstream migrant yellow-phase American eels at the Millville Dam eel ladder, lower Shenandoah River, West Virginia during 2011–2014. We categorized passage by diel periods (vespertine, nocturnal, matutinal, diurnal) and season (spring, summer, late summer/early fall, fall). We depicted passage counts as time-series histograms and used time-series spectral analysis (Fast Fourier Transformation) to identify cyclical patterns and diel periodicity of upstream migration. We created histograms to examine movement patterns within diel periods for each passage event and fit normal mixture models (2–9 mixtures) to describe multiple peaks of passage counts. Periodicity of movements for each passage event followed a 24-h activity cycle with mostly nocturnal movement. Multimodal models were supported by the data; most modes represented nocturnal movements, but modes at or near the transition between twilight and night were also common. We used mixed-model methodology to examine relationships among TL, diel period, and season. An additive-effects model of diel period + season was the best approximating model. A decreasing trend of mean TL occurred across diel movement periods, with the highest mean TL occurring during fall relative to similar mean values of TL for spring, summer, and late summer/early fall. This study increased our understanding of yellow-phase American eels by demonstrating the non-random nature of their upstream migration.

  11. Evidence of Asian carp spawning upstream of a key choke point in the Mississippi River

    USGS Publications Warehouse

    Larson, James H.; Knights, Brent C.; McCalla, S. Grace; Monroe, Emy; Tuttle-Lau, Maren T.; Chapman, Duane C.; George, Amy E.; Vallazza, Jon; Amberg, Jon J.

    2017-01-01

    Bighead Carp Hypophthalmichthys nobilis, Silver Carp H. molitrix, and Grass Carp Ctenopharyngodon idella(collectively termed “Asian carp”) were introduced into North America during the 1960s and 1970s and have become established in the lower Mississippi River basin. Previously published evidence for spawning of these species in the upper Mississippi River has been limited to an area just downstream of Dam 22 (near Saverton, Missouri). In 2013 and 2014, we sampled ichthyoplankton at 18 locations in the upper Mississippi River main stem from Dam 9 through Dam 19 and in four tributaries of the Mississippi River (Des Moines, Skunk, Iowa, and Wisconsin rivers). We identified eggs and larvae by using morphological techniques and then used genetic tools to confirm species identity. The spawning events we observed often included more than one species of Asian carp and in a few cases included eggs that must have been derived from more than one upstream spawning event. The upstream extent of genetically confirmed Grass Carp ichthyoplankton was the Wisconsin River, while Bighead Carp and Silver Carp ichthyoplankton were observed in Pool 16. In all these cases, ichthyoplankton likely drifted downstream for several hours prior to collection. Higher water velocities (and, to a lesser extent, higher temperatures) were associated with an increased likelihood of observing eggs or larvae, although the temperature range we encountered was mostly above 17°C. Several major spawning events were detected in 2013, but no major spawning events were observed in 2014. The area between Dam 15 and Dam 19 appears to be the upstream edge of spawning activity for both Silver Carp and Bighead Carp, suggesting that this area could be a focal point for management efforts designed to limit further upstream movement of these species..

  12. Upstream open reading frames regulate the expression of the nuclear Wnt13 isoforms

    SciTech Connect

    Tang Tao; Rector, Kyle; Barnett, Corey D.

    2008-02-22

    Wnt proteins control cell survival and cell fate during development. Although Wnt expression is tightly regulated in a spatio-temporal manner, the mechanisms involved both at the transcriptional and translational levels are poorly defined. We have identified a downstream translation initiation codon, AUG(+74), in Wnt13B and Wnt13C mRNAs responsible for the expression of Wnt13 nuclear forms. In this report, we demonstrate that the expression of the nuclear Wnt13C form is translationally regulated in response to stress and apoptosis. Though the 5'-leaders of both Wnt13C and Wnt13B mRNAs have an inhibitory effect on translation, they did not display an internal ribosome entrymore » site activity as demonstrated by dicistronic reporter assays. However, mutations or deletions of the upstream AUG(-99) and AUG(+1) initiation codons abrogate these translation inhibitory effects, demonstrating that Wnt13C expression is controlled by upstream open reading frames. Since long 5'-untranslated region with short upstream open reading frames characterize other Wnt transcripts, our present data on the translational control of Wnt13 expression open the way to further studies on the translation control of Wnt expression as a modulator of their subcellular localization and activity.« less

  13. Experimental study to control the upstream migration of invasive alien fish species by submerged weir

    NASA Astrophysics Data System (ADS)

    Sakuma, Masami; Kunimatsu, Fumihiro; Tsuchiya, Taku; Kawamura, Makiko; Fujita, Hiroshi

    Largemouth bass and Bluegill, major invasive alien fish species in Japan, have been extending their habitat ranges over not only Lake Biwa and the lagoons but also surrounding waters connected to them through small rivers and canals. Their increasing number is bringing about the reduction in the number of native fish species. To prevent the spread of these alien species through small rivers and canals during breeding season of the native fish (crucian carp), this study experimentally examined the effect of a submerged weir on controlling upstream migration of the alien species and the native fish. As a result of the experiment, the ratio of the alien species migrating upstream decreased as the weir height rose, whereas the ratio did not show the same trend in the case of the native fish. The ratio of the alien species also decreased as the overflow velocity over the weir rose. On the other hand, the ratio of the native fish increased as the overflow velocity rose up to 1.0m/s and decreased thereafter. These results suggest that the submerged weir may control upstream migration of the alien species to surrounding waters through small rivers and canals without interfering with the reproductive migration of the native fish.

  14. Spatial and temporal patterns of micropollutants upstream and downstream of 24 WWTPs across Switzerland

    NASA Astrophysics Data System (ADS)

    Spycher, Barbara; Deuber, Fabian; Kistler, David; Burdon, Frank; Reyes, Marta; Alder, Alfredo C.; Joss, Adriano; Eggen, Rik; Singer, Heinz; Stamm, Christian

    2015-04-01

    Treated wastewater is an important source of micropollutants in many streams. These chemicals consist of very diverse set of compounds that may vary in space and time. In order to improve our understanding of such spatio-temporal patterns of micropollutants in surface waters, we compared upstream and downstream locations at 24 sites across the Swiss Plateau and Jura (12 sites in the 2013 campaign, 12 sites during the 2014 campaign). Each site represents the most upstream treatment plant in the corresponding catchment. This survey is part of the interdisciplinary, Eawag-wide research project EcoImpact that aims at elucidating the ecological effects of micropollutants on stream ecosystems. In 2013, a broad analytical screening was applied to samples collected during winter (January) and summer conditions (June). Based in these results, the bi-monthly samples obtained in 2014 were analysed for a set of about 60 selected organic micropollutants and 10 heavy metals. The screening results demonstrate that generally pharmaceuticals, artificial sweeteners and corrosion inhibitors make up the largest part of the organic micropollutants. Pesticides including biocides and plant protection products are also regularly found but at lower concentrations. This presentation will analyse the variability of the micropollutant patterns across the different sites and how upstream conditions and the wastewater composition changes with season.

  15. Environmental correlates of upstream migration of yellow-phase American eels in the Potomac River drainage

    USGS Publications Warehouse

    Welsh, Stuart A.; Heather L. Liller,

    2013-01-01

    Assessing the relationships between upstream migration and environmental variables is important to understanding the ecology of yellow-phase American Eels Anguilla rostrata. During an American Eel migration study within the lower Shenandoah River (Potomac River drainage), we counted and measured American Eels at the Millville Dam eel ladder for three periods: 14 May–23 July 2004, 7–30 September 2004, and 1 June–31 July 2005. Using generalized estimating equations, we modeled each time series of daily American Eel counts by fitting time-varying environmental covariates of lunar illumination (LI), river discharge (RD), and water temperature (WT), including 1-d and 2-d lags of each covariate. Information-theoretic approaches were used for model selection and inference. A total of 4,847 American Eels (19–74 cm total length) used the ladder during the three periods, including 2,622 individuals during a 2-d span following a hurricane-induced peak in river discharge. Additive-effects models of RD + WT, a 2-d lag of LI + RD, and LI + RD were supported for the three periods, respectively. Parameter estimates were positive for river discharge for each time period, negative for lunar illumination for two periods and positive for water temperature during one period. Additive-effects models supported synergistic influences of environmental variables on the upstream migration of yellow-phase American Eels, although river discharge was consistently supported as an influential correlate of upstream migration.

  16. Effect of wakes from moving upstream rods on boundary layer separation from a high lift airfoil

    NASA Astrophysics Data System (ADS)

    Volino, Ralph J.

    2011-11-01

    Highly loaded airfoils in turbines allow power generation using fewer airfoils. High loading, however, can cause boundary layer separation, resulting in reduced lift and increased aerodynamic loss. Separation is affected by the interaction between rotating blades and stationary vanes. Wakes from upstream vanes periodically impinge on downstream blades, and can reduce separation. The wakes include elevated turbulence, which can induce transition, and a velocity deficit, which results in an impinging flow on the blade surface known as a ``negative jet.'' In the present study, flow through a linear cascade of very high lift airfoils is studied experimentally. Wakes are produced with moving rods which cut through the flow upstream of the airfoils, simulating the effect of upstream vanes. Pressure and velocity fields are documented. Wake spacing and velocity are varied. At low Reynolds numbers without wakes, the boundary layer separates and does not reattach. At high wake passing frequencies separation is largely suppressed. At lower frequencies, ensemble averaged velocity results show intermittent separation and reattachment during the wake passing cycle. Supported by NASA.

  17. The economic benefits of vegetation in the upstream area of Ciliwung watershed

    NASA Astrophysics Data System (ADS)

    Saridewi, T. R.; Nazaruddin

    2018-04-01

    Ciliwung watershed has strategic values since its entire downstream area is located in the Special Administrative Region of Jakarta (DKI Jakarta), the capital of Indonesia. This causes forest and farmland areas are converted into open areas or built-up areas. The existence of these areas provides enormous environmental and economic benefits. Economic benefit values are very important to be considered in developing a policy development plan, but they have not been calculated yet. This study aims to determine the economic benefits provided by trees and other vegetation anddevelops a development policy that takes into account simultaneously ecological and economic aspects. The study is conducted in the upstream Ciliwung watershed, by using land cover patterns in 1989, 2000, 2010 and 2014, and employs GIS and CITY green analysis. The results show that conversion of forest and farmland areas reduces the ability of Ciliwung upstream watershed to store water. Therefore, its ability to reduce the flow of surface has been decreased. This creates a decrease in the cost savings of annual stormwater, from US 15,175,721 in 1989 to US 13,317,469 in 2014. The Environmental Services Payment Policy (PES) for upstream community groups managing the watershed has been considered as a fairly effective policy.

  18. Upstream watershed condition predicts rural children's health across 35 developing countries.

    PubMed

    Herrera, Diego; Ellis, Alicia; Fisher, Brendan; Golden, Christopher D; Johnson, Kiersten; Mulligan, Mark; Pfaff, Alexander; Treuer, Timothy; Ricketts, Taylor H

    2017-10-09

    Diarrheal disease (DD) due to contaminated water is a major cause of child mortality globally. Forests and wetlands can provide ecosystem services that help maintain water quality. To understand the connections between land cover and childhood DD, we compiled a database of 293,362 children in 35 countries with information on health, socioeconomic factors, climate, and watershed condition. Using hierarchical models, here we find that higher upstream tree cover is associated with lower probability of DD downstream. This effect is significant for rural households but not for urban households, suggesting differing dependence on watershed conditions. In rural areas, the effect of a 30% increase in upstream tree cover is similar to the effect of improved sanitation, but smaller than the effect of improved water source, wealth or education. We conclude that maintaining natural capital within watersheds can be an important public health investment, especially for populations with low levels of built capital.Globally diarrheal disease through contaminated water sources is a major cause of child mortality. Here, the authors compile a database of 293,362 children in 35 countries and find that upstream tree cover is linked to a lower probability of diarrheal disease and that increasing tree cover may lower mortality.

  19. Simulating the effects of upstream turbulence on dispersion around a building

    SciTech Connect

    Zhang, Y.Q.; Arya, S.P.S.; Huber, A.H.

    The effects of high turbulence versus no turbulence in a sheared boundary-layer flow approaching a building are being investigated by a turbulent kinetic energy/dissipation model (TEMPEST). The effects on both the mean flow and the concentration field around a cubical building are presented. The numerical simulations demonstrate significant effects due to the differences in the incident flow. The addition of upstream turbulence results in a reduced size of the cavity directly behind the building. The velocity deficits in the wake strongly depend on the upstream turbulence intensities. The accuracy of numerical simulations is verified by comparing the predicted mean flowmore » and concentration fields with the wind tunnel measurements of Castro and Robins (1977) and Robins and Castro (1977, 1975). Comparing the results with experimental data, the authors show that the TEMPEST model can reasonably simulate the mean flow. The numerical simulations of the concentration fields due to a source on the roof-top of the building are presented. Both the value and the position of the maximum ground-level concentration are changed dramatically due to the effects of the upstream level of turblence.« less

  20. Delimiting regulatory sequences of the Drosophila melanogaster Ddc gene.

    PubMed Central

    Hirsh, J; Morgan, B A; Scholnick, S B

    1986-01-01

    We delimited sequences necessary for in vivo expression of the Drosophila melanogaster dopa decarboxylase gene Ddc. The expression of in vitro-altered genes was assayed following germ line integration via P-element vectors. Sequences between -209 and -24 were necessary for normally regulated expression, although genes lacking these sequences could be expressed at 10 to 50% of wild-type levels at specific developmental times. These genes showed components of normal developmental expression, which suggests that they retain some regulatory elements. All Ddc genes lacking the normal immediate 5'-flanking sequences were grossly deficient in larval central nervous system expression. Thus, this upstream region must contain at least one element necessary for this expression. A mutated Ddc gene without a normal TATA boxlike sequence used the normal RNA start points, indicating that this sequences is not required for start point specificity. Images PMID:3099170

  1. An upstream open reading frame represses expression of Lc, a member of the R/B family of maize transcriptional activators

    SciTech Connect

    Damiani, R.D. Jr.; Wessler, S.R.

    1993-09-01

    The R/B genes of maize encode a family of basic helix-loop-helix proteins that determine where and when the anthocyanin-pigment pathway will be expressed in the plant. Previous studies showed that allelic diversity among family members reflects differences in gene expression, specifically in transcription initiation. The authors present evidence that the R gene Lc is under translational control. They demonstrate that the 235-nt transcript leader of Lc represses expression 25- to 30-fold in an in vivo assay. Repression is mediated by the presence in cis of a 38-codon upstream open reading frame. Furthermore, the coding capacity of the upstream open readingmore » frame influences the magnitude of repression. It is proposed that translational control does not contribute to tissue specificity but prevents overexpression of the Lc protein. The diversity of promoter and 5' untranslated leader sequences among the R/B genes provides an opportunity to study the coevolution of transcriptional and translational mechanisms of gene regulation. 36 refs., 5 figs.« less

  2. Expression of Human Hemojuvelin (HJV) Is Tightly Regulated by Two Upstream Open Reading Frames in HJV mRNA That Respond to Iron Overload in Hepatic Cells

    PubMed Central

    Onofre, Cláudia; Tomé, Filipa; Barbosa, Cristina; Silva, Ana Luísa

    2015-01-01

    The gene encoding human hemojuvelin (HJV) is one of the genes that, when mutated, can cause juvenile hemochromatosis, an early-onset inherited disorder associated with iron overload. The 5′ untranslated region of the human HJV mRNA has two upstream open reading frames (uORFs), with 28 and 19 codons formed by two upstream AUGs (uAUGs) sharing the same in-frame stop codon. Here we show that these uORFs decrease the translational efficiency of the downstream main ORF in HeLa and HepG2 cells. Indeed, ribosomal access to the main AUG is conditioned by the strong uAUG context, which results in the first uORF being translated most frequently. The reach of the main ORF is then achieved by ribosomes that resume scanning after uORF translation. Furthermore, the amino acid sequences of the uORF-encoded peptides also reinforce the translational repression of the main ORF. Interestingly, when iron levels increase, translational repression is relieved specifically in hepatic cells. The upregulation of protein levels occurs along with phosphorylation of the eukaryotic initiation factor 2α. Nevertheless, our results support a model in which the increasing recognition of the main AUG is mediated by a tissue-specific factor that promotes uORF bypass. These results support a tight HJV translational regulation involved in iron homeostasis. PMID:25666510

  3. High cancer-specific expression of mesothelin (MSLN) is attributable to an upstream enhancer containing a transcription enhancer factor dependent MCAT motif.

    PubMed

    Hucl, Tomas; Brody, Jonathan R; Gallmeier, Eike; Iacobuzio-Donahue, Christine A; Farrance, Iain K; Kern, Scott E

    2007-10-01

    Identification of genes with cancer-specific overexpression offers the potential to efficiently discover cancer-specific activities in an unbiased manner. We apply this paradigm to study mesothelin (MSLN) overexpression, a nearly ubiquitous, diagnostically and therapeutically useful characteristic of pancreatic cancer. We identified an 18-bp upstream enhancer, termed CanScript, strongly activating transcription from an otherwise weak tissue-nonspecific promoter and operating selectively in cells having aberrantly elevated cancer-specific MSLN transcription. Introducing mutations into CanScript showed two functionally distinct sites: an Sp1-like site and an MCAT element. Gel retardation and chromatin immunoprecipitation assays showed the MCAT element to be bound by transcription enhancer factor (TEF)-1 (TEAD1) in vitro and in vivo. The presence of TEF-1 was required for MSLN protein overexpression as determined by TEF-1 knockdown experiments. The cancer specificity seemed to be provided by a putative limiting cofactor of TEF-1 that could be outcompeted by exogenous TEF-1 only in a MSLN-overexpressing cell line. A CanScript concatemer offered enhanced activity. These results identify a TEF family member as a major regulator of MSLN overexpression, a fundamental characteristic of pancreatic and other cancers, perhaps due to an upstream and highly frequent aberrant cellular activity. The CanScript sequence represents a modular element for cancer-specific targeting, potentially suitable for nearly a third of human malignancies.

  4. A Rich Client-Server Based Framework for Convenient Security and Management of Mobile Applications

    NASA Astrophysics Data System (ADS)

    Badan, Stephen; Probst, Julien; Jaton, Markus; Vionnet, Damien; Wagen, Jean-Frédéric; Litzistorf, Gérald

    Contact lists, Emails, SMS or custom applications on a professional smartphone could hold very confidential or sensitive information. What could happen in case of theft or accidental loss of such devices? Such events could be detected by the separation between the smartphone and a Bluetooth companion device. This event should typically block the applications and delete personal and sensitive data. Here, a solution is proposed based on a secured framework application running on the mobile phone as a rich client connected to a security server. The framework offers strong and customizable authentication and secured connectivity. A security server manages all security issues. User applications are then loaded via the framework. User data can be secured, synchronized, pushed or pulled via the framework. This contribution proposes a convenient although secured environment based on a client-server architecture using external authentications. Several features of the proposed system are exposed and a practical demonstrator is described.

  5. Flowers from Kalanchoe pinnata are a rich source of T cell-suppressive flavonoids.

    PubMed

    Coutinho, Marcela A S; Muzitano, Michelle F; Cruz, Elaine A; Bergonzi, Maria C; Kaiser, Carlos R; Tinoco, Luzineide W; Bilia, Anna R; Vincieric, Franco F; Rossi-Bergmann, Bartira; Costa, Sônia S

    2012-02-01

    The chemical composition and immunosuppressive potential of the flowers from Kalanchoe pinnata (Crassulaceae) were investigated. We found that the aqueous flower extract was more active than the leaf extract in inhibiting murine T cell mitogenesis in vitro. Flavonoids isolated from the flower extract were identified and quantitated based on NMR and HPLC-DAD-MS analysis, respectively. Along with quercetin, four quercetin glycosyl conjugates were obtained, including quercetin 3-O-beta-D-glucuronopyranoside and quercetin 3-O-beta-D-glucopyranoside, which are described for the first time in K. pinnata. All flavonoids inhibited murine T cell mitogenesis and IL-2 and IL-4 production without cell toxicity. This is the first report on the pharmacological activity of flowers of a Kalanchoe species, which are not used for curative purposes. Our findings show that K. pinnata flowers are a rich source of T-suppressive flavonoids that may be therapeutically useful against inflammatory diseases.

  6. A Tourist-like MITE insertion in the upstream region of the BnFLC.A10 gene is associated with vernalization requirement in rapeseed (Brassica napus L.)

    PubMed Central

    2012-01-01

    Background Rapeseed (Brassica napus L.) has spring and winter genotypes adapted to different growing seasons. Winter genotypes do not flower before the onset of winter, thus leading to a longer vegetative growth period that promotes the accumulation and allocation of more resources to seed production. The development of winter genotypes enabled the rapeseed to spread rapidly from southern to northern Europe and other temperate regions of the world. The molecular basis underlying the evolutionary transition from spring- to winter- type rapeseed is not known, however, and needs to be elucidated. Results We fine-mapped the spring environment specific quantitative trait locus (QTL) for flowering time, qFT10-4,in a doubled haploid (DH) mapping population of rapeseed derived from a cross between Tapidor (winter-type) and Ningyou7 (semi-winter) and delimited the qFT10-4 to an 80-kb region on chromosome A10 of B. napus. The BnFLC.A10 gene, an ortholog of FLOWERING LOCUS C (FLC) in Arabidopsis, was cloned from the QTL. We identified 12 polymorphic sites between BnFLC.A10 parental alleles of the TN-DH population in the upstream region and in intron 1. Expression of both BnFLC.A10 alleles decreased during vernalization, but decreased more slowly in the winter parent Tapidor. Haplotyping and association analysis showed that one of the polymorphic sites upstream of BnFLC.A10 is strongly associated with the vernalization requirement of rapeseed (r2 = 0.93, χ2 = 0.50). This polymorphic site is derived from a Tourist-like miniature inverted-repeat transposable element (MITE) insertion/deletion in the upstream region of BnFLC.A10. The MITE sequence was not present in the BnFLC.A10 gene in spring-type rapeseed, nor in ancestral ‘A’ genome species B. rapa genotypes. Our results suggest that the insertion may have occurred in winter rapeseed after B. napus speciation. Conclusions Our findings strongly suggest that (i) BnFLC.A10 is the gene underlying qFT10-4, the QTL for

  7. A Tourist-like MITE insertion in the upstream region of the BnFLC.A10 gene is associated with vernalization requirement in rapeseed (Brassica napus L.).

    PubMed

    Hou, Jinna; Long, Yan; Raman, Harsh; Zou, Xiaoxiao; Wang, Jing; Dai, Shutao; Xiao, Qinqin; Li, Cong; Fan, Longjiang; Liu, Bin; Meng, Jinling

    2012-12-15

    Rapeseed (Brassica napus L.) has spring and winter genotypes adapted to different growing seasons. Winter genotypes do not flower before the onset of winter, thus leading to a longer vegetative growth period that promotes the accumulation and allocation of more resources to seed production. The development of winter genotypes enabled the rapeseed to spread rapidly from southern to northern Europe and other temperate regions of the world. The molecular basis underlying the evolutionary transition from spring- to winter- type rapeseed is not known, however, and needs to be elucidated. We fine-mapped the spring environment specific quantitative trait locus (QTL) for flowering time, qFT10-4,in a doubled haploid (DH) mapping population of rapeseed derived from a cross between Tapidor (winter-type) and Ningyou7 (semi-winter) and delimited the qFT10-4 to an 80-kb region on chromosome A10 of B. napus. The BnFLC.A10 gene, an ortholog of FLOWERING LOCUS C (FLC) in Arabidopsis, was cloned from the QTL. We identified 12 polymorphic sites between BnFLC.A10 parental alleles of the TN-DH population in the upstream region and in intron 1. Expression of both BnFLC.A10 alleles decreased during vernalization, but decreased more slowly in the winter parent Tapidor. Haplotyping and association analysis showed that one of the polymorphic sites upstream of BnFLC.A10 is strongly associated with the vernalization requirement of rapeseed (r2 = 0.93, χ2 = 0.50). This polymorphic site is derived from a Tourist-like miniature inverted-repeat transposable element (MITE) insertion/deletion in the upstream region of BnFLC.A10. The MITE sequence was not present in the BnFLC.A10 gene in spring-type rapeseed, nor in ancestral 'A' genome species B. rapa genotypes. Our results suggest that the insertion may have occurred in winter rapeseed after B. napus speciation. Our findings strongly suggest that (i) BnFLC.A10 is the gene underlying qFT10-4, the QTL for phenotypic diversity of flowering time in

  8. The nucleotide sequence of the putative transcription initiation site of a cloned ribosomal RNA gene of the mouse.

    PubMed Central

    Urano, Y; Kominami, R; Mishima, Y; Muramatsu, M

    1980-01-01

    Approximately one kilobase pairs surrounding and upstream the transcription initiation site of a cloned ribosomal DNA (rDNA) of the mouse were sequenced. The putative transcription initiation site was determined by two independent methods: one nuclease S1 protection and the other reverse transcriptase elongation mapping using isolated 45S ribosomal RNA precursor (45S RNA) and appropriate restriction fragments of rDNA. Both methods gave an identical result; 45S RNA had a structure starting from ACTCTTAG---. Characteristically, mouse rDNA had many T clusters (greater than or equal to 5) upstream the initiation site, the longest being 21 consecutive T's. A pentadecanucleotide, TGCCTCCCGAGTGCA, appeared twice within 260 nucleotides upstream the putative initiation site. No such characteristic sequences were found downstream this site. Little similarity was found in the upstream of the transcription initiation site between the mouse, Xenopus laevis and Saccharomyces cerevisiae rDNA. Images PMID:6162156

  9. How downstream sub-basins depend on upstream inflows to avoid scarcity: typology and global analysis of transboundary rivers

    NASA Astrophysics Data System (ADS)

    Munia, Hafsa Ahmed; Guillaume, Joseph H. A.; Mirumachi, Naho; Wada, Yoshihide; Kummu, Matti

    2018-05-01

    Countries sharing river basins are often dependent upon water originating outside their boundaries; meaning that without that upstream water, water scarcity may occur with flow-on implications for water use and management. We develop a formalisation of this concept drawing on ideas about the transition between regimes from resilience literature, using water stress and water shortage as indicators of water scarcity. In our analytical framework, dependency occurs if water from upstream is needed to avoid scarcity. This can be diagnosed by comparing different types of water availability on which a sub-basin relies, in particular local runoff and upstream inflows. At the same time, possible upstream water withdrawals reduce available water downstream, influencing the latter water availability. By developing a framework of scarcity and dependency, we contribute to the understanding of transitions between system regimes. We apply our analytical framework to global transboundary river basins at the scale of sub-basin areas (SBAs). Our results show that 1175 million people live under water stress (42 % of the total transboundary population). Surprisingly, the majority (1150 million) of these currently suffer from stress only due to their own excessive water use and possible water from upstream does not have impact on the stress status - i.e. they are not yet dependent on upstream water to avoid stress - but could still impact on the intensity of the stress. At the same time, 386 million people (14 %) live in SBAs that can avoid stress owing to available water from upstream and have thus upstream dependency. In the case of water shortage, 306 million people (11 %) live in SBAs dependent on upstream water to avoid possible shortage. The identification of transitions between system regimes sheds light on how SBAs may be affected in the future, potentially contributing to further refined analysis of inter- and intrabasin hydro-political power relations and strategic planning

  10. Improved efficiency in amplification of Escherichia coli o-antigen gene clusters using genome-wide sequence comparison

    USDA-ARS?s Scientific Manuscript database

    Background: In many bacteria including E. coli, genes encoding O-antigens are clustered in the chromosome, with a 39-bp JUMPstart sequence and gnd gene located upstream and downstream of the cluster, respectively. For determining the DNA sequence of the E. coli O-antigen gene cluster, one set of P...

  11. Self-formed meandering river created in the laboratory using an upstream migrating boundary

    NASA Astrophysics Data System (ADS)

    van Dijk, W. M.; van de Lageweg, W. I.; Kleinhans, M. G.

    2010-12-01

    Braided rivers are relatively easily formed in the laboratory, whereas self-formed meandering rivers in the lab have proven very difficult to form, indicating a lack of understanding of the necessary and sufficient conditions for meandering. Our objective is to create self-formed dynamic meandering rivers and floodplains in a laboratory. Early experiments attempted to initiate meandering with upstream inflow at a fixed angle different from the general flow direction. The resulting bends were fixed at one position, which is not the dynamic meandering observed in nature. Another important condition for meandering is to have banks stronger than the non-cohesive bed sediment, which has been attained by growing vegetation. Furthermore, finer or light-weight sediment has been used to let chute channels fill up where otherwise multi-thread channels would have evolved, which is braiding. Yet the fixed-angle inflow kept meander migration and channel belt width and complexity limited. We accomplished dynamic meandering in the laboratory by using an upstream migrating boundary, which simulates a meander migrating into the flume. Our experiments were conducted in a circulated flume of 11x6 meter, with a constant discharge and sediment feed consisting of a sediment mixture ranging from silt to fine gravel (Kleinhans et al., 2010, this conference). The downstream boundary is a lake into which the river built a branched fan delta (Van de Lageweg et al., 2010, this conference). The morphology was recorded by high-resolution (0.5 mm) line-laser scanning and digital Single Lens Reflex (SLR) camera used for channel-floodplain segmentation and particle size estimation, at an interval of 8 hours. Furthermore a large number of smaller-scale auxiliary experiments were conducted to explore meandering tendency in a large range of parameters. Initial alternate ‘forced’ bars were formed at fixed positions with low sinuosity when the upstream boundary was at one fixed position. Migration

  12. Effects of channel constriction on upstream steering of flow around Locke Island, Columbia River, Washington

    NASA Astrophysics Data System (ADS)

    Loy, G. E.; Furbish, D. J.; Covey, A.

    2010-12-01

    Landsliding of the White Bluffs along the Columbia River in Washington State has constricted the width of the river on one side of Locke Island, a two-kilometer long island positioned in the middle of the channel. Associated changes in flow are thought to be causing relatively rapid erosion of Locke Island on the constricted side. This island is of cultural significance to Native American tribes of south-central Washington, so there are social as well as scientific reasons to understand how the alteration of stream channel processes resulting from the landsliding might be influencing observed erosion rates. Simple hydrodynamic calculations suggest that the constriction on one side of the island creates an upstream backwater effect. As a consequence a cross-stream pressure gradient upstream of the island results in steering of flow around the island into the unobstructed thread. This diversion of water decreases the discharge through the constriction. Therefore, flow velocities within the constriction are not necessarily expected to be higher than those in the unobstructed thread, contrary to initial reports suggesting that higher velocities within the constriction are the main cause of erosion. We set up streamtable experiments with lapse rate imaging to illustrate the backwater effects of the channel constriction and the associated cross-stream steering of flow around a model island. Our experiments are scaled by channel roughness and slope rather than geometrically, as the main focus is to understand the mechanical behavior of flow in this type of island-landslide system. In addition, we studied the stream velocities and flow steering as well as the magnitude of the backwater effect in both the constricted and unobstructed channels using tracer particles in the time-lapse images. These experimental data are compared with calculated upstream backwater distances determined from the known water-surface slope, flow depth, total discharge, and bed roughness

  13. An in situ Comparison of Electron Acceleration at Collisionless Shocks under Differing Upstream Magnetic Field Orientations

    SciTech Connect

    Masters, A.; Dougherty, M. K.; Sulaiman, A. H.

    A leading explanation for the origin of Galactic cosmic rays is acceleration at high-Mach number shock waves in the collisionless plasma surrounding young supernova remnants. Evidence for this is provided by multi-wavelength non-thermal emission thought to be associated with ultrarelativistic electrons at these shocks. However, the dependence of the electron acceleration process on the orientation of the upstream magnetic field with respect to the local normal to the shock front (quasi-parallel/quasi-perpendicular) is debated. Cassini spacecraft observations at Saturn’s bow shock have revealed examples of electron acceleration under quasi-perpendicular conditions, and the first in situ evidence of electron acceleration at amore » quasi-parallel shock. Here we use Cassini data to make the first comparison between energy spectra of locally accelerated electrons under these differing upstream magnetic field regimes. We present data taken during a quasi-perpendicular shock crossing on 2008 March 8 and during a quasi-parallel shock crossing on 2007 February 3, highlighting that both were associated with electron acceleration to at least MeV energies. The magnetic signature of the quasi-perpendicular crossing has a relatively sharp upstream–downstream transition, and energetic electrons were detected close to the transition and immediately downstream. The magnetic transition at the quasi-parallel crossing is less clear, energetic electrons were encountered upstream and downstream, and the electron energy spectrum is harder above ∼100 keV. We discuss whether the acceleration is consistent with diffusive shock acceleration theory in each case, and suggest that the quasi-parallel spectral break is due to an energy-dependent interaction between the electrons and short, large-amplitude magnetic structures.« less

  14. Beyond police crisis intervention: moving "upstream" to manage cases and places of behavioral health vulnerability.

    PubMed

    Wood, Jennifer D; Beierschmitt, Laura

    2014-01-01

    Law enforcement officers continue to serve on the front lines as mental health interventionists, and as such have been subject to a wave of "first generation" reform designed to enhance their crisis response capabilities. Yet, this focus on crisis intervention has not answered recent calls to move "upstream" and bolster early intervention in the name of long-term recovery. This paper reports on findings from an action research project in Philadelphia aimed at exploring opportunities for enhanced upstream engagement. Study methods include spatial analyses of police mental health transportations from an eight year period (2004-2011) and qualitative data from twenty-three "framing conversations" with partners and other stakeholders, seven focus groups with police and outreach workers, five key informant interviews as well as document reviews of the service delivery system in Philadelphia. Recommendations include the need to move beyond a focus on what police can do to a wider conception of city agencies and business stakeholders who can influence vulnerable people and vulnerable spaces of the city. We argue for the need to develop shared principles and rules of engagement that clarify roles and stipulate how best to enlist city resources in a range of circumstances. Since issues of mental health, substance use and disorder are so tightly coupled, we stress the importance of establishing a data-driven approach to crime and disorder reduction in areas of the city we term "hotspots of vulnerability". In line with a recovery philosophy, such an approach should reduce opportunities for anti-social behavior among the "dually labeled" in ways consistent with "procedural justice". Furthermore, crime and disorder data flowing from police and security to behavioral health analysts could contribute to a more focused case management of "repeat utilizers" across the two systems. Our central argument is that a twin emphasis on "case management" and "place management" may provide

  15. Upstream effects of dams on alluvial channels: state-of-the-art and future challenges

    NASA Astrophysics Data System (ADS)

    Liro, Maciej

    2017-04-01

    More than 50,000 large dams (with the height above 15 m) operate all over the world and, thus, they significantly disturb water and sediment transport in river systems. These disturbances are recognized as one of the most important factors shaping river morphology in the Anthropocene. Downstream effects of dams have been well documented in numerous case studies and supported by predictions from existing models. In contrast, little is known on the upstream effects of dams on alluvial channels. This review highlights the lack of studies on sedimentological, hydromorphological and biogeomorphological adjustments of alluvial rivers in the base-level raised zones of backwater upstream of dam reservoirs where water level fluctuations occur. Up to date, it has been documented that backwater effects may facilitate fine and coarse sediment deposition, increase groundwater level, provide higher and more frequent channel and floodplain inundation and lead to significant morphological changes. But there have been no studies quantifying short- and long-term consequences of these disturbances for the hydromorphological and biogeomorphological feedbacks that control development of alluvial channels. Some recent studies carried out on gravel-bed and fine-grained bed rivers show that the above mentioned disturbances facilitate vegetation expansion on exposed channel sediments and floodplain influencing river morphology, which suggests that backwater area of alluvial rivers may be treated as the hotspot of bio-geomorphological changes in a fluvial system. To set the stage for future research on upstream effects of dams, this work presents the existing state-of-art and proposes some hypotheses which may be tested in future studies. This study was carried out within the scope of the Research Project 2015/19/N/ST10/01526 financed by the National Science Centre of Poland

  16. Saturn's Magnetosphere and Properties of Upstream Flow at Titan: Preliminary Results

    NASA Technical Reports Server (NTRS)

    Sittler, E. C., Jr.; Hartle, R. E.; Cooper, J. F.; Lipatov, A.; Bertucci, C.; Coates, A. J.; Arridge, C.; Szego, K.; Shappirio, M.; Simipson, D. G.; hide

    2009-01-01

    Using Cassini Plasma Spectrometer (CAPS) Ion Mass Spectrometer (IMS) measurements, we present the ion fluid properties and its ion composition of the upstream flow for Titan's interaction with Saturn's magnetosphere. A 3D ion moments algorithm is used which is essentially model independent with only requirement is that ion flow is within the CAPS IMS 2(pi) steradian field-of-view (FOV) and that the ion 'velocity distribution function (VDF) be gyrotropic. These results cover the period from TA flyby (2004 day 300) to T22 flyby (2006 363). Cassini's in situ measurements of Saturn's magnetic field show it is stretched out into a magnetodisc configuration for Saturn Local Times (SLT) centered about midnight local time. Under those circumstances the field is confined near the equatorial plane with Titan either above or below the magnetosphere current sheet. Similar to Jupiter's outer magnetosphere where a magnetodisc configuration applies, one expects the heavy ions within Saturn's outer magnetosphere to be confined within a few degrees of the current sheet while at higher magnetic latitudes protons should dominate. We show that when Cassini is between dusk-midnight-dawn local time and spacecraft is not within the current sheet that light ions (H, 142) tend to dominate the ion composition for the upstream flow. If true, one may expect the interaction between Saturn's magnetosphere, locally devoid of heavy ions and Titan's upper atmosphere and exosphere to be significantly different from that for Voyager 1, TA and TB when heavy ions were present in the upstream flow. We also present observational evidence for Saturn's magnetosphere interaction with Titan's extended H and H2 corona which can extend approx. 1 Rs from Titan.

  17. Osteoblast-specific transcription factor Osterix (Osx) is an upstream regulator of Satb2 during bone formation.

    PubMed

    Tang, Wanjin; Li, Yang; Osimiri, Lindsey; Zhang, Chi

    2011-09-23

    Osterix (Osx) is an osteoblast-specific transcription factor essential for osteoblast differentiation and bone formation. Osx knock-out mice lack bone completely. Satb2 is critical for osteoblast differentiation as a special AT-rich binding transcription factor. It is not known how Satb2 is transcriptionally regulated during bone formation. In this study, quantitative real-time RT-PCR results demonstrated that Satb2 was down-regulated in Osx-null calvaria. In stable C2C12 mesenchymal cells using the tetracycline (Tet)-Off system, overexpression of Osx stimulated Satb2 expression. Moreover, inhibition of Osx by siRNA led to repression of Satb2 expression in osteoblasts. These results suggest that Osx controls Satb2 expression. Transient transfection assay showed that Osx activated 1kb Satb2 promoter reporter activity in a dose-dependent manner. To define the region of Satb2 promoter responsive to Osx activation, a series of deletion mutants of Satb2 constructs were made, and the minimal region was narrowed down to the proximal 130 bp of the Satb2 promoter. Further point mutation studies found that two GC-rich region mutations disrupted the Satb2 130bp promoter activation by Osx, suggesting that these GC-rich binding sites were responsible for Satb2 activation by Osx. Gel shift assay showed that Osx bound to the Satb2 promoter sequence directly. ChIP assays indicated that endogenous Osx associated with the native Satb2 promoter in osteoblasts. Importantly, Satb2 siRNA significantly inhibited Osx-induced osteoblast marker gene expressions. Taken together, our findings indicate that Osx is an upstream regulator of Satb2 during bone formation. This reveals a new additional link of the transcriptional regulation mechanism that Osx controls bone formation.

  18. Expression of chicken ovalbumin upstream promoter-transcription factor I (COUP-TFI) in bladder transitional cell carcinoma.

    PubMed

    Ham, Won Sik; Lee, Joo Hyoung; Yu, Ho Song; Choi, Young Deuk

    2008-10-01

    An analysis of differentially expressed genes (DEGs) between bladder transitional cell carcinoma (TCC) and the surrounding urothelium to help identify what lies behind the mechanism of multifocal tumor development has not yet been performed. We sought to find a new DEG related to the development of bladder TCC. Thirty-nine bladder TCC tissues paired with normal-appearing urothelium tissues obtained from the same patient were used as subjects. Initially, we compared the messenger RNA (mRNA) profiles between normal-appearing urothelium and TCC tissue of 1 patient by using annealing control primer (ACP)-based GeneFishing polymerase chain reaction (PCR) and selective amplification of family members (SAFM) PCR to identify potential DEGs. To validate the results of the ACP data, reverse transcriptase-polymerase chain reaction (RT-PCR) was performed on those of all 39 patients. Among the several DEGs discovered in the ACP data, 1 DEG was chosen as the candidate for the RT-PCR, that is present or markedly upregulated in normal-appearing urothelial tissue compared with TCC tissue. Gene sequence searching revealed that this DEG is chicken ovalbumin upstream promoter-transcription factor I (COUP-TFI). Downregulation of COUP-TFI mRNA expression in TCC tissue compared to normal-appearing urothelium tissue of the same patient, irrespective of tumor stage and grade, was confirmed by RT-PCR in 39 patients. Our results suggest that the loss of COUP-TFI may play a role in the transition from normal epithelium to TCC. Further characterization of the COUP-TFI gene is expected to give us informations about bladder TCC tumorigenesis.

  19. Mutations that alter a conserved element upstream of the potato virus X triple block and coat protein genes affect subgenomic RNA accumulation.

    PubMed

    Kim, K H; Hemenway, C

    1997-05-26

    The putative subgenomic RNA (sgRNA) promoter regions upstream of the potato virus X (PVX) triple block and coat protein (CP) genes contain sequences common to other potexviruses. The importance of these sequences to PVX sgRNA accumulation was determined by inoculation of Nicotiana tabacum NT1 cell suspension protoplasts with transcripts derived from wild-type and modified PVX cDNA clones. Analyses of RNA accumulation by S1 nuclease digestion and primer extension indicated that a conserved octanucleotide sequence element and the spacing between this element and the start-site for sgRNA synthesis are critical for accumulation of the two major sgRNA species. The impact of mutations on CP sgRNA levels was also reflected in the accumulation of CP. In contrast, genomic minus- and plus-strand RNA accumulation were not significantly affected by mutations in these regions. Studies involving inoculation of tobacco plants with the modified transcripts suggested that the conserved octanucleotide element functions in sgRNA accumulation and some other aspect of the infection process.

  20. The role of upstream distal electrodes in mitigating electrochemical degradation of ionic liquid ion sources

    NASA Astrophysics Data System (ADS)

    Brikner, Natalya; Lozano, Paulo C.

    2012-11-01

    Ionic liquid ion sources produce molecular ions from micro-tip emitters wetted with room-temperature molten salts. When a single ion polarity is extracted, counterions accumulate and generate electrochemical reactions that limit the source lifetime. The dynamics of double layer formation are reviewed and distal electrode contacts are introduced to resolve detrimental electrochemical decomposition effects at the micro-tip apex. By having the emitter follow the ionic liquid potential, operation can be achieved for an extended period of time with no apparent degradation of the material, indicating that electrochemistry can be curtailed and isolated to the upstream distal electrode.

  1. The control of the upstream movement of fish with pulsated direct current

    USGS Publications Warehouse

    McLain, Alberton L.

    1957-01-01

    In the Silver River, 78,648 fish comprising 21 species were taken from the trap of the direct-current diversion device. The total kill of fish moving upstream, including 289 sea lampreys, was 1,016, or 1.3 percent. This river had presented a serious problem in the operation of an alternating-current control device during previous seasons. In 1955, 85.5 percent of three important species of fish were killed at the control structure. During 1956, this mortality was reduced to 8.1 percent by the operation of the direct-current equipment.

  2. Remote radio observations of solar wind parameters upstream of planetary bow shocks

    NASA Technical Reports Server (NTRS)

    Macdowall, R. J.; Stone, R. G.; Gaffey, J. D., Jr.

    1992-01-01

    Radio emission is frequently produced at twice the electron plasma frequency 2fp in the foreshock region upstream of the terrestrial bow shock. Observations of this emission provide a remote diagnostic of solar wind parameters in the foreshock. Using ISEE-3 radio data, we present the first evidence that the radio intensity is proportional to the kinetic energy flux and to other parameters correlated with solar wind density. We provide a qualitative explanation of this intensity behavior and predict the detection of similar emission at Jupiter by the Ulysses spacecraft.

  3. Compressor Stator Time-Variant Aerodynamic Response to Upstream Rotor Wakes.

    DTIC Science & Technology

    1976-11-01

    periodic varia t i ons in pressure , velocity and flow direction in the exit field of an upstream element , wh i ch appea r as temporall y vary ing in a...compressor features blad i ng (42 rotor blades and 40 stator vanes , NACA 65 F Series ) that is aerodynamicall y l oaded to levels that are typical of...measurements were accom- — p lished by instrumenting a pair of the NACA Series 65 stator — vanes with flush mounted Ku lite thin -line des i gn dynamic

  4. Comparison of picked-up protons and water group ions upstream of Comet Halley's bow shock

    NASA Technical Reports Server (NTRS)

    Neugebauer, M.; Coates, A. J.; Neubauer, F. M.

    1990-01-01

    The similarities and differences between the picked-up cometary protons and water-group (WG) ions upstream of the bow shock of Comet Halley are examined using measurements obtained by the ion mass spectrometer and plasma analyzer experiments on board Giotto. It was found that the dependencies of the pitch angle and the energy diffusion rates of the cometary protons and WG ions on the ion densities and on the angle alpha between the interplanetary field and the solar wind velocity vector were very different. This finding could not be explained in terms of presently available theories and models.

  5. Selection of Optimal Polypurine Tract Region Sequences during Moloney Murine Leukemia Virus Replication

    PubMed Central

    Robson, Nicole D.; Telesnitsky, Alice

    2000-01-01

    Retrovirus plus-strand synthesis is primed by a cleavage remnant of the polypurine tract (PPT) region of viral RNA. In this study, we tested replication properties for Moloney murine leukemia viruses with targeted mutations in the PPT and in conserved sequences upstream, as well as for pools of mutants with randomized sequences in these regions. The importance of maintaining some purine residues within the PPT was indicated both by examining the evolution of random PPT pools and from the replication properties of targeted mutants. Although many different PPT sequences could support efficient replication and one mutant that contained two differences in the core PPT was found to replicate as well as the wild type, some sequences in the core PPT clearly conferred advantages over others. Contributions of sequences upstream of the core PPT were examined with deletion mutants. A conserved T-stretch within the upstream sequence was examined in detail and found to be unimportant to helper functions. Evolution of virus pools containing randomized T-stretch sequences demonstrated marked preference for the wild-type sequence in six of its eight positions. These findings demonstrate that maintenance of the T-rich element is more important to viral replication than is maintenance of the core PPT. PMID:11044073

  6. Optical power equalization for upstream traffic with injection-locked Fabry-Perot lasers in TDM-PON

    NASA Astrophysics Data System (ADS)

    Huang, Ting-Tsan; Sheu, Lih-Gen; Chi, Sien

    2010-10-01

    An optical power equalization of upstream traffic in time-division-multiplexed passive optical network (TDM-PON) based on injection-locked Fabry-Perot lasers has been experimentally investigated. The upstream transmitters with stable spectrum are achieved by using an external injection light source in the optical line terminal (OLT). The different upstream powers can be equalized by injection locking a Fabry-Perot laser diode (FP-LD) biased below threshold current in OLT. The dynamic upstream power range from - 8.5 to - 19.5 db m is reduced to a 1.6 dB maximal power variation, when the uplink signal is directly modulated at 1.25 Gb/s.

  7. Contaminants of emerging concern: Mass balance and comparison of wastewater effluent and upstream sources in a mixed-use watershed

    USDA-ARS?s Scientific Manuscript database

    Understanding the sources, transport, and spatiotemporal variability of contaminants of emerging concern (CECs) is important for understanding risks and developing monitoring and mitigation strategies. This study compared CEC loading and transport from a wastewater treatment plant and upstream areas...

  8. Performance of Pylons Upstream of a Cavity-Based Flameholder in Non-Reacting Supersonic Flow (Postprint)

    DTIC Science & Technology

    2006-10-01

    examine the flow field at an axial location of 0.75 inches. Measurements are performed using a pitot , cone-static probe and total temperature probe ...is the injection port, and the origin of the transverse direction (y/d = 0.0) is the upstream lip of the cavity. In each figure, the bow shock ...originates just upstream of the injection port and tends to be the strongest shock feature. In the baseline configurations, the bow shock initially

  9. Performance of Pylons Upstream of a Cavity-Based Flameholder in Non-Reacting Supersonic Flow (Postprint)

    DTIC Science & Technology

    2006-07-01

    location of 0.75 inches. Measurements are performed using a pitot , cone-static probe and total temperature probe with similar test meshes. All probes are...the transverse direction (y/d = 0.0) is the upstream lip of the cavity. In each figure, the bow shock originates just upstream of the injection port...and tends to be the strongest shock feature. In the baseline configurations, the bow shock initially penetrates perpendicular to the main flow due to

  10. Performance of Pylons Upstream of a Cavity-Based Flameholder in Non-Reacting Supersonic Flow (POSTPRINT)

    DTIC Science & Technology

    2006-07-01

    inches. Measurements are performed using a pitot , cone-static probe and total temperature probe with similar test meshes. All probes are...transverse direction (y/d = 0.0) is the upstream lip of the cavity. In each figure, the bow shock originates just upstream of the injection port and tends...to be the strongest shock feature. In the baseline configurations, the bow shock initially penetrates perpendicular to the main flow due to the

  11. Identification of the first PAR1 deletion encompassing upstream SHOX enhancers in a family with idiopathic short stature

    PubMed Central

    Benito-Sanz, Sara; Aza-Carmona, Miriam; Rodríguez-Estevez, Amaya; Rica-Etxebarria, Ixaso; Gracia, Ricardo; Campos-Barros, Ángel; Heath, Karen E

    2012-01-01

    Short stature homeobox-containing gene, MIM 312865 (SHOX) is located within the pseudoautosomal region 1 (PAR1) of the sex chromosomes. Mutations in SHOX or its downstream transcriptional regulatory elements represent the underlying molecular defect in ∼60% of Léri-Weill dyschondrosteosis (LWD) and ∼5–15% of idiopathic short stature (ISS) patients. Recently, three novel enhancer elements have been identified upstream of SHOX but to date, no PAR1 deletions upstream of SHOX have been observed that only encompass these enhancers in LWD or ISS patients. We set out to search for genetic alterations of the upstream SHOX regulatory elements in 63 LWD and 100 ISS patients with no known alteration in SHOX or the downstream enhancer regions using a specifically designed MLPA assay, which covers the PAR1 upstream of SHOX. An upstream SHOX deletion was identified in an ISS proband and her affected father. The deletion was confirmed and delimited by array-CGH, to extend ∼286 kb. The deletion included two of the upstream SHOX enhancers without affecting SHOX. The 13.3-year-old proband had proportionate short stature with normal GH and IGF-I levels. In conclusion, we have identified the first PAR1 deletion encompassing only the upstream SHOX transcription regulatory elements in a family with ISS. The loss of these elements may result in SHOX haploinsufficiency because of decreased SHOX transcription. Therefore, this upstream region should be included in the routine analysis of PAR1 in patients with LWD, LMD and ISS. PMID:22071895

  12. A Rich-Club Organization in Brain Ischemia Protein Interaction Network

    PubMed Central

    Alawieh, Ali; Sabra, Zahraa; Sabra, Mohammed; Tomlinson, Stephen; Zaraket, Fadi A.

    2015-01-01

    Ischemic stroke involves multiple pathophysiological mechanisms with complex interactions. Efforts to decipher those mechanisms and understand the evolution of cerebral injury is key for developing successful interventions. In an innovative approach, we use literature mining, natural language processing and systems biology tools to construct, annotate and curate a brain ischemia interactome. The curated interactome includes proteins that are deregulated after cerebral ischemia in human and experimental stroke. Network analysis of the interactome revealed a rich-club organization indicating the presence of a densely interconnected hub structure of prominent contributors to disease pathogenesis. Functional annotation of the interactome uncovered prominent pathways and highlighted the critical role of the complement and coagulation cascade in the initiation and amplification of injury starting by activation of the rich-club. We performed an in-silico screen for putative interventions that have pleiotropic effects on rich-club components and we identified estrogen as a prominent candidate. Our findings show that complex network analysis of disease related interactomes may lead to a better understanding of pathogenic mechanisms and provide cost-effective and mechanism-based discovery of candidate therapeutics. PMID:26310627

  13. Self-assembly of hard helices: a rich and unconventional polymorphism.

    PubMed

    Kolli, Hima Bindu; Frezza, Elisa; Cinacchi, Giorgio; Ferrarini, Alberta; Giacometti, Achille; Hudson, Toby S; De Michele, Cristiano; Sciortino, Francesco

    2014-11-07

    Hard helices can be regarded as a paradigmatic elementary model for a number of natural and synthetic soft matter systems, all featuring the helix as their basic structural unit, from natural polynucleotides and polypeptides to synthetic helical polymers, and from bacterial flagella to colloidal helices. Here we present an extensive investigation of the phase diagram of hard helices using a variety of methods. Isobaric Monte Carlo numerical simulations are used to trace the phase diagram; on going from the low-density isotropic to the high-density compact phases a rich polymorphism is observed, exhibiting a special chiral screw-like nematic phase and a number of chiral and/or polar smectic phases. We present full characterization of the latter, showing that they have unconventional features, ascribable to the helical shape of the constituent particles. Equal area construction is used to locate the isotropic-to-nematic phase transition, and the results are compared with those stemming from an Onsager-like theory. Density functional theory is also used to study the nematic-to-screw-nematic phase transition; within the simplifying assumption of perfectly parallel helices, we compare different levels of approximation, that is second- and third-virial expansions and a Parsons-Lee correction.

  14. A Rich Man, Poor Man Story of S-Adenosylmethionine and Cobalamin Revisited.

    PubMed

    Bridwell-Rabb, Jennifer; Grell, Tsehai A J; Drennan, Catherine L

    2018-06-20

    S-adenosylmethionine (AdoMet) has been referred to as both "a poor man's adenosylcobalamin (AdoCbl)" and "a rich man's AdoCbl," but today, with the ever-increasing number of functions attributed to each cofactor, both appear equally rich and surprising. The recent characterization of an organometallic species in an AdoMet radical enzyme suggests that the line that differentiates them in nature will be constantly challenged. Here, we compare and contrast AdoMet and cobalamin (Cbl) and consider why Cbl-dependent AdoMet radical enzymes require two cofactors that are so similar in their reactivity. We further carry out structural comparisons employing the recently determined crystal structure of oxetanocin-A biosynthetic enzyme OxsB, the first three-dimensional structural data on a Cbl-dependent AdoMet radical enzyme. We find that the structural motifs responsible for housing the AdoMet radical machinery are largely conserved, whereas the motifs responsible for binding additional cofactors are much more varied.

  15. Conditional Inactivation of Upstream Binding Factor Reveals Its Epigenetic Functions and the Existence of a Somatic Nucleolar Precursor Body

    PubMed Central

    Hamdane, Nourdine; Stefanovsky, Victor Y.; Tremblay, Michel G.; Németh, Attila; Paquet, Eric; Lessard, Frédéric; Sanij, Elaine; Hannan, Ross; Moss, Tom

    2014-01-01

    Upstream Binding Factor (UBF) is a unique multi-HMGB-box protein first identified as a co-factor in RNA polymerase I (RPI/PolI) transcription. However, its poor DNA sequence selectivity and its ability to generate nucleosome-like nucleoprotein complexes suggest a more generalized role in chromatin structure. We previously showed that extensive depletion of UBF reduced the number of actively transcribed ribosomal RNA (rRNA) genes, but had little effect on rRNA synthesis rates or cell proliferation, leaving open the question of its requirement for RPI transcription. Using gene deletion in mouse, we now show that UBF is essential for embryo development beyond morula. Conditional deletion in cell cultures reveals that UBF is also essential for transcription of the rRNA genes and that it defines the active chromatin conformation of both gene and enhancer sequences. Loss of UBF prevents formation of the SL1/TIF1B pre-initiation complex and recruitment of the RPI-Rrn3/TIF1A complex. It is also accompanied by recruitment of H3K9me3, canonical histone H1 and HP1α, but not by de novo DNA methylation. Further, genes retain penta-acetyl H4 and H2A.Z, suggesting that even in the absence of UBF the rRNA genes can maintain a potentially active state. In contrast to canonical histone H1, binding of H1.4 is dependent on UBF, strongly suggesting that it plays a positive role in gene activity. Unexpectedly, arrest of rRNA synthesis does not suppress transcription of the 5S, tRNA or snRNA genes, nor expression of the several hundred mRNA genes implicated in ribosome biogenesis. Thus, rRNA gene activity does not coordinate global gene expression for ribosome biogenesis. Loss of UBF also unexpectedly induced the formation in cells of a large sub-nuclear structure resembling the nucleolar precursor body (NPB) of oocytes and early embryos. These somatic NPBs contain rRNA synthesis and processing factors but do not associate with the rRNA gene loci (NORs). PMID:25121932

  16. Some Finite Difference Solutions of the Laminar Compressible Boundary Layer Showing the Effects of Upstream Transpiration Cooling

    NASA Technical Reports Server (NTRS)

    Howe, John T.

    1959-01-01

    Three numerical solutions of the partial differential equations describing the compressible laminar boundary layer are obtained by the finite difference method described in reports by I. Flugge-Lotz, D.C. Baxter, and this author. The solutions apply to steady-state supersonic flow without pressure gradient, over a cold wall and over an adiabatic wall, both having transpiration cooling upstream, and over an adiabatic wall with upstream cooling but without upstream transpiration. It is shown that for a given upstream wall temperature, upstream transpiration cooling affords much better protection to the adiabatic solid wall than does upstream cooling without transpiration. The results of the numerical solutions are compared with those of approximate solutions. The thermal results of the finite difference solution lie between the results of Rubesin and Inouye, and those of Libby and Pallone. When the skin-friction results of one finite difference solution are used in the thermal analysis of Rubesin and Inouye, improved agreement between the thermal results of the two methods of solution is obtained.

  17. Pooled genome wide association detects association upstream of FCRL3 with Graves' disease.

    PubMed

    Khong, Jwu Jin; Burdon, Kathryn P; Lu, Yi; Laurie, Kate; Leonardos, Lefta; Baird, Paul N; Sahebjada, Srujana; Walsh, John P; Gajdatsy, Adam; Ebeling, Peter R; Hamblin, Peter Shane; Wong, Rosemary; Forehan, Simon P; Fourlanos, Spiros; Roberts, Anthony P; Doogue, Matthew; Selva, Dinesh; Montgomery, Grant W; Macgregor, Stuart; Craig, Jamie E

    2016-11-18

    Graves' disease is an autoimmune thyroid disease of complex inheritance. Multiple genetic susceptibility loci are thought to be involved in Graves' disease and it is therefore likely that these can be identified by genome wide association studies. This study aimed to determine if a genome wide association study, using a pooling methodology, could detect genomic loci associated with Graves' disease. Nineteen of the top ranking single nucleotide polymorphisms including HLA-DQA1 and C6orf10, were clustered within the Major Histo-compatibility Complex region on chromosome 6p21, with rs1613056 reaching genome wide significance (p = 5 × 10 -8 ). Technical validation of top ranking non-Major Histo-compatablity complex single nucleotide polymorphisms with individual genotyping in the discovery cohort revealed four single nucleotide polymorphisms with p ≤ 10 -4 . Rs17676303 on chromosome 1q23.1, located upstream of FCRL3, showed evidence of association with Graves' disease across the discovery, replication and combined cohorts. A second single nucleotide polymorphism rs9644119 downstream of DPYSL2 showed some evidence of association supported by finding in the replication cohort that warrants further study. Pooled genome wide association study identified a genetic variant upstream of FCRL3 as a susceptibility locus for Graves' disease in addition to those identified in the Major Histo-compatibility Complex. A second locus downstream of DPYSL2 is potentially a novel genetic variant in Graves' disease that requires further confirmation.

  18. Different Types of Ion Populations Upstream of the 2013 October 8 Interplanetary Shock

    NASA Astrophysics Data System (ADS)

    Kajdič, Primož; Hietala, Heli; Blanco-Cano, Xóchitl

    2017-11-01

    We show for the first time that different types of suprathermal ion distributions may exist upstream of a single interplanetary shock. ACE and the two ARTEMIS satellites observed a shock on 2013 October 8. The ARTEMIS P1 and P2 spacecraft first observed field-aligned ions (P1) and gyrating ions (P2) arriving from the shock. These were followed by intermediate ions and later by a diffuse population. At the location of the P2 the shock exhibited an Alfvénic Mach number of M A = 5.7 and was marginally quasi-perpendicular ({θ }{Bn}=47^\\circ ). At P1 spacecraft the shock was weaker (M A = 4.9) and more perpendicular ({θ }{Bn}=61^\\circ ). Consequently, the observed suprathermal ion and ultra-low-frequency wave properties were somewhat different. At P2 the ultra-low-frequency waves are more intense and extend farther upstream from the shock. The energies of field-aligned and gyrating ions in the shock rest-frame were ˜20 keV, which is much more than in the case of the stronger (M A = 6-7) Earth’s bow shock, where they are less than 10 keV.

  19. Chandra's Observations of Jupiter's X-Ray Aurora During Juno Upstream and Apojove Intervals

    NASA Technical Reports Server (NTRS)

    Jackman, C.M.; Dunn, W.; Kraft, R.; Gladstone, R.; Branduardi-Raymont, G.; Knigge, C.; Altamirano, D.; Elsner, R.

    2017-01-01

    The Chandra space telescope has recently conducted a number of campaigns to observe Jupiter's X-ray aurora. The first set of campaigns took place in summer 2016 while the Juno spacecraft was upstream of the planet sampling the solar wind. The second set of campaigns took place in February, June and August 2017 at times when the Juno spacecraft was at apojove (expected close to the magnetopause). We report on these upstream and apojove campaigns including intensities and periodicities of auroral X-ray emissions. This new era of jovian X-ray astronomy means we have more data than ever before, long observing windows (up to 72 kiloseconds for this Chandra set), and successive observations relatively closely spaced in time. These features combine to allow us to pursue novel methods for examining periodicities in the X-ray emission. Our work will explore significance testing of emerging periodicities, and the search for coherence in X-ray pulsing over weeks and months, seeking to understand the robustness and regularity of previously reported hot spot X-ray emissions. The periods that emerge from our analysis will be compared against those which emerge from radio and UV wavelengths.

  20. Coral-inferred Variability of Upstream Kuroshio Current from 1953-2004 AD

    NASA Astrophysics Data System (ADS)

    Li, X.; Yi, L.; Shen, C. C.; Hsin, Y. C.

    2016-12-01

    The Kuroshio Current (KC), one of the most important western boundary currents in the North Pacific Ocean, strongly impacts regional climate in East Asia and upper-ocean thermal structure. However, the responses of KC to regional and remote climate forcing are poorly understood owing to lacking of long-term KC observations. Here, we present a sea surface temperature (SST) record from 1953 to 2004 AD derived from monthly skeletal δ18O data of a living coral Porites core, drilled in Nanwan, southern Taiwan (22°N, 121°E), located on the western front of the Upstream KC. The increased/reduced Kuroshio transport would generate stronger/weaker upwelling in Southern Taiwan, which can cause lower/higher SST. Agreement between dynamics of interannual coral δ18O and modern KC data shows that the regional coral δ18O can be used as a promising proxy for Upstream KC intensity. The KC-induced SST anomaly record reveals prominent interannual and decadal variability predominantly controlled by the bifurcation latitude of North Equatorial Current. We also find that the reconstructed KC intensity at east of Taiwan and south of Japan have nearly simultaneous interannual changes, suggesting the same dominant forcing(s) for the entire KC system. Additional work is needed to understand the KC system with respect to the interannual to decadal climate variability and the influences of global warming.

  1. Upstream Density for Plasma Detachment with Conventional and Lithium Vapor-Box Divertors

    NASA Astrophysics Data System (ADS)

    Goldston, Rj; Schwartz, Ja

    2016-10-01

    Fusion power plants are likely to require detachment of the divertor plasma from material targets. The lithium vapor box divertor is designed to achieve this, while limiting the flux of lithium vapor to the main plasma. We develop a simple model of near-detachment to evaluate the required upstream plasma density, for both conventional and lithium vapor-box divertors, based on particle and dynamic pressure balance between up- and down-stream, at near-detachment conditions. A remarkable general result is found, not just for lithium-induced detachment, that the upstream density divided by the Greenwald-limit density scales as (P 5 / 8 /B 3 / 8) Tdet1 / 2 / (ɛcool + γTdet) , with no explicit size scaling. Tdet is the temperature just before strong pressure loss, 1/2 of the ionization potential of the dominant recycling species, ɛcool is the average plasma energy lost per injected hydrogenic and impurity atom, and γ is the sheath heat transmission factor. A recent 1-D calculation agrees well with this scaling. The implication is that the plasma exhaust problem cannot be solved by increasing R. Instead significant innovation, such as the lithium vapor box divertor, will be required. This work supported by DOE Contract No. DE-AC02-09CH11466.

  2. Reservoir Sedimentation and Upstream Sediment Sources: Perspectives and Future Research Needs on Streambank and Gully Erosion.

    PubMed

    Fox, G A; Sheshukov, A; Cruse, R; Kolar, R L; Guertault, L; Gesch, K R; Dutnell, R C

    2016-05-01

    The future reliance on water supply and flood control reservoirs across the globe will continue to expand, especially under a variable climate. As the inventory of new potential dam sites is shrinking, construction of additional reservoirs is less likely compared to simultaneous flow and sediment management in existing reservoirs. One aspect of this sediment management is related to the control of upstream sediment sources. However, key research questions remain regarding upstream sediment loading rates. Highlighted in this article are research needs relative to measuring and predicting sediment transport rates and loading due to streambank and gully erosion within a watershed. For example, additional instream sediment transport and reservoir sedimentation rate measurements are needed across a range of watershed conditions, reservoir sizes, and geographical locations. More research is needed to understand the intricate linkage between upland practices and instream response. A need still exists to clarify the benefit of restoration or stabilization of a small reach within a channel system or maturing gully on total watershed sediment load. We need to better understand the intricate interactions between hydrological and erosion processes to improve prediction, location, and timing of streambank erosion and failure and gully formation. Also, improved process-based measurement and prediction techniques are needed that balance data requirements regarding cohesive soil erodibility and stability as compared to simpler topographic indices for gullies or stream classification systems. Such techniques will allow the research community to address the benefit of various conservation and/or stabilization practices at targeted locations within watersheds.

  3. Effect of an upstream bulge configuration on film cooling with and without mist injection.

    PubMed

    Wang, Jin; Li, Qianqian; Sundén, Bengt; Ma, Ting; Cui, Pei

    2017-12-01

    To meet the economic requirements of power output, the increased inlet temperature of modern gas turbines is above the melting point of the material. Therefore, high-efficient cooling technology is needed to protect the blades from the hot mainstream. In this study, film cooling was investigated in a simplified channel. A bulge located upstream of the film hole was numerically investigated by analysis of the film cooling effectiveness distribution downstream of the wall. The flow distribution in the plate channel is first presented. Comparing with a case without bulge, different cases with bulge heights of 0.1d, 0.3d and 0.5d were examined with blowing ratios of 0.5 and 1.0. Cases with 1% mist injection were also included in order to obtain better cooling performance. Results show that the bulge configuration located upstream the film hole makes the cooling film more uniform, and enhanceslateral cooling effectiveness. Unlike other cases, the configuration with a 0.3d-height bulge shows a good balance in improving the downstream and lateral cooling effectiveness. Compared with the case without mist at M = 0.5, the 0.3d-height bulge with 1% mist injection increases lateral average effectiveness by 559% at x/d = 55. In addition, a reduction of the thermal stress concentration can be obtained by increasing the height of the bulge configuration. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Small molecule drug A-769662 and AMP synergistically activate naive AMPK independent of upstream kinase signaling.

    PubMed

    Scott, John W; Ling, Naomi; Issa, Samah M A; Dite, Toby A; O'Brien, Matthew T; Chen, Zhi-Ping; Galic, Sandra; Langendorf, Christopher G; Steinberg, Gregory R; Kemp, Bruce E; Oakhill, Jonathan S

    2014-05-22

    The AMP-activated protein kinase (AMPK) is a metabolic stress-sensing αβγ heterotrimer responsible for energy homeostasis, making it a therapeutic target for metabolic diseases such as type 2 diabetes and obesity. AMPK signaling is triggered by phosphorylation on the AMPK α subunit activation loop Thr172 by upstream kinases. Dephosphorylated, naive AMPK is thought to be catalytically inactive and insensitive to allosteric regulation by AMP and direct AMPK-activating drugs such as A-769662. Here we show that A-769662 activates AMPK independently of α-Thr172 phosphorylation, provided β-Ser108 is phosphorylated. Although neither A-769662 nor AMP individually stimulate the activity of dephosphorylated AMPK, together they stimulate >1,000-fold, bypassing the requirement for β-Ser108 phosphorylation. Consequently A-769662 and AMP together activate naive AMPK entirely allosterically and independently of upstream kinase signaling. These findings have important implications for development of AMPK-targeting therapeutics and point to possible combinatorial therapeutic strategies based on AMP and AMPK drugs. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Potential Upstream Strategies for the Mitigation of Pharmaceuticals in the Aquatic Environment: a Brief Review.

    PubMed

    Blair, Benjamin D

    2016-06-01

    Active pharmaceutical ingredients represent a class of pollutants of emerging concern, and there is growing evidence that these pollutants can cause damage to the aquatic environment. As regulations to address these concerns are expected in developed nations, decision-makers are looking to the scientific community for potential solutions. To inform these regulatory efforts, further information on the potential strategies to reduce the levels of pharmaceuticals entering the aquatic environment is needed. End-of-pipe (i.e., wastewater treatment) technologies that can remove pharmaceuticals exist; however, they are costly to install and operate. Thus, the goal of this brief review is to look beyond end-of-pipe solutions and present various upstream mitigation strategies discussed within the scientific literature. Programs such as pharmaceutical take-back programs currently exist to attempt to reduce pharmaceutical concentrations in the environment, although access and coverage are often limited for many programs. Other potential strategies include redesigning pharmaceuticals to minimize aquatic toxicity, increasing the percent of the pharmaceuticals metabolized in the body, selecting less harmful pharmaceuticals for use, starting new prescriptions at lower dosages, selecting pharmaceuticals with lower excretion rates, and implementing source treatment such as urine separating toilets. Overall, this brief review presents a summary of the upstream preventative recommendations to mitigate pharmaceuticals from entering the aquatic environment with an emphasis on regulatory efforts in the USA and concludes with priorities for further research.

  6. Co-evolution of upstream waves and accelerated ions at parallel shocks

    NASA Astrophysics Data System (ADS)

    Fujimoto, M.; Sugiyama, T.

    2016-12-01

    Shock waves in space plasmas have been considered as the agents for various particle acceleration phenomena. The basic idea behind shock acceleration is that particles are accelerated as they move back-and-forth across a shock front. Detailed studies of ion acceleration at the terrestrial bow shock have been performed, however, the restricted maximum energies attained prevent a straight-forward application of obtained knowledge to more energetic astrophysical situations. Here we show by a large-scale self-consistent particle simulation that the co-evolution of magnetic turbulence and accelerated ion population is the foundation for continuous operation of shock acceleration to ever higher energies. Magnetic turbulence is created by ions reflected back upstream of a parallel shock front. The co-evolution arises because more energetic ions excite waves of longer wavelengths, and because longer wavelength modes are capable of scattering (in the upstream) and reflecting (at the shock front) more energetic ions. Via carefully designed numerical experiments, we show very clearly that this picture is true.

  7. Reservoir Sedimentation and Upstream Sediment Sources: Perspectives and Future Research Needs on Streambank and Gully Erosion

    NASA Astrophysics Data System (ADS)

    Fox, G. A.; Sheshukov, A.; Cruse, R.; Kolar, R. L.; Guertault, L.; Gesch, K. R.; Dutnell, R. C.

    2016-05-01

    The future reliance on water supply and flood control reservoirs across the globe will continue to expand, especially under a variable climate. As the inventory of new potential dam sites is shrinking, construction of additional reservoirs is less likely compared to simultaneous flow and sediment management in existing reservoirs. One aspect of this sediment management is related to the control of upstream sediment sources. However, key research questions remain regarding upstream sediment loading rates. Highlighted in this article are research needs relative to measuring and predicting sediment transport rates and loading due to streambank and gully erosion within a watershed. For example, additional instream sediment transport and reservoir sedimentation rate measurements are needed across a range of watershed conditions, reservoir sizes, and geographical locations. More research is needed to understand the intricate linkage between upland practices and instream response. A need still exists to clarify the benefit of restoration or stabilization of a small reach within a channel system or maturing gully on total watershed sediment load. We need to better understand the intricate interactions between hydrological and erosion processes to improve prediction, location, and timing of streambank erosion and failure and gully formation. Also, improved process-based measurement and prediction techniques are needed that balance data requirements regarding cohesive soil erodibility and stability as compared to simpler topographic indices for gullies or stream classification systems. Such techniques will allow the research community to address the benefit of various conservation and/or stabilization practices at targeted locations within watersheds.

  8. FAT1 cadherin acts upstream of Hippo signalling through TAZ to regulate neuronal differentiation.

    PubMed

    Ahmed, Abdulrzag F; de Bock, Charles E; Lincz, Lisa F; Pundavela, Jay; Zouikr, Ihssane; Sontag, Estelle; Hondermarck, Hubert; Thorne, Rick F

    2015-12-01

    The Hippo pathway is emerging as a critical nexus that balances self-renewal of progenitors against differentiation; however, upstream elements in vertebrate Hippo signalling are poorly understood. High expression of Fat1 cadherin within the developing neuroepithelium and the manifestation of severe neurological phenotypes in Fat1-knockout mice suggest roles in neurogenesis. Using the SH-SY5Y model of neuronal differentiation and employing gene silencing techniques, we show that FAT1 acts to control neurite outgrowth, also driving cells towards terminal differentiation via inhibitory effects on proliferation. FAT1 actions were shown to be mediated through Hippo signalling where it activated core Hippo kinase components and antagonised functions of the Hippo effector TAZ. Suppression of FAT1 promoted the nucleocytoplasmic shuttling of TAZ leading to enhanced transcription of the Hippo target gene CTGF together with accompanying increases in nuclear levels of Smad3. Silencing of TAZ reversed the effects of FAT1 depletion thus connecting inactivation of TAZ-TGFbeta signalling with Hippo signalling mediated through FAT1. These findings establish FAT1 as a new upstream Hippo element regulating early stages of differentiation in neuronal cells.

  9. WRNIP1 functions upstream of DNA polymerase η in the UV-induced DNA damage response

    SciTech Connect

    Yoshimura, Akari, E-mail: akari_yo@stu.musashino-u.ac.jp; Kobayashi, Yume; Tada, Shusuke

    2014-09-12

    Highlights: • The UV sensitivity of POLH{sup −/−} cells was suppressed by disruption of WRNIP1. • In WRNIP1{sup −/−/−}/POLH{sup −/−} cells, mutation frequencies and SCE after irradiation reduced. • WRNIP1 defect recovered rate of fork progression after irradiation in POLH{sup −/−} cells. • WRNIP1 functions upstream of Polη in the translesion DNA synthesis pathway. - Abstract: WRNIP1 (WRN-interacting protein 1) was first identified as a factor that interacts with WRN, the protein that is defective in Werner syndrome (WS). WRNIP1 associates with DNA polymerase η (Polη), but the biological significance of this interaction remains unknown. In this study, we analyzedmore » the functional interaction between WRNIP1 and Polη by generating knockouts of both genes in DT40 chicken cells. Disruption of WRNIP1 in Polη-disrupted (POLH{sup −/−}) cells suppressed the phenotypes associated with the loss of Polη: sensitivity to ultraviolet light (UV), delayed repair of cyclobutane pyrimidine dimers (CPD), elevated frequency of mutation, elevated levels of UV-induced sister chromatid exchange (SCE), and reduced rate of fork progression after UV irradiation. These results suggest that WRNIP1 functions upstream of Polη in the response to UV irradiation.« less

  10. Unsteady loading of a vertical-axis turbine in the interaction with an upstream deflector

    NASA Astrophysics Data System (ADS)

    Kim, Daegyoum; Gharib, Morteza

    2014-01-01

    Torque generation and flow distribution of a lift-based vertical-axis turbine with an upstream deflecting plate are investigated in water tunnel experiments. The deployment of a deflector in front of a lift-based turbine is a promising approach to increase local flow velocity and enhance energy conversion efficiency without consideration for complicated control. For the turbine with the deflector, the phase during which the blade passes near the front end of the turbine has a major contribution to torque increase from the case without the deflector. Meanwhile, the deflector can have a negative effect in torque generation at the phase when the blade moves upstream against free stream if the turbine is placed close to the deflector in a crosswise direction. The change of nearby flow distribution by the deflector is also examined to find its correlation with torque generation. When the blade rotates through the near-wake region of the deflector, the blade can collides with the vortical structure shed from the deflector. This interaction causes significant torque fluctuation.

  11. Electron distributions upstream of the Comet Halley bow shock - Evidence for adiabatic heating

    NASA Technical Reports Server (NTRS)

    Larson, D. E.; Anderson, K. A.; Lin, R. P.; Carlson, C. W.; Reme, H.; Glassmeier, K. H.; Neubauer, F. M.

    1992-01-01

    Three-dimensional plasma electron (22 eV to 30 keV) observations upstream of Comet Halley bow shock, obtained by the RPA-1 COPERNIC (Reme Plasma Analyzer - Complete Positive Ion, Electron and Ram Negative Ion Measurements near Comet Halley) experiment on the Giotto spacecraft are reported. Besides electron distributions typical of the undisturbed solar wind and backstreaming electrons observed when the magnetic field line intersects the cometary bow shock, a new type of distribution, characterized by enhanced low energy (less than 100 eV) flux which peaks at 90-deg pitch angles is found. These are most prominent when the spacecraft is on field lines which pass close to but are not connected to the bow shock. The 90-deg pitch angle electrons appear to have been adiabatically heated by the increase in the magnetic field strength resulting from the compression of the upstream solar wind plasma by the cometary mass loading. A model calculation of this effect which agrees qualitatively with the observed 90-deg flux enhancements is presented.

  12. Novel Strategies for Upstream and Downstream Processing of Tannin Acyl Hydrolase

    PubMed Central

    Rodríguez-Durán, Luis V.; Valdivia-Urdiales, Blanca; Contreras-Esquivel, Juan C.; Rodríguez-Herrera, Raúl; Aguilar, Cristóbal N.

    2011-01-01

    Tannin acyl hydrolase also referred as tannase is an enzyme with important applications in several science and technology fields. Due to its hydrolytic and synthetic properties, tannase could be used to reduce the negative effects of tannins in beverages, food, feed, and tannery effluents, for the production of gallic acid from tannin-rich materials, the elucidation of tannin structure, and the synthesis of gallic acid esters in nonaqueous media. However, industrial applications of tannase are still very limited due to its high production cost. Thus, there is a growing interest in the production, recovery, and purification of this enzyme. Recently, there have been published a number of papers on the improvement of upstream and downstream processing of the enzyme. These papers dealt with the search for new tannase producing microorganisms, the application of novel fermentation systems, optimization of culture conditions, the production of the enzyme by recombinant microorganism, and the design of efficient protocols for tannase recovery and purification. The present work reviews the state of the art of basic and biotechnological aspects of tannin acyl hydrolase, focusing on the recent advances in the upstream and downstream processing of the enzyme. PMID:21941633

  13. Sustainability of Water Resources in the Upstream Watershed- Based Community Engagement and Multistakeholder Cooperation

    NASA Astrophysics Data System (ADS)

    Brotosusilo, Agus; Utari, Dyah; Agung Satria, Afrizal

    2016-02-01

    The communities engagement become the backbone of the conservation in the Citanduy upstream watershed. It functioning as a major deal and the first one in keeping his own Watershed. This paper based on Community Engagement Grants (CEGs). Program Society-based empowerment approach is also emphasized in the viewpoint of environmental law that is useful to set governance and sanctions in watershed management. The type of activity to be undertaken are the expansion of awareness programs communities of the existence and condition of the watershed Citanduy, the formation of a cadre of conservationists environment that is primarily directed to children and women, the institutionalization of customary law environment, and afforestation by planting 100,000 prolific trees, tree conservationists, and Sunda endemic tree in the land surrounding the watershed upstream Citanduy. The Program involves several partners and stakeholders who helped in substance and operational support activities in the field.. Result of program shows that Community Engagement Grants need cooperation among stakeholders by positioning the community as main subject of changing, not as subject who does not understand their needs to change.

  14. Duplication of an upstream silencer of FZP increases grain yield in rice.

    PubMed

    Bai, Xufeng; Huang, Yong; Hu, Yong; Liu, Haiyang; Zhang, Bo; Smaczniak, Cezary; Hu, Gang; Han, Zhongmin; Xing, Yongzhong

    2017-11-01

    Transcriptional silencer and copy number variants (CNVs) are associated with gene expression. However, their roles in generating phenotypes have not been well studied. Here we identified a rice quantitative trait locus, SGDP7 (Small Grain and Dense Panicle 7). SGDP7 is identical to FZP (FRIZZY PANICLE), which represses the formation of axillary meristems. The causal mutation of SGDP7 is an 18-bp fragment, named CNV-18bp, which was inserted ~5.3 kb upstream of FZP and resulted in a tandem duplication in the cultivar Chuan 7. The CNV-18bp duplication repressed FZP expression, prolonged the panicle branching period and increased grain yield by more than 15% through substantially increasing the number of spikelets per panicle (SPP) and slightly decreasing the 1,000-grain weight (TGW). The transcription repressor OsBZR1 binds the CGTG motifs in CNV-18bp and thereby represses FZP expression, indicating that CNV-18bp is the upstream silencer of FZP. These findings showed that the silencer CNVs coordinate a trade-off between SPP and TGW by fine-tuning FZP expression, and balancing the trade-off could enhance yield potential.

  15. Mean velocities and Reynolds stresses upstream of a simulated wing-fuselage juncture

    NASA Technical Reports Server (NTRS)

    Mcmahon, H.; Hubbartt, J.; Kubendran, L. R.

    1983-01-01

    Values of three mean velocity components and six turbulence stresses measured in a turbulent shear layer upstream of a simulated wing-fuselage juncture and immediately downstream of the start of the juncture are presented nd discussed. Two single-sensor hot-wire probes were used in the measurements. The separated region just upstream of the wing contains an area of reversed flow near the fuselage surface where the turbulence level is high. Outside of this area the flow skews as it passes around the body, and in this skewed region the magnitude and distribution of the turbulent normal and shear stresses within the shear layer are modified slightly by the skewing and deceleration of the flow. A short distance downstream of the wing leading edge the secondary flow vortext is tightly rolled up and redistributes both mean flow and turbulence in the juncture. The data acquisition technique employed here allows a hot wire to be used in a reversed flow region to indicate flow direction.

  16. Structural and functional analysis of an enhancer GPEI having a phorbol 12-O-tetradecanoate 13-acetate responsive element-like sequence found in the rat glutathione transferase P gene.

    PubMed

    Okuda, A; Imagawa, M; Maeda, Y; Sakai, M; Muramatsu, M

    1989-10-05

    We have recently identified a typical enhancer, termed GPEI, located about 2.5 kilobases upstream from the transcription initiation site of the rat glutathione transferase P gene. Analyses of 5' and 3' deletion mutants revealed that the cis-acting sequence of GPEI contained the phorbol 12-O-tetradecanoate 13-acetate responsive element (TRE)-like sequence in it. For the maximal activity, however, GPEI required an adjacent upstream sequence of about 19 base pairs in addition to the TRE-like sequence. With the DNA binding gel-shift assay, we could detect protein(s) that specifically binds to the TRE-like sequence of GPEI fragment, which was possibly c-jun.c-fos complex or a similar protein complex. The sequence immediately upstream of the TRE-like sequence did not have any activity by itself, but augmented the latter activity by about 5-fold.

  17. The International Society for Sexual Medicine: A Rich History and a Bright Future.

    PubMed

    Lewis, Ronald W

    2013-07-01

    Based upon physical presence at most of the historical moments of the development of the International Society for Sexual Medicine (ISSM), extensive personal records on meetings and correspondence associated with the business and the work of the International Society for Sexual and Impotence Research and the ISSM, and information provided by the business office of the ISSM, a review paper was created to present to the reader an accurate history of the ISSM. The article is divided into the early beginnings of the idea of the field of sexual medicine, followed by the organization of what was to become eventually the International Society for Sexual Medicine, description of the development of biennial meetings and some of the major events that occurred at these meetings, a description of officers and leaders of the society and some of their key contributions, other meetings that the ISSM was actively involved in in the field of sexual medicine, a detailed discussion of publications and communications of the organization, and finally a description of the involvement of the ISSM with the recognition of scientific achievement and research in the field. This history is indeed very rich and unique for the parallelism to the development of the entire field of sexual medicine as a true science. The author has spent a great deal of time in making sure that there is written material that substantiates the history that is outlined in this document. It is provided to the reader as a true historical perspective on the ISSM. Lewis RW. The International Society for Sexual Medicine: A rich history and a bright future. Sex Med Rev 2013; 1:65-75. Copyright © 2013 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

  18. Identification and positional distribution analysis of transcription factor binding sites for genes from the wheat fl-cDNA sequences.

    PubMed

    Chen, Zhen-Yong; Guo, Xiao-Jiang; Chen, Zhong-Xu; Chen, Wei-Ying; Wang, Ji-Rui

    2017-06-01

    The binding sites of transcription factors (TFs) in upstream DNA regions are called transcription factor binding sites (TFBSs). TFBSs are important elements for regulating gene expression. To date, there have been few studies on the profiles of TFBSs in plants. In total, 4,873 sequences with 5' upstream regions from 8530 wheat fl-cDNA sequences were used to predict TFBSs. We found 4572 TFBSs for the MADS TF family, which was twice as many as for bHLH (1951), B3 (1951), HB superfamily (1914), ERF (1820), and AP2/ERF (1725) TFs, and was approximately four times higher than the remaining TFBS types. The percentage of TFBSs and TF members showed a distinct distribution in different tissues. Overall, the distribution of TFBSs in the upstream regions of wheat fl-cDNA sequences had significant difference. Meanwhile, high frequencies of some types of TFBSs were found in specific regions in the upstream sequences. Both TFs and fl-cDNA with TFBSs predicted in the same tissues exhibited specific distribution preferences for regulating gene expression. The tissue-specific analysis of TFs and fl-cDNA with TFBSs provides useful information for functional research, and can be used to identify relationships between tissue-specific TFs and fl-cDNA with TFBSs. Moreover, the positional distribution of TFBSs indicates that some types of wheat TFBS have different positional distribution preferences in the upstream regions of genes.

  19. Observations of low-energy electrons upstream of the earth's bow shock

    NASA Technical Reports Server (NTRS)

    Reasoner, D. L.

    1974-01-01

    Observations of electron fluxes with a lunar-based electron spectrometer when the moon was upstream of the earth have shown that a subset of observed fluxes are strongly controlled by the interplanetary magnetic field direction. The fluxes occur only when the IMF lines connect back to the earth's bow shock. Observed densities and temperatures were in the ranges 2-4 x 0,001/cu cm and 1.7-2.8 x 1,000,000 K. It is shown that these electrons can account for increases in effective solar wind electron temperatures on bow-shock connected field lines which have been observed previously by other investigators. It is further shown that if a model of the bow shock with an electrostatic potential barrier is assumed, the potential can be estimated to be 500 volts.

  20. e(sup +/-) Pair Loading and the Origin of the Upstream Magnetic Field in GRB Shocks

    NASA Technical Reports Server (NTRS)

    Ramirez-Ruiz, Enrico; Nishikawa, Ken-Ichi; Hededal, Christian B.

    2006-01-01

    We investigate here the effects of plasma instabilities driven by rapid e(sup +/-) pair cascades, which arise in the environment of GRB sources as a result of back-scattering of a seed fraction of their original spectrum. The injection of e(sup +/-) pairs induces strong streaming motions in the ambient medium. One therefore expects the pair-enriched medium ahead of the forward shock to be strongly sheared on length scales comparable to the radiation front thickness. Using three-dimensional particle-in-cell simulations, we show that plasma instabilities driven by these streaming e(sup +/-) pairs are responsible for the excitation of near-equipartition, turbulent magnetic fields. Our results reveal the importance of the electromagnetic filamentation instability in ensuring an effective coupling between e(sup +/-) pairs and ions, and may help explain the origin of large upstream fields in GRB shocks.

  1. e+/- Pair Loading and the Origin of the Upstream Field in GRB Shocks

    NASA Technical Reports Server (NTRS)

    Ramirez-Ruiz, Enrico; Nishikawa, Ken-Ichi; Hededal, Christian B.

    2006-01-01

    We investigate here the effects of plasma instabilities driven by rapid e(sup plus or minus) pair cascades, which arise in the environment of GRB sources as a result of back-scattering of a seed fraction of their original spectrum. The injection of e(sup plus or minus) pairs induces strong streaming motions in the ambient medium. One therefore expects the pair-enriched medium ahead of the forward shock to be strongly sheared on length scales comparable to the radiation front thickness. Using three-dimensional particle-in-cell simulations, we show that plasma instabilities driven by these streaming e(sup plus or minus) pairs are responsible for the excitation of near-equipartition, turbulent magnetic fields. Our results reveal the importance of the electromagnetic filamentation instability in ensuring an effective coupling between e(sup plus or minus) pairs and ions, and may help explain the origin of large upstream fields in GRB shocks.

  2. Effects of upstream-biased third-order space correction terms on multidimensional Crowley advection schemes

    NASA Technical Reports Server (NTRS)

    Schlesinger, R. E.

    1985-01-01

    The impact of upstream-biased corrections for third-order spatial truncation error on the stability and phase error of the two-dimensional Crowley combined advective scheme with the cross-space term included is analyzed, putting primary emphasis on phase error reduction. The various versions of the Crowley scheme are formally defined, and their stability and phase error characteristics are intercompared using a linear Fourier component analysis patterned after Fromm (1968, 1969). The performances of the schemes under prototype simulation conditions are tested using time-dependent numerical experiments which advect an initially cone-shaped passive scalar distribution in each of three steady nondivergent flows. One such flow is solid rotation, while the other two are diagonal uniform flow and a strongly deformational vortex.

  3. Toxicity assessment of sediments collected upstream and downstream from the White Dam in Clarke County, Georgia

    USGS Publications Warehouse

    Lasier, Peter J.

    2018-06-06

    The White Dam in Clarke County, Georgia, has been proposed for breaching. Efforts to determine potential risks to downstream biota included assessments of sediment collected in the vicinity of the dam. Sediments collected from sites upstream and downstream from the dam were evaluated for toxicity in 42-day exposures using the freshwater amphipod Hyalella azteca. Endpoints of the study were survival, growth, and reproduction of H. azteca. Results indicated no significant differences between the collected sediments and the water-only treatment used for comparison of the test endpoints. Therefore, based on the laboratory experiments in this study, sediment migration downstream from a breach of the Dam may not pose a toxicity risk to downstream biota.

  4. Ion distributions in the Earth's foreshock upstream from the bow shock

    NASA Technical Reports Server (NTRS)

    Fuselier, S. A.

    1995-01-01

    A variety of suprathermal and energetic ion distributions are found upstream from shocks. Some distributions, such as field-aligned beams, are generated directly at the shock either through reflection processes or through leakage from the hotter downstream region. Other distributions, such as intermediate distributions, evolve from these parent distributions through wave-particle interactions. This paper reviews our current understanding of the creation and evolution of suprathermal distributions at shocks. Examples of suprathermal ion distributions are taken from observations at the Earth's bow shock. Particular emphasis is placed on the creation of field-aligned beams and specularly reflected ion distributions and on the evolution of these distributions in the Earth's ion foreshock. However, the results from this heavily studied region are applicable to interplanetary shocks, bow shocks at other planets, and comets.

  5. Upstream regulators and downstream effectors of NF-κB in Alzheimer's disease.

    PubMed

    Shi, Zhe-Min; Han, Ya-Wei; Han, Xiao-Hui; Zhang, Kun; Chang, Ya-Nan; Hu, Zhi-Mei; Qi, Hai-Xia; Ting, Chen; Zhen, Zhang; Hong, Wei

    2016-07-15

    Since Alzheimer's disease (AD) is becoming the prevalent dementia in the whole world, more underlying mechanisms are emerging. Long time has the transcription factor NF-κB been identified to participate in AD pathogenesis, various studies have focused on the causes and effects of AD that are linked to NF-κB. In this review we discuss diverse environmental stimuli including oxidative stress, neuroinflammation and metabolism, involved signaling pathways such as PI3K/AKT, MAPK and AGE/RAGE/GSK-3 and newly found ncRNAs that mediate neuron toxicity or neuron protection through NF-κB activation and the following response associated with the same factors in AD. These may provide future orientation of investigation at transcription level and support efficient treatment to AD by a better understanding of the upstream regulators and downstream effectors of NF-κB. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Properties of ultra low frequency upstream waves at Venus and Saturn: A comparison

    NASA Technical Reports Server (NTRS)

    Orlowski, D. S.; Russell, C. T.; Krauss-Varban, D.; Omidi, N.

    1995-01-01

    The upstream regions of all planets, except Pluto, have been investigated, using in situ spacecraft measurements and a variety of analysis techniques. The detailed studies at Earth indicate that these waves are generated locally in the magnetically connected solar wind by the interaction with ions backstreaming from the shock. However, since the properties of the solar wind vary with heliocentric distance and since properties of planetary shocks depend on plasma beta, interplanetary magnetic field (IMF) spiral angle and Mach number, the amount of heating, acceleration efficiencies, etc. significantly change with heliocentric distance. In turn the waves seen at each planet propagate not in the same but different (physical) propagation modes. In this paper we compare the ULF wave observations at an outer and an inner planet. We use the results of the ratio, quantites easily derivable with sufficient accuracy at each planet. We use the full electromagnetic dispersion relation for comparison with theoretical predictions.

  7. Detection of singly ionized energetic lunar pick-up ions upstream of earth's bow shock

    NASA Technical Reports Server (NTRS)

    Hilchenbach, M.; Hovestadt, D.; Klecker, B.; Moebius, E.

    1992-01-01

    Singly ionized suprathermal ions upstream of the earth's bow shock have been detected by using the time-of-flight spectrometer SULEICA on the AMPTE/IRM satellite. The data were collected between August and December 1985. The flux of the ions in the mass range between 23 and 37 amu is highly anisotropic towards the earth. The ions are observed with a period of about 29 days around new moon (+/- 3 days). The correlation of the energy of the ions with the solar wind speed and the interplanetary magnetic field orientation indicates the relation to the pick-up process. We conclude that the source of these pick-up ions is the moon. We argue that due to the impinging solar wind, atoms are sputtered off the lunar surface, ionized in the sputtering process or by ensuing photoionization and picked up by the solar wind.

  8. Excitation of MHD waves upstream of Jupiter by energetic sulfur or oxygen ions

    NASA Technical Reports Server (NTRS)

    Goldstein, M. L.; Wong, H. K.; Eviatar, A.

    1986-01-01

    Large fluxes of heavy ions have been reported upstream of Jupiter's bow shock as Voyager 1 approached the planet (Zwickl et al., 1981; Krimigis et al., 1985). Enhanced low-frequency magnetic wave activity was also observed during the particle events. The fluctuations are left-handed, elliptically polarized in the plasma frame. The spectrum of these fluctuations contains a peak close to the Doppler-shifted resonance frequency of a sulfur or oxygen beam with streaming energy of approximately 30 keV. These fluctuations are also present in the spectrum of the magnitude of the field. It is concluded that the observations result from an instability driven by an energetic beam of either sulfur or oxygen. The wave observations can be described by a heavy ion distribution with both a streaming anisotropy and a temperature anisotropy. This class of heavy ion streaming instabilities may also play a role in wave-particle interactions in the vicinity of comets.

  9. Consumption‐Based Conservation Targeting: Linking Biodiversity Loss to Upstream Demand through a Global Wildlife Footprint

    PubMed Central

    Berlow, Eric; Conlisk, Erin; Erb, Karlheinz; Iha, Katsunori; Martinez, Neo; Newman, Erica A.; Plutzar, Christoph; Smith, Adam B.; Harte, John

    2016-01-01

    Abstract Although most conservation efforts address the direct, local causes of biodiversity loss, effective long‐term conservation will require complementary efforts to reduce the upstream economic pressures, such as demands for food and forest products, which ultimately drive these downstream losses. Here, we present a wildlife footprint analysis that links global losses of wild birds to consumer purchases across 57 economic sectors in 129 regions. The United States, India, China, and Brazil have the largest regional wildlife footprints, while per‐person footprints are highest in Mongolia, Australia, Botswana, and the United Arab Emirates. A US$100 purchase of bovine meat or rice products occupies approximately 0.1 km2 of wild bird ranges, displacing 1–2 individual birds, for 1 year. Globally significant importer regions, including Japan, the United Kingdom, Germany, Italy, and France, have large footprints that drive wildlife losses elsewhere in the world and represent important targets for consumption‐focused conservation attention. PMID:29104616

  10. High time resolution characteristics of intermediate ion distributions upstream of the earth's bow shock

    NASA Technical Reports Server (NTRS)

    Potter, D. W.

    1985-01-01

    High time resolution particle data upstream of the bow shock during time intervals that have been identified as having intermediate ion distributions often show high amplitude oscillations in the ion fluxes of energy 2 and 6 keV. These ion oscillations, observed with the particle instruments of the University of California, Berkeley, on the ISEE 1 and 2 spacecraft, are at the same frequency (about 0.04 Hz) as the magnetic field oscillations. Typically, the 6-keV ion flux increases then the 2-keV flux increases followed by a decrease in the 2-keV flux and then the 6-keV flux decreases. This process repeats many times. Although there is no entirely satisfactory explanation, the presence of these ion flux oscillations suggests that distributions often are misidentified as intermediate ion distributions.

  11. The density of cometary protons upstream of Comet Halley's bow shock

    NASA Astrophysics Data System (ADS)

    Neugebauer, M.; Goldstein, B. E.; Balsiger, H.; Neubauer, F. M.; Schwenn, R.; Shelley, E. G.

    1989-02-01

    Cometary protons picked up by the solar wind were detected by the high energy range spectrometer of the Giotto ion mass spectrometer starting at a cometocentric distance of about 12 million km. On the average, the density of cometary protons varied approximately as the inverse square of the cometocentric distance, reaching a value of 0.11/cu cm just outside the bow shock. The data can be successfully fit to models that include substantial amounts of both slow (1 km/s) and fast (8 km/s or greater) H atoms beyond the bow shock. Large local variations in the density of picked-up protons can be explained on the basis of variations in the direction of the interplanetary magnetic field in upstream regions where pitch angle scattering was weak.

  12. 8-channel prototype of SALT readout ASIC for Upstream Tracker in the upgraded LHCb experiment

    NASA Astrophysics Data System (ADS)

    Abellan Beteta, C.; Bugiel, S.; Dasgupta, R.; Firlej, M.; Fiutowski, T.; Idzik, M.; Kane, C.; Moron, J.; Swientek, K.; Wang, J.

    2017-02-01

    SALT is a new 128-channel readout ASIC for silicon strip detectors in the upgraded Upstream Tracker of the LHCb experiment. It will extract and digitise analogue signals from the sensor, perform digital processing and transmit serial output data. SALT is designed in CMOS 130 nm process and uses a novel architecture comprising of an analogue front-end and an ultra-low power (<0.5 mW) fast (40 MSps) sampling 6-bit ADC in each channel. An 8-channel prototype (SALT8), comprising all important functionalities was designed, fabricated and tested. A full 128-channel version was also submitted. The design and test results of the SALT8 prototype are presented showing its full functionality.

  13. An uncertainty analysis of the flood-stage upstream from a bridge.

    PubMed

    Sowiński, M

    2006-01-01

    The paper begins with the formulation of the problem in the form of a general performance function. Next the Latin hypercube sampling (LHS) technique--a modified version of the Monte Carlo method is briefly described. The essential uncertainty analysis of the flood-stage upstream from a bridge starts with a description of the hydraulic model. This model concept is based on the HEC-RAS model developed for subcritical flow under a bridge without piers in which the energy equation is applied. The next section contains the characteristic of the basic variables including a specification of their statistics (means and variances). Next the problem of correlated variables is discussed and assumptions concerning correlation among basic variables are formulated. The analysis of results is based on LHS ranking lists obtained from the computer package UNCSAM. Results fot two examples are given: one for independent and the other for correlated variables.

  14. Plasma and energetic particle structure upstream of a quasi-parallel interplanetary shock

    NASA Technical Reports Server (NTRS)

    Kennel, C. F.; Scarf, F. L.; Coroniti, F. V.; Russell, C. T.; Wenzel, K.-P.; Sanderson, T. R.; Van Nes, P.; Smith, E. J.; Tsurutani, B. T.; Scudder, J. D.

    1984-01-01

    ISEE 1, 2 and 3 data from 1978 on interplanetary magnetic fields, shock waves and particle energetics are examined to characterize a quasi-parallel shock. The intense shock studied exhibited a 640 km/sec velocity. The data covered 1-147 keV protons and electrons and ions with energies exceeding 30 keV in regions both upstream and downstream of the shock, and also the magnitudes of ion-acoustic and MHD waves. The energetic particles and MHD waves began being detected 5 hr before the shock. Intense halo electron fluxes appeared ahead of the shock. A closed magnetic field structure was produced with a front end 700 earth radii from the shock. The energetic protons were cut off from the interior of the magnetic bubble, which contained a markedly increased density of 2-6 keV protons as well as the shock itself.

  15. The serine protease inhibitor TLCK attenuates intrinsic death pathways in neurons upstream of mitochondrial demise.

    PubMed

    Reuther, C; Ganjam, G K; Dolga, A M; Culmsee, C

    2014-11-01

    It is well-established that activation of proteases, such as caspases, calpains and cathepsins are essential components in signaling pathways of programmed cell death (PCD). Although these proteases have also been linked to mechanisms of neuronal cell death, they are dispensable in paradigms of intrinsic death pathways, e.g. induced by oxidative stress. However, emerging evidence implicated a particular role for serine proteases in mechanisms of PCD in neurons. Here, we investigated the role of trypsin-like serine proteases in a model of glutamate toxicity in HT-22 cells. In these cells glutamate induces oxytosis, a form of caspase-independent cell death that involves activation of the pro-apoptotic protein BH3 interacting-domain death agonist (Bid), leading to mitochondrial demise and ensuing cell death. In this model system, the trypsin-like serine protease inhibitor Nα-tosyl-l-lysine chloromethyl ketone hydrochloride (TLCK) inhibited mitochondrial damage and cell death. Mitochondrial morphology alterations, the impairment of the mitochondrial membrane potential and ATP depletion were prevented and, moreover, lipid peroxidation induced by glutamate was completely abolished. Strikingly, truncated Bid-induced cell death was not affected by TLCK, suggesting a detrimental activity of serine proteases upstream of Bid activation and mitochondrial demise. In summary, this study demonstrates the protective effect of serine protease inhibition by TLCK against oxytosis-induced mitochondrial damage and cell death. These findings indicate that TLCK-sensitive serine proteases play a crucial role in cell death mechanisms upstream of mitochondrial demise and thus, may serve as therapeutic targets in diseases, where oxidative stress and intrinsic pathways of PCD mediate neuronal cell death.

  16. Chandra observations of Jupiter's X-ray Aurora during Juno upstream and apojove intervals

    NASA Astrophysics Data System (ADS)

    Dunn, W.; Jackman, C. M.; Kraft, R.; Gladstone, R.; Branduardi-Raymont, G.; Knigge, C.; Altamirano, D.; Elsner, R.; Kammer, J.

    2017-12-01

    The Chandra space telescope has recently conducted a number of campaigns to observe Jupiter's X-ray aurora. The first set of campaigns took place in summer 2016 while the Juno spacecraft was upstream of the planet sampling the solar wind. The second set of campaigns took place in February, June and August 2017 at times when the Juno spacecraft was at apojove. These campaigns were planned following the Juno orbit correction to capitalise on the opportunity to image the X-ray emission while Juno was orbiting close to the expected position of the magnetopause. Previous work has suggested that the auroral X-ray emissions map close to the magnetopause boundary [e.g. Vogt et al., 2015; Kimura et al., 2016; Dunn et al., 2016] and thus in situ spacecraft coverage in this region combined with remote observation of the X-rays afford the chance to constrain the drivers of these energetic emissions and determine if they originate on open or closed field lines. We aim to examine possible drivers of X-ray emission including reconnection and the Kelvin-Helmholtz instability and to explore the role of the solar wind in controlling the emissions. We report on these upstream and apojove campaigns including intensities and periodicities of auroral X-ray emissions. This new era of jovian X-ray astronomy means we have more data than ever before, long observing windows (up to 72 ks for this Chandra set), and successive observations relatively closely spaced in time. These features combine to allow us to pursue novel methods for examining periodicities in the X-ray emission. Our work will explore significance testing of emerging periodicities, and the search for coherence in X-ray pulsing over weeks and months, seeking to understand the robustness and regularity of previously reported hot spot X-ray emissions. The periods that emerge from our analysis will be compared against those which emerge from radio and UV wavelengths.

  17. Energy optimization for upstream data transfer in 802.15.4 beacon-enabled star formulation

    NASA Astrophysics Data System (ADS)

    Liu, Hua; Krishnamachari, Bhaskar

    2008-08-01

    Energy saving is one of the major concerns for low rate personal area networks. This paper models energy consumption for beacon-enabled time-slotted media accessing control cooperated with sleeping scheduling in a star network formulation for IEEE 802.15.4 standard. We investigate two different upstream (data transfer from devices to a network coordinator) strategies: a) tracking strategy: the devices wake up and check status (track the beacon) in each time slot; b) non-tracking strategy: nodes only wake-up upon data arriving and stay awake till data transmitted to the coordinator. We consider the tradeoff between energy cost and average data transmission delay for both strategies. Both scenarios are formulated as optimization problems and the optimal solutions are discussed. Our results show that different data arrival rate and system parameters (such as contention access period interval, upstream speed etc.) result in different strategies in terms of energy optimization with maximum delay constraints. Hence, according to different applications and system settings, different strategies might be chosen by each node to achieve energy optimization for both self-interested view and system view. We give the relation among the tunable parameters by formulas and plots to illustrate which strategy is better under corresponding parameters. There are two main points emphasized in our results with delay constraints: on one hand, when the system setting is fixed by coordinator, nodes in the network can intelligently change their strategies according to corresponding application data arrival rate; on the other hand, when the nodes' applications are known by the coordinator, the coordinator can tune the system parameters to achieve optimal system energy consumption.

  18. Statistical analysis plan for the Urodynamics for Prostate Surgery Trial; Randomised Evaluation of Assessment Methods (UPSTREAM).

    PubMed

    Young, Grace J; Lewis, Amanda L; Lane, J Athene; Winton, Helen L; Drake, Marcus J; Blair, Peter S

    2017-10-03

    Current management for men with lower urinary tract symptoms (LUTS) is a pathway that results in prostate surgery in a significant proportion. While helpful in relieving benign prostatic obstruction (BPO), surgery may be ineffective for men suffering from difficulties not relating to BPO. The UPSTREAM trial started recruitment in October 2014 with the aim of establishing whether a care pathway including urodynamics (a diagnostic tool for BPO and thus an indication of whether surgery is needed) is no worse for men, in terms of symptomatic outcome, than one without (routine care). This analysis plan outlines the main outcomes of the study and specific design choices, such as non-inferiority margins. The trial is currently recruiting in 26 hospitals across the UK, randomising men to either urodynamics or routine care, with recruitment set to end on the 31 December 2016. All outcomes will be measured 18 months after randomisation to allow sufficient time for surgical procedures and recovery. The primary outcome is based on a non-inferiority design with a margin of 1 point on the International Prostate Symptom Score (IPSS) scale. The key secondary outcome for this trial is surgery rate per arm, which is estimated to be at least 18% lower in the urodynamics arm. Surgery rates, adverse events, flow rate, urinary symptoms and sexual symptoms are secondary outcomes to be assessed for superiority. This is an update to the UPSTREAM protocol, which has already been published in this journal. This a priori statistical analysis plan aims to reduce reporting bias by allowing access to the trial's objectives and plans in advance of recruitment end. The results of the trial are expected to be published soon after the trial end date of 30 September 2018. ISRCTN registry, ISRCTN56164274 . Registered on 8 April 2014.

  19. Differences in sedge fen vegetation upstream and downstream from a managed impoundment

    USGS Publications Warehouse

    Kowalski, Kurt P.; Wilcox, Douglas A.

    2003-01-01

    The U.S. Fish and Wildlife Service proposed the restoration of wetlands impacted by a series of drainage ditches and pools located in an extensive undeveloped peatland in the Seney National Wildlife Refuge, Michigan. This study examined the nature and extent of degradation to the Marsh Creek wetlands caused by alteration of natural hydrology by a water-storage pool (C-3 Pool) that intersects the Marsh Creek channel. We tested the hypothesis that a reduction in moderate-intensity disturbance associated with natural water-level fluctuations below the C-3 dike contributed to lower species richness, reduced floristic quality and a larger tree and shrub component than vegetation upstream from the pool. Wetland plant communities were sampled quantitatively and analyzed for species richness, floristic quality and physiognomy. Aerial photographs, GIS databases and GPS data contributed to the characterization and analysis of the Marsh Creek wetlands. Results showed that there was lower species richness in vegetated areas downstream from the pool, but not the anticipated growth in shrubs. Wetland vegetation upstream and downstream from the pool had similar floristic quality, except for a greater number of weedy taxa above the pool. Seepage through the pool dike and localized ground-water discharge created conditions very similar to those observed around beaver dams in Marsh Creek. In essence, the dike containing the C-3 Pool affected hydrology and wetland plant communities in a manner similar to an enormous beaver dam, except that it did not allow seasonal flooding episodes to occur. Management actions to release water from the pool into the original Marsh Creek channel at certain times and in certain amounts that mimic the natural flow regime would be expected to promote greater plant species richness and minimize the negative impacts of the dike.

  20. Suspended sediments from upstream tributaries as the source of downstream river sites

    NASA Astrophysics Data System (ADS)

    Haddadchi, Arman; Olley, Jon

    2014-05-01

    Understanding the efficiency with which sediment eroded from different sources is transported to the catchment outlet is a key knowledge gap that is critical to our ability to accurately target and prioritise management actions to reduce sediment delivery. Sediment fingerprinting has proven to be an efficient approach to determine the sources of sediment. This study examines the suspended sediment sources from Emu Creek catchment, south eastern Queensland, Australia. In addition to collect suspended sediments from different sites of the streams after the confluence of tributaries and outlet of the catchment, time integrated suspended samples from upper tributaries were used as the source of sediment, instead of using hillslope and channel bank samples. Totally, 35 time-integrated samplers were used to compute the contribution of suspended sediments from different upstream waterways to the downstream sediment sites. Three size fractions of materials including fine sand (63-210 μm), silt (10-63 μm) and fine silt and clay (<10 μm) were used to find the effect of particle size on the contribution of upper sediments as the sources of sediment after river confluences. And then samples were analysed by ICP-MS and -OES to find 41 sediment fingerprints. According to the results of Student's T-distribution mixing model, small creeks in the middle and lower part of the catchment were major source in different size fractions, especially in silt (10-63 μm) samples. Gowrie Creek as covers southern-upstream part of the catchment was a major contributor at the outlet of the catchment in finest size fraction (<10 μm) Large differences between the contributions of suspended sediments from upper tributaries in different size fractions necessitate the selection of appropriate size fraction on sediment tracing in the catchment and also major effect of particle size on the movement and deposition of sediments.

  1. A duplication upstream of SOX9 was not positively correlated with the SRY-negative 46,XX testicular disorder of sex development: A case report and literature review

    PubMed Central

    XIA, XIN-YI; ZHANG, CUI; LI, TIAN-FU; WU, QIU-YUE; LI, NA; LI, WEI-WEI; CUI, YING-XIA; LI, XIAO-JUN; SHI, YI-CHAO

    2015-01-01

    The 46,XX male disorder of sex development (DSD) is rarely observed in humans. Patients with DSD are all male with testicular tissue differentiation. The mechanism of sex determination and differentiation remains to be elucidated. In the present case report, an 46,XX inv (9) infertile male negative for the sex-determining region of the Y chromosome (SRY) gene was examined. This infertile male was systemically assessed by semen analysis, serum hormone testing and gonadal biopsy. Formalin-fixed and paraffin-embedded gonad tissues were assessed histochemically. The SRY gene was analyzed by fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR). The other 23 specific loci, including the azoospermia factor region on the Y chromosome and the sequence-targeted sites of the SRY-box 9 (SOX9) gene were analyzed by PCR. The genes RSPO1, DAX1, SOX3, ROCK, DMRT1, SPRY2 and FGF9 were also assessed using sequencing analysis. Affymetrix Cytogenetics Whole Genome 2.7 M Arrays were used for detecting the genomic DNA from the patient and the parents. The patient with the 46,XX inv (9) (p11q13) karyotype exhibited male primary, however, not secondary sexual characteristics. However, the patient's mother with the 46, XX inv (9) karyotype was unaffected. The testicular tissue dysplasia of the patient was confirmed by tissue biopsy and absence of the SRY gene, and the other 23 loci on the Y chromosome were confirmed by FISH and/or PCR. The RSPO1, DAX1, SOX3, ROCK, DMRT1, SPRY2 and FGF9 genes were sequenced and no mutations were detected. A duplication on the 3 M site in the upstream region of SOX9 was identified in the patient as well as in the mother. The patient with the 46,XX testicular DSD and SRY-negative status was found to be infertile. The duplication on the 3 M site in the upstream region of SOX9 was a polymorphism, which indicated that the change was not a cause of 46,XX male SDS. These clinical, molecular and cytogenetic findings suggested that other

  2. A duplication upstream of SOX9 was not positively correlated with the SRY‑negative 46,XX testicular disorder of sex development: A case report and literature review.

    PubMed

    Xia, Xin-Yi; Zhang, Cui; Li, Tian-Fu; Wu, Qiu-Yue; Li, Na; Li, Wei-Wei; Cui, Ying-Xia; Li, Xiao-Jun; Shi, Yi-Chao

    2015-10-01

    The 46,XX male disorder of sex development (DSD) is rarely observed in humans. Patients with DSD are all male with testicular tissue differentiation. The mechanism of sex determination and differentiation remains to be elucidated. In the present case report, an 46,XX inv (9) infertile male negative for the sex‑determining region of the Y chromosome (SRY) gene was examined. This infertile male was systemically assessed by semen analysis, serum hormone testing and gonadal biopsy. Formalin‑fixed and paraffin‑embedded gonad tissues were assessed histochemically. The SRY gene was analyzed by fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR). The other 23 specific loci, including the azoospermia factor region on the Y chromosome and the sequence-targeted sites of the SRY‑box 9 (SOX9) gene were analyzed by PCR. The genes RSPO1, DAX1, SOX3, ROCK, DMRT1, SPRY2 and FGF9 were also assessed using sequencing analysis. Affymetrix Cytogenetics Whole Genome 2.7 M Arrays were used for detecting the genomic DNA from the patient and the parents. The patient with the 46,XX inv (9) (p11q13) karyotype exhibited male primary, however, not secondary sexual characteristics. However, the patient's mother with the 46, XX inv (9) karyotype was unaffected. The testicular tissue dysplasia of the patient was confirmed by tissue biopsy and absence of the SRY gene, and the other 23 loci on the Y chromosome were confirmed by FISH and/or PCR. The RSPO1, DAX1, SOX3, ROCK, DMRT1, SPRY2 and FGF9 genes were sequenced and no mutations were detected. A duplication on the 3 M site in the upstream region of SOX9 was identified in the patient as well as in the mother. The patient with the 46,XX testicular DSD and SRY‑negative status was found to be infertile. The duplication on the 3 M site in the upstream region of SOX9 was a polymorphism, which indicated that the change was not a cause of 46,XX male SDS. These clinical, molecular and cytogenetic findings suggested that

  3. The sequence of sequencers: The history of sequencing DNA

    PubMed Central

    Heather, James M.; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401

  4. The sequence of sequencers: The history of sequencing DNA.

    PubMed

    Heather, James M; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  5. Identification of a peroxisome proliferator-responsive element upstream of the gene encoding rat peroxisomal enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase.

    PubMed Central

    Zhang, B; Marcus, S L; Sajjadi, F G; Alvares, K; Reddy, J K; Subramani, S; Rachubinski, R A; Capone, J P

    1992-01-01

    Ciprofibrate, a hypolipidemic drug that acts as a peroxisome proliferator, induces the transcription of genes encoding peroxisomal beta-oxidation enzymes. To identify cis-acting promoter elements involved in this induction, 5.8 kilobase pairs of promoter sequence from the gene encoding rat peroxisomal enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase (EC 4.2.1.17/EC 1.1.1.35) was inserted upstream of a luciferase reporter gene. Transfection of this expression vector into rat hepatoma H4IIEC3 cells in the presence of ciprofibrate resulted in a 5- to 10-fold, cell type-specific increase in luciferase activity as compared to cells transfected in the absence of drug. A peroxisome proliferator-responsive element (PPRE) was localized to a 196-nucleotide region centered at position -2943 from the transcription start site. This PPRE conferred ciprofibrate responsiveness on a heterologous promoter and functioned independently of orientation or position. Gel retardation analysis with nuclear extracts demonstrated that ciprofibrate-treated or untreated H4IIEC3 cells, but not HeLa cells or monkey kidney cells, contained sequence-specific DNA binding factors that interact with the PPRE. These results have implications for understanding the mechanisms of coordinated transcriptional induction of genes encoding peroxisomal proteins by hypolipidemic agents and other peroxisome proliferators. Images PMID:1502166

  6. Use of the multipurpose transposon Tn KPK2 for the mutational analysis of chromosomal regions upstream and downstream of the sipF gene in Bradyrhizobium japonicum.

    PubMed

    Müller, P

    2004-04-01

    The DNA regions upstream and downstream of the Bradyrhizobium japonicum gene sipF were cloned by in vivo techniques and subsequently sequenced. In order to study the function of the predicted genes, a new transposon for in vitro mutagenesis, Tn KPK2, was constructed. This mutagenesis system has a number of advantages over other transposons. Tn KPK2 itself has no transposase gene, making transposition events stable. Extremely short inverted repeats minimize the length of the transposable element and facilitate the determination of the nucleotide sequence of the flanking regions. Since the transposable element carries a promoterless ' phoA reporter gene, the appearance of functional PhoA fusion proteins indicates that Tn KPK2 has inserted in a gene encoding a periplasmic or secreted protein. Although such events are extremely rare, because the transposon has to insert in-frame, in the correct orientation, and at an appropriate location in the target molecule, a direct screening procedure on agar indicator plates permits the identification of candidate clones from large numbers of colonies. In this study, Tn KPK2 was used for the construction of various symbiotic mutants of B. japonicum. One of the mutant strains, A2-10, which is defective in a gene encoding a protein that comigrates with bacterioferritin ( bcpB), was found to induce the formation of small and ineffective nodules.

  7. Noncanonical expression of a murine cytomegalovirus early protein CD8 T-cell epitope as an immediate early epitope based on transcription from an upstream gene.

    PubMed

    Fink, Annette; Büttner, Julia K; Thomas, Doris; Holtappels, Rafaela; Reddehase, Matthias J; Lemmermann, Niels A W

    2014-02-14

    Viral CD8 T-cell epitopes, represented by viral peptides bound to major histocompatibility complex class-I (MHC-I) glycoproteins, are often identified by "reverse immunology", a strategy not requiring biochemical and structural knowledge of the actual viral protein from which they are derived by antigen processing. Instead, bioinformatic algorithms predicting the probability of C-terminal cleavage in the proteasome, as well as binding affinity to the presenting MHC-I molecules, are applied to amino acid sequences deduced from predicted open reading frames (ORFs) based on the genomic sequence. If the protein corresponding to an antigenic ORF is known, it is usually inferred that the kinetic class of the protein also defines the phase in the viral replicative cycle during which the respective antigenic peptide is presented for recognition by CD8 T cells. We have previously identified a nonapeptide from the predicted ORFm164 of murine cytomegalovirus that is presented by the MHC-I allomorph H-2 Dd and that is immunodominant in BALB/c (H-2d haplotype) mice. Surprisingly, although the ORFm164 protein gp36.5 is expressed as an Early (E) phase protein, the m164 epitope is presented already during the Immediate Early (IE) phase, based on the expression of an upstream mRNA starting within ORFm167 and encompassing ORFm164.

  8. The dicistronic RNA from the mouse LINE-1 retrotransposon contains an internal ribosome entry site upstream of each ORF: implications for retrotransposition

    PubMed Central

    2006-01-01

    Most eukaryotic mRNAs are monocistronic and translated by cap-dependent initiation. LINE-1 RNA is exceptional because it is naturally dicistronic, encoding two proteins essential for retrotransposition, ORF1p and ORF2p. Here, we show that sequences upstream of ORF1 and ORF2 in mouse L1 function as internal ribosome entry sites (IRESes). Deletion analysis of the ORF1 IRES indicates that RNA structure is critical for its function. Conversely, the ORF2 IRES localizes to 53 nt near the 3′ end of ORF1, and appears to depend upon sequence rather than structure. The 40 nt intergenic region (IGR) is not essential for ORF2 IRES function or retrotransposition. Because of strong cis-preference for both proteins during L1 retrotransposition, correct stoichiometry of the two proteins can only be achieved post-transcriptionally. Although the precise stoichiometry is unknown, the retrotransposition intermediate likely contains hundreds of ORF1ps for every ORF2p, together with one L1 RNA. IRES-mediated translation initiation is a well-established mechanism of message-specific regulation, hence, unique mechanisms for the recognition and control of these two IRESes in the L1 RNA could explain differences in translational efficiency of ORF1 and ORF2. In addition, translational regulation may provide an additional layer of control on L1 retrotransposition efficiency, thereby protecting the integrity of the genome. PMID:16464823

  9. New approaches for moving upstream: how state and local health departments can transform practice to reduce health inequalities.

    PubMed

    Freudenberg, Nicholas; Franzosa, Emily; Chisholm, Janice; Libman, Kimberly

    2015-04-01

    Growing evidence shows that unequal distribution of wealth and power across race, class, and gender produces the differences in living conditions that are "upstream" drivers of health inequalities. Health educators and other public health professionals, however, still develop interventions that focus mainly on "downstream" behavioral risks. Three factors explain the difficulty in translating this knowledge into practice. First, in their allegiance to the status quo, powerful elites often resist upstream policies and programs that redistribute wealth and power. Second, public health practice is often grounded in dominant biomedical and behavioral paradigms, and health departments also face legal and political limits on expanding their scope of activities. Finally, the evidence for the impact of upstream interventions is limited, in part because methodologies for evaluating upstream interventions are less developed. To illustrate strategies to overcome these obstacles, we profile recent campaigns in the United States to enact living wages, prevent mortgage foreclosures, and reduce exposure to air pollution. We then examine how health educators working in state and local health departments can transform their practice to contribute to campaigns that reallocate the wealth and power that shape the living conditions that determine health and health inequalities. We also consider health educators' role in producing the evidence that can guide transformative expansion of upstream interventions to reduce health inequalities. © 2015 Society for Public Health Education.

  10. Blade-to-Blade Variations in Shocks Upstream of Both a Forward-Swept and an Aft-Swept Fan

    NASA Technical Reports Server (NTRS)

    Podboy, Gary G.; Krupar, Martin J.

    2006-01-01

    Detailed laser Doppler velocimeter (LDV) flow field measurements were made upstream of two fans, one forward-swept and one aft-swept, in order to learn more about the shocks which propagate upstream of these rotors when they are operated at supersonic tip speeds. The blade-to-blade variations in the flows associated with these shocks are thought to be responsible for generating Multiple Pure Tone (MPT) noise. The measured blade-to-blade variations are documented in this report through a series of slideshows which show relative Mach number contours computed from the velocity measurements. Data are presented for the forward-swept fan operating at three speeds (corresponding to tip relative Mach numbers of 0.817, 1.074, and 1.189), and for the aft-swept fan operating at two (tip relative Mach numbers of 1.074 and 1.189). These LDV data illustrate how the perturbations in the upstream flow field created by the rotating blades vary with axial position, radial position and rotor speed. As expected, at the highest tested speed the forward-swept fan swallowed the shocks which occur in the tip region, whereas the aftswept fan did not. This resulted in a much smaller flow disturbance just upstream of the tip of the forward-swept fan. Nevertheless, further upstream the two fan flows were much more similar.

  11. Ocean warming expands habitat of a rich natural resource and benefits a national economy.

    PubMed

    Jansen, Teunis; Post, Søren; Kristiansen, Trond; Óskarsson, Guðmundur J; Boje, Jesper; MacKenzie, Brian R; Broberg, Mala; Siegstad, Helle

    2016-10-01

    Geographic redistribution of living natural resources changes access and thereby harvesting opportunities between countries. Internationally shared fish resources can be sensitive to shifts in the marine environment and this may have great impact on the economies of countries and regions that rely most heavily on fisheries to provide employment and food supply. Here we present a climate change-related biotic expansion of a rich natural resource with substantial economic consequences, namely the appearance of northeast Atlantic mackerel (Scomber scombrus) in Greenlandic waters. In recent years, the summer temperature has reached record highs in the Irminger Current, and this development has expanded the available and realized mackerel habitat in time and space. Observations in the Irminger Current in east Greenland in 2011 of this temperature-sensitive epipelagic fish were the first records so far northwest in the Atlantic. This change in migration pattern was followed by a rapid development of a large-scale fishery of substantial importance for the national economy of Greenland (23% of Greenland's export value of all goods in 2014). A pelagic trawl survey was conducted in mid-summer 2014 and the results showed that the bulk of ~1 million Mg (=t) of mackerel in the Irminger Current in southeast Greenland were located in the relatively warm (>8.5°C) surface layer. Mackerel was also observed in southwest Greenland. Finally, 15 CMIP5 Earth System Model projections of future marine climate were used to evaluate the epipelagic environment in Greenland. These projections for moderate and high CO 2 emission scenarios (representative concentration pathways [RCP] 4.5 and 8.5) suggest how the available mackerel habitat may expand further in space and time. Overall, our results indicate that, if the stock remains large, productive, and continues its current migration pattern, then climate change has provided Greenland with a new unique opportunity for commercial exploitation

  12. An Upstream Truncation of the furA-katG Operon Confers High-Level Isoniazid Resistance in a Mycobacterium tuberculosis Clinical Isolate with No Known Resistance-Associated Mutations

    PubMed Central

    Yam, Wing Cheong; Zhang, Ying; Kao, Richard Y. T.

    2014-01-01

    Although the major causes of isoniazid (INH) resistance in Mycobacterium tuberculosis are confined to structural mutations in katG and promoter mutations in the mabA-inhA operon, a significant proportion of INH-resistant strains have unknown resistance mechanisms. Recently, we identified a high-level INH-resistant M. tuberculosis clinical isolate, GB005, with no known resistance-associated mutations. A comprehensive study was performed to investigate the molecular basis of drug resistance in this strain. Although no mutations were found throughout the katG and furA-katG intergenic region, the katG expression and the catalase activity were greatly diminished compared to those in H37Rv (P < 0.01). Northern blotting revealed that the katG transcript from the isolate was smaller than that of H37Rv. Sequencing analysis of furA and upstream genes discovered a 7.2-kb truncation extended from the 96th base preceding the initiation codon of katG. Complementation of the M. tuberculosis Δ(furA-katG) strain with katG and different portions of the truncated region identified a 134-bp upstream fragment of furA that was essential for full catalase activity and INH susceptibility in M. tuberculosis. The promoter activity of this fragment was also shown to be stronger than that of the furA-katG intergenic region (P < 0.01). Collectively, these findings demonstrate that deletion of the 134-bp furA upstream fragment is responsible for the reduction in katG expression, resulting in INH resistance in GB005. To our knowledge, this is the first report showing that deletion of the upstream region preceding the furA-katG operon causes high-level INH resistance in a clinical isolate of M. tuberculosis. PMID:25092698

  13. Multimodal sequence learning.

    PubMed

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Coordinate cytokine regulatory sequences

    DOEpatents

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

    2005-05-10

    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  15. Science sequence design

    NASA Technical Reports Server (NTRS)

    Koskela, P. E.; Bollman, W. E.; Freeman, J. E.; Helton, M. R.; Reichert, R. J.; Travers, E. S.; Zawacki, S. J.

    1973-01-01

    The activities of the following members of the Navigation Team are recorded: the Science Sequence Design Group, responsible for preparing the final science sequence designs; the Advanced Sequence Planning Group, responsible for sequence planning; and the Science Recommendation Team (SRT) representatives, responsible for conducting the necessary sequence design interfaces with the teams during the mission. The interface task included science support in both advance planning and daily operations. Science sequences designed during the mission are also discussed.

  16. Molecular architecture of the hsp70 promoter after deletion of the TATA box or the upstream regulation region.

    PubMed Central

    Weber, J A; Taxman, D J; Lu, Q; Gilmour, D S

    1997-01-01

    GAGA factor, TFIID, and paused polymerase are present on the hsp70 promoter in Drosophila melanogaster prior to transcriptional activation. In order to investigate the interplay between these components, mutant constructs were analyzed after they had been transformed into flies on P elements. One construct lacked the TATA box and the other lacked the upstream regulatory region where GAGA factor binds. Transcription of each mutant during heat shock was at least 50-fold less than that of a normal promoter construct. Before and after heat shock, both mutant promoters were found to adopt a DNase I hypersensitive state that included the region downstream from the transcription start site. High-resolution analysis of the DNase I cutting pattern identified proteins that could be contributing to the hypersensitivity. GAGA factor footprints were clearly evident in the upstream region of the TATA deletion construct, and a partial footprint possibly caused by TFIID was evident on the TATA box of the upstream deletion construct. Permanganate treatment of intact salivary glands was used to further characterize each promoter construct. Paused polymerase and TFIID were readily detected on the normal promoter construct, whereas both deletions exhibited reduced levels of each of these factors. Hence both the TATA box and the upstream region are required to efficiently recruit TFIID and a paused polymerase to the promoter prior to transcriptional activation. In contrast, GAGA factor appears to be capable of binding and establishing a DNase I hypersensitive region in the absence of TFIID and polymerase. Interestingly, purified GAGA factor was found to bind near the transcription start site, and the strength of this interaction was increased by the presence of the upstream region. GAGA factor alone might be capable of establishing an open chromatin structure that encompasses the upstream regulatory region as well as the core promoter region, thus facilitating the binding of TFIID

  17. Risk assessment in the upstream crude oil supply chain: Leveraging analytic hierarchy process

    NASA Astrophysics Data System (ADS)

    Briggs, Charles Awoala

    For an organization to be successful, an effective strategy is required, and if implemented appropriately the strategy will result in a sustainable competitive advantage. The importance of decision making in the oil industry is reflected in the magnitude and nature of the industry. Specific features of the oil industry supply chain, such as its longer chain, the complexity of its transportation system, its complex production and storage processes, etc., pose challenges to its effective management. Hence, understanding the risks, the risk sources, and their potential impacts on the oil industry's operations will be helpful in proposing a risk management model for the upstream oil supply chain. The risk-based model in this research uses a three-level analytic hierarchy process (AHP), a multiple-attribute decision-making technique, to underline the importance of risk analysis and risk management in the upstream crude oil supply chain. Level 1 represents the overall goal of risk management; Level 2 is comprised of the various risk factors; and Level 3 represents the alternative criteria of the decision maker as indicated on the hierarchical structure of the crude oil supply chain. Several risk management experts from different oil companies around the world were surveyed, and six major types of supply chain risks were identified: (1) exploration and production, (2) environmental and regulatory compliance, (3) transportation, (4) availability of oil, (5) geopolitical, and (6) reputational. Also identified are the preferred methods of managing risks which include; (1) accept and control the risks, (2) avoid the risk by stopping the activity, or (3) transfer or share the risks to other companies or insurers. The results from the survey indicate that the most important risk to manage is transportation risk with a priority of .263, followed by exploration/production with priority of .198, with an overall inconsistency of .03. With respect to major objectives the most

  18. Coral record of variability in the upstream Kuroshio Current during 1953-2004

    NASA Astrophysics Data System (ADS)

    Li, Xiaohua; Liu, Yi; Hsin, Yi-Chia; Liu, Weiguo; Shi, Zhengguo; Chiang, Hong-Wei; Shen, Chuan-Chou

    2017-08-01

    The Kuroshio Current (KC), one of the most important western boundary currents in the North Pacific Ocean, strongly affects regional hydroclimate in East Asia and upper ocean thermal structure. Limited by few on-site observations, the responses of the KC to regional and remote climate forcings are still poorly understood. Here we use monthly coral δ18O data to reconstruct a KC transport record with annual to interannual resolution for the interval 1953-2004. The field site is located in southern Taiwan on the western flank of the upstream KC. Increased (reduced) KC transport would generate strong (weak) upwelling, resulting in relatively high (low) local coral δ18O. The upstream KC transport and downstream transport, off Tatsukushi Bay, Japan, covary on interannual and decadal time scales. This suggests common forcings, such as meridional drift of the North Equatorial Current bifurcation, or zonal climatic oscillations in the Pacific. The intensities of KC transport off southeastern and northeastern Taiwan are in phase before 1990 and antiphase after 1990. This difference may be due to a poleward shift of the subtropical western boundary current as a response to global warming.Plain Language SummaryThe connection between climate and oceanic circulation has long been recognized, particularly with regard to western boundary currents such as the Gulf Stream and the Kuroshio Current (KC). These systems play a crucial role in transferring solar energy from the subtropical regions to the poles. As we begin to experience the impacts of global climate change, it is critical that we understand the affect global change has on variability leading to significant changes in the structure and heat transport of such currents. Current knowledge of the KC is limited to observations over individual 10 year periods or to paleorecords of very low resolution (one sample per roughly 1000 years). Neither data set allows for a detailed</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2002EGSGA..27.1427S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2002EGSGA..27.1427S"><span>Numerical Simulations of <span class="hlt">Upstream</span> Propagating Solitary Waves and Wave Breaking In A Stratified Fjord</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Stastna, M.; Peltier, W. R.</p> <p></p> <p>In this talk we will discuss ongoing numerical modeling of the flow of a stratified fluid over large scale topography motivated by observations in Knight Inlet, a fjord in British Columbia, Canada. After briefly surveying the work done on the topic in the past we will discuss our latest set of simulations in which we have observed the gener- ation and breaking of three different types of nonlinear internal waves in the lee of the sill topography. The first type of wave observed is a large lee wave in the weakly strat- ified main portion of the water column, The second is an upward propagating internal wave forced by topography that breaks in the strong, near-surface pycnocline. The third is a train of <span class="hlt">upstream</span> propagating solitary waves that, in certain circumstances, form as breaking waves consisting of a nearly solitary wave envelope and a highly unsteady core near the surface. Time premitting, we will comment on the implications of these results for our long term goal of quantifying tidally driven mixing in Knight Inlet.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2017AGUFMGC31F..08K','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2017AGUFMGC31F..08K"><span>Quantifying the Consumptive Landscape in the Potomac Watershed <span class="hlt">Upstream</span> From Washington DC</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Kearns, M.; Zegre, N.; Fernandez, R.</p> <p>2017-12-01</p> <p>Some of the largest and fastest-growing eastern cities depend upon Appalachian headwaters for their fresh water. Today's relative abundance of water may be at risk: changes in climate and land use could alter the availability of surface water and human consumption could increase to meet the needs of a growing population and economy. Neither the supply of surface water nor the various withdrawals that support our population, irrigation, energy, and industry are distributed uniformly throughout our watersheds. This study correlates surface water withdrawals, consumptive use coefficients, and land-use/land-cover datasets to create a model for quantifying anthropogenic water consumption. The model suggests a method for downscaling and redistributing USGS county-level surface water withdrawals to 30 meter cells. Initially completed for the Potomac River watershed <span class="hlt">upstream</span> from Washington DC's public supply intake, this approach could easily scale regionally or nationally. When combined with runoff estimates over the same landscape, the net-production or net-consumption of an area of interest may be calculated at high resolution. By better understanding the spatial relationship between hydrologic supply and demand, we can seek to improve the efficiency and security of our water resources.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li class="active"><span>17</span></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_17 --> <div id="page_18" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li class="active"><span>18</span></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="341"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015SPIE.9480E..0DB','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015SPIE.9480E..0DB"><span>Applications for fiber optic sensing in the <span class="hlt">upstream</span> oil and gas industry</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Baldwin, Chris S.</p> <p>2015-05-01</p> <p>Fiber optic sensing has been used in an increasing number of applications in the <span class="hlt">upstream</span> oil and gas industry over the past 20 years. In some cases, fiber optic sensing is providing measurements where traditional measurement technologies could not. This paper will provide a general overview of these applications and describe how the use of fiber optic sensing is enabling these applications. Technologies such as Bragg gratings, distributed temperature and acoustic sensing, interferometric sensing, and Brillouin scattering will be discussed. Applications for optic sensing include a range of possibilities from a single pressure measurement point in the wellbore to multizone pressure and flow monitoring. Some applications make use of fully distributed measurements including thermal profiling of the well. Outside of the wellbore, fiber optic sensors are used in applications for flowline and pipeline monitoring and for riser integrity monitoring. Applications to be described in this paper include in-flow profiling, well integrity, production monitoring, and steam chamber growth. These applications will cover well types such as injectors, producers, hydraulic fracturing, and thermal recovery. Many of these applications use the measurements provided by fiber optic sensing to improve enhanced oil recovery operations. The growing use of fiber optic sensors is providing improved measurement capabilities leading to the generation of actionable data for enhanced production optimization. This not only increases the recovered amount of production fluids but can also enhance wellbore integrity and safety.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4973614','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4973614"><span>Trading Land: A Review of Approaches to Accounting for <span class="hlt">Upstream</span> Land Requirements of Traded Products</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Haberl, Helmut; Kastner, Thomas; Wiedenhofer, Dominik; Eisenmenger, Nina; Erb, Karl‐Heinz</p> <p>2015-01-01</p> <p>Summary Land use is recognized as a pervasive driver of environmental impacts, including climate change and biodiversity loss. Global trade leads to “telecoupling” between the land use of production and the consumption of biomass‐based goods and services. Telecoupling is captured by accounts of the <span class="hlt">upstream</span> land requirements associated with traded products, also commonly referred to as land footprints. These accounts face challenges in two main areas: (1) the allocation of land to products traded and consumed and (2) the metrics to account for differences in land quality and land‐use intensity. For two main families of accounting approaches (biophysical, factor‐based and environmentally extended input‐output analysis), this review discusses conceptual differences and compares results for land footprints. Biophysical approaches are able to capture a large number of products and different land uses, but suffer from a truncation problem. Economic approaches solve the truncation problem, but are hampered by the limited disaggregation of sectors and products. In light of the conceptual differences, the overall similarity of results generated by both types of approaches is remarkable. Diametrically opposed results for some of the world's largest producers and consumers of biomass‐based products, however, make interpretation difficult. This review aims to provide clarity on some of the underlying conceptual issues of accounting for land footprints. PMID:27547028</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5242187','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5242187"><span>Methane-Oxidizing Enzymes: An <span class="hlt">Upstream</span> Problem in Biological Gas-to-Liquids Conversion</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Lawton, Thomas J.; Rosenzweig, Amy C.</p> <p>2017-01-01</p> <p>Biological conversion of natural gas to liquids (Bio-GTL) represents an immense economic opportunity. In nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (MMO) and methyl coenzyme M reductase (MCR) enzymes. Although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in traditional industrial hosts. With turnover numbers of 0.16–13 s−1, these enzymes pose a considerable <span class="hlt">upstream</span> problem in the biological production of fuels or chemicals from methane. Methane oxidation enzymes will need to be engineered to be faster to enable high volumetric productivities; however, efforts to do so and to engineer simpler enzymes have been minimally successful. Moreover, known methane-oxidizing enzymes have different expression levels, carbon and energy efficiencies, require auxiliary systems for biosynthesis and function, and vary considerably in terms of complexity and reductant requirements. The pros and cons of using each methane-oxidizing enzyme for Bio-GTL are considered in detail. The future for these enzymes is bright, but a renewed focus on studying them will be critical to the successful development of biological processes that utilize methane as a feedstock. PMID:27366961</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3798279','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3798279"><span>Integrated Module and Gene-Specific Regulatory Inference Implicates <span class="hlt">Upstream</span> Signaling Networks</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Roy, Sushmita; Lagree, Stephen; Hou, Zhonggang; Thomson, James A.; Stewart, Ron; Gasch, Audrey P.</p> <p>2013-01-01</p> <p>Regulatory networks that control gene expression are important in diverse biological contexts including stress response and development. Each gene's regulatory program is determined by module-level regulation (e.g. co-regulation via the same signaling system), as well as gene-specific determinants that can fine-tune expression. We present a novel approach, Modular regulatory network learning with per gene information (MERLIN), that infers regulatory programs for individual genes while probabilistically constraining these programs to reveal module-level organization of regulatory networks. Using edge-, regulator- and module-based comparisons of simulated networks of known ground truth, we find MERLIN reconstructs regulatory programs of individual genes as well or better than existing approaches of network reconstruction, while additionally identifying modular organization of the regulatory networks. We use MERLIN to dissect global transcriptional behavior in two biological contexts: yeast stress response and human embryonic stem cell differentiation. Regulatory modules inferred by MERLIN capture co-regulatory relationships between signaling proteins and downstream transcription factors thereby revealing the <span class="hlt">upstream</span> signaling systems controlling transcriptional responses. The inferred networks are enriched for regulators with genetic or physical interactions, supporting the inference, and identify modules of functionally related genes bound by the same transcriptional regulators. Our method combines the strengths of per-gene and per-module methods to reveal new insights into transcriptional regulation in stress and development. PMID:24146602</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4511863','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4511863"><span>Integrated genomic approaches identify major pathways and <span class="hlt">upstream</span> regulators in late onset Alzheimer’s disease</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Li, Xinzhong; Long, Jintao; He, Taigang; Belshaw, Robert; Scott, James</p> <p>2015-01-01</p> <p>Previous studies have evaluated gene expression in Alzheimer’s disease (AD) brains to identify mechanistic processes, but have been limited by the size of the datasets studied. Here we have implemented a novel meta-analysis approach to identify differentially expressed genes (DEGs) in published datasets comprising 450 late onset AD (LOAD) brains and 212 controls. We found 3124 DEGs, many of which were highly correlated with Braak stage and cerebral atrophy. Pathway Analysis revealed the most perturbed pathways to be (a) nitric oxide and reactive oxygen species in macrophages (NOROS), (b) NFkB and (c) mitochondrial dysfunction. NOROS was also up-regulated, and mitochondrial dysfunction down-regulated, in healthy ageing subjects. <span class="hlt">Upstream</span> regulator analysis predicted the TLR4 ligands, STAT3 and NFKBIA, for activated pathways and RICTOR for mitochondrial genes. Protein-protein interaction network analysis emphasised the role of NFKB; identified a key interaction of CLU with complement; and linked TYROBP, TREM2 and DOK3 to modulation of LPS signalling through TLR4 and to phosphatidylinositol metabolism. We suggest that NEUROD6, ZCCHC17, PPEF1 and MANBAL are potentially implicated in LOAD, with predicted links to calcium signalling and protein mannosylation. Our study demonstrates a highly injurious combination of TLR4-mediated NFKB signalling, NOROS inflammatory pathway activation, and mitochondrial dysfunction in LOAD. PMID:26202100</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/1423981-survey-magnetosheath-plasma-properties-saturn-inference-upstream-flow-conditions','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/1423981-survey-magnetosheath-plasma-properties-saturn-inference-upstream-flow-conditions"><span>Survey of Magnetosheath Plasma Properties at Saturn and Inference of <span class="hlt">Upstream</span> Flow Conditions</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Thomsen, M. F.; Coates, A. J.; Jackman, C. M.</p> <p></p> <p>A new Cassini magnetosheath data set is introduced that is based on a comprehensive survey of intervals in which the observed magnetosheath flow was encompassed within the plasma analyzer field of view and for which the computed numerical moments are therefore expected to be accurate. The data extend from 2004 day 299 to 2012 day 151 and comprise 19,155 416-s measurements. In addition to the plasma ion moments (density, temperature, and flow velocity), merged values of the plasma electron density and temperature, the energetic particle pressure, and the magnetic field vector are included in the data set. Statistical properties ofmore » various magnetosheath parameters, including dependence on local time, are presented. The magnetosheath field and flow are found to be only weakly aligned, primarily because of a relatively large z-component of the magnetic field, attributable to the field being pulled out of the equatorial orientation by flows at higher latitudes. A new procedure for using magnetosheath properties to estimate the <span class="hlt">upstream</span> solar wind speed is proposed and used to determine that the amount of electron heating at Saturn's high Mach-number bow shock is ~4% of the dissipated flow energy. The data set is available as an electronic supplement to this paper.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/pages/biblio/1423981-survey-magnetosheath-plasma-properties-saturn-inference-upstream-flow-conditions','SCIGOV-DOEP'); return false;" href="https://www.osti.gov/pages/biblio/1423981-survey-magnetosheath-plasma-properties-saturn-inference-upstream-flow-conditions"><span>Survey of Magnetosheath Plasma Properties at Saturn and Inference of <span class="hlt">Upstream</span> Flow Conditions</span></a></p> <p><a target="_blank" href="http://www.osti.gov/pages">DOE PAGES</a></p> <p>Thomsen, M. F.; Coates, A. J.; Jackman, C. M.; ...</p> <p>2018-03-01</p> <p>A new Cassini magnetosheath data set is introduced that is based on a comprehensive survey of intervals in which the observed magnetosheath flow was encompassed within the plasma analyzer field of view and for which the computed numerical moments are therefore expected to be accurate. The data extend from 2004 day 299 to 2012 day 151 and comprise 19,155 416-s measurements. In addition to the plasma ion moments (density, temperature, and flow velocity), merged values of the plasma electron density and temperature, the energetic particle pressure, and the magnetic field vector are included in the data set. Statistical properties ofmore » various magnetosheath parameters, including dependence on local time, are presented. The magnetosheath field and flow are found to be only weakly aligned, primarily because of a relatively large z-component of the magnetic field, attributable to the field being pulled out of the equatorial orientation by flows at higher latitudes. A new procedure for using magnetosheath properties to estimate the <span class="hlt">upstream</span> solar wind speed is proposed and used to determine that the amount of electron heating at Saturn's high Mach-number bow shock is ~4% of the dissipated flow energy. The data set is available as an electronic supplement to this paper.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2010SCPMA..53.1281L','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2010SCPMA..53.1281L"><span>BRCA1 and its phosphorylation involved in caffeine-inhibitable event <span class="hlt">upstream</span> of G2 checkpoint</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Li, Ning; Zhang, Hong; Wang, Yanling; Hao, Jifang</p> <p>2010-07-01</p> <p>Caffeine, which specifically inhibits ATM/ATR kinases, efficiently abrogates the ionizing radiation (IR)-induced G2 arrest and increases the sensitivity of various tumor cells to IR. Mechanisms for the effect of caffeine remain to be elucidated. As a target of ATM/ATR kinases, BRCA1 becomes activated and phosphorylated in response to IR. Thus, in this work, we investigated the possible role of BRCA1 in the effect of caffeine on G2 checkpoint and observed how BRCA1 phosphorylation was regulated in this process. For these purposes, the BRCA1 protein level and the phosphorylation states were analyzed by Western blotting by using an antibody against BRCA1 and phospho-specific antibodies against Ser-1423 and Ser-1524 residues in cells exposed to a combination of IR and caffeine. The results showed that caffeine down-regulated IR-induced BRCA1 expression and specifically abolished BRCA1 phosphorylation of Ser-1524, which was followed by an override of G2 arrest by caffeine. In addition, the ability of BRCA1 to transactivate p21 may be required for MCF-7 but not necessary for Hela response to caffeine. These data suggest that BRCA1 may be a potential target of caffeine. BRCA1 and its phosphorylation are most likely to be involved in the caffeine-inhibitable event <span class="hlt">upstream</span> of G2 arrest.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/19608661','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/19608661"><span>Offshore industry: management of health hazards in the <span class="hlt">upstream</span> petroleum industry.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Niven, Karen; McLeod, Ron</p> <p>2009-08-01</p> <p><span class="hlt">Upstream</span> oil and gas operations involve a range of activities, including exploration and drilling, conventional oil and gas production, extraction and processing of 'tar sands', heavy oil processing and pipeline operations. Firstly, to outline the nature of health risks in the offshore oil and gas industry to date. Secondly, to outline the commercial, technical and social challenges that could influence the future context of health management in the industry. Thirdly, to speculate how the health function within the industry needs to respond to these challenges. A review of the published literature was supplemented with industry subject matter and expert opinion. There was a relatively light peer-reviewed published literature base in an industry which is perceived as having changed little over three decades, so far as offshore health hazards for physical, chemical, biological hazards are concerned. Recent focus has been on musculoskeletal disorders and stress. The relative stability of the knowledge base regarding health hazards offshore may change as more innovative methods are employed to develop hydrocarbon resources in more 'difficult' environments. Society's willingness to accept risk is changing. Addressing potential health risks should be done much earlier in the planning process of major projects. This may reveal a skills gap in health professionals as a consequence of needing to employ more anticipatory tools, such as modelling exposure estimations and the skills and willingness to engage effectively with engineers and other HSSE professionals.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015MS%26E...72d2032C','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015MS%26E...72d2032C"><span>The thermal and mechanical deformation study of <span class="hlt">up-stream</span> pumping mechanical seal</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Chen, H. L.; Xu, C.; Zuo, M. Z.; Wu, Q. B.</p> <p>2015-01-01</p> <p>Taking the viscosity-temperature relationship of the fluid film into consideration, a 3-D numerical model was established by ANSYS software which can simulate the heat transfer between the <span class="hlt">upstream</span> pumping mechanical seal stationary and rotational rings and the fluid film between them as well as simulate the thermal deformation, structure deformation and the coupling deformation of them. According to the calculation result, thermal deformation causes the seal face expansion and the maximum thermal deformation appears at the inside of the seal ring. Pressure results in a mechanical deformation, the maximum deformation occurs at the top of the spiral groove and the overall trend is inward the mating face, opposite to the thermal deformation. The coupling deformation indicate that the thermal deformation can be partly counteracted by pressure deformation. Using this model, the relationship between deformation and shaft speed and the sealing liquid pressure was studied. It's found that the shaft speed will both enhance the thermal and structure deformation and the fluid pressure will enhance the structure deformation but has little to do with the thermal deformation. By changing the sealing material, it's found that material with low thermal expansion coefficient and low elastic modulus will suffer less thermal-pressure deformation.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/23962443','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/23962443"><span>Sophoraflavanone G induces apoptosis of human cancer cells by targeting <span class="hlt">upstream</span> signals of STATs.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Kim, Byung-Hak; Won, Cheolhee; Lee, Yun-Han; Choi, Jung Sook; Noh, Kum Hee; Han, Songhee; Lee, Haeri; Lee, Chang Seok; Lee, Dong-Sup; Ye, Sang-Kyu; Kim, Myoung-Hwan</p> <p>2013-10-01</p> <p>Aberrantly activated signal transducer and activator of transcription (STAT) proteins are implicated with human cancers and represent essential roles for cancer cell survival and proliferation. Therefore, the development of small-molecule inhibitors of STAT signaling bearing pharmacological activity has therapeutic potential for the treatment of human cancers. In this study, we identified sophoraflavanone G as a novel small-molecule inhibitor of STAT signaling in human cancer cells. Sophoraflavanone G inhibited tyrosine phosphorylation of STAT proteins in Hodgkin's lymphoma and tyrosine phosphorylation of STAT3 in solid cancer cells by inhibiting phosphorylation of the Janus kinase (JAK) proteins, Src family tyrosine kinases, such as Lyn and Src, Akt, and ERK1/2. In addition, sophoraflavanone G inhibited STAT5 phosphorylation in murine-bone-marrow-derived pro-B cells transfected with translocated Ets Leukemia (TEL)-JAKs and cytokine-induced rat pre-T lymphoma cells, as well as STAT5b reporter activity in TEL-JAKs and STAT5b reporter systems. Sophoraflavanone G also inhibited nuclear factor-κB (NF-κB) signaling in multiple myeloma cells. Furthermore, sophoraflavanone G inhibited cancer cell proliferation and induced apoptosis by regulating the expression of apoptotic and anti-apoptotic proteins. Our data suggest that sophoraflavanone G is a novel small-molecule inhibitor of STAT signaling by targeting <span class="hlt">upstream</span> signals of STATs that may have therapeutic potential for cancers caused by persistently activated STAT proteins. Copyright © 2013 Elsevier Inc. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2011SPIE.8045E..0EF','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2011SPIE.8045E..0EF"><span>JEFX 10 demonstration of Cooperative Hunter Killer UAS and <span class="hlt">upstream</span> data fusion</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Funk, Brian K.; Castelli, Jonathan C.; Watkins, Adam S.; McCubbin, Christopher B.; Marshall, Steven J.; Barton, Jeffrey D.; Newman, Andrew J.; Peterson, Cammy K.; DeSena, Jonathan T.; Dutrow, Daniel A.; Rodriguez, Pedro A.</p> <p>2011-05-01</p> <p>The Johns Hopkins University Applied Physics Laboratory deployed and demonstrated a prototype Cooperative Hunter Killer (CHK) Unmanned Aerial System (UAS) capability and a prototype <span class="hlt">Upstream</span> Data Fusion (UDF) capability as participants in the Joint Expeditionary Force Experiment 2010 in April 2010. The CHK capability was deployed at the Nevada Test and Training Range to prosecute a convoy protection operational thread. It used mission-level autonomy (MLA) software applied to a networked swarm of three Raven hunter UAS and a Procerus Miracle surrogate killer UAS, all equipped with full motion video (FMV). The MLA software provides the capability for the hunter-killer swarm to autonomously search an area or road network, divide the search area, deconflict flight paths, and maintain line of sight communications with mobile ground stations. It also provides an interface for an operator to designate a threat and initiate automatic engagement of the target by the killer UAS. The UDF prototype was deployed at the Maritime Operations Center at Commander Second Fleet, Naval Station Norfolk to provide intelligence analysts and the ISR commander with a common fused track picture from the available FMV sources. It consisted of a video exploitation component that automatically detected moving objects, a multiple hypothesis tracker that fused all of the detection data to produce a common track picture, and a display and user interface component that visualized the common track picture along with appropriate geospatial information such as maps and terrain as well as target coordinates and the source video.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/22924567','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/22924567"><span>Moving policies <span class="hlt">upstream</span> to mitigate the social determinants of early childbearing.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>SmithBattle, Lee</p> <p>2012-01-01</p> <p>The teen birth rate in the United States is one of the highest in the post-industrialized world. International comparisons suggest that U.S. rates reflect high levels of social disadvantage and misguided policies that frame teen parenting as costly for mothers, children, and taxpayers. Studies that control for background factors that predispose teens to become parents highlight the social inequities that contribute to early childbearing and unfavorable maternal-child outcomes, regardless of maternal age. After reviewing these studies, federal policies that target and scrutinize teenage and single mothers are described and critiqued for the ways they disregard the social determinants of early childbearing and further the marginalization and social exclusion of low-income families. This review calls for public health nurses to challenge the ideological assumptions driving downstream policies and to advocate for comprehensive reforms that reduce the wide and growing inequities in education, income, and health among U.S. citizens. Building the public support and political will to move <span class="hlt">upstream</span> will remain daunting in light of the pervasive stereotypes of teen parents and the ideological assumptions that early childbearing and poor maternal-child outcomes stem more from individual choices and lifestyles than from social inequities. © 2012 Wiley Periodicals, Inc.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2017APS..MARP16004F','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2017APS..MARP16004F"><span>Heavy tailed bacterial motor switching statistics define macroscopic transport properties during <span class="hlt">upstream</span> contamination by E. coli</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Figueroa-Morales, N.; Rivera, A.; Altshuler, E.; Darnige, T.; Douarche, C.; Soto, R.; Lindner, A.; Clément, E.</p> <p></p> <p>The motility of E. Coli bacteria is described as a run and tumble process. Changes of direction correspond to a switch in the flagellar motor rotation. The run time distribution is described as an exponential decay of characteristic time close to 1s. Remarkably, it has been demonstrated that the generic response for the distribution of run times is not exponential, but a heavy tailed power law decay, which is at odds with the motility findings. We investigate the consequences of the motor statistics in the macroscopic bacterial transport. During <span class="hlt">upstream</span> contamination processes in very confined channels, we have identified very long contamination tongues. Using a stochastic model considering bacterial dwelling times on the surfaces related to the run times, we are able to reproduce qualitatively and quantitatively the evolution of the contamination profiles when considering the power law run time distribution. However, the model fails to reproduce the qualitative dynamics when the classical exponential run and tumble distribution is considered. Moreover, we have corroborated the existence of a power law run time distribution by means of 3D Lagrangian tracking. We then argue that the macroscopic transport of bacteria is essentially determined by the motor rotation statistics.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://ntrs.nasa.gov/search.jsp?R=19960021437&hterms=moving+walk&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D20%26Ntt%3Dmoving%2Bwalk','NASA-TRS'); return false;" href="https://ntrs.nasa.gov/search.jsp?R=19960021437&hterms=moving+walk&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D20%26Ntt%3Dmoving%2Bwalk"><span>On the <span class="hlt">upstream</span> boundary of electron foreshocks in the solar wind</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Zimbardo, G.; Veltri, P.</p> <p>1995-01-01</p> <p>The <span class="hlt">upstream</span> boundary of electron foreshocks is defined as the path of the fastest electrons reflected by collisionless shocks and moving along the magnetic field in the solar wind. Considerable levels of magnetic fluctuations are found in these regions of the solar wind, and their effect is to create both a broadening and a fine structure of the electron foreshock boundary. The magnetic structure is studied by means of a 3-D numerical simulation of a turbulent magnetic field. Enhanced, anomalous diffusion is found, (Delta x(exp 2)) varies as s(sup alpha), where alpha is greater than 1 for typical values of the parameters (here, Delta x(exp 2) is the mean square width of the tangent magnetic surface and s is the field line length). This corresponds to a Levy flight regime for the magnetic field line random walk, and allows very efficient electron propagation perpendicular to the magnetic field. Implications on the observations of planetary foreshocks and of the termination shock foreshock are considered.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2018JThSc..27..117C','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2018JThSc..27..117C"><span>Numerical simulation of the effect of <span class="hlt">upstream</span> swirling flow on swirl meter performance</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Chen, Desheng; Cui, Baoling; Zhu, Zuchao</p> <p>2018-04-01</p> <p>Flow measurement is important in the fluid process and transmission system. For the need of accuracy measurement of fluid, stable flow is acquired. However, the elbows and devices as valves and rotary machines may produce swirling flow in the natural gas pipeline networks system and many other industry fields. In order to reveal the influence of <span class="hlt">upstream</span> swirling flow on internal flow fields and the metrological characteristics, numerical simulations are carried out on the swirl meter. Using RNG k-ɛ turbulent model and SIMPLE algorithm, the flow field is numerically simulated under swirling flows generated from co-swirl and counter-swirl flow. Simulation results show fluctuation is enhanced or weakened depending on the rotating direction of swirling flow. A counter- swirl flow increases the entropy production rate at the inlet and outlet of the swirler, the junction region between throat and divergent section, and then the pressure loss is increased. The vortex precession dominates the static pressure distributions on the solid walls and in the channel, especially at the end region of the throat.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4477255','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4477255"><span>Reactive Oxygen Species in Planarian Regeneration: An <span class="hlt">Upstream</span> Necessity for Correct Patterning and Brain Formation</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Pirotte, Nicky; Stevens, An-Sofie; Fraguas, Susanna; Plusquin, Michelle; Van Roten, Andromeda; Van Belleghem, Frank; Paesen, Rik; Ameloot, Marcel; Cebrià, Francesc; Artois, Tom; Smeets, Karen</p> <p>2015-01-01</p> <p>Recent research highlighted the impact of ROS as <span class="hlt">upstream</span> regulators of tissue regeneration. We investigated their role and targeted processes during the regeneration of different body structures using the planarian Schmidtea mediterranea, an organism capable of regenerating its entire body, including its brain. The amputation of head and tail compartments induces a ROS burst at the wound site independently of the orientation. Inhibition of ROS production by diphenyleneiodonium (DPI) or apocynin (APO) causes regeneration defaults at both the anterior and posterior wound sites, resulting in reduced regeneration sites (blastemas) and improper tissue homeostasis. ROS signaling is necessary for early differentiation and inhibition of the ROS burst results in defects on the regeneration of the nervous system and on the patterning process. Stem cell proliferation was not affected, as indicated by histone H3-P immunostaining, fluorescence-activated cell sorting (FACS), in situ hybridization of smedwi-1, and transcript levels of proliferation-related genes. We showed for the first time that ROS modulate both anterior and posterior regeneration in a context where regeneration is not limited to certain body structures. Our results indicate that ROS are key players in neuroregeneration through interference with the differentiation and patterning processes. PMID:26180588</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/23950723','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/23950723"><span>Gene expression regulation by <span class="hlt">upstream</span> open reading frames and human disease.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Barbosa, Cristina; Peixeiro, Isabel; Romão, Luísa</p> <p>2013-01-01</p> <p><span class="hlt">Upstream</span> open reading frames (uORFs) are major gene expression regulatory elements. In many eukaryotic mRNAs, one or more uORFs precede the initiation codon of the main coding region. Indeed, several studies have revealed that almost half of human transcripts present uORFs. Very interesting examples have shown that these uORFs can impact gene expression of the downstream main ORF by triggering mRNA decay or by regulating translation. Also, evidence from recent genetic and bioinformatic studies implicates disturbed uORF-mediated translational control in the etiology of many human diseases, including malignancies, metabolic or neurologic disorders, and inherited syndromes. In this review, we will briefly present the mechanisms through which uORFs regulate gene expression and how they can impact on the organism's response to different cell stress conditions. Then, we will emphasize the importance of these structures by illustrating, with specific examples, how disturbed uORF-mediated translational control can be involved in the etiology of human diseases, giving special importance to genotype-phenotype correlations. Identifying and studying more cases of uORF-altering mutations will help us to understand and establish genotype-phenotype associations, leading to advancements in diagnosis, prognosis, and treatment of many human disorders.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27366961','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27366961"><span>Methane-Oxidizing Enzymes: An <span class="hlt">Upstream</span> Problem in Biological Gas-to-Liquids Conversion.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Lawton, Thomas J; Rosenzweig, Amy C</p> <p>2016-08-03</p> <p>Biological conversion of natural gas to liquids (Bio-GTL) represents an immense economic opportunity. In nature, aerobic methanotrophic bacteria and anaerobic archaea are able to selectively oxidize methane using methane monooxygenase (MMO) and methyl coenzyme M reductase (MCR) enzymes. Although significant progress has been made toward genetically manipulating these organisms for biotechnological applications, the enzymes themselves are slow, complex, and not recombinantly tractable in traditional industrial hosts. With turnover numbers of 0.16-13 s(-1), these enzymes pose a considerable <span class="hlt">upstream</span> problem in the biological production of fuels or chemicals from methane. Methane oxidation enzymes will need to be engineered to be faster to enable high volumetric productivities; however, efforts to do so and to engineer simpler enzymes have been minimally successful. Moreover, known methane-oxidizing enzymes have different expression levels, carbon and energy efficiencies, require auxiliary systems for biosynthesis and function, and vary considerably in terms of complexity and reductant requirements. The pros and cons of using each methane-oxidizing enzyme for Bio-GTL are considered in detail. The future for these enzymes is bright, but a renewed focus on studying them will be critical to the successful development of biological processes that utilize methane as a feedstock.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016AGUFMSH52A..04L','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016AGUFMSH52A..04L"><span>MAVEN <span class="hlt">Upstream</span> Observations of the Cycle 24 Space Weather Conditions at Mars</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Lee, C. O.; Hara, T.; Halekas, J. S.; Thiemann, E.; Curry, S.; Lillis, R. J.; Larson, D. E.; Espley, J. R.; Gruesbeck, J.; Eparvier, F. G.; Li, Y.; Jian, L.; Luhmann, J. G.; Jakosky, B. M.</p> <p>2016-12-01</p> <p>The Mars Atmosphere and Volatile EvolutioN (MAVEN) spacecraft went into orbit around Mars during the height of the activity phase of Solar Cycle 24. The mission was designed in part to study the response of the upper atmosphere, ionosphere, and magnetosphere of Mars to solar and solar wind inputs. When MAVEN is on the Martian dayside and orbiting around its apoapsis altitude of 6200 km, the suite of instruments onboard can measure the solar wind plasma (density, velocity), interplanetary magnetic field (magnitude and direction), and particle counts of solar energetic particles (SEPs), as well as the EUV solar irradiance. We will present an overview of the <span class="hlt">upstream</span> conditions observed to date and highlight a number of Mars-impacting space weather events due to ICMEs and SEPs. We will also present events that are triggered by corotating interaction regions (CIRs), which become more prominent beyond 1 AU and are the dominant heliospheric structures during the declining phase of the solar cycle. As part of the discussion, we will compare and contrast observations from MAVEN and ACE/WIND or STEREO-A during periods when Mars and the 1-AU observer were in solar opposition or nearly aligned along the solar wind Parker spiral.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li class="active"><span>18</span></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_18 --> <div id="page_19" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li class="active"><span>19</span></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="361"> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/22067231','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/22067231"><span>Critical interactionism: an <span class="hlt">upstream</span>-downstream approach to health care reform.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Martins, Diane Cocozza; Burbank, Patricia M</p> <p>2011-01-01</p> <p>Currently, per capita health care expenditures in the United States are more than 20% higher than any other country in the world and more than twice the average expenditure for European countries, yet the United States ranks 37th in life expectancy. Clearly, the health care system is not succeeding in improving the health of the US population with its focus on illness care for individuals. A new theoretical approach, critical interactionism, combines symbolic interactionism and critical social theory to provide a guide for addressing health care problems from both an <span class="hlt">upstream</span> and downstream approach. Concepts of meaning from symbolic interactionism and emancipation from critical perspective move across system levels to inform and reform health care for individuals, organizations, and societies. This provides a powerful approach for health care reform, moving back and forth between the micro and macro levels. Areas of application to nursing practice with several examples (patients with obesity; patients who are lesbian, gay, bisexual, and transgender; workplace bullying and errors), nursing education, and research are also discussed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://ntrs.nasa.gov/search.jsp?R=19870051956&hterms=flat+earth&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D40%26Ntt%3Dflat%2Bearth','NASA-TRS'); return false;" href="https://ntrs.nasa.gov/search.jsp?R=19870051956&hterms=flat+earth&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D40%26Ntt%3Dflat%2Bearth"><span>Fast shocks at the edges of hot diamagnetic cavities <span class="hlt">upstream</span> from the earth's bow shock</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Fuselier, S. A.; Thomsen, M. F.; Gosling, J. T.; Bame, S. J.; Russell, C. T.</p> <p>1987-01-01</p> <p>Recently, several events described as hot expanding diamagnetic cavities have been observed <span class="hlt">upstream</span> from the earth's bow shock using the ISEE 1 and 2 spacecraft. It has been suggested that fast shocks may form at the edges of some of these events because of the rapid expansion of the cavities. Here, plasma density, temperature, velocity, and total field changes across the edges of several events were examined, and these changes were found to be consistent with the presence of shocks there. The presence of flat-topped electron distributions and occasional electron beams at and down-stream from the edges provides additional evidence for shocks. Plasma wave observations also show shocklike electrostatic noise at the edges of several events. It is concluded that the edges of diamagnetic cavity events are often shocks, with a range of shock strengths similar to that observed in the interplanetary medium. The range of shock strengths may be the result of different convection and/or expansion speeds of the cavities.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28064177','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28064177"><span>Nitric oxide acts <span class="hlt">upstream</span> of ethylene in cell wall phosphorus reutilization in phosphorus-deficient rice.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Zhu, Xiao Fang; Zhu, Chun Quan; Wang, Chao; Dong, Xiao Ying; Shen, Ren Fang</p> <p>2017-01-01</p> <p>Nitric oxide (NO) and ethylene are both involved in cell wall phosphorus (P) reutilization in P-deficient rice; however, the crosstalk between them remains unclear. In the present study using P-deficient 'Nipponbare' (Nip), root NO accumulation significantly increased after 1 h and reached a maximum at 3 h, while ethylene production significantly increased after 3 h and reached a maximum at 6 h, indicating NO responded more quickly than ethylene. Irrespective of P status, addition of the NO donor sodium nitroprusside (SNP) significantly increased while the NO scavenger 2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (c-PTIO) significantly decreased the production of ethylene, while neither the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) nor the ethylene inhibitor aminoethoxyvinylglycine (AVG) had any influence on NO accumulation, suggesting NO acted <span class="hlt">upstream</span> of ethylene. Under P-deficient conditions, SNP and ACC alone significantly increased root soluble P content through increasing pectin content, and c-PTIO addition to the ACC treatment still showed the same tendency; however, AVG+SNP treatment had no effect, further indicating that ethylene was the downstream signal affecting pectin content. The expression of the phosphate transporter gene OsPT2 showed the same tendency as the NO-ethylene-pectin pathway. Taken together, we conclude that ethylene functions downstream of NO in cell wall P reutilization in P-deficient rice. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4253893','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4253893"><span>The Untold Story: Examining Ontario's Community Health Centres' Initiatives to Address <span class="hlt">Upstream</span> Determinants of Health</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Collins, Patricia A.; Resendes, Sarah J.; Dunn, James R.</p> <p>2014-01-01</p> <p>Background: Unlike traditional primary care centres, part of the Community Health Centre (CHC) mandate is to address <span class="hlt">upstream</span> health determinants. In Ontario, CHCs refer to these activities as Community Initiatives (CIs); yet, little is known about how CIs operate. The objective of this study was to examine the scope, resource requirements, partnerships, successes and challenges among selected Ontario CIs. Methods: We conducted qualitative interviews with 10 CHC staff members representing 11 CIs across Ontario. CIs were identified through an online inventory, recruited by e-mail and interviewed between March and June 2011. Results: Most CIs aim to increase community participation, while addressing social isolation and poverty. They draw minimal financial resources from their CHC, and employ highly skilled staff to support implementation. Most enlist support from various partners, and use numerous methods for community engagement. Successes include improved community relations, increased opportunities for education and employment and rewarding partnerships, while insufficient funding was a commonly identified challenge. Conclusions: Despite minimal attention from researchers and funders, our findings suggest that CIs play key capacity-building roles in vulnerable communities across Ontario, and warrant further investigation. PMID:25410693</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27547028','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27547028"><span>Trading Land: A Review of Approaches to Accounting for <span class="hlt">Upstream</span> Land Requirements of Traded Products.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Schaffartzik, Anke; Haberl, Helmut; Kastner, Thomas; Wiedenhofer, Dominik; Eisenmenger, Nina; Erb, Karl-Heinz</p> <p>2015-10-01</p> <p>Land use is recognized as a pervasive driver of environmental impacts, including climate change and biodiversity loss. Global trade leads to "telecoupling" between the land use of production and the consumption of biomass-based goods and services. Telecoupling is captured by accounts of the <span class="hlt">upstream</span> land requirements associated with traded products, also commonly referred to as land footprints. These accounts face challenges in two main areas: (1) the allocation of land to products traded and consumed and (2) the metrics to account for differences in land quality and land-use intensity. For two main families of accounting approaches (biophysical, factor-based and environmentally extended input-output analysis), this review discusses conceptual differences and compares results for land footprints. Biophysical approaches are able to capture a large number of products and different land uses, but suffer from a truncation problem. Economic approaches solve the truncation problem, but are hampered by the limited disaggregation of sectors and products. In light of the conceptual differences, the overall similarity of results generated by both types of approaches is remarkable. Diametrically opposed results for some of the world's largest producers and consumers of biomass-based products, however, make interpretation difficult. This review aims to provide clarity on some of the underlying conceptual issues of accounting for land footprints.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4237342','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4237342"><span>Evaluation of Gridded Precipitation Data for Driving SWAT Model in Area <span class="hlt">Upstream</span> of Three Gorges Reservoir</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Yang, Yan; Wang, Guoqiang; Wang, Lijing; Yu, Jingshan; Xu, Zongxue</p> <p>2014-01-01</p> <p>Gridded precipitation data are becoming an important source for driving hydrologic models to achieve stable and valid simulation results in different regions. Thus, evaluating different sources of precipitation data is important for improving the applicability of gridded data. In this study, we used three gridded rainfall datasets: 1) National Centers for Environmental Prediction - Climate Forecast System Reanalysis (NCEP-CFSR); 2) Asian Precipitation - Highly-Resolved Observational Data Integration Towards Evaluation (APHRODITE); and 3) China trend - surface reanalysis (trend surface) data. These are compared with monitoring precipitation data for driving the Soil and Water Assessment Tool in two basins <span class="hlt">upstream</span> of Three Gorges Reservoir (TGR) in China. The results of one test basin with significant topographic influence indicates that all the gridded data have poor abilities in reproducing hydrologic processes with the topographic influence on precipitation quantity and distribution. However, in a relatively flat test basin, the APHRODITE and trend surface data can give stable and desirable results. The results of this study suggest that precipitation data for future applications should be considered comprehensively in the TGR area, including the influence of data density and topography. PMID:25409467</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26284497','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26284497"><span>Perturbation biology nominates <span class="hlt">upstream</span>-downstream drug combinations in RAF inhibitor resistant melanoma cells.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Korkut, Anil; Wang, Weiqing; Demir, Emek; Aksoy, Bülent Arman; Jing, Xiaohong; Molinelli, Evan J; Babur, Özgün; Bemis, Debra L; Onur Sumer, Selcuk; Solit, David B; Pratilas, Christine A; Sander, Chris</p> <p>2015-08-18</p> <p>Resistance to targeted cancer therapies is an important clinical problem. The discovery of anti-resistance drug combinations is challenging as resistance can arise by diverse escape mechanisms. To address this challenge, we improved and applied the experimental-computational perturbation biology method. Using statistical inference, we build network models from high-throughput measurements of molecular and phenotypic responses to combinatorial targeted perturbations. The models are computationally executed to predict the effects of thousands of untested perturbations. In RAF-inhibitor resistant melanoma cells, we measured 143 proteomic/phenotypic entities under 89 perturbation conditions and predicted c-Myc as an effective therapeutic co-target with BRAF or MEK. Experiments using the BET bromodomain inhibitor JQ1 affecting the level of c-Myc protein and protein kinase inhibitors targeting the ERK pathway confirmed the prediction. In conclusion, we propose an anti-cancer strategy of co-targeting a specific <span class="hlt">upstream</span> alteration and a general downstream point of vulnerability to prevent or overcome resistance to targeted drugs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/11285895','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/11285895"><span>Effect on water resources from <span class="hlt">upstream</span> water diversion in the Ganges basin.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Adel, M M</p> <p>2001-01-01</p> <p>Bangladesh faces at least 30 <span class="hlt">upstream</span> water diversion constructions of which Farakka Barrage is the major one. The effects of Farakka Barrage on water resources, socioeconomy, and culture have been investigated downstream in the basins of the Ganges and its distributaries. A diversion of up to 60% of the Ganges water over 25 yr has caused (i) reduction of water in surface water resources, (ii) increased dependence on ground water, (iii) destruction of the breeding and raising grounds for 109 species of Gangetic fishes and other aquatic species and amphibians, (iv) increased malnutrition, (v) deficiency in soil organic matter content, (vi) change in the agricultural practices, (vii) eradication of inland navigable routes, (viii) outbreak of waterborne diseases, (ix) loss of professions, and (x) obstruction to religious observances and pastimes. Further, arsenopyrites buried in the prebarrage water table have come in contact with air and formed water-soluble compounds of arsenic. Inadequate recharging of ground water hinders the natural cleansing of arsenic, and threatens about 75,000,000 lives who are likely to use water contaminated with up to 2 mg/L of arsenic. Furthermore, the depletion of surface water resources has caused environmental heating and cooling effects. Apart from these effects, sudden releases of water by the barrage during the flood season cause devestating floods. In consideration of such a heavy toll for the areas downstream, strict international rules have to be laid down to preserve the riparian ecosystems.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015EGUGA..17.4321S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015EGUGA..17.4321S"><span>On the Instability of Large Slopes in the <span class="hlt">Upstream</span> of Wu River, Taiwan</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Shou, Keh-Jian; Lin, Jia-Fei</p> <p>2015-04-01</p> <p>Considering the existence of various types of landslides (shallow and deep-seated) and the importance of protection targets (the landslide might affect a residential area, cut a road, isolate a village, etc.), this study aims to analyze the landslide susceptibility along the Lixing Industrial Road, i.e., Nantou County Road # 89, in the <span class="hlt">upstream</span> of Wu River. Focusing on the selected typical large scale landslides, the data and information of the landslides were collected from the field and the government (including the local government, the Soil and Water Conservation Bureau, and the highway agencies). Based on the data of Li-DAR and the information from boreholes, the temporal behavior and the complex mechanism of large scale landslides were analyzed. To assess the spatial hazard of the landslides, probabilistic analysis was applied. The study of the landslide mechanism can help to understand the behavior of landslides in similar geologic conditions, and the results of hazard analysis can be applied for risk prevention and management in the study area.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/20008484','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/20008484"><span>Number of children and <span class="hlt">upstream</span> intergenerational financial transfers: evidence from Hong Kong.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Chou, Kee-Lee</p> <p>2010-03-01</p> <p>This study examined financial transfers from adult children to elderly parents in Hong Kong and tested three hypotheses about the motives for such transfers. We address previous research, suggesting that family financial support for retirees will decline in the coming decades as a consequence of the reduction in the fertility rate; we also examine whether financial transfers are a function of the number of adult children in the family. We used multiple regression models based on data from a representative sample of parents aged 60 years and older to identify the correlates of the amount of transfers from adult children to their elderly parents. We found evidence for the hypothesis that <span class="hlt">upstream</span> transfers to elderly parents are their way of withdrawing savings from a "support bank" in which they made contribution for their children's education earlier in life and that transfers are altruistic in nature, but our results provide only moderate support to the old age security hypothesis that perceives family as a source of capital. The number of children has a ceiling effect on transfers, which calls into question common assumptions about the extent to which the decline in fertility will pose a severe threat to the extent of familial support of older persons over the coming decades.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://ntrs.nasa.gov/search.jsp?R=19900041003&hterms=quasi+particle&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D60%26Ntt%3Dquasi%2Bparticle','NASA-TRS'); return false;" href="https://ntrs.nasa.gov/search.jsp?R=19900041003&hterms=quasi+particle&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D60%26Ntt%3Dquasi%2Bparticle"><span>Particle injection and acceleration at earth's bow shock - Comparison of <span class="hlt">upstream</span> and downstream events</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Ellison, Donald C.; Moebius, Eberhard; Paschmann, Goetz</p> <p>1990-01-01</p> <p>The injection and acceleration of thermal solar wind ions at the quasi-parallel earth's bow shock during radial interplanetary magnetic field conditions is investigated. Active Magnetospheric Particle Tracer Explorers/Ion Release Module satellite observations of complete proton spectra, and of heavy ion spectra above 10 keV/Q, made on September 12, 1984 near the nose of the shock, are presented and compared to the predictions of a Monte Carlo shock simulation which includes diffusive shock acceleration. It is found that the spectral observations are in good agreement with the predictions of the simulation when it is assumed that all accelerated ions originate in the solar wind and are injected into the acceleration mechanism by thermal leakage from the downstream plasma. The efficiency, which is determined directly from the downstream observations, is high, with at least 15 percent of the solar wind energy flux going into accelerated particles. The comparisons allow constraints to be placed on the rigidity dependence of the scattering mean free path and suggest that the <span class="hlt">upstream</span> solar wind must be slowed substantially by backstreaming accelerated ions prior to undergoing a sharp transition in the viscous subshock.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2017AGUFMSM33D2697D','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2017AGUFMSM33D2697D"><span>Simulating the Reiner Gamma Lunar Swirl: Influence of the <span class="hlt">Upstream</span> Plasma Conditions</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Deca, J.; Gerard, M. J.; Divin, A. V.; Lue, C.; Ahmadi, T.; Lembege, B.; Horanyi, M.</p> <p>2017-12-01</p> <p>The Reiner Gamma swirl formation, co-located with one of our Moon's strongest crustal magnetic anomalies, is one of the most prominent lunar surface features. Due to Reiner Gamma's fairly moderate spatial scales, it presents an ideal test case to study the solar wind interaction with its magnetic topology from an ion-electron kinetic perspective. Using a fully kinetic particle-in-cell approach, coupled with a surface vector mapping magnetic field model based on Kaguya and Lunar Prospector observations, we are able to constrain both the reflected as well as the incident flux patterns to the lunar surface. Finding excellent agreement with the in-orbit flux measurements from the SARA:SWIM ion sensor onboard the Chandrayaan-1 spacecraft and the surface albedo images from the Lunar Reconnaissance Orbiter Wide Angle Camera we conclude that (from a pure plasma physics point of view) that solar wind standoff is a viable mechanism for the formation of lunar swirls. Here we show how the reflected and incident flux patterns change under influence of the <span class="hlt">upstream</span> plasma and magnetic field conditions. The possible consequences of crustal magnetic anomalies for lunar swirl formation are essential for the interpretation of our Moon's geological history and evolution, space weathering, and to evaluate the needs and targets for future lunar exploration opportunities.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/22361795','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/22361795"><span>Should efforts in favor of medical student diversity be focused during admissions or farther <span class="hlt">upstream</span>?</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Reiter, Harold I; Lockyer, Jocelyn; Ziola, Barry; Courneya, Carol-Ann; Eva, Kevin</p> <p>2012-04-01</p> <p>Traditional medical school admissions assessment tools may be limiting diversity. This study investigates whether the Multiple Mini-Interview (MMI) is diversity-neutral and, if so, whether applying it with greater weight would dilute the anticipated negative impact of diversity-limiting admissions measures. Interviewed applicants to six medical schools in 2008 and 2009 underwent MMI. Predictor variables of MMI scores, grade point average (GPA), and Medical College Admission Test (MCAT) scores were correlated with diversity measures of age, gender, size of community of origin, income level, and self-declared aboriginal status. A subset of the data was then combined with variable weight assigned to predictor variables to determine whether weighting during the applicant selection process would affect diversity among chosen applicants. MMI scores were unrelated to gender, size of community of origin, and income level. They correlated positively with age and negatively with aboriginal status. GPA and MCAT correlated negatively with age and aboriginal status, GPA correlated positively with income level, and MCAT correlated positively with size of community of origin. Even extreme combinations of MMI and GPA weightings failed to increase diversity among applicants who would be selected on the basis of weighted criteria. MMI could not neutralize the diversity-limiting properties of academic scores as selection criteria to interview. Using academic scores in this way causes range restriction, counteracting attempts to enhance diversity using downstream admissions selection measures such as MMI. Diversity efforts should instead be focused <span class="hlt">upstream</span>. These results lend further support for the development of pipeline programs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20080047182','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20080047182"><span>MRO <span class="hlt">Sequence</span> Checking Tool</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Fisher, Forest; Gladden, Roy; Khanampornpan, Teerapat</p> <p>2008-01-01</p> <p>The MRO <span class="hlt">Sequence</span> Checking Tool program, mro_check, automates significant portions of the MRO (Mars Reconnaissance Orbiter) <span class="hlt">sequence</span> checking procedure. Though MRO has similar checks to the ODY s (Mars Odyssey) Mega Check tool, the checks needed for MRO are unique to the MRO spacecraft. The MRO <span class="hlt">sequence</span> checking tool automates the majority of the <span class="hlt">sequence</span> validation procedure and check lists that are used to validate the <span class="hlt">sequences</span> generated by MRO MPST (mission planning and <span class="hlt">sequencing</span> team). The tool performs more than 50 different checks on the <span class="hlt">sequence</span>. The automation varies from summarizing data about the <span class="hlt">sequence</span> needed for visual verification of the <span class="hlt">sequence</span>, to performing automated checks on the <span class="hlt">sequence</span> and providing a report for each step. To allow for the addition of new checks as needed, this tool is built in a modular fashion.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28082494','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28082494"><span>Metagenome <span class="hlt">Sequencing</span> of Prokaryotic Microbiota Collected from Rivers in the Upper Amazon Basin.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Santos-Júnior, Célio Dias; Kishi, Luciano Takeshi; Toyama, Danyelle; Soares-Costa, Andrea; Oliveira, Tereza Cristina Souza; de Miranda, Fernando Pellon; Henrique-Silva, Flávio</p> <p>2017-01-12</p> <p>Tropical freshwater environments, like rivers, are important reservoirs of microbial life. This study employed metagenomic <span class="hlt">sequencing</span> to survey prokaryotic microbiota in the Solimões, Purus, and Urucu Rivers of the Amazon Basin in Brazil. We report <span class="hlt">a</span> <span class="hlt">rich</span> and diverse microbial community. Copyright © 2017 Santos-Júnior et al.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://files.eric.ed.gov/fulltext/ED384087.pdf','ERIC'); return false;" href="http://files.eric.ed.gov/fulltext/ED384087.pdf"><span>Rethinking the Undergraduate Public Relations <span class="hlt">Sequence</span>: Evolution of Thought 1975-1995.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Fischer, Rick</p> <p></p> <p>Public relations <span class="hlt">sequence</span> heads have the luxury of a strong and supportive foundation on which to build a program of instruction. The field has <span class="hlt">a</span> <span class="hlt">rich</span> collection of thinking and recommendations relating to public relations education. The Association for Education in Journalism (AEJ) and the Public Relations Society of America (PRSA) conducted a…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=64792&keyword=aerospace&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50','EPA-EIMS'); return false;" href="https://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=64792&keyword=aerospace&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50"><span>AEROSOL DEPOSITION EFFICIENCIES AND <span class="hlt">UPSTREAM</span> RELEASE POSITIONS FOR DIFFERENT INHALATION MODES IN AN UPPER BRONCHIAL AIRWAY MODELS</span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>Aerosol Deposition Efficiencies and <span class="hlt">Upstream</span> Release Positions for Different Inhalation Modes in an Upper Bronchial Airway Model <br><br>Zhe Zhang, Clement Kleinstreuer, and Chong S. Kim<br><br>Center for Environmental Medicine and Lung Biology, University of North Carolina at Ch...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.fs.usda.gov/treesearch/pubs/30011','TREESEARCH'); return false;" href="https://www.fs.usda.gov/treesearch/pubs/30011"><span>The spatial arrangement of neritina virginea (gastropoda: neritidae) during <span class="hlt">upstream</span> migration in a split-channel reach.</span></a></p> <p><a target="_blank" href="http://www.fs.usda.gov/treesearch/">Treesearch</a></p> <p>JUAN F. BLANCO; FREDERICK N. SCATENA</p> <p>2007-01-01</p> <p>This paper relates differences in flow hydraulics between a main channel (MC) and a side channel (SC) of a river to patterns of <span class="hlt">upstream</span> migration by Neritina virginea (Neritidae: Gastropoda), a dominant diadromous snail in streams of Puerto Rico (Greater Antilles). Near-bed water velocity, snail density and shell size were measured on a weekly basis between August and...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=13221&keyword=casa&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50','EPA-EIMS'); return false;" href="https://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=13221&keyword=casa&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50"><span>USING REGIONAL EXPOSURE CRITERIA AND <span class="hlt">UPSTREAM</span> REFERENCE DATA TO CHARACTERIZE SPATIAL AND TEMPORAL EXPOSURES TO CHEMICAL CONTAMINANTS</span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>Analyses of biomarkers in fish were used to evaluate exposures among locations and across time. Two types of references were used for comparison, an <span class="hlt">upstream</span> reference sample remote from known point sources and regional exposure criteria derived from a basline of fish from refere...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=96105&keyword=bile&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50','EPA-EIMS'); return false;" href="https://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=96105&keyword=bile&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50"><span>USING REGIONAL EXPOSURE CRITERIA AND <span class="hlt">UPSTREAM</span> REFERENCE DATA TO CHARACTERIZE SPATIAL AND TEMPORAL EXPOSURES TO CHEMICAL CONTAMINANTS</span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>Analyses of biomarkers in fish were used to evaluate exposures among locations and across time. Two types of references were used for comparison, an <span class="hlt">upstream</span> reference sample remote from known point sources and regional exposure criteria derived from a baseline of fish from refer...</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li class="active"><span>19</span></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_19 --> <div id="page_20" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li class="active"><span>20</span></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="381"> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/893528','SCIGOV-STC'); return false;" href="https://www.osti.gov/servlets/purl/893528"><span>White Sturgeon Mitigation and Restoration in the Columbia and Snake Rivers <span class="hlt">Upstream</span> from Bonneville Dam; 2002-2003 Annual Report.</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Ward, David L.; Kern, J. Chris; Hughes, Michele L.</p> <p>2004-02-01</p> <p>We report on our progress from April 2002 through March 2003 on determining the effects of mitigative measures on productivity of white sturgeon populations in the Columbia River downstream from McNary Dam, and on determining the status and habitat requirements of white sturgeon populations in the Columbia and Snake rivers <span class="hlt">upstream</span> from McNary Dam.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://ntrs.nasa.gov/search.jsp?R=19860060868&hterms=influence+level&qs=N%3D0%26Ntk%3DTitle%26Ntx%3Dmode%2Bmatchall%26Ntt%3Dthe%2Binfluence%2Blevel%2Bof','NASA-TRS'); return false;" href="https://ntrs.nasa.gov/search.jsp?R=19860060868&hterms=influence+level&qs=N%3D0%26Ntk%3DTitle%26Ntx%3Dmode%2Bmatchall%26Ntt%3Dthe%2Binfluence%2Blevel%2Bof"><span>The possible influence of <span class="hlt">upstream</span> upper-level baroclinic processes on the development of the QE II storm</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Uccellini, L. W.</p> <p>1986-01-01</p> <p>An analysis of the QE II storm of September 9-11, 1978 presents evidence for the existence of upper-level baroclinic processes <span class="hlt">upstream</span> of the rapidly developing cyclone. The analysis shows that a deepening shortwave trough was located 400 to 500 km <span class="hlt">upstream</span> of the site of the storm 12 h prior to rapid cyclogenesis. The trough was associated with: (1) a polar jet marked by 65 m/s winds in its core and significant vertical and horizontal wind shear, (2) positive vorticity advection and divergence at the 300 mb level, and (3) an intense frontal zone that extended from 300 mb down to the surface. It also appears that a tropopause fold likely extruded stratospheric air down to the 700-800 mb level, 400-500 km <span class="hlt">upstream</span> of the surface low and 12 h prior to the explosive development phase of the cyclone. These findings raise questions about Gyakum's (1983) assertion that the QE II storm developed in an area in which the baroclinic support was confined to the lower troposphere and the related assertion by Anthes et al. (1983) that upper-level forcing <span class="hlt">upstream</span> of the area of rapid cyclogenesis was weak and apparently not important in this case.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://pubs.er.usgs.gov/publication/70043579','USGSPUBS'); return false;" href="https://pubs.er.usgs.gov/publication/70043579"><span>A barrier to <span class="hlt">upstream</span> migration in the fish passage of Itaipu Dam (Canal da Piracema), Paraná River basin</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>,; Fontes Júnior, Hélio Martins; Makrakis, Sergio; Gomes, Luiz Carlos; Latini, João Dirço</p> <p>2012-01-01</p> <p>The majority of the fish passages built in the Neotropical region are characterised by low efficiency and high selectivity; in many cases, the benefits to fish populations are uncertain. Studies conducted in the Canal da Piracema at Itaipu dam on the Parana River indicate that the system component designated as the Discharge channel in the Bela Vista River (herein named Canal de deságue no rio Bela Vista or CABV), a 200 m long technical section, was the main barrier to the <span class="hlt">upstream</span> migration. The aim of this study was to evaluate the degree of restriction imposed by the CABV on <span class="hlt">upstream</span> movements of Prochilodus lineatus and Leporinus elongatus, Characiformes. Fish were tagged with passive integrated transponders (PIT tags) and released both downstream and <span class="hlt">upstream</span> of this critical section. Individuals of both species released downstream of the CABV took much more time to reach the upper end of the system (43.6 days vs. 15.9 days), and passed in much lower proportions (18% vs. 60.8%) than those tagged <span class="hlt">upstream</span> of this component. Although more work is needed to differentiate between fishway effects and natural variation in migratory motivation, the results clearly demonstrate passage problems at the CABV.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://eric.ed.gov/?q=health+AND+inequalities&id=EJ1056920','ERIC'); return false;" href="https://eric.ed.gov/?q=health+AND+inequalities&id=EJ1056920"><span>New Approaches for Moving <span class="hlt">Upstream</span>: How State and Local Health Departments Can Transform Practice to Reduce Health Inequalities</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Freudenberg, Nicholas; Franzosa, Emily; Chisholm, Janice; Libman, Kimberly</p> <p>2015-01-01</p> <p>Growing evidence shows that unequal distribution of wealth and power across race, class, and gender produces the differences in living conditions that are "<span class="hlt">upstream</span>" drivers of health inequalities. Health educators and other public health professionals, however, still develop interventions that focus mainly on "downstream"…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2010IEITC..91.2994K','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2010IEITC..91.2994K"><span>Performance Enhancement by Threshold Level Control of a Receiver in WDM-PON System with Manchester Coded Downstream and NRZ <span class="hlt">Upstream</span> Re-Modulation</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Kim, Bong Kyu; Chung, Hwan Seok; Chang, Sun Hyok; Park, Sangjo</p> <p></p> <p>We propose and demonstrate a scheme enhancing the performance of optical access networks with Manchester coded downstream and re-modulated NRZ coded <span class="hlt">upstream</span>. It is achieved by threshold level control of a limiting amplifier at a receiver, and the minimum sensitivity of <span class="hlt">upstream</span> is significantly improved for the re-modulation scheme with 5Gb/s Manchester coded downstream and 2.488Gb/s NRZ <span class="hlt">upstream</span> data rates.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4731297','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4731297"><span>Identification of significantly mutated regions across cancer types highlights <span class="hlt">a</span> <span class="hlt">rich</span> landscape of functional molecular alterations</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Araya, Carlos L.; Cenik, Can; Reuter, Jason A.; Kiss, Gert; Pande, Vijay S.; Snyder, Michael P.; Greenleaf, William J.</p> <p>2015-01-01</p> <p>Cancer <span class="hlt">sequencing</span> studies have primarily identified cancer-driver genes by the accumulation of protein-altering mutations. An improved method would be annotation-independent, sensitive to unknown distributions of functions within proteins, and inclusive of non-coding drivers. We employed density-based clustering methods in 21 tumor types to detect variably-sized significantly mutated regions (SMRs). SMRs reveal recurrent alterations across a spectrum of coding and non-coding elements, including transcription factor binding sites and untranslated regions mutated in up to ∼15% of specific tumor types. SMRs reveal spatial clustering of mutations at molecular domains and interfaces, often with associated changes in signaling. Mutation frequencies in SMRs demonstrate that distinct protein regions are differentially mutated among tumor types, as exemplified by a linker region of PIK3CA in which biophysical simulations suggest mutations affect regulatory interactions. The functional diversity of SMRs underscores both the varied mechanisms of oncogenic misregulation and the advantage of functionally-agnostic driver identification. PMID:26691984</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3494089','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3494089"><span>Genome-wide SNP and haplotype analyses reveal <span class="hlt">a</span> <span class="hlt">rich</span> history underlying dog domestication</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>vonHoldt, Bridgett M.; Pollinger, John P.; Lohmueller, Kirk E.; Han, Eunjung; Parker, Heidi G.; Quignon, Pascale; Degenhardt, Jeremiah D.; Boyko, Adam R.; Earl, Dent A.; Auton, Adam; Reynolds, Andy; Bryc, Kasia; Brisbin, Abra; Knowles, James C.; Mosher, Dana S.; Spady, Tyrone C.; Elkahloun, Abdel; Geffen, Eli; Pilot, Malgorzata; Jedrzejewski, Wlodzimierz; Greco, Claudia; Randi, Ettore; Bannasch, Danika; Wilton, Alan; Shearman, Jeremy; Musiani, Marco; Cargill, Michelle; Jones, Paul G.; Qian, Zuwei; Huang, Wei; Ding, Zhao-Li; Zhang, Ya-ping; Bustamante, Carlos D.; Ostrander, Elaine A.; Novembre, John; Wayne, Robert K.</p> <p>2010-01-01</p> <p>Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication1,2. To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA <span class="hlt">sequence</span> data3. Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity. PMID:20237475</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/20237475','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/20237475"><span>Genome-wide SNP and haplotype analyses reveal <span class="hlt">a</span> <span class="hlt">rich</span> history underlying dog domestication.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Vonholdt, Bridgett M; Pollinger, John P; Lohmueller, Kirk E; Han, Eunjung; Parker, Heidi G; Quignon, Pascale; Degenhardt, Jeremiah D; Boyko, Adam R; Earl, Dent A; Auton, Adam; Reynolds, Andy; Bryc, Kasia; Brisbin, Abra; Knowles, James C; Mosher, Dana S; Spady, Tyrone C; Elkahloun, Abdel; Geffen, Eli; Pilot, Malgorzata; Jedrzejewski, Wlodzimierz; Greco, Claudia; Randi, Ettore; Bannasch, Danika; Wilton, Alan; Shearman, Jeremy; Musiani, Marco; Cargill, Michelle; Jones, Paul G; Qian, Zuwei; Huang, Wei; Ding, Zhao-Li; Zhang, Ya-Ping; Bustamante, Carlos D; Ostrander, Elaine A; Novembre, John; Wayne, Robert K</p> <p>2010-04-08</p> <p>Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication. To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA <span class="hlt">sequence</span> data. Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25167811','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25167811"><span>Impacts of shape and height of <span class="hlt">upstream</span> roof on airflow and pollutant dispersion inside an urban street canyon.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Huang, Yuan-Dong; He, Wen-Rong; Kim, Chang-Nyung</p> <p>2015-02-01</p> <p>A two-dimensional numerical model for simulating flow and pollutant dispersion in an urban street canyon is firstly developed using the FLUENT code and then validated against the wind tunnel results. After this, the flow field and pollutant dispersion inside an urban street canyon with aspect ratio W/H = 1 are examined numerically considering five different shapes (vaulted, trapezoidal, slanted, upward wedged, and downward wedged roofs) as well as three different roof height to building height ratios (Z H /H = 1/6, 1/3, and 1/2) for the <span class="hlt">upstream</span> building roof. The results obtained reveal that the shape and height of an <span class="hlt">upstream</span> roof have significant influences on flow pattern and pollutant distribution in an urban canyon. A large single clockwise vortex is generated in the canyon for the vaulted <span class="hlt">upstream</span> roof at Z H /H = 1/6, 1/3, and 1/2, the trapezoidal and downward wedged roofs at Z H /H = 1/6 and 1/3, and the slanted and upward wedged roofs at Z H /H = 1/6, while a main clockwise vortex and a secondary counterclockwise vortex are established for the trapezoidal and downward wedged roofs at Z H /H = 1/2 and the slanted and upward wedged roofs at Z H /H = 1/3 and 1/2. In the one-vortex flow regime, the clockwise vortex moves upward and grows in size with increasing <span class="hlt">upstream</span> roof height for the vaulted, trapezoidal, and downward wedged roofs. In the two-vortex flow regime, the size and rotational velocity of both upper clockwise and lower counterclockwise vortices increase with the <span class="hlt">upstream</span> roof height for the slanted and upward wedged roofs. At Z H /H = 1/6, the pollution levels in the canyon are close among all the <span class="hlt">upstream</span> roof shapes studied. At Z H /H = 1/3, the pollution levels in the canyon for the upward wedged roof and slanted roof are much higher than those for the vaulted, trapezoidal, and downward wedged roofs. At Z H /H = 1/2, the lowest pollution level appears in the canyon for the vaulted <span class="hlt">upstream</span> roof, while</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://pubs.er.usgs.gov/publication/70176533','USGSPUBS'); return false;" href="https://pubs.er.usgs.gov/publication/70176533"><span>A semelparous fish continues <span class="hlt">upstream</span> migration when exposed to alarm cue, but adjusts movement speed and timing</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Luhring, Thomas M; Meckley, Trevor D.; Johnson, Nicholas S.; Siefkes, Michael J.; Hume, John B.; Wagner, C. Michael</p> <p>2016-01-01</p> <p>Animals make trade-offs between predation risk and pursuit of opportunities such as foraging and reproduction. Trade-offs between antipredator behaviours and foraging are well suited to manipulation in laboratory and field settings and have generated a vast compendium of knowledge. However, much less is known about how animals manage trade-offs between predation risk and pursuit of reproductive opportunities in the absence of the confounding effects of foraging. In the present study, we investigated how the nonfeeding migratory life stage of sea lamprey, Petromyzon marinus, responds to odour from dead conspecifics (a cue that induces avoidance behaviours in laboratory and field studies). We released groups of PIT-tagged sea lamprey 65 m from the shore of Lake Michigan or 287 m <span class="hlt">upstream</span> in Carp Lake River and used antennas to detect their movements in the river. As the breeding season progressed, sea lamprey initiated <span class="hlt">upstream</span> movement earlier and were more likely to enter the river. Sea lamprey that began the night in Lake Michigan entered Carp Lake River at higher rates and accelerated <span class="hlt">upstream</span> when exposed to high concentrations of alarm cue, consistent with animals attempting to minimize time spent in risky areas. Sea lampreys that began the night in the river delayed <span class="hlt">upstream</span> movement when exposed to alarm cue, consistent with animals sheltering and gathering information about a source of risk. We attribute this context-specific reaction to alarm cue to differences in perceived vulnerability to predation in sheltered positions in the river versus exposed positions in the lake. Once in the river, the vast majority of sea lamprey moved <span class="hlt">upstream</span> independent of alarm cue or Julian date. Although life-history-induced time and energy budgets place rigid constraints on the direction of migration, sea lamprey attend to predation risk by modifying movement timing and speed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5375686','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5375686"><span>A <span class="hlt">Sequence</span>-Independent, Unstructured Internal Ribosome Entry Site Is Responsible for Internal Expression of the Coat Protein of Turnip Crinkle Virus</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>May, Jared; Johnson, Philip; Saleem, Huma</p> <p>2017-01-01</p> <p>ABSTRACT To maximize the coding potential of viral genomes, internal ribosome entry sites (IRES) can be used to bypass the traditional requirement of a 5′ cap and some/all of the associated translation initiation factors. Although viral IRES typically contain higher-order RNA structure, an unstructured <span class="hlt">sequence</span> of about 84 nucleotides (nt) immediately <span class="hlt">upstream</span> of the Turnip crinkle virus (TCV) coat protein (CP) open reading frame (ORF) has been found to promote internal expression of the CP from the genomic RNA (gRNA) both in vitro and in vivo. An absence of extensive RNA structure was predicted using RNA folding algorithms and confirmed by selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) RNA structure probing. Analysis of the IRES region in vitro by use of both the TCV gRNA and reporter constructs did not reveal any <span class="hlt">sequence</span>-specific elements but rather suggested that an overall lack of structure was an important feature for IRES activity. The CP IRES is <span class="hlt">A-rich</span>, independent of orientation, and strongly conserved among viruses in the same genus. The IRES was dependent on eIF4G, but not eIF4E, for activity. Low levels of CP accumulated in vivo in the absence of detectable TCV subgenomic RNAs, strongly suggesting that the IRES was active in the gRNA in vivo. Since the TCV CP also serves as the viral silencing suppressor, early translation of the CP from the viral gRNA is likely important for countering host defenses. Cellular mRNA IRES also lack extensive RNA structures or <span class="hlt">sequence</span> conservation, suggesting that this viral IRES and cellular IRES may have similar strategies for internal translation initiation. IMPORTANCE Cap-independent translation is a common strategy among positive-sense, single-stranded RNA viruses for bypassing the host cell requirement of a 5′ cap structure. Viral IRES, in general, contain extensive secondary structure that is critical for activity. In contrast, we demonstrate that a region of viral RNA devoid of</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016JThSc..25..293L','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016JThSc..25..293L"><span>Effects of rising angle on <span class="hlt">upstream</span> blades and intermediate turbine duct</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Liu, Jun; Wang, Pei; Du, Qiang; Liu, Guang; Zhu, Junqiang</p> <p>2016-08-01</p> <p>With the improvement of requirement, design and manufacture technology, aero-engines for the future are characterized by further reduction in fuel consumption, cost, but increment in propulsion efficiency, which leads to ultra-high bypass ratio. The intermediate turbine duct (ITD), which connects the high pressure turbine (HPT) with the low pressure turbine (LPT), has a critical impact on the overall performances of such future engines. Therefore, it becomes more and more urgent to master the design technique of aggressive, even super-aggressive ITDs. Over the last years, a lot of research works about the flow mechanism in the diffuser ducts were carried out. Many achievements were reported, but further investigation should be performed. With the aid of numerical method, this paper focuses on the change of performance and flow field of ITD, as well as nearby turbines, brought by rising angle (RA). Eight ITDs with the same area ratio and length, but different RAs ranges from 8 degrees to 45 degrees, are compared. According to the investigation, flow field, especially outlet Ma of swirl blade is influenced by RA under potential effect, which is advisable for designers to modify HPT rotor blades after changing ITD. In addition to that, low velocity area moves towards <span class="hlt">upstream</span> until the first bend as RA increases, while pressure loss distribution at S2 stream surface shows that hub boundary layer is more sensitive to RA, and casing layer keeps almost constant. On the other hand, the overall total pressure loss could keep nearly equivalent among different RA cases, which implies the importance of optimization.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25045809','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25045809"><span>HPAEC-PAD quantification of Haemophilus influenzae type b polysaccharide in <span class="hlt">upstream</span> and downstream samples.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>van der Put, Robert M F; de Haan, Alex; van den IJssel, Jan G M; Hamidi, Ahd; Beurret, Michel</p> <p>2015-11-27</p> <p>Due to the rapidly increasing introduction of Haemophilus influenzae type b (Hib) and other conjugate vaccines worldwide during the last decade, reliable and robust analytical methods are needed for the quantitative monitoring of intermediate samples generated during fermentation (<span class="hlt">upstream</span> processing, USP) and purification (downstream processing, DSP) of polysaccharide vaccine components. This study describes the quantitative characterization of in-process control (IPC) samples generated during the fermentation and purification of the capsular polysaccharide (CPS), polyribosyl-ribitol-phosphate (PRP), derived from Hib. Reliable quantitative methods are necessary for all stages of production; otherwise accurate process monitoring and validation is not possible. Prior to the availability of high performance anion exchange chromatography methods, this polysaccharide was predominantly quantified either with immunochemical methods, or with the colorimetric orcinol method, which shows interference from fermentation medium components and reagents used during purification. Next to an improved high performance anion exchange chromatography-pulsed amperometric detection (HPAEC-PAD) method, using a modified gradient elution, both the orcinol assay and high performance size exclusion chromatography (HPSEC) analyses were evaluated. For DSP samples, it was found that the correlation between the results obtained by HPAEC-PAD specific quantification of the PRP monomeric repeat unit released by alkaline hydrolysis, and those from the orcinol method was high (R(2)=0.8762), and that it was lower between HPAEC-PAD and HPSEC results. Additionally, HPSEC analysis of USP samples yielded surprisingly comparable results to those obtained by HPAEC-PAD. In the early part of the fermentation, medium components interfered with the different types of analysis, but quantitative HPSEC data could still be obtained, although lacking the specificity of the HPAEC-PAD method. Thus, the HPAEC</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/24722816','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/24722816"><span>F 16915 prevents heart failure-induced atrial fibrillation: a promising new drug as <span class="hlt">upstream</span> therapy.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Le Grand, Bruno; Letienne, Robert; Dupont-Passelaigue, Elisabeth; Lantoine-Adam, Frédérique; Longo, Frédéric; David-Dufilho, Monique; Michael, Georghia; Nishida, Kunihiro; Catheline, Daniel; Legrand, Philippe; Hatem, Stéphane; Nattel, Stanley</p> <p>2014-07-01</p> <p>Atrial fibrillation (AF) is a common complication of heart failure. The aim of the present study was to investigate the effects of a new pure docosahexaenoic acid derivative called F 16915 in experimental models of heart failure-induced atria dysfunction. The atrial dysfunction-induced AF was investigated (1) in a dog model of tachypacing-induced congestive heart failure and (2) in a rat model of heart failure induced by occlusion of left descending coronary artery and 2 months reperfusion. F 16915 (5 g/day for 4 weeks) significantly reduced the mean duration of AF induced by burst pacing in the dog model (989 ± 111 s in the vehicle group to 79 ± 59 s with F 16915, P < 0.01). This dose of F 16915 also significantly reduced the incidence of sustained AF (5/5 dogs in the vehicle group versus 1/5 with F 16915, P < 0.05). In the rat model, the percentage of shortening fraction in the F 16915 group (100 mg/kg p.o. daily) was significantly restored after 2 months (32.6 ± 7.4 %, n = 9 vs 17.6 ± 3.4 %, n = 9 in the vehicle group, P < 0.01). F 16915 also reduced the de-phosphorylation of connexin43 from atria tissue. The present results show that treatment with F 16915 reduced the heart dilation, resynchronized the gap junction activity, and reduced the AF duration in models of heart failure. Thus, F 16915 constitutes a promising new drug as <span class="hlt">upstream</span> therapy for the treatment of AF in patients with heart failure.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/20087980','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/20087980"><span><span class="hlt">Upstream</span> petroleum degradation of mangroves and intertidal shores: the Niger Delta experience.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Osuji, Leo C; Erondu, Ebere S; Ogali, Regina E</p> <p>2010-01-01</p> <p>This article was inspired by a field reconnaissance survey of outcrops along the Nembe-Brass axis of the petroliferous Niger Delta. It reviews various tradeoffs of the impact of <span class="hlt">upstream</span> petroleum (seismic and production) operations on the mangrove ecosystems in that region, the largest in Sub-Saharan Africa. Mangroves and intertidal shores are considered critical to the economic well-being of this region owing to the people's dual occupation in fishing and farming. The mangrove ecosystem provides a nutrient medium, which serves as a nursery and spawning ground for many fish species and other biota. Oil and gas activities might destroy these spawn areas, causing reduction in resource output and community pressure. Devegetation of the mangrove forest as a result of seismic delineation leaves the fragile soil exposed, unprotected, and susceptible to erosion. Again, loss of vegetation might discourage the natural role of plants in air purification (CO(2) utilization and O(2) production). The release of nutrients (organic N(2), NH(3), and NO$\\rm{{_{3};{-}}}$) and polyaromatic hydrocarbons (PAHs) to the environment, with the attendant increase in microbial load, increases biochemical O(2) demand (BOD) and depletes dissolved O(2) (DO) in H(2)O to a level that is beyond the tolerance limit of organisms. This anoxic situation leads to asphyxiation and subsequent fish kill in affected areas. In order of increasing vulnerability, the mangroves and intertidal shores of the Niger Delta fall under categories 8 to 10 on the environmental sensitivity index (ESI) scale, which predisposes the areas to serious long-term effects and clean-up complexity. Thus, there is need to monitor mangrove systems and shoreline changes in the areas of considerable seismic and production activities, especially in the coastal Niger Delta, where pipeline corrosion due to salt intrusion into the swampy environment and 'unsighted fingers' of sabotage have increased the prevalence of oil spills.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4988899','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4988899"><span>Mechanism of arginine sensing by CASTOR1 <span class="hlt">upstream</span> of mTORC1</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Saxton, Robert A.; Chantranupong, Lynne; Knockenhauer, Kevin E.; Schwartz, Thomas U.; Sabatini, David M.</p> <p>2016-01-01</p> <p>Summary The mechanistic Target of Rapamycin Complex 1 (mTORC1) is a major regulator of eukaryotic growth that coordinates anabolic and catabolic cellular processes with inputs such as growth factors and nutrients, including amino acids1–3. In mammals, arginine is particularly important and promotes diverse physiological effects including immune cell activation, insulin secretion, and muscle growth, largely through activation of mTORC14–7. Arginine activates mTORC1 <span class="hlt">upstream</span> of the Rag GTPases8, through either the lysosomal amino acid transporter SLC38A9 or the GATOR2-interacting CASTOR1 (Cellular Arginine Sensor for mTORC1)9–12. However, the mechanism by which the mTORC1 pathway detects and transmits the arginine signal has been elusive. Here, we present the 1.8 Å crystal structure of arginine-bound CASTOR1. Homodimeric CASTOR1 binds arginine at the interface of two ACT domains, enabling allosteric control of the adjacent GATOR2-binding site to trigger dissociation from GATOR2 and the downstream activation of mTORC1. Our data reveal that CASTOR1 shares substantial structural homology with the lysine-binding regulatory domain of prokaryotic aspartate kinases, suggesting that the mTORC1 pathway exploited an ancient amino-acid-dependent allosteric mechanism to acquire arginine sensitivity. Together, these results establish a structural basis for arginine sensing by the mTORC1 pathway and provide insights into the evolution of a mammalian nutrient sensor. PMID:27487210</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/5687735','SCIGOV-STC'); return false;" href="https://www.osti.gov/servlets/purl/5687735"><span><span class="hlt">Upstream</span> H/sub 2/S removal from geothermal steam. Final report</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Not Available</p> <p>1981-11-01</p> <p>The purpose of this project was to evaluate a new heat exchanger process as a method for removing hydrogen sulfide (H/sub 2/S) gas from geothermal steam <span class="hlt">upstream</span> of a power plant turbine. The process utilizes a heat exchanger to condense geothermal steam so that noncondensable gases (including H/sub 2/S) can be removed in the form of a concentrated vent stream. Ultimate disposal of the removed H/sub 2/S gas may then be accomplished by use of other processes such as the commercially available Stretford process. The clean condensate is reevaporated on the other side of the heat exchanger using the heatmore » removed from the condensing geothermal steam. The necessary heat transfer is induced by maintaining a slight pressure difference, and consequently a slight temperature difference, between the two sides of the heat exchanger. Evaluation of this condensing and reboiling process was performed primarily through the testing of a small-scale 14 m/sup 2/ (150 ft/sup 2/) vertical tube evaporator heat exchanger at The Geysers Power Plant in northern California. The field test results demonstrated H/sub 2/S removal rates consistently better than 90 percent, with an average removal rate of 94 percent. In addition, the removal rate for all noncondensable gases is about 98 percent. Heat transfer rates were high enough to indicate acceptable economics for application of the process on a commercial scale. The report also includes an evaluation of the cost and performance of various configurations of the system, and presents design and cost estimates for a 2.5 MWe and a 55 MWe unit.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2937082','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2937082"><span>Regulation of Dpp activity by tissue-specific cleavage of an <span class="hlt">upstream</span> site within the prodomain</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Sopory, Shailaja; Kwon, Sunjong; Wehrli, Marcel; Christian, Jan L.</p> <p>2010-01-01</p> <p>BMP4 is synthesized as an inactive precursor that is cleaved at two sites during maturation: initially at a site (S1) adjacent to the ligand domain, and then at an <span class="hlt">upstream</span> site (S2) within the prodomain. Cleavage at the second site regulates the stability of mature BMP4 and this in turn influences its signaling intensity and range of action. The Drosophila ortholog of BMP4, Dpp, functions as a long- or short-range signaling molecule in the wing disc or embryonic midgut, respectively but mechanisms that differentially regulate its bioactivity in these tissues have not been explored. In the current studies we demonstrate, by dpp mutant rescue, that cleavage at the S2 site of proDpp is required for development of the wing and leg imaginal discs, whereas cleavage at the S1 site is sufficient to rescue Dpp function in the midgut. Both the S1 and S2 site of proDpp are cleaved in the wing disc, and S2-cleavage is essential to generate sufficient ligand to exceed the threshold for pMAD activation at both short- and long-range in most cells. By contrast, proDpp is cleaved at the S1 site alone in the embryonic mesoderm and this generates sufficient ligand to activate physiological target genes in neighboring cells. These studies provide the first biochemical and genetic evidence that that selective cleavage of the S2 site of proDPP provides a tissue-specific mechanism for regulating Dpp activity, and that differential cleavage can contribute to, but is not an absolute determinant of signaling range. PMID:20659445</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25662781','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25662781"><span>'Paddling <span class="hlt">upstream</span>': Fathers' involvement during pregnancy as described by expectant fathers and mothers.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Widarsson, Margareta; Engström, Gabriella; Tydén, Tanja; Lundberg, Pranee; Hammar, Lena Marmstål</p> <p>2015-04-01</p> <p>To describe the perspectives of expectant mothers and fathers on fathers' involvement during pregnancy. Becoming a father is a major life event and paternal involvement during pregnancy has a positive influence on the family. However, research into both expectant mothers' and fathers' perspectives on fathers' involvement during pregnancy is relatively scarce. A descriptive qualitative study was used. Thirty expectant parents (20 women and 10 men) were interviewed either as part of one of four focus groups or in an individual interview. Qualitative content analysis was performed on the interview transcripts. A theme of 'Paddling <span class="hlt">upstream</span>' emerged as an expression of the latent content of the interviews concerning perspectives on fathers' involvement. Five sub-themes described the manifest content: trying to participate, trying to be understanding, trying to learn, trying to be a calming influence and trying to find a balanced life. Expectant parents suggested several ways to improve fathers' involvement and to meet parents' need for shared involvement. Expectant mothers and fathers wanted the father to be more involved in the pregnancy. Although fathers attempted different strategies, they did not always perceive what was expected of them and encountered many barriers as they tried to navigate through this unique experience. The best support for the father was the mother. Expectant parents wanted their healthcare to include the father more thoroughly and to focus on the whole family. Prenatal care professionals can overcome barriers that prevent paternal involvement. Although fathers are not able to engage in the pregnancy on the same level as the mother, we suggest that their specific needs also be recognised through an increased awareness of gender norms in healthcare. © 2015 John Wiley & Sons Ltd.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/21387936','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/21387936"><span>An analysis of flaring and venting activity in the Alberta <span class="hlt">upstream</span> oil and gas industry.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Johnson, Matthew R; Coderre, Adam R</p> <p>2011-02-01</p> <p>Alberta, Canada, is an important global producer of petroleum resources. In association with this production, large amounts of gas (1.14 billion m3 in 2008) are flared or vented. Although the amount of flaring and venting has been measurably reduced since 2002, data from 2005 reveal sharp increases in venting, which have important implications in terms of resource conservation and greenhouse gas emissions (which exceeded 8 million tonnes of carbon dioxide equivalent in 2008). With use of extensive monthly production data for 18,203 active batteries spanning the years 2002-2008 obtained in close cooperation with the Alberta Energy Resources Conservation Board, a detailed analysis has been completed to examine activity patterns of flaring and venting and reasons behind these trends in the Alberta <span class="hlt">upstream</span> oil and gas industry. In any given year, approximately 6000 batteries reported flaring and/or venting, but the distribution of volumes flared and vented at individual sites was highly skewed, such that small numbers of sites handled large fractions of the total gas flaring and venting in the Province. Examination of month-to-month volume variability at individual sites, cast in terms of a nominal turndown ratio that would be required for a compressor to capture that gas and direct it into a pipeline, further revealed that volumes at a majority of sites were reasonably stable and there was no evidence that larger or more stable sites had been preferentially reduced, leaving potential barriers to future mitigation. Through linking of geospatial data with production data coupled with additional statistical analysis, the 31.2% increase in venting volumes since 2005 was revealed to be predominantly associated with increased production of heavier oils and bitumen in the Lloydminster region of the Province. Overall, the data suggest that quite significant reductions in flaring and venting could be realized by seeking mitigation solutions for only the largest batteries in</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li class="active"><span>20</span></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_20 --> <div id="page_21" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li class="active"><span>21</span></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="401"> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/14760693','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/14760693"><span>Restructuring <span class="hlt">upstream</span> bioprocessing: technological and economical aspects for production of a generic microbial feedstock from wheat.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Koutinas, A A; Wang, R; Webb, C</p> <p>2004-03-05</p> <p>Restructuring and optimization of the conventional fermentation industry for fuel and chemical production is necessary to replace petrochemical production routes. Guided by this concept, a novel biorefinery process has been developed as an alternative to conventional <span class="hlt">upstream</span> processing routes, leading to the production of a generic fermentation feedstock from wheat. The robustness of Aspergillus awamori as enzyme producer is exploited in a continuous fungal fermentation on whole wheat flour. Vital gluten is extracted as an added-value byproduct by the conventional Martin process from a fraction of the overall wheat used. Enzymatic hydrolysis of gluten-free flour by the enzyme complex produced by A. awamori during fermentation produces a liquid stream rich in glucose (320 g/L). Autolysis of fungal cells produces a micronutrient-rich solution similar to yeast extract (1.6 g/L nitrogen, 0.5 g/L phosphorus). The case-specific combination of these two liquid streams can provide a nutrient-complete fermentation medium for a spectrum of microbial bioconversions for the production of such chemicals as organic acids, amino acids, bioethanol, glycerol, solvents, and microbial biodegradable plastics. Preliminary economic analysis has shown that the operating cost required to produce the feedstock is dependent on the plant capacity, cereal market price, presence and market value of added-value byproducts, labor costs, and mode of processing (batch or continuous). Integration of this process in an existing fermentation plant could lead to the production of a generic feedstock at an operating cost lower than the market price of glucose syrup (90% to 99% glucose) in the EU, provided that the plant capacity exceeds 410 m(3)/day. Further process improvements are also suggested. Copyright 2004 Wiley Periodicals, Inc.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28651595','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28651595"><span>Identification of pathogenic genes and <span class="hlt">upstream</span> regulators in age-related macular degeneration.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Zhao, Bin; Wang, Mengya; Xu, Jing; Li, Min; Yu, Yuhui</p> <p>2017-06-26</p> <p>Age-related macular degeneration (AMD) is the leading cause of irreversible blindness in older individuals. Our study aims to identify the key genes and <span class="hlt">upstream</span> regulators in AMD. To screen pathogenic genes of AMD, an integrated analysis was performed by using the microarray datasets in AMD derived from the Gene Expression Omnibus (GEO) database. The functional annotation and potential pathways of differentially expressed genes (DEGs) were further discovered by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. We constructed the AMD-specific transcriptional regulatory network to find the crucial transcriptional factors (TFs) which target the DEGs in AMD. Quantitative real time polymerase chain reaction (qRT-PCR) was performed to verify the DEGs and TFs obtained by integrated analysis. From two GEO datasets obtained, we identified 1280 DEGs (730 up-regulated and 550 down-regulated genes) between AMD and normal control (NC). After KEGG analysis, steroid biosynthesis is a significantly enriched pathway for DEGs. The expression of 8 genes (TNC, GRP, TRAF6, ADAMTS5, GPX3, FAP, DHCR7 and FDFT1) was detected. Except for TNC and GPX3, the other 6 genes in qRT-PCR played the same pattern with that in our integrated analysis. The dysregulation of these eight genes may involve with the process of AMD. Two crucial transcription factors (c-rel and myogenin) were concluded to play a role in AMD. Especially, myogenin was associated with AMD by regulating TNC, GRP and FAP. Our finding can contribute to developing new potential biomarkers, revealing the underlying pathogenesis, and further raising new therapeutic targets for AMD.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/518528-contamination-sequence-databases-adaptor-sequences','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/518528-contamination-sequence-databases-adaptor-sequences"><span>Contamination of <span class="hlt">sequence</span> databases with adaptor <span class="hlt">sequences</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D.</p> <p></p> <p>Because of the exponential increase in the amount of DNA <span class="hlt">sequences</span> being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of <span class="hlt">sequence</span> databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host <span class="hlt">sequences</span> that have been difficult for submitters to manage or control. Examples include anomalous <span class="hlt">sequences</span> derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion <span class="hlt">sequences</span> are highly mobile and are capable ofmore » transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost <span class="hlt">sequences</span>. This category includes incorporation of cloning-vector <span class="hlt">sequences</span> and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all <span class="hlt">sequences</span> directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another <span class="hlt">sequence</span> artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2323974','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2323974"><span>Chromhome: <span class="hlt">A</span> <span class="hlt">rich</span> internet application for accessing comparative chromosome homology maps</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Nagarajan, Sridevi; Rens, Willem; Stalker, James; Cox, Tony; Ferguson-Smith, Malcolm A</p> <p>2008-01-01</p> <p>Background Comparative genomics has become a significant research area in recent years, following the availability of a number of <span class="hlt">sequenced</span> genomes. The comparison of genomes is of great importance in the analysis of functionally important genome regions. It can also be used to understand the phylogenetic relationships of species and the mechanisms leading to rearrangement of karyotypes during evolution. Many species have been studied at the cytogenetic level by cross species chromosome painting. With the large amount of such information, it has become vital to computerize the data and make them accessible worldwide. Chromhome is a comprehensive web application that is designed to provide cytogenetic comparisons among species and to fulfil this need. Results The Chromhome application architecture is multi-tiered with an interactive client layer, business logic and database layers. Enterprise java platform with open source framework OpenLaszlo is used to implement the Rich Internet Chromhome Application. Cross species comparative mapping raw data are collected and the processed information is stored into MySQL Chromhome database. Chromhome Release 1.0 contains 109 homology maps from 51 species. The data cover species from 14 orders and 30 families. The homology map displays all the chromosomes of the compared species as one image, making comparisons among species easier. Inferred data also provides maps of homologous regions that could serve as a guideline for researchers involved in phylogenetic or evolution based studies. Conclusion Chromhome provides a useful resource for comparative genomics, holding graphical homology maps of a wide range of species. It brings together cytogenetic data of many genomes under one roof. Inferred painting can often determine the chromosomal homologous regions between two species, if each has been compared with a common third species. Inferred painting greatly reduces the need to map entire genomes and helps focus only on relevant</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/18366796','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/18366796"><span>Chromhome: <span class="hlt">a</span> <span class="hlt">rich</span> internet application for accessing comparative chromosome homology maps.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Nagarajan, Sridevi; Rens, Willem; Stalker, James; Cox, Tony; Ferguson-Smith, Malcolm A</p> <p>2008-03-26</p> <p>Comparative genomics has become a significant research area in recent years, following the availability of a number of <span class="hlt">sequenced</span> genomes. The comparison of genomes is of great importance in the analysis of functionally important genome regions. It can also be used to understand the phylogenetic relationships of species and the mechanisms leading to rearrangement of karyotypes during evolution. Many species have been studied at the cytogenetic level by cross species chromosome painting. With the large amount of such information, it has become vital to computerize the data and make them accessible worldwide. Chromhome http://www.chromhome.org is a comprehensive web application that is designed to provide cytogenetic comparisons among species and to fulfil this need. The Chromhome application architecture is multi-tiered with an interactive client layer, business logic and database layers. Enterprise java platform with open source framework OpenLaszlo is used to implement the Rich Internet Chromhome Application. Cross species comparative mapping raw data are collected and the processed information is stored into MySQL Chromhome database. Chromhome Release 1.0 contains 109 homology maps from 51 species. The data cover species from 14 orders and 30 families. The homology map displays all the chromosomes of the compared species as one image, making comparisons among species easier. Inferred data also provides maps of homologous regions that could serve as a guideline for researchers involved in phylogenetic or evolution based studies. Chromhome provides a useful resource for comparative genomics, holding graphical homology maps of a wide range of species. It brings together cytogenetic data of many genomes under one roof. Inferred painting can often determine the chromosomal homologous regions between two species, if each has been compared with a common third species. Inferred painting greatly reduces the need to map entire genomes and helps focus only on relevant</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2766374','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2766374"><span>Separation of the PROX1 gene from <span class="hlt">upstream</span> conserved elements in a complex inversion/translocation patient with hypoplastic left heart</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Gill, Harinder K; Parsons, Sian R; Spalluto, Cosma; Davies, Angela F; Knorz, Victoria J; Burlinson, Clare EG; Ng, Bee Ling; Carter, Nigel P; Ogilvie, Caroline Mackie; Wilson, David I; Roberts, Roland G</p> <p>2009-01-01</p> <p>Hypoplastic left heart (HLH) occurs in at least 1 in 10 000 live births but may be more common in utero. Its causes are poorly understood but a number of affected cases are associated with chromosomal abnormalities. We set out to localize the breakpoints in a patient with sporadic HLH and a de novo translocation. Initial studies showed that the apparently simple 1q41;3q27.1 translocation was actually combined with a 4-Mb inversion, also de novo, of material within 1q41. We therefore localized all four breakpoints and found that no known transcription units were disrupted. However we present a case, based on functional considerations, synteny and position of highly conserved non-coding <span class="hlt">sequence</span> elements, and the heterozygous Prox1+/− mouse phenotype (ventricular hypoplasia), for the involvement of dysregulation of the PROX1 gene in the aetiology of HLH in this case. Accordingly, we show that the spatial expression pattern of PROX1 in the developing human heart is consistent with a role in cardiac development. We suggest that dysregulation of PROX1 gene expression due to separation from its conserved <span class="hlt">upstream</span> elements is likely to have caused the heart defects observed in this patient, and that PROX1 should be considered as a potential candidate gene for other cases of HLH. The relevance of another breakpoint separating the cardiac gene ESRRG from a conserved downstream element is also discussed. PMID:19471316</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/22561515','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/22561515"><span>Hereditary mixed polyposis syndrome is caused by a 40-kb <span class="hlt">upstream</span> duplication that leads to increased and ectopic expression of the BMP antagonist GREM1.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Jaeger, Emma; Leedham, Simon; Lewis, Annabelle; Segditsas, Stefania; Becker, Martin; Cuadrado, Pedro Rodenas; Davis, Hayley; Kaur, Kulvinder; Heinimann, Karl; Howarth, Kimberley; East, James; Taylor, Jenny; Thomas, Huw; Tomlinson, Ian</p> <p>2012-05-06</p> <p>Hereditary mixed polyposis syndrome (HMPS) is characterized by apparent autosomal dominant inheritance of multiple types of colorectal polyp, with colorectal carcinoma occurring in a high proportion of affected individuals. Here, we use genetic mapping, copy-number analysis, exclusion of mutations by high-throughput <span class="hlt">sequencing</span>, gene expression analysis and functional assays to show that HMPS is caused by a duplication spanning the 3' end of the SCG5 gene and a region <span class="hlt">upstream</span> of the GREM1 locus. This unusual mutation is associated with increased allele-specific GREM1 expression. Whereas GREM1 is expressed in intestinal subepithelial myofibroblasts in controls, GREM1 is predominantly expressed in the epithelium of the large bowel in individuals with HMPS. The HMPS duplication contains predicted enhancer elements; some of these interact with the GREM1 promoter and can drive gene expression in vitro. Increased GREM1 expression is predicted to cause reduced bone morphogenetic protein (BMP) pathway activity, a mechanism that also underlies tumorigenesis in juvenile polyposis of the large bowel.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28260621','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28260621"><span>Differential regulation of hepatitis B virus core protein expression and genome replication by a small <span class="hlt">upstream</span> open reading frame and naturally occurring mutations in the precore region.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Zong, Li; Qin, Yanli; Jia, Haodi; Ye, Lei; Wang, Yongxiang; Zhang, Jiming; Wands, Jack R; Tong, Shuping; Li, Jisu</p> <p>2017-05-01</p> <p>Hepatitis B virus (HBV) transcribes two subsets of 3.5-kb RNAs: precore RNA for hepatitis B e antigen (HBeAg) expression, and pregenomic RNA for core and P protein translation as well as genome replication. HBeAg expression could be prevented by mutations in the precore region, while an <span class="hlt">upstream</span> open reading frame (uORF) has been proposed as a negative regulator of core protein translation. We employed replication competent HBV DNA constructs and transient transfection experiments in Huh7 cells to verify the uORF effect and to explore the alternative function of precore RNA. Optimized Kozak <span class="hlt">sequence</span> for the uORF or extra ATG codons as present in some HBV genotypes reduced core protein expression. G1896A nonsense mutation promoted more efficient core protein expression than mutated precore ATG, while a +1 frameshift mutation was ineffective. In conclusion, various HBeAg-negative precore mutations and mutations affecting uORF differentially regulate core protein expression and genome replication. Copyright © 2017 Elsevier Inc. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=137018','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=137018"><span>Eukaryotic Elongation Factor 1A Interacts with the <span class="hlt">Upstream</span> Pseudoknot Domain in the 3′ Untranslated Region of Tobacco Mosaic Virus RNA</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Zeenko, Vladimir V.; Ryabova, Lyubov A.; Spirin, Alexander S.; Rothnie, Helen M.; Hess, Daniel; Browning, Karen S.; Hohn, Thomas</p> <p>2002-01-01</p> <p>The genomic RNA of tobacco mosaic virus (TMV), like that of other positive-strand RNA viruses, acts as a template for both translation and replication. The highly structured 3′ untranslated region (UTR) of TMV RNAs plays an important role in both processes; it is not polyadenylated but ends with a tRNA-like structure (TLS) preceded by a conserved <span class="hlt">upstream</span> pseudoknot domain (UPD). The TLS of tobamoviral RNAs can be specifically aminoacylated and, in this state, can interact with eukaryotic elongation factor 1A (eEF1A)/GTP with high affinity. Using a UV cross-linking assay, we detected another specific binding site for eEF1A/GTP, within the UPDs of TMV and crucifer-infecting tobamovirus (crTMV), that does not require aminoacylation. A mutational analysis revealed that UPD pseudoknot conformation and some conserved primary <span class="hlt">sequence</span> elements are required for this interaction. Its possible role in the regulation of tobamovirus gene expression and replication is discussed. PMID:11991996</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2011LNCS.6577..516W','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2011LNCS.6577..516W"><span>Nonparametric Combinatorial <span class="hlt">Sequence</span> Models</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Wauthier, Fabian L.; Jordan, Michael I.; Jojic, Nebojsa</p> <p></p> <p>This work considers biological <span class="hlt">sequences</span> that exhibit combinatorial structures in their composition: groups of positions of the aligned <span class="hlt">sequences</span> are "linked" and covary as one unit across <span class="hlt">sequences</span>. If multiple such groups exist, complex interactions can emerge between them. <span class="hlt">Sequences</span> of this kind arise frequently in biology but methodologies for analyzing them are still being developed. This paper presents a nonparametric prior on <span class="hlt">sequences</span> which allows combinatorial structures to emerge and which induces a posterior distribution over factorized <span class="hlt">sequence</span> representations. We carry out experiments on three <span class="hlt">sequence</span> datasets which indicate that combinatorial structures are indeed present and that combinatorial <span class="hlt">sequence</span> models can more succinctly describe them than simpler mixture models. We conclude with an application to MHC binding prediction which highlights the utility of the posterior distribution induced by the prior. By integrating out the posterior our method compares favorably to leading binding predictors.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/873561','DOE-PATENT-XML'); return false;" href="https://www.osti.gov/servlets/purl/873561"><span>Cellulases and coding <span class="hlt">sequences</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/doepatents">DOEpatents</a></p> <p>Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong</p> <p>2001-02-20</p> <p>The present invention provides three fungal cellulases, their coding <span class="hlt">sequences</span>, recombinant DNA molecules comprising the cellulase coding <span class="hlt">sequences</span>, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/873898','DOE-PATENT-XML'); return false;" href="https://www.osti.gov/servlets/purl/873898"><span>Cellulases and coding <span class="hlt">sequences</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/doepatents">DOEpatents</a></p> <p>Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong</p> <p>2001-01-01</p> <p>The present invention provides three fungal cellulases, their coding <span class="hlt">sequences</span>, recombinant DNA molecules comprising the cellulase coding <span class="hlt">sequences</span>, recombinant host cells and methods for producing same. The present cellulases are from Orpinomyces PC-2.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/1994navy.reptT....G','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/1994navy.reptT....G"><span>Long <span class="hlt">sequence</span> correlation coprocessor</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Gage, Douglas W.</p> <p>1994-09-01</p> <p>A long <span class="hlt">sequence</span> correlation coprocessor (LSCC) accelerates the bitwise correlation of arbitrarily long digital <span class="hlt">sequences</span> by calculating in parallel the correlation score for 16, for example, adjacent bit alignments between two binary <span class="hlt">sequences</span>. The LSCC integrated circuit is incorporated into a computer system with memory storage buffers and a separate general purpose computer processor which serves as its controller. Each of the LSCC's set of sequential counters simultaneously tallies a separate correlation coefficient. During each LSCC clock cycle, computer enable logic associated with each counter compares one bit of a first <span class="hlt">sequence</span> with one bit of a second <span class="hlt">sequence</span> to increment the counter if the bits are the same. A shift register assures that the same bit of the first <span class="hlt">sequence</span> is simultaneously compared to different bits of the second <span class="hlt">sequence</span> to simultaneously calculate the correlation coefficient by the different counters to represent different alignments of the two <span class="hlt">sequences</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/872571','DOE-PATENT-XML'); return false;" href="https://www.osti.gov/servlets/purl/872571"><span><span class="hlt">Sequence</span> information signal processor</span></a></p> <p><a target="_blank" href="http://www.osti.gov/doepatents">DOEpatents</a></p> <p>Peterson, John C.; Chow, Edward T.; Waterman, Michael S.; Hunkapillar, Timothy J.</p> <p>1999-01-01</p> <p>An electronic circuit is used to compare two <span class="hlt">sequences</span>, such as genetic <span class="hlt">sequences</span>, to determine which alignment of the <span class="hlt">sequences</span> produces the greatest similarity. The circuit includes a linear array of series-connected processors, each of which stores a single element from one of the <span class="hlt">sequences</span> and compares that element with each successive element in the other <span class="hlt">sequence</span>. For each comparison, the processor generates a scoring parameter that indicates which segment ending at those two elements produces the greatest degree of similarity between the <span class="hlt">sequences</span>. The processor uses the scoring parameter to generate a similar scoring parameter for a comparison between the stored element and the next successive element from the other <span class="hlt">sequence</span>. The processor also delivers the scoring parameter to the next processor in the array for use in generating a similar scoring parameter for another pair of elements. The electronic circuit determines which processor and alignment of the <span class="hlt">sequences</span> produce the scoring parameter with the highest value.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015AGUFMNH51B1865A','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015AGUFMNH51B1865A"><span><span class="hlt">Upstream</span> Structural Management Measures for an Urban Area Flooding in Turkey and their Consequences on Flood Risk Management</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Akyurek, Z.; Bozoglu, B.; Girayhan, T.</p> <p>2015-12-01</p> <p>Flooding has the potential to cause significant impacts to economic activities as well as to disrupt or displace populations. Changing climate regimes such as extreme precipitation events increase flood vulnerability and put additional stresses on infrastructure. In this study the flood modelling in an urbanized area, namely Samsun-Terme in Blacksea region of Turkey is done. MIKE21 with flexible grid is used in 2- dimensional shallow water flow modelling. 1/1000 scaled maps with the buildings for the urbanized area and 1/5000 scaled maps for the rural parts are used to obtain DTM needed in the flood modelling. The bathymetry of the river is obtained from additional surveys. The main river passing through the urbanized area has a capacity of Q5 according to the design discharge obtained by simple ungauged discharge estimation depending on catchment area only. The effects of the available structures like bridges across the river on the flooding are presented. The <span class="hlt">upstream</span> structural measures are studied on scenario basis. Four sub-catchments of Terme River are considered as contributing the downstream flooding. The existing circumstance of the Terme River states that the meanders of the river have a major effect on the flood situation and lead to approximately 35% reduction in the peak discharge between <span class="hlt">upstream</span> and downstream of the river. It is observed that if the flow from the <span class="hlt">upstream</span> catchments can be retarded through a detention pond constructed in at least two of the <span class="hlt">upstream</span> catchments, estimated Q100 flood can be conveyed by the river without overtopping from the river channel. The operation of the <span class="hlt">upstream</span> detention ponds and the scenarios to convey Q500 without causing flooding are also presented. Structural management measures to address changes in flood characteristics in water management planning are discussed. Flood risk is obtained by using the flood hazard maps and water depth-damage functions plotted for a variety of building types and occupancies</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/621866','SCIGOV-STC'); return false;" href="https://www.osti.gov/servlets/purl/621866"><span><span class="hlt">Upstream</span> Passage, Spawning, and Stock Identification of Fall Chinook in the Snake River, 1992 and 1993 : Final Report.</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Blankenship, H. Lee; Mendel, Glen W.</p> <p></p> <p>This final report of the 3-year study summarizes activities and results for 1993. Study objectives were to: (1) determine the source of losses (or accounting errors) for adult chinook salmon between Ice Harbor Dam (IHR) and Lower Granite Dam (LGR), and <span class="hlt">upstream</span> of LGR in the Snake River; (2) identify spawning locations <span class="hlt">upstream</span> of LGR for calibration of aerial redd surveys, redd habitat mapping, carcass recovery for genetic stock profile analysis, and correction of estimated adult/redd ratios; and (3) estimate passage and migration times at Snake River. 200 fall chinook salmon were radio tagged and tracked with aerial, fixed-site, andmore » ground mobile tracking. Fish were released <span class="hlt">upstream</span> of IHR at Charbonneau Park (CHAR). 190 of the fish were tracked or relocated away from CHAR. 59 fish descended to below IHR without crossing Lower Monumental Dam (LMO). Another 128 salmon passed <span class="hlt">upstream</span> of LMO without falling back at IHR. Only 80 salmon passed Little Goose Dam (LGO) without falling back at a downstream dam; 66 of these fish passed LGR. Many fish that fell back reascended the dams. A total of 72 salmon released at CHAR passed <span class="hlt">upstream</span> of LGR, including fish that had fallen back and reascended a dam. Over 80 percent of the salmon that entered Lyons Ferry Hatchery each year had reached LGO before descending to the hatchery. Extensive wandering was documented between LMO and <span class="hlt">upstream</span> of LGR before salmon entered Lyons Ferry Hatchery or the Tucannon River. In 1993, 41 salmon were found to be of hatchery origin when recovered. These fish entered Lyons Ferry Hatchery with similar movements to unmarked salmon. Each year a few salmon have remained near the hatchery without entering, which suggests the hatchery may have inadequate attraction flows. Fall chinook passed lower Snake River dams in 2-5 days each on average. Median travel times through LMO and LGO were 1.0-1.3 days each, which was slower than for spring chinook or steelhead in 1993. 5 refs., 21 figs., 20</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27879428','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27879428"><span>A polymorphism <span class="hlt">upstream</span> MIR1279 gene is associated with pericarditis development in Systemic Lupus Erythematosus and contributes to definition of a genetic risk profile for this complication.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ciccacci, C; Perricone, C; Politi, C; Rufini, S; Ceccarelli, F; Cipriano, E; Alessandri, C; Latini, A; Valesini, G; Novelli, G; Conti, F; Borgiani, P</p> <p>2017-07-01</p> <p>Recently, a study has shown that a polymorphism in the region of MIR1279 modulates the expression of the TRAF3IP2 gene. Since polymorphisms in the TRAF3IP2 gene have been described in association with systemic lupus erithematosus (SLE) susceptibility and with the development of pericarditis, our aim is to verify if the MIR1279 gene variability could also be involved. The rs1463335 SNP, located <span class="hlt">upstream</span> MIR1279 gene, was analyzed by allelic discrimination assay in 315 Italian SLE patients and 201 healthy controls. Moreover, the MIR1279 gene was full <span class="hlt">sequenced</span> in 50 patients. A case/control association study and a genotype/phenotype correlation analysis were performed. We also constructed a pericarditis genetic risk profile for patients with SLE. The full <span class="hlt">sequencing</span> of the MIR1279 gene in patients with SLE did not reveal any novel or known variation. The variant allele of the rs1463335 SNP was significantly associated with susceptibility to pericarditis ( P = 0.017 and OR = 1.67). A risk profile model for pericarditis considering the risk alleles of MIR1279 and three other genes (STAT4, PTPN2 and TRAF3IP2) showed that patients with 4 or 5 risk alleles have a higher risk of developing pericarditis ( OR = 4.09 with P = 0.001 and OR = 6.04 with P = 0.04 respectively). In conclusion, we describe for the first time the contribution of a MIR1279 SNP in pericarditis development in patients with SLE and a genetic risk profile model that could be useful to identify patients more susceptible to developing pericarditis in SLE. This approach could help to improve the prediction and the management of this complication.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.dtic.mil/docs/citations/AD1049774','DTIC-ST'); return false;" href="http://www.dtic.mil/docs/citations/AD1049774"><span><span class="hlt">Sequence</span> to <span class="hlt">Sequence</span> - Video to Text</span></a></p> <p><a target="_blank" href="http://www.dtic.mil/">DTIC Science & Technology</a></p> <p></p> <p>2015-12-11</p> <p>Saenko, and S. Guadarrama. Generating natural-language video descriptions using text - mined knowledge. In AAAI, July 2013. 2 [20] P. Kuznetsova, V...<span class="hlt">Sequence</span> to <span class="hlt">Sequence</span> – Video to Text Subhashini Venugopalan1 Marcus Rohrbach2,4 Jeff Donahue2 Raymond Mooney1 Trevor Darrell2 Kate Saenko3...1. Introduction Describing visual content with natural language text has recently received increased interest, especially describing images with a</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://files.eric.ed.gov/fulltext/ED471208.pdf','ERIC'); return false;" href="http://files.eric.ed.gov/fulltext/ED471208.pdf"><span>Career Academy Course <span class="hlt">Sequences</span>.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Markham, Thom; Lenz, Robert</p> <p></p> <p>This career academy course <span class="hlt">sequence</span> guide is designed to give teachers a quick overview of the course <span class="hlt">sequences</span> of well-known career academy and career pathway programs from across the country. The guide presents a variety of sample course <span class="hlt">sequences</span> for the following academy themes: (1) arts and communication; (2) business and finance; (3)…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/24512607','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/24512607"><span><span class="hlt">Sequencing</span> artifacts in the type A influenza databases and attempts to correct them.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Suarez, David L; Chester, Nikki; Hatfield, Jason</p> <p>2014-07-01</p> <p>There are over 276 000 influenza gene <span class="hlt">sequences</span> in public databases, with the quality of the <span class="hlt">sequences</span> determined by the contributor. As part of a high school class project, influenza <span class="hlt">sequences</span> with possible errors were identified in the public databases based on the size of the gene being longer than expected, with the hypothesis that these <span class="hlt">sequences</span> would have an error. Students contacted <span class="hlt">sequence</span> submitters alerting them of the possible <span class="hlt">sequence</span> issue(s) and requested they the suspect <span class="hlt">sequence(s</span>) be correct as appropriate. Type A influenza viruses were screened, and gene segments longer than the accepted size were identified for further analysis. Attention was placed on <span class="hlt">sequences</span> with additional nucleotides <span class="hlt">upstream</span> or downstream of the highly conserved non-coding ends of the viral segments. A total of 1081 <span class="hlt">sequences</span> were identified that met this criterion. Three types of errors were commonly observed: non-influenza primer <span class="hlt">sequence</span> wasn't removed from the <span class="hlt">sequence</span>; PCR product was cloned and plasmid <span class="hlt">sequence</span> was included in the <span class="hlt">sequence</span>; and Taq polymerase added an adenine at the end of the PCR product. Internal insertions of nucleotide <span class="hlt">sequence</span> were also commonly observed, but in many cases it was unclear if the <span class="hlt">sequence</span> was correct or actually contained an error. A total of 215 <span class="hlt">sequences</span>, or 22.8% of the suspect <span class="hlt">sequences</span>, were corrected in the public databases in the first year of the student project. Unfortunately 138 additional <span class="hlt">sequences</span> with possible errors were added to the databases in the second year. Additional awareness of the need for data integrity of <span class="hlt">sequences</span> submitted to public databases is needed to fully reap the benefits of these large data sets. © 2014 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li class="active"><span>21</span></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_21 --> <div id="page_22" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li class="active"><span>22</span></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="421"> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4765514','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4765514"><span>Effects of salinity on <span class="hlt">upstream</span>-migrating, spawning sea lamprey, Petromyzon marinus</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Ferreira-Martins, D.; Coimbra, J.; Antunes, C.; Wilson, J. M.</p> <p>2016-01-01</p> <p>The sea lamprey, Petromyzon marinus, is an anadromous, semelparous species that is vulnerable to endangered in parts of its native range due in part to loss of spawning habitat because of man-made barriers. The ability of lampreys to return to the ocean or estuary and search out alternative spawning river systems would be limited by their osmoregulatory ability in seawater. A reduction in tolerance to salinity has been documented in migrants, although the underlying mechanisms have not been characterized. We examined the capacity for marine osmoregulation in <span class="hlt">upstream</span> spawning migrants by characterizing the physiological effects of salinity challenge from a molecular perspective. Estuarine-captured migrants held in freshwater (FW) for ∼1 week (short-term acclimation) or 2 months (long-term acclimation) underwent an incremental salinity challenge until loss of equilibrium occurred and upper thresholds of 25 and 17.5, respectively, occurred. Regardless of salinity tolerance, all lamprey downregulated FW ion-uptake mechanisms [gill transcripts of Na+:Cl− cotransporter (NCC/slc12a3) and epithelial Na+ channel (ENaC/scnn1) and kidney Na+/K+-ATPase (NKA) protein and activity but not transcript]. At their respective salinity limits, lamprey displayed a clear osmoregulatory failure and were unable to regulate [Na+] and [Cl−] in plasma and intestinal fluid within physiological limits, becoming osmocompromised. A >90% drop in haematocrit indicated haemolysis, and higher plasma concentrations of the cytosolic enzymes alanine aminotransferase, aspartate aminotransferase and lactate dehydrogenase indicated damage to other tissues, including liver. However, >80% of short-term FW-acclimated fish were able to osmoregulate efficiently, with less haemolysis and tissue damage. This osmoregulatory ability was correlated with significant upregulation of the secretory form of Na+:K+:2Cl− cotransporter (NKCC1/slc12a2) transcript levels and the re-emergence of seawater</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/29094495','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/29094495"><span><span class="hlt">Upstream</span> kinases of plant SnRKs are involved in salt stress tolerance.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Barajas-Lopez, Juan de Dios; Moreno, Jose Ramon; Gamez-Arjona, Francisco M; Pardo, Jose M; Punkkinen, Matleena; Zhu, Jian-Kang; Quintero, Francisco J; Fujii, Hiroaki</p> <p>2018-01-01</p> <p>Sucrose non-fermenting 1-related protein kinases (SnRKs) are important for plant growth and stress responses. This family has three clades: SnRK1, SnRK2 and SnRK3. Although plant SnRKs are thought to be activated by <span class="hlt">upstream</span> kinases, the overall mechanism remains obscure. Geminivirus Rep-Interacting Kinase (GRIK)1 and GRIK2 phosphorylate SnRK1s, which are involved in sugar/energy sensing, and the grik1-1 grik2-1 double mutant shows growth retardation under regular growth conditions. In this study, we established another Arabidopsis mutant line harbouring a different allele of gene GRIK1 (grik1-2 grik2-1) that grows similarly to the wild-type, enabling us to evaluate the function of GRIKs under stress conditions. In the grik1-2 grik2-1 double mutant, phosphorylation of SnRK1.1 was reduced, but not eliminated, suggesting that the grik1-2 mutation is a weak allele. In addition to high sensitivity to glucose, the grik1-2 grik2-1 mutant was sensitive to high salt, indicating that GRIKs are also involved in salinity signalling pathways. Salt Overly Sensitive (SOS)2, a member of the SnRK3 subfamily, is a critical mediator of the response to salinity. GRIK1 phosphorylated SOS2 in vitro, resulting in elevated kinase activity of SOS2. The salt tolerance of sos2 was restored to normal levels by wild-type SOS2, but not by a mutated form of SOS2 lacking the T168 residue phosphorylated by GRIK1. Activation of SOS2 by GRIK1 was also demonstrated in a reconstituted system in yeast. Our results indicate that GRIKs phosphorylate and activate SnRK1 and other members of the SnRK3 family, and that they play important roles in multiple signalling pathways in vivo. © 2017 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2006AGUFM.H43H..02E','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2006AGUFM.H43H..02E"><span>The Evolution of Riparian Landscape Elements Following <span class="hlt">Upstream</span> Regulation and Depletion on the Rio Grande</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Everitt, B. L.</p> <p>2006-12-01</p> <p> separate the channel from its former flood plain. All areas are impacted by heavy machinery during periodic channel maintenance. I conclude that the environmental degradation caused by artificial channel modification has far outweighed any generated by <span class="hlt">upstream</span> hydrologic control.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20150015490','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20150015490"><span>A Model for Jet-Surface Interaction Noise Using Physically Realizable <span class="hlt">Upstream</span> Turbulence Conditions</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Afsar, Mohammed Z.; Leib, Stewart J.; Bozak, Richard F.</p> <p>2015-01-01</p> <p>This paper is a continuation of previous work in which a generalized Rapid Distortion Theory (RDT) formulation was used to model low-frequency trailing-edge noise. The research was motivated by proposed next-generation aircraft configurations where the exhaust system is tightly integrated with the airframe. Data from recent experiments at NASA on the interaction between high-Reynolds-number subsonic jet flows and an external flat plate showed that the power spectral density (PSD) of the far-field pressure underwent considerable amplification at low frequencies. For example, at the 900 observation angle, the low-frequency noise could be as much as 10dB greater than the jet noise itself. In this paper, we present predictions of the noise generated by the interaction of a rectangular jet with the trailing edge of a semi-infinite flat plate. The calculations are based on a formula for the acoustic spectrum of this noise source derived from an exact formal solution of the linearized Euler equations involving (in this case) one arbitrary convected scalar quantity and a Rayleigh equation Green's function. A low-frequency asymptotic approximation for the Green's function based on a two-dimensional mean flow is used in the calculations along with a physically realizable <span class="hlt">upstream</span> turbulence spectrum, which includes a finite de-correlation region. Numerical predictions, based on three-dimensional RANS solutions for a range of subsonic acoustic Mach number jets and nozzle aspect ratios are compared with experimental data. Comparisons of the RANS results with flow data are also presented for selected cases. We find that a finite decorrelation region increases the low-frequency algebraic decay (the low frequency "rolloff") of the acoustic spectrum with angular frequency thereby producing much closer agreement with noise data for Strouhal numbers less than 0.1. Secondly, the large-aspectratio theory is able to predict the low-frequency amplification due to the jet</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20160001108','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20160001108"><span>A Model for Jet-Surface Interaction Noise Using Physically Realizable <span class="hlt">Upstream</span> Turbulence Conditions</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Afsar, Mohammed Z.; Leib, Stewart J.; Bozak, Richard F.</p> <p>2016-01-01</p> <p>This paper is a continuation of previous work in which a generalized Rapid Distortion Theory (RDT) formulation was used to model low-frequency trailing-edge noise. The research was motivated by proposed next-generation aircraft configurations where the exhaust system is tightly integrated with the airframe. Data from recent experiments at NASA on the interaction between high-Reynolds-number subsonic jet flows and an external flat plate showed that the power spectral density (PSD) of the far-field pressure underwent considerable amplification at low frequencies. For example, at the 90deg observation angle, the low-frequency noise could be as much as 10 dB greater than the jet noise itself. In this paper, we present predictions of the noise generated by the interaction of a rectangular jet with the trailing edge of a semi-infinite flat plate. The calculations are based on a formula for the acoustic spectrum of this noise source derived from an exact formal solution of the linearized Euler equations involving (in this case) one arbitrary convected scalar quantity and a Rayleigh equation Green's function. A low-frequency asymptotic approximation for the Green's function based on a two-dimensional mean flow is used in the calculations along with a physically realizable <span class="hlt">upstream</span> turbulence spectrum, which includes a finite decorrelation region. Numerical predictions of the sound field, based on three-dimensional RANS solutions to determine the mean flow, turbulent kinetic energy and turbulence length and time scales, for a range of subsonic acoustic Mach number jets and nozzle aspect ratios are compared with experimental data. Comparisons of the RANS results with flow data are also presented for selected cases. We find that a finite decorrelation region in the turbulence spectrum increases the low-frequency algebraic decay (the low frequency "roll-off") of the acoustic spectrum with angular frequency thereby producing much closer agreement with noise data for Strouhal</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27501295','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27501295"><span>Can Peripheral MicroRNA Expression Data Serve as Epigenomic (<span class="hlt">Upstream</span>) Biomarkers of Alzheimer's Disease?</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Yılmaz, Şenay Görücü; Erdal, Mehmet Emin; Özge, Aynur Avcı; Sungur, Mehmet Ali</p> <p>2016-08-01</p> <p>Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the most common form of dementia. However, biomarkers that require testing in the brain tissue pose a formidable practical barrier to AD diagnostic innovation. MicroRNAs (miRNAs) are responsible for control of gene expression at the posttranscriptional level and are essential for the function of neuronal networks and neuronal survival. miRNA expression can impact the regulation of APP (amyloid beta A4 precursor protein), PSEN1 (presenilin 1), PSEN2 (presenilin 2), and BACE1 (beta-secretase 1) genes in the brain that were previously implicated in AD pathophysiology. Little is known, however, on the extent to which peripheral tissue (e.g., whole blood) miRNA variation might offer clinical predictive value for AD. Moreover, few studies have examined multiple peripheral miRNA expression data at the same time. We report here, to the best of our knowledge, the first whole-blood-based and parallel study of seven miRNAs (hsa-miR-9-5p, hsa-miR-29a-3p, hsa-miR-106a-5p, hsa-miR-106b-5p, hsa-miR-107, hsa-miR-125a-3p, and hsa-miR-125b-5p) in relation to AD susceptibility. Notably, these miRNAs are situated "<span class="hlt">upstream</span>" to the genes implicated in AD. We measured the whole-blood miRNA expression by a real-time polymerase chain reaction in a large study sample (n = 281), comprising patients with AD (n = 172) and healthy controls (n = 109). A reduction in whole-blood expression of hsa-miR-9-5p, hsa-miR-106a-5p, hsa-miR-106b-5p, and hsa-miR-107 was significantly associated with an increased risk of AD (p < 0.05). Notably, after receiver operating characteristics curve analyses, hsa-miR-106a-5p displayed, as a predictor variable, 93% specificity and 68% sensitivity. On the other hand, the expression of hsa-miR-29a-3p, hsa-miR-125a-3p, and hsa-miR-125b-5p was not significantly different between patients and controls (p > 0.05). In conclusion, these observations warrant replication in larger</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/24931615','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/24931615"><span>Avoidance of truncated proteins from unintended ribosome binding sites within heterologous protein coding <span class="hlt">sequences</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Whitaker, Weston R; Lee, Hanson; Arkin, Adam P; Dueber, John E</p> <p>2015-03-20</p> <p>Genetic <span class="hlt">sequences</span> ported into non-native hosts for synthetic biology applications can gain unexpected properties. In this study, we explored <span class="hlt">sequences</span> functioning as ribosome binding sites (RBSs) within protein coding DNA <span class="hlt">sequences</span> (CDSs) that cause internal translation, resulting in truncated proteins. Genome-wide prediction of bacterial RBSs, based on biophysical calculations employed by the RBS calculator, suggests a selection against internal RBSs within CDSs in Escherichia coli, but not those in Saccharomyces cerevisiae. Based on these calculations, silent mutations aimed at removing internal RBSs can effectively reduce truncation products from internal translation. However, a solution for complete elimination of internal translation initiation is not always feasible due to constraints of available coding <span class="hlt">sequences</span>. Fluorescence assays and Western blot analysis showed that in genes with internal RBSs, increasing the strength of the intended <span class="hlt">upstream</span> RBS had little influence on the internal translation strength. Another strategy to minimize truncated products from an internal RBS is to increase the relative strength of the <span class="hlt">upstream</span> RBS with a concomitant reduction in promoter strength to achieve the same protein expression level. Unfortunately, lower transcription levels result in increased noise at the single cell level due to stochasticity in gene expression. At the low expression regimes desired for many synthetic biology applications, this problem becomes particularly pronounced. We found that balancing promoter strengths and <span class="hlt">upstream</span> RBS strengths to intermediate levels can achieve the target protein concentration while avoiding both excessive noise and truncated protein.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4136844','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4136844"><span>Expression of Wheat High Molecular Weight Glutenin Subunit 1Bx Is Affected by Large Insertions and Deletions Located in the <span class="hlt">Upstream</span> Flanking <span class="hlt">Sequences</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Hao, Chenyang; Tang, Saijun; Zhang, Xueyong; Li, Tian</p> <p>2014-01-01</p> <p>To better understand the transcriptional regulation of high molecular weight glutenin subunit (HMW-GS) expression, we isolated four Glu-1Bx promoters from six wheat cultivars exhibiting diverse protein expression levels. The activities of the diverse Glu-1Bx promoters were tested and compared with β-glucuronidase (GUS) reporter fusions. Although all the full-length Glu-1Bx promoters showed endosperm-specific activities, the strongest GUS activity was observed with the 1Bx7OE promoter in both transient expression assays and stable transgenic rice lines. A 43 bp insertion in the 1Bx7OE promoter, which is absent in the 1Bx7 promoter, led to enhanced expression. Analysis of promoter deletion constructs confirmed that a 185 bp MITE (miniature inverted-repeat transposable element) in the 1Bx14 promoter had a weak positive effect on Glu-1Bx expression, and a 54 bp deletion in the 1Bx13 promoter reduced endosperm-specific activity. To investigate the effect of the 43 bp insertion in the 1Bx7OE promoter, a functional marker was developed to screen 505 Chinese varieties and 160 European varieties, and only 1Bx7-type varieties harboring the 43 bp insertion in their promoters showed similar overexpression patterns. Hence, the 1Bx7OE promoter should be important tool in crop genetic engineering as well as in molecular assisted breeding. PMID:25133580</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/16354835','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/16354835"><span>A 10-aa-long <span class="hlt">sequence</span> in SLP-76 <span class="hlt">upstream</span> of the Gads binding site is essential for T cell development and function.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Kumar, Lalit; Feske, Stefan; Rao, Anjana; Geha, Raif S</p> <p>2005-12-27</p> <p>The adapter SLP-76 is essential for T cell development and function. SLP-76 binds to the src homology 3 domain of Lck in vitro. This interaction depends on amino acids 185-194 of SLP-76. To examine the role of the Lck-binding region of SLP-76 in T cell development and function, SLP-76(-/-) mice were reconstituted with an SLP-76 mutant that lacks amino acids 185-194. Double and single positive thymocytes from reconstituted mice were severely reduced in numbers and exhibited impaired positive selection and increased apoptosis. Peripheral T cells were also reduced in numbers, exhibited impaired phospholipase C-gamma1 and Erk phosphorylation, and failed to flux calcium, secrete IL-2, and proliferate in response to T cell antigen receptor ligation. Delayed cutaneous hypersensitivity responses and Ab responses to T cell-dependent antigen were severely impaired. These results indicate that the Lck binding region of SLP-76 is essential for T cell antigen receptor signaling and normal T cell development and function.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2017QSRv..173..248L','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2017QSRv..173..248L"><span>Sediment <span class="hlt">sequences</span> and palynology of outer South Bay, Manitoulin Island, Ontario: Connections to Lake Huron paleohydrologic phases and <span class="hlt">upstream</span> Lake Agassiz events</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Lewis, C. F. M.; Anderson, T. W.</p> <p>2017-10-01</p> <p>South Bay on the southern coast of Manitoulin Island is a fjord-like embayment connected to Lake Huron by a natural narrow gap in the bay's outer sill 6.5-14 m above the lake. A seismic profile, pollen, plant macrofossil, grain size analyses, and other sediment properties of two piston cores from a shallow outer basin of the bay document a 9 m-thick sediment section comprising rhythmically laminated clay under silty clay containing zones with small molluscan shells and marsh detritus. A sandy pebbly layer under soft silty clay mud overlies these sediments. This stratigraphy represents inundation by deep glacial Lake Algonquin followed by the shallowing Post Algonquin series of lakes, and exposure in the early Holocene by 5 Lake Stanley lowstands in the Lake Huron basin separated by 4 Lake Mattawa highstands. Overflow from South Bay in the first lowstand is thought to have eroded the outer sill gap. Marsh environments are inferred to have formed in the bay during subsequent lowstands. The Lake Mattawa highstands are attributed to outburst floods mainly from glacial Lake Agassiz. Palynological evidence of increased spruce occurrence, an apparent regional climate reversal, during the dry pine period is attributed to cold northwest winds from the Lake Superior basin and a lake effect from the Mattawa highstands in the Lake Huron basin. Lake waters transgressed South Bay following the pine period to form the Nipissing shore on Manitoulin Island. Transfer of Lake Huron basin drainage to southern outlets and continued glacioisostatic uplift of the region led to the present configuration of South Bay and Lake Huron.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/22118691-reinterpretation-slowdown-solar-wind-mean-velocity-nonlinear-structures-observed-upstream-earth-bow-shock','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/22118691-reinterpretation-slowdown-solar-wind-mean-velocity-nonlinear-structures-observed-upstream-earth-bow-shock"><span>REINTERPRETATION OF SLOWDOWN OF SOLAR WIND MEAN VELOCITY IN NONLINEAR STRUCTURES OBSERVED <span class="hlt">UPSTREAM</span> OF EARTH'S BOW SHOCK</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Parks, G. K.; Lin, N.; Lee, E.</p> <p>2013-07-10</p> <p>Two of the many features associated with nonlinear <span class="hlt">upstream</span> structures are (1) the solar wind (SW) mean flow slows down and deviates substantially and (2) the temperature of the plasma increases in the structure. In this Letter, we show that the SW beam can be present throughout the entire <span class="hlt">upstream</span> event maintaining a nearly constant beam velocity and temperature. The decrease of the velocity is due to the appearance of new particles moving in the opposite direction that act against the SW beam and reduce the mean velocity as computed via moments. The new population, which occupies a larger velocitymore » space, also contributes to the second moment, increasing the temperature. The new particles include the reflected SW beam at the bow shock and another population of lower energies, accelerated nearby at the shock or at the boundary of the nonlinear structures.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://ascelibrary.org/action/showPublications?pubType=proceedings&sortBy=ConferenceTitleSort','USGSPUBS'); return false;" href="http://ascelibrary.org/action/showPublications?pubType=proceedings&sortBy=ConferenceTitleSort"><span>Cause and solution for false <span class="hlt">upstream</span> boat velocities measured with a StreamPro acoustic doppler current profiler</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Mueller, David S.; Rehmel, Mike S.; Wagner, Chad R.</p> <p>2007-01-01</p> <p>In 2003, Teledyne RD Instruments introduced the StreamPro acoustic Doppler current profiler which does not include an internal compass. During stationary moving-bed tests the StreamPro often tends to swim or kite from the end of the tether (the instrument rotates then moves laterally in the direction of the rotation). Because the StreamPro does not have an internal compass, it cannot account for the rotation. This rotation and lateral movement of the StreamPro on the end of the tether generates a false <span class="hlt">upstream</span> velocity, which cannot be easily distinguished from a moving-bed bias velocity. A field test was completed to demonstrate that this rotation and lateral movement causes a false <span class="hlt">upstream</span> boat velocity. The vector dot product of the boat velocity and the unit vector of the depth-averaged water velocity is shown to be an effective method to account for the effect of the rotation and lateral movement.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016SPIE.9773E..0FS','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016SPIE.9773E..0FS"><span>An <span class="hlt">upstream</span> burst-mode equalization scheme for 40 Gb/s TWDM PON based on optimized SOA cascade</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Sun, Xiao; Chang, Qingjiang; Gao, Zhensen; Ye, Chenhui; Xiao, Simiao; Huang, Xiaoan; Hu, Xiaofeng; Zhang, Kaibin</p> <p>2016-02-01</p> <p>We present a novel <span class="hlt">upstream</span> burst-mode equalization scheme based on optimized SOA cascade for 40 Gb/s TWDMPON. The power equalizer is placed at the OLT which consists of two SOAs, two circulators, an optical NOT gate, and a variable optical attenuator. The first SOA operates in the linear region which acts as a pre-amplifier to let the second SOA operate in the saturation region. The <span class="hlt">upstream</span> burst signals are equalized through the second SOA via nonlinear amplification. From theoretical analysis, this scheme gives sufficient dynamic range suppression up to 16.7 dB without any dynamic control or signal degradation. In addition, a total power budget extension of 9.3 dB for loud packets and 26 dB for soft packets has been achieved to allow longer transmission distance and increased splitting ratio.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://ntrs.nasa.gov/search.jsp?R=19810028027&hterms=ultra-low+power+sensor&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D70%26Ntt%3Dultra-low%2Bpower%2Bsensor','NASA-TRS'); return false;" href="https://ntrs.nasa.gov/search.jsp?R=19810028027&hterms=ultra-low+power+sensor&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D70%26Ntt%3Dultra-low%2Bpower%2Bsensor"><span>Composition and energy spectra of low energy ions observed <span class="hlt">upstream</span> of the earth's bow shock on ISEE-1</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Ipavich, F. M.; Galvin, A. B.; Gloeckler, G.; Hovestadt, D.; Klecker, B.; Scholer, M.; Fan, C. Y.; Fisk, L. A.; Ogallagher, J. J.</p> <p>1980-01-01</p> <p>The characteristics of eleven locally accelerated particle events in the energy range from 30 to 125 keV/Q observed <span class="hlt">upstream</span> of the earth's bow shock have been determined, including composition, energy spectra, and intensity versus time profiles. The measurements were made with the Ultra Low Energy Charge Analyzer sensor on ISEE-1. The composition in these events is similar to that of the solar wind, with a He to proton ratio of 8% and a CNO to He ratio of 6%. The composition is reasonably constant only when evaluated at equal energy per charge. The energy spectra cannot be adequately fit by a single power law in energy; an exponential or Maxwellian in energy per charge gives a satisfactory representation of the spectra. The time-intensity profiles of these <span class="hlt">upstream</span> events show an inverse velocity dispersion, which may provide clues to the responsible acceleration mechanism.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/12824373','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/12824373"><span>Regulatory <span class="hlt">sequence</span> analysis tools.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>van Helden, Jacques</p> <p>2003-07-01</p> <p>The web resource Regulatory <span class="hlt">Sequence</span> Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA <span class="hlt">sequences</span>. These tools include <span class="hlt">sequence</span> retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random <span class="hlt">sequence</span> generation and other utilities. Alternative formats are supported for the representation of regulatory motifs (strings or position-specific scoring matrices) and several algorithms are proposed for pattern discovery. RSAT currently holds >100 fully <span class="hlt">sequenced</span> genomes and these data are regularly updated from GenBank.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://pubs.er.usgs.gov/publication/70029052','USGSPUBS'); return false;" href="https://pubs.er.usgs.gov/publication/70029052"><span>The effect of thiamine injection on <span class="hlt">upstream</span> migration, survival, and thiamine status of putative thiamine-deficient coho salmon</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Fitzsimons, J.D.; Williston, B.; Amcoff, P.; Balk, L.; Pecor, C.; Ketola, H.G.; Hinterkopf, J.P.; Honeyfield, D.C.</p> <p>2005-01-01</p> <p>A diet containing a high proportion of alewives Alosa pseudoharengus results in a thiamine deficiency that has been associated with high larval salmonid mortality, known as early mortality syndrome (EMS), but relatively little is known about the effects of the deficiency on adults. Using thiamine injection (50 mg thiamine/kg body weight) of ascending adult female coho salmon Oncorhynchus kisutch on the Platte River, Michigan, we investigated the effects of thiamine supplementation on migration, adult survival, and thiamine status. The thiamine concentrations of eggs, muscle (red and white), spleen, kidney (head and trunk), and liver and the transketolase activity of the liver, head kidney, and trunk kidney of fish injected with thiamine dissolved in physiological saline (PST) or physiological saline only (PS) were compared with those of uninjected fish. The injection did not affect the number of fish making the 15-km <span class="hlt">upstream</span> migration to a collection weir but did affect survival once fish reached the <span class="hlt">upstream</span> weir, where survival of PST-injected fish was almost twice that of controls. The egg and liver thiamine concentrations in PS fish sampled after their <span class="hlt">upstream</span> migration were significantly lower than those of uninjected fish collected at the downstream weir, but the white muscle thiamine concentration did not differ between the two groups. At the upper weir, thiamine levels in the liver, spleen, head kidney, and trunk kidney of PS fish were indistinguishable from those of uninjected fish (called "wigglers") suffering from a severe deficiency and exhibiting reduced equilibrium, a stage that precedes total loss of equilibrium and death. For PST fish collected at the <span class="hlt">upstream</span> weir, total thiamine levels in all tissues were significantly elevated over those of PS fish. Based on the limited number of tissues examined, thiamine status was indicated better by tissue thiamine concentration than by transketolase activity. The adult injection method we used appears to</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://pubs.er.usgs.gov/publication/70034048','USGSPUBS'); return false;" href="https://pubs.er.usgs.gov/publication/70034048"><span>Movement Patterns of American Shad Transported <span class="hlt">Upstream</span> of Dams on The Roanoke River, North Carolina and Virginia</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Harris, Julianne E.; Hightower, J.E.</p> <p>2011-01-01</p> <p>American shad Alosa sapidissima are in decline throughout much of their native range as a result of overfishing, pollution, and habitat alteration in coastal rivers where they spawn. One approach to restoration in regulated rivers is to provide access to historical spawning habitat above dams through a trap-and-transport program. We examined the initial survival, movement patterns, spawning, and downstream passage of sonic-tagged adult American shad transported to reservoir and riverine habitats <span class="hlt">upstream</span> of hydroelectric dams on the Roanoke River, North Carolina and Virginia, during 2007–2009. Average survival to release in 2007–2008 was 85%, but survival decreased with increasing water temperature. Some tagged fish released in reservoirs migrated <span class="hlt">upstream</span> to rivers; however, most meandered back and forth within the reservoir. A higher percentage of fish migrated through a smaller (8,215-ha) than a larger (20,234-ha) reservoir, suggesting that the population-level effects of transport may depend on upper basin characteristics. Transported American shad spent little time in upper basin rivers but were there when temperatures were appropriate for spawning. No American shad eggs were collected during weekly plankton sampling in upper basin rivers. The estimated initial survival of sonic-tagged American shad after downstream passage through each dam was 71–100%; however, only 1% of the detected fish migrated downstream through all three dams and many were relocated just <span class="hlt">upstream</span> of a dam late in the season. Although adult American shad were successfully transported to <span class="hlt">upstream</span> habitats in the Roanoke River basin, under present conditions transported individuals may have reduced effective fecundity and postspawning survival compared with nontransported fish that spawn in the lower Roanoke River.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013JIEIE..94...23S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013JIEIE..94...23S"><span>Optimization of Process Parameters in Preparation of Nanoemulsions of CLn<span class="hlt">A</span> <span class="hlt">Rich</span> Oil by Response Surface Methodology</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Sengupta, Avery; Gupta, Surashree Sen; Ghosh, Mahua</p> <p>2013-03-01</p> <p>The purpose of the present study was to obtain optimal processing for preparation of uniform-sized nanoemulsion of conjugated linolenic acid (CLn<span class="hlt">A</span>) <span class="hlt">rich</span> oil to increase the oxidative stability of CLnA by using a high-speed disperser (HSD) and ultrasonication. The emulsifiers used were egg phospholipid and soya protein isolate. The effects of oil concentration [0.05 to 1.25 % (w/w)], emulsifier ratio [0.1:0.9 to 0.9:0.1 (phospholipid:protein)], speed of the HSD (2,000 to 12,000 rpm) and times of HSD and sonication treatments (10 to 50 min) were observed. Optimization was performed with and without response surface methodology (RSM). The optimum compositional variables i.e. concentration of oil was 1 % and phospholipid:protein molar ratio was 0.5:0.5. Maximum size reduction occurred at 10,000 rpm speed of HSD. HSD should be administered for 40 min followed by 40 min ultrasonication. The range of the size of the droplets in the nanoemulsion was between 173 ± 1.20 and 183 ± 0.94 nm. Nanoemulsion is a size reduction technique where the oil present in the emulsion can be easily stabilized which increases the shelf-life of the oil. The present study derived the reaction parameters were optimized using RSM to produce nanoemulsion of CLn<span class="hlt">A</span> <span class="hlt">rich</span> oils of minimum size to obtain maximum stability.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/11700586','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/11700586"><span>Biological <span class="hlt">sequence</span> compression algorithms.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Matsumoto, T; Sadakane, K; Imai, H</p> <p>2000-01-01</p> <p>Today, more and more DNA <span class="hlt">sequences</span> are becoming available. The information about DNA <span class="hlt">sequences</span> are stored in molecular biology databases. The size and importance of these databases will be bigger and bigger in the future, therefore this information must be stored or communicated efficiently. Furthermore, <span class="hlt">sequence</span> compression can be used to define similarities between biological <span class="hlt">sequences</span>. The standard compression algorithms such as gzip or compress cannot compress DNA <span class="hlt">sequences</span>, but only expand them in size. On the other hand, CTW (Context Tree Weighting Method) can compress DNA <span class="hlt">sequences</span> less than two bits per symbol. These algorithms do not use special structures of biological <span class="hlt">sequences</span>. Two characteristic structures of DNA <span class="hlt">sequences</span> are known. One is called palindromes or reverse complements and the other structure is approximate repeats. Several specific algorithms for DNA <span class="hlt">sequences</span> that use these structures can compress them less than two bits per symbol. In this paper, we improve the CTW so that characteristic structures of DNA <span class="hlt">sequences</span> are available. Before encoding the next symbol, the algorithm searches an approximate repeat and palindrome using hash and dynamic programming. If there is a palindrome or an approximate repeat with enough length then our algorithm represents it with length and distance. By using this preprocessing, a new program achieves a little higher compression ratio than that of existing DNA-oriented compression algorithms. We also describe new compression algorithm for protein <span class="hlt">sequences</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25900885','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25900885"><span>Refining the regulatory region <span class="hlt">upstream</span> of SOX9 associated with 46,XX testicular disorders of Sex Development (DSD).</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Hyon, Capucine; Chantot-Bastaraud, Sandra; Harbuz, Radu; Bhouri, Rakia; Perrot, Nicolas; Peycelon, Matthieu; Sibony, Mathilde; Rojo, Sandra; Piguel, Xavier; Bilan, Frederic; Gilbert-Dussardier, Brigitte; Kitzis, Alain; McElreavey, Ken; Siffroi, Jean-Pierre; Bashamboo, Anu</p> <p>2015-08-01</p> <p>Disorders of Sex Development (DSD) are a heterogeneous group of disorders affecting gonad and/or genito-urinary tract development and usually the endocrine-reproductive system. A genetic diagnosis is made in only around 20% of these cases. The genetic causes of 46,XX-SRY negative testicular DSD as well as ovotesticular DSD are poorly defined. Duplications involving a region located ∼600 kb <span class="hlt">upstream</span> of SOX9, a key gene in testis development, were reported in several cases of 46,XX DSD. Recent studies have narrowed this region down to a 78 kb interval that is duplicated or deleted respectively in 46,XX or 46,XY DSD. We identified three phenotypically normal patients presenting with azoospermia and 46,XX testicular DSD. Two brothers carried a 83.8 kb duplication located ∼600 kb <span class="hlt">upstream</span> of SOX9 that overlapped with the previously reported rearrangements. This duplication refines the minimal region associated with 46,XX-SRY negative DSD to a 40.7-41.9 kb element located ∼600 kb <span class="hlt">upstream</span> of SOX9. Predicted enhancer elements and evolutionary-conserved binding sites for proteins known to be involved in testis determination are located within this region. © 2015 Wiley Periodicals, Inc.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li class="active"><span>22</span></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_22 --> <div id="page_23" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li class="active"><span>23</span></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="441"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2018JHyDy..30..131C','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2018JHyDy..30..131C"><span>Influence of <span class="hlt">upstream</span> disturbance on the draft-tube flow of Francis turbine under part-load conditions</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Chen, Ting; Zheng, Xianghao; Zhang, Yu-ning; Li, Shengcai</p> <p>2018-02-01</p> <p>Owing to the part-load operations for the enhancement of grid flexibility, the Francis turbine often suffers from severe low-frequency and large-amplitude hydraulic instability, which is mostly pertinent to the highly unsteady swirling vortex rope in the draft tube. The influence of disturbances in the <span class="hlt">upstream</span> (e.g., large-scale vortex structures in the spiral casing) on the draft-tube vortex flow is not well understood yet. In the present paper, the influence of the <span class="hlt">upstream</span> disturbances on the vortical flow in the draft tube is studied based on the vortex identification method and the analysis of several important parameters (e.g., the swirl number and the velocity profile). For a small guide vane opening (representing the part-load condition), the vortices triggered in the spiral casing propagate downstream and significantly affect the swirling vortex-rope precession in the draft tube, leading to the changes of the intensity and the processional frequency of the swirling vortex rope. When the guide vane opening approaches the optimum one (representing the full-load condition), the <span class="hlt">upstream</span> disturbance becomes weaker and thus its influences on the downstream flow are very limited.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/23935075','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/23935075"><span><span class="hlt">Upstream</span> mononucleotide A-repeats play a cis-regulatory role in mammals through the DICER1 and Ago proteins.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Aporntewan, Chatchawit; Pin-on, Piyapat; Chaiyaratana, Nachol; Pongpanich, Monnat; Boonyaratanakornkit, Viroj; Mutirangura, Apiwat</p> <p>2013-10-01</p> <p>A-repeats are the simplest form of tandem repeats and are found ubiquitously throughout genomes. These mononucleotide repeats have been widely believed to be non-functional 'junk' DNA. However, studies in yeasts suggest that A-repeats play crucial biological functions, and their role in humans remains largely unknown. Here, we showed a non-random pattern of distribution of sense A- and T-repeats within 20 kb around transcription start sites (TSSs) in the human genome. Different distributions of these repeats are observed <span class="hlt">upstream</span> and downstream of TSSs. Sense A-repeats are enriched <span class="hlt">upstream</span>, whereas sense T-repeats are enriched downstream of TSSs. This enrichment directly correlates with repeat size. Genes with different functions contain different lengths of repeats. In humans, tissue-specific genes are enriched for short repeats of <10 bp, whereas housekeeping genes are enriched for long repeats of ≥10 bp. We demonstrated that DICER1 and Argonaute proteins are required for the cis-regulatory role of A-repeats. Moreover, in the presence of a synthetic polymer that mimics an A-repeat, protein binding to A-repeats was blocked, resulting in a dramatic change in the expression of genes containing <span class="hlt">upstream</span> A-repeats. Our findings suggest a length-dependent cis-regulatory function of A-repeats and that Argonaute proteins serve as trans-acting factors, binding to A-repeats.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2017PPCF...59e4007T','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2017PPCF...59e4007T"><span>Enhancement of axial momentum lost to the radial wall by the <span class="hlt">upstream</span> magnetic field in a helicon source</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Takahashi, Kazunori; Ando, Akira</p> <p>2017-05-01</p> <p>Individual measurements of forces exerted to an <span class="hlt">upstream</span> back wall, a radial source wall, and a magnetic field of a helicon plasma thruster, which has two solenoids <span class="hlt">upstream</span> and downstream of a radiofrequency antenna, are precisely measured. Two different structures of magnetic field lines in the source are tested, where the solenoid current is supplied to either only the downstream solenoid or to both the solenoids. It is observed that the high density plasma exists <span class="hlt">upstream</span> of the rf antenna when both the solenoids are powered, while the maximum density exists near the rf antenna when only the downstream solenoid is powered. Although the force exerted to the back wall is increased for the two solenoids case, the axial momentum lost to the radial wall is simultaneously enhanced; then the total force exerted to the whole structure of the thruster is found to be very similar for the two magnetic field configurations. It is shown that the individual force measurement provides useful information on the plasma momentum interacting with the physical boundaries and the magnetic fields.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://pubs.er.usgs.gov/publication/70036648','USGSPUBS'); return false;" href="https://pubs.er.usgs.gov/publication/70036648"><span>Influence of seasonal, diel, lunar, and other environmental factors on <span class="hlt">upstream</span> fish passage in the igarapava fish ladder, Brazil</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Bizzotto, P.M.; Godinho, Alexandre L.; Vono, V.; Kynard, B.; Godinho, Hugo P.</p> <p>2009-01-01</p> <p><span class="hlt">Upstream</span> fish passage was evaluated during 12 months in the vertical-slot Igarapava Fish Ladder constructed around Igarapava Dam, in the heavily dammed Grande River, Southeast Brazil. A video monitoring system was used to observe 61,621 fish that passed the ladder, of which 93.5% were identified to 15 taxa. Among the migratory species, the most abundant were Pimelodus maculatus (33.6% of all fish), Leporinus octofasciatus (31.4%), Leporinus friderici (4.5%), and Prochilodus lineatus (3.1%). Seven taxa were classified as nonmigratory, and of these taxa, the small Bryconamericus stramineus was the most abundant (12.7%) of all fishes. Passage of the 'nonmigratory' taxa <span class="hlt">upstream</span> in the ladder shows they are migratory in this system and have a strong behavioural drive to move to <span class="hlt">upstream</span> habitat. Passage of most taxa had a strong seasonal pattern. While some species passed primarily during the day, others showed a distinct nocturnal pattern. Lunar phase and water temperature also strongly affected passage of some taxa. Rainfall and dam discharge had a small or null influence on most taxa; perhaps due to the fairly small catchment area of the reservoir and the highly regulated discharge at Igarapava Dam. ?? 2009 John Wiley & Sons A/S.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2010OptFT..16..129C','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2010OptFT..16..129C"><span>Improving <span class="hlt">upstream</span> transmission performance using a receiver with decision threshold level adjustment in a loopback WDM-PON</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Cho, Seung-Hyun; Lee, Sang-Soo; Shin, Dong-Wook</p> <p>2010-06-01</p> <p>We have experimentally demonstrated that the use of an optical receiver with decision threshold level adjustment (DTLA) improved the performance of an <span class="hlt">upstream</span> transmission in reflective semiconductor optical amplifier (RSOA)-based loopback wavelength division multiplexing-passive optical network (WDM-PON). Even though the extinction ratio (ER) of the downstream signal was as much as 9 dB and the injection power into the RSOA at the optical network unit was about -24 dBm, we successfully obtained error-free transmission results for the <span class="hlt">upstream</span> signal through careful control of the decision threshold value in the optical receiver located at optical line terminal (OLT). Using an optical receiver with DTLA for <span class="hlt">upstream</span> signal detection overcame significant obstacles related to the injection power into the RSOA and the ER of the downstream signal, which were previously considered limitations of the wavelength remodulation scheme. This technique is expected to provide flexibility for the optical link design in the practical deployment of a WDM-PON.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/23991871','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/23991871"><span><span class="hlt">Upstream</span> migratory behaviour of wild and ranched Atlantic salmon Salmo salar at a natural obstacle in a coastal spate river.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Kennedy, R J; Moffett, I; Allen, M M; Dawson, S M</p> <p>2013-09-01</p> <p>The <span class="hlt">upstream</span> migratory behaviour of wild and ranched Atlantic salmon Salmo salar in a small Irish coastal spate river was investigated using acoustic telemetry. Prespawning migratory behaviour was investigated including movement patterns at a large natural waterfall in the lower reaches of the river. A strong diurnal pattern was observed for <span class="hlt">upstream</span> migrants at the waterfall indicative of the need for daylight to ascend this complex natural obstacle to migration. Successful passage of the waterfall was also associated with distinct environmental conditions and no difference in migratory ability was detected between wild and ranched origin S. salar. Wild S. salar tended to exhibit a non-erratic, stepwise <span class="hlt">upstream</span> migration pattern after ascending the waterfall while ranched S. salar had an increased probability of displaying more erratic migratory behaviour. Wild S. salar penetrated further into the river catchment than ranched S. salar, although male ranched S. salar exhibited the greatest cumulative distance moved prior to the spawning period. The management implications of escaped or released ranched S. salar and movement at natural obstacles are discussed. © 2013 The Fisheries Society of the British Isles.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27668169','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27668169"><span>Standardization and quality management in next-generation <span class="hlt">sequencing</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Endrullat, Christoph; Glökler, Jörn; Franke, Philipp; Frohme, Marcus</p> <p>2016-09-01</p> <p>DNA <span class="hlt">sequencing</span> continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation <span class="hlt">sequencing</span> devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of <span class="hlt">sequencing</span> workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the <span class="hlt">sequencing</span> workflow steps with the main focus on <span class="hlt">upstream</span> processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation <span class="hlt">sequencing</span> in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of <span class="hlt">sequence</span> data.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013EGUGA..15.4816M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013EGUGA..15.4816M"><span>Fate of <span class="hlt">Upstream</span> Anthropogenic Nitrogen Inputs in a Tropical Catchment, Athi-Galana-Sabaki River, Kenya.</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Marwick, Trent R.</p> <p>2013-04-01</p> <p> blooms downstream highlight the significant role of primary producers assimilating DIN lower in the drainage network. The intense <span class="hlt">upstream</span> N-cycling leads to a significantly enriched δ15NPN during the dry season (mean: 16.5 ± 8.2‰) comparative to the short (7.3 ± 2.6‰) and long (7.6 ± 5.9‰) rain seasons. The strong correlation found between seasonal δ15NPN and δ18OH2O (δ18OH2O as a proxy of discharge; p = 0.0258, n = 26) presents the possibility of employing a combination of proxies such as δ15NPN of sediments, corals and bivalves, to build the foundation of how historical land-use changes have influenced nitrogen cycling within the catchment whilst potentially providing foresight for future land management decisions.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015EGUGA..17.4483P','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015EGUGA..17.4483P"><span>Sediment depositions <span class="hlt">upstream</span> of open check dams: new elements from small scale models</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Piton, Guillaume; Le Guern, Jules; Carbonari, Costanza; Recking, Alain</p> <p>2015-04-01</p> <p>Torrent hazard mitigation remains a big issue in mountainous regions. In steep slope streams and especially in their fan part, torrential floods mainly result from abrupt and massive sediment deposits. To curtail such phenomenon, soil conservation measures as well as torrent control works have been undertaken for decades. Since the 1950s, open check dams complete other structural and non-structural measures in watershed scale mitigation plans1. They are often built to trap sediments near the fan apexes. The development of earthmoving machinery after the WWII facilitated the dredging operations of open check dams. Hundreds of these structures have thus been built for 60 years. Their design evolved with the improving comprehension of torrential hydraulics and sediment transport; however this kind of structure has a general tendency to trap most of the sediments supplied by the headwaters. Secondary effects as channel incision downstream of the traps often followed an open check dam creation. This sediment starvation trend tends to propagate to the main valley rivers and to disrupt past geomorphic equilibriums. Taking it into account and to diminish useless dredging operation, a better selectivity of sediment trapping must be sought in open check dams, i.e. optimal open check dams would trap sediments during dangerous floods and flush them during normal small floods. An accurate description of the hydraulic and deposition processes that occur in sediment traps is needed to optimize existing structures and to design best-adjusted new structures. A literature review2 showed that if design criteria exist for the structure itself, little information is available on the dynamic of the sediment depositions <span class="hlt">upstream</span> of open check dams, i.e. what are the geomorphic patterns that occur during the deposition?, what are the relevant friction laws and sediment transport formula that better describe massive depositions in sediment traps?, what are the range of Froude and Shields</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013NatCo...4E1826A','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013NatCo...4E1826A"><span>Engineering fluid flow using <span class="hlt">sequenced</span> microstructures</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Amini, Hamed; Sollier, Elodie; Masaeli, Mahdokht; Xie, Yu; Ganapathysubramanian, Baskar; Stone, Howard A.; di Carlo, Dino</p> <p>2013-05-01</p> <p>Controlling the shape of fluid streams is important across scales: from industrial processing to control of biomolecular interactions. Previous approaches to control fluid streams have focused mainly on creating chaotic flows to enhance mixing. Here we develop an approach to apply order using <span class="hlt">sequences</span> of fluid transformations rather than enhancing chaos. We investigate the inertial flow deformations around a library of single cylindrical pillars within a microfluidic channel and assemble these net fluid transformations to engineer fluid streams. As these transformations provide a deterministic mapping of fluid elements from <span class="hlt">upstream</span> to downstream of a pillar, we can sequentially arrange pillars to apply the associated nested maps and, therefore, create complex fluid structures without additional numerical simulation. To show the range of capabilities, we present <span class="hlt">sequences</span> that sculpt the cross-sectional shape of a stream into complex geometries, move and split a fluid stream, perform solution exchange and achieve particle separation. A general strategy to engineer fluid streams into a broad class of defined configurations in which the complexity of the nonlinear equations of fluid motion are abstracted from the user is a first step to programming streams of any desired shape, which would be useful for biological, chemical and materials automation.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2006PhDT.......154L','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2006PhDT.......154L"><span>Computational methods in <span class="hlt">sequence</span> and structure prediction</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Lang, Caiyi</p> <p></p> <p>This dissertation is organized into two parts. In the first part, we will discuss three computational methods for cis-regulatory element recognition in three different gene regulatory networks as the following: (a) Using a comprehensive "Phylogenetic Footprinting Comparison" method, we will investigate the promoter <span class="hlt">sequence</span> structures of three enzymes (PAL, CHS and DFR) that catalyze sequential steps in the pathway from phenylalanine to anthocyanins in plants. Our result shows there exists a putative cis-regulatory element "AC(C/G)TAC(C)" in the <span class="hlt">upstream</span> of these enzyme genes. We propose this cis-regulatory element to be responsible for the genetic regulation of these three enzymes and this element, might also be the binding site for MYB class transcription factor PAP1. (b) We will investigate the role of the Arabidopsis gene glutamate receptor 1.1 (AtGLR1.1) in C and N metabolism by utilizing the microarray data we obtained from AtGLR1.1 deficient lines (antiAtGLR1.1). We focus our investigation on the putatively co-regulated transcript profile of 876 genes we have collected in antiAtGLR1.1 lines. By (a) scanning the occurrence of several groups of known abscisic acid (ABA) related cisregulatory elements in the <span class="hlt">upstream</span> regions of 876 Arabidopsis genes; and (b) exhaustive scanning of all possible 6-10 bps motif occurrence in the <span class="hlt">upstream</span> regions of the same set of genes, we are able to make a quantative estimation on the enrichment level of each of the cis-regulatory element candidates. We finally conclude that one specific cis-regulatory element group, called "ABRE" elements, are statistically highly enriched within the 876-gene group as compared to their occurrence within the genome. (c) We will introduce a new general purpose algorithm, called "fuzzy REDUCE1", which we have developed recently for automated cis-regulatory element identification. In the second part, we will discuss our newly devised protein design framework. With this framework we have developed</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://pubs.usgs.gov/sir/2007/5288/','USGSPUBS'); return false;" href="https://pubs.usgs.gov/sir/2007/5288/"><span>Salinity Trends in the Upper Colorado River Basin <span class="hlt">Upstream</span> From the Grand Valley Salinity Control Unit, Colorado, 1986-2003</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Leib, Kenneth J.; Bauch, Nancy J.</p> <p>2008-01-01</p> <p>In 1974, the Colorado River Basin Salinity Control Act was passed into law. This law was enacted to address concerns regarding the salinity content of the Colorado River. The law authorized various construction projects in selected areas or 'units' of the Colorado River Basin intended to reduce the salinity load in the Colorado River. One such area was the Grand Valley Salinity Control Unit in western Colorado. The U. S. Geological Survey has done extensive studies and research in the Grand Valley Salinity Control Unit that provide information to aid the U.S. Bureau of Reclamation and the Natural Resources Conservation Service in determining where salinity-control work may provide the best results, and to what extent salinity-control work was effective in reducing salinity concentrations and loads in the Colorado River. Previous studies have indicated that salinity concentrations and loads have been decreasing downstream from the Grand Valley Salinity Control Unit, and that the decreases are likely the result of salinity control work in these areas. Several of these reports; however, also document decreasing salinity loads <span class="hlt">upstream</span> from the Grand Valley Salinity Control Unit. This finding was important because only a small amount of salinity-control work was being done in areas <span class="hlt">upstream</span> from the Grand Valley Salinity Control Unit at the time the findings were reported (late 1990?s). As a result of those previous findings, the U.S. Bureau of Reclamation entered into a cooperative agreement with the U.S. Geological Survey to investigate salinity trends in selected areas bracketing the Grand Valley Salinity Control Unit and regions <span class="hlt">upstream</span> from the Grand Valley Salinity Control Unit. The results of the study indicate that salinity loads were decreasing <span class="hlt">upstream</span> from the Grand Valley Salinity Control Unit from 1986 through 2003, but the rates of decrease have slowed during the last 10 years. The average rate of decrease in salinity load <span class="hlt">upstream</span> from the Grand Valley</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=373418','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=373418"><span>Unlocking hidden genomic <span class="hlt">sequence</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Keith, Jonathan M.; Cochran, Duncan A. E.; Lala, Gita H.; Adams, Peter; Bryant, Darryn; Mitchelson, Keith R.</p> <p>2004-01-01</p> <p>Despite the success of conventional Sanger <span class="hlt">sequencing</span>, significant regions of many genomes still present major obstacles to <span class="hlt">sequencing</span>. Here we propose a novel approach with the potential to alleviate a wide range of <span class="hlt">sequencing</span> difficulties. The technique involves extracting target DNA <span class="hlt">sequence</span> from variants generated by introduction of random mutations. The introduction of mutations does not destroy original <span class="hlt">sequence</span> information, but distributes it amongst multiple variants. Some of these variants lack problematic features of the target and are more amenable to conventional <span class="hlt">sequencing</span>. 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</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://ntrs.nasa.gov/search.jsp?R=19910036858&hterms=lean&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D80%26Ntt%3Dlean','NASA-TRS'); return false;" href="https://ntrs.nasa.gov/search.jsp?R=19910036858&hterms=lean&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D80%26Ntt%3Dlean"><span>Simulation of mixing in the quick quench region of <span class="hlt">a</span> <span class="hlt">rich</span> burn-quick quench mix-lean burn combustor</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Shih, Tom I.-P.; Nguyen, H. Lee; Howe, Gregory W.; Li, Z.</p> <p>1991-01-01</p> <p>A computer program was developed to study the mixing process in the quick quench region of <span class="hlt">a</span> <span class="hlt">rich</span> burn-quick quench mix-lean burn combustor. The computer program developed was based on the density-weighted, ensemble-averaged conservation equations of mass, momentum (full compressible Navier-Stokes), total energy, and species, closed by a k-epsilon turbulence model with wall functions. The combustion process was modeled by a two-step global reaction mechanism, and NO(x) formation was modeled by the Zeldovich mechanism. The formulation employed in the computer program and the essence of the numerical method of solution are described. Some results obtained for nonreacting and reacting flows with different main-flow to dilution-jet momentum flux ratios are also presented.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5620586','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5620586"><span>Sphenostylis stenocarpa (ex. <span class="hlt">A</span>. <span class="hlt">Rich</span>.) Harms., a Fading Genetic Resource in a Changing Climate: Prerequisite for Conservation and Sustainability</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Nnamani, Catherine Veronica; Ajayi, Sunday Adesola; Oselebe, Happiness Ogba; Atkinson, Christopher John; Igboabuchi, Anastasia Ngozi</p> <p>2017-01-01</p> <p>The southeastern part of Nigeria is one of the major hotspots of useful plant genetic resources. These endemic species are associated with <span class="hlt">a</span> <span class="hlt">rich</span> indigenous knowledge and cultural diversity in relation to their use and conservation. Sphenostylis stenocarpa (ex. <span class="hlt">A</span>. <span class="hlt">Rich</span>.) Harms., (African Yam Bean (AYB)), is one such crop within the family of Fabaceae. Its nutritional and eco-friendly characteristics have value in ameliorating malnutrition, hidden hunger and environmental degradation inherent in resource-poor rural and semi-rural communities throughout Africa. However, lack of information from the custodians of this crop is limiting its sustainable development. Therefore, ethnobotanical surveys on the diversity, uses, and constraints limiting the cultivation and use of the crop in southeastern Nigeria were carried out. Five-hundred respondents were randomly selected and data collected through oral interviews and focused group discussion (FGD). Semi-structured questionnaires (SSQ) were also used to elicit information from a spectrum of AYB users comprising community leaders, farmers, market women and consumers in five States. Results showed that the majority of the respondents lacked formal education and were of the age group of 40–50 years, while the female gender dominated with limited access to land and extension officers. Seed coat colour largely determined utilization. Long cooking time, requirement for staking materials, aging of farmers and low market demand were among the major constraints limiting further cultivation and utilization of AYB. In-situ conservation was by hanging dried fruits by the fireside, beside the house, storing in earthenware, calabash gourds, cans and bottles. It is concluded that there is urgent need to scale up conservation through robust linkages between contemporary scientific domains and indigenous peoples in order to harness and incorporate the rich indigenous knowledge in local communities for enhanced scientific knowledge</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28704944','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28704944"><span>Sphenostylis stenocarpa (ex. <span class="hlt">A</span>. <span class="hlt">Rich</span>.) Harms., a Fading Genetic Resource in a Changing Climate: Prerequisite for Conservation and Sustainability.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Nnamani, Catherine Veronica; Ajayi, Sunday Adesola; Oselebe, Happiness Ogba; Atkinson, Christopher John; Igboabuchi, Anastasia Ngozi; Ezigbo, Eucharia Chizoba</p> <p>2017-07-12</p> <p>The southeastern part of Nigeria is one of the major hotspots of useful plant genetic resources. These endemic species are associated with <span class="hlt">a</span> <span class="hlt">rich</span> indigenous knowledge and cultural diversity in relation to their use and conservation. Sphenostylis stenocarpa ( e x. <span class="hlt">A</span>. <span class="hlt">Rich</span>.) Harms., (African Yam Bean (AYB)), is one such crop within the family of Fabaceae. Its nutritional and eco-friendly characteristics have value in ameliorating malnutrition, hidden hunger and environmental degradation inherent in resource-poor rural and semi-rural communities throughout Africa. However, lack of information from the custodians of this crop is limiting its sustainable development. Therefore, ethnobotanical surveys on the diversity, uses, and constraints limiting the cultivation and use of the crop in southeastern Nigeria were carried out. Five-hundred respondents were randomly selected and data collected through oral interviews and focused group discussion (FGD). Semi-structured questionnaires (SSQ) were also used to elicit information from a spectrum of AYB users comprising community leaders, farmers, market women and consumers in five States. Results showed that the majority of the respondents lacked formal education and were of the age group of 40-50 years, while the female gender dominated with limited access to land and extension officers. Seed coat colour largely determined utilization. Long cooking time, requirement for staking materials, aging of farmers and low market demand were among the major constraints limiting further cultivation and utilization of AYB. In-situ conservation was by hanging dried fruits by the fireside, beside the house, storing in earthenware, calabash gourds, cans and bottles. It is concluded that there is urgent need to scale up conservation through robust linkages between contemporary scientific domains and indigenous peoples in order to harness and incorporate the rich indigenous knowledge in local communities for enhanced scientific knowledge</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/24833435','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/24833435"><span>Insertion <span class="hlt">sequence</span> transposition determines imipenem resistance in Acinetobacter baumannii.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Kuo, Han-Yueh; Chang, Kai-Chih; Liu, Chih-Chin; Tang, Chuan Yi; Peng, Jhih-Hua; Lu, Chia-Wei; Tu, Chi-Chao; Liou, Ming-Li</p> <p>2014-10-01</p> <p>This study employed genomewide analysis to investigate potential resistance mechanisms in Acinetobacter baumannii following imipenem exposure. Imipenem-selected mutants were generated from the imipenem-susceptible strain ATCC 17978 by multistep selection resistance. Antibiotic susceptibilities were examined, and the selected mutants originated from the ATCC 17978 strain were confirmed by pulsed-field gel electrophoresis. The genomic <span class="hlt">sequence</span> of a resistant mutant was analyzed using a next-generation <span class="hlt">sequencing</span> platform, and genetic recombination was further confirmed by PCR. The result showed that phenotypic resistance was observed with carbapenem upon exposure to various concentrations of imipenem. Genomewide analysis showed that ISAba1 transposition was initiated by imipenem exposure at concentrations up to 0.5 mg/L. Transposition of ISAba1 <span class="hlt">upstream</span> of blaOXA-95 was detected in all the selected mutants. The expression of blaOXA-95 was further analyzed by quantitative PCR, and the results demonstrated that a 200-fold increase in gene expression was required for resistance to imipenem. This study concluded that imipenem exposure at a concentration of 0.5 mg/L mediated the transposition of ISAba1 <span class="hlt">upstream</span> of the blaOXA-95 gene and resulted in the overexpression of blaOXA-95 gene, which may play a major role in the resistance to imipenem in A. baumannii.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2004APS..MAR.S8008S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2004APS..MAR.S8008S"><span>A Gibbs sampler for motif detection in phylogenetically close <span class="hlt">sequences</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Siddharthan, Rahul; van Nimwegen, Erik; Siggia, Eric</p> <p>2004-03-01</p> <p>Genes are regulated by transcription factors that bind to DNA <span class="hlt">upstream</span> of genes and recognize short conserved ``motifs'' in a random intergenic ``background''. Motif-finders such as the Gibbs sampler compare the probability of these short <span class="hlt">sequences</span> being represented by ``weight matrices'' to the probability of their arising from the background ``null model'', and explore this space (analogous to a free-energy landscape). But closely related species may show conservation not because of functional sites but simply because they have not had sufficient time to diverge, so conventional methods will fail. We introduce a new Gibbs sampler algorithm that accounts for common ancestry when searching for motifs, while requiring minimal ``prior'' assumptions on the number and types of motifs, assessing the significance of detected motifs by ``tracking'' clusters that stay together. We apply this scheme to motif detection in sporulation-cycle genes in the yeast S. cerevisiae, using recent <span class="hlt">sequences</span> of other closely-related Saccharomyces species.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/17521565','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/17521565"><span><span class="hlt">A</span> <span class="hlt">richness</span> that cures.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Pizzorusso, Tommaso; Berardi, Nicoletta; Maffei, Lamberto</p> <p>2007-05-24</p> <p>A study in Nature by Fischer et al. shows that environmental enrichment or increasing histone acetylation rescue the ability to form new memories and re-establish access to remote memories even in the presence of brain degeneration. Chromatin remodeling may be the final gate environmental enrichment opens to enhance plasticity and represents a promising target for therapeutical intervention in neurodegenerative diseases.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://eric.ed.gov/?q=wiley&pg=3&id=EJ780763','ERIC'); return false;" href="https://eric.ed.gov/?q=wiley&pg=3&id=EJ780763"><span><span class="hlt">A</span> <span class="hlt">Rich</span> History</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Hawkins, B. Denise</p> <p>2007-01-01</p> <p>This article features six Texas Historically Black Colleges and Universities (HBCU) which continue the mission of educating African-American students, while at the same time responding to the state's changing demographics. These are: (1) Huston-Tillotson University, Austin; (2) Paul Quinn College, Dallas; (3) Prairie View A&M University,…</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li class="active"><span>23</span></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_23 --> <div id="page_24" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li class="active"><span>24</span></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="461"> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/9252588','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/9252588"><span>Molecular cloning of actin genes in Trichomonas vaginalis and phylogeny inferred from actin <span class="hlt">sequences</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Bricheux, G; Brugerolle, G</p> <p>1997-08-01</p> <p>The parasitic protozoan Trichomonas vaginalis is known to contain the ubiquitous and highly conserved protein actin. A genomic library and a cDNA library have been screened to identify and clone the actin gene(s) of T. vaginalis. The nucleotide <span class="hlt">sequence</span> of one gene and its flanking regions have been determined. The open reading frame encodes a protein of 376 amino acids. The <span class="hlt">sequence</span> is not interrupted by any introns and the promoter could be represented by a 10 bp motif close to a consensus motif also found <span class="hlt">upstream</span> of most <span class="hlt">sequenced</span> T. vaginalis genes. The five different clones isolated from the cDNA library have similar <span class="hlt">sequences</span> and encode three actin proteins differing only by one or two amino acids. A phylogenetic analysis of 31 actin <span class="hlt">sequences</span> by distance matrix and parsimony methods, using centractin as outgroup, gives congruent trees with Parabasala branching above Diplomonadida.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=167512','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=167512"><span>Cloning and <span class="hlt">sequencing</span> of a laccase gene from the lignin-degrading basidiomycete Pleurotus ostreatus.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Giardina, P; Cannio, R; Martirani, L; Marzullo, L; Palmieri, G; Sannia, G</p> <p>1995-01-01</p> <p>The gene (pox1) encoding a phenol oxidase from Pleurotus ostreatus, a lignin-degrading basidiomycete, was cloned and <span class="hlt">sequenced</span>, and the corresponding pox1 cDNA was also synthesized and <span class="hlt">sequenced</span>. The isolated gene consists of 2,592 bp, with the coding <span class="hlt">sequence</span> being interrupted by 19 introns and flanked by an <span class="hlt">upstream</span> region in which putative CAAT and TATA consensus <span class="hlt">sequences</span> could be identified at positions -174 and -84, respectively. The isolation of a second cDNA (pox2 cDNA), showing 84% similarity, and of the corresponding truncated genomic clones demonstrated the existence of a multigene family coding for isoforms of laccase in P. ostreatus. PCR amplifications of specific regions on the DNA of isolated monokaryons proved that the two genes are not allelic forms. The POX1 amino acid <span class="hlt">sequence</span> deduced was compared with those of other known laccases from different fungi. PMID:7793961</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/873160','DOE-PATENT-XML'); return false;" href="https://www.osti.gov/servlets/purl/873160"><span>Lichenase and coding <span class="hlt">sequences</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/doepatents">DOEpatents</a></p> <p>Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong</p> <p>2000-08-15</p> <p>The present invention provides a fungal lichenase, i.e., an endo-1,3-1,4-.beta.-D-glucanohydrolase, its coding <span class="hlt">sequence</span>, recombinant DNA molecules comprising the lichenase coding <span class="hlt">sequences</span>, recombinant host cells and methods for producing same. The present lichenase is from Orpinomyces PC-2.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://eric.ed.gov/?q=plant+AND+parasites&id=ED267189','ERIC'); return false;" href="https://eric.ed.gov/?q=plant+AND+parasites&id=ED267189"><span>Agriculture: Scope and <span class="hlt">Sequence</span>.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Nashville - Davidson County Metropolitan Public Schools, TN.</p> <p></p> <p>This guide, which was written as an initial step in the development of a systemwide articulated curriculum <span class="hlt">sequence</span> for all vocational programs within the Metropolitan Nashville Public School System, outlines the suggested scope and <span class="hlt">sequence</span> of a 3-year program in agriculture. The guide consists of a course description; general course objectives;…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://eric.ed.gov/?q=Hair+AND+chemicals&pg=2&id=ED267213','ERIC'); return false;" href="https://eric.ed.gov/?q=Hair+AND+chemicals&pg=2&id=ED267213"><span>Cosmetology: Scope and <span class="hlt">Sequence</span>.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Nashville - Davidson County Metropolitan Public Schools, TN.</p> <p></p> <p>This scope and <span class="hlt">sequence</span> guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum <span class="hlt">sequence</span> for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://eric.ed.gov/?q=exact+AND+solutions&pg=6&id=EJ455071','ERIC'); return false;" href="https://eric.ed.gov/?q=exact+AND+solutions&pg=6&id=EJ455071"><span><span class="hlt">Sequences</span>, Series, and Mathematica.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Mathews, John H.</p> <p>1992-01-01</p> <p>Describes how the computer algebra system Mathematica can be used to enhance the teaching of the topics of <span class="hlt">sequences</span> and series. Examines its capabilities to find exact, approximate, and graphically generated approximate solutions to problems from these topics and to understand proofs about <span class="hlt">sequences</span>. (MDH)</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://eric.ed.gov/?q=Automata&pg=2&id=EJ939738','ERIC'); return false;" href="https://eric.ed.gov/?q=Automata&pg=2&id=EJ939738"><span><span class="hlt">Sequences</span> for Student Investigation</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Barton, Jeffrey; Feil, David; Lartigue, David; Mullins, Bernadette</p> <p>2004-01-01</p> <p>We describe two classes of <span class="hlt">sequences</span> that give rise to accessible problems for undergraduate research. These problems may be understood with virtually no prerequisites and are well suited for computer-aided investigation. The first <span class="hlt">sequence</span> is a variation of one introduced by Stephen Wolfram in connection with his study of cellular automata. The…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://pubs.er.usgs.gov/publication/70185039','USGSPUBS'); return false;" href="https://pubs.er.usgs.gov/publication/70185039"><span><span class="hlt">Upstream</span> movements of Atlantic Salmon in the Lower Penobscot River, Maine following two dam removals and fish passage modifications</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Izzo, Lisa K.; Maynard, George A.; Zydlewski, Joseph D.</p> <p>2016-01-01</p> <p>The Penobscot River Restoration Project (PRRP), to be completed in 2016, involved an extensive plan of dam removal, increases in hydroelectric capacity, and fish passage modifications to increase habitat access for diadromous species. As part of the PRRP, Great Works and Veazie dams were removed, making Milford Dam the first impediment to federally endangered Atlantic Salmon Salmo salar. <span class="hlt">Upstream</span> habitat access for Atlantic Salmon is dependent upon successful and timely passage at Milford Dam because nearly all suitable spawning habitat is located <span class="hlt">upstream</span>. In 2014 and 2015, a total of 73 adult salmon were radio-tagged to track their <span class="hlt">upstream</span> movements through the Penobscot River to assess potential delays at (1) the dam remnants, (2) the confluence of the Stillwater Branch and the main stem of the Penobscot River below the impassable Orono Dam, and (3) the Milford Dam fish lift (installed in 2014). Movement rates through the dam remnants and the Stillwater confluence were comparable to open river reaches. Passage efficiency of the fish lift was high in both years (95% and 100%). However, fish experienced long delays at Milford Dam, with approximately one-third of fish taking more than a week to pass in each year, well below the Federal Energy Regulatory Commission passage standard of 95% within 48 h. Telemetry indicates most fish locate the fishway entrance within 5 h of arrival and were observed at the entrance at all hours of the day. These data indicate that overall transit times through the lower river were comparable to reported movement rates prior to changes to the Penobscot River due to the substantial delays seen at Milford Dam. The results of this study show that while adult Atlantic Salmon locate the new fish lift entrance quickly, passage of these fish was significantly delayed under 2014–2015 operations.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/29476268','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/29476268"><span>Landscape-based <span class="hlt">upstream</span>-downstream prevalence of land-use/cover change drivers in southeastern rift escarpment of Ethiopia.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Temesgen, Habtamu; Wu, Wei; Legesse, Abiyot; Yirsaw, Eshetu; Bekele, Belew</p> <p>2018-02-23</p> <p>Characterized by high population density on a rugged topography, the Gedeo-Abaya landscape dominantly contains a multi-strata traditional agroforests showing the insight of Gedeo farmers on natural resource management practices. Currently, this area has been losing its resilience and is becoming unable to sustain its inhabitants. Based on both RS-derived and GIS-computed land-use/cover changes (LUCC) as well as socioeconomic validations, this article explored the LUCC and agroecological-based driver patterns in Gedeo-Abaya landscape from 1986 to 2015. A combination of geo-spatial technology and cross-sectional survey design were employed to detect the drivers behind these changes. The article discussed that LUCC and the prevalence of drivers are highly diverse and vary throughout agroecological zones. Except for the population, most downstream top drivers are perceived as insignificant in the <span class="hlt">upstream</span> region and vice versa. In the downstream, land-use/cover (LUC) classes are more dynamic, diverse, and challenged by nearly all anticipated drivers than are <span class="hlt">upstream</span> ones. Agroforestry LUC has been increasing (by 25% of its initial cover) and is becoming the predominant cover type, although socioeconomic analysis and related findings show its rapid LUC modification. A rapid reduction of woodland/shrubland (63%) occurred in the downstream, while wetland/marshy land increased threefold (158%), from 1986 to 2015 with annual change rates of - 3.7 and + 6%, respectively. Land degradation induced by changes in land use is a serious problem in Africa, especially in the densely populated sub-Saharan regions such as Ethiopia (FAO 2015). Throughout the landscape, LUCC is prominently affecting land-use system of the study landscape due to population pressure in the <span class="hlt">upstream</span> region and drought/rainfall variability, agribusiness investment, and charcoaling in the downstream that necessitate urgent action.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://pubs.er.usgs.gov/publication/70191491','USGSPUBS'); return false;" href="https://pubs.er.usgs.gov/publication/70191491"><span>Evaluating <span class="hlt">upstream</span> passage and timing of approach by adult bigheaded carps at a gated dam on the Illinois River</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Lubejko, Matthew; Whitledge, Greg; Coulter, Alison A.; Brey, Marybeth; Oliver, Devon; Garvey, James E.</p> <p>2017-01-01</p> <p>Dams are a conservation threat because they function as barriers to native fish movement; however, they may prevent the spread of invasive species. Invasive bigheaded carps (Hypophthalmichthys spp.) threaten the Great Lakes ecosystem and are advancing towards Lake Michigan via the Illinois River. Navigation dams on the Illinois River may deter bigheaded carps' <span class="hlt">upstream</span> movement. We investigated the permeability of the Starved Rock Lock and Dam (SRLD), the most downstream gated Illinois River dam, to bigheaded carps' migration by examining the timing of individuals approaching and passing through SRLD in relation to gate openness, tailwater elevation, and water temperature. Using acoustic telemetry of (N = ~104 per year) tagged fish, 13 <span class="hlt">upstream</span> passages of bigheaded carps occurred through SRLD between 2013 and 2016. Eleven passages occurred through the dam gates and 2 through the lock chamber, indicating deterrents (e.g., CO2) placed in SRLD lock chamber may only limit passage of a small proportion of all fish passing through the lock-and-dam structure. Passages were documented only in 2013 and 2015. Most of the dam gate passages occurred during high water when gates were completely out of the water. Timing of bigheaded carps approaching SRLD was positively correlated with rising water temperature and high tailwater elevation, and all fish approached during late March through mid-September. Movement through dams is rare; modifying gate operations to reduce gate openness during late spring and summer could further reduce the permeability of gated dams such as SRLD to bigheaded carps, slowing their <span class="hlt">upstream</span> advance.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/20000571-formation-burnout-region-partially-premixed-methane-air-flame-upstream-heat-loss','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/20000571-formation-burnout-region-partially-premixed-methane-air-flame-upstream-heat-loss"><span>NO formation in the burnout region of a partially premixed methane-air flame with <span class="hlt">upstream</span> heat loss</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Mokhov, A.V.; Levinsky, H.B.</p> <p></p> <p>Measurements of temperature and NO concentration in laminar, partially premixed methane-air flames stabilized on a ceramic burner in coflow are reported. The NO concentration and temperature were determined by laser-induced fluorescence (LIF) and coherent anti-Stokes Raman scattering (CARS), respectively. <span class="hlt">Upstream</span> heat loss to the burner was varied by changing the exit velocity of the fuel-air mixture at a constant equivalence ratio of 1,3; this alters the structure of the flame from an axisymmetric Bunsen-type to a strongly stabilized flat flame. To facilitate analysis of the results, a method is derived for separating the effects of dilution from those of chemicalmore » reaction based on the relation between the measured temperature and the local mixture fraction, including the effects of <span class="hlt">upstream</span> heat loss. Using this method, the amount of NO formed during burnout of the hot, fuel-rich combustion products can be ascertained. In the Bunsen-type flame, it is seen that {approximately}40 ppm of NO are produced in this burnout region, at temperatures between {approximately}2,100 K and {approximately}1,900 K, probably via the Zeldovich mechanism. Reducing the exit velocity of 12 cm/s reduces the flame temperature substantially, and effectively eliminates this contribution. At velocities of 12 and 8 cm/s, {approximately}10 ppm of NO are formed in the burnout region, even though the gas temperatures are too low for Zeldovich NO to be significant. Although the mechanism responsible for these observations is as yet unclear, the results are consistent with the idea that the low temperatures in the fuel-rich gases caused by <span class="hlt">upstream</span> heat loss retard the conversion of HCN (formed via the Fenimore mechanism) to NO, with this residual HCN then being converted to NO during burnout.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20080047211','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20080047211"><span><span class="hlt">Sequence</span> History Update Tool</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Khanampompan, Teerapat; Gladden, Roy; Fisher, Forest; DelGuercio, Chris</p> <p>2008-01-01</p> <p>The <span class="hlt">Sequence</span> History Update Tool performs Web-based <span class="hlt">sequence</span> statistics archiving for Mars Reconnaissance Orbiter (MRO). Using a single UNIX command, the software takes advantage of <span class="hlt">sequencing</span> conventions to automatically extract the needed statistics from multiple files. This information is then used to populate a PHP database, which is then seamlessly formatted into a dynamic Web page. This tool replaces a previous tedious and error-prone process of manually editing HTML code to construct a Web-based table. Because the tool manages all of the statistics gathering and file delivery to and from multiple data sources spread across multiple servers, there is also a considerable time and effort savings. With the use of The <span class="hlt">Sequence</span> History Update Tool what previously took minutes is now done in less than 30 seconds, and now provides a more accurate archival record of the <span class="hlt">sequence</span> commanding for MRO.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/22212449','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/22212449"><span>LhnR and <span class="hlt">upstream</span> operon LhnABC in Agrobacterium vitis regulate the induction of tobacco hypersensitive responses, grape necrosis and swarming motility.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Zheng, Desen; Hao, Guixia; Cursino, Luciana; Zhang, Hongsheng; Burr, Thomas J</p> <p>2012-09-01</p> <p>The characterization of Tn5 transposon insertional mutants of Agrobacterium vitis strain F2/5 revealed a gene encoding a predicted LysR-type transcriptional regulator, lhnR (for 'LysR-type regulator associated with HR and necrosis'), and an immediate <span class="hlt">upstream</span> operon consisting of three open reading frames (lhnABC) required for swarming motility, surfactant production and the induction of a hypersensitive response (HR) on tobacco and necrosis on grape. The operon lhnABC is unique to A. vitis among the <span class="hlt">sequenced</span> members in Rhizobiaceae. Mutagenesis of lhnR and lhnABC by gene disruption and complementation of ΔlhnR and ΔlhnABC confirmed their roles in the expression of these phenotypes. Mutation of lhnR resulted in complete loss of HR, swarming motility, surfactant production and reduced necrosis, whereas mutation of lhnABC resulted in loss of swarming motility, delayed and reduced HR development and reduced surfactant production and necrosis. The data from promoter-green fluorescent protein (gfp) fusions showed that lhnR suppresses the expression of lhnABC and negatively autoregulates its own expression. It was also shown that lhnABC negatively affects its own expression and positively affects the transcription of lhnR. lhnR and lhnABC constitute a regulatory circuit that coordinates the transcription level of lhnR, resulting in the expression of swarming, surfactant, HR and necrosis phenotypes. © 2012 THE AUTHORS. MOLECULAR PLANT PATHOLOGY © 2012 BSPP AND BLACKWELL PUBLISHING LTD.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19750005993','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19750005993"><span>Analysis of the dynamic response of a supersonic inlet to flow-field perturbations <span class="hlt">upstream</span> of the normal shock</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Cole, G. L.; Willoh, R. G.</p> <p>1975-01-01</p> <p>A linearized mathematical analysis is presented for determining the response of normal shock position and subsonic duct pressures to flow-field perturbations <span class="hlt">upstream</span> of the normal shock in mixed-compression supersonic inlets. The inlet duct cross-sectional area variation is approximated by constant-area sections; this approximation results in one-dimensional wave equations. A movable normal shock separates the supersonic and subsonic flow regions, and a choked exit is assumed for the inlet exit condition. The analysis leads to a closed-form matrix solution for the shock position and pressure transfer functions. Analytical frequency response results are compared with experimental data and a method of characteristics solution.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013OptCo.308..248Z','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013OptCo.308..248Z"><span>Suppression of pattern dependence in 10 Gbps <span class="hlt">upstream</span> transmission of WDM-PON with RSOA-based ONUs</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Zhang, Min; Wang, Danshi; Cao, Zhihui; Chen, Xue; Huang, Shanguo</p> <p>2013-11-01</p> <p>The finite gain recovery time of the reflective semiconductor optical amplifier (RSOA) causes distortion and pattern dependence at high bit rates in colorless optical network units (ONUs) of WDM passive optical network (WDN-PON). We propose and demonstrate a scheme of <span class="hlt">upstream</span> transmission of 10 Gbps NRZ signals directly modulated via a RSOA in a 25 km single fiber, where we use a fiber Bragg grating (FBG) as an offset filter to suppress the pattern dependence and improve the RSOA modulation bandwidth. Both experimental and simulation results are provided, which are useful results for designing cost-effective colorless transceivers.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/894650','SCIGOV-STC'); return false;" href="https://www.osti.gov/servlets/purl/894650"><span>White Sturgeon Mitgation and Restoration in the Columbia and Snake Rivers <span class="hlt">Upstream</span> from Bonneville Dam; 2003-2004 Annual Report.</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Rein, Thomas A.; Hughes, Michele L.; Kern, J. Chris</p> <p>2005-08-01</p> <p>We report on our progress from April 2003 through March 2004 on determining the effects of mitigative measures on productivity of white sturgeon populations in the Columbia River downstream from McNary Dam, and on determining the status and habitat requirements of white sturgeon populations in the Columbia and Snake rivers <span class="hlt">upstream</span> from McNary Dam. This is a multi-year study with many objectives requiring more than one year to complete; therefore, findings from a given year may be part of more significant findings yet to be reported.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26040366','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26040366"><span>Impact of the consumption of <span class="hlt">a</span> <span class="hlt">rich</span> diet in butter and it replacement for <span class="hlt">a</span> <span class="hlt">rich</span> diet in extra virgin olive oil on anthropometric, metabolic and lipid profile in postmenopausal women.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Anderson-Vasquez, Hazel Ester; Pérez-Martínez, Pablo; Ortega Fernández, Pablo; Wanden-Berghe, Carmina</p> <p>2015-06-01</p> <p>To analyze the impact of the substitution of <span class="hlt">a</span> <span class="hlt">rich</span> diet in saturated fats with <span class="hlt">a</span> <span class="hlt">rich</span> diet in monounsaturated fats on anthropometric, metabolic and lipid profile in postmenopausal women. A prospective, longitudinal and comparative study where 18 postmenopausal women participated in two periods of dietary intervention of 28 days each one: 1) (SAT diet) consumed butter. Caloric formula (CF) = 15% protein, 38% fat. [20% saturated fat (SFA), 12% monounsaturated fat (MUFA) and 47% carbohydrates and 6% polyunsaturated (PUFA)]. b) Period MONO: with extra virgin olive oil (EVOO). CF = 15% protein, 38% fat (<10% SFA, 22% PUFA and 6% MUFA) and 47% carbohydrates. Size and body composition, glucose, insulin, HOMA, TC, HDL-C, LDL-C, VLDL-C, TG, TC/HDL-C, LDL-C/HDL-C, TG/HDL-C and non-HDL-C/HDL.C were measured; dietary Anamnesis/24 hours, daily food record. ANOVA and Bonferroni statistical analysis (SPSS 20) was applied. The age was 56 ± 5 years, BMI 29.8 ± 3.1 kg/m2, waist circumference: 93.2 ± 10.1 cm, waist/hip ratio: 0.86 ± 0.14, waist/height: 0.59 ± 0.06 and 38.6 ± 4% body fat (NS). Lipid profile: SAT diet increased TC (p <0.001), LDL-C (p <0.002) and non HDL-Cholesterol (p <0.000), HDL-C increased in MONO diet (p <0.000). SAT diet: TC/HDL-c ratio, Non col HDL-c/HDL-c, LDL-c/HDL-c (p <0.000) and TG/HDL-c (p <0.000). In MONO diet decreased TC/HDL-c (p <0.015) and TG/HDL-c (p <0.016). The SAT diet increased cardiovascular risk, while the MONO diet decreased the risk to develop the metabolic syndrome components and choronary heart disease. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27768873','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27768873"><span>Positive Feedback Keeps Duration of Mitosis Temporally Insulated from <span class="hlt">Upstream</span> Cell-Cycle Events.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Araujo, Ana Rita; Gelens, Lendert; Sheriff, Rahuman S M; Santos, Silvia D M</p> <p>2016-10-20</p> <p>Cell division is characterized by a <span class="hlt">sequence</span> of events by which a cell gives rise to two daughter cells. Quantitative measurements of cell-cycle dynamics in single cells showed that despite variability in G1-, S-, and G2 phases, duration of mitosis is short and remarkably constant. Surprisingly, there is no correlation between cell-cycle length and mitotic duration, suggesting that mitosis is temporally insulated from variability in earlier cell-cycle phases. By combining live cell imaging and computational modeling, we showed that positive feedback is the molecular mechanism underlying the temporal insulation of mitosis. Perturbing positive feedback gave rise to a sluggish, variable entry and progression through mitosis and uncoupled duration of mitosis from variability in cell cycle length. We show that positive feedback is important to keep mitosis short, constant, and temporally insulated and anticipate it might be a commonly used regulatory strategy to create modularity in other biological systems. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2018LPICo2047.6014F','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2018LPICo2047.6014F"><span>Getting Ready for BepiColombo: A Modeling Approach to Infer the Solar Wind Plasma Parameters <span class="hlt">Upstream</span> of Mercury from Magnetic Field Observations</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Fatemi, S.; Poirier, N.; Holmström, M.; Wieser, M.; Barabash, S.</p> <p>2018-05-01</p> <p>We have developed a model to infer the solar wind plasma parameters <span class="hlt">upstream</span> of Mercury from magnetic field observations in Mercury's magnetosphere. This is important for observations by MESSENGER and the future mission to Mercury, BepiColombo.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27259539','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27259539"><span>Designing robust watermark barcodes for multiplex long-read <span class="hlt">sequencing</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ezpeleta, Joaquín; Krsticevic, Flavia J; Bulacio, Pilar; Tapia, Elizabeth</p> <p>2017-03-15</p> <p>To attain acceptable sample misassignment rates, current approaches to multiplex single-molecule real-time <span class="hlt">sequencing</span> require <span class="hlt">upstream</span> quality improvement, which is obtained from multiple passes over the <span class="hlt">sequenced</span> insert and significantly reduces the effective read length. In order to fully exploit the raw read length on multiplex applications, robust barcodes capable of dealing with the full single-pass error rates are needed. We present a method for designing <span class="hlt">sequencing</span> barcodes that can withstand a large number of insertion, deletion and substitution errors and are suitable for use in multiplex single-molecule real-time <span class="hlt">sequencing</span>. The manuscript focuses on the design of barcodes for full-length single-pass reads, impaired by challenging error rates in the order of 11%. The proposed barcodes can multiplex hundreds or thousands of samples while achieving sample misassignment probabilities as low as 10-7 under the above conditions, and are designed to be compatible with chemical constraints imposed by the <span class="hlt">sequencing</span> process. Software tools for constructing watermark barcode sets and demultiplexing barcoded reads, together with example sets of barcodes and synthetic barcoded reads, are freely available at www.cifasis-conicet.gov.ar/ezpeleta/NS-watermark . ezpeleta@cifasis-conicet.gov.ar. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li class="active"><span>24</span></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_24 --> <div id="page_25" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li class="active"><span>25</span></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="481"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2007HESSD...4.1407M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2007HESSD...4.1407M"><span>The "WFD-effect" on <span class="hlt">upstream</span>-downstream relations in international river basins - insights from the Rhine and the Elbe basins</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Moellenkamp, S.</p> <p>2007-06-01</p> <p>The <span class="hlt">upstream</span>-downstream relationship in international river basins is a traditional challenge in water management. Water use in <span class="hlt">upstream</span> countries often has a negative impact on water use in downstream countries. This is most evident in the classical example of industrial pollution in <span class="hlt">upstream</span> countries hindering drinking water production downstream. The European Water Framework Directive (WFD) gives new impetus to the river basin approach and to international co-operation in European catchments. It aims at transforming a mainly water quality oriented management into a more integrated approach of ecosystem management. After discussing the traditional <span class="hlt">upstream</span>-downstream relationship, this article shows that the WFD has a balancing effect on <span class="hlt">upstream</span>-downstream problems and that it enhances river basin solidarity in international basins. While it lifts the downstream countries to the same level as the <span class="hlt">upstream</span> countries, it also leads to new duties for the downstream states. Following the ecosystem approach, measures taken by downstream countries become increasingly more important. For example, downstream countries need to take measures to allow for migrating fish species to reach <span class="hlt">upstream</span> stretches of river systems. With the WFD, fish populations receive increased attention, as they are an important indicator for the ecological status. The European Commission acquires a new role of inspection and control in river basin management, which finally also leads to enhanced cooperation and solidarity among the states in a basin. In order to achieve better water quality and to mitigate <span class="hlt">upstream</span>-downstream problems, also economic instruments can be applied and the WFD does not exclude the possibility of making use of financial compensations, if at the same time the polluter pays principle is taken into account. The results presented in this article originate from a broader study on integrated water resources management conducted at Bonn University and refer to the Rhine and</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/1222684','SCIGOV-STC'); return false;" href="https://www.osti.gov/servlets/purl/1222684"><span>HIV <span class="hlt">Sequence</span> Compendium 2015</span></a></p> <p><a target="_blank" href="http://www.osti.gov/scitech">SciTech Connect</a></p> <p>Foley, Brian Thomas; Leitner, Thomas Kenneth; Apetrei, Cristian</p> <p></p> <p>This compendium is an annual printed summary of the data contained in the HIV <span class="hlt">sequence</span> database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains <span class="hlt">sequences</span> published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of <span class="hlt">sequences</span> in the HIV database ismore » still increasing. In total, at the end of 2014, there were 624,121 <span class="hlt">sequences</span> in the HIV <span class="hlt">Sequence</span> Database, an increase of 7% since the previous year. This is the first year that the number of new <span class="hlt">sequences</span> added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/ content/<span class="hlt">sequence</span>/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/23172872','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/23172872"><span>GATA3 acts <span class="hlt">upstream</span> of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Theodorou, Vasiliki; Stark, Rory; Menon, Suraj; Carroll, Jason S</p> <p>2013-01-01</p> <p>Estrogen receptor (ESR1) drives growth in the majority of human breast cancers by binding to regulatory elements and inducing transcription events that promote tumor growth. Differences in enhancer occupancy by ESR1 contribute to the diverse expression profiles and clinical outcome observed in breast cancer patients. GATA3 is an ESR1-cooperating transcription factor mutated in breast tumors; however, its genomic properties are not fully defined. In order to investigate the composition of enhancers involved in estrogen-induced transcription and the potential role of GATA3, we performed extensive ChIP-<span class="hlt">sequencing</span> in unstimulated breast cancer cells and following estrogen treatment. We find that GATA3 is pivotal in mediating enhancer accessibility at regulatory regions involved in ESR1-mediated transcription. GATA3 silencing resulted in a global redistribution of cofactors and active histone marks prior to estrogen stimulation. These global genomic changes altered the ESR1-binding profile that subsequently occurred following estrogen, with events exhibiting both loss and gain in binding affinity, implying a GATA3-mediated redistribution of ESR1 binding. The GATA3-mediated redistributed ESR1 profile correlated with changes in gene expression, suggestive of its functionality. Chromatin loops at the TFF locus involving ESR1-bound enhancers occurred independently of ESR1 when GATA3 was silenced, indicating that GATA3, when present on the chromatin, may serve as a licensing factor for estrogen-ESR1-mediated interactions between cis-regulatory elements. Together, these experiments suggest that GATA3 directly impacts ESR1 enhancer accessibility, and may potentially explain the contribution of mutant-GATA3 in the heterogeneity of ESR1+ breast cancer.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3530671','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3530671"><span>GATA3 acts <span class="hlt">upstream</span> of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Theodorou, Vasiliki; Stark, Rory; Menon, Suraj; Carroll, Jason S.</p> <p>2013-01-01</p> <p>Estrogen receptor (ESR1) drives growth in the majority of human breast cancers by binding to regulatory elements and inducing transcription events that promote tumor growth. Differences in enhancer occupancy by ESR1 contribute to the diverse expression profiles and clinical outcome observed in breast cancer patients. GATA3 is an ESR1-cooperating transcription factor mutated in breast tumors; however, its genomic properties are not fully defined. In order to investigate the composition of enhancers involved in estrogen-induced transcription and the potential role of GATA3, we performed extensive ChIP-<span class="hlt">sequencing</span> in unstimulated breast cancer cells and following estrogen treatment. We find that GATA3 is pivotal in mediating enhancer accessibility at regulatory regions involved in ESR1-mediated transcription. GATA3 silencing resulted in a global redistribution of cofactors and active histone marks prior to estrogen stimulation. These global genomic changes altered the ESR1-binding profile that subsequently occurred following estrogen, with events exhibiting both loss and gain in binding affinity, implying a GATA3-mediated redistribution of ESR1 binding. The GATA3-mediated redistributed ESR1 profile correlated with changes in gene expression, suggestive of its functionality. Chromatin loops at the TFF locus involving ESR1-bound enhancers occurred independently of ESR1 when GATA3 was silenced, indicating that GATA3, when present on the chromatin, may serve as a licensing factor for estrogen–ESR1-mediated interactions between cis-regulatory elements. Together, these experiments suggest that GATA3 directly impacts ESR1 enhancer accessibility, and may potentially explain the contribution of mutant-GATA3 in the heterogeneity of ESR1+ breast cancer. PMID:23172872</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20100010951','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20100010951"><span>Automatic Command <span class="hlt">Sequence</span> Generation</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Fisher, Forest; Gladded, Roy; Khanampompan, Teerapat</p> <p>2007-01-01</p> <p>Automatic <span class="hlt">Sequence</span> Generator (Autogen) Version 3.0 software automatically generates command <span class="hlt">sequences</span> for the Mars Reconnaissance Orbiter (MRO) and several other JPL spacecraft operated by the multi-mission support team. Autogen uses standard JPL <span class="hlt">sequencing</span> tools like APGEN, ASP, SEQGEN, and the DOM database to automate the generation of uplink command products, Spacecraft Command Message Format (SCMF) files, and the corresponding ground command products, DSN Keywords Files (DKF). Autogen supports all the major multi-mission mission phases including the cruise, aerobraking, mapping/science, and relay mission phases. Autogen is a Perl script, which functions within the mission operations UNIX environment. It consists of two parts: a set of model files and the autogen Perl script. Autogen encodes the behaviors of the system into a model and encodes algorithms for context sensitive customizations of the modeled behaviors. The model includes knowledge of different mission phases and how the resultant command products must differ for these phases. The executable software portion of Autogen, automates the setup and use of APGEN for constructing a spacecraft activity <span class="hlt">sequence</span> file (SASF). The setup includes file retrieval through the DOM (Distributed Object Manager), an object database used to store project files. This step retrieves all the needed input files for generating the command products. Depending on the mission phase, Autogen also uses the ASP (Automated <span class="hlt">Sequence</span> Processor) and SEQGEN to generate the command product sent to the spacecraft. Autogen also provides the means for customizing <span class="hlt">sequences</span> through the use of configuration files. By automating the majority of the <span class="hlt">sequencing</span> generation process, Autogen eliminates many <span class="hlt">sequence</span> generation errors commonly introduced by manually constructing spacecraft command <span class="hlt">sequences</span>. Through the layering of commands into the <span class="hlt">sequence</span> by a series of scheduling algorithms, users are able to rapidly and reliably construct the</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2017EGUGA..19.4964L','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2017EGUGA..19.4964L"><span>Numerical simulation of scouring-deposition variations caused by rainfall-induced landslides in the <span class="hlt">upstream</span> of Zengwun River, Taiwan</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Lee, Ming-Hsi; Liao, Yi-Wen; Tsai, Kuang-Jung</p> <p>2017-04-01</p> <p>In recent years, the increasing sediment disasters of severe rainfall-induced landslides on human lives and lifeline facilities worldwide have advanced the necessity to find out both economically acceptable and useful techniques to predict the occurrence and destructive power of the disasters. In August 2009, Typhoon Morakot brought a large amount of rainfall with both high intensity and long duration to a vast area of Taiwan. Unfortunately, this resulted in a catastrophic landslide in watershed of Zengwun-River reservoir, southern Taiwan. Meanwhile, large amounts of landslides were formed in the <span class="hlt">upstream</span> of Zengwun River. The major scope of this study is to apply numerical model to simulate the scouring-deposition variations caused by rainfall-induced landslides that occurred in the <span class="hlt">upstream</span> of Zengwun River during Typhoon Morakot. This study proposed the relation diagrams of the intermediate diameter (d50), recurrence interval (T) and scouring-deposition depth (D), and applied the diagrams to understand the impacts of the scouring-deposition variations on the structures for water and soil conservation and their measurements. Based on the simulation of scouring-deposition variation at the Da-Bu dam and Da-Bang dam, this study also discussed the scouring-deposition variations of different sections under different scenarios (including flow rate, intermediate diameters and structures). In summary, the result suggested that the diagrams of the intermediate diameter, recurrence interval and scouring-deposition depth could be used as the reference for designing the check dams, ground sills and lateral constructions.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2011OptEn..50i5004Y','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2011OptEn..50i5004Y"><span>Compensation of power drops in reflective semiconductor optical amplifier-based passive optical network with <span class="hlt">upstream</span> data rate adjustment</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Yeh, Chien-Hung; Chow, Chi-Wai; Chiang, Ming-Feng; Shih, Fu-Yuan; Pan, Ci-Ling</p> <p>2011-09-01</p> <p>In a wavelength division multiplexed-passive optical network (WDM-PON), different fiber lengths and optical components would introduce different power budgets to different optical networking units (ONUs). Besides, the power decay of the distributed optical carrier from the optical line terminal owing to aging of the optical transmitter could also reduce the injected power into the ONU. In this work, we propose and demonstrate a carrier distributed WDM-PON using a reflective semiconductor optical amplifier-based ONU that can adjust its <span class="hlt">upstream</span> data rate to accommodate different injected optical powers. The WDM-PON is evaluated at standard-reach (25 km) and long-reach (100 km). Bit-error rate measurements at different injected optical powers and transmission lengths show that by adjusting the <span class="hlt">upstream</span> data rate of the system (622 Mb/s, 1.25 and 2.5 Gb/s), error-free (<10-9) operation can still be achieved when the power budget drops.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25311933','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25311933"><span>Cryoablation of focal tachycardia originating from the right atrial free wall during <span class="hlt">upstream</span> phrenic pacing to avoid phrenic nerve injury.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Johnsrude, Christopher</p> <p>2015-01-01</p> <p>Recognition of the potential for phrenic nerve injury (PNI) often prompts less aggressive attempts at catheter ablation of multiple forms of tachycardia or abandoning ablation altogether. Some novel techniques to avoid PNI during catheter ablation have been described. Five patients (age: 13-57 years, three females) with ectopic atrial tachycardia originating from the right atrial free wall (RAFW) near the phrenic nerve underwent electrophysiology study with three-dimensional mapping and endocardial cryoablation. <span class="hlt">Upstream</span> phrenic pacing was performed after cryoadherence was achieved, and cryoablation of ectopic foci was performed during close observation for occurrence of PNI and tachycardia elimination. Cryoablation acutely eliminated five of six atrial tachycardias originating close to the phrenic nerve. Transient PNI during cryothermy occurred in two patients, and resolved within 3 minutes. Patients were observed overnight on telemetry, with no early recurrences of targeted atrial tachycardias and no evidence of PNI. At last follow-up of 1-39 months, four patients were arrhythmia free on no medications. Catheter cryoablation during simultaneous <span class="hlt">upstream</span> phrenic nerve pacing can lead to safe and effective elimination of focal atrial tachycardias originating from the RAFW close to the phrenic nerve. ©2014 Wiley Periodicals, Inc.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://pubs.usgs.gov/sir/2010/5048/','USGSPUBS'); return false;" href="https://pubs.usgs.gov/sir/2010/5048/"><span>Dissolved-Solids Load in Henrys Fork <span class="hlt">Upstream</span> from the Confluence with Antelope Wash, Wyoming, Water Years 1970-2009</span></a></p> <p><a target="_blank" href="http://pubs.er.usgs.gov/pubs/index.jsp?view=adv">USGS Publications Warehouse</a></p> <p>Foster, Katharine; Kenney, Terry A.</p> <p>2010-01-01</p> <p>Annual dissolved-solids load at the mouth of Henrys Fork was estimated by using data from U.S. Geological Survey streamflow-gaging station 09229500, Henrys Fork near Manila, Utah. The annual dissolved-solids load for water years 1970-2009 ranged from 18,300 tons in 1977 to 123,300 tons in 1983. Annual streamflows for this period ranged from 14,100 acre-feet in 1977 to 197,500 acre-feet in 1983. The 25-percent trimmed mean dissolved-solids load for water years 1970-2009 was 44,300 tons per year at Henrys Fork near Manila, Utah. Previous simulations using a SPAtially Referenced Regression On Watershed attributes (SPARROW) model for dissolved solids specific to water year 1991 conditions in the Upper Colorado River Basin predicted an annual dissolved-solids load of 25,000 tons for the Henrys Fork Basin <span class="hlt">upstream</span> from Antelope Wash. On the basis of computed dissolved-solids load data from Henrys Fork near Manila, Utah, together with estimated annual dissolved-solids load from Antelope Wash and Peoples Canal, this prediction was adjusted to 37,200 tons. As determined by simulations with the Upper Colorado River Basin SPARROW model, approximately 56 percent (14,000 tons per year) of the dissolved-solids load at Henrys Fork <span class="hlt">upstream</span> from Antelope Wash is associated with the 21,500 acres of irrigated agricultural lands in the upper Henrys Fork Basin.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26627697','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26627697"><span>The concentration and chemical speciation of arsenic in the Nanpan River, the <span class="hlt">upstream</span> of the Pearl River, China.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Yang, Silin; Zhao, Ning; Zhou, Dequn; Wei, Rong; Yang, Bin; Pan, Bo</p> <p>2016-04-01</p> <p>The concentration and chemical speciation of arsenic (As) in different environmental matrixes (water, sediment, agricultural soils, and non-agricultural soils) were investigated in the Nanpan River area, the <span class="hlt">upstream</span> of Pearl River, China. The results did not show any obvious transport of As along the flow direction of the river (from <span class="hlt">upstream</span> to downstream). Total As concentrations in sediment were significantly different from those in agricultural soil. According to the comparison to quality standards, the As in sediments of the studied area have potential ecological risks and a minority of the sampling sites of agricultural soils in the studied area were polluted with As. As speciations were analyzed using sequential extraction and the percentage of non-residual fraction in sediment predominated over residual fraction. We thus believe that As in the studied area was with low mobility and bioavailability in sediment, agricultural soils, and non-agricultural soils. However, the bioavailability and mobility of As in sediment were higher than in both agricultural and non-agricultural soils, and thus, special attention should be paid for the risk assessment of As in the river in future studies.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3434945','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3434945"><span>Impacts of <span class="hlt">upstream</span> drought and water withdrawals on the health and survival of downstream estuarine oyster populations</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Petes, Laura E; Brown, Alicia J; Knight, Carley R</p> <p>2012-01-01</p> <p>Increases in the frequency, duration, and severity of regional drought pose major threats to the health and integrity of downstream ecosystems. During 2007–2008, the U.S. southeast experienced one of the most severe droughts on record. Drought and water withdrawals in the <span class="hlt">upstream</span> watershed led to decreased freshwater input to Apalachicola Bay, Florida, an estuary that is home to a diversity of commercially and ecologically important organisms. This study applied a combination of laboratory experiments and field observations to investigate the effects of reduced freshwater input on Apalachicola oysters. Oysters suffered significant disease-related mortality under high-salinity, drought conditions, particularly during the warm summer months. Mortality was size-specific, with large oysters of commercially harvestable size being more susceptible than small oysters. A potential salinity threshold was revealed between 17 and 25 ppt, where small oysters began to suffer mortality, and large oysters exhibited an increase in mortality. These findings have important implications for watershed management, because <span class="hlt">upstream</span> freshwater releases could be carefully timed and allocated during stressful periods of the summer to reduce disease-related oyster mortality. Integrated, forward-looking water management is needed, particularly under future scenarios of climate change and human population growth, to sustain the valuable ecosystem services on which humans depend. PMID:22957175</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015JGRA..120.2838S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015JGRA..120.2838S"><span>Magnetosheath plasma stability and ULF wave occurrence as a function of location in the magnetosheath and <span class="hlt">upstream</span> bow shock parameters</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Soucek, Jan; Escoubet, C. Philippe; Grison, Benjamin</p> <p>2015-04-01</p> <p>We present the results of a statistical study of the distribution of mirror and Alfvén-ion cyclotron (AIC) waves in the magnetosheath together with plasma parameters important for the stability of ULF waves, specifically ion temperature anisotropy and ion beta. Magnetosheath crossings registered by Cluster spacecraft over the course of 2 years served as a basis for the statistics. For each observation we used bow shock, magnetopause, and magnetosheath flow models to identify the relative position of the spacecraft with respect to magnetosheath boundaries and local properties of the <span class="hlt">upstream</span> shock crossing. A strong dependence of both plasma parameters and mirror/AIC wave occurrence on <span class="hlt">upstream</span> ΘBn and MA is identified. We analyzed a joint dependence of the same parameters on ΘBn and fractional distance between shock and magnetopause, zenith angle, and length of the flow line. Finally, the occurrence of mirror and AIC modes was compared against the respective instability thresholds. We noted that AIC waves occurred nearly exclusively under mirror stable conditions. This is interpreted in terms of different characters of nonlinear saturation of the two modes.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2017APS..DFDM26007A','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2017APS..DFDM26007A"><span>A fast wind-farm boundary-layer model to investigate gravity wave effects and <span class="hlt">upstream</span> flow deceleration</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Allaerts, Dries; Meyers, Johan</p> <p>2017-11-01</p> <p>Wind farm design and control often relies on fast analytical wake models to predict turbine wake interactions and associated power losses. Essential input to these models are the inflow velocity and turbulent intensity at hub height, which come from prior measurement campaigns or wind-atlas data. Recent LES studies showed that in some situations large wind farms excite atmospheric gravity waves, which in turn affect the <span class="hlt">upstream</span> wind conditions. In the current study, we develop a fast boundary-layer model that computes the excitation of gravity waves and the perturbation of the boundary-layer flow in response to an applied force. The core of the model is constituted by height-averaged, linearised Navier-Stokes equations for the inner and outer layer, and the effect of atmospheric gravity waves (excited by the boundary-layer displacement) is included via the pressure gradient. Coupling with analytical wake models allows us to study wind-farm wakes and <span class="hlt">upstream</span> flow deceleration in various atmospheric conditions. Comparison with wind-farm LES results shows excellent agreement in terms of pressure and boundary-layer displacement levels. The authors acknowledge support from the European Research Council (FP7-Ideas, Grant No. 306471).</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015AGUFMSM31C2534H','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015AGUFMSM31C2534H"><span>Fine Spectral Properties of Langmuir Waves Observed <span class="hlt">Upstream</span> of the Saturn's Bowshock by the Cassini Wideband Receiver</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Hospodarsky, G. B.; Pisa, D.; Santolik, O.; Kurth, W. S.; Soucek, J.; Basovnik, M.; Gurnett, D. A.; Arridge, C. S.</p> <p>2015-12-01</p> <p>Langmuir waves are commonly observed in the <span class="hlt">upstream</span> regions of planetary and interplanetary shock. Solar wind electrons accelerated at the shock front are reflected back into the solar wind and can form electron beams. In regions with beams, the electron distribution becomes unstable and electrostatic waves can be generated. The process of generation and the evolution of electrostatic waves strongly depends on the solar wind electron distribution and generally exhibits complex behavior. Langmuir waves can be identified as intense narrowband emission at a frequency very close to the local plasma frequency and weaker broadband waves below and above the plasma frequency deeper in the downstream region. We present a detailed study of Langmuir waves detected <span class="hlt">upstream</span> of the Saturnian bowshock by the Cassini spacecraft. Using data from the Radio and Plasma Wave Science (RPWS), Magnetometer (MAG) and Cassini Plasma Spectrometer (CAPS) instruments we have analyzed several periods containing the extended waveform captures by the Wideband Receiver. Langmuir waves are a bursty emission highly controlled by variations in solar wind conditions. Unfortunately due to a combination of instrumental field of view and sampling period, it is often difficult to identify the electron distribution function that is unstable and able to generate Langmuir waves. We used an electrostatic version of particle-in-cell simulation of the Langmuir wave generation process to reproduce some of the more subtle observed spectral features and help understand the late stages of the instability and interactions in the solar wind plasma.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28545128','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28545128"><span>Common variants <span class="hlt">upstream</span> of MLF1 at 3q25 and within CPZ at 4p16 associated with neuroblastoma.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>McDaniel, Lee D; Conkrite, Karina L; Chang, Xiao; Capasso, Mario; Vaksman, Zalman; Oldridge, Derek A; Zachariou, Anna; Horn, Millicent; Diamond, Maura; Hou, Cuiping; Iolascon, Achille; Hakonarson, Hakon; Rahman, Nazneen; Devoto, Marcella; Diskin, Sharon J</p> <p>2017-05-01</p> <p>Neuroblastoma is a cancer of the developing sympathetic nervous system that most commonly presents in young children and accounts for approximately 12% of pediatric oncology deaths. Here, we report on a genome-wide association study (GWAS) in a discovery cohort or 2,101 cases and 4,202 controls of European ancestry. We identify two new association signals at 3q25 and 4p16 that replicated robustly in multiple independent cohorts comprising 1,163 cases and 4,396 controls (3q25: rs6441201 combined P = 1.2x10-11, Odds Ratio 1.23, 95% CI:1.16-1.31; 4p16: rs3796727 combined P = 1.26x10-12, Odds Ratio 1.30, 95% CI: 1.21-1.40). The 4p16 signal maps within the carboxypeptidase Z (CPZ) gene. The 3q25 signal resides within the arginine/serine-rich coiled-coil 1 (RSRC1) gene and <span class="hlt">upstream</span> of the myeloid leukemia factor 1 (MLF1) gene. Increased expression of MLF1 was observed in neuroblastoma cells homozygous for the rs6441201 risk allele (P = 0.02), and significant growth inhibition was observed upon depletion of MLF1 (P < 0.0001) in neuroblastoma cells. Taken together, we show that common DNA variants within CPZ at 4p16 and <span class="hlt">upstream</span> of MLF1 at 3q25 influence neuroblastoma susceptibility and MLF1 likely plays an important role in neuroblastoma tumorigenesis.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016OptFT..30...12Z','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016OptFT..30...12Z"><span>Proposal of DCS-OFDM-PON <span class="hlt">upstream</span> transmission with intensity modulator and collective self-coherent detection</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Zhang, Jing; Yang, Heming; Zhao, Difu; Qiu, Kun</p> <p>2016-07-01</p> <p>We introduce digital coherent superposition (DCS) into optical access network and propose a DCS-OFDM-PON <span class="hlt">upstream</span> transmission scheme using intensity modulator and collective self-coherent detection. The generated OFDM signal is real based on Hermitian symmetry, which can be used to estimate the common phase error (CPE) by complex conjugate subcarrier pairs without any pilots. In simulation, we transmit an aggregated 40 Gb/s optical OFDM signal from two ONUs. The transmission performance with DCS is slightly better after 25 km transmission without relative transmission time delay. The fiber distance for different ONUs to RN are not same in general and there is relative transmission time delay between ONUs, which causes inter-carrier-interference (ICI) power increasing and degrades the transmission performance. The DCS can mitigate the ICI power and the DCS-OFDM-PON <span class="hlt">upstream</span> transmission outperforms the conventional OFDM-PON. The CPE estimation is by using two pairs of complex conjugate subcarriers without redundancy. The power variation can be 9 dB in DCS-OFDM-PON, which is enough to tolerate several kilometers fiber length difference between the ONUs.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2008OptCo.281.2218W','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2008OptCo.281.2218W"><span><span class="hlt">Upstream</span> vertical cavity surface-emitting lasers for fault monitoring and localization in WDM passive optical networks</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Wong, Elaine; Zhao, Xiaoxue; Chang-Hasnain, Connie J.</p> <p>2008-04-01</p> <p>As wavelength division multiplexed passive optical networks (WDM-PONs) are expected to be first deployed to transport high capacity services to business customers, real-time knowledge of fiber/device faults and the location of such faults will be a necessity to guarantee reliability. Nonetheless, the added benefit of implementing fault monitoring capability should only incur minimal cost associated with upgrades to the network. In this work, we propose and experimentally demonstrate a fault monitoring and localization scheme based on a highly-sensitive and potentially low-cost monitor in conjunction with vertical cavity surface-emitting lasers (VCSELs). The VCSELs are used as <span class="hlt">upstream</span> transmitters in the WDM-PON. The proposed scheme benefits from the high reflectivity of the top distributed Bragg reflector (DBR) mirror of optical injection-locked (OIL) VCSELs to reflect monitoring channels back to the central office for monitoring. Characterization of the fault monitor demonstrates high sensitivity, low bandwidth requirements, and potentially low output power. The added advantage of the proposed fault monitoring scheme incurs only a 0.5 dB penalty on the <span class="hlt">upstream</span> transmissions on the existing infrastructure.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.osti.gov/sciencecinema/biblio/1136620','SCIGOVIMAGE-SCICINEMA'); return false;" href="http://www.osti.gov/sciencecinema/biblio/1136620"><span><span class="hlt">Sequencing</span> Complex Genomic Regions</span></a></p> <p><a target="_blank" href="http://www.osti.gov/sciencecinema/">ScienceCinema</a></p> <p>Eichler, Evan</p> <p>2018-02-12</p> <p>Evan Eichler, Howard Hughes Medical Investigator at the University of Washington, gives the May 28, 2009 keynote speech at the "<span class="hlt">Sequencing</span>, Finishing, Analysis in the Future" meeting in Santa Fe, NM. Part 1 of 2</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://ntrs.nasa.gov/search.jsp?R=19790000401&hterms=appliances&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D70%26Ntt%3Dappliances','NASA-TRS'); return false;" href="https://ntrs.nasa.gov/search.jsp?R=19790000401&hterms=appliances&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D70%26Ntt%3Dappliances"><span>Compact rotary <span class="hlt">sequencer</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Appleberry, W. T.</p> <p>1980-01-01</p> <p>Rotary <span class="hlt">sequencer</span> is assembled from conventional planetary differential gearset and latching mechanism utilizing inputs and outputs which are coaxial. Applications include automated production-line equipment in home appliances and in vehicles.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://medlineplus.gov/ency/article/001607.htm','NIH-MEDLINEPLUS'); return false;" href="https://medlineplus.gov/ency/article/001607.htm"><span>Pierre Robin <span class="hlt">sequence</span></span></a></p> <p><a target="_blank" href="http://medlineplus.gov/">MedlinePlus</a></p> <p></p> <p></p> <p>Pierre Robin syndrome; Pierre Robin complex; Pierre Robin anomaly ... The exact causes of Pierre Robin <span class="hlt">sequence</span> are unknown. It may be part of many genetic syndromes. The lower jaw develops slowly before birth, but may grow ...</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li class="active"><span>25</span></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_25 --> <center> <div class="footer-extlink text-muted"><small>Some links on this page may take you to non-federal websites. 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