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Sample records for correlating overrepresented upstream

  1. Correlating overrepresented upstream motifs to gene expression a computational approach to regulatory element discovery in eukaryotes

    CERN Document Server

    Caselle, M; Provero, P

    2002-01-01

    Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory elements in the upstream region of eukaryotic genes. The genes are grouped in sets sharing an overrepresented short motif in their upstream sequence. For each set, the average expression level from a microarray experiment is determined: If this level is significantly higher or lower than the average taken over the whole genome, then the overerpresented motif shared by the genes in the set is likely to play a role in their regulation. The method was tested by applying it to the genome of Saccharomyces cerevisiae, using the publicly available results of a DNA microarray experiment, in which expression levels for virtually all the genes were measured during the diauxic shift from fermentation to respiration. Several known motifs were correctly identified, and a new candidate regulat...

  2. Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrep-resented upstream motifs

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    Silengo Lorenzo

    2004-05-01

    Full Text Available Abstract Background Transcriptional regulation is a key mechanism in the functioning of the cell, and is mostly effected through transcription factors binding to specific recognition motifs located upstream of the coding region of the regulated gene. The computational identification of such motifs is made easier by the fact that they often appear several times in the upstream region of the regulated genes, so that the number of occurrences of relevant motifs is often significantly larger than expected by pure chance. Results To exploit this fact, we construct sets of genes characterized by the statistical overrepresentation of a certain motif in their upstream regions. Then we study the functional characterization of these sets by analyzing their annotation to Gene Ontology terms. For the sets showing a statistically significant specific functional characterization, we conjecture that the upstream motif characterizing the set is a binding site for a transcription factor involved in the regulation of the genes in the set. Conclusions The method we propose is able to identify many known binding sites in S. cerevisiae and new candidate targets of regulation by known transcritpion factors. Its application to less well studied organisms is likely to be valuable in the exploration of their regulatory interaction network.

  3. Analysis and Modeling of Time-Correlated Characteristics of Rainfall-Runoff Similarity in the Upstream Red River Basin

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    Xiuli Sang

    2012-01-01

    Full Text Available We constructed a similarity model (based on Euclidean distance between rainfall and runoff to study time-correlated characteristics of rainfall-runoff similar patterns in the upstream Red River Basin and presented a detailed evaluation of the time correlation of rainfall-runoff similarity. The rainfall-runoff similarity was used to determine the optimum similarity. The results showed that a time-correlated model was found to be capable of predicting the rainfall-runoff similarity in the upstream Red River Basin in a satisfactory way. Both noised and denoised time series by thresholding the wavelet coefficients were applied to verify the accuracy of model. And the corresponding optimum similar sets obtained as the equation solution conditions showed an interesting and stable trend. On the whole, the annual mean similarity presented a gradually rising trend, for quantitatively estimating comprehensive influence of climate change and of human activities on rainfall-runoff similarity.

  4. Gulf of Maine salinity variation and its correlation with upstream Scotian Shelf currents at seasonal and interannual time scales

    National Research Council Canada - National Science Library

    Feng, Hui; Vandemark, Doug; Wilkin, John

    2016-01-01

    ... with remote forcing of Gulf hydrography by upstream advection. These long‐term mooring data are combined with satellite altimeter estimates of upper ocean current anomaly on the adjoining Scotian Shelf (SS...

  5. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  6. Poly purine.pyrimidine sequences upstream of the beta-galactosidase gene affect gene expression in Saccharomyces cerevisiae

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    Brahmachari Samir K

    2001-10-01

    Full Text Available Abstract Background Poly purine.pyrimidine sequences have the potential to adopt intramolecular triplex structures and are overrepresented upstream of genes in eukaryotes. These sequences may regulate gene expression by modulating the interaction of transcription factors with DNA sequences upstream of genes. Results A poly purine.pyrimidine sequence with the potential to adopt an intramolecular triplex DNA structure was designed. The sequence was inserted within a nucleosome positioned upstream of the β-galactosidase gene in yeast, Saccharomyces cerevisiae, between the cycl promoter and gal 10Upstream Activating Sequences (UASg. Upon derepression with galactose, β-galactosidase gene expression is reduced 12-fold in cells carrying single copy poly purine.pyrimidine sequences. This reduction in expression is correlated with reduced transcription. Furthermore, we show that plasmids carrying a poly purine.pyrimidine sequence are not specifically lost from yeast cells. Conclusion We propose that a poly purine.pyrimidine sequence upstream of a gene affects transcription. Plasmids carrying this sequence are not specifically lost from cells and thus no additional effort is needed for the replication of these sequences in eukaryotic cells.

  7. Correlation Between ISAba1 Upstream ampC Gene and Resistance to Cefotaxime in Acinetobacter baumannii: A Serious Threat to Nosocomial Infections

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    Rezaee

    2016-01-01

    Full Text Available Background Infections due to Acinetobacter baumannii have become a significant challenge in modern healthcare systems. The global upsurge of multidrug resistance in A. baumannii has created widespread problems in the treatment of patients. Objectives We examined the prevalence ISAmpC and its correlation with cefotaxime resistance. Materials and Methods Standard biochemical tests were used to identify isolates. Genomic species of the genus Acinetobacter were confirmed by Amplified Ribosomal DNA Restriction Analysis (ARDRA. The susceptibility of 50 A. baumannii isolates to a variety of antimicrobial agents was determined using the disk diffusion method and E-test strips. PCR was used to investigate the connection of insertion sequences and the ampC gene. Clonal relatedness was determined by Repetitive Extragenic Palindromic PCR. Results ISAba1 located upstream of blaampC was found in 24 (48% of the A. baumannii isolates. In all of the studied isolates that had ISAmpC, the MIC for cefotaxime was 64 - 256 μg/mL. Based on the REP-PCR patterns among the resistant isolates, the highest number of ISAmpC positive isolates belonged to type B (n = 19 and type C (n = 12. Conclusions ISAba1 has become an important factor in A. baumannii’s resistance to cefotaxime.

  8. The far-upstream element-binding protein 2 is correlated with proliferation and doxorubicin resistance in human breast cancer cell lines.

    Science.gov (United States)

    Wang, Ying-Ying; Gu, Xiao-Ling; Wang, Chao; Wang, Hua; Ni, Qi-Chao; Zhang, Chun-Hui; Yu, Xia-Fei; Yang, Li-Yi; He, Zhi-Xian; Mao, Guo-Xin; Yang, Shu-Yun

    2016-07-01

    Far-upstream element (FUSE)-binding protein 2 (FBP2) was a member of single-stranded DNA-binding protein family; it played an important role in regulating transcription and post-transcription and is involved in the regulation of C-MYC gene expression in liver tumors. However, the role of FBP2 in breast cancer and its mechanism has not been studied yet. Here, we discovered that FBP2 was up-regulated in breast cancer tissues and breast cancer cell lines. Moreover, immunohistochemistry analysis demonstrated that up-regulated FBP2 was highly associated with tumor grade, Ki-67, and poor prognosis, which was an independent prognostic factor for survival of breast cancer patients. At the cellular level, we found that FBP2 was correlated with cell cycle progression by accelerating G1/S transition, and knockdown of FBP2 could weaken cell proliferation, anchorage-independent cell growth, while enhancing the sensitivity of breast cancer cells to doxorubicin. More importantly, we found that activation of PI3K/AKT pathway could phosphorylate FBP2, and then make FBP2 shuttle from cytoplasm into the nucleus, which was the main mechanism of breast cancer cell proliferation and drug resistance. Taken together, our findings supported the notion that FBP2 might via PI3K/AKT pathway influence breast cancer progression and drug resistance, which might provide a new target for the design of anti-cancer drugs for breast cancer patients.

  9. Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes

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    Tse Herman

    2010-09-01

    Full Text Available Abstract Background Out-of-frame stop codons (OSCs occur naturally in coding sequences of all organisms, providing a mechanism of early termination of translation in incorrect reading frame so that the metabolic cost associated with frameshift events can be reduced. Given such a functional significance, we expect statistically overrepresented OSCs in coding sequences as a result of a widespread selection. Accordingly, we examined available prokaryotic genomes to look for evidence of this selection. Results The complete genome sequences of 990 prokaryotes were obtained from NCBI GenBank. We found that low G+C content coding sequences contain significantly more OSCs and G+C content at specific codon positions were the principal determinants of OSC usage bias in the different reading frames. To investigate if there is overrepresentation of OSCs, we modeled the trinucleotide and hexanucleotide biases of the coding sequences using Markov models, and calculated the expected OSC frequencies for each organism using a Monte Carlo approach. More than 93% of 342 phylogenetically representative prokaryotic genomes contain excess OSCs. Interestingly the degree of OSC overrepresentation correlates positively with G+C content, which may represent a compensatory mechanism for the negative correlation of OSC frequency with G+C content. We extended the analysis using additional compositional bias models and showed that lower-order bias like codon usage and dipeptide bias could not explain the OSC overrepresentation. The degree of OSC overrepresentation was found to correlate negatively with the optimal growth temperature of the organism after correcting for the G+C% and AT skew of the coding sequence. Conclusions The present study uses approaches with statistical rigor to show that OSC overrepresentation is a widespread phenomenon among prokaryotes. Our results support the hypothesis that OSCs carry functional significance and have been selected in the course of

  10. Upstream profitability in Vietnam

    Energy Technology Data Exchange (ETDEWEB)

    Ingeberg, K.

    1993-12-01

    This report outlines the main characteristics of the petroleum industry in Vietnam. First, it discusses the exploration history and the fiscal regime and concession system for international companies searching for new exploration ventures in the country. Second, it presents an economic analysis of exploration and field development decisions. The analysis is based on a cash flow tax model reflecting the current economic framework. Calculations of upstream profitability are based on typical offshore oil project assumptions. The analysis includes the effects of different levels of exploration risks, tax position and tax agreements. The report also compares fiscal terms in Vietnam and Malaysia and their effect on attractivity. 20 refs., 3 figs., 19 tabs.

  11. LHCb upstream tracker

    CERN Multimedia

    Artuso, Marina

    2016-01-01

    The detector for the LHCb upgrade is designed for 40MHz readout, allowing the experiment to run at an instantaneous luminosity of 2x10^33 cm$^2$s$^-1$. The upgrade of the tracker subsystem in front of the dipole magnet, the Upstream Tracker, is crucial for charged track reconstruction and fast trigger decisions based on a tracking algorithm involving also vertex detector information. The detector consists of 4 planes with a total area of about 8.5m$^2$, made of single sided silicon strip sensors read-out by a novel custom-made ASIC (SALT). Details on the performance of prototype sensors, front-end electronics, near-detector electronics and mechanical components are presented.

  12. Upstream, downstream underground upgrading

    Energy Technology Data Exchange (ETDEWEB)

    Roche, P.

    2008-06-15

    Innovation, technology and research and development activities in the upstream oil sands industry were discussed with particular reference to new methods of upgrading bitumen in reservoirs currently being used by Shell Canada. Methods of refining residues and producing tight gas and oil sands were also discussed. Shell Canada's pilot program is currently being conducted to test the electric heat technology at a cyclic steam project that is currently preparing for significant growth. The pilot project will assess the composition of the product, determine recovery efficiency and identify geomechanical issues in order to commercialize the heaters. The project will potentially produce billions of barrels of light oil if it succeeds. It was concluded that Shell is now also using its proprietary gas-to-liquids (GTL) technology to build the world's first GTL plant in Malaysia. 3 figs.

  13. Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model

    Directory of Open Access Journals (Sweden)

    Zhai Chengxiang

    2010-05-01

    Full Text Available Abstract Background Large-scale genomic studies often identify large gene lists, for example, the genes sharing the same expression patterns. The interpretation of these gene lists is generally achieved by extracting concepts overrepresented in the gene lists. This analysis often depends on manual annotation of genes based on controlled vocabularies, in particular, Gene Ontology (GO. However, the annotation of genes is a labor-intensive process; and the vocabularies are generally incomplete, leaving some important biological domains inadequately covered. Results We propose a statistical method that uses the primary literature, i.e. free-text, as the source to perform overrepresentation analysis. The method is based on a statistical framework of mixture model and addresses the methodological flaws in several existing programs. We implemented this method within a literature mining system, BeeSpace, taking advantage of its analysis environment and added features that facilitate the interactive analysis of gene sets. Through experimentation with several datasets, we showed that our program can effectively summarize the important conceptual themes of large gene sets, even when traditional GO-based analysis does not yield informative results. Conclusions We conclude that the current work will provide biologists with a tool that effectively complements the existing ones for overrepresentation analysis from genomic experiments. Our program, Genelist Analyzer, is freely available at: http://workerbee.igb.uiuc.edu:8080/BeeSpace/Search.jsp

  14. Silent coeliac disease is over-represented in children with type 1 diabetes and their siblings.

    Science.gov (United States)

    Hansson, Tony; Dahlbom, Ingrid; Tuvemo, Torsten; Frisk, Gun

    2015-02-01

    This study measured autoantibodies against tissue transglutaminase (anti-tTG) to detect untreated coeliac disease in children with type 1 diabetes and their siblings. Anti-tTG was measured in prospectively collected sera from 169 children at the onset of diabetes, 88 of their siblings and 96 matched control children. Coeliac disease was confirmed with a small intestinal biopsy. Coeliac disease was diagnosed in five children before diabetes onset. A further 12 children were diagnosed after diabetes onset, without any gastrointestinal symptoms, and 11 of these had anti-tTG at the onset of diabetes, with the remaining child showing seroconversion within 6 months. Hence, all the children with both diseases had anti-tTG at or before diabetes diagnosis, and the prevalence of coeliac disease was 10.1%. Moreover, 6.8% of the siblings and 3.1% of the control children had elevated levels of anti-tTG. None of the siblings reported any coeliac-related symptoms, despite being positive for anti-tTG, and coeliac disease has so far been biopsy confirmed in 4.5%. Silent coeliac disease is over-represented in children with type 1 diabetes and their siblings. All diabetes children and their siblings should be tested and followed for the presence of anti-tTG and coeliac disease. ©2014 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

  15. Specific TP53 Mutants Overrepresented in Ovarian Cancer Impact CNV, TP53 Activity, Responses to Nutlin-3a, and Cell Survival

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    Lisa K. Mullany

    2015-10-01

    Full Text Available Evolutionary Action analyses of The Cancer Gene Atlas data sets show that many specific p53 missense and gain-of-function mutations are selectively overrepresented and functional in high-grade serous ovarian cancer (HGSC. As homozygous alleles, p53 mutants are differentially associated with specific loss of heterozygosity (R273; chromosome 17; copy number variation (R175H; chromosome 9; and up-stream, cancer-related regulatory pathways. The expression of immune-related cytokines was selectively related to p53 status, showing for the first time that specific p53 mutants impact, and are related to, the immune subtype of ovarian cancer. Although the majority (31% of HGSCs exhibit loss of heterozygosity, a significant number (24% maintain a wild-type (WT allele and represent another HGSC subtype that is not well defined. Using human and mouse cell lines, we show that specific p53 mutants differentially alter endogenous WT p53 activity; target gene expression; and responses to nutlin-3a, a small molecular that activates WT p53 leading to apoptosis, providing “proof of principle” that ovarian cancer cells expressing WT and mutant alleles represent a distinct ovarian cancer subtype. We also show that siRNA knock down of endogenous p53 in cells expressing homozygous mutant alleles causes apoptosis, whereas cells expressing WT p53 (or are heterozygous for WT and mutant p53 alleles are highly resistant. Therefore, despite different gene regulatory pathways associated with specific p53 mutants, silencing mutant p53 might be a suitable, powerful, global strategy for blocking ovarian cancer growth in those tumors that rely on mutant p53 functions for survival. Knowing p53 mutational status in HGSC should permit new strategies tailored to control this disease.

  16. Genome-wide upstream motif analysis of Cryptosporidium parvum genes clustered by expression profile.

    Science.gov (United States)

    Oberstaller, Jenna; Joseph, Sandeep J; Kissinger, Jessica C

    2013-07-29

    There are very few molecular genetic tools available to study the apicomplexan parasite Cryptosporidium parvum. The organism is not amenable to continuous in vitro cultivation or transfection, and purification of intracellular developmental stages in sufficient numbers for most downstream molecular applications is difficult and expensive since animal hosts are required. As such, very little is known about gene regulation in C. parvum. We have clustered whole-genome gene expression profiles generated from a previous study of seven post-infection time points of 3,281 genes to identify genes that show similar expression patterns throughout the first 72 hours of in vitro epithelial cell culture. We used the algorithms MEME, AlignACE and FIRE to identify conserved, overrepresented DNA motifs in the upstream promoter region of genes with similar expression profiles. The most overrepresented motifs were E2F (5'-TGGCGCCA-3'); G-box (5'-G.GGGG-3'); a well-documented ApiAP2 binding motif (5'-TGCAT-3'), and an unknown motif (5'-[A/C] AACTA-3'). We generated a recombinant C. parvum DNA-binding protein domain from a putative ApiAP2 transcription factor [CryptoDB: cgd8_810] and determined its binding specificity using protein-binding microarrays. We demonstrate that cgd8_810 can putatively bind the overrepresented G-box motif, implicating this ApiAP2 in the regulation of many gene clusters. Several DNA motifs were identified in the upstream sequences of gene clusters that might serve as potential cis-regulatory elements. These motifs, in concert with protein DNA binding site data, establish for the first time the beginnings of a global C. parvum gene regulatory map that will contribute to our understanding of the development of this zoonotic parasite.

  17. Upstream regulation of mycotoxin biosynthesis.

    Science.gov (United States)

    Alkhayyat, Fahad; Yu, Jae-Hyuk

    2014-01-01

    Mycotoxins are natural contaminants of food and feed products, posing a substantial health risk to humans and animals throughout the world. A plethora of filamentous fungi has been identified as mycotoxin producers and most of these fungal species belong to the genera Aspergillus, Fusarium, and Penicillium. A number of studies have been conducted to better understand the molecular mechanisms of biosynthesis of key mycotoxins and the regulatory cascades controlling toxigenesis. In many cases, the mycotoxin biosynthetic genes are clustered and regulated by one or more pathway-specific transcription factor(s). In addition, as biosynthesis of many secondary metabolites is coordinated with fungal growth and development, there are a number of upstream regulators affecting biosynthesis of mycotoxins in fungi. This review presents a concise summary of the regulation of mycotoxin biosynthesis, focusing on the roles of the upstream regulatory elements governing biosynthesis of aflatoxin and sterigmatocystin in Aspergillus.

  18. Upstream and Downstream Influence in STBLI Instability

    Science.gov (United States)

    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.

  19. The LHCb Upstream Tracker Project

    CERN Document Server

    Steinkamp, Olaf

    2015-01-01

    The LHCb detector performs searches for New Physics in CP-violating observables and rare heavy-quark decays at the LHC. A comprehensive upgrade is planned for the long shutdown of the LHC in 2018/19. A goal of this upgrade is to abolish hardware triggers and read out the full detector at 40 MHz. This requires to replace the existing TT station upstream of the LHCb magnet by a new silicon micro-strip detector, the Upstream Tracker (UT). The UT will have a new front-end chip compatible with 40 MHz readout, silicon sensors with improved radiation hardness, finer readout granularity, and improved acceptance coverage at small polar angles. The outer region of each detection layer will be covered by p-in-n sensors with 10 cm long strips and a pitch of about 180 mum, while n-in-p sensors with half the pitch and strip length will be employed in the regions of highest particle density close to the beam pipe. The innermost sensors will have a circular cutout to optimize the forward acceptance. The front-end chip is bei...

  20. Geosynchronous magnetopause crossings: upstream conditions

    CERN Document Server

    Suvorova, A; Chao, J -K; Thomsen, M; Yang, Y -H

    2011-01-01

    The experimental data on GOES magnetic measurements and plasma measurements on LANL geosynchronous satellites is used for selection of 169 case events containing 638 geosynchronous magnetopause crossings (GMCs) in 1995 to 2001. We study the necessary conditions for the geosynchronous magnetopause crossings using scatter plot of the GMCs in the coordinate space of Psw versus Bz. In such representation the upstream solar wind conditions demonstrate sharp envelope boundary under which no GMCs are occurred. The boundary has two strait horizontal branches where Bz does not influence on the magnetopause location. The first branch is located in the range of Psw=21 nPa for large positive Bz and is associated with an asymptotic regime of the pressure balance. The second branch asymptotically approaches to the range of Psw=4.8 nPa under very strong negative Bz and it is associated with a regime of the Bz influence saturation. We suggest that the saturation is caused by relatively high contribution of the magnetosphere ...

  1. Inventories and upstream gasoline price dynamics

    NARCIS (Netherlands)

    Kuper, Gerard H.

    2012-01-01

    This paper sheds new light on the asymmetric dynamics in upstream U.S. gasoline prices. The model is based on Pindyck's inventory model of commodity price dynamics. We show that asymmetry in gasoline price dynamics is caused by changes in the net marginal convenience yield: higher costs of marketing

  2. GONOME: measuring correlations between GO terms and genomic positions

    Directory of Open Access Journals (Sweden)

    Bailey Timothy L

    2006-02-01

    Full Text Available Abstract Background: Current methods to find significantly under- and over-represented gene ontology (GO terms in a set of genes consider the genes as equally probable "balls in a bag", as may be appropriate for transcripts in micro-array data. However, due to the varying length of genes and intergenic regions, that approach is inappropriate for deciding if any GO terms are correlated with a set of genomic positions. Results: We present an algorithm – GONOME – that can determine which GO terms are significantly associated with a set of genomic positions given a genome annotated with (at least the starts and ends of genes. We show that certain GO terms may appear to be significantly associated with a set of randomly chosen positions in the human genome if gene lengths are not considered, and that these same terms have been reported as significantly over-represented in a number of recent papers. This apparent over-representation disappears when gene lengths are considered, as GONOME does. For example, we show that, when gene length is taken into account, the term "development" is not significantly enriched in genes associated with human CpG islands, in contradiction to a previous report. We further demonstrate the efficacy of GONOME by showing that occurrences of the proteosome-associated control element (PACE upstream activating sequence in the S. cerevisiae genome associate significantly to appropriate GO terms. An extension of this approach yields a whole-genome motif discovery algorithm that allows identification of many other promoter sequences linked to different types of genes, including a large group of previously unknown motifs significantly associated with the terms 'translation' and 'translational elongation'. Conclusion: GONOME is an algorithm that correctly extracts over-represented GO terms from a set of genomic positions. By explicitly considering gene size, GONOME avoids a systematic bias toward GO terms linked to large genes

  3. Upstream waves and particles /Tutorial Lecture/

    Science.gov (United States)

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

    1983-02-01

    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.

  4. Mitigating Noise for the HFC Upstream Channel

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Provides the methods to mitigate noise for the upstream channel over HFC networks. We first briefly discuss the HFC network topology, then we describe the sources of noise, the mechanism to form noise, the characteristics of their spectrum, etc. In light of the mechanism to form noise and the characteristics of their spectrum, many methods are put forward in this paper. These methods are evaluated with implementation.

  5. Acyclic identification of aptamers for human alpha-thrombin using over-represented libraries and deep sequencing.

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    Gillian V Kupakuwana

    Full Text Available BACKGROUND: Aptamers are oligonucleotides that bind proteins and other targets with high affinity and selectivity. Twenty years ago elements of natural selection were adapted to in vitro selection in order to distinguish aptamers among randomized sequence libraries. The primary bottleneck in traditional aptamer discovery is multiple cycles of in vitro evolution. METHODOLOGY/PRINCIPAL FINDINGS: We show that over-representation of sequences in aptamer libraries and deep sequencing enables acyclic identification of aptamers. We demonstrated this by isolating a known family of aptamers for human α-thrombin. Aptamers were found within a library containing an average of 56,000 copies of each possible randomized 15mer segment. The high affinity sequences were counted many times above the background in 2-6 million reads. Clustering analysis of sequences with more than 10 counts distinguished two sequence motifs with candidates at high abundance. Motif I contained the previously observed consensus 15mer, Thb1 (46,000 counts, and related variants with mostly G/T substitutions; secondary analysis showed that affinity for thrombin correlated with abundance (K(d = 12 nM for Thb1. The signal-to-noise ratio for this experiment was roughly 10,000∶1 for Thb1. Motif II was unrelated to Thb1 with the leading candidate (29,000 counts being a novel aptamer against hexose sugars in the storage and elution buffers for Concanavilin A (K(d = 0.5 µM for α-methyl-mannoside; ConA was used to immobilize α-thrombin. CONCLUSIONS/SIGNIFICANCE: Over-representation together with deep sequencing can dramatically shorten the discovery process, distinguish aptamers having a wide range of affinity for the target, allow an exhaustive search of the sequence space within a simplified library, reduce the quantity of the target required, eliminate cycling artifacts, and should allow multiplexing of sequencing experiments and targets.

  6. The Netherlands Cohort Study−Meat Investigation Cohort; a population-based cohort over-represented with vegetarians, pescetarians and low meat consumers.

    Science.gov (United States)

    Gilsing, Anne M J; Weijenberg, Matty P; Goldbohm, R Alexandra; Dagnelie, Pieter C; van den Brandt, Piet A; Schouten, Leo J

    2013-11-29

    Vegetarian diets have been associated with lower risk of chronic disease, but little is known about the health effects of low meat diets and the reliability of self-reported vegetarian status. We aimed to establish an analytical cohort over-represented with vegetarians, pescetarians and 1 day/week meat consumers, and to describe their lifestyle and dietary characteristics. In addition, we were able to compare self-reported vegetarians with vegetarians whose status has been confirmed by their response on the extensive food frequency questionnaire (FFQ). Embedded within the Netherlands Cohort Study (n = 120,852; including 1150 self-reported vegetarians), the NLCS-Meat Investigation Cohort (NLCS-MIC) was defined by combining all FFQ-confirmed-vegetarians (n = 702), pescetarians (n = 394), and 1 day/week meat consumers (n = 1,396) from the total cohort with a random sample of 2-5 days/week- and 6-7 days/week meat consumers (n = 2,965 and 5,648, respectively). Vegetarians, pescetarians, and 1 day/week meat consumers had more favorable dietary intakes (e.g., higher fiber/vegetables) and lifestyle characteristics (e.g. lower smoking rates) compared to regular meat consumers in both sexes. Vegetarians adhered to their diet longer than pescetarians and 1 day/week meat consumers. 75% of vegetarians with a prevalent cancer at baseline had changed to this diet after diagnosis. 50% of self-reported vegetarians reported meat or fish consumption on the FFQ. Although the misclassification that occurred in terms of diet and lifestyle when merely relying on self-reporting was relatively small, the impact on associations with disease risk remains to be studied. We established an analytical cohort over-represented with persons at the lower end of the meat consumption spectrum which should facilitate prospective studies of major cancers and causes of death using ≥20.3 years of follow-up.

  7. Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Joshi NV

    2009-01-01

    Full Text Available Abstract Background Regulation of gene expression in Plasmodium falciparum (Pf remains poorly understood. While over half the genes are estimated to be regulated at the transcriptional level, few regulatory motifs and transcription regulators have been found. Results The study seeks to identify putative regulatory motifs in the upstream regions of 13 functional groups of genes expressed in the intraerythrocytic developmental cycle of Pf. Three motif-discovery programs were used for the purpose, and motifs were searched for only on the gene coding strand. Four motifs – the 'G-rich', the 'C-rich', the 'TGTG' and the 'CACA' motifs – were identified, and zero to all four of these occur in the 13 sets of upstream regions. The 'CACA motif' was absent in functional groups expressed during the ring to early trophozoite transition. For functional groups expressed in each transition, the motifs tended to be similar. Upstream motifs in some functional groups showed 'positional conservation' by occurring at similar positions relative to the translational start site (TLS; this increases their significance as regulatory motifs. In the ribonucleotide synthesis, mitochondrial, proteasome and organellar translation machinery genes, G-rich, C-rich, CACA and TGTG motifs, respectively, occur with striking positional conservation. In the organellar translation machinery group, G-rich motifs occur close to the TLS. The same motifs were sometimes identified for multiple functional groups; differences in location and abundance of the motifs appear to ensure different modes of action. Conclusion The identification of positionally conserved over-represented upstream motifs throws light on putative regulatory elements for transcription in Pf.

  8. The upstream tracker for the LHCb upgrade

    Energy Technology Data Exchange (ETDEWEB)

    Steinkamp, Olaf, E-mail: olafs@physik.uzh.ch

    2016-09-21

    The LHCb collaboration is planning a comprehensive upgrade of the experiment for the long shutdown of the LHC in 2019/20. As part of this upgrade, the tracking station in front of the LHCb dipole magnet will be replaced by a new planar four-layer silicon micro-strip detector with 40 MHz readout and silicon sensors with finer granularity and improved radiation hardness. Key design aspects of this new Upstream Tracker are described and a brief overview of the status of the project is given.

  9. Biodiesel byproduct bioconversion to rhamnolipids: Upstream aspects

    Directory of Open Access Journals (Sweden)

    Ana Maria Salazar-Bryam

    2017-06-01

    Full Text Available This study focused on two important aspects of the upstream process: the appropriate use of crude glycerol as a low-cost carbon source, and strain selection. The effect of different crude glycerol concentrations on rhamnolipid biosynthesis by two Pseudomonas aeruginosa strains (wild type LBI and mutant LBI 2A1 was studied. Finally, the synthesized rhamnolipids were characterized by mass spectrometry. When both strains were compared, 50 g/L was the most favorable concentration for both, but P. aeruginosa LBI 2A1 showed an increase in rhamnolipid production (2.55 g/L of 192% over wild type (1.3 g/L. The higher rhamnolipid production could be related to a possible mechanism developed after the mutation process at high antibiotic concentrations. Mass spectrometry confirmed the glycolipid nature of the produced biosurfactant, and the homologue composition showed a wide mixture of mono and di-rhamnolipids. These results show that high glycerol concentrations can inhibit microbial metabolism, due to osmotic stress, leading to a better understanding of glycerol metabolism towards its optimization in fermentation media. Since P. aeruginosa LBI 2A1 showed higher conversion yields than P. aeruginosa LBI, the use of a mutant strain associated with a low cost carbon source might improve biosurfactant biosynthesis, therefore yielding an important upstream improvement.

  10. Internal hydraulic jumps with large upstream shear

    Science.gov (United States)

    Ogden, Kelly; Helfrich, Karl

    2015-11-01

    Internal hydraulic jumps in approximately two-layered flows with large upstream shear are investigated using numerical simulations. The simulations allow continuous density and velocity profiles, and a jump is forced to develop by downstream topography, similar to the experiments conducted by Wilkinson and Wood (1971). High shear jumps are found to exhibit significantly more entrainment than low shear jumps. Furthermore, the downstream structure of the flow has an important effect on the jump properties. Jumps with a slow upper (inactive) layer exhibit a velocity minimum downstream of the jump, resulting in a sub-critical downstream state, while flows with the same upstream vertical shear and a larger barotropic velocity remain super-critical downstream of the jump. A two-layer theory is modified to account for the vertical structure of the downstream density and velocity profiles and entrainment is allowed through a modification of the approach of Holland et al. (2002). The resulting theory can be matched reasonably well with the numerical simulations. However, the results are very sensitive to how the downstream vertical profiles of velocity and density are incorporated into the layered model, highlighting the difficulty of the two layer approximation when the shear is large.

  11. Upstream pipelines : inspection, corrosion and integrity management

    Energy Technology Data Exchange (ETDEWEB)

    Paez, J.; Stephenson, M. [Talisman Energy Inc., Calgary, AB (Canada)] (comps.)

    2009-07-01

    Accurate inspection techniques are needed to ensure the integrity of pipelines. This working group discussed methods of reducing pipeline failures for a variety of pipes. A summary of recent pipeline performance statistics was presented, as well as details of third party damage and fiberglass pipe failures. A batch inhibitor joint industry project was described. The session demonstrated that integrity program need to be developed at the field-level as well as at the upper management level. Fiberglass pipeline failures are significant problem for pipeline operators. Corrosion monitoring, pigging and specific budgets are needed in order to ensure the successful management of pipeline integrity. New software developed to predict pipeline corrosion rates was discussed, and methods of determining mole fractions and flow regimes were presented. The sessions included updates from regulators and standards agencies as well as discussions of best practices, regulations, codes and standards related to pipeline integrity. The working group was divided into 4 sessions: (1) updates since 2007 with input from the Canadian Association of Petroleum Producers (CAPP) and the Upstream Pipeline Integrity Management Association (UPIMA); (2) integrity of non-metallic pipelines; (3) upstream pipeline integrity issues; and (4) hot topics. tabs., figs.

  12. The Netherlands Cohort Study – Meat Investigation Cohort; a population-based cohort over-represented with vegetarians, pescetarians and low meat consumers

    Science.gov (United States)

    2013-01-01

    Background Vegetarian diets have been associated with lower risk of chronic disease, but little is known about the health effects of low meat diets and the reliability of self-reported vegetarian status. We aimed to establish an analytical cohort over-represented with vegetarians, pescetarians and 1 day/week meat consumers, and to describe their lifestyle and dietary characteristics. In addition, we were able to compare self-reported vegetarians with vegetarians whose status has been confirmed by their response on the extensive food frequency questionnaire (FFQ). Study methods Embedded within the Netherlands Cohort Study (n = 120,852; including 1150 self-reported vegetarians), the NLCS-Meat Investigation Cohort (NLCS-MIC) was defined by combining all FFQ-confirmed-vegetarians (n = 702), pescetarians (n = 394), and 1 day/week meat consumers (n = 1,396) from the total cohort with a random sample of 2–5 days/week- and 6–7 days/week meat consumers (n = 2,965 and 5,648, respectively). Results Vegetarians, pescetarians, and 1 day/week meat consumers had more favorable dietary intakes (e.g. higher fiber/vegetables) and lifestyle characteristics (e.g. lower smoking rates) compared to regular meat consumers in both sexes. Vegetarians adhered to their diet longer than pescetarians and 1 day/week meat consumers. 75% of vegetarians with a prevalent cancer at baseline had changed to this diet after diagnosis. 50% of self-reported vegetarians reported meat or fish consumption on the FFQ. Although the misclassification that occurred in terms of diet and lifestyle when merely relying on self-reporting was relatively small, the impact on associations with disease risk remains to be studied. Conclusion We established an analytical cohort over-represented with persons at the lower end of the meat consumption spectrum which should facilitate prospective studies of major cancers and causes of death using ≥20.3 years of follow-up. PMID:24289207

  13. Moving stormwater P management upstream (Invited)

    Science.gov (United States)

    Baker, L. A.; Hobbie, S. E.; Finlay, J. C.; Kalinosky, P.; Janke, B.

    2013-12-01

    Reducing stormwater phosphorus loading using current approaches, which focus on treatment at the end of the pipe, is unlikely to reduce P loads enough to restore nutrient-impaired urban lakes. An indication of this is that of the nearly 150 nutrient impaired lakes in the Twin Cities region, only one has been restored. We hypothesize that substantial reduction of eutrophication will require reductions of P inputs upstream from storm drains. Developing source reduction strategies will required a shift in thinking about system boundaries, moving upstream from the storm drain to the curb, and from the curb to the watershed. Our Prior Lake Street Sweeping Project, a 2-year study of enhanced street sweeping, will be used to illustrate the idea of moving the system boundary to the curb. This study showed that P load recovery from sweeping increases with both sweeping frequency and overhead tree canopy cover. For high canopy streets, coarse organic material (tree leaves; seed pods, etc.) comprised 42% of swept material. We estimate that P inputs from trees may be half of measured storm P yields in 8 urban catchments in St. Paul, MN. Moreover, the cost of removing P during autumn was often 1000/lb P for stormwater ponds. We can also move further upstream, to the watershed boundary. P inputs to urban watersheds that enter lawns include lawn fertilizer, polyphosphates added to water supplies (and hence to lawns via irrigation), and pet food (transformed to pet waste). Minnesota enacted a lawn P fertilizer restriction in 2003, but early reductions in stormwater P loads were modest, probably reflecting reduction in direct wash-off of applied fertilizer. Because urban soils are enriched in P, growing turf has continued to extract available soil P. When turf is mowed, cut grass decomposes, generating P in runoff. As soil P becomes depleted, P concentrations in lawn runoff will gradually decline. Preliminary modeling suggests that substantial reductions in P export from lawns may

  14. Upstream from OPERA: extreme attention to detail

    CERN Multimedia

    CERN Bulletin

    2011-01-01

    Two weeks ago, at a seminar held at CERN, the OPERA collaboration revealed their astonishing observation: neutrinos might move faster than light. The finding is currently under scrutiny in the scientific community. While the result downstream at Gran Sasso speaks for itself, upstream at CERN things are no less intriguing, with high-tech GPS systems, novel techniques for accurately measuring the time, and unique ways keeping the initial particle beam stable. Take away one ingredient and the accuracy needed for the final measurement is spoiled.   Underground installations of the CERN Neutrinos to Gran Sasso (CNGS) project. First ingredient: a stable beam CERN produces neutrinos by sending a beam of protons to hit a target. The collisions produce a secondary beam, which mostly consists of pions and kaons that decay in flight within an evacuated tunnel. Their decay products are muons and muon-neutrinos. An absorber stops the pions and kaons that do not decay, while the resulting muons are absorb...

  15. Partial Crosstalk Cancellation for Upstream VDSL

    Directory of Open Access Journals (Sweden)

    Raphael Cendrillon

    2004-09-01

    Full Text Available Crosstalk is a major problem in modern DSL systems such as VDSL. Many crosstalk cancellation techniques have been proposed to help mitigate crosstalk, but whilst they lead to impressive performance gains, their complexity grows with the square of the number of lines within a binder. In binder groups which can carry up to hundreds of lines, this complexity is outside the scope of current implementation. In this paper, we investigate partial crosstalk cancellation for upstream VDSL. The majority of the detrimental effects of crosstalk are typically limited to a small subset of lines and tones. Furthermore, significant crosstalk is often only seen from neighbouring pairs within the binder configuration. We present a number of algorithms which exploit these properties to reduce the complexity of crosstalk cancellation. These algorithms are shown to achieve the majority of the performance gains of full crosstalk cancellation with significantly reduced run-time complexity.

  16. DOWNSTREAM ECOCIDE FROM UPSTREAM WATER PIRACY

    Directory of Open Access Journals (Sweden)

    Miah Muhammad Adel

    2012-01-01

    Full Text Available Upstream India and downstream Bangladesh share more than 50 international rivers. India has set up water diversion constructions in more than 50% of these rivers, the largest one being on the Bangladesh’s northwest upon the Ganges River, puts Bangladesh’s Gangetic ecosystem at stake. In some border rivers, India has set up groins on her side of river banks. Also, Indian side pumps Bangladesh river water stealthily from border-rivers. Further, India is constructing another dam and reservoir upstream on the Barak River on the northeast of Bangladesh. Furthermore, India has chalked out a grand plan for river networking. Exploration has been made to assess the degree of the ecosystem degradation both inland and on the coast due to all water diversion constructions around the border, except for the Tipaimukh Dam in which case estimation of projected ecosystem degradation has been mentioned. Finally, Indian grand plan of river networking plan has been briefly touched upon. Site visitations, observations, surveys, measurements and interviews of professionals were made in the project country. Relevant literatures on this issue were reviewed in electronic and print databases. Related published articles in electronic and print media were systematically searched following the key words for the case. Finally, both electronic and print news media have been closely followed to know the latest developments on this issue. The reduced flow of the Ganges in Bangladesh has caused scarcity of fresh water, species endangerment and extinction, obstruction to livestock raising, loss of livelihoods, people’s displacement, changes in crop production, reduction in navigable routes, extreme weather, increased flood occurrences, scarcity of potable water, groundwater contamination, reduction in coastal sediment deposition, deterioration of the Ganges water quality and inland intrusion of saline water front. Water diversion constructions in other rivers have

  17. Computational identification of conserved transcription factor binding sites upstream of genes induced in rat brain by transient focal ischemic stroke.

    Science.gov (United States)

    Pulliam, John V K; Xu, Zhenfeng; Ford, Gregory D; Liu, Cuimei; Li, Yonggang; Stovall, Kyndra C; Cannon, Virginetta S; Tewolde, Teclemichael; Moreno, Carlos S; Ford, Byron D

    2013-02-07

    Microarray analysis has been used to understand how gene regulation plays a critical role in neuronal injury, survival and repair following ischemic stroke. To identify the transcriptional regulatory elements responsible for ischemia-induced gene expression, we examined gene expression profiles of rat brains following focal ischemia and performed computational analysis of consensus transcription factor binding sites (TFBS) in the genes of the dataset. In this study, rats were sacrificed 24 h after middle cerebral artery occlusion (MCAO) stroke and gene transcription in brain tissues following ischemia/reperfusion was examined using Affymetrix GeneChip technology. The CONserved transcription FACtor binding site (CONFAC) software package was used to identify over-represented TFBS in the upstream promoter regions of ischemia-induced genes compared to control datasets. CONFAC identified 12 TFBS that were statistically over-represented from our dataset of ischemia-induced genes, including three members of the Ets-1 family of transcription factors (TFs). Microarray results showed that mRNA for Ets-1 was increased following tMCAO but not pMCAO. Immunohistochemical analysis of Ets-1 protein in rat brains following MCAO showed that Ets-1 was highly expressed in neurons in the brain of sham control animals. Ets-1 protein expression was virtually abolished in injured neurons of the ischemic brain but was unchanged in peri-infarct brain areas. These data indicate that TFs, including Ets-1, may influence neuronal injury following ischemia. These findings could provide important insights into the mechanisms that lead to brain injury and could provide avenues for the development of novel therapies. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. Spatial distribution of upstream magnetospheric ≥50 keV ions

    Directory of Open Access Journals (Sweden)

    G. Kaliabetsos

    Full Text Available We present for the first time a statistical study of geq50 keV ion events of a magnetospheric origin upstream from Earth's bow shock. The statistical analysis of the 50-220 keV ion events observed by the IMP-8 spacecraft shows: (1 a dawn-dusk asymmetry in ion distributions, with most events and lower intensities upstream from the quasi-parallel pre-dawn side (4 LT-6 LT of the bow shock, (2 highest ion fluxes upstream from the nose/dusk side of the bow shock under an almost radial interplanetary magnetic field (IMF configuration, and (3 a positive correlation of the ion intensities with the solar wind speed and the index of geomagnetic index Kp, with an average solar wind speed as high as 620 km s-1 and values of the index Kp > 2. The statistical results are consistent with (1 preferential leakage of ~50 keV magnetospheric ions from the dusk magnetopause, (2 nearly scatter free motion of ~50 keV ions within the magnetosheath, and (3 final escape of magnetospheric ions from the quasi-parallel dawn side of the bow shock. An additional statistical analysis of higher energy (290-500 keV upstream ion events also shows a dawn-dusk asymmetry in the occurrence frequency of these events, with the occurrence frequency ranging between ~16%-~34% in the upstream region.Key words. Interplanetary physics (energetic particles; planetary bow shocks

  19. CD19(+) CD20(-) CD27(hi) IL-s10-producing B cells are overrepresented in R-CHOP-treated DLBCL patients in complete remission.

    Science.gov (United States)

    Qiu, Huiying; Li, Junguo; Feng, Zhenjun; Yuan, Joanna; Lu, Jie; Hu, Xiaoxia; Gao, Lei; Lv, Shuqing; Yang, Jianmin; Chen, Lei

    2016-09-01

    Treatment of diffuse large B cell lymphoma (DLBCL) with rituximab, an anti-CD20 monoclonal antibody, has resulted in significantly improved patient responses with longer event-free intervals and higher overall survival rates. However, since rituximab depletes all CD20-expressing cells, including noncancerous B cells, the effects of rituximab on the normal immunity of DLBCL patients under remission need to be examined. Here, we observed that DLBCL patients under remission contained significantly lower frequencies of total B cells, with a significantly overrepresented interleukin (IL)-10-producing B cell (B10) population in the peripheral blood. Further examination confirmed that a large fraction of B10 cells was CD20(-) CD27(hi) plasmablasts, possibly explaining the persistence of B10 cells after R-CHOP treatment. We also observed that the percentage of B10 cells in DLBCL patients in remission gradually reduced during the first year of achieving complete remission, primarily due to the replenishment of non-B10 B cells. Despite this, the percentage of B10 cells in DLBCL patients after 1 year of achieving complete remission was still higher than that in controls. CD4(+) and CD8(+) T cells cocultured with B10-enriched B cells secreted significantly lower levels of proinflammatory cytokines IFN-g and TNF-a, compared to those incubated with B10-depleted B cells. Together, our data observed a long-lasting overrepresentation of B10 cells in DLBCL patients under remission. Whether this change could impact on the overall anti-tumor immunity during remission requires further studies.

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

    Science.gov (United States)

    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.

  1. Characteristics of upstream energetic (E>=50keV) ion events during intense geomagnetic activity

    Science.gov (United States)

    Anagnostopoulos, G. C.; Rigas, A. G.; Sarris, E. T.; Krimigis, S. M.

    1998-05-01

    In this work we examine the statistical presence of some important features of upstream energetic (>=50 keV) ion events under some special conditions in the upstream region and the magnetosphere. The 125 ion events considered in the statistic were observed by the IMP 7 and IMP 8 spacecraft, at ~35RE from the Earth, during nine long time intervals of a total of 153 hours. The time intervals analyzed were selected under the following restrictions: existence of high proton flux (i.e., >=900 pcm-2s-1sr-1) and of a great number of events (an occurrence frequency of ~10 events per 12 hours in the whole statistics) in the energy range 50-220 keV. The most striking findings are the following: (1) The upstream events were observed during times with high values of the geomagnetic activity index Kp(>=3-) (2) all of the upstream events (100%) have energy spectra extending up to energies E>=290keV (3) 86% of these events are accompanied by relativistic (E>=220keV) electrons; and (4) the majority of the upstream ion events (82%) showed noninverse velocity dispersion during their onset phase (22% of the events showed forward velocity dispersion, and 60% showed no velocity dispersion at all when 5.5-min averaged observations were analyzed). Further statistical analysis of this sample of upstream particle events shows that the 50- to 220-keV proton flux shows a positive correlation with the following parameters: the Kp index of geomagnetic activity and the flux of the high-energy (290-500 keV) protons and (>=220 keV) electrons. More specific findings are the following: (1) The spectral index γ for a power law distribution of ions detected by the National Oceanic and Atmospheric Administration Energetic Particle Experiment (EPE) instrument (50=220-keV electrons increases with the time duration of upstream events. We infer that the vast majority of the upstream ion events considered in this study (under conditions of intense particle activity in the upstream region and enhanced

  2. Study of prototype sensors for the Upstream Tracker Upgrade

    CERN Document Server

    Abba, Andrea; Blusk, Steven R.; Bursche, Albert; Davis, Adam; Dendek, Adam Mateusz; Dey, Biplab; Ely, Scott Edward; Forshaw, Dean Charles; Fu, Jinlin; Kelsey, Matthew Jordan; Lionetto, Federica; Manning Jr, Peter Michael; Mountain, Ray; Neri, Nicola; Papula, Alana Leigh; Petruzzo, Marco; Pikies, Malgorzata Maria; Rudolph, Matthew Scott; Sokoloff, Michael David; Stone, Sheldon; Szumlak, Tomasz; Wang, Jianchun

    2016-01-01

    Three testbeams were carried out in 2015 to test the performance of prototype sensors for the Upstream Tracker. Two of the testbeams were devoted to studying full size n-in-p sensors, and one was devoted to testing mini-sensors, all from Hamamatsu. Results on the performance of these Upstream Tracker sensor prototypes are presented.

  3. Willingness of upstream and downstream resource managers to engage in compensation schemes for environmental services

    Directory of Open Access Journals (Sweden)

    Chapika Sangkapitux

    2009-04-01

    Full Text Available Providing compensation for agricultural conservation practices adopted by upstream farmers is still an alien concept in the Thai political context. The governance of common-pool natural resources, such as forest and water, has traditionally been under the control of powerful government line agencies, while the contribution of local communities to natural resource conservation have been hardly recognized by policy-makers. Drawing on a case study in Mae Sa watershed, Chiang Mai province, northern Thailand, this paper discusses the potential of developing compensation schemes in a socio-political context where upland farmers – mostly belonging to ethnic minority groups – tend to be considered a threat to the natural resource base rather than providers of environmental services. Based on data obtained from 371 households in the upstream communities and 151 households in the downstream communities of the watershed, upstream resource managers’ willingness to accept compensation for the conservation measures and downstream resource managers’ willingness to pay for water resource improvements were estimated through the use of choice experiments. Results from the study suggest that downstream resource managers would be willing to provide on average nearly 1% of their annual income for a substantial improvement of the quantity and quality of water resources, which could be achieved by compensating upstream farmers’ change of their agricultural systems towards more environment-friendly practices. Both willingness to pay of downstream respondents and willingness of upstream resource managers to accept compensation were positively correlated with age, education, participation in environmental conservation activities and previous experiences with droughts and/or erosion. The paper concludes that there is a clear potential for establishing compensation schemes for provision of environmental services in northern Thai watersheds. The important policy

  4. Upstream petroleum industry flaring and venting report : industry performance for year ending December 31, 2008

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2009-06-15

    The Energy Resources Conservation Board (ERCB) has developed recommendations for a flaring and venting management framework for the province of Alberta. This report fulfilled the ERCB's information mandate regarding flaring and venting as part of a commitment made in Directive 060 for upstream petroleum industry flaring, incineration, and venting to make flaring and venting data more accessible. It included data on upstream petroleum industry flaring and venting with particular reference to solution gas conserved, flared and vented, from 1996 to 2008; solution gas flaring and venting performance; flaring from all upstream oil and gas sources, from 2000 to 2008; venting from all upstream oil and gas sources, from 2000 to 2008; solution gas flaring and venting maps; and solution gas emissions ranking of operators for 2007. The report also provided a summary of flaring and venting from various oil and gas industry sources, such as well tests, gas plants, gas gathering systems, transmission lines, and batteries. Ranking of companies was established based on solution gas flared plus vented; solution gas flared; and solution gas vented from crude oil and bitumen batteries. The data used in the preparation of this report was submitted by companies. The report revealed that considerable progress has been made in the reduction of flaring and venting volumes for all upstream oil and gas sources. The reduction can be attributed to the decline in new conventional oil production. It can also be correlated to the decline in volumes of solution gas formerly being flared, and now being vented. Solution gas vented in 2008 was 40.7 per cent less than the 2000 venting baseline. However, in 2008, there was a 25.9 per cent increase in venting from crude bitumen batteries which can be correlated to the increase in crude bitumen production. The ERCB is continuing to work with the Clean Air Strategic Alliance to examine options to further address solution gas venting. tabs., figs.

  5. Reattachment heating upstream of short compression ramps in hypersonic flow

    Science.gov (United States)

    Estruch-Samper, David

    2016-05-01

    Hypersonic shock-wave/boundary-layer interactions with separation induce unsteady thermal loads of particularly high intensity in flow reattachment regions. Building on earlier semi-empirical correlations, the maximum heat transfer rates upstream of short compression ramp obstacles of angles 15° ⩽ θ ⩽ 135° are here discretised based on time-dependent experimental measurements to develop insight into their transient nature (Me = 8.2-12.3, Re_h= 0.17× 105-0.47× 105). Interactions with an incoming laminar boundary layer experience transition at separation, with heat transfer oscillating between laminar and turbulent levels exceeding slightly those in fully turbulent interactions. Peak heat transfer rates are strongly influenced by the stagnation of the flow upon reattachment close ahead of obstacles and increase with ramp angle all the way up to θ =135°, whereby rates well over two orders of magnitude above the undisturbed laminar levels are intermittently measured (q'_max>10^2q_{u,L}). Bearing in mind the varying degrees of strength in the competing effect between the inviscid and viscous terms—namely the square of the hypersonic similarity parameter (Mθ )^2 for strong interactions and the viscous interaction parameter bar{χ } (primarily a function of Re and M)—the two physical factors that appear to most globally encompass the effects of peak heating for blunt ramps (θ ⩾ 45°) are deflection angle and stagnation heat transfer, so that this may be fundamentally expressed as q'_max∝ {q_{o,2D}} θ ^2 with further parameters in turn influencing the interaction to a lesser extent. The dominant effect of deflection angle is restricted to short obstacle heights, where the rapid expansion at the top edge of the obstacle influences the relaxation region just downstream of reattachment and leads to an upstream displacement of the separation front. The extreme heating rates result from the strengthening of the reattaching shear layer with the increase in

  6. Experimental Investigation of Upstream Boundary Layer Acceleration on Unsteadiness of Shock-Induced Separation

    Science.gov (United States)

    2007-11-02

    part of the upstream boundary layer and the shock foot motion. Furthermore, their measurements confirmed the observation that there is no correlation...The “dot card” target is composed of equally spaced dots and a single cross in the lower part of the image (an example image is shown in Fig. 9...University of Tokyo, Hongo Bunkyo-ku, Tokyo 113, Japan, Oct. 25-29, 1987. 12 Figure 1. Schematic diagram of the test section with compression

  7. Correction of upstream flow and hydraulic state with data assimilation in the context of flood forecasting

    Directory of Open Access Journals (Sweden)

    S. Ricci

    2011-11-01

    Full Text Available The present study describes the assimilation of river water level observations and the resulting improvement in flood forecasting. The Kalman Filter algorithm was built on top of a one-dimensional hydraulic model which describes the Saint-Venant equations. The assimilation algorithm folds in two steps: the first one was based on the assumption that the upstream flow can be adjusted using a three-parameter correction; the second one consisted of directly correcting the hydraulic state. This procedure was applied using a four-day sliding window over the flood event. The background error covariances for water level and discharge were represented with anisotropic correlation functions where the correlation length upstream of the observation points is larger than the correlation length downstream of the observation points. This approach was motivated by the implementation of a Kalman Filter algorithm on top of a diffusive flood wave propagation model. The study was carried out on the Adour and the Marne Vallage (France catchments. The correction of the upstream flow as well as the control of the hydraulic state during the flood event leads to a significant improvement in the water level and discharge in both analysis and forecast modes.

  8. Working group 3: upstream pipelines: inspection, corrosion and integrity management

    Energy Technology Data Exchange (ETDEWEB)

    Paez, Jorge; Stephenson, Mark [Talisman Energy, (Canada)

    2011-07-01

    The third topic investigated the latest challenges to upstream pipeline operation and the areas for improvement in upstream integrity in the pipeline industry. The first session of talks reported on the pipeline incident analysis conducted by the CAPP on several companies from 2006 to 2010 in order to identify best management practises and to drive improvement in pipeline integrity management. Reviews of primary failure statistics and failure frequency were conducted with respect to the various materials of pipes. A summary of changes to the CSA standard related to non-metallic pipes was also presented to complete this background overview of the upstream industry. The second session provided more information about these non-metallic pipes, focusing on construction and quality issues with large diameter HDPE pipelines. The third session discussed the ERW pipeline in relation to upstream industry. An integrity management panel discussion was carried out to close this third working group.

  9. Emergence of upstream swimming via a hydrodynamic transition.

    Science.gov (United States)

    Tung, Chih-Kuan; Ardon, Florencia; Roy, Anubhab; Koch, Donald L; Suarez, Susan S; Wu, Mingming

    2015-03-13

    We demonstrate that upstream swimming of sperm emerges via an orientation disorder-order transition. The order parameter, the average orientation of the sperm head against the flow, follows a 0.5 power law with the deviation from the critical flow shear rate (γ-γ_{c}). This transition is successfully explained by a hydrodynamic bifurcation theory, which extends the sperm upstream swimming to a broad class of near surface microswimmers that possess front-back asymmetry and circular motion.

  10. Attractiveness of the brazilian petroleum and gas industries upstream; Atratividade do upstream da industria de petroleo e gas brasileiros

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Edmar Fagundes de; Araujo, Leandro dos Reis

    2007-07-01

    This article performs an analysis on the upstream attractiveness of the Brazilian petroleum and gas industries, in accordance with the following parameters: the country risks, the sector risk, the country geologic potential, the government take, and the market potential.

  11. Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes

    Directory of Open Access Journals (Sweden)

    Kohane Isaac

    2005-11-01

    Full Text Available Abstract Background Recent advances in genome sequencing suggest a remarkable conservation in gene content of mammalian organisms. The similarity in gene repertoire present in different organisms has increased interest in studying regulatory mechanisms of gene expression aimed at elucidating the differences in phenotypes. In particular, a proximal promoter region contains a large number of regulatory elements that control the expression of its downstream gene. Although many studies have focused on identification of these elements, a broader picture on the complexity of transcriptional regulation of different biological processes has not been addressed in mammals. The regulatory complexity may strongly correlate with gene function, as different evolutionary forces must act on the regulatory systems under different biological conditions. We investigate this hypothesis by comparing the conservation of promoters upstream of genes classified in different functional categories. Results By conducting a rank correlation analysis between functional annotation and upstream sequence alignment scores obtained by human-mouse and human-dog comparison, we found a significantly greater conservation of the upstream sequence of genes involved in development, cell communication, neural functions and signaling processes than those involved in more basic processes shared with unicellular organisms such as metabolism and ribosomal function. This observation persists after controlling for G+C content. Considering conservation as a functional signature, we hypothesize a higher density of cis-regulatory elements upstream of genes participating in complex and adaptive processes. Conclusion We identified a class of functions that are associated with either high or low promoter conservation in mammals. We detected a significant tendency that points to complex and adaptive processes were associated with higher promoter conservation, despite the fact that they have emerged

  12. A polymorphic variant in the human electron transfer flavoprotein alpha-chain (alpha-T171) displays decreased thermal stability and is overrepresented in very-long-chain acyl-CoA dehydrogenase-deficient patients with mild childhood presentation

    DEFF Research Database (Denmark)

    Bross, P; Pedersen, P; Nyholm, M;

    1999-01-01

    The consequences of two amino acid polymorphisms of human electron transfer flavoprotein (alpha-T/I171 in the alpha-subunit and beta-M/T154 in the beta-subunit) on the thermal stability of the enzyme are described. The alpha-T171 variant displayed a significantly decreased thermal stability...... thermal stability) was significantly overrepresented. Subgrouping of the VLCAD patients into three phenotypic classes (severe childhood, mild childhood, and adult presentation) revealed that the overrepresentation of the alpha-T171 variant was significant only in patients with mild childhood presentation...

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Naoki Masuda

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  16. Emergence of upstream swimming through a hydrodynamic transition

    Science.gov (United States)

    Tung, Chih-kuan; Ardon, Florencia; Roy, Anubhab; Koch, Donald L.; Suarez, Susan S.; Wu, Mingming

    2015-01-01

    We demonstrate that upstream swimming of sperm emerges via an orientation disorder-order transition. The order parameter, the average orientation of the sperm head against the flow, follows a 0.5 power law with the deviation from the critical flow shear rate (γ − γc). This transition is successfully explained by a hydrodynamic bifurcation theory, which extends the sperm upstream swimming to a broad class of near surface micro-swimmers that possess front-back asymmetry and circular motion. PMID:25815969

  17. Exploring Social Learning through Upstream Engagement in Science and Technology

    DEFF Research Database (Denmark)

    Mortensen, Jonas Egmose

    This discussion paper deliberates on how the concept of social learning can be used for evaluating upstream engagement initiatives in science and technology.  The paper briefly introduces to the concept of upstream engagement and a concrete case, the UK Citizen Science for Sustainability project...... (SuScit), as an outset for discussing how the concept of social learning can be used for analysing and understanding relations between citizen participation, Science and research, and sustainability. A number of relevant research questions and methodological considerations are distilled...

  18. Transition duct with divided upstream and downstream portions

    Energy Technology Data Exchange (ETDEWEB)

    McMahan, Kevin Weston; LeBegue, Jeffrey Scott; Maldonado, Jaime Javier; Dillard, Daniel Jackson; Flanagan, James Scott

    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 the upstream portion and the downstream portion.

  19. MAGNETIC VARIANCES AND PITCH-ANGLE SCATTERING TIMES UPSTREAM OF INTERPLANETARY SHOCKS

    Energy Technology Data Exchange (ETDEWEB)

    Perri, Silvia; Zimbardo, Gaetano, E-mail: silvia.perri@fis.unical.it, E-mail: gaetano.zimbardo@fis.unical.it [Dipartimento di Fisica, Universita della Calabria, Ponte P. Bucci, Cubo 31C, I-87036 Arcavacata di Rende (Italy)

    2012-07-20

    Recent observations of power-law time profiles of energetic particles accelerated at interplanetary shocks have shown the possibility of anomalous, superdiffusive transport for energetic particles throughout the heliosphere. Those findings call for an accurate investigation of the magnetic field fluctuation properties at the resonance frequencies upstream of the shock's fronts. Normalized magnetic field variances, indeed, play a crucial role in the determination of the pitch-angle scattering times and then of the transport regime. The present analysis investigates the time behavior of the normalized variances of the magnetic field fluctuations, measured by the Ulysses spacecraft upstream of corotating interaction region (CIR) shocks, for those events which exhibit superdiffusion for energetic electrons. We find a quasi-constant value for the normalized magnetic field variances from about 10 hr to 100 hr from the shock front. This rules out the presence of a varying diffusion coefficient and confirms the possibility of superdiffusion for energetic electrons. A statistical analysis of the scattering times obtained from the magnetic fluctuations upstream of the CIR events has also been performed; the resulting power-law distributions of scattering times imply long range correlations and weak pitch-angle scattering, and the power-law slopes are in qualitative agreement with superdiffusive processes described by a Levy random walk.

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

    Directory of Open Access Journals (Sweden)

    Feng-Yu Wang

    Full Text Available 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.

  1. Interactive Learning-driven Innovation in Upstream-Downstream Relations

    DEFF Research Database (Denmark)

    Machikita, Tomohiro; Ueki, Yasushi

    2012-01-01

    This paper presents a simple framework of the innovations that result from interfirm learning through exchanges of engineers in upstream-downstream relations within a production chain. To examine the framework, we empirically investigate the impact of mutual knowledge exchanges on product and pro...

  2. Sediment Deposition Risk Analysis and PLSR Model Research for Cascade Reservoirs Upstream of the Yellow River

    Directory of Open Access Journals (Sweden)

    Jie Yang

    2015-01-01

    Full Text Available It is difficult to effectively identify and eliminate the multiple correlation influence among the independent factors by least-squares regression. Focusing on this insufficiency, the sediment deposition risk of cascade reservoirs and fitting model of sediment flux into the reservoir are studied. The partial least-squares regression (PLSR method is adopted for modeling analysis; the model fitting is organically combined with the non-model-style data content analysis, so as to realize the regression model, data structure simplification, and multiple correlations analysis among factors; meanwhile the accuracy of the model is ensured through cross validity check. The modeling analysis of sediment flux into the cascade reservoirs of Long-Liu section upstream of the Yellow River indicates that partial least-squares regression can effectively overcome the multiple correlation influence among factors, and the isolated factor variables have better ability to explain the physical cause of measured results.

  3. Conserved-peptide upstream open reading frames (CPuORFs are associated with regulatory genes in angiosperms

    Directory of Open Access Journals (Sweden)

    Richard A Jorgensen

    2012-08-01

    Full Text Available Upstream open reading frames (uORFs are common in eukaryotic transcripts, but those that encode conserved peptides (CPuORFs occur in less than 1% of transcripts. The peptides encoded by three plant CPuORF families are known to control translation of the downstream ORF in response to a small signal molecule (sucrose, polyamines and phosphocholine. In flowering plants, transcription factors are statistically over-represented among genes that possess CPuORFs, and in general it appeared that many CPuORF genes also had other regulatory functions, though the significance of this suggestion was uncertain (Hayden and Jorgensen, 2007. Five years later the literature provides much more information on the functions of many CPuORF genes. Here we reassess the functions of 27 known CPuORF gene families and find that 22 of these families play a variety of different regulatory roles, from transcriptional control to protein turnover, and from small signal molecules to signal transduction kinases. Clearly then, there is indeed a strong association of CPuORFs with regulatory genes. In addition, 16 of these families play key roles in a variety of different biological processes. Most strikingly, the core sucrose response network includes three different CPuORFs, creating the potential for sophisticated balancing of the network in response to three different molecular inputs. We propose that the function of most CPuORFs is to modulate translation of a downstream major ORF (mORF in response to a signal molecule recognized by the conserved peptide and that because the mORFs of CPuORF genes generally encode regulatory proteins, many of them centrally important in the biology of plants, CPuORFs play key roles in balancing such regulatory networks.

  4. Turbulence Analysis Upstream of a Wind Turbine: a LES Approach to Improve Wind LIDAR Technology

    Science.gov (United States)

    Calaf, M.

    2015-12-01

    upstream, much can be learned about the incoming turbulence, hence allowing improved wind turbine readjustments. Time correlations with the upstream incoming turbulence have been computed through an entire diurnal cycle, and a non-dimensional analysis shows the existence of different behaviors throughout the day.

  5. Upstream-downstream cooperation approach in Guanting Reservoir watershed

    Institute of Scientific and Technical Information of China (English)

    YANG Zhi-feng; ZHANG Wen-guo

    2005-01-01

    A case study is introduced and discussed concerning water dispute of misuse and pollution between up- and down-stream parts.The relations between water usage and local industrial structures are analyzed. Results show it is important to change industrial structures of the target region along with controlling water pollution by technical and engineering methods. Three manners of upstream-downstream cooperation are presented and discussed based on the actual conditions of Guangting Reservoir watershed, Two typical scenarios are supposed and studied along with the local plan on water resources development. The best solution for this cooperation presents a good way to help the upstream developing in a new pattern of eco-economy.

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

    CERN Document Server

    Yates, J N; Guio, P

    2010-01-01

    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...

  7. Whistler wave bursts upstream of the Uranian bow shock

    Science.gov (United States)

    Smith, Charles W.; Goldstein, Melvyn L.; Wong, Hung K.

    1989-01-01

    Observations of magnetic field wave bursts upstream of the Uranian bow shock are reported which were recorded prior to the inbound shock crossing. Three wave types are identified. One exhibits a broad spectral enhancement from a few millihertz to about 50 mHz and is seen from 17 to 10 hr prior to the inbound shock crossing. It is argued that these waves are whistler waves that have propagated upstream from the shock. A second wave type has a spacecraft frame frequency between 20 and 40 mHz, is seen only within or immediately upstream of the shock pedestal, is right-hand polarized in the spacecraft frame, and has a typical burst duration of 90 s. The third wave type has a spacecraft frame frequency of about 0.15 Hz, is seen exclusively within the shock pedestal, is left-hand polarized in the spacecraft frame, and has a burst duration lasting up to 4 min. It is argued that the low-frequency bursts are whistler waves with phase speed comparable to, but in excess of, the solar wind speed.

  8. Conflict Approaches of Effective Project Manager in the Upstream Sector of Indonesian Oil & Gas Industry

    Directory of Open Access Journals (Sweden)

    Adhi Cahyono

    2012-10-01

    Full Text Available Conflict can be functional or dysfunctional to the organization’s performance. This study focused on the relationship between conflict approaches implemented by the project manager based on project team member’s perception on the effectiveness of the project manager in managing project’s conflict. Questionnaires were modified from Barker et al. (1988 to measure conflict management approaches and outcomes of managing project conflict. Data were gathered from 57 respondents who worked in the Engineering, Procurement, and Construction (EPC contractors serving the upstream sector of the Oil and Gas industry in Indonesia. By using Pearson correlation, result of this study indicated that project managers were perceived to be effective in managing project conflict when implementing cooperative and confi rmative approaches, but ineffective when combining competitive and avoidance approaches. Further research should investigate correlation between cultural dimensions with conflict approaches and outcomes of managing conflict.

  9. Increased risk of oesophageal adenocarcinoma among upstream petroleum workers

    Science.gov (United States)

    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

  10. Multiple upstream modules regulate zebrafish myf5 expression

    Directory of Open Access Journals (Sweden)

    Weng Chih-Wei

    2007-01-01

    Full Text Available Abstract Background Myf5 is one member of the basic helix-loop-helix family of transcription factors, and it functions as a myogenic factor that is important for the specification and differentiation of muscle cells. The expression of myf5 is somite- and stage-dependent during embryogenesis through a delicate regulation. However, this complex regulatory mechanism of myf5 is not clearly understood. Results We isolated a 156-kb bacterial artificial chromosome clone that includes an upstream 80-kb region and a downstream 70-kb region of zebrafish myf5 and generated a transgenic line carrying this 156-kb segment fused to a green fluorescent protein (GFP reporter gene. We find strong GFP expression in the most rostral somite and in the presomitic mesoderm during segmentation stages, similar to endogenous myf5 expression. Later, the GFP signals persist in caudal somites near the tail bud but are down-regulated in the older, rostral somites. During the pharyngula period, we detect GFP signals in pectoral fin buds, dorsal rostral myotomes, hypaxial myotomes, and inferior oblique and superior oblique muscles, a pattern that also corresponds well with endogenous myf5 transcripts. To characterize the specific upstream cis-elements that regulate this complex and dynamic expression pattern, we also generated several transgenic lines that harbor various lengths within the upstream 80-kb segment. We find that (1 the -80 kb/-9977 segment contains a fin and cranial muscle element and a notochord repressor; (2 the -9977/-6213 segment contains a strong repressive element that does not include the notochord-specific repressor; (3 the -6212/-2938 segment contains tissue-specific elements for bone and spinal cord; (4 the -2937/-291 segment contains an eye enhancer, and the -2937/-2457 segment is required for notochord and myocyte expression; and (5 the -290/-1 segment is responsible for basal transcription in somites and the presomitic mesoderm. Conclusion We suggest

  11. POSTRANSLATIONAL MODIFICATIONS OF P53: UPSTREAM SIGNALING PATHWAYS.

    Energy Technology Data Exchange (ETDEWEB)

    ANDERSON,C.W.APPELLA,E.

    2003-10-23

    The p53 tumor suppressor is a tetrameric transcription factor that is posttranslational modified at >20 different sites by phosphorylation, acetylation, or sumoylation in response to various cellular stress conditions. Specific posttranslational modifications, or groups of modifications, that result from the activation of different stress-induced signaling pathways are thought to modulate p53 activity to regulate cell fate by inducing cell cycle arrest, apoptosis, or cellular senescence. Here we review recent progress in characterizing the upstream signaling pathways whose activation in response to various genotoxic and non-genotoxic stresses result in p53 posttranslational modifications.

  12. Simulation of Upstream Tracker Detector Response for Modernised LHCb Experiment

    CERN Document Server

    Pikies, M

    2015-01-01

    LHCb experiment operates a forward spectrometer that collects proton–proton collision data at the Large Hadron Collider at CERN. During the so-called Long Shutdown 2 period in years 2018–2019, LHCb detector will undergo a major modernisation. A vital part of this upgrade process is building a silicon micro-strip tracking detector — Upstream Tracker (UT) — that will be placed before the bending magnet. The UT will play a critical role in the upgraded trigger system. This paper contains a general discussion of the UT detector and presents description of a silicon response simulation platform that is being currently designed by the AGH UST LHCb group.

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

    Science.gov (United States)

    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.

  14. Doublesex: a conserved downstream gene controlled by diverse upstream regulators

    Indian Academy of Sciences (India)

    J. N. Shukla; J. Nagaraju

    2010-09-01

    Sex determination, an integral precursor to sexual reproduction, is required to generate morphologically distinct sexes. The molecular components of sex-determination pathways regulating sexual differentiation have been identified and characterized in different organisms. The Drosophila doublesex (dsx) gene at the bottom of the sex-determination cascade is the best characterized candidate so far, and is conserved from worms (mab3 of Caenorhabditis elegans) to mammals (Dmrt-1). Studies of dsx homologues from insect species belonging to different orders position them at the bottom of their sex-determination cascade. The dsx homologues are regulated by a series of upstream regulators that show amazing diversity in different insect species. These results support the Wilkin’s hypothesis that evolution of the sex-determination cascade has taken place in reverse order, the bottom most gene being most conserved and the upstream genes having been recruited at different times during evolution. The pre-mRNA of dsx is sex-specifically spliced to encode male or female-specific transcription factors that play an important role in the regulation of sexually dimorphic characters in different insect species. The generalization that dsx is required for somatic sexual differentiation culminated with its functional analysis through transgenesis and knockdown experiments in diverse species of insects. This brief review will focus on the similarities and variations of dsx homologues that have been investigated in insects to date.

  15. Computational sciences in the upstream oil and gas industry.

    Science.gov (United States)

    Halsey, Thomas C

    2016-10-13

    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'.

  16. A Large Eddy Simulation Study for upstream wind energy conditioning

    Science.gov (United States)

    Sharma, V.; Calaf, M.; Parlange, M. B.

    2013-12-01

    The wind energy industry is increasingly focusing on optimal power extraction strategies based on layout design of wind farms and yaw alignment algorithms. Recent field studies by Mikkelsen et al. (Wind Energy, 2013) have explored the possibility of using wind lidar technology installed at hub height to anticipate incoming wind direction and strength for optimizing yaw alignment. In this work we study the benefits of using remote sensing technology for predicting the incoming flow by using large eddy simulations of a wind farm. The wind turbines are modeled using the classic actuator disk concept with rotation, together with a new algorithm that permits the turbines to adapt to varying flow directions. This allows for simulations of a more realistic atmospheric boundary layer driven by a time-varying geostrophic wind. Various simulations are performed to investigate possible improvement in power generation by utilizing upstream data. Specifically, yaw-correction of the wind-turbine is based on spatio-temporally averaged wind values at selected upstream locations. Velocity and turbulence intensity are also considered at those locations. A base case scenario with the yaw alignment varying according to wind data measured at the wind turbine's hub is also used for comparison. This reproduces the present state of the art where wind vanes and cup anemometers installed behind the rotor blades are used for alignment control.

  17. Shape and shear guide sperm cells spiraling upstream

    Science.gov (United States)

    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.

  18. Current-driven filamentation upstream of magnetized relativistic collisionless shocks

    CERN Document Server

    Lemoine, M; Gremillet, L; Plotnikov, I

    2014-01-01

    The physics of instabilities in the precursor of relativistic collisionless shocks is of broad importance in high energy astrophysics, because these instabilities build up the shock, control the particle acceleration process and generate the magnetic fields in which the accelerated particles radiate. Two crucial parameters control the micro-physics of these shocks: the magnetization of the ambient medium and the Lorentz factor of the shock front; as of today, much of this parameter space remains to be explored. In the present paper, we report on a new instability upstream of electron-positron relativistic shocks and we argue that this instability shapes the micro-physics at moderate magnetization levels and/or large Lorentz factors. This instability is seeded by the electric current carried by the accelerated particles in the shock precursor as they gyrate around the background magnetic field. The compensation current induced in the background plasma leads to an unstable configuration, with the appearance of ...

  19. Ingestion into the upstream wheelspace of an axial turbine stage

    Science.gov (United States)

    Green, T.; Turner, A. B.

    1994-04-01

    The upstream wheelspace of an axial air turbine stage complete with nozzle guide vanes (NGVs) and rotor blades (430 mm mean diameter) has been tested with the objective of examining the combined effect of NGVs and rotor blades on the level of mainstream ingestion for different seal flow rates. A simple axial clearance seal was used with the rotor spun up to 6650 rpm by drawing air through it from atmospheric pressure with a large centrifugal compressor. The effect of rotational speed was examined for several constant mainstream flow rates by controlling the rotor speed with an air brake. The circumferential variation in hub static pressure was measured at the trailing edge of the NGVs upstream of the seal gap and was found to affect ingestion significantly. The hub static pressure distribution on the rotor blade leading edges was rotor speed dependent and could not be measured in the experiments. The Denton three-dimensional CFD computer code was used to predict the smoothed time-dependent pressure field for the rotor together with the pressure distribution downstream of the NGVs. The level and distribution of mainstream ingestion, and thus, the seal effectiveness, was determined from nitrous oxide gas concentration measurements and related to static pressure measurements made throughout the wheelspace. With the axial clearance rim seal close to the rotor the presence of the blades had a complex effect. Rotor blades in connection with NGVs were found to reduce mainstream ingestion seal flow rates significantly, but a small level of ingestion existed even for very high levels of seal flow rate.

  20. Landscape pattern and eco-hydrological charactedstics at the upstream of Minjiang River,China

    Institute of Scientific and Technical Information of China (English)

    LI Chongwei; GE Jianping; LIU Shirong; SUN Pengsen

    2006-01-01

    Based on three scenes of Landsat 5 Thematic Mapper (TM) satellite images acquired on June 26,1994,12 land cover types were identified by the supervised classification techniques.The precipitation,runoff,and normalized difference vegetation index (NDVI) data of six catchments were accumulated from April to September in 1992,1993,and 1995.A new eco-hydrological index,expressed by the difference between precipitation and runoff divided by the product of precipitation and NDVI,was used in this study to represent the eco-hydrological functions of different catchments.The results were:(1) The selected six catchments at the upstream of Minjiang River,China were different in landscape patterns in terms of landscape type and cover.There were higher contagion,lower edge density and diversity index in the Shouxi catchments and lower contagion,higher edge density and diversity index in the Zagunao catchments.(2)Eco-hydrological indexes had remarkable differences among different catchments.The highest eco-hydrological index was found in the Shouxi catchments,which indicated higher precipitation holding capacity of vegetation therein.While the lower eco-hydrological index was found in the Zagunao catchments,which indicated its lower precipitation holding capacity of vegetation.(3) High correlation was detected between the landscape indexes and eco-hydrological indexes.Eco-hydrological index was positively correlated with landscape contagion in contrast with the negative correlation with landscape diversity and edge density.

  1. Upstream ORFs are prevalent translational repressors in vertebrates.

    Science.gov (United States)

    Johnstone, Timothy G; Bazzini, Ariel A; Giraldez, Antonio J

    2016-04-01

    Regulation of gene expression is fundamental in establishing cellular diversity and a target of natural selection. Untranslated mRNA regions (UTRs) are key mediators of post-transcriptional regulation. Previous studies have predicted thousands of ORFs in 5'UTRs, the vast majority of which have unknown function. Here, we present a systematic analysis of the translation and function of upstream open reading frames (uORFs) across vertebrates. Using high-resolution ribosome footprinting, we find that (i)uORFs are prevalent within vertebrate transcriptomes, (ii) the majority show signatures of active translation, and (iii)uORFs act as potent regulators of translation and RNA levels, with a similar magnitude to miRNAs. Reporter experiments reveal clear repression of downstream translation by uORFs/oORFs. uORF number, intercistronic distance, overlap with the CDS, and initiation context most strongly influence translation. Evolution has targeted these features to favor uORFs amenable to regulation over constitutively repressive uORFs/oORFs. Finally, we observe that the regulatory potential of uORFs on individual genes is conserved across species. These results provide insight into the regulatory code within mRNA leader sequences and their capacity to modulate translation across vertebrates.

  2. Thyroid-disrupting chemicals: interpreting upstream biomarkers of adverse outcomes.

    Science.gov (United States)

    Miller, Mark D; Crofton, Kevin M; Rice, Deborah C; Zoeller, R Thomas

    2009-07-01

    There is increasing evidence in humans and in experimental animals for a relationship between exposure to specific environmental chemicals and perturbations in levels of critically important thyroid hormones (THs). Identification and proper interpretation of these relationships are required for accurate assessment of risk to public health. We review the role of TH in nervous system development and specific outcomes in adults, the impact of xenobiotics on thyroid signaling, the relationship between adverse outcomes of thyroid disruption and upstream causal biomarkers, and the societal implications of perturbations in thyroid signaling by xenobiotic chemicals. We drew on an extensive body of epidemiologic, toxicologic, and mechanistic studies. THs are critical for normal nervous system development, and decreased maternal TH levels are associated with adverse neuropsychological development in children. In adult humans, increased thyroid-stimulating hormone is associated with increased blood pressure and poorer blood lipid profiles, both risk factors for cardiovascular disease and death. These effects of thyroid suppression are observed even within the "normal" range for the population. Environmental chemicals may affect thyroid homeostasis by a number of mechanisms, and multiple chemicals have been identified that interfere with thyroid function by each of the identified mechanisms. Individuals are potentially vulnerable to adverse effects as a consequence of exposure to thyroid-disrupting chemicals. Any degree of thyroid disruption that affects TH levels on a population basis should be considered a biomarker of adverse outcomes, which may have important societal outcomes.

  3. Harbor seal whiskers synchronize with frequency of upstream wake

    Science.gov (United States)

    Beem, Heather; Triantafyllou, Michael

    2013-11-01

    Harbor seals are able to use their whiskers to track minute water movements, such as those left in the wake of a fish. The current study is a simple representation of what the whiskers experience as the seal chases a fish. A scaled whisker model (average cross-flow diameter: dw) is first tested in a towing tank by itself and then towed behind a larger cylinder (dc = 2 . 5dw), which serves as a wake generator. A flexing plate attached to the model base allows the whisker to freely vibrate in response to the flow. Measurements from strain gages on the plate are calibrated to tip deflections. While in the cylinder wake, the whisker vibrates with an amplitude up to ten times higher than it does on its own (A /dw = 0 . 15). Also, the whisker synchronizes with the vortex shedding frequency (fs =0/. 2 U dc) of the upstream cylinder over the range of reduced velocities tested, whereas on its own, the whisker oscillates around its own natural frequency in water. Seals may use the difference in vibration amplitude and frequency between these two cases to help detect the presence of a vortex wake.

  4. Conserved upstream open reading frames in higher plants

    Directory of Open Access Journals (Sweden)

    Schultz Carolyn J

    2008-07-01

    Full Text Available Abstract Background Upstream open reading frames (uORFs can down-regulate the translation of the main open reading frame (mORF through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are in closely related plants. Results We used a homology-based approach to identify conserved uORFs in five cereals (monocots that could potentially regulate translation. Our approach used a modified reciprocal best hit method to identify putative orthologous sequences that were then analysed by a comparative R-nomics program called uORFSCAN to find conserved uORFs. Conclusion This research identified new genes that may be controlled at the level of translation by conserved uORFs. We report that conserved uORFs are rare (

  5. Mercury pollution in Rana Chensinensis in Weisha River reach, in the upstream region of Songhua River

    Institute of Scientific and Technical Information of China (English)

    WANG Ning; ZHU Yanming; SHENG Lianxi; MENG Dan

    2005-01-01

    Twice a year continuous samples of Rana Chensinensis and sediments have been collected near gold mine in the upstream region of Songhua River from 2000 to 2002, for analyzing the total mercury (THg), methylmercury (MeHg) concentration and correlation in sediments, muscles, livers of the frog. The study indicates that THg and MeHg concentrations in polluted samples near the gold mine are higher than those in unpolluted ones. THg and MeHg concentrations are higher in autumn, in female, and in livers than those in spring, in male, in muscles respectively. The order of concentration degree in the frog organizations is as follows: liver>muscle>ovum>Fallopian tube. MeHg is the main form of mercury (Hg) existing in autumn, while inorganic Hg is in spring. There is no distinct difference of CMeHg/CTHg between male and female, livers and muscles. The correlation between MeHg concentrations in the river sediments and in the frog's livers and muscles are significant, which is related to disorderly discharge of Hg.

  6. Deceleration of the solar wind upstream from the earth's bow shock and the origin of diffuse upstream ions

    Science.gov (United States)

    Bame, S. J.; Asbridge, J. R.; Feldman, W. C.; Gosling, J. T.; Paschmann, G.; Skopke, N.

    1980-01-01

    Observations with the Los Alamos Scientific Laboratory/Max-Planck-Institut crossed-fan solar wind ion experiment on ISEE I reveal that the solar wind is decelerated and deflected away from the direction of the earth's bow shock as it enters that portion of the upstream region populated by diffuse bow shock ions and long-period (10-60 s) waves. Typically, the average directed velocity vector changes by 7-10 km/s as it enters the wave region. At times, average speed changes as large as 25-40 km/s are observed. Superposed upon these changes in average flow speed are large amplitude (+ or - 15) fluctuations in flow speed associated with the waves themselves. The observations suggest that the solar wind deceleration is the result of momentum transfer from reflected bow shock ions to the wind via the long-period waves as the reflected ion beams go unstable. The broad angular distributions of the diffuse ions thus appear to be produced as a consequence of the disruption of reflected ion beams.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  9. Upstream plasticity and downstream robustness in evolution of molecular networks

    Directory of Open Access Journals (Sweden)

    Eriksen Kasper

    2004-03-01

    Full Text Available Abstract Background Gene duplication followed by the functional divergence of the resulting pair of paralogous proteins is a major force shaping molecular networks in living organisms. Recent species-wide data for protein-protein interactions and transcriptional regulations allow us to assess the effect of gene duplication on robustness and plasticity of these molecular networks. Results We demonstrate that the transcriptional regulation of duplicated genes in baker's yeast Saccharomyces cerevisiae diverges fast so that on average they lose 3% of common transcription factors for every 1% divergence of their amino acid sequences. The set of protein-protein interaction partners of their protein products changes at a slower rate exhibiting a broad plateau for amino acid sequence similarity above 70%. The stability of functional roles of duplicated genes at such relatively low sequence similarity is further corroborated by their ability to substitute for each other in single gene knockout experiments in yeast and RNAi experiments in a nematode worm Caenorhabditis elegans. We also quantified the divergence rate of physical interaction neighborhoods of paralogous proteins in a bacterium Helicobacter pylori and a fly Drosophila melanogaster. However, in the absence of system-wide data on transcription factors' binding in these organisms we could not compare this rate to that of transcriptional regulation of duplicated genes. Conclusions For all molecular networks studied in this work we found that even the most distantly related paralogous proteins with amino acid sequence identities around 20% on average have more similar positions within a network than a randomly selected pair of proteins. For yeast we also found that the upstream regulation of genes evolves more rapidly than downstream functions of their protein products. This is in accordance with a view which puts regulatory changes as one of the main driving forces of the evolution. In this

  10. Augmented reality graphic interface for upstream dam inspection

    Science.gov (United States)

    Cote, Jean; Lavallee, Jean

    1995-12-01

    This paper presents a 3D graphic interface for the inspection of cracks along a dam. The monitoring of concrete dams is restricted by the accessibility of the various parts of the structure. Since the upstream face of a dam is not usually exposed, as in our case at Hydro- Quebec, a systematic and even ad hoc inspection become extremely complex. The piloting of a ROV (Remotely Operated Vehicle) underwater is like driving in a snowstorm. The view from the camera is similar to the visibility a driver would have in a snowstorm. Sensor fusion has to be performed by the operator since each sensor is specialized for its task. Even with a 2D positioning system or sonar scan, the approach to the inspection area is very tedious. A new 3D interface has been developed using augmented reality since the position and orientation of the vehicle are known. The point of view of the observer can easily be changed during a manipulation of the ROV. A shared memory based server can access the position data of the ROV and update the graphics in real time. The graphic environment can be used as well to drive the ROV with computer generated trajectories. A video card will be added to the Silicon Graphics workstation to display the view of the camera fixed to the ROV. This visual feedback will only be available when the ROV is close enough to the dam. The images will be calibrated since the position of the camera is known. The operator interface also includes a set of stereoscopic camera, hydrophonic (sound) feedback and imaging tools for measuring cracks.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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...

  14. Upstream proton cyclotron waves at Venus near solar maximum

    Science.gov (United States)

    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

  15. Upstream drivers of poleward moving auroral forms by satellite-imager coordinated observations

    Science.gov (United States)

    Wang, B.; Nishimura, T.; Lyons, L. R.; Angelopoulos, V.; Frey, H. U.; Mende, S. B.

    2015-12-01

    Poleward moving auroral forms (PMAFs) are observed near the dayside poleward auroral oval boundary. PMAFs are thought to be an ionospheric signature of dayside reconnection and flux transfer events. PMAFs tend to occur when the IMF is southward. Although a limited number of PMAFs has been found in association with IMF southward turning, events without appreciable changes in IMF have also been reported. While those PMAFs could be triggered spontaneously, many of the past studies used solar wind measurements far away from the bow shock nose and may have used inaccurate time shift or missed small-scale structures in the solar wind. To examine how often PMAFs are triggered by upstream structures using solar wind measurements close to the bow shock nose, we use the AGO all sky imager in Antarctic and THEMIS B and C satellites in 2008, 2009 and 2011. We identified 24 conjunction events, where at least one of the THEMIS satellites is in the solar wind and the AGO imager is located within 3 MLT from the THEMIS MLT. We found that, in 14 out of 24 conjunction events, PMAFs occur soon after IMF southward turning, indicating that IMF southward turning could be the major triggering of PMAFs. Interestingly, among these 14 cases, there are 7 cases with different IMF structures between THEMIS B/C and OMNI, which obtained IMF information from WIND and ACE. And the larger correlation coefficients between PMAFs and IMFs observed by THMEIS B/C than OMNI present the advantages of THEMIS B/C. Among the 10 cases without correlating with IMF structures, PMAFs in two events are shown to have good correlation with reflected ions in the foreshock. Based on all the conjunction events we identified, IMF southward turning is the major trigger of PMAFs and reflected ions have minor effects. The rest of the cases could be spontaneous PMAFs, although foreshock activities, even if exists, may be missed due to the IMF orientation.

  16. Isolation and Characterization of Cucumber ACC Oxidase Gene and Its Upstream

    Institute of Scientific and Technical Information of China (English)

    CHEN Yin-hua; OUYANG Bo; LI Han-xia; ZHANG Jun-hong; YE Zhi-biao

    2005-01-01

    Ethylene has been implicated as a sex-determining hormone in cucumber. Its exogenous application increases femaleness,and gynoecious genotypes were reported to produce more ethylene. 1-aminocyclopropane-1-carboxylate (ACC) oxidase (ACO) is the key enzyme in ethylene biosynthesis. In this study, a 1 200 base pair (bp) candidate fragment was amplified from the cucumber genome with degenerated primers derived from the ACO amino acid consensus sequence among different plant species. The coding region and its upstream (1 155 bp) were obtained by vector-mediated inverse PCR. The novel gene was analyzed by bioinformatics tools. Four exons and three introns were identified in the coding sequence.The spliced length of mRNA was 933 nucleotides (nts) and it encoded 311 amino acids. Phylogenic analysis result of the new gene (CsACO4, GenBank accession number AY450356) was in accordance with the evolution relationship of genetics among various plant species. Northern blotting showed that the gene expressed among female flowers of gynoecious and monoecious genotypes, it could not express in other organs. This implied that the gene might be correlated with the female behavior positively. Further work is on the way to demonstrate the complexity of the relationship between the endogenous ethylene and the sex determination.

  17. Resistance to selective BRAF inhibition can be mediated by modest upstream pathway activation.

    Science.gov (United States)

    Su, Fei; Bradley, William D; Wang, Qiongqing; Yang, Hong; Xu, Lizhong; Higgins, Brian; Kolinsky, Kenneth; Packman, Kathryn; Kim, Min Jung; Trunzer, Kerstin; Lee, Richard J; Schostack, Kathleen; Carter, Jade; Albert, Thomas; Germer, Soren; Rosinski, Jim; Martin, Mitchell; Simcox, Mary Ellen; Lestini, Brian; Heimbrook, David; Bollag, Gideon

    2012-02-15

    A high percentage of patients with BRAF(V600E) mutant melanomas respond to the selective RAF inhibitor vemurafenib (RG7204, PLX4032) but resistance eventually emerges. To better understand the mechanisms of resistance, we used chronic selection to establish BRAF(V600E) melanoma clones with acquired resistance to vemurafenib. These clones retained the V600E mutation and no second-site mutations were identified in the BRAF coding sequence. Further characterization showed that vemurafenib was not able to inhibit extracellular signal-regulated kinase phosphorylation, suggesting pathway reactivation. Importantly, resistance also correlated with increased levels of RAS-GTP, and sequencing of RAS genes revealed a rare activating mutation in KRAS, resulting in a K117N change in the KRAS protein. Elevated levels of CRAF and phosphorylated AKT were also observed. In addition, combination treatment with vemurafenib and either a MAP/ERK kinase (MEK) inhibitor or an AKT inhibitor synergistically inhibited proliferation of resistant cells. These findings suggest that resistance to BRAF(V600E) inhibition could occur through several mechanisms, including elevated RAS-GTP levels and increased levels of AKT phosphorylation. Together, our data implicate reactivation of the RAS/RAF pathway by upstream signaling activation as a key mechanism of acquired resistance to vemurafenib, in support of clinical studies in which combination therapy with other targeted agents are being strategized to combat resistance.

  18. Gene expression regulation by upstream open reading frames and human disease.

    Directory of Open Access Journals (Sweden)

    Cristina Barbosa

    Full Text Available Upstream 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.

  19. Does Tacit Knowledge Predict Organizational Performance? A Scrutiny of Firms in the Upstream Sector in Nigeria

    Directory of Open Access Journals (Sweden)

    Vincent I.O Odiri

    2016-02-01

    Full Text Available This paper examined tacit knowledge so as to see whether tacit knowledge when properly put to use can lead to improved performance by upstream sector firms in Nigeria. Knowledge as we believe, is very vital to both corporate entities and individuals. Knowledge encompasses both explicit and tacit. This paper focused on one aspect of knowledge – ‘tacit’ which is in the psyche or brain of the individual possessing it. Inspite of the central role it plays, tacit knowledge has been downplayed by most firms. However, we adopted a survey research design via questionnaires administered to 504 employees randomly selected from 3 different oil firms. The data obtained were analyzed using inferential statistics. Also, multi-collinearity diagnoses of tacit knowledge and organizational performance was performed. The result suggests that tacit knowledge is linearly correlated with organizational performance. This implies that tacit knowledge predicts organizational performance. This study is significant in that the findings would be useful to management of firms, as it divulge how tacit knowledge when properly harnessed can lead to increased performance. Most prior studies in this area were conducted in other countries, hence our study is one of the first in Nigeria that examined tacit knowledge and organizational performance.

  20. PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters

    DEFF Research Database (Denmark)

    Preker, Pascal; Almvig, Kristina; Christensen, Marianne Skovgaard

    2011-01-01

    RNAs, PROMPTs are largely nuclear and rapidly turned over by the RNA exosome. PROMPT-transcribing DNA is occupied by RNA polymerase II (RNAPII) complexes with serine 2 phosphorylated C-terminal domains (CTDs), mimicking that of the associated genic region. Thus, the inefficient elongation capacity of PROMPT...... or RNAPIII also produce PROMPTs that are targeted by the exosome. RNAPIII PROMPTs bear hallmarks of RNAPII promoter-associated RNAs, explaining the physical presence of RNAPII upstream of many RNAPIII-transcribed genes. We propose that RNAPII activity upstream gene promoters are wide-spread and integral...

  1. Experimental demonstration of CW light injection effect in upstream traffic TDM-PON

    Science.gov (United States)

    Yeh, Chien-Hung; Chow, Chi-Wai; Wu, Yu-Fu; Shih, Fu-Yuan; Chi, Sien

    2010-06-01

    High capacity time-division-multiplexed passive optical network (TDM-PON) is an emerging fiber access network that deploys optical access lines between a carrier's central office (CO) and a customer sites. In this investigation, we demonstrate and analyze the continuous wave (CW) upstream effect in TDM-PONs. Besides, we also propose and design a protection apparatus in each optical network unit (ONU) to avoid a CW upstream traffic in TDM-PONs due to sudden external environment change or ONU failure. When an upstream CW injection occurs in TDM access network, the protection scheme can stop the CW effect within a few ms to maintain the entire data traffic.

  2. Effects on the upstream flood inundation caused from the operation of Chao Phraya Dam

    OpenAIRE

    Sutham Visutimeteegorn; Kanchit Likitdecharote; Suphat Vongvisessomjai

    2007-01-01

    During the flooding events, the operation of Chao Phraya Dam to control downstream water discharge is one of the causes of the inundation occuring over the upstream area. The purposes of this research are to study the effects of the operation of Chao Phraya Dam upon the upstream flood inundation and to find out the new measures of the flood mitigation in the upstream areas of Chao Phraya Dam by using a hydrodynamic model. The results show that Manning's n in the Chao Phraya River and its trib...

  3. AN IMPROVED EPON UPSTREAM TRANSMISSION SCHEME WITH ZERO INTER-PERIOD IDLE LOSS

    Institute of Scientific and Technical Information of China (English)

    Shen Jianhua; Guo Hongmei; Mi Zhengkun

    2011-01-01

    Existing Ethernet Passive Optical Network (EPON) Dynamic Bandwidth Allocation (DBA) algorithms suffer from the disadvantage of idle time loss,which lower the upstream bandwidth utilization.This letter proposes an improved upstream transmission scheme with idle-time eliminating mechanism.Theoretical analysis and numerical calculation prove that the improved scheme can effectively eliminate the idle time and enhance the efficiency of upstream link utilization.Simulation results have shown that the bandwidth utilization can be raised up to 15% in heavy-load scenarios while the time delay performance of Assured Forwarding (AF) and Best Effort (BE) services are improved simultaneously.

  4. Effects of upstream dams versus groundwater pumping on stream temperature under varying climate conditions

    National Research Council Canada - National Science Library

    John C. Risley; Jim Constantz; Hedeff Essaid; Stewart Rounds

    2010-01-01

      The relative impact of a large upstream dam versus in-reach groundwater pumping on stream temperatures was analyzed for humid, semiarid, and arid conditions with long dry seasons to represent typical...

  5. Non-E x B ordered ion beams upstream of the earth's bow shock

    Science.gov (United States)

    Gurgiolo, C.; Parks, G. K.; Mauk, B. H.; Anderson, K. A.; Lin, R. P.; Reme, H.; Lin, C. S.

    1981-01-01

    The unexpected appearance of spin modulations in the fixed voltage electrostatic analyzer detectors on ISEE 1 and 2 has made it possible to study the plasma properties of the upstream ions in high time resolution. Using an isotropic flowing Maxwellian distribution to model the count rate modulations, estimates have been obtained of the local plasma temperature and three-dimensional flow velocity of the observed upstream ion population. It is found that in almost all of the observations of upstream particles there exist beam-like ions with temperatures in the range 5-80 eV. Their flow velocities cannot be ordered by E x B. This last point separates these observations from the previously reported reflected and diffuse populations of upstream ions. Mechanisms that can gyrophase bunch the ions reflected at the bow shock are discussed as a method of explaining the data.

  6. Power efficient and colorless PON upstream system using asymmetric clipping optical OFDM and TDMA technologies

    Science.gov (United States)

    Zhao, Yuan; Qiao, Yaojun; Ji, Yuefeng

    2012-04-01

    Asymmetric clipping optical orthogonal frequency division multiplexing (ACO-OFDM) based time division multiple access (TDMA) Passive Optical Network (PON) upstream transmission architecture is proposed. The system features low power consumption, colorless, and cost effectiveness. Performance and validity of 10 Gb/s upstream transmission are studied and confirmed by simulation. Performance degradation due to interference from rogue Optical Network Unit (ONU) is also studied.

  7. Low power consumption O-band VCSEL sources for upstream channels in PON systems

    DEFF Research Database (Denmark)

    Vegas Olmos, Juan José; Rodes Lopez, Roberto; Tafur Monroy, Idelfonso

    2012-01-01

    This paper presents an experimental validation of a low power optical network unit employing vertical-cavity surface-emitting lasers as upstream sources for passive optical networks with an increased power budget, enabling even larger splitting ratios.......This paper presents an experimental validation of a low power optical network unit employing vertical-cavity surface-emitting lasers as upstream sources for passive optical networks with an increased power budget, enabling even larger splitting ratios....

  8. Survey: UPSTREAM SECTOR OIL AND NATURAL GAS MOST PROFITABLE IN CHINA

    Institute of Scientific and Technical Information of China (English)

    Huang Zuxi

    2006-01-01

    @@ The upstream sector of oil and natural gas industry becomes the most profitable industry in China in 2005, according to a survey released by the China's State Information Center in mid-February. The results of the study show that oil and natural gas mining made a profit of 292.7 billion yuan (about US$36 billion) made in the upstream sector of oil and gas industry, up 68 percent from 2004.

  9. Potentially toxic metals in rivers upstream of Pantanal Norte

    Directory of Open Access Journals (Sweden)

    Geizibel Campos de Magalhães

    2016-11-01

    Full Text Available Cuiabá (CBA and São Lourenço (SL rivers are considered strategic once they integrate regions, which are economically, socially and environmentally relevant for Brazil and the world. However, several activities developed in their watersheds may represent sources of metals and be a threat to the environmental quality. Thus, in this study we evaluated the spatial and temporal variability of potentially toxic metals in water and sediment and the relationship of their concentration with water quality parameters. Surface water samples were collected monthly in 15 points and bottom sediment in nine points distributed throughout both rivers from August 2012 to July 2013. Cr, Cu, Fe, Mn, Pb and Zn were determined in water by inducted coupled plasma optical emission spectrometry and in sediment by flame atomic absorption spectrometry. Fe, Mn, Pb and Cr had high concentrations in water and sediment but only Pb and Cr represent environmental risk. Fe and Mn were in higher concentrations in at the upper points of SL River and Cu and Pb in the urban area of both rivers. Temporally, the metal concentrations were associated with precipitation variation. The observed correlations amongst metal concentrations indicate common sources. Thus, the metals occurrence and concentrations in water and sediment of both rivers showed a natural contribution, as a reflex of soil type associated to the region's precipitation regimen as well as the anthropic contribution due to agricultural and cattle breeding activities, and disposal of untreated urban effluents.

  10. Sedimentation Study on Upstream Reach of Selected Rivers in Pahang River Basin, Malaysia

    Directory of Open Access Journals (Sweden)

    Mohd Khairul Amri Kamarudin

    2017-02-01

    Full Text Available The sedimentation study on the upstream reach of Pahang River is located in the Bentong River Basin. The detail hydrographic survey for each river in the Bentong River Basin was carried out in May 2016. Nine stations were selected to represent the sediment concentration at Bentong River, Pahang, Malaysia. Bentong River Basin is one of the river catchment in Pahang River Basin, Malaysia. Before this, Bentong River deterioration in water quality, resulting from the sedimentation problems and unsustainable development management around the river basin. This study was implemented to prove the sedimentation problem, especially the formation of Total  Suspended Solid (TSS in the Bentong River. There are two important parameters were quantified in this study such as the concentration of suspended solid (mg/L and the river discharge (Q values (m³/s. The method used in this study to analysis the concentration of TSS using Gravimetric Method. The result showed the sedimentation in the Bentong River was unstable and the highest of TSS up to 367.6 mg/L that is categorized under the class V which > 300 mg/L based on the National Water Quality Standard (NWQS result showed the coefficient correlation between the observed Q and the TSS concentration in the Bentong River is significant R² = 0.919, there are strong positive relationship between TSS concentration production and the river discharge value in the Bentong River. The study found that the contributors to the high sedimentation problems resulting from the sediments generated from the unsustainable land use, which effectively trapping the bed sediments, rainfall intensity, backflow that carries out high sediments as well as sedimentation produced due to the river bank erosion.

  11. Water stress in global transboundary river basins: significance of upstream water use on downstream stress

    Science.gov (United States)

    Munia, H.; Guillaume, J. H. A.; Mirumachi, N.; Porkka, M.; Wada, Y.; 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 analysed 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. We found 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.

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

    Science.gov (United States)

    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.

  13. Observations of a New Foreshock Region Upstream of a Foreshock Bubble's Shock

    Science.gov (United States)

    Liu, T. Z.; Hietala, H.; Angelopoulos, V.; Turner, D. L.

    2016-12-01

    Earth's foreshock is a region within the solar wind upstream of Earth's bow shock filled with back-streaming solar wind particles reflected at the shock. Within this region, when the interplanetary field is approximately radial, foreshock bubbles (FBs) can be formed when the back-streaming particles interact with approaching discontinuities embedded in the solar wind. Foreshock bubbles can grow to 5-10 RE in scale, well upstream of the bow shock. Having a high concentration of thermalized upstream ions and slow, or even sunward, speeds within them, these transient phenomena deflect the solar wind by forming a new shock ahead of them. Although FBs eventually succumb to solar wind dynamic pressure and crash onto Earth's bow-shock and magnetopause, they may last long enough to allow solar wind reflection at their own shocks, which forms a new FB foreshock region upstream of them. The FB shock may be of different obliquity than the parent bow-shock providing new and diverse opportunities for particle acceleration. Using a case study from THEMIS, we demonstrate that ions and electrons are reflected at the FB shock, where they acquire energies consistent with shock acceleration theory. These are the first definitive observations of a new ion and electron foreshock region upstream of the FB shock with implications for shock acceleration in general.

  14. A Review of Density Holes Upstream of Earth's Bow Shock%A Review of Density Holes Upstream of Earth's Bow Shock

    Institute of Scientific and Technical Information of China (English)

    G K Parks; E Lee; N Lin; J B Cao; S Y Fu; J K Shi

    2011-01-01

    Larmor size transient structures with density depletions as large as 99% of ambient solar wind density levels occur commonly upstream of Earth's collisionless bow shock. These "density holes" have a mean duration of 17.9±10.4s but holes as short as 4 s have been observed. The average fractional density depletion (Sn/n) inside the holes is 0.68±0.14. The density of the upstream edge moving in the sunward direction can be enhanced by five or more times the solar wind density. Particle distributions show the steepened edge can behave like a shock, and measured local field geometries and Mach number support this view. Similarly shaped magnetic holes accompany the density holes indicating strong coupling between fields and particles. Current densities as large as 150 nA·m^-2 are observed at the leading compressed edge. The waves are elliptically polarized and rotating in the sense of ions (left hand) in the plasma frame. The waves appear to grow and steepen as the density holes convect with the solar wind toward the Earth. The transient nature of density holes suggests that the temporal features could represent the different stages of nonlinear evolutionary processes that produce a shock-like structure. The density holes are only observed with upstream particles, suggesting that back-streaming particles interacting with the solar wind are important. The significance of these observations is still being investigated.

  15. Particles upstream of the pre-dawn bow shock - ISEE-3 observations

    Energy Technology Data Exchange (ETDEWEB)

    Terasawa, T.; Scholer, M.; Hovestadt, D.; Klecker, B.; Ipavich, F.M.; Gloeckler, G.; Sanderson, T.R.; Wenzel, K.P.; Smith, E.J.

    1985-06-01

    The first observations of energetic ions (equal to or greater than 30 keV) in the region upstream of the pre-dawn bow shock (X between 0 and -60 Re inclusively) are presented. The intensity in this region is controlled by the direction of the interplanetary magnetic field (IMF) and is maximized when the IMF is around the spiral direction. The particle distributions are highly anisotropic with the anisotropy directed perpendicular to the magnetic field. In the E x B frame this perpendicular anisotropy is conserved and it is argued that the distribution is pancake-like. This indicates that the energetic particles in the pre-dawn upstream region have their origin in the near-earth upstream region, from where they are convected by the solar wind perpendicular to the magnetic field. It is therefore concluded that acceleration occurs mainly near the nose of the bow shock, and particle acceleration at the distant bow shock is weak. 15 references.

  16. The scheme optimization on construction diversion with discharge control feature of upstream operational reservoir

    Institute of Scientific and Technical Information of China (English)

    Liu Quan; Hu Zhigen; Fan Wuyi; Ni Jinchu; Li Qinjun

    2012-01-01

    There is a discharge control feature of construction diversion system with the upstream operational reservoir. The risk evaluation model of construction diversion is established by taking into consideration the risk factors of construc- tion diversion system with discharge control feature as well as their composition. And the risk factors include the up- stream operational reservoir discharge control, the interval flood and branch flood and the diversion system itself. And then based on analyzing of the conversion relation between risk index and investment index of diversion scheme, the risk control and conversion principals of diversion system are put forward, and the feasible diversion scheme model is built. At last, the risk and economic evaluation and scheme economic feasibility analysis method of diversion scheme are shown by an example of construction diversion scheme optimization with the discharge control condition of upstream hydropower station. The study is valuable for establishment and optimization of construction diversion scheme with upstream reservoir discharge control.

  17. Strategic human resources study of the upstream petroleum industry : the decade ahead

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-10-01

    This report presents the results of a 10 month study of the human resources issues in Canada's upstream petroleum industry. The study identifies workforce demographics, skills, and supply and demand. It also discusses the impact of technology and other key challenges facing human resources issues. The upstream petroleum industry includes exploration and production, service industries, pipeline transmission, natural gas processing, and heavy oil and bitumen extracting and upgrading. The study defined four regions in Canada: Western Canada Sedimentary Basin, the oil sands, the north, and the east coast. The main influences on the management practices within the upstream petroleum industry are: globalization; cyclical economic conditions; operational excellence business models; government regulatory requirements; stakeholder expectations for involvement; technological advances; changing demographics, and workplace skills. The study also presented suggestions for changes in best practices to improve the efficiency and effectiveness of product and service delivery. refs., tabs., figs.

  18. Institutional preparation for relaxation of control over the upstream petroleum industry in China

    Institute of Scientific and Technical Information of China (English)

    Chen Shouhai; Zhang Baosheng

    2009-01-01

    Relaxation of control over the upstream business of the petroleum industry in China is discussed. The authors suggest that a basic institutional preparation should be made before relaxing control over the upstream business, and that the institutional preparation includes at least four parts: 1) setting up the admission standards, 2) perfecting the management system of mining rights, 3) reforming the royalty and taxation system for oil and gas resources, and 4) improving the supervision and management system. Stressing the institutional preparation before relaxation of control does not mean that China could not relax control over the upstream business until the management systems are perfected, but the authors suggest that China could establish a necessary system for relaxation of control and to improve it with future practice.

  19. Observational evidence on the origin of ions upstream of the earth's bow shock

    Science.gov (United States)

    Thomsen, M. F.; Gosling, J. T.; Schwartz, S. J.

    1983-01-01

    The kinematic formalism described by Schwartz et al. (1983) is used to quantitatively compare the zeroth order predicted energies for four different source hypotheses for ions detected upstream of the earth's bow shock with previously published observations of upstream field-aligned beams and gyrating ion events. Specular reflection of a fraction of the incident solar wind is found to be the most credible explanation of gyrating ion events observed upstream of shocks ranging from quasi-parallel to nearly perpendicular. The recent hypothesis that field-aligned beams are the result of leakage from the magnetosheath of ions which were originally specularly reflected at quasi-perpendicular portions of the shock provides good agreement with observed energies of many field-aligned beams. Only magnetic moment conserving reflection of solar wind ions is capable of accounting for two very energetic beam events.

  20. A scheme for regulating toxic substances to water quality of Chamsil upstream water system

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kang Suk; Kim, Jee Hoon [Korea Environment Institute, Seoul (Korea)

    1998-12-01

    This study asserts to reflect a concept of toxicity thoroughly in the present water quality concept. It presents an appropriate solution to control toxic substances flowing into the Chamsil upstream water system. Although a regulation of toxic substances into major rivers in Korea other than Han river is also required urgently, it will be studied in future. It is expected that this study on Chamsil upstream would be a cornerstone for establishing a national regulation policy of toxic substances into water system. 28 refs., 1 fig., 36 tabs.

  1. Regulating water extraction in a river basin with upstream-downstream communities

    DEFF Research Database (Denmark)

    Graversen, Mette Kildegaard

    This paper proposes a tax mechanism modelled for water extraction in a river system with upstream and downstream farmers. The tax mechanism is based on the regulator’s own estimation of aggregate extraction and for that reason the tax addresses the problem of asymmetric information. It is demonst......This paper proposes a tax mechanism modelled for water extraction in a river system with upstream and downstream farmers. The tax mechanism is based on the regulator’s own estimation of aggregate extraction and for that reason the tax addresses the problem of asymmetric information...

  2. Antibiotic resistance in Aeromonas upstream and downstream of a water resource recovery facility.

    Science.gov (United States)

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

    2014-09-01

    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 13 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 resistance phenotypes (p 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.

  3. On the upstream mobility scheme for two-phase flow in porous media

    CERN Document Server

    Mishra, Siddhartha

    2009-01-01

    When neglecting capillarity, two-phase incompressible flow in porous media is modelled as a scalar nonlinear hyperbolic conservation law. A change in the rock type results in a change of the flux function. Discretizing in one-dimensional with a finite volume method, we investigate two numerical fluxes, an extension of the Godunov flux and the upstream mobility flux, the latter being widely used in hydrogeology and petroleum engineering. Then, in the case of a changing rock type, one can give examples when the upstream mobility flux does not give the right answer.

  4. Sound generation and upstream influence due to instability waves interacting with non-uniform mean flows

    Science.gov (United States)

    Goldstein, M. E.

    1984-01-01

    Attention is given to the sound produced by artificially excited, spatially growing instability waves on subsonic shear layers. Real flows that always diverge in the downstream direction allow sound to be produced by the interaction of the instability waves with the resulting streamwise variations of the flow. The upstream influence, or feedback, can interact with the splitter plate lip to produce a downstream-propagating instability wave that may under certain conditions be the same instability wave that originally generated the upstream influence. The present treatment is restricted to very low Mach number flows, so that compressibility effects can only become important over large distances.

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

    Science.gov (United States)

    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.

  6. Guide 71 : Emergency preparedness and response requirements for the upstream petroleum industry

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-06-01

    This guide presents current emergency preparedness and response requirements for the upstream petroleum industry. It applies to any hazard related to upstream petroleum operations and describes requirements specific to sour wells, sour production facilities and gathering systems, high vapour pressure pipelines, spills of hydrocarbons and produced water, and hydrocarbon storage in caverns. The report describes initial planning requirements for specific emergency response plans (ERP) with reference to how an emergency planning zone is determined. It also describes requirements for corporate level ERPs. Compliance and enforcement programs for ERPs were also presented. 8 tabs., 2 figs., 6 appendices.

  7. Wind tunnel testing of a full scale helicopter blade section with an upstream active Gurney flap

    NARCIS (Netherlands)

    Loendersloot, R.; Freire Gomez, J.; Booker, J.D.

    2014-01-01

    Wind tunnel tests were performed on an aerofoil section comparable to that of a full scale helicopter blade section with an upstream active Gurney flap in the framework of the European project CleanSky ITD Green RotorCraft. A modified NACA0012 profile was used, with 23 Kulite pressure transducers em

  8. Upstream Channel Utilization of CSMA/CD-Based Ethernet over Passive Optical Networks

    Institute of Scientific and Technical Information of China (English)

    Elaine; Wong; Chang-Joon; Chae

    2003-01-01

    We demonstrate that an asynchronous CSMA/CD protocol with an optical loop-back star coupler can achieve high upstream channel utilizatbn in an Ethernet PON, readily supporting a large installed base of Ethernet 10BaseT and 100BaseT interfaces.

  9. The WW domain protein Kibra acts upstream of Hippo in Drosophila

    DEFF Research Database (Denmark)

    Baumgartner, Roland; Poernbacher, Ingrid; Buser, Nathalie;

    2010-01-01

    inactivating the transcriptional coactivator Yorkie is well established, much less is known about the upstream events that regulate Hippo signaling activity. The FERM domain proteins Expanded and Merlin appear to represent two different signaling branches that feed into the Hippo pathway. Signaling...

  10. Asymmetric dispersal allows an upstream region to control population structure throughout a species' range.

    Science.gov (United States)

    Pringle, James M; Blakeslee, April M H; Byers, James E; Roman, Joe

    2011-09-13

    In a single well-mixed population, equally abundant neutral alleles are equally likely to persist. However, in spatially complex populations structured by an asymmetric dispersal mechanism, such as a coastal population where larvae are predominantly moved downstream by currents, the eventual frequency of neutral haplotypes will depend on their initial spatial location. In our study of the progression of two spatially separate, genetically distinct introductions of the European green crab (Carcinus maenas) along the coast of eastern North America, we captured this process in action. We documented the shift of the genetic cline in this species over 8 y, and here we detail how the upstream haplotypes are beginning to dominate the system. This quantification of an evolving genetic boundary in a coastal system demonstrates that novel genetic alleles or haplotypes that arise or are introduced into upstream retention zones (regions whose export of larvae is not balanced by import from elsewhere) will increase in frequency in the entire system. This phenomenon should be widespread when there is asymmetrical dispersal, in the oceans or on land, suggesting that the upstream edge of a species' range can influence genetic diversity throughout its distribution. Efforts to protect the upstream edge of an asymmetrically dispersing species' range are vital to conserving genetic diversity in the species.

  11. Exploring Patterns of Upstream Internationalization: The Role of Home-region ‘Stickiness’

    NARCIS (Netherlands)

    A.R. Muller (Allan); R.J.M. van Tulder (Rob)

    2005-01-01

    textabstractRecent work has emphasized the importance of regional strategies downstream, adding new depth to the debate on ‘globalization’. This paper adds to the debate by exploring the regional dimension upstream for a sample of Triad-based Fortune 500 firms. We find support for our hypothesis tha

  12. Water stress in global transboundary river basins : Significance of upstream water use on downstream stress

    NARCIS (Netherlands)

    Munia, H.; Guillaume, J. H A; Mirumachi, N.; Porkka, M.; Wada, Y.; 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 analysed in many of these international river basins, this has n

  13. Upstream Channel Utilization of CSMA/CD-Based Ethernet over Passive Optical Networks

    Institute of Scientific and Technical Information of China (English)

    Elaine Wong; Chang-Joon Chae

    2003-01-01

    We demonstrate that an asynchronous CSMA/CD protocol with an optical loop-back star coupler can achieve high upstream channel utilization in an Ethernet PON, readily supporting a large installed base of Ethernet 10BaseT and 100BaseT interfaces.

  14. Water stress in global transboundary river basins : Significance of upstream water use on downstream stress

    NARCIS (Netherlands)

    Munia, H.; Guillaume, J. H A; Mirumachi, N.; Porkka, M.; Wada, Y.|info:eu-repo/dai/nl/341387819; 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 analysed in many of these international river basins, this has

  15. Going against the flow: a case for upstream dispersal and detection of uncommon dispersal events

    NARCIS (Netherlands)

    Wubs, E.R.J.; Fraaije, Rob G.A.; Groot, de G.A.; Erkens, R.H.J.; Garsen, Annemarie G.; Kleyheeg, Erik; Raven, Bart M.; Soons, Merel B.

    2016-01-01

    1.Dispersal and colonisation are key processes determining species survival, and their importance is increasing as a consequence of ongoing habitat fragmentation, land-use change and climate change. Identification of long-distance dispersal events, including upstream dispersal, and of the dispersal

  16. Going against the flow: a case for upstream dispersal and detection of uncommon dispersal events

    NARCIS (Netherlands)

    Wubs, E. R. Jasper; Fraaije, Rob G. A.; de Groot, G. Arjen; Erkens, Roy H. J.; Garssen, Annemarie G.; Kleyheeg, Erik; Raven, Bart M.; Soons, Merel B.

    2016-01-01

    * Dispersal and colonisation are key processes determining species survival, and their importance is increasing as a consequence of ongoing habitat fragmentation, land-use change and climate change. Identification of long-distance dispersal events, including upstream dispersal, and of the dispersal

  17. Effects on the upstream flood inundation caused from the operation of Chao Phraya Dam

    Directory of Open Access Journals (Sweden)

    Sutham Visutimeteegorn

    2007-11-01

    Full Text Available During the flooding events, the operation of Chao Phraya Dam to control downstream water discharge is one of the causes of the inundation occuring over the upstream area. The purposes of this research are to study the effects of the operation of Chao Phraya Dam upon the upstream flood inundation and to find out the new measures of the flood mitigation in the upstream areas of Chao Phraya Dam by using a hydrodynamic model. The results show that Manning's n in the Chao Phraya River and its tributaries is 0.030-0.035 in the main channels and 0.050-0.070 in the flood plain areas. The backwater due to the operation of the Chao Praya dam affects as far as 110 kilometers upstream. New methods of water diversion can mitigate the flood inundation without the effect on the floating rice fields. The construction of reservoirs in the Upper Sakaekang River Basin and the Upper Yom River Basin will mitigate the flood not only in their own basins but also in the Lower Chao Phraya River Basin. The coordinated operation of the Chao Phraya Dam, the regulators and the upper basin reservoirs will efficiently mitigate the flood inundation.

  18. MIIT Convened Work Meeting for Upstream and Downstream Cooperation Mechanism of Aluminum Material For Civilian Aircraft

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    On September 15,2015,the Department of Raw Material Industry and the Department of Equipment Industry of the Ministry of Industry and Information Technology(MIIT)jointly organized and convened the first work meeting for upstream and downstream cooperation mechanism of aluminum material for civilian aircraft in Shanghai.Entrusted by Vice

  19. Experimental demonstration of a scalable transmitter frontend technique in IMDD-OFDMA-PON upstream scheme

    Science.gov (United States)

    Ju, Cheng; Liu, Na; Wang, Dongdong; Zhang, Zhiguo; Chen, Xue

    2016-11-01

    Scalable transmitter frontend scheme is proposed to reduce the sampling rate of digital-to-analog converter (DAC) and the complexity of digital signal processing (DSP) in intensity modulation and direct detection (IMDD) OFDMA-PON upstream scenarios. The hardware cost of each ONU is substantially decreased. The feasibility of the proposed scheme is experimentally demonstrated.

  20. Nucleotides upstream of the Kozak sequence strongly influence gene expression in the yeast S. cerevisiae.

    Science.gov (United States)

    Li, Jing; Liang, Qiang; Song, Wenjiang; Marchisio, Mario Andrea

    2017-01-01

    In the yeast Saccharomyces cerevisiae, as in every eukaryotic organism, the mRNA 5(')-untranslated region (UTR) is important for translation initiation. However, the patterns and mechanisms that determine the efficiency with which ribozomes bind mRNA, the elongation of ribosomes through the 5(')-UTR, and the formation of a stable translation initiation complex are not clear. Genes that are highly expressed in S. cerevisiae seem to prefer a 5(')-UTR rich in adenine and poor in guanine, particularly in the Kozak sequence, which occupies roughly the first six nucleotides upstream of the START codon. We measured the fluorescence produced by 58 synthetic versions of the S. cerevisiae minimal CYC1 promoter (pCYC1min), each containing a different 5(')-UTR. First, we replaced with adenine the last 15 nucleotides of the original pCYC1min 5(')-UTR-a theoretically optimal configuration for high gene expression. Next, we carried out single and multiple point mutations on it. Protein synthesis was highly affected by both single and multiple point mutations upstream of the Kozak sequence. RNAfold simulations revealed that significant changes in the mRNA secondary structures occur by mutating more than three adenines into guanines between positions -15 and -9. Furthermore, the effect of point mutations turned out to be strongly context-dependent, indicating that adenines placed just upstream of the START codon do not per se guarantee an increase in gene expression, as previously suggested. New synthetic eukaryotic promoters, which differ for their translation initiation rate, can be built by acting on the nucleotides upstream of the Kozak sequence. Translation efficiency could, potentially, be influenced by another portion of the 5(')-UTR further upstream of the START codon. A deeper understanding of the role of the 5(')-UTR in gene expression would improve criteria for choosing and using promoters inside yeast synthetic gene circuits.

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

    Science.gov (United States)

    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.

  2. Potential transcriptional regulatory regions exist upstream of the human ezrin gene promoter in esophageal carcinoma cells

    Institute of Scientific and Technical Information of China (English)

    Shuying Gao; Yanpeng Dai; Meijun Yin; Jing Ye; Gang Li; Jie Yu

    2011-01-01

    We previously demonstrated that the region -87/+ 134 of the human ezrin gene (VIL2) exhibited promoter activity in human esophageal carcinoma EC109 cells, and a further upstream region -1324/-890 positively regulated transcription.In this study, to identify the transcriptional regulatory regions upstream of the VIL2 promoter, we cloned VIL2 - 1541/- 706 segment containing the -1324/-890, and investigated its transcriptional regulatory properties via luciferase assays in transiently transfected cells.In EC109 cells, it was found that VIL2 -1541/-706 possessed promoter and enhancer activities.We also localized transcriptional regulatory regions by fusing 5′- or 3′-deletion segments of VIL2 -1541/-706 to a luciferase reporter.We found that there were three positive and one negative transcriptional regulatory regions ithin VIL2 -1541/-706 in EC109 cells.When these regions were separately located upstream of the luciferase gene without promoter, or located upstream of the VIL2 promoter or SV40 promoter directing the luciferase gene, only VIL2 -1297/-1186 exhibited considerable promoter and enhancer activities, which were lower than those of -1541/-706.In addition, transient expression of Sp1 increased ezrin expression and the transcriptional activation of VIL2 -1297/-1186.Other three regions,although exhibiting significantly positive or negative transcriptional regulation in deletion experiments, showed a weaker or absent regulation.These data suggested that more than one region upstream of the VIL2 promoter participated in VIL2 transcription, and the VIL2 -1297/-1186, probably as a key transcriptional regulatory region, regulated VIL2 transcription in company with other potential regulatory regions.

  3. Upstream ORF affects MYCN translation depending on exon 1b alternative splicing

    Directory of Open Access Journals (Sweden)

    Tutrone Giovani

    2009-12-01

    Full Text Available Abstract Background The MYCN gene is transcribed into two major mRNAs: one full-length (MYCN and one exon 1b-spliced (MYCNΔ1b mRNA. But nothing is known about their respective ability to translate the MYCN protein. Methods Plasmids were prepared to enable translation from the upstream (uORF and major ORF of the two MYCN transcripts. Translation was studied after transfection in neuroblastoma SH-EP cell line. Impact of the upstream AUG on translation was evaluated after directed mutagenesis. Functional study with the two MYCN mRNAs was conducted by a cell viability assay. Existence of a new protein encoded by the MYCNΔ1b uORF was explored by designing a rabbit polyclonal antibody against a specific epitope of this protein. Results Both are translated, but higher levels of protein were seen with MYCNΔ1b mRNA. An upstream ORF was shown to have positive cis-regulatory activity on translation from MYCN but not from MYCNΔ1b mRNA. In transfected SH-EP neuroblastoma cells, high MYCN dosage obtained with MYCNΔ1b mRNA translation induces an antiapoptotic effect after serum deprivation that was not observed with low MYCN expression obtained with MYCN mRNA. Here, we showed that MYCNOT: MYCN Overlap Transcript, a new protein of unknown function is translated from the upstream AUG of MYCNΔ1b mRNA. Conclusions Existence of upstream ORF in MYCN transcripts leads to a new level of MYCN regulation. The resulting MYCN dosage has a weak but significant anti-apoptotic activity after intrinsic apoptosis induction.

  4. Genetic mapping of habitual substance use, obesity-related traits, responses to mental and physical stress, and heart rate and blood pressure measurements reveals shared genes that are overrepresented in the neural synapse.

    Science.gov (United States)

    Nikpay, Majid; Šeda, Ondrej; Tremblay, Johanne; Petrovich, Milan; Gaudet, Daniel; Kotchen, Theodore A; Cowley, Allen W; Hamet, Pavel

    2012-06-01

    Links between substance use habits, obesity, stress and the related cardiovascular outcomes can be, in part, because of loci with pleiotropic effects. To investigate this hypothesis, we performed genome-wide mapping in 119 multigenerational families from a population in the Saguenay-Lac-St-Jean region with a known founder effect using 58,000 single-nucleotide polymorphisms and 437 microsatellite markers to identify genetic components of the following factors: habitual alcohol, tobacco and coffee use; response to mental and physical stress; obesity-related traits; and heart rate (HR) and blood pressure (BP) measures. Habitual alcohol and/or tobacco users had attenuated HR responses to mental stress compared with non-users, whereas hypertensive individuals had stronger HR and systolic BP responses to mental stress and a higher obesity index than normotensives. Genetic mappings uncovered numerous shared genes among substance use, stress response, obesity and hemodynamic traits, including CAMK4, CNTN4, DLG2, FHIT, GRID2, ITPR2, NOVA1 and PRKCE, forming network of interacting proteins, sharing synaptic function and display higher and patterned expression profiles in brain-related tissues; moreover, pathway analysis of shared genes pointed to long-term potentiation. Subgroup genetic mappings uncovered additional shared synaptic genes, including CAMK4, CNTN5 and DNM3 (hypertension-specific); CNTN4, DNM3, FHIT and ITPR1 (sex-specific), having protein interactions with genes driven from general analysis. In summary, consistent with the observed phenotypic correlations, we found substantial overlap among genomic determinants of these traits in synapse, which supports the notion that the neural synapse may be a shared interface behind substance use, stress, obesity, HR, BP as well as the observed sex- and hypertension-specific genetic differences.

  5. Determination of viscous pressure losssand resistance upstream from the choke point from breathing gases of different physical properties

    DEFF Research Database (Denmark)

    Pedersen, O.F.

    2007-01-01

      Determination of viscous pressure loss and resistance upstream from the choke point from breathing gases of different physical properties Ole F. Pedersen, Institute of Public Health, University of Aarhus, Denmark. AIM. To determine viscous pressure losses and resistances  upstream to CP...

  6. Measurements of energy spectra of fast electrons from PF-1000 in the upstream and downstream directions

    Energy Technology Data Exchange (ETDEWEB)

    Kwiatkowski, R.; Czaus, K.; Skladnik-Sadowska, E.; Malinowski, K.; Zebrowski, J. [The Andrzej Soltan Institute for Nuclear Studies (IPJ), 05-400 Otwock-Swierk (Poland); Sadowski, M.J. [The Andrzej Soltan Institute for Nuclear Studies (IPJ), 05-400 Otwock-Swierk (Poland); Karpinski, L.; Paduch, M.; Scholz, M. [Institute of Plasma Physics and Laser Microfusion (IPPLM), 01-497 Warsaw (Poland); Kubes, P. [Czech Technical University (CVUT), 166-27 Prague, (Czech Republic)

    2011-07-01

    The paper describes measurements of energy spectra of electrons emitted in the upstream direction along the symmetry-axis of the PF-1000 facility, operated with the deuterium filling at 21 kV, 290 kJ. The measurements were performed with a magnetic analyzer. The same analyzer was used to measure also electron beams emitted in along the symmetry-axis in the downstream direction. The recorded spectra showed that the electron-beams emitted in the upstream direction have energies in the range from about 40 keV to about 800 keV, while those in the downstream direction have energies in the range from about 60 keV to about 200 keV. These spectra confirm that in the PF (Plasma Focus) plasma column there appear strong local fields accelerating charged particles in different directions. This document is composed of a paper and a poster. (authors)

  7. Parameter estimation of superdiffusive motion of energetic particles upstream of heliospheric shocks

    CERN Document Server

    Perri, Silvia; Effenberger, Frederic; Fichtner, Horst

    2015-01-01

    In-situ spacecraft observations recently suggested that the transport of energetic particles accelerated at heliospheric shocks can be anomalous, i.e. the mean square displacement can grow non-linearly in time. In particular, a new analysis technique has permitted the study of particle transport properties from energetic particle time profiles upstream of interplanetary shocks. Indeed, the time/spatial power laws of the differential intensity upstream of several shocks are indicative of superdiffusion. A complete determination of the key parameters of superdiffusive transport comprises the power-law index, the superdiffusion coefficient, the related transition scale at which the energetic particle profiles turn to decay as power laws, and the energy spectral index of the shock accelerated particles. Assuming large-scale spatial homogeneity of the background plasma, the power-law behaviour can been derived from both a (microscopic) propagator formalism and a (macroscopic) fractional transport equation. We comp...

  8. Long wavelength unstable modes in the far upstream of relativistic collisionless shocks

    CERN Document Server

    Rabinak, Itay; Waxman, Eli

    2010-01-01

    The growth rate of long wavelength kinetic instabilities arising due to the interaction of a collimated beam of relativistic particles and a cold unmagnetized plasma are calculated in the ultra relativistic limit. For sufficiently culminated beams, all long wave-length modes are shown to be Weibel-unstable, and a simple analytic expression for their growth rate is derived. For large transverse velocity spreads, these modes become stable. An analytic condition for stability is given. These analytic results, which generalize earlier ones given in the literature, are shown to be in agreement with numerical solutions of the dispersion equation and with the results of novel PIC simulations in which the electro-magnetic fields are restricted to a given k-mode. The results may describe the interaction of energetic cosmic rays, propagating into the far upstream of a relativistic collisionless shock, with a cold unmagnetized upstream. The long wavelength modes considered may be efficient in deflecting particles and co...

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

    Science.gov (United States)

    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.

  10. Immediate-early Inducible Function in Upstream Region of junB Gene

    Institute of Scientific and Technical Information of China (English)

    HONG WAN; HIROSHI ISHIHARA; IZUMI TANAKA

    2006-01-01

    Objective To analyze the upstream region of radiation-induced junB gene. Methods Four plasmids containing 250 bp, 590 bp, 900 bp and 1650 bp, and CAT reporter gene were constructed separately and introduced to L8704 cells. The cells were irradiated with 2 Gy X-rays and incubated at different intervals. Total RNA was extracted from the cells and fluctuation of the CAT mRNA level was assessed by the RNA ratio of CAT/β-actin measured by quantitative Northern blot hybridization. Results CAT mRNA expression containing 900 bp and 1560 bpjunB promoter remarkably and rapidly increased, and reached its peak 30 min after 2 Gy X-ray irradiation. Conclusions 590~900 bp fragments located in the upstream region ofjunB gene play an important role in the early process of cells against radiation.

  11. A numerical study on the flow upstream of a wind turbine on complex terran

    DEFF Research Database (Denmark)

    Meyer Forsting, Alexander Raul; Bechmann, Andreas; Troldborg, Niels

    2016-01-01

    running ridges. Simulating various wind directions with and without rotor, the impact of the rotor on the flow-field upstream is determined. This is compared and related to simulations with sheared and uniform inflow. The induction zones forming for these two inflows agree to such an extent, that shear...... the wind turbine wake trajectory which in turn governs the orientation of the induction zone...

  12. Engineering ribosomal leaky scanning and upstream open reading frames for precise control of protein translation

    OpenAIRE

    Joshua P Ferreira; Noderer, William L; Diaz de Arce, Alexander J; Wang, Clifford L.

    2014-01-01

    We have employed upstream open reading frames (uORFs) to systematically tune the translation levels of recombinant proteins. We present the design principles that guided the development of this technology and provide information that may help others in implementing synthetic uORFs for their own applications. We also report on recent applications to our own research projects, including the coupling of uORF and translation initiation site (TIS) engineering with small molecule-inducible post-tra...

  13. Experimental investigation of a vibrating axial turbine cascade in presence of upstream generated aerodynamic gusts

    OpenAIRE

    Rottmeier, Fabrice; Bölcs, Albin

    2005-01-01

    An experimental investigation has been conducted in the non-rotating annular test facility of the "Laboratoire de Thermique Appliquée et de Turbomachines" (LTT), "École Polytechnique Fédérale de Lausanne" (EPFL). During this investigation, the unsteady aerodynamic response of a turbine cascade was investigated for three different cases: (1) the clamped blades subjected to periodic, upstream generated aerodynamic gusts, (2) the cascade forced to vibrate in the travelling wave mode in a uniform...

  14. Experimental investigation of a vibrating axial turbine cascade in presence of upstream generated aerodynamic gusts

    OpenAIRE

    Rottmeier, Fabrice

    2003-01-01

    An experimental investigation has been conducted in the non-rotating annular test facility of the "Laboratoire de Thermique Appliquée et de Turbomachines" (LTT), "École Polytechnique Fédérale de Lausanne" (EPFL). During this investigation, the unsteady aerodynamic response of a turbine cascade was investigated for three different cases: (1) the clamped blades subjected to periodic, upstream generated aerodynamic gusts, (2) the cascade forced to vibrate in the travelling wave mode in a uniform...

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

    Science.gov (United States)

    Masters, A.; Sulaiman, A. H.; Stawarz, Ł.; Reville, B.; Sergis, N.; Fujimoto, M.; Burgess, D.; Coates, A. J.; Dougherty, M. K.

    2017-07-01

    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 a 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.

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

    Science.gov (United States)

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

    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..

  17. Experimental Branch Retinal Vein Occlusion Induces Upstream Pericyte Loss and Vascular Destabilization.

    Directory of Open Access Journals (Sweden)

    Elisa Dominguez

    Full Text Available Branch retinal vein occlusion (BRVO leads to extensive vascular remodeling and is important cause of visual impairment. Although the vascular morphological changes following experimental vein occlusion have been described in a variety of models using angiography, the underlying cellular events are ill defined.We here show that laser-induced experimental BRVO in mice leads to a wave of TUNEL-positive endothelial cell (EC apoptosis in the upstream vascular network associated with a transient edema and hemorrhages. Subsequently, we observe an induction of EC proliferation within the dilated vein and capillaries, detected by EdU incorporation, and the edema resolves. However, the pericytes of the upstream capillaries are severely reduced, which was associated with continuing EC apoptosis and proliferation. The vascular remodeling was associated with increased expression of TGFβ, TSP-1, but also FGF2 expression. Exposure of the experimental animals to hypoxia, when pericyte (PC dropout had occurred, led to a dramatic increase in endothelial cell proliferation, confirming the vascular instability induced by the experimental BRVO.Experimental BRVO leads to acute endothelial cells apoptosis and increased permeability. Subsequently the upstream vascular network remains destabilized, characterized by pericyte dropout, un-physiologically high endothelial cells turnover and sensitivity to hypoxia. These early changes might pave the way for capillary loss and subsequent chronic ischemia and edema that characterize the late stage disease.

  18. A conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans piRNAs.

    Directory of Open Access Journals (Sweden)

    Allison C Billi

    Full Text Available Piwi-interacting RNAs (piRNAs fulfill a critical, conserved role in defending the genome against foreign genetic elements. In many organisms, piRNAs appear to be derived from processing of a long, polycistronic RNA precursor. Here, we establish that each Caenorhabditis elegans piRNA represents a tiny, autonomous transcriptional unit. Remarkably, the minimal C. elegans piRNA cassette requires only a 21 nucleotide (nt piRNA sequence and an ∼50 nt upstream motif with limited genomic context for expression. Combining computational analyses with a novel, in vivo transgenic system, we demonstrate that this upstream motif is necessary for independent expression of a germline-enriched, Piwi-dependent piRNA. We further show that a single nucleotide position within this motif directs differential germline enrichment. Accordingly, over 70% of C. elegans piRNAs are selectively expressed in male or female germline, and comparison of the genes they target suggests that these two populations have evolved independently. Together, our results indicate that C. elegans piRNA upstream motifs act as independent promoters to specify which sequences are expressed as piRNAs, how abundantly they are expressed, and in what germline. As the genome encodes well over 15,000 unique piRNA sequences, our study reveals that the number of transcriptional units encoding piRNAs rivals the number of mRNA coding genes in the C. elegans genome.

  19. Formation Flight: Upstream Influence of a Wing on a Streamwise Vortex

    Science.gov (United States)

    McKenna, Chris; Rockwell, Donald; Lehigh University Fluids Lab Team

    2015-11-01

    Aircraft flying together in formation can experience aerodynamic advantages. Impingement of the tip vortex of the leader wing on the trailer wing can increase the lift to drag ratio L/D and the unsteady loading on the trailer wing. These increases are sensitive to the impingement location of the vortex on the wing. Particle image velocimetry is employed to determine patterns of velocity and vorticity on successive crossflow planes along the vortex, which lead to volume representations and thereby characterization of the streamwise evolution of the vortex structure as it approaches the trailer wing. This evolution of the incident vortex is affected by the upstream influence of the trailer wing, and is highly dependent on the location of vortex impingement. As the spanwise impingement location of the vortex moves from outboard of the wing tip to inboard, the upstream influence on the development of the vortex increases. For spanwise locations close to or intersecting the vortex core, the effects of upstream influence of the wing on the vortex are to: increase the streamwise velocity deficit; decrease the streamwise vorticity; increase the in-plane vorticity; decrease the downwash; and increase the root-mean-square of both streamwise velocity and vorticity.

  20. Upstream to downstream: stormwater quality in Mayagüez, Puerto Rico.

    Science.gov (United States)

    Wengrove, Meagan E; Ballestero, Thomas P

    2012-08-01

    The focus of this research was upon consequences of urban stormwater runoff entering two streams in Mayagüez, Puerto Rico. Mayagüez is the largest urban area of the western side of the island of Puerto Rico and provides an excellent point of reference to monitor the affects of urban development on water quality in a tropical climate. The two monitored streams were Quebrada del Oro and Cano Majagual. The research hypothesis asks, "Does stormwater runoff from urban development measurably affect the water quality of downstream receiving water by raising the conductivity, temperature, and flow quantity characteristics during storm events in comparison to upstream water quality?" In essence, the results for Quebrada del Oro agreed with the hypothesis of this project, while Cano Majagual produced results different from the hypothesis primarily due to the absence of non-urbanized land use for both upstream and downstream sections as well as the buffering capacity of a large wetland just upstream of the downstream instrument location of Cano Majagual. Both streams showed signs of stream impairment according to the temperature criteria (32°C or 90°F) set by the Junta de Calidad Ambiental and the US Environmental Protection Agency. Dissolved oxygen levels of the streams were severely affected by water temperature and oxygen-consuming matter within these stream systems, making dissolved oxygen and temperature important water quality parameters for tropical climates.

  1. Propagation of ULF waves from the upstream region to the midnight sector of the inner magnetosphere

    Science.gov (United States)

    Takahashi, Kazue; Hartinger, Michael D.; Malaspina, David M.; Smith, Charles W.; Koga, Kiyokazu; Singer, Howard J.; Frühauff, Dennis; Baishev, Dmitry G.; Moiseev, Alexey V.; Yoshikawa, Akimasa

    2016-09-01

    Ultralow frequency (ULF) waves generated in the ion foreshock are a well-known source of Pc3-Pc4 waves (7-100 mHz) observed in the dayside magnetosphere. We use data acquired on 10 April 2013 by multiple spacecraft to demonstrate that ULF waves of upstream origin can propagate to the midnight sector of the inner magnetosphere. At 1130-1730 UT on the selected day, the two Van Allen Probes spacecraft and the geostationary ETS-VIII satellite detected compressional 20 to 40 mHz magnetic field oscillations between L ˜ 4 and L ˜ 7 in the midnight sector, along with other spacecraft located closer to noon. Upstream origin of the oscillations is concluded from the wave frequency that matches a theoretical model, globally coherent amplitude modulation, and duskward propagation that is consistent with expected entry of the upstream wave energy through the dawnside flank under the observed interplanetary magnetic field. The oscillations are attributed to magnetohydrodynamic fast-mode waves based on their propagation velocity of ˜300 km/s and the relationship between the electric and magnetic field perturbations. The magnitude of the azimuthal wave number is estimated to be ˜30. There is no evidence that the oscillations propagated to the ground in the midnight sector.

  2. Researches on the ice jam formation in the upstream of Izvoru Muntelui reservoir

    Directory of Open Access Journals (Sweden)

    Maria RĂDOANE

    2008-03-01

    Full Text Available The current work provides a description of the ice jam phenomena along the riverof Bistrita, which has the longest mountainous course in Romania (216km. During the coldseason of the year, in the upstream of the Izvoru Muntelui Reservoir over a length of 25-30km, there are generated with a almost yearly frequency ice blocks accumulations known asice jams. Analysis of the hidroclimatical and morphological conditions of the river bed hasrevealed that they are favorable to formation of ice jam provided there is present a certaincombination of their temporal variations. Hidraulic geometry of the Bistrita river bed isfavorable to flow of frazil slush, frazil pans and ice floes while the air temperature is -7 oC aslong as the level of Izvoru Muntelui Reservoir is below 500 m. Over this level, the river bed isblocked with ice jam during the submerse phase of the lake and this blockage advancesupstream with velocities of several hudreds of meters per day. The most dramatic phenomenahas been recorded during the winter of 2002-2003 when the thickness of the ice was of 6meters and it caused floods that provoked damages and claimed human lives. Aparition in2003 of the Topoliceni Reservoir, placed 6 km upstream of the Izvoru Muntelui Reservoir, hascomplicated the evolution of the phenomena, the lake itself acting as an accumulation poolfor the ices in the upstream.

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

    Science.gov (United States)

    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.

  4. Rearrangement of Upstream Regulatory Elements Leads to Ectopic Expression of the Drosophila Mulleri Adh-2 Gene

    Science.gov (United States)

    Falb, D.; Fischer, J.; Maniatis, T.

    1992-01-01

    The Adh-2 gene of Drosophila mulleri is expressed in the larval fat body and the adult fat body and hindgut, and a 1500-bp element located 2-3 kb upstream of the Adh-2 promoter is necessary for maximal levels of transcription. Previous work demonstrated that deletion of sequences between this upstream element and the Adh-2 promoter results in Adh-2 gene expression in a novel larval tissue, the middle midgut. In this study we show that the upstream element possesses all of the characteristics of a transcriptional enhancer: its activity is independent of orientation, it acts on a heterologous promoter, and it functions at various positions both 5' and 3' to the Adh-2 gene. Full enhancer function can be localized to a 750-bp element, although other regions possess some redundant activity. The ectopic expression pattern is dependent on the proximity of at least two sequence elements. Thus, tissue-specific transcription can involve complex proximity-dependent interactions among combinations of regulatory elements. PMID:1459428

  5. Effects of optimal initial errors on predicting the seasonal reduction of the upstream Kuroshio transport

    Science.gov (United States)

    Zhang, Kun; Wang, Qiang; Mu, Mu; Liang, Peng

    2016-10-01

    With the Regional Ocean Modeling System (ROMS), we realistically simulated the transport variations of the upstream Kuroshio (referring to the Kuroshio from its origin to the south of Taiwan), particularly for the seasonal transport reduction. Then, we investigated the effects of the optimal initial errors estimated by the conditional nonlinear optimal perturbation (CNOP) approach on predicting the seasonal transport reduction. Two transport reduction events (denoted as Event 1 and Event 2) were chosen, and CNOP1 and CNOP2 were obtained for each event. By examining the spatial structures of the two types of CNOPs, we found that the dominant amplitudes are located around (128°E, 17°N) horizontally and in the upper 1000 m vertically. For each event, the two CNOPs caused large prediction errors. Specifically, at the prediction time, CNOP1 (CNOP2) develops into an anticyclonic (cyclonic) eddy-like structure centered around 124°E, leading to the increase (decrease) of the upstream Kuroshio transport. By investigating the time evolution of the CNOPs in Event 1, we found that the eddy-like structures originating from east of Luzon gradually grow and simultaneously propagate westward. The eddy-energetic analysis indicated that the errors obtain energy from the background state through barotropic and baroclinic instabilities and that the latter plays a more important role. These results suggest that improving the initial conditions in east of Luzon could lead to better prediction of the upstream Kuroshio transport variation.

  6. Optical correlation

    NARCIS (Netherlands)

    Boden, J.A.

    1974-01-01

    A survey is given of the most common types of coherent optical correlators, which are classified as spatial plane correlators, frequency plane correlators and special reference correlators. Only the spatial plane correlators are dealt with rather thoroughly. Basic principles, some special features,

  7. Unified translation repression mechanism for microRNAs and upstream AUGs

    Directory of Open Access Journals (Sweden)

    Ajay Subramanian S

    2010-03-01

    Full Text Available Abstract Background MicroRNAs (miRNAs are endogenous small RNAs that modulate gene expression at the post-transcriptional level by binding complementary sites in the 3'-UTR. In a recent genome-wide study reporting a new miRNA target class (miBridge, we identified and validated interactions between 5'-UTRs and miRNAs. Separately, upstream AUGs (uAUGs in 5'-UTRs are known to regulate genes translationally without affecting mRNA levels, one of the mechanisms for miRNA-mediated repression. Results Using sequence data from whole-genome cDNA alignments we identified 1418 uAUG sequences on the 5'-UTR that specifically interact with 3'-ends of conserved miRNAs. We computationally identified miRNAs that can target six genes through their uAUGs that were previously reported to suppress translation. We extended this meta-analysis by confirming expression of these miRNAs in cell-lines used in the uAUG studies. Similarly, seven members of the KLF family of genes containing uAUGs were computationally identified as interacting with several miRNAs. Using KLF9 as an example (whose protein expression is limited to brain tissue despite the mRNA being expressed ubiquitously, we show computationally that miRNAs expressed only in HeLa cells and not in neuroblastoma (N2A cells can bind the uAUGs responsible for translation inhibition. Our computed results demonstrate that tissue- or cell-line specific repression of protein translation by uAUGs can be explained by the presence or absence of miRNAs that target these uAUG sequences. We propose that these uAUGs represent a subset of miRNA interaction sites on 5'-UTRs in miBridge, whereby a miRNA binding a uAUG hinders the progression of ribosome scanning the mRNA before it reaches the open reading frame (ORF. Conclusions While both miRNAs and uAUGs are separately known to down-regulate protein expression, we show that they may be functionally related by identifying potential interactions through a sequence

  8. Celiac disease is overrepresented in patients with constipation

    NARCIS (Netherlands)

    Pelleboer, Rolf A. A.; Janssen, Rob L. H.; Deckers-Kocken, Judith M.; Wouters, Edward; Nissen, Annemieke C.; Bolz, Werner E. A.; Ten, Walther E. Tjon A.; van der Feen, Cathelijne; Oosterhuis, Koen J.; Rovekamp, Mechelien H.; Nikkels, Peter G. J.; Houwen, Roderick H. J.

    2012-01-01

    Objective: It is suggested that patients with constipation should be screened for celiac disease. Similarly, it is recommended to investigate these patients for hypothyroidism and hypercalcemia. However, no evidence for these recommendations is available so far. We therefore set out to determine the

  9. Celiac disease is overrepresented in patients with constipation

    NARCIS (Netherlands)

    Pelleboer, Rolf A. A.; Janssen, Rob L. H.; Deckers-Kocken, Judith M.; Wouters, Edward; Nissen, Annemieke C.; Bolz, Werner E. A.; Ten, Walther E. Tjon A.; van der Feen, Cathelijne; Oosterhuis, Koen J.; Rovekamp, Mechelien H.; Nikkels, Peter G. J.; Houwen, Roderick H. J.

    2012-01-01

    Objective: It is suggested that patients with constipation should be screened for celiac disease. Similarly, it is recommended to investigate these patients for hypothyroidism and hypercalcemia. However, no evidence for these recommendations is available so far. We therefore set out to determine the

  10. Synergistic and singular effects of river discharge and lunar illumination on dam passage of upstream migrant yellow-phase American eels

    Science.gov (United States)

    Welsh, Stuart; Aldinger, Joni L.; Braham, Melissa; Zimmerman, Jennifer L.

    2016-01-01

    Monitoring of dam passage can be useful for management and conservation assessments of American eel, particularly if passage counts can be examined over multiple years. During a 7-year study (2007–2013) of upstream migration of American eels within the lower Shenandoah River (Potomac River drainage), we counted and measured American eels at the Millville Dam eel pass, where annual study periods were determined by the timing of the eel pass installation during spring or summer and removal during fall. Daily American eel counts were analysed with negative binomial regression models, with and without a year (YR) effect, and with the following time-varying environmental covariates: river discharge of the Shenandoah River at Millville (RDM) and of the Potomac River at Point of Rocks, lunar illumination (LI), water temperature, and cloud cover. A total of 17 161 yellow-phase American eels used the pass during the seven annual periods, and length measurements were obtained from 9213 individuals (mean = 294 mm TL, s.e. = 0.49, range 183–594 mm). Data on passage counts of American eels supported an additive-effects model (YR + LI + RDM) where parameter estimates were positive for river discharge (β = 7.3, s.e. = 0.01) and negative for LI (β = −1.9, s.e. = 0.34). Interestingly, RDM and LI acted synergistically and singularly as correlates of upstream migration of American eels, but the highest daily counts and multiple-day passage events were associated with increased RDM. Annual installation of the eel pass during late spring or summer prevented an early spring assessment, a period with higher RDM relative to those values obtained during sampling periods. Because increases in river discharge are climatically controlled events, upstream migration events of American eels within the Potomac River drainage are likely linked to the influence of climate variability on flow regime.

  11. The worst moment of superposed surge wave in upstream series double surge tanks of hydropower station

    Science.gov (United States)

    Teng, Y.; Yang, J. D.; Guo, W. C.; Chen, J. P.

    2016-11-01

    It is a consensus to consider the superposed working conditions when calculating the surge wave in surge tank of hydropower station with long diversion tunnel. For the hydropower station with single surge tank, the method of determining the worst superposed moment is mature. However, for the hydropower station with upstream series double surge tanks, research in this field is still blank. Based on an engineering project, this paper investigated the worst moments and the control superposed working conditions about the maximum surge level and the minimum surge level of upstream series double surge tanks using numerical simulation. In addition, the incidence relations between the worst moment of superposed surge wave and the different areal array and distance between the two surge tanks are also carried out. The results showed that: With the decrease of the distance between auxiliary surge tank and upstream reservoir, the maximum values of the highest surge levels in the two surge tanks always reach close to but a little earlier than the bigger one time when the inflowing discharges of the two surge tanks reach the maximum. It is similar to the minimum values of lowest surge levels in the two surge tanks which also reach close to but a little later than the bigger one time when the outflowing discharges of the two surges reach the maximum. Moreover, the closer the area of auxiliary surge tank to the area of main surge tank is, the closer the worst moment to the bigger one time when inflow or outflow of the two surges reach the maximum will become.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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

  14. Performance of a large-scale barrier discharge plume improved by an upstream auxiliary barrier discharge

    Science.gov (United States)

    Li, Xuechen; Chu, Jingdi; Zhang, Qi; Zhang, Panpan; Jia, Pengying; Geng, Jinling

    2016-11-01

    Enhanced by an upstream auxiliary dielectric barrier discharge (ADBD), a transverse barrier discharge plume with a fairly large scale is generated downstream of a narrow slit. Electrical and optical characteristics are compared for the two discharges with and without the ADBD. Results indicate that the plume with the ADBD is longer, more uniform, and dissipates a higher power. Moreover, its inception voltage is much lower. High-speed imaging presents that the uniform plasma plume with the ADBD comprises a series of moving micro-discharge filaments in a glow regime, which are much smoother than those without the ADBD.

  15. Engineering ribosomal leaky scanning and upstream open reading frames for precise control of protein translation

    Science.gov (United States)

    Ferreira, Joshua P; Noderer, William L; Diaz de Arce, Alexander J; Wang, Clifford L

    2014-01-01

    We have employed upstream open reading frames (uORFs) to systematically tune the translation levels of recombinant proteins. We present the design principles that guided the development of this technology and provide information that may help others in implementing synthetic uORFs for their own applications. We also report on recent applications to our own research projects, including the coupling of uORF and translation initiation site (TIS) engineering with small molecule-inducible post-translational control. Finally, we discuss opportunities to investigate and potentially engineer gene-specific translational responses to cellular stress. PMID:24637490

  16. How to use Big Data technologies to optimize operations in Upstream Petroleum Industry

    Directory of Open Access Journals (Sweden)

    Abdelkader Baaziz

    2013-12-01

    Full Text Available “Big Data is the oil of the new economy” is the most famous citation during the three last years. It has even been adopted by the World Economic Forum in 2011. In fact, Big Data is like crude! It’s valuable, but if unrefined it cannot be used. It must be broken down, analyzed for it to have value. But what about Big Data generated by the Petroleum Industry and particularly its upstream segment? Upstream is no stranger to Big Data. Understanding and leveraging data in the upstream segment enables firms to remain competitive throughout planning, exploration, delineation, and field development.Oil & Gas Companies conduct advanced geophysics modeling and simulation to support operations where 2D, 3D & 4D Seismic generate significant data during exploration phases. They closely monitor the performance of their operational assets. To do this, they use tens of thousands of data-collecting sensors in subsurface wells and surface facilities to provide continuous and real-time monitoring of assets and environmental conditions. Unfortunately, this information comes in various and increasingly complex forms, making it a challenge to collect, interpret, and leverage the disparate data. As an example, Chevron’s internal IT traffic alone exceeds 1.5 terabytes a day.Big Data technologies integrate common and disparate data sets to deliver the right information at the appropriate time to the correct decision-maker. These capabilities help firms act on large volumes of data, transforming decision-making from reactive to proactive and optimizing all phases of exploration, development and production. Furthermore, Big Data offers multiple opportunities to ensure safer, more responsible operations. Another invaluable effect of that would be shared learning.The aim of this paper is to explain how to use Big Data technologies to optimize operations. How can Big Data help experts to decision-making leading the desired outcomes?Keywords:Big Data; Analytics

  17. Experimental studies of the properties of 'simulated' upstream turbulence using a statistical multipoint method

    Science.gov (United States)

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

    1995-01-01

    In this report we present a different approach to the multipoint measurement of magnetic fields and plasma. This is called the multi-spacecraft ensemble technique (MET), essentially free of process restrictions, such as linearity and stationarity. We comprehensively discuss the other conditions and limitations intrinsic to this statistical method. We also show the results of the application of the ensemble method to the synthetic data obtained from a hybrid simulation in the region upstream of a quasi-parallel shock. The important implications of the above approach for the CLUSTER mission are discussed.

  18. Characterization of an upstream regulatory element of adenovirus L1 poly (A) site.

    Science.gov (United States)

    Liu, Li

    2005-06-20

    The transition from early to late stage infection by adenovirus involves a change in mRNA expression from the adenovirus major late transcription unit (AdMLTU). This early to late switch centers around alternative selection of one of five poly (A) sites (L1-L5) that code for the major structural proteins of Adenovirus. During the early stage of infection, steady state mRNA is primarily derived from the L1 poly (A) site. During the late stage of infection, each of the MLTU poly (A) sites is represented in the steady state mRNA pool (Falck-Pedersen, E., Logan, J., 1989. Regulation of poly(A) site selection in adenovirus. J. Virol. 63 (2), 532-541.). Using transient transfection of a plasmid expressing Chloramphenicol Acetyl Transferase with a tandem poly (A) minigene system (L13) (DeZazzo, J.D., Falck-Pedersen, E., Imperiale, M.J., 1991. Sequences regulating temporal poly(A) site switching in the adenovirus major late transcription unit. Mol. Cell. Biol. 11 (12), 5977-5984; Prescott, J., Falck-Pedersen, E., 1994. Sequence elements upstream of the 3' cleavage site confer substrate strength to the adenovirus L1 and L3 polyadenylation sites. Mol. Cell. Biol. 14 (7), 4682-4693.), it has been demonstrated that the promoter-proximal L1 poly (A) site which is poorly recognized by the 3' end processing machinery, contains an upstream repressor element (URE) that influences steady state levels of mRNA (Prescott, J.C., Liu, L., Falck-Pedersen, E., 1997. Sequence-mediated regulation of adenovirus gene expression by repression of mRNA accumulation. Mol. Cell. Biol. 17 (4), 2207-2216.). In this study, we have further characterized the elements that mediate L1URE function. These studies indicate that the L1 upstream regulatory element (L1 URE) contains a complex RNA architecture that serves to repress gene expression through multiple sub-effectors. The L1URE functions when located upstream of a heterologous poly (A) site, and is able to strongly suppress steady state m

  19. Diabetes mellitus and atrial fibrillation: Pathophysiological mechanisms and potential upstream therapies.

    Science.gov (United States)

    Goudis, Christos A; Korantzopoulos, Panagiotis; Ntalas, Ioannis V; Kallergis, Eleftherios M; Liu, Tong; Ketikoglou, Dimitrios G

    2015-04-01

    Diabetes mellitus (DM) represents one of the most important risk factors for atrial fibrillation (AF) while AF is a strong and independent marker of overall mortality and cardiovascular morbidity in diabetic patients. Autonomic, electrical, electromechanical, and structural remodeling, including oxidative stress, connexin remodeling and glycemic fluctuations seem to be implicated in AF pathophysiology in the setting of DM. The present review highlights the association between DM and AF, provides a comprehensive overview of the responsible pathophysiological mechanisms and briefly discusses potential upstream therapies for DM-related atrial remodeling.

  20. New polymorphisms for the BoLA-DRB3 upstream regulatory region.

    Science.gov (United States)

    Ripoli, M V; Villegas-Castagnasso, E E; Peral-Garcia, P; Giovambattista, G

    2005-08-01

    Two new alleles, named BoLA-DRB3-P*06 and BoLA-DRB3-P*07, have been identified for the upstream regulatory region of the BoLA-DRB3 gene. The 228-bp nucleotide sequences of the promoter comprising the W, X, Y, CAAT and TATA regulatory boxes were analysed. The BoLA-DRB3-P*06 exhibits one insertion between the W and X boxes, and one transition between the X and Y boxes. On the other hand, the BoLA-DRB3-P*07 showed one insertion in the X box.

  1. 8-channel prototype of SALT readout ASIC for Upstream Tracker in the upgraded LHCb experiment

    Science.gov (United States)

    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 (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.

  2. Impacts of water and soil erosion in upstream watershed of Nenjiang River

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Making a brief analysis of the water and soil loss present situation in Daxing'anling area which locates to the upstream region of Nenjiang River, and giving the water and soil loss of this area that have been made near 20 years, as well as the factors of the water and soil loss. According to the factors corresponding prevention measure and forecast model have been put forward, make a brief introduction to this model in this article. It is helpful to improve the local soil conservation and sustainable development.

  3. Minimum cost maximum flow algorithm for upstream bandwidth allocation in OFDMA passive optical networks

    Science.gov (United States)

    Wu, Yating; Kuang, Bin; Wang, Tao; Zhang, Qianwu; Wang, Min

    2015-12-01

    This paper presents a minimum cost maximum flow (MCMF) based upstream bandwidth allocation algorithm, which supports differentiated QoS for orthogonal frequency division multiple access passive optical networks (OFDMA-PONs). We define a utility function as the metric to characterize the satisfaction degree of an ONU on the obtained bandwidth. The bandwidth allocation problem is then formulated as maximizing the sum of the weighted total utility functions of all ONUs. By constructing a flow network graph, we obtain the optimized bandwidth allocation using the MCMF algorithm. Simulation results show that the proposed scheme improves the performance in terms of mean packet delay, packet loss ratio and throughput.

  4. Attenuation Distance of Low Frequency Waves Upstream of the Pre-Dawn Bow Shock: GEOTAIL snd ISEE-3 Comparison

    Science.gov (United States)

    Sugiyama, T.; Terasawa, T.; Kawano, H.; Yamamoto, T.; Kokubun, S.; Frank, L.; Ackerson, K.; Tsurutani, B.

    1994-01-01

    This paper presents a statistical study of the spatial distribution of low frequency waves in the region upstream of the pre-dawn to dawn side bow shock using both GEOTAIL and ISEE-3 magnetometer data.

  5. Individual Target Data-Collection Points Upstream of the Siltation Dam at Prairie Rose Lake, Shelby County, Iowa

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — Point coverage of bathymetry target points upstream of the siltation dam at Prairie Rose Lake in Shelby Co., Iowa. The U.S. Geological Survey conducted a...

  6. Determination of viscous pressure losssand resistance upstream from the choke point from breathing gases of different physical properties

    DEFF Research Database (Denmark)

    Pedersen, O.F.

    2007-01-01

      Determination of viscous pressure loss and resistance upstream from the choke point from breathing gases of different physical properties Ole F. Pedersen, Institute of Public Health, University of Aarhus, Denmark. AIM. To determine viscous pressure losses and resistances  upstream to CP...... flows after breathing air,  20% oxygen in He and 20% oxygen in SF6 . For construction of MFSR-curves. Lung elastic recoil pressures were estimated  from ECCS reference values (Bull. europ. Physiopath. resp. 1983, 19  (suppl 5),28-31). The model described in the figure was used. The extrapolated flow FY...... 1, but certainly different from1.5, indicating predominant laminar flow upstream to CP. The upstream resistance is low, and lower than directly measured (JAP 83:1721-32,1997). This is a possibility if CP is more peripheral than assumed in that study.  ...

  7. Photosynthetic Genes and Genes Associated with the C4 Trait in Maize Are Characterized by a Unique Class of Highly Regulated Histone Acetylation Peaks on Upstream Promoters.

    Science.gov (United States)

    Perduns, Renke; Horst-Niessen, Ina; Peterhansel, Christoph

    2015-08-01

    Histone modifications contribute to gene regulation in eukaryotes. We analyzed genome-wide histone H3 Lysine (Lys) 4 trimethylation and histone H3 Lys 9 acetylation (two modifications typically associated with active genes) in meristematic cells at the base and expanded cells in the blade of the maize (Zea mays) leaf. These data were compared with transcript levels of associated genes. For individual genes, regulations (fold changes) of histone modifications and transcript levels were much better correlated than absolute intensities. When focusing on regulated histone modification sites, we identified highly regulated secondary H3 Lys 9 acetylation peaks on upstream promoters (regulated secondary upstream peaks [R-SUPs]) on 10% of all genes. R-SUPs were more often found on genes that were up-regulated toward the blade than on down-regulated genes and specifically, photosynthetic genes. Among those genes, we identified six genes encoding enzymes of the C4 cycle and a significant enrichment of genes associated with the C4 trait derived from transcriptomic studies. On the DNA level, R-SUPs are frequently associated with ethylene-responsive elements. Based on these data, we suggest coevolution of epigenetic promoter elements during the establishment of C4 photosynthesis.

  8. Regulation of CCL2 expression by an upstream TALE homeodomain protein-binding site that synergizes with the site created by the A-2578G SNP.

    Science.gov (United States)

    Page, Stephen H; Wright, Edward K; Gama, Lucio; Clements, Janice E

    2011-01-01

    CC Chemokine Ligand 2 (CCL2) is a potent chemoattractant produced by macrophages and activated astrocytes during periods of inflammation within the central nervous system. Increased CCL2 expression is correlated with disease progression and severity, as observed in pulmonary tuberculosis, HCV-related liver disease, and HIV-associated dementia. The CCL2 distal promoter contains an A/G polymorphism at position -2578 and the homozygous -2578 G/G genotype is associated with increased CCL2 production and inflammation. However, the mechanisms that contribute to the phenotypic differences in CCL2 expression are poorly understood. We previously demonstrated that the -2578 G polymorphism creates a TALE homeodomain protein binding site (TALE binding site) for PREP1/PBX2 transcription factors. In this study, we identified the presence of an additional TALE binding site 22 bp upstream of the site created by the -2578 G polymorphism and demonstrated the synergistic effects of the two sites on the activation of the CCL2 promoter. Using chromatin immunoprecipitation (ChIP) assays, we demonstrated increased binding of the TALE proteins PREP1 and PBX2 to the -2578 G allele, and binding of IRF1 to both the A and G alleles. The presence of TALE binding sites that form inverted repeats within the -2578 G allele results in increased transcriptional activation of the CCL2 distal promoter while the presence of only the upstream TALE binding site within the -2578 A allele exerts repression of promoter activity.

  9. PCR analysis of the upstream regulatory region of human papillomavirus genomes in cervical intraepithelial neoplasia and cervical carcinoma.

    OpenAIRE

    Donaldson, Y K; Arends, M. J.; Duvall, E.; Bird, C C

    1993-01-01

    AIMS--To test whether human papillomavirus (HPV) variants with large scale sequence alterations to the upstream regulatory region are present in cervical intraepithelial neoplasias (CIN) and cervical carcinomas. METHODS--New PCR based assays were designed specifically to detect large scale insertion/deletion alterations in the upstream regulatory region of HPV 16 and 18. The assays were applied to 24 cases of CIN and 34 cases of cervical carcinoma previously shown to contain these two high ri...

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

    Science.gov (United States)

    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.

  11. Comparing effects of oligotrophication and upstream hydropower dams on plankton and productivity in perialpine lakes

    Science.gov (United States)

    Finger, David; Schmid, Martin; Wüest, Alfred

    2007-12-01

    In recent decades, many perialpine lakes have been affected by oligotrophication due to efficient sewage treatment and by altered water turbidity due to upstream hydropower operations. Such simultaneous environmental changes often lead to public debate on the actual causes of observed productivity reductions. We evaluate the effects of those two changes by a combined approach of modeling and data interpretation for a case study on Lake Brienz (Switzerland), a typical oligotrophic perialpine lake, located downstream of several hydropower reservoirs. A physical k-ɛ scheme and a biogeochemical advection-diffusion-reaction model were implemented and applied for several hypothetical scenarios with different nutrient loads and different particle input dynamics. The simulation results are compared to long-term biotic data collected from 1999 to 2004. The analysis shows that enhanced nutrient supply increases the nutritious value of algae, stimulating zooplankton growth, while phytoplankton growth is limited by stronger top-down control. Annually integrated productivity is only slightly influenced by altered turbidity, as phosphorous limitation prevails. Simulations indicate that the spring production peak is delayed because of increased turbidity in winter caused by upstream hydropower operation. As a consequence, the entire nutrient cycle is seasonally delayed, creating an additional stress for zooplankton and fish in the downstream lake.

  12. Performance of upstream interaction region detectors for the FIRST experiment at GSI

    CERN Document Server

    Abou-Haidar, Z; Alvarez, M A G; Anelli, M; Aumann, T; Battistoni, G; Bocci, A; Bohlen, T T; Boudard, A; Brunetti, A; Carpinelli, M; Cirrone, G A P; Cortes-Giraldo, M A; Cuttone, G; De Napoli, M; Durante, M; Fernandez-Garcia, J P; Finck, C; Gallardo, M I; Golosio, B; Iarocci, E; Iazzi, F; Ickert, G; Introzzi, R; Juliani, D; Krimmer, J; Kurz, N; Labalme, M; Leifels, Y; Le Fevre, A; Leray, S; Marchetto, F; Monaco, V; Morone, M C; Oliva, P; Paoloni, A; Patera, V; Piersanti, L; Pleskac, R; Quesada, J M; Randazzo, N; Romano, F; Rossi, D; Rosso, V; Rousseau, M; Sacchi, R; Sala, P; Sarti, A; Schuy, C; Sciubba, A; Sfienti, C; Simon, H; Sipala, V; Spiriti, E; Stuttge, L; Tropea, S; Younis, H

    2012-01-01

    The FIRST (Fragmentation of Ions Relevant for Space and Therapy) experiment at GSI has been designed to study carbon fragmentation, measuring (12)C double differential cross sections (- (2)I /- - E) for different beam energies between 100 and 1000 MeV/u. The experimental setup integrates newly designed detectors in the, so called, Interaction Region around the graphite target. The Interaction Region upstream detectors are a 250 mum thick scintillator and a drift chamber optimized for a precise measurement of the ions interaction time and position on the target. In this article we review the design of the upstream detectors along with the preliminary results of the data taking performed on August 2011 with 400 MeV/u fully stripped carbon ion beam at GSI. Detectors performances will be reviewed and compared to those obtained during preliminary tests, performed with 500 MeV electrons (at the BTF facility in the INFN Frascati Laboratories) and 80 MeV/u protons and carbon ions (at the INFN LNS Laboratories in Cata...

  13. Dynamics in phosphorus retention in wetlands upstream of Delavan Lake, Wisconsin

    Science.gov (United States)

    Robertson, Dale M.; Elder, John F.; Goddard, Gerald L.; James, William F.

    2009-01-01

    A phosphorus budget was constructed for Delavan Lake Inlet, a perennial riverine wetland with submersed and floating aquatic vegetation in southeastern Wisconsin, to better understand the phosphorus dynamics in natural wetlands and the role of wetlands in lake-rehabilitation efforts. During the growing season, the inlet served as a net source of phosphorus, primarily due to the release of phosphorus from the sediments. More phosphorus was released from the sediments of the inlet (600 kg) than was input from the upstream watershed (460 kg). This release was caused by high pH associated with high photosynthetic activity. During the remainder of the year, the inlet served as a net sink for phosphorus, retaining 6% of die phosphorus input from the watershed. Over the entire year, this wetland was a net source of over 500 kg of phosphorus to downstream Delavan Lake. A constructed riverine wetland upstream of Delavan Lake Inlet demonstrated a similar periodic release of phosphorus. However, in this case, the summer release of phosphorus was less than that trapped during the remainder of the year. The constructed wetland served as a net sink for approximately 20% of the input phosphorus on an annual time scale. The role of existing and constructed wetlands as phosphorus traps is complex. Wetlands can act as a source or a sink for phosphorus depending on the ambient conditions in die wetland. Howa wetland fits into a rehabilitation plan depends upon its net retention efficiency and the importance of the periodic releases of phosphorus to downstream waters.

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

    Science.gov (United States)

    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.

  15. Experience of molecular monitoring techniques in upstream oil and gas operations

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, Anthony F.; Anfindsen, Hilde; Liengen, Turid; Molid, Solfrid [Statoil ASA (Denmark)

    2011-07-01

    For a numbers of years, molecular monitoring tools have been used in upstream oil and gas operations but the results have given only limited added value. This paper discusses the various techniques available for upstream molecular monitoring which provides scope for identification of microbial influenced problems. The methodology, which consists of analyzing solid samples using traditional as well as molecular techniques, is detailed. Two cases were studied with the objective of determining if microbial contamination was contributing to the problem. The first case was a study of amorphous deposits in production wells and mainly iron sulphide was found. The second study was of amorphous deposits in water injection wells and the analysis showed typical components of drilling and completion fluids with some organic material. Two more cases, corrosion of tubing in a water injection well and flow line corrosion, are discussed and the results are given. From the study, it can be concluded that failure can be due to several factors, chemical and biological.

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    Luis V. Rodríguez-Durán

    2011-01-01

    Full Text Available 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.

  18. Comparative genomic analysis reveals a distant liver enhancer upstream of the COUP-TFII gene

    Energy Technology Data Exchange (ETDEWEB)

    Baroukh, Nadine; Ahituv, Nadav; Chang, Jessie; Shoukry, Malak; Afzal, Veena; Rubin, Edward M.; Pennacchio, Len A.

    2004-08-20

    COUP-TFII is a central nuclear hormone receptor that tightly regulates the expression of numerous target lipid metabolism genes in vertebrates. However, it remains unclear how COUP-TFII itself is transcriptionally controlled since studies with its promoter and upstream region fail to recapitulate the genes liver expression. In an attempt to identify liver enhancers in the vicinity of COUP-TFII, we employed a comparative genomic approach. Initial comparisons between humans and mice of the 3,470kb gene poor region surrounding COUP-TFII revealed 2,023 conserved non-coding elements. To prioritize a subset of these elements for functional studies, we performed further genomic comparisons with the orthologous pufferfish (Fugu rubripes) locus and uncovered two anciently conserved non-coding sequences (CNS) upstream of COUP-TFII (CNS-62kb and CNS-66kb). Testing these two elements using reporter constructs in liver (HepG2) cells revealed that CNS-66kb, but not CNS-62kb, yielded robust in vitro enhancer activity. In addition, an in vivo reporter assay using naked DNA transfer with CNS-66kb linked to luciferase displayed strong reproducible liver expression in adult mice, further supporting its role as a liver enhancer. Together, these studies further support the utility of comparative genomics to uncover gene regulatory sequences based on evolutionary conservation and provide the substrates to better understand the regulation and expression of COUP-TFII.

  19. Upstream proton cyclotron waves at Venus observed by Venus Express magnetometer

    Science.gov (United States)

    Delva, Magda; Volwerk, Martin; Bertucci, Cesar; Mazelle, Christian; Romanelli, Norberto; Voeroes, Zoltan

    2016-07-01

    An overview of the observations of proton cyclotron waves (PCWs) upstream of the Venus bow shock from the magnetometer data on Venus Express is given. The first detection of this specific type of upstream waves proved that newborn planetary ions from the upper exosphere are directly picked up by the instreaming solar wind. Their occurrence up to large distances (~ 9 Rv) from the planet raises the question of the existence of an extended reservoir of planetary neutral hydrogen. Also, the loss of exospheric hydrogen directly to the solar wind has implications for the evolution of the planetary atmosphere over the age of the solar system. The successful long duration of the Venus Express mission allows to study the occurrence of PCWs under solar minimum and solar maximum conditions. Results of long term studies for both cases are presented and compared. Explanations for the differences are found in the unusual nature of the current solar maximum, which was characterized by low sunspot numbers, low density and mainly moderate speed.

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

    Science.gov (United States)

    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.

  1. Upstream petroleum industry flaring and venting report : industry performance for year ending December 31, 2005

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2006-10-15

    This report provided statistical data concerning solution gas flaring and venting in the upstream petroleum industry in Alberta. In their 2003 Upstream Petroleum Industry Flaring and Venting Report, the Alberta Energy and Utilities Board (EUB) made commitments to identify and implement a number of conservation measures aimed at reducing the volumes of solution gas vented from crude bitumen operations. As a result of the measures, venting from crude bitumen batteries decreased by 18.9 per cent in 2005. Solution gas conservation for 2005 was 96.3 per cent, the highest conservation level achieved to date. Solution gas flaring for 2005 was 71.9 per cent less than the 1996 baseline. A slight increase in solution gas flaring was attributed to crude bitumen operations. Solution gas venting for 2005 was 58.6 per cent less than the 2000 venting baseline. An analysis of the data suggested that significant progress has been made in reducing solution gas flaring in Alberta, and that venting reductions realized in 2005 continue the trend of significant reductions since 2000. Although the downward trend in the reduction of venting since 2000 is encouraging, the EUB continues to be concerned about solution gas venting associated with crude bitumen projects. It was concluded that the EUB will continue to work with all stakeholders to identify additional venting reduction strategies. 5 tabs., 3 figs.

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

    Science.gov (United States)

    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. Production of Magnetic Turbulence by Cosmic Rays Drifting Upstream of Supernova Remnant Shocks

    CERN Document Server

    Niemiec, Jacek; Stroman, Thomas; Nishikawa, and Ken-Ichi

    2008-01-01

    We present results of 2D and 3D PIC simulations of magnetic turbulence production by isotropic cosmic-ray ions drifting upstream of SNR shocks. The studies aim at testing recent predictions of a strong amplification of short wavelength non-resonant wave modes and at studying the evolution of the magnetic turbulence and its backreaction on cosmic rays. We confirm the generation of the turbulent magnetic field due to the drift of cosmic rays in the upstream plasma, but show that an oblique filamentary mode grows more rapidly than the non resonant parallel modes found in analytical theory. The growth rate of the field perturbations is much slower than is estimated using a quasi-linear approach, and the amplitude of the turbulence saturates at about dB/B~1. The backreaction of the turbulence on the particles leads to an alignment of the bulk-flow velocities of the cosmic rays and the background medium, which is an essential characteristic of cosmic-ray modified shocks. It accounts for the saturation of the instab...

  4. Research on Cavitation Regions of Upstream Pumping Mechanical Seal Based on Dynamic Mesh Technique

    Directory of Open Access Journals (Sweden)

    Huilong Chen

    2014-08-01

    Full Text Available In order to study the cavitation area of the Upstream Pumping Mechanical Seal, three-dimensional microgap inner flow field of the Upstream Pumping Mechanical Seal was simulated with multiphase flow cavitation model and dynamic mesh technique based on hydrodynamic lubrication theory. Furthermore, the simulated result was compared with the experimental data. The results show that the simulated result with the Zwart-Gerber-Belamri cavitation model was much closer to the experimental data. The area of cavitation inception mainly occurred at the concave side of the spiral groove and surrounding region without spiral grooves, which was nearly covered by the inner diameter to roots of grooves; in addition, the region near the surface of the stationary ring was primary cavitation location. The area of cavitation has little relationship with the medium pressure; however, it became larger following increasing rotating speed in the range of researched operating conditions. Moreover the boundary of cavitated area was transformed from smooth to rough, which occurred in similar film thickness. When cavitation number was decreasing, which was conducive to improving the lubrication performance of sealed auxiliary, it made the sealing stability decline.

  5. VIP gene transcription is regulated by far upstream enhancer and repressor elements.

    Science.gov (United States)

    Liu, D; Krajniak, K; Chun, D; Sena, M; Casillas, R; Lelièvre, V; Nguyen, T; Bravo, D; Colburn, S; Waschek, J A

    2001-06-01

    SK-N-SH human neuroblastoma subclones differ widely in basal and second messenger induction of the gene encoding the neuropeptide vasoactive intestinal peptide (VIP). These differences were recapitulated by a chimeric gene which consisted of 5.2 kb of the human VIP gene 5' flanking sequence fused to a reporter. Subsequent gene deletion experiments revealed several regulatory regions on the gene, including a 645-bp sequence located approximately 4.0 upstream from the transcription start site. Here we examined this upstream region in detail. Inhibitory sequences were found to be present on each end of the 645-bp fragment. When removed, basal transcription increased more than 50-fold. Subsequent deletion/mutation analysis showed that the 213-bp fragment contained at least two enhancer elements. One of these was localized to an AT-rich 42-bp sequence shown by others to bind Oct proteins in neuroblastoma cells, while the other corresponded to a composite AP-1/ets element. In addition to these enhancers, a 28-bp sequence on the 213-bp fragment with no apparent homology to known silencers inhibited transcription. The studies provide molecular details of a complex regulatory region on the VIP gene that is likely to be used to finely tune the level of gene transcription in vivo.

  6. Sediment trapping analysis of flood control reservoirs in Upstream Ciliwung River using SWAT Model

    Science.gov (United States)

    Rofiq Ginanjar, Mirwan; Putra, Santosa Sandy

    2017-06-01

    The plans of Sukamahi dam and Ciawi dam construction for Jakarta flood risk reduction purpose had been proposed as feasible solutions to be implemented. However, the risk of the dam outlets clogging, caused by the sediment, is important to be anticipated. The prediction of the max sediment concentration in the reservoir is crucial for the dam operation planning. It is important to avoid the flood outlet tunnel clogging. This paper present a hydrologic sediment budget model of The Upstream Ciliwung River Basin, with flood control dam existence scenarios. The model was constructed within SWAT (Soil and Water Assessment Tools) plugin and run inside the QGIS framework. The free hydrological data from CFSR, soil data from FAO, and topographical data from CGIAR-CSI were implemented as the model input. The model resulted the sediment concentration dynamics of the Sukamahi and Ciawi reservoirs, on some suspended sediment parameter ranges. The sediment trapping efficiency was also computed by different possible dam capacity alternatives. The research findings will give a scientific decision making base for the river authority, in term of flood control dam planning, especially in The Upstream Ciliwung River Basin.

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

    Energy Technology Data Exchange (ETDEWEB)

    Yoshimura, Akari, E-mail: akari_yo@stu.musashino-u.ac.jp [Molecular Cell Biology Laboratory, Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585 (Japan); Kobayashi, Yume [Molecular Cell Biology Laboratory, Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585 (Japan); Tada, Shusuke [Department of Medical Biochemistry, Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi-shi, Chiba 274-8510 (Japan); Seki, Masayuki [Department of Biochemistry, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai-shi, Miyagi 981-8558 (Japan); Enomoto, Takemi [Molecular Cell Biology Laboratory, Research Institute of Pharmaceutical Sciences, Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo 202-8585 (Japan)

    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 analyzed 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.

  8. Identifying emerging smart grid impacts to upstream and midstream natural gas operations.

    Energy Technology Data Exchange (ETDEWEB)

    McIntyre, Annie

    2010-09-01

    The Smart Grid has come to describe a next-generation electrical power system that is typified by the increased use of communications and information technology in the generation, delivery and consumption of electrical energy. Much of the present Smart Grid analysis focuses on utility and consumer interaction. i.e. smart appliances, home automation systems, rate structures, consumer demand response, etc. An identified need is to assess the upstream and midstream operations of natural gas as a result of the smart grid. The nature of Smart Grid, including the demand response and role of information, may require changes in upstream and midstream natural gas operations to ensure availability and efficiency. Utility reliance on natural gas will continue and likely increase, given the backup requirements for intermittent renewable energy sources. Efficient generation and delivery of electricity on Smart Grid could affect how natural gas is utilized. Things that we already know about Smart Grid are: (1) The role of information and data integrity is increasingly important. (2) Smart Grid includes a fully distributed system with two-way communication. (3) Smart Grid, a complex network, may change the way energy is supplied, stored, and in demand. (4) Smart Grid has evolved through consumer driven decisions. (5) Smart Grid and the US critical infrastructure will include many intermittent renewables.

  9. Full-Scale Testing of a Mercury Oxidation Catalyst Upstream of a Wet FGD System

    Energy Technology Data Exchange (ETDEWEB)

    Gary Blythe; Jennifer Paradis

    2010-06-30

    This document presents and discusses results from Cooperative Agreement DE-FC26-06NT42778, 'Full-scale Testing of a Mercury Oxidation Catalyst Upstream of a Wet FGD System,' which was conducted over the time-period July 24, 2006 through June 30, 2010. The objective of the project was to demonstrate at full scale the use of solid honeycomb catalysts to promote the oxidation of elemental mercury in pulverized-coal-fired flue gas. Oxidized mercury is removed downstream in wet flue gas desulfurization (FGD) absorbers and collected with the byproducts from the FGD system. The project was co-funded by EPRI, the Lower Colorado River Authority (LCRA), who also provided the host site, Great River Energy, Johnson Matthey, Southern Company, Salt River Project (SRP), the Tennessee Valley Authority (TVA), NRG Energy, Ontario Power and Westar. URS Group was the prime contractor and also provided cofunding. The scope of this project included installing and testing a gold-based catalyst upstream of one full-scale wet FGD absorber module (about 200-MW scale) at LCRA's Fayette Power Project (FPP) Unit 3, which fires Powder River Basin coal. Installation of the catalyst involved modifying the ductwork upstream of one of three wet FGD absorbers on Unit 3, Absorber C. The FGD system uses limestone reagent, operates with forced sulfite oxidation, and normally runs with two FGD modules in service and one spare. The full-scale catalyst test was planned for 24 months to provide catalyst life data. Over the test period, data were collected on catalyst pressure drop, elemental mercury oxidation across the catalyst module, and mercury capture by the downstream wet FGD absorber. The demonstration period began on May 6, 2008 with plans for the catalyst to remain in service until May 5, 2010. However, because of continual increases in pressure drop across the catalyst and concerns that further increases would adversely affect Unit 3 operations, LCRA decided to end the

  10. Multipronged approach to identify and validate a novel upstream regulator of Sncg in mouse retinal ganglion cells.

    Science.gov (United States)

    Chintalapudi, Sumana R; Morales-Tirado, Vanessa M; Williams, Robert W; Jablonski, Monica M

    2016-02-01

    Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Mechanistic studies on RGCs are hindered by the lack of sufficient primary cells and consensus regarding their signature markers. Recently, γ-synuclein (SNCG) has been shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the role of Sncg in RGCs, we used a novel systems genetics approach to identify a gene that modulates Sncg expression, followed by confirmatory studies in both healthy and diseased retinae. We found that chromosome 1 harbors an expression quantitative trait locus that modulates Sncg expression in the mouse retina, and identified the prefoldin-2 (PFDN2) gene as the candidate upstream modulator of Sncg expression. Our immunohistochemical analyses revealed similar expression patterns in both mouse and human healthy retinae, with PFDN2 colocalizing with SNCG in RGCs and their axons. In contrast, in retinae from glaucoma subjects, SNCG levels were significantly reduced, although PFDN2 levels were maintained. Using a novel flow cytometry-based RGC isolation method, we obtained viable populations of murine RGCs. Knocking down Pfdn2 expression in primary murine RGCs significantly reduced Sncg expression, confirming that Pfdn2 regulates Sncg expression in murine RGCs. Gene Ontology analysis indicated shared mitochondrial function associated with Sncg and Pfdn2. These data solidify the relationship between Sncg and Pfdn2 in RGCs, and provide a novel mechanism for maintaining RGC health.

  11. Comparison of accelerated ion populations observed upstream of the bow shocks at Venus and Mars

    Directory of Open Access Journals (Sweden)

    M. Yamauchi

    2011-03-01

    Full Text Available Foreshock ions are compared between Venus and Mars at energies of 0.6~20 keV using the same ion instrument, the Ion Mass Analyser, on board both Venus Express and Mars Express. Venus Express often observes accelerated protons (2~6 times the solar wind energy that travel away from the Venus bow shock when the spacecraft location is magnetically connected to the bow shock. The observed ions have a large field-aligned velocity compared to the perpendicular velocity in the solar wind frame, and are similar to the field-aligned beams and intermediate gyrating component of the foreshock ions in the terrestrial upstream region. Mars Express does not observe similar foreshock ions as does Venus Express, indicating that the Martian foreshock does not possess the intermediate gyrating component in the upstream region on the dayside of the planet. Instead, two types of gyrating protons in the solar wind frame are observed very close to the Martian quasi-perpendicular bow shock within a proton gyroradius distance. The first type is observed only within the region which is about 400 km from the bow shock and flows tailward nearly along the bow shock with a similar velocity as the solar wind. The second type is observed up to about 700 km from the bow shock and has a bundled structure in the energy domain. A traversal on 12 July 2005, in which the energy-bunching came from bundling in the magnetic field direction, is further examined. The observed velocities of the latter population are consistent with multiple specular reflections of the solar wind at the bow shock, and the ions after the second reflection have a field-aligned velocity larger than that of the de Hoffman-Teller velocity frame, i.e., their guiding center has moved toward interplanetary space out from the bow shock. To account for the observed peculiarity of the Martian upstream region, finite gyroradius effects of the solar wind protons compared to the radius of the bow shock curvature and

  12. Meta-analysis of Arabidopsis KANADI1 direct target genes identifies basic growth-promoting module acting upstream of hormonal signaling pathways

    DEFF Research Database (Denmark)

    Xie, Yakun; Straub, Daniel; Eguen, Teinai Ebimienere;

    2015-01-01

    -wide datasets. Our analysis revealed that KAN1 acts upstream of several genes encoding auxin biosynthetic enzymes. When exposed to shade, we find three YUCCA genes, YUC2, YUC5 and YUC8 to be transcriptionally upregulated, which correlates with an increase in the levels of free auxin. When ectopically expressed......, KAN1 is able to transcriptionally repress these three YUC genes and thereby block shade-induced auxin biosynthesis. Consequently, KAN1 is able to strongly suppress shade avoidance responses. Taken together, we hypothesize that HD-ZIPIII/KAN form the basis of a basic growth-promoting module. Hypocotyl...... extension in the shade and outgrowth of new leaves both involve auxin-synthesis and -signaling, which are under the direct control by HD-ZIPIII/KAN....

  13. A spider tRNA(Ala) requires a far upstream sequence element for expression.

    Science.gov (United States)

    Cintrón, I; Capó, L; Plazaola, A; Arroyo, G; Candelas, G C

    1999-04-29

    Within the series of timed differential accumulations of small RNAs we have shown to prelude the synthesis of fibroin in the large ampullate glands of Nephila clavipes (Nc), we are currently directing our attention to the alanine tRNAs. This work reports the subcloning of the members of a tRNAAla gene cluster and the optimization of their transcription in a heterologous cell-free system derived from Bombyx mori (Bm) silkglands. Our data show that the heterologous cell-free system supports the faithful and differential transcription of the individual spider alanine tRNA genes. We are thus making use of the extract to characterize the individual genes with respect to flank-contained regulatory elements through cell-free transcription of gene derivatives. The work has been initiated with pNTA3 because of its high transcriptional activity. Interestingly, the transcription of this gene requires a far upstream sequence, an uncommon modality in tRNA genes.

  14. Strategy and technical considerations of an upstream pipeline risk assessment process

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, D.; Santander, M.; Yu, B. [Husky Energy Inc., Calgary, AB (Canada)

    2010-07-01

    This paper presented an upstream pipeline integrity management program developed by Husky Energy. Three levels of risk assesment were used to optimize technical expertise and resources. The first level consisted of prioritizing gathering systems for the net assessment level. Level 2 was comprised of a subject matter expert (SME) based assessment performed in collaboration with industry operators and integrity management specialists. The assessment focused on the development of a mitigation strategy for higher risk pipelines. Level 3 investigated frequent failures of systematic mechanisms and pipelines with a high risk of failure. The risk assessment process was shown to effectively manage pipeline integrity when risk validation and mitigation actions were implemented, closely followed up, and evaluated in relation to their consistency. 9 refs., 3 tabs., 7 figs.

  15. A Study on the Active Induction Control of Upstream Wind Turbines for total power increases

    Science.gov (United States)

    Kim, Hyungyu; Kim, Kwansoo; Paek, Insu; Bottasso, Carlo L.; Campagnolo, Filippo

    2016-09-01

    In this study, the effect of active induction control of upstream wind turbines is investigated. Two scaled wind turbines having a rotor diameter of 1 m with a spacing of four times of the rotor diameter were used to experimentally validate the concept. Also, an in-house c code was used to simulate the same two wind turbines and see if the experimental observations can be obtained. From the experiment, approximately 0.81% increase of total power could be observed. Although the simulation results were not exactly the same as the experimental results but the shape was similar and the maximum power increase of 0.27% was predicted. Also from further simulation using NREL 5MW wind turbines instead of scaled wind turbines with realistic ambient turbulence intensity, it was found that the power increase could become more than 1%.

  16. Relativistic electrons produced by foreshock disturbances observed upstream of the Earth's bow shock

    Science.gov (United States)

    Wilson, Lynn Bruce, III; Sibeck, David G.; Turner, Drew L.; Osmane, Adnane; Caprioli, Damiano; Angelopoulos, Vassilis

    2017-04-01

    It has been known for years that charged particles can be accelerated by high Mach number collisionless shock waves. The accelerated particles can stream away upstream to form a foreshock region in communication with the shock. Due to differences in gyroradii, ions are more readily accelerated than electrons by collisionless shocks. These energetic, suprathermal ions stream against the incident flow providing free energy that can generate foreshock disturbances - large-scale (i.e., tens to thousands of thermal ion gyroradii), transient ( 5-10 per day) structures. They have recently been found to accelerate ions to energies of several keV [e.g., Wilson et al., 2013] and even produce their own mini foreshocks [e.g., Liu et al., 2016]. While the high Mach number (M > 40) Kronian bow shock can generate MeV electrons [e.g., Masters et al., 2013], the much weaker Earth's bow shock (1 ≤ M questions in heliospheric and astrophysical plasmas.

  17. Identification of a Positive Cis-Element Upstream of Human NKX3.1 Gene

    Institute of Scientific and Technical Information of China (English)

    An-Li JIANG; Peng-Ju ZHANG; Xiao-Yan HU; Wei-Wen CHEN; Feng KONG; Zhi-Fang LIU; Hui-Qing YUAN; Jian-Ye ZHANG

    2005-01-01

    NKX3.1 is a prostate-specific homeobox gene related to prostate development and prostate cancer. In this work, we aimed to identify precisely the functional cis-element in the 197 bp region (from -1032 to -836 bp) of the NKX3.1 promoter (from -1032 to +8 bp), which was previously identified to present positive regulatory activity on NKX3.1 expression, by deletion mutagenesis analysis and electrophoretic mobility shift assay (EMSA). A 16 bp positive cis-element located between -920 and -905 bp upstream of the NKX3.1 gene was identified by deletion mutation analysis and proved to be a functional positive cis-element by EMSA. It will be important to further study the functions and regulatory mechanisms of this positive cis-element in NKX3.1 gene expression.

  18. A NUMERICAL SIMULATION OF 3-D INNER FLOW IN UP-STREAM PUMPING MECHANICAL SEAL

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jin-feng; YUAN Shou-qi; FU Yong-hong; FANG Yu-jian

    2006-01-01

    Numerical simulation of 3-D inner flow between Up-stream Pumping Mechanical Face Seals (UPMFS) faces was initially done by CFD software, which made the flow visualization come true.Simulation results directly discover the action of hydrodynamic lubrication, and by comparison with that of Conventional Mechanic Face Seals (CMFS), the advantage over bigger bearing capability, less friction and much less leakage are explained clearly.Otherwise there are also some different ideas and results from precedent analysis and computational research results: dynamic and static pressure profiles can be obtained respectively instead of the analytic total pressure distribution only, pressure distribution is nonlinear, while always be solved as linear, lower pressure is observed at the area of inner diameter caused by the grooves, but its possible cavitations effects to the performance of UPMFS still need further study.

  19. Proton Cyclotron Waves Upstream from Mars: Observations from Mars Global Surveyor

    CERN Document Server

    Romanelli, Norberto; Gomez, Daniel; Mazelle, Christian; Delva, Magda

    2013-01-01

    We present a study on the properties of electromagnetic plasma waves in the region upstream of the Martian bow shock, detected by the magnetometer and electron reflectometer (MAG / ER) onboard the Mars Global Surveyor (MGS) spacecraft during the period known as Science Phasing Orbits (SPO). The frequency of these waves, measured in the MGS reference frame (SC), is close to the local proton cyclotron frequency. Minimum variance analysis (MVA) shows that these 'proton cyclotron frequency' waves (PCWs) are characterized - in the SC frame - by a left-hand, elliptical polarization and propagate almost parallel to the background magnetic field. They also have a small degree of compressibility and an amplitude that decreases with the increase of the interplanetary magnetic field (IMF) cone angle and radial distance from the planet. The latter result supports the idea that the source of these waves is Mars. In addition, we find that these waves are not associated with the foreshock . Empirical evidence and theoretica...

  20. DEVELOPMENT OF A VIRTUAL INTELLIGENCE TECHNIQUE FOR THE UPSTREAM OIL INDUSTRY

    Energy Technology Data Exchange (ETDEWEB)

    Iraj A. Salehi; Shahab D. Mohaghegh; Samuel Ameri

    2004-09-01

    The objective of the research and development work reported in this document was to develop a Virtual Intelligence Technique for optimization of the Preferred Upstream Management Practices (PUMP) for the upstream oil industry. The work included the development of a software tool for identification and optimization of the most influential parameters in upstream common practices as well as geological, geophysical and reservoir engineering studies. The work was performed in cooperation with three independent producing companies--Newfield Exploration, Chesapeake Energy, and Triad Energy--operating in the Golden Trend, Oklahoma. In order to protect data confidentiality, these companies are referred to as Company One, Two, Three in a randomly selected order. These producing companies provided geological, completion, and production data on 320 wells and participated in frequent technical discussions throughout the project. Research and development work was performed by Gas Technology Institute (GTI), West Virginia University (WVU), and Intelligent Solutions Inc. (ISI). Oklahoma Independent Petroleum Association (OIPA) participated in technology transfer and data acquisition efforts. Deliverables from the project are the present final report and a user-friendly software package (Appendix D) with two distinct functions: a characterization tool that identifies the most influential parameters in the upstream operations, and an optimization tool that seeks optimization by varying a number of influential parameters and investigating the coupled effects of these variations. The electronic version of this report is also included in Appendix D. The Golden Trend data were used for the first cut optimization of completion procedures. In the subsequent step, results from soft computing runs were used as the guide for detailed geophysical and reservoir engineering studies that characterize the cause-and-effect relationships between various parameters. The general workflow and the main

  1. On a source of electron impact ionization in Io's upstream atmosphere

    Science.gov (United States)

    Shaposhnikov, V. E.; Zaitsev, V. V.; Rucker, H. O.; Litvinenko, G. V.; Konovalenko, A. A.

    2013-09-01

    A mechanism for the ionization of Io's atmosphere due to the moon's motion through the Jovian magnetic field is considered. Attention is paid to the important role of charge separation in the upstream part of Io's ionosphere and accumulation of electrons and positive ions on the low and top ionospheric boundaries which results in (a) the creation of longitudinal component (with respect to the Jovian magnetic field lines) of polarization electric field, (b) the driving of Bounemann plasma turbulence, and (c) the heating of electrons and the ionization of neutrals. Estimations show that the proposed mechanism can essentially heat the electrons and increase the electron density. The increase with the plasma density and the electron temperature can result in an ionospheric plasma distribution and overcomes the difficulty with generation of the most bright part of UV emission of the Io's equatorial spots.

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

    Science.gov (United States)

    Yoshimura, Akari; Kobayashi, Yume; Tada, Shusuke; Seki, Masayuki; Enomoto, Takemi

    2014-09-12

    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 analyzed the functional interaction between WRNIP1 and Polη by generating knockouts of both genes in DT40 chicken cells. Disruption of WRNIP1 in Polη-disrupted (POLH(-/-)) 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.

  3. HTL heavy oil upgrading a key solution for heavy oil upstream and midstream operations

    Energy Technology Data Exchange (ETDEWEB)

    Silverman, M.A.; Pavel, S. K.; Hillderman, M. D. [Ivanhoe Energy (Canada)

    2011-07-01

    In the oil industry, heavy oil has become a strategic resource due to the decline of light crude oil reserves and the rising energy demand. Many challenges have to be overcome during heavy oil development and Ivanhoe Energy has developed a new process to address these issues. The heavy to light (HTL) upgrading process converts heavy crude oil into lighter and more valuable synthetic oil. This process can be used upstream, midstream or near the well head. The aim of this paper is to present the history of HTL's development, the technology itself and its performance and advantages. HTL captures the majority of the market value difference between heavy and light oil while eliminating diluent requirement; in addition this technology is economic at small scales. The HTL upgrading process presented herein is a simple and efficient solution for exploiting heavy oil and bitumen reserves.

  4. Moving upstream: why rehabilitative justice in military discharge proceedings serves a public health interest.

    Science.gov (United States)

    Seamone, Evan R; McGuire, James; Sreenivasan, Shoba; Clark, Sean; Smee, Daniel; Dow, Daniel

    2014-10-01

    The cultural divide between US military and civilian institutions amplifies the consequences of military discharge status on public health and criminal justice systems in a manner that is invisible to a larger society. Prompt removal of problematic wounded warriors through retributive justice is more expedient than lengthy mental health treatment. Administrative and punitive discharges usually preclude Department of Veterans Affairs eligibility, posing a heavy public health burden. Moving upstream--through military rehabilitative justice addressing military offenders' mental health needs before discharge--will reduce the downstream consequences of civilian maladjustment and intergenerational transmission of mental illness. The public health community can play an illuminating role by gathering data about community effect and by advocating for policy change at Department of Veterans Affairs and community levels.

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

    Directory of Open Access Journals (Sweden)

    Masfique Mehedi

    Full Text Available 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.

  6. Effects of fuel injection on mixing and upstream interactions in supersonic flow

    Science.gov (United States)

    Tu, Qiuya

    Scramjet engine performance has been studied experimentally and computationally almost under steady-state conditions. Transients of the airflow and fueling in the scramjet's isolator or combustor create important fluid-dynamic/ combustion interactions. Spark schlieren photography was employed to study the effects of pressure rise in the combustion chamber on the isolator flow at three conditions with isolator entrance Mach number of 1.6, 1.9 and 2.5, covering the range of dual-mode combustion and transition to full scramjet operation. Heat release through combustion in the model scramjet was simulated by incrementally blocking the flow exit until upstream-interaction was induced and a shock train formed in the isolator. Theoretical predictions of the pressure rise in the isolator under separated flow conditions were calculated, which agreed well with the experimental data. The prediction is sensitive to the accurate modeling of the isolator inlet conditions and the correct selection of wall friction coefficient. Gaseous helium and argon have been transversely injected into a Mach 1.6 airflow simulating a light and a heavy fuel injection behind a thin triangular pylon placed upstream, in the isolator, which has a negligible impact on pressure losses. Planar laser-induced fluorescence (PLIF) was used to observe the penetration and mixing in the test section at three cross-sections including the recirculation region and beyond. Results were compared to the no-pylon cases, which showed the presence of the pylon resulted in improving both penetration and spreading of the jet. Simulation for shock wave/ boundary-layer interaction was conducted in Fluent for case of M=1.9 at 60% blockage by using k-ε RNG model with two different near wall treatments. In both cases, the shock ran out of isolator before the computation converged, this is different from experimental results. Proper actual wall friction force may have a very important effect on the computation, which needs

  7. Energy optimization for upstream data transfer in 802.15.4 beacon-enabled star formulation

    Science.gov (United States)

    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.

  8. A bow-shaped thermal structure traveling upstream of the zonal wind flow of Venus atmosphere

    Science.gov (United States)

    Taguchi, Makoto; Fukuhara, Tetsuya; Imamura, Takeshi; Kouyama, Toru; Nakamura, Masato; Sato, Takao M.; Ueno, Munetaka; Suzuki, Makoto; Iwagami, Naomoto; Sato, Mitsuteru; Hashimoto, George L.; Takagi, Seiko; Akatsuki Science Team

    2016-10-01

    The Longwave Infrared Camera (LIR) onboard the Japanese Venus orbiter Akatsuki acquires a snap shot of Venus in the middle infrared region, and provides a brightness temperature distribution at the cloud-top altitudes of about 65 km. Hundreds of images taken by LIR have been transferred to the ground since the successful Venus orbit insertion of Akatsuki on Dec. 7, 2015. Here we report that a bow shaped thermal structure extending from the northern high latitudes to the southern high latitudes was found in the brightness temperature map on Dec. 7, 2015, and that it lasted for four days at least surprisingly at almost same geographical position. The bow shape structure looks symmetrical with the equator, and consists of a high temperature region in east or upstream of the background strong westward wind or the super rotation of the Venus atmosphere followed by a low temperature region in west with an amplitude of 5 K. It appeared close to the evening terminator in the dayside, and seems not to have stayed in the same local time rather to have co-rotated with the slowly rotating ground where the western part of Aphrodite Continent was below the center of the bow shape. Meridionally aligned dark filaments similar to the bow shape structure in shape but in much smaller scale were also identified in the brightness temperature map on Dec. 7, and they propagated upstream of the zonal wind as well. The bow shape structure disappeared when LIR observed the same local time and longitude in the earliest opportunity on Jan. 16, 2016. Similar events, though their amplitudes were less than 1 K, were found on Apr. 15 and 26, 2016, but they appeared in different local times and longitudes. A simulation of a gravity wave generated in the lower atmosphere and propagating upward reproduces the observed bow shape structure. The bow shape structure could be a signature of transferring momentum from the ground to the upper atmosphere.

  9. Automation and control trends in the upstream sector of the oil industry

    Energy Technology Data Exchange (ETDEWEB)

    Plucenio, Agustinho; Pagano, Daniel J. [Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil). Programa de Recursos Humanos da ANP em Automacao, Controle e Instrumentacao para a Industria do Petroleo e Gas, PRH-34

    2004-07-01

    The need to continuously improve the aspects of Health, Safety and Environment to operators, installation's security, optimization of oil reservoir recovery in wells operating with different artificial lift methods, subject to different secondary recovery techniques, has motivated the development of technologies in the automation and control for the upstream sector of the oil industry. While the application of control and automation techniques is well established in the downstream sector of the oil industry that is not the case in the downstream sector. One tendency in this sector is the utilization of control via Field bus Networks. This technology uses equipment that communicate with each other in a two wire digital network and can be programmed to execute function blocks algorithms designed to perform a designed control strategy. The most noticeable benefits are the improvements in the process performance and the equipment reusability and interoperability. Proprietary solutions can be replaced by systems composed of equipment supplied by different manufacturers connected in the same network. These equipment operate according to a strategy designed by automation and control engineers under the supervision of professionals working in computer terminals located in different company departments. Other gains are a better understanding about the industry processes, application of optimization techniques, fault detection, equipment maintenance follow-up, and improved operators working conditions and workers qualification. Other tendencies are: permanent well monitoring. Either with installation of down hole sensors based on fiber grating sensors or surface sensors using embedded electronic processors. Developments of instrumentation technology for low cost multiphase flow measurements. Application of control techniques for flow regime control and optimization of reservoir recovery through better identification, optimization and Model Based Predictive Control

  10. Circadian and Light Regulated Expression of CBFs and their Upstream Signalling Genes in Barley

    Science.gov (United States)

    Novák, Aliz; Ahres, Mohamed; Gulyás, Zsolt; Monostori, István; Galiba, Gábor; Vágújfalvi, Attila

    2017-01-01

    CBF (C-repeat binding factor) transcription factors show high expression levels in response to cold; moreover, they play a key regulatory role in cold acclimation processes. Recently, however, more and more information has led to the conclusion that, apart from cold, light—including its spectra—also has a crucial role in regulating CBF expression. Earlier, studies established that the expression patterns of some of these regulatory genes follow circadian rhythms. To understand more of this complex acclimation process, we studied the expression patterns of the signal transducing pathways, including signal perception, the circadian clock and phospholipid signalling pathways, upstream of the CBF gene regulatory hub. To exclude the confounding effect of cold, experiments were carried out at 22 °C. Our results show that the expression of genes implicated in the phospholipid signalling pathway follow a circadian rhythm. We demonstrated that, from among the tested CBF genes expressed in Hordeum vulgare (Hv) under our conditions, only the members of the HvCBF4-phylogenetic subgroup showed a circadian pattern. We found that the HvCBF4-subgroup genes were expressed late in the afternoon or early in the night. We also determined the expression changes under supplemental far-red illumination and established that the transcript accumulation had appeared four hours earlier and more intensely in several cases. Based on our results, we propose a model to illustrate the effect of the circadian clock and the quality of the light on the elements of signalling pathways upstream of the HvCBFs, thus integrating the complex regulation of the early cellular responses, which finally lead to an elevated abiotic stress tolerance. PMID:28829375

  11. Score Correlation

    OpenAIRE

    Fabián, Z. (Zdeněk)

    2010-01-01

    In this paper, we study a distribution-dependent correlation coefficient based on the concept of scalar score. This new measure of association of continuous random variables is compared by means of simulation experiments with the Pearson, Kendall and Spearman correlation coefficients.

  12. Upstream dams and downstream water allocation: The case of the Hadejia-Jama'are floodplain, northern Nigeria

    Science.gov (United States)

    Barbier, Edward B.

    2003-11-01

    This paper models the economic and hydrological impacts of upstream water diversion on downstream floodplain activities. The model is illustrated and applied to the example of the Hadejia-Jama'are River Basin, northern Nigeria. Full implementation of all the upstream dams and large-scale irrigation schemes in the river basin would produce losses of US20.2-20.9 million in present value terms in terms of flooplain agriculture, forestry, and fishing. The associated annual losses from declining groundwater levels in surrounding areas would be around 1.2 million for tube well irrigation and 4.76 million for domestic water consumption. The introduction of a regulated flooding regime for upstream dams would probably protect the groundwater recharge function of the downstream floodplain and reduce substantially the losses to agriculture, forestry, and fishing to around 15.4-16.5 million.

  13. Temperature Influences on the Expression of GFP Promoted by the Upstream Sequence of cpcB from Arthrospira platensis

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In order to investigate the regulation mechanism of the phycocyanin gene, a series of functional analyses of the upstream sequence of cpcB gene from Arthrospira platensis were conducted in E. coli with green fluorescent protein encoding gene (gfp) as the reporter. Results showed that the gfp gene could express at a high level under the promotion of the upstream sequence, suggesting the existence of some strong promoter elements in it. The expression of GFP was influenced by temperature. Higher temperature led to higher expression level. The bioinformatics analyses followed by mutation analyses on the secondary structure of translation initiation region (TIR) revealed that RNA thermosensor might account for the temperature regulation.

  14. Temperature influences on the expression of GFP promoted by the upstream sequence of cpcB from Arthrospira platensis

    Science.gov (United States)

    Lu, Yongzhong; Zhang, Xuecheng

    2007-07-01

    In order to investigate the regulation mechanism of the phycocyanin gene, a series of functional analyses of the upstream sequence of cpcB gene from Arthrospira platensis were conducted in E. coli with green fluorescent protein encoding gene (gfp) as the reporter. Results showed that the gfp gene could express at a high level under the promotion of the upstream sequence, suggesting the existence of some strong promoter elements in it. The expression of GFP was influenced by temperature. Higher temperature led to higher expression level. The bioinformatics analyses followed by mutation analyses on the secondary structure of translation initiation region (TIR) revealed that RNA thermosensor might account for the temperature regulation.

  15. Impact of groundwater pumping vs. a large upstream dam on streamflows and temperature under varying climate

    Science.gov (United States)

    Risley, J. C.; Constantz, J. E.; Essaid, H.; Rounds, S. A.

    2009-12-01

    The relative impact of in-reach groundwater pumping versus a large upstream dam on streamflows and stream temperature was analyzed for humid, semiarid, and arid conditions with long dry seasons representing typical climate conditions where large dams are present, such as the western US or eastern Australia. A MODFLOW-2000 model, with the SFR1 stream-aquifer interaction module, the streamflow-routing package, and the grid-block rewetting option, was constructed to simulate monthly streamflows for 12 watershed scenarios described below. For each scenario streamflow output became input into a stream temperature simulation model. Stream temperatures were simulated using the CE-QUAL-W2 water quality model over a 110 km model grid, with the presence/absence of a dam at the top of the reach and pumping in the lower 60 km of the reach. Measured meteorological data from three representative locations in Oregon and California were used as model input to simulate the impact of varying climate conditions on streamflows and stream temperature. For each climate condition four hypothetical watershed scenarios were modeled: (1) natural [no dam or pumping], (2) large upstream dam present, (3) dam with in-reach pumping, and (4) no dam with pumping continued, resulting in 12 cases. Dam removal, in the presence or absence of pumping, created significant changes in streamflow resulting in significant changes in stream temperature throughout the year for all three climate conditions. From March to August, the presence of a dam caused monthly-mean stream temperatures to decrease on average by approximately 3.0, 2.5, and 2.0 oC for the humid, semiarid, and arid conditions, respectively; however, stream temperatures generally increased from September to February. Pumping caused stream temperatures to warm in summer and cool in winter by generally less than 0.5 oC. Though the impact of a large dam led to greater changes in stream temperature than the impact of pumping, ephemeral conditions

  16. Pilot Testing of Mercury Oxidation Catalysts for Upstream of Wet FGD Systems

    Energy Technology Data Exchange (ETDEWEB)

    Gary Blythe; Conor Braman; Katherine Dombrowski; Tom Machalek

    2010-12-31

    This document is the final technical report for Cooperative Agreement DE-FC26-04NT41992, 'Pilot Testing of Mercury Oxidation Catalysts for Upstream of Wet FGD Systems,' which was conducted over the time-period January 1, 2004 through December 31, 2010. The objective of this project has been to demonstrate at pilot scale the use of solid catalysts and/or fixed-structure mercury sorbents to promote the removal of total mercury and oxidation of elemental mercury in flue gas from coal combustion, followed by wet flue gas desulfurization (FGD) to remove the oxidized mercury at high efficiency. The project was co-funded by the U.S. DOE National Energy Technology Laboratory (DOE-NETL), EPRI, Great River Energy (GRE), TXU Energy (now called Luminant), Southern Company, Salt River Project (SRP) and Duke Energy. URS Group was the prime contractor. The mercury control process under development uses fixed-structure sorbents and/or catalysts to promote the removal of total mercury and/or oxidation of elemental mercury in the flue gas from coal-fired power plants that have wet lime or limestone FGD systems. Oxidized mercury not adsorbed is removed in the wet FGD absorbers and leaves with the byproducts from the FGD system. The project has tested candidate materials at pilot scale and in a commercial form, to provide engineering data for future full-scale designs. Pilot-scale catalytic oxidation tests have been completed for periods of approximately 14 to19 months at three sites, with an additional round of pilot-scale fixed-structure sorbent tests being conducted at one of those sites. Additionally, pilot-scale wet FGD tests have been conducted downstream of mercury oxidation catalysts at a total of four sites. The sites include the two of three sites from this project and two sites where catalytic oxidation pilot testing was conducted as part of a previous DOE-NETL project. Pilot-scale wet FGD tests were also conducted at a fifth site, but with no catalyst or fixed

  17. Risk assessment in the upstream crude oil supply chain: Leveraging analytic hierarchy process

    Science.gov (United States)

    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. Assessment of Total Suspended Sediment and Bed Sediment Grains in Upstream Areas of Lata Berangin, Terengganu

    Directory of Open Access Journals (Sweden)

    Noorjima Abd Wahab

    2016-10-01

    Full Text Available The amount of suspended sediment yield and the size of sediment grains an indicator of hydrological cycle, especially in the river. The sediment transportation process is one of the measurements of water resources management. Equilibrium of the river depends on the flow rate of water and by several factors such as frequency of rainfall, climate changes and land use activities that changes then effected to the river flow. Sedimentation problems occur in reservoirs, rivers, lakes, flood plains and offshore. This study was carried out in the upstream area, Lata Berangin, Hulu Keruak, Besut, Terengganu. This study was implemented to prove the sedimentation problem, especially the formation of total suspended sediment (TSS and the bed sediment grain size. There are three important parameters were quantified in this study such as the distribution of sediment grain size (phi, TSS (mg/L and the river discharge values (Q (m³/s. The technique of analysis of primary data obtained which determine the bed sediment grain size according with the procedure of Gerald and Kenneth and the phi (ϕ value in this study using the scale Udden-Wentworth that included median, mean, standard deviation, skewness, kurtosis and the Gravimetric Method used to analyze the concentration TSS is the Gravimetric Method. From the result, the highest TSS up to 6.0 mg/L which is categorized under the class I, based on the National Water Quality Standard. Overall, the estimated daily-suspended sediment load values up to 1.1649 tonne/day at Station 2.  Then, from the statistics for the median, mean, standard deviation, skewness and kurtosis showed that the size of sediment falls between phi -0.30φ to phi -1.00 φ which classified as very coarse and the majority of the sediment texture and a very leptokurtic, leptokurtic texture showed sedimentation production is not so high. Overall, the sedimentation problem in Lata Berangin, Hulu Keruak still in stable level. Most of this upstream

  19. CalA, a Cyanobacterial AbrB Protein, Interacts with the Upstream Region of hypC and Acts as a Repressor of Its Transcription in the Cyanobacterium Nostoc sp. Strain PCC 7120▿ †

    Science.gov (United States)

    Agervald, Åsa; Zhang, Xiaohui; Stensjö, Karin; Devine, Ellenor; Lindblad, Peter

    2010-01-01

    The filamentous, heterocystous, nitrogen-fixing cyanobacterium Nostoc sp. strain PCC 7120 may contain, depending on growth conditions, up to two hydrogenases directly involved in hydrogen metabolism. HypC is one out of at least seven auxiliary gene products required for synthesis of a functional hydrogenase, specifically involved in the maturation of the large subunit. In this study we present a protein, CalA (Alr0946 in the genome), belonging to the transcription regulator family AbrB, which in protein-DNA assays was found to interact with the upstream region of hypC. Transcriptional investigations showed that calA is cotranscribed with the downstream gene alr0947, which encodes a putative protease from the abortive infection superfamily, Abi. CalA was shown to interact specifically not only with the upstream region of hypC but also with its own upstream region, acting as a repressor on hypC. The bidirectional hydrogenase activity was significantly downregulated when CalA was overexpressed, demonstrating a correlation with the transcription factor, either direct or indirect. In silico studies showed that homologues to both CalA and Alr0947 are highly conserved proteins within cyanobacteria with very similar physical organizations of the corresponding structural genes. Possible functions of the cotranscribed downstream protein Alr0947 are presented. In addition, we present a three-dimensional (3D) model of the DNA binding domain of CalA and putative DNA binding mechanisms are discussed. PMID:20023111

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

    Science.gov (United States)

    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.

  1. Genome-Wide Search for Translated Upstream Open Reading Frames in Arabidopsis Thaliana.

    Science.gov (United States)

    Hu, Qiwen; Merchante, Catharina; Stepanova, Anna N; Alonso, Jose M; Heber, Steffen

    2016-03-01

    Upstream open reading frames (uORFs) are open reading frames that occur within the 5' UTR of an mRNA. uORFs have been found in many organisms. They play an important role in gene regulation, cell development, and in various metabolic processes. It is believed that translated uORFs reduce the translational efficiency of the main coding region. However, only few uORFs are experimentally characterized. In this paper, we use ribosome footprinting together with a semi-supervised approach based on stacking classification models to identify translated uORFs in Arabidopsis thaliana. Our approach identified 5360 potentially translated uORFs in 2051 genes. GO terms enriched in genes with translated uORFs include catalytic activity, binding, transferase activity, phosphotransferase activity, kinase activity, and transcription regulator activity. The reported uORFs occur with a higher frequency in multi-isoform genes, and some uORFs are affected by alternative transcript start sites or alternative splicing events. Association rule mining revealed sequence features associated with the translation status of the uORFs. We hypothesize that uORF translation is a complex process that might be regulated by multiple factors. The identified uORFs are available online at:https://www.dropbox.com/sh/zdutupedxafhly8/AABFsdNR5zDfiozB7B4igFcja?dl=0. This paper is the extended version of our research presented at ISBRA 2015.

  2. Reactive Oxygen Species in Planarian Regeneration: An Upstream Necessity for Correct Patterning and Brain Formation

    Directory of Open Access Journals (Sweden)

    Nicky Pirotte

    2015-01-01

    Full Text Available Recent research highlighted the impact of ROS as upstream 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.

  3. Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells.

    Science.gov (United States)

    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

    2015-08-18

    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 upstream alteration and a general downstream point of vulnerability to prevent or overcome resistance to targeted drugs.

  4. Obese locus in WNIN/obese rat maps on chromosome 5 upstream of leptin receptor.

    Directory of Open Access Journals (Sweden)

    Rajender Rao Kalashikam

    Full Text Available WNIN/Obese (WNIN/Ob rat a new mutant model of metabolic syndrome was identified in 1996 from an inbred Wistar rat strain, WNIN. So far several papers are published on this model highlighting its physical, biochemical and metabolic traits. WNIN/Ob is leptin resistant with unaltered leptin or its receptor coding sequences--the two well-known candidate genes for obesity. Genotyping analysis of F2 progeny (raised from WNIN/Ob × Fisher--344 in the present study localized the mutation to a recombinant region of 14.15cM on chromosome 5. This was further corroborated by QTL analysis for body weight, which narrowed this region to 4.43 cM with flanking markers D5Rat256 & D5Wox37. Interval mapping of body weight QTL shows that the LOD score peak maps upstream of leptin receptor and shows an additive effect suggesting this as a novel mutation and signifying the model as a valuable resource for studies on obesity and metabolic syndrome.

  5. The role of upstream-migrating knick points in turbidity current channels

    Science.gov (United States)

    Cartigny, Matthieu; Hughes Clarke, John; Stacey, Cooper; Hage, Sophie; Parsons, Daniel; Talling, Peter; Azpiroz, Maria; Clare, Michael; Eggenhuisen, Joris; Hizzett, Jamie; Hunt, James; Lintern, Gwyn; Sumner, Esther; Vellinga, Age; Vendettouli, Daniella; Wood, Jon

    2017-04-01

    High-resolution bathymetric images of turbidity current channels reveal the existence of a wide range of bedforms within these systems. Knick points are the dominant kilometre-scale bedform in most sandy systems. These knick points are thought to initiate and maintain submarine channels, and they would therefore play a key role the transport of sediment and nutrients to the deep sea. In contrast to their important role very little is known about knick points. What drives the formation of a knick point? Are they remnant headwalls of landslide, or are they related to supercritical turbidity currents? Are they a purely erosional feature? Do they have any preservation potential in the rock record? Here we present data collected from knick points in an active turbidity current channel on a fjord floor in British Colombia, Canada. These data show how trains of knick points migrate several hundred metres upstream every year. We use repeat surveys to show how knick points are a combined erosional-depositional feature. Furthermore, we have deployed several instruments over the knick points to study how the knick points interact with the passing turbidity currents. Finally, we use repeat surveys and cores to explore the potential architecture and facies association associated to knick points.

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

    Science.gov (United States)

    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.

  7. Moving policies upstream to mitigate the social determinants of early childbearing.

    Science.gov (United States)

    SmithBattle, Lee

    2012-01-01

    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 upstream 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.

  8. SEQUENCING DELIVERIES TO MINIMIZE INVENTORY HOLDING COST WITH DOMINANT UPSTREAM SUPPLY CHAIN PARTNER

    Institute of Scientific and Technical Information of China (English)

    Sushil GUPTA; Manoj VANAJAKUMARI; Chelliah SRISKANDARAJAH

    2009-01-01

    This paper studies a two stage supply chain with a dominant upstream partner. Manufacturer is the dominant partner and operates in a Just-in-Time environment. Production is done in a single manufacturing line capable of producing two products without stopping the production for switching from one product to the other. The manufacturer imposes constraints on the distributor by adhering to his favorable production schedule which minimizes his manufacturing cost. Distributor on the other hand caters to retailers' orders without incurring any shortages and is responsible for managing the inventory of finished goods. Adhering to manufacturer's schedule may lead to high inventory carrying costs for the distributor. Distributor's problem, which is to find an optimal distribution sequence which minimizes the distributor's inventory cost under the constraint imposed by the manufacturer is proved NP-Hard by Manoj et al. (2008). Therefore, solving large size problems require efficient heuristics. We develop algorithms for the distribution problem by exploiting its structural properties. We propose two heuristics and use their solutions in the initial population of a genetic algorithm to arrive at solutions with an average deviation of less than 3.5% from the optimal solution for practical size problems.

  9. STEREO/SEPT observations of upstream particle events: almost monoenergetic ion beams

    Directory of Open Access Journals (Sweden)

    A. Klassen

    2009-05-01

    Full Text Available We present observations of Almost Monoenergetic Ion (AMI events in the energy range of 100–1200 keV detected with the Solar Electron and Proton Telescope (SEPT onboard both STEREO spacecraft. The energy spectrum of AMI events contain 1, 2, or 3 narrow peaks with the relative width at half maximum of 0.1–0.7 and their energy maxima varies for different events from 120 to 1200 keV. These events were detected close to the bow-shock (STEREO-A&B and to the magnetopause at STEREO-B as well as unexpectedly far upstream of the bow-shock and far away from the magnetotail at distances up to 1100 RE (STEREO-B and 1900 RE (STEREO-A. We discuss the origin of AMI events, the connection to the Earth's bow-shock and to the magnetosphere, and the conditions of the interplanetary medium and magnetosphere under which these AMI bursts occur. Evidence that the detected spectral peaks were caused by quasi-monoenergetic beams of protons, helium, and heavier ions are given. Furthermore, we present the spatial distribution of all AMI events from December 2006 until August 2007.

  10. Mapping Uncertainties in the Upstream: The Case of PLGA Nanoparticles in Salmon Vaccines.

    Science.gov (United States)

    Nielsen, Kåre Nolde; Fredriksen, Børge Nilsen; Myhr, Anne Ingeborg

    2011-04-01

    The diversity of nanotechnologies and of the governance challenges that their applications raise calls for exploration and learning across different cases. We present an Upstream Oversight Assessment (UOA) of expected benefits and potential harms of nanoparticles made of a synthetic polymer (PLGA) to improve vaccines for farmed salmon. Suggested by Jennifer Kuzma and colleagues, an UOA may help identify and prioritise research needs, and it may support evaluations of the adequacy of relevant existing regulatory frameworks. In this work, the UOA approach is modified and supported with elements from the uncertainty analysis framework developed by Warren Walker and colleagues. Empirically, we draw on relevant available published literature and insights generated in an ongoing nanoparticle salmon vaccine project, in which one of the authors participates. Nanotechnologies have not previously been encountered in the regulatory context of fish vaccines, which in part raises unique challenges due to prospective large scale vaccine use in semi-open aquatic systems. Strengthened through cooperation between ELSA and technology researchers we found the UOA useful for an early mapping of benefits and concerns, and for identifying areas in need of further research prior to a nanoparticle based salmon vaccine is developed and taken into use. We consider our approach to represent one among several complementing initiatives that seek to contribute to early stage evaluations of possible negative side effects, broadly conceived, in order to facilitate a more robust nanotechnology development.

  11. Translation efficiency of mRNAs is increased by antisense oligonucleotides targeting upstream open reading frames.

    Science.gov (United States)

    Liang, Xue-Hai; Shen, Wen; Sun, Hong; Migawa, Michael T; Vickers, Timothy A; Crooke, Stanley T

    2016-08-01

    Increasing the levels of therapeutic proteins in vivo remains challenging. Antisense oligonucleotides (ASOs) are often used to downregulate gene expression or to modify RNA splicing, but antisense technology has not previously been used to directly increase the production of selected proteins. Here we used a class of modified ASOs that bind to mRNA sequences in upstream open reading frames (uORFs) to specifically increase the amounts of protein translated from a downstream primary ORF (pORF). Using ASO treatment, we increased the amount of proteins expressed from four genes by 30-150% in a dose-dependent manner in both human and mouse cells. Notably, systemic treatment of mice with ASO resulted in an ∼80% protein increase of LRPPRC. The ASO-mediated increase in protein expression was sequence-specific, occurred at the level of translation and was dependent on helicase activity. We also found that the type of RNA modification and the position of modified nucleotides in ASOs affected translation of a pORF. ASOs are a useful class of therapeutic agents with broad utility.

  12. Numerical Analyses of Earthquake Induced Liquefaction and Deformation Behaviour of an Upstream Tailings Dam

    Directory of Open Access Journals (Sweden)

    Muhammad Auchar Zardari

    2017-01-01

    Full Text Available Much of the seismic activity of northern Sweden consists of micro-earthquakes occurring near postglacial faults. However, larger magnitude earthquakes do occur in Sweden, and earthquake statistics indicate that a magnitude 5 event is likely to occur once every century. This paper presents dynamic analyses of the effects of larger earthquakes on an upstream tailings dam at the Aitik copper mine in northern Sweden. The analyses were performed to evaluate the potential for liquefaction and to assess stability of the dam under two specific earthquakes: a commonly occurring magnitude 3.6 event and a more extreme earthquake of magnitude 5.8. The dynamic analyses were carried out with the finite element program PLAXIS using a recently implemented constitutive model called UBCSAND. The results indicate that the magnitude 5.8 earthquake would likely induce liquefaction in a limited zone located below the ground surface near the embankment dikes. It is interpreted that stability of the dam may not be affected due to the limited extent of the liquefied zone. Both types of earthquakes are predicted to induce tolerable magnitudes of displacements. The results of the postseismic slope stability analysis, performed for a state after a seismic event, suggest that the dam is stable during both the earthquakes.

  13. Analysis of apyrase 5' upstream region validates improved Anopheles gambiae transformation technique

    Directory of Open Access Journals (Sweden)

    Lanfrancotti Alessandra

    2009-02-01

    Full Text Available Abstract Background Genetic transformation of the malaria mosquito Anopheles gambiae has been successfully achieved in recent years, and represents a potentially powerful tool for researchers. Tissue-, stage- and sex-specific promoters are essential requirements to support the development of new applications for the transformation technique and potential malaria control strategies. During the Plasmodium lifecycle in the invertebrate host, four major mosquito cell types are involved in interactions with the parasite: hemocytes and fat body cells, which provide humoral and cellular components of the innate immune response, midgut and salivary glands representing the epithelial barriers traversed by the parasite during its lifecycle in the mosquito. Findings We have analyzed the upstream regulatory sequence of the An. gambiae salivary gland-specific apyrase (AgApy gene in transgenic An. gambiae using a piggyBac transposable element vector marked by a 3xP3 promoter:DsRed gene fusion. Efficient germ-line transformation in An. gambiae mosquitoes was obtained and several integration events in at least three different G0 families were detected. LacZ reporter gene expression was analyzed in three transgenic lines/groups, and in only one group was tissue-specific expression restricted to salivary glands. Conclusion Our data describe an efficient genetic transformation of An. gambiae embryos. However, expression from the selected region of the AgApy promoter is weak and position effects may mask tissue- and stage- specific activity in transgenic mosquitoes.

  14. Optimization of Upstream Detention Reservoir Facilities for Downstream Flood Mitigation in Urban Areas

    Directory of Open Access Journals (Sweden)

    Thi Thuy Ngo

    2016-07-01

    Full Text Available A detention reservoir is one of the most effective engineered solutions for flood damage mitigation in urban areas. Detention facilities are constructed to temporarily store storm water and then slowly drain when the peak period has passed. This delayed drainage may coincide with upstream floods and aggravate the flood risk downstream. Optimal operation and design are needed to improve the performance of detention reservoirs for flood reduction. This study couples hydrologic simulation software (EPA-SWMM with an evolutional optimizer (extraordinary particle swarm optimization, EPSO to minimize flood damage downstream while considering the inundation risk at the detention reservoir. The optimum design and operation are applied to an urban case study in Seoul, Korea, for historical severe flooding events and designed rainfall scenarios. The optimal facilities outperform the present facilities in terms of flood damage reduction both downstream and in the detention reservoir area. Specifically, the peak water level at the detention pond under optimal conditions is significantly smaller than that of the current conditions. The comparison of the total flooded volume in the whole watershed shows a dramatic reduction of 79% in a severe flooding event in 2010 and around 20% in 2011 and in 180 min designed rainfall scenarios.

  15. Upstream petroleum industry flaring and venting report : Industry performance for year ending December 31, 2002

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2003-09-01

    The largest source of flaring and venting in Alberta is solution gas, accounting for 66 per cent of total emissions in 2002. A summary of flared and vented volumes for the different oil and gas industry sources, such as well tests, gas plants, gas gathering systems, transmission lines, and batteries was presented in this report. It also contained detailed information on solution gas conserved, flared, and vented during 2002. Rankings of companies was established based on solution gas flared plus vented, solution gas flared, and solution gas vented, from crude oil and bitumen batteries. The ranking is provincial and also by the Energy Utilities Board (EUB) Field Centre area. The data used in the preparation of this report is submitted by companies. Considerable progress was made in the reduction of flaring and venting volumes for all upstream oil and gas sources, as demonstrated by the data. A reduction of 62 per cent from the 1996 flaring baseline was achieved. A reduction of 29 per cent was achieved for the venting of solution gas from the 2000 venting baseline. There was a 44 per cent reduction in the volume of solution gas flared and vented from the 1996 volume. tabs., figs.

  16. Arctic sea ice decline and continental cold anomalies: Upstream and downstream effects of Greenland blocking

    Science.gov (United States)

    Chen, Xiaodan; Luo, Dehai

    2017-04-01

    The influence of Greenland blocking on continental cold anomalies in the Northern Hemisphere is examined. It is found that westward moving Greenland blocking (WGB) events in the recent decade are more strongly related to the sea ice decline over the Baffin Bay, Davis Strait, and Labrador Sea (BDL), while the quasi-stationary Greenland blocking (QGB) events are more strongly related to the negative phase of the North Atlantic Oscillation. The frequency of WGB events is significantly increased owing to reduced mid-high-latitude westerly winds in the North Atlantic and its upstream region because of intensified Arctic warming related to the large BDL sea ice decline. It is further revealed that North American low temperatures are more sensitive to the WGB, while European low temperatures are more sensitive to the QGB. For the WGB, an intense cold anomaly is seen over the eastern North America. But for the QGB, strong cold anomalies appear over the North Europe and eastern Asia. Thus, it is concluded that more winter cold air outbreaks should occur over the eastern North America, if large BDL sea ice decline continues in the recent decade.

  17. A decision model for financial assurance instruments in the upstream petroleum sector

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, D. [State University of Campinas (UNICAMP) (Brazil). Dept. of Geology and Natural Resources; Suslick, S. [State University of Campinas (UNICAMP) (Brazil). Dept. of Geology and Natural Resources; Center for Petroleum Studies, Campinas (Brazil); Farley, J.; Costanza, R.; Krivov, S. [Maryland Univ., Solomons, MD (United States). Inst. for Ecological Economics

    2004-07-01

    The main objective of this paper is to deepen the discussion regarding the application of financial assurance instruments, bonds, in the upstream oil sector. This paper will also attempt to explain the current choice of instruments within the sector. The concepts of environmental damages and internalization of environmental and regulatory costs will be briefly explored. Bonding mechanisms are presently being adopted by several governments with the objective of guaranteeing the availability of funds for end-of-leasing operations. Regulators are mainly concerned with the prospect of inheriting liabilities from lessees. Several forms of bonding instruments currently available were identified and a new instrument classification was proposed. Ten commonly used instruments were selected and analyzed under the perspective of both regulators and industry (surety, paid-in and periodic payment collateral accounts, letters of credit, self-guarantees, investment grade securities, real estate collaterals, insurance policies, pools, and special funds). A multiattribute value function model was then proposed to examine current instrument preferences. Preliminary simulations confirm the current scenario where regulators are likely to require surety bonds, letters of credit, and periodic payment collateral account tools. (author)

  18. Upstream control of the frontal jet regulating plankton production in the Alboran Sea (Western Mediterranean)

    Science.gov (United States)

    Oguz, Temel; Mourre, Baptiste; Tintoré, Joaquín.

    2016-09-01

    Using a coupled physical-biological model, we document that a ˜30 km wide meandering jet constitutes a major source of biological enrichment in the Alboran Sea (Western Mediterranean) even in the absence of wind forcing and tidal dynamics. The level of enrichment is shown to vary markedly during the year depending on the upstream characteristics of the jet as it exits from the Gibraltar Strait. When its intensity is sufficiently low and characterized by weaker cross-frontal density gradients during winter-spring, the jet is weakly nonlinear and may not fulfill the necessary conditions for frontogenesis. It then remains weakly productive. In the case of stronger jet intensity (>1.1 Sv) accompanied by stronger cross-frontal density and velocity gradients within the Alboran Sea during summer-autumn, the frontal jet becomes strongly nonlinear and ageostrophic with large cross-frontal vorticity changes on the order of planetary vorticity. Under these conditions, upward vertical velocities in the range 10-50 m d-1 supply nutrients into the euphotic layer more effectively and support high-level frontogenesis-induced phytoplankton production on the anticyclonic side of the main jet axis. The strong eddy pumping mechanism also provides a comparable level of plankton production within strongly nonlinear elongated cyclonic eddies along the outer periphery of the frontal jet. The plankton biomass is advected partially by the jet along its trajectory and dispersed within the basin by mesoscale eddies and meanders.

  19. The IAP-antagonist ARTS initiates caspase activation upstream of cytochrome C and SMAC/Diablo

    Science.gov (United States)

    Edison, N; Zuri, D; Maniv, I; Bornstein, B; Lev, T; Gottfried, Y; Kemeny, S; Garcia-Fernandez, M; Kagan, J; Larisch, S

    2012-01-01

    ARTS (Sept4_i2) is a pro-apoptotic tumor suppressor protein that functions as an antagonist of X-linked IAP (XIAP) to promote apoptosis. It is generally thought that mitochondrial outer membrane permeabilization (MOMP) occurs before activation of caspases and is required for it. Here, we show that ARTS initiates caspase activation upstream of MOMP. In living cells, ARTS is localized to the mitochondrial outer membrane. In response to apoptotic signals, ARTS translocates rapidly to the cytosol in a caspase-independent manner, where it binds XIAP and promotes caspase activation. This translocation precedes the release of cytochrome C and SMAC/Diablo, and ARTS function is required for the normal timing of MOMP. We also show that ARTS-induced caspase activation leads to cleavage of the pro-apoptotic Bcl-2 family protein Bid, known to promote MOMP. We propose that translocation of ARTS initiates a first wave of caspase activation that can promote MOMP. This leads to the subsequent release of additional mitochondrial factors, including cytochrome C and SMAC/Diablo, which then amplifies the caspase cascade and causes apoptosis. PMID:21869827

  20. Methane-Oxidizing Enzymes: An Upstream Problem in Biological Gas-to-Liquids Conversion.

    Science.gov (United States)

    Lawton, Thomas J; Rosenzweig, Amy C

    2016-08-03

    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 upstream 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.

  1. BRCA1 and its phosphorylation involved in caffeine-inhibitable event upstream of G2 checkpoint

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    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 upstream of G2 arrest.

  2. A barrier to upstream migration in the fish passage of Itaipu Dam (Canal da Piracema), Paraná River basin

    Science.gov (United States)

    ,; Fontes Júnior, Hélio Martins; Makrakis, Sergio; Gomes, Luiz Carlos; Latini, João Dirço

    2012-01-01

    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 upstream migration. The aim of this study was to evaluate the degree of restriction imposed by the CABV on upstream movements of Prochilodus lineatus and Leporinus elongatus, Characiformes. Fish were tagged with passive integrated transponders (PIT tags) and released both downstream and upstream 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 upstream 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.

  3. New Approaches for Moving Upstream: How State and Local Health Departments Can Transform Practice to Reduce Health Inequalities

    Science.gov (United States)

    Freudenberg, Nicholas; Franzosa, Emily; Chisholm, Janice; Libman, Kimberly

    2015-01-01

    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"…

  4. Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation.

    Science.gov (United States)

    Zhang, Gong; Lukoszek, Radoslaw; Mueller-Roeber, Bernd; Ignatova, Zoya

    2011-04-01

    In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the tRNA genes. Using a systematic bioinformatic analysis of 11 multicellular eukaryotic genomes we identified a highly conserved TATA motif followed by a CAA-motif in the tRNA upstream regions of all plant genomes. Strikingly, the 5'-flanking tRNA regions of the animal genomes are highly heterogeneous and lack a common conserved sequence signature. Interestingly, in the animal genomes the tRNA species that read the same codon share conserved motifs in their upstream regions. Deep-sequencing analysis of 16 human tissues revealed multiple splicing variants of two of the TFIIIB subunits, Bdp1 and Brf1, with tissue-specific expression patterns. These multiple forms most likely modulate the TFIIIB-DNA interactions and explain the lack of a uniform signature motif in the tRNA upstream regions of animal genomes. The anticodon-dependent 5'-flanking motifs provide a possible mechanism for independent regulation of the tRNA transcription in various human tissues.

  5. The spatial arrangement of neritina virginea (gastropoda: neritidae) during upstream migration in a split-channel reach.

    Science.gov (United States)

    JUAN F. BLANCO; FREDERICK N. SCATENA

    2007-01-01

    This paper relates differences in flow hydraulics between a main channel (MC) and a side channel (SC) of a river to patterns of upstream 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...

  6. Characterization of wind velocities in the upstream induction zone of a wind turbine using scanning continuous-wave lidars

    DEFF Research Database (Denmark)

    Simley, Eric; Angelou, Nikolas; Mikkelsen, Torben Krogh;

    2016-01-01

    an estimated axial induction factor of 0.25. The velocity reductions relative to the freestream velocity become smaller when the turbine’s coefficient of power decreases; for a low CP of 0.16 resulting in an estimated induction factor of 0.04, the velocity deficits are 1% of the freestream value 1 D upstream......As a wind turbine generates power, induced velocities, lower than the freestream velocity, will be present upstream of the turbine due to perturbation of the flow by the rotor. In this study, the upstream induction zone of a 225kW horizontal axis Vestas V27 wind turbine located at the Danish....... Velocity deficits of 1%–3% of the freestream value were observed 1 D upstream of the rotor, increasing at the rotor plane to 7.4% near the edge of the rotor and 18% near the center of the rotor while the turbine was operating with a high estimated mechanical coefficient of power (CP) of 0.56 yielding...

  7. The impact of upstream water abstractions on reservoir yield: the case of the Orós Reservoir in Brazil

    NARCIS (Netherlands)

    van Oel, P.R.; Krol, Martinus S.; Hoekstra, Arjen Ysbert; de Araújo, José C.

    2008-01-01

    Water abstraction for irrigation upstream of a reservoir and its impact on reservoir yield and reliability are studied. Water demand and availability are strongly related in semi-arid environments where the irrigation sector is responsible for a large part of consumptive water use. Variations in

  8. Investigating altered nitric oxide signalling as an up-stream mediator of the antidepressant action of ketamine

    DEFF Research Database (Denmark)

    Liebenberg, N.; Muller, H. K.; Elfving, B.

    2012-01-01

    to increased synaptic protein synthesis in the frontal cortex as vital processes that underlie its antidepressant action. However, the upstream mechanism(s) that are affected, i.e. immediately downstream of NMDA receptors, remain unclear. Neuronal nitric oxide synthase (nNOS) is directly coupled...

  9. Upstream Tracking and the Decay $B^{0} \\to K^{+}\\pi^{-}\\mu^{+}\\mu^{-}$ at the LHCb Experiment

    CERN Document Server

    Bowen, Espen Eie; Serra, Nicola; Steinkamp, Olaf; Storaci, Barbara

    The LHCb detector is a single-arm forward spectrometer covering the pseudorapidity range $2 < \\eta < 5$, designed to search for indirect evidence of New Physics in $C\\!P$ violation and rare decays of beauty and charm hadrons. The unique geometry takes advantage of the large $b$ and $c$ quark production in the forward region at the LHC. The detector includes a high granularity silicon-strip vertex detector, a silicon-strip detector upstream of the magnet and three stations of silicon-strip detectors and straw drift tubes downstream of the magnet. This thesis is divided into two main parts. The first part details the development of improved algorithms to perform track reconstruction using the sub-detectors upstream of the LHCb magnet. A novel idea to perform upstream tracking as an intermediate step of the track reconstruction sequence was investigated. The vast gains in tracking performance obtained when using upstream tracks led to the algorithm being adopted into the default reconstruction sequence for...

  10. White Sturgeon Mitigation and Restoration in the Columbia and Snake Rivers Upstream from Bonneville Dam; 2002-2003 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Ward, David L.; Kern, J. Chris; Hughes, Michele L. (Oregon Department of Fish and Wildlife)

    2004-02-01

    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 upstream from McNary Dam.

  11. Counterstreaming suprathermal electron events upstream of corotating shocks in the solar wind beyond approximately 2 AU: Ulysses

    Science.gov (United States)

    Gosling, J. T.; Bame, S. J.; Feldman, W. C.; Mccomas, D. J.; Phillips, J. L.; Goldstein, B. E.

    1993-01-01

    Enhanced fluxes of suprathermal electrons are commonly observed upstream of corotating forward and reverse shocks in the solar wind at heliocentric distances beyond approximately 2 AU by the Los Alamos plasma experiment on Ulysses. The average duration of these events, which are most intense immediately upstream from the shocks and which fade with increasing distance from them, is approximately 2.4 days near 5 AU. These events are caused by the leakage of shock-heated electrons into the upstream region. The upstream regions of these shocks face back toward the Sun along the interplanetary magnetic field, so these leaked electrons commonly counterstream relative to the normal solar wind electron heat flux. The observations suggest that conservation of magnetic moment and scattering typically limit the sunward propagation of these electrons as beams to field-aligned distances of approximately 15 AU. Although it seems unlikely that these shock-associated events are an important source of counterstreaming events near 1 AU, remnants of the backstreaming beams may contribute importantly to the diffuse solar wind halo electron population there.

  12. White Sturgeon Mitigation and Restoration in the Columbia and Snake Rivers Upstream from Bonneville Dam; 2001-2002 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Ward, David L.; Kern, J. Chris; Hughes, Michele L.

    2003-12-01

    We report on our progress from April 2001 through March 2002 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 upstream from McNary Dam.

  13. Analysis of Environmental Issues Related to Small-Scale Hydroelectric Development II: Design Consideration for Passing Fish Upstream Around Dams

    Energy Technology Data Exchange (ETDEWEB)

    Hildebrandt, S. G. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bell, M. C. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Anderson, J. J. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Richey, E. P. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Parkhurst, Z. E. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    1980-08-01

    The purpose of this report is to provide general information for use by potential developers of small scale hydroelectric projects that will include facilities to pass migrating fish upstream around dams. The document is not intended to be a textbook on design of fish passage facilities, but rather to be a general guide to some factors that are important when designing such facilities.

  14. Using temporal detrending to observe the spatial correlation of traffic.

    Science.gov (United States)

    Ermagun, Alireza; Chatterjee, Snigdhansu; Levinson, David

    2017-01-01

    This empirical study sheds light on the spatial correlation of traffic links under different traffic regimes. We mimic the behavior of real traffic by pinpointing the spatial correlation between 140 freeway traffic links in a major sub-network of the Minneapolis-St. Paul freeway system with a grid-like network topology. This topology enables us to juxtapose the positive and negative correlation between links, which has been overlooked in short-term traffic forecasting models. To accurately and reliably measure the correlation between traffic links, we develop an algorithm that eliminates temporal trends in three dimensions: (1) hourly dimension, (2) weekly dimension, and (3) system dimension for each link. The spatial correlation of traffic links exhibits a stronger negative correlation in rush hours, when congestion affects route choice. Although this correlation occurs mostly in parallel links, it is also observed upstream, where travelers receive information and are able to switch to substitute paths. Irrespective of the time-of-day and day-of-week, a strong positive correlation is witnessed between upstream and downstream links. This correlation is stronger in uncongested regimes, as traffic flow passes through consecutive links more quickly and there is no congestion effect to shift or stall traffic. The extracted spatial correlation structure can augment the accuracy of short-term traffic forecasting models.

  15. A semelparous fish continues upstream migration when exposed to alarm cue, but adjusts movement speed and timing

    Science.gov (United States)

    Luhring, Thomas M; Meckley, Trevor D.; Johnson, Nicholas S.; Siefkes, Michael J.; Hume, John B.; Wagner, C. Michael

    2016-01-01

    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 upstream in Carp Lake River and used antennas to detect their movements in the river. As the breeding season progressed, sea lamprey initiated upstream 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 upstream 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 upstream 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 upstream 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.

  16. Extreme floods in the Mekong River Delta under climate change: combined impacts of upstream hydrological changes and sea level rise

    Science.gov (United States)

    Hoang, Long; Nguyen Viet, Dung; Kummu, Matti; Lauri, Hannu; Koponen, Jorma; van Vliet, Michelle T. H.; Supit, Iwan; Leemans, Rik; Kabat, Pavel; Ludwig, Fulco

    2016-04-01

    Extreme floods cause huge damages to human lives and infrastructure, and hamper socio-economic development in the Mekong River Delta in Vietnam. Induced by climate change, upstream hydrological changes and sea level rise are expected to further exacerbate future flood hazard and thereby posing critical challenges for securing safety and sustainability. This paper provides a probabilistic quantification of future flood hazard for the Mekong Delta, focusing on extreme events under climate change. We developed a model chain to simulate separate and combined impacts of two drivers, namely upstream hydrological changes and sea level rise on flood magnitude and frequency. Simulation results show that upstream changes and sea level rise substantially increase flood hazard throughout the whole Mekong Delta. Due to differences in their nature, two drivers show different features in their impacts on floods. Impacts of upstream changes are more dominant in floodplains in the upper delta, causing an increase of up to +0.80 m in flood depth. Sea level rise introduces flood hazard to currently safe areas in the middle and coastal delta zones. A 0.6 m rise in relative sea level causes an increase in flood depth between 0.10 and 0.70 m, depending on location by 2050s. Upstream hydrological changes and sea level rise tend to intensify each other's impacts on floods, resulting in stronger combined impacts than linearly summed impacts of each individual driver. Substantial increase of future flood hazard strongly requires better flood protection and more flood resilient development for the Mekong Delta. Findings from this study can be used as quantified physical boundary conditions to develop flood management strategies and strategic delta management plans.

  17. Potential control of human immunodeficiency virus type 1 asp expression by alternative splicing in the upstream untranslated region.

    Science.gov (United States)

    Barbagallo, Michael S; Birch, Katherine E; Deacon, Nicholas J; Mosse, Jennifer A

    2012-07-01

    The negative-sense asp open reading frame (ORF) positioned opposite to the human immunodeficiency virus type 1 (HIV-1) env gene encodes the 189 amino acid, membrane-associated ASP protein. Negative-sense transcription, regulated by long terminal repeat sequences, has been observed early in HIV-1 infection in vitro. All subtypes of HIV-1 were scanned to detect the negative-sense asp ORF and to identify potential regulatory sequences. A series of highly conserved upstream short open reading frames (sORFs) was identified. This potential control region from HIV-1(NL4-3), containing six sORFs, was cloned upstream of the reporter gene EGFP. Expression by transfection of HEK293 cells indicated that the introduction of this sORF region inhibits EGFP reporter expression; analysis of transcripts revealed no significant changes in levels of EGFP mRNA. Reverse transcriptase-polymerase chain reaction analysis (RT-PCR) further demonstrated that the upstream sORF region undergoes alternative splicing in vitro. The most abundant product is spliced to remove sORFs I to V, leaving only the in-frame sORF VI upstream of asp. Sequence analysis revealed the presence of typical splice donor- and acceptor-site motifs. Mutation of the highly conserved splice donor and acceptor sites modulates, but does not fully relieve, inhibition of EGFP production. The strong conservation of asp and its sORFs across all HIV-1 subtypes suggests that the asp gene product may have a role in the pathogenesis of HIV-1. Alternative splicing of the upstream sORF region provides a potential mechanism for controlling expression of the asp gene.

  18. Correlator technology

    NARCIS (Netherlands)

    Schooneveld, C. van

    1968-01-01

    The paper reviews a number of designs of cross-correlation receivers for the detection of active underwater transmissions. Particular attention is given to the various structures of phase insensitive receivers, and to the problems concerned with clipping of the input signal and the reference functio

  19. Effects of rising angle on upstream blades and intermediate turbine duct

    Science.gov (United States)

    Liu, Jun; Wang, Pei; Du, Qiang; Liu, Guang; Zhu, Junqiang

    2016-08-01

    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 upstream 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.

  20. An analysis of flaring and venting activity in the Alberta upstream oil and gas industry.

    Science.gov (United States)

    Johnson, Matthew R; Coderre, Adam R

    2011-02-01

    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 upstream 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

  1. Tying Down Loose Ends in the Chlamydomonas Genome: Functional Significance of Abundant Upstream Open Reading Frames

    Directory of Open Access Journals (Sweden)

    Frederick R. Cross

    2016-02-01

    Full Text Available The Chlamydomonas genome has been sequenced, assembled, and annotated to produce a rich resource for genetics and molecular biology in this well-studied model organism. The annotated genome is very rich in open reading frames upstream of the annotated coding sequence (‘uORFs’: almost three quarters of the assigned transcripts have at least one uORF, and frequently more than one. This is problematic with respect to the standard ‘scanning’ model for eukaryotic translation initiation. These uORFs can be grouped into three classes: class 1, initiating in-frame with the coding sequence (CDS (thus providing a potential in-frame N-terminal extension; class 2, initiating in the 5′ untranslated sequences (5UT and terminating out-of-frame in the CDS; and class 3, initiating and terminating within the 5UT. Multiple bioinformatics criteria (including analysis of Kozak consensus sequence agreement and BLASTP comparisons to the closely related Volvox genome, and statistical comparison to cds and to random sequence controls indicate that of ∼4000 class 1 uORFs, approximately half are likely in vivo translation initiation sites. The proposed resulting N-terminal extensions in many cases will sharply alter the predicted biochemical properties of the encoded proteins. These results suggest significant modifications in ∼2000 of the ∼20,000 transcript models with respect to translation initiation and encoded peptides. In contrast, class 2 uORFs may be subject to purifying selection, and the existent ones (surviving selection are likely inefficiently translated. Class 3 uORFs are found in more than half of transcripts, frequently multiple times per transcript; however, they are remarkably similar to random sequence expectations with respect to size, number, and composition, and therefore may in most cases be selectively neutral.

  2. Quantitative assessment of upstream source influences on total gaseous mercury observations in Ontario, Canada

    Directory of Open Access Journals (Sweden)

    D. Wen

    2011-02-01

    Full Text Available Hourly total gaseous mercury (TGM concentrations at three monitoring sites (receptors in Ontario were predicted for four selected periods at different seasons in 2002 using the Stochastic Time-Inverted Lagrangian Transport (STILT model, which transports Lagrangian air parcels backward in time from the receptors to provide linkages to the source region in the upwind area. The STILT model was modified to deal with Hg deposition and high stack Hg emissions. The model-predicted Hg concentrations were compared with observations at three monitoring sites. Estimates of transport errors (uncertainties in simulated concentrations due to errors in wind fields are also provided that suggest such errors can reach approximately 10% of simulated concentrations. Results from a CMAQ chemical transport model (CTM simulation in which the same emission and meteorology inputs were used are also reported. The comparisons show that STILT-predicted Hg concentrations usually agree better with observations than CMAQ except for a subset of cases that are subject to biases in the coarsely resolved boundary conditions. In these comparisons STILT captures high frequency concentration variations better than the Eulerian CTM, likely due to its ability to account for the sub-grid scale position of the receptor site and to minimize numerical diffusion. Thus it is particularly valuable for the interpretation of plumes (short-term concentration variations that require the use of finer mesh sizes or controls on numerical diffusion in Eulerian models. We report quantitative assessments of the relative importance of different upstream sources for the selected episodes, based on emission fluxes and STILT footprints. The STILT simulations indicate that natural sources (which include re-emission from historical anthropogenic activities contribute much more than current-day anthropogenic emissions to the Hg concentrations observed at the three sites.

  3. Quantitative assessment of upstream source influences on total gaseous mercury observations in Ontario, Canada

    Directory of Open Access Journals (Sweden)

    D. Wen

    2010-11-01

    Full Text Available Hourly total gaseous mercury (TGM concentrations at three monitoring sites (receptors in Ontario were predicted for four selected periods at different seasons in 2002 using the Stochastic Time-Inverted Lagrangian Transport (STILT model, which transports Lagrangian air parcels backward in time from the receptors to provide linkages to the source region in the upwind area. The STILT model was modified to deal with Hg deposition and high stack Hg emissions. The model-predicted Hg concentrations were compared with observations at three monitoring sites. Estimates of transport errors (uncertainties in simulated concentrations due to errors in wind fields are also provided that suggest such errors can reach approximately 10% of simulated concentrations. Results from a CMAQ chemical transport model (CTM simulation in which the same emission and meteorology inputs were used are also reported. The comparisons show that STILT-predicted Hg concentrations usually agree better with observations than CMAQ except for a subset of cases that are subject to biases in the coarsely resolved boundary conditions. STILT captures high frequency concentration variations better than the Eulerian CTM, due to its ability to account for near-field influences that are not resolved by typical grid sizes in Eulerian CTMs. Thus it is particularly valuable for the interpretation of plumes (short-term concentration variations that require complex sub-grid treatments in Eulerian models. We report quantitative assessments of the relative importance of different upstream sources for the selected episodes, based on emission fluxes and STILT footprints. The STILT simulations indicate that natural sources (which include re-emission from historical anthropogenic activities contribute much more than current-day anthropogenic emissions to the Hg concentrations observed at the three sites.

  4. Upstream petroleum licensing: a comparative approach on regulatory frameworks and economic impacts

    Energy Technology Data Exchange (ETDEWEB)

    Cunha, Amanda L. [Felsberg e Associados, Sao Paulo, SP (Brazil)

    2008-07-01

    The recent discoveries hit in the pre-salt area, such as Tupi, Jupiter, Bem-te-vi and Carioca may place Brazil amongst the largest oil producers in the world. As a result, the Brazilian regulatory framework, which was originally envisaged in a scenario of higher exploration risk, has been under heavy public scrutiny. The Brazilian Government has already taken the first steps towards substantial changes in the country's contracting model for upstream activities. By means of Resolution No. 6/2007, the National Council for Energy Policy ('CNPE') not only determined the removal of 41 blocks with sub-salt geology from the ANP 9 Th Bid Round, but also stressed the need for a different regime for E and P activities in the country's continental shelf. At this moment, there is a great deal of controversy on the contracting model to be adopted, mainly whether the concession model should be maintained, but subject to higher levels of government take, or a production sharing model should apply. This paper goes through the evolution of international oil agreements, from early concessions to modern agreements. A special emphasis is placed on concession/license regimes as well as on production sharing agreements (PSAs). Besides drawing a comparative line between such models, this article assesses their economic impacts and whether the regulatory framework currently in force in Brazil is suitable for a scenario of lower risk, showing that any desired level of regulation may be achieved in the context of a PSA as easily as in a exclusive concession. (author)

  5. Quantification of the advected CO2 concentration due to upstream surface fluxes in aircraft vertical profiles

    Science.gov (United States)

    Font, A.; Morguí, J.-A.; Curcoll, R.; Rodó, X.

    2009-04-01

    A model framework which couples the Lagrangian Particle Dispersion Model FLEXPART (LPDM) with the new global surface flux inversion CarbonTracker from NOAA-ESRL (2007B release) is used to quantify the advected CO2 concentration from outbound surface fluxes to measured vertical profiles carried out during different seasons in 2006 at La Muela site in Spain (LMU; 41.60°N, 1.1°W). The Lagrangian Particle Dispersion Model FLEXPART (LPDM) calculates the influence of surface CO2 fluxes upwind of the study area, allowing us to identify those sources or sink areas that strongly modify the CO2 content of air masses that arrives at different altitudes of measured profiles. CarbonTracker is a new assimilation system that informs of global carbon fluxes at 1°x1° at 3 hours resolution. Coupling LPDM results with surface fluxes allows assessing the net CO2 contribution of identified areas to measured concentrations along the profiles above a reference or background concentration. Furthermore, it allows the quantification of the percentage of each component flux (biospheric, anthropogenic and oceanic) to each vertical layer. At LMU, biospheric fluxes account ~70% of total CO2 advection; fossil fuel ~25%; and ~5% is attributed to the oceanic ones. By far, late spring and summer profiles are largely influence by the biospheric component (~90%). Finally, the CO2 concentration above the background value of profiles measured on 22nd February, 13th October and 30th November 2006 are well explained by the advection of upstream surface fluxes. In other profiles examined, the variation of CO2 along the profile is partially explained by the advection of CO2 outbound fluxes.

  6. PILOT TESTING OF MERCURY OXIDATION CATALYSTS FOR UPSTREAM OF WET FGD SYSTEMS

    Energy Technology Data Exchange (ETDEWEB)

    Gary M. Blythe

    2003-05-01

    This document summarizes progress on Cooperative Agreement DE-FC26-01NT41185, ''Pilot Testing of Mercury Oxidation Catalysts for Upstream of Wet FGD Systems,'' during the time period January 1, 2003 through March 31, 2003. The objective of this project is to demonstrate at pilot scale the use of solid honeycomb catalysts to promote the oxidation of elemental mercury in the flue gas from coal combustion. The project is being funded by the U.S. DOE National Energy Technology Laboratory under Cooperative Agreement DE-FC26-01NT41185. EPRI, Great River Energy (GRE), and City Public Service (CPS) of San Antonio are project cofunders. URS Group is the prime contractor. The mercury control process under development uses catalyst materials applied to honeycomb substrates to promote the oxidation of elemental mercury in the flue gas from coal-fired power plants that have wet lime or limestone flue gas desulfurization (FGD) systems. Oxidized mercury is removed in the wet FGD absorbers and co-precipitates with the byproducts from the FGD system. The current project is testing previously identified, effective catalyst materials at a larger, pilot scale and in a commercial form, to provide engineering data for future full-scale designs. The pilot-scale tests will continue for up to 14 months at each of two sites to provide longer-term catalyst life data. This is the sixth full reporting period for the subject Cooperative Agreement. During this period, project efforts included continued operation of the pilot unit with three catalysts, conducting catalyst activity measurements, and procuring the fourth catalyst, all for the GRE Coal Creek pilot unit site. Laboratory efforts were also conducted to support catalyst selection for the second pilot unit site, at CPS' Spruce Plant. This technical progress report provides an update on these efforts.

  7. Identification of transcription factor AML-1 binding site upstream of human cytomegalovirus UL111A gene.

    Directory of Open Access Journals (Sweden)

    Xiaoqun Zheng

    Full Text Available Human cytomegalovirus (HCMV interleukin-10 (hcmvIL-10, encoded by HCMV UL111A gene, is a homolog of human IL-10. It exerts immunomodulatory effects that allow HCMV to evade host defense mechanisms. However, the exact mechanism underlying the regulation of hcmvIL-10 expression is not well understood. The transcription factor acute myeloid leukemia 1 (AML-1 plays an important role in the regulation of various genes involved in the differentiation of hematopoietic lineages. A putative AML-1 binding site is present within the upstream regulatory region (URR of UL111A gene. To provide evidence that AML-1 is involved in regulating UL111A gene expression, we examined the interaction of AML-1 with the URR of UL111A in HCMV-infected human monocytic THP-1 cells using a chromatin immunoprecipitation assay. HcmvIL-10 transcription was detected in differentiated THP-1 cells, but not in undifferentiated ones. Furthermore, the URR of UL111A showed a higher intensity of AML-1 binding, a higher level of histone H3 acetyl-K9, but a lower level of histone H3 dimethyl-K9 in differentiated THP-1 cells than undifferentiated cells. Down-regulation of AML1 by RNA interference decreased the expression of the UL111A gene. Our results suggest that AML-1 may contribute to the epigenetic regulation of UL111A gene via histone modification in HCMV-infected differentiated THP-1 cells. This finding could be useful for the development of new anti-viral therapies.

  8. Restructuring upstream bioprocessing: technological and economical aspects for production of a generic microbial feedstock from wheat.

    Science.gov (United States)

    Koutinas, A A; Wang, R; Webb, C

    2004-03-05

    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 upstream 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.

  9. Upstream petroleum industry flaring and venting report : Industry performance for year ending December 31, 2004

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2005-08-01

    Since 1938, the Alberta Energy and Utilities Board (EUB) has made the reduction of routine flaring and venting of solution gas a priority. The EUB has been acknowledged internationally for its achievements in reducing flaring and venting. The EUB's goal is to eliminate the routine flaring and venting of solution gas in order to address energy conservation and public safety. This report describes how the EUB fulfills its information mandate regarding flaring and venting. It is published in response to a commitment made by the EUB to make flaring and venting data more accessible. The EUB and the Clean Air Strategic Alliance have established baselines for flaring and venting. Regulations, enforcement and industry cooperation have resulted in major reductions in the amount of solution gas flared and vented. This report provides a summary of flared and vented volumes for the different oil and gas industry sources, such as well tests, gas plants, gas gathering systems, transmission lines, and batteries. It also contains detailed information on solution gas conserved, flared, and vented during 2003. Ranking of companies was established based on solution gas flared plus vented, solution gas flared, and solution gas vented, from crude oil and bitumen batteries. The data used in the preparation of this report was submitted by companies. The data demonstrates that considerable progress has been made in the reduction of flaring and venting volumes for all upstream oil and gas sources. Solution gas conservation for 2004 was 96.0 per cent, the highest conservation level achieved to date. Solution gas flaring for 2004 was 72.2 per cent less than the 1996 flaring baseline, compared to 70.0 per cent less than the baseline in 2003. tabs., figs.

  10. Upstream petroleum industry flaring and venting report : Industry performance for year ending December 31, 2003

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2004-05-01

    Solution gas is the largest source of flaring and venting in Alberta. The Alberta Energy and Utilities Board (EUB) has been acknowledged internationally for its success in reducing flaring and venting. The EUB's target is to eliminate the routine flaring and venting of solution gas to address conservation and public safety. This report describes how the EUB fulfills its information mandate regarding flaring and venting. It is published in response to a commitment made by the EUB to make flaring and venting data more accessible. The EUB and the Clean Air Strategic Alliance have established baselines for flaring and venting. Regulations, enforcement and industry cooperation have resulted in major reductions in the amount of solution gas flared and vented. This report provides a summary of flared and vented volumes for the different oil and gas industry sources, such as well tests, gas plants, gas gathering systems, transmission lines, and batteries. It also contains detailed information on solution gas conserved, flared, and vented during 2003. Ranking of companies was established based on solution gas flared plus vented, solution gas flared, and solution gas vented, from crude oil and bitumen batteries. The data used in the preparation of this report was submitted by companies. The data demonstrates that considerable progress has been made in the reduction of flaring and venting volumes for all upstream oil and gas sources. Solution gas conservation for 2003 was 95.4 per cent, the highest conservation level achieved to date. Solution gas flaring for 2003 was 70 per cent less than the 1996 flaring baseline. tabs., figs.

  11. Impact of Climate Change on Drought in the Upstream Yangtze River Region

    Directory of Open Access Journals (Sweden)

    Guihua Lu

    2016-12-01

    Full Text Available Based on Coupled Model Intercomparison Project Phase 5 (CMIP5 dataset and a variable infiltration capacity (VIC hydrological model, this study assesses the possible influence of climate change in the upstream region of the Yangtze River on droughts in the future 30 years. Long-term daily soil moisture content were simulated by VIC model at a 50 km × 50 km resolution from 1951 to 2013. Regional historical drought events were then recognized based on soil moisture anomaly percentage index and validated with field data. Five relatively independent representative global circulation models were selected and the outputs of them were downscaled temporally and spatially as the inputs of VIC model for daily soil moisture content simulations both in the period of 1971–2000 for the present-day climate and in the period of 2021–2050 for the future. The results show that the projected annual mean temperature is likely to increase from 1.4 °C to 1.8 °C. The projected change in mean annual precipitation could be increased slightly by 0.6% to 1.3%, but the trend of precipitation change in summer and autumn might be opposite of that. Comparing the drought characteristics values recognized in 1971–2000, seven to eight additional regional drought events are likely to happen in 2021–2050. Drought duration and drought intensity are also likely to extend for 18 d to 25 d and increase by 1.2% to 6.2%, respectively. But, drought area could decrease slightly by 1.3% to 2.7% on average. These changes in drought characteristics values suggest that regional drought could become more severely prolonged and frequent in future.

  12. Chicken ovalbumin upstream promoter transcription factor II regulates renin gene expression.

    Science.gov (United States)

    Mayer, Sandra; Roeser, Marc; Lachmann, Peter; Ishii, Sumiyashi; Suh, Jae Mi; Harlander, Sabine; Desch, Michael; Brunssen, Coy; Morawietz, Henning; Tsai, Sophia Y; Tsai, Ming-Jer; Hohenstein, Bernd; Hugo, Christian; Todorov, Vladimir T

    2012-07-13

    This study aimed to investigate the possible involvement of the orphan nuclear receptor chicken ovalbumin upstream promoter transcription factor II (COUP-TFII) in the regulation of renin gene expression. COUP-TFII colocalized with renin in the juxtaglomerular cells of the kidney, which are the main source of renin in vivo. Protein-DNA binding studies demonstrated that COUP-TFII binds to an imperfect direct repeat COUP-TFII recognition sequence (termed hereafter proxDR) in the proximal renin promoter. Because cAMP signaling plays a central role in the control of the renin gene expression, we suggested that COUP-TFII may modulate this cAMP effect. Accordingly, knockdown of COUP-TFII in the clonal renin-producing cell lines As4.1 and Calu-6 diminished the stimulation of the renin mRNA expression by cAMP agonists. In addition, the mutation of the proxDR element in renin promoter reporter gene constructs abrogated the inducibility by cAMP. The proxDR sequence was found to be necessary for the function of a proximal renin promoter cAMP-response element (CRE). Knockdown of COUP-TFII or cAMP-binding protein (CREB), which is the archetypal transcription factor binding to CRE, decreased the basal renin gene expression. However, the deficiency of COUP-TFII did not further diminish the renin expression when CREB was knocked down. In agreement with the cell culture studies, mutant mice deficient in COUP-TFII have lower renin expression than their control strain. Altogether our data show that COUP-TFII is involved in the control of renin gene expression.

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

    Science.gov (United States)

    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.

  14. PILOT TESTING OF MERCURY OXIDATION CATALYSTS FOR UPSTREAM OF WET FGD SYSTEMS

    Energy Technology Data Exchange (ETDEWEB)

    Gary M. Blythe

    2003-01-21

    This document summarizes progress on Cooperative Agreement DE-FC26-01NT41185, Pilot Testing of Mercury Oxidation Catalysts for Upstream of Wet FGD Systems, during the time period October 1, 2002 through December 31, 2002. The objective of this project is to demonstrate at pilot scale the use of solid honeycomb catalysts to promote the oxidation of elemental mercury in the flue gas from coal combustion. The project is being funded by the U.S. DOE National Energy Technology Laboratory under Cooperative Agreement DE-FC26-01NT41185. EPRI, Great River Energy (GRE), and City Public Service (CPS) of San Antonio are project co-funders. URS Group is the prime contractor. The mercury catalytic oxidation process under development uses catalyst materials applied to honeycomb substrates to promote the oxidation of elemental mercury in the flue gas from coal-fired power plants that have wet lime or limestone flue gas desulfurization (FGD) systems. Oxidized mercury is removed in the wet FGD absorbers and co-precipitates with the byproducts from the FGD system. The co-precipitated mercury does not appear to adversely affect the disposal or reuse properties of the FGD byproduct. The current project testing previously identified, effective catalyst materials at a larger, pilot scale and in a commercial form, to provide engineering data for future fullscale designs. The pilot-scale tests will continue for up to 14 months at each of two sites to provide longer-term catalyst life data. This is the fifth full reporting period for the subject Cooperative Agreement. During this period, project efforts included starting up the pilot unit with three catalysts at the first site, conducting catalyst activity measurements, completing comprehensive flue gas sampling and analyses, and procuring additional catalysts for the pilot unit. This technical progress report provides an update on these efforts.

  15. Monitoring of endangered Roanoke logperch (Percina rex) in Smith River upstream from the Philpott Reservoir on U.S. Army Corps of Engineers property near Martinsville, Virginia

    Science.gov (United States)

    Roberts, James H.; Angermeier, Paul L.

    2012-01-01

    The purpose of this study was to continue annual monitoring of Roanoke logperch (Percina rex), an endangered fish, in the Smith River immediately upstream from Philpott Reservoir. This river reach is owned by the U.S. Army Corps of Engineers (USACE), which must ensure that appropriate actions are undertaken to aid in recovery of logperch. Monitoring of fish abundance and habitat conditions provides a means for assessing the species’ status and its responses to USACE management actions. The Roanoke logperch is a large darter (Percidae: Etheostomatinae) endemic to the Roanoke, Dan, and Nottoway River basins of Virginia and North Carolina, where it occupies third- to sixth-order streams containing relatively silt-free substrate (Jenkins and Burkhead, 1994). Because of its rarity, small range, and vulnerability to siltation, the Roanoke logperch was listed in 1989 as endangered under the U.S. Endangered Species Act (ESA) (U.S. Federal Register 54:34468-34472). Within the Dan basin, Roanoke logperch have long been known to occupy the Smith River and one of its largest tributaries, Town Creek (Jenkins and Burkhead, 1994). Logperch also recently were discovered in other tributaries of the Dan River, including North Carolina segments of the Mayo River, Cascade Creek, Big Beaver Island Creek, Wolf Island Creek (William Hester, U.S. Fish and Wildlife Service, personal commun., 2012). Within the Smith River, Roanoke logperch are present both upstream and downstream from Philpott Reservoir, a hydroelectric and water storage project owned and operated by the USACE. Although logperch have not been observed in the reservoir itself, the species is relatively abundant in a free-flowing, ≈ 2.5-km-long segment of Smith River upstream from the reservoir on USACE property (Lahey and Angermeier, 2006). This segment is bounded on the downstream end by the lentic conditions of the reservoir and on the upstream end by White Falls, a natural waterfall that presumably allows fish passage

  16. Upstream Structural Management Measures for an Urban Area Flooding in Turkey and their Consequences on Flood Risk Management

    Science.gov (United States)

    Akyurek, Z.; Bozoglu, B.; Girayhan, T.

    2015-12-01

    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 upstream 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 upstream and downstream of the river. It is observed that if the flow from the upstream catchments can be retarded through a detention pond constructed in at least two 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. Flood risk is obtained by using the flood hazard maps and water depth-damage functions plotted for a variety of building types and occupancies

  17. Development of sediment slug upstream from the Czorsztyn Reservoir (southern Poland) and its interaction with river morphology

    Science.gov (United States)

    Liro, Maciej

    2016-01-01

    The effects of base-level rising upstream of dam reservoirs on in-channel sedimentation and interaction of the stored sediments with the gravel-bed channel morphology have received little attention so far. Previous studies, however, suggested that the feedback mechanism between in-channel sedimentation and bank erosion may affect channel morphology. Here, the pattern of the bar area, bank erosion, and morphology of the gravel-bed Dunajec River upstream from the Czorsztyn Reservoir (CR), constructed in 1997 in southern Poland were analyzed from aerial images (1982-2012) and LiDAR data (2013). In the part of the post-dam period with a large flood, the average bar area increased significantly in the backwater section, and at some distance upstream, and then extended in the upstream direction at an average rate of above 40 m/y, reaching 2.2 km upstream from the CR in 2012. The bar area variation was 40% and 77% explained by local bank erosion in the periods of large and low to moderate floods, respectively. The sum of bank erosion from the post-dam period explained 80% of the variation in the present width/depth ratio, significantly increased in the backwater section. The results showed that the large floods in 1997, in conjunction with backwater inundation, initiated intensive bank erosion and bar growth. Subsequently, in the period with low and moderate floods, the localized bar-bank interaction, connected with the flow divergence around the deposited bar, led to localized bank erosion and additional bar growth promoting bend development. These processes, propagating in the upstream direction, were facilitated by the existence of a large amount of easily remobilized sediment stored in the floodplain connected with the sedimentation zone from the end of the nineteenth century. Bend development was controlled by valley confinement causing downstream bend translation in the narrower valley-confined section and its extension in the wider unconfined section of past

  18. Routine versus aggressive upstream rhythm control for prevention of early atrial fibrillation in heart failure : background, aims and design of the RACE 3 study

    NARCIS (Netherlands)

    Alings, M.; Smit, M. D.; Moes, M. L.; Crijns, H. J. G. M.; Tijssen, J. G. P.; Brugemann, J.; Hillege, H. L.; Lane, D. A.; Lip, G. Y. H.; Smeets, J. R. L. M.; Tieleman, R. G.; Tukkie, R.; Willems, F. F.; Vermond, R. A.; Van Veldhuisen, D. J.; Van Gelder, I. C.

    2013-01-01

    Rhythm control for atrial fibrillation (AF) is cumbersome because of its progressive nature caused by structural remodelling. Upstream therapy refers to therapeutic interventions aiming to modify the atrial substrate, leading to prevention of AF. The Routine versus Aggressive upstream rhythm Control

  19. Inflammation, insulin resistance, and diabetes--Mendelian randomization using CRP haplotypes points upstream.

    Directory of Open Access Journals (Sweden)

    Eric J Brunner

    2008-08-01

    linkage disequilibrium with our tagging SNPs also demonstrated null associations. CONCLUSIONS: Observed associations between serum CRP and insulin resistance, glycemia, and diabetes are likely to be noncausal. Inflammation may play a causal role via upstream effectors rather than the downstream marker CRP.

  20. The Upstream Regulatory Region of Human Papillomavirus Type 31 Is Insensitive to Glucocorticoid Induction

    Science.gov (United States)

    Bromberg-White, Jennifer L.; Meyers, Craig

    2002-01-01

    The upstream regulatory region (URR) of various types of human papillomaviruses (HPVs) has been shown to contain functional glucocorticoid response elements (GREs), including HPV type 11 (HPV11), HPV16, and HPV18. Glucocorticoids have been demonstrated to induce the transcriptional activity of the early promoters of these HPV types. Although it has been assumed that the URR of HPV31 contains at least one GRE, no functionality has been demonstrated. We attempt to show here inducibility of the URR of HPV31 by the synthetic glucocorticoid dexamethasone (dex). By sequence analysis we identified three potential GREs in the URR of HPV31. Gel shift analysis indicated that each of these three sites has the potential to be a functional GRE. However, constructs containing the full-length URR, 5′ deletions of the URR, and an internal fragment of the URR containing all three putative GREs were only weakly inducible by dex. Linker scanning mutants, whereby each potential GRE was replaced individually, in double combination, or in triple combination by a unique polylinker, had no effect on dex inducibility. Replacement of each of the three HPV31 GREs with the GRE of HPV18 failed to induce a response to dex. Placement of the HPV18 GRE into the URR of HPV31 in a region similar to its location in the HPV18 URR was also unable to result in a strong dex induction of the HPV31 URR. These data suggest that the lack of dex inducibility is due to the overall context of the HPV31 URR and may be dependent on the requirements of the major early promoter for transcriptional activation. Finally, replacement of the HPV18 GRE with each of the HPV31 GREs in HPV18 only showed weak inducibility, indicating that the three GREs of HPV31 are in fact only weak inducers of dex. Overall, these data suggest that dex responsiveness, along with oncogenic potential, may provide a possible explanation for the classification of HPV31 as an intermediate-risk virus and demonstrate the complexity of

  1. Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation

    Directory of Open Access Journals (Sweden)

    Bilsland Elizabeth

    2007-08-01

    Full Text Available Abstract Background The translational efficiency of an mRNA can be modulated by upstream open reading frames (uORFs present in certain genes. A uORF can attenuate translation of the main ORF by interfering with translational reinitiation at the main start codon. uORFs also occur by chance in the genome, in which case they do not have a regulatory role. Since the sequence determinants for functional uORFs are not understood, it is difficult to discriminate functional from spurious uORFs by sequence analysis. Results We have used comparative genomics to identify novel uORFs in yeast with a high likelihood of having a translational regulatory role. We examined uORFs, previously shown to play a role in regulation of translation in Saccharomyces cerevisiae, for evolutionary conservation within seven Saccharomyces species. Inspection of the set of conserved uORFs yielded the following three characteristics useful for discrimination of functional from spurious uORFs: a length between 4 and 6 codons, a distance from the start of the main ORF between 50 and 150 nucleotides, and finally a lack of overlap with, and clear separation from, neighbouring uORFs. These derived rules are inherently associated with uORFs with properties similar to the GCN4 locus, and may not detect most uORFs of other types. uORFs with high scores based on these rules showed a much higher evolutionary conservation than randomly selected uORFs. In a genome-wide scan in S. cerevisiae, we found 34 conserved uORFs from 32 genes that we predict to be functional; subsequent analysis showed the majority of these to be located within transcripts. A total of 252 genes were found containing conserved uORFs with properties indicative of a functional role; all but 7 are novel. Functional content analysis of this set identified an overrepresentation of genes involved in transcriptional control and development. Conclusion Evolutionary conservation of uORFs in yeasts can be traced up to 100

  2. ANN modeling for flood prediction in the upstream Eure's catchment (France)

    Science.gov (United States)

    Kharroubi, Ouissem; masson, Eric; Blanpain, Olivier; Lallahem, Sami

    2013-04-01

    Rainfall-Runoff relationship at basin scale is strongly depending on the catchment complexity including multi-scale interactions. In extreme events cases (i.e. floods and droughts) this relationship is even more complex and differs from average hydrological conditions making extreme runoff prediction very difficult to achieve. However, flood warning, flood prevention and flood mitigation rely on the possibility to predict both flood peak runoff and lag time. This point is crucial for decision making and flood warning to prevent populations and economical stakes to be damaged by extreme hydrological events. Since 2003 in France, a dedicated state service is in charge of producing flood warning from national level (i.e. SCHAPI) to regional level (i.e. SPC). This flood warning service is combining national weather forecast agency (i.e. Meteo France) together with a fully automated realtime hydrological network (i.e. Rainfall-Runoff) in order to produce a flood warning national map online and provide a set of hydro-meteorological data to the SPC in charge of flood prediction from regional to local scale. The SPC is in fact the flood service delivering hydrological prediction at operational level for decision making about flood alert for municipalities and first help services. Our research in collaboration with the SPC SACN (i.e. "Seine Aval et fleuves Côtiers Normands") is focused on the implementation of an Artificial Neural Network model (ANN) for flood prediction in deferent key points of the Eure's catchment and main subcatchment. Our contribution will focus on the ANN model developed for Saint-Luperce gauging station in the upstream part of the Eure's catchment. Prediction of extreme runoff at Saint-Luperce station is of high importance for flood warning in the Eure's catchment because it gives a good indicator on the extreme status and the downstream propagation of a potential flood event. Despite a good runoff monitoring since 27 years Saint Luperce flood

  3. Dispersion of low frequency plasma waves upstream of the quasi-perpendicular terrestrial bow shock

    Directory of Open Access Journals (Sweden)

    A. P. Dimmock

    2013-08-01

    Full Text Available Low frequency waves in the foot of a supercritical quasi-perpendicular shock front have been observed since the very early in situ observations of the terrestrial bow shock (Guha et al., 1972. The great attention that has been devoted to these type of waves since the first observations is explained by the key role attributed to them in the processes of energy redistribution in the shock front by various theoretical models. In some models, these waves play the role of the intermediator between the ions and electrons. It is assumed that they are generated by plasma instability that exist due to the counter-streaming flows of incident and reflected ions. In the second type of models, these waves result from the evolution of the shock front itself in the quasi-periodic process of steepening and overturning of the magnetic ramp. However, the range of the observed frequencies in the spacecraft frame are not enough to distinguish the origin of the observed waves. It also requires the determination of the wave vectors and the plasma frame frequencies. Multipoint measurements within the wave coherence length are needed for an ambiguous determination of the wave vectors. In the main multi-point missions such as ISEE, AMPTE, Cluster and THEMIS, the spacecraft separation is too large for such a wave vector determination and therefore only very few case studies are published (mainly for AMPTE UKS AMPTE IRM pair. Here we present the observations of upstream low frequency waves by the Cluster spacecraft which took place on 19 February 2002. The spacecraft separation during the crossing of the bow shock was small enough to determine the wave vectors and allowed the identification of the plasma wave dispersion relation for the observed waves. Presented results are compared with whistler wave dispersion and it is shown that contrary to previous studies based on the AMPTE data, the phase velocity in the shock frame is directed downstream. The consequences of this

  4. Isotopes and groundwater management strategies under semi-arid area: case of the Souss upstream basin (Morocco).

    Science.gov (United States)

    Bouragba, L; Mudry, J; Bouchaou, L; Hsissou, Y; Krimissa, M; Tagma, T; Michelot, J L

    2011-07-01

    This study concerns the Souss upstream basin. The objective is to investigate the characteristics of surface water and groundwater, to assess the impact of artificial recharge as reinforcement of the natural replenishment and assess the renewal of groundwater under semi-arid area. Two major water types are observed: (i) surface waters and upstream springs (least mineralized) and (ii) all groundwater samples (prevailing calcium and magnesium bicarbonate water type). Water isotopes show a low evaporation of precipitations during infiltration. Impoverishment in heavy isotopes is the characteristic of mountain rainfalls, or of a climate colder and wetter than present. Carbon-14 activities (34-94 pmc) indicate a long residence time. The artificial recharge is low compared to the reservoir volume, due to which the renewal rate is also low.

  5. Improvement in Product Development: Use of back-end data to support upstream efforts of Robust Design Methodology

    Directory of Open Access Journals (Sweden)

    Vanajah Siva

    2012-12-01

    Full Text Available In the area of Robust Design Methodology (RDM less is done on how to use and work with data from the back-end of the product development process to support upstream improvement. The purpose of this paper is to suggest RDM practices for the use of customer claims data in early design phases as a basis for improvements. The back-end data, when systematically analyzed and fed back into the product development process, aids in closing the product development loop from claims to improvement in the design phase. This is proposed through a flow of claims data analysis tied to an existing tool, namely Failure Mode and Effects Analysis (FMEA. The systematic and integrated analysis of back-end data is suggested as an upstream effort of RDM to increase understanding of noise factors during product usage based on the feedback of claims data to FMEA and to address continuous improvement in product development.

  6. PATTERNS AND TOURIST ACTIVITIES INDUCED BY THE UNDERGROUND RIVERS AND LAKES IN THE ARIEŞ BASIN UPSTREAM OF BURU

    Directory of Open Access Journals (Sweden)

    Marius CIGHER

    2011-11-01

    Full Text Available Patterns and tourist activities induced by the underground rivers and lakes in the Arieş basin upstream of Buru – The presence of carbonate deposits in the Arieş basin, upstream of Buru induced certain organization of groundwater resources. Depending on local genetic factors – geological, climatic, biotic, temporal, etc – the extension and characteristics of karst aquifers engenders exploitable hydro units in terms of tourism: underground rivers and lakes. Identification and analysis of morphometrical, morphological, quantitative, qualitative, dynamic and biotic characteristics have provided the approach to ranking the hydro entities. Forms and tourism activities are subsumed to the established typological categories: recreational and pleasure tourism and multipurpose tourism.

  7. THE ACTUAL CONDITIONS OF WETLANDS FROM THE UPSTREAM OF HĂRPĂŞEŞETI RIVER (BAHLUI HYDROGRAPHICAL BASIN

    Directory of Open Access Journals (Sweden)

    Gheorghe Romanescu

    2005-10-01

    Full Text Available The Hărpăşeşti river is a right side affluent of the Bahluieţ river. It junctions with the latter in the river-collecting “market” from near Podu Iloaiei. The physico-chemical analysis conducted in the waters and the marshes of the creek relieve an increase of the content of dissolved salts and of the water chemical content as we advance upstream, as a consequence of the fact that these salts are transported from the upstream hydrographical basin. The temperature is higher in the low waters, and the dissolved oxygen has a higher importance in the waters with high depths, lower temperatures and rare aquatic vegetation.

  8. Upstream Analysis”: An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data

    Directory of Open Access Journals (Sweden)

    Jeannette Koschmann

    2015-05-01

    Full Text Available A strategy is presented that allows a causal analysis of co-expressed genes, which may be subject to common regulatory influences. A state-of-the-art promoter analysis for potential transcription factor (TF binding sites in combination with a knowledge-based analysis of the upstream pathway that control the activity of these TFs is shown to lead to hypothetical master regulators. This strategy was implemented as a workflow in a comprehensive bioinformatic software platform. We applied this workflow to gene sets that were identified by a novel triclustering algorithm in naphthalene-induced gene expression signatures of murine liver and lung tissue. As a result, tissue-specific master regulators were identified that are known to be linked with tumorigenic and apoptotic processes. To our knowledge, this is the first time that genes of expression triclusters were used to identify upstream regulators.

  9. Structural and functional characterization of the 5' upstream region of a glutamine synthetase gene from Scots pine

    OpenAIRE

    Avila, Concepción; Cantón, Francisco; Barnestein, Pilar; Suárez, María-Fernanda; Marraccini, Pierre; Rey, Manuel; Humara, Jaime; Ordás, Ricardo; Cánovas, Francisco

    2002-01-01

    International audience; We report here the isolation and characterization of a genomic clone encoding Scots pine (P. sylvestris) cytosolic glutamine synthetase GS1a. The clone contains the 5' half of the gene including part of the coding region organized in seven exons, interrupted by 6 introns and 980 bp upstream of the translation initiation codon. Earlier experiments carried out in our lab have shown that the GS1a gene is expressed in a light dependent fashion during the initial stages of ...

  10. Numerical investigation of the interaction between upstream cavity purge flow and main flow in low aspect ratio turbine cascade

    Institute of Scientific and Technical Information of China (English)

    Jia Wei; Liu Huoxing

    2013-01-01

    In modem gas turbines,rim seal located between the stator-disc and rotor-disc is used to prevent hot-gas ingestion into the inner stage-gap of high pressure turbine.However,the purge flow supplied to the cavity through the rim seal interacts with the main flow,producing additional aerodynamic loss due to the mixing process which plays a significant role in the formation,development and evolution of downstream secondary flow.In this paper,a set of cascade representative of low aspect ratio turbine is selected to numerically investigate the influence of upstream cavity purge flow on the hub secondary flow structure and aerodynamic loss.Cascade with/without upstream cavity and four different purge mass flow rates are all taken into account in this simulation.Then,a deep insight into the loss mechanism of interaction between purge flow and main flow is gained.The results show that the presence of cavity and purge flow has a significant impact on the main flow which not only changes the vortex structure in both the passage and upstream cavity,but also alters the cascade exit flow angle distribution along the spanwise.Moreover,aerodynamic loss in the cascade rises with the increase of purge flow rate while the sealing effect is also enhanced.Therefore,the effect of upstream cavity purge flow must be considered in the process of turbine aerodynamic design.What is more,it is necessary to minimize the purge flow rate in order to reduce aerodynamic loss on the premise of satisfying cooling requirements.

  11. Identification of novel craniofacial regulatory domains located far upstream ofSOX9and disrupted in Pierre Robin sequence

    OpenAIRE

    2014-01-01

    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 fo...

  12. Effects of Salinity Challenge on Ion Regulation in Early and Late Upstream Migrating Sea Lamprey, Petromyzon marinus.

    Directory of Open Access Journals (Sweden)

    Diogo Ferreira-Martins

    2015-10-01

    Full Text Available The sea lamprey, Petromyzon marinus, is an anadromous species in which the adults re-enter freshwater, and migrate upstream for terminal spawning. A reduction in salinity tolerance has been document in migrants although the underlying mechanisms have not been characterized. The aim of this study was to determine the capacity for marine osmoregulation in late, upstream migrants by characterizing the morphological and physiological effects of salinity challenge from a molecular perspective. For this two experiments were performed using early and late upstream migrants. Animals salinity limited was found to be 17.5‰ for late upstream migrants, thought some early migrants were able to perform at 24‰. A number of relevant blood and intestinal parameters were measured to assess ionoregulatory and biochemical changes as well as the expression of key ion-transport related proteins by immunoblotting (IB [Na+/K+-ATPase (NKA, vacuolar-type H+-ATPase, carbonic anhydrase, and Na+:K+:2Cl-contransporter]. NKA activity was also measured, in addition to oxidative stress indicators. The Na+ and Cl- levels with plasma and intestinal fluid were quantified and it was found that in non performing animals these fluids approached environmental concentrations (osmoconforming and failure of drinking mechanism, respectively. A drop in hematocrit was also observed with plasma lactate indicating hemolytic anemia. Plasma [ALT], GST activity and [GSH] were used to assess oxidative damage to tissues. An increase in Na+/K+-ATPase activity in mid-intestine in late migrants and posterior intestine in early migrates showed a potentially adaptive ionoregulatory response to salinity increase. (FCT grant PTDC/MAR/98035/2008.

  13. Pilot Testing of Mercury Oxidation Catalysts for Upstream of Wet FGD Systems

    Energy Technology Data Exchange (ETDEWEB)

    Richard Rhudy

    2006-06-30

    This final report presents and discusses results from a mercury control process development project entitled ''Pilot Testing of Mercury Oxidation Catalysts for Upstream of Wet FGD Systems''. The objective of this project was to demonstrate at pilot scale a mercury control technology that uses solid honeycomb catalysts to promote the oxidation of elemental mercury in the flue gas from coal combustion. Oxidized mercury is removed in downstream wet flue gas desulfurization (FGD) absorbers and leaves with the FGD byproducts. The goal of the project was to achieve 90% oxidation of elemental mercury in the flue gas and 90% overall mercury capture with the downstream wet FGD system. The project was co-funded by EPRI and the U.S. Department of Energy's National Energy Technology Laboratory (DOE NETL) under Cooperative Agreement DE-FC26-01NT41185. Great River Energy (GRE) and City Public Service (now CPS Energy) of San Antonio were also project co-funders and provided host sites. URS Group, Inc. was the prime contractor. Longer-term pilot-scale tests were conducted at two sites to provide catalyst life data. GRE provided the first site, at their Coal Creek Station (CCS), which fires North Dakota lignite, and CPS Energy provided the second site, at their Spruce Plant, which fires Powder River Basin (PRB) coal. Mercury oxidation catalyst testing began at CCS in October 2002 and continued through the end of June 2004, representing nearly 21 months of catalyst operation. An important finding was that, even though the mercury oxidation catalyst pilot unit was installed downstream of a high-efficiency ESP, fly ash buildup began to plug flue gas flow through the horizontal catalyst cells. Sonic horns were installed in each catalyst compartment and appeared to limit fly ash buildup. A palladium-based catalyst showed initial elemental mercury oxidation percentages of 95% across the catalyst, declining to 67% after 21 months in service. A carbon

  14. Correlation spectrometer

    Science.gov (United States)

    Sinclair, Michael B.; Pfeifer, Kent B.; Flemming, Jeb H.; Jones, Gary D.; Tigges, Chris P.

    2010-04-13

    A correlation spectrometer can detect a large number of gaseous compounds, or chemical species, with a species-specific mask wheel. In this mode, the spectrometer is optimized for the direct measurement of individual target compounds. Additionally, the spectrometer can measure the transmission spectrum from a given sample of gas. In this mode, infrared light is passed through a gas sample and the infrared transmission signature of the gasses present is recorded and measured using Hadamard encoding techniques. The spectrometer can detect the transmission or emission spectra in any system where multiple species are present in a generally known volume.

  15. Influence of seasonal, diel, lunar, and other environmental factors on upstream fish passage in the igarapava fish ladder, Brazil

    Science.gov (United States)

    Bizzotto, P.M.; Godinho, Alexandre L.; Vono, V.; Kynard, B.; Godinho, Hugo P.

    2009-01-01

    Upstream 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 upstream in the ladder shows they are migratory in this system and have a strong behavioural drive to move to upstream 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.

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

    Science.gov (United States)

    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

    2014-08-01

    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 harboring 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 noncoding elements contribute to the craniofacial regulation of SOX9 expression, and that their disruption results in PRS.

  17. Sediment depositions upstream of open check dams: new elements from small scale models

    Science.gov (United States)

    Piton, Guillaume; Le Guern, Jules; Carbonari, Costanza; Recking, Alain

    2015-04-01

    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 upstream 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

  18. Development of recommended practices and guidance documents for upstream oil and gas flow measurement

    Energy Technology Data Exchange (ETDEWEB)

    Dahl, Eivind; Scheers, Lex; Ting, Frank; Letton, Chip

    2005-07-01

    As first stated in the Introduction, improvements in multiphase flow meters during the last 15 years have resulted in their increased usage in upstream oil and gas applications, especially in difficult offshore locations both topside and deep subsea. To address user needs for information and standardization in the area, documentation has recently been created under the auspices of the NFOGM, API, and ISO. Our intent here was to familiarize potential users with the three new documents, which should be helpful in a number of respects, e.g., (a) distribution of best knowledge and operational practices on the subject, (b) provision of a common language for discussing multiphase flow, and (c) accounting for the requirements of governing regulatory authorities. At this stage of completion of NFOGM, API, and ISO reports, a natural question arises as to what the future holds for another round of flow measurement documentation. Candidate areas include: 1) In Situ Verification of Multiphase Flow Meters. 2) Wet Gas Flow Measurement. 3) Flare Gas Meters. 4) Virtual Metering. 5) Composition and Phase Behavior Issues In Measurement. 6) Flow Measurement Uncertainty. Addressing certain of these is already being proposed in several possible venues, among which are (1) the DeepStar Consortium, (2) a JIP for investigating total system (meter + flowline + separator) uncertainty organized by a group at Tulsa University, and (3) a program for development of drilling and production capabilities in ultradeep water to be sponsored by the US Department of Energy. The creation of the three documents discussed in this paper demonstrates the benefits that strong international cooperation can achieve in producing standardization documents, ensuring their true global input and acceptance. On the other hand, it should also be questioned why two or more documents are required, which are the result of much duplication of effort. For example, although there are differences between API RP86 and the

  19. Sources and the distribution of heavy metals in the particle size of soil polluted by gold mining upstream of Miyun Reservoir, Beijing: implications for assessing the potential risks.

    Science.gov (United States)

    Li, Qian; Ji, Hongbing; Qin, Fei; Tang, Lei; Guo, Xinyue; Feng, Jinguo

    2014-10-01

    Mining has been carried out upstream of Miyun Reservoir, Beijing, for several decades, and has caused metal emissions to the environment, threatening human health. We conducted a soil survey to assess metal contamination in this area and to determine distribution of heavy metals in the particle size. We attempted to determine the possible sources of the metals and the significance of metals in the fine particle fractions to soil risk assessments. Thirty-four soil samples were collected, and eight samples were partitioned into seven size fractions. Most of the metal concentrations in the soils were higher than the background levels in Beijing, and the metal concentrations and total organic matter (TOC) contents generally increased as the particle size decreased. Each metal except Hg significantly positively correlated with the TOC. The metals in the coarse-grained soils were mainly derived from parent materials, but the metals in the fine fractions were mostly anthropogenic. Statistical analyses showed that there were three metal sources: Cd, Cu, Hg, Pb, and Zn had anthropogenic sources; Co, Cr, Ni, and V had mixed anthropogenic and natural sources; and As and Be had natural sources. The trace metals were primarily in the clay and fine silt fractions, and they might pose health risks through the inhalation of resuspended soil particles (PM10 and PM2.5). The elevated accumulation factors, enrichment factors, and ecological risk indices for the metals in the fine fractions suggest that risk assessments should be based on the fine particle size.

  20. Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Kaushik; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302 (India)

    2015-07-28

    Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging the ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.

  1. Influences of Water Conservancy and Hydropower Projects on Runoff in Qingjiang River Upstream Basin

    Institute of Scientific and Technical Information of China (English)

    Yi Sun; Junwei Wan; Songyuan Yang; Xinghua Xue; Kun Huang

    2016-01-01

    ABSTRACT:Hydrological data on the Upper Qingjiang River from 1960 to 2012 document trends of runoff caused by hydropower engineering projects and long-term changes in rainfall. Annual runoff correlates strongly with annual precipitation, but is significantly reduced after reservoir construction compared to earlier values. Comparisons of intense, pre-and post-construction rainfall events suggest that the Chebahe and Dalongtan reservoir projects respectively clips the magnitude of the flood peaks and delays runoff delivery.

  2. TATA-binding protein (TBP)-like protein is required for p53-dependent transcriptional activation of upstream promoter of p21Waf1/Cip1 gene.

    Science.gov (United States)

    Suzuki, Hidefumi; Ito, Ryo; Ikeda, Kaori; Tamura, Taka-Aki

    2012-06-01

    TATA-binding protein-like protein (TLP) is involved in development, checkpoint, and apoptosis through potentiation of gene expression. TLP-overexpressing human cells, especially p53-containing cells, exhibited a decreased growth rate and increased proportion of G(1) phase cells. TLP stimulated expression of several growth-related genes including p21 (p21(Waf1/Cip1)). TLP-mediated activation of the p21 upstream promoter in cells was shown by a promoter-luciferase reporter assay. The p53-binding sequence located in the p21 upstream promoter and p53 itself are required for TLP-mediated transcriptional activation. TLP and p53 bound to each other and synergistically enhanced activity of the upstream promoter. TLP specifically activated transcription from the endogenous upstream promoter, and p53 was required for this activation. Etoposide treatment also resulted in activation of the upstream promoter as well as nuclear accumulation of TLP and p53. Moreover, the upstream promoter was associated with endogenous p53 and TLP, and the p53 recruitment was enhanced by TLP. The results of the present study suggest that TLP mediates p53-governed transcriptional activation of the p21 upstream promoter.

  3. Correlations for the Vineland Adaptive Behavior Scales with Kaufman Brief Intelligence Test in a forensic sample.

    Science.gov (United States)

    Hayes, Susan; Farnill, Douglas

    2003-04-01

    People with an intellectual disability are over-represented in the criminal justice system in many western countries. Identifying accused persons with intellectual disability is important if they are to receive protections available under the law. Accurate diagnosis is also relevant for correctional administrators, probation and parole services, and community services. Diagnosis of intellectual disability must be made on the basis of both cognitive skills (intelligence) and adaptive behavior. In this study, the Kaufman Brief Intelligence Test assessed intelligence, and the Vineland Adaptive Behavior Scales assessed adaptive behavior, through self-report. Tests were administered to 150 offenders, ranging in age from 13 to 53 years, in Australian prisons, juvenile detention centers, legal aid offices, and probation services. Pearson product-moment correlation coefficients calculated among all subtests and between total scores were significant. ROC curve analyses demonstrated that performance on each effectively predicted a standard score of less than 70 on the other one.

  4. Pilot Testing of Mercury Oxidation Catalysts for Upstream of Wet FGD Systems

    Energy Technology Data Exchange (ETDEWEB)

    Richard Rhudy

    2006-06-30

    This final report presents and discusses results from a mercury control process development project entitled ''Pilot Testing of Mercury Oxidation Catalysts for Upstream of Wet FGD Systems''. The objective of this project was to demonstrate at pilot scale a mercury control technology that uses solid honeycomb catalysts to promote the oxidation of elemental mercury in the flue gas from coal combustion. Oxidized mercury is removed in downstream wet flue gas desulfurization (FGD) absorbers and leaves with the FGD byproducts. The goal of the project was to achieve 90% oxidation of elemental mercury in the flue gas and 90% overall mercury capture with the downstream wet FGD system. The project was co-funded by EPRI and the U.S. Department of Energy's National Energy Technology Laboratory (DOE NETL) under Cooperative Agreement DE-FC26-01NT41185. Great River Energy (GRE) and City Public Service (now CPS Energy) of San Antonio were also project co-funders and provided host sites. URS Group, Inc. was the prime contractor. Longer-term pilot-scale tests were conducted at two sites to provide catalyst life data. GRE provided the first site, at their Coal Creek Station (CCS), which fires North Dakota lignite, and CPS Energy provided the second site, at their Spruce Plant, which fires Powder River Basin (PRB) coal. Mercury oxidation catalyst testing began at CCS in October 2002 and continued through the end of June 2004, representing nearly 21 months of catalyst operation. An important finding was that, even though the mercury oxidation catalyst pilot unit was installed downstream of a high-efficiency ESP, fly ash buildup began to plug flue gas flow through the horizontal catalyst cells. Sonic horns were installed in each catalyst compartment and appeared to limit fly ash buildup. A palladium-based catalyst showed initial elemental mercury oxidation percentages of 95% across the catalyst, declining to 67% after 21 months in service. A carbon

  5. NO formation in the burnout region of a partially premixed methane-air flame with upstream heat loss

    Energy Technology Data Exchange (ETDEWEB)

    Mokhov, A.V.; Levinsky, H.B.

    1999-09-01

    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. Upstream 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 chemical reaction based on the relation between the measured temperature and the local mixture fraction, including the effects of upstream 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 upstream 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.

  6. Improving AVSWAT Stream Flow Simulation by Incorporating Groundwater Recharge Prediction in the Upstream Lesti Watershed, East Java, Indonesia

    Directory of Open Access Journals (Sweden)

    Christina Rahayuningtyas

    2014-01-01

    Full Text Available The upstream Lesti watershed is one of the major watersheds of East Java in Indonesia, covering about 38093 hectares. Although there are enough water resources to meet current demands in the basin, many challenges including high spatial and temporal variability in precipitation from year to year exist. It is essential to understand how the climatic condition affects Lesti River stream flow in each sub basin. This study investigated the applicability of using the Soil and Water Assessment Tool (SWAT with the incorporation of groundwater recharge prediction in stream flow simulation in the upstream Lesti watershed. Four observation wells in the upstream Lesti watershed were used to evaluate the seasonal and annual variations in the water level and estimate the groundwater recharge in the deep aquifer. The results show that annual water level rise was within the 2800 - 5700 mm range in 2007, 3900 - 4700 mm in 2008, 3200 - 5100 mm in 2009, and 2800 - 4600 mm in 2010. Based on the specific yield and the measured water level rise, the area-weighted groundwater predictions at the watershed outlet are 736, 820.9, 786.7, 306.4 mm in 2007, 2008, 2009, and 2010, respectively. The consistency test reveals that the R-square statistical value is greater than 0.7, and the DV (% ranged from 32 - 55.3% in 2007 - 2010. Overall, the SWAT model performs better in the wet season flow simulation than the dry season. It is suggested that the SWAT model needs to be improved for stream flow simulation in tropical regions.

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

    Science.gov (United States)

    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.

  8. Upstream sample processing facilitates PCR detection of Listeria monocytogenes in mayonnaise-based ready-to-eat (RTE) salads.

    Science.gov (United States)

    Isonhood, Jamie; Drake, MaryAnne; Jaykus, Lee-Ann

    2006-09-01

    Sample pretreatment to reduce volume and concentrate cells of the target organism(s) prior to molecular detection offers a useful supplement or alternative to cultural enrichment. The purpose of this study was to develop an upstream processing method to facilitate the detection of Listeria monocytogenes in ready-to-eat (RTE) salads by PCR. Potato salad, a model RTE commodity, was seeded with L. monocytogenes and processed by two alternative upstream sample processing methods (designated one-step and two-step centrifugation), followed by DNA extraction, PCR amplification, and Southern hybridization. The two-step method resulted in 1,000-fold improvements in the PCR detection limit, from 10(6) Cfu/g (no sample processing) to 10(3) Cfu/g. The two-step method was applied for upstream sample processing of four representative deli salad items artificially inoculated with L. monocytogenes at levels ranging from 10(1)-10(6) Cfu/g. Following DNA extraction, PCR amplification, and Southern hybridization, detection was achieved at input levels of 10(5) Cfu/g for chicken salad, 10(4) Cfu/g for macaroni salad, and 10(3) Cfu/g for potato and seafood salads. The two-step method reported here facilitates the production of a final sample concentrate of reduced volume and improved purity which was compatible with PCR amplification. This approach offers further progress in our efforts to reduce or eliminate cultural enrichment in an effort to speed time to results when applying molecular methods to the detection of pathogens in foods.

  9. Upstream movements of Atlantic Salmon in the Lower Penobscot River, Maine following two dam removals and fish passage modifications

    Science.gov (United States)

    Izzo, Lisa K.; Maynard, George A.; Zydlewski, Joseph

    2016-01-01

    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. Upstream habitat access for Atlantic Salmon is dependent upon successful and timely passage at Milford Dam because nearly all suitable spawning habitat is located upstream. In 2014 and 2015, a total of 73 adult salmon were radio-tagged to track their upstream 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.

  10. Formula for Upstream Pressure, Nozzle Geometry and Frequency Correlation in Shedding/Discharging Cavitation Clouds Determined by Visualization of Submerged Cavitating Jet

    Science.gov (United States)

    Hutli, E. A. F.; Nedeljkovic, M. S.

    Visualization of high-submerged cavitating water jet was done by a high-speed camera photography in order to study and understand the jet structure and the behaviour of cloud cavitation within the time and space. The influencing parameters, such as: injection pressure, nozzle diameter and geometry, nozzle direction (convergent and divergent) were experimentally proven to be very significant. Periodical shedding and discharging of cavitation clouds has been also analysed and corresponding frequency was determined by clouds shape analysis. Additionally, dependence of this frequency on injection pressure and nozzle geometry has been analysed and a simple formula of correspondence has been proposed. The formula has been tested on self-measured and literature data.

  11. Annual and seasonal variations In the gamma activities in Sava river sediments upstream and downstream of NPP Krsko

    Energy Technology Data Exchange (ETDEWEB)

    Stipe, Lulic [Rudjer Boskovic Institute, Lab. for radioecology, Zagreb (Croatia)

    2006-07-01

    Results of the five years monitoring of artificial and natural occurring radionuclides in the Sava river sediments are presented. Measurements were conducted as a part of the regular Krsko Nuclear Power Plant radioactivity control and the independent supervisions of the input of radionuclides into larger environment (immission). In order to estimate seasonal variations samples were taken from seven locations (one upstream and five downstream of the Krsko NPP) during four sampling period (seasonal) in each year. Selected radionuclides in the sediment fractiess than 0.5 mm were determined with gamma spectrometer equipped with BE3830 model High Purity Ge detector with 30% relative efficiency. (authors)

  12. An upstream open reading frame controls translation of var2csa, a gene implicated in placental malaria

    DEFF Research Database (Denmark)

    Amulic, Borko; Salanti, Ali; Lavstsen, Thomas

    2009-01-01

    to only be expressed in the presence of a placenta, suggesting that its expression is actively repressed in men, children or non-pregnant women; however, the mechanism of repression is not understood. Using cultured parasite lines and reporter gene constructs, we show that the gene encoding VAR2CSA...... contains a small upstream open reading frame that acts to repress translation of the resulting mRNA, revealing a novel form of gene regulation in malaria parasites. The mechanism underlying this translational repression is reversible, allowing high levels of protein translation upon selection, thus...... potentially enabling parasites to upregulate expression of this variant antigen in the presence of the appropriate host tissue....

  13. White Sturgeon Mitigation and Restoration in the Columbia and Snake Rivers Upstream from Bonneville Dam; 2004-2005 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Rien, Thomas A.; Hughes, Michele L.; Kern, J. Chris (Oregon Department of Fish and Wildlife, Clackamas, OR)

    2006-03-01

    We report on our progress from April 2004 through March 2005 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 upstream 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.

  14. White Sturgeon Mitgation and Restoration in the Columbia and Snake Rivers Upstream from Bonneville Dam; 2003-2004 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Rein, Thomas A.; Hughes, Michele L.; Kern, J. Chris (Oregon Department of Fish and Wildlife, Clackamas, OR)

    2005-08-01

    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 upstream 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.

  15. Activation of the Klebsiella pneumoniae nifU promoter: identification of multiple and overlapping upstream NifA binding sites.

    OpenAIRE

    1990-01-01

    The Klebsiella pneumoniae nifU promoter is positively controlled by the NifA protein and requires a form of RNA polymerase holoenzyme containing the rpoN encoded sigma factor, sigma 54. Occupancy of the K. pneumoniae nifU promoter by NifA was examined using in vivo dimethyl sulphate footprinting. Three binding sites for NifA (Upstream Activator Sequences, UASs 1, 2 and 3) located at -125, -116 and -72 were identified which conform to the UAS consensus sequence TGT-N10-ACA. An additional NifA ...

  16. On the relative importance of the climate change factors along the river Scheldt considering climate scenarios for upstream inland and downstream coastal (mean sea level and surge) boundary conditions

    Science.gov (United States)

    Ntegeka, V.; Willems, P.; Monbaliu, J.

    2012-04-01

    To improve on the efficacy of flood risk mitigation measures, it is essential to investigate the relative importance of the future impact pressures. This is more so in areas which are found to be hot spots for flooding. One such area was identified in the Scheldt region located in Belgium. The Dendermonde area is a place where both the downstream coastal and the upstream river flow boundary conditions interact and jointly control the flood risk. Downstream of this area, the coastal level changes include both the sea level rise and storm surge changes due to climate change impacts on the wind climate over the North Atlantic and North Sea region. Upstream of the Dendermonde area lies the Dender river which introduces an extra pressure on the Dendermonde area. Against this back drop, impact analysis was performed using a hydrodynamic model that accounts for such changes. The climate data for future scenarios were extracted from the climate databases PRUDENCE (http://prudence.dmi.dk), ENSEMBLES (http://www.ensembles-eu.org/), IPCC AR4 (www-pcmdi.llnl.gov/ipcc/about_ipcc.php) and CERA (CLM from MPI-M/MaD). Future changes were derived from the large ensemble set of climate model runs and their effects simulated in the hydrodynamic model based on statistically processed climate change scenarios of sea level rise, SLP change and related storm surge changes and upstream runoff due to changes in rainfall and potential evapotranspiration. Changes in SLP were transferred to changes in storm surges at the Scheldt mouth (at Vlissingen) based on a correlation model between the SLP at the Baltic Sea and the storm surge level. This model was derived after analysis of SLP composite maps and SLP-surge correlation maps for days where the surge exceeds given thresholds (for different return periods). Correlations between the inland (rainfall, runoff) and coastal climatic changes were considered. The impact analysis to analyze the importance of the pressures for the Dendermonde area was

  17. Model for the Study of Automating a System of Pumping Water from Upstream to Downstream Hydropower Plant Using Siemens S7-200 PLC

    OpenAIRE

    Eugen Raduca; Mihaela Răduca; Lucian Ghinea; Aki Uyetani

    2010-01-01

    This paper shows the realization of an experimental model for studying didactic use automation system pumping water from upstream to downstream hydropower. As command and control unit was used PLC Siemens S7-200.

  18. Model for the Study of Automating a System of Pumping Water from Upstream to Downstream Hydropower Plant Using Siemens S7-200 PLC

    Directory of Open Access Journals (Sweden)

    Eugen Raduca

    2010-10-01

    Full Text Available This paper shows the realization of an experimental model for studying didactic use automation system pumping water from upstream to downstream hydropower. As command and control unit was used PLC Siemens S7-200.

  19. A statistical study into the spatial distribution and dawn‐dusk asymmetry of dayside magnetosheath ion temperatures as a function of upstream solar wind conditions

    National Research Council Canada - National Science Library

    Dimmock, A. P; Nykyri, K; Karimabadi, H; Osmane, A; Pulkkinen, T. I

    2015-01-01

    ... and nonisotropic and differs between the dawn and dusk flanks. The present study attempts to study the spatial distribution of magnetosheath ion temperature as a function of upstream solar wind conditions...

  20. Symmetric 10 Gb/s wavelength reused bidirectional RSOA based WDM-PON with DPSK modulated downstream and OFDM modulated upstream signals

    Science.gov (United States)

    Choudhury, Pallab K.; Khan, Tanvir Zaman

    2016-08-01

    A 10 Gb/s bidirectional wavelength division multiplexing passive optical network (WDM-PON) with reflective semiconductor optical amplifier (RSOA) based colorless optical network unit (ONU) is proposed and analyzed for next generation gigabit class optical access network. Differential phase shift keying (DPSK) modulated signal is used in downstream and further reused as a seeding wavelength for upstream data modulation. By exploiting the constant envelope property of DPSK seed signal, the re-modulation noise in upstream receiver is effectively minimized without employing any constraint on extinction ratio of downstream signal. Orthogonal frequency division multiplexing (OFDM) signal is used in upstream transmission to overcome the limited bandwidth (∼1 GHz) response of RSOA remodulation. The results show that the proposed 10 Gb/s symmetric WDM-PON can achieve good performance over 25 km fiber transmission with error free operation in downstream and bit error rate (BER) lower than forward error correction (FEC) limit in upstream.

  1. Harbor seal whiskers synchronize with upstream wake over a range of distances

    Science.gov (United States)

    Beem, Heather; Triantafyllou, Michael

    2014-11-01

    Harbor seal whiskers have been shown to exhibit unique vibration properties as they encounter vortex wakes. Seals may use this information to detect hydrodynamic trails left by fish prey. A scaled model, which captures the undulatory morphology of the harbor seal whisker and is designed to freely vibrate, is tested here to explore these properties in more detail. This model is towed downstream of a larger cylinder, which generates a vortex wake. Effects of downstream distance, lateral distance, and diameter ratio between the two objects are explored. Frequency measurements are collected simultaneously through use of a pressure sensor placed in the wake. Cross-correlation of the whisker motion and cylinder wake pressure provides evidence that frequency synchronization holds for a range of separation distances and wake generator sizes.

  2. The "WFD-effect" on upstream-downstream relations in international river basins – insights from the Rhine and the Elbe basins

    Directory of Open Access Journals (Sweden)

    S. Moellenkamp

    2007-06-01

    Full Text Available The upstream-downstream relationship in international river basins is a traditional challenge in water management. Water use in upstream countries often has a negative impact on water use in downstream countries. This is most evident in the classical example of industrial pollution in upstream 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 upstream-downstream relationship, this article shows that the WFD has a balancing effect on upstream-downstream problems and that it enhances river basin solidarity in international basins. While it lifts the downstream countries to the same level as the upstream 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 upstream 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 upstream-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

  3. Relationships between locomotor behavior, morphometric characters and thyroid hormone levels give evidence of stage-dependent mechanisms in European eel upstream migration.

    Science.gov (United States)

    Imbert, Hélène; Arrowsmith, Rory; Dufour, Sylvie; Elie, Pierre

    2008-01-01

    In order to decipher movements during freshwater eel colonization, we experimentally characterized individual locomotor behavior of two eel life history stages: elvers and yellow eels. A ramp located at the flume tank upstream side required a specific locomotor behavior to be ascended. Placing individually tagged eels in the middle of the tank three times successively tested behavioral consistency. Eels climbing the ramp on each trial were classified as "upstream climbers" whereas eels settling in the tank middle were classified as "inactive". Both stages exhibited these two opposite consistent behaviors. However, elvers were predominantly "upstream climbers" (58.1%) whereas yellow eels were predominantly "inactive" (79.6%). We measured morphometric characters and thyroid hormones to determine if upstream activity was related to body condition and thyroid status. Elver upstream climbers had higher body condition as well as higher thyroxine (T(4)) and triiodothyronine (T(3)) levels compared with inactive elvers. Yellow eel upstream climbers had lower body length as well as higher T(3) and (T(3):T(4)) ratio compared with inactive yellow eels. This indicated that the physiological release factors for eel upstream migration may be stage dependent. For elvers, high thyroid gland activity, together with high body condition, may be the physiological release factors for migration. In contrast, for yellow eels, physiological stress may be the release factor with an increase in T(4) deiodination activity in the smallest eels. Our study revealed inter-stage and intra-stage locomotor behavior plasticity and suggested stage-dependent opposite impacts of physiological condition on eel upstream migration.

  4. S tatu s a n dC omparativ e An aly sis of Overseas Upstream Businesses of China'sOil Majors%S tatu s a n dC omparativ e An aly sis of Overseas Upstream Businesses of China'sOil Majors

    Institute of Scientific and Technical Information of China (English)

    LiYushun

    2012-01-01

    In recent years, China's three oil majors has taken .the opportunity of rising oil price and financialcrisis, implemented the "going out" strategy and done international businesses. They have been actively engaged in overseas oil/gas development and petroleum engineering services. They have completed market existence in overseas upstream business successively and their overseas upstream business is on a fast track of development.

  5. 基于NASH谈判模型的上下游企业R&D合作与协调机制研究%R&D Cooperation and Benefit Coordination between Upstream and Downstream Firms Based on NASH Negotiation Model

    Institute of Scientific and Technical Information of China (English)

    李卫红; 陈圻; 王强

    2012-01-01

    profit in the abovementioned two conditions. The comparison shows that; (1) simultaneously horizontal and vertical R&D cooperation may create higher equilibrium output, R&D investment level and industry profit than sole horizontal R&D cooperation; (2) when R&D cost-sharing ratio is low (high), the upstream firm has (lack) the R&D cooperation motivation. This result has no correlation with the level of technology spillover; (3) the downstream firm will choose vertical R&D cooperation when the upstream R&D cost-sharing ratio is high or the level of technology spillovers is low. The fourth part discusses the cost-sharing problem when the upstream and downstream firms choose horizontal and vertical R&D cooperation simultaneously. On the basis of bargaining theory, this part uses the degree of satisfaction as an objective function and designs a benefit coordination mechanism based on the NASH negotiation model. The fifth part demonstrates the flaw of the existing R&D cost-sharing method through numerical simulation, and shows that benefit conflicts of all parties in the R&D cooperation could be avoided effectively under the proposed coordination mechanisms. The sixth part summarizes this article and suggests future research directions.In summary, upstream and downstream firms can achieve great efficiency and innovation benefits by horizontal and vertical R&D cooperation, and the stability of R&D cooperation can be promoted due to agreeable coordination mechanisms. Understanding the characteristics of horizontal and vertical R&D cooperation, firms will efficiently implement technical innovation and promote socio-technical progress rapidly.%已有研究往往孤立地分析企业横向或纵向R&D合作问题,而现实中,企业有可能同时采用两种合作形式进行技术创新.针对这一现象,建立了上下游企业同时进行横向与纵向R&D合作的博弈模型,并与下游企业只选择横向R&D合作的情形进行了比较.研究发现:(1)与下游企业

  6. Mitochondrial DNA evidence indicates the local origin of domestic pigs in the upstream region of the Yangtze River.

    Directory of Open Access Journals (Sweden)

    Long Jin

    Full Text Available Previous studies have indicated two main domestic pig dispersal routes in East Asia: one is from the Mekong region, through the upstream region of the Yangtze River (URYZ to the middle and upstream regions of the Yellow River, the other is from the middle and downstream regions of the Yangtze River to the downstream region of the Yellow River, and then to northeast China. The URYZ was regarded as a passageway of the former dispersal route; however, this assumption remains to be further investigated. We therefore analyzed the hypervariable segements of mitochondrial DNA from 513 individual pigs mainly from Sichuan and the Tibet highlands and 1,394 publicly available sequences from domestic pigs and wild boars across Asia. From the phylogenetic tree, most of the samples fell into a mixed group that was difficult to distinguish by breed or geography. The total network analysis showed that the URYZ pigs possessed a dominant position in haplogroup A and domestic pigs shared the same core haplotype with the local wild boars, suggesting that pigs in group A were most likely derived from the URYZ pool. In addition, a region-wise network analysis determined that URYZ contains 42 haplotypes of which 22 are unique indicating the high diversity in this region. In conclusion, our findings confirmed that pigs from the URYZ were domesticated in situ.

  7. High copy arrays containing a sequence upstream of mec-3 alter cell migration and axonal morphology in C. elegans

    Directory of Open Access Journals (Sweden)

    Patchen Brandi

    2001-01-01

    Full Text Available Abstract Background The Caenorhabditis elegans gene mec-3 encodes a LIM-homeodomain protein that is a master regulator of touch receptor neuron genes. Two of the touch neurons, the ALM neurons, are generated in the anterior of the animal and then migrate to near the middle of the animal. In animals transformed with a sequence upstream of mec-3, the ALM touch receptor neurons failed to migrate to their normal positions and sometimes migrated in the wrong direction, and the PLM touch receptor neurons showed axonal defects. Here we characterize this effect and identify the sequence causing the cell migration and axonal defects. Results The ALM migration defect did not result from RNA interference (RNAi, nonspecific effects of carrying a transgenic array, expression of GFP, or the marker gene used to make the transformants. Instead, the ALM migration defect resulted from transgenic arrays containing many copies of a specific 104 bp DNA sequence. Transgenic arrays containing this sequence did not affect all cell migrations. Conclusions The mec-3 upstream sequence appeared to be sequestering (titrating out a specific DNA-binding factor that is required for the ALMs to migrate correctly. Because titration of this factor could reverse the direction of ALM migrations, it may be part of a program that specifies both the direction and extent of ALM migrations. mec-3 is a master regulator of touch receptor neuron genes, so the factor or factors that bind this sequence may also be involved in specifying the fate of touch receptor neurons.

  8. Zebrafish hoxd4a acts upstream of meis1.1 to direct vasculogenesis, angiogenesis and hematopoiesis.

    Directory of Open Access Journals (Sweden)

    Aseervatham Anusha Amali

    Full Text Available Mice lacking the 4th-group paralog Hoxd4 display malformations of the anterior vertebral column, but are viable and fertile. Here, we report that zebrafish embryos having decreased function of the orthologous hoxd4a gene manifest striking perturbations in vasculogenesis, angiogenesis and primitive and definitive hematopoiesis. These defects are preceded by reduced expression of the hemangioblast markers scl1, lmo2 and fli1 within the posterior lateral plate mesoderm (PLM at 13 hours post fertilization (hpf. Epistasis analysis revealed that hoxd4a acts upstream of meis1.1 but downstream of cdx4 as early as the shield stage in ventral-most mesoderm fated to give rise to hemangioblasts, leading us to propose that loss of hoxd4a function disrupts hemangioblast specification. These findings place hoxd4a high in a genetic hierarchy directing hemangioblast formation downstream of cdx1/cdx4 and upstream of meis1.1. An additional consequence of impaired hoxd4a and meis1.1 expression is the deregulation of multiple Hox genes implicated in vasculogenesis and hematopoiesis which may further contribute to the defects described here. Our results add to evidence implicating key roles for Hox genes in their initial phase of expression early in gastrulation.

  9. A study on the relationship between vegetation pattern and environment in the upstream of Minjiang River,China

    Institute of Scientific and Technical Information of China (English)

    Li Chongwei; Lin Yong; Liu Lijuan; Ge Jianping

    2006-01-01

    The vegetation pattern in the upstream of Minjiang River,and its relationship with environment factors,such as landscape position(elevation,slope,aspect),precipitation and temperature and soil are analyzed in this paper.The data used in this Paper were based on the landscape map derived from 1994 TM imagery.The results were as follows:1)dominant landscape types were forest,shrub land and grassland,which were very similar in terms of area ratio(32.87%,31.85% and 28.44%,respectively);2)the patch shape of conifer forest and mixed forest was complicated while that of broad-leaved forest and cultivated land was simple;3)the fragmentation of conifer forest and mixed forest was serious in contrast with low fragmentation of broad-leaved forest and cultivated land;and 4)closed scrub and grassland had a high contagion and good connectivity while mixed forest had a lower contagion and bad connectivity.In addition,the vegetation distribution pattern of upstream of Minjiang River Was closely related with elevation and temperature,but the relationship between vegetation and precipitation was not statistically significant.

  10. Assessment of the impacts of land use changes on nonpoint source pollution inputs upstream of the Three Gorges Reservoir.

    Science.gov (United States)

    Yang, Huicai; Wang, Guoqiang; Yang, Yan; Xue, Baolin; Wu, Binbin

    2014-01-01

    In recent years, land use upstream of the Three Gorges Reservoir (TGR) has changed significantly because of the TGR project. In this study, the Soil and Water Assessment Tool (SWAT) model was examined for its ability to assess relationships between land use changes and nonpoint pollutant indexes upstream of the TGR. Results indicated that the SWAT model, calibrated with the adjusted parameters, could successfully reproduce the nonpoint indexes at the water quality monitoring sites in the two rivers. The different land use change types were shown to be sensitive to nonpoint pollutants in the study area. The land use change type from upland to water was the strongest influence on changes in total nitrogen and total phosphorus. An empirical regression equation between nonpoint indexes and different land use change types was developed for the study area by partial least squares regression (PLSR) as follows: Y = b 0 + ∑ i=1 (m) b i X i. This regression equation was useful for evaluating the influence of land use change types on changes in nonpoint pollutants over a long time period. The results from this study may be useful for the TGR management and may help to reduce nonpoint pollutant loads into downstream water bodies.

  11. Polycyclic aromatic hydrocarbons in upstream riverine runoff of the Pearl River Delta, China: an assessment of regional input sources.

    Science.gov (United States)

    Zhang, Kai; Liang, Bo; Wang, Ji-Zhong; Guan, Yu-Feng; Zeng, Eddy Y

    2012-08-01

    Water samples collected from upstream tributaries of the Pearl River Delta (PRD) and from locations within the PRD (South China) were analyzed for 27 polycyclic aromatic hydrocarbons (PAHs). Average concentrations (aqueous plus particulate) of total 27 PAHs (Σ(27)PAH), 16 priority PAHs designated by the United States Environmental Protection Agency (USEPA) except naphthalene (Σ(15)PAH), and the seven carcinogenic PAHs (Σ(7)PAH) classified by the USEPA were 260 ± 410, 130 ± 310, and 15 ± 12 ng/L, respectively. Riverine PAHs were predominantly generated from coal and vegetation combustion, coke production, vehicle exhausts, and petroleum residues, accounting for 28%, 25%, 22% and 21%, respectively, on average. Upstream riverine fluxes of Σ(27)PAH and Σ(15)PAH amounted to 38.9 and 12.9 tons/year, respectively. The net contributions of Σ(27)PAH and Σ(15)PAH from sources within the PRD were estimated at 21.4 and 21.0 tons/year, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

  12. Influences of increased daily repeated upstream releases and varying meteorological conditions on temperature distributions in a river-reservoir system

    Science.gov (United States)

    Chen, G.; Fang, X.

    2016-08-01

    Temperature distribution in a river-reservoir system was simulated using a calibrated three-dimensional Environmental Fluid Dynamics Code model under various hypothetical weather conditions and daily repeated large releases (DRLRs) from the upstream boundary. Both DRLRs and weather conditions affect and control the formation and spread of density currents and then affect the bottom-layer temperatures. The DRLRs with longer durations (e.g., 6 or 8 hours) can relatively quickly push cooler release water to the Gorgas upstream monitoring station (GOUS) and the river intake. With the air temperature drops in the first 6 days, simulated bottom temperatures at GOUS for 6- and 8-hr DRLRs are lower than one under 4-hr DRLR, but relatively larger bottom-layer temperature drops only primarily occur during the air-temperature drop and rise period. The release with larger flow rate can also maintain the cooler water temperature downstream. Releasing the same amounts of water, with different release durations and flow rates, has a very similar effect on the downstream water temperatures.

  13. Common Health, Safety and Environmental Concerns in Upstream Oil and Gas Sector: Implications for HSE Management in Ghana

    Directory of Open Access Journals (Sweden)

    Seth Oppong

    2014-01-01

    Full Text Available This paper explores the literature to identify common occupational injuries, diseases, and psychological wellbeing on oil rigs as well as the negative environmental impacts of the upstream oil and gas sector. It ends by making recommendations for effective health, safety, and environmental (HSE management. Review of the literature showed that contusion (bruise, cuts, and laceration are the commonest occupational injuries that workers on the oil rig suffer and that the injuries mostly affect the hand and finger, leg, and eyes of the offshore workers. These injuries were found to be caused mostly by direct stroke, jamming and overstrain. Similarly, accidental poisoning, musculoskeletal disorders, respiratory disorders and diseases of the digestive system were also documented as the commonest occupational diseases among offshore workers. The literature also shows that working offshore is associated with poorer psychological wellbeing or health; this is to say that offshore workers tend to experience higher levels of stress, burnout, anxiety, depression, low job satisfaction (particularly with the environmental conditions associated with their work, and sleep disorders. Finally, the literature review indicated that land-use problems, air pollution, acid rain, climate change, habitat disruption, environmental degradation, oil spills and leakages are some of environmental impacts of upstream oil production. This review was concluded by recommending some measures for the management of the HSE hazards associated with the oil and gas sector.

  14. Fine structure of Langmuir waves observed upstream of the bow shock at Venus

    Science.gov (United States)

    Hospodarsky, G. B.; Gurnett, D. A.; Kurth, W. S.; Kivelson, M. G.; Strangeway, R. J.; Bolton, S. J.

    1994-01-01

    Highly structured Langmuir waves, also known as electron plasma oscillations, have been observed in the foreshock of Venus using the plasma wave experiment on the Galileo spacecraft during the gravity assist flyby on February 10, 1990. The Galileo wideband sampling system provides digital electric field waveform measurements at sampling rates up to 201,600 samples per second, much higher than any previous instrument of this type. The main Langmuir wave emission band occurs near the local electron plasma frequency, which was approximately 43 kHz. The Langmuir waves are observed to shift above and below the plasma frequency, sometimes by as much as 20 kHz. The shifts in frequency are closely correlated with the downstream distance from the tangent field line, implying that the shifts are controlled by the electron beam velocity. Considerable fine structure is also evident, with timescales as short as 0.15 ms, corresponding to spatial scales of a few tens of Debye lengths. The frequency spectrum often consists of beat-type waveforms, with beat frequencies ranging from 0.2 to 7 kHz, and in a few cases, isolated wave packets. The peak electric field strengths are approximately 1 mV/m. These field strengths are too small for strongly nonlinear processes to be important. The beat-type waveforms are suggestive of a parametric decay process.

  15. Positive Feedback Keeps Duration of Mitosis Temporally Insulated from Upstream Cell-Cycle Events.

    Science.gov (United States)

    Araujo, Ana Rita; Gelens, Lendert; Sheriff, Rahuman S M; Santos, Silvia D M

    2016-10-20

    Cell division is characterized by a sequence 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.

  16. Human gene correlation analysis (HGCA): a tool for the identification of transcriptionally co-expressed genes.

    Science.gov (United States)

    Michalopoulos, Ioannis; Pavlopoulos, Georgios A; Malatras, Apostolos; Karelas, Alexandros; Kostadima, Myrto-Areti; Schneider, Reinhard; Kossida, Sophia

    2012-06-06

    Bioinformatics and high-throughput technologies such as microarray studies allow the measure of the expression levels of large numbers of genes simultaneously, thus helping us to understand the molecular mechanisms of various biological processes in a cell. We calculate the Pearson Correlation Coefficient (r-value) between probe set signal values from Affymetrix Human Genome Microarray samples and cluster the human genes according to the r-value correlation matrix using the Neighbour Joining (NJ) clustering method. A hyper-geometric distribution is applied on the text annotations of the probe sets to quantify the term overrepresentations. The aim of the tool is the identification of closely correlated genes for a given gene of interest and/or the prediction of its biological function, which is based on the annotations of the respective gene cluster. Human Gene Correlation Analysis (HGCA) is a tool to classify human genes according to their coexpression levels and to identify overrepresented annotation terms in correlated gene groups. It is available at: http://biobank-informatics.bioacademy.gr/coexpression/.

  17. Attenuation distance of low frequency waves upstream of the pre-dawn bow shock: GEOTAIL and ISEE 3 comparison

    Science.gov (United States)

    Sugiyama, T.; Terasawa, T.; Kawano, H.; Yamamoto, T.; Kokubun, S.; Frank, L. A.; Ackerson, K.; Tsurutani, B. T.

    1995-01-01

    We have made a statistical study of the spatial distribution of low frequency waves (approx. 0.01-0.1 Hz) in the region upstream of the pre-dawn to dawn side bow shock (-50 Re less than X less than 15 Re) using both GEOTAIL and international sun earth explorer 3 (ISEE-3) magnetometer data. We have found that the wave amplitude dependence on D and X(sub s), where D is the distance from the bow shock and X(sub s) the x-coordinate position of shock foot point of the IMF, can be described by a functional form of A exp (X(sub s)/L(sub X)-D/L(sub D), with the characteristic attenuation distances, L(sub X) = 62 +/- 12 Re and L(sub D) = 59 +/- 38 Re.

  18. Attenuation distance of low frequency waves upstream of the pre-dawn bow shock: GEOTAIL and ISEE comparison

    Energy Technology Data Exchange (ETDEWEB)

    Sugiyama, T.; Terasawa, T.; Kawano, H. [Univ. of Tokoyo (Japan)] [and others

    1995-01-15

    The authors have made a statistical study of the spatial distribution of low frequency waves ({approximately}0.01-0.1 Hz) in the region upstream of the pre-dawn to dawn side bow shock ({minus}50 Re

  19. Temporal Variability of Waves at the Proton Cyclotron Frequency Upstream from Mars: Implications for Mars Distant Hydrogen Exosphere

    CERN Document Server

    Bertucci, Cesar; Chaufray, Jean-Yves; Gomez, Daniel; Mazelle, Christian; Delva, Magda; Modolo, Ronan; Gonzalez-Galindo, Francisco; Brain, David Andrew

    2013-01-01

    We report on the temporal variability of the occurrence of waves at the local proton cyclotron frequency upstream from the Martian bow shock from Mars Global Surveyor observations during the first aerobraking and science phasing orbit periods. Observations at high southern latitudes during minimum-to-mean solar activity show that the wave occurrence rate is significantly higher around perihelion southern summer solstice and lower around the same hemisphere's spring and autumn equinoxes. A similar trend is observed in the hydrogen (H) exospheric density profiles over the Martian South Pole obtained from a model including UV thermospheric heating effects. In spite of the complexity in the ion pick-up and plasma wave generation and evolution processes, these results support the idea that variations in the occurrence of waves could be used to study the temporal evolution of the distant Martian H corona and its coupling with the thermosphere at altitudes currently inaccessible to direct measurements.

  20. Upstream expansion of round goby (Neogobius Melanostomus – first record in the upper reaches of the Elbe river

    Directory of Open Access Journals (Sweden)

    Buřič M.

    2015-01-01

    Full Text Available The round goby Neogobius melanostomus (Pallas, 1814 is one of the most problematic invasive fish species in recent years in Europe. It has proliferated from its native Ponto-Caspian region to several European river systems including their mouths and coastal brackish waters and was also introduced to and became widely established in the Great Lakes in North America. Despite recent reports about further invasions of round goby in the Odra and Vistula Rivers, including penetration of Baltic and North Seas, in the Elbe River this species was only recorded near its mouth close to Hamburg. Here we report the occurrence of round goby 622 km upstream from the previous record in Geesthacht (Germany in the upper part of the Elbe River in Usti nad Labem (Czech Republic. This report illustrates the fast spread of round goby through several possible pathways, but the most certain is an introduction in ballast water.

  1. Identification of four novel alleles of the BoLA-DRB3 upstream regulatory region in Chinese yellow cattle.

    Science.gov (United States)

    Wang, K; Sun, D-X; Li, K-Y; Wang, X-Q; Zhang, F

    2012-07-01

    The sequence of upstream regulatory region (URR) of BoLA-DRB3 gene was amplified with polymerase chain reaction followed by DNA sequencing from six animals of Chinese yellow cattle. A total of five alleles including four newly identified ones, named BoLA-DRB3*R-03-U2, BoLA-DRB3*R-06-U2, BoLA-DRB3*R-07-U and BoLA-DRB3*R-12-U for the BoLA-DRB3 URR were found. Result of sequence analysis showed that the regulatory elements W, X, Y, CCAAT and TATA-like boxes existed in such URRs and 16 polymorphic sites (11 transitions, 3 transversions, 1 deletion and 1 insertion) located in the spacers between the conserved consensus boxes and 1 insertion within X box, while no new polymorphic site within the consensus boxes.

  2. Abundant Early Expression of gpUL4 from a Human Cytomegalovirus Mutant Lacking a Repressive Upstream Open Reading Frame

    Science.gov (United States)

    Alderete, John P.; Child, Stephanie J.; Geballe, Adam P.

    2001-01-01

    The human cytomegalovirus UL4 gene encodes a 48-kDa glycoprotein, expression of which is repressed at the translational level by a short upstream open reading frame (uORF2) within the UL4 transcript leader. Mutation of the uORF2 initiation codon in the viral genome eliminates ribosomal stalling at the uORF2 termination site, resulting in early and abundant gpUL4 protein synthesis. This mutation does not appear to affect viral replication kinetics in human fibroblasts. These results reveal that the unusual uORF2 inhibitory mechanism is a principal determinant of the abundance and timing of gpUL4 expression but is nonessential for replication in cell culture. PMID:11435600

  3. The composition of upstream open reading frames (uORF) in four genes from Trypanosoma cruzi typical strains.

    Science.gov (United States)

    Jaeger, Lauren Hubert; Brandão, Adeilton

    2011-10-01

    Upstream open reading frames (uORF) are small open reading frames located in the 5' untranslated region (5' utr) of a mature mRNA. We analysed in four strains representing the Trypanosoma cruzi groups Tc I, Tc II, Tc IV and Tc VI the uORF present in 5' utr sequences of four genes: P-type H+-ATPase 1, DEAD/H RNA helicase, casein kinase 1.1 and ferredoxin-NADP+ reductase. A segment in the 5' utr at each of these genes encompassing one or more uORF was PCR amplified and sequenced. An analysis of these sequences reveals that the uORF in T. cruzi show minor variations; however, these nucleotide substitutions mirror the divergence of T. cruzi strains into major groups.

  4. Relative role of upstream regulators of Akt, ERK and CREB in NCAM- and FGF2-mediated signalling

    DEFF Research Database (Denmark)

    Ditlevsen, D.K.; Owczarek, S.; Berezin, V.

    2008-01-01

    demonstrated previously to be involved in NCAM signalling. For comparison, we also evaluated the role of upstream signalling cascades on fibroblast growth factor 2 (FGF2)-mediated phosphorylation of ERK, Akt, and CREB and found that FGF2 required the activity of both FGFR and Src-family kinases...... for phosphorylation of ERK, Akt, and CREB. MEK was required for phosphorylation of ERK and CREB, but not Akt, whereas G(0)/G(i)-proteins were necessary for phosphorylation of Akt and CREB, and cGMP was necessary for Akt phosphorylation. We thus demonstrate that even though NCAM and FGF2 have many signalling features...... in common, and even though both are known to activate FGFR, there are a number of differences in the intracellular signalling network activated by the NCAM ligand C3d and the FGFR ligand FGF2....

  5. Water quality assessment in piracicamirim creek upstream and downstream a sugar and ethanol industry through toxicity tests with cladocerans

    Directory of Open Access Journals (Sweden)

    Rafael Grossi Botelho

    2012-08-01

    Full Text Available An environmental impact study was conducted to determine the Piracicamirim's creek water quality in order to assess the influence of effluents from a sugar industry in this water body. For this, toxicity tests were performed with a water sample upstream and downstream the industry using the microcrustaceans Daphnia magna, Ceriodaphnia dubia and Ceriodaphnia silvestrii as test organisms, as well as physical and chemical analysis of water. Results showed that physical and chemical parameters did not change during the sampling period, except for the dissolved oxygen. No toxicity was observed for D. magna and reproduction of C. dubia and C. silvestrii in both sampling points. Thus, the industry was not negatively impacting the quality of this water body.

  6. twin of eyeless, a second Pax-6 gene of Drosophila, acts upstream of eyeless in the control of eye development.

    Science.gov (United States)

    Czerny, T; Halder, G; Kloter, U; Souabni, A; Gehring, W J; Busslinger, M

    1999-03-01

    The Drosophila Pax-6 gene eyeless (ey) plays a key role in eye development. Here we show tht Drosophila contains a second Pax-6 gene, twin of eyeless (toy), due to a duplication during insect evolution. Toy is more similar to vertebrate Pax-6 proteins than Ey with regard to overall sequence conservation, DNA-binding function, and early expression in the embryo, toy and ey share a similar expression pattern in the developing visual system, and targeted expression of Toy, like Ey, induces the formation of ectopic eyes. Genetic and biochemical evidence indicates, however, that Toy functions upstream of ey by directly regulating the eye-specific enhancer of ey. Toy is therefore required for initiation of ey expression in the embryo and acts through Ey to activate the eye developmental program.

  7. Upstream promoter sequences and αCTD mediate stable DNA wrapping within the RNA polymerase–promoter open complex

    Science.gov (United States)

    Cellai, Sara; Mangiarotti, Laura; Vannini, Nicola; Naryshkin, Nikolai; Kortkhonjia, Ekaterine; Ebright, Richard H; Rivetti, Claudio

    2007-01-01

    We show that the extent of stable DNA wrapping by Escherichia coli RNA polymerase (RNAP) in the RNAP–promoter open complex depends on the sequence of the promoter and, in particular, on the sequence of the upstream region of the promoter. We further show that the extent of stable DNA wrapping depends on the presence of the RNAP α-subunit carboxy-terminal domain and on the presence and length of the RNAP α-subunit interdomain linker. Our results indicate that the extensive stable DNA wrapping observed previously in the RNAP–promoter open complex at the λ PR promoter is not a general feature of RNAP–promoter open complexes. PMID:17290289

  8. Upstream promoter sequences and alphaCTD mediate stable DNA wrapping within the RNA polymerase-promoter open complex.

    Science.gov (United States)

    Cellai, Sara; Mangiarotti, Laura; Vannini, Nicola; Naryshkin, Nikolai; Kortkhonjia, Ekaterine; Ebright, Richard H; Rivetti, Claudio

    2007-03-01

    We show that the extent of stable DNA wrapping by Escherichia coli RNA polymerase (RNAP) in the RNAP-promoter open complex depends on the sequence of the promoter and, in particular, on the sequence of the upstream region of the promoter. We further show that the extent of stable DNA wrapping depends on the presence of the RNAP alpha-subunit carboxy-terminal domain and on the presence and length of the RNAP alpha-subunit interdomain linker. Our results indicate that the extensive stable DNA wrapping observed previously in the RNAP-promoter open complex at the lambda P(R) promoter is not a general feature of RNAP-promoter open complexes.

  9. Investigating Sources of Toxicity in Stormwater: Algae Mortality in Runoff Upstream of the Lawrence Livermore National Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Campbell, C G; Folks, K; Mathews, S; Martinelli, R

    2003-10-06

    A source evaluation case study is presented for observations of algae toxicity in an intermittent stream passing through the Lawrence Livermore National Laboratory near Livermore, California. A five-step procedure is discussed to determine the cause of water toxicity problems and to determine appropriate environmental management practices. Using this approach, an upstream electrical transfer station was identified as the probable source of herbicides causing the toxicity. In addition, an analytical solution for solute transport in overland flow was used to estimate the application level of 40 Kg/ha. Finally, this source investigation demonstrates that pesticides can impact stream water quality regardless of application within levels suggested on manufacturer labels. Environmental managers need to ensure that pesticides that could harm aquatic organisms (including algae) not be used within close proximity to streams or storm drainages and that application timing should be considered for environmental protection.

  10. Design and performance investigation of LDPC-coded upstream transmission systems in IM/DD OFDM-PONs

    Science.gov (United States)

    Gong, Xiaoxue; Guo, Lei; Wu, Jingjing; Ning, Zhaolong

    2016-12-01

    In Intensity-Modulation Direct-Detection (IM/DD) Orthogonal Frequency Division Multiplexing Passive Optical Networks (OFDM-PONs), aside from Subcarrier-to-Subcarrier Intermixing Interferences (SSII) induced by square-law detection, the same laser frequency for data sending from Optical Network Units (ONUs) results in ONU-to-ONU Beating Interferences (OOBI) at the receiver. To mitigate those interferences, we design a Low-Density Parity Check (LDPC)-coded and spectrum-efficient upstream transmission system. A theoretical channel model is also derived, in order to analyze the detrimental factors influencing system performances. Simulation results demonstrate that the receiver sensitivity is improved 3.4 dB and 2.5 dB under QPSK and 8QAM, respectively, after 100 km Standard Single-Mode Fiber (SSMF) transmission. Furthermore, the spectrum efficiency can be improved by about 50%.

  11. Emulation and Calibration of the SALT Read-out Chip for the Upstream Tracker for Modernised LHCb Detector

    CERN Document Server

    Dendek, Adam

    2015-01-01

    The LHCb is one of the four major experiments currently operating at CERN. The main reason for constructing the LHCb forward spectrometer was a precise measurement of the CP violation in heavy quarks section as well as search for a New Physics. To obtain interesting results, the LHCb is mainly focused on study of B meson decays. Unfortunately, due to the present data acquisition architecture, the LHCb experiment is statistically limited for collecting such events. This fact led the LHCb Collaboration to decide to perform far-reaching upgrade. Key part of this upgrade will be replacement of the TT detector. To perform this action, it was requited to design new tracking detector with entirely new front-end electronics. This detector will be called the Upstream Tracker (UT) and the read-out chip — SALT. This note presents an overall discussion on SALT chip. In particular, the emulation process of the SALT data preformed via the software written by the author.

  12. San Joaquin River Up-Stream DO TMDL Project Task 4: MonitoringStudy Interim Task Report #3

    Energy Technology Data Exchange (ETDEWEB)

    Stringfellow, William; Borglin, Sharon; Dahlgren, Randy; Hanlon,Jeremy; Graham, Justin; Burks, Remie; Hutchinson, Kathleen

    2007-03-30

    The purpose of the Dissolved Oxygen Total Maximum Daily LoadProject (DO TMDLProject) is to provide a comprehensive understanding ofthe sources and fate of oxygen consuming materials in the San JoaquinRiver (SJR) watershed between Channel Point and Lander Avenue (upstreamSJR). When completed, this study will provide the stakeholders anunderstanding of the baseline conditions of the basin, provide input foran allocation decision, and provide the stakeholders with a tool formeasuring the impact of any waterquality management program that may beimplemented as part of the DO TMDL process. Previous studies haveidentified algal biomass as the most significant oxygen-demandingsubstance in the DO TMDL Project study-area between of Channel Point andLander Ave onthe SJR. Other oxygen-demanding substances found in theupstream SJR include ammonia and organic carbon from sources other thanalgae. The DO TMDL Project study-area contains municipalities, dairies,wetlands, cattle ranching, irrigated agriculture, and industries thatcould potentially contribute biochemical oxygen demand (BOD) to the SJR.This study is designed to discriminate between algal BOD and othersources of BOD throughout the entire upstream SJR watershed. Algalbiomass is not a conserved substance, but grows and decays in the SJR;hence, characterization of oxygen-demanding substances in the SJR isinherently complicated and requires an integrated effort of extensivemonitoring, scientific study, and modeling. In order to achieve projectobjectives, project activities were divided into a number of Tasks withspecific goals and objectives. In this report, we present the results ofmonitoring and research conducted under Task 4 of the DO TMDL Project.The major objective of Task 4 is to collect sufficient hydrologic (flow)and water quality (WQ) data to characterize the loading of algae, otheroxygen-demanding materials, and nutrients fromindividual tributaries andsub-watersheds of the upstream SJR between Mossdale and

  13. Loss of proteostatic control as a substrate for Atrial Fibrillation; a novel target for upstream therapy by Heat Shock Proteins

    Directory of Open Access Journals (Sweden)

    Roelien Amanda Marjolein Meijering

    2012-02-01

    Full Text Available Atrial Fibrillation (AF is the most common, sustained clinical tachyarrhythmia associated with significant morbidity and mortality. AF is a persistent condition with progressive structural remodeling of the atrial cardiomyocytes due to the AF itself, resulting in cellular changes commonly observed in ageing and in other heart diseases. While rhythm control by electrocardioversion or drug treatment is the treatment of choice in symptomatic AF patients, its effectiveness is still limited. Current research is directed at preventing new-onset AF by limiting the development of substrates underlying AF promotion and resembles mechanism-based therapy. Upstream therapy refers to the use of non-ion channel anti-arrhythmic drugs that modify the atrial substrate- or target-specific mechanisms of AF, with the ultimate aim to prevent the occurrence (primary prevention or recurrence of the arrhythmia following (spontaneous conversion (secondary prevention.Heat shock proteins (HSPs are molecular chaperones and comprise a large family of proteins involved in the protection against various forms of cellular stress. Their classical function is the conservation of proteostasis via prevention of toxic protein aggregation by binding to (partially unfolded proteins. Our recent data reveal that HSPs prevent electrical, contractile and structural remodeling of cardiomyocytes, thus attenuating the AF substrate in cellular, Drosophila melanogaster and animal experimental models. Furthermore, studies in humans suggest a protective role for HSPs against the progression from paroxysmal AF to persistent AF and in recurrence of AF. In this review, we discuss upregulation of the heat shock response system as a novel target for upstream therapy to prevent derailment of proteostasis and consequently promotion and recurrence of AF.

  14. Toll-Like Receptor 4 Is an Essential Upstream Regulator of On-Time Parturition and Perinatal Viability in Mice.

    Science.gov (United States)

    Wahid, Hanan H; Dorian, Camilla L; Chin, Peck Yin; Hutchinson, Mark R; Rice, Kenner C; Olson, David M; Moldenhauer, Lachlan M; Robertson, Sarah A

    2015-10-01

    An inflammatory response is instrumental in the physiological process of parturition but the upstream signals initiating inflammation are undefined. Because endogenous ligands for Toll-like receptor 4 (TLR4) are released in late gestation, we hypothesized that on-time labor requires TLR4 signaling, to trigger a cytokine and leukocyte response and accelerate the parturition cascade. In pregnant TLR4-deficient (Tlr4-/-) mice, average gestation length was extended by 13 hours and increased perinatal mortality was seen compared with wild-type controls. Quantification of cytokine and uterine activation gene expression showed that late gestation induction of Il1b, Il6, Il12b, and Tnf expression seen in control placenta and fetal membranes was disrupted in Tlr4-/- mice, and accompanied by a transient delay in expression of uterine activation genes, including prostaglandin F receptor, oxytocin receptor, and connexin-43. Leukocyte populations were altered before birth in TLR4-deficient females, with fewer neutrophils and macrophages in the placenta, and fewer dendritic cells and more regulatory T cells in the myometrium. Administration of TLR4 ligand lipopolysaccharide to pregnant wild-type mice induced cytokine expression and fetal loss, whereas Tlr4-/- pregnancies were protected. The small molecule TLR4 antagonist (+)-naloxone increased mean duration of gestation by 16 hours in wild-type mice. Collectively, these data demonstrate that TLR4 is a key upstream regulator of the inflammatory response acting to drive uterine activation and control the timing of labor. Because causal pathways for term and preterm labor converge with TLR4, interventions to manipulate TLR4 signaling may have therapeutic utility for women at risk of preterm labor, or in postterm pregnancy.

  15. Effects of a Guide Field on the Larmor Electric Field and Upstream Electron Temperature Anisotropy in Collisionless Asymmetric Magnetic Reconnection

    Science.gov (United States)

    Ek-In, Surapat; Malakit, Kittipat; Ruffolo, David; Shay, Michael A.; Cassak, Paul A.

    2017-08-01

    We perform the first study of the properties of the Larmor electric field (LEF) in collisionless asymmetric magnetic reconnection in the presence of an out-of-plane (guide) magnetic field for different sets of representative upstream parameters at Earth’s dayside magnetopause with an ion temperature greater than the electron temperature (the ion-to-electron temperature ratio fixed at 2) using two-dimensional particle-in-cell simulations. We show that the LEF does persist in the presence of a guide field. We study how the LEF thickness and strength change as a function of guide field and the magnetospheric temperature and reconnecting magnetic field strength. We find that the thickness of the LEF structure decreases, while its magnitude increases when a guide field is added to the reconnecting magnetic field. The added guide field makes the Larmor radius smaller, so the scaling with the magnetospheric ion Larmor radius is similar to that reported for the case without a guide field. Note, however, that the physics causing the LEF is not well understood, so future work in other parameter regimes is needed to fully predict the LEF for arbitrary conditions. We also find that a previously reported upstream electron temperature anisotropy arises in the vicinity of the LEF region both with and without a guide field. We argue that the generation of the anisotropy is linked to the existence of the LEF. The LEF can be used in combination with the electron temperature anisotropy as a signature to effectively identify dayside reconnection sites in observations.

  16. Suspended-sediment loads, reservoir sediment trap efficiency, and upstream and downstream channel stability for Kanopolis and Tuttle Creek Lakes, Kansas, 2008-10

    Science.gov (United States)

    Juracek, Kyle E.

    2011-01-01

    Continuous streamflow and turbidity data collected from October 1, 2008, to September 30, 2010, at streamgage sites upstream and downstream from Kanopolis and Tuttle Creek Lakes, Kansas, were used to compute the total suspended-sediment load delivered to and released from each reservoir as well as the sediment trap efficiency for each reservoir. Ongoing sedimentation is decreasing the ability of the reservoirs to serve several purposes including flood control, water supply, and recreation. River channel stability upstream and downstream from the reservoirs was assessed using historical streamgage information. For Kanopolis Lake, the total 2-year inflow suspended-sediment load was computed to be 600 million pounds. Most of the suspended-sediment load was delivered during short-term, high-discharge periods. The total 2-year outflow suspended-sediment load was computed to be 31 million pounds. Sediment trap efficiency for the reservoir was estimated to be 95 percent. The mean annual suspended-sediment yield from the upstream basin was estimated to be 129,000 pounds per square mile per year. No pronounced changes in channel width were evident at five streamgage sites located upstream from the reservoir. At the Ellsworth streamgage site, located upstream from the reservoir, long-term channel-bed aggradation was followed by a period of stability. Current (2010) conditions at five streamgages located upstream from the reservoir were typified by channel-bed stability. At the Langley streamgage site, located immediately downstream from the reservoir, the channel bed degraded 6.15 feet from 1948 to 2010. For Tuttle Creek Lake, the total 2-year inflow suspended-sediment load was computed to be 13.3 billion pounds. Most of the suspended-sediment load was delivered during short-term, high-discharge periods. The total 2-year outflow suspended-sediment load was computed to be 327 million pounds. Sediment trap efficiency for the reservoir was estimated to be 98 percent. The mean

  17. Factors Affecting the Survival of Upstream Migrant Adult Salmonids in the Columbia River Basin : Recovery Issues for Threatened and Endangered Snake River Salmon : Technical Report 9 of 11.

    Energy Technology Data Exchange (ETDEWEB)

    Dauble, Dennis D.; Mueller, Robert P.

    1993-06-01

    The Bonneville Power Administration (BPA) is developing conservation planning documentation to support the National Marine Fisheries Service`s (NMFS) recovery plan for Columbia Basin salmonid stocks that are currently listed under the Endangered Species Act (ESA). Information from the conservation planning documentation will be used as a partial scientific basis for identifying alternative conservation strategies and to make recommendations toward conserving, rebuilding, and ultimately removing these salmon stocks from the list of endangered species. This report describes the adult upstream survival study, a synthesis of biological analyses related to conditions affecting the survival of adult upstream migrant salmonids in the Columbia River system. The objective of the adult upstream survival study was to analyze existing data related to increasing the survival of adult migrant salmonids returning to the Snake River system. The fate and accountability of each stock during its upstream migration period and the uncertainties associated with measurements of escapement and survival were evaluated. Operational measures that affected the survival of adult salmon were evaluated including existing conditions, augmented flows from upstream storage release, and drawdown of mainstem reservoirs. The potential impacts and benefits of these measures to each ESA stock were, also described based on considerations of species behavior and run timing.

  18. A cost-effective structure of a centralized-light-source WDM-PON utilizing inverse-duobinary-RZ downstream and DPSK upstream

    Science.gov (United States)

    Chen, Long-Quan; Qiao, Yao-Jun; Ji, Yue-Feng

    2013-05-01

    In this paper, we propose a new structure of a centralized-light-source wavelength division multiplexed passive optical network (WDM-PON) utilizing inverse-duobinary-return-to-zero (inverse-duobinary-RZ) downstream and DPSK upstream. It reuses downstream light for the upstream modulation, which retrenches lasers assembled at each optical network unit (ONU), and ultimately cuts down the cost of ONUs a great deal. Meanwhile, a 50-km-reach WDM-PON experiment with 10-Gb/s inverse-duobinary-RZ downstream and 6-Gb/s DPSK upstream is demonstrated here. It is revealed to be a novel cost-effective alternative for the next generation access network.

  19. Upstream WDM-PON transmission scheme based on PDM-OOK modulation and digital coherent detection with dual-modulus algorithm.

    Science.gov (United States)

    Zhu, Paikun; Li, Juhao; Zhou, Peng; Lin, Bangjiang; Chen, Zhangyuan; He, Yongqi

    2015-05-18

    Wavelength-division-multiplexing passive optical network (WDM-PON) is a promising architecture for next-generation access networks because of its large bandwidth, protocol transparency and scalability. In this paper, we propose a cost-effective, high-speed upstream WDM-PON scheme adopting polarization division multiplexed (PDM) on-off keying (OOK) modulation at the optical network unit (ONU) and digital coherent/self-coherent detection with a novel blind dual-modulus equalization algorithm at the optical line terminal (OLT). As such, the upstream capacity can be directly enhanced at low ONU expenditure, and receiver sensitivity as well as power budget can be also improved. Enabled by the scheme, 40-Gb/s upstream transmission in 80-km WDM-PON is experimentally demonstrated.

  20. A cost-effective structure of a centralized-light-source WDM-PON utilizing inverse-duobinary-RZ downstream and DPSK upstream

    Institute of Scientific and Technical Information of China (English)

    Chen Long-Quan; Qiao Yao-Jun; Ji Yue-Feng

    2013-01-01

    In this paper,we propose a new structure of a centralized-light-source wavelength division multiplexed passive optical network (WDM-PON) utilizing inverse-duobinary-return-to-zero (inverse-duobinary-RZ) downstream and DPSK upstream.It reuses downstream light for the upstream modulation,which retrenches lasers assembled at each optical network unit (ONU),and ultimately cuts down the cost of ONUs a great deal.Meanwhile,a 50-km-reach WDM-PON experiment with 10-Gb/s inverse-duobinary-RZ downstream and 6-Gb/s DPSK upstream is demonstrated here.It is revealed to be a novel cost-effective alternative for the next generation access network.

  1. A WDM-PON with DPSK modulated downstream and OOK modulated upstream signals based on symmetric 10 Gbit/s wavelength reused bidirectional reflective SOA

    Science.gov (United States)

    El-Nahal, Fady I.

    2017-01-01

    We investigate a wavelength-division-multiplexing passive optical network (WDM-PON) with centralized lightwave and direct detection. The system is demonstrated for symmetric 10 Gbit/s differential phase-shift keying (DPSK) downstream signals and on-off keying (OOK) upstream signals, respectively. A wavelength reused scheme is employed to carry the upstream data by using a reflective semiconductor optical amplifier (RSOA) as an intensity modulator at the optical network unit (ONU). The constant-intensity property of the DPSK modulation format can keep high extinction ratio ( ER) of downstream signal and reduce the crosstalk to the upstream signal. The bit error rate ( BER) performance of our scheme shows that the proposed 10 Gbit/s symmetric WDM-PON can achieve error free transmission over 25-km-long fiber transmission with low power penalty.

  2. Bidirectional 3.125 Gbps downstream / 2 Gbps upstream impulse radio ultrawide-band (UWB) over combined fiber and wireless link

    DEFF Research Database (Denmark)

    Jensen, Jesper Bevensee; Gibbon, Timothy Braidwood; Yu, Xianbin;

    2010-01-01

    We demonstrate bidirectional fiber and wireless transmission of impulse radio ultra-wideband at 3.125 Gbps downstream and 2 Gbps upstream. After transmission over 50 km fiber and 1.85 m wireless link both signals are recovered without errors.......We demonstrate bidirectional fiber and wireless transmission of impulse radio ultra-wideband at 3.125 Gbps downstream and 2 Gbps upstream. After transmission over 50 km fiber and 1.85 m wireless link both signals are recovered without errors....

  3. Asymmetrical TWDM-PON with 4 × 25-Gb/s downstream DSB OFDM and 4 × 10-Gb/s upstream OOK modulations

    Science.gov (United States)

    Lin, Bangjiang; Li, Yiwei; Zhang, Shihao; Tang, Xuan

    2015-12-01

    We propose and experimentally demonstrate an asymmetrical time wavelength division multiplexing passive optical network (TWDM-PON) scheme with 100-Gb/s downstream and 40-Gb/s upstream capacity using four pairs of wavelengths. Double sideband (DSB) orthogonal frequency division multiplexing (OFDM) with 16-QAM mapping is used for downstream transmission, while on-off keying (OOK) modulation is used for upstream transmission. The experimental results show that the power budget for bidirectional transmission is more than 35.5-dB. This scheme can be a promising solution for 100-Gb/s TWDM-PON with high power budget.

  4. Risk assessment for the reintroduction of anadromous salmonids upstream of Chief Joseph and Grand Coulee Dams, Northeastern Washington

    Science.gov (United States)

    Hardiman, Jill M.; Breyta, Rachel B.; Haskell, Craig A.; Ostberg, Carl O.; Hatten, James R.; Connolly, Patrick J.

    2017-09-12

    The Upper Columbia United Tribes (UCUT; Spokane, Colville, Kootenai, Coeur d’Alene, and Kalispel Tribes) and Washington Department of Fish and Wildlife want to reintroduce anadromous salmonids to their historical range to restore ecosystem function and lost cultural and spiritual relationships in the upper Columbia River, northeastern Washington. The UCUT contracted with the U.S. Geological Survey to assess risks to resident taxa (existing fish populations in the reintroduction area upstream of Chief Joseph and Grand Coulee Dams) and reintroduced salmon associated with reintroduction. We developed a risk assessment framework for reintroduction of anadromous salmonids upstream of Chief Joseph and Grand Coulee Dams. To accomplish this goal, we applied strategies identified in previous risk assessment frameworks for reintroduction. The risk assessment is an initial step towards an anadromous reintroduction strategy. An initial list of potential donor sources for reintroduction species was developed from previous published sources for Chinook Salmon (Oncorhynchus tshawytscha) donors in the Transboundary Reach of the Columbia River, British Columbia; an ecological risk assessment of upper Columbia River hatchery programs on non-target taxa of concern; and a review of existing hatchery programsDuring two workshops, we further identified and ranked potential donor sources of anadromous Redband Trout (steelhead; O. mykiss), Chinook Salmon, Sockeye Salmon (O. nerka), and Coho Salmon (O. kisutch). We also identified resident fish populations of interest and their primary habitat, location, status, and pathogen concerns to determine the potential risks of reintroduction. Species were deemed of interest based on resource management and potential interactions (that is, genetics, competition, and predation) with introduced species. We developed tables of potential donors by species and characterized potential sources (hatchery and natural origins), populations (individual runs

  5. From C-Reactive Protein to Interleukin-6 to Interleukin-1: Moving Upstream To Identify Novel Targets for Atheroprotection.

    Science.gov (United States)

    Ridker, Paul M

    2016-01-08

    Plasma levels of the inflammatory biomarker high-sensitivity C-reactive protein (hsCRP) predict vascular risk with an effect estimate as large as that of total or high-density lipoprotein cholesterol. Further, randomized trial data addressing hsCRP have been central to understanding the anti-inflammatory effects of statin therapy and have consistently demonstrated on-treatment hsCRP levels to be as powerful a predictor of residual cardiovascular risk as on-treatment levels of low-density lipoprotein cholesterol. Yet, although hsCRP is clinically useful as a biomarker for risk prediction, most mechanistic studies suggest that CRP itself is unlikely to be a target for intervention. Moving upstream in the inflammatory cascade from CRP to interleukin (IL)-6 to IL-1 provides novel therapeutic opportunities for atheroprotection that focus on the central IL-6 signaling system and ultimately on inhibition of the IL-1β-producing NOD-like receptor family pyrin domain containing 3 inflammasome. Cholesterol crystals, neutrophil extracellular traps, atheroprone flow, and local tissue hypoxia activate the NOD-like receptor family pyrin domain containing 3 inflammasome. As such, a unifying concept of hsCRP as a downstream surrogate biomarker for upstream IL-1β activity has emerged. From a therapeutic perspective, small ischemia studies show reductions in acute-phase hsCRP production with the IL-1 receptor antagonist anakinra and the IL-6 receptor blocker tocilizumab. A phase IIb study conducted among diabetic patients at high vascular risk indicates that canakinumab, a human monoclonal antibody that targets IL-1β, markedly reduces plasma levels of IL-6, hsCRP, and fibrinogen with little change in atherogenic lipids. Canakinumab in now being tested as a method to prevent recurrent cardiovascular events in a randomized trial of 10 065 post-myocardial infarction patients with elevated hsCRP that is fully enrolled and due to complete in 2017. Clinical trials using alternative anti

  6. LHCb: LHCb Upstream Tracker

    CERN Multimedia

    Manning Jr, P; Stone, S

    2014-01-01

    The LHCb upgrade requires replacing the silicon strip tracker between the vertex locator and the magnet. A new design has been developed and tested based on the "stave" concept planned for the ATLAS upgrade. We will describe the new detector being constructed and show its improved performance in charged particle tracking and triggering.

  7. LHCb Upstream Tracker

    CERN Multimedia

    Gandini, P

    2014-01-01

    The LHCb upgrade requires replacing the silicon strip tracker between the vertex locator (VELO) and the magnet. A new design has been developed and tested based on the "stave" concept planned for the ATLAS upgrade

  8. LHCb Upstream Tracker

    CERN Multimedia

    Gandini, Paolo

    2014-01-01

    The LHCb upgrade requires replacing the silicon strip tracker between the vertex locator (VELO) and the magnet. A new design has been developed and tested based on the "stave" concept planned for the ATLAS upgrade.

  9. Upstream/Downstream

    Science.gov (United States)

    Slack, Amy

    2014-01-01

    In our increasingly digital world, students are often disconnected from the natural environment and may not understand how human actions affect it. One of the most significant human impacts on ecosystems is water pollution. Measuring the water quality of a local stream, river, or lake can be a valuable learning experience but is often impractical.…

  10. The long non-coding RNA PARROT is an upstream regulator of c-Myc and affects proliferation and translation

    Science.gov (United States)

    Vučićević, Dubravka; Gehre, Maja; Dhamija, Sonam; Friis-Hansen, Lennart; Meierhofer, David; Sauer, Sascha; Ørom, Ulf Andersson

    2016-01-01

    Long non-coding RNAs are important regulators of gene expression and signaling pathways. The expression of long ncRNAs is dysregulated in cancer and other diseases. The identification and characterization of long ncRNAs is often challenging due to their low expression level and localization to chromatin. Here, we identify a functional long ncRNA, PARROT (Proliferation Associated RNA and Regulator Of Translation) transcribed by RNA polymerase II and expressed at a relatively high level in a number of cell lines. The PARROT long ncRNA is associated with proliferation in both transformed and normal cell lines. We characterize the long ncRNA PARROT as an upstream regulator of c-Myc affecting cellular proliferation and translation using RNA sequencing and mass spectrometry following depletion of the long ncRNA. PARROT is repressed during senescence of human mammary epithelial cells and overexpressed in some cancers, suggesting an important association with proliferation through regulation of c-Myc. With this study, we add to the knowledge of cytoplasmic functional long ncRNAs and extent the long ncRNA-Myc regulatory network in transformed and normal cells. PMID:27129154

  11. Trace Elements, With Special Reference to Mercury, in Fish Collected Upstream and Downstream of Los Alamos National Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    P. R. Fresquez; J. D. Huchton; M. A. Mullen

    1999-11-01

    Trace elements (Ag, As, Ba, Be, Cr, Cd, Cu, Hg, Ni, Pb, Sb, Se, and Tl) were determined in muscle (fillet) of average sized fish (mostly carp, catfish, and sucker) collected from the confluences of major canyons that cross Los Alamos National Laboratory (LANL) lands with the Rio Grande (RG). Also, trace elements were determined in fish from reservoirs upstream (Abiquiu [AR]) and downstream (Cochiti [CR]) of LANL from 1991 through 1999. In general, all of the (mean) trace elements, including Hg, were either at the limits of detection (LOD) or in low concentrations at all study sites. Of the trace elements (e.g., Ba, Cu, and Hg) that were found to be above the LOD in fish muscle collected from LANL canyons/RG, none were in significantly higher (p < 0.05) concentrations than in muscle of fish collected from background locations. Mercury concentrations (mean of means) in fish from AR (all other trace elements were at LOD) were significantly higher (p < 0.10) than Hg concentrations in fish from CR, and Hg concentrations in fish collected from both reservoirs exhibited significantly (AR = p <0.05 and CR = p < 0.10) decreasing trends over time.

  12. Mercury in Fish Collected Upstream and Downstream of Los Alamos National Laboratory, New Mexico: 1991--2004.

    Energy Technology Data Exchange (ETDEWEB)

    P.R. Fresquez

    2004-10-15

    Small amounts of mercury (Hg) may exist in some canyon drainage systems within Los Alamos National Laboratory lands as a result of past discharges of untreated effluents. This paper reports on the concentrations of Hg in muscle (fillets) of various types of fish species collected downstream of LANL's influence from 1991 through 2004. The mean Hg concentration in fish from Cochiti reservoir (0.22 {micro}g/g wet weight), which is located downstream of LANL, was similar to fish collected from a reservoir upstream of LANL (Abiquiu) (0.26 {micro}g/g wet weight). Mercury concentrations in fish collected from both reservoirs exhibited significantly (Abiquiu = p < 0.05 and Cochiti = p < 0.10) decreasing trends over time. Predator fish like the northern pike (Esox lucius) contained significantly higher concentrations of Hg (0.39 {micro}g/g wet weight) than bottom-feeding fish like the white sucker (Catostomus commersoni) (0.10 {micro}g/g wet weight).

  13. The upstream conserved regions (UCRs) mediate homo- and hetero-oligomerization of type 4 cyclic nucleotide phosphodiesterases (PDE4s).

    Science.gov (United States)

    Xie, Moses; Blackman, Brigitte; Scheitrum, Colleen; Mika, Delphine; Blanchard, Elise; Lei, Tao; Conti, Marco; Richter, Wito

    2014-05-01

    PDE4s (type 4 cyclic nucleotide phosphodiesterases) are divided into long and short forms by the presence or absence of conserved N-terminal domains termed UCRs (upstream conserved regions). We have shown previously that PDE4D2, a short variant, is a monomer, whereas PDE4D3, a long variant, is a dimer. In the present study, we have determined the apparent molecular masses of various long and short PDE4 variants by size-exclusion chromatography and sucrose density-gradient centrifugation. Our results indicate that dimerization is a conserved property of all long PDE4 forms, whereas short forms are monomers. Dimerization is mediated by the UCR domains. Given their high sequence conservation, the UCR domains mediate not only homo-oligomerization, but also hetero-oligomerization of distinct PDE4 long forms as detected by co-immunoprecipitation assays and FRET microscopy. Endogenous PDE4 hetero-oligomers are, however, low in abundance compared with homo-dimers, revealing the presence of mechanisms that predispose PDE4s towards homo-oligomerization. Oligomerization is a prerequisite for the regulatory properties of the PDE4 long forms, such as their PKA (protein kinase A)-dependent activation, but is not necessary for PDE4 protein-protein interactions. As a result, individual PDE4 protomers may independently mediate protein-protein interactions, providing a mechanism whereby PDE4s contribute to the assembly of macromolecular signalling complexes.

  14. The SLO1 PPR protein is required for RNA editing at multiple sites with similar upstream sequences in Arabidopsis mitochondria.

    Science.gov (United States)

    Sung, Tzu-Ying; Tseng, Ching-Chih; Hsieh, Ming-Hsiun

    2010-08-01

    In Arabidopsis, RNA editing changes more than 500 cytidines to uridines in mitochondrial transcripts. The editing enzyme and co-factors involved in these processes are largely unknown. We have identified a nuclear gene SLOW GROWTH1 (SLO1) encoding an E motif-containing pentatricopeptide repeat protein that is required for RNA editing of nad4 and nad9 in Arabidopsis mitochondria. The SLO1 protein is localized to the mitochondrion, and its absence gives rise to small plants with slow growth and delayed development. A survey of approximately 500 mitochondrial RNA editing sites in Arabidopsis reveals that the editing of two sites, nad4-449 and nad9-328, is abolished in the slo1 mutants. Sequence comparison in the upstream (from -1 to -15 bp) of nad4-449 and nad9-328 editing sites shows that nine of the 15 nucleotides are identical. In addition to RNA editing, we used RNA gel blot analysis to compare the abundance and banding patterns of mitochondrial transcripts between the wild type and slo1 mutants. Of the 79 genes and open reading frames examined, steady-state levels of 56 mitochondrial transcripts are increased in the slo1 mutants. These results suggest that the SLO1 protein may indirectly regulate plant growth and development via affecting mitochondrial RNA editing and gene expression.

  15. Bifurcation analysis of hydro-turbine regulating system with saturation nonlinearity for hydropower station with upstream and downstream surge chambers

    Science.gov (United States)

    Chen, J. P.; Yang, J. D.; Guo, W. C.

    2016-11-01

    A nonlinear mathematical model of hydraulic turbine regulating system is applied to describe hydropower stations with upstream and downstream surge chambers. This model features saturation nonlinearity including pipeline system and turbine regulating system used in stability analysis. First, the existence conditions and direction of Hopf bifurcation are obtained. Second, based on the algebraic criteria for the occurrence of Hopf bifurcation, the stability domain is drawn in a coordinate system, where the proportional gain Kp is the abscissa and the integral gain Ki is the ordinate. Third, the nonlinear dynamic behaviour of a regulating system with different state parameters are analyzed, and the variations of the system stability around the two sides of the bifurcation point are numerically calculated. Based on this work we conclude that the Hopf bifurcation of system is supercritical. The bifurcation parameters that are far from the bifurcation point would be advantageous to the rapid system regulation needed to sustain equilibrium. Furthermore, it is established that using a PID controller is more conducive to stability than a PI controller. The unit stability regulation gets worse by taking into account the saturation nonlinearity.

  16. An upstream open reading frame controls translation of var2csa, a gene implicated in placental malaria.

    Directory of Open Access Journals (Sweden)

    Borko Amulic

    2009-01-01

    Full Text Available Malaria, caused by the parasite Plasmodium falciparum, is responsible for substantial morbidity, mortality and economic losses in tropical regions of the world. Pregnant women are exceptionally vulnerable to severe consequences of the infection, due to the specific adhesion of parasite-infected erythrocytes in the placenta. This adhesion is mediated by a unique variant of PfEMP1, a parasite encoded, hyper-variable antigen placed on the surface of infected cells. This variant, called VAR2CSA, binds to chondroitin sulfate A on syncytiotrophoblasts in the intervillous space of placentas. VAR2CSA appears to only be expressed in the presence of a placenta, suggesting that its expression is actively repressed in men, children or non-pregnant women; however, the mechanism of repression is not understood. Using cultured parasite lines and reporter gene constructs, we show that the gene encoding VAR2CSA contains a small upstream open reading frame that acts to repress translation of the resulting mRNA, revealing a novel form of gene regulation in malaria parasites. The mechanism underlying this translational repression is reversible, allowing high levels of protein translation upon selection, thus potentially enabling parasites to upregulate expression of this variant antigen in the presence of the appropriate host tissue.

  17. NDV-induced apoptosis in absence of Bax; evidence of involvement of apoptotic proteins upstream of mitochondria

    Directory of Open Access Journals (Sweden)

    Molouki Aidin

    2012-08-01

    Full Text Available Abstract Background Recently it was shown that following infection of HeLa cells with Newcastle disease virus (NDV, the matrix (M protein binds to Bax and subsequently the intrinsic pathway of apoptosis is activated. Moreover, there was very little alteration on mRNA and protein levels of Bax and Bcl-2 after infection with NDV. Finding In order to further investigate the role of members of the Bcl-2 family, Bax-knockout and wild-type HCT116 cells were infected with NDV strain AF2240. Although both cells underwent apoptosis through the activation of the intrinsic pathway and the release of cytochrome c from mitochondria, the percentage of dead Bax-knockout cells was significantly lower than wt cells (more than 10% at 48 h post-infection. In a parallel experiment, the effect of NDV on HT29 cells, that are originally Bcl-2-free, was studied. Apoptosis in HT29 cells was associated with Bax redistribution from cytoplasm to mitochondria, similar to that of HeLa and wt HCT116 cells. Conclusion Although the presence of Bax during NDV-induced apoptosis contributes to a faster cell death, it was concluded that other apoptotic protein(s upstream of mitochondria are also involved since cancer cells die whether in the presence or absence of Bax. Therefore, the classic Bax/Bcl-2 ratio may not be a major determinant in NDV-induced apoptosis.

  18. An AP1 binding site upstream of the kappa immunoglobulin intron enhancer binds inducible factors and contributes to expression.

    Science.gov (United States)

    Schanke, J T; Marcuzzi, A; Podzorski, R P; Van Ness, B

    1994-01-01

    Expression of the kappa immunoglobulin light chain gene requires developmental- and tissue-specific regulation by trans-acting factors which interact with two distinct enhancer elements. A new protein-DNA interaction has been identified upstream of the intron enhancer, within the matrix-associated region of the J-C intron. The binding activity is greatly inducible in pre-B cells by bacterial lipopolysaccharide and interleukin-1 but specific complexes are found at all stages of B cell development tested. The footprinted binding site is homologous to the consensus AP1 motif. The protein components of this complex are specifically competed by an AP1 consensus motif and were shown by supershift to include c-Jun and c-Fos, suggesting that this binding site is an AP1 motif and that the Jun and Fos families of transcription factors play a role in the regulation of the kappa light chain gene. Mutation of the AP1 motif in the context of the intron enhancer was shown to decrease enhancer-mediated activation of the promoter in both pre-B cells induced with LPS and constitutive expression in mature B cells. Images PMID:7816634

  19. Keratins regulate protein biosynthesis through localization of GLUT1 and -3 upstream of AMP kinase and Raptor

    Science.gov (United States)

    Vijayaraj, Preethi; Kröger, Cornelia; Reuter, Ursula; Windoffer, Reinhard; Leube, Rudolf E.

    2009-01-01

    Keratin intermediate filament proteins form cytoskeletal scaffolds in epithelia, the disruption of which affects cytoarchitecture, cell growth, survival, and organelle transport. However, owing to redundancy, the global function of keratins has not been defined in full. Using a targeted gene deletion strategy, we generated transgenic mice lacking the entire keratin multiprotein family. In this study, we report that without keratins, embryonic epithelia suffer no cytolysis and maintain apical polarity but display mislocalized desmosomes. All keratin-null embryos die from severe growth retardation at embryonic day 9.5. We find that GLUT1 and -3 are mislocalized from the apical plasma membrane in embryonic epithelia, which subsequently activates the energy sensor adenosine monophosphate kinase (AMPK). Analysis of the mammalian target of rapamycin (mTOR) pathway reveals that AMPK induction activates Raptor, repressing protein biosynthesis through mTORC1's downstream targets S6 kinase and 4E-binding protein 1. Our findings demonstrate a novel keratin function upstream of mTOR signaling via GLUT localization and have implications for pathomechanisms and therapy approaches for keratin disorders and the analysis of other gene families. PMID:19841136

  20. [Estimation of topographical factors in revised universal soil loss model based on maximum up-stream flow path].

    Science.gov (United States)

    Luo, Hong; Ma, You-xin; Liu, Wen-jun; Li, Hong-mei

    2010-05-01

    By using maximum upstream flow path, a self-developed new method for calculating slope length value based on Arc Macro Language (AML), five groups of DEM data for different regions in Bijie Prefecture of Guizhou Province were extracted to compute the slope length and topographical factors in the Prefecture. The time cost for calculating the slope length and the values of the topographical factors were analyzed, and compared with those by iterative slope length method based on AML (ISLA) and on C++ (ISLC). The results showed that the new method was feasible to calculate the slope length and topographical factors in revised universal soil loss model, and had the same effect as iterative slope length method. Comparing with ISLA, the new method had a high computing efficiency and greatly decreased the time consumption, and could be applied to a large area to estimate the slope length and topographical factors based on AML. Comparing with ISLC, the new method had the similar computing efficiency, but its coding was easily to be written, modified, and debugged by using AML. Therefore, the new method could be more broadly used by GIS users.

  1. Polymorphism in the bovine BOLA-DRB3 upstream regulatory regions detected through PCR-SSCP and DNA sequencing.

    Science.gov (United States)

    Ripoli, M V; Peral-García, P; Dulout, F N; Giovambattista, G

    2004-09-15

    In the present work, we describe through polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and DNA sequencing the polymorphism within the URR-BoLA-DRB3 in 15 cattle breeds. In total, seven PCR-SSCP defined alleles were detected. The alignment of studied sequences showed six polymorphic sites (four transitions, one transversion and one deletion) in the interconsensus regions of the BoLA-DRB3 upstream regulatory region (URR), while the consensus boxes were invariant. Five out of six detected polymorphic sites were of one nucleotide substitution in the interconsensus regions. It is expected that these mutations do not affect significantly the level of expression. In contrast, the deletion observed in the sequence between CCAAT and TATA boxes could have some effect on affinity interactions between the promoter region and the transcription factors. The URR-BoLA-DRB3 DNA analyzed sequences showed moderate level of nucleotide diversity, high level of identity among them and were grouped in the same clade in the phylogenetic tree. In addition, the phylogenetic tree, the similarity analysis and the sequence structure confirmed that the fragment analyzed in this study corresponds to the URR-BoLA-DRB3. The functional role of the observed polymorphic sites among the regulatory motifs in bovine needs to be analyzed and confirmed by means of gene expression assays.

  2. High-Throughput siRNA Screening to Reveal GATA-2 Upstream Transcriptional Mechanisms in Hematopoietic Cells.

    Directory of Open Access Journals (Sweden)

    Yo Saito

    Full Text Available Hematopoietic stem cells can self-renew and differentiate into all blood cell types. The transcription factor GATA-2 is expressed in both hematopoietic stem and progenitor cells and is essential for cell proliferation, survival, and differentiation. Recently, evidence from studies of aplastic anemia, MonoMAC syndrome, and lung cancer has demonstrated a mechanistic link between GATA-2 and human pathophysiology. GATA-2-dependent disease processes have been extensively analyzed; however, the transcriptional mechanisms upstream of GATA-2 remain less understood. Here, we conducted high-throughput small-interfering-RNA (siRNA library screening and showed that YN-1, a human erythroleukemia cell line, expressed high levels of GATA-2 following the activation of the hematopoietic-specific 1S promoter. As transient luciferase reporter assay in YN-1 cells revealed the highest promoter activity in the 1S promoter fused with GATA-2 intronic enhancer (+9.9 kb/1S; therefore, we established a cell line capable of stably expressing +9.9 kb/1S-Luciferase. Subsequently, we screened 995 transcription factor genes and revealed that CITED2 acts as a GATA-2 activator in human hematopoietic cells. These results provide novel insights into and further identify the regulatory mechanism of GATA-2.

  3. Different papillomaviruses have different repertoires of transcription factor binding sites: convergence and divergence in the upstream regulatory region

    Directory of Open Access Journals (Sweden)

    Alonso Ángel

    2006-03-01

    Full Text Available Abstract Background Papillomaviruses (PVs infect stratified squamous epithelia in warm-blooded vertebrates and have undergone a complex evolutionary process. The control of the expression of the early ORFs in PVs depends on the binding of cellular and viral transcription factors to the upstream regulatory region (URR of the virus. It is believed that there is a core of transcription factor binding sites (TFBS common to all PVs, with additional individual differences, although most of the available information focuses only on a handful of viruses. Results We have studied the URR of sixty-one PVs, covering twenty different hosts. We have predicted the TFBS present in the URR and analysed these results by principal component analysis and genetic algorithms. The number and nature of TFBS in the URR might be much broader than thus far described, and different PVs have different repertoires of TFBS. Conclusion There are common fingerprints in the URR in PVs that infect primates, although the ancestors of these viruses diverged a long time ago. Additionally, there are obvious differences between the URR of alpha and beta PVs, despite these PVs infect similar histological cell types in the same host, i.e. human. A thorough analysis of the TFBS in the URR might provide crucial information about the differential biology of cancer-associated PVs.

  4. Long-term fructose consumption prolongs hepatic stearoyl-CoA desaturase 1 activity independent of upstream regulation in rats.

    Science.gov (United States)

    Liu, Li; Wang, Shang; Yao, Ling; Li, Jin-Xiu; Ma, Peng; Jiang, Li-Rong; Ke, Da-Zhi; Pan, Yong-Quan; Wang, Jian-Wei

    2016-10-28

    Dietary fructose is considered a risk factor for metabolic disorders, such as fatty liver disease. However, the mechanism underlying the effects of fructose is not well characterized. We investigated the hepatic expression of key regulatory genes related to lipid metabolism following fructose feeding under well-defined conditions. Rats were fed standard chow supplemented with 10% w/v fructose solution for 5 weeks, and killed after chow-fasting and fructose withdrawal (fasting) or chow-fasting and continued fructose (fructose alone) for 14 h. Hepatic deposition of triglycerides was found in rats from both groups. As expected, fructose alone increased mRNA levels of lipogenesis-related genes and correspondingly decreased mRNA levels of lipid oxidative genes in the liver. Interesting, hepatic levels of stearoyl-CoA desaturase (SCD)1 mRNA remained elevated under fructose withdrawn conditions, although expression levels of other genes, including two key transcription factors (carbohydrate response element binding protein (ChREBP) and sterol regulatory element-binding protein (SREBP)-1c) fell to normal levels, indicating that long-term fructose intake increased SCD1 activity, independent of upstream regulatory genes, such as ChREBP and SREBP-1c. In conclusion, SCD1 overexpression in fatty liver disease is not affected by fasting after long-term fructose consumption in rats. Regulation of SCD1 plays an important role in fructose-induced hepatic steatosis. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. In vivo analysis of Aicda gene regulation: a critical balance between upstream enhancers and intronic silencers governs appropriate expression.

    Directory of Open Access Journals (Sweden)

    Le Thi Huong

    Full Text Available The Aicda gene encodes activation-induced cytidine deaminase (AID. Aicda is strongly transcribed in activated B cells to diversify immunoglobulin genes, but expressed at low levels in various other cells in response to physiological or pathological stimuli. AID's mutagenic nature has been shown to be involved in tumor development. Here, we used a transgenic strategy with bacterial artificial chromosomes (BACs to examine the in vivo functions of Aicda regulatory elements, which cluster in two regions: in the first intron (region 2, and approximately 8-kb upstream of the transcription start site (region 4. Deleting either of these regions completely abolished the expression of Aicda-BAC reporters, demonstrating these elements' critical roles. Furthermore, we found that selectively deleting two C/EBP-binding sites in region 4 inactivated the enhancer activity of the region despite the presence of intact NF-κB-, STAT6- and Smad-binding sites. On the other hand, selectively deleting E2F- and c-Myb-binding sites in region 2 increased the frequency of germinal-center B cells in which the Aicda promoter was active, indicating that E2F and c-Myb act as silencers in vivo. Interestingly, the silencer deletion did not cause ectopic activation of the Aicda promoter, indicating that Aicda activation requires enhancer-specific stimulation. In summary, precise regulation of the Aicda promoter appears to depend on a coordinated balance of activities between enhancer and silencer elements.

  6. Experimental study of the solid-liquid interface in a yield-stress fluid flow upstream of a step

    Science.gov (United States)

    Luu, Li-Hua; Pierre, Philippe; Guillaume, Chambon

    2014-11-01

    We present an experimental study where a yield-stress fluid is implemented to carefully examine the interface between a liquid-like unyielded region and a solid-like yielded region. The studied hydrodynamics consists of a rectangular pipe-flow disturbed by the presence of a step. Upstream of the step, a solid-liquid interface between a dead zone and a flow zone appears. This configuration can both model geophysical erosion phenomenon in debris flows or find applications for industrial extrusion processes. We aim to investigate the dominant physical mechanism underlying the formation of the static domain, by combining the rheological characterization of the yield-stress fluid with local measurements of the related hydrodynamic parameters. In this work, we use a model fluid, namely polymer micro-gel Carbopol, that exhibits a Hershel-Bulkley viscoplastic rheology. Exploiting the fluid transparency, the flow is monitored by Particle Image Velocimetry thanks to internal visualization technique. In particular, we demonstrate that the flow above the dead zone roughly behaves as a plug flow whose velocity profile can successfully be described by a Poiseuille equation including a Hershel-Bulkley rheology (PHB theory), with exception of a thin zone at the close vicinity of the static domain. The border inside the flow zone above which the so-called PHB flow starts, is found to be the same regardless of the flow rate and to move with a constant velocity that increases with the flow rate. We interpret this feature as a slip frontier.

  7. OsWRKY03, a rice transcriptional activator that functions in defense signaling pathway upstream of OsNPR1

    Institute of Scientific and Technical Information of China (English)

    Xiao Qiang LIU; Xian Quan BAI; Qian QIAN; Xiu Jie WANG; Ming Sheng CHEN; Cheng Cai CHU

    2005-01-01

    WRKY family proteins are a class of plant specific transcription factors that involve in many stress response pathways.It has been shown that one Arabidopsis WRKY protein, AtWRKY29/22, is activated by MAP kinase signaling cascade and confers resistance to both bacterial and fungal pathogens. However, little is known about the biological roles of WRKY proteins in rice. In this study, we investigated the expression patterns of rice AtWRKY29/22 homolog, OsWRKY03,under different conditions, and also its possible role involved in plant defense. Our results showed that OsWRKY03 was up-regulated by several defense signaling molecules or different treatments. Further analysis revealed that the expression of OsWRKY03 was light dependent. Transcriptional activation activity of OsWRKY03 was also demonstrated by yeast functional assay. Transient expression of OsWRKY03-GFP fusion protein in onion epidermis cells showed that OsWRKY03 was a nuclear localized protein. OsNPR1 as well as several other pathogenesis-related genes, such as OsPR1b, phenylalanine ammonia-lyase (ZB8) and peroxidase (POX22.3), were induced in OsWRKY03-overexpressing transgenic plants. These results indicated that OsWRKY03 is located upstream of OsNPR1 as a transcriptional activator in salicylic acid (SA)-dependent or jasmonic acid (JA)-dependent defense signaling cascades.

  8. A test of the Hall-MHD model: Application to low-frequency upstream waves at Venus

    Science.gov (United States)

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

    1994-01-01

    Early studies suggested that in the range of parameter space where the wave angular frequency is less than the proton gyrofrequency and the plasma beta, the ratio of the thermal to magnetic pressure, is less than 1 magnetohydrodynamics provides an adequate description of the propagating modes in a plasma. However, recently, Lacombe et al. (1992) have reported significant differences between basic wave characteristics of the specific propagation modes derived from linear Vlasov and Hall-magnetohydrodynamic (MHD) theories even when the waves are only weakly damped. In this paper we compare the magnetic polarization and normalization magnetic compression ratio of ultra low frequency (ULF) upstream waves at Venus with magnetic polarization and normalized magnetic compression ratio derived from both theories. We find that while the 'kinetic' approach gives magnetic polarization and normalized magnetic compression ratio consistent with the data in the analyzed range of beta (0.5 less than beta less than 5) for the fast magnetosonic mode, the same wave characteristics derived from the Hall-MHD model strongly depend on beta and are consistent with the data only at low beta for the fast mode and at high beta for the intermediate mode.

  9. Sustaining Competitiveness: Moving Towards Upstream Manufacturing in Specialized-Market-Based Clusters in the Chinese Toy Industry

    Directory of Open Access Journals (Sweden)

    Huasheng Zhu

    2016-02-01

    Full Text Available Western industrial cluster literature pays little attention to specialized markets (SMs and the geographical agglomeration of distributors or sale agencies (SAs. This paper takes Linyin, Shandong, a famous commodity city in Northeastern China, as an example, to discuss the determinants that make SAs in SMs of the toy industry move towards upstream manufacturing. A structured questionnaire survey and subsequent interviews were carried out during 2011 and 2012 to collect data, and a Binary Logistic Regression Model was used to process the data. This paper looks from the perspective of global production networks theory, establishes an analytical framework that combines individual motivations of intra-firm coordination, local inter-firm relationships and dynamic cross-regional level relationships. The findings indicate that the expansion of SAs towards manufacturing allows them to sustain competitiveness under changing circumstances. The local inter-firm relationships within SM-based clusters not only makes it easy to obtain material and human resources with lower manufacturing costs, but also facilitates the access to production knowledge and technologies for an expansion of production scale. Cross-regional relationships with suppliers provide an informal channel for SAs to obtain skills, which is fundamental for an expansion into manufacturing. In addition, it is a preference for strengthening competitiveness rather than the simple pursuit of economic profit that encourages SAs to invest in manufacturing.

  10. Heterozygous triplication of upstream regulatory sequences leads to dysregulation of matrix metalloproteinase 19 in patients with cavitary optic disc anomaly.

    Science.gov (United States)

    Hazlewood, Ralph J; Roos, Benjamin R; Solivan-Timpe, Frances; Honkanen, Robert A; Jampol, Lee M; Gieser, Stephen C; Meyer, Kacie J; Mullins, Robert F; Kuehn, Markus H; Scheetz, Todd E; Kwon, Young H; Alward, Wallace L M; Stone, Edwin M; Fingert, John H

    2015-03-01

    Patients with a congenital optic nerve disease, cavitary optic disc anomaly (CODA), are born with profound excavation of the optic nerve resembling glaucoma. We previously mapped the gene that causes autosomal-dominant CODA in a large pedigree to a chromosome 12q locus. Using comparative genomic hybridization and quantitative PCR analysis of this pedigree, we report identifying a 6-Kbp heterozygous triplication upstream of the matrix metalloproteinase 19 (MMP19) gene, present in all 17 affected family members and no normal members. Moreover, the triplication was not detected in 78 control subjects or in the Database of Genomic Variants. We further detected the same 6-Kbp triplication in one of 24 unrelated CODA patients and in none of 172 glaucoma patients. Analysis with a Luciferase assay showed that the 6-Kbp sequence has transcription enhancer activity. A 773-bp fragment of the 6-Kbp DNA segment increased downstream gene expression eightfold, suggesting that triplication of this sequence may lead to dysregulation of the downstream gene, MMP19, in CODA patients. Lastly, immunohistochemical analysis of human donor eyes revealed strong expression of MMP19 in optic nerve head. These data strongly suggest that triplication of an enhancer may lead to overexpression of MMP19 in the optic nerve that causes CODA. © 2015 WILEY PERIODICALS, INC.

  11. Analysis of the opening model of the Brazilian upstream business; Analise da adequacao do modelo de E e P brasileiro

    Energy Technology Data Exchange (ETDEWEB)

    Canelas, Andre [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia. Programa de Planejamento Energetico]. E-mail: canelas@ppe.ufrj.br

    2004-07-01

    This paper analyses the institutional model adopted for the reform of the oil industry in Brazil, beginning with the approval of Law n. 9.478 by the Brazilian Parliament in 1997. The reform of the Brazilian oil industry took place in the context of the reforms of the world's national economies throughout the 1980's and 1990's. From this worldwide process of reform stemmed a huge increase in the international capital flow directed to long-run investment opportunities in the economic infrastructure sectors. The aim of this paper is to analyse both the regulatory model for the oil and gas upstream activities in Brazil and the bidding model adopted at Brazil's National Petroleum Agency's auctions for the acquisition of exploration areas. This paper is dedicated, in its entirety, to Prof. Carmen Alveal (in memoriam), whose knowledge, support, encouragement and friendship were, for me, the most important of all, professionally and morally. (author)

  12. Mitigation/adaptation and health: health policymaking in the global response to climate change and implications for other upstream determinants.

    Science.gov (United States)

    Wiley, Lindsay F

    2010-01-01

    The time is ripe for innovation in global health governance if we are to achieve global health and development objectives in the face of formidable challenges. Integration of global health concerns into the law and governance of other, related disciplines should be given high priority. This article explores opportunities for health policymaking in the global response to climate change. Climate change and environmental degradation will affect weather disasters, food and water security, infectious disease patterns, and air pollution. Although scientific research has pointed to the interdependence of the global environment and human health, policymakers have been slow to integrate their approaches to environmental and health concerns. A robust response to climate change will require improved integration on two fronts: health concerns must be given higher priority in the response to climate change and threats associated with climate change and environmental degradation must be more adequately addressed by global health law and governance. The mitigation/adaptation response paradigm developing within and beyond the United Nations Framework Convention on Climate Change provides a useful framework for thinking about global health law and governance with respect to climate change, environmental degradation, and possibly other upstream determinants of health as well.

  13. Estimated natural streamflow in the Rio San Jose upstream from the pueblos of Acoma and Laguna, New Mexico

    Science.gov (United States)

    Risser, D.W.

    1982-01-01

    The development of surface and ground water, which began about 1870 in the upper Rio San Jose drainage basin, has decreased the flow of the Rio San Jose on the Pueblo of Acoma and the Pueblo of Laguna. The purpose of this study was to estimate the natural streamflow in the Rio San Jose that would have entered the pueblos if no upstream water development had taken place. Estimates of natural flow were based upon streamflow and precipitation records, historical accounts of streamflow, records of irrigated acreage, and empirically-derived estimates of the effects on streamflow of Bluewater Lake, groundwater withdrawals, and irrigation diversions. Natural streamflow in the Rio San Jose at the western boundary of the Pueblo of Acoma is estimated to be between 13,000 and 15,000 acre-feet per year, based on 55 years of recorded and reconstructed streamflow data from water years 1913 to 1972. Natural streamflow at the western boundary of the Pueblo of Laguna is estimated to be between 17 ,000 and 19,000 acre-feet per year for the same period. The error in these estimates of natural streamflow is difficult to assess accurately, but it probably is less than 25 percent. (USGS)

  14. White Sturgeon Mitigation and Restoration in the Columbia and Snake Rivers Upstream from Bonneville Dam; 1998-1999 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Ward, David L.

    2000-12-01

    The authors report on their progress from April 1998 through March 1999 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 upstream from McNary Dam. The study is a cooperative effort by the Oregon Department of Fish and Wildlife (ODFW; Report A), Washington Department of Fish and Wildlife (WDFW; Report B), U.S. Geological Survey Biological Resources Division (USGS; Report C), U.S. Fish and Wildlife Service (USFWS; Report D), Columbia River Inter-Tribal Fish Commission (CRITFC; Report E), and the University of Idaho (UI; Report F). 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. Highlights of results of our work from April 1998 through March 1999 are given.

  15. White Sturgeon Mitigation and Restoration in the Columbia and Snake Rivers Upstream from Bonneville Dam, 1999-2000 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Ward, David L. (Oregon Department of Fish and Wildlife, Portland, OR)

    2001-04-01

    We report on our progress from April 1999 through March 2000 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 upstream from McNary Dam. The study is a cooperative effort by the Oregon Department of Fish and Wildlife (ODFW; Report A), Washington Department of Fish and Wildlife (WDFW; Report B), U.S. Geological Survey Biological Resources Division (USGS; Report C), Columbia River Inter-Tribal Fish Commission (CRITFC; Report D), and the U.S. Fish and Wildlife Service (USFWS; Report E). 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. Highlights of results of our work from April 1999 through March 2000 are given.

  16. Analysis of upstream promoter region and corresponding 5’ UTR of glucokinase (GCK gene in horse breeds

    Directory of Open Access Journals (Sweden)

    L. Minieri

    2010-04-01

    Full Text Available A region of glucokinase (GCK gene was sequenced in 14 horses of 14 different breeds. The resulting GCK nucleotide sequence (GenBank number EF136885 showed 77% homology with human GCK gene portion containing the upstream promoter region and the corresponding 5’ UTR of the exon 1. Conserved regulatory sequences near the putative transcriptional start site were identified. The obtained sequences were aligned to detect polymorphism. A new C>T transition within the 5’ UTR of exon 1 was found. Allele frequencies of this polymorphism were studied by PCR-RFLP in 193 horses of 14 breeds (Bardigiano, 21; Esperia Pony, 5; Haflinger, 10; Italian Heavy Draught Horse, 28; Italian Saddle, 25; Italian Trotter, 16; Lipizzan, 12; Maremmano, 15; Murgese, 14; Norico, 10; Salernitano, 12; Thoroughbred, 10; Tolfetano, 7 and Ventasso Horse, 8. The polymorphism was found in all breeds and differences in allelic frequencies among the breeds were observed. The new SNP identified within a regulative region of GCK gene, which plays an important role in insulin secretion and feeding behaviour, could be used for association studies with performance traits of the horses.

  17. White Sturgeon Mitigation and Restoration in the Columbia and Snake Rivers Upstream from Bonneville Dam; 2000-2001 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Kern, J. Chris; Ward, David L.; Farr, Ruth A. (Oregon Department of Fish and Wildlife)

    2002-02-01

    We report on our progress from April 2000 through March 2001 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 upstream from McNary Dam. The study is a cooperative effort by the Oregon Department of Fish and Wildlife (ODFW; Report A), Washington Department of Fish and Wildlife (WDFW; Report B), U.S. Geological Survey Biological Resources Division (USGS; Report C), Columbia River Inter-Tribal Fish Commission (CRITFC; Report D), the U.S. Fish and Wildlife Service (USFWS; Report E), and Oregon State University (OSU; Report F). 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. Highlights of results of our work from April 2000 through March 2001 are listed.

  18. Interaction of a nodule specific, trans-acting factor with distinct DNA elements in the soybean leghaemoglobin Ibc(3) 5' upstream region

    DEFF Research Database (Denmark)

    Jensen, Erik Østergaard; Marcker, Kjeld A; Schell, J;

    1988-01-01

    Nuclear extracts from soybean nodules, leaves and roots were used to investigate protein-DNA interactions in the 5' upstream (promoter) region of the soybean leghaemoglobin lbc(3) gene. Two distinct regions were identified which strongly bind a nodule specific factor. A Bal31 deletion analysis de...

  19. Restructuring: new relationships between the oil companies and the upstream oil firms; Alliances et restructurations: nouvelles relations entre maitres d'oeuvre et parapetrolier

    Energy Technology Data Exchange (ETDEWEB)

    Barreau, S

    2001-11-01

    Since the 1986 oil shock, international oil companies have focused on their base competencies, concentrating on activities viewed as their core businesses and steadily increasing the number of tasks to be subcontracted to the upstream oil and gas service sector. The upstream oil and gas service companies had to be restructured to face this new challenge. The strategies they launched at the end of the 80's were varied. Some firms became largely integrated (Schlumberger, Baker Hughes, Halliburton) whereas other firms chose to broaden their range of services. However generally, they opted for external investment which led to an important wave of mergers and acquisitions. The first part characterizes the upstream oil and gas sector by introducing the main oil and gas service firms and their recent strategic evolution. This concludes with both an economic valuation and a typology of attempted growth strategies. To illustrate this, a matrix has been created to characterise the dynamic paths of the oil and gas service firms. The purpose of the second part is to consider the economic theories related to industrial strategies. The strategies of innovation, market protection, vertical integration and diversification have been studied to illustrate the main conclusion which is that the aim of all these strategies was to change the relationships between the oil companies and the upstream oil and gas service firms. (author)

  20. The economic impacts of the upstream activities after the reform of the Brazilian oil industry; Impactos economicos da exploracao e producao apos a abertura da industria petrolifera brasileira

    Energy Technology Data Exchange (ETDEWEB)

    Canelas, Andre [Universidade Federal, Rio de Janeiro, RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia. Programa de Planejamento Energetico]. E-mail: canelas@ppe.ufrj.br

    2004-07-01

    This paper analyzes the macroeconomic impacts of the investments in the oil and gas upstream, which took place after the reform of the Brazilian oil industry. The reason why I chose to analyze such a period of time was the institutional change which took place in the Brazilian oil industry after the Brazilian Parliament approved Law n. 9.478 in 1997. The law represented the new regulation of the activities related to the oil industry in Brazil. Since then, there has been a very large amount of capital spending in the oil and gas upstream, not only by PETROBRAS, the state-owned oil company, but also by the oil companies which entered the Brazilian oil industry after it was opened to foreign and private upstream investments. This paper analyses the economic impacts of these upstream investments by PETROBRAS and by the new players in Brazil, addressing the impacts of these investments on the generation of aggregate value and yield and the economic activity of other industries. This paper is dedicated, in its entirety, to Prof. Carmen Alveal, whose knowledge, support, encouragement and friendship were, for me, the most important of all, professionally and morally. (author)

  1. Muscleblind-like 1 activates insulin receptor exon 11 inclusion by enhancing U2AF65 binding and splicing of the upstream intron.

    Science.gov (United States)

    Echeverria, Gloria V; Cooper, Thomas A

    2014-02-01

    Alternative splicing regulates developmentally and tissue-specific gene expression programs, disruption of which have been implicated in numerous diseases. Muscleblind-like 1 (MBNL1) regulates splicing transitions, which are disrupted on loss of MBNL1 function in myotonic dystrophy type 1 (DM1). One such event is MBNL1-mediated activation of insulin receptor exon 11 inclusion, which requires an intronic enhancer element downstream of exon 11. The mechanism of MBNL1-mediated activation of exon inclusion is unknown. We developed an in vitro splicing assay, which robustly recapitulates MBNL1-mediated splicing activation of insulin receptor exon 11 and found that MBNL1 activates removal of the intron upstream of exon 11 upon binding its functional response element in the downstream intron. MBNL1 enhances early spliceosome assembly as evidenced by enhanced complex A formation and binding of U2 small nuclear ribonucleoprotein auxiliary factor 65 kDa subunit (U2AF65) on the upstream intron. We demonstrated that neither the 5' splice site nor exon 11 sequences are required for MBNL1-activated U2AF65 binding. Interestingly, the 5' splice site is required for MBNL1-mediated activation of upstream intron removal, although MBNL1 has no effect on U1 snRNA recruitment. These results suggest that MBNL1 directly activates binding of U2AF65 to enhance upstream intron removal to ultimately activate alternative exon inclusion.

  2. Analysis of environmental issues related to small scale hydroelectric development. II. Design considerations for passing fish upstream around dams. Environmental Sciences Division Publication No. 1567

    Energy Technology Data Exchange (ETDEWEB)

    Hildebrand, S.G. (ed.)

    1980-08-01

    The possible requirement of facilities to move migrating fish upstream around dams may be a factor in determining the feasibility of retrofitting small dams for hydroelectric generation. Basic design considerations are reported that should be evaluated on a site-specific basis if upstream fish passage facilities are being considered for a small scale hydroelectric project (defined as an existing dam that can be retrofitted to generate 25 MW or less). Information on general life history and geographic distribution of fish species that may require passage is presented. Biological factors important in the design of upstream passage facilities are discussed: gas bubble disease, fish swimming speed, oxygen consumption by fish, and diel and photo behavior. Three general types of facilities (fishways, fish locks, and fish lifts) appropriate for upstream fish passage at small scale hydroelectric projects are described, and size dimensions are presented. General design criteria for these facilities (including fish swimming ability and behavior) and general location of facilities at a site are discussed. Basic cost considerations for each type of passage facility, including unit cost, operation and maintenance costs, and costs for supplying attraction water, are indicated.

  3. Looking upstream to prevent HIV transmission: can interventions with sex workers alter the course of HIV epidemics in Africa as they did in Asia?

    NARCIS (Netherlands)

    Steen, R. van der; Hontelez, J.A.; Veraart, A.; White, R.G.; Vlas, S.J. de

    2014-01-01

    BACKGROUND: High rates of partner change in 'upstream' sex work networks have long been recognized to drive 'downstream' transmission of sexually transmitted infections (STIs). We used a stochastic microsimulation model (STDSIM) to explore such transmission dynamics in a generalized African HIV epid

  4. A novel mutation in the upstream open reading frame of the CDKN1B gene causes a MEN4 phenotype.

    Directory of Open Access Journals (Sweden)

    Gianluca Occhi

    2013-03-01

    Full Text Available The CDKN1B gene encodes the cyclin-dependent kinase inhibitor p27(KIP1, an atypical tumor suppressor playing a key role in cell cycle regulation, cell proliferation, and differentiation. Impaired p27(KIP1 expression and/or localization are often observed in tumor cells, further confirming its central role in regulating the cell cycle. Recently, germline mutations in CDKN1B have been associated with the inherited multiple endocrine neoplasia syndrome type 4, an autosomal dominant syndrome characterized by varying combinations of tumors affecting at least two endocrine organs. In this study we identified a 4-bp deletion in a highly conserved regulatory upstream ORF (uORF in the 5'UTR of the CDKN1B gene in a patient with a pituitary adenoma and a well-differentiated pancreatic neoplasm. This deletion causes the shift of the uORF termination codon with the consequent lengthening of the uORF-encoded peptide and the drastic shortening of the intercistronic space. Our data on the immunohistochemical analysis of the patient's pancreatic lesion, functional studies based on dual-luciferase assays, site-directed mutagenesis, and on polysome profiling show a negative influence of this deletion on the translation reinitiation at the CDKN1B starting site, with a consequent reduction in p27(KIP1 expression. Our findings demonstrate that, in addition to the previously described mechanisms leading to reduced p27(KIP1 activity, such as degradation via the ubiquitin/proteasome pathway or non-covalent sequestration, p27(KIP1 activity can also be modulated by an uORF and mutations affecting uORF could change p27(KIP1 expression. This study adds the CDKN1B gene to the short list of genes for which mutations that either create, delete, or severely modify their regulatory uORFs have been associated with human diseases.

  5. A novel mutation in the upstream open reading frame of the CDKN1B gene causes a MEN4 phenotype.

    Science.gov (United States)

    Occhi, Gianluca; Regazzo, Daniela; Trivellin, Giampaolo; Boaretto, Francesca; Ciato, Denis; Bobisse, Sara; Ferasin, Sergio; Cetani, Filomena; Pardi, Elena; Korbonits, Márta; Pellegata, Natalia S; Sidarovich, Viktoryia; Quattrone, Alessandro; Opocher, Giuseppe; Mantero, Franco; Scaroni, Carla

    2013-03-01

    The CDKN1B gene encodes the cyclin-dependent kinase inhibitor p27(KIP1), an atypical tumor suppressor playing a key role in cell cycle regulation, cell proliferation, and differentiation. Impaired p27(KIP1) expression and/or localization are often observed in tumor cells, further confirming its central role in regulating the cell cycle. Recently, germline mutations in CDKN1B have been associated with the inherited multiple endocrine neoplasia syndrome type 4, an autosomal dominant syndrome characterized by varying combinations of tumors affecting at least two endocrine organs. In this study we identified a 4-bp deletion in a highly conserved regulatory upstream ORF (uORF) in the 5'UTR of the CDKN1B gene in a patient with a pituitary adenoma and a well-differentiated pancreatic neoplasm. This deletion causes the shift of the uORF termination codon with the consequent lengthening of the uORF-encoded peptide and the drastic shortening of the intercistronic space. Our data on the immunohistochemical analysis of the patient's pancreatic lesion, functional studies based on dual-luciferase assays, site-directed mutagenesis, and on polysome profiling show a negative influence of this deletion on the translation reinitiation at the CDKN1B starting site, with a consequent reduction in p27(KIP1) expression. Our findings demonstrate that, in addition to the previously described mechanisms leading to reduced p27(KIP1) activity, such as degradation via the ubiquitin/proteasome pathway or non-covalent sequestration, p27(KIP1) activity can also be modulated by an uORF and mutations affecting uORF could change p27(KIP1) expression. This study adds the CDKN1B gene to the short list of genes for which mutations that either create, delete, or severely modify their regulatory uORFs have been associated with human diseases.

  6. Demographic population model for American shad: will access to additional habitat upstream of dams increase population sizes?

    Science.gov (United States)

    Harris, Julianne E.; Hightower, Joseph E.

    2012-01-01

    American shad Alosa sapidissima are in decline in their native range, and modeling possible management scenarios could help guide their restoration. We developed a density-dependent, deterministic, stage-based matrix model to predict the population-level results of transporting American shad to suitable spawning habitat upstream of dams on the Roanoke River, North Carolina and Virginia. We used data on sonic-tagged adult American shad and oxytetracycline-marked American shad fry both above and below dams on the Roanoke River with information from other systems to estimate a starting population size and vital rates. We modeled the adult female population over 30 years under plausible scenarios of adult transport, effective fecundity (egg production), and survival of adults (i.e., to return to spawn the next year) and juveniles (from spawned egg to age 1). We also evaluated the potential effects of increased survival for adults and juveniles. The adult female population size in the Roanoke River was estimated to be 5,224. With no transport, the model predicted a slow population increase over the next 30 years. Predicted population increases were highest when survival was improved during the first year of life. Transport was predicted to benefit the population only if high rates of effective fecundity and juvenile survival could be achieved. Currently, transported adults and young are less likely to successfully out-migrate than individuals below the dams, and the estimated adult population size is much smaller than either of two assumed values of carrying capacity for the lower river; therefore, transport is not predicted to help restore the stock under present conditions. Research on survival rates, density-dependent processes, and the impacts of structures to increase out-migration success would improve evaluation of the potential benefits of access to additional spawning habitat for American shad.

  7. Midkine-A functions upstream of Id2a to regulate cell cycle kinetics in the developing vertebrate retina

    Directory of Open Access Journals (Sweden)

    Luo Jing

    2012-10-01

    Full Text Available Abstract Background Midkine is a small heparin binding growth factor expressed in numerous tissues during development. The unique midkine gene in mammals has two paralogs in zebrafish: midkine-a (mdka and midkine-b (mdkb. In the zebrafish retina, during both larval development and adult photoreceptor regeneration, mdka is expressed in retinal stem and progenitor cells and functions as a molecular component of the retina’s stem cell niche. In this study, loss-of-function and conditional overexpression were used to investigate the function of Mdka in the retina of the embryonic zebrafish. Results The results show that during early retinal development Mdka functions to regulate cell cycle kinetics. Following targeted knockdown of Mdka synthesis, retinal progenitors cycle more slowly, and this results in microphthalmia, a diminished rate of cell cycle exit and a temporal delay of cell cycle exit and neuronal differentiation. In contrast, Mdka overexpression results in acceleration of the cell cycle and retinal overgrowth. Mdka gain-of-function, however, does not temporally advance cell cycle exit. Experiments to identify a potential Mdka signaling pathway show that Mdka functions upstream of the HLH regulatory protein, Id2a. Gene expression analysis shows Mdka regulates id2a expression, and co-injection of Mdka morpholinos and id2a mRNA rescues the Mdka loss-of-function phenotype. Conclusions These data show that in zebrafish, Mdka resides in a shared Id2a pathway to regulate cell cycle kinetics in retinal progenitors. This is the first study to demonstrate the function of Midkine during retinal development and adds Midkine to the list of growth factors that transcriptionally regulate Id proteins.

  8. Unsteady Analysis of Blade and Tip Heat Transfer as Influenced by the Upstream Momentum and Thermal Wakes

    Science.gov (United States)

    Ameri, Ali A.; Rigby, David L.; Steinthorsson, Erlendur; Heidmann, James D.; Fabian, John C.

    2008-01-01

    The effect of the upstream wake on the blade heat transfer has been numerically examined. The geometry and the flow conditions of the first stage turbine blade of GE s E3 engine with a tip clearance equal to 2 percent of the span was utilized. Based on numerical calculations of the vane, a set of wake boundary conditions were approximated, which were subsequently imposed upon the downstream blade. This set consisted of the momentum and thermal wakes as well as the variation in modeled turbulence quantities of turbulence intensity and the length scale. Using a one-blade periodic domain, the distributions of unsteady heat transfer rate on the turbine blade and its tip, as affected by the wake, were determined. Such heat transfer coefficient distribution was computed using the wall heat flux and the adiabatic wall temperature to desensitize the heat transfer coefficient to the wall temperature. For the determination of the wall heat flux and the adiabatic wall temperatures, two sets of computations were required. The results were used in a phase-locked manner to compute the unsteady or steady heat transfer coefficients. It has been found that the unsteady wake has some effect on the distribution of the time averaged heat transfer coefficient on the blade and that this distribution is different from the distribution that is obtainable from a steady computation. This difference was found to be as large as 20 percent of the average heat transfer on the blade surface. On the tip surface, this difference is comparatively smaller and can be as large as four percent of the average.

  9. Coding potential and transcript analysis of fowl adenovirus 4: insight into upstream ORFs as common sequence features in adenoviral transcripts.

    Science.gov (United States)

    Griffin, Bryan D; Nagy, Eva

    2011-06-01

    Recombinant fowl adenoviruses (FAdVs) have been successfully used as veterinary vaccine vectors. However, insufficient definitions of the protein-coding and non-coding regions and an incomplete understanding of virus-host interactions limit the progress of next-generation vectors. FAdVs are known to cause several diseases of poultry. Certain isolates of species FAdV-C are the aetiological agent of inclusion body hepatitis/hydropericardium syndrome (IBH/HPS). In this study, we report the complete 45667 bp genome sequence of FAdV-4 of species FAdV-C. Assessment of the protein-coding potential of FAdV-4 was carried out with the Bio-Dictionary-based Gene Finder together with an evaluation of sequence conservation among species FAdV-A and FAdV-D. On this basis, 46 potentially protein-coding ORFs were identified. Of these, 33 and 13 ORFs were assigned high and low protein-coding potential, respectively. Homologues of the ancestral adenoviral genes were, with few exceptions, assigned high protein-coding potential. ORFs that were unique to the FAdVs were differentiated into high and low protein-coding potential groups. Notable putative genes with high protein-coding capacity included the previously unreported fiber 1, hypothetical 10.3K and hypothetical 10.5K genes. Transcript analysis revealed that several of the small ORFs less than 300 nt in length that were assigned low coding potential contributed to upstream ORFs (uORFs) in important mRNAs, including the ORF22 mRNA. Subsequent analysis of the previously reported transcripts of FAdV-1, FAdV-9, human adenovirus 2 and bovine adenovirus 3 identified widespread uORFs in AdV mRNAs that have the potential to act as important translational regulatory elements.

  10. Directing the biosynthesis of putrebactin or desferrioxamine B in Shewanella putrefaciens through the upstream inhibition of ornithine decarboxylase.

    Science.gov (United States)

    Soe, Cho Z; Pakchung, Amalie A H; Codd, Rachel

    2012-09-01

    To manage iron acquisition in an oxic environment, Shewanella putrefaciens produces the macrocyclic dihydroxamic acid putrebactin (PB) as its native siderophore. In this work, we have established the siderophore profile of S. putrefaciens in cultures augmented with the native PB precursor putrescine and in putrescine-depleted cultures. Compared to base medium, PB increased by two-fold in cultures of S. putrefaciens with 10 mM NaCl and 20 mM exogenous putrescine. In cultures augmented with 1,4-diaminobutan-2-one (DAB), PB decreased with only 0.02-fold PB detectable at 10 mM DAB. As an ornithine decarboxylase (ODC) inhibitor, DAB depleted levels of endogenous putrescine which attenuated downstream PB assembly. Under putrescine-depleted conditions, S. putrefaciens produced as its replacement siderophore the cadaverine-based desferrioxamine B (DFO-B), as characterised by ESI-MS of the Fe(III)-loaded form (m/z(obs) 614.13; m/z(calc) 614.27). A third siderophore, independent of DAB, was observed in low levels. LC/MS Analysis of the Fe(III)-loaded extract gave m/z(obs) 440.93, which, formulated as a 1:1 Fe(III) complex with a macrocyclic dihydroxamic acid, comprising one putrescine- and one cadaverine-based precursor (m/z(calc) 440.14). These results show that the production of native PB or non-native DFO-B by S. putrefaciens can be directed though upstream inhibition of ODC. This approach could be used to increase the molecular diversity of siderophores produced by S. putrefaciens and to map alternative diamine-dependent metabolites. Copyright © 2012 Verlag Helvetica Chimica Acta AG, Zürich.

  11. An evaluation of fish behavior upstream of the water temperature control tower at Cougar Dam, Oregon, using acoustic cameras, 2013

    Science.gov (United States)

    Adams, Noah S.; Smith, Collin; Plumb, John M.; Hansen, Gabriel S.; Beeman, John W.

    2015-07-06

    This report describes the initial year of a 2-year study to determine the feasibility of using acoustic cameras to monitor fish movements to help inform decisions about fish passage at Cougar Dam near Springfield, Oregon. Specifically, we used acoustic cameras to measure fish presence, travel speed, and direction adjacent to the water temperature control tower in the forebay of Cougar Dam during the spring (May, June, and July) and fall (September, October, and November) of 2013. Cougar Dam is a high-head flood-control dam, and the water temperature control tower enables depth-specific water withdrawals to facilitate adjustment of water temperatures released downstream of the dam. The acoustic cameras were positioned at the upstream entrance of the tower to monitor free-ranging subyearling and yearling-size juvenile Chinook salmon (Oncorhynchus tshawytscha). Because of the large size discrepancy, we could distinguish juvenile Chinook salmon from their predators, which enabled us to measure predators and prey in areas adjacent to the entrance of the tower. We used linear models to quantify and assess operational and environmental factors—such as time of day, discharge, and water temperature—that may influence juvenile Chinook salmon movements within the beam of the acoustic cameras. Although extensive milling behavior of fish near the structure may have masked directed movement of fish and added unpredictability to fish movement models, the acoustic-camera technology enabled us to ascertain the general behavior of discrete size classes of fish. Fish travel speed, direction of travel, and counts of fish moving toward the water temperature control tower primarily were influenced by the amount of water being discharged through the dam.

  12. Translational Effects of Mutations and Polymorphisms in a Repressive Upstream Open Reading Frame of the Human Cytomegalovirus UL4 Gene

    Science.gov (United States)

    Alderete, John P.; Jarrahian, Sohail; Geballe, Adam P.

    1999-01-01

    The human cytomegalovirus (HCMV) gpUL4 mRNA contains a 22-codon upstream open reading frame (uORF2), the peptide product of which represses downstream translation by blocking translation termination at its own stop codon and by causing ribosomes to stall on the mRNA. A distinctive feature of this unusual mechanism is its strict dependence on the uORF2 peptide sequence. To delineate sequence elements that function in the inhibitory mechanism, deletions and missense mutations affecting the previously uncharacterized amino-terminal region of uORF2 were analyzed in transient-transfection and infection assays. These experiments identified multiple codons in this region that are necessary for inhibition of downstream translation by uORF2 and, in conjunction with previous results, demonstrated that amino acids dispersed throughout the uORF2 peptide participate in the repressive mechanism. In contrast to the highly conserved carboxy terminus, the amino-terminal portion of the uORF2 peptide is polymorphic. A survey of uORF2 sequences in HCMV clinical isolates revealed that although most have uORF2 sequences that are predicted to retain the uORF2 inhibitory activity, ∼15% contain polymorphisms at codons that are essential for full inhibition by uORF2. Consistent with predictions based on analyses of engineered mutations, two viral isolates with uORF2 sequences that do not inhibit downstream translation in transfection assays expressed much more gpUL4 protein but similar levels of UL4 mRNA compared to the levels produced by the prototypic laboratory strain HCMV (Towne) and another clinical isolate with an inhibitory variant uORF2. These results demonstrate that uORF2 is polymorphic in sequence and repressive activity and suggest that the uORF2 regulatory mechanism, although prevalent among natural HCMV isolates, is not absolutely essential for viral replication. PMID:10482583

  13. Vegetation response to upstream water yield in the Heihe river by time series analysis of MODIS data

    Directory of Open Access Journals (Sweden)

    L. Jia

    2010-07-01

    Full Text Available Liquid and solid precipitation is abundant in the high elevation, upper reach of the Heihe basin. The development of modern irrigation schemes in the middle reach of the basin is taking up an increasing share of fresh water resources, endangering the oasis and traditional irrigation systems in the lower reach. In this study, the response of vegetation in the Ejina Oasis in the lower reach of the Heihe River to the water yield of the upper catchment was analyzed by time series analysis of monthly observations of precipitation in the upper and lower catchment, river streamflow downstream of the modern irrigation schemes and satellite observations of vegetation index. Firstly, remote sensing data were used to monitor the vegetation dynamic for a long time period. Due to cloud-contamination, atmospheric influence and different solar angles, however, the quality and consistence of time series of remote sensing data is degraded. In this research we used a Fourier Transform method – the Harmonic Analysis of Time Series (HANTS algorithm – to reconstruct cloud-free NDVI time series data from the Terra-MODIS dataset. Anomalies in precipitation, streamflow, and vegetation index are detected by comparing each year with the average year. The relationship between the anomalies in vegetation growth, the local precipitation and upstream water yield were analyzed. The same approach is used to identify, remove and gap-filling cloud contaminated observations in the satellite data for each year in the dataset. The results showed that: the previous year total runoff had a significant relationship with the vegetation growth in Ejina Oasis and that anomalies in monthly runoff of the Heihe River influenced the phenology of vegetation in the entire oasis during drier years. The time of maximum green-up was uniform throughout the oasis during wetter years, but showed a clear S–N gradient (downstream during drier years.

  14. Anthropogenic phosphorus (P) inputs to a river basin and their impacts on P fluxes along its upstream-downstream continuum

    Science.gov (United States)

    Zhang, Wangshou; Swaney, Dennis; Hong, Bongghi; Howarth, Robert

    2017-04-01

    Phosphorus (P) originating from anthropogenic sources as a pollutant of surface waters has been an environmental issue for decades because of the well-known role of P in eutrophication. Human activities, such as food production and rapid urbanization, have been linked to increased P inputs which are often accompanied by corresponding increases in riverine P export. However, uneven distributions of anthropogenic P inputs along watersheds from the headwaters to downstream reaches can result in significantly different contributions to the riverine P fluxes of a receiving water body. So far, there is still very little scientific understanding of anthropogenic P inputs and their impacts on riverine flux in river reaches along the upstream to downstream continuum. Here, we investigated P budgets in a series of nested watersheds draining into Hongze Lake of China, and developed a simple empirical function to describe the relationship between anthropogenic inputs and riverine TP fluxes. The results indicated that an average of 1.1% of anthropogenic P inputs are exported into rivers, with most of the remainder retained in the watershed landscape over the period studied. Fertilizer application was the main contributor of P loading to the lake (55% of total loads), followed by legacy P stock (30%), food and feed P inputs (12%) and non-food P inputs (4%). From 60% to 89% of the riverine TP loads generated from various locations within this basin were ultimately transported into the receiving lake of the downstream, with an average rate of 1.86 tons P km-1 retaining in the main stem of the inflowing river annually. Our results highlight that in-stream processes can significantly buffer the riverine P loading to the downstream receiving lake. An integrated P management strategy considering the influence of anthropogenic inputs and hydrological interactions is required to assess and optimize P management for protecting fresh waters.

  15. Comprehensive study of ULF upstream waves observed in the topside ionosphere by CHAMP and on the ground

    Directory of Open Access Journals (Sweden)

    B. Heilig

    2007-03-01

    Full Text Available Based on magnetic field measurements from the satellite CHAMP, a detailed picture could be obtained of the upstream wave (UW distribution in the topside ionosphere. The low, near-polar orbit of CHAMP, covering all local times, allows the global distribution of this type of pulsation to be revealed. The observations from space are compared to recordings of the ground-based MM100 meridional array covering the latitude range 66° to 42° in magnetic coordinates. UWs show up very clearly in the compressional component of the satellite magnetic field data, whereas on the ground, their signature is found in the H component, but it is mixed with oscillations from field line resonant pulsations. Here we first introduce a procedure for an automated detection of UW signatures, both in ground and space data. Then a statistical analysis is presented of UW pulsations recorded during a 132-day period, centred on the autumn 2001 equinox. Observations in the top-side ionosphere reveal a clear latitudinal distribution of the amplitudes. Largest signals are observed at the equator. Minima show up at about 40° latitude. The coherence between ground and satellite wave signatures is high over wide latitude and longitude ranges. We make suggestions about the entry mechanism of UWs from the foreshock region into the magnetosphere. The clear UW signature in satellite recordings between −60° and 60° latitude allows for detailed investigations of the dependence on solar wind conditions. We test the control of solar wind speed, interplanetary magnetic field strength and cone angle on UWs. For the first time, it is possible to derive details of the Doppler-shift effect by modifying the UW frequency from direct observations. The results reconcile foreshock wave generation predictions with near-Earth observations.

  16. Is forage productivity of meadows influenced by the afforestation of upstream hillsides? A study in NW Patagonia

    Energy Technology Data Exchange (ETDEWEB)

    Weigandt, M.; Gyenge, J.; Fernandez, M. E.; Varela, S.; Schlichter, T.

    2011-07-01

    Meadows are important reserves of water, with a key role in the maintenance of the biodiversity and productivity of ecosystems. In Patagonia, Argentina, afforestation with fast-growing exotic conifers has slowly but continuously increased over recent decades; though unfortunately, knowledge of the effects of afforestation on water resources remains scarce, with no information at all related to its impact on water dynamics and productivity of meadows located down slope to it. The effects of Pinus ponderosa afforestation on water dynamics (soil moisture contents and groundwater level) and productivity (aboveground forage productivity) of Northwest Patagonia meadows under xeric and humid conditions were analyzed. In the humid meadow, gravimetric soil water content, groundwater level and forage productivity were similar down slope of forested and non-forested slopes, with a trend towards higher forage productivity on the forested slope. In the xeric meadow, gravimetric soil water content was always higher down slope of the non-forested slope, with no difference in groundwater level between treatments. Forage productivity was statistically similar between situations (down slope of forested and non-forested slopes), with a trend towards higher productivity in the zone with higher soil water content. The main difference in the latter was related to differences in soil texture between zones. These results suggest that coniferous plantations located upstream of this type of meadow do not produce a direct effect on its aboveground forage productivity. These systems have high complexity linked to precipitation, geomorphology and previous history of land use, which determine primarily soil water dynamics and consequently, forage productivity. (Author) 42 refs.

  17. Upstream migration, reproduction and fishery of sea lamprey (Petromyzon marinus Linnaeus, 1758 in the River Ulla (NW Spain

    Directory of Open Access Journals (Sweden)

    Sergio Silva

    2015-11-01

    Full Text Available After a juvenile haematophagous stage developed mainly at sea, the sea lamprey Petromyzon marinus Linnaeus, 1758 stop feeding and return to the river to spawn. One of the main pressures in this stage is the presence of obstacles that reduce the accessible habitat, the mobility of individuals within this section and the energy resources available for gonad development and spawning. In addition, in the River Ulla, adults are targeted in a commercial fishery, using fyke-nets in the upper estuary and fishing in pesqueiras, which are stone constructions placed on the river bed, in the low section of the river. This study advances in the knowledge of the upstream migration (and related impact of barriers, reproduction and fishery of P. marinus in the River Ulla. The study combined fieldwork (radiotelemetry tracking of 19 adults in years 2012 and 2013 and inventory and characterization of obstacles, with information on the capture of lampreys (years 2000 to 2010 by commercial fishing and by a fixed trap located in the middle section of the river. The migration period in this river runs from January, or even December, until June, followed by reproduction in May and June. A total of 48 anthropogenic obstacles (all small-medium sized barriers except the last three, which are impassable, including 20 pesqueiras, were identified as a relevant obstacle for sea lamprey migration (which joins the impact of fishing performed in these sites. Hence, still more attention must be paid to "small" barriers, as pesqueiras, and to fisheries to properly conserve and manage populations of this and other anadromous lamprey species.

  18. Correlation and Entanglement

    Institute of Scientific and Technical Information of China (English)

    Shun-long Luo; You-feng Luo

    2003-01-01

    In quantum mechanics, it is long recognized that there exist correlations between observables which are much stronger than the classical ones. These correlations are usually called entanglement, and cannot be accounted for by classical theory. In this paper, we will study correlations between observables in terms of covariance and the Wigner-Yanase correlation, and compare their merits in characterizing entanglement. We will show that the Wigner-Yanase correlation has some advantages over the conventional covariance.

  19. General correlation and partial correlation analysis in finding interactions: with Spearman rank correlation and proportion correlation as correlation measures

    OpenAIRE

    WenJun Zhang; Xin Li

    2015-01-01

    Between-taxon interactions can be detected by calculating the sampling data of taxon sample type. In present study, Spearman rank correlation and proportion correlation are chosen as the general correlation measures, and their partial correlations are calculated and compared. The results show that for Spearman rank correlation measure, in all predicted candidate direct interactions by partial correlation, about 16.77% (x, 0-45.4%) of them are not successfully detected by Spearman rank correla...

  20. Subchannel analysis and correlation of the Rod Bundle Heat Transfer (RBHT) steam cooling experimental data

    Energy Technology Data Exchange (ETDEWEB)

    Riley, M.P.; Mohanta, L.; Miller, D.J.; Cheung, F.B. [Pennsylvania State Univ., University Park, PA (United States); Bajorek, S.M.; Tien, K.; Hoxie, C.L. [U.S. Nuclear Regulatory Commission, Washington, DC (United States). Office of Nuclear Regulatory Research

    2016-07-15

    A subchannel analysis of the steam cooling data obtained in the Rod Bundle Heat Transfer (RBHT) test facility has been performed in this study to capture the effect of spacer grids on heat transfer. The RBHT test facility has a 7 x 7 rod bundle with heater rods and with seven spacer grids equally spaced along the length of the rods. A method based on the concept of momentum and heat transport analogy has been developed for calculating the subchannel bulk mean temperature from the measured steam temperatures. Over the range of inlet Reynolds number, the local Nusselt number was found to exhibit a minimum value between the upstream and downstream spacer grids. The presence of a spacer grid not only affects the local Nusselt number downstream of the grid but also affects the local Nusselt number upstream of the next grid. A new correlation capturing the effect of Reynolds number on the local flow restructuring downstream as well as upstream of the spacer grids was proposed for the minimum Nusselt number. In addition, a new enhancement factor accounting for the effects of the upstream as well as downstream spacer grids was developed from the RBHT data. The new enhancement factor was found to compare well with the data from the ACHILLLES test facility.

  1. Selection against spurious promoter motifs correlates withtranslational efficiency across bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Froula, Jeffrey L.; Francino, M. Pilar

    2007-05-01

    Because binding of RNAP to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of DNA motifs capable of RNAP-binding across the genome. Here we analyze the distribution of the -10 promoter motifs that bind the {sigma}{sup 70} subunit of RNAP in 42 bacterial genomes. We show that selection on these motifs operates across the genome, maintaining an over-representation of -10 motifs in regulatory sequences while eliminating them from the nonfunctional and, in most cases, from the protein coding regions. In some genomes, however, -10 sites are over-represented in the coding sequences; these sites could induce pauses effecting regulatory roles throughout the length of a transcriptional unit. For nonfunctional sequences, the extent of motif under-representation varies across genomes in a manner that broadly correlates with the number of tRNA genes, a good indicator of translational speed and growth rate. This suggests that minimizing the time invested in gene transcription is an important selective pressure against spurious binding. However, selection against spurious binding is detectable in the reduced genomes of host-restricted bacteria that grow at slow rates, indicating that components of efficiency other than speed may also be important. Minimizing the number of RNAP molecules per cell required for transcription, and the corresponding energetic expense, may be most relevant in slow growers. These results indicate that genome-level properties affecting the efficiency of transcription and translation can respond in an integrated manner to optimize gene expression. The detection of selection against promoter motifs in nonfunctional regions also implies that no sequence may evolve free of selective constraints, at least in the relatively small and unstructured genomes of bacteria.

  2. Explicit correlation factors

    Science.gov (United States)

    Johnson, Cole M.; Hirata, So; Ten-no, Seiichiro

    2017-09-01

    We analyze the performance of 17 different correlation factors in explicitly correlated second-order many-body perturbation calculations for correlation energies. Highly performing correlation factors are found to have near-universal shape and size in the short range of electron-electron distance (0 1.5 a.u.) is insignificant insofar as the factor becomes near constant, leaving an orbital expansion to describe decoupled electrons. An analysis based on a low-rank Taylor expansion of the correlation factor seems limited, except that a negative second derivative with the value of around -1.3 a.u. correlates with high performance.

  3. Quantifying the Effects of Upstream Farm Dams on inflows into the Gaborone Dam in Botswana: An integrated approach

    Science.gov (United States)

    Helmschrot, J.; Kenabatho, P. K.; Parida, B.; Kralisch, S.; Fleischer, M.

    2014-12-01

    One of the major challenges of hydrological modelling in semiarid areas is the high spatial and temporal variability of rainfall and subsequent associated hydrological processes, coupled with an inherent non-linearity of response between rainfall and runoff. The problem often gets worse due to a lack of instrumentation of good spatial coverage, which increases input errors and uncertainties when spatial rainfall estimates are made from limited observations for use as input to rainfall-runoff models. This particular problem is well documented for many catchments in the world, including the semiarid southern Africa and has largely promoted the use of lumped models over distributed models in data scarce areas which often fail to adequately represent hydrological processes, and, thus, in addressing key water resources management issues at sub basin levels. One of the major issues these models are unable to address, is the effect of upstream land use changes on flow regimes in the downstream watershed. The Gaborone dam catchment located within a 20 km radius from Gaborone city in Botswana has been experiencing challenges of reduced inflows into the dam, despite some recorded heavy storms in the head streams and within the catchment. Recent studies indicate that there are more than 200 farm dams spread across the 400 km2 catchment which may have led to reduced inflows into the dam, representing a main source of water supply to the greater Gaborone area. However, due to insufficient rainfall recording instruments and flow gauging stations in the catchment, no studies had been able to adequately address runoff generation processes and associated inflow dynamics in this important catchment. Through the present study, an experimental hydrological site has been established, consisting of five automated weather stations and two gauging stations to capture spatial rainfall and flow variability within the catchment. This study has taken an integrated approach by considering (i

  4. Phenological response of vegetation to upstream river flow in the Heihe Rive basin by time series analysis of MODIS data

    Directory of Open Access Journals (Sweden)

    L. Jia

    2011-03-01

    Full Text Available Liquid and solid precipitation is abundant in the high elevation, upper reach of the Heihe River basin in northwestern China. The development of modern irrigation schemes in the middle reach of the basin is taking up an increasing share of fresh water resources, endangering the oasis and traditional irrigation systems in the lower reach. In this study, the response of vegetation in the Ejina Oasis in the lower reach of the Heihe River to the water yield of the upper catchment was analyzed by time series analysis of monthly observations of precipitation in the upper and lower catchment, river streamflow downstream of the modern irrigation schemes and satellite observations of vegetation index. Firstly, remotely sensed NDVI data acquired by Terra-MODIS are used to monitor the vegetation dynamic for a seven years period between 2000 and 2006. Due to cloud-contamination, atmospheric influence and different solar and viewing angles, however, the quality and consistence of time series of remotely sensed NDVI data are degraded. A Fourier Transform method – the Harmonic Analysis of Time Series (HANTS algorithm – is used to reconstruct cloud- and noise-free NDVI time series data from the Terra-MODIS NDVI dataset. Modification is made on HANTS by adding additional parameters to deal with large data gaps in yearly time series in combination with a Temporal-Similarity-Statistics (TSS method developed in this study to seek for initial values for the large gap periods. Secondly, the same Fourier Transform method is used to model time series of the vegetation phenology. The reconstructed cloud-free NDVI time series data are used to study the relationship between the water availability (i.e. the local precipitation and upstream water yield and the evolution of vegetation conditions in Ejina Oasis from 2000 to 2006. Anomalies in precipitation, streamflow, and vegetation index are detected by comparing each year with the average year. The results showed that

  5. Elastic plate flexure above mantle plumes explains the upstream offset of volcanic activity at la Réunion and Hawaii

    Science.gov (United States)

    Gerbault, Muriel; Fontaine, Fabrice; Rabinowicz, Michel; Bystricky, Micha

    2017-04-01

    Surface volcanism at la Réunion and Hawaii occurs with an offset of 150-180 km upstream to the plume axis with respect to the plate motion. This striking observation raises questions about the forcing of plume-lithosphere thermo-mechanical interactions on melt trajectories beneath these islands. Based on visco-elasto-plastic numerical models handled at kilometric resolution, we propose to explain this offset by the development of compressional stresses at the base of the lithosphere, that result from elastic plate bending above the upward load exerted by the plume head. This horizontal compression adopts a disc shape centered around the plume axis, 20 km thick and 150 km in radius, at 50-70 km depth where the temperature varies from 600°C to 750°C. It lasts for 5 to 10 My in an oceanic plate of age greater than 70 My, a timing that is controlled by the visco-elastic relaxation time at 50-70 km depth. This period of time exceeds the time during which both the Somalian/East-African and Pacific plates drift over the Reunion and Hawaii plumes, respectively, thus rendering this basal compression a persistent feature. It is inferred that the buoyant melts percolating in the plume head pond below this zone of compression and eventually spread laterally until the most compressive principal elastic stresses reverse to the vertical, i.e., 150 km away from the plume head. There, melts propagate through dikes upwards to 35 km depth, where the plate curvature reverses and ambient compression diminishes. This 30-35 km depth may thus host magmatic reservoirs where melts pond, until further differentiation can relaunch ascension up to the surface and form a volcanic edifice. In a second stage, as the volcano grows because of melt accumulation at the top of the plate, the lithosphere is flexed downwards, inducing extra tensile stress at 30-35 km depth and compression at 15 km depth. It implies that now the melts pond at 15 km and form another magmatic reservoir lying just

  6. Travel times, streamflow velocities, and dispersion rates in the Missouri River upstream from Canyon Ferry Lake, Montana

    Science.gov (United States)

    Whiteman, Aroscott

    2012-01-01

    In 2010, the U.S. Geological Survey, in cooperation with the Montana Department of Environmental Quality, initiated a dye-tracer study to determine travel times, streamflow velocities, and longitudinal dispersion rates for the Missouri River upstream from Canyon Ferry Lake. For this study, rhodamine WT (RWT) dye was injected at two locations, Missouri River Headwaters State Park in early September and Broadwater-Missouri Dam (Broadwater Dam) in late August 2010. Dye concentrations were measured at three sites downstream from each dye-injection location. The study area was a 41.2-mile reach of the Missouri River from Trident, Montana, at the confluence of the Jefferson, Madison, and Gallatin Rivers (Missouri River Headwaters) at river mile 2,319.40 downstream to the U.S. Route 12 Bridge (Townsend Bridge), river mile 2,278.23, near Townsend, Montana. Streamflows were reasonably steady and ranged from 3,070 to 3,700 cubic feet per second. Mean velocities were calculated for each subreach between measurement sites for the leading edge, peak concentration, centroid, and trailing edge at 10 percent of the peak concentration of the dye plume. Calculated velocities for the centroid of the dye plume ranged from 0.80 to 3.02 feet per second within the study reach from Missouri River Headwaters to Townsend Bridge, near Townsend. The mean velocity of the dye plume for the entire study reach, excluding the subreach between the abandoned Milwaukee Railroad bridge at Lombard, Montana (Milwaukee Bridge) and Broadwater-Missouri Dam (Broadwater Dam), was 2.87 feet per second. The velocity of the centroid of the dye plume for the subreach between Milwaukee Bridge and Broadwater Dam (Toston Reservoir) was 0.80 feet per second. The residence time for Toston Reservoir was 8.2 hours during this study. Estimated longitudinal dispersion rates of the dye plume for this study ranged from 0.72 feet per second for the subreach from Milwaukee Bridge to Broadwater Dam to 2.26 feet per second for

  7. Conditional inactivation of Upstream Binding Factor reveals its epigenetic functions and the existence of a somatic nucleolar precursor body.

    Directory of Open Access Journals (Sweden)

    Nourdine Hamdane

    2014-08-01

    Full Text Available 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.

  8. Comparing dependent robust correlations.

    Science.gov (United States)

    Wilcox, Rand R

    2016-11-01

    Let r1 and r2 be two dependent estimates of Pearson's correlation. There is a substantial literature on testing H0  : ρ1  = ρ2 , the hypothesis that the population correlation coefficients are equal. However, it is well known that Pearson's correlation is not robust. Even a single outlier can have a substantial impact on Pearson's correlation, resulting in a misleading understanding about the strength of the association among the bulk of the points. A way of mitigating this concern is to use a correlation coefficient that guards against outliers, many of which have been proposed. But apparently there are no results on how to compare dependent robust correlation coefficients when there is heteroscedasicity. Extant results suggest that a basic percentile bootstrap will perform reasonably well. This paper reports simulation results indicating the extent to which this is true when using Spearman's rho, a Winsorized correlation or a skipped correlation.

  9. Optomechanical Quantum Correlation Thermometry

    Science.gov (United States)

    Purdy, T. P.; Grutter, K. E.; Davanco, M. I.; Srinivasan, K.; Taylor, J. M.

    We present an optomechanical approach for producing accurate thermometry over a wide temperature range using quantum Brownian motion. Optical measurements induce quantum correlations in an optomechanical system when quantum-limited intensity fluctuations of a probe laser drive mechanical motion. The size of the correlations in the weak probe limit are dictated by the scale of individual phonons. We have recently measured optomechanical quantum correlations in the cross correlation spectrum between the amplitude and phase fluctuations of a single probe laser interacting with a silicon nitride optomechanical crystal. These correlations are independent of thermally-induced Brownian motion. However, Brownian motion does simultaneously produce much larger correlation signals between other optical quadratures. A comparison of the size of thermally-induced correlations to quantum correlations allows us to absolutely calibrate Brownian motion thermometry to the mechanical energy quantization scale.

  10. The Correlation Confocal Microscope

    CERN Document Server

    Simon, D S

    2010-01-01

    A new type of confocal microscope is described which makes use of intensity correlations between spatially correlated beams of light. It is shown that this apparatus leads to significantly improved transverse resolution.

  11. Facilities to monitor the upstream migration at the double slot fish pass Geesthacht; Einrichtungen zum Monitoring des Fischaufstiegs im Doppelschlitzpass Geesthacht

    Energy Technology Data Exchange (ETDEWEB)

    Adam, Beate [Institut fuer angewandte Oekologie, Kirtorf-Wahlen (Germany); Neumann, Christof [Knabe Enders Duehrkop Ingenieure GmbH, Hamburg (Germany)

    2012-07-01

    Both fish passes at the Geesthacht dam are continuously monitored to not only provide long term data about fish movements through the passes, but also to verify the correct functioning of the recently constructed double slot pass. To evaluate the traceability of fish passes by upstream moving fishes, transponder technology is used on a grand scale for the first time. Here, antennas located within fish passes automatically detect movements of individuals marked with transponder tags. In addition, a specially designed trap is used to confirm the presence of upstream moving fish of all species and sizes and thereby validate the functionality of the double slot pass. The use of this trap facilitates the collection of continuous and reliable monitoring data even during high discharges and harsh environmental conditions, whilst maintaining health and safety regulations for the personnel in charge. (orig.)

  12. Optimal Replenishment Decisions under Two-Level Trade Credit with Partial Upstream Trade Credit Linked to Order Quantity and Limited Storage Capacity

    Directory of Open Access Journals (Sweden)

    Chih-Te Yang

    2014-01-01

    Full Text Available This paper extends the previous economic order quantity (EOQ models under two-level trade credit such as Goyal (1985, Teng (2002, Huang (2003, 2007, Kreng and Tan (2010, Ouyang et al. (2013, and Teng et al. (2007 to reflect the real-life situations by incorporating the following concepts: (1 the storage capacity is limited, (2 the supplier offers the retailer a partially upstream trade credit linked to order quantity, and (3 both the dispensable assumptions that the upstream trade credit is longer than the downstream trade credit N

  13. Power Budget Analysis of Colorless Hybrid WDM/TDM-PON Scheme Using Downstream DPSK and Re-modulated Upstream OOK Data Signals

    Science.gov (United States)

    Khan, Yousaf; Afridi, Muhammad Idrees; Khan, Ahmed Mudassir; Rehman, Waheed Ur; Khan, Jahanzeb

    2014-09-01

    Hybrid wavelength-division multiplexed/time-division multiplexed passive optical access networks (WDM/TDM-PONs) combine the advance features of both WDM and TDM PONs to provide a cost-effective access network solution. We demonstrate and analyze the transmission performances and power budget issues of a colorless hybrid WDM/TDM-PON scheme. A 10-Gb/s downstream differential phase shift keying (DPSK) and remodulated upstream on/off keying (OOK) data signals are transmitted over 25 km standard single mode fiber. Simulation results show error free transmission having adequate power margins in both downstream and upstream transmission, which prove the applicability of the proposed scheme to future passive optical access networks. The power budget confines both the PON splitting ratio and the distance between the Optical Line Terminal (OLT) and Optical Network Unit (ONU).

  14. International Correlation Risk

    OpenAIRE

    Philippe Mueller; Andreas Stathopoulos; Andrea Vedolin

    2012-01-01

    Foreign exchange correlation is a key driver of risk premia in the cross-section of carry trade returns. First, we show that the correlation risk premium, defined as the difference between the risk-neutral and objective measure correlation is large (15% per year) and highly time-varying. Second, sorting currencies according to their exposure with correlation innovations yields portfolios with attractive risk and return characteristics. We also find that high (low) interest rate currencies hav...

  15. Correlation in business networks

    Science.gov (United States)

    Souma, Wataru; Aoyama, Hideaki; Fujiwara, Yoshi; Ikeda, Yuichi; Iyetomi, Hiroshi; Kaizoji, Taisei

    2006-10-01

    This paper considers business networks. Through empirical study, we show that business networks display characteristics of small-world networks and scale-free networks. In this paper, we characterize firms as sales and bankruptcy probabilities. A correlation between sales and a correlation between bankruptcy probabilities in business networks are also considered. The results reveal that the correlation between sales depends strongly on the type of network, whereas the correlation between bankruptcy probabilities does so only weakly.

  16. Teager Correlation Function

    DEFF Research Database (Denmark)

    Bysted, Tommy Kristensen; Hamila, R.; Gabbouj, M.

    1998-01-01

    A new correlation function called the Teager correlation function is introduced in this paper. The connection between this function, the Teager energy operator and the conventional correlation function is established. Two applications are presented. The first is the minimization of the Teager error...... norm and the second one is the use of the instantaneous Teager correlation function for simultaneous estimation of TDOA and FDOA (Time and Frequency Difference of Arrivals)....

  17. 淮河上游暴雨事件评估模型%Torrential Rain Events Assessment Model for the Upstream of the Huaihe River Basin

    Institute of Scientific and Technical Information of China (English)

    郑国; 薛建军; 范广洲; 李泽椿

    2011-01-01

    events indicator vector and each column vector of the assessment matrix, the degree of this torrential rain event can be determined. Through the assessment of historical and live torrential rain events which happen in the upstream of the Huaihe River Basin, the assessment results correspond well with the actual impact of the torrential rain disaster, which indicates that the degrees of torrential rain events assessed by this torrential rain events assessment model is reasonable. The pre-as^ sessment can be made by this torrential rain events assessment model to publish warning information when the forecast data are used, and the assessment accuracy has a positive effect on the forecast accuracy.Through the assessment of historical torrential rain events by this model, the results show that in 226 historical torrential fain events, there are 47 times belonging to level 1, 86 times belonging to level 2, 55 times belonging to level 3, 25 times belonging to level 4, 9 times belonging to level 5, 3 times belonging to level 6, and just 1 time belonging to level 7, which are consistent with the theoretical analysis. According to the assessment results, the most serious torrential rain events happen in 2007, which is consistent with the historical facts.The correlation between the assessment levels of torrential rain events and the Wangjiaba water levels passes the test of 0. 005 level, inferring that the selection of the assessment region and the assessment results of the torrential rain events of this research are rational.The analysis of the assessment results shows that, the torrential rain events happen 2 days before the peak of Wangjiaba water level, which has important significance to guide the disaster prevention and mitigation. However, the assessments of the influences of torrential rain events are insufficient, which need further research.

  18. Universal correlators from geometry

    Energy Technology Data Exchange (ETDEWEB)

    Dijkgraaf, Robbert [Institute for Theoretical Physics, University of Amsterdam, Valckenierstraat 65, 1018 XE Amsterdam (Netherlands); Korteweg-de Vries Institute for Mathematics, University of Amsterdam, Valckenierstraat 65, 1018 XE Amsterdam (Netherlands); Temuerhan, Mine; Sinkovics, Annamaria [Institute for Theoretical Physics, University of Amsterdam, Valckenierstraat 65, 1018 XE Amsterdam (Netherlands)]. E-mail: sinkovic@science.uva.nl

    2004-11-01

    Matrix model correlators show universal behaviour at short distances. We provide a derivation for these universal correlators by inserting probe branes in the underlying effective geometry. We generalize these results to study correlators of branes and their universal behaviour in the Calabi-Yau crystals, where we find a role for a generalized brane insertion. (author)

  19. Universal Correlators from Geometry

    Science.gov (United States)

    Dijkgraaf, Robbert; Sinkovics, Annamaria; Temurhan, Mine

    2004-11-01

    Matrix model correlators show universal behaviour at short distances. We provide a derivation for these universal correlators by inserting probe branes in the underlying effective geometry. We generalize these results to study correlators of branes and their universal behaviour in the Calabi-Yau crystals, where we find a role for a generalized brane insertion.

  20. Universal Correlators from Geometry

    CERN Document Server

    Dijkgraaf, R; Temurhan, M; Dijkgraaf, Robbert; Sinkovics, Annamaria; Temurhan, Mine

    2004-01-01

    Matrix model correlators show universal behaviour at short distances. We provide a derivation for these universal correlators by inserting probe branes in the underlying effective geometry. We generalize these results to study correlators of branes and their universal behaviour in the Calabi-Yau crystals, where we find a role for a generalized brane insertion.

  1. Modified Biserial Correlation Coefficients.

    Science.gov (United States)

    Kraemer, Helena Chmura

    1981-01-01

    Asymptotic distribution theory of Brogden's form of biserial correlation coefficient is derived and large sample estimates of its standard error obtained. Its relative efficiency to the biserial correlation coefficient is examined. Recommendations for choice of estimator of biserial correlation are presented. (Author/JKS)

  2. End-review of the development programme 'Strengthening the state petroleum administration of the upstream petroleum sector in Uganda'; Commissioned by Norad

    Energy Technology Data Exchange (ETDEWEB)

    2011-06-15

    The purpose of this end-review is to review the overall results of the Petrad Capacity Building Programme for strengthening the State Petroleum Administration of the upstream petroleum sector in Uganda ('the Programme') and assess the extent to which the Programme has achieved its objectives. The Programme commenced in January 2006 and ended in June 2009. This end-review has been carried out in the period February-June 2011. (Author)

  3. CARACTERIZACIÓN DE LA FASE UPSTREAM DE LA CADENA DE VALOR Y ABASTECIMIENTO DE LA AGROINDUSTRIA DE LA PALMA DE ACEITE EN COLOMBIA

    Directory of Open Access Journals (Sweden)

    Rafael García Cáceres

    2013-01-01

    Full Text Available Este artículo proporciona una descripción de la fase upstream de la cadena agroindustrial de la palma de aceite. El trabajo caracteriza la funcionalidad y relaciones de eslabones y escalones de la cadena de abastecimiento y de valor de la cadena en Colombia. El trabajo representa un esfuerzo pionero que busca contribuir a mejorar la eficiencia y eficacia del sector palmero colombiano.

  4. Energy transformations associated with the synoptic and planetary scales during the evolution of a blocking anticyclone and an upstream explosively-developing cyclone

    OpenAIRE

    Smith, Phillip J.; Tsou, Chih-Hua

    2011-01-01

    Energy transformations associated with a wave system that included the development of a blocking anticyclone over the North Atlantic Ocean and the upstream explosive-development of an extratropical cyclone are studied for the period 17–21 January 1979. Included in the investigation are eddy kinetic energy (KE), release of eddy potential energy (CE), generation of eddy kinetic energy (GK), and exchange between eddy and zonal kinetic energy (CK). In addition, these quantities were partitioned i...

  5. A novel approach to propagate flavivirus infectious cDNA clones in bacteria by introducing tandem repeat sequences upstream of virus genome.

    Science.gov (United States)

    Pu, Szu-Yuan; Wu, Ren-Huang; Tsai, Ming-Han; Yang, Chi-Chen; Chang, Chung-Ming; Yueh, Andrew

    2014-07-01

    Despite tremendous efforts to improve the methodology for constructing flavivirus infectious cDNAs, the manipulation of flavivirus cDNAs remains a difficult task in bacteria. Here, we successfully propagated DNA-launched type 2 dengue virus (DENV2) and Japanese encephalitis virus (JEV) infectious cDNAs by introducing seven repeats of the tetracycline-response element (7×TRE) and a minimal cytomegalovirus (CMVmin) promoter upstream of the viral genome. Insertion of the 7×TRE-CMVmin sequence upstream of the DENV2 or JEV genome decreased the cryptic E. coli promoter (ECP) activity of the viral genome in bacteria, as measured using fusion constructs containing DENV2 or JEV segments and the reporter gene Renilla luciferase in an empty vector. The growth kinetics of recombinant viruses derived from DNA-launched DENV2 and JEV infectious cDNAs were similar to those of parental viruses. Similarly, RNA-launched DENV2 infectious cDNAs were generated by inserting 7×TRE-CMVmin, five repeats of the GAL4 upstream activating sequence, or five repeats of BamHI linkers upstream of the DENV2 genome. All three tandem repeat sequences decreased the ECP activity of the DENV2 genome in bacteria. Notably, 7×TRE-CMVmin stabilized RNA-launched JEV infectious cDNAs and reduced the ECP activity of the JEV genome in bacteria. The growth kinetics of recombinant viruses derived from RNA-launched DENV2 and JEV infectious cDNAs displayed patterns similar to those of the parental viruses. These results support a novel methodology for constructing flavivirus infectious cDNAs, which will facilitate research in virology, viral pathogenesis and vaccine development of flaviviruses and other RNA viruses. © 2014 The Authors.

  6. [The effects of SV40 PolyA sequence and its AATAAA signal on upstream GFP gene expression and transcription termination].

    Science.gov (United States)

    Li, Shu-Ping; Feng, Jing-Jing; Wang, Hong-Gang; Wang, Xiu-Fang; Lv, Zhan-Jun

    2012-01-01

    SV40 PolyA (Simian virus 40 PolyA, also called PolyA) sequence is DNA sequence (240 bp) that possesses the activity of transcription termination and can add PolyA tail to mRNA. PolyA contains AATAAA hexanucleotide polyadenylation signal. Fourteen copies of Alu in sense orientation (Alu14) were inserted downstream of GFP in pEGFP-C1 to construct pAlu14 plasmid, and then HeLa cells were transiently transfected with pAlu14. Northern blot and fluorescence microscope were used to observe GFP RNA and protein expressions. Our results found that Alu tandem sequence inhibited remarkably GFP gene expression, but produced higher-molecular-mass GFP fusion RNA. PolyA and its sequence that was deleted AATAAA signal in sense or antisense orientation were inserted between GFP and Alu tandem sequence in pAlu14. The results showed that all the inserted PolyA sequences partly eliminated the inhibition induced by Alu14. PolyA sequences without AATAAA signal in sense or antisense orientation still induced transcription termination. Antisense PolyA (PolyAas) was divided into four fragments that all are 60 bp long and the middle two fragments were named 2F2R and 3F3R. 2F2R or 3F3R was inserted upstream of Alu tandem sequence in pAlu14. The molecular mass of GFP fusion RNA increased when the copy number of 2F2R increased. 2F2R can support transcription elongation when 2F2R is located upstream of other 2F2R. Nevertheless, 2F2R located upstream of Alu tandem sequence can induce transcription termination. Inserting one copy or 64 copies of 3F3R in upstream of Alu tandem sequence caused the production of lower-molecular-mass GFP RNA.

  7. Soggy, a spermatocyte-specific gene, lies 3.8 kb upstream of and antipodal to TEAD-2, a transcription factor expressed at the beginning of mouse development.

    Science.gov (United States)

    Kaneko, K J; DePamphilis, M L

    2000-10-15

    Investigation of the regulatory region of mTEAD-2, a gene expressed at the beginning of mouse pre-implantation development, led to the surprising discovery of another gene only 3.8 kb upstream of mTEAD-2. Here we show that this new gene is a single copy, testis-specific gene called SOGGY: (mSgy) that produces a single, dominant mRNA approximately 1.3 kb in length. It is transcribed in the direction opposite to mTEAD-2, thus placing the regulatory elements of these two genes in close proximity. mSgy contains three methionine codons that could potentially act as translation start sites, but most mSGY protein synthesis in vitro was initiated from the first Met codon to produce a full-length protein, suggesting that mSGY normally consists of 230 amino acids (26.7 kDa). Transcription began at a cluster of nucleotides approximately 150 bp upstream of the first Met codon using a TATA-less promoter contained within the first 0.9 kb upstream. The activity of this promoter was repressed by upstream sequences between -0.9 and -2.5 kb in cells that did not express mSgy, but this repression was relieved in cells that did express mSgy. mSgy mRNA was detected in embryos only after day 15 and in adult tissues only in the developing spermatocytes of seminiferous tubules, suggesting that mSgy is a spermatocyte-specific gene. Since mTEAD-2 and mSgy were not expressed in the same cells, the mSgy/mTEAD-2 locus provides a unique paradigm for differential regulation of gene expression during mammalian development.

  8. Caracterización de la fase upstream de la cadena de valor y abastecimiento de la agroindustria de la palma de aceite en colombia

    OpenAIRE

    Rafael García Cáceres; Adriana Núñez Moreno; Tatiana Ramírez Ortiz; Sonia Jaimes Suárez

    2013-01-01

    Este artículo proporciona una descripción de la fase upstream de la cadena agroindustrial de la palma de aceite. El trabajo caracteriza la funcionalidad y relaciones de eslabones y escalones de la cadena de abastecimiento y de valor de la cadena en Colombia. El trabajo representa un esfuerzo pionero que busca contribuir a mejorar la eficiencia y eficacia del sector palmero colombiano.

  9. Expression of NAC1 up-stream regulatory region and its relationship to the lateral root initiation induced by gibberellins and auxins.

    Science.gov (United States)

    Wang, Youhua; Duan, Liusheng; Lu, Mengzhu; Li, Zhaohu; Wang, Minjie; Zhai, Zhixi

    2006-10-01

    A 1050 bp up-stream regulatory fragment of the transcription factor gene NAC1 in Arabidopsis thaliana was isolated using polymerase chain reaction (PCR) based techniques. The fragment was used to substitute the 35S promoter of the pBI121 plasmid to construct a beta-glucuronidase gene (GUS) expression system. The construct was introduced into tobacco (Nicotiana tabaccum) plants by the Agrobacterium-mediated transferring method. GUS expression pattern was studied by using the transgenic lines. The results showed that the GUS driven by the NAC1 up-stream regulatory region was specifically expressed in the root meristem region, basal areas of the lateral root primordium and the lateral roots. The GUS expression was induced by 3-indolebutyric acid (IBA) and gibberellins (GA3 and GA4+7). The results indicated that the up-stream regulatory fragment of NAC1 responded to plant hormones. The fragment might be involved in both auxins and gibberellins signaling in promoting the development of lateral roots.

  10. Demonstrations of 10 and 40 Gbps upstream transmissions using 1.2 GHz RSOA-based ONU in long-reach access networks

    Science.gov (United States)

    Yeh, C. H.; Chow, C. W.; Wu, Y. F.; Chen, H. Y.

    2012-03-01

    Carrier-distributed long-reach passive optical network (LR-PON) is a promising candidate for future access networks. In this work, we analyze and compare the 4 × 2.5 Gb/s and 4 × 10 Gb/s upstream traffics in a carrier-distributed LR-PON using four wavelength-multiplexed 2.5 Gb/s on-off keying (OOK) and 10 Gb/s optical orthogonal frequency division multiplexing-quadrature amplitude modulation (OFDM-QAM) signals. Four commercial 1.2 GHz bandwidth reflective semiconductor optical amplifiers (RSOAs) are used in each optical networking unit (ONU) for the generation of the upstream signal. Due to the limited bandwidth of the RSOA, only up to 2.5 Gb/s upstream OOK signal can be generated. However, by using the spectral efficient modulation, such as OFDM-QAM, 10 Gb/s data rate can be achieved. 20, 50 and 75 km fiber transmissions are also compared using the two different kinds of modulation respectively.

  11. Sequences more than 500 base pairs upstream of the human U3 small nuclear RNA gene stimulate the synthesis of U3 RNA in frog oocytes

    Energy Technology Data Exchange (ETDEWEB)

    Suh, D.; Reddy, R. (Baylor Coll. of Medicine, Houston, TX (United States)); Wright, D. (Texas Medical Center, Houston (United States))

    1991-06-04

    Small nuclear RNA (snRNA) genes contain strong promoters capable of initiating transcription once every 4 s. Studies on the human U1 snRNA gene, carried out in other laboratories, showed that sequences within 400 bp of the 5' flanking region are sufficient for maximal levels of transcription both in vivo and in frog oocytes (reviewed in Dahlberg and Lund (1988)). The authors studied the expression of a human U3 snRNA gene by injecting 5' deletion mutants into frog oocytes. The results show that sequences more than 500 bp upstream of the U3 snRNA gene have a 2-3-fold stimulatory effect on the U3 snRNA synthesis. These results indicate that the human U3 snRNA gene is different from human U1 snRNA gene in containing regulatory elements more than 500 bp upstream. The U3 snRNA gene upstream sequences contain an AluI homologous sequence in the {minus}1,200 region; these AluI sequences were transcribed in vitro and in frog oocytes but were not detectable in Hela cells.

  12. Expression of NAC1 up-stream regulatory region and its relationship to the lateral root initiation induced by gibberellins and auxins

    Institute of Scientific and Technical Information of China (English)

    WANG; Youhua; DUAN; Liusheng; LU; Mengzhu; LI; Zhaohu; WANG; Minjie; ZHAI; Zhixi

    2006-01-01

    A 1050 bp up-stream regulatory fragment of the transcription factor gene NAC1 in Arabidopsis thaliana was isolated using polymerase chain reaction (PCR) based techniques. The fragment was used to substitute the 35S promoter of the pBI121 plasmid to construct a β-glucuronidase gene (GUS) expression system. The construct was introduced into tobacco (Nicotiana tabaccum) plants by the Agrobacterium-mediated transferring method. GUS expression pattern was studied by using the transgenic lines. The results showed that the GUS driven by the NAC1up-stream regulatory region was specifically expressed in the root meristem region, basal areas of the lateral root primordium and the lateral roots. The GUS expression was induced by 3-indolebutyric acid (IBA) and gibberellins (GA3 and GA4+7). The results indicated that the up-stream regulatory fragment of NAC1 responded to plant hormones. The fragment might be involved in both auxins and gibberellins signaling in promoting the development of lateral roots.

  13. Adaptive upstream rate adjustment by RSOA-ONU depending on different injection power of seeding light in standard-reach and long-reach PON systems

    Science.gov (United States)

    Yeh, C. H.; Chow, C. W.; Shih, F. Y.; Pan, C. L.

    2012-08-01

    The wavelength division multiplexing-time division multiplexing (WDM-TDM) passive optical network (PON) using reflective semiconductor optical amplifier (RSOA)-based colorless optical networking units (ONUs) is considered as a promising candidate for the realization of fiber-to-the-home (FTTH). And this architecture is actively considered by Industrial Technology Research Institute (ITRI) for the realization of FTTH in Taiwan. However, different fiber distances and optical components would introduce different power budgets to different ONUs in the PON. Besides, due to the aging of optical transmitter (Tx), the power decay of the distributed optical carrier from the central office (CO) could also reduce the injection power into each ONU. The situation will be more severe in the long-reach (LR) PON, which is considered as an option for the future access. In this work, we investigate a WDM-TDM PON using RSOA-based ONU for upstream data rate adjustment depending on different continuous wave (CW) injection powers. Both standard-reach (25 km) and LR (100 km) transmissions are evaluated. Moreover, a detail analysis of the upstream signal bit-error rate (BER) performances at different injection powers, upstream data rates, PON split-ratios under stand-reach and long-reach is presented.

  14. Correlations in Werner States

    Institute of Scientific and Technical Information of China (English)

    DONG Li; LUO Shun-Long; XIU Xiao-Ming; LI Nan; GAO Ya-Jun; CHI Feng

    2008-01-01

    Werner states are paradigmatic examples of quantum states and play an innovative role in quantum information theory. In investigating the correlating capability of Werner states, we find the curious phenomenon that quantum correlations, as quantified by the entanglement of formation, may exceed the total correlations, as measured by the quantum mutual information. Consequently, though the entanglement of formation is so widely used in quantifying entanglement, it cannot be interpreted as a consistent measure of quantum correlations per se if we accept the folklore that total correlations are measured (or rather upper bounded) by the quantum mutual information.

  15. Experimental fully contextual correlations

    CERN Document Server

    Amselem, Elias; Lopez-Tarrida, Antonio J; Portillo, Jose R; Bourennane, Mohamed; Cabello, Adan

    2011-01-01

    Quantum correlations are contextual yet, in general, nothing prevents the existence of even more contextual correlations. We identify and test a simple noncontextual inequality in which the quantum violation cannot be improved by any hypothetical post-quantum resource, and use it to experimentally obtain correlations in which the maximum noncontextual content, defined as the maximum fraction of noncontextual correlations, is less than 0.06. Our correlations are experimentally generated from the outcomes of sequential compatible measurements on a four-state quantum system encoded in the polarization and path of a single photon.

  16. Four-fold increase in users of time-wavelength division multiplexing (TWDM) passive optical network (PON) by delayed optical amplitude modulation (AM) upstream

    Science.gov (United States)

    Kachhatiya, Vivek; Prince, Shanthi

    2016-12-01

    In this paper, we have proposed and simulated optical time division multiplexed passive optical network (TDM-PON) using delayed optical amplitude modulation (AM). Eight upstream wavelengths are demonstrated to show optical time wavelength division multiplexed (TWDM) by combining optical network units (ONU) users data at the remote node (RN). Each ONU generates 2.5 Gb/s user data, and it is modulated using novel return to zero (RZ) delayed AM. Optical TDM aggregates 10 Gb/s data per wavelength from four 2.5 Gb/s upstream user data, which facilitates four different ONU data on the same wavelength as 10 Gb/s per upstream wavelength and, simplify the laser requirements (2.5 Gb/s) at each optical network unit (ONU) transmitter. Upstream optical TWDM-PON is investigated for eight wavelengths with wavelength spacing of 100 GHz. Novel optical TDM for upstream increased the number of the simultaneous user to fourfold from conventional TWDM-PON using delayed AM with a high-quality-factor of received signal. Despite performance degradation due to different fiber reach and dispersion compensation technique, Optical TWDM link shows significant improvement regarding receiver sensitivity when compared with common TWDM link. Hence, it offers optimistic thinking to show optical TDM at this phase as one of the future direction, where complex digital signal processing (DSP) and coherent optical communication are frequently demonstrated to serve the access network. Downstream side conventional TWDM eight wavelengths are multiplexed at the OLT and sent downstream to serve distributed tunable ONU receivers through an optical distribution network (ODN). Each downstream wavelengths are modulated at the peak rate of 10 Gb/s using non-return to zero external modulation (NRZ-EM). The proposed architecture is cost efficient and supports high data rates as well as ;pay as you grow; network for both service providers and the users perspectives. Users are classified into two categories viz home

  17. Polychlorinated Biphenyls (PCBs) in Catfish and Carp Collected from the Rio Grande Upstream and Downstream of Los Alamos National Laboratory: Revision 1

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert J. Gonzales

    2008-05-12

    Concern has existed for years that the Los Alamos National Laboratory (LANL), a complex of nuclear weapons research and support facilities, has released polychlorinated biphenyls (PCBs) to the environment that may have reached adjacent bodies of water through canyons that connect them. In 1997, LANL's Ecology Group began measuring PCBs in fish in the Rio Grande upstream and downstream of ephemeral streams that cross LANL and later began sampling fish in Abiquiu and Cochiti reservoirs, which are situated on the Rio Chama and Rio Grande upstream and downstream of LANL, respectively. In 2002, we electroshocked channel catfish (Ictalurus punctatus) and common carp (Carpiodes carpio) in the Rio Grande upstream and downstream of LANL and analyzed fillets for PCB congeners. We also sampled soils along the Rio Chama and Rio Grande drainages to discern whether a background atmospheric source of PCBs that could impact surface water adjacent to LANL might exist. Trace concentrations of PCBs measured in soil (mean = 4.7E-05 {micro}g/g-ww) appear to be from background global atmospheric sources, at least in part, because the bimodal distribution of low-chlorinated PCB congeners and mid-chlorinated PCB congeners in the soil samples is interpreted to be typical of volatilized PCB congeners that are found in the atmosphere and dust from global fallout. Upstream catfish (n = 5) contained statistically (P = 0.047) higher concentrations of total PCBs (mean = 2.80E-02 {micro}g/g-ww) than downstream catfish (n = 10) (mean = 1.50E-02 {micro}g/g-ww). Similarly, upstream carp (n = 4) contained higher concentrations of total PCBs (mean = 7.98E-02 {micro}g/g-ww) than downstream carp (n = 4) (3.07E-02 {micro}g/g-ww); however, the difference was not statistically significant (P = 0.42). The dominant PCB homologue in all fish samples was hexachlorobiphenyls. Total PCB concentrations in fish in 2002 are lower than 1997; however, differences in analytical methods and other uncertainties

  18. Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

    Science.gov (United States)

    Sharov, Alexei A.; Ko, Minoru S.H.

    2009-01-01

    We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cells based on published chromatin immunoprecipitation sequencing data. Furthermore, CisFinder successfully identified alternative binding motifs of TFs (e.g. POU5F1, ESRRB, and CTCF) and motifs for known and unknown co-factors of genes associated with the pluripotent state of ES cells. CisFinder also showed robust performance in the identification of motifs that were only slightly enriched in a set of DNA sequences. PMID:19740934

  19. Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

    OpenAIRE

    Sharov, Alexei A; Minoru S.H. Ko

    2009-01-01

    We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cel...

  20. Hybrid neurofibroma/schwannoma is overrepresented among schwannomatosis and neurofibromatosis patients.

    Science.gov (United States)

    Harder, Anja; Wesemann, Martin; Hagel, Christian; Schittenhelm, Jens; Fischer, Susan; Tatagiba, Marcos; Nagel, Christoph; Jeibmann, Astrid; Bohring, Axel; Mautner, Victor-Felix; Paulus, Werner

    2012-05-01

    We analyzed the histologic features of peripheral nerve sheath tumors occurring in 14 patients with schwannomatosis. Among a total of 31 tumors, 19 tumors (61%) showed schwannoma-like nodules within a neurofibroma-like tumor, corresponding to hybrid neurofibroma/schwannoma. At least 1 hybrid tumor occurred in 10 of 14 (71%) schwannomatosis patients. We then retrieved cases of hybrid tumors without documented relation to schwannomatosis from our database and identified 41 tumors arising in 23 patients. More than half of these patients (14/23) were reported to suffer from multiple peripheral nerve sheath tumors, favoring a tumor syndrome. Indeed, analysis of clinical records revealed the diagnosis of neurofibromatosis type 2 (NF2) in 26% (6/23), neurofibromatosis type 1 (NF1) in 9% (2/23), definite schwannomatosis in 4% (1/23), and possible schwannomatosis in 13% (3/23) of patients with multiple nerve sheath tumors. Our findings suggest that hybrid neurofibroma/schwannoma represents a common tumor type in schwannomatosis and shows a striking association with neurofibromatoses.

  1. Methylated DNA is over-represented in whole-genome bisulfite sequencing data

    Directory of Open Access Journals (Sweden)

    Lexiang eJi

    2014-10-01

    Full Text Available The development of whole-genome bisulfite sequencing (WGBS has led to a number of exciting discoveries about the role of DNA methylation leading to a plethora of novel testable hypotheses. Methods for constructing sodium bisulfite-converted and amplified libraries have recently advanced to the point that the bottleneck for experiments that use WGBS has shifted to data analysis and interpretation. Here we present empirical evidence for an over-representation of reads from methylated DNA in WGBS. This enrichment for methylated DNA is exacerbated by higher cycles of PCR and is influenced by the type of uracil-insensitive DNA polymerase used for amplifying the sequencing library. Future efforts to computationally correct for this enrichment bias will be essential to increasing the accuracy of determining methylation levels for individual cytosines. It is especially critical for studies that seek to accurately quantify DNA methylation levels in populations that may segregate for allelic DNA methylation states.

  2. Neurodevelopmental disorders are highly over-represented in children with obesity: A cross-sectional study.

    Science.gov (United States)

    Wentz, Elisabet; Björk, Anna; Dahlgren, Jovanna

    2017-01-01

    To investigate prevalence of neurodevelopmental disorders in children with obesity and to compare body mass index (BMI) and metabolic profile in the children. Seventy-six children (37 girls, 39 boys) were consecutively recruited from a university outpatient clinic specialized in severe obesity. Neurodevelopmental disorders including attention-deficit/hyperactivity disorder (ADHD), autism spectrum disorder (ASD), and developmental coordination disorder (DCD) were assessed using interviews and questionnaires. Neurodevelopmental diagnoses were collected retrospectively in medical records. BMI ranged between 1.9 and 5.9 SDS and age between 5.1 and 16.5 years. In 13.2% and 18.4% ASD and ADHD was assigned, respectively. In addition, 25% screened positive for DCD, 31.6% had at least one neurodevelopmental disorder, and 18.4% had a parent who screened positive for adult ADHD. Girls with ASD/ADHD had higher BMI SDS than girls without neurodevelopmental disorder (P = 0.006). One third of children with obesity referred to specialist centers have a neurodevelopmental disorder including deviant motor skills, and these problems may deteriorate weight status. One fifth of the parents exhibit ADHD symptomatology which could partly explain the poor adherence by some families in obesity units. Future obesity therapy could benefit from incorporating a neurodevelopmental treatment approach. © 2016 The Obesity Society.

  3. Is the SPINK1 variant p.N34S overrepresented in patients with acute pancreatitis?

    DEFF Research Database (Denmark)

    Jøergensen, Maiken Thyregod; Brusgaard, Klaus; Novovic, Srdan;

    2012-01-01

    Serine Protease Inhibitor Kazal type 1 (SPINK1) protects against premature intracellular activation of trypsinogen and development of acute pancreatitis. Our aim was to determine the prevalence of SPINK1 mutations (a) in unselected patients with first-time acute pancreatitis and (b) in the Danish...

  4. Effects of upstream tirofiban versus downstream tirofiban on myocardial damage and 180-day clinical outcomes in high-risk acute coronary syndromes patients undergoing percutaneous coronary interventions

    Institute of Scientific and Technical Information of China (English)

    LIU Tao; XIE Ying; ZHOU Yu-jie; LI Yue-ping; MA Han-ying; GUO Yong-he; LIU Yu-yang; ZHAO Ying-xin; SHI Dong-mei

    2009-01-01

    Background For patients with moderate to high-risk acute coronary syndromes(ACS)who undergo early,invasive treatment strategies,current guidelines recommend the usage of glycoprotein(GP)lib/Illa inhibitors as an upstream treatment for a coronary care unit or as an downstream provisional treatment for selected patients who are undergoing percutaneous coronary intervention(PCI).The relative advantage of either strategy is unknown.The purpose of this study was to evaluate the effects of upstream tirofiban versus the effects of downstream tirofiban on myocardial damage and 180-day major adverse cardiovascular events(MACE)after PCI in high-risk non-ST-segment elevation ACS (NSTE-ACS)undergoing PCI.Methods From July 2006 to July 2007,160 high-risk NSTE-ACS undergoing PCI were randomized to receive upstream (within 4-6 hours before coronary angiography)tirofiban or downstream(the guidewire crossing the lesion)tirofiban,to evaluate the extent of myocardial damage after PCI by quantitatively and qualitatively analyzing the value of cardiac troponin I(cTnl)as well as MB isoenzyme of creatine kinase(CK-MB)before and after PCI.The incidences of 24-hour,3-day,7-day,30-day and 180-day MACE after PCI were followed up and the rates of bleeding complications and thrombocytopenia during tirofiban administration were recorded.Results The peak release and cumulative release of cTnl levels within 48 hours after PCI were significantly lower with upstream tirefiban than downstream tirofiban(0.45 vs 0.63 and 0.32 vs 0.43,respectively;P<0.05).Post-procedural cTnl elevation within 48 hours was significantly less frequent among patients who received the upstream tirofiban than those who received the downstream tirefiban(66.3%vs 87.5%,P<0.05).The peak and cumulative release of CK-MB levels as well as post-procedural CK-MB elevation within 48 hours after PCI were not significantly different between the two groups (16 vs 14,5 vs 3 and 26.3%vs 36.3%,respectively;P>0.05).The incidences of

  5. Particle Correlations at LEP

    CERN Document Server

    Kress, Thomas

    2002-01-01

    Particle correlations are extensively studied to obtain information about the dynamics of hadron production. From 1989 to 2000 the four LEP collaborations recorded more than 16 million hadronic Z0 decays and several thousand W+W- events. In Z0 decays, two-particle correlations were analysed in detail to study Bose-Einstein and Fermi-Dirac correlations for various particle species. In fully-hadronic W+W- decays, particle correlations were used to study whether the two W bosons decay independently. A review of selected results is presented.

  6. Learning efficient correlated equilibria

    KAUST Repository

    Borowski, Holly P.

    2014-12-15

    The majority of distributed learning literature focuses on convergence to Nash equilibria. Correlated equilibria, on the other hand, can often characterize more efficient collective behavior than even the best Nash equilibrium. However, there are no existing distributed learning algorithms that converge to specific correlated equilibria. In this paper, we provide one such algorithm which guarantees that the agents\\' collective joint strategy will constitute an efficient correlated equilibrium with high probability. The key to attaining efficient correlated behavior through distributed learning involves incorporating a common random signal into the learning environment.

  7. Correlation Functions and Spin

    CERN Document Server

    Tyc, T

    2000-01-01

    The k-electron correlation function of a free chaotic electron beam is derived with the spin degree of freedom taken into account. It is shown that it can be expressed with the help of correlation functions for a polarized electron beam of all orders up to k and the degree of spin polarization. The form of the correlation function suggests that if the electron beam is not highly polarized, observing multi-particle correlations should be difficult. The result can be applied also to chaotic photon beams, the degree of spin polarization being replaced by the degree of polarization.

  8. HFC宽带接入网上行带宽分配策略的改进%Improving the Upstream Bandwidth Allocation Policy for the HFC Broadband Access Networks

    Institute of Scientific and Technical Information of China (English)

    宋军; 甘育裕; 吴资玉

    2003-01-01

    The request/transmit based upstream bandwidth resource allocation policy of DOCSIS introduces a trouble to the quality of the data service provided in the I-IFC networks. In this paper, the mechanism of the upstream data transrmitting and the process of data service transmitting in the HFC networks are described in detail, and the perfor- mance of the data service in HFC networks is analyzed. An advanced upstream bandwidth resource allocation policy is proposed to improve the quality of the data service in the HFC networks.

  9. Concomitant expression of far upstream element (FUSE) binding protein (FBP) interacting repressor (FIR) and its splice variants induce migration and invasion of non-small cell lung cancer (NSCLC) cells.

    Science.gov (United States)

    Müller, Benedikt; Bovet, Michael; Yin, Yi; Stichel, Damian; Malz, Mona; González-Vallinas, Margarita; Middleton, Alistair; Ehemann, Volker; Schmitt, Jennifer; Muley, Thomas; Meister, Michael; Herpel, Esther; Singer, Stephan; Warth, Arne; Schirmacher, Peter; Drasdo, Dirk; Matthäus, Franziska; Breuhahn, Kai

    2015-11-01

    Transcription factors integrate a variety of oncogenic input information, facilitate tumour growth and cell dissemination, and therefore represent promising therapeutic target structures. Because over-expression of DNA-interacting far upstream element binding protein (FBP) supports non-small cell lung cancer (NSCLC) migration, we asked whether its repressor, FBP-interacting repressor (FIR) is functionally inactivated and how FIR might affect NSCLC cell biology. Different FIR splice variants were highly expressed in the majority of NSCLCs, with the highest levels in tumours carrying genomic gains of chromosome 8q24.3, which contained the FIR gene locus. Nuclear FIR expression was significantly enriched at the invasion front of primary NSCLCs, but this did not correlate with tumour cell proliferation. FIR accumulation was associated with worse patient survival and tumour recurrence; in addition, FIR over-expression significantly correlated with lymph node metastasis in squamous cell carcinomas (SCCs). In vitro, we applied newly developed methods and modelling approaches for the quantitative and time-resolved description of the pro-migratory and pro-invasive capacities of SCC cells. siRNA-mediated silencing of all FIR variants significantly reduced the speed and directional movement of tumour cells in all phases of migration. Furthermore, sprouting efficiency and single cell invasiveness were diminished following FIR inhibition. Interestingly, the silencing of FIR isoforms lacking exon 2 (FIR(Δexon2)) alone was sufficient to reduce lateral migration and invasion. In summary, by using scale-spanning data derived from primary human tissues, quantitative cellular analyses and mathematical modelling, we have demonstrated that concomitant over-expression of FIR and its splice variants drives NSCLC migration and dissemination.

  10. Correlations in multiparticle production

    CERN Document Server

    Troshin, S M

    2011-01-01

    We discuss correlations in the hadron production in the $pp$-collision with emphasize on the ridge-like structure origin in the two-particle correlation function. We suggest that this structure can appear due to a rotating nature of the transient state of matter generated in the intermidiate stage of proton collison.

  11. ALMA correlator computer systems

    Science.gov (United States)

    Pisano, Jim; Amestica, Rodrigo; Perez, Jesus

    2004-09-01

    We present a design for the computer systems which control, configure, and monitor the Atacama Large Millimeter Array (ALMA) correlator and process its output. Two distinct computer systems implement this functionality: a rack- mounted PC controls and monitors the correlator, and a cluster of 17 PCs process the correlator output into raw spectral results. The correlator computer systems interface to other ALMA computers via gigabit Ethernet networks utilizing CORBA and raw socket connections. ALMA Common Software provides the software infrastructure for this distributed computer environment. The control computer interfaces to the correlator via multiple CAN busses and the data processing computer cluster interfaces to the correlator via sixteen dedicated high speed data ports. An independent array-wide hardware timing bus connects to the computer systems and the correlator hardware ensuring synchronous behavior and imposing hard deadlines on the control and data processor computers. An aggregate correlator output of 1 gigabyte per second with 16 millisecond periods and computational data rates of approximately 1 billion floating point operations per second define other hard deadlines for the data processing computer cluster.

  12. Higher-spin correlators

    CERN Document Server

    Alday, Luis F

    2013-01-01

    We analyze the properly normalized three-point correlator of two protected scalar operators and one higher spin twist-two operator in N=4 super Yang-Mills, in the limit of large spin j. The relevant structure constant can be extracted from the OPE of the four-point correlator of protected scalar operators. We show that crossing symmetry of the four point correlator plus a judicious guess for the perturbative structure of the three-point correlator, allow to make a prediction for the structure constant at all loops in perturbation theory, up to terms that remain finite as the spin becomes large. Furthermore, the expression for the structure constant allows to propose an expression for the all loops four-point correlator G(u,v), in the limit u,v -> 0. Our predictions are in perfect agreement with the large j expansion of results available in the literature.

  13. Quantitative Infrared Image Analysis Of Simultaneous Upstream and Downstream Microgravity Flame Spread over Thermally-Thin Cellulose in Low Speed Forced Flow

    Science.gov (United States)

    Olson, S. L.; Lee, J. R.; Fujita, O.; Kikuchi, M.; Kashiwagi, T.

    2013-01-01

    The effect of low velocity forced flow on microgravity flame spread is examined using quantitative analysis of infrared video imaging. The objective of the quantitative analysis is to provide insight into the mechanisms of flame spread in microgravity where the flame is able to spread from a central location on the fuel surface, rather than from an edge. Surface view calibrated infrared images of ignition and flame spread over a thin cellulose fuel were obtained along with a color video of the surface view and color images of the edge view using 35 mm color film at 2 Hz. The cellulose fuel samples were mounted in the center of a 12 cm wide by 16 cm tall flow duct and were ignited in microgravity using a straight hot wire across the center of the 7.5 cm wide by 14 cm long samples. Four cases, at 1 atm. 35%O2 in N2, at forced flows from 2 cm/s to 20 cm/s are presented here. This flow range captures flame spread from strictly upstream spread at low flows, to predominantly downstream spread at high flow. Surface temperature profiles are evaluated as a function of time, and temperature gradients for upstream and downstream flame spread are measured. Flame spread rates from IR image data are compared to visible image spread rate data. IR blackbody temperatures are compared to surface thermocouple readings to evaluate the effective emissivity of the pyrolyzing surface. Preheat lengths and pyrolysis lengths are evaluated both upstream and downstream of the central ignition point. A surface energy balance estimates the net heat flux from the flame to the fuel surface along the length of the fuel. Surface radiative loss and gas-phase radiation from soot are measured relative to the net heat feedback from the flame. At high surface heat loss relative to heat feedback, the downstream flame spread does not occur.

  14. Quantitative Infrared Image Analysis Of Thermally-Thin Cellulose Surface Temperatures During Upstream and Downstream Microgravity Flame Spread from A Central Ignition Line

    Science.gov (United States)

    Olson, Sandra L.; Lee, J. R.; Fujita, O.; Kikuchi, M.; Kashiwagi, T.

    2012-01-01

    Surface view calibrated infrared images of ignition and flame spread over a thin cellulose fuel were obtained at 30 Hz during microgravity flame spread tests in the 10 second Japan Microgravity Center (JAMIC). The tests also used a color video of the surface view and color images of the edge view using 35 millimeter 1600 Kodak Ektapress film at 2 Hz. The cellulose fuel samples (50% long fibers from lumi pine and 50% short fibers from birch) were made with an area density of 60 grams per square meters. The samples were mounted in the center of a 12 centimeter wide by 16 centimeter tall flow duct that uses a downstream fan to draw the air through the flow duct. Samples were ignited after the experiment package was released using a straight hot wire across the center of the 7.5 centimeter wide by 14 centimeter long samples. One case, at 1 atmosphere 35%O2 in N2, at a forced flow of 10 centimeters per second, is presented here. In this case, as the test progresses, the single flame begins to separate into simultaneous upstream and downstream flames. Surface temperature profiles are evaluated as a function of time, and temperature gradients for upstream and downstream flame spread are measured. Flame spread rates from IR image data are compared to visible image spread rate data. IR blackbody temperatures are compared to surface thermocouple readings to evaluate the effective emissivity of the pyrolyzing surface. Preheat lengths are evaluated both upstream and downstream of the central ignition point. A surface energy balance estimates the net heat flux from the flame to the fuel surface along the length of the fuel.

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

    Directory of Open Access Journals (Sweden)

    Adam G Marsh

    Full Text Available 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

  16. Complexes between the LKB1 tumor suppressor, STRADα/β and MO25α/β are upstream kinases in the AMP-activated protein kinase cascade

    Directory of Open Access Journals (Sweden)

    Alessi Dario R

    2003-09-01

    Full Text Available Abstract Background The AMP-activated protein kinase (AMPK cascade is a sensor of cellular energy charge that acts as a 'metabolic master switch' and inhibits cell proliferation. Activation requires phosphorylation of Thr172 of AMPK within the activation loop by upstream kinases (AMPKKs that have not been identified. Recently, we identified three related protein kinases acting upstream of the yeast homolog of AMPK. Although they do not have obvious mammalian homologs, they are related to LKB1, a tumor suppressor that is mutated in the human Peutz-Jeghers cancer syndrome. We recently showed that LKB1 exists as a complex with two accessory subunits, STRADα/β and MO25α/β. Results We report the following observations. First, two AMPKK activities purified from rat liver contain LKB1, STRADα and MO25α, and can be immunoprecipitated using anti-LKB1 antibodies. Second, both endogenous and recombinant complexes of LKB1, STRADα/β and MO25α/β activate AMPK via phosphorylation of Thr172. Third, catalytically active LKB1, STRADα or STRADβ and MO25α or MO25β are required for full activity. Fourth, the AMPK-activating drugs AICA riboside and phenformin do not activate AMPK in HeLa cells (which lack LKB1, but activation can be restored by stably expressing wild-type, but not catalytically inactive, LKB1. Fifth, AICA riboside and phenformin fail to activate AMPK in immortalized fibroblasts from LKB1-knockout mouse embryos. Conclusions These results provide the first description of a physiological substrate for the LKB1 tumor suppressor and suggest that it functions as an upstream regulator of AMPK. Our findings indicate that the tumors in Peutz-Jeghers syndrome could result from deficient activation of AMPK as a consequence of LKB1 inactivation.

  17. Identification of a novel first exon in the human dystrophin gene and of a new promoter located more than 500 kb upstream of the nearest known promoter

    Energy Technology Data Exchange (ETDEWEB)

    Yanagawa, H.; Nishio, H.; Takeshima, Y. [Kobe Univ. School of Medicine (Japan)] [and others

    1994-09-01

    The dystrophin gene, which is muted in patients with Duchenne and Becker muscular dystrophies, is the largest known human gene. Five alternative promoters have been characterized until now. Here we show that a novel dystrophin isoform with a different first exon can be produced through transcription initiation at a previously-unidentified alternative promoter. The case study presented is that of patient with Duchenne muscular dystrophy who had a deletion extending from 5{prime} end of the dystrophin gene to exon 2, including all promoters previously mapped in the 5{prime} part of the gene. Transcripts from lymphoblastoid cells were found to contain sequences corresponding to exon 3, indicating the presence of new promoter upstream of this exon. The nucleotide sequence of amplified cDNA corresponding to the 5{prime} end of the new transcript indicated that the 5{prime} end of exon 3 was extended by 9 codons, only the last (most 3{prime}) of which codes for methionine. The genomic nucleotide sequence upstream from the new exon, as determined using inverse polymerase chain reaction, revealed the presence of sequences similar to a TATA box, an octamer motif and an MEF-2 element. The identified promoter/exon did not map to intron 2, as might have been expected, but to a position more than 500 kb upstream of the most 5{prime} of the previously-identified promoters, thereby adding 500 kb to the dystrophin gene. The sequence of part of the new promoter region is very similar to that of certain medium reiteration frequency repetitive sequences. These findings may help us understand the molecular evolution of the dystrophin gene.

  18. Transcription of the Escherichia coli dcw cluster: evidence for distal upstream transcripts being involved in the expression of the downstream ftsZ gene.

    Science.gov (United States)

    de la Fuente, A; Palacios, P; Vicente, M

    2001-01-01

    Escherichia coli strains VIP596 and VIP597 have been constructed to compare the amount of transcription of the ftsZ gene derived from proximal promoters in the ddlB-ftsZ region with that originating in the upstream regions of the dcw cluster. Both strains have in common a beta-galactosidase reporter fusion located at the ddlB locus, but differ in that VIP597 has a transcription terminator Omega interposon located downstream from lacZ. In addition, these strains have the ddlB, ftsQ, ftsA and ftsZ genes under the control of the IPTG-inducible promoter P(tac), allowing to control artificially ftsZ expression for normal cell division to take place. When beta-galactosidase activity was measured in VIP596 and VIP597 and compared to the levels measured in strain VIP407, in which the lacZ reporter fusion is located in the ftsZ gene, they were found to account for nearly 66% of the total transcription entering into ftsZ. This result indicates that the reduction in ftsZ transcription observed when the promoters in the ddlB-ftsA region are disconnected from the upstream sequences of the dcw cluster (as observed by Flärdh et al., Mol. Microbiol. 30 (1998) 305-316) in strain VIP490) is the direct consequence of the interruption in the transcription originated upstream and not due to the effect of such sequences on the promoters proximal to ftsZ.

  19. A distinct DNA-methylation boundary in the 5'- upstream sequence of the FMR1 promoter binds nuclear proteins and is lost in fragile X syndrome.

    Science.gov (United States)

    Naumann, Anja; Hochstein, Norbert; Weber, Stefanie; Fanning, Ellen; Doerfler, Walter

    2009-11-01

    We have discovered a distinct DNA-methylation boundary at a site between 650 and 800 nucleotides upstream of the CGG repeat in the first exon of the human FMR1 gene. This boundary, identified by bisulfite sequencing, is present in all human cell lines and cell types, irrespective of age, gender, and developmental stage. The same boundary is found also in different mouse tissues, although sequence homology between human and mouse in this region is only 46.7%. This boundary sequence, in both the unmethylated and the CpG-methylated modes, binds specifically to nuclear proteins from human cells. We interpret this boundary as carrying a specific chromatin structure that delineates a hypermethylated area in the genome from the unmethylated FMR1 promoter and protecting it from the spreading of DNA methylation. In individuals with the fragile X syndrome (FRAXA), the methylation boundary is lost; methylation has penetrated into the FMR1 promoter and inactivated the FMR1 gene. In one FRAXA genome, the upstream terminus of the methylation boundary region exhibits decreased methylation as compared to that of healthy individuals. This finding suggests changes in nucleotide sequence and chromatin structure in the boundary region of this FRAXA individual. In the completely de novo methylated FMR1 promoter, there are isolated unmethylated CpG dinucleotides that are, however, not found when the FMR1 promoter and upstream sequences are methylated in vitro with the bacterial M-SssI DNA methyltransferase. They may arise during de novo methylation only in DNA that is organized in chromatin and be due to the binding of specific proteins.

  20. A Distinct DNA-Methylation Boundary in the 5′- Upstream Sequence of the FMR1 Promoter Binds Nuclear Proteins and Is Lost in Fragile X Syndrome

    Science.gov (United States)

    Naumann, Anja; Hochstein, Norbert; Weber, Stefanie; Fanning, Ellen; Doerfler, Walter

    2009-01-01

    We have discovered a distinct DNA-methylation boundary at a site between 650 and 800 nucleotides upstream of the CGG repeat in the first exon of the human FMR1 gene. This boundary, identified by bisulfite sequencing, is present in all human cell lines and cell types, irrespective of age, gender, and developmental stage. The same boundary is found also in different mouse tissues, although sequence homology between human and mouse in this region is only 46.7%. This boundary sequence, in both the unmethylated and the CpG-methylated modes, binds specifically to nuclear proteins from human cells. We interpret this boundary as carrying a specific chromatin structure that delineates a hypermethylated area in the genome from the unmethylated FMR1 promoter and protecting it from the spreading of DNA methylation. In individuals with the fragile X syndrome (FRAXA), the methylation boundary is lost; methylation has penetrated into the FMR1 promoter and inactivated the FMR1 gene. In one FRAXA genome, the upstream terminus of the methylation boundary region exhibits decreased methylation as compared to that of healthy individuals. This finding suggests changes in nucleotide sequence and chromatin structure in the boundary region of this FRAXA individual. In the completely de novo methylated FMR1 promoter, there are isolated unmethylated CpG dinucleotides that are, however, not found when the FMR1 promoter and upstream sequences are methylated in vitro with the bacterial M-SssI DNA methyltransferase. They may arise during de novo methylation only in DNA that is organized in chromatin and be due to the binding of specific proteins. PMID:19853235