Molecular analysis of the microbial community structures in water-flooding petroleum reservoirs with different temperatures

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Vibration suppression and angle tracking of a fire-rescue ladder

This paper mainly considers vibration suppression and angle tracking of a fire-rescue ladder system. The dynamical model is regarded as a segmented Euler–Bernoulli beam with gravity and tip mass, described by a set of motion equations and boundary conditions. Based on the nonlinear Euler–Bernoulli beam model, two active boundary controllers are proposed to achieve the control objectives. The elastic deflection and the angular error in the closed-loop system are proven to converge exponentially to a small neighborhood of zero. Numerical simulations based on finite difference method verify the effectiveness and the ascendancy of active boundary controllers

Two-pion Bose-Einstein correlations in central Pb-Pb collisions at sNN\sqrt{s_{\rm NN}} = 2.76 TeV

The first measurement of two-pion Bose-Einstein correlations in central Pb-Pb collisions at $\sqrt{s_{\rm NN}} = 2.76$ TeV at the Large Hadron Collider is presented. We observe a growing trend with energy now not only for the longitudinal and the outward but also for the sideward pion source radius. The pion homogeneity volume and the decoupling time are significantly larger than those measured at RHIC.Comment: 17 pages, 5 captioned figures, 1 table, authors from page 12, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/388

Suppression of charged particle production at large transverse momentum in central Pb-Pb collisions at sNN=2.76\sqrt{s_{\rm NN}} = 2.76 TeV

Inclusive transverse momentum spectra of primary charged particles in Pb-Pb collisions at $\sqrt{s_{_{\rm NN}}}$ = 2.76 TeV have been measured by the ALICE Collaboration at the LHC. The data are presented for central and peripheral collisions, corresponding to 0-5% and 70-80% of the hadronic Pb-Pb cross section. The measured charged particle spectra in $|\eta|<0.8$ and $0.3 < p_T < 20$ GeV/$c$ are compared to the expectation in pp collisions at the same $\sqrt{s_{\rm NN}}$, scaled by the number of underlying nucleon-nucleon collisions. The comparison is expressed in terms of the nuclear modification factor $R_{\rm AA}$. The result indicates only weak medium effects ($R_{\rm AA} \approx$ 0.7) in peripheral collisions. In central collisions, $R_{\rm AA}$ reaches a minimum of about 0.14 at $p_{\rm T}=6$-7GeV/$c$ and increases significantly at larger $p_{\rm T}$. The measured suppression of high-$p_{\rm T}$ particles is stronger than that observed at lower collision energies, indicating that a very dense medium is formed in central Pb-Pb collisions at the LHC.Comment: 15 pages, 5 captioned figures, 3 tables, authors from page 10, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/98

The P2X1 receptor and platelet function

Extracellular nucleotides are ubiquitous signalling molecules, acting via the P2 class of surface receptors. Platelets express three P2 receptor subtypes, ADP-dependent P2Y1 and P2Y12 G-protein-coupled receptors and the ATP-gated P2X1 non-selective cation channel. Platelet P2X1 receptors can generate significant increases in intracellular Ca2+, leading to shape change, movement of secretory granules and low levels of αIIbβ3 integrin activation. P2X1 can also synergise with several other receptors to amplify signalling and functional events in the platelet. In particular, activation of P2X1 receptors by ATP released from dense granules amplifies the aggregation responses to low levels of the major agonists, collagen and thrombin. In vivo studies using transgenic murine models show that P2X1 receptors amplify localised thrombosis following damage of small arteries and arterioles and also contribute to thromboembolism induced by intravenous co-injection of collagen and adrenaline. In vitro, under flow conditions, P2X1 receptors contribute more to aggregate formation on collagen-coated surfaces as the shear rate is increased, which may explain their greater contribution to localised thrombosis in arterioles compared to venules within in vivo models. Since shear increases substantially near sites of stenosis, anti-P2X1 therapy represents a potential means of reducing thrombotic events at atherosclerotic plaques

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Non-standard errors

In statistics, samples are drawn from a population in a data-generating process (DGP). Standard errors measure the uncertainty in estimates of population parameters. In science, evidence is generated to test hypotheses in an evidence generating process (EGP). We claim that EGP variation across researchers adds uncertainty: Non-standard errors (NSEs). We study NSEs by letting 164 teams test the same hypotheses on the same data. NSEs turn out to be sizable, but smaller for better reproducible or higher rated research. Adding peer-review stages reduces NSEs. We further find that this type of uncertainty is underestimated by participants

Nitrate-reducing community in production water of three oil reservoirs and their responses to different carbon sources revealed by nitrate-reductase encoding gene (napA)

The nitrate-reducing microbial community in oil reservoirs was examined by PCR using primers to amplify a segment of napA gene encoding for a subunit of the nitrate reductase, and the effects of different organic carbon additions on the nitrate-reducing community were also evaluated. The orders Rhodocyclales and Burkholderiales within Betaproteobacteria and Pseudomonadales within Gammaproteobacteria were recovered in production water of all three oil reservoirs. Amendment of organic acids promoted Enterobacteriales within Gammaproteobacteria and orders of Rhodocyclales, Pseudomonadales, and Burkholderiales, while alkanes favored the Rhizobiaceae family within Alphaproteobacteria and orders of Rhodocyclales and Pseudomonadales. Results indicated that the functional gene napA can be used as a valuable biomarker in analyzing the diversity of nitrate reducers in oil reservoirs. Nitrate-reducing microbial community shifts following the available carbon sources. Information about napA gene in oil reservoirs environment is scarce. This is the first study that combines molecular and culture-dependent approaches to reveal the diversity of the nitrate-reducing microbial community in production water of oil reservoirs by using the napA gene. © 2011.link_to_subscribed_fulltex

Production processes affected prokaryotic amoA gene abundance and distribution in high-temperature petroleum reservoirs

Although the presence and activity of ammonia-oxidation archaea (AOA) and ammonia-oxidation bacteria (AOB) were observed in thermophilic habitats recently, their existence in the geothermal subterranean oil reservoirs is still not available. This study investigated the abundance and distribution of AOA and AOB in the production waters of high-temperature oil reservoirs by using real-time PCR and phylogenetic analysis based on amoA genes. The results indicated the occurrence of both AOA and AOB in 9 out of totally 17 wells. The AOA-like phylotypes are mainly clustered within two major clades of archaeal amoA sequences known from water columns, sediments and soils: clusters A and B, and a few clones are related to the new genera: Candidatus 'Nitrosocaldus yellowstonii'. The AOB-like phylotypes mainly belong to Nitrosospira and Nitrosomonas clusters, while two of them are deep-branched in Nitrosospira cluster and showed no substantial alignment to the known cultured AOB, indicating the possibility of new AOB phylotypes. The abundance of AOA and AOB-like amoA genes ranged from 2.92 × 10 3 to 9.21 × 10 4 and from 2.91 × 10 2 to 8.12 × 10 3 amoA gene copy numbers per ml production water with the ratios of AOA to AOB ranging from 5.10 to 95.5. Statistical analysis showed that amoA gene fell into five groups and the distribution of amoA gene is significantly correlated with the environmental factors, e.g., temperature and recovery process. Our study showed distribution of prokaryotic amoA gene in various oil reservoirs was affected by production processes. © Taylor & Francis Group, LLC.link_to_subscribed_fulltex

Microbial community characteristics of petroleum reservoir production water amended with n-alkanes and incubated under nitrate-, sulfate-reducing and methanogenic conditions

Methanogenic, sulfate- and nitrate-reducing enrichment cultures amended with long-chain n-alkanes (C 15-C 20) were established with production water from Huabei oilfield in China in the present study. Chemical analyses indicated that degradation of n-alkanes was evident under all three conditions after 356 days of incubation. Phylogenetic analyses based on 16S rRNA gene amplification indicated that α-, β-, γ-Proteobacteria and Bacteroidetes were detected in the nitrate-reducing enrichment; Actinobacteria, Nitrospira and δ-Proteobacteria were recovered from both the sulfate-reducing and methanogenic enrichments. Actinobacteria and Nitrospira were the most abundant in methanogenic and sulfate-reducing enrichment, respectively. The archaeal clone libraries showed that the order Methanomicrobiales within the phylum Euryarchaeota predominated methanogenic enrichment; whereas the unclassified class Thermoprotei within the phylum Crenarchaeota prevailed in sulfate-reducing enrichment. Comparison of 16S rRNA gene sequences from genomic DNA extracted directly from the petroleum reservoir production water with those from the three active enrichments showed that the available electron acceptors had a strong influence on the microbial community composition. In addition, genes encoding the alkylsuccinate synthase (assA) and methyl coenzyme-M reductase (mcrA) were amplified from the methanogenic enrichment and the results suggested that fumarate addition was probably involved in the degradation of n-alkanes. These results shed light on the potential utilization of microbial metabolism in remediation of hydrocarbon contamination or in enhancing the recovery of residual oil for energy. © 2012 Elsevier Ltd.link_to_subscribed_fulltex