STUDY OF THE MECHANlSM OF FLOW-INDUCED VIBRATIONS OF A CYLINDER IN PROXIMITY TO A WALL

Flexible bluff bodies exposed to a uniform fluid flow undergo vibration due to vortex-shedding from the body. This phenomenon is known as vortex-induced vibration (VIV). Structural members, such as cables, conduits, and pipes, are susceptible to VIV. Vortex-induced vibrations result in structural stresses due to elastic structural deformation from the flow-induced loading. Cylindrical structures in proximity to planar surfaces can undergo vortex-induced vibrations when the gap between the cylinder and the planar surfaces is above a critical value. This laboratory study investigated the mechanism of vibration and planar wall proximity effect on the cylinder response to the vortex shedding process. The vibration mechanism at subcritical gap ratios is hypothesized to be movement-induced vibrations (MIV) caused by unsteady fluid flow interactions. On the other hand, vortex-induced vibration has been established as the vibration mechanism at large gap ratios in uniform flow (Blevins, 1990). A circular cylinder, mounted on two degree-of-freedom (DOF) leaf springs at each end, was positioned in a tolerant, open return subsonic wind tunnel at Bucknell University. At a reduced velocity of Ur = 5 and a Reynolds number, using the cylinder’s diameter, of 1.73 x 104, a series measurement of two-DOF structural accelerations along with the fluctuating wake velocity at a fixed position relative to the cylinder was recorded. This study provides data on the relationship between two DOF vibrations and the proximity of a circular structure to a planar surface. For gap ratios of G/D \u3e 1.0 and δ/G ≈ 0.30, the alternate shedding of vortices (the von Kármán vortex street) produces a fluctuating y-direction acceleration of the body at the same frequency as that of vortex shedding. Furthermore, the transverse y-direction acceleration has an associated streamwise x-direction acceleration at twice the vortex shedding frequency, indicating a fluid-structure interaction due to von Kármán vortex shedding as expected for a cylinder in a uniform flow. For G/D \u3c 0.5 and δ/G ≈ 0.61, it is theorized that the bistable upstream wall boundary layer separation bubble periodically detaches and reattaches to the outer front top quarter surface of the cylinder as the cylinder moves upstream and towards the wall. As a result, coherent vortices are shed only from the outer side of the cylinder. The cylinder’s resulting MIV from the fluid forces has an oblong acceleration trajectory, reinforcing the single-sided vortex shedding from the cylinder. The bistable wall boundary layer is suggested as a possible mechanism for the near-wall region

Structure and hydration of polyvinylpyrrolidone-hydrogen peroxide

The structure of the commercially important polyvinylpyrrolidone-hydrogen peroxide complex can be understood by reference to the co-crystal structure of a hydrogen peroxide complex and its mixed hydrates of a two-monomer unit model compound, bisVP·2H2O2. The mixed hydrates involve selective water substitution into one of the two independent hydrogen peroxide binding sites

High-resolution sequencing of DNA G-quadruplex secondary structures in the human genome

This is the author accepted manuscript. The final version is available from NPG via http://dx.doi.org/10.1038/nbt.3295During active transcription and replication chromatin architecture is altered, allowing formation of DNA secondary structures. G-quadruplexes (G4s) have emerged as important regulatory DNA structures and have been associated with genomic instability, genetic diseases and cancer progression. Experimental evidence for G4 prevalence in the entire human genome is still lacking. We present a high-resolution sequencing-based method that detected 716,310 distinct G4s in the human genome, more than predicted by computational methods, including structural variants previously uncharacterised in a genomic context. We observed high G4-density in functional regions, such as 5’ UTRs and splicing sites, and in genes not predicted to have such structures (BRCA1 and BRCA2). We found a significant association of G4 formation with oncogenes and tumor suppressors, and with Somatic Copy-Number Alterations (SCNAs) that act as cancer drivers. Our results support that G4s are promising targets for cancer intervention and suggest novel candidates for further biological and mechanistic studies.We are grateful to the Biotechnology and Biological Sciences Research Council (BBSRC) and Illumina® for the studentship supporting V.C (BB/I015477/1). The S.B. research group is supported by programme funding from Cancer Research UK and from the European Research Council and project funding from BBSRC

Whole genome experimental maps of DNA G-quadruplexes in multiple species.

Genomic maps of DNA G-quadruplexes (G4s) can help elucidate the roles that these secondary structures play in various organisms. Herein, we employ an improved version of a G-quadruplex sequencing method (G4-seq) to generate whole genome G4 maps for 12 species that include widely studied model organisms and also pathogens of clinical relevance. We identify G4 structures that form under physiological K+ conditions and also G4s that are stabilized by the G4-targeting small molecule pyridostatin (PDS). We discuss the various structural features of the experimentally observed G-quadruplexes (OQs), highlighting differences in their prevalence and enrichment across species. Our study describes diversity in sequence composition and genomic location for the OQs in the different species and reveals that the enrichment of OQs in gene promoters is particular to mammals such as mouse and human, among the species studied. The multi-species maps have been made publicly available as a resource to the research community. The maps can serve as blueprints for biological experiments in those model organisms, where G4 structures may play a role.The S.B. research group is supported by programme grant funding from Cancer Research UK (C9681/A18618), European Research Council Advanced Grant No. 339778, a Wellcome Trust Senior Investigator Award (grant 209441/z/17/z) and by core funding from Cancer Research UK (C14303/A17197). We are grateful to the Biotechnology and Biological Sciences Research Council (BBSRC) and Illumina for the CASE studentship supporting V.S.C. (BB/I015477/1)

Identification of Differential Gene Expression in Brassica rapa Nectaries through Expressed Sequence Tag Analysis

BACKGROUND: Nectaries are the floral organs responsible for the synthesis and secretion of nectar. Despite their central roles in pollination biology, very little is understood about the molecular mechanisms underlying nectar production. This project was undertaken to identify genes potentially involved in mediating nectary form and function in Brassica rapa. METHODOLOGY AND PRINCIPAL FINDINGS: Four cDNA libraries were created using RNA isolated from the median and lateral nectaries of B. rapa flowers, with one normalized and one non-normalized library being generated from each tissue. Approximately 3,000 clones from each library were randomly sequenced from the 5' end to generate a total of 11,101 high quality expressed sequence tags (ESTs). Sequence assembly of all ESTs together allowed the identification of 1,453 contigs and 4,403 singleton sequences, with the Basic Localized Alignment Search Tool (BLAST) being used to identify 4,138 presumptive orthologs to Arabidopsis thaliana genes. Several genes differentially expressed between median and lateral nectaries were initially identified based upon the number of BLAST hits represented by independent ESTs, and later confirmed via reverse transcription polymerase chain reaction (RT PCR). RT PCR was also used to verify the expression patterns of eight putative orthologs to known Arabidopsis nectary-enriched genes. CONCLUSIONS/SIGNIFICANCE: This work provided a snapshot of gene expression in actively secreting B. rapa nectaries, and also allowed the identification of differential gene expression between median and lateral nectaries. Moreover, 207 orthologs to known nectary-enriched genes from Arabidopsis were identified through this analysis. The results suggest that genes involved in nectar production are conserved amongst the Brassicaceae, and also supply clones and sequence information that can be used to probe nectary function in B. rapa

Chemistry in Infrared Dark Cloud Clumps: a Molecular Line Survey at 3 mm

We have observed 37 Infrared Dark Clouds (IRDCs), containing a total of 159 clumps, in high-density molecular tracers at 3 mm using the 22-meter ATNF Mopra Telescope located in Australia. After determining kinematic distances, we eliminated clumps that are not located in IRDCs and clumps with a separation between them of less than one Mopra beam. Our final sample consists of 92 IRDC clumps. The most commonly detected molecular lines are (detection rates higher than 8%): N2H+, HNC, HN13C, HCO+, H13CO+, HCN, C2H, HC3N, HNCO, and SiO. We investigate the behavior of the different molecular tracers and look for chemical variations as a function of an evolutionary sequence based on Spitzer IRAC and MIPS emission. We find that the molecular tracers behave differently through the evolutionary sequence and some of them can be used to yield useful relative age information. The presence of HNC and N2H+ lines do not depend on the star formation activity. On the other hand, HC3N, HNCO, and SiO are predominantly detected in later stages of evolution. Optical depth calculations show that in IRDC clumps the N2H+ line is optically thin, the C2H line is moderately optically thick, and HNC and HCO+ are optically thick. The HCN hyperfine transitions are blended, and, in addition, show self-absorbed line profiles and extended wing emission. These factors combined prevent the use of HCN hyperfine transitions for the calculation of physical parameters. Total column densities of the different molecules, except C2H, increase with the evolutionary stage of the clumps. Molecular abundances increase with the evolutionary stage for N2H+ and HCO+. The N2H+/HCO+ and N2H+/HNC abudance ratios act as chemical clocks, increasing with the evolution of the clumps.Comment: Accepted to ApJ. 29 page

Optimized survey design for electrical resistivity tomography: combined optimization of measurement configuration and electrode placement

Within geoelectrical imaging, the choice of measurement configurations and electrode locations is known to control the image resolution. Previous work has shown that optimized survey designs can provide a model resolution that is superior to standard survey designs. This paper demonstrates a methodology to optimize resolution within a target area, while limiting the number of required electrodes, thereby selecting optimal electrode locations. This is achieved by extending previous work on the ‘Compare-R’ algorithm, which by calculating updates to the resolution matrix optimizes the model resolution in a target area. Here, an additional weighting factor is introduced that allows to preferentially adding measurement configurations that can be acquired on a given set of electrodes. The performance of the optimization is tested on two synthetic examples and verified with a laboratory study. The effect of the weighting factor is investigated using an acquisition layout comprising a single line of electrodes. The results show that an increasing weight decreases the area of improved resolution, but leads to a smaller number of electrode positions. Imaging results superior to a standard survey design were achieved using 56 per cent fewer electrodes. The performance was also tested on a 3-D acquisition grid, where superior resolution within a target at the base of an embankment was achieved using 22 per cent fewer electrodes than a comparable standard survey. The effect of the underlying resistivity distribution on the performance of the optimization was investigated and it was shown that even strong resistivity contrasts only have minor impact. The synthetic results were verified in a laboratory tank experiment, where notable image improvements were achieved. This work shows that optimized surveys can be designed that have a resolution superior to standard survey designs, while requiring significantly fewer electrodes. This methodology thereby provides a means for improving the efficiency of geoelectrical imaging

Rucaparib maintenance treatment for recurrent ovarian carcinoma after response to platinum therapy (ARIEL3): a randomised, double-blind, placebo-controlled, phase 3 trial

Background: Rucaparib, a poly(ADP-ribose) polymerase inhibitor, has anticancer activity in recurrent ovarian carcinoma harbouring a BRCA mutation or high percentage of genome-wide loss of heterozygosity. In this trial we assessed rucaparib versus placebo after response to second-line or later platinum-based chemotherapy in patients with high-grade, recurrent, platinum-sensitive ovarian carcinoma. Methods: In this randomised, double-blind, placebo-controlled, phase 3 trial, we recruited patients from 87 hospitals and cancer centres across 11 countries. Eligible patients were aged 18 years or older, had a platinum-sensitive, high-grade serous or endometrioid ovarian, primary peritoneal, or fallopian tube carcinoma, had received at least two previous platinum-based chemotherapy regimens, had achieved complete or partial response to their last platinum-based regimen, had a cancer antigen 125 concentration of less than the upper limit of normal, had a performance status of 0–1, and had adequate organ function. Patients were ineligible if they had symptomatic or untreated central nervous system metastases, had received anticancer therapy 14 days or fewer before starting the study, or had received previous treatment with a poly(ADP-ribose) polymerase inhibitor. We randomly allocated patients 2:1 to receive oral rucaparib 600 mg twice daily or placebo in 28 day cycles using a computer-generated sequence (block size of six, stratified by homologous recombination repair gene mutation status, progression-free interval after the penultimate platinum-based regimen, and best response to the most recent platinum-based regimen). Patients, investigators, site staff, assessors, and the funder were masked to assignments. The primary outcome was investigator-assessed progression-free survival evaluated with use of an ordered step-down procedure for three nested cohorts: patients with BRCA mutations (carcinoma associated with deleterious germline or somatic BRCA mutations), patients with homologous recombination deficiencies (BRCA mutant or BRCA wild-type and high loss of heterozygosity), and the intention-to-treat population, assessed at screening and every 12 weeks thereafter. This trial is registered with ClinicalTrials.gov, number NCT01968213; enrolment is complete. Findings: Between April 7, 2014, and July 19, 2016, we randomly allocated 564 patients: 375 (66%) to rucaparib and 189 (34%) to placebo. Median progression-free survival in patients with a BRCA-mutant carcinoma was 16·6 months (95% CI 13·4–22·9; 130 [35%] patients) in the rucaparib group versus 5·4 months (3·4–6·7; 66 [35%] patients) in the placebo group (hazard ratio 0·23 [95% CI 0·16–0·34]; p<0·0001). In patients with a homologous recombination deficient carcinoma (236 [63%] vs 118 [62%]), it was 13·6 months (10·9–16·2) versus 5·4 months (5·1–5·6; 0·32 [0·24–0·42]; p<0·0001). In the intention-to-treat population, it was 10·8 months (8·3–11·4) versus 5·4 months (5·3–5·5; 0·36 [0·30–0·45]; p<0·0001). Treatment-emergent adverse events of grade 3 or higher in the safety population (372 [99%] patients in the rucaparib group vs 189 [100%] in the placebo group) were reported in 209 (56%) patients in the rucaparib group versus 28 (15%) in the placebo group, the most common of which were anaemia or decreased haemoglobin concentration (70 [19%] vs one [1%]) and increased alanine or aspartate aminotransferase concentration (39 [10%] vs none). Interpretation: Across all primary analysis groups, rucaparib significantly improved progression-free survival in patients with platinum-sensitive ovarian cancer who had achieved a response to platinum-based chemotherapy. ARIEL3 provides further evidence that use of a poly(ADP-ribose) polymerase inhibitor in the maintenance treatment setting versus placebo could be considered a new standard of care for women with platinum-sensitive ovarian cancer following a complete or partial response to second-line or later platinum-based chemotherapy. Funding: Clovis Oncology