Amplified fragment length polymorphism genotyping of metronidazole-resistant Helicobacter pylori infecting dyspeptics in England

ObjectiveIntra-specific diversity of Helicobacter pylori infecting stomachs of different individuals was investigated by numerical analysis of amplified fragment length polymorphisms (AFLP), to determine the existence of clones within the strain population and the effect that antibiotic treatment, particularly with metronidazole (Mtz), had on the balance of types/subtypes present before and after treatment.MethodsThe 92 cultures studied comprised 89 single or multiple (pre- and post-treatment) isolates from gastric biopsies from 35 dyspeptic patients at two geographical locations in England, and three reference strains. HindIII restriction fragments tagged with specific adaptors were used as template DNA for AFLP. Patterns were coded in binary format according to deduced sizes of amplified fragments, and numerical analysis was performed.ResultsH. pylori isolated from different individuals were highly diverse (43 AFLP types) with a continuum of similarities that included three putative strain clusters at the 55% similarity level. Twelve sets each comprised identical isolates but subclonal variants with similarities of 82-99% coexisted in isolate sets from 19 patients. Seven sets contained strains with different AFLP types which for several corresponded with vacA/cagA genotypic differences. Mtz resistance was a feature of clonal as well as unrelated isolates.ConclusionsAFLP profiling was a robust, reproducible and highly discriminatory means of indexing H. pylori strain diversity, and the numerical analysis enabled clonal/subclonal variants infecting an individual to be defined and contrasted with the general species diversity. The majority (65%) of patients had co-infections with different strain types/subtypes but antibiotic treatment apparently did not markedly modify H. pylori population diversity in individual stomachs. Mtz sensitivity was generally associated with greater strain diversity as several subtypes often coexisted in sensitive pretreatment strain sets. In contrast, Mtz-resistant strain populations were less diverse, which was attributed to selection by previous exposure to nitroimidazoles in the same or a different host

Evidence for a three-nucleon-force effect in proton-deuteron elastic scattering

Developments in spin-polarized internal targets for storage rings have permitted measurements of 197 MeV polarized protons scattering from vector polarized deuterons. This work presents measurements of the polarization observables A_y, iT_11, and C_y,y in proton-deuteron elastic scattering. When compared to calculations with and without three-nucleon forces, the measurements indicate that three-nucleon forces make a significant contribution to the observables. This work indicates that three-body forces derived from static nuclear properties appear to be crucial to the description of dynamical properties.Comment: 8 pages 2 figures Latex, submitted to Phys. Rev. Letter

Contribution of nuclei accelerated by gamma-ray pulsars to cosmic rays in the Galaxy

We consider the galactic population of gamma-ray pulsars as possible sources of cosmic rays at and just above the ``knee'' in the observed cosmic ray spectrum at $10^{15}$--$10^{16}$ eV. We suggest that iron nuclei may be accelerated in the outer gaps of pulsars, and then suffer partial photo-disintegration in the non-thermal radiation fields of the outer gaps. As a result, protons, neutrons, and surviving heavier nuclei are injected into the expanding supernova remnant. We compute the spectra of nuclei escaping from supernova remnants into the interstellar medium, taking into account the observed population of radio pulsars. Our calculations, which include a realistic model for acceleration and propagation of nuclei in pulsar magnetospheres and supernova remnants, predict that heavy nuclei accelerated directly by gamma-ray pulsars could contribute about 20% of the observed cosmic rays in the knee region. Such a contribution of heavy nuclei to the cosmic ray spectrum at the knee can significantly increase the average value of $$ with increasing energy as is suggested by recent observations.Comment: 21 pages, 5 figures, accepted for publication in Astroparticle Physic

Real-time Classification of Vehicle Types within Infra-red Imagery

Real-time classification of vehicles into sub-category types poses a significant challenge within infra-red imagery due to the high levels of intra-class variation in thermal vehicle signatures caused by aspects of design, current operating duration and ambient thermal conditions. Despite these challenges, infra-red sensing offers significant generalized target object detection advantages in terms of all-weather operation and invariance to visual camouflage techniques. This work investigates the accuracy of a number of real-time object classification approaches for this task within the wider context of an existing initial object detection and tracking framework. Specifically we evaluate the use of traditional feature-driven bag of visual words and histogram of oriented gradient classification approaches against modern convolutional neural network architectures. Furthermore, we use classical photogrammetry, within the context of current target detection and classification techniques, as a means of approximating 3D target position within the scene based on this vehicle type classification. Based on photogrammetric estimation of target position, we then illustrate the use of regular Kalman filter based tracking operating on actual 3D vehicle trajectories. Results are presented using a conventional thermal-band infra-red (IR) sensor arrangement where targets are tracked over a range of evaluation scenarios

An entomocentric view of the Janzen-Connell hypothesis

In 1987, in the first issue of Conservation Biology, Edward O. Wilson wrote about the “little things that run the world” – the importance and conservation of insects (Wilson, 1987). Readers of Insect Conservation and Diversity will no doubt be very familiar with the concept. Sadly, however, this perception is not as widely shared among the rest of the scientific community as it should be, and insects are still comparatively neglected as a prime focus of scientific investigations

Searching for Gravitational Waves from the Inspiral of Precessing Binary Systems: Astrophysical Expectations and Detection Efficiency of "Spiky'' Templates

Relativistic spin-orbit and spin-spin couplings has been shown to modify the gravitational waveforms expected from inspiraling binaries with a black hole and a neutron star. As a result inspiral signals may be missed due to significant losses in signal-to-noise ratio, if precession effects are ignored in gravitational-wave searches. We examine the sensitivity of the anticipated loss of signal-to-noise ratio on two factors: the accuracy of the precessing waveforms adopted as the true signals and the expected distributions of spin-orbit tilt angles, given the current understanding of their physical origin. We find that the results obtained using signals generated by approximate techniques are in good agreement with the ones obtained by integrating the 2PN equations. This shows that a complete account of all high-order post-Newtonian effects is usually not necessary for the determination of detection efficiencies. Based on our current astrophysical expectations, large tilt angles are not favored and as a result the decrease in detection rate varies rather slowly with respect to the black hole spin magnitude and is within 20--30% of the maximum possible values.Comment: 7 fig., accepted by Phys. Rev. D Minor modification

A Mathematical Model of Liver Cell Aggregation In Vitro

The behavior of mammalian cells within three-dimensional structures is an area of intense biological research and underpins the efforts of tissue engineers to regenerate human tissues for clinical applications. In the particular case of hepatocytes (liver cells), the formation of spheroidal multicellular aggregates has been shown to improve cell viability and functionality compared to traditional monolayer culture techniques. We propose a simple mathematical model for the early stages of this aggregation process, when cell clusters form on the surface of the extracellular matrix (ECM) layer on which they are seeded. We focus on interactions between the cells and the viscoelastic ECM substrate. Governing equations for the cells, culture medium, and ECM are derived using the principles of mass and momentum balance. The model is then reduced to a system of four partial differential equations, which are investigated analytically and numerically. The model predicts that provided cells are seeded at a suitable density, aggregates with clearly defined boundaries and a spatially uniform cell density on the interior will form. While the mechanical properties of the ECM do not appear to have a significant effect, strong cell-ECM interactions can inhibit, or possibly prevent, the formation of aggregates. The paper concludes with a discussion of our key findings and suggestions for future work

Middle pleistocene glaciation in Patagonia dated by cosmogenic-nuclide measurements on outwash gravels

The well-preserved glacial record in Argentine Patagonia offers a ~ 1 Ma archive of terrestrial climate extremes in southern South America. These glacial deposits remain largely undated beyond the range of radiocarbon dating at ca. 40 ka. Dating old glacial deposits (> several 105 a) by cosmogenic surface exposure methods is problematic because of the uncertainty in moraine degradation and boulder erosion rates. Here, we show that cobbles on outwash terraces can reliably date ‘old’ glacial deposits in the Lago Pueyrredón valley, 47.5° S, Argentina. Favorable environmental conditions (e.g., aridity and strong winds) have enabled continuous surface exposure of cobbles and preservation of outwash terraces. The data demonstrate that nuclide inheritance is negligible and we therefore use the oldest surface cobbles to date the deposit. 10Be concentrations in outwash cobbles reveal a major glacial advance at ca. 260 ka, concurrent with Marine Isotope Stage 8 (MIS 8) and dust peaks in Antarctic ice cores. A 10Be concentration depth-profile in the outwash terrace supports the age and suggests a low terrace erosion rate of ca. 0.5 mm ka− 1. We compare these data to exposure ages obtained from associated moraines and find that surface boulders underestimate the age of the glaciation by ~ 100 ka; thus the oldest boulders in this area do not date closely moraine deposition. The 10Be concentration in moraine cobbles help to constrain moraine degradation rates. These data together with constraints from measured 26Al/10Be ratios suggest that all moraine boulders were likely exhumed after original deposition. We determine the local Last Glacial Maximum (LGM) occurred at ~ 27–25 ka, consistent with the maximum LGM in other parts of Patagonia

Split-off dimer defects on the Si(001)2x1 surface

Dimer vacancy (DV) defect complexes in the Si(001)2x1 surface were investigated using high-resolution scanning tunneling microscopy and first principles calculations. We find that under low bias filled-state tunneling conditions, isolated 'split-off' dimers in these defect complexes are imaged as pairs of protrusions while the surrounding Si surface dimers appear as the usual 'bean-shaped' protrusions. We attribute this to the formation of pi-bonds between the two atoms of the split-off dimer and second layer atoms, and present charge density plots to support this assignment. We observe a local brightness enhancement due to strain for different DV complexes and provide the first experimental confirmation of an earlier prediction that the 1+2-DV induces less surface strain than other DV complexes. Finally, we present a previously unreported triangular shaped split-off dimer defect complex that exists at SB-type step edges, and propose a structure for this defect involving a bound Si monomer.Comment: 8 pages, 7 figures, submitted to Phys. Rev.

Fatty acid metabolism in marine fish: Low activity of fatty acyl Δ5 desaturation in gilthead sea bream ( Sparus aurata ) cells

Marine fish are known to have an absolute dietary requirement for C20 and C22 highly unsaturated fatty acids. Previous studies using cultured cell lines indicated that underlying this requirement in marine fish was either a deficiency in fatty acyl Δ5 desaturase or C18-20 elongase activity. Recently, Ghioni et al. (Biochim. Biophys. Acta, 1437, 170-181, 1999) presented evidence that in turbot cells there was low activity of C18-20 elongase whereas Δ5 desaturase had high activity. In the present study, the fatty acid desaturase/elongase pathway was investigated in a cell line (SAF-1) from another carnivorous marine fish, sea bream. The metabolic conversions of a range of radiolabelled polyunsaturated fatty acids that comprised the direct substrates for Δ6 desaturase ([1-14C]18:2n-6 and [1-14C]18:3n-3), C18-20 elongase ([U-14C]18:4n-3), Δ5 desaturase ([1-14C]20:3n-6 and [U-14C]20:4n-3) and C20-22 elongase ([1-14C]20:4n-6 and [1-14C]20:5n-3) were utilized. The results showed that fatty acyl Δ6 desaturase in SAF-1 cells was highly active and there was substantial C18-20 elongase and C20-22 elongase activities. A deficiency in the desaturation/elongation pathway was clearly identified at the level of the fatty acyl Δ5 desaturase which was very low, particularly with 20:4n-3 as substrate. In comparison, the apparent activities of Δ6 desaturase, C18-20 elongase and C20-22 elongase were approximately 94-fold, 27-fold and 16-fold greater than that for Δ5 desaturase towards their respective n-3 polyunsaturated fatty acid substrates. The evidence obtained in the SAF-1 cell line is consistent with the dietary requirement for C20 and C22 highly unsaturated fatty acids in the marine fish, the sea bream, being primarily due to a deficiency in fatty acid Δ5 desaturase activity