A universally applicable method of operon map prediction on minimally annotated genomes using conserved genomic context.

An important step in understanding the regulation of a prokaryotic genome is the generation of its transcription unit map. The current strongest operon predictor depends on the distributions of intergenic distances (IGD) separating adjacent genes within and between operons. Unfortunately, experimental data on these distance distributions are limited to Escherichia coli and Bacillus subtilis. We suggest a new graph algorithmic approach based on comparative genomics to identify clusters of conserved genes independent of IGD and conservation of gene order. As a consequence, distance distributions of operon pairs for any arbitrary prokaryotic genome can be inferred. For E.coli, the algorithm predicts 854 conserved adjacent pairs with a precision of 85%. The IGD distribution for these pairs is virtually identical to the E.coli operon pair distribution. Statistical analysis of the predicted pair IGD distribution allows estimation of a genome-specific operon IGD cut-off, obviating the requirement for a training set in IGD-based operon prediction. We apply the method to a representative set of eight genomes, and show that these genome-specific IGD distributions differ considerably from each other and from the distribution in E.coli

Solar Neutron Events of October-November 2003

During the period when the Sun was intensely active on October-November 2003, two remarkable solar neutron events were observed by the ground-based neutron monitors. On October 28, 2003, in association with an X17.2 large flare, solar neutrons were detected with high statistical significance (6.4 sigma) by the neutron monitor at Tsumeb, Namibia. On November 4, 2003, in association with an X28 class flare, relativistic solar neutrons were observed by the neutron monitors at Haleakala in Hawaii and Mexico City, and by the solar neutron telescope at Mauna Kea in Hawaii simultaneously. Clear excesses were observed at the same time by these detectors, with the significance calculated as 7.5 sigma for Haleakala, and 5.2 sigma for Mexico City. The detector onboard the INTEGRAL satellite observed a high flux of hard X-rays and gamma-rays at the same time in these events. By using the time profiles of the gamma-ray lines, we can explain the time profile of the neutron monitor. It appears that neutrons were produced at the same time as the gamma-ray emission.Comment: 35 pages, 21 figures, accepted for publication in Ap

Anomalous strength of membranes with elastic ridges

We report on a simulational study of the compression and buckling of elastic ridges formed by joining the boundary of a flat sheet to itself. Such ridges store energy anomalously: their resting energy scales as the linear size of the sheet to the 1/3 power. We find that the energy required to buckle such a ridge is a fixed multiple of the resting energy. Thus thin sheets with elastic ridges such as crumpled sheets are qualitatively stronger than smoothly bent sheets.Comment: 4 pages, REVTEX, 3 figure

Competition between normal and intruder states inside the "Island of Inversion"

The beta decay of the exotic 30Ne (N=20) is reported. For the first time, the low-energy level structure of the N=19, 30Na (Tz = 4), is obtained from beta-delayed gamma spectroscopy using fragment-beta-gamma-gamma coincidences. The level structure clearly displays "inversion", i.e., intruder states with mainly 2p2h configurations displacing the normal states to higher excitation energies. The good agreement in excitation energies and the weak and electromagnetic decay patterns with Monte Carlo Shell Model calculations with the SDPF-M interaction in the sdpf valence space illustrates the small d3/2 - f7/2 shell gap. The relative position of the "normal dominant" and "intruder dominant" excited states provides valuable information to understand better the N=20 shell gap.Comment: 4 pages, 5 figure

Hypovitaminosis D and cervical disk herniation among adults undergoing spine surgery

Study Design Single-center, retrospective study. Objective Suboptimal concentrations of vitamin D have been linked to hip and knee osteoarthritis in large, population-based cohort studies. We sought to examine the association of vitamin D levels with intervertebral disk disease. Methods From January 2010 through May 2011, 91 consecutive, eligible adult spine surgery patients who had undergone cervical magnetic resonance imaging (MRI) and preoperative serum 25-hydroxyvitamin D (s25D) measurement were retrospectively included. MRI was read for C2–T1 disk herniation and degeneration (grades I to V). Logistic regressions were performed. Results Compared with the 384 disks of nondeficient patients, 162 disks of vitamin D-deficient (< 20 ng/mL) patients were more frequently herniated (40% versus 27%, p = 0.004); deficiency was not predictive of individual disk grade (unadjusted odds ratio [uOR] = 0.98, p = 0.817). On regression analysis, deficiency was associated with increased number of herniations per patient (uOR = 2.17, 95% confidence interval [CI] = 1.22 to 3.87, p = 0.009; adjusted odds ratio [aOR] = 2.12, 95% CI = 1.11 to 4.03, p = 0.023). When disks were analyzed individually, and levels (e.g., C5 to C6), additionally controlled for, deficiency correlated with greater likelihood of herniation per disk (uOR = 1.81, 95% CI = 1.22 to 2.66, p = 0.003; aOR = 2.06, 95% CI = 1.25 to 3.41, p = 0.005). Conclusion Among adults undergoing spine surgery at our institution, vitamin D deficiency was associated with cervical disk herniation. Considering the current epidemics of vitamin D insufficiency and neck pain, further investigation is warranted, as these data were retrospectively collected and subject to sampling bias

The second ESGAR consensus statement on CT colonography

To update quality standards for CT colonography based on consensus among opinion leaders within the European Society of Gastrointestinal and Abdominal Radiology (ESGAR). A multinational European panel of nine members of the ESGAR CT colonography Working Group (representing six EU countries) used a modified Delphi process to rate their level of agreement on a variety of statements pertaining to the acquisition, interpretation and implementation of CT colonography. Four Delphi rounds were conducted, each at 2 months interval. The panel elaborated 86 statements. In the final round the panelists achieved complete consensus in 71 of 86 statements (82 %). Categories including the highest proportion of statements with excellent Cronbach's internal reliability were colon distension, scan parameters, use of intravenous contrast agents, general guidelines on patient preparation, role of CAD and lesion measurement. Lower internal reliability was achieved for the use of a rectal tube, spasmolytics, decubitus positioning and number of CT data acquisitions, faecal tagging, 2D vs. 3D reading, and reporting. The recommendations of the consensus should be useful for both the radiologist who is starting a CTC service and for those who have already implemented the technique but whose practice may need updating

An overview of the Upper Paleozoic-Mesozoic stratigraphy of the NE Atlantic region

This study describes the distribution and stratigraphic range of the Upper Paleozoic–Mesozoic succession in the NE Atlantic region, and is correlated between conjugate-margins and along the axis of the NE Atlantic rift system. The stratigraphic framework has yielded important new constraints on the timing and nature of sedimentary basin development in the NE Atlantic, with implications for rifting and the breakup of the Pangaean supercontinent. From a regional perspective, the Permian–Triassic succession records a northward transition from an arid interior to a passively-subsiding, mixed carbonate/siliciclastic shelf margin. A Late Permian–earliest Triassic rift pulse has regional expression in the stratigraphic record. A fragmentary paralic to shallow-marine Lower Jurassic succession reflects Early Jurassic thermal subsidence and mild extensional tectonism; this was interrupted by widespread Mid-Jurassic uplift and erosion, and followed by an intense phase of Late Jurassic rifting in some (but not all) parts of the NE Atlantic region. The Cretaceous succession is dominated by thick basinal-marine deposits, which accumulated within and along a broad zone of extension and subsidence between Rockall and NE Greenland. There is no evidence for a substantive and continuous rift system along the proto-NE Atlantic until the Late Cretaceous

Observation of Sommerfeld precursors on a fluid surface

We report the observation of two types of Sommerfeld precursors (or forerunners) on the surface of a layer of mercury. When the fluid depth increases, we observe a transition between these two precursor surface waves in good agreement with the predictions of asymptotic analysis. At depths thin enough compared to the capillary length, high frequency precursors propagate ahead of the ''main signal'' and their period and amplitude, measured at a fixed point, increase in time. For larger depths, low frequency ''precursors'' follow the main signal with decreasing period and amplitude. These behaviors are understood in the framework of the analysis first introduced for linear transient electromagnetic waves in a dielectric medium by Sommerfeld and Brillouin [1].Comment: to be published in Physical Review Letter