Inferring DNA sequences from mechanical unzipping data: the large-bandwidth case

The complementary strands of DNA molecules can be separated when stretched apart by a force; the unzipping signal is correlated to the base content of the sequence but is affected by thermal and instrumental noise. We consider here the ideal case where opening events are known to a very good time resolution (very large bandwidth), and study how the sequence can be reconstructed from the unzipping data. Our approach relies on the use of statistical Bayesian inference and of Viterbi decoding algorithm. Performances are studied numerically on Monte Carlo generated data, and analytically. We show how multiple unzippings of the same molecule may be exploited to improve the quality of the prediction, and calculate analytically the number of required unzippings as a function of the bandwidth, the sequence content, the elasticity parameters of the unzipped strands

Impact of droughts on the carbon cycle in European vegetation : a probabilistic risk analysis using six vegetation models

Peer reviewedPublisher PD

Закономерности распределения аномальных концентраций гелия в палеозойских отложениях Донбасса

Підвищені концентрації гелію у вільних і розчинених газах у вугільно-породному масиві Донбасу приурочені до зон зчленування Донбасу з Приазовським і Воронезьким кристалічними масивами і Головної антикліналі. Диз'юнктивні тектонічні порушення глибокого закладення служили, ймовірно, шляхами транзиту гелію від кристалічних порід фундаменту в палеозойські відклади Донбасу, і підвищений вміст гелію може служити індикатором шляхів транзиту газів з глибоких горизонтів Донецького вугільного басейну.Elevated concentrations of helium in free and dissolved gases in coal-rock mass of the Donets Coal Basin are confined to the junction zones of the Donets Coal Basin with the Priazovie and Voronezh crystalline core-areas and Glavnaya (Principal) Anticline. Deep-laid disjunctive dislocations were probably the ways for transit of helium from crystalline basement rocks into Paleozoic deposits of the Basin. Elevated concentrations of helium can also serve as indicators of the ways for transit of gases from deep levels of the Donets Coal Basin

Mechanism of membrane fusion induced by vesicular stomatitis virus G protein

The glycoproteins (G proteins) of vesicular stomatitis virus (VSV) and related rhabdoviruses (e.g., rabies virus) mediate both cell attachment and membrane fusion. The reversibility of their fusogenic conformational transitions differentiates them from many other low-pH-induced viral fusion proteins. We report single-virion fusion experiments, using methods developed in previous publications to probe fusion of influenza and West Nile viruses. We show that a three-stage model fits VSV single-particle fusion kinetics: (i) reversible, pH-dependent, G-protein conformational change from the known prefusion conformation to an extended, monomeric intermediate; (ii) reversible trimerization and clustering of the G-protein fusion loops, leading to an extended intermediate that inserts the fusion loops into the target-cell membrane; and (iii) folding back of a cluster of extended trimers into their postfusion conformations, bringing together the viral and cellular membranes. From simulations of the kinetic data, we conclude that the critical number of G-protein trimers required to overcome membrane resistance is 3 to 5, within a contact zone between the virus and the target membrane of 30 to 50 trimers. This sequence of conformational events is similar to those shown to describe fusion by influenza virus hemagglutinin (a “class I” fusogen) and West Nile virus envelope protein (“class II”). Our study of VSV now extends this description to “class III” viral fusion proteins, showing that reversibility of the low-pH-induced transition and architectural differences in the fusion proteins themselves do not change the basic mechanism by which they catalyze membrane fusion

Prognostic value of patient-reported quality of life for survival in oesophagogastric cancer:Analysis from the population-based POCOP study

BACKGROUND: Accumulating evidence of trials demonstrates that patient-reported health-related quality of life (HRQoL) at diagnosis is prognostic for overall survival (OS) in oesophagogastric cancer. However, real-world data are lacking. Moreover, differences in disease stages and tumour-specific symptoms are usually not taken into consideration. The aim of this population-based study was to assess the prognostic value of HRQoL, including tumour-specific scales, on OS in patients with potentially curable and advanced oesophagogastric cancer. METHODS: Data were derived from the Netherlands Cancer Registry and the patient reported outcome registry (POCOP). Patients included in POCOP between 2016 and 2018 were stratified for potentially curable (cT1-4aNallM0) or advanced (cT4b or cM1) disease. HRQoL was measured with the EORTC QLQ-C30 and the tumour-specific OG25 module. Cox proportional hazards models assessed the impact of HRQoL, sociodemographic and clinical factors (including treatment) on OS. RESULTS: In total, 924 patients were included. Median OS was 38.9 months in potentially curable patients (n = 795) and 10.6 months in patients with advanced disease (n = 129). Global Health Status was independently associated with OS in potentially curable patients (HR 0.89, 99%CI 0.82-0.97), together with several other HRQoL items: appetite loss, dysphagia, eating restrictions, odynophagia, and body image. In advanced disease, the Summary Score was the strongest independent prognostic factor (HR 0.75, 99%CI 0.59-0.94), followed by fatigue, pain, insomnia and role functioning. CONCLUSION: In a real-world setting, HRQoL was prognostic for OS in patients with potentially curable and advanced oesophagogastric cancer. Several HRQoL domains, including the Summary Score and several OG25 items, could be used to develop or update prognostic models

Discovery of a bow shock around Vela X-1

We report the discovery of a symmetric bow shock around the well-known high-mass X-ray binary (HMXB) Vela X-1. Wind bow shocks are a ubiquitous phenomenon around OB-runaway stars, but now such a structure is found around a HMXB. The presence of a bow shock indicates that the system has a high (supersonic) velocity with respect to the interstellar medium. From the symmetry of the bow shock, the direction of motion and, moreover, the origin and age of the system can be derived. Our observation supports Blaauw's scenario for the formation of an OB-runaway star by the supernova explosion of the binary companion.Comment: 14 pages, latex (including style file), 3 postscript figures, ApJ Letters, in pres

Excitons in a Photosynthetic Light-Harvesting System: A Combined Molecular Dynamics/Quantum Chemistry and Polaron Model Study

The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with a novel approach which combines molecular dynamics (MD) simulations with quantum chemistry (QC) calculations. The MD simulations of an LH-II complex, solvated and embedded in a lipid bilayer at physiological conditions (with total system size of 87,055 atoms) revealed a pathway of a water molecule into the B800 binding site, as well as increased dimerization within the B850 BChl ring, as compared to the dimerization found for the crystal structure. The fluctuations of pigment (B850 BChl) excitation energies, as a function of time, were determined via ab initio QC calculations based on the geometries that emerged from the MD simulations. From the results of these calculations we constructed a time-dependent Hamiltonian of the B850 exciton system from which we determined the linear absorption spectrum. Finally, a polaron model is introduced to describe quantum mechanically both the excitonic and vibrational (phonon) degrees of freedom. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function are derived from the MD/QC simulations. It is demonstrated that, in the framework of the polaron model, the absorption spectrum of the B850 excitons can be calculated from the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined MD/QC simulations. The obtained result is in good agreement with the experimentally measured absorption spectrum.Comment: REVTeX3.1, 23 pages, 13 (EPS) figures included. A high quality PDF file of the paper is available at http://www.ks.uiuc.edu/Publications/Papers/PDF/DAMJ2001/DAMJ2001.pd

Probing Single-Electron Spin Decoherence in Quantum Dots using Charged Excitons

We propose to use optical detection of magnetic resonance (ODMR) to measure the decoherence time T_{2} of a single electron spin in a semiconductor quantum dot. The electron is in one of the spin 1/2 states and a circularly polarized laser can only create an optical excitation for one of the electron spin states due to Pauli blocking. An applied electron spin resonance (ESR) field leads to Rabi spin flips and thus to a modulation of the photoluminescence or, alternatively, of the photocurrent. This allows one to measure the ESR linewidth and the coherent Rabi oscillations, from which the electron spin decoherence can be determined. We study different possible schemes for such an ODMR setup, including cw or pulsed laser excitation.Comment: 8 pages, 7 figures. Proceedings of the PASPS3 conference, Santa Barbara, CA (USA). To appear in the Journal of Superconductivit

Cutoff value determines the performance of a semi-quantitative immunochemical faecal occult blood test in a colorectal cancer screening programme

BACKGROUND: The cutoff of semi-quantitative immunochemical faecal occult blood tests (iFOBTs) influences colonoscopy referrals and detection rates. We studied the performance of an iFOBT (OC-Sensor) in colorectal cancer (CRC) screening at different cutoffs. METHODS: Dutch screening participants, 50-75 years of age, with average CRC risk and an iFOBT value >or=50 ng ml(-1) were offered colonoscopy. The detection rate was the percentage of participants with CRC or advanced adenomas (>or=10 mm, >or=20% villous, high-grade dysplasia). The number needed to scope (NNTScope) was the number of colonoscopies to be carried out to find one person with CRC or advanced adenomas. RESULTS: iFOBT values >or=50 ng ml(-1) were detected in 526 of 6157 participants (8.5%) and 428 (81%) underwent colonoscopy. The detection rate for advanced lesions (28 CRC and 161 with advanced adenomas) was 3.1% (95% confidence interval: 2.6-3.5%) and the NNTScope was 2.3. At 75 ng ml(-1), the detection rate was 2.7%, the NNTScope was 2.0 and the CRC miss rate compared with 50 ng ml(-1) was <5% (N=1). At 100 ng ml(-1), the detection rate was 2.4% and the NNTScope was <2. Compared with 50 ng ml(-1), up to 200 ng ml(-1) CRC miss rates remained at 16% (N=4). CONCLUSIONS: Cutoffs below the standard 100 ng ml(-1) resulted in not only higher detection rates of advanced lesions but also more colonoscopies. With sufficient capacity, 75 ng ml(-1) might be advised; if not, up to 200 ng ml(-1) CRC miss rates are acceptable compared with the decrease in performed colonoscopies