A mutate-and-map protocol for inferring base pairs in structured RNA

Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resolution and used to constrain structural modeling. This experimental framework has been extensively revisited in the past decade with new strategies for high-throughput read-outs, chemical modification, and rapid data analysis. Recently, we have coupled the technique to high-throughput mutagenesis. Point mutations of a base-paired nucleotide can lead to exposure of not only that nucleotide but also its interaction partner. Carrying out the mutation and mapping for the entire system gives an experimental approximation of the molecules contact map. Here, we give our in-house protocol for this mutate-and-map strategy, based on 96-well capillary electrophoresis, and we provide practical tips on interpreting the data to infer nucleic acid structure.Comment: 22 pages, 5 figure

Virtual finger boosts three-dimensional imaging and microsurgery as well as terabyte volume image visualization and analysis

Three-dimensional (3D) bioimaging, visualization and data analysis are in strong need of powerful 3D exploration techniques. We develop virtual finger (VF) to generate 3D curves, points and regions-of-interest in the 3D space of a volumetric image with a single finger operation, such as a computer mouse stroke, or click or zoom from the 2D-projection plane of an image as visualized with a computer. VF provides efficient methods for acquisition, visualization and analysis of 3D images for roundworm, fruitfly, dragonfly, mouse, rat and human. Specifically, VF enables instant 3D optical zoom-in imaging, 3D free-form optical microsurgery, and 3D visualization and annotation of terabytes of whole-brain image volumes. VF also leads to orders of magnitude better efficiency of automated 3D reconstruction of neurons and similar biostructures over our previous systems. We use VF to generate from images of 1,107 Drosophila GAL4 lines a projectome of a Drosophila brain. © 2014 Macmillan Publishers Limited. All rights reserved

Quantum corrections and black hole spectroscopy

In the work \cite{BRM,RBE}, black hole spectroscopy has been successfully reproduced in the tunneling picture. As a result, the derived entropy spectrum of black hole in different gravity (including Einstein's gravity, Einstein-Gauss-Bonnet gravity and Ho\v{r}ava-Lifshitz gravity) are all evenly spaced, sharing the same forms as $S_n=n$, where physical process is only confined in the semiclassical framework. However, the real physical picture should go beyond the semiclassical approximation. In this case, the physical quantities would undergo higher-order quantum corrections, whose effect on different gravity shares in different forms. Motivated by these facts, in this paper we aim to observe how quantum corrections affect black hole spectroscopy in different gravity. The result shows that, in the presence of higher-order quantum corrections, black hole spectroscopy in different gravity still shares the same form as $S_n=n$, further confirming the entropy quantum is universal in the sense that it is not only independent of black hole parameters, but also independent of higher-order quantum corrections. This is a desiring result for the forthcoming quantum gravity theory.Comment: 14 pages, no figure, use JHEP3.cls. to be published in JHE

Back reaction, emission spectrum and entropy spectroscopy

Recently, an interesting work, which reformulates the tunneling framework to directly produce the Hawking emission spectrum and entropy spectroscopy in the tunneling picture, has been received a broad attention. However, during the emission process, most related observations have not incorporated the effects of back reaction on the background spacetime, whose derivations are therefore not the desiring results for the real physical process. With this point as a central motivation, in this paper we suitably adapt the \emph{reformulated} tunneling framework so that it can well accommodate the effects of back reaction to produce the Hawking emission spectrum and entropy spectroscopy. Consequently, we interestingly find that, when back reaction is considered, the Parikh-Wilczek's outstanding observations that, an isolated radiating black hole has an unitary-evolving emission spectrum that is \emph{not} precisely thermal, but is related to the change of the Bekenstein-Hawking entropy, can also be reproduced in the reformulated tunneling framework, meanwhile the entropy spectrum has the same form as that without inclusion of back reaction, which demonstrates the entropy quantum is \emph{independent} of the effects of back reaction. As our final analysis, we concentrate on the issues of the black hole information, but \emph{unfortunately} find that, even including the effects of back reaction and higher-order quantum corrections, such tunneling formalism can still not provide a mechanism for preserving the black hole information.Comment: 16 pages, no figure, use JHEP3.cls. to be published in JHE

Perception of epidemic's related anxiety in the General French Population: a cross-sectional study in the Rhône-Alpes region

International audienceBackgroundTo efficiently plan appropriate public health interventions during possible epidemics, governments must take into consideration the following factors about the general population: their knowledge of epidemics, their fears of and psychological responses to them, their level of compliance with government measures and their communities' trusted sources of information. However, such surveys among the French general population are rare.MethodsA cross-sectional study was conducted in 2006 in a representative sample of 600 subjects living in the Rhône-Alpes region (south-east France) to investigate self-reported knowledge about infectious diseases and anxiety generated by epidemic risk with particular reference to avian influenza. Data on reactions to potentially new epidemics and the confidence level in various sources of information were also collected.ResultsRespondents were most knowledgeable about AIDS, followed by avian influenza. Overall, 75% of respondents had adequate knowledge of avian influenza. The percentage was even higher (88%) among inhabitants of the Ain district, where an avian influenza epidemic had previously been reported. However, 39% expressed anxiety about this disease. In total, 20% of respondents with knowledge about avian influenza stated that they had changed their behaviours during the epizooty. Epidemics were perceived as a real threat by 27% of respondents. In the event of a highly contagious outbreak, the majority of respondents said they would follow the advice given by authorities. The study population expressed a high level of confidence in physicians and scientists, but had strong reservations about politicians, deputies and the media.ConclusionsAlthough the survey was conducted only four months after the avian influenza outbreak, epidemics were not perceived as a major threat by the study population. The results showed that in the event of a highly infectious disease, the population would comply with advice given by public authorities

Genetic alterations on chromosome 17p associated with response to radiotherapy in bulky cervical cancer

Chromosome 17 alterations are found in more cancers than those of any other chromosome, and frequently involve the p53 gene on 17p13. The aim of this study was to identify the correlations between the presence of loss of heterozygosity (LOH) and microsatellite instability (MI) on chromosome 17p13 in patients with cervical cancer and the patients’ response to radiotherapy. A total of 50 patients were treated with definitive radiotherapy. We performed biopsies and took specimens from the tumour and venous blood of all patients. Tumour and normal DNAs were analysed by polymerase chain reaction for genetic losses and instability at three polymorphic microsatellite loci mapped to 17p13. Nineteen of the 50 tumours (38%) displayed a genetic alteration (GA) on 17p13, 16 (32%) were found to have LOH, and three (6%) showed MI. The sizes of the tumours of the GA-positive patients were significantly greater than those of the GA-negative patients (P = 0.009). The mean tumour diameter of all patients was 6 ± 2.4 cm. We divided the patients into those with tumours smaller than 6 cm in diameter (n = 26) and those with tumours equal to or greater than 6 cm in diameter (n = 24). The former group survived significantly longer compared to the latter group (P = 0.0002). Among the patients with < 6 cm tumours, all six GA-positive patients are alive with no evidence of disease (NED), whereas of the 20 GA-negative patients, 18 have NED and two are alive with disease (AWD) or suffered cancer-caused death (CD). Thus, there was no correlation between GA and radiotherapy response in the tumours smaller than 6 cm. However, among the patients with ≥ 6 cm tumours, two of the GA-positive patients have NED and 11 are AWD/CD, whereas seven of the GA-negative patients have NED and four are AWD/CD. Among the patients with ≥ 6 cm tumours, the response to radiotherapy of the GA-positive patients were significantly poorer than those of the GA-negative patients (P = 0.02). In addition, the GA-negative patients survived significantly longer compared to the GA-positive patients (P = 0.026). The results of this study suggest that GA increases with tumour growth. Improved success in the management of bulky cervical cancer requires a better understanding of its biological behaviour. © 1999 Cancer Research Campaig

Blue carbon stock of the Bangladesh Sundarban mangroves: what could be the scenario after a century?

The total blue carbon stock of the Bangladesh Sundarban mangroves was evaluated and the probable future status after a century was predicted based on the recent trend of changes in the last 30 years and implementing a hybrid model of Markov Chain and Cellular automata. At present 36.24 Tg C and 54.95 Tg C are stored in the above-ground and below-ground compartments respectively resulting in total blue carbon stock of 91.19 Tg C. According to the prediction 15.88 Tg C would be lost from this region by the year 2115. The low saline species composition classes dominated mainly by Heritiera spp. accounts for the major portion of the carbon sock at present (45.60 Tg C), while the highly saline regions stores only 14.90 Tg C. The prediction shows that after a hundred years almost 22.42 Tg C would be lost from the low saline regions accompanied by an increase of 8.20 Tg C in the high saline regions dominated mainly by Excoecaria sp. and Avicennia spp. The net carbon loss would be due to both mangrove area loss (~ 510 km2) and change in species composition leading to 58.28 Tg of potential CO2 emission within the year 2115

Studying the Underlying Event in Drell-Yan and High Transverse Momentum Jet Production at the Tevatron

We study the underlying event in proton-antiproton collisions by examining the behavior of charged particles (transverse momentum pT > 0.5 GeV/c, pseudorapidity |\eta| < 1) produced in association with large transverse momentum jets (~2.2 fb-1) or with Drell-Yan lepton-pairs (~2.7 fb-1) in the Z-boson mass region (70 < M(pair) < 110 GeV/c2) as measured by CDF at 1.96 TeV center-of-mass energy. We use the direction of the lepton-pair (in Drell-Yan production) or the leading jet (in high-pT jet production) in each event to define three regions of \eta-\phi space; toward, away, and transverse, where \phi is the azimuthal scattering angle. For Drell-Yan production (excluding the leptons) both the toward and transverse regions are very sensitive to the underlying event. In high-pT jet production the transverse region is very sensitive to the underlying event and is separated into a MAX and MIN transverse region, which helps separate the hard component (initial and final-state radiation) from the beam-beam remnant and multiple parton interaction components of the scattering. The data are corrected to the particle level to remove detector effects and are then compared with several QCD Monte-Carlo models. The goal of this analysis is to provide data that can be used to test and improve the QCD Monte-Carlo models of the underlying event that are used to simulate hadron-hadron collisions.Comment: Submitted to Phys.Rev.

Precision measurement of the top quark mass from dilepton events at CDF II

We report a measurement of the top quark mass, M_t, in the dilepton decay channel of $t\bar{t}\to b\ell'^{+}\nu_{\ell'}\bar{b}\ell^{-}\bar{\nu}_{\ell}$ using an integrated luminosity of 1.0 fb^{-1} of p\bar{p} collisions collected with the CDF II detector. We apply a method that convolutes a leading-order matrix element with detector resolution functions to form event-by-event likelihoods; we have enhanced the leading-order description to describe the effects of initial-state radiation. The joint likelihood is the product of the likelihoods from 78 candidate events in this sample, which yields a measurement of M_{t} = 164.5 \pm 3.9(\textrm{stat.}) \pm 3.9(\textrm{syst.}) \mathrm{GeV}/c^2, the most precise measurement of M_t in the dilepton channel.Comment: 7 pages, 2 figures, version includes changes made prior to publication by journa