345 research outputs found
Inferring DNA sequences from mechanical unzipping: an ideal-case study
We introduce and test a method to predict the sequence of DNA molecules from
in silico unzipping experiments. The method is based on Bayesian inference and
on the Viterbi decoding algorithm. The probability of misprediction decreases
exponentially with the number of unzippings, with a decay rate depending on the
applied force and the sequence content.Comment: Source as TeX file with ps figure
A glance into mthfr deficiency at a molecular level
MTHFR deficiency still deserves an investigation to associate the phenotype to protein structure variations. To this aim, considering the MTHFR wild type protein structure, with a catalytic and a regulatory domain and taking advantage of state‐of‐the‐art computational tools, we explore the properties of 72 missense variations known to be disease associated. By computing the thermodynamic ΔΔG change according to a consensus method that we recently introduced, we find that 61% of the disease‐related variations destabilize the protein, are present both in the catalytic and regulatory domain and correspond to known biochemical deficiencies. The propensity of solvent accessible residues to be involved in protein‐protein interaction sites indicates that most of the interacting residues are located in the regulatory domain, and that only three of them, located at the interface of the functional protein homodimer, are both disease‐related and destabilizing. Finally, we compute the protein architecture with Hidden Markov Models, one from Pfam for the catalytic domain and the second computed in house for the regulatory domain. We show that patterns of disease‐associated, physicochemical variation types, both in the catalytic and regulatory domains, are unique for the MTHFR deficiency when mapped into the protein architecture
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
Parylene C-based, breathable tattoo electrode for high-quality biopotential measurements
A breathable tattoo electrode for bio-potential recording based on a Parylene C nanofilm is presented in this study. The proposed approach allows for the fabrication of micro-perforated epidermal submicrometer-thick electrodes that conjugate the unobtrusiveness of Parylene C nanofilms and the very important feature of breathability. The electrodes were fully validated for electrocardiography (ECG) measurements showing performance comparable to that of conventional disposable gelled Ag/AgCl electrodes, with no visible negative effect on the skin even many hours after their application. This result introduces interesting perspectives in the field of epidermal electronics, particularly in applications where critical on-body measurements are involved
The X-Gamma Imaging Spectrometer (XGIS) onboard THESEUS
A compact and modular X and gamma-ray imaging spectrometer (XGIS) has been
designed as one of the instruments foreseen on-board the THESEUS mission
proposed in response to the ESA M5 call. The experiment envisages the use of
CsI scintillator bars read out at both ends by single-cell 25 mm 2 Silicon
Drift Detectors. Events absorbed in the Silicon layer (lower energy X rays) and
events absorbed in the scintillator crystal (higher energy X rays and
Gamma-rays) are discriminated using the on-board electronics. A coded mask
provides imaging capabilities at low energies, thus allowing a compact and
sensitive instrument in a wide energy band (~2 keV up to ~20 MeV). The
instrument design, expected performance and the characterization performed on a
series of laboratory prototypes are discussed.Comment: To be published in the Proceedings of the THESEUS Workshop 2017
(http://www.isdc.unige.ch/theseus/workshop2017.html), Journal of the Italian
Astronomical Society (Mem.SAIt), Editors L. Amati, E. Bozzo, M. Della Valle,
D. Gotz, P. O'Brien. Details on the THESEUS mission concept can be found in
the white paper Amati et al. 2017 (arXiv:171004638) and Stratta et al. 2017
(arXiv:1712.08153
Development and tests of a new prototype detector for the XAFS beamline at Elettra Synchrotron in Trieste
The XAFS beamline at Elettra Synchrotron in Trieste combines X-ray absorption
spectroscopy and X-ray diffraction to provide chemically specific structural
information of materials. It operates in the energy range 2.4-27 keV by using a
silicon double reflection Bragg monochromator. The fluorescence measurement is
performed in place of the absorption spectroscopy when the sample transparency
is too low for transmission measurements or the element to study is too diluted
in the sample. We report on the development and on the preliminary tests of a
new prototype detector based on Silicon Drift Detectors technology and the
SIRIO ultra low noise front-end ASIC. The new system will be able to reduce
drastically the time needed to perform fluorescence measurements, while keeping
a short dead time and maintaining an adequate energy resolution to perform
spectroscopy. The custom-made silicon sensor and the electronics are designed
specifically for the beamline requirements.Comment: Proceeding of the 6YRM 12th-14th Oct 2015 - L'Aquila (Italy).
Accepted for publication on Journal of Physics: Conference Serie
LOFT - a Large Observatory For x-ray Timing
The high time resolution observations of the X-ray sky hold the key to a
number of diagnostics of fundamental physics, some of which are unaccessible to
other types of investigations, such as those based on imaging and spectroscopy.
Revealing strong gravitational field effects, measuring the mass and spin of
black holes and the equation of state of ultradense matter are among the goals
of such observations. At present prospects for future, non-focused X-ray timing
experiments following the exciting age of RXTE/PCA are uncertain. Technological
limitations are unavoidably faced in the conception and development of
experiments with effective area of several square meters, as needed in order to
meet the scientific requirements. We are developing large-area monolithic
Silicon Drift Detectors offering high time and energy resolution at room
temperature, which require modest resources and operation complexity (e.g.,
read-out) per unit area. Based on the properties of the detector and read-out
electronics that we measured in the lab, we developed a realistic concept for a
very large effective area mission devoted to X-ray timing in the 2-30 keV
energy range. We show that effective areas in the range of 10-15 square meters
are within reach, by using a conventional spacecraft platform and launcher of
the small-medium class.Comment: 13 pages, 8 figures, 1 table, Proceedings of SPIE Vol. 7732, Paper
No. 7732-66, 201
Silicon strip detectors for two-dimensional soft X-ray imaging at normal incidence
A simple prototype system for static two-dimensional soft X-ray imaging using silicon microstrip detectors irradiated at normal incidence is presented. Radiation sensors consist of single-sided silicon detectors made from 300 mum thick wafers, read by RX64 ASICs. Data acquisition and control is performed by a Windows PC workstation running dedicated LabVIEW routines, connected to the sensors through a PCI-DIO-96 interface. Two-dimensional images are obtained by scanning a lead collimator with a thin slit perpendicular to the strip axis, along the whole detector size; the several strip profiles (slices) taken at each position are then put together to form a planar image. Preliminary results are presented, illustrating the high-resolution imaging capabilities of the system with soft X-rays. (C) 2003 Elsevier B.V. All rights reserved.info:eu-repo/semantics/publishedVersio
Steps towards the hyperfine splitting measurement of the muonic hydrogen ground state: pulsed muon beam and detection system characterization
The high precision measurement of the hyperfine splitting of the
muonic-hydrogen atom ground state with pulsed and intense muon beam requires
careful technological choices both in the construction of a gas target and of
the detectors. In June 2014, the pressurized gas target of the FAMU experiment
was exposed to the low energy pulsed muon beam at the RIKEN RAL muon facility.
The objectives of the test were the characterization of the target, the
hodoscope and the X-ray detectors. The apparatus consisted of a beam hodoscope
and X-rays detectors made with high purity Germanium and Lanthanum Bromide
crystals. In this paper the experimental setup is described and the results of
the detector characterization are presented.Comment: 22 pages, 14 figures, published and open access on JINS
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