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Measuring the accuracy of genome-size multiple alignments
Amol Prakash, Martin Tompa
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-6-r124
Abstract: With the rapid sequencing of so many related genomes, comparative genomics has emerged as one of the most important areas of computational biology. The workhorse of comparative genomics is the multiple sequence alignment, particularly whole-genome multiple sequence alignments such as those provided by the UCSC Genome Browser [1]. These alignments are marvelous tools for anyone working in comparative genomics. More and more sophisticated analyses rely implicitly on the correctness of these alignments. For example, it is already standard practice to search for functional genomic elements (more precisely, those constrained by purifying selection) by scanning a whole-genome alignment, looking for regions that are better conserved across the species than expected [2-12].When such methods find surprisingly well conserved sites across all aligned species, that portion of the alignment is likely to be correct. Conversely, in regions where the sequences are misaligned, these methods may fail to find conserved sites that exist. Even the designers of the alignment algorithms and genome browsers would not claim that the alignments are correct at all sites across entire genomes. How can users decide which portions of the alignment are trustworthy and which portions less so, particularly in noncoding regions?We present a method to assess a whole-genome multiple sequence alignment, classifying it into well aligned and suspiciously aligned regions. Before carrying out any further analysis that relies on the alignment's correctness, such as those listed above, the user should be aware of possible misalignment in those regions classified as suspicious. In addition, efforts should be made to either realign the regions with suspicious alignments or increase the confidence in their current alignments by other evidence.Without any well established methodology for estimating the quality of the whole-genome alignments, scientists have either trusted the alignments completely or developed t
The Effect of Accompanying In Situ Ductal Carcinoma on Accuracy of Measuring Malignant Breast Tumor Size Using B-Mode Ultrasonography and Real-Time Sonoelastography  [PDF]
A. A. Soliman,S. Wojcinski,F. Degenhardt
International Journal of Breast Cancer , 2012, DOI: 10.1155/2012/376032
Abstract: Objectives. Clinical estimation of malignant breast tumor size is critical for preoperative planning and is crucial for following up the tumor’s response to the therapy in case she receives a neoadjuvant chemotharapy. Ductal carcinoma in situ (DCIS) accompanies about 25.4% of detected invasive breast cancers. The aim of this study was to examine the effect of the presence of DCIS on the accuracy of the ultrasonographic measuring malignant breast tumor size using B-mode and real time elastography. Materials and Methods. We recruited histologically confirmed breast cancer patients in a prospective observational study. Results. We recruited 50 breast cancer patients with a median age of 57.5 years. DCIS was confirmed to accompany 42% ( ?? = 2 1 ) of the cases. Tumor size estimation using B-mode sonography ( ?? < 0 . 0 0 1 ) as well as using real time elastography ( ?? < 0 . 0 0 1 ). was statistically significant correlated to the actual tumor size. Presence of DCIS in 42% of our recruited patients affected the tumor size estimation using both methods thus losing the correlation between both estimations ( ?? = 0 . 7 9 4 ). Conclusion. This study shows that the presence of DCIS significantly affects the accuracy of measuring the sizes of malignant breast tumors when using either B-mode ultrasonography or real time elastography. 1. Introduction Breast cancer is the most common cancer affecting women in Germany. With 58 thousand new cases every year, it is estimated that every tenth woman in Germany will get breast cancer by the age of 74 [1, 2]. That is why breast cancer diagnostic technology occupies a very important position in the scientific community. Clinical estimation of malignant breast tumor size is very important. Most importantly, it is critical for preoperative planning, for whether a patient will receive a mastectomy, or be treated using a breast conservation operation. Without an accurate estimation of tumor size, the preoperative decision can be wrong [3]. Moreover, if tumor sizes are incorrectly estimated, the rate of reoperation will increase, with its risks, or a small tumor-free resection margin may be left behind that can lead to increased rates of local recurrence [4]. With the numbers of patients receiving neoadjuvant chemotherapy for treatment of breast cancer currently increasing, sonographic estimation of tumor size is very important for setting up the initial treatment plan, and then for following up the tumor’s response to the therapy [5, 6]. Moreover, tumor size is one of the most important prognostic factors in breast cancer;
On measuring the size of nuclei of comets  [PDF]
S. N. Dolya
Physics , 2014,
Abstract: Possibilities of measuring the size of nuclei of comets hidden by dust clouds are discussed. To this end, the dust cloud should be irradiated with a flow of rods accelerated in a linear mass accelerator to the velocity six kilometers per second. Each rod should be equipped with a transmitter with a power of one microwatt, which is destroyed in a collision with a comet's nucleus, or continues to work if the rod passes through the dust cloud without collision. Radio signals are received by three independent ground stations. At a distance of one thousand kilometers from the nucleus of the comet the power of the received signals is ten to the minus seventeenth Watt power, the receiver noise power is ten to the minus twentieth Watt power.
Measuring the elements of the optical density matrix  [PDF]
K. L. Pregnell,D. T. Pegg
Physics , 2002, DOI: 10.1103/PhysRevA.66.013810
Abstract: Most methods for experimentally reconstructing the quantum state of light involve determining a quasiprobability distribution such as the Wigner function. In this paper we present a scheme for measuring individual density matrix elements in the photon number state representation. Remarkably, the scheme is simple, involving two beam splitters and a reference field in a coherent state.
Accuracy of Measuring Camera Position by Marker Observation  [PDF]
Vladimir A. Grishin
Journal of Software Engineering and Applications (JSEA) , 2010, DOI: 10.4236/jsea.2010.310107
Abstract: A lower bound to errors of measuring object position is constructed as a function of parameters of a monocular computer vision system (CVS) as well as of observation conditions and a shape of an observed marker. This bound justifies the specification of the CVS parameters and allows us to formulate constraints for an object trajectory based on required measurement accuracy. For making the measurement, the boundaries of marker image are used.
Investigation of correlation measuring method accuracy for two types of test signals
Vladimir GAVRILJUK,Roman RYBALKA,Victor BEZRUKOV
Transport Problems : an International Scientific Journal , 2008,
Abstract: On the base of developed computer simulation program the comparative investigations of correlation measuring method accuracy with two types of test signals have been provided.
On the Spectroscopic Method of Measuring the Size of the Semiconductor Nanocrystals  [PDF]
I. V. Beloussov,V. I. Pavlenko,I. I. Dobinda
Physics , 2014,
Abstract: The dependences of the fundamental transition on the semiconductor quantum dot size obtained experimentally at various temperatures using different measuring methods are analyzed and compared. The possibility to extrapolate the results for the case of arbitrary temperature is discussed.
Accuracy of Protein Size Estimates Based on Light Scattering Measurements  [PDF]
Ken Takeuchi, Yoichi Nakatani, Osamu Hisatomi
Open Journal of Biophysics (OJBIPHY) , 2014, DOI: 10.4236/ojbiphy.2014.42009
Abstract:
There are two types of light scattering measurements: static light scattering (SLS) and dynamic light scattering (DLS). The SLS method is used to estimate the molecular weight (MW) of particles by measuring the time-averaged intensity of light scattered by the particles, whereas the DLS method is used to estimate the diffusion coefficient of particles by observing the time-correlation of scattered light intensity. These techniques have recently been applied to the investigation of the aggregation, denaturation and folding, and complex formation of proteins in solution. However, the accuracy of protein size measurement by light scattering is poorly understood. In the present study, we carried out the size measurements of five globular proteins by SLS and DLS at a detection angle of 90 and compared these data to measurements made by size exclusion chromatography (SEC). The difference (%) between the MW estimated from each method and the MW calculated from the amino acid sequence (namely the calibration residual error) was regarded as an index of measurement accuracy. The averaged calibration residual errors were 5.2 and 4.7 for SEC and SLS measurements, respectively. For the DLS measurements, the extrapolation of the apparent hydrodynamic radii to a protein concentration of zero may effectively eliminate the interparticle and hydrodynamic interactions and significantly reduced the averaged calibration residual error to 4.8%. Our results suggested that the size of globular proteins can be estimated using light scattering measurements with an accuracy equivalent to that of SEC.
The Impact of Questionnaire Size on the Accuracy of the Rasch Measure
Silvia Golia
Journal of Applied Sciences , 2011,
Abstract: The study aims at evaluating the impact of the questionnaire size on the accuracy and stability of the Rasch measure. The Rasch measurement model is used to obtain a reliable and objective measurement of a latent trait of interest. A simulation study is performed in order to deal with the issue.
Diffracto-Astrometry measurements: accuracy of the measuring algorithm  [PDF]
A. Ruelas-Mayorga,L. J. Sanchez,J. Olivares,C. Allen,A. Poveda,R. Costero,A. Nigoche-Netro
Physics , 2011, DOI: 10.1086/662952
Abstract: We present a theoretical analysis of the measuring algorithm we use when applying the Diffracto-Astrometry technique to Hubble Space Telescope Wide Field Planetary Camera 2 (WFPC2) saturated stellar images. Theoretical Point Spread Functions (PSFs) were generated using the Tiny Tim software for the four CCDs in the WFPC2 and for some of the available filters. These images were then measured with our Diffracto-Astrometry measuring algorithm using only their diffraction pattern, and positions for the simulated PSFs on each generated CCD-frame were obtained. The measuring algorithm recovers the original positions reasonably well ($\pm 0.1\ \rm{to} \ \pm 0.4$ pixels). However, slight deviations from the original values are observed. These also vary with position over the entire surface of the CCD. We adjust the difference between the real and the measured position with a quadratic function of the coordinates. The transformation coefficients also present a slight correlation with the filter effective wavelength. Application of these transformation coefficients allows us to determine the position of a stellar image with a precision of a few hundredths of a pixel.
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