Quantitative Comparison of ChIP-Seq Data Sets Using MAnorm

Author(s):  
Zhen Shao ◽  
Yijing Zhang
2019 ◽  
Author(s):  
Ketan Khare ◽  
Frederick R. Phelan Jr.

<a></a><a>Quantitative comparison of atomistic simulations with experiment for glass-forming materials is made difficult by the vast mismatch between computationally and experimentally accessible timescales. Recently, we presented results for an epoxy network showing that the computation of specific volume vs. temperature as a function of cooling rate in conjunction with the time–temperature superposition principle (TTSP) enables direct quantitative comparison of simulation with experiment. Here, we follow-up and present results for the translational dynamics of the same material over a temperature range from the rubbery to the glassy state. Using TTSP, we obtain results for translational dynamics out to 10<sup>9</sup> s in TTSP reduced time – a macroscopic timescale. Further, we show that the mean squared displacement (MSD) trends of the network atoms can be collapsed onto a master curve at a reference temperature. The computational master curve is compared with the experimental master curve of the creep compliance for the same network using literature data. We find that the temporal features of the two data sets can be quantitatively compared providing an integrated view relating molecular level dynamics to the macroscopic thermophysical measurement. The time-shift factors needed for the superposition also show excellent agreement with experiment further establishing the veracity of the approach</a>.


Paleobiology ◽  
2015 ◽  
Vol 41 (4) ◽  
pp. 640-660 ◽  
Author(s):  
Sam M. Slater ◽  
Charles H. Wellman

AbstractDetailed quantitative data has previously been collected from plant megafossil assemblages from a Middle Jurassic (Aalenian) plant bed from Hasty Bank, North Yorkshire, UK. We conducted a similar analysis of palynological dispersed sporomorph (spore and pollen) assemblages collected from the same section using the same sampling regime: 67 sporomorph taxa were recorded from 50 samples taken at 10 cm intervals through the plant bed. Basic palynofacies analysis was also undertaken on each sample. Both dispersed sporomorph and plant megafossil assemblages display consistent changes in composition, diversity (richness), and abundance through time. However, the dispersed sporomorph and plant megafossil records provide conflicting evidence for the nature of parent vegetation. Specifically, conifers and ferns are underrepresented in plant megafossil assemblages, bryophytes and lycopsids are represented only in sporomorph assemblages, and sphenophytes, pteridosperms, Caytoniales, Cycadales, Ginkgoales and Bennettitales are comparatively underrepresented in sporomorph assemblages. Combined multivariate analysis (correspondence analysis and nonmetric multidimensional scaling) of sporomorph occurrence/abundance data demonstrates that temporal variation in sporomorph assemblages is the result of depositional change through the plant bed. The reproductive strategies of parent plants are considered to be a principal factor in shaping many of the major abundance and diversity irregularities between dispersed sporomorph and plant megafossil data sets that seemingly reflects different parent vegetation. Preferential occurrence/preservation of sporomorphs and equivalent parent plants is a consequence of a complex array of biological, ecological, geographical, taphonomic, and depositional factors that act inconsistently between and within fossil assemblages, which results in notable discrepancies between data sets.


2012 ◽  
Vol 23 (4) ◽  
pp. 509-532 ◽  
Author(s):  
Amber M. VanDerwarker ◽  
Robert P. Kruger

AbstractThis article presents an archaeobotanical analysis from the site of San Carlos, a small Early/Middle Formative period homestead situated in the Coatzacoalcos River basin in the southern Veracruz lowlands, approximately 9 km southeast of San Lorenzo. Although archaeobotanical data from the Olmec heartland have become more widely reported in recent years, we still lack sufficient data to capture regional and temporal variation in plant foodways. Thus, we report the macrobotanical data from San Carlos and provide a quantitative comparison with existing data sets from other southern Veracruz sites with Early and Middle Formative components (La Joya and Tres Zapotes). Comparative analysis reveals that these three sites vary dramatically in terms of the ubiquity and abundance of maize, in addition to the frequencies of different fruit types. We interpret these differences in terms of (1) settlement location with respect to geographical positioning in terms of access to riverine wetlands and their resources and (2) their association with areas of developing sociopolitical power structures.


2019 ◽  
Author(s):  
Ketan Khare ◽  
Frederick R. Phelan Jr.

<a></a><a>Quantitative comparison of atomistic simulations with experiment for glass-forming materials is made difficult by the vast mismatch between computationally and experimentally accessible timescales. Recently, we presented results for an epoxy network showing that the computation of specific volume vs. temperature as a function of cooling rate in conjunction with the time–temperature superposition principle (TTSP) enables direct quantitative comparison of simulation with experiment. Here, we follow-up and present results for the translational dynamics of the same material over a temperature range from the rubbery to the glassy state. Using TTSP, we obtain results for translational dynamics out to 10<sup>9</sup> s in TTSP reduced time – a macroscopic timescale. Further, we show that the mean squared displacement (MSD) trends of the network atoms can be collapsed onto a master curve at a reference temperature. The computational master curve is compared with the experimental master curve of the creep compliance for the same network using literature data. We find that the temporal features of the two data sets can be quantitatively compared providing an integrated view relating molecular level dynamics to the macroscopic thermophysical measurement. The time-shift factors needed for the superposition also show excellent agreement with experiment further establishing the veracity of the approach</a>.


Neurosurgery ◽  
2008 ◽  
Vol 62 (suppl_5) ◽  
pp. A44-A52 ◽  
Author(s):  
Klaus D. Hamm ◽  
Joachim Klisch ◽  
Gunnar Surber ◽  
Gabriele Kleinert ◽  
Cornelia Eger ◽  
...  

ABSTRACT OBJECTIVE Radiosurgery can be considered a well-established option for the treatment of arteriovenous malformations (AVMs). The exact application of the therapeutic dose is based on the availability of imaging data sets with superior image quality that can be superimposed using an image fusion algorithm. For follow-up studies, the quantitative comparison of the respective image data sets also plays an important role. Until now, digital subtraction angiography (DSA) has been a mandatory tool for treatment planning and follow-up procedures. The aim of this study was to investigate whether a suitable computed tomographic (CT) and/or magnetic resonance (MR) angiography procedure can replace DSA and, if so, in which cases. METHODS For 34 AVM patients, various MR data sets were used together with the stereotactically localized CT and DSA data sets for treatment planning. To define the AVM nidus precisely, all available MR data sets were fused onto the CT data set by the use of an automatic image fusion algorithm. The nidus was outlined in both localized DSA projections, resulting in the DSA target volume. Subsequently, the DSA target volume was adapted by inclusion of the available CT/MR data sets (localized and/or fused, slice by slice), resulting in the final target volume. Finally, both volumes were compared and analyzed. For precise comparison purposes, all available digital follow-up studies were fused. RESULTS In all cases, the thin-slice MR data sets (1-mm slice width) that included T1-weighted series and time of flight angiographies have been precisely fused onto the stereotactically localized treatment planning CT. The final target volume was compared with the DSA target volume as follows. In 19 cases, the final target volume was larger than the DSA target volume; in six cases, it was smaller; and in five cases, it was approximately equal. The difference was significant (Wilcoxon test, difference &lt;0.0001; t test, t = 3.01; P &gt; 0.005). In four cases, outlining the AVM was not possible without DSA. In five patients, a two- or three-vessel DSA was needed because there were different AVM compartments. In cases in which a previous partial embolization had been undergone by the patient, the use of superimposed CT sets with and without contrast medium was important to define the completely embolized partial volumes that were not subject to treatment. The inclusion of the DSA images enabled a better identification of those arterialized veins that did not belong to the nidus. In six cases, the follow-up MR studies showed contrast enhancements overlapping the AVM nidus as a result of brain-blood barrier disturbances (T1-weighted series with contrast). In seven cases, perifocal reactions were primarily observed (T2-weighted series) 12 months after treatment with rather low clinical relevance. CONCLUSION By integrating all available imaging modalities, the exact three-dimensional definition of the AVM nidus was safely realized for all patients. Stereotactic DSA data acquisition remains a crucial tool for safe nidus definition in radiosurgery treatment planning and cannot, therefore, be discarded at present. It is recommended that a quantitative comparison of all MR follow-up studies be established.


2012 ◽  
Vol 13 (3) ◽  
pp. R16 ◽  
Author(s):  
Zhen Shao ◽  
Yijing Zhang ◽  
Guo-Cheng Yuan ◽  
Stuart H Orkin ◽  
David J Waxman

Author(s):  
P.R. Smith ◽  
W.E. Fowler ◽  
U. Aebi

An understanding of the specific interactions of actin with regulatory proteins has been limited by the lack of information about the structure of the actin filament. Molecular actin has been studied in actin-DNase I complexes by single crystal X-ray analysis, to a resolution of about 0.6nm, and in the electron microscope where two dimensional actin sheets have been reconstructed to a maximum resolution of 1.5nm. While these studies have shown something of the structure of individual actin molecules, essential information about the orientation of actin in the filament is still unavailable.The work of Egelman & DeRosier has, however, suggested a method which could be used to provide an initial quantitative estimate of the orientation of actin within the filament. This method involves the quantitative comparison of computed diffraction data from single actin filaments with diffraction data derived from synthetic filaments constructed using the molecular model of actin as a building block. Their preliminary work was conducted using a model consisting of two juxtaposed spheres of equal size.


Author(s):  
John A. Hunt

Spectrum-imaging is a useful technique for comparing different processing methods on very large data sets which are identical for each method. This paper is concerned with comparing methods of electron energy-loss spectroscopy (EELS) quantitative analysis on the Al-Li system. The spectrum-image analyzed here was obtained from an Al-10at%Li foil aged to produce δ' precipitates that can span the foil thickness. Two 1024 channel EELS spectra offset in energy by 1 eV were recorded and stored at each pixel in the 80x80 spectrum-image (25 Mbytes). An energy range of 39-89eV (20 channels/eV) are represented. During processing the spectra are either subtracted to create an artifact corrected difference spectrum, or the energy offset is numerically removed and the spectra are added to create a normal spectrum. The spectrum-images are processed into 2D floating-point images using methods and software described in [1].


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