1,720,956 research outputs found
Radcomp
No full text<p>DCM now uses the "Radau" integration method if there is a transition rate or transfer coefficient greater than 10 inverse hours in the ODE. Such an ODE is "stiff" and the "Radau" method performs much better than the "RK45" method in this case. The "RK45" method is used otherwise.</p>If you use this software, please cite it as below
Spatio-temporal, multicellular and Monte Carlo track-based model of radiotherapy in silico
Full text linkA notable short-coming in the way radiotherapy is currently practised is that patient-specific radiobiology is minimally and rarely accounted for in the treatment planning process. If this is to be remedied, in silico radiobiological models of radiotherapy will play an essential role. By increasing the complexity of such models, greater accuracy and utility are gained, along with opportunities for new radiobiological insights. A new computational model was developed called “Stochastic Squared Radiotherapy” (S2RT). It is a spatio-temporal/four-dimensional radiotherapy model for head and neck squamous cell carcinoma (HNSCC), that uses stochastic modelling of tumour cells and Monte Carlo track structure simulations. The four main components of the model are tumour growth, tumour irradiation, DNA damage induction and cell death/survival. The tumour growth module generates the initial multicellular tumour and evolves it spatio-temporally in-between dose fractions. Ellipsoidal tumour cells occupy randomised, non-overlapping locations. Cells are pushed outward and fall inward following cell division and cell death, respectively. An epithelial cell hierarchy of stem, transit and differentiated cells is modelled. A connected and chaotic network of blood vessels grows interwoven between the cells. Chronic hypoxia and necrotic cells are simulated at distances far from blood vessels. Hypoxic cells divide slower and necrotic cells are gradually resorbed. Accelerated repopulation may be simulated by increasing the symmetric division of cancer stem cells. Dose fractions are delivered to the tumour in Monte Carlo simulations of radiation tracks. The multicellular tumour is voxelised into nucleus, cytoplasm and intercellular voxels of size 2 μm and imported into Geant4 to perform irradiation. A Geant4 application was developed that uses Geant4-DNA to simulate low-energy physical interactions and radiolytic chemical tracks to account for the indirect effect. The tracks through cell nuclei are converted to DNA damage, including doublestrand breaks (DSBs). This was done by spatially clustering physical interactions such as ionisations and excitations and hydroxyl radical interactions into simulated DNA volumes, each of size 10 base pairs. The DNA damage was made dependent upon the cellular pO2 by increasing the efficiency of DNA radical-to-strand break conversion with increasing pO2. In the model, complex DSBs (cDSBs) produced DNA free-ends that can misrejoin with one another and produce exchange-type chromosome aberrations. Complete exchanges are assumed. The misrejoining probability is modelled as an exponential function of the initial distance between the two cDSBs involved. Cells die if they contain an asymmetric chromosome aberration. Notable findings from the S2RT model include: 1. Symmetric division of cancer stem cells may be as high as 50% during accelerated repopulation. 2. The decrease in the oxygen enhancement ratio for DSB induction with increasing LET can be attributed to spatial clustering alone; i.e., at higher LET, the additional strand breaks produced in the presence of oxygen seldom result in additional DSBs. Instead, they increase DSB complexity. 3. For MV x-rays, misrejoinings between cDSBs produced by the same primary x-ray (including its secondary electrons) do not contribute appreciably to the linear components of chromosome aberration production and cell killing. For HNSCC, which does have an appreciable linear component of cell killing, unrejoined DNA ends (i.e. incomplete exchanges and terminal deletions) may be important. There is promise of accuracy and utility in S2RT because it is predicated on simulating Monte Carlo tracks through a multicellular tumour and simulating cellular tumour growth in-between dose fractions. DNA damage induction and subsequent processes like DNA free-end misrejoining and cell death are modelled stochastically using the track structure. Simulated tumours have realistic spatial distributions of cellular pO2 in relation to the blood vessels, so one can carefully investigate the effect of microscopic regions of tumour hypoxia on treatment efficacy. Since tumour irradiation is performed with track structure, the radiation quality modelled can easily be extended to high LET beams. Modelling a connected network of blood vessels in the tumour also enables consideration of vascular damages. In particular, the model may be used in the future to investigate the extent to which wide-spread vascular damages are responsible for the efficacy of high dose per fraction treatments such as stereotactic body radiotherapy.Thesis (Ph.D.) -- University of Adelaide, School of Physical Sciences, 201
Dorn
No full text<p>The release on GitHub includes a zip file Dorn_1-10-1_Win.zip. This zip file contains an executable file Dorn.exe that can be used to run Dorn on Windows 10 and 11 computers without needing to install Python and Dorn's other dependencies.</p>
<p>Changes since version 1.10.0 (excerpt from CHANGELOG.md)</p>
<p>### Added<br>Added radionuclide Tc-99m.</p>
<p>### Fixed<br>Fixed a bug that occurred when a single dose rate measurement was entered and the administration time or residual was subsequently changed.</p>If you use this software, please cite both the article from preferred-citation and the software itself
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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