Simul software
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We introduce the mathematical model of electromigration of electrolytes in free solution together with free software Simul, version 5, designed for simulation of electrophoresis. The mathematical model is based on principles of mass conservation, acid-base equilibria, and electroneutrality. It accounts for any number of multivalent electrolytes or ampholytes and yields a complete picture about dynamics of electromigration and diffusion in the separation channel. Additionally, the model accounts for the influence of ionic strength on ionic mobilities and electrolyte activities. The typical use of Simul is: inspection of system peaks (zones), stacking and preconcentrating analytes, resonance phenomena, and optimization of separation conditions, in either CZE, ITP, or IEF.
Quantitative structure-property/activity relationships (QSPRs/QSARs) are a tool (in silico) to rapidly predict various endpoints in general, and drug toxicity in particular. However, this dynamic evolution of experimental data (expansion of existing experimental data on drugs toxicity) leads to the problem of critical estimation of the data. The carcinogenicity, mutagenicity, liver effects and cardiac toxicity should be evaluated as the most important aspects of the drug toxicity. The toxicity is a multidimensional phenomenon. It is apparent that the main reasons for the increase in applications of in silico prediction of toxicity include the following: (i) the need to reduce animal testing; (ii) computational models provide reliable toxicity prediction; (iii) development of legislation that is related to use of new substances; (iv) filling data gaps; (v) reduction of cost and time; (vi) designing of new compounds; (vii) advancement of understanding of biology and chemistry. This mini-review provides analysis of existing databases and software which are necessary for use of robust computational assessments and robust prediction of potential drug toxicities by means of in silico methods.
- MeSH
- databáze faktografické * MeSH
- kvantitativní vztahy mezi strukturou a aktivitou * MeSH
- lidé MeSH
- nežádoucí účinky léčiv * MeSH
- počítačová simulace MeSH
- software MeSH
- testy toxicity MeSH
- výpočetní biologie * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
Described is a computer software package, EPIZOO, which has been developed specifically for undergraduate and postgraduate education, self-training, problem-solving, and simulation studies in veterinary epidemiology. The program is based on action-oriented animal population health/disease analyses and programming. EPIZOO runs on IBM-compatible personal computers and can be used for any animal population diseases, including those transmissible to man. The software comprises an integral system of selected indicators contained in twelve modules, with about 200 widely applicable methods used in epizootiology. It is user-friendly and includes general methods related to the following: animal population characteristics of health/disease importance; analysis of animal population health and disease situations, structures, dynamics, diagnoses, and consequences; preparation, cost, and evaluation of animal population health programmes; and selected statistical techniques.
- MeSH
- epidemiologie výchova MeSH
- nemoci zvířat epidemiologie MeSH
- počítačem řízená výuka * MeSH
- software * MeSH
- studium veterinárního lékařství * MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Česká republika MeSH
Předmět sdělení: V posledních letech dochází k rozvoji a pronikání 3D technologií do mnoha medicínských oborů. Stomatologie, ortodoncie a čelistní chirurgie nejsou výjimkou. Prověřené metody plánování ortognátních operací, jako jsou operace na sádrových modelech či 2D simulace, jsou považovány za „zlatý standard“ a vedou k osvědčeným výsledkům. Ovšem i tyto metody mají své hranice a omezení. Trojrozměrné (3D) prostředí přináší do plánování další, třetí rozměr, čímž se obraz přibližuje reálnému světu. To nám rozšiřuje možnosti např. při diagnostice některých asymetrií a umožňuje přesnější plánování ortognátních operací. Využívá přitom moderních 3D zobrazovacích metod, jako jsou Cone Beam CT, stereofotogrammetrie či digitální modely zubních oblouků. Vzájemnou registrací (překrytím) zhotovených 3D snímků (3D modelů) vznikne virtuální 3D model pacienta. Tento model dokonale zobrazuje obličejový skelet (Cone Beam CT), měkké tkáně obličeje (stereofotogrammetrický snímek) a zubní oblouky (digitální modely), někdy také označovaný jako tzv. triáda. Ve specializovaných počítačových programech, jako je např. Dolphin Imaging 3D 11.7? (Dolphin Imaging, Chatsworth, USA), provedeme na tomto virtuálním modelu 3D simulaci ortognátní operace. Cílem tohoto článku je prezentovat tuto relativně novou metodu plánování ortognátních operací a zároveň i 3D zobrazovací metody, které jsou k 3D plánování využívány a dále popsat jednotlivé kroky při vlastní 3D simulaci ortognátní operace v počítačovém programu Dolphin Imaging 3D?. Klíčová slova: ortognátní chirurgie – ortodoncie – 3D simulace – Cone Beam CT – obličejový sken – digitální ortodontické modely
AIM: Recently there has been a great progress in three-dimensional (3D) technologies in field of medicine. Dentistry and maxillofacial surgery haven't been exceptions. Methods such as model surgery or cephalometric methods of prediction (2D prediction) including video imaging are considered as “gold standards” in orthognathic surgery. However, these techniques, despite being routine part of the diagnosis and treatment planning process, have their limitations. 3D environment adds the third dimension to planning, which moves planning closer to reality and gives us more information for diagnosing a wider range of dentofacial anomalies. Furthermore, 3D planning increases accuracy of overall orthognatic planning by using modern 3D imaging methods, such as Cone Beam CT, stereophotogrammetry or digital models of dental arches. By merging these 3D images is created virtual model of patient head, described by some authors as triad. It depicts facial skeleton (Cone Beam CT), facial soft tissues (stereophotogrammetry scan) and dental arches (digital models) in the most suitable way. The next step is to perform 3D simulation on this virtual model by using a planning software, e.g. Dolphin imaging 3D?. The aim of this article is to present relatively new method of orthognatic surgery planning and brings some information about 3D imaging technologies, which are essential as part of that process. Simultaneously fundamental steps (procedures) in orthognatic surgery 3D simulation using program Dolphin Imaging 3D? process are described. Keywords: orthognatic surgery, orthodontics – Cone-Beam Computed Tomography – facial scan – digital dental models/casts
- MeSH
- estetika stomatologická MeSH
- fotogrammetrie metody MeSH
- lidé MeSH
- obličej MeSH
- ortognátní chirurgické výkony * metody MeSH
- počítačová simulace MeSH
- počítačová tomografie s kuželovým svazkem metody MeSH
- počítačové zpracování obrazu MeSH
- software MeSH
- zdravotnické prostředky ekonomika MeSH
- zobrazování trojrozměrné * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- přehledy MeSH
In this paper we determine acid dissociation constants, limiting ionic mobilities, complexation constants with β-cyclodextrin or heptakis(2,3,6-tri-O-methyl)-β-cyclodextrin, and mobilities of resulting complexes of profens, using capillary zone electrophoresis and affinity capillary electrophoresis. Complexation parameters are determined for both neutral and fully charged forms of profens and further corrected for actual ionic strength and variable viscosity in order to obtain thermodynamic values of complexation constants. The accuracy of obtained complexation parameters is verified by multidimensional nonlinear regression of affinity capillary electrophoretic data, which provides the acid dissociation and complexation parameters within one set of measurements, and by NMR technique. A good agreement among all discussed methods was obtained. Determined complexation parameters were used as input parameters for simulations of electrophoretic separation of profens by Simul 5 Complex. An excellent agreement of experimental and simulated results was achieved in terms of positions, shapes, and amplitudes of analyte peaks, confirming the applicability of Simul 5 Complex to complex systems, and accuracy of obtained physical-chemical constants. Simultaneously, we were able to demonstrate the influence of electromigration dispersion on the separation efficiency, which is not possible using the common theoretical approaches, and predict the electromigration order reversals of profen peaks. We have shown that determined acid dissociation and complexation parameters in combination with tool Simul 5 Complex software can be used for optimization of separation conditions in capillary electrophoresis.
- MeSH
- antiflogistika nesteroidní chemie MeSH
- beta-cyklodextriny chemie MeSH
- elektroforéza kapilární metody MeSH
- flurbiprofen chemie MeSH
- ibuprofen chemie MeSH
- ketoprofen chemie MeSH
- koncentrace vodíkových iontů MeSH
- magnetická rezonanční spektroskopie MeSH
- naproxen chemie MeSH
- osmolární koncentrace MeSH
- počítačová simulace MeSH
- software MeSH
- termodynamika MeSH
- viskozita MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
In this study, in silico mutagenesis and docking in Ralstonia solanacearum lectin (RSL) were carried out, and the ability of several docking software programs to calculate binding affinity was evaluated. In silico mutation of six amino acid residues (Agr17, Glu28, Gly39, Ala40, Trp76, and Trp81) was done, and a total of 114 in silico mutants of RSL were docked with Me-α-L-fucoside. Our results show that polar residues Arg17 and Glu28, as well as nonpolar amino acids Trp76 and Trp81, are crucial for binding. Gly39 may also influence ligand binding because any mutations at this position lead to a change in the binding pocket shape. The Ala40 residue was found to be the most interesting residue for mutagenesis and can affect the selectivity and/or affinity. In general, the docking software used performs better for high affinity binders and fails to place the binding affinities in the correct order.
- MeSH
- krystalografie rentgenová MeSH
- lektiny chemie genetika metabolismus MeSH
- molekulární modely MeSH
- molekulární sekvence - údaje MeSH
- mutageneze MeSH
- počítačová simulace MeSH
- Ralstonia solanacearum chemie genetika metabolismus MeSH
- receptory buněčného povrchu chemie MeSH
- sacharidové sekvence MeSH
- software MeSH
- vazebná místa MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: Simulators used in teaching are interactive applications comprising a mathematical model of the system under study and a graphical user interface (GUI) that allows the user to control the model inputs and visualize the model results in an intuitive and educational way. Well-designed simulators promote active learning, enhance problem-solving skills, and encourage collaboration and small group discussion. However, creating simulators for teaching purposes is a challenging process that requires many contributors including educators, modelers, graphic designers, and programmers. The availability of a toolchain of user-friendly software tools for building simulators can facilitate this complex task. OBJECTIVE: This paper aimed to describe an open-source software toolchain termed Bodylight.js that facilitates the creation of browser-based client-side simulators for teaching purposes, which are platform independent, do not require any installation, and can work offline. The toolchain interconnects state-of-the-art modeling tools with current Web technologies and is designed to be resilient to future changes in the software ecosystem. METHODS: We used several open-source Web technologies, namely, WebAssembly and JavaScript, combined with the power of the Modelica modeling language and deployed them on the internet with interactive animations built using Adobe Animate. RESULTS: Models are implemented in the Modelica language using either OpenModelica or Dassault Systèmes Dymola and exported to a standardized Functional Mock-up Unit (FMU) to ensure future compatibility. The C code from the FMU is further compiled to WebAssembly using Emscripten. Industry-standard Adobe Animate is used to create interactive animations. A new tool called Bodylight.js Composer was developed for the toolchain that enables one to create the final simulator by composing the GUI using animations, plots, and control elements in a drag-and-drop style and binding them to the model variables. The resulting simulators are stand-alone HyperText Markup Language files including JavaScript and WebAssembly. Several simulators for physiology education were created using the Bodylight.js toolchain and have been received with general acclaim by teachers and students alike, thus validating our approach. The Nephron, Circulation, and Pressure-Volume Loop simulators are presented in this paper. Bodylight.js is licensed under General Public License 3.0 and is free for anyone to use. CONCLUSIONS: Bodylight.js enables us to effectively develop teaching simulators. Armed with this technology, we intend to focus on the development of new simulators and interactive textbooks for medical education. Bodylight.js usage is not limited to developing simulators for medical education and can facilitate the development of simulators for teaching complex topics in a variety of different fields.
- MeSH
- internet MeSH
- lidé MeSH
- software normy MeSH
- studium lékařství metody MeSH
- uživatelské rozhraní počítače * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Super-resolution optical fluctuation imaging (SOFI) allows one to perform sub-diffraction fluorescence microscopy of living cells. By analyzing the acquired image sequence with an advanced correlation method, i.e. a high-order cross-cumulant analysis, super-resolution in all three spatial dimensions can be achieved. Here we introduce a software tool for a simple qualitative comparison of SOFI images under simulated conditions considering parameters of the microscope setup and essential properties of the biological sample. This tool incorporates SOFI and STORM algorithms, displays and describes the SOFI image processing steps in a tutorial-like fashion. Fast testing of various parameters simplifies the parameter optimization prior to experimental work. The performance of the simulation tool is demonstrated by comparing simulated results with experimentally acquired data.
- MeSH
- algoritmy MeSH
- fluorescenční mikroskopie * MeSH
- HeLa buňky MeSH
- lidé MeSH
- počítačové zpracování obrazu metody MeSH
- software * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
