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arXiv2014

Efficiency and comfort of knee braces: A parametric study based on computational modelling

Knee orthotic devices are widely proposed by physicians and medical practitioners for preventive or therapeutic objectives in relation with their effects, usually known as to stabilize joint or restrict ranges of motion. This study focuses on the understanding of force transfer mechanisms from the brace to the joint thanks to a Finite Element Model. A Design Of Experiments approach was used to characterize the stiffness and comfort of various braces in order to identify their mechanically influent characteristics. Results show conflicting behavior: influent parameters such as the brace size or textile stiffness improve performance in detriment of comfort. Thanks to this computational tool, novel brace designs can be tested and evaluated for an optimal mechanical efficiency of the devices and a better compliance of the patient to the treatment.

physics.med-ph↗

arXiv2014

Assess Sleep Stage by Modern Signal Processing Techniques

In this paper, two modern adaptive signal processing techniques, Empirical Intrinsic Geometry and Synchrosqueezing transform, are applied to quantify different dynamical features of the respiratory and electroencephalographic signals. We show that the proposed features are theoretically rigorously supported, as well as capture the sleep information hidden inside the signals. The features are used as input to multiclass support vector machines with the radial basis function to automatically classify sleep stages. The effectiveness of the classification based on the proposed features is shown to be comparable to human expert classification -- the proposed classification of awake, REM, N1, N2 and N3 sleeping stages based on the respiratory signal (resp. respiratory and EEG signals) has the overall accuracy $81.7\%$ (resp. $89.3\%$) in the relatively normal subject group. In addition, by examining the combination of the respiratory signal with the electroencephalographic signal, we conclude that the respiratory signal consists of ample sleep information, which supplements to the information stored in the electroencephalographic signal.

physics.med-ph↗

arXiv2014

Modelling beam transport and biological effectiveness to develop treatment planning for ion beam radiotherapy

Radiation therapy with carbon ions is a novel technique of cancer radiotherapy, applicable in particular to treating radioresistant tumours at difficult localisations. Therapy planning, where the medical physicist, following the medical prescription, finds the optimum distribution of cancer cells to be inactivated by their irradiation over the tumour volume, is a basic procedure of cancer radiotherapy. The main difficulty encountered in therapy planning for ion radiotherapy is to correctly account for the enhanced radiobiological effectiveness of ions in the Spread Out Bragg Peak (SOBP) region over the tumour volume. In this case, unlike in conventional radiotherapy with photon beams, achieving a uniform dose distribution over the tumour volume does not imply achieving uniform cancer cell inactivation. In this thesis, an algorithm of the basic element (kernel) of a treatment planning system (TPS) for carbon ion therapy is developed. The algorithm consists of a radiobiological part which suitably corrects for the enhanced biological effect of ion irradiation of cancer cells, and of a physical beam transport model. In the radiobiological component, Katz's track structure model of cellular survival is applied, after validating its physical assumptions and improving some aspects of this model. The Katz model offers fast and accurate predictions of cell survival in mixed fields of the primary carbon ions and of their secondary fragments. The physical beam model was based on available tabularized data, prepared earlier by Monte Carlo simulations. Both components of the developed TPS kernel are combined within an optimization tool, allowing the entrance energy-fluence spectra of the carbon ion beam to be selected in order to achieve a pre-assumed uniform (flat) depth-survival profile over the SOBP region, assuring uniform cancer cell inactivation over the tumour depth.

physics.med-ph↗

arXiv2017

Evaluation of Electric and Magnetic Fields Distribution and SAR Induced in 3D Models of Water Containers by Radiofrequency Radiation and Their Relationship to the Non-Thermal Effects of Microwaves

The research works on the biological effects of electromagnetic (EM) radiation have increased globally. Computer simulation models were developed to assess exposure of square, rectangular, pyramidal, and cylindrical water containers to microwave radiation at 300, 900, and 2,400 MHz. The development of the models included determination of EM field distribution and the resulting specific absorption rate (SAR) in the stored water. These models employed CST STUDIO SUITE 2014 package to solve EM field equations by applying the finite-difference time-domain (FDTD) method. The effect of frequency, packaging shape, and polarization on SAR induced in water was determined. High electric field and point SAR were obtained over the whole azimuth and elevation angles range in the pyramidal container model. The highest values of SAR were induced in water at the sharp edges of the four water container models. The order of the effect on total SAR and maximum point SAR is cylindrical < square < rectangular < pyramidal model at 300, 900, and 2,400 MHz for both vertical and horizontal polarizations. It can be concluded that the variation in the packaging shape of the containers, polarization, irradiation geometry, and frequency. In addition, the sharp edges of the container models significantly affect the calculation and distribution of electric and magnetic fields and SAR values induced in the stored water, which in turn could cause variations in the non-thermal effects of the electromagnetic fields in the stored water.

physics.med-ph↗

arXiv2014

Stochastic model for computer simulation of the number of cancer cells and lymphocytes in homogeneous sections of cancer tumors

We deal with a small enough tumor section to consider it homogeneous, such that populations of lymphocytes and cancer cells are independent of spatial coordinates. A stochastic model based in one step processes is developed to take into account natural birth and death rates. Other rates are also introduced to consider medical treatment: natural birth rate of lymphocytes and cancer cells; induced death rate of cancer cells due to self-competition, and other ones caused by the activated lymphocytes acting on cancer cells. Additionally, a death rate of cancer cells due to induced apoptosis is considered. Weakness due to the advance of sickness is considered by introducing a lymphocytes death rate proportional to proliferation of cancer cells. Simulation is developed considering different combinations of the parameters and its values, so that several strategies are taken into account to study the effect of anti-angiogenic drugs as well the self-competition between cancer cells. Immune response, with the presence of a kind of specialized lymphocytes, is introduced such that they appear once cancer cells are detected. Induced apoptosis of cancer cells is introduced to model the action of several drugs under development right now. Besides, the model predicts the cancer relapse even from a very small number of cells. Simulation is done by using Gillespie algorithm.

physics.med-ph↗

arXiv2014

Analysis of EEG signal by Flicker Noise Spectroscopy: Identification of right/left hand movement imagination

Flicker Noise Spectroscopy (FNS) has been used for the analysis of electroencephalography (EEG) signal related to the movement imagination. The analysis of sensorimotor rhythms in time-frequency maps reveals the event-related desynchronization (ERD) and the post-movement event-related synchronization (ERS), observed mainly in the contralateral hemisphere to the hand moved for the motor imagery. The signal has been parameterized in accordance with FNS method. The significant changes of the FNS parameters, at the time when the subject imagines the movement, have been observed. The analysis of these parameters allows to distinguish between imagination of right and left hands movement. Our study shows that the flicker-noise spectroscopy can be an alternative method of analyzing EEG signal related to the imagination of movement in terms of a potential application in the brain-computer interface (BCI).

physics.med-ph↗

arXiv2014

Track structure modelling for ion radiotherapy

In its broadest terms, doctoral dissertation entitled "Track structure modelling for ion radiotherapy" is part of the supporting research background in the development of the ambitious proton radiotherapy project currently under way at the Institute of Nuclear Physics PAN in Kraków. Another broad motivation was the desire to become directly involved in research on a topical and challenging subject of possibly developing a therapy planning system for carbon beam radiotherapy, based in its radiobiological part on the Track Structure model developed by prof. Robert Katz over 50 years ago. Thus, the general aim of this work was, firstly, to recapitulate the Track Structure model and to propose an updated and complete formulation of this model by incorporating advances made by several authors who had contributed to its development in the past. Secondly, the updated and amended (if necessary) formulation of the model was presented in a form applicable for use in computer codes which would constitute the "radiobiological engine" of the future therapy planning system for carbon radiotherapy, which the Kraków ion radiotherapy research group wishes to develop. Lastly, currently available radiobiology data were analysed in terms of Track Structure Theory to supply exemplary parameters for cell lines (preferably, exposed in normal and anoxic conditions) to be used as possible input for carbon ion radiotherapy planning studies.

physics.med-ph↗

arXiv2014

Automated placement of stereotactic injections using a laser scan of the skull

Stereotactic targeting is a commonly used technique for performing injections in the brains of mice and other animals. The most common method for targeting stereoscopic injections uses the skull indentations bregma and lambda as reference points and is limited in its precision by factors such as skull curvature and individual variation, as well as an incomplete correspondence between skull landmarks and brain locations. In this software tool, a 3D laser scan of the mouse skull is taken in vitro and registered onto a reference skull using a point cloud matching algorithm, and the parameters of the transformation are used to position a glass pipette to place tracer injections. The software was capable of registering sample skulls with less than 100 micron error, and was able to target an injection in a mouse with error of roughly 500 microns. These results indicate that using skull scan registration has the potential to be widely applicable in automating stereotactic targeting of tracer injections.

q-bio.QM↗

arXiv2014

Efficient, high-speed ablation of soft tissue with few-microjoule, femtosecond pulse bursts

Femtosecond pulses hold great promise for high-precision tissue removal. However, ablation rates are severely limited by the need to keep average laser power low to avoid collateral damage due to heat accumulation. Furthermore, previously reported pulse energies preclude delivery in flexible fibers, hindering in vivo operation. Both of these problems can be addressed through use of groups of high-repetition-rate pulses, or bursts. Here, we report a novel fiber laser and demonstrate ultrafast burst-mode ablation of brain tissue at rates approaching 1 mm$^3$/min, an order of magnitude improvement over previous reports. Burst mode operation is shown to be superior in terms of energy required and avoidance of thermal effects, compared to uniform repetition rates. These results can pave the way to in vivo operation at medically relevant speeds, delivered via flexible fibers to surgically hard-to-reach targets, or with simultaneous magnetic resonance imaging.

physics.optics↗

arXiv2015

SPIKY: A graphical user interface for monitoring spike train synchrony

Techniques for recording large-scale neuronal spiking activity are developing very fast. This leads to an increasing demand for algorithms capable of analyzing large amounts of experimental spike train data. One of the most crucial and demanding tasks is the identification of similarity patterns with a very high temporal resolution and across different spatial scales. To address this task, in recent years three time-resolved measures of spike train synchrony have been proposed, the ISI-distance, the SPIKE-distance, and event synchronization. The Matlab source codes for calculating and visualizing these measures have been made publicly available. However, due to the many different possible representations of the results the use of these codes is rather complicated and their application requires some basic knowledge of Matlab. Thus it became desirable to provide a more user-friendly and interactive interface. Here we address this need and present SPIKY, a graphical user interface which facilitates the application of time-resolved measures of spike train synchrony to both simulated and real data. SPIKY includes implementations of the ISI-distance, the SPIKE-distance and SPIKE-synchronization (an improved and simplified extension of event synchronization) which have been optimized with respect to computation speed and memory demand. It also comprises a spike train generator and an event detector which makes it capable of analyzing continuous data. Finally, the SPIKY package includes additional complementary programs aimed at the analysis of large numbers of datasets and the estimation of significance levels.

physics.data-an↗

arXiv2014

Specific Absorbed Fractions of Electrons and Photons for Rad-HUMAN Phantom Using Monte Carlo Method

The specific absorbed fractions (SAF) for self- and cross-irradiation are effective tools for the internal dose estimation of inhalation and ingestion intakes of radionuclides. A set of SAFs of photon and electron were calculated using the Rad-HUMAN phantom, a computational voxel phantom of Chinese adult female and created using the color photographic image of the Chinese Visible Human (CVH) data set. The model can represent most of Chinese adult female anatomical characteristics and can be taken as an individual phantom to investigate the difference of internal dose with Caucasians. In this study, the emission of mono-energetic photons and electrons of 10keV to 4MeV energy were calculated using the Monte Carlo particle transport calculation code MCNP. Results were compared with the values from ICRP reference and ORNL models. The results showed that SAF from Rad-HUMAN have the similar trends but larger than those from the other two models. The differences were due to the racial and anatomical differences in organ mass and inter-organ distance. The SAFs based on the Rad-HUMAN phantom provide an accurate and reliable data for internal radiation dose calculations for Chinese female.

physics.med-ph↗

arXiv2014

Improved Scatter Correction in X-Ray Cone Beam CT with Moving Beam Stop Array Using Johns' Equation

In this paper, an improved scatter correction with moving beam stop array (BSA) for x-ray cone beam (CB) CT is proposed. Firstly, correlation between neighboring CB views is deduced based on John's Equation. Then, correlation-based algorithm is presented to complement the incomplete views by using the redundancy (over-determined information) in CB projections. Finally, combining the algorithm with scatter correction method using moving BSA, where part of primary radiation is blocked and incomplete projections are acquired, an improved correction method is proposed. Effectiveness and robustness is validated by Monte Carlo (MC) simulation with EGSnrc on humanoid phantom.

physics.med-ph↗

arXiv2014

Single-scan scatter correction in CBCT by using projection correlation based view interpolation (PC-VI) and a stationary ring-shaped beam stop array (BSA)

In the scatter correction for x-ray Cone Beam (CB) CT, the single-scan scheme with moving Beam Stop Array (BSA) offers reliable scatter measurement with low dose, and by using Projection Correlation based View Interpolation (PC-VI), the primary fluence shaded by the moving BSA (during scatter measurement) could be recovered with high accuracy. However, the moving BSA may increase the mechanical burden in real applications. For better practicability, in this paper we proposed a PC-VI based single-scan scheme with a ring-shaped stationary BSA, which serves as a virtual moving BSA during CB scan, so the shaded primary fluence by this stationary BSA can be also well recovered by PC-VI. The principle in designing the whole system is deduced and evaluated. The proposed scheme greatly enhances the practicability of the single-scan scatter correction scheme.

physics.med-ph↗

arXiv2014

Why are public health authorities not concerned about Ebola in the US? Part I. Fat tailed distributions

US public health authorities claim imposing quarantines on healthcare workers returning from West Africa is incorrect according to science. Their positions rely upon a set of studies and experience about outbreaks and transmission mechanisms in Africa as well as assumptions about what those studies imply about outbreaks in the US. According to this view the probability of a single infection is low and that of a major outbreak is non-existent. In a series of brief reports we will provide insight into why properties of networks of contagion that are not considered in traditional statistics suggest that risks are higher than those assumptions suggest. We begin with the difference between thin and fat tailed distributions applied to the number of infected individuals that can arise from a single one. Traditional epidemiological models consider the contagion process as described by $R_0$, the average number of new infected individuals arising from a single case. However, in a complex interdependent society it is possible for the actual number due to a single individual to dramatically differ from the average number, with severe consequences for the ability to contain an outbreak when it is just beginning. Our analysis raises doubts about the scientific validity of policy recommendations of public health authorities. We also point out that existing CDC public health policies and actions are inconsistent with their claims.

physics.soc-ph↗

arXiv2014

Feasibility of Simulated Annealing Tomography

Simulated annealing tomography (SAT) is a simple iterative image reconstruction technique which can yield a superior reconstruction compared with filtered back-projection (FBP). However, the very high computational cost of iteratively calculating discrete Radon transform (DRT) has limited the feasibility of this technique. In this paper, we propose an approach based on the pre-calculated intersection lengths array (PILA) which helps to remove the step of computing DRT in the simulated annealing procedure and speed up SAT by over 300 times. The enhancement of convergence speed of the reconstruction process using the best of multiple-estimate (BoME) strategy is introduced. The performance of SAT under different conditions and in comparison with other methods is demonstrated by numerical experiments.

physics.comp-ph↗

arXiv2014

Exact Modeling of Cardiovascular System Using Lumped Method

Electrical analogy (Lumped method) is an easy way to model human cardiovascular system. In this paper Lumped method is used for simulating a complete model. It describes a 36-vessel model and cardiac system of human body with details that could show hydrodynamic parameters of cardiovascular system. Also this paper includes modeling of pulmonary, atrium, left and right ventricles with their equivalent circuits. Exact modeling of right and left ventricles pressure increases the accuracy of our simulation. In this paper we show that a calculated pressure for aorta from our complex circuit is near to measured pressure by using advanced medical instruments.

physics.med-ph↗

arXiv2014

Raman spectroscopy as a tool for reagent free estimation

We present results of Raman spectroscopic studies of urine to determine the suitability of near-infrared Raman spectroscopy for quantitative estimation of urinary urea. The Raman spectra were acquired from the urine samples with an inbuilt Raman spectroscopy setup that employs a 785-nm diode laser as the Raman excitation source. A multivariate algorithm based on partial least square (PLS) regression was developed to predict the concentration of urea depending on the measured sets of Raman spectra and the reference urea concentration. The computed results shows that Raman spectroscopy in amalgamation with PLS-based multivariate chemometric algorithm can detect urea in urine samples with an accuracy of >90 %

physics.med-ph↗

arXiv2014

Biological effects of pulsating magnetic fields: role of solitons

In this paper, we analyze biological effects produced by magnetic fields in order to elucidate the physical mechanisms, which can produce them. We show that there is a chierarchy of such mechanisms and that the mutual interplay between them can result in the synergetic outcome. In particular, we analyze the biological effects of magnetic fields on soliton mediated charge transport in the redox processes in living organisms. Such solitons are described by nonlinear systems of equations and represent electrons that are self-trapped in alpha-helical polypeptides due to the moderately strong electron-lattice interaction. They represent a particular type of disssipativeless large polarons in low-dimensional systems. We show that the effective mass of solitons in the is different from the mass of free electrons, and that there is a resonant effect of the magnetic fields on the dynamics of solitons, and, hence, on charge transport that accompanies photosynthesis and respiration. These effects can result in non-thermal resonant effects of magnetic fields on redox processes in particular, and on the metabolism of the organism in general. This can explain physical mechanisms of therapies based on applying magnetic fields.

physics.bio-ph↗